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Celebrating 2019 Biomedical Breakthroughs

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Science 2019 Biomedical Breakthroughs and a Breakdown

Happy New Year! As we say goodbye to the Teens, let’s take a look back at 2019 and some of the groundbreaking scientific discoveries that closed out this remarkable decade.

Each December, the reporters and editors at the journal Science select their breakthrough of the year, and the choice for 2019 is nothing less than spectacular: An international network of radio astronomers published the first image of a black hole, the long-theorized cosmic singularity where gravity is so strong that even light cannot escape [1]. This one resides in a galaxy 53 million light-years from Earth! (A light-year equals about 6 trillion miles.)

Though the competition was certainly stiff in 2019, the biomedical sciences were well represented among Science’s “runner-up” breakthroughs. They include three breakthroughs that have received NIH support. Let’s take a look at them:

In a first, drug treats most cases of cystic fibrosis: Last October, two international research teams reported the results from phase 3 clinical trials of the triple drug therapy Trikafta to treat cystic fibrosis (CF). Their data showed Trikafta effectively compensates for the effects of a mutation carried by about 90 percent of people born with CF. Upon reviewing these impressive data, the Food and Drug Administration (FDA) approved Trikafta, developed by Vertex Pharmaceuticals.

The approval of Trikafta was a wonderful day for me personally, having co-led the team that isolated the CF gene 30 years ago. A few years later, I wrote a song called “Dare to Dream” imagining that wonderful day when “the story of CF is history.” Though we’ve still got more work to do, we’re getting a lot closer to making that dream come true. Indeed, with the approval of Trikafta, most people with CF have for the first time ever a real chance at managing this genetic disease as a chronic condition over the course of their lives. That’s a tremendous accomplishment considering that few with CF lived beyond their teens as recently as the 1980s.

Such progress has been made possible by decades of work involving a vast number of researchers, many funded by NIH, as well as by more than two decades of visionary and collaborative efforts between the Cystic Fibrosis Foundation and Aurora Biosciences (now, Vertex) that built upon that fundamental knowledge of the responsible gene and its protein product. Not only did this innovative approach serve to accelerate the development of therapies for CF, it established a model that may inform efforts to develop therapies for other rare genetic diseases.

Hope for Ebola patients, at last: It was just six years ago that news of a major Ebola outbreak in West Africa sounded a global health emergency of the highest order. Ebola virus disease was then recognized as an untreatable, rapidly fatal illness for the majority of those who contracted it. Though international control efforts ultimately contained the spread of the virus in West Africa within about two years, over 28,600 cases had been confirmed leading to more than 11,000 deaths—marking the largest known Ebola outbreak in human history. Most recently, another major outbreak continues to wreak havoc in northeastern Democratic Republic of Congo (DRC), where violent civil unrest is greatly challenging public health control efforts.

As troubling as this news remains, 2019 brought a needed breakthrough for the millions of people living in areas susceptible to Ebola outbreaks. A randomized clinical trial in the DRC evaluated four different drugs for treating acutely infected individuals, including an antibody against the virus called mAb114, and a cocktail of anti-Ebola antibodies referred to as REGN-EB3. The trial’s preliminary data showed that about 70 percent of the patients who received either mAb114 or the REGN-EB3 antibody cocktail survived, compared with about half of those given either of the other two medicines.

So compelling were these preliminary results that the trial, co-sponsored by NIH’s National Institute of Allergy and Infectious Diseases (NIAID) and the DRC’s National Institute for Biomedical Research, was halted last August. The results were also promptly made public to help save lives and stem the latest outbreak. All Ebola patients in the DRC treatment centers now are treated with one or the other of these two options. The trial results were recently published.

The NIH-developed mAb114 antibody and the REGN-EB3 cocktail are the first therapeutics to be shown in a scientifically rigorous study to be effective at treating Ebola. This work also demonstrates that ethically sound clinical research can be conducted under difficult conditions in the midst of a disease outbreak. In fact, the halted study was named Pamoja Tulinde Maisha (PALM), which means “together save lives” in Kiswahili.

