For more than two decades, research teams have investigated gene therapy strategies that deliver DNA sequences carrying genetic code to produce clotting factor in patients with hemophilia, an inherited bleeding disorder. However, this approach has been frustrated by the body's immune response against vectors — the non-disease-causing viruses used to transport the DNA.

Valder R. Arruda, MD, PhD, a hematology researcher at The Children’s Hospital of Philadelphia and an associate professor of Pediatrics at the Perelman School of Medicine at the University of Pennsylvania, and colleagues therefore investigated gene therapy that used lower dosages of vector to produce a “turbocharged” potent clotting factor — a variant protein called FIX-Padua that is hyperfunctional. It clots blood 8 to 12 times more strongly than normal, wild-type factor IX, a clotting protein. It also eliminated pre-existing antibodies that often weaken conventional treatments for people with hemophilia.

“Our findings may provide a new approach to gene therapy for hemophilia and perhaps other genetic diseases that have similar complications from inhibiting antibodies,” Dr. Arruda said.

The investigators tested the safety of FIX-Padua in three dogs, all with naturally occurring types of hemophilia B very similar to that found in people. Two of the dogs had never been exposed to clotting factor and had never developed antibodies. The gene therapy injections changed their hemophilia from severe to mild, with no bleeding episodes for up to two years. They did not develop inhibitory antibodies, nor was there evidence of thrombosis.

The third dog, named Wiley, already had inhibitory antibodies before receiving the gene therapy. Wiley also experienced safe and effective treatment of hemophilia, persisting over a sustained period of three years. The treatment also eradicated the inhibitory antibodies, the first time this occurred in an animal model with pre-existing antibodies.

Another set of preclinical safety studies in mice supported the safety and efficacy of gene therapy using FIX-Padua. Dr. Arruda published the findings in the journal Blood and added that additional studies are needed to confirm these encouraging early results.

Mitochondria are tiny energy-producing structures within our cells that contain their own DNA. Although mitochondrial DNA (mtDNA) holds far fewer genes than nuclear DNA, mtDNA exchanges signals with nuclear DNA and participates in complicated networks of biochemical reactions essential to life. New research shows that small changes in the ratio of mutant to normal mtDNA can cause abrupt changes in the expression of numerous genes within cells’ nuclear DNA.

“The findings in this study provide strong support for the concept that common metabolic diseases such as diabetes and obesity, heart and muscle diseases, and neurodegenerative diseases have underpinnings in energy deficiencies from malfunctioning mitochondria,” said Douglas C. Wallace, PhD, director of the Center for Mitochondrial and Epigenomic Medicine at The Children’s Hospital of Philadelphia.

Dr. Wallace’s team investigated the impacts of steadily increasing levels of a pathogenic mutation in one particular base of mtDNA. Researchers already knew that if 10 to 30 percent of a person’s mtDNA has this mutation, a person has diabetes and sometimes autism. Individuals with an mtDNA mutation level of 50 to 90 percent have other multisystem diseases, particularly MELAS syndrome, a severe condition that involves brain and muscle impairments. Above the 90 percent level, patients die in infancy.

In the current study, conducted in cultured human cells, Dr. Wallace and colleagues analyzed cells with different levels of this pathogenic mtDNA mutation to determine the effects on the cell’s gene expression. The researchers measured variations in cellular structure and function, nuclear gene expression, and production of different proteins.

“By showing that subtle changes in the cellular proportion of the same mitochondrial DNA mutation can result in a wide range of different clinical manifestations, these findings challenge the traditional model that a single mutation causes a single disease,” Dr. Wallace said.

While Dr. Wallace’s paradigm-shifting hypotheses remain controversial in biomedicine, the study, published in the Proceedings of the National Academy of Sciences, reinforces the argument that he has presented over the course of his career: Mitochondria play a central, largely under-recognized role in all common human diseases.

Investigators at The Children’s Hospital of Philadelphia want to identify ways to avert the lifetime of medical, developmental, and social problems associated with obesity. They are intrigued by the emerging idea that the microbial population that begins to colonize in infants’ intestines shortly after birth, known as the microbiome, plays an important role in establishing energy metabolism.

“As pediatricians, we’re interested in whether there is anything happening early in life that resets this ‘thermostat’ and has a long-term effect on how your body regulates its weight,” said L. Charles Bailey, MD, PhD, lead author of a retrospective study based on electronic health records that looked at how tendencies toward obesity develop early in life. “The thought is that the microbiome may be critically dependent on what is going on during infancy.”

