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Tag: Nishikura

Learning How to Read the Book of Life

Research in the Gene Expression & Regulation Program at Wistar continues to reveal new knowledge on RNA and its functions to regulate how our genes are expressed and how that can go awry.

The advent of mRNA vaccines for COVID-19 — touted as the next-generation tool in vaccinology — brought RNA to the fore, giving popularity to this once less-publicized cousin of DNA.

In high school biology, we learned that our genes are the repositories of the blueprint to make all of our proteins. Our genes carry out most of the functions in our cells. RNA is the carrier of information from DNA to ribosomes — the machines that manufacture proteins.

The process of reading and executing the instruction book of life involves strict oversight and multiple levels of regulation to allow a relatively small number of genes to orchestrate all the functions of our body. Control of gene expression plays a critical role in determining what proteins are present in a cell and in what amounts at any given time.

It is becoming abundantly clear that this control process happens both during and after RNA transcription.

Wistar scientists have pioneered the study of RNA biology, discovering new RNA types and unraveling some of the mechanisms that modify RNA to regulate its functions for gene expression. Following along that path, labs in the Gene Expression and Regulation Program continue to delve deep into the RNA world and make exciting discoveries related to RNA structure and functions.

R-LOOPS: Friend-Foes

Dr. Kavitha Sarma, assistant professor, focuses on particular nucleic acid structures called R-loops that contain both DNA and RNA and form during transcription, the first step of gene expression.

In our DNA book, consider genes as the individual words and nucleotides as the letters that make up those words. When a DNA template is “transcribed” into messenger RNA (mRNA), the sequence of letters that form each gene gets “read” and copied into an RNA molecule that will leave the nucleus and travel to the cytoplasm, where words will be read by ribosomes to provide instructions for making proteins.

Sometimes during transcription, the newly synthesized RNA molecule sticks to its template DNA strand, forming a stable DNA/RNA hybrid that appears like a loop when visualized by electron microscopy, hence the name R-loop.

This is a normal occurrence — R-loops are constantly formed and removed throughout the genome and their presence can be beneficial for transcriptional regulation. However, accumulation of R-loops can cause DNA damage, chromosome rearrangements and genomic instability and underlie a host of diseases from cancer to neurodegenerative disorders and possibly autism.

The Sarma lab is interested in R-loops for their potential in causing disease and in serving as new therapeutic targets. They have been busy developing new, improved techniques to detect R-loops to study the contributions of these structures in gene regulation and the consequences of their accumulation in the cell1.

Thanks to these technological advances, Dr. Sarma and her colleagues were able to identify new factors that regulate R-loops and are now closing in on their function in glioblastoma and colon cancer.

The lab received funding from the W.W. Smith Charitable Trust to study the role of R-loops in brain cancer and with support from the Basser Center for BRCA and the Margaret Q. Landenberger Research Foundation they are dissecting the correlation between R-loop formation and BRCA1/2 gene mutations in breast and ovarian cancer to eventually use R-loops for novel diagnostic and therapeutic applications. The Simons Foundation supports the lab’s work elucidating the consequences of unregulated R-loops in autism spectrum disorders.


Dr. Kazuko Nishikura, professor, has published a new function of R-loops2 in preserving the integrity of our chromosome ends — the telomeres.

Dr. Nishikura has been a pillar of Wistar science for almost four decades with a career overlapping with the rise and expansion of the RNA biology field. She was one of the first to characterize a process called RNA editing and its multiple functions in the cell, and to discover the enzyme ADAR1 that is responsible for it.

RNA editing changes one or more letters in RNA “words,” allowing cells to make discrete modifications to an RNA molecule. RNA editing is a good example of how our cells make the most of their genes and create different protein products from a single gene by slightly modifying the RNA sequence.

With support from grants from the National Institutes of Health and Emerson Collective, the Nishikura lab recently showed that ADAR1 helps the cells resolve R-loops formed at the chromosome ends and prevents their accumulation by facilitating degradation of the RNA strand.

Nishikura and colleagues found that depletion of a particular form of the ADAR1 protein leads to extensive telomeric DNA damage and arrested proliferation specifically in cancer cells, indicating this process as a new target for cancer therapy.

