siRNA-mediated RNA Interference Research Articles

Transcriptomic analysis reveals PC4's participation in thermotolerance of scallop Argopecten irradians irradians by regulating myocardial bioelectric activity

Rising ocean temperatures due to global warming pose a significant threat to the bay scallop aquaculture industry. Understanding the mechanisms of thermotolerance in bay scallops is crucial for developing thermotolerant breeds. Our prior research identified Arg0230340.1, part of the positive cofactor 4 (PC4) family, as a key gene associated with the thermotolerance index Arrhenius break temperature (ABT) in bay scallops. Further validation through RNA interference (RNAi) reinforced PC4's role in thermotolerance, offering a solid basis for investigating thermal response mechanisms in these scallops. In this study, we performed a comparative transcriptomic analysis on the temperature-sensitive hearts of bay scallops after siRNA-mediated RNAi targeting Arg0230340.1, to delve into the detailed molecular mechanism of PC4's participation in thermotolerance regulation. The analysis revealed that silencing Arg0230340.1 significantly reduced the expression of mitochondrial tRNA and rRNA, potentially affecting mitochondrial function and the heart's blood supply capacity. Conversely, the up-regulation of genes involved in energy metabolism, RNA polymerase II (RNAPII)-mediated basal transcription, and aminoacyl-tRNA synthesis pathways points to an intrinsic protective response, providing energy and substrates for damage repair and maintenance of essential functions under stress. GO and KEGG enrichment analyses indicated that the up-regulated genes were primarily associated with energy metabolism and spliceosome pathways, likely contributing to myocardial remodeling post-Arg0230340.1 knockdown. Down-regulated genes were enriched in ion channel pathways, particularly those for Na+, K+, and Ca2+ channels, whose dysfunction could disrupt normal myocardial bioelectric activity. The impaired cardiac performance resulting from RNAi targeting Arg0230340.1 reduced the cardiac workload in scallop hearts, thus affecting myocardial oxygen consumption and thermotolerance. We propose a hypothetical mechanism where PC4 down-regulation impairs cardiac bioelectric activity, leading to decreased thermotolerance in bay scallops, providing theoretical guidance for breeding thermotolerant scallop varieties and developing strategies for sustainable aquaculture in the face of long-term environmental changes.

Role of CRISPR in Crop Improvement: A Review

The meals and agriculture sectors have witnessed good sized advancements due to the state-of-the-art improvements in agricultural biotechnology and genetic engineering, that have more advantageous the essential characteristics of plant agronomic tendencies. A extensively used technique for inducing focused deletions, insertions, and precise sequence adjustments throughout numerous species and mobile kinds is collection-particular nucleases (SSNs)-based centered genome editing. Commercial adoption of genome modifying gear, which include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and siRNA-mediated RNA interference, has been significant. However, the whole landscape of lifestyles sciences underwent a paradigm shift with the invention of the CRISPR/Cas9 machine as a flexible tool for genome modifying. Initially recognized as a virological defense DNA segment in bacteria and archaea, the clustered Regularly interspaced short palindromic repeats (CRISPR) machine has revolutionized molecular biology. Through modern molecular organic strategies, CRISPR/Cas9 enables unique modifications in any crop species. Its efficacy, reproducibility, and specificity have earned CRISPR/Cas9 the moniker of a "leap forward" in biotechnology.

Improvement of economic and useful characters of wheat using RNA interference technology