Dr. Bailey is an attending physician at CHOP and an assistant professor of Pediatrics at the Perelman School of Medicine at the University of Pennsylvania.

Previous studies have shown that antibiotic exposure influences the microbiome’s diversity and composition. With these findings in mind, Dr. Bailey and colleagues analyzed electronic health records from 2001 to 2013 of 64,580 children with annual visits at ages 0 to 23 months, as well as one or more visits at ages 24 to 59 months within the network of primary care practices affiliated with CHOP. They assessed the relationships between antibiotic prescription and related diagnoses before age 24 months and the development of obesity in the following three years.

The results showed an increased risk of obesity with greater antibiotic use, particularly for children with four or more exposures to broad-spectrum antibiotics in early childhood, but they reported no significant association between obesity and narrow-spectrum drugs.

“What we think we’re seeing here with these associations is that the more we choose to use narrow-spectrum antibiotics, the less likely it may be that we’re doing something that will affect a patient’s risk of obesity later on,” Dr. Bailey said.

Christopher Forrest, MD, PhD; Peixin Zhang, PhD; Thomas M. Richards, MS; Alice Livshits, BS; and Patricia DeRusso, MD, MS; contributed to the article published in JAMA Pediatrics.

A painful condition that brings half a million patients a year to U.S. emergency rooms, kidney stones have increased in prevalence markedly in the past three decades, especially in children. When stones do not pass on their own, surgery may be necessary.

Gregory E. Tasian, MD, MSc, MSCE, a pediatric urologist and epidemiologist at The Children’s Hospital of Philadelphia, along with Ron Keren, MD, MPH, of the Center for Pediatric Clinical Effectiveness, conducted a research study that found as daily temperatures increase, so does the number of patients seeking treatment for kidney stones.

“With some experts predicting that extreme temperatures will become the norm in 30 years, children will bear the brunt of climate change,” predicted Dr. Tasian, who is also an assistant professor of Urology in Surgery at the Perelman School of Medicine at the University of Pennsylvania.

The investigators analyzed medical records of more than 60,000 adults and children with kidney stones between 2005 and 2011 in Atlanta, Chicago, Dallas, Los Angeles, and Philadelphia, in connection with weather data.The delay between high daily temperatures and kidney stone presentation was short, peaking within three days of exposure to hot days.

The researchers suggest that the number of hot days in a given year may better predict kidney stone risk in those people predisposed to stone formation than the mean annual temperature. Dehydration leads to higher concentrations of calcium and other minerals in the urine that promote the growth of kidney stones.

The researchers also found that very low outdoor temperatures increased the risk of kidney stones in three cities: Atlanta, Chicago, and Philadelphia. The authors suggest that as frigid weather keeps people indoors more, higher indoor temperatures, changes in diet, and decreased physical activity may increase their risk of kidney stones.

Dr. Tasian added that while the five U.S. cities have climates representative of those found throughout the world, future studies should analyze how risk patterns vary in different populations, including among children, who were represented by a small sample size in the current study.

The study team published its findings in Environmental Health Perspectives, the journal of the National Institute of Environmental Health Sciences.

Sickle cell disease is an inherited condition that distorts the red blood cells into a sickle shape, like the letter “C,” that blocks blood flow and damages blood vessels and many organs. A sickle cell gene mutation tells the body to make a defective type of hemoglobin, which is the oxygen transport protein in red blood cells.

Pre-empting the effects of this sickle cell gene mutation has been a focus of Children’s Hospital of Philadelphia hematology researcher Gerd A. Blobel, MD, PhD, and the August 2014 edition of Cell reported his novel findings. Dr. Blobel and his co-authors described how they altered the genetic architecture behind a developmentally controlled process called hemoglobin switching, in which adult hemoglobin (HbA) almost completely replaces fetal hemoglobin (HbF) within six months after birth.

“A major driver in the field for many years has been to understand the molecular basis and the machinery that controls that switch,” Dr. Blobel said. “The goal is ultimately to overcome the silencing of the fetal globin genes and turn them back on.”

His research team’s strategy was to manipulate gene expression in order to elevate the amount of HbF and also downregulate the amount of faulty HbA, thereby reducing the sickle cell inducing properties of the mutated form of HbA. They employed artificial zinc finger protein technology that Dr. Blobel and colleagues adapted for use in hemoglobin regulation and described in Cell two years ago.

