The future of ribosomes

0:00This is Stanford Engineering's The Future of Everything, and I'm your host Russ Altman. I thought it would be good to revisit the original intent of this show. In 2017, when we started, we wanted to create a forum to dive into and discuss the motivations and the research that my colleagues do across the campus in science, technology, engineering, medicine, and other topics. Stanford University and all universities, for the most part, have a long history of doing important work that impacts the world. and it's a joy to share with you how this work is motivated by humans who are working hard to create a better future for everybody.

0:37In that spirit, I hope you will walk away from every episode with a deeper understanding of the work that's in progress here and that you'll share it with your friends, family, neighbors, co-workers as well. So one of the things that we're attempting to do is to say, okay, cancer evolved, like we had discussed, it's customized ribosome to generate a customized cancer proteome. So now can we put in a payload, for example, something that would kill a cancer cell and make it highly specific only for that cancer cell by making use of those cancer ribosomes. So basically now saying, can we reshift the focus of what these cancer ribosomes are actually translating and make it a death signal for these cells as opposed to a normal cell.

1:35This is Stanford Engineering's The Future of Everything, and I'm your host, Russ Altman. If you're enjoying this show or if it's helped you, please consider sharing it with friends, neighbors, colleagues, anyone who you respect and love, because personal recommendations are the best way to spread news about the future of everything. Today, Maria Barna will tell us that the molecular machines that make proteins, proteins which are key to many aspects of life, are critical for cancer, for infections, and for neurological disease. It's the future of ribosomes. Today, we are continuing our new feature called The Future in a Minute.

2:12At the end of the interview, I will ask Maria a few rapid-fire questions, and she'll give me a few rapid-fire answers. Before we get started, a reminder to tell your friends, neighbors, and everyone else you meet throughout the day about the Future of Everything podcast and how much you're enjoying it. Personal recommendations are what it's all about.

2:37So when we talk about biology, we often talk about the central dogma, the organizing principle of all biological research and knowledge. And it's called the central dogma because it's central. And it goes like this. DNA in the genome gets transcribed into RNA, another molecule. That RNA becomes protein, and proteins do all the work in the cell. So the central dogma is simply DNA to RNA to protein. Well, that RNA to protein link is implemented by a molecular machine called the ribosome, which takes RNA as input and produces proteins as output. It's literally a tiny little factory. And for a long time, we thought that all ribosomes in each cell were identical.

3:26They simply take the input, like a little computer, and make the output. Well, in the last few years, we've learned that ribosomes are actually much more variable. In a cell, you might have 10 million ribosomes, and there might be hundreds or even thousands of different types of ribosome that are specialized to do specialized things. In addition, these ribosomes can sometimes go awry, and you have abnormal, I like to call them diabolical ribosomes, that cause problems because they're not normal, and they're doing things that are not advantageous to the cell. They're advantageous to the disease.

4:04Well, Maria Barna is a professor of genetics at Stanford University and an expert on ribosomes. She's been studying them for many years, and she's going to tell us about recent discoveries that ribosomes are not all the same and that they're implicated in an unbelievable variety of diseases. So, Maria, why have you focused so much of your life's research on the ribosome? Well, I think it's one of life's most ancient and spectacular molecular machines. And just to think about it from the beginning, just to give you a perspective, so the earth is thought to have arisen 4.5 billion years ago. And when we think about what was the first molecule that actually was present, I think the knee-jerk reaction for a lot of people would be DNA.

4:55And actually, on the contrary, it's sort of the carbon copy of DNA that's commonly referred to as RNA that really was the ancient origins of what we favor as a hypothesis as the RNA world. And that's because RNA was shown and really in a remarkable series of discoveries that it had this core catalytic property. So it can encode nucleotides, but at the same time, it acted almost like an enzyme. And the most ancient molecule that ever arose gave rise to this machinery. So the core of the ribosome is all RNA-based. It functions as a way of getting two amino acids together to form a peptide bond, and that is all catalyzed by an RNA activity.

