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Feng SJ, Voruz F, Leong S, Hammer DR, Breil E, Aksit A, Yu M, Chiriboga L, Olson ES, Kysar JW, Lalwani AK. Microneedle-Mediated Delivery of siRNA via Liposomal-Based Transfection for Inner Ear Gene Therapy. Otol Neurotol 2024; 45:1068-1077. [PMID: 39165134 DOI: 10.1097/mao.0000000000004297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
HYPOTHESIS Microneedle-mediated intracochlear injection of siRNA-Lipofectamine through the round window membrane (RWM) can be used to transfect cells within the cochlea. BACKGROUND Our laboratory has developed 100-μm diameter hollow microneedles for intracochlear injection through the guinea pig RWM. In this study, we test the feasibility of microneedle-mediated injection of siRNA and Lipofectamine, a commonly used reagent with known cellular toxicity, through the RWM for cochlear transfection. METHODS Fluorescently labeled scramble siRNA was diluted into Lipofectamine RNAiMax and OptiMEM. One microliter of 5 μM siRNA was injected through the RWM of Hartley guinea pigs at a rate of 1 μl/min (n = 22). In a control group, 1.0 μl of Lipofectamine, with no siRNA, was diluted into OptiMEM and injected in a similar fashion (n = 5). Hearing tests were performed before and either at 24 hours, 48 hours, or 5 days after injection. Afterward, animals were euthanized, and cochleae were harvested for imaging. Control cochleae were processed in parallel to untreated guinea pigs. RESULTS Fluorescence, indicating successful transfection, was observed within the basal and middle turns of the cochlea with limited distribution in the apex at 24 and 48 hours. Signal was most intense in the organ of Corti, spiral ligament, and spiral ganglion. Little to no fluorescence was observed at 5 days post-injection. No significant changes in auditory brainstem response (ABR) were noted post-perforation at 5 days, suggesting that siRNA-Lipofectamine at low doses does not cause cochlear toxicity. CONCLUSIONS Small volumes of siRNA and Lipofectamine can be effectively delivered to cochlear structures using microneedles, paving the way for atraumatic cochlear gene therapy.
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Affiliation(s)
| | - François Voruz
- Department of Otolaryngology-Head and Neck Surgery, Columbia University, New York, New York
| | | | - Daniella R Hammer
- Department of Mechanical Engineering, Columbia University, New York, New York
| | - Eugénie Breil
- Department of Otolaryngology-Head and Neck Surgery, Columbia University, New York, New York
| | - Aykut Aksit
- Department of Mechanical Engineering, Columbia University, New York, New York
| | - Michelle Yu
- Department of Otolaryngology-Head and Neck Surgery, Columbia University, New York, New York
| | - Lauren Chiriboga
- Department of Biomedical Engineering, Columbia University, New York, New York
| | | | - Jeffrey W Kysar
- Department of Mechanical Engineering, Columbia University, New York, New York
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Mota L, Zhu M, Tomeo JN, Recarey M, Patel N, Pradhan-Nabzdyk L, LoGerfo FW, Liang P. The impact of heparin and direct thrombin inhibitors on cell-penetrating polymer siRNA transfection. Gene Ther 2024; 31:467-476. [PMID: 39013986 DOI: 10.1038/s41434-024-00460-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/18/2024]
Abstract
Gene therapy using siRNA has become a promising strategy to achieve targeted gene knockdown for treatment of cardiovascular pathologies. However, efficient siRNA transfection often relies on cationic delivery vectors such as synthetic cell-penetrating polymers which are susceptible to interference by negatively charged molecules. Anticoagulants such as heparin, which is negatively charged and widely used in cardiovascular applications, may pose a significant barrier to effective siRNA delivery. We therefore conducted in vitro studies utilizing human smooth muscle and endothelial cells transfected with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β2-microglobulin (B2M) siRNA in the presence of heparin, argatroban, and bivalirudin in order to determine which anticoagulant therapy is most compatible for siRNA delivery. We observed that while heparin, at clinical doses, decreases the efficiency of siRNA targeted mRNA knockdown, mRNA knockdown is not inhibited in the presence of either argatroban or bivalirudin. Our data suggests that heparin should be avoided during siRNA therapy with cationic transfection agents, and argatroban and bivalirudin should be used in its stead.
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Affiliation(s)
- Lucas Mota
- Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Max Zhu
- Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - John N Tomeo
- Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Melina Recarey
- Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nyah Patel
- Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Leena Pradhan-Nabzdyk
- Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Frank W LoGerfo
- Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Patric Liang
- Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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Zuo Y, He J, Zhou Z, Sun J, Ouyang C, Huang H, Wang Y, Liu H, Reed SH. Long non-coding RNA LIP interacts with PARP-1 influencing the efficiency of base excision repair. Noncoding RNA Res 2024; 9:649-658. [PMID: 38577022 PMCID: PMC10987297 DOI: 10.1016/j.ncrna.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
In recent years, various long non-coding RNAs (lncRNAs) involved in DNA damage response (DDR) have been identified and studied to deepen our understanding. However, there are rare reports on the association between lncRNAs and base excision repair (BER). Our designed DNA microarray identified dozens of functionally unknown lncRNAs, and their transcription levels significantly increased upon exposure to DNA damage inducers. One of them, named LIP (Long noncoding RNA Interacts with PARP-1), exhibited a significant alteration in transcription in response to methyl methanesulfonate (MMS) and temozolomide (TMZ) treatments. LIP knockdown or knockout cell lines are sensitive to MMS and TMZ, indicating that LIP plays a crucial role in DDR. The loss or insufficiency of LIP significantly influences the efficiency of BER in human cells, and it suggests that LIP participates in the BER pathway. The interaction between LIP and a key factor in BER, poly (ADP-ribose) polymerase 1 (PARP-1), has been confirmed. We identified and characterized LIP, a lncRNA, which is involved in DDR, significantly influences BER efficiency, and interacts with the BER key factor PARP-1. This advances our understanding of the connection between lncRNAs and BER, presenting the potential for the discovery of new drug targets.
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Affiliation(s)
- You Zuo
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Jiaqian He
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Zheng Zhou
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Jingjing Sun
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Can Ouyang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Hui Huang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Yajuan Wang
- College of Biology, Hunan University, Changsha, 410082, PR China
| | - Hairong Liu
- College of Material Science and Engineering, Hunan University, Changsha, 410082, PR China
| | - Simon H. Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
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Safarkhani M, Ahmadi S, Ipakchi H, Saeb MR, Makvandi P, Ebrahimi Warkiani M, Rabiee N, Huh Y. Advancements in Aptamer-Driven DNA Nanostructures for Precision Drug Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401617. [PMID: 38713753 PMCID: PMC11234471 DOI: 10.1002/advs.202401617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/08/2024] [Indexed: 05/09/2024]
Abstract
DNA nanostructures exhibit versatile geometries and possess sophisticated capabilities not found in other nanomaterials. They serve as customizable nanoplatforms for orchestrating the spatial arrangement of molecular components, such as biomolecules, antibodies, or synthetic nanomaterials. This is achieved by incorporating oligonucleotides into the design of the nanostructure. In the realm of drug delivery to cancer cells, there is a growing interest in active targeting assays to enhance efficacy and selectivity. The active targeting approach involves a "key-lock" mechanism where the carrier, through its ligand, recognizes specific receptors on tumor cells, facilitating the release of drugs. Various DNA nanostructures, including DNA origami, Tetrahedral, nanoflower, cruciform, nanostar, nanocentipede, and nanococklebur, can traverse the lipid layer of the cell membrane, allowing cargo delivery to the nucleus. Aptamers, easily formed in vitro, are recognized for their targeted delivery capabilities due to their high selectivity for specific targets and low immunogenicity. This review provides a comprehensive overview of recent advancements in the formation and modification of aptamer-modified DNA nanostructures within drug delivery systems.
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Affiliation(s)
- Moein Safarkhani
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
- School of Chemistry, Damghan University, Damghan, 36716-45667, Iran
| | - Sepideh Ahmadi
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
| | - Hossein Ipakchi
- Department of Chemical Engineering, McMaster University, Hamilton, L8S 4L8, Canada
| | - Mohammad Reza Saeb
- Department of Pharmaceutical Chemistry, Medical University of Gdańsk, J. Hallera 107, Gdańsk, 80-416, Poland
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, 324000 Quzhou, Zhejiang, China
- Centre of Research Impact and Outreach, Chitkara University, Rajpura, Punjab, 140417, India
- Department of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai, 600077, India
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Institute for Biomedical Materials and Devices (IBMD), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Navid Rabiee
- Department of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai, 600077, India
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, 6150, Australia
| | - YunSuk Huh
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
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Zhao X, Liu Z, Liu Y, Lu M, Xu J, Wu F, Jin W. Development and application of an RNA nanostructure to induce transient RNAi in difficult transgenic plants. Biotechnol J 2024; 19:e2400024. [PMID: 38797726 DOI: 10.1002/biot.202400024] [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: 01/10/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
The development of RNA interference (RNAi) is crucial for studying plant gene function. Its use, is limited to a few plants with well-established transgenic techniques. Spray-induced gene silencing (SIGS) introduces exogenous double-stranded RNA (dsRNA) into plants by spraying, injection, or irrigation, triggering the RNAi pathway to instantly silence target genes. As is a transient RNAi technology that does not rely on transgenic methods, SIGS has significant potential for studying gene function in plants lacking advanced transgenic technology. In this study, to enhance their stability and delivery efficiency, siRNAs were used as structural motifs to construct RNA nanoparticles (NPs) of four shapes: triangle, square, pentagon, and hexagon. These NPs, when synthesized by Escherichia coli, showed that triangular and square shapes accumulated more efficiently than pentagon and hexagon shapes. Bioassays revealed that RNA squares had the highest RNAi efficiency, followed by RNA triangles, with GFP-dsRNA showing the lowest efficiency at 4 and 7 days post-spray. We further explored the use of RNA squares in inducing transient RNAi in plants that are difficult to transform genetically. The results indicated that Panax notoginseng-derived MYB2 (PnMYB2) and Camellia oleifera-derived GUT (CoGUT) were significantly suppressed in P. notoginseng and C. oleifera, respectively, following the application of PnMYB2- and CoGUT-specific RNA squares. These findings suggest that RNA squares are highly effective in SIGS and can be utilized for gene function research in plants.
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Affiliation(s)
- Xiayang Zhao
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zhekai Liu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co. Ltd., Shaoxing, Zhejiang, China
| | - Yiqing Liu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co. Ltd., Shaoxing, Zhejiang, China
| | - Mingdong Lu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co. Ltd., Shaoxing, Zhejiang, China
| | - Jinfeng Xu
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co. Ltd., Shaoxing, Zhejiang, China
| | - Fangli Wu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Weibo Jin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co. Ltd., Shaoxing, Zhejiang, China
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Dahal S, Bastola S, Ramamurthi A. JNK2 silencing lipid nanoparticles for elastic matrix repair. J Biomed Mater Res A 2024; 112:562-573. [PMID: 37815147 DOI: 10.1002/jbm.a.37618] [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: 04/10/2023] [Revised: 08/08/2023] [Accepted: 09/07/2023] [Indexed: 10/11/2023]
Abstract
The over-expression of c-Jun N-terminal kinase (JNK2), a stress activated mitogen kinase, in the aortic wall plays a critical role in the formation and progression of abdominal aortic aneurysm (AAA). This triggers chronic downstream upregulation of elastolytic matrix metalloproteinases (MMPs), MMPs2 and 9 to cause progressive proteolytic breakdown of the wall elastic matrix. We have previously shown that siNRA knockdown of JNK2 gene expression in an AAA culture model stimulates downstream elastin gene expression, elastic fiber formation, crosslinking and reduces elastolytic MMPs2 and 9. Since naked siRNA poorly routes to intracellular targets, has poor stability in blood, and could be potentially toxic and immunogenic, this project is aimed to develop PEGylated lipid nanoparticles (LNPs) for delivery of JNK siRNA and to generate evidence of successful JNK2 knockdown and downstream attenuation of MMP2 gene and protein expressions. LNPs were formulated using thin-film hydration technique and had the size of 100-200 nm with zeta-potential ranging between 30 and 40 mV. JNK siRNA loaded PEGylated LNPs successfully knocked down JNK2 in cytokine-activated rat aneurysmal smooth muscle (EaRASMC) cultures. This resulted in a downstream decrease in MMP2 gene and protein expression and an upward trend in expression of genes for proteins critical for elastic fiber assembly such as elastin (ELN) and lysyl oxidase (LOX). Our result indicates cationic LNPs to be potential carriers for JNK siRNA delivery improving potency for elastin homeostasis required for AAA repair which could possibly provide benefits in preventing the progression of small AAAs.