Dr. Blobel’s team designed zinc fingers in a way that they would promote looped contacts between the locus control region and the fetal genes in adult red blood cells. This approach worked well and indeed enhanced the expression of fetal genes and reduced the level of the adult-type genes. In the context of sickle cell disease, this would be a double benefit since both high fetal gene expression and low levels of the mutated toxic form of adult hemoglobin would ameliorate the disease.

“This is a novel way to manipulate gene expression via altering chromatin architecture,” Dr. Blobel said.

Results of a study published in Pediatrics suggest that short 10- to 20-minute observations, such as an office visit, may be insufficient when it comes to assessing autism risk.

Led by Judith S. Miller PhD, MS, a senior scientist at the Center for Autism Research (CAR) at The Children’s Hospital of Philadelphia, the researchers studied a group of children age 15 to 33 months with autism, speech delays, and typical development. The researchers asked two licensed psychologists with toddler and autism expertise — who were unaware of the study participants’ status — to analyze two 10-minute video samples of the participants’ autism evaluations. The experts measured five behaviors, including responding, initiating, vocalizing, play, and response to name.

The researchers found the experts missed referrals for 39 percent of the children in the autism group. Detecting autism risk based on the brief observations alone was challenging because the children who had autism showed more typical behavior (89 percent of the time) than atypical behavior (11 percent) during that short window.

In March of 2014, the Centers for Disease Control and Prevention announced that one in 68 children in the U.S. has an autism spectrum disorder (ASD) — a 29 percent increase over the 2012 rate of one in 88. The seemingly growing prevalence of ASD demonstrates the need for accurate autism referral decisions. This decision-making process should include parent observations, developmental testing, a detailed history, and autism screening tools, in addition to clinical judgment, the research team concluded.

A description of the diagnostic tests and other information on how parents can spot the developmental delays associated with ASD is available in the diagnosis section of Autism Roadmap, an online resource developed by the CAR. The roadmap provides directories of service providers, community resources, government programs, ideas for various stages of childhood and beyond, and explanations of the latest research on ASD treatments and interventions.

Studying a family in which three generations had blood disorders, researchers discovered a defect in a gene that regulates telomeres, complex chromosomal structures with crucial roles in normal cell function.

Telomeres are made of DNA and protein that are located on the end of chromosomes, where they protect the chromosomes’ stability. They are sometimes compared to plastic tips at the end of shoelaces. Certain inherited and acquired disorders may shorten telomeres and injure rapidly dividing blood-forming cells produced in bone marrow. This leads to bone marrow failure, one example of which is aplastic anemia.

Hakon Hakonarson, MD, PhD, director of the Center for Applied Genomics at The Children’s Hospital of Philadelphia, and a number of other CHOP investigators collaborated with Australian scientists on the study that focused on an Australian family with aplastic anemia and other blood disorders, including leukemia. The investigators performed whole-exome sequencing on DNA from the families and identified an inherited mutation on the ACD gene, which codes for the telomere-binding protein TPP1. They determined that the mutation shortened telomeres and interrupted their ability to attract the enzyme telomerase, which counteracts telomere shortening and thus protects cells.

“Identifying this causal defect may help suggest future molecular-based treatments that bypass the gene defect and restore blood cell production,” Dr. Hakonarson said.

Nine other genes were previously found to play a role in bone marrow failure disorders. The current study, which appeared in the journal Blood, adds ACD to the list, the first time the gene has been shown to have a disease-causing role.

Children born with a DNA abnormality on chromosome 16, which already has been linked to neurodevelopmental problems, show measurable delays in processing sound and language, according to a team of radiologists and psychologists led by an expert from The Children’s Hospital of Philadelphia.

“This study shows an important connection between gene differences and differences in neurophysiology,” said the study’s leader, Timothy P.L. Roberts, PhD, vice chair of Radiology Research at CHOP and a researcher at CHOP’s Center for Autism Research. Dr. Roberts is also a professor of Radiology at the Perelman School of Medicine at the University of Pennsylvania.

The researchers examined 115 children with some neurological or learning disabilities who had copy number variants — either deletions or duplications of DNA — at the genetic site 16p11.2. Previous researchers had found that this location on chromosome 16 was associated with a subset of autism spectrum disorders (ASDs) and with language impairments and developmental delays.

