In one second, 1 million cells in the human body die! The “death” methods are different...

Death may seem like a pure loss, but if we zoom out to the cellular level, death takes on a different and more nuanced meaning. Simply defining what makes a cell "alive" or "dead" is a challenge.

Today, scientists are working to understand the various ways and reasons why cells disappear, and what these processes mean for biological systems. Cell biologist Shai Shaham joins podcast host Steven Strogatz to discuss the different forms of cell death, their roles in evolution and disease, and why the right type and pattern of cell death is so important to our development and health. In the second you play this episode, a million cells in your body die. Some of these cells are programmed to die through naturally regulated processes, such as apoptosis ; some actively end their lives after infection to prevent the spread of a viral invasion; and some undergo necrosis due to physical damage, where the cell membrane ruptures and the contents leak out. We know that cells have nearly a dozen different ways to die. And learning how to control these processes can make a world of difference to patients.

Apoptosis of mouse preadipocytes. © wikimedia

Strogatz: I was very curious to learn more about cell death, so I thought maybe we could start by talking about the life of the cell. What are the things that a cell does that allow us to tell it's alive?

Shaham: It's a pretty complicated question. It really depends on what criteria or measurements you use to determine whether a cell is alive or dead. For example, if a cell is moving, we might say it's alive. But if the cell is stationary, you have to ask: What does it mean to be alive? Is it metabolizing food? Is it sending signals to other cells? However, some people believe that this type of activity can also occur in cells that are chemically active but not performing any biological function. One of the long-standing problems in the field of cell death research is how to define a "dead cell." And the definition that I agree with most, at least for me, is that if a cell disappears completely, then it is dead. Beyond that, it is difficult to make a judgment.

SB: It's interesting how subtle this question is. Many people think that cells divide to stay alive. I wonder if cell division is a key feature of being alive? Must cells divide to be considered alive?

SS: If a cell is dividing, then it's obviously alive. But the question is, if it's not dividing, is it necessarily dead? Again, the answer to this depends on the context. For example, some bacterial spores can go years without dividing, but when the time is right, they wake up from the spore state and start dividing and reproducing again. So during this period, which can be decades, is the cell dead or alive?

© Heiti Paves/SPL/Science Source

Here’s an example that I’m very fond of, because my lab studies the nematode Caenorhabditis elegans. Recently, someone extracted a nematode from the Siberian permafrost that had been frozen about 40,000 years ago and then revived in the lab [1]. So you can’t help but ask: was this creature dead or alive during those 40,000 years?

SB: Incredible! This is so interesting. In everyday language we have a concept called suspended animation. The spores you mentioned, in layman's terms, seem to be waiting to be "resurrected." But when they are in this state of suspended animation, what is their nature? This brings up a question about irreversibility.

SS: Yes, and the problem you're struggling with is one that has long plagued our field. It all comes down to the method of measurement. For example, suppose you have a spore that waits 100 years to start dividing. If you observe it in the 30th year and test it for activity over a few weeks, then by any standard it is dead. Only when it comes back to life 100 years later do you say, ah, it's alive. But if we use a different criterion, such as measuring its metabolic activity, the accumulation of mutations in its genome, or the signals it sends to other cells, as long as it shows "activity" in your test, you would consider it alive. But this is just an operational definition. I don't think it's necessary to introduce an element of mysticism into this question.

S: You made it very clear that we can use some operational definitions to determine whether a cell is alive. This method is relatively objective, such as detecting whether it is metabolizing, whether it is dividing, etc. In order to better define life and death, I would like to introduce some new angles, such as certain parts of the cell. Can part of a cell also "die"? Or does death have to occur in the entire cell?

SS: Absolutely. If you remember what I mentioned earlier, my preferred definition of a "dead cell" is that a cell is dead when it disappears completely. But there are cases where parts of a cell disappear. This can be a programmed event (a normal biological process) or it can be caused by injury or other unexpected events.

© Cell Press

For example, as animals develop, nerve axons extend from neurons. Axons are long, thin projections that extend from neurons and connect to other neurons, allowing the brain to function properly. During normal development, some axons may begin to retract, a phenomenon known as “dying back” [2]. Functionally, these retracting axons have lost their function and are actually disappearing. Therefore, you can say that part of the cell is “dying.”

SB: So, you mentioned programmed cell death, which is a topic I wanted to learn about next. I read about a form of cell death called necrosis. What happens when a cell dies necrotically?

