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Gut-Dwelling Bacterium Consumes Parkinson’s Drug

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Gut bacteria eating a pill

Scientists continue to uncover the many fascinating ways in which the trillions of microbes that inhabit the human body influence our health. Now comes yet another surprising discovery: a medicine-eating bacterium residing in the human gut that may affect how well someone responds to the most commonly prescribed drug for Parkinson’s disease.

There have been previous hints that gut microbes might influence the effectiveness of levodopa (L-dopa), which helps to ease the stiffness, rigidity, and slowness of movement associated with Parkinson’s disease. Now, in findings published in Science, an NIH-funded team has identified a specific, gut-dwelling bacterium that consumes L-dopa [1]. The scientists have also identified the bacterial genes and enzymes involved in the process.

Parkinson’s disease is a progressive neurodegenerative condition in which the dopamine-producing cells in a portion of the brain called the substantia nigra begin to sicken and die. Because these cells and their dopamine are critical for controlling movement, their death leads to the familiar tremor, difficulty moving, and the characteristic slow gait. As the disease progresses, cognitive and behavioral problems can take hold, including depression, personality shifts, and sleep disturbances.

For the 10 million people in the world now living with this neurodegenerative disorder, and for those who’ve gone before them, L-dopa has been for the last 50 years the mainstay of treatment to help alleviate those motor symptoms. The drug is a precursor of dopamine, and, unlike dopamine, it has the advantage of crossing the blood-brain barrier. Once inside the brain, an enzyme called DOPA decarboxylase converts L-dopa to dopamine.

Unfortunately, only a small fraction of L-dopa ever reaches the brain, contributing to big differences in the drug’s efficacy from person to person. Since the 1970s, researchers have suspected that these differences could be traced, in part, to microbes in the gut breaking down L-dopa before it gets to the brain.

To take a closer look in the new study, Vayu Maini Rekdal and Emily Balskus, Harvard University, Cambridge, MA, turned to data from the NIH-supported Human Microbiome Project (HMP). The project used DNA sequencing to identify and characterize the diverse collection of microbes that populate the healthy human body.

The researchers sifted through the HMP database for bacterial DNA sequences that appeared to encode an enzyme capable of converting L-dopa to dopamine. They found what they were looking for in a bacterial group known as Enterococcus, which often inhabits the human gastrointestinal tract.

Next, they tested the ability of seven representative Enterococcus strains to transform L-dopa. Only one fit the bill: a bacterium called Enterococcus faecalis, which commonly resides in a healthy gut microbiome. In their tests, this bacterium avidly consumed all the L-dopa, using its own version of a decarboxylase enzyme. When a specific gene in its genome was inactivated, E. faecalis stopped breaking down L-dopa.

These studies also revealed variability among human microbiome samples. In seven stool samples, the microbes tested didn’t consume L-dopa at all. But in 12 other samples, microbes consumed 25 to 98 percent of the L-dopa!

The researchers went on to find a strong association between the degree of L-dopa consumption and the abundance of E. faecalis in a particular microbiome sample. They also showed that adding E. faecalis to a sample that couldn’t consume L-dopa transformed it into one that could.

So how can this information be used to help people with Parkinson’s disease? Answers are already appearing. The researchers have found a small molecule that prevents the E. faecalis decarboxylase from modifying L-dopa—without harming the microbe and possibly destabilizing an otherwise healthy gut microbiome.

The finding suggests that the human gut microbiome might hold a key to predicting how well people with Parkinson’s disease will respond to L-dopa, and ultimately improving treatment outcomes. The finding also serves to remind us just how much the microbiome still has to tell us about human health and well-being.

Reference:

[1] Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism. Maini Rekdal V, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP. Science. 2019 Jun 14;364(6445).

Links:

Parkinson’s Disease Information Page (National Institute of Neurological Disorders and Stroke/NIH)

NIH Human Microbiome Project

Balskus Lab (Harvard University, Cambridge, MA)

NIH Support: National Institute of General Medical Sciences; National Heart, Lung, and Blood Institute


Farrar Delivers Barmes Lecture

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Francis Collins and Jeremy Farrar
Jeremy Farrar (left), director of the Wellcome Trust, London, delivered the 2019 David E. Barmes Global Health Lecture on June 19 in NIH’s Masur Auditorium. The lecture was titled, “Global Health in a Changing World.” Jeremy also presented me with a copy of the just-released Wellcome Global Monitor 2018. It offers the results of Wellcome’s survey of 140,000 people worldwide about science and global health challenges. The inside front cover included his handwritten inscription, which he asked me to read aloud to the audience, “Francis and all colleagues and friends at the N.I.H. We admire, respect, and give all our thanks for your leadership and friendship. Very best wishes, Jeremy.” The annual lecture honors the late David Edward Barmes, special expert for international health in the NIH’s National Institute of Dental and Craniofacial Research (NIDCR). The NIDCR cosponsors the Barmes Lecture with NIH’s Fogarty International Center. Credit: Marleen Van den Neste.

