I recently spoke with Dr. Suneil Malik about genomics and outbreak preparedness.
Dr. Malik is a Manager and Team Leader for Toxicology at Health Canada, a government agency directed by the Canadian Minister of Health. He is based in Ottawa, Ontario, Canada.
Our conversation will be posted in two parts. Part I (below) is about the role of genomics in biodefense and outbreak preparedness. Part II (to be posted next week) will examine the benefits and potential pitfalls of the so-called “omics”-revolution, which consists of new technologies such as transcriptomics and proteomics that are changing the field of medicine.
About Dr. Malik:
- He was a Biologist at the Office of Biotechnology, Genomics, and Population Health at the Public Health Agency of Canada (PHAC).
- He is an investigator at the McGill International Tuberculosis Centre in Ottawa.
- He is the author of numerous publications in the field of genomics, including the highly regarded article “Genomics Research: The Underpinning of Infectious Disease Prevention and Control Strategies” (2013) and a landmark paper on the association of the NRAMP1 gene with pediatric tuberculosis
- He currently works as a Manager for the Mechanistic Studies Division and the Hazard Identification Division in the Environmental Health and Science Research Bureau at Health Canada, a department of the Government of Canada focused on promoting and maintaining the health of Canadians.
Q: Dr. Malik, thank you for taking the time to speak with me today. Could you start by telling me a little about how Canada prepares for biological emergency situations, like pandemics and deliberate biological attacks?
Dr. Malik: The Public Safety governmental department is in charge of coordinating other departments in the event of biological emergency. Depending on nature of the emergency they would coordinate with the Public Health Agency of Canada (PHAC), which is where I worked and/or Health Canada, or other departments. PHAC is very well positioned to address infectious outbreaks. Their main laboratory is in Winnipeg, Manitoba, and is referred to as the National Microbiology Laboratory (NML). They have outstanding capacity and expertise to sequence and identify pathogens and to do so rapidly.
A little bit of history on this: The need for a center like PHAC became clear during the SARS outbreak early ‘90s. The Minister of Health at the time recognized that there was a need to have a dedicated body with the infrastructure, capacity, and expertise to address infectious-based outbreaks. This is how PHAC was born. And if it is something that is in our food, the Canadian Food Inspection Agency would also be on board.
Q: You spent time developing intervention strategies that focused on genomics. Please tell me more about that. How can genomics research help with emergency and bioterror preparedness?
Dr. Malik: My work in genomics was not directly related to bioterrorism preparedness. When I was working in genomics with PHAC, the idea was to understand why people who are exposed to an infection, for instance influenza or M. tuberculosis, do not respond equally. Most people exposed to these pathogens recover, but some people (about 10%) develop severe outcomes. Our research was focused on this subgroup. Why are some people so much more vulnerable to infection? It could be that the people who develop severe outcomes have co-morbidities or other issues, but that does not explain the entire burden of disease. As such, a lot of work has gone into studying the genetic makeup of the host.
We decided to use genetics to understand why an individual’s immune system is not adequately dealing with the infection. And if we understand that, maybe we can develop intervention strategies to prevent people from getting ill. For example, some individuals carry a polymorphism (a common genetic mutation) that may affect the way in which they metabolize micronutrients like vitamin D and this could be important since vitamin D has been linked with immunity to infections. If we find evidence for this, perhaps we can supplement a vulnerable subsection of the population with vitamin D to prevent severe illness.
Just to make it clear, this research was not being used directly in the context of bioterrorism and emergency preparedness at the moment but potentially can be in the future.
Q: In one of my recent interviews with public health experts, a gene was mentioned that might impact flu severity. It seems that not much research has been conducted on this gene, IFITM3, to date. Is this something you might be working on in the future?
Dr. Malik: Yes, this was associated with susceptibility and it is a gene worth exploring further. Once a gene is identified, the next challenge is to understand how genetic variants lead to susceptibility of disease. Only by knowing ‘how’ this gene modifies immunity can we start to develop rational intervention strategies to prevent severe influenza.
The newspapers often write that scientists have found a gene that is associated with cancer or some other disease. But that is often where the story ends. Again, you have to know the role of this gene in a given disease before prevention strategies or treatments can be developed.
Q: Will genomics work help make people more resistant to viruses? Or will it mainly help identify those who are most vulnerable?
Dr. Malik: That’s a very good question. It could do both! By using genomics you may parse out the molecular mechanism underlying a viral infection. Once you have this understanding you may develop markers to identify vulnerable subpopulations and, further, to develop rational intervention or treatment strategies.
Q: Do you think genomic research could be used to help us in other areas, such as biodefense?
Dr. Malik: Yes, genomics itself can help identify the biological agent. We are able to sequence the DNA of the pathogen to identity what type of bug we are dealing with. In terms of the genetics of the host (people), we use genetics to identify people who are more susceptible to the agent. Right now, in terms of biodefense, our best defense is to be able to identify the type of bug we have and that’s where we use genomics. Genomics can help us identify targets on the bug for which we can develop treatments. On the flip side, if we understand why individuals are susceptible to the bug, we can focus on enhancing the host’s immune function, zeroing in on very specific biological pathways. Genomics gives us a lot of information.
We study diseases using genomics as a tool, but we use other tools as well. These tools fall under the umbrella of “-omics” tools, namely transcriptomics, proteomics, metabolomics etc. The challenge is to bring all that data together and try to understand what is going on.
Q: Is this work being done by governments? Or is it mainly universities and academics who are focused on it?
Dr. Malik: When I was doing research on infectious diseases in PHAC, we worked extensively with academia. Oftentimes, one institution does not have the capacity or expertise to do everything. So, it is important for us to collaborate with other universities, and not just within the country, but internationally as well. When I worked on tuberculosis, I collaborated with McGill University that had a cohort of patients from which we could obtain DNA to identify genetic susceptibility genes. In another study we worked with the University of Montreal for their statistical analysis in genetics. These are just a couple of our many collaborations with academia.
Part II of this conversation will be posted next week. Stay tuned!
“Alleles of the NRAMP1 gene are risk factors for pediatric tuberculosis disease”. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1189316/