Wheat is a strategic cereal crop of global importance and plays a leading role in the food supply of mankind. Despite the general trend to increase in its production, climatic changes leading to significant temperature changes, unpredictable precipitation or droughts and the appearance of new races of pathogens and pests significantly affect its yield. In order to prevent the negative impact of changes in climatic conditions on the productivity of this crop, it is necessary to develop innovative technologies for improving the resistance of wheat to environmental stresses. RNA interference (RNAi) represents a new potential tool for wheat breeding by introducing small non-coding RNA sequences with the ability to silence gene expression in a sequence-specific manner. A decrease in the expression of a certain gene determines the acquisition of a new characteristic through the elimination or accumulation of certain plant traits, which leads to biochemical or phenotypic changes that the original plants do not have. This literature review describes the progress achieved over the past decades in the application of RNAi to create wheat plants with improved economic and valuable traits. The main stages of the gene silencing mechanism mediated by short interfering RNA (siRNA) and microRNA (miRNA), features of their biogenesis, modes of action and distribution are presented. Examples of the use of various biotechnological approaches to wheat improvement using gene transformation, endogenous and exogenous double-stranded RNA molecules (dsRNA) are given. The possibility of using RNAi technology to increase the nutritional value and quality of grain, remove toxic compounds and allergens is highlighted. Considerable attention is paid to the practical results of various applications of RNAi to increase the resistance of wheat to biotic stress factors, in particular, viruses, bacteria, fungi, insect pests, and nematodes. Examples of the use of siRNA-mediated RNAi and the role of miRNA in improving wheat tolerance to abiotic stresses are summarized.

Three alternative splicing variants of Loquacious play different roles in miRNA- and siRNA-mediated RNAi pathways in Locusta migratoria

ABSTRACT RNA interference (RNAi) is a specific post-transcriptional gene-silencing phenomenon, which plays an important role in the regulation of gene expression and the protection from transposable elements in eukaryotic organisms. In Drosophila melanogaster, RNAi can be induced by microRNA (miRNA), endogenous small interfering RNA (siRNA), or exogenous siRNA. However, the biogenesis of miRNA and siRNA in these RNAi pathways is aided by the double-stranded RNA binding proteins (dsRBPs) Loquacious (Loqs)-PB, Loqs-PD or R2D2. In this study, we identified three alternative splicing variants of Loqs, namely Loqs-PA, -PB, and -PC in the orthopteran Locusta migratoria. We performed in vitro and in vivo experiments to study the roles of the three Loqs variants in the miRNA- and siRNA-mediated RNAi pathways. Our results show that Loqs-PB assists the binding of pre-miRNA to Dicer−1 to lead to the cleavage of pre-miRNA to yield matured miRNA in the miRNA-mediated RNAi pathway. In contrast, different Loqs proteins participate in different siRNA-mediated RNAi pathways. In exogenous siRNA-mediated RNAi pathway, binding of Loqs-PA or LmLoqs-PB to exogenous dsRNA facilitates the cleavage of dsRNA by Dicer−2, whereas in endogenous siRNA-mediated RNAi pathway, binding of Loqs-PB or Loqs-PC to endogenous dsRNA facilitates the cleavage of dsRNA by Dicer−2. Our findings provide new insights into the functional importance of different Loqs proteins derived from alternative splicing variants of Loqs in achieving high RNAi efficiency in different RNAi pathways in insects.

Both LmDicer-1 and two LmDicer-2s participate in siRNA-mediated RNAi pathway and contribute to high gene silencing efficiency in Locusta migratoria

Dicers belong to a class of large RNase III multidomain ribonucleases and are central components of the RNA interference (RNAi) pathways. In insects, Dicer-2 has been known to cleave long double-stranded RNA (dsRNA) in small interfering RNA (siRNA)-mediated-RNAi pathway. However, Dicer-1 is responsible for cleaving precursor microRNAs (pre28 miRNAs) in miRNA-mediated RNAi pathway. In this study, we identified one LmDicer-1 and two LmDicer-2 (LmDicer-2a and LmDicer-2b) genes in Locusta migratoria. The RNAi of RNAi assay showed that knockdown of each of the Dicer genes reduced RNAi efficiency against a target gene (Lmβ-Tubulin), suggesting that all these genes participated in the siRNA-mediated RNAi pathway. Sequence analyses of the siRNAs generated from dsLmβ-Tubulin after silencing each LmDicer gene showed no significant difference in the pattern of siRNAs mapped to dsLmβ-Tubulin. This result indicated that all the three LmDicers are capable of generating siRNAs from the dsRNA. We then generated recombinant proteins consisting of different domains using Escherichia coli expression system and incubated each recombinant protein with dsLmβ-Tubulin. We found that the recombinant Dicer proteins successfully cleaved dsLmβ-Tubulin. However, LmDicer-2a-R lacking dsRBD domain lost activity, suggesting that dsRBD domain is critical for Dicer function. Furthermore, overexpression of these proteins in Drosophila S2 cells improved RNAi efficiency. Our siRNA affinity chromatography and LC-MS/MS analysis identified LmDicer-2a, LmDicer-2b, LmR2D2, LmAgo2a, LmAgo1, LmStaufen and LmTARBP2 as constituents of RNA-induced silencing complex. Taken together, these data show that both LmDicer-1 and two LmDicer-2s all participate in siRNA-mediated RNAi pathway and likely contribute to high RNAi efficiency in L. migratoria.

