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International collaboration discovers new cause for dwarfism

DNA

An international collaboration resulted in the identification of a new cause of dwarfism: mutations in a gene known as DNMT3A.

Beyond diabetes, short stature is the most common reason for children in the U.S. to visit an endocrinologist. For the vast majority of children with short stature, the cause remains unknown – even though many of these conditions stem from an as-yet unidentified genetic cause, says Andrew Dauber, M.D., M.M.Sc., division chief of Endocrinology at Children’s National Health System.

“Parents are concerned about why their child isn’t growing and if there are other complications or health problems they’ll need to watch out for,” he says. “Without a diagnosis, it’s very hard to answer those questions.”

Dauber’s research focuses on using cutting-edge genetic techniques to unravel the minute differences in DNA that limit growth. This research recently led him and his colleagues to identify a new cause of dwarfism: mutations in a gene known as DNMT3A. The discovery, which the team published in the January 2019 Nature Genetics, didn’t happen in isolation – it required a rich collaboration of labs spread across the world in Scotland, Spain, France and New Zealand, in addition to Dauber’s lab in the U.S.

The journey that brought Dauber into this group effort got its start with a young patient in Spain. The boy, then four years old, was at less than 0.1 percentile on the growth curve for height with a very small head circumference and severe developmental delays. This condition, known as microcephalic dwarfism, is incredibly rare and could stem from one of several different genetic causes. But his doctors didn’t know the reason for this child’s specific syndrome.

To better understand this condition, Dauber used a technique known as whole exome sequencing, a method that sequences all the protein-coding regions in an individual’s entire genome. He found a mutation in DNMT3A – a change known as a de novo missense mutation, meaning that the mutation happened in a single letter of the boy’s genetic code in a way that hadn’t been inherited from his parents. But although this mutation was clear, its meaning wasn’t. The only clue that Dauber had as to DNMT3A’s function was that he’d read about overgrowth syndromes in which the function of this gene is lost, leading to large individuals with large heads, the exact opposite of this patient’s condition.

To gather more information, Dauber reached out to Andrew Jackson, Ph.D., a researcher who studies human genes for growth at the University of Edinburgh in Scotland. Coincidentally, Jackson had already started studying this gene after two patients with a shared mutation in a neighboring letter in the genetic code – who also had short stature and other related problems – were referred to him.

Dauber and his colleagues sent the results from their genetic analysis back across the Atlantic to Jackson’s Edinburgh lab, and the doctors from Spain sent more information to Jackson’s lab, including the patient’s clinical information, blood samples and skin biopsy samples. Then the whole team of collaborators from around the globe set to work to discover the processes influencing short stature in each of these three patients.

Their results showed that these mutations appear to cause a gain of function in DNMT3A. This gene codes for a type of enzyme known as a methyltransferse, which places methyl groups on other genes and on the protein spools called histones that DNA wraps around. Each of these functions changes how cells read the instructions encoded in DNA. While the mutations that cause the overgrowth syndromes appear to allow stem cells to keep dividing long past when they should taper off and differentiate into different cell types – both normal processes in development – the gain of function that appears to be happening in these three patients prompts the opposite situation: Stem cells that should be dividing for a long time during development stop dividing and differentiate earlier, leading to smaller individuals with far fewer cells overall.

The researchers confirmed their findings by inserting one of the gain-of-function human DNMT3A mutations into a mouse, leading to short animals with small heads.

Eventually, says Dauber, these findings could help lead to new treatments for this and other types of dwarfism that act on these genetic pathways and steer them toward normal growth. These and other scientific discoveries hinge on the type of international collaboration that he and his colleagues engaged in here, he adds – particularly for the types of rare genetic syndromes that affect the patients that he and his colleagues study. With only a handful of individuals carrying mutations in certain genes, it’s increasingly necessary to combine the power of many labs to better understand the effects of these differences and how doctors might eventually intervene.

“The expertise for all aspects of any single research project is rarely centered in one institution, one city, or even one country,” Dauber says. “Often, you really need to reach out to people with different areas of expertise around the world to make these types of new discoveries that can have pivotal impacts on human health.”

