Skip to main content

Tag: Nishikura

The Wistar Institute’s Dr. Kazuko Nishikura Launches Preclinical Testing of New Melanoma Immunotherapy

Written by The Wistar Institute on . Posted in Featured News.

Melanoma Research Foundation Grant Supports Preclinical Research

Wistar professor Kazuko Nishikura, Ph.D., has led the way in foundational biomedical research on RNA for decades. Her laboratory discovered the role genes in the ADAR family play in editing RNA. A new grant from the Melanoma Research Foundation supports Dr. Nishikura’s approach to a new immunotherapy for melanoma.

What problem does your project aim to solve?

We want to improve cancer immunotherapy, a class of cancer treatment that marshals the immune system against tumors. With funding from the Melanoma Research Foundation, we want to overcome resistance to immunotherapy in melanoma, which has posed a challenge for researchers and treatment providers.

Because cancers like melanoma develop resistance to immunotherapy through adaptive mutations, only about one in five patients receives the benefit of treatment. My hope for this project is that our approach will prevent resistance to immunotherapy and expand the potential benefits of treatment to more patients. In this case, we aim to improve immune therapy response in a melanoma model, but hopefully, this method will work for other immunotherapy-resistant cancers as well.

Can you explain your lab’s research?

My lab focuses on the role of the A-to-I RNA editing process in regulating the immune system, which is overseen by the ADAR1 gene that my lab discovered. The A-to-I RNA editing that ADAR1 causes is critical to our approach to cancer immunotherapy.

How we get from RNA editing to a new cancer therapy is a little complicated, so let’s start with the basics. RNA, unlike DNA, usually has just one strand. Instead of DNA’s double helix, single-stranded RNA is more or less a line, with the sugar molecules A, C, G, and U studded along its length.

But even though most of the RNA that our body makes is single-stranded, some is double-stranded, which we call dsRNA — and that can pose a problem because dsRNA triggers the immune system.

Even though the dsRNA we produce naturally is harmless, the immune system mounts a response against dsRNA because so many viruses are based on dsRNA. So the immune system needs a way to distinguish between viral dsRNA, which poses a threat, and naturally occurring dsRNA, which does not.

When our bodies make dsRNA, the ADAR1 gene kicks off A-to-I RNA editing, which swaps the A molecule in the dsRNA for an I. That way, the immune system has a signal that functions like a security badge. If a piece of dsRNA has A’s instead of I’s, then the immune system triggers a response.

How does your research on RNA editing help in cancer immunotherapy?

Our fundamental idea is that we can stop A-to-I RNA editing in and around tumors as a way of setting off the immune system’s alarms. By injecting our drug candidate in models of melanoma tumors, we anticipate that our molecule will prevent treatment resistance and allow immunotherapy to destroy the tumor.

At the most basic level, it works like this: we shut off ADAR1 in and around the tumor; dsRNAs in that area don’t get their security badges; the immune system’s alarms are triggered in and around the tumor; and the immune system attacks the tumor.

We’ll test our molecule’s ability to fight melanoma by disabling A-to-I RNA editing, which is exciting because this is the first small-molecule ADAR1 inhibitor molecule that anyone has identified, and from our preliminary testing, it seems to work well. With this melanoma project, I anticipate an exciting proof-of-concept for our drug candidate.

What are your hopes for the future of your molecule and its use in cancer treatment?

I’ve been at this work for quite a long time; I discovered the ADAR A-to-I editing mechanism back in 1989. Finally, after decades of foundational research, my lab has advanced our work to a point where it’s ready to be tested as a possible cancer therapy.

People ask me, ‘Kazuko, are you going to start a company?’ and I tell them, ‘What do you think? I’m almost ready to retire!’ No, I’m interested in doing the preclinical testing that will hopefully prepare our molecule for the next stage. It’s my job to make sure that it’s ready.

We scientists are driven by that search for the new; we want to discover something nobody else has found. I’ve done that, and it looks like my curiosity has led me to something that will help advance human health. And that’s a very satisfying experience.

Learning How to Read the Book of Life

Written by The Wistar Institute on . Posted in Featured News.

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.

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.

EDITING RNA TO RESOLVE R-LOOPS

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

Dr. Kazuko Nishikura

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

Written by The Wistar Institute on . Posted in Press Releases.

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. wistar.org.