small activating RNA
{{short description|Type of RNA that activates transcription of specific genes }}
{{distinguish|Self-amplifying RNA|text=Self-amplifying RNA}}
Small activating RNAs (saRNAs) are double-stranded RNA molecules that induce gene expression at the transcriptional level, a phenomenon known as RNA activation (RNAa). This contrasts with the gene silencing typically associated with small interfering RNAs (siRNAs) in RNA interference. saRNAs offer a novel approach to upregulate genes of therapeutic interest, and have progressed to clinical trials.
== Mechanism of Action ==
saRNAs, typically 19 nucleotides in length with 2-nucleotide overhangs (similar to siRNAs),{{cite journal | vauthors = Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H, Dahiya R | title = Small dsRNAs induce transcriptional activation in human cells | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 46 | pages = 17337–42 | date = November 2006 | pmid = 17085592 | pmc = 1859931 | doi = 10.1073/pnas.0607015103 | doi-access = free | bibcode = 2006PNAS..10317337L }} mediate RNAa through the RNA-induced transcriptional activation (RITA) complex. This complex includes Argonaute 2 (AGO2), RNA helicase A (RHA), and CTR9 (a component of the PAF1 complex).{{cite journal | vauthors = Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H, Li LC | title = saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription | journal = Cell Research | volume = 26 | issue = 3 | pages = 320–335 | date = March 2016 | pmid = 26891992 | pmc = 4778170 | doi = 10.1038/cr.2016.22 }} The RITA complex facilitates the transition of RNA polymerase II from a paused to an elongating state at the target gene's promoter, leading to increased transcription. (For a more detailed explanation of the mechanism, see RNA activation.)
== saRNA Design and Use ==
Designing effective saRNAs involves careful consideration of several factors. Unlike siRNAs, which primarily target mRNA sequences for degradation, saRNAs target promoter regions, and their efficacy is highly dependent on the specific target location.{{cite journal |last1=Wang |first1=J |last2=Place |first2=RF |last3=Portnoy |first3=V |last4=Huang |first4=V |last5=Kang |first5=MR |last6=Kosaka |first6=M |last7=Ho |first7=MKC |last8=Li |first8=LC |title=Inducing gene expression by targeting promoter sequences using small activating RNAs. |journal=Journal of Biological Methods |date=11 March 2015 |volume=2 |issue=1 |page=1 |doi=10.14440/jbm.2015.39 |pmid=25839046|pmc=4379447 }}{{cite journal |last1=Wang |first1=J |last2=Huang |first2=V |last3=Ye |first3=L |last4=Bárcena |first4=A |last5=Lin |first5=G |last6=Lue |first6=TF |last7=Li |first7=LC |title=Identification of small activating RNAs that enhance endogenous OCT4 expression in human mesenchymal stem cells. |journal=Stem Cells and Development |date=1 February 2015 |volume=24 |issue=3 |pages=345–53 |doi=10.1089/scd.2014.0290 |pmid=25232932|pmc=4303016 }} Proximity to the transcription start site (TSS), sequence context, and local chromatin state are critical determinants of activation versus silencing outcomes.{{cite journal |last1=Janowski |first1=BA |last2=Younger |first2=ST |last3=Hardy |first3=DB |last4=Ram |first4=R |last5=Huffman |first5=KE |last6=Corey |first6=DR |title=Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. |journal=Nature Chemical Biology |date=March 2007 |volume=3 |issue=3 |pages=166–73 |doi=10.1038/nchembio860 |pmid=17259978}}{{cite book |last1=Li |first1=LC |title=Small RNA-Guided Transcriptional Gene Activation (RNAa) in Mammalian Cells. |series=Advances in Experimental Medicine and Biology |date=2017 |volume=983 |pages=1–20 |doi=10.1007/978-981-10-4310-9_1 |pmid=28639188|isbn=978-981-10-4309-3 }}
Key considerations for saRNA design include:
- Target Site Selection: saRNAs typically target promoter regions, often within a few hundred base pairs upstream of the TSS. Computational tools and empirical testing are used to identify optimal target sites.