Multiple Argonaute family genes contribute to the siRNA-mediated RNAi pathway in Locusta migratoria

Argonautes (Ago) are important core proteins in RNA interference (RNAi) pathways of eukaryotic cells. Generally, it is thought that Ago1, Ago2 and Ago3 are involved in the miRNA (microRNA), siRNA (small interfering RNA) and piRNA (Piwi-interacting RNA)-mediated RNAi pathways, respectively. As a main component of the RNA-induced silencing complex (RISC), Ago2 plays an indispensable role in using siRNA to recognize and cut target messenger RNAs resulting in suppression of transcript levels, but the contributions of Ago1 and Ago3 to the siRNA-mediated RNAi pathway remain to be explored in many insect species. In this study, we investigated the contributions of four Ago genes (named LmAgo1, LmAgo2a and LmAgo2b and LmAgo3) to RNAi efficiency in Locusta migratoria by using both in vivo and in vitro experiments. Our results showed that suppression of each of the Ago genes significantly impaired RNAi efficiency when targeting Lmβ-tubulin transcripts, resulting in recovery of 48, 43.3, 61.4 or 26% of Lmβ-tubulin transcripts following RNAi-mediated suppression of LmAgo1, LmAgo2a, LmAgo2b, and LmAgo3, respectively. Furthermore, overexpression of LmAgo1, LmAgo2a, LmAgo2b, or LmAgo3 in a PAc5.1-V5/HisB vector and co-transfection with psicheck2 fluorescence vector in S2 cells reduced luciferase fluorescence by 38.3, 58.9, 53.3 or 55.6%, respectively. Taken together, our results showed that LmAgo1, LmAgo2a, LmAgo2b, and LmAgo3 each make significant contributions to RNAi efficiency in L. migratoria and suggest that the involvement of all four enzymes could be one of the major factors supporting robust RNAi responses observed in this species.

CircRNA_104889 promotes lung adenocarcinoma cell invasion via sponging miR4458

BackgroundLung adenocarcinoma is metastatic cancer with a high mortality rate. Circular RNAs (circRNAs) are a type of noncoding RNA and play a vital role in cancer progression. However, the expression and function of circRNAs in lung adenocarcinoma are still mostly unknown.MethodsIn this study, we screened the differential expression of circRNAs in human bronchial epithelial cells (HBE) and A549 human lung adenocarcinoma cell line (A549) by human circRNA microarray and RT-qPCR. The role of overexpressed circRNA_104889 in A549 cell proliferation, apoptosis, migration, and invasion was studied extensively. Intracellular localization of circRNA_104889 was visualized by FISH assay. MiRNA sponging, ERK1/2 signaling, and caspase-3 expression were analyzed in siRNA-mediated circRNA_104889 knockdowned A549 cells.ResultsCircRNA microarray showed overexpression of circRNA_104889 (> 13-fold) in A459 cells compared to HBE. This finding was further corroborated by the RT-qPCR result. CircRNA_104889 was mainly localized in the cytoplasm of A549 cells. The knockdown of circRNA_104889 in A549 cells by si-RNA mediated RNA interference did not affect cell proliferation and apoptosis but significantly inhibited cell migration and invasion in vitro. Furthermore, knockdown of circRNA_104889 led to an increase of miR4458 expression. Overexpression of miR4458 inhibited A549 cell migration. Both the knockdown of circRNA_104889 and overexpression of miR4458 inhibited the caspase-3 expression and ERK1/2 phosphorylation in A549 cells.ConclusionsCircRNA_104889 promotes lung adenocarcinoma cell migration and invasion by sponging miR4458 and targeting ERK1/2 signaling and caspase-3 expression.

