RNA interference

delivery of designed shRNAs and the mechanism of RNA interference in mammalian cells RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translational or transcriptional repression. Historically, RNAi was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. The detailed study of each of these seemingly different processes elucidated that the identity of these phenomena were all actually RNAi. Andrew Fire and Craig Mello shared the 2006 Nobel Prize in Physiology or Medicine for their work on RNAi in the nematode worm Caenorhabditis elegans, which they published in 1998¹. Since the discovery of RNAi and its regulatory potentials, it has become evident that RNAi has immense potential in suppression of desired genes. RNAi is now known as precise, efficient, stable and better than antisense therapy for gene suppression. Antisense RNA produced intracellularly by an expression vector may be developed and find utility as novel therapeutic agents. Two types of small ribonucleic acid (RNA) molecules, microRNA (miRNA) and small interfering RNA (siRNA), are central to components to the RNAi pathway. Once mRNA is degraded, post-transcriptional silencing occurs as protein translation is prevented.…

delivery of designed shRNAs and the mechanism of RNA interference in mammalian cells]] RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translational or transcriptional repression. Historically, RNAi was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. The detailed study of each of these seemingly different processes elucidated that the identity of these phenomena were all actually RNAi. Andrew Fire and Craig Mello shared the 2006 Nobel Prize in Physiology or Medicine for their work on RNAi in the nematode worm Caenorhabditis elegans, which they published in 1998. Since the discovery of RNAi and its regulatory potentials, it has become evident that RNAi has immense potential in suppression of desired genes. RNAi is now known as precise, efficient, stable and better than antisense therapy for gene suppression. Antisense RNA produced intracellularly by an expression vector may be developed and find utility as novel therapeutic agents. Two types of small ribonucleic acid (RNA) molecules, microRNA (miRNA) and small interfering RNA (siRNA), are central to components to the RNAi pathway. Once mRNA is degraded, post-transcriptional silencing occurs as protein translation is prevented. Transcription can be inhibited via the pre-transcriptional silencing mechanism of RNAi, through which an enzyme complex catalyzes DNA methylation at genomic positions complementary to complexed siRNA or miRNA. RNAi has an important role in defending cells against parasitic nucleotide sequences (e.g., viruses or transposons) and also influences development of organisms. The RNAi pathway is a naturally occurring process found in many eukaryotes. It is initiated by the enzyme Dicer, which cleaves long double-stranded RNA (dsRNA) molecules into short double-stranded fragments of approximately 21 to 23 nucleotide siRNAs. Each siRNA is unwound into two single-stranded RNAs (ssRNAs), the passenger (sense) strand and the guide (antisense) strand. The passenger strand is then cleaved by the protein Argonaute 2 (Ago2). The passenger strand is degraded and the guide strand is incorporated into the RNA-induced silencing complex (RISC). The RISC assembly then binds and degrades the target mRNA. Specifically, this is accomplished when the guide strand pairs with a complementary sequence in a mRNA molecule and induces cleavage by Ago2, a catalytic component of the RISC. In some organisms, this process spreads systemically, despite the initially limited molar concentrations of siRNA. RNAi is a valuable research tool, both in cell culture and in living organisms, because synthetic dsRNA introduced into cells can selectively and robustly induce suppression of specific genes of interest. RNAi may be used for large-scale screens that systematically shut down each gene (and the subsequent proteins it codes for) in the cell, which can help to identify the components necessary for a particular cellular process or an event such as cell division. The pathway is also used as a practical tool for food, medicine and insecticides.

