Skip to Main Content

Kazuko Nishikura, Ph.D.

Kazuko Nishikura, Ph.D.

Laboratory

The Nishikura Laboratory

Contact

215-898-3828
kazuko@wistar.org

Professor, Gene Expression & Regulation Program, The Wistar Institute Cancer Center

About the Scientist

Nishikura studies the process of RNA editing and has made pioneering strides in the understanding of how our cells utilize RNA to control gene expression and protein synthesis and how the malfunction of this process can lead to disease. She discovered and characterized a family of enzymes called ADAR, which are responsible for editing the RNA transcribed from DNA.

Nishikura received both a bachelor’s and master’s degree in biochemistry from Kanazawa University, Japan, and obtained her Ph.D. in medical science from Osaka University, Japan, performing much of her thesis work at the Medical Research Council Laboratory of Molecular Biology (LMB) in Cambridge, England. She returned to the LMB for her first postdoctoral fellowship before obtaining a second fellowship at Stanford University. Nishikura first joined The Wistar Institute in 1982 and became a full professor in 1995.

View Publications

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.

Staff

Associate Staff Scientist

Yusuke Shiromoto, Ph.D.

Postdoctoral Fellow

Moeko Minakuchi, Ph.D.

Undergraduate Student

Brian Song

Visiting Research Associate

YuChen Hwang, Ph.D.

Research

The research focus of the laboratory is to better understand the functions of ADAR and the 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. 

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). 


Figure 1 - Kazuko_final

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.  


Figure 2 - Kazuko_final

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.

Selected Publications

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.

Shiromoto, Y., Sakurai, M., Qu, H., Kossenkov, A., Nishikura, K. "Processing of Alu small RNAs by DICER/ADAR1 complexes and their RNAi targets." RNA. 2020 Aug 17;rna.076745.120. doi: 10.1261/rna.076745.120. 

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.

View Additional Publications