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Dr. Francis Collins

Finding Beauty in the Nervous System of a Fruit Fly Larva

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Wow! Click on the video. If you’ve ever wondered where those pesky flies in your fruit bowl come from, you’re looking at it right now. It’s a fruit fly larva. And this 3D movie offers never-before-seen details into proprioception—the brain’s sixth sense of knowing the body’s location relative to nearby objects or, in this case, fruit.

This live-action video highlights the movement of the young fly’s proprioceptive nerve cells. They send signals to the fly brain that are essential for tracking the body’s position in space and coordinating movement. The colors indicate the depth of the nerve cells inside the body, showing those at the surface (orange) and those further within (blue).

Such movies make it possible, for the first time, to record precisely how every one of these sensory cells is arranged within the body. They also provide a unique window into how body positions are dynamically encoded in these cells, as a segmented larva inches along in search of food.

The video was created using a form of confocal microscopy called Swept Confocally Aligned Planar Excitation, or SCAPE. It captures 3D images by sweeping a sheet of laser light back and forth across a living sample. Even better, it does this while the microscope remains completely stationary—no need for a researcher to move any lenses up or down, or hold a live sample still.

Most impressively, with this new high-speed technology, developed with support from the NIH’s BRAIN Initiative, researchers are now able to capture videos like the one seen above in record time, with each whole volume recorded in under 1/10th of a second! That’s hundreds of times faster than with a conventional microscope, which scans objects point by point.

As reported in Current Biology, the team, led by Elizabeth Hillman and Wesley Grueber, Columbia University, New York, didn’t stop at characterizing the structural details and physical movements of nerve cells involved in proprioception in a crawling larva. In another set of imaging experiments, they went a step further, capturing faint flashes of green in individual labeled nerve cells each time they fired. (You have to look very closely to see them.) With each wave of motion, proprioceptive nerve cells light up in sequence, demonstrating precisely when they are sending signals to the animal’s brain.

From such videos, the researchers have generated a huge amount of data on the position and activity of each proprioceptive nerve cell. The data show that the specific position of each cell makes it uniquely sensitive to changes in position of particular segments of a larva’s body. While most of the proprioceptive nerve cells fired when their respective body segment contracted, others were attuned to fire when a larval segment stretched.

Taken together, the data show that proprioceptive nerve cells provide the brain with a detailed sequence of signals, reflecting each part of a young fly’s undulating body. It’s clear that every proprioceptive neuron has a unique role to play in the process. The researchers now will create similar movies capturing neurons in the fly’s central nervous system.

A holy grail of the BRAIN Initiative is to capture the brain in action. With these advances in imaging larval flies, researchers are getting ever closer to understanding the coordinated activities of an organism’s complete nervous system—though this one is a lot simpler than ours! And perhaps this movie—and the anticipation of the sequels to come—may even inspire a newfound appreciation for those pesky flies that sometimes hover nearby.


[1] Characterization of Proprioceptive System Dynamics in Behaving Drosophila Larvae Using High-Speed Volumetric Microscopy. Vaadia RD, Li W, Voleti V, Singhania A, Hillman EMC, Grueber WB. Curr Biol. 2019 Mar 18;29(6):935-944.e4.


Using Research Organisms to Study Health and Disease (National Institute of General Medical Sciences/NIH)

The Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative (NIH)

Hillman Lab (Columbia University, New York)

Grueber Lab (Columbia University, New York)

NIH Support: National Institute of Neurological Disorders and Stroke; Eunice Kennedy Shriver National Institute of Child Health and Human Development

Making the Case for Down Syndrome Research

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Francis Collins standing with Frank Stephens
Great to see Frank Stephens at a hearing on NIH’s budget for Fiscal Year 2020! As I told the House Labor/HHS Appropriations Subcommittee on April 2, 2019, I’m inspired by his advocacy for research that will benefit people with Down syndrome and many other diseases. Credit: NIH

Testifying Before House Subcommittee

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On April 2, 2019, I testified before the House Labor/HHS Appropriations Subcommittee on NIH’s budget for Fiscal Year 2020. Here I am waiting for the hearing to start with my colleagues (left to right) Gary Gibbons, director of the National Heart, Lung, and Blood Institute; Diana Bianchi, director of the Eunice Kennedy Shriver National Institute of Child Health and Human Development; and Anthony Fauci, director of National Institute of Allergy and Infectious Diseases. Credit: NIH

A CRISPR Approach to Treating Sickle Cell

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Unedited and edited sickle cells
Caption: Red blood cells from patient with sickle cell disease. The cells were differentiated from bone marrow with unedited and edited hematopoietic stem cells, and the red arrows show the sickled cells. Credit: Wu et al. Nature Medicine. March 25, 2019

Recently, CBS’s “60 Minutes” highlighted the story of Jennelle Stephenson, a brave young woman with sickle cell disease (SCD). Jennelle now appears potentially cured of this devastating condition, thanks to an experimental gene therapy being tested at the NIH Clinical Center in Bethesda, MD. As groundbreaking as this research may be, it’s among a variety of innovative strategies now being tried to cure SCD and other genetic diseases that have long seemed out of reach.