Andrew Dauber at his computer doing a Reddit AMA

Thirteen questions for a pediatric endocrinologist

Andrew Dauber at his computer doing a Reddit AMA

Andrew Dauber, M.D., hosts an AMA chat with Reddit’s science community and offers feedback about height, growth disorders and pediatric endocrinology.

Andrew Dauber, M.D., MMSc., the division chief of endocrinology at Children’s National, spoke about epigenetics – how genes are expressed – and about all things related to pediatric endocrinology in a recent Ask Me Anything (AMA) chat with Reddit’s science community.

We’ve selected highlights from several questions Dr. Dauber received. You can view the full AMA discussion on Reddit.

Q1: What will the future of type 1 diabetes treatment look like?

As a pediatric endocrinologist, Dr. Dauber sees a lot of patients with type 1 diabetes. He predicts technology will pave the way for advancements with continuous glucose monitoring and encourage a ‘real-time’ interaction between patients and providers:

“I anticipate that within a few years, everyone will have access to continuous glucose monitoring technology and that these will be seamlessly connected to insulin pumps or artificial pancreas technologies,” types Dr. Dauber in response to the first AMA question. “I also think there will be more virtual interaction between medical providers and patients with doctors and nurses reviewing blood sugar data in the cloud.”

Q2: What height range is considered normal for a growing child? What is the difference between short stature and a height problem?

The Centers for Disease Control and Prevention has a growth chart, which shows ‘normal’ ranges, based on statistical definitions of height in the general population.

“The truth is that I know plenty of people who have heights below the ‘normal’ population, and they don’t think they have a problem at all,” says Dr. Dauber. “From a genetics point of view, the question can be reframed: When do we call a genetic variant a ‘mutation’ versus a rare variant in the population? For example: If there is a genetic change that 1 in a 1,000 people have that causes you to be 2 inches shorter – is that a problem? Is that a disease?”

“From a clinical perspective, I tend to have a discussion with my patients and their families and ask them how their stature is affecting their lives and whether changing that would really make a meaningful difference,” adds Dr. Dauber. “I believe that this is a very personal decision but people need to be realistic about expected outcomes.”

Q3: What are your favorite case studies about atypical growth or height patterns?

Dr. Dauber references two case studies about growth and puberty:

The growth case study refers to the PAPPA2 gene, which was particularly meaningful for Dr. Dauber since he got to know the family and was able to provide answers to a previously undiagnosed medical mystery about short stature. This research is also opening future studies and analysis about the regulation of IGF-1 bioavailability.

The puberty case study looks at the opposite end of growth and development: precocious puberty. In this case an inherited MKRN3 gene mutation resulted in new insight about the regulation of pubertal timing: Deficiency of MKRN3 caused central precocious puberty in humans. Girls who had inherited the mutated genes from their father (an imprint gene) started to develop breasts before age 6. The results were published in The New England Journal of Medicine.

Q4: What are the differences with consistent and inconsistent growth disorders? Could one arm or leg experience accelerated or stunted growth?

“Most genetic disorders that affect growth will have a uniform effect throughout the body as they are likely to affect all aspects of the skeleton,” says Dr. Dauber. “That being said, there are some notable exceptions such as Russell-Silver syndrome which presents with body asymmetry. There are also somatic mutations (mutations which are just present in some cells in the body) that can lead to segmental areas of overgrowth leading to asymmetry.”

Q5: Can you predict height and growth by looking at genetic factors? What are your thoughts about polygenic risk scores?

“Polygenic risk scores will probably play more of a role in the future to help determine risk of a certain disease,” says Dr. Dauber. “Right now, for most conditions, the risk score does not explain a substantial enough fraction of the variation to help with prediction.”

Dr. Dauber discusses how this works for height, a highly hereditable trait, in The Journal for Clinical Endocrinology and Metabolism. In the review, Dr. Dauber and the study co-authors note that individuals with extreme heights are more likely to have abnormal stature as a result of a severe mutation that causes a growth disorder. For these individuals, whole exome sequencing may reveal gene mutations.

