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Topology of cancer

The Columbia University Center for Topology of Cancer Evolution and Heterogeneity will combine mathematical approaches from topological data analysis with new single-cell experimental technologies to study cellular diversity in solid tumors. Image courtesy of Raul Rabadan.

The National Cancer Institute’s Physical Sciences in Oncology program has announced the creation of a new center for research and education based at Columbia University. The Center for Topology of Cancer Evolution and Heterogeneity will develop and utilize innovative mathematical and experimental techniques to explore how genetic diversity emerges in the cells that make up solid tumors. In this way it will address a key challenge facing cancer research in the age of precision medicine — how to identify the clonal variants within a tumor that are responsible for its growth, spread, and resistance to therapy. Ultimately, the strategies the Center develops could be used to identify more effective biomarkers of disease and new therapeutic strategies.

Gut-Brain Microbiota
A grant from the Office of Naval Research will support the development of three foundational synthetic biology technologies for engineering the human gut microbiota.

Harris Wang, an assistant professor in the Columbia University Department of Systems Biology, has been selected for the Office of Naval Research 2015 Young Investigators Program. This highly selective program promotes the development of early-career academic scientists whose research shows exceptional promise and creativity. With the support of this award, Dr. Wang will extend his research in the field of synthetic biology to develop new technologies for engineering the gut microbiome, the ecosystem of bacteria that inhabit the human digestive system. These new methods, Wang anticipates, could provide new ways of designing communities of different microbial species and ultimately modulating interactions between the gut, the immune system, and the brain.

Rodney Rothstein
Rodney Rothstein

The Columbia University Department of Systems Biology congratulates Rodney Rothstein on his election to the National Academy of Sciences. The NAS is a private, non-profit society of distinguished scholars that provides independent, objective advice to the nation on matters related to science and technology. Scientists elected to the NAS are chosen by their peers in recognition of their distinguished and continuing achievements in original research.

Comorbidity between Mendelian disease and cancer
Researchers in the Rabadan Lab have found that comorbidity between Mendelian diseases and cancer may result from shared genetic factors.

Genetic diseases can arise in a variety of ways. Mendelian disorders, for example, occur when specific mutations in single genes — called germline mutations — are inherited from either of one’s two parents. Well-known examples of Mendelian diseases include cystic fibrosis, sickle cell disease, and Duchenne muscular dystrophy. Other genetic diseases, including cancer, result from somatic mutations, which occur in individual cells during a person’s lifetime. Because the genetic origins of Mendelian diseases and cancer are so different, they are typically understood to be distinct phenomena. However, scientists in the Columbia University Department of Systems Biology have found evidence that there might be interesting genetic connections between them. 

In a paper just published in Nature Communications, postdoctoral research scientist Rachel Melamed and colleagues in the laboratory of Associate Professor Raul Rabadan report on a new method that uses knowledge about Mendelian diseases to suggest mutations involved in cancer. The study takes advantage of an enormous collection of electronic health records representing over 110 million patients, a substantial percentage of US residents. The authors show that clinical co-occurrence of Mendelian diseases and cancer, known as comorbidity, can be tied to genetic changes that play roles in both diseases. The paper also identifies several specific relationships between Mendelian diseases and the cancers melanoma and glioblastoma.

Some factors in the expo some

The exposome incorporates factors such as the environment we inhabit, the food we eat, and the drugs we take.

Although genomics has dramatically improved our understanding of the molecular origins of certain human genetic diseases, our health is also influenced by exposures to our surrounding environment. Molecules found in food, air and water pollution, and prescription drugs, for example, interact with genetic, molecular, and physiologic features within our bodies in highly personalized ways. The nature of these relationships is important in determining who is immune to such exposures and who becomes sick because of them.

In the past, methods for studying this interface have been limited because of the complexity of the problem. After all, how could we possibly cross-reference a lifetime’s worth of exposures with individual genetic profiles in any kind of meaningful way? Recently, however, an explosion in the generation of quantitative data related to the environment, health, and genetics — along with new computational methods based in machine learning and bioinformatics — have made this landscape ripe for exploration.

At this year’s South by Southwest Interactive Festival in Austin, Texas, Department of Systems Biology Assistant Professor Nicholas Tatonetti and his collaborator Chirag Patel (Harvard Medical School) discussed the remarkable new opportunities that “big data” approaches offer for investigating this landscape. Driving Tatonetti and Patel’s approach is a concept called the exposome. First proposed by Christopher Wild (University of Leeds) in 2005, an exposome represents all of the environmental exposures a person has experienced during his or her life that could play a role in the onset of chronic diseases. Tatonetti and Chirag’s presentation highlighted how investigation of the exposome has become tractable, as well as the important roles that individuals can play in supporting this effort.

In the following interview, Dr. Tatonetti discusses some of the approaches his team is using to explore the exposome, and how the project has evolved out of his previous research.