Embryonic MTHFR contributes to blastocyst development.

Reduction in methylenetetrahydrofolate reductase (MTHFR) activity due to genetic variations in the MTHFR gene has been controversially implicated in subfertility in human in vitro fertilization. However, there is no direct gene-knockdown study of embryonic MTHFR to assess its involvement in mammalian preimplantation development. The purpose of this study is to investigate expression profiles and functional roles of MTHFR in bovine preimplantation development. Reverse transcription-quantitative PCR (RT-qPCR) and analysis of publicly available RNA-seq data were performed to reveal expression levels of MTHFR during bovine preimplantation development. We knocked down MTHFR by siRNA-mediated RNA interference from the 8- to 16-cell stage and assessed the effects on preimplantation development. The RT-qPCR analysis showed relatively high MTHFR expression at the GV oocyte stage, which was decreased toward the 8- to 16-cell stage and then slightly restored at the blastocyst stage. Public data-based analysis also showed the similar pattern of expression with substantial embryonic expression at the blastocyst stage. MTHFR knockdown reduced the blastocyst rate (P < 0.01) and the numbers of total (P < 0.0001), trophectoderm (P < 0.0001), and inner cell mass (P < 0.001) cells. The results indicate that embryonic MTHFR is indispensable for normal blastocyst development. The findings provide insight into the debatable roles of MTHFR in fertility and may be applicable for the improvement of care for early embryos via modulation of surrounding folate-related nutritional conditions in vitro and/or in utero, depending on the parental and embryonic MTHFR genotype.

Interaction of a Trichinella spiralis cathepsin B with enterocytes promotes the larval intrusion into the cells

Cathepsin B is one member of cysteine protease family and widely distributed in organisms, it plays an important function in parasite penetrating, migrating, molting and immune escaping. The aim of this work was to investigate whether exist interaction between a Trichinella spiralis cathepsin B (TsCB) and mouse intestinal epithelium cells (IECs), and its influence in the process of larva cell invasion. The results of ELISA, indirect immunofluorescence assay (IIFA), confocal microscopy and Far western blotting showed that there was a strong specific binding of rTsCB and IEC proteins, and the binding positions were located in cytoplasm and nuclei of IECs. The results of the in vitro larva penetration test revealed that rTsCB facilitated the larva invasion of IECs, whereas anti-rTsCB antibodies impeded partially the larva intrusion of enterocytes, this promotive or inhibitory roles were dose-dependent of rTsCB or anti-rTsCB antibodies. Silencing TsCB by siRNA mediated RNA interference reduced the TsCB expression in T. spiralis larvae, and markedly inhibited the larva penetration of enterocytes. The results indicated that TsCB binding to IECs promoted larva penetration of host's enteral epithelia, and it is a promising molecular target against intestinal invasive stages of T. spiralis.