One particularly exciting approach involves using gene editing to increase levels of fetal hemoglobin (HbF) in the red blood cells of people with SCD. Shortly after birth, babies usually stop producing HbF, and switch over to the adult form of hemoglobin. But rare individuals continue to make high levels of HbF throughout their lives. This is referred to as hereditary persistence of fetal hemoglobin (HPFH). (My own postdoctoral research in the early 1980s discovered some of the naturally occurring DNA mutations that lead to this condition.)

Individuals with HPFH are entirely healthy. Strikingly, rare individuals with SCD who also have HPFH have an extremely mild version of sickle cell disease—essentially the presence of significant quantities of HbF provides protection against sickling. So, researchers have been exploring ways to boost HbF in everyone with SCD—and gene editing may provide an effective, long-lasting way to do this.

Clinical trials of this approach are already underway. And new findings reported in Nature Medicine show it may be possible to make the desired edits even more efficiently, raising the possibility that a single infusion of gene-edited cells might be able to cure SCD [1].

Sickle cell disease is caused by a specific point mutation in a gene that codes for the beta chain of hemoglobin. People with just one copy of this mutation have sickle cell trait and are generally healthy. But those who inherit two mutant copies of this gene suffer lifelong consequences of the presence of this abnormal protein. Their red blood cells—normally flexible and donut-shaped—assume the sickled shape that gives SCD its name. The sickled cells clump together and stick in small blood vessels, resulting in severe pain, anemia, stroke, pulmonary hypertension, organ failure, and far too often, early death.

Eleven years ago, a team led by Vijay Sankaran and Stuart Orkin at Boston Children’s Hospital and the Dana-Farber Cancer Institute discovered that a protein called BCL11A seemed to determine HbF levels [2]. Subsequent work showed the protein actually works as a master mediator of the switch from fetal to adult hemoglobin, which normally occurs shortly after birth.

Five years ago, Orkin and Daniel Bauer identified a specific enhancer of BCL11A expression that could be an attractive target for gene editing [3]. They could knock out the enhancer in the bone marrow, and BCL11A would not be produced, allowing HbF to stay switched on.

Because the BCL11A protein is required to turn off production of HbF in red cells. the researchers had another idea. They thought it might be possible to keep HbF on permanently by disrupting BCL11A in blood-forming hematopoietic stem cells (HSCs). The hope was that such a treatment might offer people with SCD a permanent supply of healthy red blood cells.

Fast-forward to the present, and researchers are now testing the ability of gene editing tools to cure the disease. A favorite editing system is CRISPR, which I’ve highlighted on my blog.

CRISPR is a highly precise gene-editing tool that relies on guide RNA molecules to direct a scissor-like Cas9 enzyme to just the right spot in the genome to correct the misspelling. The gene-editing treatment involves removing bone marrow from a patient, modifying the HSCs outside the body using CRISPR gene-editing tools, and then returning them back to the patient. Preclinical studies had shown that CRISPR can be effective in editing BCL11A to boost HbF production.

But questions lingered about the editing efficiency in HSCs versus more common, shorter-lived progenitor cells found in bone marrow samples. The efficiency greatly influences how long the edited cells might benefit patients. Bauer’s team saw room for improvement and, as the new study shows, they were right.

To produce lasting HbF production, it’s important to edit as many HSCs as possible. But it turns out that HSCs are more resistant to editing than other types of cells in bone marrow. With a series of adjustments to the gene-editing protocol, including use of an optimized version of the Cas9 protein, the researchers showed they could push the number of edited genes from about 80 percent to about 95 percent.

Their studies show that the most frequent Cas9 edits in HSCs are tiny insertions of a single DNA “letter.” With that slight edit to the BCL11A gene, HSCs reprogram themselves in a way that ensures long-term HbF production.

As a first test of their CRISPR-edited human HSCs, the researchers carried out the editing on HSCs derived from patients with SCD. Then they transferred the editing cells into immune-compromised mice. Four months later, the mice continued to produce red blood cells that produced high levels of HbF and resisted sickling. Bauer says they’re already taking steps to begin testing cells edited with their optimized protocol in a clinical trial.

What’s truly exciting is that the first U.S. human clinical trials of such a gene-editing approach for SCD are already underway, led by CRISPR Therapeutics/Vertex Pharmaceuticals and Sangamo Therapeutics/Sanofi. In January, CRISPR Therapeutics/Vertex Pharmaceuticals announced that the U.S. Food and Drug Administration (FDA) had granted Fast Track Designation for their CRISPR-based treatment called CTX001 [4].

In that recent “60 Minutes” segment, I dared to suggest that we now have what looks like a cure for SCD. As shown by this new work and the clinical trials underway, we in fact may soon have multiple different strategies to provide cures for this devastating disease. And if this can work for sickle cell, a similar strategy might work for other genetic conditions that currently lack any effective treatment.


[1] Highly efficient therapeutic gene editing of human hematopoietic stem cells. Wu Y, Zeng J, Roscoe BP, Liu P, Yao Q, Lazzarotto CR, Clement K, Cole MA, Luk K, Baricordi C, Shen AH, Ren C, Esrick EB, Manis JP, Dorfman DM, Williams DA, Biffi A, Brugnara C, Biasco L, Brendel C, Pinello L, Tsai SQ, Wolfe SA, Bauer DE. Nat Med. 2019 Mar 25.

