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1.
Stem Cells Transl Med ; 12(8): 527-535, 2023 08 16.
Article En | MEDLINE | ID: mdl-37440203

The progressive appreciation that multiple types of RNAs regulate virtually all aspects of tissue function and the availability of effective tools to deliver RNAs in vivo now offers unprecedented possibilities for obtaining RNA-based therapeutics. For the heart, RNA therapies can be developed that stimulate endogenous repair after cardiac damage. Applications in this area include acute cardioprotection after ischemia or cancer chemotherapy, therapeutic angiogenesis to promote new blood vessel formation, regeneration to form new cardiac mass, and editing of mutations to cure inherited cardiac disease. While the potential of RNA therapeutics for all these conditions is exciting, the field is still in its infancy. A number of roadblocks need to be overcome for RNA therapies to become effective, in particular, related to the problem of delivering RNA medicines into the cells and targeting them specifically to the heart.


Aptamers, Nucleotide , Heart , RNA, Antisense , RNA, Guide, CRISPR-Cas Systems , Heart/physiology , Regeneration , RNA, Antisense/therapeutic use , Aptamers, Nucleotide/therapeutic use , RNA Interference/drug effects , RNA, Guide, CRISPR-Cas Systems/therapeutic use , Gene Editing , Humans , Animals
2.
J Virol ; 96(4): e0177821, 2022 02 23.
Article En | MEDLINE | ID: mdl-34908449

RNA interference (RNAi) functions as the major host antiviral defense in insects, while less is understood about how to utilize antiviral RNAi in controlling viral infection in insects. Enoxacin belongs to the family of synthetic antibacterial compounds based on a fluoroquinolone skeleton that has been previously found to enhance RNAi in mammalian cells. In this study, we show that enoxacin efficiently inhibited viral replication of Drosophila C virus (DCV) and cricket paralysis virus (CrPV) in cultured Drosophila cells. Enoxacin promoted the loading of Dicer-2-processed virus-derived small interfering RNA (siRNA) into the RNA-induced silencing complex, thereby enhancing the antiviral RNAi response in infected cells. Moreover, enoxacin treatment elicited RNAi-dependent in vivo protective efficacy against DCV or CrPV challenge in adult fruit flies. In addition, enoxacin also inhibited the replication of flaviviruses, including dengue virus and Zika virus, in Aedes mosquito cells in an RNAi-dependent manner. Together, our findings demonstrate that enoxacin can enhance RNAi in insects, and enhancing RNAi by enoxacin is an effective antiviral strategy against diverse viruses in insects, which may be exploited as a broad-spectrum antiviral agent to control the vector transmission of arboviruses or viral diseases in insect farming. IMPORTANCE RNAi has been widely recognized as one of the most broadly acting and robust antiviral mechanisms in insects. However, the application of antiviral RNAi in controlling viral infections in insects is less understood. Enoxacin is a fluoroquinolone compound that was previously found to enhance RNAi in mammalian cells, while its RNAi-enhancing activity has not been assessed in insects. Here, we show that enoxacin treatment inhibited viral replication of DCV and CrPV in Drosophila cells and adult fruit flies. Enoxacin promoted the loading of Dicer-generated virus-derived siRNA into the Ago2-incorporated RNA-induced silencing complex and in turn strengthened the antiviral RNAi response in the infected cells. Moreover, enoxacin displayed effective RNAi-dependent antiviral effects against flaviviruses, such as dengue virus and Zika virus, in mosquito cells. This study is the first to demonstrate that enhancing RNAi by enoxacin elicits potent antiviral effects against diverse viruses in insects.


Antiviral Agents/pharmacology , Enoxacin/pharmacology , Insect Viruses/drug effects , RNA Interference/drug effects , Aedes , Animals , Cell Line , Drosophila , Flavivirus/classification , Flavivirus/drug effects , Insect Viruses/classification , RNA, Small Interfering/metabolism , RNA, Viral/metabolism , RNA-Induced Silencing Complex/metabolism , Virus Replication/drug effects
3.
Osteoarthritis Cartilage ; 30(3): 481-493, 2022 03.
Article En | MEDLINE | ID: mdl-34958937