Progress Toward 3D Printed Human Organs

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There’s considerable excitement that 3D printing technology might one day allow scientists to produce fully functional replacement organs from one’s own cells. While there’s still a lot to learn, this video shows just some of the amazing progress that’s now being made.

The video comes from a bioengineering team at Rice University, Houston, that has learned to bioprint the small air sacs in the lungs. When hooked up to a machine that pulsed air in and out of the air sacs, the rhythmic movement helped to mix red blood cells traveling through an associated blood vessel network. Those red cells also took up oxygen in much the way that blood vessels do when surrounding the hundreds of millions of air sacs in our lungs.

As mentioned in the video, one of the biggest technical hurdles in growing fully functional replacement tissues and organs is to find a way to feed the growing tissues with a blood supply and to remove waste products. In this study recently published in Science [1], the NIH-supported team cleared this hurdle by creating an open-source bioprinting technology they call SLATE, which is short for “stereo-lithography apparatus for tissue engineering.”

The SLATE system “grows” soft hydrogel scaffolds one layer at a time. Each layer is printed using a liquid pre-hydrogel solution that solidifies when exposed to blue light. By also projecting light into the hydrogel as a pixelated 3D shape, it’s possible to print complex 3D structures within minutes.

When the researchers first started, their printouts lacked the high resolution, submillimeter-scale channels needed to generate intricate vascular networks. In other manufacturing arenas, light-absorbing chemicals have helped control the conversion from liquid to solid in a very fine polymer layer. But these industrial light-absorbing chemicals are highly toxic and therefore unsuitable for scaffolds that grow living tissues and organs.

The researchers, including Bagrat Grigoryan, Jordan Miller, and Kelly Stevens, wondered whether they could swap out those noxious ingredients with synthetic and natural food dyes widely used in the food industry. These dyes include curcumin, anthocyanin, and tartrazine (yellow dye #5). Their studies showed that those fully biocompatible dyes worked as effective light absorbers, allowing the scientists to recreate the complex architectures of human vasculature. Importantly, the living cells survived within the soft scaffold!

These models are already yielding intriguing new insights into the vascular structures found within our organs and how those architectures may influence function in ways that hadn’t been well understood. In the near term, tissues and organs grown on such scaffolds might also find use as sophisticated, 3D tissue “chips,” with potential for use in studies to predict whether drugs will be safe in humans.

In the long term, this technology may allow production of replacement organs from those needing them. More than 100,000 men, women, and children are on the national transplant waiting list in the United States alone and 20 people die each day waiting for a transplant [2]. Ultimately, with the aid of bioprinting advances like this one, perhaps one day we’ll have a ready supply of perfectly matched and fully functional organs.

References:

[1] Multivascular networks and functional intravascular topologies within biocompatible hydrogels. Grigoryan B, Paulsen SJ, Corbett DC, Sazer DW, Fortin CL, Zaita AJ, Greenfield PT, Calafat NJ, Gounley JP, Ta AH, Johansson F, Randles A, Rosenkrantz JE, Louis-Rosenberg JD, Galie PA, Stevens KR, Miller JS. Science. 2019 May 3;364(6439):458-464.

[2] Organ Donor Statistics, Health Resources & Services Administration, October 2018.

Links:

Tissue Engineering and Regenerative Medicine (National Institute of Biomedical Imaging and Bioengineering/NIH)

Tissue Chip for Drug Screening (National Center for Advancing Translational Sciences/NIH)

Miller Lab (Rice University, Houston)

NIH Support: National Heart, Lung, and Blood Institute; National Institute of Biomedical Imaging and Bioengineering; National Institute of General Medical Sciences; Common Fund


Study Finds Genetic Mutations in Healthy Human Tissues

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General mutations throughout the body

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.

Reference:

[1] 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).

Links:

Genotype-Tissue Expression Program

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


In Memory of Andrew Lee

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Andrew Lee Composite
Caption: Clockwise from left, Andrew Lee with his Nissan GT-R; Andrew Lee and me; Isaac Barchus with his parents, Steve and Kathe Barchus, and Andrew’s father Bruce Lee. Credits: Driven to Cure, Foundation for the NIH, The Children’s Inn at NIH

A lot of young people are driven—driven to get a good education, land a great job, find true love, or see the world. But, today, I want to honor the life of a young man who was driven by something even bigger. Andrew Lee was driven to cure kidney cancer—not only for himself, but for others as well.