Sand: Let me distinguish two different types of cell death here. One is genetically programmed cell death, which is a set of specific genes present in the cell's DNA that are specifically designed to direct the cell to die. This process is selected by evolution and passed on to the cell's descendants in order for the cell to terminate itself. The other type of death is similar to what happens when you step on a cell. As you can imagine, there are countless unnatural ways to damage a cell, and necrosis is one of them. Necrosis is a vaguely defined term, but it is generally described as an unregulated cell death that is not genetically controlled and usually manifests as the cell swelling, abnormal formation of the cell membrane, and eventually leakage of the cell's contents into the surrounding environment.

SB: I guess that triggers a reaction in the immune system?

SS: Yes, and generally speaking, the difference between genetically programmed cell death and cell death caused by external forces is that the former is designed to be very "clean" so that it does not disturb the surrounding environment as much as possible. In fact, this type of death will do everything it can to minimize the damage to surrounding cells. But the other type of death will usually trigger a strong response, both from neighboring cells and, if the animal has an immune system, immune cells that will also try to deal with the damage that the bursting cell has caused to the surrounding environment.

SB: I mentioned the word apoptosis earlier, which is this relatively clean form of programmed death. Am I right? Is that what we are talking about?

Sha: I would say that people who work in this field often equate programmed cell death with apoptosis, but that’s not entirely accurate. Apoptosis is just one form of programmed cell death. Our own lab has discovered a different form of cell death called linker cell–type death, or LCD.[3] There is also at least one other form of cell death that I know of that my colleagues have studied in fruit flies. So there are three true genetically programmed cell death pathways that we know of.

SB: Can you describe for us what they look like? How should we imagine when a cell undergoes any of these three types of death?

SHA: The term apoptosis was actually first coined in a paper by John F. R. Cole and Andrew Wylie in the early 1970s (the word is derived from the Greek for leaves falling off a tree, a process of death). It is characterized by the condensation of the DNA or chromatin in the nucleus, which becomes so compact that it can no longer function. In addition, the cytoplasm, which is the bulk of the cell, shrinks. Often, organelles such as mitochondria in the cytoplasm break apart, but this usually happens later in the process. Overall, the whole process is very rapid. It's only when you sit there and count the number of cells that go through this process that you realize how common this method of death is.

© Kyoto University

So it's a very compact breakdown process, and the cells get cleaned up. These dying cells have special signals on their surface called "eat me" signals that signal to neighboring cells or professional phagocytes to come and eat and break down these dead cells. Most programmed cell death follows this path, and apoptosis has these characteristics that I just mentioned. And the linker cell type of death is almost a "mirror" of apoptosis in some ways. In this type of death, there is very little chromatin condensation. In fact, the hallmark of this type of cell death is that the chromatin is very loose. In addition, the organelles do not show defects until later in the death process like apoptosis, but tend to be swollen from the beginning. But importantly, this type of cell death still has "eat me" signals on its surface, and these cells are still cleaned up and degraded by neighboring cells or professional phagocytes.

SB: I was very interested in this second type of cell death. First, I had never heard of it, and second, my first scientific paper in my career was on mathematical modeling of the structure of the chromatin fiber. So when you mention "linkers," do you mean the connecting DNA between nucleosomes?

SHA: Actually not. We discovered this cell death in C. elegans. It's the death of a single cell in the male worm called the linker cell. It's called a linker cell because it connects the developing male gonad to the sperm release channel. This cell is like a "plug" between the gonad and the exit channel. The animal eliminates it through this new linker cell-type death program, which allows the two channels to fuse together and sperm to be released.

© Cell Press

Using electron microscopy, we observed this signature of cell death—not just in this cell in C. elegans, but also very common in mammalian and human development. In fact, many cell deaths that occur in our nervous system have this signature. Another notable feature of linker cell death is that the nuclear membrane has indentations, which we call “crenellations,” and a wavy appearance. This is also a hallmark of cell death in many human diseases. We are very curious whether linker cell death plays a role in certain human diseases, such as when this type of cell death is mistakenly activated in pathological conditions.

BS: I want to return to the relationship between cell death and human disease, but if I may, I would like to move on to discussing several cell death pathways that are associated with defense functions, such as when cells die in response to an attack caused by a virus or other pathogen.