- Sequence Specificity: The saRNA sequence must be carefully designed to ensure specific binding to the target promoter and avoid off-target effects.
- Chemical Modifications: Chemical modifications, similar to those used in siRNA therapeutics, can be incorporated to enhance saRNA stability, reduce off-target effects, and improve delivery.{{cite journal |last1=Place |first1=RF |last2=Noonan |first2=EJ |last3=Földes-Papp |first3=Z |last4=Li |first4=LC |title=Defining features and exploring chemical modifications to manipulate RNAa activity. |journal=Current Pharmaceutical Biotechnology |date=August 2010 |volume=11 |issue=5 |pages=518–26 |doi=10.2174/138920110791591463 |pmid=20662764|pmc=3413318 }}{{cite journal |last1=Voutila |first1=J |last2=Reebye |first2=V |last3=Roberts |first3=TC |last4=Protopapa |first4=P |last5=Andrikakou |first5=P |last6=Blakey |first6=DC |last7=Habib |first7=R |last8=Huber |first8=H |last9=Saetrom |first9=P |last10=Rossi |first10=JJ |last11=Habib |first11=NA |title=Development and Mechanism of Small Activating RNA Targeting CEBPA, a Novel Therapeutic in Clinical Trials for Liver Cancer. |journal=Molecular Therapy |date=6 December 2017 |volume=25 |issue=12 |pages=2705–2714 |doi=10.1016/j.ymthe.2017.07.018 |pmid=28882451|pmc=5768526 }}
- Delivery: Efficient delivery to the target tissue and into the cell nucleus is crucial for saRNA activity. Delivery methods include lipid nanoparticles (LNPs), GalNAc conjugates, lipid conjugates and other approaches.{{cite journal |last1=Kwok |first1=A |last2=Raulf |first2=N |last3=Habib |first3=N |title=Developing small activating RNA as a therapeutic: current challenges and promises. |journal=Therapeutic Delivery |date=March 2019 |volume=10 |issue=3 |pages=151–164 |doi=10.4155/tde-2018-0061 |pmid=30909853|doi-access=free }}{{cite journal |last1=Pandey |first1=Shalini |last2=Bednarz |first2=Patrick T. |last3=Oberli |first3=Matthias A. |last4=Veiseh |first4=Omid |title=Small activating RNA delivery in vivo: Challenges, prospects, and lessons learned from siRNA delivery |journal=Nano Research |date=October 2024 |volume=17 |issue=10 |pages=8990–9002 |doi=10.1007/s12274-024-6862-4|bibcode=2024NaRes..17.8990P }}
A set of guidelines for designing saRNAs has been published and an [http://bioinfo.imtech.res.in/manojk/sarna/ online resource for saRNAs] has been developed to integrate experimentally verified saRNAs and proteins involved.{{Cite journal|last1=Dar|first1=Showkat Ahmad|last2=Kumar|first2=Manoj|date=July 2018|title=saRNAdb: Resource of Small Activating RNAs for Up-regulating the Gene Expression|journal=Journal of Molecular Biology|volume=430|issue=15|pages=2212–2218|doi=10.1016/j.jmb.2018.03.023|pmid=29625201|s2cid=4936884}}
== Therapeutic Applications ==
saRNAs represent a promising therapeutic modality for diseases where increasing the expression of a specific gene is beneficial. This approach is particularly attractive for targeting genes considered "undruggable" by conventional small molecule or antibody-based therapies.{{cite journal | vauthors = Qian Y, Liu C, Zeng X, Li LC | title = RNAa: Mechanisms, Therapeutic Potential, and Clinical Progress | journal = Molecular Therapy - Nucleic Acids | date = 2025 | volume = 36 | issue = 2 | doi = 10.1016/j.omtn.2025.102494| pmid = 40125270 | pmc = 11930103 }}{{cite journal |last1=Ghanbarian |first1=H |last2=Aghamiri |first2=S |last3=Eftekhary |first3=M |last4=Wagner |first4=N |last5=Wagner |first5=KD |title=Small Activating RNAs: Towards the Development of New Therapeutic Agents and Clinical Treatments. |journal=Cells |date=8 March 2021 |volume=10 |issue=3 |page=591 |doi=10.3390/cells10030591 |doi-access=free |pmid=33800164|pmc=8001863 }}