I knew and loved Andrew. And so did the legion of doctors, nurses, researchers, and other team members who had the privilege of fighting cancer with him over four very challenging years. Andrew was 19, just finishing his freshman year of college, when he received a devastating diagnosis: stage 4 kidney cancer, a rare type called Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC). There is no known cure for HLRCC, and doctors estimated his survival at about a year at best.

Still, Andrew and his family weren’t about to go hide somewhere and wait for the end. They began a journey that led him to take part in at least seven clinical trials, including ones at Yale University, New Haven, CT; Georgetown University, Washington, DC; and the NIH Clinical Center, Bethesda, MD. Experimental treatments slowed down the cancer, but sometimes made him terribly sick. Yet, Andrew always remained optimistic and cheerful. If a trial didn’t help him, maybe it would help someone else.

Andrew’s generosity didn’t stop there. Inspired by his father’s gift of a totally awesome 2015 Liberty Walk Nissan GT-R, he founded the Driven To Cure (DTC) nonprofit and traveled the country in his orange sports car to raise funds for kidney cancer research. According to the National Cancer Institute, nearly 63,000 Americans are diagnosed with kidney and renal pelvis cancers each year.

Andrew figured out how to put the “fun” in fundraising, drawing crowds at car shows and raising more than $500,000 in donations in just three years. His efforts were recognized by the Foundation for the NIH’s Charlie Sanders Award, which I had the privilege of presenting to him last fall.

But I think it was Andrew’s humanity that touched us the most. He always had time to share his story, to encourage another child or adult struggling with a frightening diagnosis. He’d give thrills to kids at The Children’s Inn at NIH when he rumbled into the parking lot with his 700 horsepower GT-R. At car shows, throngs of people were drawn in by the turbocharged ride and then captivated by the young man with the bright smile and compelling story. Andrew wrote: “I realized that the vehicle of my dreams was also the vehicle which gave me the opportunity to make a difference; to do something bigger than myself.”

Still, on the personal level, kidney cancer proved relentless. Options for treatment eventually ran out. As the disease progressed, Andrew and his family had to make another difficult transition—choosing to celebrate life, even in the face of its approaching end. He needed a wheelchair, so family and friends came up with one, keeping in mind one of Andrew’s last wishes. When Andrew needed 24-hour care and pain control, he was admitted to the NIH Clinical Center Hospice Unit, where comfort could be provided and his loved ones could gather around. That even included getting government permission for a visit from his dog Milo! Surrounded by friends and family, he died peacefully on April 21.

Andrew made friends with everyone—especially kids at The Children’s Inn. One special buddy was Isaac Barchus, who has a rare autoinflammatory disease called CANDLE Syndrome. When he was back home in Omaha, NE, Isaac enjoyed challenging Andrew to long-distance video games, especially FIFA Soccer.

Although Isaac can walk, it can be very painful, so he sometimes turned to an old, beat-up wheelchair to cover long distances. But not anymore. When Isaac turned 15 on June 7, Andrew’s father Bruce Lee fulfilled his son’s wish for the future of his wheelchair. He presented Isaac with Andrew’s wheelchair, which had now been painted the same orange color as Andrew’s GT-R and emblazoned with the feisty slogan on Andrew’s personalized license plate—F CANCR. What a cool birthday gift!

During his final weeks and days, Andrew and his dad often listened to the Andy Grammer song, “Don’t Give Up on Me.” Andrew’s family never gave up on him, and he never gave up on them either. In fact, Andrew never gave up caring, loving, and believing. He wouldn’t want us to either, as his favorite song reminds us: “I will fight, I will fight for you; I always do until my heart is black and blue.”

Yes, Andrew, our hearts are black and blue from losing you. But we won’t give up on all you stood for in your short but inspiring life. Race In Peace, dear Andrew.

Links:

Remembering Andrew Lee (Foundation for the National Institutes of Health)

NIH Cancer Patient Receives Humanitarian Award (The NIH Record)

The Children’s Inn at NIH

Driven To Cure (Silver Spring, MD)

Video: Fighting Cancer With a 700-hp Nissan GT-R (The Drive)

Video: Andy Grammer—”Don’t Give Up On Me” [Official Lyric Video] from the film Five Feet Apart

Hereditary Leiomyomatosis and Renal Cell Cancer (National Library of Medicine/NIH)

Kidney (Renal Cell) Cancer (National Cancer Institute/NIH)

CANDLE Syndrome (Genetic and Rare Diseases Information Center/NIH)

Treating CANDLE Syndrome (National Institute of Allergy and Infectious Diseases/NIH)


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