OBJECTIVE: In the largest avascular low-nutrient intervertebral disc, resident cells would utilize autophagy, a stress-response survival mechanism by self-digestion and recycling wastes. Our goal was to elucidate the involvement of autophagy in disc homeostasis through RNA interference of autophagy-related gene 5 (Atg5). DESIGN: In vitro, small interfering RNAs (siRNAs) targeting autophagy-essential Atg5 were transfected into rat disc cells. Cell viability with levels of autophagy including Atg5 expression, apoptosis, and senescence was assessed under serum starvation and/or pro-inflammatory interleukin-1 beta (IL-1ß) stimulation. In vivo, time-course autophagic flux was monitored following Alexa Fluor® 555-labeled Atg5-siRNA injection into rat tail discs. Furthermore, 24-h temporary static compression-induced disruption of Atg5 siRNA-injected discs was observed by radiography, histomorphology, and immunofluorescence. RESULTS: In disc cells, three different Atg5 siRNAs consistently suppressed autophagy with Atg5 protein knockdown (mean 44.4% [95% confidence interval: -51.7, -37.1], 51.5% [-80.5, -22.5], 62.3% [-96.6, -28.2]). Then, Atg5 knockdown reduced cell viability through apoptosis and senescence not in serum-supplemented medium (93.6% [-0.8, 21.4]) but in serum-deprived medium (66.4% [-29.8, -8.6]) further with IL-1ß (44.5% [-36.9, -23.5]). In disc tissues, immunofluorescence detected intradiscal signals for the labeled siRNA even at 56-d post-injection. Immunoblotting found 56-d autophagy suppression with prolonged Atg5 knockdown (33.2% [-52.8, -5.3]). With compression, Atg5 siRNA-injected discs presented radiographic height loss ([-43.9, -0.8]), histological damage ([-5.5, -0.2]), and immunofluorescent apoptosis ([2.2, 22.2]) and senescence ([4.1, 19.9]) induction compared to control siRNA-injected discs at 56 d. CONCLUSIONS: This loss-of-function study suggests Atg5-dependent autophagy-mediated anti-apoptosis and anti-senescence. Autophagy could be a molecular therapeutic target for degenerative disc disease.


Apoptosis/drug effects , Autophagy-Related Protein 5/administration & dosage , Autophagy/drug effects , Cellular Senescence/drug effects , Intervertebral Disc/drug effects , RNA, Small Interfering/administration & dosage , Animals , Disease Models, Animal , Male , RNA Interference/drug effects , Rats , Rats, Sprague-Dawley , Tail , Transfection
4.
Eur J Endocrinol ; 185(4): 539-552, 2021 Aug 27.
Article En | MEDLINE | ID: mdl-34342596

OBJECTIVE: Sex steroid hormones like estrogens have a key role in the regulation of energy homeostasis and metabolism. In transwomen, gender-affirming hormone therapy like estradiol (in combination with antiandrogenic compounds) could affect metabolism as well. Given that the underlying pathophysiological mechanisms are not fully understood, this study assessed circulating estradiol-driven microRNAs (miRs) in transwomen and their regulation of genes involved in metabolism in mice. METHODS: Following plasma miR-sequencing (seq) in a transwomen discovery (n = 20) and validation cohort (n = 30), we identified miR-224 and miR-452. Subsequent systemic silencing of these miRs in male C57Bl/6 J mice (n = 10) was followed by RNA-seq-based gene expression analysis of brown and white adipose tissue in conjunction with mechanistic studies in cultured adipocytes. RESULTS: Estradiol in transwomen lowered plasma miR-224 and -452 carried in extracellular vesicles (EVs) while their systemic silencing in mice and cultured adipocytes increased lipogenesis (white adipose) but reduced glucose uptake and mitochondrial respiration (brown adipose). In white and brown adipose tissue, differentially expressed (miR target) genes are associated with lipogenesis (white adipose) and mitochondrial respiration and glucose uptake (brown adipose). CONCLUSION: This study identified an estradiol-drive post-transcriptional network that could potentially offer a mechanistic understanding of metabolism following gender-affirming estradiol therapy.


Cell-Derived Microparticles/genetics , Estradiol/physiology , MicroRNAs/genetics , Transsexualism , Adipocytes/drug effects , Adipocytes/physiology , Adipogenesis/drug effects , Adipogenesis/genetics , Adult , Animals , Cell-Derived Microparticles/drug effects , Cell-Derived Microparticles/metabolism , Cohort Studies , Down-Regulation/drug effects , Down-Regulation/genetics , Energy Metabolism/drug effects , Energy Metabolism/genetics , Estradiol/blood , Estradiol/pharmacology , Extracellular Vesicles/genetics , Extracellular Vesicles/metabolism , Female , Gene Expression Regulation/drug effects , Homeostasis/drug effects , Hormone Replacement Therapy , Humans , Male , Mice , Mice, Inbred C57BL , MicroRNAs/metabolism , Middle Aged , RNA Interference/drug effects , Transgender Persons , Transsexualism/genetics , Transsexualism/metabolism , Young Adult
5.
PLoS One ; 16(6): e0251719, 2021.
Article En | MEDLINE | ID: mdl-34157051

