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Small interfering RNA
Small interfering RNA
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Mediating RNA interference in cultured mammalian cells.

Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded non-coding RNA molecules, typically 20–24 base pairs in length, similar to microRNA (miRNA), and operating within the RNA interference (RNAi) pathway. It interferes with the expression of specific genes with complementary nucleotide sequences by degrading messenger RNA (mRNA) after transcription, preventing translation.[1][2] It was discovered in 1998 by Andrew Fire at the Carnegie Institution for Science in Washington, D.C. and Craig Mello at the University of Massachusetts in Worcester.

Structure

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Naturally occurring siRNAs have a well-defined structure that is a short (usually 20 to 24-bp) double-stranded RNA (dsRNA) with phosphorylated 5' ends and hydroxylated 3' ends with two overhanging nucleotides. The Dicer enzyme catalyzes production of siRNAs from long dsRNAs and small hairpin RNAs.[3] siRNAs can also be introduced into cells by transfection. Since in principle any gene can be knocked down by a synthetic siRNA with a complementary sequence, siRNAs are an important tool for validating gene function and drug targeting in the post-genomic era.

History

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In 1998, Andrew Fire at Carnegie Institution for Science in Washington DC and Craig Mello at University of Massachusetts in Worcester discovered the RNAi mechanism while working on the gene expression in the nematode, Caenorhabditis elegans.[4] They won the Nobel prize for their research with RNAi in 2006. siRNAs and their role in post-transcriptional gene silencing (PTGS) was discovered in plants by David Baulcombe's group at the Sainsbury Laboratory in Norwich, England and reported in Science in 1999.[5] Thomas Tuschl and colleagues soon reported in Nature that synthetic siRNAs could induce RNAi in mammalian cells.[6] In 2001, the expression of a specific gene was successfully silenced by introducing chemically synthesized siRNA into mammalian cells (Tuschl et al.) These discoveries led to a surge in interest in harnessing RNAi for biomedical research and drug development. Significant developments in siRNA therapies have been made with both organic (carbon based) and inorganic (non-carbon based) nanoparticles, which have been successful in drug delivery to the brain, offering promising methods to deliver therapeutics into human subjects. However, human applications of siRNA have had significant limitations to its success. One of these being off-targeting.[2] There is also a possibility that these therapies can trigger innate immunity.[4] Animal models have not been successful in accurately representing the extent of this response in humans. Hence, studying the effects of siRNA therapies has been a challenge.  

In recent years, siRNA therapies have been approved and new methods have been established to overcome these challenges. There are approved therapies available for commercial use and several currently in the pipeline waiting to get approval.[7][8]

Mechanism

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The mechanism by which natural siRNA causes gene silencing through repression of translation occurs as follows:

siRNA Mechanism
  1. Long dsRNA (which can come from hairpin, complementary RNAs, and RNA-dependent RNA polymerases) is cleaved by an endo-ribonuclease called Dicer. Dicer cuts the long dsRNA to form short interfering RNA or siRNA; this is what enables the molecules to form the RNA-Induced Silencing Complex (RISC).
  2. Once siRNA enters the cell it gets incorporated into other proteins to form the RISC.
  3. Once the siRNA is part of the RISC complex, the siRNA is unwound to form single stranded siRNA.
  4. The strand that is thermodynamically less stable due to its base pairing at the 5´end is chosen to remain part of the RISC-complex
  5. The single stranded siRNA which is part of the RISC complex now can scan and find a complementary mRNA
  6. Once the single stranded siRNA (part of the RISC complex) binds to its target mRNA, it induces mRNA cleavage.
  7. The mRNA is now cut and recognized as abnormal by the cell. This causes degradation of the mRNA and in turn no translation of the mRNA into amino acids and then proteins. Thus silencing the gene that encodes that mRNA.

siRNA is also similar to miRNA, however, miRNAs are derived from shorter stemloop RNA products. miRNAs typically silence genes by repression of translation and have broader specificity of action, while siRNAs typically work with higher specificity by cleaving the mRNA before translation, with 100% complementarity.[9][10]

RNAi induction using siRNAs or their biosynthetic precursors

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Dicer protein colored by protein domain.

Gene knockdown by transfection of exogenous siRNA is often unsatisfactory because the effect is only transient, especially in rapidly dividing cells. This may be overcome by creating an expression vector for the siRNA. The siRNA sequence is modified to introduce a short loop between the two strands. The resulting transcript is a short hairpin RNA (shRNA), which can be processed into a functional siRNA by Dicer in its usual fashion.[11] Typical transcription cassettes use an RNA polymerase III promoter (e.g., U6 or H1) to direct the transcription of small nuclear RNAs (snRNAs) (U6 is involved in RNA splicing; H1 is the RNase component of human RNase P). It is theorized that the resulting siRNA transcript is then processed by Dicer.

The gene knockdown efficiency can also be improved by using cell squeezing.[12]

The activity of siRNAs in RNAi is largely dependent on its binding ability to the RNA-induced silencing complex (RISC). Binding of the duplex siRNA to RISC is followed by unwinding and cleavage of the sense strand with endonucleases. The remaining anti-sense strand-RISC complex can then bind to target mRNAs for initiating transcriptional silencing.[13]

RNA activation

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In addition to their role in RNAi, siRNAs can also activate gene expression, a phenomenon termed "RNA activation" or RNAa. This was first observed when synthetic siRNAs, termed "small activating RNA" (saRNA), targeting gene promoters were found to induce potent transcriptional activation of target genes.[14] RNAa has been demonstrated to be a conserved mechanism, observed across species from insects, C. elegans, and plants, to mammals (including humans).[15][16][17][18]

The mechanism of RNAa involves the targeting of promoter regions by saRNAs, leading to the recruitment of transcriptional machinery and epigenetic changes that promote gene expression. This process often involves the RNA-induced transcriptional activation (RITA) complex, which includes Argonaute proteins (particularly Ago2), RNA helicase A (RHA), and CTR9.[19][20] Endogenous miRNAs can also mediate RNAa, expanding the regulatory roles of these small RNAs beyond gene silencing.

Several saRNA-based therapeutics are currently in clinical development. MTL-CEBPA, developed by MiNA Therapeutics, targets the CEBPA gene and is in Phase II trials for liver cancer.[21] RAG-01, developed by Ractigen Therapeutics, targets the p21 gene and is in Phase I trials for non-muscle invasive bladder cancer (NMIBC).[22] These clinical trials represent a significant step towards translating the RNAa phenomenon into novel therapeutic strategies.

Post-transcriptional gene silencing

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The siRNA-induced post transcriptional gene silencing is initiated by the assembly of the RNA-induced silencing complex (RISC). The complex silences certain gene expression by cleaving the mRNA molecules coding the target genes. To begin the process, one of the two siRNA strands, the guide strand (anti-sense strand), will be loaded into the RISC while the other strand, the passenger strand (sense strand), is degraded. Certain Dicer enzymes may be responsible for loading the guide strand into RISC.[23] Then, the siRNA scans for and directs RISC to perfectly complementary sequence on the mRNA molecules.[24] The cleavage of the mRNA molecules is thought to be catalyzed by the Piwi domain of Argonaute proteins of the RISC. The mRNA molecule is then cut precisely by cleaving the phosphodiester bond between the target nucleotides which are paired to siRNA residues 10 and 11, counting from the 5'end.[25] This cleavage results in mRNA fragments that are further degraded by cellular exonucleases. The 5' fragment is degraded from its 3' end by exosome while the 3' fragment is degraded from its 5' end by 5' -3' exoribonuclease 1(XRN1).[26] Dissociation of the target mRNA strand from RISC after the cleavage allow more mRNA to be silenced. This dissociation process is likely to be promoted by extrinsic factors driven by ATP hydrolysis.[25]

Sometimes cleavage of the target mRNA molecule does not occur. In some cases, the endonucleolytic cleavage of the phosphodiester backbone may be suppressed by mismatches of siRNA and target mRNA near the cleaving site. Other times, the Argonaute proteins of the RISC lack endonuclease activity even when the target mRNA and siRNA are perfectly paired.[25] In such cases, gene expression will be silenced by an miRNA induced mechanism instead [24]

A simplified version of the Ping-Pong Method, involving proteins Aubergine (Aub) and Argonaute-3 (Ago3) cleaving the 3' and 5' ends of piRNA.

[2]

Piwi-interacting RNAs are responsible for the silencing of transposons and are not siRNAs.[27] PIWI-interacting RNAs (piRNAs) are a recently discovered class of small non-coding RNAs (ncRNAs) with a length of 21-35 nucleotides. They play a role in gene expression regulation, transposon silencing, and viral infection inhibition. Once considered as "dark matter" of ncRNAs, piRNAs emerged as important players in multiple cellular functions in different organisms.[28]

Transcriptional Gene Silencing

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Many model organism, such as plants (Arabidopsis thaliana), yeast (Saccharomyces cerevisiae ), flies (Drosophila melanogaster) and worms (C. elegans), have been used to study small non coding RNA-directed Transcriptional gene silencing. In human cell, RNA-directed transcriptional gene silencing was observed a decade ago when exogenous siRNAs silenced a transgenic elongation factor 1 α promoter driving a Green Fluorescent Protein (GFP) reporter gene.[29] The main mechanisms of transcriptional gene silencing (TGS) involving the RNAi machinery include DNA methylation, histone post-translational modifications, and subsequent chromatin remodeling around the target gene into a heterochromatic state.[29] SiRNAs can be incorporated into a RNA-induced transcriptional silencing (RITS) complex. An active RITS complex will trigger the formation of heterochromatin around DNA matching the siRNA, effectively silencing the genes in that region of the DNA.