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Affiliation(s)
- Shataakshi Dahal
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Suraj Bastola
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Anand Ramamurthi
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
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Chandran C, Santra M, Rubin E, Geary ML, Yam GHF. Regenerative Therapy for Corneal Scarring Disorders. Biomedicines 2024; 12:649. [PMID: 38540264 PMCID: PMC10967722 DOI: 10.3390/biomedicines12030649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 05/09/2024] Open
Abstract
The cornea is a transparent and vitally multifaceted component of the eye, playing a pivotal role in vision and ocular health. It has primary refractive and protective functions. Typical corneal dysfunctions include opacities and deformities that result from injuries, infections, or other medical conditions. These can significantly impair vision. The conventional challenges in managing corneal ailments include the limited regenerative capacity (except corneal epithelium), immune response after donor tissue transplantation, a risk of long-term graft rejection, and the global shortage of transplantable donor materials. This review delves into the intricate composition of the cornea, the landscape of corneal regeneration, and the multifaceted repercussions of scar-related pathologies. It will elucidate the etiology and types of dysfunctions, assess current treatments and their limitations, and explore the potential of regenerative therapy that has emerged in both in vivo and clinical trials. This review will shed light on existing gaps in corneal disorder management and discuss the feasibility and challenges of advancing regenerative therapies for corneal stromal scarring.
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Affiliation(s)
- Christine Chandran
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
| | - Mithun Santra
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
| | - Elizabeth Rubin
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
| | - Moira L. Geary
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
| | - Gary Hin-Fai Yam
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
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Jiang Y, Shen L, Wang B. Non-electrophysiological techniques targeting transient receptor potential (TRP) gene of gastrointestinal tract. Int J Biol Macromol 2024; 262:129551. [PMID: 38367416 DOI: 10.1016/j.ijbiomac.2024.129551] [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: 10/25/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/19/2024]
Abstract
Transient receptor potential (TRP) channels are cation channels related to a wide range of physical and chemical stimuli, they are expressed all along the gastrointestinal system, and a myriad of diseases are often associated with aberrant expression or mutation of the TRP gene, suggesting that TRPs are promising targets for drug therapy. Therefore, a better understanding of the information of TRPs in health and disease could facilitate the development of effective drugs for the treatment of gastrointestinal diseases like IBD. But there are very few generalizations about the experimental techniques studied in this field. In view of the promise of TRP as a therapeutic target, we discuss experimental methods that can be used for TRPs including their distribution, function and interaction with other proteins, as well as some promising emerging technologies to provide experimental methods for future studies.
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Affiliation(s)
- Yuting Jiang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Center for Pharmaceutics Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China
| | - Lan Shen
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Bing Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Center for Pharmaceutics Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China.
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Manzoor HB, Asare-Werehene M, Pereira SD, Satyamoorthy K, Tsang BK. The regulation of plasma gelsolin by DNA methylation in ovarian cancer chemo-resistance. J Ovarian Res 2024; 17:15. [PMID: 38216951 PMCID: PMC10785480 DOI: 10.1186/s13048-023-01332-w] [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: 10/05/2023] [Accepted: 12/22/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Ovarian cancer (OVCA) is the most lethal gynecologic cancer and chemoresistance remains a major hurdle to successful therapy and survival of OVCA patients. Plasma gelsolin (pGSN) is highly expressed in chemoresistant OVCA compared with their chemosensitive counterparts, although the mechanism underlying the differential expression is not known. Also, its overexpression significantly correlates with shortened survival of OVCA patients. In this study, we investigated the methylation role of Ten eleven translocation isoform-1 (TET1) in the regulation of differential pGSN expression and chemosensitivity in OVCA cells. METHODS Chemosensitive and resistant OVCA cell lines of different histological subtypes were used in this study to measure pGSN and TET1 mRNA abundance (qPCR) as well as protein contents (Western blotting). To investigate the role of DNA methylation specifically in pGSN regulation and pGSN-induced chemoresistance, DNMTs and TETs were pharmacologically inhibited in sensitive and resistant OVCA cells using specific inhibitors. DNA methylation was quantified using EpiTYPER MassARRAY system. Gain-and-loss-of-function assays were used to investigate the relationship between TET1 and pGSN in OVCA chemoresponsiveness. RESULTS We observed differential protein and mRNA expressions of pGSN and TET1 between sensitive and resistant OVCA cells and cisplatin reduced their expression in sensitive but not in resistant cells. We observed hypomethylation at pGSN promoter upstream region in resistant cells compared to sensitive cells. Pharmacological inhibition of DNMTs increased pGSN protein levels in sensitive OVCA cells and decreased their responsiveness to cisplatin, however we did not observe any difference in methylation level at pGSN promoter region. TETs inhibition resulted in hypermethylation at multiple CpG sites and decreased pGSN protein level in resistant OVCA cells which was also associated with enhanced response to cisplatin, findings that suggested the methylation role of TETs in the regulation of pGSN expression in OVCA cells. Further, we found that TET1 is inversely related to pGSN but positively related to chemoresponsiveness of OVCA cells. CONCLUSION Our findings broaden our knowledge about the epigenetic regulation of pGSN in OVCA chemoresistance and reveal a novel potential target to re-sensitize resistant OVCA cells. This may provide a future therapeutic strategy to improve the overall OVCA patient survival.
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Affiliation(s)
- Hafiza Bushra Manzoor
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Meshach Asare-Werehene
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Department of Obstetrics & Gynecology, & The Centre for Infection, Immunity and Inflammation (CI3), Faculty of Medicine & Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, K1H 8L1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Satyajit Dey Pereira
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kapaettu Satyamoorthy
- Shri Dharmasthala Manjunatheshwara University, Manjushree Block, Manjushree Nagar Sattur, Dharwad, Karnataka, 580 009, India
| | - Benjamin K Tsang
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
- Department of Obstetrics & Gynecology, & The Centre for Infection, Immunity and Inflammation (CI3), Faculty of Medicine & Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, K1H 8L1, Canada.
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10
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Turan FB, Ercan ME, Firat-Karalar EN. A Chemically Inducible Organelle Rerouting Assay to Probe Primary Cilium Assembly, Maintenance, and Disassembly in Cultured Cells. Methods Mol Biol 2024; 2725:55-78. [PMID: 37856017 DOI: 10.1007/978-1-0716-3507-0_3] [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: 10/20/2023]
Abstract
The primary cilium is a conserved, microtubule-based organelle that protrudes from the surface of most vertebrate cells as well as sensory cells of many organisms. It transduces extracellular chemical and mechanical cues to regulate diverse cellular processes during development and physiology. Loss-of-function studies via RNA interference and CRISPR/Cas9-mediated gene knockouts have been the main tool for elucidating the functions of proteins, protein complexes, and organelles implicated in cilium biology. However, these methods are limited in studying acute spatiotemporal functions of proteins as well as the connection between their cellular positioning and functions. A powerful approach based on inducible recruitment of plus or minus end-directed molecular motors to the protein of interest enables fast and precise control of protein activity in time and in space. In this chapter, we present a chemically inducible heterodimerization method for functional perturbation of centriolar satellites, an emerging membrane-less organelle involved in cilium biogenesis and function. The method we present is based on rerouting of centriolar satellites to the cell center or the periphery in mammalian epithelial cells. We also describe how this method can be applied to study the temporal functions of centriolar satellites during primary cilium assembly, maintenance, and disassembly.
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Affiliation(s)
- F Basak Turan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - M Erdem Ercan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.
- Koc University School of Medicine, Istanbul, Turkey.
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Jeon T, Makabenta JMV, Park J, Nabawy A, Cicek YA, Mirza SS, Welton J, Hassan MA, Huang R, Mager J, Rotello VM. Antimicrobial polymer-siRNA polyplexes as a dual-mode platform for the treatment of wound biofilm infections. MATERIALS HORIZONS 2023; 10:5500-5507. [PMID: 37815454 PMCID: PMC10841859 DOI: 10.1039/d3mh01108a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Treatment of wound biofilm infections faces challenges from both pathogens and uncontrolled host immune response. Treating both issues through a single vector would provide enhanced wound healing. Here, we report the use of a potent cationic antimicrobial polymer to generate siRNA polyplexes for dual-mode treatment of wound biofilms in vivo. These polyplexes act both as an antibiofilm agent and a delivery vehicle for siRNA for the knockdown of biofilm-associated pro-inflammatory MMP9 in host macrophages. The resulting polyplexes were effective in vitro, eradicating MRSA biofilms and efficiently delivering siRNA to macrophages in vitro with concomitant knockdown of MMP9. These polyplexes were likewise effective in an in vivo murine wound biofilm model, significantly reducing bacterial load in the wound (∼99% bacterial clearance) and reducing MMP9 expression by 80% (qRT-PCR). This combination therapeutic strategy dramatically reduced wound purulence and significantly expedited wound healing. Taken together, these polyplexes provide an effective and translatable strategy for managing biofilm-infected wounds.
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Affiliation(s)
- Taewon Jeon
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 230 Stockbridge Road, Amherst, Massachusetts, 01003, USA.
| | - Jessa Marie V Makabenta
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Jungmi Park
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Ahmed Nabawy
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Yagiz Anil Cicek
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Sarah S Mirza
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, 661 N Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Janelle Welton
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, 661 N Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Muhammad Aamir Hassan
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Rui Huang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, 661 N Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Vincent M Rotello
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 230 Stockbridge Road, Amherst, Massachusetts, 01003, USA.
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
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12
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Haiduk TS, Sicking M, Brücksken KA, Espinoza-Sánchez NA, Eder KM, Kemper B, Eich HT, Götte M, Greve B, Troschel FM. Dysregulated Stem Cell Markers Musashi-1 and Musashi-2 are Associated with Therapy Resistance in Inflammatory Breast Cancer. Arch Med Res 2023; 54:102855. [PMID: 37481823 DOI: 10.1016/j.arcmed.2023.102855] [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: 01/20/2023] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND AND AIM While preliminary evidence points to pro-tumorigenic roles for the Musashi (MSI) RNA-binding proteins Musashi-1 (MSI1) and Musashi-2 (MSI2) in some breast cancer subtypes, no data exist for inflammatory breast cancer (IBC). METHODS MSI gene expression was quantified in IBC SUM149PT cells. We then used small interfering RNA-based MSI1 and MSI2 double knockdown (DKD) to understand gene expression and functional changes upon MSI depletion. We characterized cancer stem cell characteristics, cell apoptosis and cell cycle progression via flow cytometry, mammospheres via spheroid assays, migration and proliferation via digital holographic microscopy, and cell viability using BrdU assays. Chemoresistance was determined for paclitaxel and cisplatin with MTT assays and radioresistance was assessed with clonogenic analyses. In parallel, we supported our in vitro data by analyzing publicly available patient IBC gene expression datasets. RESULTS MSI1 and MSI2 are upregulated in breast cancer generally and IBC specifically. MSI2 is more commonly expressed compared to MSI1. MSI DKD attenuated proliferation, cell cycle progression, migration, and cell viability while increasing apoptosis. Stem cell characteristics CD44(+)/CD24(-), TERT and Oct4 were associated with MSI expression in vivo and were decreased in vitro after MSI DKD as was ALDH expression and mammosphere formation. In vivo, chemoresistant tumors were characterized by MSI upregulation upon chemotherapy application. In vitro, MSI DKD was able to alleviate chemo- and radioresistance. CONCLUSIONS The Musashi RNA binding proteins are dysregulated in IBC and associated with tumor proliferation, cancer stem cell phenotype, chemo- and radioresistance. MSI downregulation alleviates therapy resistance and attenuates tumor proliferation in vitro.