Overexpression and persistent activation of STAT5 play an important role in the development and progression of acute lymphoblastic leukemia (ALL), the most common pediatric cancer. Small interfering RNA (siRNA)-mediated downregulation of STAT5 represents a promising therapeutic approach for ALL to overcome the limitations of current treatment modalities such as high relapse rates and poor prognosis. However, to effectively transport siRNA molecules to target cells, development of potent carriers is of utmost importance to surpass hurdles of delivery. In this study, we investigated the use of lipopolymers as non-viral delivery systems derived from low molecular weight polyethylenimines (PEI) substituted with lauric acid (Lau), linoleic acid (LA) and stearic acid (StA) to deliver siRNA molecules to ALL cell lines and primary samples. Among the lipid-substituted polymers explored, Lau- and LA-substituted PEI displayed excellent siRNA delivery to SUP-B15 and RS4;11 cells. STAT5A gene expression was downregulated (36-92%) in SUP-B15 and (32%) in RS4;11 cells using the polymeric delivery systems, which consequently reduced cell growth and inhibited the formation of colonies in ALL cells. With regard to ALL primary cells, siRNA-mediated STAT5A gene silencing was observed in four of eight patient cells using our leading polymeric delivery system, 1.2PEI-Lau8, accompanied by the significant reduction in colony formation in three of eight patients. In both BCR-ABL positive and negative groups, three of five patients demonstrated marked cell growth inhibition in both MTT and trypan blue exclusion assays using 1.2PEI-Lau8/siRNA complexes in comparison with their control siRNA groups. Three patient samples did not show any positive results with our delivery systems. Differential therapeutic responses to siRNA therapy observed in different patients could result from variable genetic profiles and patient-to-patient variability in delivery. This study supports the potential of siRNA therapy and the designed lipopolymers as a delivery system in ALL therapy.


Down-Regulation/drug effects , Drug Carriers/administration & dosage , Polymers/administration & dosage , Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy , RNA, Small Interfering/administration & dosage , STAT5 Transcription Factor/genetics , Tumor Suppressor Proteins/genetics , B-Lymphocytes/drug effects , Cell Line, Tumor , Fusion Proteins, bcr-abl/genetics , Gene Silencing/drug effects , Humans , Linoleic Acid/administration & dosage , Polyethyleneimine/administration & dosage , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , RNA Interference/drug effects , RNA, Double-Stranded/genetics
6.
Sci Rep ; 11(1): 10271, 2021 05 13.
Article En | MEDLINE | ID: mdl-33986351

COVID-19 has currently become the biggest challenge in the world. There is still no specific medicine for COVID-19, which leaves a critical gap for the identification of new drug candidates for the disease. Recent studies have reported that the small-molecule enoxacin exerts an antiviral activity by enhancing the RNAi pathway. The aim of this study is to analyze if enoxacin can exert anti-SARS-CoV-2 effects. We exploit multiple computational tools and databases to examine (i) whether the RNAi mechanism, as the target pathway of enoxacin, could act on the SARS-CoV-2 genome, and (ii) microRNAs induced by enoxacin might directly silence viral components as well as the host cell proteins mediating the viral entry and replication. We find that the RNA genome of SARS-CoV-2 might be a suitable substrate for DICER activity. We also highlight several enoxacin-enhanced microRNAs which could target SARS-CoV-2 components, pro-inflammatory cytokines, host cell components facilitating viral replication, and transcription factors enriched in lung stem cells, thereby promoting their differentiation and lung regeneration. Finally, our analyses identify several enoxacin-targeted regulatory modules that were critically associated with exacerbation of the SARS-CoV-2 infection. Overall, our analysis suggests that enoxacin could be a promising candidate for COVID-19 treatment through enhancing the RNAi pathway.


Anti-Bacterial Agents/pharmacology , COVID-19 Drug Treatment , Enoxacin/pharmacology , RNA Interference/drug effects , SARS-CoV-2/drug effects , COVID-19/genetics , Computer Simulation , Drug Discovery , Gene Regulatory Networks/drug effects , Genomics , Humans , MicroRNAs/genetics , SARS-CoV-2/genetics
7.
J Biol Chem ; 296: 100264, 2021.
Article En | MEDLINE | ID: mdl-33837743

Recent studies have demonstrated that embryonic stem cells (ESCs) are deficient in expressing type I interferons (IFN), the cytokines that play key roles in antiviral responses. However, the underlying molecular mechanisms and biological implications of this finding are poorly understood. In this study, we developed a synthetic RNA-based assay that can simultaneously assess multiple forms of antiviral responses. Dicer is an enzyme essential for RNA interference (RNAi), which is used as a major antiviral mechanism in invertebrates. RNAi activity is detected in wild-type ESCs but is abolished in Dicer knockout ESCs (D-/-ESCs) as expected. Surprisingly, D-/-ESCs have gained the ability to express IFN, which is otherwise deficient in wild-type ESCs. Furthermore, D-/-ESCs have constitutively active double-stranded RNA (dsRNA)-activated protein kinase (PKR), an enzyme that is also involved in antiviral response. D-/-ESCs show increased sensitivity to the cytotoxicity resulting from RNA transfection. The effects of dsRNA can be partly replicated with a synthetic B2RNA corresponding to the retrotransposon B2 short interspersed nuclear element. B2RNA has secondary structure features of dsRNA and accumulates in D-/-ESCs, suggesting that B2RNA could be a cellular RNA that activates PKR and contributes to the decreased cell proliferation and viability of D-/-ESCs. Treatment of D-/-ESCs with a PKR inhibitor and IFNß-neutralizing antibodies increased cell proliferation rate and cell viability. Based on these findings, we propose that, in ESCs, Dicer acts as a repressor of antiviral responses and plays a key role in the maintenance of proliferation, viability, and pluripotency of ESCs.