Applications: Allele-specific gene silencing

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One of the potent applications of siRNAs is the ability to distinguish the target versus non-target sequence with a single-nucleotide difference. This approach has been considered as therapeutically crucial for the silencing dominant gain-of-function (GOF) disorders, where mutant allele causing disease is differed from wt-allele by a single nucleotide (nt). These types of siRNAs with the capability to distinguish a single-nt difference, are termed as, allele-specific siRNAs.[2]

ASP-RNAi is an innovative category of RNAi with the objective of suppressing the dominant mutant allele while sparing expression of the corresponding normal allele with the specificity of single-nucleotide differences between the two.[2] ASP-siRNAs are potentially a novel and better remedial alternative for the treatment of autosomal dominant genetic disorders especially in cases where wild-type allele expression is crucial for organism survival such as Huntington disease (HD),DYT1 dystonia (Gonzalez-Alegre et al. 2003, 2005), Alzheimer's disease (Sierant et al. 2011), Parkinson's disease (PD) (Takahashi et al. 2015), amyloid lateral sclerosis (ALS) (Schwarz et al. 2006), and Machado–Joseph disease (Alves et al. 2008). Their therapeutic potential has also been assessed for various skin disorders like epidermolysis bullosa simplex (Atkinson et al. 2011), epidermolytic palmoplantar keratoderma (EPPK) (Lyu et al. 2016), and lattice corneal dystrophy type I (LCDI) (Courtney et al. 2014).[2]

Challenges: avoiding nonspecific effects

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RNAi intersects with a number of other pathways; as of 2010 it was not surprising that on occasion, nonspecific effects are triggered by the experimental introduction of an siRNA.[30][31] When a mammalian cell encounters a double-stranded RNA such as an siRNA, it may mistake it as a viral by-product and mount an immune response. Furthermore, because structurally related microRNAs modulate gene expression largely via incomplete complementarity base pair interactions with a target mRNA, the introduction of an siRNA may cause unintended off-targeting. Chemical modifications of siRNA may alter the thermodynamic properties that also result in a loss of single nucleotide specificity.[32]

Innate immunity

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Introduction of too many siRNA can result in nonspecific events due to activation of innate immune responses.[33] Most evidence to date suggests that this is probably due to activation of the dsRNA sensor PKR, although retinoic acid-inducible gene I (RIG-I) may also be involved.[34] The induction of cytokines via toll-like receptor 7 (TLR7) has also been described. Chemical modification of siRNA is employed to reduce in the activation of the innate immune response for gene function and therapeutic applications. One promising method of reducing the nonspecific effects is to convert the siRNA into a microRNA.[35] MicroRNAs occur naturally, and by harnessing this endogenous pathway it should be possible to achieve similar gene knockdown at comparatively low concentrations of resulting siRNAs. This should minimize nonspecific effects.

Off-targeting

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Off-targeting is another challenge to the use of siRNAs as a gene knockdown tool.[31] Here, genes with incomplete complementarity are inadvertently downregulated by the siRNA (in effect, the siRNA acts as a miRNA), leading to problems in data interpretation and potential toxicity. This, however, can be partly addressed by designing appropriate control experiments, and siRNA design algorithms are currently being developed to produce siRNAs free from off-targeting. Genome-wide expression analysis, e.g., by microarray technology, can then be used to verify this and further refine the algorithms. A 2006 paper from the laboratory of Dr. Khvorova implicates 6- or 7-basepair-long stretches from position 2 onward in the siRNA matching with 3'UTR regions in off-targeted genes.[36] The tool of siRNA off-target predition is available at http://crdd.osdd.net/servers/aspsirna/asptar.php and published as ASPsiRNA resource.[37]

Adaptive immune responses

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Plain RNAs may be poor immunogens, but antibodies can easily be created against RNA-protein complexes. Many autoimmune diseases see these types of antibodies. There haven't yet been reports of antibodies against siRNA bound to proteins. Some methods for siRNA delivery adjoin polyethylene glycol (PEG) to the oligonucleotide reducing excretion and improving circulating half-life. However recently a large Phase III trial of PEGylated RNA aptamer against factor IX had to be discontinued by Regado Biosciences because of a severe anaphylactic reaction to the PEG part of the RNA. This reaction led to death in some cases and raises significant concerns about siRNA delivery when PEGylated oligonucleotides are involved.[38]

Saturation of the RNAi machinery

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siRNAs transfection into cells typically lowers the expression of many genes, however, the upregulation of genes is also observed. The upregulation of gene expression can partially be explained by the predicted gene targets of endogenous miRNAs. Computational analyses of more than 150 siRNA transfection experiments support a model where exogenous siRNAs can saturate the endogenous RNAi machinery, resulting in the de-repression of endogenous miRNA-regulated genes.[39] Thus, while siRNAs can produce unwanted off-target effects, i.e. unintended downregulation of mRNAs via a partial sequence match between the siRNA and target, the saturation of RNAi machinery is another distinct nonspecific effect, which involves the de-repression of miRNA-regulated genes and results in similar problems in data interpretation and potential toxicity.[40]

Chemical modification

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siRNAs have been chemically modified to enhance their therapeutic properties, Short interfering RNA (siRNA) must be delivered to the site of action in the cells of target tissues in order for RNAi to fulfill its therapeutic promise. A detailed database of all such chemical modifications is manually curated as siRNAmod in scientific literature.[41] Chemical modification of siRNA can also inadvertently result in loss of single-nucleotide specificity.[42]

Therapeutic applications and challenges

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Given the ability to knock down, in essence, any gene of interest, RNAi via siRNAs has generated a great deal of interest in both basic[43] and applied biology.[44]

One of the biggest challenges to siRNA and RNAi based therapeutics is intracellular delivery.[45] siRNA also has weak stability and pharmacokinetic behavior.[46] Delivery of siRNA via nanoparticles has shown promise.[45] siRNA oligos in vivo are vulnerable to degradation by plasma and tissue endonucleases and exonucleases[47] and have shown only mild effectiveness in localized delivery sites, such as the human eye.[48] Delivering pure DNA to target organisms is challenging because its large size and structure prevents it from diffusing readily across membranes.[45] siRNA oligos circumvent this problem due to their small size of 21-23 oligos.[49] This allows delivery via nano-scale delivery vehicles called nanovectors.[48]

A good nanovector for siRNA delivery should protect siRNA from degradation, enrich siRNA in the target organ and facilitate the cellular uptake of siRNA.[47] The three main groups of siRNA nanovectors are: lipid based, non-lipid organic-based, and inorganic.[47] Lipid based nanovectors are excellent for delivering siRNA to solid tumors,[47] but other cancers may require different non-lipid based organic nanovectors such as cyclodextrin based nanoparticles.[47][50]

siRNAs delivered via lipid based nanoparticles have been shown to have therapeutic potential for central nervous system (CNS) disorders.[51] Central nervous disorders are not uncommon, but the blood brain barrier (BBB) often blocks access of potential therapeutics to the brain.[51] siRNAs that target and silence efflux proteins on the BBB surface have been shown to create an increase in BBB permeability.[51] siRNA delivered via lipid based nanoparticles is able to cross the BBB completely.[51]

A huge difficulty in siRNA delivery is the problem of off-targeting.[45][48] Since genes are read in both directions, there exists a possibility that even if the intended antisense siRNA strand is read and knocks out the target mRNA, the sense siRNA strand may target another protein involved in another function.[52]

Phase I results of the first two therapeutic RNAi trials (indicated for age-related macular degeneration, aka AMD) reported at the end of 2005 that siRNAs are well tolerated and have suitable pharmacokinetic properties.[53]

In a phase 1 clinical trial, 41 patients with advanced cancer metastasised to liver were administered RNAi delivered through lipid nanoparticles. The RNAi targeted two genes encoding key proteins in the growth of the cancer cells, vascular endothelial growth factor, (VEGF), and kinesin spindle protein (KSP). The results showed clinical benefits, with the cancer either stabilized after six months, or regression of metastasis in some of the patients. Pharmacodynamic analysis of biopsy samples from the patients revealed the presence of the RNAi constructs in the samples, proving that the molecules reached the intended target.[54][55]

Proof of concept trials have indicated that Ebola-targeted siRNAs may be effective as post-exposure prophylaxis in humans, with 100% of non-human primates surviving a lethal dose of Zaire Ebolavirus, the most lethal strain.[56]

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Currently, SiRNA are currently chemically synthesized and so, are legally categorized inside EU and in USA as simple medicinal products. But as bioengineered siRNA (BERAs) are in development, these would be classified as biological medicinal products, at least in EU. The development of the BERAs technology raises the question of the categorization of drugs having the same mechanism of action but being produced chemically or biologically. This lack of consistency should be addressed.[57]

Intracellular delivery

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There is great potential for RNA interference (RNAi) to be used therapeutically to reversibly silence any gene. For RNAi to realize its therapeutic potential, small interfering RNA (siRNA) must be delivered to the site of action in the cells of target tissues. But finding safe and efficient delivery mechanisms is a major obstacle to achieving the full potential of siRNA-based therapies.  Unmodified siRNA is unstable in the bloodstream, has the potential to cause immunogenicity, and has difficulty readily navigating cell membranes.[58] As a result, chemical alterations and/or delivery tools are needed to safely transfer siRNA to its site of action.[58] There are three main techniques of delivery for siRNA that differ on efficiency and toxicity.

