Putting patients first in the translational research pipeline

During a follow-up visit, pediatric hematologist/oncologist Sung-Yun Pai, MD, hugs a patient who received gene therapy for X-linked severe combined immunodeficiency.
During a follow-up visit at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, pediatric hematologist/oncologist Sung-Yun Pai, MD, hugs a patient who received gene therapy for X-linked severe combined immunodeficiency.

This is part II of a two-part blog series recapping the 2018 BIO International Convention. Read part I: Forecasting the convergence of artificial intelligence and precision medicine.

The hope to improve people’s lives is what drives many members of industry and academia to bring new products and therapies to market. At the BIO International Convention last week in Boston, there was lots of discussion about how translational science intersects with patients’ needs and why the best therapeutic developmental pipelines are consistently putting patients first.

As a case in point, Mustafa Sahin, MD, PhD, of Boston Children’s discussed his work to improve testing and translation of new therapies for autism spectrum disorder (ASD). As a member of PACT (Preclinical Autism Consortium for Therapeutics) and director of Boston Children’s Translational Neuroscience Program, Sahin aims to bridge the gap between drug discovery and clinical translation.

“Our mission is to de-risk entry of new therapies in the ASD drug discovery and development space,” said Sahin, who is also a professor of neurology at Harvard Medical School.

One big challenge, says Sahin, is knowing how well — or how poorly — autism therapies are actually affecting people with ASD. Externally, ASD is recognized by its core symptoms of repetitive behaviors and social deficits.

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Forecasting the convergence of artificial intelligence and precision medicine

Image of artificial DNA, which in combination with other artificial intelligence could contribute to an artificial model of the immune system
Will an artificial model of the immune system be the key to discovering new, precision vaccines?

This is part I of a two-part blog series recapping the 2018 BIO International Convention.

At the 2018 BIO International Convention last week, it was clear what’s provoking scientific minds in industry and academia — or at least those of the Guinness-world-record-making 16,000 people in attendance. Artificial intelligence, machine learning and their implications for tailor-made medicine bubbled up across all BIO’s educational tracks and a majority of discussions about the future state of biotechnology. Panelists from Boston Children’s Hospital also contributed their insights to what’s brewing at the intersection of these burgeoning fields.

Isaac Kohane, MD, PhD, former chair of Boston Children’s Computational Health and Informatics Program, spoke on a panel about how large-scale patient data — if properly harnessed and analyzed for health and disease trends — is a virtual goldmine for precision medicine insights. Patterns gleaned from population health data or electronic health records, for example, could help identify which subgroups of patients who might respond better to specific therapies.

According to Kohane, who is currently the Marion J. Nelson Professor of Biomedical Informatics and Pediatrics at Harvard Medical School (HMS), we will soon be leveraging artificial intelligence to go through patient records and determine exactly what doctors were thinking when they saw patients.

“We’ve seen again and again that data abstraction by artificial intelligence is better than abstraction by human analysts when performed at the scale of millions of clinical notes across thousands of patients,” said Kohane.

And based on what we heard at BIO, artificial intelligence will revolutionize more than patient data mining. It will also transform the way we design precision therapeutics — and even vaccines — from the ground up.

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Why blood stem cells are in our bones: Evolutionary observation may inform better bone marrow transplants

blood stem cells melanocytes hematopoietic stem cells
In normal zebrafish, blood stem cells in the kidney are protected from sunlight by melanocytes. When this layer is stripped away, stem cell numbers go down. (Image and video below courtesy of the Zon Laboratory and the Howard Hughes Medical Institute.)

Since the late 1970s, biologists have known that blood develops in a specific body location. But they’ve wondered why different creatures house their blood stem cells in different places. In humans and other mammals, they’re in the bone. In fish, they’re in the kidney. Why?

Strange as it seems, the two stem cell “niches” share something in common, say researchers led by Leonard Zon, MD, of Boston Children’s Stem Cell Program, the Harvard Department of Stem Cell and Regenerative Biology (HSCRB) and the Harvard Stem Cell Institute. Both protect blood stem cells from sunlight’s harmful ultraviolet rays. The findings, published today in Nature, may contain lessons for improving blood stem cell transplants for cancer, blood disorders and other conditions.