DEAD-box RNA Helicases/genetics , Interferon Type I/genetics , Interferon-gamma/genetics , Mouse Embryonic Stem Cells/drug effects , Ribonuclease III/genetics , eIF-2 Kinase/genetics , Animals , Antiviral Agents/pharmacology , Cell Proliferation/drug effects , Cell Survival/drug effects , Humans , Mice , Mouse Embryonic Stem Cells/metabolism , Protein Kinase Inhibitors/pharmacology , RNA Interference/drug effects , RNA, Double-Stranded/drug effects , RNA, Double-Stranded/genetics , Retroelements/genetics , eIF-2 Kinase/antagonists & inhibitors
8.
RNA Biol ; 18(5): 604-618, 2021 05.
Article En | MEDLINE | ID: mdl-33622174

A persisting obstacle in human immunology is that blood-derived leukocytes are notoriously difficult to manipulate at the RNA level. Therefore, our knowledge about immune-regulatory RNA-networks is largely based on tumour cell-line and rodent knockout models, which do not fully mimic human leukocyte biology. Here, we exploit straightforward cell penetrating peptide (CPP) chemistry to enable efficient loss-of-function phenotyping of regulatory RNAs in primary human blood-derived cells. The classical CPP octaarginine (R8) enabled antisense peptide-nucleic-acid (PNA) oligomer delivery into nearly 100% of human blood-derived macrophages without apparent cytotoxicity even up to micromolar concentrations. In a proof-of-principle experiment, we successfully de-repressed the global microRNA-155 regulome in primary human macrophages using a PNA-R8 oligomer, which phenocopies a CRISPR-Cas9 induced gene knockout. Interestingly, although it is often believed that fairly high concentrations (µM) are needed to achieve antisense activity, our PNA-R8 was effective at 200 nM. RNA-seq characterized microRNA-155 as a broad-acting riboregulator, feedback restraining a late myeloid differentiation-induced pro-inflammatory network, comprising MyD88-signalling and ubiquitin-proteasome components. Our results highlight the important role of the microRNA machinery in fine-control of blood-derived human phagocyte immunity and open the door for further studies on regulatory RNAs in difficult-to-transfect primary human immune cells.


Inflammation/genetics , MicroRNAs/physiology , Oligonucleotides, Antisense/pharmacology , Phagocytes/drug effects , Cells, Cultured , Gene Knockdown Techniques , Humans , Inflammation/metabolism , MicroRNAs/genetics , Myeloid Cells/drug effects , Myeloid Cells/metabolism , Myeloid Cells/physiology , Phagocytes/immunology , Phagocytes/metabolism , Primary Cell Culture , RNA Interference/drug effects , Transcriptome/drug effects , U937 Cells
9.
Biochem Pharmacol ; 189: 114468, 2021 07.
Article En | MEDLINE | ID: mdl-33577889

Physiologically based pharmacokinetic (PBPK) modeling is a powerful tool with many demonstrated applications in various phases of drug development and regulatory review. RNA interference (RNAi)-based therapeutics are a class of drugs that have unique pharmacokinetic properties and mechanisms of action. With an increasing number of RNAi therapeutics in the pipeline and reaching the market, there is a considerable amount of active research in this area requiring a multidisciplinary approach. The application of PBPK models for RNAi therapeutics is in its infancy and its utility to facilitate the development of this new class of drugs is yet to be fully evaluated. From this perspective, we briefly discuss some of the current computational modeling approaches used in support of efficient development and approval of RNAi therapeutics. Considerations for PBPK model development are highlighted both in a relative context between small molecules and large molecules such as monoclonal antibodies and as it applies to RNAi therapeutics. In addition, the prospects for drawing upon other recognized avenues of PBPK modeling and some of the foreseeable challenges in PBPK model development for these chemical modalities are briefly discussed. Finally, an exploration of the potential application of PBPK model development for RNAi therapeutics is provided. We hope these preliminary thoughts will help initiate a dialogue between scientists in the relevant sectors to examine the value of PBPK modeling for RNAi therapeutics. Such evaluations could help standardize the practice in the future and support appropriate guidance development for strengthening the RNAi therapeutics development program.