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Affiliation(s)
- Tiffany S Haiduk
- Department of Radiation Oncology, University Hospital Münster, Münster, Germany
| | - Mark Sicking
- Department of Radiation Oncology, University Hospital Münster, Münster, Germany
| | - Kathrin A Brücksken
- Department of Radiation Oncology, University Hospital Münster, Münster, Germany
| | - Nancy A Espinoza-Sánchez
- Department of Radiation Oncology, University Hospital Münster, Münster, Germany; Department of Gynecology and Obstetrics, University Hospital Münster, Münster, Germany
| | - Kai Moritz Eder
- Biomedical Technology Center, Medical Faculty, University of Münster, Münster, Germany
| | - Björn Kemper
- Biomedical Technology Center, Medical Faculty, University of Münster, Münster, Germany
| | - Hans Theodor Eich
- Department of Radiation Oncology, University Hospital Münster, Münster, Germany
| | - Martin Götte
- Department of Gynecology and Obstetrics, University Hospital Münster, Münster, Germany
| | - Burkhard Greve
- Department of Radiation Oncology, University Hospital Münster, Münster, Germany
| | - Fabian M Troschel
- Department of Radiation Oncology, University Hospital Münster, Münster, Germany.
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13
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Moraleva A, Deryabin A, Kordyukova M, Polzikov M, Shishova K, Dobrochaeva K, Rubtsov Y, Rubtsova M, Dontsova O, Zatsepina O. Human nucleolar protein SURF6/RRP14 participates in early steps of pre-rRNA processing. PLoS One 2023; 18:e0285833. [PMID: 37450438 PMCID: PMC10348582 DOI: 10.1371/journal.pone.0285833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/02/2023] [Indexed: 07/18/2023] Open
Abstract
The biogenesis of ribosomes requires tightly controlled transcription and processing of pre-rRNA which comprises ribosomal RNAs forming the core of large and small ribosomal subunits. Early steps of the pre-rRNA processing and assembly of the ribosomal subunits require a large set of proteins that perform folding and nucleolytic cleavage of pre-rRNAs in the nucleoli. Structure and functions of proteins involved in the pre-rRNA processing have been extensively studied in the budding yeast S. cerevisiae. Functional characterization of their human homologues is complicated by the complexity of mammalian ribosomes and increased number of protein factors involved in the ribosomal biogenesis. Homologues of human nucleolar protein SURF6 from yeast and mouse, Rrp14 and Surf6, respectively, had been shown to be involved in the early steps of pre-rRNA processing. Rrp14 works as RNA chaperone in complex with proteins Ssf1 and Rrp15. Human SURF6 knockdown and overexpression were used to clarify a role of SURF6 in the early steps of pre-rRNA processing in human cell lines HeLa and HTC116. By analyzing the abundance of the rRNA precursors in cells with decreased level or overexpression of SURF6, we demonstrated that human SURF6 is involved in the maturation of rRNAs from both small and large ribosomal subunits. Changes in the SURF6 level caused by knockdown or overexpression of the protein do not result in the death of HeLa cells in contrast to murine embryonic fibroblasts, but significantly alter the distribution of cells among the phases of the cell cycle. SURF6 knockdown in both p53 sufficient and p53 deficient HCT116 human cancer cells results in elongation of G0/G1 and shortening of G2/M phase. This surprising result suggests p53 independence of SURF6 effects on the cell cycle and possible multiple functions of SURF6. Our data point to the shift from pathway 1 to pathway 2 of the rRNA biogenesis caused by the SURF6 knockdown and its likely association with p53 pathway.
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Affiliation(s)
- Anastasiia Moraleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Alexander Deryabin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Maria Kordyukova
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russian Federation
| | - Mikhail Polzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Kseniya Shishova
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russian Federation
| | - Kira Dobrochaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Yury Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Maria Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Olga Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
- SkolTech, Moscow, Russian Federation
| | - Olga Zatsepina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
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14
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Dubey SM, Han S, Stutzman N, Prigge MJ, Medvecká E, Platre MP, Busch W, Fendrych M, Estelle M. The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in Arabidopsis thaliana. MOLECULAR PLANT 2023; 16:1120-1130. [PMID: 37391902 PMCID: PMC10720607 DOI: 10.1016/j.molp.2023.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/31/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFB auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified. Here we show that the N-terminal region of AFB1, including the F-box domain and residues that contribute to auxin binding, is essential and sufficient for its specific role in the rapid response. Substitution of the N-terminal region of AFB1 with that of TIR1 disrupts its distinct cytoplasm-enriched localization and activity in rapid root growth inhibition by auxin. Importantly, the N-terminal region of AFB1 is indispensable for auxin-triggered calcium influx, which is a prerequisite for rapid root growth inhibition. Furthermore, AFB1 negatively regulates lateral root formation and transcription of auxin-induced genes, suggesting that it plays an inhibitory role in canonical auxin signaling. These results suggest that AFB1 may buffer the transcriptional auxin response, whereas it regulates rapid changes in cell growth that contribute to root gravitropism.
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Affiliation(s)
- Shiv Mani Dubey
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Soeun Han
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Nathan Stutzman
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Michael J Prigge
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Eva Medvecká
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Matthieu Pierre Platre
- Plant Molecular and Cellular Biology Laboratory and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Prague, Czech Republic.
| | - Mark Estelle
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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15
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Uppaluri KR, Challa HJ, Gaur A, Jain R, Krishna Vardhani K, Geddam A, Natya K, Aswini K, Palasamudram K, K SM. Unlocking the potential of non-coding RNAs in cancer research and therapy. Transl Oncol 2023; 35:101730. [PMID: 37406550 PMCID: PMC10366642 DOI: 10.1016/j.tranon.2023.101730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have emerged as key regulators of gene expression, with growing evidence implicating their involvement in cancer development and progression. The potential of ncRNAs as diagnostic and prognostic biomarkers for cancer is promising, with emphasis on their use in liquid biopsy and tissue-based diagnostics. In a nutshell, the review comprehensively summarizes the diverse classes of ncRNAs implicated in cancer, including microRNAs, long non-coding RNAs, and circular RNAs, and their functions and mechanisms of action. Furthermore, we describe the potential therapeutic applications of ncRNAs, including anti-miRNA oligonucleotides, siRNAs, and other RNA-based therapeutics in cancer treatment. However, significant challenges remain in developing effective ncRNA-based diagnostics and therapeutics, including the lack of specificity, limited understanding of mechanisms, and delivery challenges. This review also covers the current state-of-the-art non-coding RNA research technologies and bioinformatic analysis tools. Lastly, we outline future research directions in non-coding RNA research in cancer, including developing novel biomarkers, therapeutic targets, and modalities. In summary, this review provides a comprehensive understanding of non-coding RNAs in cancer and their potential clinical applications, highlighting both the opportunities and challenges in this rapidly evolving field.
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Affiliation(s)
- Kalyan Ram Uppaluri
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India.
| | - Hima J Challa
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - Ashish Gaur
- Department of Biotechnology, GLA University, Mathura, India
| | - Rajul Jain
- Dayalbagh Educational Institute, Agra, India
| | - K Krishna Vardhani
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - Anusha Geddam
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - K Natya
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - K Aswini
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - Kalyani Palasamudram
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - Sri Manjari K
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India.
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16
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Yadav K, Sahu KK, Sucheta, Gnanakani SPE, Sure P, Vijayalakshmi R, Sundar VD, Sharma V, Antil R, Jha M, Minz S, Bagchi A, Pradhan M. Biomedical applications of nanomaterials in the advancement of nucleic acid therapy: Mechanistic challenges, delivery strategies, and therapeutic applications. Int J Biol Macromol 2023; 241:124582. [PMID: 37116843 DOI: 10.1016/j.ijbiomac.2023.124582] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/30/2023]
Abstract
In the past few decades, substantial advancement has been made in nucleic acid (NA)-based therapies. Promising treatments include mRNA, siRNA, miRNA, and anti-sense DNA for treating various clinical disorders by modifying the expression of DNA or RNA. However, their effectiveness is limited due to their concentrated negative charge, instability, large size, and host barriers, which make widespread application difficult. The effective delivery of these medicines requires safe vectors that are efficient & selective while having non-pathogenic qualities; thus, nanomaterials have become an attractive option with promising possibilities despite some potential setbacks. Nanomaterials possess ideal characteristics, allowing them to be tuned into functional bio-entity capable of targeted delivery. In this review, current breakthroughs in the non-viral strategy of delivering NAs are discussed with the goal of overcoming challenges that would otherwise be experienced by therapeutics. It offers insight into a wide variety of existing NA-based therapeutic modalities and techniques. In addition to this, it provides a rationale for the use of non-viral vectors and a variety of nanomaterials to accomplish efficient gene therapy. Further, it discusses the potential for biomedical application of nanomaterials-based gene therapy in various conditions, such as cancer therapy, tissue engineering, neurological disorders, and infections.
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Affiliation(s)
- Krishna Yadav
- Raipur Institute of Pharmaceutical Education and Research, Sarona, Raipur, Chhattisgarh 492010, India
| | - Kantrol Kumar Sahu
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Sucheta
- School of Medical and Allied Sciences, K. R. Mangalam University, Gurugram, Haryana 122103, India
| | | | - Pavani Sure
- Department of Pharmaceutics, Vignan Institute of Pharmaceutical Sciences, Hyderabad, Telangana, India
| | - R Vijayalakshmi
- Department of Pharmaceutical Analysis, GIET School of Pharmacy, Chaitanya Knowledge City, Rajahmundry, AP 533296, India
| | - V D Sundar
- Department of Pharmaceutical Technology, GIET School of Pharmacy, Chaitanya Knowledge City, Rajahmundry, AP 533296, India
| | - Versha Sharma
- Department of Biotechnology, School of Biological Sciences, Dr. Harisingh Gour Central University, Sagar, M.P. 470003, India
| | - Ruchita Antil
- Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, England, United Kingdom of Great Britain and Northern Ireland
| | - Megha Jha
- Department of Biotechnology, School of Biological Sciences, Dr. Harisingh Gour Central University, Sagar, M.P. 470003, India
| | - Sunita Minz
- Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak, M.P., 484887, India
| | - Anindya Bagchi
- Tumor Initiation & Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road La Jolla, CA 92037, USA
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17
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Hu D, Xia M, Wu L, Liu H, Chen Z, Xu H, He C, Wen J, Xu X. Challenges and advances for glioma therapy based on inorganic nanoparticles. Mater Today Bio 2023; 20:100673. [PMID: 37441136 PMCID: PMC10333687 DOI: 10.1016/j.mtbio.2023.100673] [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: 03/15/2023] [Revised: 05/10/2023] [Accepted: 05/18/2023] [Indexed: 07/15/2023] Open
Abstract
Glioma is one of the most serious central nervous system diseases, with high mortality and poor prognosis. Despite the continuous development of existing treatment methods, the median survival time of glioma patients is still only 15 months. The main treatment difficulties are the invasive growth of glioma and the obstruction of the blood-brain barrier (BBB) to drugs. With rapid advancements in nanotechnology, inorganic nanoparticles (INPs) have shown favourable application prospects in the diagnosis and treatment of glioma. Due to their extraordinary intrinsic features, INPs can be easily fabricated, while doping with other elements and surface modification by biological ligands can be used to enhance BBB penetration, targeted delivery and biocompatibility. Guided glioma theranostics with INPs can improve and enhance the efficacy of traditional methods such as chemotherapy, radiotherapy and gene therapy. New strategies, such as immunotherapy, photothermal and photodynamic therapy, magnetic hyperthermia therapy, and multifunctional inorganic nanoplatforms, have also been facilitated by INPs. This review emphasizes the current state of research and clinical applications of INPs, including glioma targeting and BBB penetration enhancement methods, in vivo and in vitro biocompatibility, and diagnostic and treatment strategies. As such, it provides insights for the development of novel glioma treatment strategies.