Transfection

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In this technique siRNA first must be designed against the target gene. Once the siRNA is configured against the gene it has to be effectively delivered through a transfection protocol. Delivery is usually done by cationic liposomes, polymer nanoparticles, and lipid conjugation.[59] This method is advantageous because it can deliver siRNA to most types of cells, has high efficiency and reproducibility, and is offered commercially. The most common commercial reagents for transfection of siRNA are Lipofectamine and Neon Transfection. However, it is not compatible with all cell types and has low in vivo efficiency.[60][61]

Electroporation

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Electrical pulses are also used to intracellularly deliver siRNA into cells. The cell membrane is made of phospholipids which makes it susceptible to an electric field. When quick but powerful electrical pulses are initiated the lipid molecules reorient themselves, while undergoing thermal phase transitions because of heating. This results in the making of hydrophilic pores and localized perturbations in the lipid bilayer cell membrane also causing a temporary loss of semipermeability. This allows for the escape of many intracellular contents, such as ions and metabolites as well as the simultaneous uptake of drugs, molecular probes, and nucleic acids. For cells that are difficult to transfect electroporation is advantageous however cell death is more probable under this technique.[62]

This method has been used to deliver siRNA targeting VEGF into the xenografted tumors in nude mice, which resulted in a significant suppression of tumor growth.[63]

Viral-mediated delivery

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The gene silencing effects of transfected designed siRNA are generally transient, but this difficulty can be overcome through an RNAi approach. Delivering this siRNA from DNA templates can be done through several recombinant viral vectors based on retrovirus, adeno-associated virus, adenovirus, and lentivirus.[64] The latter is the most efficient virus that stably delivers siRNA to target cells as it can transduce nondividing cells as well as directly target the nucleus.[65] These specific viral vectors have been synthesized to effectively facilitate siRNA that is not viable for transfection into cells. Another aspect is that in some cases synthetic viral vectors can integrate siRNA into the cell genome which allows for stable expression of siRNA and long-term gene knockdown. This technique is advantageous because it is in vivo and effective for difficult to transfect cell. However problems arise because it can trigger antiviral responses in some cell types leading to mutagenic and immunogenic effects.

This method has potential use in gene silencing of the central nervous system for the treatment of Huntington's disease.[66]

Therapies

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A decade after the discovery of RNAi mechanism in 1993, the pharmaceutical sector heavily invested in the research and development of siRNA therapy. There are several advantages that this therapy has over small molecules and antibodies. It can be administered quarterly or every six months. Another advantage is that, unlike small molecule and monoclonal antibodies that need to recognize specific conformation of a protein, siRNA functions by Watson-Crick basepairing with mRNA. Therefore, any target molecule that needs to be treated with high affinity and specificity can be selected if the right nucleotide sequence is available.[46] One of the biggest challenges researchers needed to overcome was the identification and establishment of a delivery system through which the therapies would enter the body. And that the immune system often mistakes the RNAi therapies as remnants of infectious agents, which can trigger an immune response.[4] Animal models did not accurately represent the degree of immune response that was seen in humans and despite the promise in the treatment investors divested away from RNAi.[4]

However, there were a few companies that continued with the development of RNAi therapy for humans. Alnylam Pharmaceuticals, Sirna Therapeutics and Dicerna Pharmaceuticals are few of the companies still working on bringing RNAi therapies to market. It was learned that almost all siRNA therapies administered in the bloodstream accumulated in the liver. That is why most of the early drug targets were diseases that affected the liver. Repeated developmental work also shed light on improving the chemical composition of the RNA molecule to reduce the immune response, subsequently causing little to no side effects.[67] Listed below are some of approved therapies or therapies in pipeline.

Alnylam Pharmaceuticals

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In 2018, Alnylam Pharmaceuticals became the first company to have a siRNA therapy approved by the FDA. Onpattro (patisiran) was approved for the treatment of polyneuropathy of hereditary transthyretin-mediated (hATTR) amyloidosis in adults. hATTR is a rare, progressively debilitating condition. During hATTR amyloidosis, misfolded transthyretin (TTR) protein is deposited in the extracellular space. Under typical folding conditions, TTR tetramers are made up of four monomers. Hereditary ATTR amyloidosis is caused by a fault or mutation in the transthyretin (TTR) gene which is inherited. Changing just one amino-acid changes the tetrameric transthyretin proteins, resulting in unstable tetrameric transthyretin protein that aggregates in monomers and forms insoluble extracellular amyloid deposits. Amyloid buildup in various organ systems causes cardiomyopathy, polyneuropathy, gastrointestinal dysfunction. It affects 50,000 people worldwide. To deliver the drug directly to the liver, siRNA is encased in a lipid nanoparticle. The siRNA molecule halts the production of amyloid proteins by interfering with the RNA production of abnormal TTR proteins. This prevents the accumulation of these proteins in different organs of the body and helps the patients manage this disease.[68][69]

Traditionally, liver transplantation has been the standard treatment for hereditary transthyretin amyloidosis, however its effectiveness may be limited by the persistent deposition of wild-type transthyretin amyloid after transplantation. There are also small molecule medications that provide temporary relief. Before Onpattro was released, the treatment options for hATTR were limited. After the approval of Onpattro, FDA awarded Alnylam with the Breakthrough Therapy Designation, which is given to drugs that are intended to treat a serious condition and are a substantial improvement over any available therapy. It was also awarded Orphan Drug Designations given to those treatments that are intended to safely treat conditions affecting less than 200,000 people.[70]

Along with Onpattro, another RNA interference therapeutic drug has also been discovered (Partisiran) which has property of inhibiting hepatic synthesis of transthyretin. Target messenger RNA (mRNA) is cleaved as a result by tiny interfering RNAs coupled to the RNA-induced silencing complex. Patisiran, an investigational RNAi therapeutic drug, uses this process to decrease the production of mutant and wild-type transthyretin by cleaving on 3-untranslated region of transthyretin mRNA.[71]

In 2019, FDA approved the second RNAi therapy, Givlaari (givosiran) used to treat acute hepatic porphyria (AHP). The disease is caused due to the accumulation of toxic porphobilinogen (PBG) molecules which are formed during the production of heme. These molecules accumulate in different organs and this can lead to the symptoms or attacks of AHP.

Givlaari is an siRNA drug that downregulates the expression of aminolevulinic acid synthase 1 (ALAS1), a liver enzyme involved in an early step in heme production. The downregulation of ALAS1 lowers the levels of neurotoxic intermediates that cause AHP symptoms.[46]

Years of research has led to a greater understanding of siRNA therapies beyond those affecting the liver. As of 2019, Alnylam Pharmaceuticals was involved in therapies that may treat amyloidosis and CNS disorders like Huntington's disease and Alzheimer's disease.[4] They have also partnered with Regeneron Pharmaceuticals to develop therapies for CNS, eye and liver diseases.

As of 2020, ONPATTRO and GIVLAARI, were available for commercial application, and two siRNAs, lumasiran (ALN-GO1) and inclisiran, have been submitted for new drug application to the FDA. Several siRNAs are undergoing phase 3 clinical studies, and more candidates are in the early developmental stage.[46] In 2020, Alnylam and Vir pharmaceuticals announced a partnership and have started working on a RNAi therapy that would treat severe cases of COVID-19.[72]

Other companies that have had success in developing a pipeline of siRNA therapies are Dicerna Pharmaceuticals, partnered Eli Lilly and Company and Arrowhead Pharmaceuticals partnered with Johnson and Johnson. Several other big pharmaceutical companies such as Amgen and AstraZeneca have also invested heavily in siRNA therapies as they see the potential success of this area of biological drugs.[73]

See also

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References

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Further reading

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Revisions and contributorsEdit on WikipediaRead on Wikipedia
from Grokipedia
Small interfering RNA (siRNA) is a class of double-stranded, molecules, typically 20–25 in length, that mediate (RNAi) to silence by targeting and degrading complementary (mRNA) transcripts. These molecules feature 3′ overhangs of two and are generated endogenously from long double-stranded precursors or introduced synthetically for experimental or therapeutic purposes. The discovery of siRNA stemmed from observations of RNAi in the 1990s, with the phenomenon first noted in petunia plants in 1990 and mechanistically elucidated in Caenorhabditis elegans by Andrew Fire and Craig Mello in 1998, who demonstrated that double-stranded RNA triggers potent, sequence-specific —work that earned them the 2006 in Physiology or Medicine. Subsequent studies identified siRNA as the key effector in this process, with Hamilton and Baulcombe characterizing it in in 1999 and Elbashir et al. demonstrating its efficacy in mammalian cells using synthetic siRNAs in 2001. At the molecular level, siRNA is processed by the endoribonuclease into duplexes, which are then loaded into the (RISC); within RISC, the passenger strand is discarded, and the guide strand directs 2 (Ago2) to cleave target mRNA with near-perfect complementarity, preventing protein . This mechanism provides precise , distinguishing siRNA from microRNAs (miRNAs), which typically repress with partial complementarity rather than inducing cleavage. Biologically, siRNA functions in genome defense against viruses and transposons, chromatin modification, and developmental gene regulation across eukaryotes, from plants to mammals. Therapeutically, siRNA has revolutionized targeted gene silencing, overcoming delivery challenges like nuclease degradation and cellular uptake through chemical modifications (e.g., 2′-O-methyl groups) and conjugates (e.g., GalNAc for liver targeting); the first FDA-approved siRNA drug was patisiran in 2018 for hereditary transthyretin-mediated (hATTR) amyloidosis, followed by six more as of November 2025 for conditions including rare genetic disorders like acute hepatic porphyria and primary hyperoxaluria, hypercholesterolemia, and hemophilia. Ongoing research expands siRNA applications to cancer, viral infections, and neurological disorders, highlighting its potential as a versatile modality in precision .

