Not lost in space Episode #1

This podcast is about two scientists, Dr. Patrik Ståhl and Dr. Fredrik Salmén, who are joint first authors of a paper that kickstarted a field. It's about finding work they did with colleagues to enable finding out where in tissue gene expressions is happening. It's called spatially resolved transcriptomics. It is a Nature Methods Method of the Year and I did a story about it here: https://www.nature.com/articles/s41592-020-01033-y . This is a podcast series that shares more of what I found out in my reporting. The piece is about patience, stamina, friendship, surfing the Baltic Sea, genomics and imaging. [00:00:05.560] - Vivien Marx Hi and welcome to Conversations with Scientists, I'm Vivien Marx. This podcast is with and about two scientists and about space space in biology. Actually, you'll meet Patrik Ståhl. He's on the faculty of KTH Royal Institute of Technology in Stockholm, Sweden, and Fredrik Salmén, who is currently a postdoctoral fellow at Hubrecht Institute in the Netherlands. They will talk about a field. [00:00:33.280] - Patrik Ståhl The whole field. It's really it's it's an awesome field. [00:00:36.940] - Vivien That's Patrik Ståhl. Their work led to a major publication in the journal Science, and they are both joint first authors of this paper, [00:00:47.710] - Patrik Ståhl We share the honor [00:00:47.710] - Fredrik Salmén and the pain. [00:00:47.710] - Vivien The honor and the pain. That's research for you. Just briefly, before we get to that about this podcast series, in my reporting, I speak with scientists around the world, and this podcast is a way to share more of what I find out. This podcast takes you into the science, and it's about the people doing the science. You can find some of my work, for example, in Nature journals that are part of the nature portfolio. That's where you find studies by working scientists. [00:01:19.960] - Vivien And those are about the latest aspect of their research in a number of these journals offer science journalism. These are pieces by science journalists like me. This podcast episode is one of several I'm producing about space in biology. Months ago, I interviewed researchers who work on Spatially resolved transcriptomics for a story and in my slowpokey DIY podcast production. This is part one in a series about this field of study. So Patrik Stahl and Fredrik Salmen here they are introducing themselves to help me learn how to pronounce their names. [00:02:02.890] - Patrik Ståhl Fredrik you go first. [00:02:03.560] - Fredrik Salmén Fredrik Salmén. [00:02:12.290] - Vivien All right. I have to practice. OK, so in [00:02:16.750] - Patrik Ståhl English it's Patrick. It's Patrik Stahl. [00:02:21.650] - Vivien Patrick Sahl? So no t, Stahl [00:02:29.210] all right, you have to brace yourselves. [00:02:33.980] - Patrik Ståhl Stahl means steel in English, [00:02:36.393] - Patrik Ståhl Patrik Ståhl [00:02:36.780] - Vivien Wow I apologize . Despite their lessons, I am doing the Swedish pronunciation of their names badly. I hope they and Sweden will forgive me. So I interviewed these two Swedish scientists together and when we started to chat, I noticed a poster on the wall behind Fredrik Salmen. It showed a surfer riding a big wave. So I asked about that. [00:03:03.530] - Patrik Ståhl Fredrik actually quite advanced surfer, like wave surfer at the time when we started this project. [00:03:14.540] - Fredrik Salmén Yah, it's true. Oh, it's actually me. It's a little bit self-centered, I guess, to have their own picture on the wall. But it's fun, though. It's [00:03:27.620] - Vivien where was this taken? [00:03:30.290] - Fredrik Salmén This is actually Sweden. So it's the Baltic Sea. [00:03:35.900] - Vivien The Baltic Sea is cold. You need to wear a special suit if you want to surf there. [00:03:41.240] - Fredrik Salmén Yeah. It's like a frog suit with hood and gloves and boots. [00:03:45.920] - Vivien So do you still do this or. [00:03:48.320] - Fredrik Salmén Yeah, I still do. I'm a little bit, I would say much less nowadays and I'm also a little bit heavier these days, so not as agile anymore. But still when I get the opportunity I try to surf, it's nice. [00:04:06.020] - Vivien The two researchers worked together along with many others, but their connection was quite intense and you will hear more about that in this podcast. [00:04:13.260] - Vivien It was work that took around six years and led to a publication in the journal Science. And that publication kick-started a field. And there was a company spin out to the field of study is called spatially resolved transcriptomics, and it was crowned a Nature Methods method of the year. In this area of spatially resolved transcriptomics, scientists want to know where something takes place. It's part of understanding larger issues, such as why does the head grow where it does? [00:04:44.750] - Vivien Why does a part of the brain develop where it does? Why does a tumor grow where it does? It's genes that tune such events, genes are turned on or off, they are expressed at high levels or low levels or silenced, their expression can shift. With gene expression, it's like tissues are playing a kind of music, just one you need to find ways to hear. Patrik Stahl and Fredrik Salmen and their colleagues found one way to do just that. [00:05:15.370] - Vivien The work took place in Sweden. It involved surfing the cold waves of the Baltic, as you just heard. It's about friendship. It's about patience, about science, careers. If you're interested in any of that, as well as biology, genomics and imaging, please stick around. So this work in particular took six years and Fredrik Salmen and Patrik Stahl worked intensely together. They are the first authors of this paper in Science published in 2016, and it led to a company called Spatial Transcriptomics. [00:05:45.790] - Vivien What these scientists and their colleagues developed was a way to see where, for example, in a tissue genes are expressed. It's not the first way to do this, but it was a way to analyze a lot of mRNAs, a lot of gene transcripts at the same time. To understand why this matters, we can step back for a moment and consider a practical example that they told me about. A pathologist gets a tissue sample. It might be from a person who was just on the operating table. [00:06:13.300] - Vivien The tissue is prepared with chemical stains and then studied. The pathologist interprets what is going on in this tissue. Sometimes pathologists look at many tissue slides from many patients and want to compare them. In other cases, it is information that has to travel quickly to determine how a patient might need to be treated. Or the analysis is for a basic research lab that is studying a particular disease or development. As Patrik Stahl explains, scientists can look at a tissue slide and use stains and dyes to see what is happening there. [00:06:46.630] - Vivien Well, sort of. This immunohistochemistry doesn't always answer all the questions of pathologist or other scientists might have [00:06:55.990] - Patrik Ståhl So I think this was like late 2009 and it was Jonas Frisen, who is a who is, s stem cell professor working at Karolinska Institute who is subjected to this kind of immunohistorchemistry a lot during his daily work. And I think that he was the one who first grew tired of a lack of spatial information that they could get out of a stain. And so late 2009, he contacted Joakim Lundeberg and they together in early 2010, initiated this project , trying and then...