The researchers used magnetoencephalography (MEG), which detects magnetic fields in the brain, just as electroencephalography (EEG) detects electrical fields. As each child heard a series of tones, the MEG machine analyzed changing magnetic fields in the child’s brain, measuring an auditory processing delay called the M100 response latency.

In children with the deletion, the researchers found a significant delay: 23 milliseconds, about one-fortieth of a second, a figure that Dr. Roberts called “stunningly high” compared to the healthy children. There was no such delay among children with the duplication, who actually had a non-significant tendency to process sounds faster than the control subjects.

Because the severity of neurodevelopmental symptoms did not correlate with the length of the auditory processing delay, the M100 delay may not become a clear-cut diagnostic biomarker in neurological disorders, but it may be a clue to an important common pathway in neurobiology, Dr. Roberts said. Further studies will investigate other genes previously implicated ASDs and other psychiatric disorders, to determine whether they also involve M100 response delays.

“Our goal is to unify diverse genes along a few common pathways, some of which may be treatable with specific therapies,” Dr. Roberts said.

Initiating antipsychotics may elevate a child’s risk not only for significant weight gain, but also for Type II diabetes by nearly 50 percent, according to a study conducted by researchers from PolicyLab at The Children’s Hospital of Philadelphia.

Moreover, among children who are also receiving antidepressants, the risk may double. Previous PolicyLab research showed that one in three youth receiving antidepressants in the Medicaid program were receiving an antipsychotic at the same time.

“These new findings should give us pause,” wrote PolicyLab Director David Rubin, MD, MSCE, in a blog post about the study. “With such vast numbers of children being exposed to these medications, the implications for potential long-lasting harm can be jarring.” Dr Rubin is also a professor of Pediatrics at the Perelman School of Medicine at the University of Pennsylvania.

Traditionally, antipsychotics have been narrowly prescribed to children with a diagnosis of schizophrenia or bipolar disorder, or to those with significant developmental delays who were displaying aggressive behaviors that were potentially injurious to themselves or others.

In recent years, however, antipsychotics are increasingly being prescribed in the absence of strong supporting safety and efficacy data to treat healthier children and adolescents with disruptive behaviors, such as those who are diagnosed with attention-deficit/hyperactivity disorder. Despite the number of children being exposed to antipsychotics, the researchers remain cautious about over-reacting to these findings.

“We need to incorporate these new revelations about the risk for diabetes into a more thoughtful consideration of the true risks and benefits of prescribing an antipsychotic to a child,” Dr. Rubin said. “Yes, we should try, by all means possible, to minimize the numbers of children and adolescents exposed to these powerful medications. But for some children in immediate crisis, we must also concede that the benefit of the antipsychotic for acute management may still outweigh the risk.”

The study’s authors recommend that clinicians and families who are making medication decisions periodically revisit the treatment strategy to address challenging behaviors. For example, when planning to prescribe antipsychotics to a child, professional organizations recommend beginning cautiously with the lowest dose possible, while strictly monitoring for early evidence of weight gain or abnormal lab tests that often predict later onset of diabetes.

The study’s results appeared in JAMA Pediatrics.

Catheter-associated urinary tract infections (CAUTIs) have received national attention as a high-priority, preventable hospital-acquired condition because they are common and costly. Yet, most of the research on CAUTI epidemiology and evidence-based prevention guidelines focused on adults, until the multidisciplinary “Prevent CAUTI” team at The Children’s Hospital of Philadelphia published an observational study in Pediatrics that established a plan to reduce the infection in a pediatric setting.

In July 2010, the team initiated a bundle of quality-improvement practices that focused on placing indwelling urinary catheters only when indicated, using sterile techniques at all points of care, and reviewing catheter necessity daily. A crucial part of the intervention was institution-wide training on proper urinary catheter insertion technique and maintenance practices. In all, about 1,500 clinicians over a three-month period received training on the CAUTI prevention bundle.

“It was an incredible example of multidisciplinary work,” said Katherine Finn Davis, PhD, RN, CPNP, a nurse researcher for CHOP’s Center for Pediatric Nursing Research and Evidence-Based Practice who helped to lead the CAUTI team. “People from different aspects of the clinical world drew on their strengths and worked together toward a common goal to get our rate down.”

