Posted on by Dr. Francis Collins
These colorful lights might look like a video vignette from one of the spectacular evening light shows taking place this holiday season. But they actually aren’t. These lights are illuminating the way to a much fuller understanding of the mammalian brain.
The video features a new research method called BARseq (Barcoded Anatomy Resolved by Sequencing). Created by a team of NIH-funded researchers led by Anthony Zador, Cold Spring Harbor Laboratory, NY, BARseq enables scientists to map in a matter of weeks the location of thousands of neurons in the mouse brain with greater precision than has ever been possible before.
How does it work? With BARseq, researchers generate uniquely identifying RNA barcodes and then tag one to each individual neuron within brain tissue. As reported recently in the journal Cell, those barcodes allow them to keep track of the location of an individual cell amid millions of neurons . This also enables researchers to map the tangled paths of individual neurons from one region of the mouse brain to the next.
The video shows how the researchers read the barcodes. Each twinkling light is a barcoded neuron within a thin slice of mouse brain tissue. The changing colors from frame to frame correspond to one of the four letters, or chemical bases, in RNA (A=purple, G=blue, U=yellow, and C=white). A neuron that flashes blue, purple, yellow, white is tagged with a barcode that reads GAUC, while yellow, white, white, white is UCCC.
By sequencing and reading the barcodes to distinguish among seemingly identical cells, the researchers mapped the connections of more than 3,500 neurons in a mouse’s auditory cortex, a part of the brain involved in hearing. In fact, they report they’re now able to map tens of thousands of individual neurons in a mouse in a matter of weeks.
What makes BARseq even better than the team’s previous mapping approach, called MAPseq, is its ability to read the barcodes at their original location in the brain tissue . As a result, they can produce maps with much finer resolution. It’s also possible to maintain other important information about each mapped neuron’s identity and function, including the expression of its genes.
Zador reports that they’re continuing to use BARseq to produce maps of other essential areas of the mouse brain with more detail than had previously been possible. Ultimately, these maps will provide a firm foundation for better understanding of human thought, consciousness, and decision-making, along with how such mental processes get altered in conditions such as autism spectrum disorder, schizophrenia, and depression.
Here’s wishing everyone a safe and happy holiday season. It’s been a fantastic year in science, and I look forward to bringing you more cool NIH-supported research in 2020!
 High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. Chen X, Sun YC, Zhan H, Kebschull JM, Fischer S, Matho K, Huang ZJ, Gillis J, Zador AM. Cell. 2019 Oct 17;179(3):772-786.e19.
 High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA. Kebschull JM, Garcia da Silva P, Reid AP, Peikon ID, Albeanu DF, Zador AM. Neuron. 2016 Sep 7;91(5):975-987.
Zador Lab (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY)
NIH Support: National Institute of Neurological Disorders and Stroke; National Institute on Drug Abuse; National Cancer Institute
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
Posted on by Dr. Francis Collins
The standard view of biology is that every normal cell copies its DNA instruction book with complete accuracy every time it divides. And thus, with a few exceptions like the immune system, cells in normal, healthy tissue continue to contain exactly the same genome sequence as was present in the initial single-cell embryo that gave rise to that individual. But new evidence suggests it may be time to revise that view.
By analyzing genetic information collected throughout the bodies of nearly 500 different individuals, researchers discovered that almost all had some seemingly healthy tissue that contained pockets of cells bearing particular genetic mutations. Some even harbored mutations in genes linked to cancer. The findings suggest that nearly all of us are walking around with genetic mutations within various parts of our bodies that, under certain circumstances, may have the potential to give rise to cancer or other health conditions.
Efforts such as NIH’s The Cancer Genome Atlas (TCGA) have extensively characterized the many molecular and genomic alterations underlying various types of cancer. But it has remained difficult to pinpoint the precise sequence of events that lead to cancer, and there are hints that so-called normal tissues, including blood and skin, might contain a surprising number of mutations —perhaps starting down a path that would eventually lead to trouble.
In the study published in Science, a team from the Broad Institute at MIT and Harvard, led by Gad Getz and postdoctoral fellow Keren Yizhak, along with colleagues from Massachusetts General Hospital, decided to take a closer look. They turned their attention to the NIH’s Genotype-Tissue Expression (GTEx) project.
The GTEx is a comprehensive public resource that shows how genes are expressed and controlled differently in various tissues throughout the body. To capture those important differences, GTEx researchers analyzed messenger RNA sequences within thousands of healthy tissue samples collected from people who died of causes other than cancer.
Getz, Yizhak, and colleagues wanted to use that extensive RNA data in another way: to detect mutations that had arisen in the DNA genomes of cells within those tissues. To do it, they devised a method for comparing those tissue-derived RNA samples to the matched normal DNA. They call the new method RNA-MuTect.
