Corporate Banner
Satellite Banner
Technology
Networks
Scientific Communities
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Pan-Cancer Studies Find Common Patterns Shared by Different Tumor Types

Published: Wednesday, October 02, 2013
Last Updated: Wednesday, October 02, 2013
Bookmark and Share
Findings may open up new treatment options by extending therapies effective in one cancer type to others with a similar genomic profile.

Cancer encompasses a complex group of diseases traditionally defined by where in the body it originates, as in lung cancer or colon cancer. This framework for studying and treating cancer has made sense for generations, but molecular analysis now shows that cancers of different organs have many shared features, while cancers from the same organ or tissue are often quite distinct.

The Pan-Cancer Initiative, a major effort to analyze the molecular aberrations in cancer cells across a range of tumor types, has yielded an abundance of new findings reported in 18 forthcoming papers, including four published in the October issue of Nature Genetics. The initiative, launched in October 2012 at a meeting in Santa Cruz, California, is part of the Cancer Genome Atlas (TCGA) project led by the National Cancer Institute and the National Human Genome Research Institute.

Josh Stuart, professor of biomolecular engineering at the University of California, Santa Cruz, helped organize the Pan-Cancer Initiative and is lead author of a commentary in Nature Genetics giving an overview of the project and its initial findings.

"For years we've been looking at one tumor type at a time, but there are patterns you can only spot by making connections across different tissues and tumor types. Finding these similarities across tissues can have important implications for treatment," Stuart said.

For example, some types of bladder cancer look very similar to certain lung and head-and-neck cancers, and recognizing those similarities may open up new therapeutic options. "This could allow oncologists to apply all they know about treating head-and-neck squamous cell tumors to the ten percent of bladder cancers that have the same characteristics," Stuart said.

TCGA is generating comprehensive maps of the key genomic changes in major types and subtypes of cancer, eventually covering at least 20 different cancer types. TCGA researchers are profiling thousands of tumors to discover molecular aberrations at the DNA, RNA, protein, and epigenetic levels. The Pan-Cancer Initiative has done comparative analyses of the first 12 tumor types profiled by TCGA.

The analyses show that the tissue of origin is an important factor, producing a dominant signal that groups tumors mostly according to their tissue of origin. But the data also reveal a number of interesting signals that cut across tumor types and suggest new ways of categorizing tumors, Stuart said. In addition, the statistical power gained by combining all of the data available from different tumor types has enabled researchers to see new patterns of genomic aberrations.

"In ovarian cancer, for example, we were able to identify mutations that correlate with the response to treatment, but only by using data from other types of cancer," Stuart said.

A persistent problem in cancer genomics has been distinguishing "driver" mutations from "passenger" mutations. Cancer cells often accumulate large numbers of genetic mutations that do not play a role in driving the uncontrolled cell growth that is a hallmark of cancer. These passenger mutations greatly complicate efforts to identify the genomic drivers of cancer. Aggregating data from the 12 tumor types gave Pan-Cancer researchers enough statistical power to see patterns that weren't apparent before. One of the forthcoming papers identifies with high confidence many new genomic drivers of cancer, Stuart said.

The Pan-Cancer analyses have also revealed the importance of new classes of mutations, such as those that affect how a cell's DNA is packaged in the chromosomes. As cells differentiate into specialized cell types during an organism's development, some genes are turned off and others are turned on depending on how the DNA is packaged together with specialized proteins to make "chromatin." Genomic changes (gene amplification, deletion or mutation) affecting genes that control the packaging of DNA can disrupt this key regulatory mechanism. One of the Nature Genetics papers (Zack et al.) analyzed amplifications and deletions and found 104 novel regions that had not been associated with cancer previously, and these regions contain a rich supply of genes involved in "epigenetic" modifications of chromatin.

"There are so many different ways to mess up the packaging of DNA that the mutations look random in any one tumor type, but now we have enough data to see that chromatin remodeling is a big factor in a lot of these tumors," Stuart said.

Stuart played a central role in creating the organizational framework that made the Pan-Cancer analyses possible. The project started as an informal collaboration among members of the TCGA research network, but then quickly expanded to include many other interested researchers. Coordinating all these efforts was a major task. Stuart worked with the bioinformatics company Sage Bionetworks to create a data repository called Synapse for the project. To ensure that everyone was working from the same data set, a data "freeze" was established in December 2012. But Stuart realized that many important analyses would depend on the results of other analyses carried out by different research groups.

"The interdependencies are so complicated that everybody had to abide by a schedule in order to play the game," Stuart said. "The system worked really well, and the project has ballooned because there are so many interesting things to look at. We have 18 papers coming out in this first release, and there are 60 more Pan-Cancer papers coming that I'm currently tracking."

The Synapse system created by Sage Bionetworks is described in one of the Nature Genetics papers (Omberg et al.). "This beautifully organized data repository is now available for scientists around the world to use to go beyond these initial analyses and discover even more about cancer," Stuart said.

Researchers will continue to use the framework and procedures Stuart established as they integrate new tumor types and new data from TCGA, as well as data from other cancer genomics projects. Stuart has just been named, along with Gad Getz of the Broad Institute of MIT and Harvard, to lead an international pan-cancer initiative that will combine TCGA data with data from other cancer genomics efforts around the world.