Discovery and History

Initial Discovery

The foundational experiments leading to the discovery of small interfering RNA (siRNA) built upon earlier observations of in and fungi. In 1990, researchers attempting to overexpress the chalcone synthase in unexpectedly observed post-transcriptional silencing (PTGS), where introduction of a led to co-suppression of both the and the endogenous homologous , resulting in reduced production. Similarly, in 1992, transformation of the fungus with sequences homologous to the albino-1 caused transient, sequence-specific inactivation of the endogenous , a phenomenon termed quelling. These findings hinted at a conserved mechanism for RNA-mediated regulation but lacked insight into the molecular triggers. The breakthrough came in 1998 when and demonstrated (RNAi) in the Caenorhabditis elegans. By injecting double-stranded (dsRNA) corresponding to the unc-22 muscle into nematodes, they observed potent, heritable, and sequence-specific silencing of the target , manifesting as twitching phenotypes, whereas single-stranded sense or antisense had minimal effects. Further experiments confirmed that dsRNA triggered targeted degradation of complementary mRNA, distinguishing RNAi from prior antisense approaches and establishing dsRNA as the key effector. This discovery elucidated the mechanism underlying PTGS and quelling, revealing RNAi as a widespread eukaryotic process for post-transcriptional . In 1999, Andrew Hamilton and David Baulcombe identified small antisense RNAs of approximately 25 in plants undergoing PTGS, providing the first evidence of these short RNAs—later termed siRNAs—as mediators of silencing. In 2001, Sayda M. Elbashir and colleagues identified the precise molecular intermediates of RNAi, showing that long dsRNAs are diced into 21- to 23-nucleotide double-stranded fragments that direct the silencing. These short RNAs, dubbed small interfering RNAs (siRNAs), were found to mediate specific mRNA cleavage in Drosophila embryo lysates and, when synthetically introduced, efficiently silenced genes in cultured mammalian cells without activating nonspecific responses. The work by Fire and Mello earned them the 2006 in Physiology or Medicine for uncovering RNAi as a fundamental regulatory mechanism.

Key Milestones and Developments

The discovery of in 1998 laid the groundwork for subsequent advancements in siRNA research. In 2001, the first demonstration of synthetic siRNAs effectively mediating in mammalian cells was reported by Elbashir et al., marking a pivotal shift from long double-stranded RNA to short, 21-nucleotide duplexes that avoided nonspecific responses. This breakthrough enabled precise, targeted RNAi in human cells, facilitating broader experimental applications. The field gained international recognition in 2006 when Andrew Z. Fire and Craig C. Mello were awarded the in Physiology or Medicine for their discovery of by double-stranded RNA. Concurrently, the development and commercialization of genome-wide siRNA libraries spurred the rise of high-throughput functional screening, allowing systematic identification of gene functions in mammalian systems. These libraries, often comprising thousands of siRNAs targeting the , transformed RNAi into a powerful tool for and . The transition from research tool to therapeutic modality accelerated with regulatory approvals. In 2018, the U.S. (FDA) approved (Onpattro), the first siRNA-based drug, for treating the of hereditary transthyretin-mediated , validating lipid nanoparticle delivery for hepatic targeting. Between 2019 and 2022, four additional siRNA therapeutics received FDA approval: givosiran in 2019 for acute hepatic , lumasiran in 2020 for primary type 1, in 2021 for hypercholesterolemia, and in 2022 for hereditary transthyretin-mediated . In 2023, nedosiran was approved for primary type 1 in patients aged 9 years and older. By 2024, these approvals totaled six siRNA drugs, highlighting the maturation of siRNA as a clinical platform for rare genetic diseases and metabolic disorders. From 2024 to 2025, emerged as a key driver in siRNA optimization, with models like graph neural networks predicting siRNA efficacy and off-target effects to enhance design efficiency. These AI approaches integrated structural features and empirical rules, accelerating the development of more potent and specific siRNAs. The global siRNA therapeutics market reached approximately $2.5 billion by 2025, reflecting robust growth fueled by expanded pipelines and manufacturing scales. Early siRNA research faced challenges in distinguishing it from endogenous microRNA (miRNA) pathways, as both involve small RNAs guiding proteins in RNA-induced silencing complexes; however, siRNAs were recognized as deriving primarily from exogenous or perfectly complementary duplexes for precise mRNA cleavage, while miRNAs typically arise from endogenous with imperfect binding for translational repression, delineating distinct evolutionary branches in eukaryotic gene regulation. This clarification refined siRNA's role in exogenous silencing mechanisms.

Structure and Biogenesis

Molecular Structure

Small interfering RNA (siRNA) is a class of double-stranded molecules, typically comprising 20-25 per strand, that play a central role in . These molecules feature characteristic 2-nucleotide 3' overhangs on both ends and monophosphate groups at the 5' termini, which are essential structural hallmarks derived from RNase III-like processing. The duplex consists of two complementary strands: the sense (passenger) strand and the antisense (guide) strand, with the latter being preferentially selected for incorporation into the (RISC). A key feature of siRNA architecture is thermodynamic asymmetry between the two ends of the duplex, where the end with relatively weaker base-pairing stability facilitates the directional loading of the antisense strand into RISC by promoting cleavage or release of the sense strand. Structurally, siRNA is composed of a sugar-phosphate backbone with ribose sugars linked by phosphodiester bonds, and the nucleobases adenine (A), uracil (U), guanine (G), and cytosine (C), forming Watson-Crick base pairs along the duplex. Unlike microRNAs (miRNAs), which are generally 21-23 nucleotides long and form imperfect heteroduplexes with central bulges or mismatches, siRNAs exhibit near-perfect base-pairing across their entire length, enhancing specificity in target recognition. The secondary structure of siRNA adopts a right-handed A-form , typical of double-stranded , with approximately 11 base pairs per helical turn and a deep, narrow major groove. The 2-nucleotide 3' overhangs, composed of unpaired ribonucleotides terminating in 3' hydroxyl groups, mimic the products of cleavage and aid in recognition by Dicer during the processing of longer double-stranded precursors into mature siRNAs. Both endogenous siRNAs, produced from cellular double-stranded RNA sources, and synthetic siRNAs designed for experimental use maintain this perfect base-pairing and overhang configuration, distinguishing them from miRNAs that often include structural imperfections such as internal loops or bulges for regulatory flexibility.

Biosynthetic Pathways

Small interfering RNAs (siRNAs) are primarily generated endogenously through the processing of double-stranded RNA (dsRNA) precursors or self-complementary hairpin transcripts by enzymes, which belong to the RNase III family and cleave these precursors into ~21-23 duplexes with 2-nucleotide 3' overhangs. These precursors, often derived from intermediates, transposon transcripts, or natural antisense transcripts, vary in length but are processed iteratively by . In animals, the resulting siRNA duplexes associate with accessory proteins that enhance activity and facilitate the loading of the siRNA into the (RISC), such as TRBP in mammals, Loquacious in flies, and RDE-4 in C. elegans. The core RISC assembly involves the siRNA duplex binding to an protein, where the passenger strand is unwound and discarded, leaving the guide strand to direct silencing; proteins, particularly AGO2 in animals, provide the endonucleolytic activity for subsequent target recognition. In plants and nematodes like , this primary pathway is amplified by RNA-dependent RNA polymerases (RdRPs), which use the primary siRNA-targeted transcripts as templates to synthesize secondary siRNAs, expanding the silencing response through phased register production. For instance, in C. elegans, primary siRNAs are rare and trigger RdRP-mediated amplification into abundant 22-nucleotide secondary siRNAs loaded into worm-specific (WAGOs). Biosynthetic pathways vary across species, reflecting adaptations to endogenous threats like transposons and viruses. In mammals, endogenous siRNAs are uncommon and primarily arise from bidirectional transcription of pseudogene loci or transposons, relying solely on Dicer without RdRP amplification, though short hairpin RNAs (shRNAs) can mimic this process. Plants, such as Arabidopsis thaliana, employ multiple Dicer-like (DCL) enzymes—DCL2 for 22-nucleotide antiviral siRNAs, DCL3 for 24-nucleotide heterochromatin-associated siRNAs from transposons, and DCL4 for 21-nucleotide trans-acting siRNAs from hairpin precursors—with RdRPs like RDR2 and RDR6 driving secondary amplification in pathways like RNA-directed DNA methylation. In flies (Drosophila melanogaster), Dicer-2, aided by Loquacious, processes transposon-derived dsRNAs into siRNAs without secondary amplification, highlighting a streamlined animal-specific route.

Mechanism of Action

RNA Interference Pathway

The RNA interference (RNAi) pathway mediated by small interfering RNA (siRNA) represents a highly conserved eukaryotic mechanism for post-transcriptional gene regulation, originating from the last eukaryotic common ancestor and persisting across diverse lineages from plants to humans. Core components, including Dicer-like enzymes for siRNA processing and Argonaute proteins within the RNA-induced silencing complex (RISC), exhibit structural and functional homology, enabling siRNA-directed silencing of viral and transposon-derived nucleic acids in both kingdoms. In this pathway, exogenous or endogenous double-stranded siRNA duplexes, typically 21-23 nucleotides long, are incorporated into RISC to guide sequence-specific nucleic acid targeting, with the process ensuring precise selection of the functional guide strand. The pathway initiates with the loading of the siRNA duplex into a pre-RISC complex, primarily involving the Argonaute 2 (Ago2) protein in mammals, facilitated by ATP-dependent chaperones such as and associated factors like Hsc70, which stabilize the interaction and promote duplex insertion into Ago2's and MID domains. The antisense (guide) strand is preferentially selected based on thermodynamic asymmetry, where the strand with the less stable 5' end binds more favorably to Ago2's MID domain, often recognizing a 5' or adenine. Subsequent passenger strand ejection follows, occurring via two main mechanisms: slicer-dependent cleavage by Ago2's endonucleolytic activity in the PIWI domain when the duplex exhibits perfect base-pairing, or slicer-independent unwinding driven by the N-terminal domain of Ago2 and thermal instability at physiological temperatures, without requiring additional for strand separation. This ejection step activates RISC, yielding a mature holo-RISC complex with the guide strand anchored in Ago2, poised for target recognition. Ago2 serves as the central effector and slicer enzyme in mammalian RISC, harboring the catalytic residues (Asp, Asp, His) in its domain that enable precise , a function essential for efficient passenger strand removal and subsequent target cleavage in siRNA-mediated . Unlike the (miRNA) pathway, where imperfect base-pairing in RISC typically results in translational repression or mRNA deadenylation without direct cleavage, the siRNA pathway enforces strict complementarity to trigger Ago2-mediated endonucleolytic slicing of the target, distinguishing their mechanistic outcomes while sharing initial loading machinery. This divergence underscores siRNA's role in precise, destructive , conserved evolutionarily to counter invasive genetic elements.

