The Nishikura Laboratory
The Nishikura laboratory explores the phenomenon of RNA editing, which regulates expression of certain gene products by changing the sequence context of mRNAs. One type of RNA editing involves the conversion of adenosine residues into inosine specifically in double-stranded RNA (dsRNA). This A-to-I RNA editing is catalyzed by members of the ADAR (adenosine deaminases acting on RNA) gene family, discovered in the lab.
Moeko Minakuchi, Ph.D.
The research focus of the laboratory is to better understand the functions of ADAR as well as cellular processes regulated by A-to-I RNA editing and to identify possible new therapies based on these processes.
Two ADAR1 isoforms, p150 and p110, are known. ADAR1p150 is mostly located in the cytoplasm, whereas ADAR1p110 mainly localizes in the nucleus. The cytoplasmic ADAR1p150 edits 3’UTR dsRNAs and regulates the dsRNA sensing mechanism mediated by MDA5-MAVS-IFN signaling. In contrast, the biological functions of the nuclear ADAR1p110 have remained mostly unknown.
The Nishikura laboratory found that ADAR1p110 plays an important role in the stress response mechanism. This isoform is phosphorylated at five sites in response to stress, such as UV irradiation and heat shock, by p38-activated MAP kinases, MSK1 and MSK2. Phosphorylation increases the binding affinity of ADAR1p110 to the nuclear exporter protein Xpo5, resulting in translocation of ADAR1p110 to the cytoplasm. Approximately 500 anti-apoptotic gene transcripts containing 3’UTR dsRNA structures, primarily made from inverted Alu repeats, are protected by the cytoplasmic ADAR1p110 from Staufen1-mediated mRNA decay. These studies thus revealed a new function of ADAR1p110 that suppresses apoptosis of stressed cells.
In collaboration with Wistar’s Rugang Zhang laboratory, the Nishikura laboratory co-discovered that ADAR1p110 suppresses cell senescence by promoting the expression of SIRT1, a major suppressor of senescence. ADAR1p110 phosphorylated by MAP kinases (see above) prevents HuR mediated degradation of SIRT1 mRNAs, independently of its A-to-I RNA editing activity, via its dsRNA binding activity.
Nascent RNA usually dissociates from its template DNA strand but occasionally the newly transcribed RNA forms a stable RNA:DNA hybrid, leaving the sense DNA in a single-stranded form. This structure is called an R-loop and causes abortive transcription and instability of the genome. R-loop accumulation leads to human diseases including cancer. We recently discovered that ADAR1p110 regulates R-loop formation and genome stability at telomeres in cancer cells carrying non-canonical variants of telomeric repeats. ADAR1p110 edits the A-C mismatches within RNA:DNA hybrids formed between canonical and non-canonical variant repeats. Editing of A-C mismatches to I:C matched pairs facilitates resolution of telomeric R-loops by RNase H2 (Fig. 1).
Fig. 1. ADAR1p110 together with RNase H2 resolves telomeric R-loops in non-ALT cancer cells. Telomeric variant repeats cause formation of RNA:DNA hybrids containing A-C mismatches. In telomerase-positive cancer cells, ADAR1p110 edits these A-C mismatches to I:C matched base pairs, which is essential for removal of the RNA strands by RNase H2 during G2-M. In the absence of ADAR1p110, cancer cells die due to genome instability caused by accumulation of telomeric R-loops and mitotic arrest.
The newly discovered function of ADAR1p110 in suppressing telomeric R-loops is essential for continued proliferation of telomerase-reactivated cancer cells, revealing the pro-oncogenic nature of ADAR1p110 and identifying ADAR1 as a promising therapeutic target in telomerase-positive cancers, which represent 70-80% of all cancers.
In addition to the pro-oncogenig role of ADAR1p110 discovered by the lab, Nick Haining’s group identified ADAR1p150 as a critical factor that regulates immunotherapy resistance. They found that ADAR1-mediated A-to-I editing of Alu dsRNAs prevents them from activating inflammatory responses in tumors via MDA5-MAVS-IFN signaling, which in turn dampens responsiveness to immunotherapy (Fig. 2). Thus, ADAR1 inhibitors are anticipated to restore responsiveness to immunotherapy and increase the success rate of the PD-1 based immunotherapy.
