Bench to Bedside

January 2014

Flipping Gene Switch Could Lead to Sickle Cell Disease Treatment


Hematology researchers at Children’s Hospital have manipulated key biological events in adult blood cells to produce a form of hemoglobin normally absent after the newborn period. Because this fetal hemoglobin is unaffected by the genetic defect in sickle cell disease (SCD), the cell culture findings may open the door to a new therapy for the debilitating blood disorder.

“Our study shows the power of a technique called forced chromatin looping in reprogramming gene expression in blood-forming cells,” said hematology researcher Jeremy W. Rupon, MD, PhD. “If we can translate this approach to humans, we may enable new treatment options for patients.”

Dr. Rupon presented the study team’s findings during the American Society of Hematology (ASH) annual meeting in New Orleans. Dr. Rupon worked in collaboration with a former postdoctoral fellow, Wulan Deng, PhD, in the laboratory of Gerd Blobel, MD, PhD.

Hematologists have long sought to reactivate fetal hemoglobin as a treatment for children and adults with SCD, a painful, sometimes life-threatening genetic disorder that deforms red blood cells and disrupts normal circulation. In the normal course of development, a biological switch flips during the production of hemoglobin, the oxygen-carrying component of red blood cells.

Shortly after birth, regulatory elements in DNA shift the body from producing the fetal form of hemoglobin to producing the adult form instead.

But when patients with SCD undergo this transition, their inherited gene mutation distorts adult hemoglobin, forcing red blood cells to assume a sickled shape. Drs. Rupon and Blobel reprogrammed gene expression to reverse the biological switch, causing cells to resume producing fetal hemoglobin, which is not affected by the SCD mutation, and produces normally shaped red blood cells.

The scientists built on previous work by Dr. Blobel’s team showing that chromatin looping, a tightly regulated interaction between widely separated DNA sequences, drives gene transcription — the conversion of DNA code into RNA messages to carry out biological processes.

In the current study, the researchers used a specialized tool, a genetically engineered zinc finger protein, which they custom-designed to latch onto a specific DNA site carrying the code for fetal hemoglobin. They attached the zinc finger to another protein that forced a chromatin loop to form. The loop then activated gene expression that produced embryonic hemoglobin in blood-forming cells from adult mice. The team obtained similar results in human adult red blood cells, forcing the cells to produce fetal hemoglobin.

Drs. Rupon and Blobel will continue investigations aimed at moving their research toward clinical application. The approach may also prove useful in treating other diseases of hemoglobin, such as thalassemia, Dr. Rupon added.

For more information, see the press release about this study.

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Project Seeks to Understand Molecular Mechanisms That Cause Aging


It’s no secret that as we age, our bodies change. Though the signs of aging — from wrinkles to graying hair to changes in metabolism — vary from person to person, the truth is that every day everyone is getting a little bit older.

And the aging process, as we also know, can have implications for our health. As the National Institute on Aging (NIA) succinctly puts it, “getting older can come with a variety of health challenges.” Besides the usual aches and pains that aging can bring, there are a number of diseases typically seen in older populations. These include osteoporosis, osteoarthritis, cardiovascular issues, and Alzheimer’s disease.

One Children’s Hospital researcher, Marc Vermulst, PhD, of the Center for Mitochondrial and Epigenomic Medicine, is very interested in the mechanics of aging. Much of Dr. Vermulst’s research has focused on better understanding the aging process, and he recently received a four-year grant from the NIA to investigate the role biological errors play in aging.

“Most diseases that are endemic in our society are age-related diseases — cancer, Alzheimer’s disease, Parkinson’s disease — so there’s something about the aging process that predisposes different types of tissues to these diseases, so if we can find that thing we might be able to stave off some of these age-related diseases or push them out of our natural lifespan,” Dr. Vermulst said.

The NIA grant will support Dr. Vermulst’s investigation of the role non-genetic errors made during cell transcription and translation play in age-related diseases. This is a new, “non-DNA centric way to understand how aging results ultimately in age-related diseases,” Dr. Vermulst said. He has been working with the National Cancer Institute’s Jeffrey N. Strathern, PhD, and the University of North Carolina’s Dorothy Erie, PhD, on the project.

Dr. Vermulst developed a number of novel assays to conduct this research, which he hopes “may significantly deepen our understanding of aging and age-related pathology and help identify new targets for treatments or prevention strategies in the clinic.” The investigators are currently focused on four diseases: Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and Amyotrophic Lateral Sclerosis, also known as ALS or Lou Gehrig’s disease.

