Bioinformatics in stem cell research

Rendezvous with a scientist- Dr. Vivek Tanavde

Rendezvous with a scientist- Dr. Vivek Tanavde

Dr. Vivek Tanavde
Principal Investigator, Bioinformatics Institute, A*STAR, Singapore
Adjunct Principal Investigator, Institute of Medical Biology, A*STAR Singapore

Dr. Vivek Tanavde obtained his Ph.D in Applied Biology at the Cancer Research Institute in Mumbai. In 1999, he joined as a postdoctoral fellow at Johns Hopkins and worked on expansion of umbilical cord blood stem cells. He then joined Reliance Life Sciences India and was heading the hematopoietic stem cell lab. In 2006, Dr. Vivek Tanavde joined Bioinformatics Institute.

We met with Dr. Tanavde and talked to him about stem cells and the role of bioinformatics in stem cell research. This rendezvous piece is a dialogue between Dr. Tanavde, Laxmi Sankaran and me (Sandhya Sriram).

In recent times, stem cells have been one of the most discussed topics. What do you think is the impact of stem cells on the society?

Stem cells definitely has had an impact on the society, however, the challenge faced by researchers especially, is to meet the high expectations of the society. It is tough for researchers to meet the urgent requirements of patients. In the media, stem cells have been referred to as a ‘cure’. It is true in some cases but the fact is it takes a long time to establish stem cell therapy. Most patients will not have that kind of time, that is the reality and this proves to be a big challenge. However, given the role that stem cells play and the progress that has been made in the field of stem cell therapeutics, it is quite amazing as to what can be achieved. The pace at which stem cell research is moving forward is reasonable but it cannot meet the expectations of people as of yet in terms of timeline.

Billions of dollars are being poured into ‘stem cell’ research and Singapore is actively doing research on stem cells. What can we look forward to in the coming years?

Singapore was very active in stem research from 2005 to 2010 with dedicated funding for basic stem cell research. Now, the focus is moving more towards translational medicine and using stem cells for therapeutic applications. The present trend is clinical and diagnostic assay based.

Since stem cell therapy is expensive, do you foresee a common man being able to afford it?

Definitely, maybe ten to fifteen years down the line. Currently, it is expensive due to the way we do things. I was exposed to this in my previous company, Reliance Life Sciences; where in a market like India, it is very difficult to get people to pay such a high price. Also the regulatory bodies in charge of stem cell ethics make it hard for researchers to perform certain experiments. Researchers tend to generate a lot of data and finally only a small percentage of it is actually published for everyone to access. This causes the high pricing of stem cell products. For example, let us take the method in which we culture stem cells in the lab. We scale up the process from a lab dish, which is actually not an efficient way of doing it, but we have no other choice at present. It is similar to the transition of a mainframe computer to a personal computer. Nowadays, we have smartphones that are more powerful than desktop computers! Therefore, we are hoping for a breakthrough to happen in mass production of stem cells. We are still in infancy and I do not know how long it is going to take for you to just walk into a clinic and get stem cell therapy done. It needs to happen and it will happen over the next few years.

Stem cell banking is gaining popularity world over. Other than cord blood banking, how do you think adults can bank their stem cells?

Cord blood banking has become quite famous in recent years and the prices have come down from what it was ten years back. It used to be around SGD 13,000 to 15,000 for a ten-year period, but at present it is about half the price. This has happened due to pure economy of scale- more people want to do cord blood banking.

Increasingly, we are moving towards the notion that the best source of stem cells is dependent on the application. For example, stem cells from the adipose tissue/fat are the easiest to get and many a times non-invasive as these can be collected during liposuction procedures. These adipose stem cells are suitable for obtaining fat tissue or a new blood vessel formation, to a certain extent. But if you want to make bone out of these adipose stem cells, it is not very efficient. Hence, the stem cell source is highly dependent on its application. I think we should have stem cell source specific banks in place.

In line with this, I would like to add that in the advent of iPSC (induced pluripotent stem cell) technology, we can get tailor made stem cells with the characteristics that you want.

How is bioinformatics helping stem cell research and what are its pros and cons?

Bioinformatics gives you an additional tool set along with everything else that is out there. Bioinformatics helps to reduce lengthy and time-consuming biological experiments when they need to be performed on a large scale. Bioinformatics helps understand biological processes and signaling at the cellular level giving an insight to researchers as to what is happening inside a cell. This will help them manipulate the cell or improve its condition to use for therapy. Bioinformatics is complementary to all the existing tools. More tools means more chances to analyze precisely what is happening. That is how bioinformatics is revolutionizing stem research and perhaps therapy. For example, when I was a post doc I was looking at designing media to grow hematopoietic stem cells in vitro. The way I did it then was using trial and error method, which has its limits in terms of quantity. When I came to Singapore, we did a similar project with a biotech company to manufacture serum-free media. We looked at all the genes expressed, the cytokines and receptors expressed and based on that large amount of information; we were able to come up with a series of critical growth factors, which helped us develop the media. This method was much more rational than actually performing everything on the lab bench. Bioinformatics helps reduce time and is an efficient ‘cost cutting’ method.

When I came to Singapore, I said that there will be no bioinformatics in the future and it still holds true. Bioinformatics will stop being a separate entity or a distinct field. It will become an integral and essential part of biology. Bioinformatics is defined as data generated in a computer to study a biological question. Nowadays there is not a single biological equipment that does not use or is not connected to a computer! This is because the data generated by experiments is immense especially in case of high throughput imaging, gene microarray, proteomics etc. Bioinformatics is needed to collect, manage, organize and interpret the data generated by performing experiments in the lab.

What is the work that your lab at BII is doing currently?

Currently, my lab is interested in looking at how microRNAs are important in stem cell differentiation. The human body uses microRNAs to regulate numerous signaling pathways and cell growth and differentiation. We work with adult mesenchymal stem cells, which have many applications including cardiac to orthopedic uses. We think that microRNAs hold the key for targeted differentiation; if I want a stem cell to become a cardiac muscle cell; it should become a cardiac muscle cell and not a bone cell! Imagine having a bone cell in your heart-it is definitely not a good idea.

I am sure there are many researchers out there who would like to acquire bioinformatics skills to aid their present line of work. Are there any courses available for biologists to take to learn various tools of bioinformatics?

That is a good question. There is definitely a need for biologists to get hands on with bioinformatics tools since only you will know your dataset and the specifics of the experiment as such. Currently, there are no short-term courses available for biologists to attend in Singapore. There is definitely a gap there and the need for skill-based technology platform courses is immense. A company in Ahmedabad, India called IBio Analysis Pvt Ltd is providing such 5-day workshops and training courses for biologists. The course would deal with basics of bioinformatics and at least teach biologists how to analyze sequencing data or the huge amount of data generated from a microarray experiment. This kind of workshop is yet to happen in Singapore, and I hope the private sector takes part to a greater extent to answer this unmet need.

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