Programmable CRISPR interference for gene silencing using Cas13a in mosquitoes

In the CRISPR-Cas systems, Cas13a is an RNA-guided RNA nuclease specifically targeting single strand RNA. We developed a Cas13a mediated CRISPR interference tool to target mRNA for gene silencing in mosquitoes. A Cas13a expressing plasmid was delivered to mosquitoes by intrathoracic injection, and Cas13a transcripts were detectable at least 10 days post-delivery. The target specific crRNA was synthesized in vitro using T7 RNA polymerase. The Cas13a plasmid and target crRNA can be delivered by intrathoracic injection together, or the Cas13a construct can be provided first, and then target crRNA can be given later when appropriate. The machinery was tested in two mosquito species. In Anopheles gambiae, vitellogenin gene was silenced by Cas13a/Vg-crRNA, which was accompanied by a significant reduction in egg production. In Aedes aegypti, the α- and δ-subunits of COPI genes were silenced by Cas13a/crRNA, which resulted in mortality and fragile midguts, reproducing a phenotype reported previously. Co-silencing genes simultaneously is achievable when a cocktail of target crRNAs is given. No detectable collateral cleavages of non-target transcripts were observed in the study. In addition to dsRNA or siRNA mediated RNA interference, the programmable CRISPR interference method offers an alternative to knock down genes in mosquitoes.

RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference

The influenza A virus is a human pathogen that poses a serious public health threat due to rapid antigen changes and emergence of new, highly pathogenic strains with the potential to become easily transmitted in the human population. The viral genome is encoded by eight RNA segments, and all stages of the replication cycle are dependent on RNA. In this study, we designed small interfering RNA (siRNA) targeting influenza segment 5 nucleoprotein (NP) mRNA structural motifs that encode important functions. The new criterion for choosing the siRNA target was the prediction of accessible regions based on the secondary structure of segment 5 (+)RNA. This design led to siRNAs that significantly inhibit influenza virus type A replication in Madin-Darby canine kidney (MDCK) cells. Additionally, chemical modifications with the potential to improve siRNA properties were introduced and systematically validated in MDCK cells against the virus. A substantial and maximum inhibitory effect was achieved at concentrations as low as 8 nM. The inhibition of viral replication reached approximately 90% for the best siRNA variants. Additionally, selected siRNAs were compared with antisense oligonucleotides targeting the same regions; this revealed that effectiveness depends on both the target accessibility and oligonucleotide antiviral strategy. Our new approach of target-site preselection based on segment 5 (+)RNA secondary structure led to effective viral inhibition and a better understanding of the impact of RNA structural motifs on the influenza replication cycle.

Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2.

RNA interference (RNAi) is an evolutionary ancient innate immune response in plants, nematodes, and arthropods providing natural protection against viral infection. Viruses have also gained counter‐defensive measures by producing virulence determinants called viral‐suppressors‐of‐RNAi (VSRs). Interestingly, in spite of dominance of interferon‐based immunity over RNAi in somatic cells of higher vertebrates, recent reports are accumulating in favour of retention of the antiviral nature of RNAi in mammalian cells. The present study focuses on the modulation of intracellular RNAi during infection with rotavirus (RV), an enteric virus with double‐stranded RNA genome. Intriguingly, a time point‐dependent bimodal regulation of RNAi was observed in RV‐infected cells, where short interfering RNA (siRNA)‐based RNAi was rendered non‐functional during early hours of infection only to be reinstated fully beyond that early infection stage. Subsequent investigations revealed RV nonstructural protein 1 to serve as a putative VSR by associating with and triggering degradation of Argonaute2 (AGO2), the prime effector of siRNA‐mediated RNAi, via ubiquitin–proteasome pathway. The proviral significance of AGO2 degradation was further confirmed when ectopic overexpression of AGO2 significantly reduced RV infection. Cumulatively, the current study presents a unique modulation of host RNAi during RV infection, highlighting the importance of antiviral RNAi in mammalian cells.

Functional analysis of a novel parasitic nematode-specific protein of Setaria digitata larvae in Culex quinquefasciatus by siRNA mediated RNA interference