SHA: Many of these conditions have a lot in common with apoptosis, and their names are often based on the specific context. For example, pyroptosis is a type of apoptotic cell death that occurs in response to inflammation. The word "pyro" refers to the concept of inflammation or this "hot" state.

Neutrophils engulf anthrax bacteria (orange). © Cell Press

The basic principle is that when a cell is infected with a virus or bacteria, it chooses to self-destruct for the benefit of the host organism, so that the virus or bacteria does not spread throughout the body. In addition to apoptotic cell death, there are many ways to target infected cells. For example, cytotoxic T cells release proteins called perforins after recognizing virus-infected cells . These proteins are just as their name implies, they punch holes in the target cell membrane, which triggers apoptosis or causes the cell contents to leak out, and eventually the cell disintegrates and is cleared away by circulating phagocytes. Similar situations also occur in complement-mediated cell death, which is another response of the body to cells invaded by pathogens. Usually, this is a very complex protein cascade that culminates in the infected cell being covered with a protein that acts as a "eat me" mark. Unlike the other examples, in this case, the cell itself is not destroyed from the inside, but is marked as "harmful" so that phagocytes can clear it out.

SB: My impression from these discussions is that cells are doing this for the "collective good" when they perform these programs or allow themselves to be labeled "eat me." It's to help the cells or tissues around them. This seems to be a phenomenon that is unique to multicellular organisms. If you were a single-celled organism, you might not have the drive to do these things. These processes occur in the context of multicellular organisms. Am I correct in understanding this?

SS: You're basically right, but I wouldn't limit it to just multicellular organisms. This principle applies whenever a group of cells is in an environment where they need to depend on each other to survive. So in multicellular organisms, individual cells have to follow the principle of "I may need to sacrifice for the good of the group," but this is also true in bacteria. For example, bacteria tend to form what are called biofilms, which are sheets of bacteria. Under starvation conditions, when the biofilm can't provide enough food, some of the bacteria will choose to self-destruct in order to provide nutrients for the other bacteria that survive. This principle applies to collections of cells, both within a single multicellular organism and in the broader multicellular environment.

SS: So, we can think of "multicellularity" in a broad sense, not necessarily limited to a single multicellular organism, but to include all forms of multicellular life. SS: We can find important examples of this principle in the context of animals. For example, in ant colonies, which are essentially what we call "superorganisms," each ant plays an important role in the colony. Often, the ants need to sacrifice themselves to create structures that are essential to the survival of the colony, or even to provide food.

© The Conversation

There are some amazing videos you can find on YouTube or National Geographic that show ants building bridges so other ants can walk across. Often the ants that are the bridge die, and their exoskeletons become part of the bridge, allowing other ants to walk. This example of individual animals sacrificing themselves for the good of the whole is common.

SB: That's very interesting. I wanted to ask you one more thing, because you mentioned C. elegans, a little worm that's only about a millimeter long, that has taught us a lot in all areas of biology, including development, genetics, behavior, neurobiology, and aging. We've learned an incredible amount from this little organism. For those of us listening who may not be familiar with it, could you briefly introduce C. elegans and how it helps us understand the cell death process and why it's important?

SHA: Absolutely. If you want to study cell death, it’s helpful to know that a cell will die at a certain time and in a certain location. Because that predictability allows you to manipulate the system in advance and ask all kinds of questions. In most model systems, that predictability doesn’t exist. But in nematodes, and in particular in C. elegans, we can do that. One of the remarkable things about C. elegans is that the pattern of cell division from the fertilized egg to the adult worm is almost identical across individuals in the same population, with only a few exceptions. And the pattern of cell death is also exactly the same. We demonstrate this consistency by naming the cells in the nematode. We can say this cell is Moe and that one is Coley (of course, we actually give them much more boring names, like ASE, NSM, or CEP sheath). In us or other vertebrates, you can’t name a cell and find the same cell in every individual. We can tell you exactly that a cell called Coley will die 4 hours and 20 minutes after the fertilized egg starts dividing, and the death process will take 25 minutes. These details were determined in the late 1970s and early 1980s by two brilliant scientists, Bob Horvitz and John Sulston.[4] They mapped the complete pattern of cell division from fertilized egg to adult worm. As they watched these divisions unfold, they noticed that some cells eventually disappeared. These were the dead cells.