Three prime untranslated regions and microRNAs

Three prime untranslated regions (3′UTRs) of mRNAs often contain regulatory sequences that post-transcriptionally cause RNAi. Such 3′-UTRs often contain both binding sites for miRNAs as well as for regulatory proteins. By binding to specific sites within the 3′-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting translation or directly causing degradation of the transcript. The 3′-UTR also may have silencer regions that bind repressor proteins that inhibit the expression of a mRNA. The 3′-UTR often contains microRNA response elements (MREs). MREs are sequences to which miRNAs bind, primarily through evolutionarily conserved seed sequences six to eight nucleobases in length. These are prevalent motifs within 3′-UTRs. Among all regulatory motifs within the 3′-UTRs (e.g. including silencer regions), MREs make up about half of the motifs. As of 2023, the miRBase web site, an archive of miRNA sequences and annotations, listed 28,645 entries in 271 biologic species. Of these, 1,917 miRNAs were in annotated human miRNA loci. miRNAs were predicted to have an average of about four hundred target mRNAs (affecting expression of several hundred genes). Friedman et al. estimate that >45,000 miRNA target sites within human mRNA 3′UTRs are conserved above background levels, and >60% of human protein-coding genes have been under selective pressure to maintain pairing to miRNAs. Direct experiments show that a single miRNA can reduce the stability of hundreds of unique mRNAs. Other experiments show that a single miRNA may repress the production of hundreds of proteins, but that this repression often is relatively mild (less than 2-fold). The effects of miRNA dysregulation of gene expression seem to be important in cancer. For instance, in gastrointestinal cancers, nine miRNAs have been identified as epigenetically altered and effective in down regulating DNA repair enzymes. The let-7 family of miRNAs provides a well-characterized example of miRNA dysregulation in cancer. Let-7-5p isoforms are among the most consistently downregulated miRNAs in hepatocellular carcinoma and several other malignancies, and their suppression is associated with upregulation of oncogenes including c-MYC, CDK6, and the RNA-binding protein LIN28B, as well as efflux ATP-binding cassette (ABC) transporters that govern multidrug resistance. Loss of let-7 activity establishes a self-reinforcing circuit, as LIN28B actively suppresses let-7 maturation, further sustaining the expression of let-7 target genes and contributing to a chemotherapy-resistant phenotype. Reintroduction of depleted tumor-suppressive miRNAs has therefore been explored as a strategy to restore natural post-transcriptional regulation of oncogenic targets and resensitize resistant cancer cells to treatment. Because the let-7 family comprises multiple isoforms that share a conserved seed sequence but differ outside it, the choice of isoform influences which targets are most effectively regulated and to what degree, underscoring that even closely related miRNA family members are not functionally interchangeable. The effects of miRNA dysregulation of gene expression also seem to be important in neuropsychiatric disorders, such as schizophrenia, bipolar disorder, major depression, Parkinson's disease, Alzheimer's disease and autism spectrum disorders.

Bioengineered RNA agents to study miRNA function and replacement therapy

A longstanding limitation in miRNA research has been the reliance on chemically synthesized miRNA mimics or biosimilars, which bear extensive non-natural chemical modifications—including altered ribose subunits and backbone linkages—whose physiochemical and biological properties may not faithfully recapitulate those of endogenous, genome-derived miRNA species. While chemical modifications may improve metabolic stability and binding affinity, their inclusion introduces structural divergence from natural miRNA and may increase immunogenic risk, raising questions about how accurately commercial mimics model endogenous miRNA biology. To address these concerns, RNA molecular bioengineering platforms have been developed that produce recombinant miRNA molecules—termed bioengineered RNAs (BioRNAs)—through in vivo fermentation in bacteria using human transfer RNA (htRNA) fused precursor miRNA carriers. This approach yields agents with high purity, low endotoxin content, and structural and chemical properties that more closely represent those of naturally processed, endogenous miRNA, including post-transcriptional modifications acquired during biogenesis in living cells. BioRNA agents have been produced successfully across a diverse panel of miRNA sequences and have demonstrated functional equivalence to or improvement over commercial LNA mimics in regulating target gene expression—including known cancer-relevant targets such as EGFR, MRP1, and VDAC1—in human cancer cell lines. Beyond their utility as research tools, BioRNA agents have been applied to miRNA replacement therapy, a strategy that seeks to reintroduce tumor-suppressive miRNAs depleted in disease tissue to harness endogenous RNAi machinery for treatment. In preclinical cancer models, bioengineered miRNA agents have demonstrated antitumor activity, the ability to suppress multidrug resistance by downregulating efflux transporter expression, and pharmacological synergism with co-administered chemotherapeutic drugs—providing a mechanistic rationale for their development as combination therapeutics.