BackgroundFunctional analysis of animal parasitic nematode genes is often quite challenging due to the unavailability of standardised in vitro culture conditions and lack of adequate tools to manipulate these genes. Therefore, this study was undertaken to investigate the suitability of Culex quinquefasciatus, as an in vivo culture platform for Setaria digitata larvae and RNA interference (RNAi), as a post-transcriptional gene silencing tool to study the roles of a vital gene that encodes a novel parasitic nematode-specific protein (SDNP).ResultsThe red colour fluorescence detected following RNAi injection to the thorax of C. quinquefasciatus indicated the uptake of dsRNA by S. digitata larvae. The reduction of SDNP transcripts in siRNA treated larvae compared to non-treated larvae, as determined by qPCR, indicated that the siRNA pathway is operational in S. digitata larvae. The observation of motility reductions and deformities during the development indicated the association of SDNP in larvae locomotion and development processes, respectively. The irregularities in the migration of larvae in mosquitoes and elevated survival rates of mosquitoes compared to their untreated counterparts indicated reduced parasitism of S. digitata larvae in mosquitoes upon targeted downregulation of SDNP by siRNA treatment.ConclusionSDNP plays vital roles in muscle contraction, locomotion, development processes, larval development and parasitism of S. digitata. Its ubiquitous presence in parasitic nematodes and its absence in their hosts provide a tantalising prospect of the possibility of targeting SDNP for future development of anthelmintic drugs. The susceptibility of the larval stages of S. digitata for RNAi in Culex quinquefasciatus was also demonstrated for the first time in this study.

Regulation of IRE1 RNase activity by the Ribonuclease inhibitor 1 (RNH1)

ABSTRACT Adaptation to endoplasmic reticulum (ER) stress depends on the activation of the sensor inositol-requiring enzyme 1α (IRE1), an endoribonuclease that splices the mRNA of the transcription factor XBP1 (X-box-binding protein 1). To better understand the protein network that regulates the activity of the IRE1 pathway, we systematically screened the proteins that interact with IRE1 and identified a ribonuclease inhibitor called ribonuclease/angiogenin inhibitor 1 (RNH1). RNH1 is a leucine-rich repeat domains-containing protein that binds to and inhibits ribonucleases. Immunoprecipitation experiments confirmed this interaction. Docking experiments indicated that RNH1 physically interacts with IRE1 through its cytosolic RNase domain. Upon ER stress, the interaction of RNH1 with IRE1 in the ER increased at the expense of the nuclear pool of RNH1. Inhibition of RNH1 expression using siRNA mediated RNA interference upon ER stress led to an increased splicing activity of XBP1. Modulation of IRE1 RNase activity by RNH1 was recapitulated in a cell-free system, suggesting direct regulation of IRE1 by RNH. We conclude that RNH1 attenuates the activity of IRE1 by interacting with its ribonuclease domain. These findings have implications for understanding the molecular mechanism by which IRE1 signaling is attenuated upon ER stress.

Cloning and Characterization of Two Toll Receptors (PcToll5 and PcToll6) in Response to White Spot Syndrome Virus in the Red Swamp Crayfish Procambarus clarkii.

Toll/Toll-like receptors are key components in the innate immune responses of invertebrates. In this study, we identified two novel Toll receptors (PcToll5 and PcToll6) from the red swamp crayfish Procambarus clarkii. The complete cDNA sequence of PcToll5 is 4247 bp, encoding a 1293 amino acid polypeptide. The full-length 4688 bp PcToll6 encodes a putative protein of 1195 amino acids. Quantitative RT-PCR analysis indicated that PcToll5 and PcToll6 were constitutively expressed in all tissues studied. The highest expression levels of PcToll5 and PcToll6 were found in the intestine and gills, respectively, and were significantly upregulated from 24 to 48 h during white spot syndrome virus (WSSV) challenge. siRNA-mediated RNA interference results showed that PcToll5 and PcToll6 might regulate the expression of anti-lipopolysaccharide factors (PcALF2 and PcALF3) in vivo. Overexpression of PcToll5 and PcToll6 in Drosophila Schneider 2 (S2) cells activated the transcription of Drosophila antimicrobial peptides, including drosomycin (Drs), metchnikowin (Mtk), and attacin A (AttA), and shrimp Penaeidin-4 (Pen4). These findings provide significant information that PcToll5 and PcToll6 may contribute to host immune defense against WSSV in P. clarkii.

