Collaborative research on novel biomarkers for pancreatic cancer

The scientists at the Institute of Bioinformatics using bioinformatics tools in this collaborative effort with Johns Hopkins have reanalysed all the acquired data and thereby mapping previously undecipherable data into precise genes involved in pancreatic cancer

In the post genomic era we live in, bioinformatics is a buzz word. Careful bioinformatics analysis can indeed drive fundamental research at an unbelievably faster pace. As better treatment of diseases demands additional research into disease mechanisms, such research demands researchers to be more innovative in their thinking, to explore new dimensions. Bioinformatics is one such area which is demanding by all means.

At the Institute of Bioinformatics (IOB), a not-for-profit research organisation in Bangalore, the scientists are rising to this challenge to drive the frontiers of science in order to make the world a better place. One of such challenging tasks that was undertaken in the recent past was to help cancer scientists at America’s leading hospital, the Johns Hopkins Hospital in Baltimore, to identify new markers for pancreatic cancer, said a release issued by IOB.

Pancreatic cancer is one of the leading causes of cancer deaths worldwide. Even though all cancers have some common properties, every cancer is unique from a molecular standpoint. If one has to identify a possible cure, it is absolutely crucial to understand the key molecular details which are unique and special for a particular cancer type. Realising the need, the scientists at the Johns Hopkins Hospital, who are world-renowned, set out on a pioneering mission to identify the genes involved in pancreatic cancer.

Genes are the physical units of chemical information that form the core of our genetic material and are responsible for essentially making us who we are. A subtle change in the behaviour of a key gene or a set of genes can have an inappropriate physical effect which could sometimes be lethal to that particular individual. Cancers are one such example where changes in the behaviour of a set of genes causes a normal cell to lose its control mechanisms making it cancerous.

The pancreatic cancer team at the Johns Hopkins were monitoring the intricate changes in gene behaviour between a normal pancreatic cell and the cancerous cell. One has to admit at this juncture that the limit of technology is the limit of understanding.

In this context, understanding the behaviour patterns for tens of thousands of genes in humans will not be possible without two key technologies: the DNA Microarray technology and Serial Analysis of Gene expression (SAGE). These techniques together allow us to conquer the world of cancer research as these are the major ways through which one can monitor the subtle changes at the level of genes.

Microarray and SAGE measure the level of gene expression between the normal and cancerous cell, the difference in which is noted as the change in gene behaviour. These techniques are highly complicated in its nature and it needs a trained eye not only to perform these experiments but also to interpret the results. It is at this moment that the Institute of Bioinformatics came into the picture as bioinformatics play a major role in interpreting the results from both Microarray and SAGE experiments.

As every technology has its own limitations, the same goes true for both these techniques. In a microarray experiment, one can always be sure that some gene is changing in its level of gene expression when compared between a normal cell and a cancerous cell but not always it can tell, which gene is changing. Without knowing which gene is altered in its behaviour, the data itself is relatively useless. At least a quarter of the data from every microarray experiment is in the form of uncharacterised sequences which cannot be ascribed to any gene puzzling the cancer scientists.

At the Institute of Bioinformatics, the scientists are well aware of this problem and are using a careful bioinformatics approach to find a solution to this problem. The scientists at IOB, under the leadership of Dr Akhilesh Pandey, the Chief Scientific Advisor of the Institute, used their bioinformatics tools in this collaborative effort with Johns Hopkins to reanalyse all the data acquired by scientists at Johns Hopkins in their quest to find genes which are novel markers of pancreatic cancer. This led to mapping of previously undecipherable data into precise genes which were never been known to involve in pancreatic cancer before.

Most strikingly, these bioinformatics predictions are experimentally verified by scientists at Johns Hopkins and were published in the international scientific journal, Cancer Biology and Therapy. This analysis was made possible by a software tool that the scientists at IOB developed specifically for this purpose called TagMapper — this resource is freely available to the scientific community at: http://tagmapper.ibioinformatics.org.

As identification of genes involved in a particular cancer is directly related to bringing a possible solution for the cure, this identification of responsible genes through bioinformatics efforts can change the world of cancer research in a way that could not be previously imagined. The success of this project as well as the previous projects by IOB highlight the capacity of research institutes in India to emerge as globally competitive centers in applying bioinformatics.

The Institute of Bioinformatics, a non-profit research organisation, was set up in 2002 as a center of excellence for bioinformatics in India. IOB has a staff of 70 scientists with experts in varying fields of biology and information technology. It has already received worldwide recognition for developing unique databases such as Human Protein Reference Database (HPRD), an extremely popular protein repository which is freely accessible to the scientific community.

Oncomine, another database developed by this institute enabled discovery of a unique genetic signature for cancers. This database was covered in many prominent international news media including the Discover magazine as a revolutionary resource. Also, IOB recently received a research grant from Human Proteome Organisation, the world’s premier body on proteins and their characterisation for collaborative research.

Courtesy: Institute of Bioinformatics, Bangalore