To top off the life-saving progress in 2019, the FDA just approved the first vaccine for Ebola. Called Ervebo (earlier rVSV-ZEBOV), this single-dose injectable vaccine is a non-infectious version of an animal virus that has been genetically engineered to carry a segment of a gene from the Zaire species of the Ebola virus—the virus responsible for the current DRC outbreak and the West Africa outbreak. Because the vaccine does not contain the whole Zaire virus, it can’t cause Ebola. Results from a large study in Guinea conducted by the WHO indicated that the vaccine offered substantial protection against Ebola virus disease. Ervebo, produced by Merck, has already been given to over 259,000 individuals as part of the response to the DRC outbreak. The NIH has supported numerous clinical trials of the vaccine, including an ongoing study in West Africa.

Microbes combat malnourishment: Researchers discovered a few years ago that abnormal microbial communities, or microbiomes, in the intestine appear to contribute to childhood malnutrition. An NIH-supported research team followed up on this lead with a study of kids in Bangladesh, and it published last July its groundbreaking finding: that foods formulated to repair the “gut microbiome” helped malnourished kids rebuild their health. The researchers were able to identify a network of 15 bacterial species that consistently interact in the gut microbiomes of Bangladeshi children. In this month-long study, this bacterial network helped the researchers characterize a child’s microbiome and/or its relative state of repair.

But a month isn’t long enough to determine how the new foods would help children grow and recover. The researchers are conducting a similar study that is much longer and larger. Globally, malnutrition affects an estimated 238 million children under the age 5, stunting their normal growth, compromising their health, and limiting their mental development. The hope is that these new foods and others adapted for use around the world soon will help many more kids grow up to be healthy adults.

Measles Resurgent: The staff at Science also listed their less-encouraging 2019 Breakdowns of the Year, and unfortunately the biomedical sciences made the cut with the return of measles in the U.S. Prior to 1963, when the measles vaccine was developed, 3 to 4 million Americans were sickened by measles each year. Each year about 500 children would die from measles, and many more would suffer lifelong complications. As more people were vaccinated, the incidence of measles plummeted. By the year 2000, the disease was even declared eliminated from the U.S.

But, as more parents have chosen not to vaccinate their children, driven by the now debunked claim that vaccines are connected to autism, measles has made a very preventable comeback. Last October, the Centers for Disease Control and Prevention (CDC) reported an estimated 1,250 measles cases in the United States at that point in 2019, surpassing the total number of cases reported annually in each of the past 25 years.

The good news is those numbers can be reduced if more people get the vaccine, which has been shown repeatedly in many large and rigorous studies to be safe and effective. The CDC recommends that children should receive their first dose by 12 to 15 months of age and a second dose between the ages of 4 and 6. Older people who’ve been vaccinated or have had the measles previously should consider being re-vaccinated, especially if they live in places with low vaccination rates or will be traveling to countries where measles are endemic.

Despite this public health breakdown, 2019 closed out a memorable decade of scientific discovery. The Twenties will build on discoveries made during the Teens and bring us even closer to an era of precision medicine to improve the lives of millions of Americans. So, onward to 2020—and happy New Year!

Reference:

[1] 2019 Breakthrough of the Year. Science, December 19, 2019.

NIH Support: These breakthroughs represent the culmination of years of research involving many investigators and the support of multiple NIH institutes.


Whole-Genome Sequencing Plus AI Yields Same-Day Genetic Diagnoses

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Sebastiana
Caption: Rapid whole-genome sequencing helped doctors diagnose Sebastiana Manuel with Ohtahara syndrome, a neurological condition that causes seizures. Her data are now being used as part of an effort to speed the diagnosis of other children born with unexplained illnesses. Credits: Getty Images (left); Jenny Siegwart (right).



Back in April 2003, when the international Human Genome Project successfully completed the first reference sequence of the human DNA blueprint, we were thrilled to have achieved that feat in just 13 years. Sure, the U.S. contribution to that first human reference sequence cost an estimated $400 million, but we knew (or at least we hoped) that the costs would come down quickly, and the speed would accelerate. How far we’ve come since then! A new study shows that whole genome sequencing—combined with artificial intelligence (AI)—can now be used to diagnose genetic diseases in seriously ill babies in less than 24 hours.