Fig. 2. ADAR1p150 suppresses cancer responsiveness to immune checkpoint blockade by hyper-editing 3’UTR Alu dsRNAs.Long Alu dsRNAs present in 3’UTRs of certain mRNAs that remain unedited in the absence of cytoplasmic ADAR1p150 have been proposed as endogenous inducers of the MDA5-MAVS-IFN signaling pathway. IFNs and inflammatory conditions induced by loss of ADAR1 and dsRNA editing activities play important roles in cancer responsiveness to immune checkpoint blockade (upper panel). Hyper-editing of these Alu dsRNAs by ADAR1p150 in the cytoplasm dampens MDA5-MAVS-IFN signaling and thereby contributes to development of immunotherapy resistance in cancer patients (bottom panel). ADAR1 inhibitors are expected to potentiate the cancer responsiveness to immunotherapy.
ADAR1 inhibitors are expected to be very effective therapeutics for cancer treatment because they will interfere with two different pro-oncogenic ADAR1 functions: suppression of MDA5-MAVS-IFN signaling by the cytoplasmic ADAR1p150 and maintenance of telomere stability in telomerase-reactivated cancer cells by the nuclear ADAR1p110. ADAR1 inhibitors are likely to initiate a major change in the treatment of patients with telomerase-reactivated cancers and patients who have developed resistance to immunotherapy.
The Nishikura laboratory recently developed a high-throughput molecular screening strategy and identified ADAR1 inhibitor candidate compounds. They are currently being further evaluated for their ADAR1 inhibitory effects in vitro and in vivo in various cancer cell lines and for their potential for cancer therapeutics in mouse model systems.
Nishikura Lab in the News
ADAR1 Downregulation by Autophagy Drives Senescence Independently of RNA Editing by Enhancing p16INK4a Levels.
Hao, X., Shiromoto, Y., Sakurai, M., Towers, M., Zhang, Q., Wu, S., Havas, A., Wang, L., Berger, S., Adams, P.D., et al. “ADAR1 Downregulation by Autophagy Drives Senescence Independently of RNA Editing by Enhancing p16INK4a Levels.” Nat Cell Biol. 2022 Aug;24(8):1202-1210. doi: 10.1038/s41556-022-00959-z. Epub 2022 Jul 18.
ADAR1 RNA Editing Enzyme Regulates R-loop Formation And Genome Stability At Telomeres In Cancer Cells.
Shiromoto, Y., Sakurai, M., Minakuchi, M., Ariyoshi, K., and Nishikura, K. ”ADAR1 RNA Editing Enzyme Regulates R-loop Formation And Genome Stability At Telomeres In Cancer Cells.” Nat Commun. 2021 Mar 12;12(1):1654. doi: 10.1038/s41467-021-21921-x.
Tan, M.H., Li, Q., Shanmugam, R., Piskol, R., Kohler, J., Young, A.N., Liu, K.I., Zhang, R., Ramaswami, G., Ariyoshi, K., et al. “Dynamic landscape and regulation of RNA editing in mammals.” Nature. 2017 Oct 11;550(7675):249-254. doi: 10.1038/nature24041.
Sakurai, M., Shiromoto, Y., Ota, H., Song, C., Kossenkov, A.V., Wickramasinghe, J., Showe, L.C., Skordalakes, E., Tang, H.Y., Speicher, D.W., et al. ”ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay.” Nat Struct Mol Biol. 2017 Jun;24(6):534-543. doi: 10.1038/nsmb.3403. Epub 2017 Apr 24.
Song, C., Sakurai, M., Shiromoto, Y., Nishikura, K. ”Functions of the RNA Editing Enzyme ADAR1 and Their Relevance to Human Diseases.” Genes (Basel). 2016 Dec 17;7(12). pii: E129. doi: 10.3390/genes7120129.