© Carolina Biological

So we know, for example, that in a developing C. elegans hermaphrodite, 1090 somatic cells are generated, 131 of which die, resulting in a total of 959 somatic cells. With this level of precision, we can do all kinds of genetic and cell biology studies where we look at the same cells over and over again to try to understand what drives cell death. I think that's the biggest advantage of using C. elegans to study cell death.

SB: So if anyone is curious, they're not that hard to catch, right? Like, if you take a handful of dirt, there's a lot of these C. elegans in there?

SHA: C. elegans is a nematode that is found all over the world. In fact, when I first started working in the lab at Rockefeller University, one of my first ideas was to try to find the "Rockefeller version" of C. elegans. I went out and got some soil samples, put them on petri dishes with agar (which is how we grow nematodes), and waited for them to appear. Sure enough, we found them. I was very excited because we had found the "Rockefeller version" of nematodes, but it turned out that the soil at Rockefeller University was actually imported from upstate New York. So these nematodes were not really "native nematodes" but were from upstate New York.

SB: Haha, it's like a "country worm" moved to the "city". The story you just told is very fascinating, the development process of C. elegans from fertilized egg to adult is as precise as a machine. You mentioned that this phenomenon is not as predictable in humans or other complex organisms. I am sure some people may wonder: Is this special nematode unique in the entire biological world? Please convince us that studying this strange nematode is really meaningful to us.

Sand: First of all, I should say that they are indeed special. They can do certain things that other organisms cannot do. That cannot be ignored. But if you look at their relatedness to other animals, you can see that just by looking at their DNA sequence and their genome.[5] The DNA sequence and genome of C. elegans are almost identical to ours. For example, the process of apoptosis is carried out by a protein called caspase. This protein's function is to cut up other proteins, and this protein is encoded by a gene that is almost identical in C. elegans and humans. To paraphrase Nietzsche, "Man is a worm" might be more appropriate.

SB: I am not familiar with this quote. Is this Nietzsche's original statement?

SS: Yes, it was in German, but this is the translated version.

SB: I didn't realize he was a cell biologist (laughs), maybe he did have an insight. Next, I want to talk about the various experimental systems used to study cell death, from bacteria in a dish to C. elegans to more complex organisms. What is the best scale for us to study cell death?

SHA: I think it’s important to start at different levels of scale. The smallest level is the individual cell. Cell death in bacteria is very important, not only for health issues, but also to answer some basic scientific curiosities: How does a bacterium decide that it needs to die? It’s very interesting to study this question in bacteria. Studying it in cell culture can also tell us a lot. For example, if we take cells from humans or mice, put them in culture, and let them divide or die, we may not understand the context in which they execute their death program. But we can learn a lot about the molecular mechanisms and signaling pathways, and figure out what signals tell cells to die or not die. Once we have established some principles in this simplified cell culture model, we can try to extend these understandings to organisms. For example, we can explore what effects a gene discovered in cell culture might have on cells in an organism. At the organism level, there are also some questions that can only be explored in this context, such as the phenomenon of cell death in groups. It’s not just the death of individual cells, but the collective behavior of groups of cells. This is most beautifully studied in the field of developmental biology, especially in processes related to morphogenesis. Morphogenesis is how multicellular organisms develop their specific shapes. The sculptor Rodin once said that he was trying to reveal the statue hidden in the stone (Editor's note: this sentence may also be said by Michelangelo). Cell death is similar: we have a group of cells, and through the death of certain cells, a specific shape is formed. One of the most famous examples is the formation of fingers and toes in vertebrates.

SS: You mean the formation of fingers or toes?

© ResearchGate

SHA: Yes. For example, in human embryonic development, all vertebrate embryos have very distinct membranes between the fingers.[6] In vertebrates like us, these membrane cells die in large numbers, eventually forming separate fingers. But in ducks, most of this cell death does not occur, so they have webbed feet.

SB: That's amazing. It's not that ducks grow webbed feet, it's that other animals "cut" off the webbed structure! I also wonder if there is some genetic variation? Some of my relatives often say, "Look at my toes, there's a web in the middle."

Sandy: These are probably vestigial structures that were not completely eliminated during embryonic development.

BS: Coming back to the human aspect, regarding cell death, could this help us reverse organ failure or address the problem of massive cell death?

SHA: Cell death is associated with almost every disease state in humans. Broadly speaking, these problems can be divided into two categories. One is diseases where there is too much cell death, such as in an organ infarction. For example, the death of heart muscle cells during a heart attack, or the death of cells in the brain in neurodegenerative diseases such as Alzheimer's and Parkinson's. The other is when cells that should die don't die, which is the underlying problem in almost all cancers. In cancer cells, some program stops working, so these harmful cells cannot be properly cleared away, and they survive inappropriately.

