Millions of Single-Cell Analyses Yield Most Comprehensive Human Cell Atlas Yet
Posted on by Lawrence Tabak, D.D.S., Ph.D.
There are 37 trillion or so cells in our bodies that work together to give us life. But it may surprise you that we still haven’t put a good number on how many distinct cell types there are within those trillions of cells.
That’s why in 2016, a team of researchers from around the globe launched a historic project called the Human Cell Atlas (HCA) consortium to identify and define the hundreds of presumed distinct cell types in our bodies. Knowing where each cell type resides in the body, and which genes each one turns on or off to create its own unique molecular identity, will revolutionize our studies of human biology and medicine across the board.
Since its launch, the HCA has progressed rapidly. In fact, it has already reached an important milestone with the recent publication in the journal Science of four studies that, together, comprise the first multi-tissue drafts of the human cell atlas. This draft, based on analyses of millions of cells, defines more than 500 different cell types in more than 30 human tissues. A second draft, with even finer definition, is already in the works.
Making the HCA possible are recent technological advances in RNA sequencing. RNA sequencing is a topic that’s been mentioned frequently on this blog in a range of research areas, from neuroscience to skin rashes. Researchers use it to detect and analyze all the messenger RNA (mRNA) molecules in a biological sample, in this case individual human cells from a wide range of tissues, organs, and individuals who voluntarily donated their tissues.
By quantifying these RNA messages, researchers can capture the thousands of genes that any given cell actively expresses at any one time. These precise gene expression profiles can be used to catalogue cells from throughout the body and understand the important similarities and differences among them.
In one of the published studies, funded in part by the NIH, a team co-led by Aviv Regev, a founding co-chair of the consortium at the Broad Institute of MIT and Harvard, Cambridge, MA, established a framework for multi-tissue human cell atlases . (Regev is now on leave from the Broad Institute and MIT and has recently moved to Genentech Research and Early Development, South San Francisco, CA.)
Among its many advances, Regev’s team optimized single-cell RNA sequencing for use on cell nuclei isolated from frozen tissue. This technological advance paved the way for single-cell analyses of the vast numbers of samples that are stored in research collections and freezers all around the world.
Using their new pipeline, Regev and team built an atlas including more than 200,000 single-cell RNA sequence profiles from eight tissue types collected from 16 individuals. These samples were archived earlier by NIH’s Genotype-Tissue Expression (GTEx) project. The team’s data revealed unexpected differences among cell types but surprising similarities, too.
For example, they found that genetic profiles seen in muscle cells were also present in connective tissue cells in the lungs. Using novel machine learning approaches to help make sense of their data, they’ve linked the cells in their atlases with thousands of genetic diseases and traits to identify cell types and genetic profiles that may contribute to a wide range of human conditions.
By cross-referencing 6,000 genes previously implicated in causing specific genetic disorders with their single-cell genetic profiles, they identified new cell types that may play unexpected roles. For instance, they found some non-muscle cells that may play a role in muscular dystrophy, a group of conditions in which muscles progressively weaken. More research will be needed to make sense of these fascinating, but vital, discoveries.
The team also compared genes that are more active in specific cell types to genes with previously identified links to more complex conditions. Again, their data surprised them. They identified new cell types that may play a role in conditions such as heart disease and inflammatory bowel disease.
Two of the other papers, one of which was funded in part by NIH, explored the immune system, especially the similarities and differences among immune cells that reside in specific tissues, such as scavenging macrophages [2,3] This is a critical area of study. Most of our understanding of the immune system comes from immune cells that circulate in the bloodstream, not these resident macrophages and other immune cells.
These immune cell atlases, which are still first drafts, already provide an invaluable resource toward designing new treatments to bolster immune responses, such as vaccines and anti-cancer treatments. They also may have implications for understanding what goes wrong in various autoimmune conditions.
Scientists have been working for more than 150 years to characterize the trillions of cells in our bodies. Thanks to this timely effort and its advances in describing and cataloguing cell types, we now have a much better foundation for understanding these fundamental units of the human body.
But the latest data are just the tip of the iceberg, with vast flows of biological information from throughout the human body surely to be released in the years ahead. And while consortium members continue making history, their hard work to date is freely available to the scientific community to explore critical biological questions with far-reaching implications for human health and disease.
 Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Eraslan G, Drokhlyansky E, Anand S, Fiskin E, Subramanian A, Segrè AV, Aguet F, Rozenblatt-Rosen O, Ardlie KG, Regev A, et al. Science. 2022 May 13;376(6594):eabl4290.
 Cross-tissue immune cell analysis reveals tissue-specific features in humans. Domínguez Conde C, Xu C, Jarvis LB, Rainbow DB, Farber DL, Saeb-Parsy K, Jones JL,Teichmann SA, et al. Science. 2022 May 13;376(6594):eabl5197.
 Mapping the developing human immune system across organs. Suo C, Dann E, Goh I, Jardine L, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA, et al. Science. 2022 May 12:eabo0510.
Ribonucleic acid (RNA) (National Human Genome Research Institute/NIH)
Studying Cells (National Institute of General Medical Sciences/NIH)
Regev Lab (Broad Institute of MIT and Harvard, Cambridge, MA)
NIH Support: Common Fund; National Cancer Institute; National Human Genome Research Institute; National Heart, Lung, and Blood Institute; National Institute on Drug Abuse; National Institute of Mental Health; National Institute on Aging; National Institute of Allergy and Infectious Diseases; National Institute of Neurological Disorders and Stroke; National Eye Institute
Meet an Inspiring Researcher Who Helped Create COVID-19 mRNA Vaccines
Posted on by Dr. Francis Collins
More than 170 million Americans already have received COVID-19 vaccines. As this number continues to grow and expand to younger age groups, I’m filled with overwhelming gratitude for all of the researchers who worked so diligently, over the course of decades, to build the scientific foundation for these life-saving vaccines. One of them is Dr. Kizzmekia Corbett, who played a central role in the fact that, in the span of less than a year, we were able to develop safe and effective mRNA-based vaccines to protect against this devastating infectious disease.
As leader of the immunopathogenesis team at NIH’s Dale and Betty Bumpers Vaccine Research Center in Bethesda, MD, Dr. Corbett was ready, willing, and able when the COVID-19 pandemic emerged to take the critical first steps in developing what would become the Moderna and Pfizer/BioNTech mRNA vaccines. Recently, she accepted a position at Harvard University T.H. Chan School of Public Health, Boston, where she will soon open her own viral immunology lab to help inform future vaccine development for coronaviruses and other respiratory viruses.
While she was preparing for her move to Harvard, I had a chance to speak with Dr. Corbett about her COVID-19 research experience and what it was like to get immunized with the vaccine that she helped to create. Our conversation was part of an NIH Facebook Live event in which we connected virtually from our homes in Maryland. Here is a condensed version of our chat.
Collins: You’ve studied SARS, MERS, and other coronaviruses for many years. Then, in early January 2020, like all of us, you heard that something was going on that sounded worrisome in Wuhan, China. What did you think?
Corbett: Well, the story actually began for me on December 31, 2019. My boss Dr. Barney Graham sent me an email at 6 a.m. that said: “Get ready for 2020.” There had been some news of a respiratory virus outbreak in the Wuhan district of China. I honestly wrote it off as probably a strain of the flu. Then, we got back to NIH after the holidays, and it was determined around January 6 that the virus was for certain a coronavirus. That meant our team would be responding to it.
We sat down and planned to monitor the situation very closely. We knew exactly what to do, based on our past work. We would go into full force to make a vaccine—the one now known as “the Moderna vaccine” —as quickly as possible for testing in a clinical trial. The goal was to make the vaccine in 100 days. And so when the genetic sequence of this new virus came out on January 10, I sprung out of bed and so did everyone on the team. It’s been kind of a whirlwind ever since.
Collins: Tell us a little bit more about that. The sequence got posted on the internet by a Chinese scientist. So you have this sequence, and everyone gathers in NIH’s Vaccine Research Center. Then what happens?
Corbett: The cool thing about this type of technology is you don’t even need the lab to design the vaccine. All you need are the letters, or sequence, that encodes the virus’ genetic material displayed on your computer screen. We could actually do the work from our homes, obviously in close conversation with each other.
This sequence is the virus’s genetic code. Just like humans have families—brothers, sisters, cousins—viruses also have families. So, we could see when looking at the sequence of letters, how similar this particular virus was to viruses that we’ve worked with before in the coronavirus family. It was almost like “A-ha! This is the part of the sequence that represents the protein on the surface of the virus.”