Take a moment to absorb this. I would submit that there is no other technology in the history of planet Earth that has experienced this degree of progress in speed and affordability. And, at the same time, DNA sequence technology has achieved spectacularly high levels of accuracy. The time-honored adage that you can only get two out of three for “faster, better, and cheaper” has been broken—all three have been dramatically enhanced by the advances of the last 16 years.

Rapid diagnosis is critical for infants born with mysterious conditions because it enables them to receive potentially life-saving interventions as soon as possible after birth. In a study in Science Translational Medicine, NIH-funded researchers describe development of a highly automated, genome-sequencing pipeline that’s capable of routinely delivering a diagnosis to anxious parents and health-care professionals dramatically earlier than typically has been possible [1].

While the cost of rapid DNA sequencing continues to fall, challenges remain in utilizing this valuable tool to make quick diagnostic decisions. In most clinical settings, the wait for whole-genome sequencing results still runs more than two weeks. Attempts to obtain faster results also have been labor intensive, requiring dedicated teams of experts to sift through the data, one sample at a time.

In the new study, a research team led by Stephen Kingsmore, Rady Children’s Institute for Genomic Medicine, San Diego, CA, describes a streamlined approach that accelerates every step in the process, making it possible to obtain whole-genome test results in a median time of about 20 hours and with much less manual labor. They propose that the system could deliver answers for 30 patients per week using a single genome sequencing instrument.

Here’s how it works: Instead of manually preparing blood samples, his team used special microbeads to isolate DNA much more rapidly with very little labor. The approach reduced the time for sample preparation from 10 hours to less than three. Then, using a state-of-the-art DNA sequencer, they sequence those samples to obtain good quality whole genome data in just 15.5 hours.

The next potentially time-consuming challenge is making sense of all that data. To speed up the analysis, Kingsmore’s team took advantage of a machine-learning system called MOON. The automated platform sifts through all the data using artificial intelligence to search for potentially disease-causing variants.

The researchers paired MOON with a clinical language processing system, which allowed them to extract relevant information from the child’s electronic health records within seconds. Teaming that patient-specific information with data on more than 13,000 known genetic diseases in the scientific literature, the machine-learning system could pick out a likely disease-causing mutation out of 4.5 million potential variants in an impressive 5 minutes or less!

To put the system to the test, the researchers first evaluated its ability to reach a correct diagnosis in a sample of 101 children with 105 previously diagnosed genetic diseases. In nearly every case, the automated diagnosis matched the opinions reached previously via the more lengthy and laborious manual interpretation of experts.

Next, the researchers tested the automated system in assisting diagnosis of seven seriously ill infants in the intensive care unit, and three previously diagnosed infants. They showed that their automated system could reach a diagnosis in less than 20 hours. That’s compared to the fastest manual approach, which typically took about 48 hours. The automated system also required about 90 percent less manpower.

The system nailed a rapid diagnosis for 3 of 7 infants without returning any false-positive results. Those diagnoses were made with an average time savings of more than 22 hours. In each case, the early diagnosis immediately influenced the treatment those children received. That’s key given that, for young children suffering from serious and unexplained symptoms such as seizures, metabolic abnormalities, or immunodeficiencies, time is of the essence.

Of course, artificial intelligence may never replace doctors and other healthcare providers. Kingsmore notes that 106 years after the invention of the autopilot, two pilots are still required to fly a commercial aircraft. Likewise, health care decisions based on genome interpretation also will continue to require the expertise of skilled physicians.

Still, such a rapid automated system will prove incredibly useful. For instance, this system can provide immediate provisional diagnosis, allowing the experts to focus their attention on more difficult unsolved cases or other needs. It may also prove useful in re-evaluating the evidence in the many cases in which manual interpretation by experts fails to provide an answer.

The automated system may also be useful for periodically reanalyzing data in the many cases that remain unsolved. Keeping up with such reanalysis is a particular challenge considering that researchers continue to discover hundreds of disease-associated genes and thousands of variants each and every year. The hope is that in the years ahead, the combination of whole genome sequencing, artificial intelligence, and expert care will make all the difference in the lives of many more seriously ill babies and their families.

