MJM MedTalks
Genomes and Japan (Part 2): How international collaborations are shaping science
S03E04Jan Pack1, Guillaume Bourque2, Susan Joanne Wang 1, Maryia Samuel1, Lilian Alkhalaileh1, Renée-Claude Bider3,
Published Online: 15-Jun-2026
1McGill University, Montréal, Québec, Canada
2Department of Human Genetics, Victor Phillip Dahdaleh Institute of Genomic Medicine, Canadian Centre for Computational Genomics
3University of Ottawa, Ottawa, Ontario, Canada
mjm.med@mcgill.ca
Abstract
The human genome consists of about 6.2 billion base pairs. Almost half of these consist of repeated sequences, also called transposable elements, which have long been regarded as biologically inactive. However, we are now starting to realize that they may play a bigger role in the regulation of our genes than previously thought, and even give clues to our evolution. In this two-part episode, we are talking to Prof. Guillaume Bourque of the Department of Human Genetics at McGill. His goal is to understand mammalian genomes via comparative analyses and investigate the role of transposable elements in gene regulation and the impact of genome rearrangements in evolution and cancer. He also shares with us his experiences in running a successful collaboration between Canada and Japan, and how we can continue to do meaningful work despite global tensions and the rise of AI in research.
Content Overview
[00:00] The future for international collaborations
[04:25] Pros and cons of double degrees and advice to students
[09:30] Cultural differences between Canada and Japan
[12:04] Current political unrest and its consequence for research collaborations
Glossary
- AlphaFold: An AI program which predicts protein folding in a virtual space (in silico). One of the first AI tools for biomedical research.
- Illumina: A company developing sequencing technology.
- CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR-associated protein 9 (CRISPR-Cas9) is a protein adapted from bacteria and used to selectively edit DNA.
- Endogenous Retrovirus (EV): Ancient viral DNA sequences integrated into the genome that play a role in evolution, placenta development, and disease.
- Genome: The complete set of genetic instructions in the form of DNA (or RNA in some viruses). It contains all the necessary information for an organism to function, grow, and develop.
- Haplotype: Derived from “haploid genotype,” a set of closely linked DNA variations (alleles or SNPs) on a single chromosome that are inherited together from a single parent.
- Long Terminal Repeats (LTR): Identical sequences of DNA, typically 200–1,100 base pairs long, found at both ends of retrotransposons and retroviral proviruses.
- p53: A regulatory transcription factor that helps prevent cancer by monitoring cellular health.
- Point Mutation: A genetic mutation in which a single DNA or RNA nucleotide is substituted, added, or deleted.
- Promoter: A sequence in the genome that enables the binding of polymerases and transcription factors to initiate RNA transcription.
- Reference Genome: A standardized digital database compiled from multiple genomes, serving as a representative scaffold against which DNA sequences are compared.
- SNP: Single-nucleotide polymorphisms are a common type of genetic variation in which a single nucleotide differs among individuals or from the reference genome.
- SOX Family: A family of transcription factors that play a critical role in cell fate, embryonic development, and homeostasis.
- Transcription Factor (TF): Proteins that regulate gene expression by binding to specific DNA sequences (promoters or enhancers) and turning gene transcription on or off.
- Transposable Elements (TE): Also known as “jumping genes,” these are DNA sequences (100–10,000 base pairs long) that move within genomes, drive evolution, induce mutations, and comprise over 45% of the human genome.
- Zinc Finger (ZNF): Structural motifs in proteins that can recognize and bind to DNA, often found in transcription factors.