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Affiliation(s)
- Die Hu
- Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Miao Xia
- Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Linxuan Wu
- Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Hanmeng Liu
- Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Zhigang Chen
- Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Hefeng Xu
- Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Chuan He
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Jian Wen
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Xiaoqian Xu
- Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
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18
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Phanindhar K, Mishra RK. Auxin-inducible degron system: an efficient protein degradation tool to study protein function. Biotechniques 2023; 74:186-198. [PMID: 37191015 DOI: 10.2144/btn-2022-0108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Targeted protein degradation, with its rapid protein depletion kinetics, allows the measurement of acute changes in the cell. The auxin-inducible degron (AID) system, rapidly degrades AID-tagged proteins only in the presence of auxin. The AID system being inducible makes the study of essential genes and dynamic processes like cell differentiation, cell cycle and genome organization feasible. The AID degradation system has been adapted to yeast, protozoans, C. elegans, Drosophila, zebrafish, mouse and mammalian cell lines. Using the AID system, researchers have unveiled novel functions for essential proteins at developmental stages that were previously difficult to investigate due to early lethality. This comprehensive review discusses the development, advancements, applications and drawbacks of the AID system and compares it with other available protein degradation systems.
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Affiliation(s)
- Kundurthi Phanindhar
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- Tata Institute for Genetics & Society (TIGS), Bangalore, 560065, India
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19
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Tao GY, Xie YH, Li WF, Li KP, Sun C, Wang HM, Sun XM. LkARF7 and LkARF19 overexpression promote adventitious root formation in a heterologous poplar model by positively regulating LkBBM1. Commun Biol 2023; 6:372. [PMID: 37020138 PMCID: PMC10076273 DOI: 10.1038/s42003-023-04731-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Cuttage propagation involves adventitious root formation induced by auxin. In our previous study, Larix kaempferi BABY BOOM 1 (LkBBM1), which is known to regulate adventitious root formation, was affected by auxin. However, the relationship between LkBBM1 and auxin remains unclear. Auxin response factors (ARFs) are a class of important transcription factors in the auxin signaling pathway and modulate the expression of early auxin-responsive genes by binding to auxin response elements. In the present study, we identified 14 L. kaempferi ARFs (LkARFs), and found LkARF7 and LkARF19 bound to LkBBM1 promoter and enhanced its transcription using yeast one-hybrid, ChIP-qPCR, and dual-luciferase assays. In addition, the treatment with naphthalene acetic acid promoted the expression of LkARF7 and LkARF19. We also found that overexpression of these two genes in poplar promoted adventitious root formation. Furthermore, LkARF19 interacted with the DEAD-box ATP-dependent RNA helicase 53-like protein to form a heterodimer to regulate adventitious root formation. Altogether, our results reveal an additional regulatory mechanism underlying the control of adventitious root formation by auxin.
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Affiliation(s)
- Gui-Yun Tao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yun-Hui Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wan-Feng Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Kui-Peng Li
- Guangxi Forestry Research Institute, Guangxi, 530009, China
| | - Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Hong-Ming Wang
- College of Bioengineering and Biotechnology, Tianshui Normal University, Gansu, 741000, China
| | - Xiao-Mei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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20
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Santos C, Malheiro S, Correia M, Damásio J. Gene Suppression Therapies in Hereditary Cerebellar Ataxias: A Systematic Review of Animal Studies. Cells 2023; 12:cells12071037. [PMID: 37048110 PMCID: PMC10093402 DOI: 10.3390/cells12071037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 03/30/2023] Open
Abstract
Introduction: Hereditary cerebellar ataxias (HCAs) are a heterogenous group of neurodegenerative disorders associated with severe disability. Treatment options are limited and overall restricted to symptomatic approaches, leading to poor prognoses. In recent years, there has been extensive research on gene suppression therapies (GSTs) as a new hope for disease-modifying strategies. In this article, we aim to perform a review of in vivo studies investigating the efficacy and safety profile of GSTs in HCAs. Methods: A structured PubMed® search on GSTs in HCAs from January 1993 up to October 2020 was performed. Inclusion and exclusion criteria were defined, and the selection process was conducted accordingly. The screening process was independently carried out by two authors and was initially based on title and abstract, followed by full-text reading. The risk-of-bias assessment was performed with SYRCLE’s tool. A data extraction sheet was created to collect relevant information from each selected article. Results: The initial search yielded 262 papers, of which 239 were excluded. An additional article was obtained following reference scrutiny, resulting in a total of 24 articles for final analysis. Most studies were not clear on the tools used to assess bias. In SCA1, SCA2, MJD/SCA3 and SCA7, RNA interference (iRNA) and antisense oligonucleotide (ASO) therapies proved to be well tolerated and effective in suppressing mutant proteins, improving neuropathological features and the motor phenotype. In SCA6, the phenotype was improved, but no investigation of adverse effects was performed. In FRDA, only the suppression efficacy of the electroporation of the clustered regularly interspaced short palindromic repeats associated with Cas9 enzyme system (CRISPR-Cas9) system was tested and confirmed. Conclusion: The literature reviewed suggests that GSTs are well tolerated and effective in suppressing the targeted proteins, improving neuropathological features and the motor phenotype in vivo. Nonetheless, there is no guarantee that these results are free of bias. Moreover, further investigation is still needed to clarify the GST effect on HCAs such as FRDA, SCA6 and SCA2.
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Strazzer P, Verbree B, Bliek M, Koes R, Quattrocchio FM. The Amsterdam petunia germplasm collection: A tool in plant science. FRONTIERS IN PLANT SCIENCE 2023; 14:1129724. [PMID: 37025133 PMCID: PMC10070740 DOI: 10.3389/fpls.2023.1129724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
Petunia hybrida is a plant model system used by many researchers to investigate a broad range of biological questions. One of the reasons for the success of this organism as a lab model is the existence of numerous mutants, involved in a wide range of processes, and the ever-increasing size of this collection owing to a highly active and efficient transposon system. We report here on the origin of petunia-based research and describe the collection of petunia lines housed in the University of Amsterdam, where many of the existing genotypes are maintained.
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Huber A, Dijkstra C, Ernst M, Eissmann MF. Generation of gene-of-interest knockouts in murine organoids using CRISPR-Cas9. STAR Protoc 2023; 4:102076. [PMID: 36853714 PMCID: PMC9918790 DOI: 10.1016/j.xpro.2023.102076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/11/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Gene-of-interest knockout organoids present a powerful and versatile research tool to study a gene's effects on many biological and pathological processes. Here, we present a straightforward and broadly applicable protocol to generate gene knockouts in mouse organoids using CRISPR-Cas9 technology. We describe the processes of transient transfecting organoids with pre-assembled CRISPR-Cas9 ribonucleoprotein complexes, organoid cell sorting, and establishing clonal organoid culture pairs. We then detail how to confirm the knockout via Western blot analysis.
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Affiliation(s)
- Anne Huber
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia.
| | - Christine Dijkstra
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
| | - Moritz F Eissmann
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia.
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23
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Hou J, Meng S, Zhang B, Ruan R, Zhang Y, Wang Z, Song M, Bai Z. Effect of RNA interference with glutamate decarboxylase on acid resistance of Trichinella spiralis. Acta Trop 2023; 241:106869. [PMID: 36849092 DOI: 10.1016/j.actatropica.2023.106869] [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: 11/25/2022] [Revised: 01/24/2023] [Accepted: 02/18/2023] [Indexed: 02/27/2023]
Abstract
Trichinella spiralis is a zoonotic parasite that infects most mammals, even humans. Glutamate decarboxylase (GAD) is an important enzyme in glutamate-dependent acid resistance system 2 (AR2), but the GAD of T. spiralis in AR2 is unclear. We aimed to investigate the role of T. spiralis glutamate decarboxylase (TsGAD) in AR2. We silenced the TsGAD gene to evaluate the AR of T. spiralis muscle larvae (ML) in vivo and in vitro via siRNA. The results showed that recombinant TsGAD was recognized by anti-rTsGAD polyclonal antibody (57 kDa), and qPCR indicated that TsGAD transcription peaked at pH 2.5 for 1 h compared to that with pH 6.6 phosphate-buffered saline. Indirect immunofluorescence assays revealed that TsGAD was expressed in the epidermis of ML. After TsGAD silencing in vitro, TsGAD transcription and the survival rate of ML decreased by 15.2% and 17%, respectively, compared with those of the PBS group. Both TsGAD enzymatic activity and the acid adjustment of siRNA1-silenced ML were weakened. In vivo, each mouse was orally infected with 300 siRNA1-silenced ML. On days 7 and 42 post-infection, the reduction rates of adult worms and ML were 31.5% and 49.05%, respectively. Additionally, the reproductive capacity index and larvae per gram of ML were 62.51±7.32 and 1250.22±146.48, respectively, lower than those of the PBS group. Haematoxylin-eosin staining revealed many inflammatory cells infiltrating the nurse cells in the diaphragm of mice infected with siRNA1-silenced ML. The survival rate of the F1 generation ML was 27% higher than that of the F0 generation ML, but there was no difference from the PBS group. These results first indicated that GAD plays a crucial role in AR2 of T. spiralis. TsGAD gene silencing reduced the worm burden in mice, providing data for the comprehensive study of the AR system of T. spiralis and a new idea for the prevention of trichinosis.
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Affiliation(s)
- Jiaming Hou
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Shi Meng
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Bohan Zhang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Rulin Ruan
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Yan Zhang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Ze Wang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Mingxin Song
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China.
| | - Zhikun Bai
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China.
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Liang J, Liang J, Tan Q, Wang Z. ELAC2 Functions as a Key Gene in the Early Development of Placental Formation Based on WGCNA. Cells 2023; 12:cells12040613. [PMID: 36831280 PMCID: PMC9954566 DOI: 10.3390/cells12040613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The placenta plays a crucial role in mammalian fetal growth. The most important cell type in the placenta is the trophoblast cell. Many genes have been reported to play important functions in the differentiation of early placental trophoblast cells. Weighted gene co-expression network analysis (WGCNA) is a systematic biological method for describing the correlation patterns among genes across microarray samples. We used WGCNA to screen placental trophoblast development-related genes, and through experimental confirmation, we showed that, among these genes, ELAC2 may play an important regulatory role in the early development of mammalian placental formation. ELAC2 regulates early placental trophoblast differentiation by affecting cell migration and cell proliferation. In addition, ELAC2 may be involved in regulating cell migration processes in a manner that affects epithelial mesenchymal transition (EMT).