Dr. Davis and her colleagues conducted a retrospective, observational analysis that compared CHOP’s hospital-wide CAUTI rates before and after implementation of the quality improvement project. Using data from July 2009 to June 2012, they found that the multifaceted intervention was associated with a 50 percent reduction in the hospital’s monthly CAUTI rate.

“That reduction was impressive,” Dr. Davis said. “After analysis, we also determined that the children getting catheters were still the right kids — everyone had an indication. The usage rate of catheters did not decrease during that time period, but we were using them appropriately.”

In addition to understanding better which children are at risk for CAUTIs, Dr. Davis said the study is important because it is one of the first to provide information to healthcare institutions on how to prevent CAUTIs from a pediatric perspective. Other pediatric institutions can assess their CAUTI rates and then use CHOP’s tools to implement similar CAUTI prevention bundles.

Researchers suspect that mutations in the genes associated with common variable immunodeficiency (CVID) result in a shortage of antibodies that leaves the body vulnerable to infections from bacteria and viruses. Children with CVID experience recurrent respiratory infections that can lead to chronic lung disease, and they also may have joint inflammation, stomach and bowel disorders, and a higher risk of cancers.

A study team from the Center for Applied Genomics (CAG) at The Children’s Hospital of Philadelphia performed an association analysis that focused on immune-related genes in a cohort of 360 CVID patients and 21,610 healthy controls. They compared regions of the genome using a genotyping chip specialized to search for gene variants previously implicated in autoimmune and inflammatory diseases.

The researchers found 11 single nucleotide polymorphisms (SNPs) associated with CVID on the 16p11.2 locus of chromosome 16. SNPs are changes in a single DNA building block (A, T, C, or G), compared to the more typical sequence in a certain stretch of DNA. Of particular interest, the study team found variants in the gene ITGAM, which carries codes for an integrin protein that regulates cellular contact and adhesion.

“This association is of high biological relevance because ITGAM plays an important role in normal immune responses,” said Hakon Hakonarson, MD, PhD, director of the CAG, who led the study team. “Other researchers have shown that mice in which this gene has been knocked out have immune deficiencies.”

The new findings may promote better understanding of ITGAM’s functional role and eventually lead to targeted therapies for patients with CVID. Dr. Hakonarson added that the research, published in the Journal of Allergy and Clinical Immunology, may have broader implications for other patients who do not have these novel gene variants because the integrin protein affects many important pathways in immune function.

One in 125 babies in the U.S. is not born with a perfect heart. For example, a heart defect called ventricular septal defect (VSD) involves an opening in the dividing wall between the two lower chambers of the heart. The hole allows an extra volume of blood to be pumped into the lungs, creating increased pressure, stress, and congestion.

At The Children’s Hospital of Philadelphia, investigators reported that mutations in the gene NTRK3 may be involved in the development of VSDs. NTRK3 regulates cell survival and encodes a protein called neurotrophic tyrosine kinase receptor C (TrkC).

“We picked NTRK3 as a candidate gene because deletion of this gene in mice will result in heart defects, and we had identified a patient with a VSD that had a large deletion encompassing NTRK3,” said Petra Werner, DVM, PhD, a senior research associate in the laboratory of Elizabeth Goldmuntz, MD, professor of pediatrics in the Division of Cardiology.

In an article published in Human Mutation, Dr. Werner and colleagues described how they screened 467 patients with related heart defects for NTRK3 mutations. They identified four of those patients with VSDs who had a missense mutation, which means an amino acid substitution occurred in the TrkC protein made by the gene that may modify how it works.

Next, the study team conducted experiments to see if the mutated TrkC lost any function. As a receptor, TrkC sits on cells’ membranes and waits for a signal from its ligand, a protein called neurotrophin-3 (NT-3). The results showed that one of the mutations significantly reduced TrkC’s ability to respond to the ligand, and subsequently TrkC failed to activate essential downstream signaling pathways. In addition, the investigators found that cells expressing mutant TrkC showed altered cell growth.

Dr. Werner and her colleagues hypothesize that if TrkC’s function is impaired and allows the wrong heart cells to differentiate and migrate, then flaws could occur during the rapid remodeling of embryonic heart development.

“They may end up in the wrong location in the heart and be missed in other locations, resulting in malformations or holes,” Dr. Werner said. “But much more research must be done before we fully understand all of TrkC’s functions.”