Post-Transcriptional Gene Silencing

Post-transcriptional gene silencing (PTGS) by small interfering RNA (siRNA) primarily occurs through the (RISC), where the siRNA guide strand directs sequence-specific cleavage of complementary target mRNAs in the cytoplasm. This process requires near-perfect base-pairing between the siRNA antisense strand and the target mRNA, enabling the endonucleolytic activity of (Ago2), the catalytic component of RISC. Ago2 cleaves the target mRNA phosphodiester backbone precisely between nucleotides 10 and 11, counting from the 5' end of the siRNA guide strand, generating fragments with 5'-phosphate and 3'-hydroxyl ends. Following cleavage, the mRNA fragments undergo rapid exonucleolytic degradation independent of deadenylation or . The 5' fragment is primarily degraded in a 5'-to-3' direction by the XRN1, while the 3' fragment is processed in a 3'-to-5' direction by the exosome complex, ensuring complete elimination of the target transcript and preventing its . This decay pathway is distinct from general mRNA turnover mechanisms and is highly efficient. The efficiency of siRNA-mediated PTGS is influenced by the degree of complementarity, particularly in the seed region (positions 2-8 of the guide strand), which facilitates initial target recognition and RISC loading, though full complementarity across the siRNA length is essential for Ago2 slicing. Mismatches outside the seed can reduce cleavage but may still allow translational repression; however, perfect matching maximizes endonucleolytic activity.

Transcriptional Gene Silencing

Small interfering RNAs (siRNAs) mediate transcriptional gene silencing (TGS) through nuclear RNA interference (RNAi), where they guide Argonaute-containing complexes to chromatin-associated targets, leading to epigenetic modifications that repress transcription. In fission yeast (Schizosaccharomyces pombe), siRNAs direct the RNA-induced transcriptional silencing (RITS) complex—containing Ago1—to pericentromeric repeats, recruiting the Clr4 methyltransferase for H3K9 trimethylation (H3K9me3) and promoting heterochromatin assembly. Similarly, in plants like Arabidopsis thaliana, 24-nucleotide siRNAs facilitate RNA-directed DNA methylation (RdDM) by guiding Ago4 to RNA polymerase V-transcribed non-coding RNAs at target loci, resulting in cytosine methylation and heterochromatin reinforcement at transposons and repetitive elements. These processes ensure genome stability by suppressing transposon activity and aberrant transcription. The nuclear localization of RNAi components distinguishes TGS from cytoplasmic pathways, enabling direct interference with transcription initiation. The core mechanisms of siRNA-induced TGS involve the formation of and promoter to establish stable silencing. In mammals, siRNA-mediated TGS is more limited and context-specific compared to lower eukaryotes, though evidence exists in oocytes and embryonic stem cells, where siRNAs contribute to epigenetic and maintenance. Nuclear proteins loaded with siRNAs can bind promoter-associated transcripts, recruiting factors like SETDB1 for and inducing stable repression of genes such as the . However, mammalian TGS often relies more on piRNAs in the , and siRNA effects require nuclear import of cytoplasmic complexes. The extent of siRNA-mediated TGS in mammals remains a subject of ongoing , with some on its robustness outside specific contexts. Unlike post-transcriptional (PTGS), which degrades mature mRNAs in the , TGS by siRNAs targets pre-mRNA transcripts or DNA in the nucleus to block transcription elongation or initiation. Experimental studies demonstrate that siRNA-directed can spread over 1-2 kb from nucleation sites, as seen in fission yeast models where propagates bidirectionally along fibers to amplify . This localized spreading provides a mechanism for precise, heritable repression without widespread genomic disruption.

Induction and Activation

RNAi Induction Methods

Small interfering RNAs (siRNAs) are commonly introduced into cells through synthetic duplexes that mimic the products of processing, enabling direct of the (RISC). of these synthetic siRNAs, typically 21 nucleotides in length, is achieved using lipid-based reagents or , allowing transient in cultured mammalian cells within hours of delivery. This method provides rapid onset of silencing but is limited to short-term effects due to siRNA degradation and dilution during . For sustained RNAi, short hairpin RNAs (shRNAs) are expressed from plasmid or viral vectors, where they are transcribed by RNA polymerase III promoters such as U6 or H1, folding into stem-loop structures that are processed into siRNAs by Dicer. These expression vectors enable stable integration into the genome via lentiviral transduction, achieving long-term knockdown in dividing cells without repeated transfections. shRNA systems are particularly useful for high-throughput screening and creating knockout cell lines, though they require careful design to avoid toxicity from overexpression. In non-mammalian organisms like C. elegans and , long double-stranded RNAs (dsRNAs) exceeding 200 base pairs serve as biosynthetic precursors, processed by into siRNAs to trigger widespread RNAi. In mammals, where long dsRNAs induce responses, Dicer substrate RNAs such as 27-mer duplexes ( dsiRNAs) are used as enhanced precursors; these are more efficiently cleaved by Dicer, leading to greater RISC loading and up to 10-fold higher potency than standard 21-mer siRNAs, with silencing persisting for 10 days in some cases. These substrates target sites refractory to conventional siRNAs and improve efficacy in therapeutic applications. In vivo induction in animal models often employs hydrodynamic tail vein injection in mice, delivering high volumes of siRNA or shRNA vectors rapidly to achieve liver-specific silencing, as demonstrated by up to 90% reduction in target . Viral vectors, including lentiviruses and adeno-associated viruses (AAVs), facilitate shRNA delivery for stable, tissue-specific knockdown; for instance, AAV-shRNA constructs have silenced genes in hepatocytes for months without eliciting strong immune responses. These approaches are foundational for preclinical studies of RNAi-based therapies. Effective siRNA design adheres to principles established for optimal RISC incorporation and stability, featuring a 19-base-pair duplex with 2-nucleotide 3' UU overhangs on both strands to mimic natural products. Sequences with 30-50% are preferred, as higher GC levels reduce silencing efficiency by hindering duplex unwinding, while lower content compromises thermodynamic stability. Tools incorporating these rules, such as those from Reynolds et al., predict functionality with over 80% accuracy. To minimize off-target effects, where siRNAs inadvertently silence unintended transcripts via partial complementarity, multiple siRNAs (typically 3-5 per target) are pooled, diluting gene-specific off-targets while maintaining robust on-target knockdown, as validated in genome-wide studies showing reduced false positives. This strategy enhances specificity in without relying on chemical modifications.

RNA Activation Processes

RNA activation (RNAa) refers to a process in which small interfering RNAs (siRNAs), also known as small activating RNAs (saRNAs), target promoter regions of genes to upregulate their transcription, contrasting with the canonical (RNAi) pathway that silences . This phenomenon was first discovered in 2006 when researchers demonstrated that 21-nucleotide dsRNAs targeting sequences approximately 30-50 upstream of the transcription start site (TSS) could activate transcription in cells, as shown in experiments with the p21WAF1/CIP1 gene promoter. The mechanisms underlying RNAa involve epigenetic modifications and transcriptional machinery recruitment. saRNAs promote histone acetylation at promoter regions, including increased levels of , which correlates with enhanced accessibility and activation. Additionally, these saRNAs facilitate the recruitment of (Pol II) to the promoter and may involve demethylases to alleviate repressive marks, leading to sustained transcriptional upregulation. For instance, in cancer models, saRNA targeting the E-cadherin (CDH1) promoter has been used to restore expression, inhibiting and in renal and breast cancer cells, highlighting potential therapeutic applications. Unlike traditional RNAi, which degrades target mRNAs in the , RNAa operates by binding to non-coding promoter-associated transcripts, forming complexes with proteins that localize to the nucleus to modulate structure. The activation induced by RNAa is typically transient, lasting several days, rather than the more stable silencing effects of RNAi. Despite its promise, RNAa faces limitations, including species specificity primarily observed in and systems, with limited efficacy in other organisms. Activation levels generally achieve 2- to 10-fold upregulation of target , which may constrain its potency compared to other approaches. Recent clinical progress as of 2025 includes Phase I trials of saRNA therapeutics. For example, RAG-01, targeting p21 for non-muscle invasive (NMIBC) post-BCG failure, showed a 66.7% complete response rate in patients across low-dose cohorts, with no dose-limiting toxicities and mostly mild adverse events. Similarly, MTL-CEBPA, upregulating C/EBPα for advanced , demonstrated safety and potential efficacy in combination with in Phase I/II studies, including improved immune modulation. These trials mark the transition of RNAa towards clinical application in .