5:56So when we think about life, life in essence is the ribosome. It predated the protein. It predated the DNA. and it's been around, it's the oldest molecule that's been around in the evolution of life itself. So that's great. And I am aware of this RNA world hypothesis and I'm glad you mentioned it because it's so exciting and it's so cool because as you said, catalysis and a lot of the things in terms of speeding up molecular reactions, that's often thought to be the domain of proteins, but information carrying like the genome and the four bases that everybody knows about is always thought to be the province of DNA.

6:40But what you just said is basically RNA can do both of those things. And it kind of therefore makes sense that it might have been the first thing around. And then it kind of helped create subsequently the DNA as a modification of the RNA. You can even tell by the names. And then proteins might have been something that RNA created just to help it do its job. And as you know very well, and this is what we're going to talk about, the ribosome is kind of where all of these ideas come together. So tell me, what does the ribosome do in a cell? Right. So the ribosome is actually decoding the genome. We think about genes and DNA, and those are very common.

7:22but the actual executors of every single cellular decision across all kingdoms of life is actually the protein. And the way our genomes are decoded into proteins is via these molecular machines. And to give you a sense of scale, so a typical cell has 10 million, up to 10 million of these molecular machines that are packed in. Each is about 100 ,000 times smaller than the width of a human hair. 60 % of the energy of the cell goes into making these machines. 90 % of our transcriptome. So what actually is made into an RNA molecule is this machine. and actually 20 % of the proteome actually goes into making this machine.

8:19So essentially, you can think of a cell in different ways. The way my lab views it is a cell is a sack of ribosomes. Really, this is great. And so when you say machine, these really are machines. I mean, people say, oh, yeah, she's just using that as an easy-to-understand metaphor. for, but they are actually where they take input, which is the RNA, as you know, and they actually create the proteins as output. And they very much look and act like a synthesizing machine. Correct. And what I think is becoming incredibly exciting is the notion that in the past, we've kind of thought of these as simply being these static machines that, of course, play the most foundational role in life and health in producing all of these proteins, Russ, but not having sort of decision-making processes in terms of which proteins are made, in which cell types, where subcellularly in a cell.

9:31And what I think the newest discoveries are is the notion that these machines can be incredibly different. There can be hundreds of different kinds of this machinery that could have specificity inherent to that machinery to how it's decoding these genomes. What proteins are being produced, when, where, and how. Great. Now this gets us to, I know, some of the really exciting work that your group has done and published recently in some very high profile journals. So you said at the beginning that a cell might have, I think you said, tens of millions of ribosomes or tens of thousands? Up to 10 million ribosomes.

10:14So, okay. So it's filled with ribosomes. And as you said, when I went to school, all the ribosomes were the same. They took their input and they made their output. So tell me about this kind of very kind of paradigm shifting discovery that you made that those 10 million or up to 10 million are not all the same. And tell me the ways in which they differ. Like we don't really have a, I don't have a, maybe a clear picture of what a ribosome looks like. And so tell me what they look like and how they can make different decisions based on changing their makeup. Right. So in the most simplest way, the way that our lab describes a ribosome and its regulation is sort of as an onion.

10:57So there's layers upon layers of regulation to it. So it's true, at its core, it's this most ancient machinery that's made up of RNA. And I've already told you that 60 % of the energy goes into making this RNA core. And to do that, there are hundreds of copies of what are known as ribosomal RNA that basically make up this core. And recent discoveries have sort of started to look at these sequences more carefully. So there's more than 500 copies of what is known as this ribosomal RNA that's spread across five different chromosomes. And scientists ignored it. So until a couple of years ago, we only had the sequence of one of these RNA units.

11:54The rest, we couldn't even fill in. It was a complete, we thought we had sequenced the whole genome, but we didn't have or bother to sequence the rest of it. And so now we know that even in this ancient core, not all of these RNA units are the same and they can have slight variations in their sequences. Okay, okay. Then there's an outer shell of proteins. And these proteins can be either proteins that we've always thought to be what are the principal components of this machinery, because with the highest level of salt wash that we can throw on it, these are proteins that remain bound to this core ribosomal RNA.