Links and Papers
Studies- Chen X, et al. A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage. Sci Adv. 2025;11:eads9164. doi:10.1126/sciadv.ads9164. https://doi.org/10.1126/sciadv.ads9164
- Gill EE, et al. The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. Microb Genom. 2024 Oct;10(10):001293. doi:10.1099/mgen.0.001293. PMID: 39401061; PMCID: PMC11472881. https://doi.org/10.1099/mgen.0.001293
- Aracena KA, et al. Epigenetic variation impacts individual differences in the transcriptional response to influenza infection. Nat Genet. 2024;56:408–419. doi:10.1038/s41588-024-01668-z. https://doi.org/10.1038/s41588-024-01668-z
- Ancient viral DNA may play a key role in early human development, new study suggests. CNN. 2025 Aug 9. https://edition.cnn.com/2025/08/09/science/ancient-viruses-junk-dna-primate-genome
- Bourque Lab – Computational Genomics Laboratory
- Guillaume Bourque – McGill University profile
- Guillaume Bourque – Kyoto University profile
- Kyoto–McGill Joint PhD Program
Transcript
Introduction
Jan Pack (JP): This is the second part of our two-part interview with Guillaume Bourque of McGill University. You can find the first part, in which we talk about Genomic research, and how viruses may have influenced Human evolution, along with many other interviews on the MJM Spotify page. Enjoy!
Interview
JP: So changing a bit the topic from the research itself a bit more to the collaboration between Canada and Japan. I think that also very much connects to that because of the change that we're experiencing now with AI, but also the world in itself is changing a lot. So these kind of collaborations, which comes back to, you are in a camp, but you should absolutely talk to the other camp too, which is kind of what you're doing with this Canadian-Japanese collaboration, right?
So yeah, you're pretty much deeply involved in that with Kyoto University specifically. There's a joint PhD program that's running between the two institutions, so can you tell us about that, how it started and how it culminated in the recent publications?
Dr. Guillaume Bourque (GB): Yeah. So, I mean, it started a long, long time ago. Well, I mentioned that I started my lab in Singapore and, you know, I've always been interested in looking for opportunities to continue to come to Asia. But McGill, even when I joined, already had a strong connection with Kyoto University, organizing regular events and symposia.
And this started more than 10 years ago, looking at collaborative work because, yeah, indeed, it's great sometimes in science in particular to think about collaboration and bringing different perspectives in certain things. And one thing led to another, and there were opportunities, I think, initially in Japan, to propose a more formal collaboration through a joint PhD program.
And so Matsuda Sensei, who is a professor here in Kyoto University, was successful with an application to put forward- to get resources from a funding agency in Japan, to sort of formalize the collaboration that we had and part of that was to create a joint PhD program between the two universities and convert our ad hoc meetings into more regular meetings and so on.
And so similarly on the McGill side, there was all of these interests, of course, there's many international students coming to McGill and, promoting international collaboration is, I think, an important part of science and then viewed positively by institutes. But it's not easy and it takes time because you need to build links and it's a lot of effort and in some ways, and especially with Japan and McGill, in Canada, especially with Montreal, it's a 12-hour difference and so it leads to some logistical challenges, but it's still, I think it's a great, it's been a great partnership.
And I believe we launched a program in 2018, and by now, we've graduated or have close to 20 students in the joint PhD program. So very nice, I think. And I should say the students can either start on the McGill side or start on the Kyoto side, and then do a one-year exchange as a minimum component of their PhD, and then can either return to their home institution or continue sort of the back and forth between the two institutions.
JP: Yeah, I'm very well aware of what kind of logistical problems that sometimes brings with the 12-hour difference there. It's challenging but exciting sometimes. And I'm very happy to see this collaboration. I think that's a great thing to do and I think that's kind of a bit the future going forward as well, to do more of these rather than less.
As a student who's thinking about doing this kind of joint PhD, in that perspective, what do you think would be the pros and cons of doing such a degree?
GB: Well, yeah. Lots to say on both sides of the equation. I mean, maybe we start with the cons. So I think the cons are really, logistically, it's more challenging and a PhD is hard to begin with, right? And often takes time and always takes quite a bit of time, right?
And so adding, one layer of complexity to a PhD can then add even more time to a successful PhD. And so that's- you need, you need to coordinate with two supervisors and sometimes coordinating with one can be a challenge and so coordinating with two can be a challenge. And so, those are some of the cons.
But on the pro side, and if I continue on the idea of co-supervision, I think having co-supervision is both good and bad. I think it's also good because it gives you different perspectivs on the project. I think there's a lot of pros to that. I think it exposes you to two different lab cultures and I mean, literally two different cultures in this case. So I think that's quite clear.