Research Applications

Allele-Specific Gene Silencing

Allele-specific gene silencing using small interfering RNAs (siRNAs) enables the selective targeting of mutant alleles in heterozygous dominant disorders, sparing wild-type to minimize therapeutic side effects. This approach is particularly valuable for conditions like and familial (ALS), where a single mutant drives pathology. By designing siRNAs that exploit single-nucleotide polymorphisms (SNPs) linked to the mutation, researchers achieve discrimination through sequence-specific mismatches, leveraging the (RISC) machinery for precise post-transcriptional knockdown. siRNA design for allele specificity typically incorporates a deliberate mismatch in the seed region (positions 2-8 of the guide strand), which disrupts base-pairing stability with the wild-type while maintaining efficacy against the mutant. Thermodynamic principles guide this process, as the free energy difference (ΔΔG) at the mismatch site influences RISC loading and target recognition; central or seed-region mismatches enhance selectivity by increasing the energetic barrier for non-cognate binding. For instance, in models of type 3, siRNAs with mismatches at positions 7-8 or 10 achieved up to 92.6% reduction in mutant expression versus only 6.4% for wild-type. Algorithms incorporating these thermodynamic parameters, such as (SVM)-based predictors, evaluate potential siRNA candidates for bias by modeling duplex stability and off-target potential. In , where expanded CAG repeats in the HTT gene cause toxicity, allele-specific siRNAs target SNPs such as rs362273 or rs362307, which are heterozygous in 35-48% of patients and linked to alleles. Chemically modified siRNAs with mismatches (e.g., at position 6) and secondary mismatches (e.g., position 11) demonstrated over 50-fold selectivity , with >85% HTT knockdown in BACHD mouse brains following intracerebroventricular delivery, while preserving wild-type levels. Similarly, in SOD1-linked models, siRNAs targeting SNPs in the allele achieved 70-90% specific knockdown in neuronal cells, with mismatches in the region enabling discrimination despite high sequence similarity; related studies using allele-specific RNAi extended survival in transgenic mice. These efficiencies highlight the approach's potential, though optimization via 2'-fluoro and phosphorothioate modifications is often required to boost potency. As of 2025, allele-specific siRNA approaches remain in for and related neuropathies, building on safety data from non-allele-specific RNAi therapies like (an approved in 2023), with designs tailored to common heterozygous SNPs for broader applicability. Design tools, including thermodynamic modeling software like BIOPREDsi adapted for allele bias, facilitate rapid screening of SNP-spanning sequences to predict >80% specificity . Challenges in allele-specific silencing arise from heterozygosity, necessitating precise to ensure the targeted variant is mutant-linked, as mismatched patient alleles reduce efficacy. Limited sequence space around SNPs often yields 2-4-fold lower potency compared to pan-targeting siRNAs, requiring extensive for therapeutic dosing, particularly in non-CNS tissues where delivery barriers amplify this issue. Despite these hurdles, the strategy's high specificity mitigates broader off-target risks, positioning it as a for personalized RNAi therapeutics in dominant genetic disorders.

Functional Genomics Studies

Small interfering RNA (siRNA) libraries have revolutionized functional genomics by enabling systematic loss-of-function studies across the human genome, which comprises approximately 20,000 protein-coding genes. These libraries consist of synthetic siRNAs designed to target individual genes, often with multiple siRNAs per gene to enhance reliability and mitigate off-target effects. Computational modeling is integral to the rational design and optimization of these siRNA sequences, allowing prediction of maximum gene silencing efficacy and specificity while minimizing off-target effects and toxicity. This approach employs thermodynamic parameters, machine learning algorithms, and structural predictions to select potent candidates, facilitating the construction of high-quality libraries for research applications. Genome-wide siRNA screens typically involve transfecting these libraries into cultured cells, followed by phenotypic readout assays to identify genes whose knockdown alters specific cellular processes, such as proliferation, apoptosis, or migration. This approach provides direct insights into gene function and genetic interactions without relying on prior knowledge of protein structures or pathways. In applications to phenotypic assays, siRNA screens have been instrumental in cell line models for discovering drug targets, particularly in cancer pathways. For instance, early genome-wide screens conducted between 2005 and 2010 identified key regulators of tumor cell survival and , such as components of the Wnt/β-catenin signaling pathway that promote progression when overexpressed. These studies often employed high-content imaging or viability assays to quantify phenotypes, revealing novel therapeutic vulnerabilities like dependency on mitotic kinases in cells. By linking to observable traits, siRNA screening has accelerated the identification of actionable targets, informing subsequent efforts. siRNA screens can be performed in arrayed or pooled formats, each suited to different experimental needs. Arrayed screens, where individual siRNAs are tested in separate wells, allow for precise phenotypic analysis using or but require higher reagent volumes and automation. In contrast, pooled formats combine multiple siRNAs into a single population, enabling selection-based readouts like survival under stress, though they are less common for transient siRNA due to delivery challenges and are more typically used with stable shRNA libraries. To validate initial hits from siRNA screens, researchers often integrate CRISPR-Cas9 approaches, which provide permanent disruption for confirmatory loss-of-function studies, reducing false positives from transient knockdown. Hit validation routinely involves testing 2-3 independent siRNAs per to confirm specificity and rule out off-target artifacts. Recent advances in multiplexed siRNA screening have enhanced the detection of complex genetic interactions, such as in tumor cells. In , a single-cell encoded platform enabled high-throughput testing of siRNA cocktails targeting multiple genes simultaneously, uncovering combinatorial dependencies in cancer models that single-agent knockdowns miss. This multiplexed approach facilitates the exploration of pathway redundancies and tumor-specific vulnerabilities, bridging with precision .

Challenges and Limitations

Nonspecific Off-Target Effects

Nonspecific off-target effects in small interfering RNA (siRNA) applications arise primarily from partial sequence complementarity between the siRNA guide strand and non-target mRNAs, leading to unintended gene silencing that mimics microRNA (miRNA)-like regulation rather than precise cleavage. These effects compromise the specificity of RNA interference (RNAi), as the RNA-induced silencing complex (RISC) can bind and repress transcripts beyond the intended target, often through translational repression or mRNA destabilization. A key mechanism is seed-dependent off-targeting, where complementarity in the seed region—typically nucleotides 2–8 (a 6–8 match) of the siRNA guide strand—sufficiently engages RISC to cause repression of non-cognate mRNAs. This partial matching, analogous to miRNA targeting, prioritizes the seed sequence over full-length complementarity, resulting in widespread but subtle downregulation of unintended transcripts. Transcriptome-wide studies reveal the scale of these impacts, with individual siRNAs potentially affecting up to 100 off-target transcripts, as identified through microarray and RNA sequencing (RNA-seq) analyses that capture global changes in gene expression. These off-targets are often enriched in the 3' untranslated regions (UTRs) of mRNAs and can alter cellular phenotypes, confounding experimental interpretations in functional genomics. Mitigation strategies include chemical modifications to the siRNA backbone or sugar moieties, such as 2'-O-methyl or unlocked nucleic acids, which disrupt non-specific RISC loading and reduce off-target binding while preserving on-target efficacy. Pooled siRNAs, comprising multiple distinct sequences targeting the same , dilute individual off-target profiles by averaging effects across the pool. Recent advances in AI-driven design platforms, leveraging models like graph neural networks, have achieved up to 50% reductions in predicted off-target binding compared to traditional algorithms, enhancing specificity in therapeutic development.

Immune Response Issues

Small interfering RNA (siRNA) molecules, due to their double-stranded RNA structure resembling viral pathogens, can activate the primarily through Toll-like receptors (TLRs). TLR3 recognizes dsRNA in endosomes, while TLR7 and TLR8 detect single-stranded RNA motifs, particularly GU-rich sequences, leading to downstream signaling via myeloid differentiation primary response 88 (MyD88) and TIR-domain-containing adapter-inducing interferon-β (TRIF) pathways. This activation triggers the production of type I interferons (IFN-α and IFN-β) and pro-inflammatory cytokines such as interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and IL-12, which can escalate to severe cytokine release if siRNA is unmodified or delivered in high doses. In preclinical models, this innate response has been linked to toxicity, including inflammation and organ stress, distinguishing it from sequence-specific off-target gene silencing as a receptor-mediated process independent of the siRNA's target mRNA complementarity. Species differences amplify these effects, with non-human primates exhibiting stronger cytokine induction compared to rodents due to closer alignment of their TLR7/8 expression and sensitivity with humans, complicating translational safety assessments. Adaptive immune responses to siRNA arise mainly with repeated dosing, where the host may develop (IgG) antibodies against the siRNA cargo or associated delivery vehicles, potentially reducing efficacy and causing . For instance, in clinical use of , an approved siRNA therapeutic, infusion-related reactions have been observed in approximately 19% of patients, sometimes linked to excipients in the lipid nanoparticle formulation such as PEG2000-DMG rather than the siRNA itself. To mitigate these issues, recent innovations in coatings, such as (PEG) or lipid-polymer hybrids, have demonstrated reduced TLR binding and in 2024 preclinical studies by shielding siRNA from endosomal recognition. In Phase I clinical trials, immune activation is monitored through serial profiling (e.g., measuring IFN-α, IL-6, and TNF-α levels in serum), enabling early detection and dose adjustment to prevent adverse events.