Off-Target Effects of Gene Knockdown

Extensive efforts in computational biology have been directed toward the design of successful dsRNA reagents that maximize gene knockdown but minimize "off-target" effects. Off-target effects arise when an introduced RNA has a base sequence that can pair with and thus reduce the expression of multiple genes. Such problems occur more frequently when the dsRNA contains repetitive sequences. It has been estimated from studying the genomes of humans, C. elegans and S. pombe that about 10% of possible siRNAs have substantial off-target effects. A multitude of software tools have been developed implementing algorithms for the design of general mammal-specific, and virus-specific siRNAs that are automatically checked for possible cross-reactivity. Depending on the organism and experimental system, the exogenous RNA may be a long strand designed to be cleaved by Dicer, or short RNAs designed to serve as siRNA substrates. In most mammalian cells, shorter RNAs are used because long double-stranded RNA molecules induce the mammalian interferon response, a form of innate immunity that reacts nonspecifically to foreign genetic material. Mouse oocytes and cells from early mouse embryos lack this reaction to exogenous dsRNA and are therefore a common model system for studying mammalian gene-knockdown effects. Specialized laboratory techniques have also been developed to improve the utility of RNAi in mammalian systems by avoiding the direct introduction of siRNA, for example, by stable transfection with a plasmid encoding the appropriate sequence from which siRNAs can be transcribed, or by more elaborate lentiviral vector systems allowing the inducible activation or deactivation of transcription, known as conditional RNAi.

Drug–drug interactions with siRNA therapeutics

As the number of approved RNAi therapeutics has grown, reaching seven in 2025 (patisiran, givosiran, lumasiran, inclisiran, vutrisiran, nedosiran, and fitusiran), a distinct challenge has emerged in assessing drug–drug interactions (DDIs) for this drug class. Unlike small-molecule drugs, siRNA therapeutics are not major substrates of cytochrome P450 enzymes and do not rely on classical hepatic or renal uptake transporters. Instead, they are metabolized by endogenous endo- and exonucleases to shortened oligonucleotide chains, and their systemic pharmacokinetic parameters often do not reflect target-tissue distribution or pharmacodynamic (PD) outcomes. A clinically observed example of an unexpected DDI is givosiran, which produced a 2- to 3-fold increase in systemic exposure to cytochrome P450 substrates dextromethorphan (CYP2D6) and caffeine (CYP1A2) in patients with acute intermittent porphyria—an effect not predicted by standard in vitro CYP enzyme studies. The proposed mechanism involves indirect interference with hepatic heme biosynthesis via on-target suppression of aminolevulinate synthase 1 (ALAS1), rather than direct enzyme inhibition. More broadly, siRNA drugs may compete with endogenous microRNAs (miRNAs) for shared components of the RNA-induced silencing complex (RISC), particularly Argonaute (AGO) proteins. This competition could alter the post-transcriptional gene regulation (PTGR) of ADME-related genes, leading to indirect modulation of the expression of drug-metabolizing enzymes or transporters and causing DDIs with co-administered drugs. Short hairpin RNAs (shRNAs) may additionally compete with pre-miRNAs for the nuclear export protein Exportin-5 (XPO5) and the cytoplasmic ribonuclease Dicer, disrupting global miRNA biogenesis and posing further DDI risk. The U.S. Food and Drug Administration has issued guidance specific to oligonucleotide therapeutics, recommending assessment of QTc interval prolongation, immunogenicity, organ-impairment effects on PD endpoints, and the potential for RNAi machinery competition as part of the DDI risk framework for this drug class.