ALTERNATIVE POLYADENYLATION: Tell Me What Your APA Is and I Will Tell You Where to Go

An important level of mRNA regulation involves modifying its structure, especially at the tail end of the sequence, termed 3’ end. A process called polyadenylation adds a stretch of specific nucleotides to protein-coding mRNAs to regulate their stability, transportation from nucleus to cytoplasm and translation into proteins.

Dr. Bin Tian, professor, and his lab study this process to understand regulatory mechanisms and to identify new drug targets. They have contributed important knowledge on polyadenylation in normal and diseased conditions, including the discovery that alternative polyadenylation (APA) is widespread across genes.

This is a dynamic mechanism of gene regulation that generates different 3′ ends in mRNA molecules, resulting in multiple mRNAs from the same gene, which scientists call isoforms.

The lab’s latest research is uncovering the role APA plays in facilitating protein production in certain sites within the cell where those proteins are most needed.

When mRNAs leave the nucleus and move to the cytoplasm, they need to be properly directed to reach the ribosomes and be translated into proteins. Although too small to be seen with the naked eye, a cell is a huge space for something as tiny as an mRNA molecule that has to find its way. Imagine finding yourself in a baseball stadium and not knowing how to get to your seat.

The Tian lab discovered that some mRNAs possess specific properties in their sequence and structure that enable them to associate with the endoplasmic reticulum (ER), a network of tubes that build, package and transport proteins and where a large fraction of ribosomes in the cell are located3.

These mRNAs tend to encode for proteins involved in cell signaling, the process that allows the cells to communicate with neighboring cells by sending, receiving and processing signals to respond to changes in their environment.

Dr. Tian and his team hypothesize that association with the ER anchors certain mRNA isoforms in specific cellular locations where important signaling events happen, making the whole process more efficient. According to this model, the ER would serve a new function as a scaffold to keep proteins at hand where they are needed, representing a platform that provides venues for signaling events to happen quickly and effectively.

The lab also creates computer-based data mining tools to analyze APA using large data sets, such as those from The Cancer Genome Atlas (TCGA) program.

The extraordinary biological complexity of human life is a reflection of the many sophisticated ways in which gene expression can be fine-tuned.

The cutting-edge science underway at Wistar pushes the limits of RNA research to advance our understanding of how the human genome is decoded, how the messengers of genetic information are guided, and how accidental mistakes that happen while reading and interpreting the DNA book can be fixed, all of which may enable researchers to develop novel and more precise ways to treat diseases.

1 A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide, Elife 2021
2 ADAR1 RNA editing enzyme regulates R-loop formation and genome stability at telomeres in cancer cells, Nature Communications 2021
3 Alternative 3’UTRs play a widespread role in translation-independent mRNA association with endoplasmic reticulum, Cell Reports 2021

RNA Editing Protein ADAR1 Protects Telomeres and Supports Proliferation in Cancer Cells

PHILADELPHIA — (March 12, 2021) — Scientists at The Wistar Institute identified a new function of ADAR1, a protein responsible for RNA editing, discovering that the ADAR1p110 isoform regulates genome stability at chromosome ends and is required for continued proliferation of cancer cells. These findings, reported in Nature Communications, reveal an additional oncogenic function of ADAR1 and reaffirm its potential as a therapeutic target in cancer.

The lab of Kazuko Nishikura, Ph.D., professor in the Gene Expression & Regulation Program of The Wistar Institute Cancer Center, was one of the first to discover ADAR1 in mammalian cells and to characterize the process of RNA editing and its multiple functions in the cell.

Similar to changing one or more letters in a written word, RNA editing allows cells to make discrete modifications to single nucleotides within an RNA molecule. This process can affect RNA metabolism and how it is translated into proteins and has implications for neurological and developmental disorders and antitumor immunity.

There are two forms of the ADAR1 protein, ADAR1p150 and ADAR1p110. While the RNA editing role of the former, located in the cytoplasm, has been extensively characterized, the function of the nuclear ADAR1p110 isoform remained elusive.

“We discovered that in the nucleus, ADAR1p110 oversees a similar mechanism to ADAR1p150, the better-known cytoplasmic variant, but the editing process in this case targets particular nucleic acid structures called R-loops when formed at the chromosome ends,” said Nishikura. “Through this function, ADAR1p110 seems to be essential for cancer cell proliferation.”