I think it allows you to potentially have a project that's maybe more challenging to do, but also more interesting to do in a way, because it's going to, you know, it's going to force really thinking about some things that is going to use the resources from both of these labs. And so it's the idea of high risk, high return a little bit, right?
I think it's a little bit more challenging, but has more potential as well and gives you access again to two resources and to two countries and universities. And so that's interesting.
One thing on the pro side that maybe I'll add, and this is something that, now that I've been going through this for some time, I'm realizing is important is, it'sort of more if you think beyond your PhD itself, but more long term. Well, and again, if the goal is just to do a PhD and then move to industry and be able to say you've done a PhD, you know, maybe it's not as needed or interesting, although, you know, still this gives you opportunity and exposes you to two different countries.
But in the academic sense, if you decide to stay in that stream, you know, the Ph.D is really the beginning of building a network of people and sort of thinking about science and collaboration in ways that it will grow.
So if I look at my career path, right, you start doing a PhD, it's sort of a narrow project, postdoc maybe a bit more and broader, but when you start building a lab and you start growing a lab and by now, like my lab is doing all sorts of things, but this process really goes through, you know, both thinking about expanding your knowledge of science and then working on broader and broader research topics, but also building a network of people that you know and expanding the collaborations and the connections.
And so, if you think about the PhD as a first step in that path, then I think the joint PhD is very interesting as well because it will expose you, early on, to this kind of broader network, not just one lab, one department, but two universities, two labs. And so, you know, in that context, it's a bit of a gamble because it makes the PhD maybe a little bit more challenging in the short term. But I think in the long term, you know, there's just more potential as well.
And again, through that process, you will have met people in two different countries, for sure. And, often people say that it's good to, if you do your PhD in one place, to do your postdoc in a different place. And then that is facilitated by doing a PhD, that's a joint PhD. Whether, well, I think it would facilitate on your CV, you know, showing that you've already, not just been in your own city, but you've already been exposed to this kind of international thing. And it would facilitate doing a postdoc, of course, in the other institute, but also anywhere else. So in that sense, I think these are- these are- there's lots of pros, I think. I mean, and this is. Yeah.
JP: Yeah, as someone who was being co-supervised by a Japanese PI (Principal Investigator/Professor) and a Canadian PI, I can definitely confirm your points.
GB: I mean, you could flip this around and talk about the cons because, you know, the culture shock between Japan and McGill, it's quite striking, right? And so, and this is like at all level, including at the level of the PhD itself. And, you know, the administration and doing a thesis and doing a (PhD) defense, like at all levels, it's actually quite complex, right?
So it's like, it's, yeah, you would know well, it's like, it's, I don't want to make it sound like it's easy. So there's, you know, and in terms of cons, I think there's definitely this added complexity.
It's like, and every case also, and this is true, I mean, you're a unique case because you're not part of the joint PhD and you sort of have your own joint PhD. But even within the joint PhD in McGill and Kyoto, I would say that every student is a bit unique in the sense that, you know, it's hard because, when you start and you start on this side or that side, and then, we end up having to sort of have a special case with every student in a way because it's just hard to fit everybody into the same mold, because of the sort of the logistical challenges of this joint PhD. But- so you need to be comfortable with that, but then it comes with all these pros.
I mean, the other pro I would have said, this is my bias, is just the food and the experience in Japan. So coming from McGill, I mean, well, it's such a wonderful place to be exposed to, Japan, for something like a year. I mean, I think that's an amazing opportunity. And probably true, the reverse is also true, but definitely for people coming from McGill.
JP: Yes, I can confirm, yes.
GB: Yeah.
JP: All right, maybe a little bit concludingly and looking a bit more into the future and the big picture. Since you're exposed to this very international, intercontinental collaboration on a very high level, you definitely have some insights that we normal (PhD) students probably don't have.