12:40Those proteins, once thought to be invariable, now have been shown to be sometimes present in a ribosome and sometimes not. Okay. And there are hundreds of additional proteins that we've now characterized, which we've termed the ribointeractome, that have expanded our vision of what actually a ribosome is and its definition. And on top of that, there are hundreds of modifications, so little tiny changes to both the proteins as well as the ribosomal RNA. So if you were going to factor in, based on this knowledge, how many possible variant ribosomes could there be? It's actually, in theory, astronomical.

13:30It's something like 10 to the 20th different types of ribosomes. Which is way more than 10 million. 10 million is 10 to the 6th, and you're talking 10 to the 20th. Right. So it's almost like as many as there are sands of grain on the earth. And so, of course, we don't think that's what's actually happening because that would mean that each ribosome could only have one change. Right. And so we think that these are concordantly changing, and we feel confident in saying that probably there are hundreds of different types of ribosomes, and each can be attuned to varying which proteins are going to be made in specific cells, the speed at which these proteins are being made, the accuracy in which these proteins are being made.

14:26So essentially creating an additional layer of regulation to what's commonly known as genetic code. Great, great. So this is really helpful. So I mean, just to summarize, the ribosome as it's encoded in the DNA has many, many variations. The proteins that it can interact with has many variations. And then there's these little molecules making changes to the ribosome and your group, and this is now getting to the fun stuff, your group has not only shown all of this along with others, but now you're connecting that, tell me if I'm wrong, to some diseases and to some things very relevant to how human biology and other biology work.

15:07So how did you make that jump? Yeah. And so basically, I think that it is It's incredible to think about that, for example, every single neurodegenerative disorder, and this is really true for ALS, Alzheimer's disease, Huntington's, Parkinson's. There's a dysfunction. ALS is Lou Gehrig's, is also known as Lou Gehrig's. Yes. Yeah. There's a dysfunction of ribosomes or their regulatory pathways. So there's a decline in activity of these ribosomes. there is an incredible change that happens during aging. So because 60 % of the energy of the cell is going towards making these ribosomes, what's happening is as we age, and especially in the brain and in our neurons, that require such tight and dynamic regulation of how proteins are produced because they are sort of locally produced where synapses become active.

16:16There's a decline in the production of proteins by the ribosome. There's a decline in the stoichiometries. And by stoichiometries, I mean the compositions of ribosomes in these diseases and even in cancer. So it seems that in cancer, cancer cells have literally hijacked the ribosome, creating a completely customized ribosome that is decoding a cancer proteome. So it's a diabolical ribosome. Yes, it's the most diabolical ribosome. It basically says, I want to translate proteins that are going to be made that will promote my growth, my tolerance to highly hypoxic conditions, to therapies, and tailor it completely in a different way than a normal cell.

17:12Yeah, and it kind of makes sense because you said there are so many potential ribosomes. We only see some of them, but it's not that surprising to me, knowing how diabolical cancer is, that it would see all of those possibilities and see an opportunity to say, oh, I can put together a certain set of choices that actually don't help normal biology as much as it helps me, the cancer. And it sounds like that's what's starting to happen. Exactly. And you can equate that even to a viral infection, which is the most extreme version of this. When a virus infects a cell, again, it's all about the ribosome.

17:45So basically, the virus will shut down its cells host ribosomes and create a ribosome that is dedicated towards translating and producing viral mRNAs at the expense of the host proteome. Wow. So yes, it's a very powerful paradigm that I think will extend to neurodegenerative diseases, cancers, virology, and just how we think about normal cell behavior and disease. So I don't want to put words in your mouth, so I'm going to make it a question and not a statement, but it sounds to me like from your perspective, many of the diseases you just mentioned, neurodegenerative disease, some infectious diseases, and some cancers can be thought of at least in part as a disease of ribosomal function.

18:36Correct. And there are even more direct connections because core components of the ribosome themselves can be mutated. And I think this has been dogma changing because they give rise to a wide array of congenital birth defects. Sometimes they have been entirely ignored because people were seeing these components and saying, how can this be? There was a clinician at Rockefeller University that was characterizing children that were born without a spleen. So it's all the organs in the body are fine. They're just missing their spleens. And it turns out to be a mutation in only one of the components of the ribosome.