- Cancer: A major focus of saRNA research has been on reactivating tumor suppressor genes that are silenced in cancer cells. Examples include:
:* p21: RAG-01, an saRNA targeting p21, has received FDA approval for Phase I trials for non-muscle invasive bladder cancer (NMIBC).{{cite web | title = Ractigen Therapeutics Announces FDA Approval for RAG-01, a First-in-Class saRNA Therapy for BCG-Unresponsive NMIBC | url = https://www.ractigen.com/ractigen-therapeutics-announces-fda-approval-for-rag-01-a-first-in-class-sarna-therapy-for-bcg-unresponsive-nmibc/ | publisher = Ractigen Therapeutics | date = April 2024 | access-date = 2024-11-21 }}{{cite journal |last1=Kang |first1=MR |last2=Yang |first2=G |last3=Place |first3=RF |last4=Charisse |first4=K |last5=Epstein-Barash |first5=H |last6=Manoharan |first6=M |last7=Li |first7=LC |title=Intravesical delivery of small activating RNA formulated into lipid nanoparticles inhibits orthotopic bladder tumor growth. |journal=Cancer Research |date=1 October 2012 |volume=72 |issue=19 |pages=5069–79 |doi=10.1158/0008-5472.CAN-12-1871 |pmid=22869584}}{{cite book |last1=Kang |first1=MR |last2=Li |first2=G |last3=Pan |first3=T |last4=Xing |first4=JC |last5=Li |first5=LC |chapter=Development of Therapeutic dsP21-322 for Cancer Treatment |title=RNA Activation |series=Advances in Experimental Medicine and Biology |date=2017 |volume=983 |pages=217–229 |doi=10.1007/978-981-10-4310-9_16 |pmid=28639203|isbn=978-981-10-4309-3 }}
:* C/EBP-α: MTL-CEBPA, the first saRNA drug candidate, targets C/EBP-α and has shown efficacy in hepatocellular carcinoma (HCC) in Phase II clinical trials.{{cite journal |last1=Sarker |first1=D |last2=Plummer |first2=R |last3=Meyer |first3=T |last4=Sodergren |first4=MH |last5=Basu |first5=B |last6=Chee |first6=CE |last7=Huang |first7=KW |last8=Palmer |first8=DH |last9=Ma |first9=YT |last10=Evans |first10=TRJ |last11=Spalding |first11=DRC |last12=Pai |first12=M |last13=Sharma |first13=R |last14=Pinato |first14=DJ |last15=Spicer |first15=J |last16=Hunter |first16=S |last17=Kwatra |first17=V |last18=Nicholls |first18=JP |last19=Collin |first19=D |last20=Nutbrown |first20=R |last21=Glenny |first21=H |last22=Fairbairn |first22=S |last23=Reebye |first23=V |last24=Voutila |first24=J |last25=Dorman |first25=S |last26=Andrikakou |first26=P |last27=Lloyd |first27=P |last28=Felstead |first28=S |last29=Vasara |first29=J |last30=Habib |first30=R |last31=Wood |first31=C |last32=Saetrom |first32=P |last33=Huber |first33=HE |last34=Blakey |first34=DC |last35=Rossi |first35=JJ |last36=Habib |first36=N |title=MTL-CEBPA, a Small Activating RNA Therapeutic Upregulating C/EBP-α, in Patients with Advanced Liver Cancer: A First-in-Human, Multicenter, Open-Label, Phase I Trial. |journal=Clinical Cancer Research |date=1 August 2020 |volume=26 |issue=15 |pages=3936–3946 |doi=10.1158/1078-0432.CCR-20-0414 |pmid=32357963|url=https://discovery.ucl.ac.uk/id/eprint/10097721/1/Meyer_MTL-CEBPA%2C%20a%20small%20activating%20RNA%20therapeutic%20up-regulating%20C%3AEBP-%CE%B1_AAM.pdf }}{{cite journal |last1=Hashimoto |first1=A |last2=Sarker |first2=D |last3=Reebye |first3=V |last4=Jarvis |first4=S |last5=Sodergren |first5=MH |last6=Kossenkov |first6=A |last7=Sanseviero |first7=E |last8=Raulf |first8=N |last9=Vasara |first9=J |last10=Andrikakou |first10=P |last11=Meyer |first11=T |last12=Huang |first12=KW |last13=Plummer |first13=R |last14=Chee |first14=CE |last15=Spalding |first15=D |last16=Pai |first16=M |last17=Khan |first17=S |last18=Pinato |first18=DJ |last19=Sharma |first19=R |last20=Basu |first20=B |last21=Palmer |first21=D |last22=Ma |first22=YT |last23=Evans |first23=J |last24=Habib |first24=R |last25=Martirosyan |first25=A |last26=Elasri |first26=N |last27=Reynaud |first27=A |last28=Rossi |first28=JJ |last29=Cobbold |first29=M |last30=Habib |first30=NA |last31=Gabrilovich |first31=DI |title=Upregulation of C/EBPα Inhibits Suppressive Activity of Myeloid Cells and Potentiates Antitumor Response in Mice and Patients with Cancer. |journal=Clinical Cancer Research |date=1 November 2021 |volume=27 |issue=21 |pages=5961–5978 |doi=10.1158/1078-0432.CCR-21-0986 |pmid=34407972|pmc=8756351 }}
:* LHPP: saRNAs targeting LHPP have shown preclinical efficacy in HCC.{{cite journal | vauthors = Bi CQ, Kang T, Qian YK, Kang M, Zeng XH, Li LC | title = Upregulation of LHPP by saRNA inhibited hepatocellular cancer cell proliferation and xenograft tumor growth | journal = PLOS ONE | volume = 19 | issue = 3 | pages = 810–818 | date = March 2024 | pmid = 38489487 | pmc = 10941452 | doi = 10.1371/journal.pone.0299522 | doi-access = free | bibcode = 2024PLoSO..1999522B }}
:* PTPRO: saRNAs have been used to overcome trastuzumab resistance in HER2-positive breast cancer by reactivating PTPRO.{{cite journal | vauthors = Wang L, Lin Y, Yao Z, Babu N, Lin W, Chen C, Du L, Cai S, Pan Y, Xiong X, et al. | title = Targeting undruggable phosphatase overcomes trastuzumab resistance by inhibiting multi-oncogenic kinases | journal = Drug Resistance Updates | volume = 76 | pages = 101118 | date = September 2024 | issue = 6 | pmid = 38913624 | doi = 10.1016/j.drup.2024.101118 | pmc = 11195946 }}
:* CDH13 saRNAs have been used to upregulate CDH13 expression in CML cells overcoming imatinib-resistance{{cite journal | vauthors = Su R, Wen Z, Zhan X, Long Y, Wang X, Li C, Su Y, Fei J | title = Small RNA activation of CDH13 expression overcome BCR-ABL1-independent imatinib-resistance and their signaling pathway studies in chronic myeloid leukemia | journal = Cell Death & Disease | volume = 15 | issue = 9 | pages = 3910–3913 | date = September 2024 | pmid = 39008739 | pmc = 11405707 | doi = 10.1038/s41419-024-07006-9 }}
- Acute Lung Injury: saRNAs targeting CEBPA have shown potential in preclinical models of acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) by reducing inflammation.{{cite journal | vauthors = Zhang L, Chen S, Zheng Z, Lin Y, Wang C, Gong Y, Qin A, Su J, Tang S | title = Artificial Neutrophil-Mediated CEBPA-saRNA Delivery to Ameliorate ALI/ARDS | journal = ACS Applied Materials & Interfaces | volume = 16 | issue = 46 | pages = 51957–51969 | date = 2024-11-06 | pmid = 37930896 | doi = 10.1021/acsami.4c09022| pmc = 10627407 }}
- Cardiovascular Diseases: saRNAs have been used to activate genes like βII spectrin to improve cardiac function in preclinical models.{{cite journal | vauthors = Yang R, Ruan B, Wang R, Zhang X, Xing P, Li C, Zhang Y, Chang X, Song H, Zhang S, et al. | title = Cardiomyocyte betaII spectrin plays a critical role in maintaining cardiac function by regulating mitochondrial respiratory function | journal = Cardiovascular Research | volume = 120 | issue = 14 | pages = 1312–1326 | date = 2024-06-01 | pmid = 38747816 | doi = 10.1093/cvr/cvae116| pmc = 11376619 }}