Reference:

[1] Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation. Clark MM, Hildreth A, Batalov S, Ding Y, Chowdhury S, Watkins K, Ellsworth K, Camp B, Kint CI, Yacoubian C, Farnaes L, Bainbridge MN, Beebe C, Braun JJA, Bray M, Carroll J, Cakici JA, Caylor SA, Clarke C, Creed MP, Friedman J, Frith A, Gain R, Gaughran M, George S, Gilmer S, Gleeson J, Gore J, Grunenwald H, Hovey RL, Janes ML, Lin K, McDonagh PD, McBride K, Mulrooney P, Nahas S, Oh D, Oriol A, Puckett L, Rady Z, Reese MG, Ryu J, Salz L, Sanford E, Stewart L, Sweeney N, Tokita M, Van Der Kraan L, White S, Wigby K, Williams B, Wong T, Wright MS, Yamada C, Schols P, Reynders J, Hall K, Dimmock D, Veeraraghavan N, Defay T, Kingsmore SF. Sci Transl Med. 2019 Apr 24;11(489).

Links:

DNA Sequencing Fact Sheet (National Human Genome Research Institute/NIH)

Genomics and Medicine (NHGRI/NIH)

Genetic and Rare Disease Information Center (National Center for Advancing Translational Sciences/NIH)

Stephen Kingsmore (Rady Children’s Institute for Genomic Medicine, San Diego, CA)

NIH Support: National Institute of Child Health and Human Development; National Human Genome Research Institute; National Center for Advancing Translational Sciences


More Progress Toward Gene Editing for Kids with Muscular Dystrophy

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Normal and treated muscles with DMD
Caption: Muscles of untreated mouse model of Duchenne muscular dystrophy (left) compared to muscles of similar mice one year after gene-editing treatment (right). Dystrophin production (green) is restored in treated animals, despite therapy-related immune response to the Cas9 editing enzyme (dark spots in white inset). Credit: Charles Gersbach, Duke University, Durham, NC

Thanks to CRISPR and other gene editing technologies, hopes have never been greater for treating or even curing Duchenne muscular dystrophy (DMD) and many other rare, genetic diseases that once seemed tragically out of reach. The latest encouraging news comes from a study in which a single infusion of a CRISPR editing system produced lasting benefits in a mouse model of DMD.

There currently is no way to cure DMD, an ultimately fatal disease that mainly affects boys. Caused by mutations in a gene that codes for a critical protein called dystrophin, DMD progressively weakens the skeletal and heart muscles. People with DMD are usually in wheelchairs by the age of 10, with most dying before the age of 30.

The exquisite targeting ability of CRISPR/Cas9 editing systems rely on a sequence-specific guide RNA to direct a scissor-like, bacterial enzyme (Cas9) to just the right spot in the genome, where it can be used to cut out, replace, or repair disease-causing mutations. In previous studies in mice and dogs, researchers directly infused CRISPR systems directly into the animals bodies. This “in vivo” approach to gene editing successfully restored production of functional dystrophin proteins, strengthening animals’ muscles within weeks of treatment.

But an important question remained: would CRISPR’s benefits persist over the long term? The answer in a mouse model of DMD appears to be “yes,” according to findings published recently in Nature Medicine by Charles Gersbach, Duke University, Durham, NC, and his colleagues [1]. Specifically, the NIH-funded team found that after mice with DMD received one infusion of a specially designed CRISPR/Cas9 system, the abnormal gene was edited in a way that restored dystrophin production in skeletal and heart muscles for more than a year. What’s more, lasting improvements were seen in the structure of the animals’ muscles throughout the same time period.

As exciting as these results may be, much more research is needed to explore both the safety and the efficacy of in vivo gene editing before it can be tried in humans with DMD. For instance, the researchers found that older mice that received the editing system developed an immune response to the bacterially-derived Cas9 protein. However, this response didn’t prevent the CRISPR/Cas9 system from doing its job or appear to cause any adverse effects. Interestingly, younger animals didn’t show such a response.

