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Research team awarded $9 million to study extracellular RNA in colorectal cancer

Apr. 9, 2020, 10:52 AM

The extracellular RNA in colorectal cancer team includes, from left, Jeffrey Franklin, PhD, Yu Shyr, PhD, Qi Liu, PhD, Alissa Weaver, MD, PhD, James Higginbotham, PhD, and James Patton, PhD. Not pictured: Robert Coffey, MD, Kasey Vickers, PhD, and John Karijolich, PhD. (photo taken before social distancing)
The extracellular RNA in colorectal cancer team includes, from left, Jeffrey Franklin, PhD, Yu Shyr, PhD, Qi Liu, PhD, Alissa Weaver, MD, PhD, James Higginbotham, PhD, and James Patton, PhD. Not pictured: Robert Coffey, MD, Kasey Vickers, PhD, and John Karijolich, PhD. (photo by Erin O. Smith taken before social distancing).

by Leigh MacMillan

A multidisciplinary team of investigators at Vanderbilt University and Vanderbilt University Medical Center has received a program project grant from the National Cancer Institute to explore extracellular RNA in colorectal cancer.

The five-year, $9 million award will support multiple projects that aim to define fundamental biological principles about extracellular RNA signaling and the development and aggressiveness of colorectal cancer, the second leading cause of cancer death in the United States.

RNA (ribonucleic acid) has historically been understood to function inside cells, where it is primarily involved in protein production. About 10 years ago, researchers discovered RNA inside small membrane “packages” — extracellular vesicles — being shipped out of cells.

“It was already known that cells released vesicles, but it wasn’t known what the vesicles did or if they were functional. The finding that these vesicles contained RNAs — and the idea that they might change the epigenetic phenotype and gene expression profiles of recipient cells — really captured researchers’ imaginations and brought a lot of new investigators into the extracellular vesicle field,” said Alissa Weaver, MD, PhD, Cornelius Vanderbilt Chair and Professor of Cell and Developmental Biology and Pathology, Microbiology and Immunology.

“We know that extracellular vesicles are a major part of the tumor microenvironment and are involved in all aspects of tumor development and metastasis,” said Weaver, principal investigator of the new program project grant. “Our goal is to use colorectal cancer as a model to understand how cells make vesicles that contain RNA and how these vesicles get into recipient cells and change cellular functions. We want to define the ‘rules of the game’ for extracellular RNA communication.”

Many of the investigators involved in the current program have been collaborating on the study of extracellular RNA for more than five years.

They were part of the Extracellular RNA Communication Consortium (ERCC), which at Vanderbilt was led by Robert Coffey, MD, professor of Medicine and Cell and Developmental Biology.

As part of the ERCC, the researchers studied how KRAS mutations affected the formation of extracellular vesicles in colorectal cancer and their RNA and RNA-binding protein content.

The KRAS gene, which encodes a signaling protein, is mutated in about 25% of all cancers and in 30-40% of colorectal cancers. KRAS mutations in colorectal cancer are associated with increased tumor aggressiveness, resistance to EGFR-targeted treatments like cetuximab, and poorer survival.

“We found that mutant KRAS affected the trafficking of RNA and RNA-binding proteins into vesicles,” Weaver said.

The new grant will support three main projects focused on:

  • How different organelles (specialized cellular compartments) interact as RNAs are trafficked into extracellular vesicles;
  • The RNA sequences and modifications that govern RNA interaction with RNA-binding proteins and how complexes are selected for transfer into extracellular vesicles; and
  • How RNA and growth factors in extracellular vesicles affect signaling, tissue patterning and colon cancer aggressiveness in the colon crypt.

The investigators will be supported by an RNA sequencing and data analysis core and an extracellular vesicle purification and analysis core.

Project leaders are Weaver, Coffey and James Patton, PhD, professor of Biological Sciences. Project co-investigators are Jeffrey Franklin, PhD, research assistant professor of Medicine, James Higginbotham, PhD, research instructor in Medicine, John Karijolich, PhD, assistant professor of Pathology, Microbiology and Immunology, and Kasey Vickers, PhD, assistant professor of Medicine. Leaders and co-leaders of core resources are Weaver, Higginbotham, Qi Liu, PhD, assistant professor of Biostatistics, Yu Shyr, PhD, professor and chair of Biostatistics, and Vickers.

“We know that extracellular vesicles in the tumor microenvironment carry more than just RNA; they carry all kinds of proteins and bioactive lipids,” Weaver said.

“Sorting that out and providing deep proof-of-principle examples for the field is an important goal for us.”

In addition to their participation in the new program project grant, the investigators are members of the recently established Vanderbilt Program for Extracellular Vesicle Research, which is directed by Weaver and Andries Zijlstra, PhD, associate professor of Pathology, Microbiology and Immunology.

The program provides a structure to engage investigators already doing extracellular vesicle research and those who are interested in getting started. It supports an invited seminar series, a work-in-progress data club, shared instrumentation, and other events and workshops.

“We have deep and broad expertise in extracellular vesicles at Vanderbilt,” Weaver said. “The new program and grant have the potential to launch Vanderbilt to the forefront of extracellular vesicle research and to advance our understanding of a variety of physiological and pathological states that rely on extracellular vesicles for communication.”

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