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Affiliation(s)
- Junyong Liang
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
| | - Jingjie Liang
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
| | - Qiang Tan
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
| | - Zhengguang Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310000, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
- Correspondence:
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25
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Han Y, Li B, Li Y, Niu D. The Inhibitory Effects of RNA-Interference-Mediated Guanylate Cyclase Knockdown on Larval Metamorphosis and Early Progeny Growth of Razor Clam. Genes (Basel) 2023; 14:459. [PMID: 36833386 PMCID: PMC9956218 DOI: 10.3390/genes14020459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/10/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Guanylate cyclase (GC, cGMPase) is a key enzyme in organisms, catalyzing the synthesis of cGMP from GTP, thus making cGMP work. cGMP plays a vital role in the regulation of cell and biological growth as a second messenger in signaling pathways. In this study, we screened and identified cGMPase from the razor clam Sinonovacula constricta, which encoded 1257 amino acids and was widely expressed in different tissues, especially the gill and liver. We also screened one double-stranded RNA (dsRNA), cGMPase, which was used to knockdown cGMPase at three larval metamorphosis development stages: trochophores-veliger larve, veliger larve-umbo larve, and umbo larve-creeping larvae. We showed that interference at these stages significantly inhibited larval metamorphosis and survival rates. cGMPase knockdown resulted in an average metamorphosis rate of 60% and an average mortality rate of 50% when compared with control clams. After 50 days, shell length and body weight were inhibited to 53% and 66%, respectively. Thus, cGMPase appeared to regulate metamorphosis development and growth in S. constricta. By examining the role of the key gene in the metamorphosis development of S. constricta larvae and the growth and development period, we can provide some data reference for studying the growth and development mechanism of shellfish, and the results provided basic information for the breeding of S. constricta.
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Affiliation(s)
- Yuting Han
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai 201306, China
| | - Beibei Li
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai 201306, China
| | - Yifeng Li
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Donghong Niu
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
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26
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Zhang M, Lin D, Luo C, Wei P, Cui K, Chen K, Chen Z. saKLK1-374 is more difficult to induce KLK1 expression in normal prostate cell lines than that in prostate cancer cell lines: Rethinking the universality of RNA activation. Biochem Biophys Res Commun 2023; 643:157-168. [PMID: 36610381 DOI: 10.1016/j.bbrc.2022.12.075] [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: 11/28/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
RNA activation, as a method of regulating gene expression at the transcriptional level, is far less widely used than RNA interference because of the insufficient understanding of the mechanism and the unstable success rate. It is necessary to analyze the failure cases of RNA activation to promote the application of RNA activation. When we validated the saRNAs designed to induce KLK1 expression, we found that saKLK1-374 can upregulate KLK1 expression in prostate tumor cell lines, but failed in normal prostate cell lines. To determine whether the RNA activation of normal cells is difficult only when the target gene is KLK1, we tested p21WAF1/CIP1 as the target gene in RNA activation experiments of normal and cancer prostate cells. Next, to determine whether the above phenomenon exists in other tissues, we used normal and cancerous bladder cells to perform RNA activation experiments with KLK1 and p21WAF1/CIP1 as targets. We have also extended the time from transfection to detection to evaluate whether a longer incubation time can make saRNA upregulate the target genes in normal cells. Fluorescently labeled dsRNA was transfected to evaluate the transfection efficiency, and the expression of Ago2 and IPO8 necessary for RNA activation was also detected. The p21WAF1/CIP1 could be significantly upregulated by saRNA in prostate cancer cells, but not in normal prostate cells. The expression of KLK1 in bladder-derived cell lines was extremely low and could not be induced by saRNA. The p21WAF1/CIP1 was upregulated by saRNA to a higher extent in bladder cancer cells but to a lower extent in normal bladder cells. Prolonging incubation time could not make saRNA induce the expression of target genes in normal cells. Compared with tumor cells used in this study, normal cells had lower transfection efficiency or lower expression of Ago2 and IPO8. Although it has been currently found that normal cell lines in the prostate and bladder might be more difficult to be successfully induced target gene expression by exogenous saRNA than tumor cells due to low transfection efficiency or Ago2 and IPO8 expression, it is not certain that this phenomenon occurs in other types of tissue. However, researchers still need to pay attention to the transfection efficiency and/or the expression levels of Ago2 and IPO8 when conducting RNA activation experiments in normal cells.
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Affiliation(s)
- Mengyang Zhang
- Department of Urology, Tongji Hospital Affiliated to Tongji Medical College of Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China
| | - Dongxu Lin
- Department of Urology, Tongji Hospital Affiliated to Tongji Medical College of Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China
| | - Changcheng Luo
- Department of Urology, Tongji Hospital Affiliated to Tongji Medical College of Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China
| | - Pengyu Wei
- Department of Urology, Tongji Hospital Affiliated to Tongji Medical College of Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China
| | - Kai Cui
- Department of Urology, Tongji Hospital Affiliated to Tongji Medical College of Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China
| | - Ke Chen
- Department of Urology, Tongji Hospital Affiliated to Tongji Medical College of Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China
| | - Zhong Chen
- Department of Urology, Tongji Hospital Affiliated to Tongji Medical College of Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China.
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Dubey SM, Han S, Stutzman N, Prigge MJ, Medvecká E, Platre MP, Busch W, Fendrych M, Estelle M. The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in Arabidopsis thaliana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522696. [PMID: 36711737 PMCID: PMC9881920 DOI: 10.1101/2023.01.04.522696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFBs auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified. Here we show that the N-terminal region of AFB1, including the F-box domain and residues that contribute to auxin binding, are essential and sufficient for its specific role in the rapid response. Substitution of the N-terminal region of AFB1 with that of TIR1 disrupts its distinct cytoplasm-enriched localization and activity in rapid root growth inhibition. Importantly, the N-terminal region of AFB1 is indispensable for auxin-triggered calcium influx which is a prerequisite for rapid root growth inhibition. Furthermore, AFB1 negatively regulates lateral root formation and transcription of auxin-induced genes, suggesting that it plays an inhibitory role in canonical auxin signaling. These results suggest that AFB1 may buffer the transcriptional auxin response while it regulates rapid changes in cell growth that contribute to root gravitropism.
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Affiliation(s)
- Shiv Mani Dubey
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Soeun Han
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| | - Nathan Stutzman
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| | - Michael J Prigge
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| | - Eva Medvecká
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Matthieu Pierre Platre
- Plant Molecular and Cellular Biology Laboratory and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Prague, Czech Republic,For correspondence: and
| | - Mark Estelle
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States,For correspondence: and
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28
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Sil S, Bertilla J, Rupachandra S. A comprehensive review on RNA interference-mediated targeting of interleukins and its potential therapeutic implications in colon cancer. 3 Biotech 2023; 13:18. [PMID: 36568500 PMCID: PMC9768089 DOI: 10.1007/s13205-022-03421-x] [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: 04/18/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Colon cancer is the world's fourth leading cause of death. It is cancer of the latter part of the large intestine, i.e. the colon. Chronic inflammation over a long period also leads to the development of cancer. Cancer in the colon region is arduous to diagnose and is detected at a later stage when it metastasizes to other parts of the body like the liver, lungs, peritoneum, etc. Colon cancer is a great example of solid tumours associated with chronic inflammation. Although conventional therapies are effective, they lose their effectiveness beyond a certain point. Relapse of the disease occurs frequently. RNA interference (RNAi) is emerging as a great tool to specifically attack the cancer cells of a target site like the colon. RNAi deals with epigenetic changes made in the defective cells which ultimately leads to their death without harming the healthy cells. In this review, two types of epigenetic modulators have been considered, namely siRNA and miRNA, and their effect on interleukins. Interleukins, a class of cytokines, are major inflammatory responses of the body that are released by immune cells like leukocytes and macrophages. Some of these interleukins are pro-inflammatory, thereby promoting inflammation which eventually causes cancer. RNAi can prevent colon cancer by inhibiting pro-inflammatory interleukins.
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Affiliation(s)
- Sagari Sil
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu 603 203 India
| | - Janet Bertilla
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu 603 203 India
| | - S. Rupachandra
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu 603 203 India
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29
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Tarverdizadeh Y, Khalili M, Esmaeili S, Ahmadian G, Golchin M, Hajizade A. Targeted gene inactivation in Salmonella Typhi by CRISPR/Cas9-assisted homologous recombination. World J Microbiol Biotechnol 2022; 39:58. [PMID: 36572753 DOI: 10.1007/s11274-022-03504-0] [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: 09/09/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Targeted gene inactivation (TGI) is a widely used technique for the study of genes' functions. There are many different methods for TGI, however, most of them are so complicated and time-consuming. New promising genetic engineering tools are developing for this purpose. In the present study, for the first time we disrupted a virulence gene from Salmonella enterica serovar Typhi (S. Typhi), located in the bacterial chromosome using CRISPR/Cas9 system and homology directed repair (HDR). METHODS For this aim, pCas9 plasmid containing Cas9 enzyme and required proteins for homology directed recombination was transferred to S. Typhi by electroporation. On the other hand, a specific guide RNA (gRNA) was designed using CRISPOR online tool. Synthetic gRNA was cloned into pTargetF plasmid. Also, a DNA fragment (HDR fragment) was designed to incorporate into the bacterial chromosome following the cleavage of the bacterial genome by Cas9 enzyme. pTargetF containing gRNA and HDR fragment were co-transferred to S. Typhi containing pcas9 plasmid. The transformed bacteria were screened for recombination using PCR, restriction digestion and sequencing. RESULTS The results of PCR, restriction digestion and sequencing showed the successful recombination of S. Typhi, in which the gidA gene is disrupted. CONCLUSION In the present study we aimed to develop a rapid and robust method for targeted gene inactivation in a bacterial species, S. Typhi. This procedure can be exploited for disruption of other Salmonella as well as other bacteria's genes.
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Affiliation(s)
- Yousof Tarverdizadeh
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Khalili
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Saber Esmaeili
- Department of Epidemiology and Biostatics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mehdi Golchin
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Abbas Hajizade
- Biology Research Center, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran.
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Liang Z, Yang Y, Sun X, Du J, Wang Q, Zhang G, Zhang J, Yin X, Singh D, Su P, Zhang X. Integrated Analysis of MicroRNA and mRNA Expression Profiles in the Fat Bodies of MbMNPV-Infected Helicoverpa armigera. Viruses 2022; 15:19. [PMID: 36680059 PMCID: PMC9861407 DOI: 10.3390/v15010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs), are a novel class of gene expression regulators, that have been found to participate in regulating host-virus interactions. However, the function of insect-derived miRNAs in response to virus infection is poorly understood. We analyzed miRNA expression profiles in the fat bodies of Helicoverpa armigera (H. armigera) infected with Mamestra brassicae multiple nucleopolyhedroviruses (MbMNPV). A total of 52 differentially expressed miRNAs (DEmiRNAs) were filtered out through RNA-seq analysis. The targets of 52 DEmiRNAs were predicted and 100 miRNA-mRNA interaction pairs were obtained. The predicted targets of DEmiRNAs were mainly enriched in the Wnt signaling pathway, phagosome, and mTOR signaling pathway, which are related to the virus infection. Real-time PCR was used to verify the RNA sequencing results. ame-miR-317-3p, mse-miR-34, novel1-star, and sfr-miR-6094-5p were shown to be involved in the host response to MbMNPV infection. Results suggest that sfr-miR-6094-5p can negatively regulate the expression of four host genes eIF3-S7, CG7583, CG16901, and btf314, and inhibited MbMNPV infection significantly. Further studies showed that RNAi-mediated knockdown of eIF3-S7 inhibited the MbMNPV infection. These findings suggest that sfr-miR-6094-5p inhibits MbMNPV infection by negatively regulating the expression of eIF3-S7. This study provides new insights into MbMNPV and H. armigera interaction mechanisms.