We knew that we could take the sequence of that surface protein and use all of the knowledge that we had from previous years to design a vaccine. And that’s what we did. We took that sequence on our computer screen and said we said this is exactly how we want this vaccine to look. The process was as straightforward as that.
Collins: In other words, you already knew that these coronaviruses have spike proteins on their surface and that’s the thing that’s going to be really useful for making an antibody. You’d already taken this approach in developing a vaccine for MERS, right?
Corbett: Exactly, we’d done that for MERS. Vaccines are basically a way to teach your body how to see a pathogen. Over the years, as vaccinology and technology have progressed, different scientists have figured out that you don’t really need the whole virus as a part of the vaccine. You can just take a small portion of that virus to alert your body.
In this case, taking the spike protein and teaching your immune system how to specifically spot and attack it, you can now protect yourself from COVID-19. So, we used the sequence of that spike protein, with some modifications to make it much better as a vaccine. We then deliver that to you as a message—messenger RNA (mRNA) —to get your muscle cells briefly to make the spike protein. Then, your body sees that spike protein hanging out on your cells and makes a really specific immune response to it. That way the next time your body sees the spike protein, if you ever come into contact with the virus, your immune system is armed and ready to attack.
Collins: Say more about this messenger RNA approach. It’s been so revolutionary and one of the reasons that we got vaccines into people’s arms in just 11 months. Had this approach ever been used before?
Corbett: Yes, messenger RNA technologies have been in development from a basic science perspective for over 15 years. A lot of that work was funded by NIH. Soon after I got to NIH, I attended a meeting in London called Transforming Vaccinology. At the time, Moderna was a smaller company that was working to make messenger RNA technologies, mostly centered around cancer therapies. But they had started to test some flu vaccines that used messenger RNA. My question to the presenter was: “Every single time I see you guys present, it looks like mRNA technology has always worked. Can you tell me a time that it hasn’t?” And he said, “I can’t.”
So, our understanding of how this technology works to make really good vaccines predates this pandemic. I think one of the worries that many people have is how fast and how new this technology is. But all science is compounded knowledge—everything builds on itself.
Collins: Right! We only learned about messenger RNA, because back in the 1950s and 1960s, some researchers decided to figure out how the information in our genetic instruction book, our DNA, can ultimately turn into proteins. It turned out that the message that carries that information is made of RNA.
So, you knew which kinds of letters to program into the messenger RNA vaccine. Would you explain how this vaccine, its messenger RNA, produces a spike protein. Where does that step happen?
Corbett: Your cells are machines built for this kind of thing. I like to remind people that, on a day-in, day-out basis, our cells make proteins—all of the hormones and other things our bodies needs to survive. So, we’re not teaching the cells to do anything different than they would normally do. That’s important to understand.
The way that cells do this is by reading the mRNA sequence. As they’re reading that sequence, they chew it up, like eating it, and say, “Okay, this sequence is for this very specific protein.” Then, they make that protein and push it to the surface of your cells. That’s how it happens.
Collins: And for mRNA vaccines, that’s the point when your immune system says “Wait a minute! I don’t recognize that as part of me, so I’ve got to make an antibody to it.” Then you’re off to the races and develop your immunity. Now that this mRNA vaccine strategy has succeeded for COVID-19, could it be applied to other infectious diseases or even non-infectious conditions?
Corbett: Yes, I heard that about 60 new companies have sprouted up in the last year around messenger RNA technology. They have ideas for different types of infectious disease vaccines and cancer therapies. I expect that this technology will be transformative to medicine in general.
Collins: Here’s a question from social media: “Why does it take two shots for the Pfizer and the Moderna mRNA vaccines? Why isn’t one good enough?”
Corbett: The way that these vaccines work is much like an alarm clock. Imagine your immune system is in bed and the first shot is the alarm clock going off to say, “Hey, wake up and get ready.” And just like I did this morning, the immune system pressed snooze and took a little nap. But when you hear the alarm clock the second time, it’s like someone rushing into your room and pouring a cold bucket of water on you. You have no choice but to get out of bed.
That’s what the second dose of the vaccine does. It pushes your immune response to the next level. That’s why you need two shots to get the type of efficacy that you want and be fully protected for the optimal immune response.