It’s worth noting that the immune systems of mice and people often respond quite differently. But the findings do highlight some possible challenges of such treatments, as well as approaches to reduce possible side effects. For instance, the latest findings suggest CRISPR/Cas9 treatment might best be done early in life, before an infant’s immune system is fully developed. Also, if it’s necessary to deliver CRISPR/Cas9 to older individuals, it may be beneficial to suppress the immune system temporarily.

Another concern about CRISPR technology is the potential for damaging, “off-target” edits to other parts of the genome. In the new work, the Duke team found that its CRISPR system made very few “off-target” edits. However, the system did make a surprising number of complex edits to the targeted dystrophin gene, including integration of the viral vector used to deliver Cas9. While those editing “errors” might reduce the efficacy of treatment, researchers said they didn’t appear to affect the health of the mice studied.

It’s important to emphasize that this gene editing research aimed at curing DMD is being done in non-reproductive (somatic) cells, primarily muscle tissue. The NIH does not support the use of gene editing technologies in human embryos or human reproductive (germline) cells, which would change the genetic makeup of future offspring.

As such, the Duke researchers’ CRISPR/Cas9 system is designed to work optimally in a range of muscle and muscle-progenitor cells. Still, they were able to detect editing of the dystrophin-producing gene in the liver, kidney, brain, and other tissues. Importantly, there was no evidence of edits in the germline cells of the mice. The researchers note that their CRISPR system can be reconfigured to limit gene editing to mature muscle cells, although that may reduce the treatment’s efficacy.

It’s truly encouraging to see that CRISPR gene editing may confer lasting benefits in an animal model of DMD, but a great many questions remain before trying this new approach in kids with DMD. But that time is coming—so let’s boldly go forth and get answers to those questions on behalf of all who are affected by this heartbreaking disease.

Reference:

[1] Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nelson CE, Wu Y, Gemberling MP, Oliver ML, Waller MA, Bohning JD, Robinson-Hamm JN, Bulaklak K, Castellanos Rivera RM, Collier JH, Asokan A, Gersbach CA. Nat Med. 2019 Feb 18.

Links:

Muscular Dystrophy Information Page (National Institute of Neurological Disorders and Stroke/NIH)

Gersbach Lab (Duke University, Durham, NC)

Somatic Cell Genome Editing (Common Fund/NIH)

NIH Support: National Institute of Arthritis and Musculoskeletal and Skin Diseases; National Institute of Biomedical Imaging and Bioengineering


Working Toward Greater Precision in Childhood Cancers

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Pediatric Cancer

Credit: National Cancer Institute, NIH

Each year, more than 15,000 American children and teenagers will be diagnosed with cancer. While great progress has been made in treating many types of childhood cancer, it remains the leading cause of disease-related death among kids who make it past infancy in the United States [1]. One reason for that sobering reality is our relatively limited knowledge about the precise biological mechanisms responsible for childhood cancers—information vital for designing targeted therapies to fight the disease in all its varied forms.

Now, two complementary studies have brought into clearer focus the genomic landscapes of many types of childhood cancer [2, 3]. The studies, which analyzed DNA data representing tumor and normal tissue from more than 2,600 young people with cancer, uncovered thousands of genomic alterations in about 200 different genes that appear to drive childhood cancers. These so-called “driver genes” included many that were different than those found in similar studies of adult cancers, as well as a considerable number of mutations that appear amenable to targeting with precision therapies already available or under development.


NIH Family Members Giving Back: Rebecca Shlafer

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Rebecca Shlafer

Rebecca Shlafer/Credit: Brady Willette

When Rebecca Shlafer clicks on her office lights each morning at the University of Minnesota Medical Center, Minneapolis, she usually has a good idea of what to expect from the day ahead as lead of a nine-person research team that studies the effects of incarceration on children and families. It’s her volunteer work that can be unpredictable.

For the past eight years, this developmental child psychologist has donated her free time to serve as a guardian ad litem for abused or neglected children who’ve been removed from their homes and placed under protective supervision of Minnesota’s Fourth Judicial District. In that volunteer capacity, Shlafer advocates in court for the well-being of the child, but doesn’t foster the youngster or provide any day-to-day care.


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