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Mothers’ life experiences may affect their newborns’ telomeres — especially boys’

mother and newborn with telomeres

A new study adds to a growing body of evidence that mothers’ experiences affect their babies’ chromosomes. For the first time, it also shows a gender difference — with male babies more susceptible to maternal influence. And it even implicates experiences dating back to the mother’s own childhood.

The study, led by psychologist Michelle Bosquet Enlow, PhD, at Boston Children’s Hospital, may help explain why stress can have intergenerational effects within a family. It was published last month in the journal Psychoneuroendocrinology.

The researchers enrolled 151 socioeconomically diverse mothers and their infants, all born at Beth Israel Deaconess Medical Center in Boston. The mothers completed in-depth interviews during pregnancy. Cord blood was collected from the newborns so that their chromosomes could be examined — and in particular, the little caps at their tips known as telomeres.

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Precision medicine for end-stage kidney failure? 40 percent of kids needing transplants have identifiable mutations

People forming a kidney shape - indicating that not all ESRD is alike and that it can have multiple genetic causes

In adults, end-stage renal disease, or ESRD, is most commonly a complication of diabetes or hypertension. In children, teens and young adults, it’s a different picture entirely. New research finds that more than half of people needing a kidney transplant before age 25 have a congenital anomaly of the kidney or urinary tract, and that 40 percent have an identifiable genetic cause of ESRD. Knowing these genetic underpinnings can inform better care for patients with kidney disease, says study leader Friedhelm Hildebrandt, MD, chief of the Division of Nephrology at Boston Children’s Hospital.

Hildebrandt and his colleagues drew on 263 families whose child received a new kidney at Boston Children’s between 2007 and 2017, before the age of 25. In 68 families, the team was able to perform whole-exome sequencing, comparing their DNA with a normal reference sample.

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Poised pluripotency: A glimpse of the early embryo just as it’s implanting

poised pluripotency - a newly defined stem cell state
Fawn Gracey illustration (click to enlarge)

Stem cell researchers at Boston Children’s Hospital have, for the first time, profiled a highly elusive kind of stem cell in the early embryo – a cell so fleeting that it makes its entrance and exit within a 12-hour span. They describe this “poised pluripotent” cell in the journal Cell Stem Cell.

In mice, poised cells appear 4.75 to 5.25 days after egg and sperm join to form the embryo, right at the time when the embryo stops floating around and implants itself in the uterine wall.

“People have had a hard time capturing the peri-implantation period because it’s really hard to define,” says Richard Gregory, PhD, who led the research. “It’s a very dynamic stage. Everything happens within a few hours, which is quite remarkable considering the extent of the changes occurring in the properties of the cells.”

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Solving the DIPG puzzle a single cell at a time

Image depicting the cellular makeup of DIPG/DMG tumors vs normal brain tissue development
Scientists have discovered that DIPG/DMG tumors are made up of H3K27M-mutated cell populations that contain many cells stuck in a stem-cell-like state, fueling tumor growth. Cells that can differentiate despite the H3K27M mutation could hold the key to unlocking a new therapy for DIPG/DMG.

For more than 15 years, pediatric neuro-oncologist Mariella Filbin, MD, PhD, has been on a scientific crusade to understand DIPG (diffuse intrinsic pontine glioma). She hopes to one day be able to cure a disease that has historically been thought of as an incurable type of childhood brain cancer.

“While I was in medical school, I met a young girl who was diagnosed with DIPG,” Filbin recalls. “When I heard that there was no treatment available, I couldn’t believe that was the case. It really made a huge impression on me and since then, I’ve dedicated all my research to fighting DIPG.”

Her mission brought her to Boston Children’s Hospital for her medical residency program and later, to do postdoctoral research at the Dana-Farber/Boston Children’s Cancer and Blood Disorders Center. Now, she’s starting her own research laboratory focused on DIPG — which has also been called diffuse midline glioma (DMG) in recent years — and continuing to treat children with brain tumors at the Dana-Farber/Boston Children’s pediatric brain tumor treatment center. She’s also a scientist affiliated with the Broad Institute Cancer Program.

