Ed Chuong

Yuanyuan Xie awarded National Cancer Center fellowship to explore the pathological role of transposons

Anonymous — Wed, 12 Jun 2019 14:56:18 +0000

Yuanyuan Xie awarded National Cancer Center fellowship to explore the pathological role of transposons Anonymous (not verified) Wed, 06/12/2019 - 08:56

Lindsay Diamond

Nearly all species’ genomes are littered with millions of genetic sequences called transposons, which are virus-like parasitic elements that can replicate and spread within host genomes. Collectively, transposon-derived sequences constitute about 50 percent of the human genome sequence, and are believed to have - over tens of millions of years - played a critical role in our evolution. Transposons are increasingly recognized to have influenced human biology and adaptation, particularly in the realms of development and immunity. Transposons may also contribute to disease.

Yuanyuan Xie, a postdoctoral researcher in the Chuong Lab, was recently awarded a National Cancer Center Postdoctoral Fellowship to explore the pathological role of transposon-derived sequences known as retrocopies in colorectal cancer.

For the cell to create proteins, the DNA sequence of a gene is transcribed into RNA, which is then normally translated into a protein. However, cellular RNAs are occasionally reverse-transcribed back to DNA and inserted into a different location in the genome, forming a type of gene duplication known as a retrocopy. Retrocopies originate from the activity of retrotransposons, which replicate by reverse transcribing their own RNA into host DNA, but occasionally capture cellular RNAs by accident. While over 8,000 retrocopies can be detected in the human genome, they are often assumed to be nonfunctional. Nevertheless, genomic studies have revealed that many retrocopies have transcribed RNAs or even translated proteins, often with distinct activities from their parental genes.

Repeat sequences can have deleterious effects in the genome and underlie several human disease conditions including Huntington’s disease, fragile X syndrome, several ataxias, and myotonic dystrophy. To protect against potential harm, all organisms have evolved genomic defenses to repress transposons through epigenetic manipulation. Yet, repression is inherently reversible, and inappropriate reactivation of transposons are common in many cancers. However, the specific cellular functions of retrocopies and whether they play a genome-wide role in cancer progression remain unknown.

Answering these questions is what drew Yuanyuan to the interdisciplinarity of Chuong Lab and the BioFrontiers Institute. “My previous experience was in cell signaling pathways and stem cell models, and I was interested in joining the Chuong Lab where I can learn computational genomics to study gene regulatory networks in evolution and disease,” says Xie.

Taking a break from the bench, Yuanyuan scoured The Cancer Genome Atlas (TCGA), a joint effort between the National Cancer Institute and the National Human Genome Research Institute that has characterized over 20,000 primary cancer and normal samples across a variety of different cancers, in search of candidates where there is increased expression of retrocopies, rather than parental genes, in primary tumors.

Now with the fellowship funding, Yuanyuan will head back to the bench to test his hypotheses. “Through activities like DNA and histone modification, these repetitive elements are derepressed in states like cancer and aging. The question remains whether this derepression is a consequence or a cause,” says Xie.

Looking forward, Yuanyuan plans to extend the analysis to a genome-wide CRISPR screen to identify novel protein-coding and non-coding retrocopies involved in tumorigenesis. Overall these experiments seek to uncover an understudied yet potentially extensive pathological role for retrocopies in colorectal cancers wherein the mechanism may be applied to other types of cancers. These studies may help pave the road for more precise cancer therapies that specifically target retrocopies.

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2 researchers awarded 2019 Sloan Research Fellowships

Anonymous — Tue, 19 Feb 2019 07:00:00 +0000

2 researchers awarded 2019 Sloan Research Fellowships Anonymous (not verified) Tue, 02/19/2019 - 00:00

Assistant Professors Edward Chuong (left) and Sandeep Sharma. Photo: CU Boulder

CU Boulder assistant professors Edward Chuong and Sandeep Sharma have been awarded prestigious Sloan Research Fellowships for 2019, one of the highest honors for early-career researchers.

The fellowships, awarded yearly by the Alfred P. Sloan Foundation since 1955, mark Chuong and Sharma as among the most promising researchers in their fields. The 2019 recipients include 126 scientists from across 57 research institutions in the U.S. and Canada.

“I’m very pleased to represent CU Boulder with this award,” said Sharma, an assistant professor in the Department of Chemistry. “I’m grateful to my senior colleagues, many of whom have been very supportive and helped me build a strong, thriving lab group.”

Sharma’s research focuses on developing algorithms to perform computer simulations that can help understand and predict the unusual and intriguing properties of quantum materials and enzymes. This will potentially help in the development of materials for high-density computer memory, quantum qubits and efficient catalysts.