Collins: You were a co-leader of the team that created what became the Moderna vaccine—and you ended up getting immunized with the Moderna vaccine. What did that feel like?
Corbett: It was pretty surreal. I cried. At the end of it, I felt a lot of relief after getting my vaccine, particularly after getting the second dose. There was this breath of fresh air. It was also a birthday present. I got my second dose the day before my 35th birthday, as a birthday present to myself.
Collins: I have to admit, I cried a little bit too after my second dose. It’s just the sense of relief and incredible gratitude that we’ve reached this point. Here we are with vaccines that have 95 percent effectiveness and an incredibly good safety record, which is almost better than we could have hoped for. I’m a person of faith, so there were a lot of my prayers that went into this and it sure felt like they got answered.
Corbett: Yes, same.
Collins: You are out there a lot talking to people about the vaccines. There are still about 100 million Americans that have not yet received their first dose. Many of them still unsure about getting vaccinated. What do you say to those who are on the fence?
Corbett: In this past year, I’ve spent a lot of time talking about the vaccine with people in the community. One thing that I realized, is that I don’t need to say anything unless I’m asked. I think it’s important that I listen first, instead of just speaking.
So I do that, and I try to answer people’s inquiries as specifically as possible. But people have some very broad questions. One thing that is happening is people are seeing vaccines being developed right before their eyes. That can be a little confusing. I try to explain the process, how we went from the preclinical stage all the way to the point of getting the vaccine to hundreds of millions of people. I explain how each step along the way is very highly vetted by regulatory agencies and data safety monitoring committees. I also tell them that the monitoring continues. People from the clinical trials are still being evaluated, and there’s monitoring in the real world as the vaccine is being rolled out. I think that all of those things are really important for people to know.
Collins: Another question from social media: “As a successful scientist, what advice would you give to people who are thinking about a career in science?”
Corbett: If you think you’re interested, you just have to start. There are internship programs, there are scholarship programs, there are shadowing programs all over this country and even globally that can help you get your feet wet. I think the first thing that you want to do with any career is to figure out whether or not you like it. The only way that you can do that is to just explore, explore, explore.
Collins: Didn’t you kind of roll up your sleeves and take the plunge at a young age?
Corbett: Yes, at age 16, I went off and did summer internships at the University of North Carolina. I was able to see first-hand the day-to-day life of science and what being a scientist would look like. That was really important for me. That’s what I mean by exploring.
Collins: And a follow-up question: “Is the biomedical research community welcoming to women of color?”
Corbett: Not always, frankly. I was very fortunate to have been under the wings of a lot of mentors and advocates, who have helped to advance my career to where it is now. I had great mentors at NIH. My graduate school mentor was amazing, and my main collaborator in the coronavirus field was on my dissertation committee. Even prior to this pandemic, when I was doing work that was very obscure, he checked on me very often and made sure that he had a sense of where I wanted to go and how he could help me get there, including collaborating with me.
That kind of thing is very important, particularly for women of color or anyone from a marginalized community. That’s because there will be a point where there might be a glass ceiling. Unfortunately, we don’t necessarily have the tools to break those just yet. So, someone else is going to have to break those down, and most often than not, that person is going to have to be a white man. Finding those people who are allies with you and joining in your fight for your career trajectory is very helpful.
I remember when I was choosing a college, it was a very difficult decision for me. I got accepted into Ivy League schools, and I’d gone to all of the scholarship weekends all over the country. When I was making the decision, my dad said, “Kizzy, just always go where there is love.”
That really sticks to me with every single choice that I make around my career. You want to be at a place that’s welcoming, a place that understands you, and a place that fosters the next version of who you are destined to be. You need to make sure to step back outside of the day-to-day stuff and say, “Okay, does this place love me and people like me?” It’s important to remember that’s how you thrive: when you are comfortable in and in love with your environment.
Collins: Yes, we have to move our scientific workforce into a place where it is not necessary for a white man to advocate for a talented Black woman. There’s something very wrong with that particular circumstance. As NIH Director, I want to assure you, we are motivated more than ever to change that, including through a new initiative called UNITE. We’re missing out on welcoming the talents of so many folks who currently don’t see our research agenda as theirs, and we need to change that.