19:16You can have another component of the ribosome that's mutated and patients are born without body hair. And you can have another protein that's mutated in the ribosome and it causes devastating bone marrow failure that's only affecting the red blood cell lineage. This is the future of everything. we'll have more with Maria Barna next.

19:53Welcome back to the Future of Everything. I'm Russ Altman and I'm speaking with Maria Barna from Stanford University. In the last segment, we learned a lot about the basics of ribosomes, where they fit into the central dogma, and that they are not all the same, that they're quite different. And these differences help them do specialized functions, but these differences can also be hijacked in disease to create ribosomes that are not being helpful. In this segment, I'm going to ask Maria about how we might have therapies based on this knowledge, and also what is the relationship between transcription, that's when we go from DNA to RNA and translation, which is what the ribosome does going from RNA to proteins.

20:35Don't forget, at the end of this episode, I'll be doing the future in a minute with Maria, and I'll ask her some rapid fire questions and she'll give me some rapid answers. So Maria, one of the things is, as you know very well, what goes into the ribosome is RNA. And people, because of the genome revolution, people have figured out not only how to sequence DNA, but they've gotten very good at sequencing RNA. And they say, well, look, we know that the RNA goes into the ribosome and that a protein pops out. It's a little bit harder to measure proteins. So let's just measure the RNA because that'll tell us which proteins are being made by the cell and therefore what it cares about at this moment.

21:14But I know that that's not a great model. And I know that you have strong feelings about that. So talk to me about why just measuring the inputs is not such a great way to estimate the quantity of output. Yeah. So I'm sure your listeners through all of your podcasts will probably have heard of what you were referring to, which is RNA sequencing. And we've gotten so good at it. We can do single cell RNA sequencing from one cell. And the little hidden secret in biology is we're, as you mentioned, it's easy to do. Everyone is able to do it. But if we actually look at how much of it is a predictor for ultimately protein expression, which is the execution side of what the genome is doing, it's only about 40%.

22:08So remarkably, our best guesstimates are that only 40 % of this transcriptome is predicting for the proteome. So I think in the life of every single biologist, our dream is almost to paint a picture of what life is. Yes. And the way I view it is we have a sketch. And that sketch is the transcriptome. And I hope that people that are listening to this will become savvy in always questioning whether that's the absolute truth to unlock the secret of life. Or is it just a sketch and we really need to fill it in? by knowing exactly the quantities, the proteins, where in a cell they actually can be produced and how they can dynamically change.

22:57And as you said, in our entire revolution of genetics, we have the poorest tools available to do that. And I think that's where the next few decades of research really have to go to unlock what life is, both in health and in disease. I mean, two things I want to highlight. First of all, I love your idea of a sketch because it's like the RNA is giving us like a impressionistic painting of the cell. It's very beautiful and simple with colors. But what we kind of want is a high resolution photograph more than the sketch. And the other thing that I like about what you just said is that the RNA is the input.

23:40But now that you've told, and if all ribosomes were the same, you might imagine that that RNA was 100 % predictive of what's going to come out on the other end with the proteins. But now that you've told us in the previous discussion that we have thousands of different ones, it's not a surprise that that RNA has many different fates because there are all these different ribosomes that have like an opinion. And I'm using that with scare quotes. There's all these ribosomes that have an opinion of when, where, and how much of the protein to make. And they're all going to be voting. And that creates the lack of a high resolution picture.

24:16Okay. So I want to make sure we get to therapies. You mentioned some like really scary diseases, actually right across the whole range of human disease, cancer, infectious disease, and neurological diseases. Is there an opportunity in all of this science to say, okay, how could we actually intervene to like stop disease processes that are hijacking ribosomes or doing other things that we just don't want to happen? Yeah. So I think the ultimate vision is to create customized ribosomes. So could we create, with the knowledge of this code, so a ribosome being fine-tuned for the translation of selective mRNAs, could we make a customized version of this machinery to now say, okay, can we make a cell, for example, a muscle cell, produce more of a titan protein, which is so critical for the elasticity of the muscle fiber?