Edward Chuong, an assistant professor of Molecular Cellular and Developmental Biology, studies ancient genetic parasites known as “transposons,” which latch on to a host’s DNA and replicate themselves throughout the genome and rewire the expression of genes.

Collectively, the virus-like bits of genetic material constitute about 50 percent of the human genome sequence, and they are believed to have—over tens of millions of years—played a key role in the evolution of gene networks controlling immunity and development.

“We are interested not only in how these transposons have influenced our biology and helped us adapt as a species, but also in how they may contribute to disease today,” he said. “This grant provides much needed support for that line of inquiry.”

Chuong, who is also an evolutionary geneticist with the BioFrontiers Institute, uses modern gene-editing and computational tools to determine whether transposons have played a similar role in the evolution of other species, including mice, dogs and cows.

“Ultimately this work could help us understand what differences there are across mammals when it comes to immune response and how those differences evolved,” he said.

Open to scholars in eight scientific and technical fields—chemistry, computer science, economics, mathematics, computational and evolutionary molecular biology, neuroscience, ocean sciences, and physics—the Sloan Research Fellowships are awarded in close coordination with the scientific community. Winners receive a two-year, $70,000 fellowship to further their research.

“Sloan Research Fellows are the best young scientists working today,” said Adam F. Falk, president of the Alfred P. Sloan Foundation in a statement. “Sloan Fellows stand out for their creativity, for their hard work, for the importance of the issues they tackle, and the energy and innovation with which they tackle them. To be a Sloan Fellow is to be in the vanguard of 21st century science.”

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New Faculty Member Ed Chuong Named Boettcher Investigator

Anonymous — Mon, 18 Jun 2018 20:41:33 +0000

New Faculty Member Ed Chuong Named Boettcher Investigator Anonymous (not verified) Mon, 06/18/2018 - 14:41

Six University of Colorado researchers at the CU Anschutz Medical Campus and CU Boulder have been named Boettcher Investigators in the Boettcher Webb-Waring Biomedical Research Awards Program for 2018.

The awards support promising, early career scientific researchers, allowing them to establish their independent research and compete in the future for major federal and private awards. Recipients are awarded $235,000 in grant funding to sustain up to three years of biomedical research. They also receive the title of Boettcher Investigator.

“The 2018 class of Boettcher Investigators represents Colorado’s most dynamic emerging scientists, leaders who are committed to improving human health,” said Katie Kramer, president and CEO of the Boettcher Foundation. “The Boettcher Foundation is honored to support their research at this critical juncture in their careers and to elevate scientific innovation across our state.”

The 2018 Class of Boettcher Investigators and their research topics are:

CU Anschutz Medical Campus

Kathleen M. Gavin, Ph.D., assistant professor of medicine, Division of Geriatric Medicine – Cellular composition of adipose tissue
Jean M. Mulcahy Levy, M.D., assistant professor, Center for Cancer and Blood Disorders – New therapy development for pediatric brain tumors
Matthew Taliaferro, Ph.D., assistant professor of biochemistry and molecular genetics – Regulation of subcellular RNA localization
Eszter K. Vladar, Ph.D., assistant professor of medicine and cell and developmental biology – Airway epithelial development, homeostasis and dysfunction

CU Boulder

Edward Chuong, Ph.D., assistant professor of molecular, cellular and developmental biology – Evolution of gene regulatory networks
David H. Root, Ph.D., assistant professor of psychology and neuroscience – Neurobiology of drug addiction

Also named to the 2018 class of Boettcher Investigators: Jesse W. Wilson, Ph.D., of Colorado State University.

The Boettcher Foundation Board of Trustees formally announced its annual class of Boettcher Investigators on June 7. The year’s total funding from the Boettcher Foundation’s Webb-Waring Biomedical Research Awards program is $1.41 million.

With the addition of the ninth class, there are 39 Boettcher Investigators at CU receiving over $9 million in biomedical research support.

See all CU Boettcher Investigators.

In its ninth year, the Webb-Waring Biomedical Research Awards honor the commitments that the Webb and Waring families made to scientific research. Including the class of 2018, 61 Boettcher Investigators have received funding through the Webb-Waring program.

Since 2010, Boettcher Investigators have gone on to earn a collective $34 million in subsequent independent research funding. Some 95 percent of award recipients still reside at Colorado research institutions, advancing the foundation’s mission of keeping Colorado’s top scientific minds in the state.

“We are continually impressed by the caliber of the community of Boettcher Investigators and the promise of their research to build better lives” said April Giles, president and CEO of the Colorado BioScience Association. “The research supported by the Webb-Waring Biomedical Research Awards undoubtedly improves the health of the bioscience industry and the residents of Colorado.”

Original publication https://connections.cu.edu/spotlights/six-cu-researchers-named-boettcher-investigators

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