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Affiliation(s)
- Zhenpu Liang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanqing Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoyan Sun
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Junyang Du
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Qiuyun Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Guozhi Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiran Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Deepali Singh
- School of Biotechnology, Gautam, Buddha University, Greater Noida 201312, India
| | - Ping Su
- Institute of Agricultural Sciences of the 14th Division of Xinjiang Production and Construction Corps, Kunyu 848116, China
| | - Xiaoxia Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
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31
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Zhang L, Liang Y, Liang G, Tian Z, Zhang Y, Liu Z, Ji X. The therapeutic prospects of N-acetylgalactosamine-siRNA conjugates. Front Pharmacol 2022; 13:1090237. [PMID: 36588695 PMCID: PMC9794871 DOI: 10.3389/fphar.2022.1090237] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
RNA interference has become increasingly used for genetic therapy following the rapid development of oligonucleotide drugs. Significant progress has been made in its delivery system and implementation in the treatment of target organs. After a brief introduction of RNA interference technology and siRNA, the efficiency and stability of GalNAc-siRNA conjugates are highlighted since several oligonucleotide drugs of GalNAc have been approved for clinical use in recent years. The structure and features of GalNAc-siRNA conjugates are studied and the clinical efficiency and limitations of oligonucleotide-based drugs are summarized and investigated. Furthermore, another delivery system, lipid nanoparticles, that confer many advantages, is concluded, includ-ing stability and mass production, compared with GalNAc-siRNA conjugates. Importantly, developing new approaches for the use of oligonucleotide drugs brings hope to genetic therapy.
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Affiliation(s)
- Lei Zhang
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yayu Liang
- School of Stomatology, Henan University, Kaifeng, China
| | - Guohui Liang
- School of Clinical Medical Sciences, Henan University, Kaifeng, China
| | - Zhili Tian
- School of Clinical Medical Sciences, Henan University, Kaifeng, China
| | - Yue Zhang
- Department of Obstetrics and Gynecology, Zhengzhou, China
| | - Zhihui Liu
- Department of General Practice, Henan Provincial People’s Hospital, Zhengzhou University, Zhengzhou, China
| | - Xinying Ji
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
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32
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Li J, Zhu D, Hu S, Nie Y. CRISPR-CasRx knock-in mice for RNA degradation. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2248-2256. [PMID: 35412223 DOI: 10.1007/s11427-021-2059-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
The RNA editing tool CRISPR-CasRx has provided a platform for a range of transcriptome analysis tools and therapeutic approaches with its broad efficacy and high specificity. To enable the application of CasRx in vivo, we established a Credependent CasRx knock-in mouse. Using these mice, we specifically knocked down the expression of Meis1 and Hoxb13 in cardiomyocytes, which induced cardiac regeneration after myocardial infarction. We also knocked down the lncRNA Mhrt in cardiomyocytes with the CasRx knock-in mice, causing hypertrophic cardiomyopathy. In summary, we generated a Credependent CasRx knock-in mouse that can efficiently knock down coding gene and lncRNA expression in specific somatic cells. This in vivo CRISPR-CasRx system is promising for gene function research and disease modeling.
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Affiliation(s)
- Jiacheng Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100037, China
| | - Dekun Zhu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100037, China
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100037, China.
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100037, China.
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central-China Branch of National Center for Cardiovascular Diseases, Zhengzhou, 450046, China.
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Dong F, Su L, Tan J, Luo H. The anticancer effect of
EGFR
‐targeting artificial
microRNA
controlled by
SLPI
promoter in nasopharyngeal carcinoma. J Clin Lab Anal 2022; 36:e24729. [DOI: 10.1002/jcla.24729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/12/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Feilin Dong
- Medical College Soochow University Suzhou China
- Department of Otolaryngology, Otolaryngology & Head and Neck Center, Cancer Center Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College) Hangzhou China
| | - Lizhong Su
- Department of Otolaryngology, Otolaryngology & Head and Neck Center, Cancer Center Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College) Hangzhou China
| | - Jun Tan
- Department of Otolaryngology, Otolaryngology & Head and Neck Center, Cancer Center Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College) Hangzhou China
| | - Hui Luo
- Department of Otolaryngology, Otolaryngology & Head and Neck Center, Cancer Center Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College) Hangzhou China
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34
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Li X, Qi H, Cui W, Wang Z, Fu X, Li T, Ma H, Yang Y, Yu T. Recent advances in targeted delivery of non-coding RNA-based therapeutics for atherosclerosis. Mol Ther 2022; 30:3118-3132. [PMID: 35918894 PMCID: PMC9552813 DOI: 10.1016/j.ymthe.2022.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 10/16/2022] Open
Abstract
Cardiovascular disease (CVD) has overtaken infectious illnesses as the leading cause of mortality and disability worldwide. The pathology that underpins CVD is atherosclerosis, characterized by chronic inflammation caused by the accumulation of plaques in the arteries. As our knowledge about the microenvironment of blood vessel walls deepens, there is an opportunity to fine-tune treatments to target the mechanisms driving atherosclerosis more directly. The application of non-coding RNAs (ncRNAs) as biomarkers or intervention targets is increasing. Although these ncRNAs play an important role in driving atherosclerosis and vascular dysfunction, the cellular and extracellular environments pose a challenge for targeted transmission and therapeutic regulation of ncRNAs. Specificity, delivery, and tolerance have hampered the clinical translation of ncRNA-based therapeutics. Nanomedicine is an emerging field that uses nanotechnology for targeted drug delivery and advanced imaging. Recently, nanoscale carriers have shown promising results and have introduced new possibilities for nucleic acid targeted drug delivery, particularly for atherosclerosis. In this review, we discuss the latest developments in nanoparticles to aid ncRNA-based drug development, particularly miRNA, and we analyze the current challenges in ncRNA targeted delivery. In particular, we highlight the emergence of various kinds of nanotherapeutic approaches based on ncRNAs, which can improve treatment options for atherosclerosis.
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Affiliation(s)
- Xiaoxin Li
- Center for Regenerative Medicine, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, Qingdao 266021, People's Republic of China
| | - Hongzhao Qi
- Center for Regenerative Medicine, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, Qingdao 266021, People's Republic of China
| | - Weigang Cui
- Department of Cardiology, People's Hospital of Rizhao, No. 126 Taian Road, Rizhao 276827, People's Republic of China
| | - Zhibin Wang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, No.16 Jiangsu Road, Qingdao 266000, China
| | - Xiuxiu Fu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, No.16 Jiangsu Road, Qingdao 266000, China
| | - Tianxiang Li
- Center for Regenerative Medicine, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, Qingdao 266021, People's Republic of China
| | - Huibo Ma
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao 266021, People's Republic of China.
| | - Tao Yu
- Center for Regenerative Medicine, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, Qingdao 266021, People's Republic of China; Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, No.16 Jiangsu Road, Qingdao 266000, China.
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35
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Seçilmiş D, Hillerton T, Tjärnberg A, Nelander S, Nordling TEM, Sonnhammer ELL. Knowledge of the perturbation design is essential for accurate gene regulatory network inference. Sci Rep 2022; 12:16531. [PMID: 36192495 PMCID: PMC9529923 DOI: 10.1038/s41598-022-19005-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
The gene regulatory network (GRN) of a cell executes genetic programs in response to environmental and internal cues. Two distinct classes of methods are used to infer regulatory interactions from gene expression: those that only use observed changes in gene expression, and those that use both the observed changes and the perturbation design, i.e. the targets used to cause the changes in gene expression. Considering that the GRN by definition converts input cues to changes in gene expression, it may be conjectured that the latter methods would yield more accurate inferences but this has not previously been investigated. To address this question, we evaluated a number of popular GRN inference methods that either use the perturbation design or not. For the evaluation we used targeted perturbation knockdown gene expression datasets with varying noise levels generated by two different packages, GeneNetWeaver and GeneSpider. The accuracy was evaluated on each dataset using a variety of measures. The results show that on all datasets, methods using the perturbation design matrix consistently and significantly outperform methods not using it. This was also found to be the case on a smaller experimental dataset from E. coli. Targeted gene perturbations combined with inference methods that use the perturbation design are indispensable for accurate GRN inference.
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Affiliation(s)
- Deniz Seçilmiş
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Thomas Hillerton
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Andreas Tjärnberg
- Center for Developmental Genetics, New York University, New York, USA
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, 75185, Uppsala, Sweden
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, 701, Taiwan, ROC
- Department of Applied Physics and Electronics, Umeå University, 90187, Umeå, Sweden
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden.
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36
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Chen T, Wang Y, Wang YH, Hang CH. The Mfn1-βIIPKC Interaction Regulates Mitochondrial Dysfunction via Sirt3 Following Experimental Subarachnoid Hemorrhage. Transl Stroke Res 2022; 13:845-857. [PMID: 35192161 DOI: 10.1007/s12975-022-00999-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 10/19/2022]
Abstract
Neuronal injury following subarachnoid hemorrhage (SAH) has been shown to be associated with mitochondrial dysfunction and oxidative stress. βIIPKC, a subtype of protein kinase C (PKC), accumulates on the mitochondrial outer membrane and phosphorylates mitofusin 1 (Mfn1) at serine 86. Here, we investigated the role of Mfn1-βIIPKC interaction in brain damage and neurological function in both in vivo and in vitro experimental SAH models. The expression of βIIPKC protein and the interaction of Mfn1-βIIPKC were found to be increased after OxyHb treatment in primary cultured cortical neurons and were also observed in the brain following SAH in rats. Treatment with the βIIPKC inhibitor βIIV5-3 or SAMβA, a peptide that selectively antagonizes Mfn1-βIIPKC association, significantly attenuated the OxyHb-induced neuronal injury and apoptosis. These protective effects were accompanied by inhibited mitochondrial dysfunction and preserved mitochondrial biogenesis. The results of western blot showed that βIIV5-3 or SAMβA markedly increased the expression of Sirt3 and enhanced the activities of its downstream mitochondrial antioxidant enzymes in OxyHb-treated neurons. Knockdown of Sirt3 via specific targeted small interfering RNA (siRNA) partially prevented the βIIV5-3- or SAMβA-induced protection and antioxidative effects. In addition, treatment with βIIV5-3 or SAMβA in vivo was found to obviously reduce brain edema, alleviate neuroinflammation, and preserve neurological function after experimental SAH in rats. In congruent with in vitro data, the protection induced by βIIV5-3 or SAMβA was reduced by Sirt3 knockdown in vivo. In summary, our present results showed that blocking Mfn1-βIIPKC interaction protects against brain damage and mitochondrial dysfunction via Sirt3 following experimental SAH.
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Affiliation(s)
- Tao Chen
- Department of Neurosurgery, Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210000, Jiangsu, China
- Department of Neurosurgery, The 904Th Hospital of PLA, Medical School of Anhui Medical University, Wuxi, 214044, Jiangsu, China
| | - Yue Wang
- Department of Neurosurgery, The 904Th Hospital of PLA, Medical School of Anhui Medical University, Wuxi, 214044, Jiangsu, China
| | - Yu-Hai Wang
- Department of Neurosurgery, The 904Th Hospital of PLA, Medical School of Anhui Medical University, Wuxi, 214044, Jiangsu, China.
| | - Chun-Hua Hang
- Department of Neurosurgery, Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210000, Jiangsu, China.
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37
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Liu Q, Zhang Y, Huang J, Xu Z, Li X, Yang J, Huang H, Tang S, Chai Y, Lin J, Yang C, Liu J, Lin S. Mesoporous silica-coated silver nanoparticles as ciprofloxacin/siRNA carriers for accelerated infected wound healing. J Nanobiotechnology 2022; 20:386. [PMID: 35999547 PMCID: PMC9400313 DOI: 10.1186/s12951-022-01600-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/14/2022] [Indexed: 12/14/2022] Open
Abstract
The colonization of bacterial pathogens is a major concern in wound infection and becoming a public health issue. Herein, a core–shell structured Ag@MSN (silver core embedded with mesoporous silica, AM)-based nanoplatform was elaborately fabricated to co-load ciprofloxacin (CFL) and tumor necrosis factor-α (TNF-α) small interfering RNA (siTNF-α) (AMPC@siTNF-α) for treating the bacterial-infected wound. The growth of bacterial pathogens was mostly inhibited by released silver ions (Ag+) and CFL from AMPC@siTNF-α. Meanwhile, the loaded siTNF-α was internalized by macrophage cells, which silenced the expression of TNF-α (a pro-inflammatory cytokine) in macrophage cells and accelerated the wound healing process by reducing inflammation response. In the in vivo wound model, the Escherichia coli (E. coli)-infected wound in mice almost completely disappeared after treatment with AMPC@siTNF-α, and no suppuration symptom was observed during the course of the treatment. Importantly, this nanoplatform had negligible side effects both in vitro and in vivo. Taken together, this study strongly demonstrates the promising potential of AMPC@siTNF-α as a synergistic therapeutic agent for clinical wound infections.