Drug Development/methods , Models, Biological , RNA Interference/drug effects , RNAi Therapeutics/methods , Animals , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/metabolism , Drug Development/trends , Humans , Oligonucleotides/antagonists & inhibitors , Oligonucleotides/genetics , Oligonucleotides/metabolism , RNA Interference/physiology , RNAi Therapeutics/trends
10.
Mol Pharm ; 18(3): 796-806, 2021 03 01.
Article En | MEDLINE | ID: mdl-33464088

The small interference RNA (siRNA)-assisted RNA interference approach in stem cells for differentiating into cell-specific lineages is gaining importance for its therapeutic potential. An effective gene delivery platform is crucial to achieve this goal. In this context, self-fluorescent, cell-penetrating peptide (CPP)-functionalized hydroxyapatite nanoparticles (R8HNPs) were synthesized by a modified sol gel technique. R8HNPs were crystalline, displayed characteristic bands, and exhibited broad emission spectra from 350 to 750 nm corresponding to green and red fluorescence. The biocompatible R8HNPs displayed robust binding with siRNA and excellent uptake in R1 ESCs. This was attributed to functionalization with CPP. Moreover, the R8HNP-complexed siRNA exhibited excellent serum and room temperature stability. The NPs protected the siRNA from sonication, pH, and temperature-induced stress and efficiently delivered siRNA to trigger 80% silencing of a pluripotency marker gene, Oct4, in R1 ESCs at 48 h. The transient downregulation was also observed at the protein level. Our findings demonstrate R8HNPs as a promising delivery agent for siRNA therapeutics with the potential for lineage-specific differentiation and future applications in regenerative medicine.


Durapatite/chemistry , Mouse Embryonic Stem Cells/drug effects , Nanoparticles/administration & dosage , RNA, Small Interfering/administration & dosage , Animals , Cell Differentiation/drug effects , Cell Line, Tumor , Cell-Penetrating Peptides/administration & dosage , Cell-Penetrating Peptides/chemistry , Down-Regulation/drug effects , Gene Transfer Techniques , Mice , Nanoparticles/chemistry , RNA Interference/drug effects , RNA, Small Interfering/chemistry
11.
Cardiovasc Drugs Ther ; 35(6): 1269-1279, 2021 12.
Article En | MEDLINE | ID: mdl-32997212

PURPOSE: While low density lipoprotein cholesterol (LDL-C) remains a key contributor of atherosclerotic cardiovascular disease (ASCVD), additional risk factors identified through epidemiological and genetic studies have ushered in a fertile era of drug discovery in lipid-lowering therapy. Unlike contemporary small molecule medications, many of the novel agents are biologics utilizing monoclonal antibody (mAb) or RNA interference (RNAi) technologies. This report aims to review the evidence to date, focusing on completed and ongoing clinical trials and how these new agents will impact clinical practice. METHODS: We review data from pertinent studies on lipid-lowering biologics in clinical use or have translated to human studies and are undergoing clinical trials. RESULTS: Several targets affecting lipid metabolism have been identified to be causally associated with ASCVD including proprotein convertase subtilisin/kexin type 9 (PCSK9), angiopoietin-like protein 3 (ANGPTL3), apolipoprotein C3 (APOC3), and lipoprotein (a) (Lp[a]). Biotechnological modalities that have been developed for these targets include mAb, small interfering RNA (siRNA), and anti-sense oligonucleotide (ASO) agents. Agents such as alirocumab and evolocumab have shown efficacy in risk reduction of ASCVD in cardiovascular outcome trials and have been incorporated into evidence-based practice guidelines. Other agents included in this review are in various stages of clinical trials and have shown significant efficacy in the reduction of lipid parameters. CONCLUSION: The development of new biologics targeting lipid risk factors will provide clinicians additional tools to reduce the risk for ASCVD. Important factors to consider will be cost-effectiveness and improving methods to personalize treatments to risk factors.


Antibodies, Monoclonal/pharmacology , Antibodies, Monoclonal/therapeutic use , Biological Products/pharmacology , Biological Products/therapeutic use , Hypolipidemic Agents/pharmacology , Hypolipidemic Agents/therapeutic use , Animals , Antibodies, Monoclonal/administration & dosage , Antibodies, Monoclonal/adverse effects , Biological Products/administration & dosage , Biological Products/adverse effects , Humans , Hypolipidemic Agents/administration & dosage , Hypolipidemic Agents/adverse effects , Lipid Metabolism/drug effects , Oligonucleotides, Antisense/pharmacology , Oligonucleotides, Antisense/therapeutic use , RNA Interference/drug effects , RNA, Small Interfering/pharmacology , RNA, Small Interfering/therapeutic use
12.
Methods Mol Biol ; 2234: 99-111, 2021.
Article En | MEDLINE | ID: mdl-33165783

Trichoderma reesei is capable of secreting large amounts of lignocellulose-degrading enzymes. Although the genome sequence of T. reesei has been available, the molecular mechanisms of the hyper-production of cellulases, including the transcriptional regulation and the protein secretion, have not been completely elucidated yet. This is partially due to the lack of genetic manipulation approaches. RNA interference (RNAi) is a powerful tool for functional genomic studies in eukaryotes. Some successful examples of RNAi have already been reported; however, these systems were either uncontrolled or relied on a nutrient source inducible promoter. Here, we present a copper-controlled RNAi system in T. reesei for reversible silencing of different target genes. As the proof of concept, T.reesei xyr1, the key transcriptional activator of cellulase genes, has been knocked down using this method.