Machinery Saturation Effects

High concentrations of exogenous small interfering RNA (siRNA) can overload the endogenous (RNAi) machinery, leading to competition for key components such as Exportin-5 and 2 (Ago2). Exportin-5, responsible for nuclear export of pre-miRNAs and short hairpin RNAs (shRNAs), becomes saturated when siRNA or shRNA levels exceed cellular capacity, typically at doses greater than 100 nM in models. Similarly, Ago2, the core effector of the (RISC), experiences saturation during RISC loading, where excessive siRNAs displace endogenous microRNAs (miRNAs) from the pathway. This competition disrupts the normal balance of endogenous RNAi processes, as siRNAs and shRNAs share the same export and loading mechanisms as miRNAs. The primary consequences of this saturation include impaired miRNA-mediated gene regulation, which can result in cellular and physiological disruptions. For instance, reduced activity of endogenous miRNAs leads to of target genes, contributing to phenotypes such as developmental defects observed in model organisms like mice and , where high siRNA loads mimic loss-of-function in miRNA pathways. In vivo, sustained high-level shRNA expression has been shown to cause in mice due to oversaturation of the miRNA/shRNA pathway, manifesting as and multi-organ after prolonged exposure. Optimal siRNA dosing mitigates these effects, with 10-50 nM typically sufficient for effective in cell-based assays without significant saturation. Long-term shRNA delivery, even at moderate levels, risks cumulative saturation and in mammalian models, underscoring the need for dose optimization. Recent 2025 studies on extrahepatic siRNA delivery highlight that targeting non-liver tissues with lower systemic doses reduces the risk of machinery saturation, particularly beneficial for therapies focused on peripheral organs where liver accumulation is minimized. Saturation can be assessed by monitoring endogenous miRNA levels, such as miR-21, as a proxy for pathway overload; decreased miR-21 activity in reporter assays indicates competition and potential toxicity.

Chemical Modifications

Stability Enhancements

Chemical modifications to the siRNA backbone and sugar moieties are essential for enhancing stability against nuclease degradation, a primary barrier to therapeutic efficacy. Unmodified siRNAs are rapidly degraded in biological fluids, with half-lives often limited to minutes due to susceptibility to endonucleases and exonucleases. Backbone modifications, particularly phosphorothioate (PS) linkages, replace the non-bridging oxygen in the phosphodiester bond with sulfur, conferring resistance to enzymatic hydrolysis and increasing the half-life from minutes to hours in serum. This modification also improves protein binding, further protecting the siRNA from degradation, though it introduces chirality at each linkage site, which can influence pharmacokinetics. Sugar modifications target the ring to bolster resistance while preserving the RNA-like conformation necessary for RISC incorporation. The 2'-O-methyl (2'-OMe) substitution adds a to the 2' hydroxyl, reducing susceptibility to RNase A-family s by sterically hindering cleavage, while 2'-fluoro (2'-F) replaces the 2' hydroxyl with , enhancing and resistance to both endo- and exonucleases without significantly altering duplex stability. These modifications are often alternated or combined with PS linkages to achieve synergistic effects, as seen in early therapeutic designs where partial 2'-OMe/2'-F incorporation extended in preclinical models. A prominent example of stability enhancement is the use of (GalNAc) conjugation in siRNAs like givosiran, an FDA-approved drug for acute hepatic porphyria. GalNAc-siRNAs incorporate multiple chemical modifications, including PS and 2'-F/2'-OMe, alongside the GalNAc ligand for targeting, resulting in serum stability extended to days and prolonged . In , these conjugates exhibit liver-specific with a biophase of approximately 50 days, enabling subcutaneous dosing every few months due to slow hepatic clearance and minimal . However, excessive chemical modifications can introduce trade-offs, such as reduced potency from impaired RISC loading or altered duplex if over-applied. For instance, full 2'-OMe substitution at certain positions may diminish , necessitating balanced patterns to maintain activity. Recent advancements in chemical modifications have enhanced overall durability. In 2025, the 5'-(E)-vinylphosphonate modification on strand extended siRNA duration to over 30 days and .

Specificity Improvements

To enhance the specificity of small interfering RNAs (siRNAs), chemical modifications target the seed region and strand selection mechanisms, minimizing unintended interactions while preserving on-target silencing efficacy. Unlocked nucleic acids () incorporated at position 7 of the antisense strand disrupt seed-mediated off-target effects by altering the helical geometry, which reduces binding to non-cognate mRNAs without significantly compromising potency. This modification has been shown to lower off-target repression by up to 90% in cellular assays, as demonstrated in studies using systems. Additional modifications at the 5' terminus, such as morpholino or abasic substitutions, further refine specificity by blocking immune sensor recognition and improving antisense strand bias. The 5'-morpholino modification on the prevents 5'-phosphorylation, favoring RISC loading of the antisense strand and thereby reducing passenger strand-mediated off-targeting and innate immune via TLR pathways. Similarly, abasic modifications at the 5' end abrogate TLR3 and TLR7/8 stimulation, eliminating induction while maintaining RNAi activity, as these sites mimic non-nucleic acid structures that evade receptors. Recent advances in have accelerated specificity optimization by predicting sequence features that minimize off-target profiles. These AI-driven approaches integrate structural and thermodynamic parameters to generate candidates that outperform traditional empirical designs in high-throughput validation. A practical example is , an approved siRNA therapeutic targeting for hypercholesterolemia management, which employs 2'-fluoro (2'-F) and phosphorothioate (PS) modifications to achieve precise without TLR activation. The 2'-F substitutions in the seed region enhance base-pairing fidelity, while PS linkages at select positions stabilize the duplex against immune nucleases, resulting in allele-specific knockdown ratios exceeding 100:1 in dual- reporter assays. Such assays, which co-transfect siRNAs with mismatched and perfect-match reporters, quantify specificity by comparing normalized Renilla-to-firefly ratios, confirming minimal cross-reactivity. In 2025, single alkyl modifications in the seed region further improved specificity and therapeutic profiles compared to unmodified siRNAs. These specificity-focused modifications address core challenges like seed-dependent off-targeting, as explored in related sections on nonspecific effects, by prioritizing precision over broad reactivity.

Delivery Strategies

Non-Viral Delivery Techniques

Non-viral delivery techniques for small interfering RNA (siRNA) encompass physical and chemical methods that facilitate cellular uptake without the use of viral vectors, addressing key challenges in RNA interference applications such as stability and targeting. These approaches are particularly valuable in research settings for their simplicity and control, though they often face limitations due to barriers like endosomal entrapment. Common strategies include lipid-based , , and emerging physical methods like sonoporation, each balancing efficiency, toxicity, and applicability across cell types. Lipid-based transfection reagents, such as Lipofectamine, form lipoplexes by electrostatically binding siRNA, promoting cellular internalization via endocytosis in vitro. These complexes achieve transfection efficiencies of up to 70-90% in adherent cell lines, with low cytotoxicity when optimized, making them a standard for high-throughput gene silencing studies. However, their efficacy diminishes in primary or non-dividing cells due to poor endosomal escape, where mechanisms like the proton sponge effect—enabled by cationic lipids buffering endosomal pH and inducing osmotic swelling—help release siRNA into the cytosol. Electroporation employs short electric pulses to create transient pores in the , enabling direct siRNA entry and bypassing ; it is especially effective for hard-to-transfect cells like primary neurons, achieving near-100% delivery in some protocols with minimal off-target effects. Despite high efficiency, can cause cell stress or viability loss if parameters like voltage and pulse duration are not tuned, limiting its use to smaller-scale experiments. Other physical methods include , which delivers siRNA precisely into individual cells via a fine needle, offering 100% but at the cost of low throughput and technical expertise, and sonoporation, which uses ultrasound-induced to permeabilize membranes, enabling siRNA uptake in immune cells like T lymphocytes with reduced toxicity compared to . Recent 2024 advances in nanoparticles (LNPs) have expanded non-viral capabilities beyond the liver, incorporating ionizable and targeting ligands for extrahepatic delivery to organs like the lungs and kidneys, overcoming clearance barriers through optimized surface charge and ApoE-independent pathways. While these techniques provide versatile tools for siRNA delivery, their clinical translation remains constrained by scalability and stability issues.

Viral and Nanoparticle Delivery

Viral vectors, including (AAV) and lentiviral systems, facilitate the delivery of short hairpin RNAs (shRNAs) that are intracellularly processed into siRNAs, enabling prolonged through continuous expression. AAV serotype 9 (AAV9) demonstrates pronounced for the (CNS), efficiently crossing the blood-brain barrier upon intravenous administration to transduce neurons and . Lentiviral vectors integrate shRNA expression cassettes into the host genome, supporting stable, long-term silencing in both dividing and non-dividing cells, with expression persisting for months to over two years in preclinical models. These vectors achieve expression durations of several months, contrasting with transient siRNA effects, though they require careful engineering to minimize off-target . Nanoparticle-based approaches enhance siRNA delivery by encapsulating or conjugating the RNA to protect it from nucleases and improve cellular uptake. (GalNAc)-siRNA conjugates specifically target s via binding to the , resulting in rapid and high liver-specific uptake, with knockdown efficiencies reaching 70-85% in preclinical studies. Lipid nanoparticles (LNPs), composed of ionizable cationic lipids, , and polyethylene glycol-lipids, encapsulate siRNA for , mimicking mRNA delivery platforms to promote endosomal escape and cytoplasmic release in target tissues. These systems yield efficiencies of 70-85% and sustain silencing for weeks to months through optimized formulations. Emerging innovations as of 2025 include exosome-based carriers loaded with siRNA for cancer therapy, leveraging natural to evade immune detection and enhance tumor-specific delivery, as demonstrated in models of and where they inhibit oncogenic pathways. For CNS applications, temporarily disrupts the blood- barrier to enable LNP-siRNA penetration, achieving targeted in brain tumors with minimal invasiveness. Overall, viral and methods exhibit lower than naked siRNA due to shielding and receptor-mediated uptake, reducing innate immune activation while maintaining therapeutic efficacy.