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Affiliation(s)
- Qiqi Liu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Ying Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China.,Central Laboratory, The Second Affiliated Hospital, School of Medicine, Longgang District People's Hospital of Shenzhen, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Jingkai Huang
- Dermatology Department, Southern University of Science and Technology Hospital (SUSTech Hospital), Shenzhen, 518055, China
| | - Zhourui Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Xiang Li
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Jingyu Yang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Haoqiang Huang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Shiqi Tang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Yujuan Chai
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Jinbo Lin
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, Longgang District People's Hospital of Shenzhen, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Chengbin Yang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China.
| | - Jia Liu
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, Longgang District People's Hospital of Shenzhen, The Chinese University of Hong Kong, Shenzhen, 518172, China.
| | - Suxia Lin
- Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, 518048, China.
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38
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Zhang Y, Xu Q, Wang G, Shi K. Indole-Acetic Acid Promotes Ammonia Removal Through Heterotrophic Nitrification, Aerobic Denitrification With Mixed Enterobacter sp. Z1 and Klebsiella sp. Z2. Front Microbiol 2022; 13:929036. [PMID: 35875564 PMCID: PMC9304994 DOI: 10.3389/fmicb.2022.929036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
Mixed Enterobacter sp. Z1 and Klebsiella sp. Z2 displayed an outstanding ammonia removal capacity than using a single strain. Metabolomics, proteomics, and RNA interference analysis demonstrated that the HNAD process was closely related to indole-acetic acid (IAA). Under the cocultured conditions, the excess IAA produced by Z2 could be absorbed by Z1 to compensate for the deficiency of IAA in the cells. IAA directly induced the expression of denitrifying enzymes and further activated the IAA metabolism level, thus greatly improving the nitrogen removal ability of Z1. In turn, nitrate and nitrite induced the expression of key enzymes in the IAA pathways. Moreover, Z1 and Z2 enhanced two IAA metabolic pathways in the process of mixed removal process. The activated hydrolysis-redox pathway in Z1 reduced the oxidative stress level, and the activated decarboxylation pathway in Z2 promoted intracellular energy metabolism, which indirectly promoted the process of HNAD in the system.
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39
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Kotsaridis K, Tsakiri D, Sarris PF. Understanding enemy's weapons to an effective prevention: common virulence effects across microbial phytopathogens kingdoms. Crit Rev Microbiol 2022:1-15. [PMID: 35709325 DOI: 10.1080/1040841x.2022.2083939] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Plant-pathogens interaction is an ongoing confrontation leading to the emergence of new diseases. The majority of the invading microorganisms inject effector proteins into the host cell, to bypass the sophisticated defense system of the host. However, the effectors could also have other specialized functions, which can disrupt various biological pathways of the host cell. Pathogens can enrich their effectors arsenal to increase infection success or expand their host range. This usually is accomplished by the horizontal gene transfer. Nowadays, the development of specialized software that can predict proteins structure, has changed the experimental designing in effectors' function research. Different effectors of distinct plant pathogens tend to fold alike and have the same function and focussed structural studies on microbial effectors can help to uncover their catalytic/functional activities, while the structural similarity can enable cataloguing the great number of pathogens' effectors. In this review, we collectively present phytopathogens' effectors with known enzymatic functions and proteins structure, originated from all the kingdoms of microbial plant pathogens. Presentation of their common domains and motifs is also included. We believe that the in-depth understanding of the enemy's weapons will help the development of new strategies to prevent newly emerging or re-emerging plant pathogens.
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Affiliation(s)
| | | | - Panagiotis F Sarris
- Department of Biology, University of Crete, Crete, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Crete, Greece.,Biosciences, University of Exeter, Exeter, UK
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40
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Genenger B, Perry JR, Ashford B, Ranson M. A tEMTing target? Clinical and experimental evidence for epithelial-mesenchymal transition in the progression of cutaneous squamous cell carcinoma (a scoping systematic review). Discov Oncol 2022; 13:42. [PMID: 35666359 PMCID: PMC9170863 DOI: 10.1007/s12672-022-00510-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is a disease with globally rising incidence and poor prognosis for patients with advanced or metastatic disease. Epithelial-mesenchymal transition (EMT) is a driver of metastasis in many carcinomas, and cSCC is no exception. We aimed to provide a systematic overview of the clinical and experimental evidence for EMT in cSCC, with critical appraisal of type and quality of the methodology used. We then used this information as rationale for potential drug targets against advanced and metastatic cSCC. All primary literature encompassing clinical and cell-based or xenograft experimental studies reporting on the role of EMT markers or related signalling pathways in the progression of cSCC were considered. A screen of 3443 search results yielded 86 eligible studies comprising 44 experimental studies, 22 clinical studies, and 20 studies integrating both. From the clinical studies a timeline illustrating the alteration of EMT markers and related signalling was evident based on clinical progression of the disease. The experimental studies reveal connections of EMT with a multitude of factors such as genetic disorders, cancer-associated fibroblasts, and matrix remodelling via matrix metalloproteinases and urokinase plasminogen activator. Additionally, EMT was found to be closely tied to environmental factors as well as to stemness in cSCC via NFκB and β-catenin. We conclude that the canonical EGFR, canonical TGF-βR, PI3K/AKT and NFκB signalling are the four signalling pillars that induce EMT in cSCC and could be valuable therapeutic targets. Despite the complexity, EMT markers and pathways are desirable biomarkers and drug targets for the treatment of advanced or metastatic cSCC.
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Affiliation(s)
- Benjamin Genenger
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia.
| | - Jay R Perry
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Bruce Ashford
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
| | - Marie Ranson
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia.
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41
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Fang F, Xu W, Zhang J, Gu J, Yang G. Ultrasound microbubble-mediated RNA interference targeting WNT1 inducible signaling pathway protein 1(WISP1) suppresses the proliferation and metastasis of breast cancer cells. Bioengineered 2022; 13:11050-11060. [PMID: 35481425 PMCID: PMC9208516 DOI: 10.1080/21655979.2022.2068738] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
In the context of relatively sufficient research that annotated WNT1 inducible signaling pathway protein 1 (WISP1) as a promoting factor in tumor progression of breast cancer, and identified the effects of ultrasound microbubble technology on enhancing the transfection efficiency and achieving better gene interference, this study managed to investigate the effects of ultrasound microbubble-mediated siWISP1 transfection on proliferation and metastasis of breast cancer cells. To achieve our research objectives, the expression of WISP1 in breast cancer tissues was retrieved from GEPIA website, and the viability of breast cancer cells (SK-BR-3 and MCF7) was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay for ultrasound intensity screening. After the transfection of siWISP1 by ultrasound microbubble or lipofectamine 6000, the content of WISP1 secreted by cells was detected through Enzyme-linked immunosorbent assay (ELISA), and WISP1 expression in cells was determined by quantitative reverse transcription polymerase-chain reaction (qRT-PCR). Besides, the cell invasion, migration, and proliferation were evaluated by wound healing, transwell, and EdU assays, respectively. In accordance with experimental results, WISP1 was highly expressed in breast cancer tissues, and the 1 W/cm2 intensity was the onset of a notable decrease in cell viability. Compared with lipofectamine 6000 transfection, the transfection of siWISP1 mediated by ultrasound microbubble further reduced the expression of WISP1, and meanwhile suppressed cell invasion, migration, and proliferation. Collectively, ultrasound microbubble-mediated transfection of siWISP1 worked rather effectively in improving transfection efficiency and inhibiting the progression of breast cancer.
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Affiliation(s)
- Faying Fang
- Department of Special Examination, Maternal and Child Health Hospital of Chun'an County, Hangzhou, Zhejiang, China
| | - Weizhi Xu
- Department of Ultrasound, Sanmen People's Hospital, Taizhou, Zhejiang, China
| | - Jian Zhang
- Department of Ultrasound, Pingyi County Hospital of Traditional Chinese Medicine, Linyi, Shandong, China
| | - Jin Gu
- Department of Ultrasound, Chongqing Public Health Medical Center, Chongqing, Shandong, China
| | - Gaoyi Yang
- Department of Ultrasound, Sanmen People's Hospital, Taizhou, Zhejiang, China
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42
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Li T, Geng Y, Hu Y, Zhang L, Cui X, Zhang W, Gao F, Liu Z, Luo X. Dentin Matrix Protein 1 Silencing Inhibits Phosphorus Utilization in Primary Cultured Tibial Osteoblasts of Broiler Chicks. Front Vet Sci 2022; 9:875140. [PMID: 35558889 PMCID: PMC9087580 DOI: 10.3389/fvets.2022.875140] [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: 02/13/2022] [Accepted: 02/21/2022] [Indexed: 12/19/2022] Open
Abstract
Three experiments were carried out in the present study to investigate whether dentin matrix protein 1 (DMP1) was involved in regulating phosphorus (P) metabolic utilization in primary cultured tibial osteoblasts of broiler chicks. Experiment 1 was conducted to select the optimal osteogenic inductive culture medium and the optimal induction time in primary cultured tibial osteoblasts of broiler chicks. In experiment 2, the siRNAs against DMP1 were designed, synthesized and transfected into primary cultured tibial osteoblasts of broiler chicks, and then the inhibitory efficiencies of siRNAs against DMP1 were determined, and the most efficacious siRNA was selected to be used for the DMP1 silencing. In experiment 3, with or without siRNA against DMP1, primary cultured tibial osteoblasts of broiler chicks were treated with the medium supplemented with 0.0, 1.0 or 2.0 mmol/L of P as NaH2PO4 for 12 days. The P metabolic utilization-related parameters were measured. The results showed that the osteogenic induced medium 2 and 12 days of the optimal induction time were selected; Among the designed siRNAs, the si340 was the most effective (P < 0.05) in inhibiting the DMP1 expression; DMP1 silencing decreased (P < 0.05) the expressions of DMP1 mRNA and protein, P retention rate, mineralization formation, alkaline phosphatase activity and bone gla-protein content in tibial osteoblasts at all of added P levels. It is concluded that DMP1 silencing inhibited P utilization, and thus DMP1 was involved in regulating P metabolic utilization in primary cultured tibial osteoblasts of broiler chicks, which provides a novel insight into the regulation of the P utilization in the bone of broilers, and will contribute to develop feasible strategies to improve the bone P utilization efficiency of broilers so as to decrease its excretion.
