Circular RNA reveals tumor
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Circular RNA reveals tumor progression & Cancer Identification 

Mona Batish, molecular biologist, University of Delaware and collaborators at Harvard Medical School and University of California, Los Angeles, have now identified a new circular ribonucleic acid (RNA) that increases the tumor activity in soft tissues and connective tissue tumors.

Finding this new genetic unit circular RNA has the potential to advance understanding of the genetics of cancer and how cancer is identified and treated.

Scientists recently reported their study findings in a new paper in a Nature Journal, Cell Research. Batish was a co-author on the research team that included Jlenia Guarnerio who is the paper’s lead author and assistant professor of biomedical science at UCLA and at Pier Paolo Pandolfi, and professor of medicine and pathology at Harvard Medical School; and his colleagues from Harvard Medical School’s Beth Israel Deaconess Medical Center, Rutgers University and Aalborg University Hospital in Denmark.

RNA is a single-stranded molecule which is made by the DNA in our bodies. The messenger RNA acts as a courier i.e, transports instructions from the DNA code to protein-making machines and thus dictating the compositions of proteins in a cell. There are other types of RNA, which do not

carry any code for proteins but perform other important functions in cells. All these are known as non-coding RNAs.

One f the new class of non-coding RNA, called circular RNA, was discovered in the 1970s. Circular RNA or circRNA was initially thought to be a virus. This was because most RNA molecules are linear,(meaning that their genetic sequence always moves in a forward direction). In contrast to this, circRNA is circular as its name indicates, even though it shares the same genetic sequence as linear RNA.

Batish who is an assistant professor of medical and molecular sciences in UD’s College of Health Sciences said that under certain conditions, RNA processing systems can get tricked into thinking they are supposed to join the ends. When this error occurs, it creates a backward loop in the RNA’s genetic sequences and then keeps on going — just like when you get a kink in the middle of a necklace. Now, this loop separates off and persists as a circular RNA inside the cell.

Formerly, scientists thought this error, a process is known as back splicing, did not mean anything. When the genome sequencing came about in the 1990s, researchers started finding circular RNA in brain tissue and other tissues. By 2014, scientists realized that circRNA was important. Today there is a whole field looking at circRNA as a biomarker for disease, especially in cancers.

The role of circular RNA that reveals tumor progression has been understudied according to Batish.

In this research paper, the scientists describe a new circular RNA, that reveals tumor progression, is generated by a gene called Zbtb7a which is found in soft tissue tumors, like mesenchymal tumors. In circ RNA’s linear form, this makes a tumor-suppressing protein which stops the growth of cancer, according to the previous study out of Pandolfi’s Harvard research lab. Once the same RNA makes a circRNA, the circular RNA works independently to make the tumor more active, effectively silencing the tumor-suppressing proteins.

This is the first time that this type of antagonistic, tumor-promoting role of circular RNA has been shown in connection with linear RNA with the same gene sequence, according to Batish.

Both the RNA strands should perform the same function, theoretically, because they originate from the same genetic material, but they don’t.

In order to validate their findings, the scientists needed a way to tell whether an RNA was linear or circular since they share the same genetic code. This is where Batish’s expertise came in.

Batish said that to see an RNA we will have to label it, But, if we label it with something that is sequence-specific, it becomes so hard to tell if it’s linear or circular because their genetic code looks the same.

Batish had previously worked on probes that can light up each RNA in an individual cell as a single bright spot under a fluorescence microscope. This was to understand how biological systems operate on a cellular level. She adapted this method of using probes for distinguishing circRNA from its linear RNA counterpart from the same gene using a color combination method.

She added that essentially, it is like creating a pattern of beads on a necklace. Imagine the RNA we are working with contains both red and green beads. Suppose circular RNA is a closed circle of only green beads, so we add probes for both red and green beads, after which we image them under a fluorescence microscope. If they see a signal for both red and green at the same spot, which appears as yellow (a combination of green and red color) in the sample, we know that it is a linear RNA. If it doesn’t have any red, it must be a circular RNA.

This method of labeling allowed researchers to simultaneously visualize linear and circular RNA within a single cell.

She said that this is the first time that the team has realized that RNA with the same genetic sequences can sometimes perform two roles, in this case, both as a cancer suppressor and also a cancer promoter and that this change in role occurs at the RNA-level. She explained that the identification of these new genetic units opens up new opportunities to understand both the genetics of cancer and also the role of circRNA in cancer biology.

As a unique junction is created where the ends of circular RNA come together, Batish said this may be able to develop treatment protocols to uniquely target the circRNA, but leave the linear RNA alone. This could provide ways to target treatment to stop the circRNA from turning off the cancer-suppressing effect in the body.

While this study focused on connective and soft tissue tumors or diseases like mesenchymal tumors, she said the technique developed in her laboratory could be used on any kind of cancer, because every cancer has circular RNA.

Batish also has some plans to conduct an experiment to see if what they have observed at the cellular level occurs in tissue samples. By studying this expression in both healthy and diseased tissue, she said, would help her in getting a better understanding about the biosignature of circular RNA.

She said that if we can show that it persists in samples that are left out and which are not treated properly, that has real value. This is because circRNA is differentially expressed, meaning the lungs will express different circular RNA than the brain and other tissues or organs.

Batish wants to study whether circRNA found in tumors is present in cell signaling molecules known as the extracellular vesicles. She describes these extracellular vesicles as letters, FedEx packages that cells put together and delivers to neighboring cells to tell them what is going on nearby.

Since every cancer starts within one single cell, she wants to explore the role circRNA may play in this messaging process. This might provide pathways to understand how cell to cell communications are used by tumor cells.

Batish also wants to develop tools to enable live imaging of circRNA in cells. By working in collaboration with Jeff Caplan who is the director of the BioImaging Center at the Delaware Biotechnology Institute, she is exploring ways to add a tracking device of sorts into the cells that would allow them to follow the signal in a real-time as circRNA is formed.

The study on new circular RNA that reveals tumor activity would be really groundbreaking research if we can do it, said Batish.

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Ria Roy completed her Post Grad degree at the Visvesvaraya Technological University. She has a great grounding in the skills, including technical, analytical and research skills. She is a motivated life science professional with experience of working in famous research institutes