R-loops form during gene transcription when, instead of dissociating from its template DNA strand, the newly synthesized RNA remains attached to it, leading to a stable DNA/RNA hybrid. While these structures can be beneficial for transcriptional regulation in certain conditions, accumulation of R-loops can cause DNA damage, chromosome rearrangements and genomic instability and is linked to neurological disorders and cancer.

Nishikura and colleagues found that ADAR1p110 helps the cells resolve R-loops and prevent their accumulation by editing both the DNA and the RNA strands involved in the structure and facilitating degradation of the RNA strand by the RNase H2 enzyme.

Notably, researchers found that ADAR1p110 depletion results in accumulation of R-loops at the chromosome ends, indicating that ADAR1p110 acts on R-loops formed in the telomeric regions and is required to preserve telomere stability.

Telomeres serve as an internal clock that tells normal cells when it’s time to stop proliferating. Just like the plastic coating on the tips of shoelaces, telomeres protect chromosome ends from the loss of genetic material at each cell division, by their progressive shortening eventually triggers growth arrest or cell death.

Cancer cells bypass this mechanism to become immortal. Researchers found that ADAR1p110 depletion leads to extensive telomeric DNA damage and arrested proliferation specifically in cancer cells.

“It has recently been suggested ADAR1 inhibitors could potentiate tumor response to immunotherapy by interfering with certain cytoplasmic ADAR1p150 functions,” said Nishikura. “Based on our findings on the role of nuclear ADAR1p110 in maintaining telomere stability in cancer cells, we predict that ADAR1 inhibitors would be very effective anticancer therapeutics by interfering with two different and independent pro-oncogenic ADAR1functions exerted by the two isoforms.”

Co-authors: Yusuke Shiromoto*, Masayuki Sakurai*, Moeko Minakuchi*, and Kentaro Ariyoshi from The Wistar Institute. *Co-first authors.

Work supported by: National Institutes of Health (NIH) grants GM040536, CA175058, and GM130716; additional support was provided by the Emerson Collective, the Japan Society for the Promotion of Science (JSPS), and the Uehara Memorial Foundation. Core support for The Wistar Institute was provided by the Cancer Center Support Grant P30CA010815.

Publication information: ADAR1 RNA editing enzyme regulates R-loop formation and genome stability at telomeres in cancer cells, Nature Communications, 2021. Online publication.


The Wistar Institute is an international leader in biomedical research with special expertise in cancer research and vaccine development. Founded in 1892 as the first independent nonprofit biomedical research institute in the United States, Wistar has held the prestigious Cancer Center designation from the National Cancer Institute since 1972. The Institute works actively to ensure that research advances move from the laboratory to the clinic as quickly as possible.

Dr. Kazuko Nishikura: the RNA Explorer

Nishikura has been a pillar of Wistar science for the past 37 years with a career overlapping with the rise and expansion of the RNA biology field, which explores the alternative functions of RNA in the cell, besides carrying the genetic information from DNA to proteins. Her foray into research happened at a time when scientists were only beginning to understand the function of RNA and its molecular mechanisms; she would end up contributing fundamental knowledge to the field.

Nishikura discovered the process of RNA editing, an important mechanism of genetic regulation. Her scientific journey has taken her on to explore several aspects and functions of RNA editing and its interplay with other molecular pathways.

Passion for Science Sparks

Born and educated in Japan, Nishikura was encouraged by her high school science teacher who recognized her scientific talent. She obtained her PhD at Osaka University and pursued postdoctoral training at the Medical Research Council (MRC) Laboratory of Molecular Biology in Cambridge, England, and Stanford University, two of the birthplaces of molecular biology.

Photos of those times hang from the wall in her office, memories of a cherished past, and portray some very famous scientists who left their mark in history and in Nishikura’s career: Nobel Prize winners Max Perutz, Ph.D., who discovered the structure of hemoglobin and was her doctoral thesis advisor, and John Gurdon, Ph.D., whose work on reprogramming mature cells to stem cells laid the foundation for major advances in cloning and stem cell research.