However, the study authors note that for now, the role of these technologies in individuals with extreme stature but without any syndromic features has not been rigorously and systematically explored. (Dr. Dauber and a team of endocrinologists from leading children’s hospitals are currently using electronic health records to study and track these types of genetic clues over time.)

Q6: The general public is excited about genetics and ongoing research, especially with consumer applications – such as genetic tests, including 23andMe. What misconceptions about genetics do people have? What ethical concerns do geneticists share right now?

“Many people think that genetics is completely deterministic,” says Dr. Dauber. “In reality, most genetic variants influence a person’s predisposition toward a trait or disease but don’t actually determine the outcome. Also, the genetic sequence itself is just the first step. Epigenetics, gene regulation, and gene-environment interactions are all important and we are just scratching the surface of understanding these areas.”

“I think that people engaged in genetics research are very interested in the ethical questions,” adds Dr. Dauber. “The problem is that technology is advancing at such a rapid pace, that often consumers are using technologies in ways that we haven’t yet had time to figure out the ethics for. The medical community is often playing catch up.”

Q7: Aside from using gene modifications to cure diseases, where or when should we draw the line in terms of enhancement?

“I think genetic modification for enhancement is a very dangerous slippery slope that we should avoid,” says Dr. Dauber. “We really don’t know the full effect of many genes and by enhancing them, we could be causing lots of problems that we can’t anticipate. There is a reason that evolution is a slow process that happens over millions of years. I think we need to start with the most devastating diseases and try to cure those first.”

Q8: Would it be ethical to use CRISPR on the genes for short stature to produce tall offspring if the risks are sufficiently small? This would be similar to what Dr. He did, but without the ethical violations.

This is a fascinating question and it will become more of an issue over time,” says Dr. Dauber. “Where do we draw the line between fixing, preventing disease and enhancing physical function? Personally, I think using genome editing to promote height is a terrible idea. Our current perception that taller height is more desirable is a social construct and varies by culture. This idea also changes over time.”

Q9: Overall, how does this fit into meeting unmet medical needs?

I would be very wary about trying to design our children’s physical features,” Dr. Dauber notes. “We need to figure out as a society what diseases are sufficiently problematic that we feel comfortable trying to eliminate them via genome editing.”

Q10: How many genes control acromegaly? Is it possible (in theory) to Top of Formselect them just to gain the positive effects of gigantism without the health risks?

Dr. Dauber explains that acromegaly, a condition often referred to as gigantism, is caused by a growth hormone-producing tumor. There are a few genes known to cause these tumors, including the AIP, and there was recently a genetic cause of X-linked gigantism, which was published in The New England Journal of Medicine.

“This basic idea is a good one,” notes Dr. Dauber. “We can find genes that when mutated can cause tall stature – and then try to manipulate those pathways. A great example is the NPR2 gene, which when mutated can cause short or tall stature. This pathway is being targeted for therapeutics related to achondroplasia.”

The National Institutes of Health (NIH) refers to achondroplasia as ‘short-limbed dwarfism,’ which results in an average-sized trunk with short limbs, especially arms and legs, due to a lack of cartilage turning into bone. The average height of an adult male with achondroplasia is 4 feet, 4 inches, while the average height of adult females with achondroplasia is less than 4 feet, 1 inch. In this case, manipulating growth pathways may help alleviate health problems associated with achondroplasia: lack of mobility or range of motion, an enlarged head, apnea, ear infections and spinal stenosis, or a compression or pinching of the spinal cord.

Q11: Give us a history lesson. Why are there variations of height within populations, such as Asia and Latin America?

“The average height in a population is due to the influence of literally thousands of common genetic variants,” says Dr. Dauber. “These population differences have evolved over thousands of years due to a combination of migration and selection. There is a well-known difference in the genetic makeup of various populations which likely underlies the differences across the globe. There are even differences within Europe.”

Q12: Are there examples of pseudoscience or theories about growth, such as recommendations to eat a certain food instead of taking growth hormones to correct for a growth disorder, which runs contrary to scientific evidence, that drive you crazy?

“I don’t really get bothered by crazy theories, but it is upsetting when patients and their families get swindled into spending their money on therapies that aren’t truly effective,” says Dr. Dauber. “People ask me all the time if a certain food or exercise can make their child taller. The bottom line is that in a well-nourished (and healthy) child, there is no magical food that is going to make them tall.”