Kizzmekia, this has been a lot of fun. Thank you for giving us a half-hour of your time when you’re in the midst of this crazy two-week period of moving from Bethesda to Boston. We wish you the very best for this next chapter, which I know is going to be just amazing.
Corbett: Thank you so much.
Video: COVID-19 mRNA Vaccine Q & A – Kizzmekia Corbett and Francis Collins (NIH)
Video: Lead COVID-19 scientist Kizzmekia Corbett to join Harvard Chan School faculty (Harvard University, Boston)
COVID-19 Research (NIH)
Dale and Betty Bumpers Vaccine Research Center (National Institute of Allergy and Infectious Diseases/NIH)
UNITE Initiative (NIH)
Using MicroRNA to Starve a Tumor?
Posted on by Dr. Francis Collins
Tumor cells thrive by exploiting the willingness of normal cells in their neighborhood to act as accomplices. One of their sneakier stunts involves tricking the body into helping them form new blood vessels. This growth-enabling process of sprouting new blood vessels, called tumor angiogenesis, remains a vital area of cancer research and continues to yield important clues into how to beat this deadly disease.
The two-panel image above shows one such promising lead from recent lab studies with endothelial cells, specialized cells that line the inside of all blood vessels. In tumors, endothelial cells are induced to issue non-stop SOS signals that falsely alert the body to dispatch needed materials to rescue these cells. The endothelial cells then use the help to replicate and sprout new blood vessels.
The left panel demonstrates the basics of this growth process under normal conditions. Endothelial cells (red and blue) were cultured under special conditions that help them grow in the lab. When given the right cues, those cells sprout spiky extensions to form new vessels.
But in the right panel, the cells can’t sprout. The reason is because the cells are bathed in a molecule called miR-30c, which isn’t visible in the photo. These specialized microRNA molecules—and humans make a few thousand different versions of them—control protein production by binding to and disabling longer RNA templates, called messenger RNA.
This new anti-angiogenic lead, published in the Journal of Clinical Investigation, comes from a research team led by Andrew Dudley, University of Virginia Medical School, Charlottesville . The team made its discovery while studying a protein called TGF-beta that tumors like to exploit to fuel their growth.
Their studies in mice showed that loss of TGF-beta signals in endothelial cells blocked the growth of new blood vessels and thus tumors. Further study showed that those effects were due in part to elevated levels of miR-30c. The two interact in endothelial cells as part of a previously unrecognized signaling pathway that coordinates the growth of new blood vessels in tumors.
Dudley’s team went on to show that levels of miR-30c vary widely amongst endothelial cells, even when those cells come from the very same tumor. Cells rich in miR-30c struggled to sprout new vessels, while those with less of this microRNA grew new vessels with ease.
Intriguingly, they found that levels of this microRNA also predicted the outcomes for patients with breast cancer. Those whose cancers had high levels of the vessel-stunting miR-30c fared better than those with lower miR-30c levels. While more research is needed, it does offer a potentially promising new lead in the fight against cancer.
 Endothelial miR-30c suppresses tumor growth via inhibition of TGF-β-induced Serpine1. McCann JV, Xiao L, Kim DJ, Khan OF, Kowalski PS, Anderson DG, Pecot CV, Azam SH, Parker JS, Tsai YS, Wolberg AS, Turner SD, Tatsumi K, Mackman N, Dudley AC. J Clin Invest. 2019 Mar 11;130:1654-1670.
Angiogenesis Inhibitors (National Cancer Institute/NIH)
Dudley Lab (University of Virginia School of Medicine, Charlottesville)
NIH Support: National Cancer Institute; National Heart, Lung, and Blood Institute
A New Piece of the Alzheimer’s Puzzle
Posted on by Dr. Francis Collins
For the past few decades, researchers have been busy uncovering genetic variants associated with an increased risk of Alzheimer’s disease (AD) . But there’s still a lot to learn about the many biological mechanisms that underlie this devastating neurological condition that affects as many as 5 million Americans .
As an example, an NIH-funded research team recently found that AD susceptibility may hinge not only upon which gene variants are present in a person’s DNA, but also how RNA messages encoded by the affected genes are altered to produce proteins . After studying brain tissue from more than 450 deceased older people, the researchers found that samples from those with AD contained many more unusual RNA messages than those without AD.