So looking at that, in the light of recent political turmoil in North America and many US-based researchers getting their funding cut, actually, And I hear a lot of talk that people would love to emigrate from the US to some other places because of this. How do you think that the ties between Canada and Japan will change? Will it be strengthened? Will it be deepened? Or will there be more insecurities as an obstacle?
GB: Well, good, very good question. Before I talk about Japan, let me maybe answer that question more generally. You know, I think that- okay, yes, uncertain times, we don't know exactly what's going to happen in the US and elsewhere. But to me, being connected to a broader network.. there's strength in that because you're not tied to just one place and one thing.
And so, you know, I'm a strong believer in sort of spreading my eggs a little bit. And I just find that, you know, not not not just putting all my eggs in one basket puts me in a position that even if the situation is more difficult, it's easier to pivot because you have some other ways. And so I think this would apply generally to staying open and looking for these kinds of international opportunities because I think it does strengthen your position even in this uncertain world.
And more specifically then to your question on- and in terms of what's coming, I really don't know because it is an uncertain world for me too. So I think it is really a concern in terms of what's going to happen in- I mean, we see it already now in the US. I think it's very likely going to come to Canada much worse than it currently is. We'll see in what form, but I think there's definitely some uncertain times ahead.
But going back to your more specific question about Canada and Japan partnership, I think there's an opportunity now to indeed strengthen these ties. I think there's an opportunity for stronger ties with between Canada and Europe as well. So there's new programs and we see it again at the political level and that sort of trickles down at the scientific level.
You know, I think we were over-reliant on the US from the Canadian perspective for many things in the economy, but also in science. So I think it is an opportunity, and maybe that's the positive way to look at all of this. I think there is movement towards more opportunities to collaborate with others. And I think, again, this is true both on the political and economy side of things, but also true for science. And I think that is a good opportunity now.
So maybe in this uncertain time, still, you know, a positive outcome and then something maybe to try to focus on. So in the short term, I'm not too worried for these collaboration, and I think it's worth continuing to pursue and encourage. And yeah, and I do see some support for these types of international efforts, at least for now in Canada. So, you know, that's good. And then, you know, the good ideas in the end prevail.
So, you know, sometimes it takes longer to get funded for certain things. And sometimes it takes a long time. And like this collaboration between McGill and Kyoto, I think, took more than 10 years to be in full steam ahead, right. But I think right now we're in a very good position with having, you know, being patient and setting all of these things.
And this, you know, if I maybe finish on something, you know, I think that, you know, you do need to be patient. Certain things can move fast and then certain things you do need to be patient on. And I think that is reasonable advice also for PhD students. I mean, I think you do need to think about things you want to do that are good in the short term and there are things that will be good in the long term and sometimes you just, if you are confident that these are good things.
You need to be patient on them and continue to push on that and sometimes the positive outcome of those efforts will just come later as opposed to in the short term. And I, again, didn't expect this, but I see that now, you know, I'm getting closer to the end of my career and I see how things that were important to me - and I continued even if, you know, they weren't supported - are paying off now because, it just took longer for people around me to appreciate that.
But if you continue doing it, at some point, you're ready to jump on these opportunities because you've made the progress on these things, even though they weren't popular at the time. So don't only do things that are popular right now. Like, do things that are, it's also very difficult to know what's going to be popular later. You can not really do that, but you can pick things that are important to you now.
And so even if they're not popular, you do them and hopefully that's going to be, that's going to pay off later on.
JP: Yeah, that's great advice. I think that's a perfect note to end it on. I'm sure we could talk much longer, but unfortunately we're running out of your time, so.
GB: I know, but thanks a lot, thanks for the interview.
JP: Thank you so much. This was amazing, I had a lot of fun and who knows, maybe there'll be another one at some point!
GB: All right. Well, thanks for all the questions. You really, I thought you really led me into, you know, talking about all the things I like a lot in a very systematic way. So thank you for this as well. All right. Thank you. Bye.
JP: and thank you, our audience for joining us on an other episode of MJM podcast the MedShow series. Please consult our show notes where you will find a transcript of our conversation as well as links to any projects or papers we have discussed. As always, see you next time.

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