Copper/pharmacology , Hypocreales/genetics , RNA Interference/drug effects , DNA, Fungal/genetics , Electrophoresis, Polyacrylamide Gel , Fermentation/drug effects , Hypocreales/drug effects , Phenotype , Plasmids/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transformation, Genetic/drug effects
13.
Carcinogenesis ; 42(1): 21-30, 2021 02 11.
Article En | MEDLINE | ID: mdl-33196828

AT-rich interactive domain 1A (ARID1A), which is a tumor suppressor gene, is frequently mutated in Epstein-Barr virus-positive gastric cancer [EBV (+) GC]. While most ARID1A mutations in GC are truncating mutations, leading to loss of ARID1A protein expression, epigenetic modifications appear to contribute to ARID1A deficiency in EBV (+) GC harboring wild-type ARID1A. Based on the significant role of epigenetic modifications in EBV (+) GC that contributes to ARID1A deficiency, the methylation status of ARID1A was evaluated in EBV-infected cells and GC patients using a publicly available microarray and the Cancer Genome Atlas (TCGA) database. EBV-encoded miRNAs that potentially target ARID1A were identified as an additional epigenetic modulator by computational prediction. In vitro experiments were conducted to evaluate how EBV-encoded miRNAs affected ARID1A mRNA and protein levels. In clinical GC samples, the expression of predicted miRNAs and ARID1A and the mutation status of ARID1A was evaluated. As results, ARID1A was not hypermethylated in EBV (+) GC samples or EBV-infected GC cells. EBV infection did not alter ARID1A mRNA levels, suggesting that ARID1A protein deficiency was caused by post-transcriptional gene silencing in ARID1A-WT EBV (+) GC. Overexpression of miR-BART11-3p and miR-BART12, which were identified as miRNAs that potentially bind ARID1A, suppressed ARID1A protein expression in MKN7 and NCI-N87 cells. Highly expressed miR-BART11-3p and miR-BART12 were correlated with decreased ARID1A levels in GC tumors which did not harbor ARID1A mutations. The present findings revealed that ARID1A expression was epigenetically regulated by miR-BART11-3p and miR-BART12 in EBV (+) GC.


DNA-Binding Proteins/genetics , Epstein-Barr Virus Infections/genetics , Herpesvirus 4, Human/genetics , MicroRNAs/metabolism , Stomach Neoplasms/genetics , Transcription Factors/genetics , Aged , Aged, 80 and over , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Proliferation/genetics , Computational Biology , DNA Methylation , DNA-Binding Proteins/deficiency , Datasets as Topic , Epigenesis, Genetic , Epstein-Barr Virus Infections/pathology , Epstein-Barr Virus Infections/surgery , Epstein-Barr Virus Infections/virology , Female , Gene Expression Regulation, Neoplastic/drug effects , Gene Expression Regulation, Neoplastic/genetics , Host-Pathogen Interactions/genetics , Humans , Male , MicroRNAs/agonists , Middle Aged , Oligonucleotide Array Sequence Analysis , Promoter Regions, Genetic/genetics , RNA Interference/drug effects , Retrospective Studies , Stomach/pathology , Stomach/surgery , Stomach/virology , Stomach Neoplasms/pathology , Stomach Neoplasms/surgery , Stomach Neoplasms/virology , Transcription Factors/deficiency
14.
Mol Pharm ; 18(1): 377-385, 2021 01 04.
Article En | MEDLINE | ID: mdl-33295773

RNAi therapy has been developed and explored for treating retinal conditions since last decades. The progression of retinal diseases including the age-related macular degeneration and glaucoma is associated with the malfunction of specific retinal cells. Therefore, to deliver therapeutic RNAi to selective retinal tissues with desired gene downregulation is crucial for the treatment of retinal diseases via RNAi therapy. Lipid-based nanoparticles are potent delivery vectors for RNAi therapeutics to achieve high gene silencing efficiency. The surface charge has been demonstrated to affect the intraocular behaviors and retinal distribution of intravitreally administered lipid nanoparticles (LNPs), which could subsequently affect the gene knockdown efficiency in specific retinal layers. Here, we evaluated three charged LNPs for their ability to deliver siRNA and facilitate gene downregulation both in vitro and in vivo. LNPs with different surface charges ranging from neutral to positive (5-34 mV) were successfully formulated. All types of charged LNPs managed gene knockdown in both mammalian cell line and primary neurons. At 48 h post intravitreal injection, neutral LNPs (6.2 mV) and mildly positive LNPs (15.9 mV) mediated limited retinal gene suppression (<10%) and the more positive LNPs (31.2 mV) led to ∼25% gene suppression in the retinal ganglion cell (RGC) layer. No gene silencing in the retinal pigmented epithelium layer was facilitated by any LNPs independent of the charges. In summary, this study has shown that positive LNPs with an optimized charge managed specific gene downregulation in the RGC layer. These RNAi carriers hold potential for the treatment of RGC-associated retinal diseases.