25:17Can we produce proteins in neurons that are critical for how these neurons fire and are linked to long-term memory? Can we revert the defects in ribosomes that are happening during neurodegeneration? And can we be clever about it? So one of the things that we're attempting to do is to say, okay, cancer evolved, like we had discussed. it's customized ribosome to generate a customized cancer proteome. So now can we put in a payload, for example, something that would kill a cancer cell and make it highly specific only for that cancer cell by making use of those cancer ribosomes. So basically now saying, can we reshift the focus of what these cancer ribosomes are actually translating and make it a death signal for these cells as opposed to a normal cell.

26:16Yeah. And it sounds like there might be a similar idea for the virus example that you gave, where the virus is also creating its own bespoke ribosome. And if you can hijack that system... So let me ask, is this going to require big-time genetic engineering going into the genomes of either the cancer or the host? Or is it possible that there'll be like drugs, like small molecules or proteins that we just kind of, that we use all the time in current medicine? What's your, and I know that part of this is guessing, but you think about this all the time. What's your vision of how these therapies are going to develop and what are going to be the vehicles?

26:52Is it going to be small molecules, new kinds of proteins, or are we going to have to actually edit the genome? Well, one of the huge ongoing efforts in the lab is the small molecules. Okay. So people have screened small molecule libraries. And again, it's so focused on this transcriptional view of the ribosome. But we know that small molecules, a transcriptional view of gene expression, but we know that small molecules can bind to the ribosome. So for example, the best examples of that are antibiotics. Yes. So antibiotics can bind to the prokaryotic ribosome directly and shut off its activity.

27:32And no one has attempted to do screens for molecules that directly target the ribosome. And one of the chemical screens that is still unpublished and ongoing is we're screening the largest library of compounds. We have a screening center at Stanford to do that to basically increase the activity of ribosomes. And where we think that's going to fit in really well is in all of these, for example, neurodegenerative states where you have a decline in ribosome activity. Can we increase or augment how these ribosomes are functioning to produce more protein? Can we do this in these congenital birth defects where there is a problem in ribosomes?

28:20Can we boost up their ability to make them super at producing proteins? And we've remarkably have identified compounds that can do that. And so we're really excited to bring into the clinic this notion of these ribo-targeted. Yeah, ribotherapy. Okay, so this is a little bit of a technical question, but it rises just from what you just said. Now that we know that ribosomes can be very different, even in the same cell, have you or others figured out how to isolate particular types of these ribosomes? Because I'm now thinking if you're trying to develop drugs, you're going to want them to be very specific.

29:01And you might not want a drug that clobbers all the ribosomes. You kind of want to be very surgical. So what's the status of our ability to isolate particular types of ribosomes so that you can study them in detail? Okay. So this is my dream and this is predicting science 20 years from now. Perfect. It's called the future of everything, Maria. Okay. So basically I told you 10 million cells, 10 million ribosomes per cell, they're tiny. They're 35 nanometers, 100 ,000 times smaller than a single width of a hair. But my dream is to be able to literally, using microfluidics, isolate every single ribosome.

29:45There you go. Ribosome by ribosome by ribosome and characterize it, what mRNA is it being bound to and to unlock the code. If we had that magic understanding of this process, we can then, as you're saying, isolate selective classes of ribosomes and even sort of creating an in vitro system, an in vitro lysate for these specific types of ribosomes. So they can even work with like minimal components to execute their functions in translating selected classes of mRNAs and then redo our chemical screens. So for redoing our libraries of small molecules to say, can we find small molecules that would target this specific class?

30:36Super specific. Well, that's great. And thank you so much. And this is a great place to end. But before we go on, I want to do our new segment, which we're calling the future in a minute. So what I'd like to do is I'd like to ask you, in this case, five questions, rapid fire and get your rapid fire answers. And I'm wondering if you're ready. I think I am. I'll go for the challenge. OK, so here's the first question. What is the one thing that gives you the most hope about the future? This is the best time to do science. Just the speed at which we can test a hypothesis is unbelievable. So essentially, you can dream up a hypothesis and go into the lab and test it so quickly that I think we will get answers to any of the remaining questions of biology and medicine at a rate that's never been possible before.