Therapeutic Applications

Approved siRNA Drugs

As of November 2025, seven small interfering RNA (siRNA) therapeutics have received approval from the U.S. (FDA) or the (EMA), primarily targeting rare genetic disorders and metabolic conditions through liver-specific . These drugs represent a milestone in RNA interference-based medicine, leveraging chemical modifications and targeted delivery systems to achieve durable effects with infrequent dosing. Most are administered subcutaneously and focus on hepatic expression of disease-causing proteins, demonstrating clinical benefits such as reduced disease progression and normalization with generally manageable safety profiles. The first approved siRNA drug, (Onpattro), received FDA approval in August 2018 for the treatment of in adults with hereditary transthyretin-mediated (hATTR) . It targets (TTR) mRNA to reduce both mutant and wild-type TTR protein production by approximately 80%, using encapsulation for intravenous delivery every three weeks. In the phase 3 APOLLO trial, patisiran improved neuropathy impairment scores by 6.0 points compared to over 18 months, halting disease progression and enhancing in patients with this progressive neuropathy. Givosiran (Givlaari) was approved by the FDA in November 2019 for adults with acute hepatic porphyria (AHP), a rare disorder causing recurrent neurovisceral attacks. This GalNAc-conjugated siRNA targets aminolevulinic acid synthase 1 (ALAS1) mRNA in hepatocytes, administered subcutaneously at 2.5 mg/kg monthly, leading to near-complete suppression of ALAS1 and toxic porphyrin precursors. The phase 3 ENVISION trial showed a 74% reduction in annualized porphyria attack rates versus placebo, with sustained benefits over six months and reduced healthcare utilization. Lumasiran (Oxlumo), approved by the FDA in November 2020, addresses primary hyperoxaluria type 1 (PH1), a leading to oxalate overproduction and kidney damage. It targets glycolate oxidase (GOX, encoded by HAO1) mRNA via GalNAc-mediated subcutaneous delivery (initial loading doses followed by quarterly maintenance at 3 mg/kg). Clinical data from the phase 3 ILLUMINATE-A trial indicated a mean 65% reduction in urinary levels from baseline by month 6, with over 50% of patients achieving normal levels, thereby mitigating risks of nephrolithiasis and renal failure. Inclisiran (Leqvio), approved by the FDA in December 2021 (initial dose plus one at three months, then every six months), is indicated for lowering cholesterol (LDL-C) in adults with primary hypercholesterolemia or mixed , including as adjunctive or monotherapy. This GalNAc-conjugated siRNA targets proprotein convertase subtilisin/kexin type 9 (PCSK9) mRNA for hepatic delivery via subcutaneous injection, achieving up to 52% LDL-C reduction sustained over one year in the ORION-10 and ORION-11 trials, with benefits in cardiovascular risk reduction. Vutrisiran (Amvuttra), approved by the FDA in June 2022, treats in hATTR and was expanded in March 2025 to include . Administered subcutaneously every three months (25 mg) with GalNAc conjugation targeting TTR mRNA, it offers advantages over through outpatient dosing and potentially better tolerability. The HELIOS-A phase 3 trial demonstrated a mean change from baseline in mNIS+7 of −2.7 points for compared to +20.8 points for external at 18 months, representing an 87.5% reduction in the rate of neuropathy progression and quality-of-life gains, with deeper TTR reduction (up to 85%) than in head-to-head comparisons. Nedosiran (Rivfloza), approved by the FDA in October 2023, is for lowering urinary in patients aged 9 years and older with PH1 and relatively preserved renal function. This GalNAc-conjugated siRNA targets (LDHA) mRNA via monthly subcutaneous doses (up to 160 mg), providing an alternative pathway to oxalate reduction independent of GOX. In the phase 3 PHYOX-2 trial, it achieved a 55% mean reduction in 24-hour urinary oxalate from baseline by month 6, with 56% of patients normalizing levels and slowing estimated decline. The most recent approval, fitusiran (Qfitlia), received FDA clearance in March 2025 for routine prophylaxis in patients aged 12 years and older with hemophilia A or B, with or without inhibitors. This GalNAc-conjugated siRNA targets (AT) mRNA for subcutaneous monthly delivery (80 mg), reducing AT levels to 15-35% to enhance generation and clotting. Phase 3 ATLAS trials reported approximately 70% reductions in annualized rates versus enhanced or standard prophylaxis arms, marking the first siRNA for hemophilia and offering a genotype-independent option with convenient dosing. These approved siRNA drugs share key features: liver-targeted delivery predominantly via N-acetylgalactosamine (GalNAc) conjugates (except ), infrequent subcutaneous administration for rare diseases like , , , and hemophilia, and focus on reducing pathogenic for long-term biomarker control. Common adverse effects are mild, including injection-site reactions (affecting 20-30% of patients), , and transient elevations in liver enzymes, with no evidence of severe or off-target silencing in long-term use.

Emerging Therapies and Companies

Computational modeling serves as a key strategy in developing siRNA therapeutics, enabling rational design and optimization of sequences for maximal gene silencing efficacy and specificity while minimizing off-target effects and toxicity, as further explored in Research Applications. maintains a robust pipeline of over 25 investigational RNAi therapeutics in clinical development as of late , spanning rare diseases, cardiovascular conditions, and . Key candidates include zilebesiran, an siRNA targeting angiotensinogen for , which advanced to global Phase 3 trials in to evaluate cardiovascular risk reduction with quarterly subcutaneous dosing. In , nucresiran targets (TTR) mRNA for hATTR amyloidosis-related and in Phase 3, while ALN-SOD, an siRNA against 1, entered Phase 1 for SOD1-mediated (ALS), demonstrating potential for (CNS) delivery. Fitusiran, previously in Phase 3 for hemophilia A and B, received FDA approval as Qfitlia in March , marking Alnylam's sixth approved RNAi therapeutic and highlighting the transition of pipeline candidates to market. In , siRNA therapies are advancing against challenging targets like mutants and polo-like kinase 1 (), with preclinical and early clinical efforts focusing on solid tumors. Chimeric siRNAs cotargeting and have shown synergistic tumor inhibition and reduced growth in -driven models. For , siRNA approaches complement small-molecule inhibitors, enhancing anti-tumor effects in -mutant by blocking progression, as evidenced in 2025 preclinical studies. Lipid nanoparticle (LNP)-encapsulated siRNAs are entering 2025 trials for solid tumors, improving targeted delivery and overcoming resistance in pancreatic and lung cancers driven by oncogenic . Extrahepatic applications are expanding siRNA's reach beyond the liver, with promising results in ocular and CNS disorders. In wet age-related (AMD), Sylentis's SYL1801, an siRNA targeting integrin subunit alpha 5, met its primary endpoint in a Phase 2a trial in 2025, reducing neovascularization and improving visual outcomes with topical administration. For CNS delivery in , Voyager Therapeutics selected an siRNA candidate against in 2025, using intravenous AAV vectors for blood-brain barrier penetration, while RAG-17 employs a smart chemistry-aided delivery system for in SOD1- patients. AI-optimized siRNA designs are emerging for tumor applications, enhancing specificity and potency in silencing oncogenes like those in , as shown in 2025 computational models integrated with delivery platforms. Other companies are driving siRNA innovation, including Pharmaceuticals, which advanced ARO-MAPT into clinical development in 2025 using a novel proprietary delivery system for CNS targets, and partnered with on ARO-SNCA, a preclinical siRNA for . Dicerna Pharmaceuticals, acquired by in 2021 for $3.3 billion, has integrated its GalXC platform into Novo’s pipeline, yielding candidates like those in Phase 2 for cardiometabolic diseases. The global RNAi therapeutics market, dominated by siRNA modalities, is projected to reach approximately $20 billion by 2030, fueled by expanded indications and delivery improvements. Despite progress, challenges persist in extrahepatic siRNA delivery, particularly achieving sufficient uptake and silencing in tissues like the CNS and tumors without off-target effects. Combinations with , such as siRNAs silencing alongside checkpoint inhibitors, show preclinical synergy in enhancing T-cell responses against solid tumors, but require optimized formulations to balance and immune .

Regulatory and Ethical Considerations

Small interfering RNA (siRNA) therapeutics are classified by the U.S. Food and Drug Administration (FDA) as drugs, subject to (IND) applications for clinical trials and (NDA) pathways for approval, with many qualifying for accelerated approval in rare diseases due to unmet needs and surrogate endpoints like neuropathy impairment scores. For instance, received accelerated approval in 2018 for hereditary transthyretin-mediated , a rare condition, based on clinical response data with post-approval confirmatory studies required. Patent landscapes for siRNA have evolved significantly, with core (RNAi) technologies, such as the Tuschl patents covering siRNA structures and mechanisms, largely expiring between 2018 and 2023, opening pathways for broader development but leaving delivery innovations protected. holds key patents on siRNA delivery systems, including nanoparticle formulations, which remain active and have led to ongoing disputes with generic entrants seeking to replicate therapeutic formulations as of 2025. Ethical considerations in siRNA therapy emphasize avoidance of germline modifications, as these agents act transiently on somatic cells without altering the genome, thereby sidestepping heritable risks associated with permanent editing technologies. Equity in access poses a major concern, particularly for orphan drug indications, where high development and manufacturing costs—often exceeding $1 million per patient annually—limit availability in low-resource settings despite incentives like the Orphan Drug Act. As of 2025, development for siRNA faces challenges in demonstrating analytical sameness, including purity, impurity profiles, and complex formulations, as highlighted in FDA's initiatives for . International harmonization efforts between the FDA and (EMA) continue to address discrepancies in chemistry, manufacturing, and controls (CMC) requirements for , with EMA's 2025 reflection paper proposing streamlined clinical data reliance to align with FDA frameworks. Looking ahead, regulations on off-label siRNA use will likely follow existing FDA guidelines, permitting physician-prescribed applications beyond approved indications for rare diseases while prohibiting manufacturer promotion, with increased scrutiny on data from programs. In agriculture, RNAi-based pesticides raise environmental concerns, including potential non-target effects on pollinators and ecosystems, necessitating assessments and public engagement to mitigate risks of unintended in non-pest species.

References

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