Q13: According to almost every theory of how life evolved on Earth, from religion to evolution, we all have one common ancestor. In theory doesn’t that make us all cousins?

“Yes, just very distant ones,” says Dr. Dauber. “People always point out the vast number of differences between races but in fact we are all more than 99.9 percent identical on a genetic level.”

Stay on top of the latest pediatric endocrinology news by following @EndoDocDauber and @ChildrensHealth on Twitter: #GrowUpStronger.

Test tube that says IGF-1 test

PAPPA2: A genetic mystery

Test tube that says IGF-1 test

What would happen if you suddenly stopped growing at age 12 or 13?

Solving genetic growth mysteries and scheduling regular appointments with pediatric endocrinologists is atypical for most parents and pediatricians.

However, for children with growth disorders – a classification that typically describes children below the third or above the 97th percentile of growth charts for their age – receiving a diagnosis is half the battle to reaching average height. Understanding and creating treatment for a growth disorder, which could stem from an underlying medical illness, a genetic mutation or a problem with endocrine function, such as the production or action of growth hormone, is often the next step.

For Andrew Dauber, M.D., MMSc., the chief of endocrinology at Children’s National Health System, a third step is to use these clues to create larger datasets and blueprints to identify risk factors for rare growth disorders. By understanding genetic markers of growth disorders, endocrinologists can identify solutions and create plans for multidisciplinary care to help children reach developmental milestones and receive coordinated care throughout their lifespan.

A case study that Dauber and his research team continue to explore is how to correct for mutations in the PAPPA2 gene, which regulates human growth by releasing a key growth factor called insulin-like growth factor 1 (IGF-1). Dauber and his colleagues recently described a mutation in PAPPA2, observed in two families with multiple children affected with significant short stature. He found that this mutation decreased the bioavailability of IGF-1, stunting the growth and development of the children who carry this mutation.

While the PAPPA2 mutation is rare, endocrinologists, like Dauber, who understand its function and dysregulation can create solutions to support IGF-1 bioavailability, thereby supporting healthy growth and development in children.

Understanding barriers to IGF-1 function can also help researchers gain insight into the relationship between PAPPA2, levels of circulating insulin in the body, which could cause insulin resistance, and other growth hormones. For now, Dauber and his research team are exploring how to use PAPPA2 to increase IGF-1 in circulation among people with height disorders in the hopes of improving their growth.

“The population of children who have PAPPA2 mutations is small and we’re finding out that two children could respond to the same treatment in different ways,” says Dauber. “One medication could work modestly in one child and support short growth spurts, such as growing by 5 or 6 cm a year. It could also create undesirable side effects, such as headaches and migraines in another, and render it ineffective. However, the clues we walk away with enable us to test new solutions, and confirm or dissolve our hunches, about what may be preventing the bioactive release of essential growth hormones.”

To generate controls for healthy patterns of growth and development, Dauber and his research team are analyzing the relationship between PAPPA2, STC2 and IGFBP-3 concentrations among 838 relatively healthy pediatric participants, ages 3-18, with traditional growth patterns.

They are studying PAPPA2, STC2 and intact IGFBP-3 concentrations throughout childhood and the researchers are already surprised to find PAPPA2, a positive modulator of growth and IGF- bioavailability, decreased with age, while STC2, a negative modulator and traditional growth inhibitor, increased with age.

“As pediatric endocrinology researchers and clinicians, we’re looking at the pathology of traditional growth patterns and growth disorders with an open mind,” says Dr. Dauber. “These data sets are invaluable as they confirm or challenge our theories, which enable us to create and test new forms of personalized treatments. We’ll continue to share this knowledge, which informs other researchers and accelerates the field of pediatric endocrinology.”

This research was presented at the annual meeting of the European Society of Pediatric Endocrinology in Athens on Sept. 28, 2018.

Dauber and his research team will present their findings at endocrinology conferences and grand rounds throughout 2018 and 2019.

To view Dr. Dauber’s most recent research and pediatric endocrinology reviews, visit PubMed.