The hope is that these cross-tumor investigations will lead to new and improved cancer treatments. One goal is to identify biomarkers that can be used across a range of tumor types to indicate which therapies are likely to be most effective. The results of these studies may also point toward targets for novel therapeutic agents that can be tested clinically.

"These initial papers are just the first step, and we expect much more to come from the Pan-Cancer Initiative," Stuart said. "With the infrastructure now in place, we can scale up to look at more types of data, especially whole genome sequencing data, and to include many more tumor types, including rare tumors."


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 3,200+ scientific posters on ePosters
  • More Than 4,600+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

‘Human-on-a-Chip’ Could Replace Animal Testing
Researchers are developing a “human-on-a-chip,” a miniature external replication of the human body, integrating biology and engineering with a combination of microfluidics and multi-electrode arrays.
Monday, June 13, 2016
Unveiling the Complexity of Mysterious Protein Folding
Imagine trying to reverse engineer a car when all you have is a finished product or a box full of parts — no instructions.
Wednesday, June 01, 2016
Study Identifies How Brain Connects Memories Across Time
UCLA Neuroscientists have boost ability of aging brain to recapture links between related memories.
Tuesday, May 31, 2016
Transcription Factor Isoforms Implicated in Colon Diseases
UC Riverside study explains how distribution of two forms of a transcription factor in the colon influence risk of disease.
Thursday, May 19, 2016
An E.coli Detector May be in Your Hands Soon
Hand-held device that can be used to detect a variety of pathogens—including foodborne pathogens like E. coli—at all stages in the food supply chain, from fields to restaurants may be available soon.
Monday, May 16, 2016
Fructose Alters Hundreds of Brain Genes
UCLA scientists report that diet rich in omega-3 fatty acids can reverse the damage.
Tuesday, April 26, 2016
Study Yields the Key to Effective Personalized Medicine
A team of UCLA bioengineers and surgeons has taken a major step toward making personalized medicine a reality.
Monday, April 11, 2016
Tracking RNA in Live Cells
Technique may open doors to new treatments for many conditions, from cancer to autism.
Friday, March 18, 2016
Cat Stem Cell Therapy Gives Humans Hope
By the time Bob the cat came to the UC Davis veterinary hospital, he had used up most of his nine lives.
Monday, February 08, 2016
Crowdfunding the Fight Against Cancer
From budding social causes to groundbreaking businesses to the next big band, crowdfunding has helped connect countless worthy projects with like-minded people willing to support their efforts, even in small ways. But could crowdfunding help fight cancer?
Monday, February 08, 2016
Toxic Pollutants Found in Fish Across the World's Oceans
Scripps researchers' analysis shows highly variable pollutant concentrations in fish meat.
Friday, January 29, 2016
Key Enzyme in Pierce’s Disease Grapevine Damage Uncovered
UC Davis plant scientists have identified an enzyme that appears to play a key role in the insect-transmitted bacterial infection of grapevines with Pierce’s disease, which annually costs California’s grape and wine industries more than $100 million.
Wednesday, January 13, 2016
Science Magazine Names CRISPR ‘Breakthrough of the Year’
In its year-end issue, the journal Science chose the CRISPR genome-editing technology invented at UC Berkeley 2015’s Breakthrough of the Year.
Monday, December 21, 2015
Genome Sequencing May Save California's Legendary Sugar Pine
The genome of California’s legendary sugar pine, which naturalist John Muir declared to be “king of the conifers” more than a century ago, has been sequenced by a research team led by UC Davis scientists.
Thursday, December 17, 2015
Cellular “ORACLs” to Aid Drug Discovery
New approach for finding therapeutics is inspired by face-recognition software.
Wednesday, December 16, 2015
Scientific News
Platelets are the Pathfinders for Leukocyte Extravasation During Inflammation
Findings from the study could help in the prevention and treatment of inflammatory pathologies.
ASMS 2016: Targeting Mass Spectrometry Tools for the Masses
The expanding application range of MS in life sciences, food, energy, and health sciences research was highlighted at this year's ASMS meeting in San Antonio, Texas.
Benchtop Automation Trends
Gain a better understanding of current interest in and future deployment of benchtop automated systems.
Manufactured Stem Cells to Advance Clinical Research
Clinical-grade cell line will enable development of new therapies and accelerate early-stage clinical research.
Dengue Virus Exposure May Amplify Zika Infection
Researchers at Imperial College London have found that the previous exposure to the dengue virus may increase the potency of Zika infection.
Gender Determination in Forensic Investigations
This study investigated the effectiveness of lip print analysis as a tool in gender determination.
Identifying Novel Types of Forensic Markers in Degraded DNA
Scientists have tried to verify the nucleosome protection hypothesis by discovering STRs within nucleosome core regions, using whole genome sequencing.
Proteins in Blood of Heart Disease Patients May Predict Adverse Events
Nine-protein test shown superior to conventional assessments of risk.
Higher Frequency of Huntington's Disease Mutations Discovered
University of Aberdeen study shows that the gene change that causes Huntington's disease is much more common than previously thought.
Starving Stem Cells May Enable Scientists To Build Better Blood Vessels
Researchers from the University of Illinois at Chicago College of Medicine have uncovered how changes in metabolism of human embryonic stem cells help coax them to mature into specific cell types — and may improve their function in engineered organs or tissues.
Scroll Up
Scroll Down
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
3,200+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,600+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!