Development of siRNA mediated RNA interference and functional analysis of novel parasitic nematode-specific protein of Setaria digitata

Despite the differences of the host, parasitic nematodes may share commonalities in their parasitizing genes. Setaria digitata novel protein (SDNP) is such an entity which is parasitic nematode-specific and having sequence similarities with those of W. bancrofti, B. malayi, Loa loa and Onchocerca volvulus. Post-transcriptional gene silencing by siRNA mediated RNA interference (RNAi) is a widely used technique in functional genomics. Though the technique has been used in several free-living, plant and animal parasitic nematodes, it has not yet been tried out for the filarial worm S. digitata. In this study, we developed an effective siRNA delivery method by microinjection and utilized the siRNAi tool to knockdown SDNP to study the phenotypic and cellular changes associated with the interference.qPCR analysis revealed, a significant reduction of SDNP transcript levels following siRNA microinjection into S. digitata adult worms. Similarly, immunohistochemical staining indicated a reduction of SDNP protein expression. Furthermore, worms treated with siRNA showed a significant reduction of microfilariae release together with embryonic lethality by arresting an early developmental stage compared to non-treated worms. A distinct motility reduction was also observed in treated worms compared to non-treated counterparts.This is the first report of the amenability of S. digitata to the siRNA induced RNAi. The presence of inter-domain linkers of muscle-specific twitchin kinase and calcium-dependent protein kinase isoform CDPK1 together with what our results revealed suggest that SDNP is most likely a protein involved in muscle movement and growth and development of the nematode. Hence SDNP has the characteristics of a potential drug target.

SiRNA-Mediated RNA Interference in Precision-Cut Tissue Slices Prepared from Mouse Lung and Kidney

Small interfering RNA (siRNA)-mediated RNAi interference (RNAi) is a powerful post-transcriptional gene silencing mechanism which can be used to study the function of genes in vitro (cell cultures) and in vivo (animal models). However, there is a translational gap between these models. Hence, there is a need for novel experimental models that combine the advantages of in vitro and in vivo models (e.g., simplicity, flexibility, throughput, and representability) to study the effects of siRNA. This need may be addressed by precision-cut tissue slices (PCTS), which represent an ex vivo model that mimics the structural and functional characteristics of a whole organ. The goal of this study was to investigate whether self-deliverable siRNA (Accell siRNA) can be used in precision-cut lung slices (PCLuS) and precision-cut kidney slices (PCKS) to achieve RNAi ex vivo. PCLuS and PCKS were prepared from mouse tissue, and they were subsequently incubated up to 48 h with no siRNA (untransfected), non-targeting Accell siRNA, or Gapdh-targeting Accell siRNA. Significant Gapdh mRNA silencing was achieved (PCLuS ~ 55%; PCKS ~ 40%) without compromising the viability and morphology of slices. Fluorescence microscopy confirmed that Accell siRNA diffused into PCLuS and PCKS. Spontaneous inflammation upon incubation was observed in PCLuS and PCKS as shown by a higher mRNA expression of pro-inflammatory cytokines Il1b, Il6, and Tnfa, although Accell siRNA appeared to diminish this response in PCLuS after 24 h. In conclusion, this ex vivo transfection model can be used to evaluate the effects of siRNA in relevant biological environments.

Abstract 3131: Ubiquitin ligases: a new target for RNAi therapy of hepatocellular carcinoma

