Cellular book of knowledge

Cellular book of knowledge

The University of Toronto’s Gary Bader is compiling information about gene function from around the world in a database that has already shown the potential to save lives
November 20, 2014

Gary Bader cringes when he recalls life as a biochemistry undergrad, particularly the toil of memorizing immense amounts of information about cellular mechanisms. “Given my interest in computers, I always dreamed it would be great to put all that information in a computer and have it available at your fingertips,” says Bader. “Later, I learned it was not just a matter of having it at your fingertips — you could actually use it to make discoveries.”

As a graduate student in 1998, Bader was among the first to become involved in an international effort to create a “cell map” — what would become a vast digital archive of mechanistic details of how human cells work, which began its life at the University of Toronto. Today, researchers can use the map in two ways: as an educational textbook to learn how genes function and interact (“It’s like Google for biologists and cell biologists,” says Bader) or as an online database to access existing knowledge of the workings of genes specific to their research. If they want to find out more about a single human gene they’ve isolated, for example, researchers can query the map from virtually anywhere and access all the compiled information about that gene. Bader is leading this ongoing effort to grow and further refine his map, which is now used by scientists from more than 100 countries and includes hundreds of separate “cellular pathways.” Each pathway is a series of interactions among molecules that carry out a cellular function, such as creating a new molecule or turning a gene on or off.

In 2006, Bader established the Computational Network Biology lab at the University of Toronto, which serves as the bricks-and-mortar headquarters for work on the cell map. Over the years, Bader has selectively incorporated publicly available information to grow the map, focusing on pathways related to cancer, heart disease and autoimmune diseases like rheumatoid arthritis.

WATCH: Gary Bader explains how his lab merges computer science and biology to understand disease

This accumulation of knowledge has already shown the potential to save lives. Earlier this year, Bader collaborated with neurosurgeon Michael Taylor at Toronto’s Hospital for Sick Children, who is conducting genetic research into ependymoma, a little-understood, often lethal form of brain cancer found in very young children. Taylor had sequenced the DNA in many tumours and eventually came calling to Bader with 2,000 abnormal genes that were a mystery, since no one knew what they did. Using the cell map, Bader’s lab was able to pinpoint a molecular system that was active in the most serious cancer samples and later discovered that new drugs already in development could specifically target the workings of this system.

The results so far are early but promising: A child in the very late stages of this disease, with cancer metastasized to the lung, was recently given a therapy that targeted the molecular machinery pinpointed using the cell map, and the growth of the tumour stopped. “It’s an amazing result for us,” says Bader, who hopes that the cell map will soon be applied across a broad range of diseases beyond cancer.