- Metabolic Disorders: saRNAs targeting SIRT1 have shown potential for reversing metabolic syndrome in preclinical studies.{{cite journal |last1=Andrikakou |first1=P |last2=Reebye |first2=V |last3=Vasconcelos |first3=D |last4=Yoon |first4=S |last5=Voutila |first5=J |last6=George |first6=AJT |last7=Swiderski |first7=P |last8=Habib |first8=R |last9=Catley |first9=M |last10=Blakey |first10=D |last11=Habib |first11=NA |last12=Rossi |first12=JJ |last13=Huang |first13=KW |title=Enhancing SIRT1 Gene Expression Using Small Activating RNAs: A Novel Approach for Reversing Metabolic Syndrome. |journal=Nucleic Acid Therapeutics |date=December 2022 |volume=32 |issue=6 |pages=486–496 |doi=10.1089/nat.2021.0115 |pmid=35895511}}
- Proliferative Vitreoretinopathy (PVR): A saRNA designed to upregulate the p21 gene has shown therapeutic efficacy in a rabbit model of proliferative vitreoretinopathy.{{cite journal |last1=Zhang |first1=Q |last2=Guo |first2=Y |last3=Kang |first3=M |last4=Lin |first4=WH |last5=Wu |first5=JC |last6=Yu |first6=Y |last7=Li |first7=LC |last8=Sang |first8=A |title=p21CIP/WAF1 saRNA inhibits proliferative vitreoretinopathy in a rabbit model. |journal=PLOS ONE |date=2023 |volume=18 |issue=2 |pages=e0282063 |doi=10.1371/journal.pone.0282063 |doi-access=free |pmid=36821623|pmc=9949646 |bibcode=2023PLoSO..1882063Z }}
- Neurodegenerative Diseases: saRNAs have been explored for modulating gene expression in diseases like Alzheimer's disease, for example, targeting BACE2.{{cite journal | vauthors = Liu H, Chen S, Sun Q, Sha Q, Tang Y, Jia W, Chen L, Zhao J, Wang T, Sun X | title = Let-7c increases BACE2 expression by RNAa and decreases Abeta production | journal = American Journal of Translational Research | date = 2022 | volume = 14 | issue = 2 | pages = 899–908 | pmid = 35273693 | pmc = 8902526}}
== Clinical Progress ==
saRNA based therapeutics have advanced from preclinical studies to human clinical trials.
- MTL-CEBPA: Developed by MiNA Therapeutics, MTL-CEBPA is the first saRNA drug candidate to enter clinical trials. It targets the C/EBP-α gene. A Phase I trial in patients with advanced HCC showed an acceptable safety profile and anticancer efficacy. Phase II trials are ongoing (NCT04710641).
- RAG-01: Developed by Ractigen Therapeutics, RAG-01 is an saRNA designed to activate the p21 tumor suppressor gene. It has received FDA approval for Phase I trials for the treatment of non-muscle invasive bladder cancer (NMIBC). A Phase I trial is underway in Australia (NCT06351904).
== Challenges and Future Directions ==
While saRNAs hold significant therapeutic promise, challenges remain:
- Delivery: Efficient and targeted delivery to the nucleus of target cells remains a major hurdle. Advances in delivery technologies, such as improved lipid nanoparticles, novel conjugates and targeted extrahepatic delivery, are crucial.
- Off-target Effects: Ensuring sequence specificity and minimizing unintended effects on other genes is essential.
- Durability of Effect: While RNAa effects are generally more durable than RNAi, long-term efficacy and potential for repeated dosing need further investigation.
== See Also ==
== References ==
{{Reflist}}