Abstract Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide and the third leading cause of cancer-related deaths in the world. HCC is a very aggressive cancer, resistant to all conventional chemotherapies and capable of acquiring resistance to Sorafenib, which is the only approved chemotherapeutic drug for HCC. This highlights the need to look for new therapeutic options and improve the survival of patients with advanced HCC. The N-end rule pathway is an emerging player in the field of cancer biology, because of its capacity to positively regulate many hallmarks of cancer including angiogenesis, cell proliferation, motility and survival. Therefore, the N-end rule pathway offers the potential to be a target for highly effective anti-tumor treatment. The aim of this study is to investigate the role of the N-end rule pathway in the context of hepatocellular carcinoma in vivo. We used siRNA-mediated RNA interference as the main approach for selective downregulation of the four N-end rule-dependent cognate ubiquitin ligases: UBR1, UBR2, UBR4 and UBR5. Initial screening of siRNAs was performed in Hepa 1-6 cells, followed by in vitro phenotyping using proliferation assays, migration assays, and TUNEL assays. The most potent siRNA against Ubr1, Ubr2, Ubr4 and Ubr5 were formulated into lipid nanoparticles (LNPs) and injected into mice in order to modulate the function of the N-end rule in vivo. We have confirmed that Ubr1, Ubr2, Ubr4 and Ubr5 are overexpressed in Hepa 1-6 cells and in mouse liver tumors, in comparison to normal liver. Upon transfection of siRNAs in Hepa 1-6 cells or injection of LNPs loaded with the same siRNAs into mice, we obtained successful down regulation of Ubr1, Ubr2, Ubr4 and Ubr5 both in vitro and in vivo (in the liver and in tumor tissue). We have also demonstrated that down regulation of these four Ubr proteins negatively affects cell migration and proliferation, and renders cells more susceptible to apoptosis. Bi-weekly injections of the LNPs in mice for a period up to 6 weeks efficiently downregulates the expression of Ubr1, Ubr2, Ubr4 and Ubr5 without any toxic effects. Indeed, we found no significant increase of ALT, AST or total bilirubin in the blood compared to controls. Considering that all four Ubrs are overexpressed in mouse liver tumors, and that the N-end rule plays a major role in many key pathways of cancer development, we expect that even a partial down regulation of this pathway will have prominent effects on tumor development and progression due to the suppression of tumor vascularization, cell proliferation and viability. Citation Format: Dominique Leboeuf, Timofei Zatsepin, Daniel G. Anderson, Konstantin Piatkov. Ubiquitin ligases: a new target for RNAi therapy of hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3131. doi:10.1158/1538-7445.AM2017-3131

Polymers in the co-delivery of siRNA and anticancer drugs to treat multidrug-resistant tumors

Traditional chemotherapeutic agents have long been associated with serious drawbacks due to the heterogeneity and complexity of human cancer. One of the major hurdles regarding chemotherapy is the development of multidrug resistance by the cancer cells. Combination therapy of cancer using different anticancer vectors holds great promise in clinical settings and has been accepted as a current treatment standard for cancer. Recently, siRNA-mediated RNA interference has gained significant attention for cancer treatment due to its ability to knock down genes and proteins with great specificity. Combination of this fast evolving approach to downregulation of genes associated with multidrug resistance in cancer with the simultaneous delivery of traditional chemotherapeutics is fast becoming an effective approach in the cancer therapy. This article provides a view focused on the polymers used to develop multifunctional co-delivery systems that specifically encapsulate siRNAs targeted against MDR and conventional chemotherapeutics. The many studies reviewed here that reported successful in vitro and in vivo results emphasize the promise of this combination therapy approach to overcome multidrug resistance in cancer.

RNAi revised--target mRNA-dependent enhancement of gene silencing.

The discovery of RNA interference (RNAi) gave rise to the development of new nucleic acid-based technologies as powerful investigational tools and potential therapeutics. Mechanistic key details of RNAi in humans need to be deciphered yet, before such approaches take root in biomedicine and molecular therapy.We developed and validated an in silico-based model of siRNA-mediated RNAi in human cells in order to link in vitro-derived pre-steady state kinetic data with a quantitative and time-resolved understanding of RNAi on the cellular level. The observation that product release by Argonaute 2 is accelerated in the presence of an excess of target RNA in vitro inspired us to suggest an associative mechanism for the RNA slicer reaction where incoming target mRNAs actively promote dissociation of cleaved mRNA fragments. This novel associative model is compatible with high multiple turnover rates of RNAi-based gene silencing in living cells and accounts for target mRNA concentration-dependent enhancement of the RNAi machinery.