Lipids/chemistry , Nanoparticles/administration & dosage , Nanoparticles/chemistry , RNA, Small Interfering/administration & dosage , RNA, Small Interfering/chemistry , Retinal Ganglion Cells/drug effects , Animals , Gene Silencing/drug effects , HEK293 Cells , Humans , Male , Mice , Mice, Inbred C57BL , RNA Interference/drug effects , RNAi Therapeutics/methods
15.
RNA ; 27(2): 151-162, 2021 02.
Article En | MEDLINE | ID: mdl-33177187

A key approach for improving siRNA efficacy is chemical modifications. Through an in silico screening of modifications at the 5'-end nucleobase of the guide strand, an adenine-derived compound called 6-(3-(2-carboxyethyl)phenyl)-purine (6-mCEPh-purine) was identified to improve the RNAi activity in cultured human cells and in vivo mouse models. Nevertheless, it remains unclear how this chemical modification enhances the siRNA potency. Here, we used a series of biochemical approaches to quantitatively evaluate the effect of the 6-mCEPh-purine modification at each step in the assembly of the RNAi effector complex called RISC. We found that the modification improves the formation of mature RISC at least in two different ways, by fixing the loading orientation of siRNA duplexes and increasing the stability of mature RISC after passenger strand ejection. Our data will provide a molecular platform for further development of chemically modified siRNA drugs.


Adenine/pharmacology , Argonaute Proteins/genetics , RNA Interference/drug effects , RNA, Double-Stranded/genetics , RNA, Small Interfering/agonists , RNA-Induced Silencing Complex/agonists , Adenine/analogs & derivatives , Adenine/chemical synthesis , Argonaute Proteins/metabolism , Base Pairing , Base Sequence , HEK293 Cells , Humans , Methylation , Protein Binding , RNA, Double-Stranded/metabolism , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , RNA-Induced Silencing Complex/genetics , RNA-Induced Silencing Complex/metabolism
16.
RNA ; 27(2): 163-173, 2021 02.
Article En | MEDLINE | ID: mdl-33177188

Small interfering RNAs (siRNAs) can be utilized not only as functional biological research tools but also as therapeutic agents. For the clinical use of siRNA as drugs, various chemical modifications have been used to improve the activity of siRNA drugs, and further chemical modifications are expected to improve the utility of siRNA therapeutics. As the 5' nucleobase of the guide strand affects the interaction between an siRNA and AGO2 and target cleavage activity, structural optimization of this specific position may be a useful strategy for improving siRNA activity. Here, using the in silico model of the complex between human AGO2 MID domain and nucleoside monophosphates, we screened and synthesized an original adenine-derived analog, 6-(3-(2-carboxyethyl)phenyl)purine (6-mCEPh-purine), that fits better than the natural nucleotide bases into the MID domain of AGO2. Introduction of the 6-mCEPh-purine analog at the 5'-end of the siRNA guide strand significantly enhanced target knockdown activity in both cultured cell lines and in vivo animal models. Our findings can help expand strategies for rationally optimizing siRNA activity via chemical modifications of nucleotide bases.


Adenine/pharmacology , Argonaute Proteins/genetics , RNA Interference/drug effects , RNA, Double-Stranded/genetics , RNA, Small Interfering/agonists , RNA-Induced Silencing Complex/agonists , Adenine/analogs & derivatives , Adenine/chemical synthesis , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/metabolism , Animals , Apolipoprotein B-100/antagonists & inhibitors , Apolipoprotein B-100/blood , Apolipoprotein B-100/chemistry , Apolipoprotein B-100/genetics , Argonaute Proteins/metabolism , Base Pairing , Base Sequence , Binding Sites , Cholesterol/blood , HeLa Cells , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Male , Methylation , Mice , Mice, Knockout , Models, Molecular , Protein Binding , RNA, Double-Stranded/metabolism , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , RNA-Induced Silencing Complex/genetics , RNA-Induced Silencing Complex/metabolism , Uridine Monophosphate/chemistry , Uridine Monophosphate/metabolism
17.
Bioorg Med Chem Lett ; 30(24): 127637, 2020 12 15.
Article En | MEDLINE | ID: mdl-33132114

We found that sulfisomidine, a sulfonamide antibiotic, potently binds to the Piwi/Argonaute/Zwille (PAZ) domain of human Argonaute protein 2 and inhibits RNA interference (RNAi). To elucidate the effect on RNAi of strong affinity of the 3'-ends in small interfering RNA (siRNA) to the PAZ domain, chemically modified siRNAs bearing sulfisomidine at the 3'-end were synthesized.