[2] Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Sankaran VG, Menne TF, Xu J, Akie TE, Lettre G, Van Handel B, Mikkola HK, Hirschhorn JN, Cantor AB, Orkin SH.Science. 2008 Dec 19;322(5909):1839-1842.

[3] An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH. Science. 2013 Oct 11;342(6155):253-257.

[4] CRISPR Therapeutics and Vertex Announce FDA Fast Track Designation for CTX001 for the Treatment of Sickle Cell Disease, CRISPR Therapeutics News Release, Jan. 4, 2019.


Sickle Cell Disease (National Heart, Lung, and Blood Institute/NIH)

Cure Sickle Cell Initiative (NHLBI)

What are Genome Editing and CRISPR-Cas9? (National Library of Medicine/NIH)

Could Gene Therapy Cure Sickle Cell Anemia? (CBS News)

Daniel Bauer (Dana-Farber Cancer Institute, Boston)

Somatic Cell Genome Editing Program (Common Fund/NIH)

NIH Support: National Heart, Lung, and Blood Institute; National Institute of General Medical Sciences; National Institute of Allergy and Infectious Diseases; National Institute of Diabetes and Digestive and Kidney Diseases

World’s Smallest Tic-Tac-Toe Game Built from DNA

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Check out the world’s smallest board game, a nanoscale match of tic-tac-toe being played out in a test tube with X’s and O’s made of DNA. But the innovative approach you see demonstrated in this video is much more than fun and games. Ultimately, researchers hope to use this technology to build tiny DNA machines for a wide variety of biomedical applications.

Here’s how it works. By combining two relatively recent technologies, an NIH-funded team led by Lulu Qian, California Institute of Technology, Pasadena, CA, created a “swapping mechanism” that programs dynamic interactions between complex DNA nanostructures [1]. The approach takes advantage of DNA’s modular structure, along with its tendency to self-assemble, based on the ability of the four letters of DNA’s chemical alphabet to pair up in an orderly fashion, A to T and C to G.

To make each of the X or O tiles in this game (displayed here in an animated cartoon version), researchers started with a single, long strand of DNA and many much shorter strands, called staples. When the sequence of DNA letters in each of those components is arranged just right, the longer strand will fold up into the desired 2D or 3D shape. This technique is called DNA origami because of its similarity to the ancient art of Japanese paper folding.

In the early days of DNA origami, researchers showed the technique could be used to produce miniature 2D images, such as a smiley face [2]. Last year, the Caltech group got more sophisticated—using DNA origami to produce the world’s smallest reproduction of the Mona Lisa [3].

In the latest work, published in Nature Communications, Qian, Philip Petersen and Grigory Tikhomirov first mixed up a solution of nine blank DNA origami tiles in a test tube. Those DNA tiles assembled themselves into a tic-tac-toe grid. Next, two players took turns adding one of nine X or O DNA tiles into the solution. Each of the game pieces was programmed precisely to swap out only one of the tile positions on the original, blank grid, based on the DNA sequences positioned along its edges.

When the first match was over, player X had won! More importantly for future biomedical applications, the original, blank grid had been fully reconfigured into a new structure, built of all-new, DNA-constructed components. That achievement shows not only can researchers use DNA to build miniature objects, they can also use DNA to repair or reconfigure such objects.

Of course, the ultimate aim of this research isn’t to build games or reproduce famous works of art. Qian wants to see her DNA techniques used to produce tiny automated machines, capable of performing basic tasks on a molecular scale. In fact, her team already has used a similar approach to build nano-sized DNA robots, programmed to sort molecules in much the same way that a person might sort laundry [4]. Such robots may prove useful in miniaturized approaches to drug discovery, development, manufacture, and/or delivery.

Another goal of the Caltech team is to demonstrate to the scientific community what’s possible with this leading-edge technology, in hopes that other researchers will pick up their innovative tools for their own applications. That would be a win-win for us all.


[1] Information-based autonomous reconfiguration in systems of DNA nanostructures. Petersen P, Tikhomirov G, Qian L. Nat Commun. 2018 Dec 18;9(1):5362

[2] Folding DNA to create nanoscale shapes and patterns. Rothemund PW. Nature. 2006 Mar 16;440(7082):297-302.

[3] Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns. Tikhomirov G, Petersen P, Qian L. Nature. 2017 Dec 6;552(7683):67-71.

[4] A cargo-sorting DNA robot. Thubagere AJ, Li W, Johnson RF, Chen Z, Doroudi S, Lee YL, Izatt G, Wittman S, Srinivas N, Woods D, Winfree E, Qian L. Science. 2017 Sep 15;357(6356).


Paul Rothemund—DNA Origami: Folded DNA as a Building Material for Molecular Devices (Cal Tech, Pasadena)

The World’s Smallest Mona Lisa (Caltech)

Qian Lab (Caltech, Pasadena, CA)

NIH Support: National Institute of General Medical Sciences

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