The division and proliferation of cancer cells. © wikipedia

In principle, these issues involve almost all major diseases. Although cell death is not the root cause of every disease, in some cases, if we can prevent cell death, we can at least buy some time to treat cells that would otherwise disappear completely. In terms of application, there have been some drug studies that try to solve problems by inhibiting or promoting cell death in various disease contexts. For example, there are currently some drugs in the clinic that specifically trigger the death of specific cells in tumors, and the development of these drugs is based on our understanding of the cell death mechanism and related molecules.

SS: When you mentioned earlier the “eat me” signal on the cell surface, I couldn’t help but wonder whether this mechanism could be applied to cancer immunotherapy or similar treatments?

SHA: There are no clinical trials specifically targeting "eat me" signals, but we can artificially create them. If we can find some unique markers on the surface of cancer cells that are completely different from other normal cells, we can generate a specific antibody to trigger apoptosis in cancer cells. This can precisely kill cancer cells without harming other cells in the body. In fact, there is a remarkable revolution going on in cancer treatment called immunotherapy. This is the basis of it. The idea is to get the body to recognize specific unique markers on tumor cells, generate an immune response against those markers, and then the immune cells will destroy these tumor cells in many of the ways we mentioned before.

SB: We’ve spent a lot of time looking at what’s been discovered about cell death over the last few decades. I was wondering if there are any questions you hope to see answered in your lifetime, or what other exciting unanswered questions you think there are in this field?

SHA: Yes, I think we still have a lot to learn. As you mentioned at the beginning of this conversation, one of the most widely studied cell death processes is called apoptosis. For many years, we thought that this process was sufficient to explain many of the cell death-related events that occur during animal development. However, in the past few decades of research, we have found that this cell death program can be completely removed from the genome of an animal and the animal still survives normally. This means that there may be other ways for cells to die. One way may be the linker cell type of death that I mentioned, but it may not be the only way. So this "black box" of other death programs is a very interesting direction, especially if we want to use cell death as an important angle to deal with disease. Another big question that we hope to understand is: I mentioned that in C. elegans, we know exactly which cell will die when. In vertebrates, we don't know. If there are two human cells next to each other, why does one undergo cell death and the other doesn't? We have no idea about this. So I think it becomes a larger question about how cells respond to their environment. Cell death is just a manifestation of this response at this point, but it is still a very fascinating question that is completely unanswered at present.

Cell biologist Shay Shaham. © The Rockefeller University

SB: Great! These are very exciting directions. Finally, as a scientist involved in this great endeavor, is there anything about your research that makes you particularly happy?

SS: I love to discover new things. I've always been interested in discovering new things that nobody else knows about. In a way, the specific details of what I discover aren't even that important. Because once you get into the details, everything seems interesting and exciting. As long as there are problems to explore and I can imagine ways to solve them, that's what motivates me to work every day. And that passion has never gone away.

SB: I understand that feeling. I sometimes tell my graduate students that it hardly matters what the problem is; the process of discovery itself is deeply satisfying. Once you get into it, everything becomes interesting.

Sand: I totally agree. It’s a rare but fulfilling feeling.

SB: Francis Crick once said that it is better to study an important problem than a trivial or uninteresting one. Has this statement influenced the research goals you choose?

Sand: I often think of this quote when deciding what to aim for next. But to be honest, I don’t think I have the arrogance to decide what is important and what is not. Science has proven time and again that seemingly unimportant, marginal discoveries often become hot decades later. This may be true in biology, physics, or mathematics. So if I limit myself to this framework that Crick suggests, I may exclude some areas of discovery that are more exciting than I thought. I think even if my imagination is good, it is not good enough to foresee future developments.

SB: I'm very inspired by your answer. This humility is not only a virtue, but from the perspective you describe, it can also be a very practical attitude. After all, we really can't predict the future. This has been a great conversation, and I could talk to you all day.

SHA: Thank you, Stephen. I really enjoyed this conversation.

By Steven Strogatz

Translated by gross

Proofreading/tamiya2

Original article/www.quantamagazine.org/how-is-cell-death-essential-to-life-20241205/

This article is based on the Creative Commons License (BY-NC) and is published by gross on Leviathan

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