RNAi discovery

plants in which genes for pigmentation are silenced by RNAi. The left plant is wild-type; the right plants contain transgenes that induce suppression of both transgene and endogenous gene expression, giving rise to the unpigmented white areas of the flower. ]] The process of RNAi was referred to as "co-suppression" and "quelling" when observed prior to the knowledge of an RNA-related mechanism. The discovery of RNAi was preceded first by observations of transcriptional inhibition by antisense RNA expressed in transgenic plants, and more directly by reports of unexpected outcomes in experiments performed by plant scientists in the United States and the Netherlands in the early 1990s. In an attempt to alter flower colors in petunias, researchers introduced additional copies of a gene encoding chalcone synthase, a key enzyme for flower pigmentation into petunia plants of normally pink or violet flower color. The overexpressed gene was expected to result in darker flowers, but instead caused some flowers to have less visible purple pigment, sometimes in variegated patterns, indicating that the activity of chalcone synthase had been substantially decreased or became suppressed in a context-specific manner. Another early observation of RNAi came from a study of the fungus Neurospora crassa, although it was not immediately recognized as related. Further investigation of the phenomenon in plants indicated that the downregulation was due to post-transcriptional inhibition of gene expression via an increased rate of mRNA degradation. This phenomenon was called co-suppression of gene expression, but the molecular mechanism remained unknown. Not long after, plant virologists working on improving plant resistance to viral diseases observed a similar unexpected phenomenon. While it was known that plants expressing virus-specific proteins showed enhanced tolerance or resistance to viral infection, it was not expected that plants carrying only short, non-coding regions of viral RNA sequences would show similar levels of protection. Researchers believed that viral RNA produced by transgenes could also inhibit viral replication. The reverse experiment, in which short sequences of plant genes were introduced into viruses, showed that the targeted gene was suppressed in an infected plant. This phenomenon was labeled "virus-induced gene silencing" (VIGS), and the set of such phenomena were collectively called post transcriptional gene silencing. After these initial observations in plants, laboratories searched for this phenomenon in other organisms. The first instance of RNA silencing in animals was documented in 1996, when Guo and Kemphues observed that, by introducing sense and antisense RNA to par-1 mRNA in Caenorhabditis elegans caused degradation of the par-1 message. It was thought that this degradation was triggered by single-stranded RNA (ssRNA), but two years later, in 1998, Fire and Mello discovered that this ability to silence the par-1 gene expression was actually triggered by double-stranded RNA (dsRNA). Craig C. Mello and Andrew Fire's 1998 Nature paper reported a potent gene silencing effect after injecting double stranded RNA into C. elegans. In investigating the regulation of muscle protein production, they observed that neither mRNA nor antisense RNA injections had an effect on protein production, but double-stranded RNA successfully silenced the targeted gene. As a result of this work, they coined the term RNAi. This discovery represented the first identification of the causative agent for the phenomenon. Fire and Mello were awarded the 2006 Nobel Prize in Physiology or Medicine.

RNAi therapeutics

Just after Fire and Mello's ground-breaking discovery, Elbashir et al. discovered, by using synthetically made siRNA, it was possible to target the silencing of specific sequences in a gene, rather than silencing the entire gene. Only a year later, McCaffrey and colleagues demonstrated that this sequence-specific silencing had therapeutic applications by targeting a sequence from the Hepatitis C virus in transgenic mice. Since then, multiple researchers have been attempting to expand the therapeutic applications of RNAi, specifically looking to target genes that cause various types of cancer. By 2006, the first applications to reach clinical trials were in the treatment of macular degeneration and respiratory syncytial virus. Four years later the first-in-human Phase I clinical trial was started, using a nanoparticle delivery system to target solid tumors. The FDA approved the first siRNA-based drug (patisiran) in 2018. Givosiran and lumasiran later won FDA approval for the treatment of AHP and PH1 in 2019 and 2020, respectively. Inclisiran received EMA approval in 2020 for the treatment of high cholesterol and is currently under review by the FDA.

See also

DNA-directed RNA interference

References

External links

Overview of the RNAi process, from Cambridge University's The Naked Scientists Animation of the RNAi process, from Nature NOVA scienceNOW explains RNAi – A 15-minute video of the Nova broadcast that aired on PBS, 26 July 2005 Silencing Genomes RNA interference (RNAi) experiments and bioinformatics in C. elegans for education. From the Dolan DNA Learning Center of Cold Spring Harbor Laboratory. RNAi screens in C. elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions (a protocol) 2 American 'Worm People' Win Nobel for RNA Work, from NY Times Molecular Therapy web focus: "The development of RNAi as a therapeutic strategy", a collection of free articles about RNAi as a therapeutic strategy. GenomeRNAi: a database of phenotypes from RNA interference screening experiments in Drosophila melanogaster and Homo sapiens RNAi tools Pre-designed and custom RNA Interference tools

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