Anti-Bacterial Agents/pharmacology , Argonaute Proteins/metabolism , RNA Interference/drug effects , Sulfisomidine/pharmacology , Argonaute Proteins/chemistry , Humans , Protein Domains/drug effects , RNA, Small Interfering/antagonists & inhibitors , Sulfonamides/pharmacology
18.
Chem Commun (Camb) ; 56(98): 15406-15409, 2020 Dec 21.
Article En | MEDLINE | ID: mdl-33196071

Gene therapy is highly suited for prostate cancer (PC). Metal-organic-frameworks (MOFs) are potential gene delivery systems. Target-specific cytoplasmic and nuclear knockdown in host gene expression using ZIF-C is shown for the first time through RNAi and CRISPR/Cas9 based gene editing in PC cells. A green tea phytochemical coating enhances intracellular delivery.


CRISPR-Associated Protein 9/antagonists & inhibitors , Metal-Organic Frameworks/pharmacology , Prostatic Neoplasms/drug therapy , RNA Interference/drug effects , CRISPR-Associated Protein 9/genetics , Gene Editing , Gene Transfer Techniques , Humans , Male , Metal-Organic Frameworks/chemistry , PC-3 Cells , Prostatic Neoplasms/genetics
19.
Biochem Biophys Res Commun ; 531(3): 305-311, 2020 10 20.
Article En | MEDLINE | ID: mdl-32800558

Mitochondrial dysfunction and oxidative stress are pathophysiologic mechanisms implicated in Parkinson's disease (PD). In recent years, environmental toxins are employed to increase oxidative stress mediated neuropathology and sporadic PD. Disruption of iron homeostasis has been implicated in PD patients for many years, but the functional role of iron in sporadic PD pathogenesis is still not well clarified in vivo. To address this question, we set out to investigate the effect of iron on a Drosophila rotenone model of sporadic PD. Iron homeostasis is maintained by many transporters. We found that inhibition of transferrin1 (Tsf1) expression in the central nervous system (CNS) results in reduced iron levels in brains and significantly ameliorates the neurodegenerative phenotypes of rotenone exposure Drosophila; moreover, the rotenone induced reactive oxygen species (ROS) levels in the brain, the damaged complex I activity and the decreased ATP generation were dramatically rescued by Tsf1 knockdown. Further study indicated that all the rescue effects of Tsf1 knockdown on sporadic PD could be inhibited by malvolio (Mvl) overexpression, an iron transporter responsible for iron uptake. These results imply that Tsf1 knockdown in the CNS could attenuate rotenone toxicity by decreasing the ROS levels in brains through reducing iron levels, and manipulation of iron transporters in brains may provide a novel therapeutic strategy for sporadic PD.


Drosophila Proteins/metabolism , Drosophila melanogaster/metabolism , Homeostasis , Iron/metabolism , Parkinson Disease/metabolism , Rotenone/pharmacology , Transferrins/metabolism , Animals , Brain Injuries/metabolism , Brain Injuries/pathology , Disease Progression , Head , Homeostasis/drug effects , Neurons/drug effects , Neurons/metabolism , Neurons/pathology , Neurotoxins/toxicity , Oxidative Stress/drug effects , Parkinson Disease/pathology , Phenotype , RNA Interference/drug effects
20.
Exp Cell Res ; 395(1): 112175, 2020 10 01.
Article En | MEDLINE | ID: mdl-32679233

Autophagy is a basic catabolic response that eukaryotic cells use to degrade unnecessary or dysfunctional cellular components in an orderly and regulated manner. It plays important roles in maintaining cellular homeostasis, energy homeostasis, response to environmental stimuli, and the development of cancer. In solid tumors, hypoxia induces an increased HIF-1a that activates autophagy. However, the exact mechanism by which induced HIF-1a stimulates autophagy in cancer cells remains elusive. In the present study, we confirmed that ANKRD37 is upregulated in colon cancer tissue. Moreover, the higher expression level of ANKRD37 is related to a poorer survival rate. Using RNA interference, immunoblot, and immunofluorescence, we discovered that in cancer cell line RKO, hypoxia-induced HIF-1a regulates autophagy activity by increasing ANKRD37 level. In addition, intranuclear ANKRD37 played an important role in the regulation of hypoxia-induced autophagy. The translocation of ANKRD37 into cell nuclear is required for promoting cell growth and HIF-1a induced autophagy. These findings provide new insights to understand the hypoxia regulation mechanisms and the role of autophagy in cancer development.


Autophagy/drug effects , Colonic Neoplasms/genetics , Gene Expression Regulation, Neoplastic/genetics , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Autophagy/genetics , Autophagy/physiology , Cell Hypoxia/drug effects , Cell Hypoxia/physiology , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Proliferation/physiology , Colonic Neoplasms/metabolism , Colonic Neoplasms/pathology , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/pharmacology , RNA Interference/drug effects , RNA Interference/physiology , Transcriptional Activation/physiology
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