Biology is no longer restricted to studying living organisms in the wild, or working with cells in the confines of a lab. Interdisciplinary influences from fields like mathematics, physics, chemistry and statistics on biology are increasing by the day in relentless attempts to comprehend the complexity of life. Bioinformatics is a result of one such effort, where computational approaches are used to solve problems that are practically either impossible to resolve or are highly time-consuming to pursue. Bioinformatics provides analytical solutions in the form of computer programs that trained researchers can use to interpret data.
With an increasing understanding of the subject and use of interdisciplinary approaches, are we now better equipped to fight near-fatal diseases like cancer? Every day, numerous research labs are generating massive bodies of knowledge in the form of research data and publications that have helped us understand the different tenets of this disease like never before. How, then, can we scoop out specific bits of research evidence or nuggets of information from the enormous number of research papers that can help us tackle cancer better? Using bioinformatics is what Sunita Yadavalli and Dr Prashant Kumar from the Institute of Bioinformatics in Bengaluru, propose.
“It is imperative to note the importance of data resources available online,” says Sunita. “It is possible to infer and deliver important insights from exhaustive data curation, and without using bench resources. Particularly in the realm of cancer, any information is valuable as it has not been elucidated completely,” she adds. In a recent study, Sunita and Prashant, along with a team of researchers from the Indian Institute of Science and the National University of Singapore, have attempted to figure out what molecules and mechanisms are involved in the movement of cancer cells. The researchers have analysed cancer cells and the genes involved in the process using just a computer!
Cancer starts as tumours — a solid clump of cells that are static. Circulating tumour cells (CTCs) are cells that break free from the tumours and squeeze their way through the walls of the nearest blood vessel and enter the bloodstream. While most cancer cells don’t have the inherent ability to migrate, they acquire this ability through a cellular mechanism called Epithelial Mesenchymal Transition or EMT. This mechanism kicks in when certain genes in our cells are turned ‘on’. In the case of CTCs, the tumour cells turn on
specific genes that allow them to change from being sedentary to being nomadic. CTCs play a great role in cancer diagnosis and prognosis since they can be collected by simply drawing some blood from the patient as ‘liquid biopsy’. However, isolating and detecting CTCs in blood is not as easy as it may sound and is limited to a handful of validated techniques. This is because CTCs are not yet completely characterised at the molecular level.
Sunita’s work involves examining the cellular pathways involved in the migration of tumour cells into the bloodstream, a study that could help in cancer diagnosis and therapy. During the study, she scoured through thousands of research papers by scientists who had already worked in the lab and had generated large sets of data using different experiments. She then narrowed this down to five studies where the scientists used one or more advanced techniques in their isolation of CTCs to overcome the problem of contamination. The diverse data set that she began with had data from CTCs obtained from skin, prostate, breast, colorectal and pancreatic cancer patients.
After a thorough analysis, the researchers found that to move into a blood vessel, CTCs tend to switch on the same genes that white blood cells normally use to enter and exit the bloodstream. “However, when we investigated further, we saw that across cancers, these cells turn on various genes that have already been categorised under the leukocyte extravasation pathway and more,” comments Sunita. The study reveals a number of key molecules that can be exploited for both diagnosis and therapeutic purposes for cancer.
The power of analysing data provides valuable interpretations that vary from study to study, thus helping us gain new perspectives and insights. “With big data that exists today in the scientific research community, all you need is a computer, basic bioinformatics know-how and the dedication and inclination to process large data sets,” signs off Sunita.
(The author is with Gubbi Labs, a Bengaluru-based Research collective)