All told, the researchers analyzed RNA sequences from 29 tissues, including heart, stomach, pancreas, and fat, and matched DNA from 488 individuals in the GTEx database. Those analyses showed that the vast majority of people—a whopping 95 percent—had one or more tissues with pockets of cells carrying new genetic mutations.
While many of those genetic mutations are most likely harmless, some have known links to cancer. The data show that genetic mutations arise most often in the skin, esophagus, and lung tissues. This suggests that exposure to environmental elements—such as air pollution in the lung, carcinogenic dietary substances in the esophagus, or the ultraviolet radiation in sunlight that hits the skin—may play important roles in causing genetic mutations in different parts of the body.
The findings clearly show that, even within normal tissues, the DNA in the cells of our bodies isn’t perfectly identical. Rather, mutations constantly arise, and that makes our cells more of a mosaic of different mutational events. Sometimes those altered cells may have a subtle growth advantage, and thus continue dividing to form larger groups of cells with slightly changed genomic profiles. In other cases, those altered cells may remain in small numbers or perhaps even disappear.
It’s not yet clear to what extent such pockets of altered cells may put people at greater risk for developing cancer down the road. But the presence of these genetic mutations does have potentially important implications for early cancer detection. For instance, it may be difficult to distinguish mutations that are truly red flags for cancer from those that are harmless and part of a new idea of what’s “normal.”
To further explore such questions, it will be useful to study the evolution of normal mutations in healthy human tissues over time. It’s worth noting that so far, the researchers have only detected these mutations in large populations of cells. As the technology advances, it will be interesting to explore such questions at the higher resolution of single cells.
Getz’s team will continue to pursue such questions, in part via participation in the recently launched NIH Pre-Cancer Atlas. It is designed to explore and characterize pre-malignant human tumors comprehensively. While considerable progress has been made in studying cancer and other chronic diseases, it’s clear we still have much to learn about the origins and development of illness to build better tools for early detection and control.
 RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Yizhak K, Aguet F, Kim J, Hess JM, Kübler K, Grimsby J, Frazer R, Zhang H, Haradhvala NJ, Rosebrock D, Livitz D, Li X, Arich-Landkof E, Shoresh N, Stewart C, Segrè AV, Branton PA, Polak P, Ardlie KG, Getz G. Science. 2019 Jun 7;364(6444).
The Cancer Genome Atlas (National Cancer Institute/NIH)
Pre-Cancer Atlas (National Cancer Institute/NIH)
Getz Lab (Broad Institute, Cambridge, MA)
NIH Support: Common Fund; National Heart, Lung, and Blood Institute; National Human Genome Research Institute; National Institute of Mental Health; National Cancer Institute; National Library of Medicine; National Institute on Drug Abuse; National Institute of Neurological Diseases and Stroke
Posted on by Dr. Francis Collins
A Happy New Year to one and all! While many of us were busy wrapping presents, the journal Science announced its much-anticipated scientific breakthroughs of 2018. In case you missed the announcement , it was another banner year for the biomedical sciences.
The 2018 Breakthrough of the Year went to biomedical science and its ability to track the development of life—one cell at a time—in a variety of model organisms. This newfound ability opens opportunities to understand the biological basis of life more systematically than ever before. Among Science’s “runner-up” breakthroughs, more than half had strong ties to the biomedical sciences and NIH-supported research.
Sound intriguing? Let’s take a closer look at some of the amazing science conducted in 2018, starting with Science’s Breakthrough of the Year.
Development Cell by Cell: For millennia, biologists have wondered how a single cell develops into a complete multicellular organism, such as a frog or a mouse. But solving that mystery was almost impossible without the needed tools to study development systematically, one cell at a time. That’s finally started to change within the last decade. I’ve highlighted the emergence of some of these powerful tools on my blog and the interesting ways that they were being applied to study development.
Over the past few years, all of this technological progress has come to a head. Researchers, many of them NIH-supported, used sophisticated cell labeling techniques, nucleic acid sequencing, and computational strategies to isolate thousands of cells from developing organisms, sequence their genetic material, and determine their location within that developing organism.
In 2018 alone, groundbreaking single-cell analysis papers were published that sequentially tracked the 20-plus cell types that arise from a fertilized zebrafish egg, the early formation of organs in a frog, and even the creation of a new limb in the Axolotl salamander. This is just the start of amazing discoveries that will help to inform us of the steps, or sometimes missteps, within human development—and suggest the best ways to prevent the missteps. In fact, efforts are now underway to gain this detailed information in people, cell by cell, including the international Human Cell Atlas and the NIH-supported Human BioMolecular Atlas Program.