This year, Filbin has made new impact in the field by leveraging the newest single-cell genetic sequencing technologies to analyze exactly how DIPG develops in the first place. Her latest research, published in Science, entailed profiling more than 3,300 individual brain cells from biopsies of six different patients.

Using what’s known as a single-cell RNA sequencing approach to interrogate the makeup of DIPG/DMG tumors, Filbin was able to identify a particularly problematic type of brain cell that acts forever young, constantly dividing over and over again in a manner similar to stem cells.

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Probing the brain’s earliest development, with a detour into rare childhood cancers

In early brain development there is an increase in ribosomes, contained in these nucleoli
Nucleoli, the structures in the cell nucleus that manufacture ribosomes, are enlarged in very early brain development, indicating an increase in ribosome production. Here, a 3D reconstruction of individual nucleoli. (Kevin Chau, Boston Children’s Hospital)

In our early days as embryos, before we had brains, we had a neural fold, bathed in amniotic fluid. Sometime in the early-to-mid first trimester, the fold closed to form a tube, capturing some of the fluid inside as cerebrospinal fluid. Only then did our brains begin to form.

In 2015, a team led by Maria Lehtinen, PhD, Kevin Chau, PhD and Hanno Steen, PhD, at Boston Children’s Hospital, showed that the profile of proteins in the fluid changes during this time. They further showed that these proteins “talk” to the neural stem cells that form the brain.

In new research just published in the online journal eLife, Lehtinen and Chau shed more light on this little-known early stage of brain development.

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Scientists find link between increases in local temperature and antibiotic resistance

Image representing the rise of antibiotic resistance
Illustration by Fawn Gracey

Over-prescribing has long been thought to increase antibiotic resistance in bacteria. But could much bigger environmental pressures be at play?

While studying the role of climate on the distribution of antibiotic resistance across the geography of the U.S., a multidisciplinary team of epidemiologists from Boston Children’s Hospital found that higher local temperatures and population densities correlate with higher antibiotic resistance in common bacterial strains. Their findings were published today in Nature Climate Change.

“The effects of climate are increasingly being recognized in a variety of infectious diseases, but so far as we know this is the first time it has been implicated in the distribution of antibiotic resistance over geographies,” says the study’s lead author, Derek MacFadden, MD, an infectious disease specialist and research fellow at Boston Children’s Hospital. “We also found a signal that the associations between antibiotic resistance and temperature could be increasing over time.”

During their study, the team assembled a large database of U.S. antibiotic resistance in E. coli, K. pneumoniae and S. aureus, pulling from hospital, laboratory and disease surveillance data documented between 2013 and 2015. Altogether, their database comprised more than 1.6 million bacterial specimens from 602 unique records across 223 facilities and 41 states.

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Elusive epilepsy mutations begin to yield up their secrets

mosaic epilepsy mutations concept
Fawn Gracey illustration

Anti-seizure drugs don’t work in about a third of people with epilepsy. But for people with focal epilepsy, whose seizures originate in a discrete area of the brain, surgery is sometimes an option. The diseased brain tissue that’s removed also offers a rare opportunity to discover epilepsy-related genes.

Many mutations causing epilepsy have been discovered by testing DNA taken from the blood. But it’s becoming clear that not all epilepsy mutations show up on blood tests. So-called somatic mutations can arise directly in tissues like the brain during early prenatal development. Even within the brain, these mutations may affect only a fraction of the cells — those descended from the original mutated cell. This can create a “mosaic” pattern, with affected and unaffected cells sometimes intermingling.

One of the first such mutations to be described, by Ann Poduri, MD, MPH, and colleagues at Boston Children’s Hospital in 2012, was in Dante, a young boy who was having relentless daily seizures. The entire right side of Dante’s brain was malformed and enlarged, and he underwent a drastic operation, hemispherectomy, to remove it. Only later, studying brain samples from Dante and similar children, did Poduri find the genetic cause: a mutation in the gene AKT3. It affected only about a third of Dante’s brain cells. 

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