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Affiliation(s)
- Tingting Li
- Poultry Mineral Nutrition Laboratory, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yanqiang Geng
- Poultry Mineral Nutrition Laboratory, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yun Hu
- Poultry Mineral Nutrition Laboratory, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Liyang Zhang
- Mineral Nutrition Research Division, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyan Cui
- Poultry Mineral Nutrition Laboratory, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Weiyun Zhang
- Poultry Mineral Nutrition Laboratory, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Feiyu Gao
- Poultry Mineral Nutrition Laboratory, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zongping Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xugang Luo
- Poultry Mineral Nutrition Laboratory, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- *Correspondence: Xugang Luo
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43
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Aripova T, Muratkhodjaev J. A novel concept of human antiviral protection: It's all about RNA (Review). Biomed Rep 2022; 16:29. [PMID: 35251616 PMCID: PMC8889527 DOI: 10.3892/br.2022.1512] [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: 11/24/2021] [Accepted: 01/10/2022] [Indexed: 11/06/2022] Open
Abstract
The comparative analysis of the antiviral protective mechanisms, including protozoa and RNA interference in multicellular organisms, has revealed their similarity and provided a basic understanding of adaptive immunity. The present article summarizes the latest studies on RNA-guided gene regulation in human antiviral protection, and its importance. Additionally, the role of both neutralizing antibodies and the interferon system in viral invasion is considered. The interferon system is an additional mechanism for suppressing viral infections in humans, which shifts cells into an 'alarm' mode to attempt to prevent further contagion. The primary task of the human central immune system is to maintain integrity and to protect against foreign organisms. In this review, a novel concept is proposed: Antiviral protection in all organisms can be achieved through an intracellular RNA-guided mechanism. A simple and effective defence against viruses is incorporation of a part of a virus's DNA (spacer) into the hosts chromosomes. Following reinfection, RNA transcripts of this spacer are created to direct nuclease enzymes to destroy the viral genome. This is an example of real-time adaptive immunity potentially possessed by every cell with a full complement of chromosomes, and an indicator that antiviral immunity is not only mediated by the presence of neutralizing antibodies and memory B- and T-cells, but also by the presence of specific spacers in the DNA of individuals who have recovered from a viral infection.
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Affiliation(s)
- Tamara Aripova
- Institute of Immunology and Human Genomics, Academy of Sciences of Uzbekistan, Tashkent 100060, Uzbekistan
| | - Javdat Muratkhodjaev
- Institute of Immunology and Human Genomics, Academy of Sciences of Uzbekistan, Tashkent 100060, Uzbekistan
- GENEX LLC Pharmaceutical Company, Tashkent 100052, Uzbekistan
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44
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Bacteroides fragilis Toxin Induces Intestinal Epithelial Cell Secretion of Interleukin-8 by the E-Cadherin/β-Catenin/NF-κB Dependent Pathway. Biomedicines 2022; 10:biomedicines10040827. [PMID: 35453577 PMCID: PMC9032310 DOI: 10.3390/biomedicines10040827] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022] Open
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) has emerged as a gut microbiome pathogen that can promote colitis associated cancer in humans. ETBF secretes the metalloprotease, B. fragilis toxin (BFT), which can induce ectodomain cleavage of E-cadherin and IL-8 secretion through the β-catenin, NF-κB, and MAPK pathways in intestinal epithelial cells. However, it is still unclear whether E-cadherin cleavage is required for BFT induced IL-8 secretion and the relative contribution of these signaling pathways to IL-8 secretion. Using siRNA knockdown and CRISPR knockout studies, we found that E-cadherin cleavage is required for BFT mediated IL-8 secretion. In addition, genetic ablation of β-catenin indicates that β-catenin is required for the BFT induced increase in transcriptional activity of NF-κB, p65 nuclear localization and early IL-8 secretion. These results suggest that BFT induced β-catenin signaling is upstream of NF-κB activation. However, despite β-catenin gene disruption, BFT still activated the MAPK pathway, suggesting that the BFT induced activation of the MAPK signaling pathway is independent from the E-cadherin/β-catenin/NF-κB pathway. These findings show that E-cadherin and β-catenin play a critical role in acute inflammation following ETBF infection through the inflammatory response to BFT in intestinal epithelial cells.
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45
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Fan X, Yang J, Wu G, Wang M, Cheng X, Liu C, Liu Q, Wen Y, Meng S, Wang Z, Lin X, An L. Optimization of cationic polymer-mediated transfection for RNA interference. Genet Mol Biol 2022; 45:e20210237. [PMID: 35275159 PMCID: PMC8915406 DOI: 10.1590/1678-4685-gmb-2021-0237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/12/2022] [Indexed: 11/27/2022] Open
Abstract
Transfection efficiency was estimated to optimize the conditions for RNA interference (RNAi), including transfection time, validity, and nucleic acid concentration and type, using the EZ Trans Cell Reagent, a cationic polymer. An shRNA against GFP was designed and transfected into cells using the EZ transfection reagent. The shRNA significantly decreased the expression of GFP. In addition, pre-diluted transfection reagent at room temperature and small nucleic acids increased the transfection efficiency, which peaked at 24 h. Compared with circular nucleic acids, linear nucleic acids showed higher transfection efficiency and a higher genome integration rate. We optimized cationic polymer-mediated RNAi conditions, and our data will be useful for future RNAi studies.
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Affiliation(s)
- Xiaojie Fan
- Huaihe Hospital of Henan University, Kaifeng, Henan, China
| | - Jingnan Yang
- Huaihe Hospital of Henan University, Kaifeng, Henan, China
| | - Guangyao Wu
- Huaihe Hospital of Henan University, Kaifeng, Henan, China
| | - Meiyi Wang
- Henan University, School of Medicine, Kaifeng, Henan, China
| | - Xiaoxia Cheng
- Henan University, School of Medicine, Kaifeng, Henan, China
| | - Chang Liu
- Henan University, School of Medicine, Kaifeng, Henan, China
| | - Qian Liu
- Henan University, School of Medicine, Kaifeng, Henan, China
| | - Yanan Wen
- Huaihe Hospital of Henan University, Kaifeng, Henan, China
| | | | - Zhenxing Wang
- Huaihe Hospital of Henan University, Kaifeng, Henan, China
| | - Xuhong Lin
- Huaihe Hospital of Henan University, Kaifeng, Henan, China
| | - Lei An
- Huaihe Hospital of Henan University, Kaifeng, Henan, China.,Henan University, School of Medicine, Kaifeng, Henan, China
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46
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Susgun S, Kasan K, Yucesan E. Gene Hunting Approaches through the Combination of Linkage Analysis with Whole-Exome Sequencing in Mendelian Diseases: From Darwin to the Present Day. Public Health Genomics 2022; 24:207-217. [PMID: 34237751 DOI: 10.1159/000517102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/27/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In the context of medical genetics, gene hunting is the process of identifying and functionally characterizing genes or genetic variations that contribute to disease phenotypes. In this review, we would like to summarize gene hunting process in terms of historical aspects from Darwin to now. For this purpose, different approaches and recent developments will be detailed. SUMMARY Linkage analysis and association studies are the most common methods in use for explaining the genetic background of hereditary diseases and disorders. Although linkage analysis is a relatively old approach, it is still a powerful method to detect disease-causing rare variants using family-based data, particularly for consanguineous marriages. As is known that, consanguineous marriages or endogamy poses a social problem in developing countries, however, this same condition also provides a unique opportunity for scientists to identify and characterize pathogenic variants. The rapid advancements in sequencing technologies and their parallel implementation together with linkage analyses now allow us to identify the candidate variants related to diseases in a relatively short time. Furthermore, we can now go one step further and functionally characterize the causative variant through in vitro and in vivo studies and unveil the variant-phenotype relationships on a molecular level more robustly. Key Messages: Herein, we suggest that the combined analysis of linkage and exome analysis is a powerful and precise tool to diagnose clinically rare and recessively inherited conditions.
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Affiliation(s)
- Seda Susgun
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey.,Graduate School of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Koray Kasan
- Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Emrah Yucesan
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
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Srivichit B, Thonusin C, Chattipakorn N, Chattipakorn SC. Impacts of bisphosphonates on the bone and its surrounding tissues: mechanistic insights into medication-related osteonecrosis of the jaw. Arch Toxicol 2022; 96:1227-1255. [PMID: 35199244 DOI: 10.1007/s00204-021-03220-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/23/2021] [Indexed: 01/20/2023]
Abstract
Bisphosphonates are widely used as anti-resorptive agents for the treatment of various bone and joint diseases, including advanced osteoporosis, multiple myeloma, bone metastatic cancers, Paget's disease of bone, and rheumatoid arthritis. Bisphosphonates act as an anti-osteoclast via the induction of osteoclast apoptosis, resulting in a decreased rate of bone resorption. Unfortunately, there is much evidence to demonstrate that the long-term use of bisphosphonates is associated with osteonecrosis. The pathogenesis of osteonecrosis includes the death of osteoblasts, osteoclasts, and osteocytes. In addition, the functions of endothelial cells, epithelial cells, and fibroblasts are impaired in osteonecrosis, leading to disruptive angiogenesis, and delayed wound healing. Osteonecrosis is most commonly found in the jawbone and the term medication-related osteonecrosis of the jaw (MRONJ) has become the condition of greatest clinical concern among patients receiving bisphosphonates. Although surgical treatment is an effective strategy for the treatment of MRONJ, several non-surgical interventions for the attenuation of MRONJ have also been investigated. With the aim of increasing understanding around MRONJ, we set out to summarize and discuss the holistic effects of bisphosphonates on the bone and its surrounding tissues. In addition, non-surgical interventions for the attenuation of bisphosphonate-induced osteonecrosis were reviewed and discussed.
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Affiliation(s)
- Bhumrapee Srivichit
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Cardiac Electrophysiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
| | - Chanisa Thonusin
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Cardiac Electrophysiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nipon Chattipakorn
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Cardiac Electrophysiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Siriporn C Chattipakorn
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center of Excellence in Cardiac Electrophysiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand. .,Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand.
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48
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Simple Gene Knockdown in Endothelial Cells Using Short Interfering RNA Oligonucleotides. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2441:251-255. [PMID: 35099742 DOI: 10.1007/978-1-0716-2059-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Cell transfection using short interfering RNAs (siRNAs) is a widely used technique to perform loss of function studies by "knocking down" genes of interest. Oftentimes, primary cells can be difficult to transfect, but here we provide a simple and robust method using cultured endothelial cells and routine transfection reagents. Knockdown studies can be used to complement overexpression studies and validate biochemical pathway analysis, as well as functional assays. The enclosed protocol will compliment other in vitro assays detailed in this edition.
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49
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Zambrano RAI, Hernandez-Perez C, Takahashi MK. RNA Structure Prediction, Analysis, and Design: An Introduction to Web-Based Tools. Methods Mol Biol 2022; 2518:253-269. [PMID: 35666450 DOI: 10.1007/978-1-0716-2421-0_15] [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] [Indexed: 06/15/2023]
Abstract
Understanding RNA structure has become critical in the study of RNA in their roles as mediators of biological processes. To aid in these studies, computational algorithms that utilize thermodynamics have been developed to predict RNA secondary structure. Due to the importance of intermolecular interactions, the algorithms have been expanded to determine and predict RNA-RNA hybridization. This chapter discusses popular webservers with the tools for RNA secondary structure prediction, RNA-RNA hybridization, and design. We address key features that distinguish common-functioning programs and their purposes for the interests of the user. Ultimately, we hope this review elucidates web-based tools researchers may take advantage of in their investigations of RNA structure and function.
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Affiliation(s)
| | | | - Melissa K Takahashi
- Department of Biology, California State University Northridge, Northridge, CA, USA.
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50
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An Overview of Zebrafish Modeling Methods in Drug Discovery and Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1387:145-169. [PMID: 34961915 DOI: 10.1007/5584_2021_684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Animal studies are recognized as a significant step forward in the bridging between drug discovery and clinical applications. Animal models, due to their relative genetic, molecular, physiological, and even anatomical similarities to humans, can provide a suitable platform for unraveling the mechanisms underlying human diseases and discovering new therapeutic approaches as well. Recently, zebrafish has attracted attention as a valuable experimental and pharmacological model in drug discovery and development studies due to its prominent characteristics such as the high degree of genetic similarity with humans, genetic manipulability, and prominent clinical features. Since advancing a theory to a valid and reliable observation requires the manipulation of animals, it is, therefore, essential to use efficient modeling methods appropriate to the different aspects of experimental conditions. In this context, applying several various approaches such as using chemicals, pathogens, and genetic manipulation approaches allows zebrafish development into a preferable model that mimics some human disease pathophysiology. Thus, such modeling approaches not only can provide a framework for a comprehensive understanding of the human disease mechanisms that have a counterpart in zebrafish but also can pave the way for discovering new drugs that are accompanied by higher amelioration effects on different human diseases.
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