Cookies

Like most websites The Pathologist uses cookies. In order to deliver a personalized, responsive service and to improve the site, we remember and store information about how you use it. Learn more.
Subscribe to Newsletter
Inside the Lab Oncology, Omics, Bioinformatics

Driving Discovery

A collaborative effort between researchers in Europe and the US has resulted in the combination of two publicly available “omics” databases, to create a catalog of cancer drivers. The study has discovered over 70 new candidate cancer driver genes (1), and could help to explain how the same affected gene can lead to different outcomes or therapy responses in patients.

The computational program, called E-driver, uses tumor data from ~6,000 patients from the Cancer Genome Atlas (TCGA), and more than 18,000 three-dimensional protein structures from the Protein Data Bank. An algorithm then analyzes the information to see if structural alterations of protein-protein interaction (PPI) interfaces are enriched in cancer mutations, therefore identifying candidate driver genes.

The motivation behind the study? It was based on the theory that, as genes can have a variety of functions, information on the structures, pathways, and protein complexes involved in disease would give insight into how mutations in different genetic regions may produce different characteristics in the resulting cancer.

“I was surprised that almost all existing tools for the analysis of cancer mutations are not using available structural information on proteins, which happen to be my main field of interest,” says co-author Adam Godzik. “Insights can be gained from even very rudimentary structural analysis, and we set out to do this on a large scale”.

As well as identifying possible new cancer drivers, the study has given further insight into this area of oncology, adds Godzik. “We have learned two things: mutations in different regions of a gene can have different, sometimes opposite effects on cancer and treatment outcomes. And the growing list of cancer driver genes is slowly eroding the current model of driver vs. passenger mutations. It is clear now that as well as a small number of major drivers, there are a lot of genes that play a role of ‘enablers’ or ‘mini-drivers’, which when mutated, could provide an important advantage to a growing tumor, but may not be able to start cancer by themselves”, he says.

Godzik admits that more analysis is needed to better understand the entire landscape of molecular events in cancer in order to identify optimal treatments and predict patient outcomes. However, at this point it remains unclear if these newly-discovered drivers are likely to become targets for therapy, as many are relatively rare.

Receive content, products, events as well as relevant industry updates from The Pathologist and its sponsors.
Stay up to date with our other newsletters and sponsors information, tailored specifically to the fields you are interested in

When you click “Subscribe” we will email you a link, which you must click to verify the email address above and activate your subscription. If you do not receive this email, please contact us at [email protected].
If you wish to unsubscribe, you can update your preferences at any point.

  1. E Porta-Pardo et al., “A pan-cancer catalogue of cancer driver protein interaction interfaces”, PloS Comput Biol, 11, e1004518 (2015). PMID: 26485003.
About the Author
Roisin McGuigan

I have an extensive academic background in the life sciences, having studied forensic biology and human medical genetics in my time at Strathclyde and Glasgow Universities. My research, data presentation and bioinformatics skills plus my ‘wet lab’ experience have been a superb grounding for my role as an Associate Editor at Texere Publishing. The job allows me to utilize my hard-learned academic skills and experience in my current position within an exciting and contemporary publishing company.

Related Application Notes
Subspecialties Oncology
Invitae microsatellite instability detection

| Contributed by Invitae

Superior Determination of HPV using RNAscope™ In Situ Hybridization

| Contributed by Bio-Techne

Biomarker Optimization on LabSat® Research

| Contributed by Lunaphore Technologies

Related Product Profile
Diagnostics Genetics and epigenetics
QIAseq® Pan Cancer Multimodal cuts user interventions by 50%

| Contributed by QIAGEN

Register to The Pathologist

Register to access our FREE online portfolio, request the magazine in print and manage your preferences.

You will benefit from:
  • Unlimited access to ALL articles
  • News, interviews & opinions from leading industry experts
  • Receive print (and PDF) copies of The Pathologist magazine

Register