An RNA Drug Enters the Clinic: Twenty years ago, researchers Andrew Fire and Craig Mello showed that certain small, noncoding RNA molecules can selectively block genes in our cells from turning “on” through a process called RNA interference (RNAi). This work, for the which these NIH grantees received the 2006 Nobel Prize in Physiology or Medicine, soon sparked a wave of commercial interest in various noncoding RNA molecules for their potential to silence the expression of a disease-causing gene.
After much hard work, the first gene-silencing RNA drug finally came to market in 2018. It’s called Onpattro™ (patisiran), and the drug uses RNAi to treat the peripheral nerve disease that can afflict adults with a rare disease called hereditary transthyretin-mediated amyloidosis. This hard-won success may spark further development of this novel class of biopharmaceuticals to treat a variety of conditions, from cancer to cardiovascular disorders, with potentially greater precision.
Rapid Chemical Structure Determination: Last October, two research teams released papers almost simultaneously that described an incredibly fast new imaging technique to determine the structure of smaller organic chemical compounds, or “small molecules“ at atomic resolution. Small molecules are essential components of molecular biology, pharmacology, and drug development. In fact, most of our current medicines are small molecules.
News of these papers had many researchers buzzing, and I highlighted one of them on my blog. It described a technique called microcrystal electron diffraction, or MicroED. It enabled these NIH-supported researchers to take a powder form of small molecules (progesterone was one example) and generate high-resolution data on their chemical structures in less than a half-hour! The ease and speed of MicroED could revolutionize not only how researchers study various disease processes, but aid in pinpointing which of the vast number of small molecules can become successful therapeutics.
How Cells Marshal Their Contents: About a decade ago, researchers discovered that many proteins in our cells, especially when stressed, condense into circumscribed aqueous droplets. This so-called phase separation allows proteins to gather in higher concentrations and promote reactions with other proteins. The NIH soon began supporting several research teams in their groundbreaking efforts to explore the effects of phase separation on cell biology.
Over the past few years, work on phase separation has taken off. The research suggests that this phenomenon is critical in compartmentalizing chemical reactions within the cell without the need of partitioning membranes. In 2018 alone, several major papers were published, and the progress already has some suggesting that phase separation is not only a basic organizing principle of the cell, it’s one of the major recent breakthroughs in biology.
Forensic Genealogy Comes of Age: Last April, police in Sacramento, CA announced that they had arrested a suspect in the decades-long hunt for the notorious Golden State Killer. As exciting as the news was, doubly interesting was how they caught the accused killer. The police had the Golden Gate Killer’s DNA, but they couldn’t determine his identity, that is, until they got a hit on a DNA profile uploaded by one of his relatives to a public genealogy database.
Though forensic genealogy falls a little outside of our mission, NIH has helped to advance the gathering of family histories and using DNA to study genealogy. In fact, my blog featured NIH-supported work that succeeded in crowdsourcing 600 years of human history.
The researchers, using the online profiles of 86 million genealogy hobbyists with their permission, assembled more than 5 million family trees. The largest totaled more than 13 million people! By merging each tree from the crowd-sourced and public data, they were able to go back about 11 generations—to the 15th century and the days of Christopher Columbus. Though they may not have caught an accused killer, these large datasets provided some novel insights into our family structures, genes, and longevity.
An Ancient Human Hybrid: Every year, researchers excavate thousands of bone fragments from the remote Denisova Cave in Siberia. One such find would later be called Denisova 11, or “Denny” for short.
Oh, what a fascinating genomic tale Denny’s sliver of bone had to tell. Denny was at least 13 years old and lived in Siberia roughly 90,000 years ago. A few years ago, an international research team found that DNA from the mitochondria in Denny’s cells came from a Neanderthal, an extinct human relative.
In 2018, Denny’s family tree got even more interesting. The team published new data showing that Denny was female and, more importantly, she was a first generation mix of a Neanderthal mother and a father who belonged to another extinct human relative called the Denisovans. The Denisovans, by the way, are the first human relatives characterized almost completely on the basis of genomics. They diverged from Neanderthals about 390,000 years ago. Until about 40,000 years ago, the two occupied the Eurasian continent—Neanderthals to the west, and Denisovans to the east.
Denny’s unique genealogy makes her the first direct descendant ever discovered of two different groups of early humans. While NIH didn’t directly support this research, the sequencing of the Neanderthal genome provided an essential resource.
As exciting as these breakthroughs are, they only scratch the surface of ongoing progress in biomedical research. Every field of science is generating compelling breakthroughs filled with hope and the promise to improve the lives of millions of Americans. So let’s get started with 2019 and finish out this decade with more truly amazing science!
 “2018 Breakthrough of the Year,” Science, 21 December 2018.
NIH Support: These breakthroughs represent the culmination of years of research involving many investigators and the support of multiple NIH institutes.