New Pathology Atlas maps genes in cancer to accelerate progress in personalized medicine

August 17, 2017, KTH Royal Institute of Technology
The KRT7 gene, important for epithelial differentiation, is a prognostic marker with unfavorable outcome in ovarian carcinoma. Credit: Human Protein Atlas

A new Pathology Atlas is launched today with an analysis of all human genes in all major cancers showing the consequence of their corresponding protein levels for overall patient survival. The difference in expression patterns of individual cancers observed in the study strongly reinforces the need for personalized cancer treatment based on precision medicine. In addition, the systems level approach used to construct the Pathology Atlas demonstrates the power of "big data" to change how medical research is performed.

The dream of personalized treatment for patients takes a major step forward today with the launch by Swedish researchers of the Human Pathology Atlas. Published in Science, the Atlas is based on the analysis of 17 main cancer types using data from 8,000 patients. In addition, a new concept for showing patient survival data is introduced, called Interactive Survival Scatter plots, and the atlas includes more than 400,000 such plots. A national supercomputer center was used to analyze more than 2.5 petabytes of underlying publicly available data from the Cancer Genome Atlas (TCGA) to generate more than 900,000 survival plots describing the consequence of RNA and protein levels on clinical survival. The Pathology Atlas also contains 5 million -based images generated by the Human Protein Atlas consortium.

Professor Mathias Uhlen, Director of the Human Protein Atlas consortium and leader of the Pathology Atlas effort says: "This study differs from earlier cancer investigations, since it is not focused on the mutations in cancers, but the downstream effects of such mutations across all protein-coding . We show, for the first time, the influence of the gene expression levels demonstrating the power of "big data" to change how is performed. It also shows the advantage of open access policies in science in which researchers share data with each other to allow integration of huge amounts of data from different sources."

The JDP2 gene, encoding a transcription factor protein, is a prognostic marker with unfavorable outcome in colon adenocarcinoma. Credit: Human Protein Atlas

The Research Article in Science reports several important findings related to cancer biology and treatment. Firstly, a large fraction of genes is differentially expressed in cancers - and in many cases - have an impact on overall patient survival. The research also showed that gene expression patterns of individual tumors varied considerably, and could exceed the variation observed between different cancer types. Shorter patient survival was generally associated with up-regulation of genes involved in mitosis and cell growth, and down-regulation of genes involved in cellular differentiation. The data allowed the researchers to generate personalized genome-scale metabolic models for cancer patients to identify key genes involved in tumor growth.

The work depends heavily on the supercomputing power available to the Human Protein Atlas consortium through the Science for Life Laboratory (SciLifeLab). According to Dr. Adil Mardinoglu, SciLifeLab Fellow and leader of the systems biology effort in the project: "We are now in possession of incredibly powerful systems biology tools for medical research, allowing, for the first time, genome-wide analysis of individual with regards to the consequence of their expression profiles for clinical survival."

The Pathology Atlas team also looked to demonstrate the utility of the new tool in two particular cancers. "For lung and colorectal cancer, a selection of prognostic genes identified in the Atlas were also analyzed in independent, prospective cancer cohorts using immunohistochemistry to validate the at the protein level," says Fredrik Ponten, Professor in Pathology of Uppsala University. "We are pleased to provide a stand-alone open-access resource for cancer researchers worldwide, which we hope will help accelerate their efforts to find the biomarkers needed to develop personalized cancer treatments."

The Pathology Atlas is available via an interactive open-access database.

The CBX3 gene, encoding a DNA-binding protein, is a prognostic marker with unfavorable outcome in breast cancer. Credit: Human Protein Atlas

Explore further: The IASLC Atlas of PD-L1 Immunohistochemistry (IHC) Testing in Lung Cancer released

More information: M. Uhlen el al., "A pathology atlas of the human cancer transcriptome," Science (2017). science.sciencemag.org/cgi/doi … 1126/science.aan2507

Related Stories

The IASLC Atlas of PD-L1 Immunohistochemistry (IHC) Testing in Lung Cancer released

May 3, 2017
Media Contact: Becky Bunn, MSc Public Relations ManagerBecky.Bunn@IASLC.org | 720-325-2946

Comprehensive cancer study assesses potential targets for personalized medicine and finds new ones

May 18, 2017
Looking to improve cancer treatment, a multi-institutional research team has taken a comprehensive approach to evaluating which molecular changes in cancer cells are most likely involved in the development of the disease. ...

Recommended for you

Everything big data claims to know about you could be wrong

June 19, 2018
When it comes to understanding what makes people tick—and get sick—medical science has long assumed that the bigger the sample of human subjects, the better. But new research led by UC Berkeley suggests this big-data ...

Are you sticking to your diet? Scientists may be able to tell from a blood sample

June 19, 2018
An analysis of small molecules called "metabolites" in a blood sample may be used to determine whether a person is following a prescribed diet, scientists at Johns Hopkins Bloomberg School of Public Health have shown.

Diagnosing and treating disorders of early sex development

June 19, 2018
Diagnosing, advising on and treating disorders of early sex development represent a huge medical challenge, both for those affected and for treating physicians. In contrast to the earlier view, DSD (Difference of Sex Development) ...

BPA can induce multigenerational effects on ability to communicate

June 18, 2018
Past studies have shown that biparental care of offspring can be affected negatively when females and males are exposed to bisphenol A (BPA); however, previous studies have not characterized how long-term effects of BPA exposure ...

New compound shown to be as effective as FDA-approved drugs against life-threatening infections

June 15, 2018
Purdue University researchers have identified  a new compound that in preliminary testing has shown itself to be as effective as antibiotics approved by the Food and Drug Administration to treat life-threatening infections ...

Foods combining fats and carbohydrates more rewarding than foods with just fats or carbs

June 14, 2018
Researchers show that the reward center of the brain values foods high in both fat and carbohydrates—i.e., many processed foods—more than foods containing only fat or only carbs. A study of 206 adults, to appear June ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.