Nishikura spent two very formative years in his lab in Cambridge as a postdoctoral fellow, before moving to Stanford to work with another outstanding mentor, Roger Kornberg, Ph.D., also a Nobel laureate, who described how genetic information is passed from DNA to RNA.

Training with great minds of the time was the fertile scientific soil of her education as a scientist. Nishikura absorbed their intellectual curiosity and learned how to properly follow the scientific method as part of her training. “I consider myself very lucky for having had a chance to observe in person how those big scientists addressed important biological questions,” she said.

An Expanding Field of RNA Biology

RNA biology became Nishikura’s main research interest, which she has continued to cultivate throughout her career. It was a nascent field, rapidly expanding with fundamental discoveries, but so many questions were still unanswered.

However, at the time when she joined Wistar as an assistant professor, the Institute was mainly invested in cancer biology. Oncogenes were protagonists on the cancer research scene and Wistar scientists were pursuing seminal studies on chromosomal alterations, demonstrating their causative role in leukemia.

Nishikura was drawn into this line of investigation until the end of the 80s, when a paper by a former MRC colleague came out and described a mysterious biological activity that appeared to unwind double stranded RNA, which immediately caught Nishikura’s attention.

“I couldn’t resist looking into it,” she said. “For some time it was my pet project; no study section would believe in it and it was very risky too.”

That didn’t discourage her, and she kept pursuing the investigation with the resources she could spare from her other projects on oncogenes, which had much more success in securing funds for her lab.

“When you find something unusual you have to follow it,” said Nishikura. “Pursuing something unique will make you stand out from the crowd.”

This has been her favorite piece of advice for the young scientists training in her lab. “It’s sad and unfortunate that the current climate of high competition for funding pushes young independent investigators away from basic science. They hesitate to embark in risky projects, but these are often the source of breakthroughs.”

Nishikura considers herself fortunate to have had big opportunities that gave her the resources and the support to both follow her scientific interest and, at the same time, establish herself as a successful scientist, even though as a young investigator she wasn’t particularly focused on cultivating her academic career.

“I was only after my scientific questions and was content to just do my work and search for the answers,” she said. “In retrospect, I was probably naïve, even a little foolish. I didn’t worry much about problems and setbacks. This simplified my decision-making process and helped me stick to it.”

Thanks to her determination, Nishikura was able to secure her first grant on RNA editing when she found the gene responsible for the process. The rest is history.

“In the early 90s, RNA editing was a very new concept, with only two or three labs chasing it,” said Nishikura. “Today, it’s a large field with dozens of labs. It’s very satisfying to look back and see that I contributed to opening that path.”

The institutes where she trained put her on the right track and equipped her with a successful approach to science, then Wistar was the ideal landing ground to grow and establish herself. “Being at Wistar is a great asset, because of our collaborative environment and vocation of always being at the forefront of new trends and technologies,” said Nishikura. “It has helped substantially when I came across new themes and needed support to acquire different expertise or catch up with new develoments.”

Nishikura’s passion and curiosity are unchanged and she still finds great inspiration in science. In 2017, she successfully renewed a large federal grant that had continuously supported her work on RNA editing for 26 years, with a proposal to investigate a novel function she had recently discovered.

Outside the Lab

Meanwhile, when not in her lab, Nishikura cultivates other “side projects.”

She enjoys traveling the world, especially to places that are interesting from a biological point of view. She recently visited the Galapagos Islands and Antarctica and went on a safari in Africa. The exploration component of such trips resonates with her scientific mind.

“I love going to music concerts too,” she said. “Whenever I go to Europe for conferences, I try to catch the opera or a classic music concert.” That’s not to say that she doesn’t enjoy some good classic rock. “I’ve recently seen Eric Clapton, the Rolling Stones and Paul McCartney.”

At home, Nishikura is an experienced cook, specializing in many types of cuisine. She enjoys cooking for friends and neighbors. “I like cooking because I’m a foodie and because it takes method and creativity, just like science.”

These days, she’s been making a tasty and healthy beet salad. She will gladly share the recipe.

In the photo, Dr. Nishikura with the group of John Gurdon at the MRC Laboratory of Molecular Biology at the University of Cambridge, England. Courtesy of Dr. Nishikura.