In their experiments, Dr. Vermulst and his team increased the error rate of transcription in living cells and found “features that are indicative of accelerated aging,” he said. For example, Dr. Vermulst pointed out that some age-related diseases are caused by an aggregation of proteins. And as the researchers increased the error rate of transcription, they also increased the rate at which these proteins aggregated, which suggests that a link exists between transcription errors and age-related diseases.

While his investigation is basic and clinical applications of the work remain in the future, Dr. Vermulst says the project’s focus on establishing a better understanding of the mechanisms of aging could lead to future treatment strategies. “If we understand the reason why aging causes age-related diseases, we can pinpoint targets for intervention,” he said.

To learn more about the groundbreaking research being conducted at the Center for Mitochondrial and Epigenomic Medicine, visit CMEM’s website.

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Defining The Future: The 2013 CHOP Research Annual Report


In many ways, 2013 was a banner year for The Children’s Hospital of Philadelphia and the Research Institute. We achieved a number of firsts, notably being named the best children’s hospital in the country by both U.S. News & World Report and Parents magazine. And in April it was announced that the Research Institute received more NIH funding than any other independent children’s hospital.

These achievements have helped further cement our reputation as the leader in both the lab and the clinic. However, it’s important not to look at these accomplishments individually, but instead to view them in the broader context of our tradition of pioneering research.

And as bright as the promise is today of improving the health and well-being of children around the world, the future is even brighter.

We are pleased to bring you this year’s Research Annual Report, which highlights how we are leading the way in innovative therapies that save lives of children every day. The passion and expertise of our hundreds of investigators contribute to the collective scientific knowledge and, most importantly, deliver promising therapies to patients’ bedsides. We are bringing the potential of personalized medicine to the forefront of care and enhancing the depth of our knowledge on the genetic underpinnings of disease.

Childhood cancer, fetal therapy, diabetes, hemophilia, pediatric heart disease, cystic fibrosis, nutrition disorders, mental retardation, AIDS, sickle cell disease, and injury prevention are a few of the many areas where our state-of-the-art technologies, innovations, and expertise are advancing our understanding of diseases and health.

In addition, our investigators have assumed leadership positions that help shape legislation and propel change broadly, and our commitment to training the next generation of scientists has never waivered.

In essence, we are not only leading pediatric research. We are defining its future.

We hope you have an opportunity to peruse the Research Annual Report, which is available as an interactive website and a downloadable PDF. As always, we thank you for your continued support!

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CHOP-Led Research Network Set to Join National Clinical Research Network


A network of children’s hospitals, data partners, and specialty networks led by Children’s Hospital was recently approved for an award from the Patient-Centered Outcomes Research Institute (PCORI) to develop and expand its work as part of PCORnet: the National Patient-Centered National Clinical Research Network. PEDSnet, A National Pediatric Learning Health System, was one of 28 multi-institutional and patient-powered research networks approved for a total of $93.5 million from PCORI on December 17 to form this new national resource that aims to boost the efficiency of health research.

PEDSnet combines a clinical data research network — including eight of the nation’s largest children’s hospital systems — with three condition-specific networks and two national data partners. Led by The Children’s Hospital of Philadelphia, PEDSnet is also comprised of Cincinnati Children’s Hospital Medical Center, Children’s Hospital Colorado, Nemour’s Children’s Health System, Nationwide Children’s Hospital, St. Louis Children’s Hospital, Seattle Children’s Hospital, and Boston Children’s Hospital. The specialty networks include the National Pediatric Cardiology Improvement Collaborative and ImproveCareNow, as well as a new childhood obesity network. The data partners are Express Scripts and the health analytics company IMS Health.

The Children’s Hospital of Philadelphia’s Christopher Forrest, MD, PhD, serves as the principal investigator of PEDSnet, which is set to combine its efforts with 10 other clinical data research networks in PCORI’s new PCORnet. Focused on comparative effectiveness research (CER), PCORI is “is authorized by Congress to conduct research to provide information about the best available evidence to help patients and their health care providers make more informed decisions,” according to the PCORI website. Since it began funding CER in 2012, PCORI has awarded a total of $464.4 million.

PCORnet will be a secure, national data network that will improve the speed, efficiency, and use of patient-centered CER, PCORI says. By integrating data available in the individual networks, PCORnet aims to provide access to a large amount of diverse, nationally representative health information that can support a range of study designs. The network will reduce the time and effort needed to launch new studies and focus research on questions and outcomes especially useful to patients and those who care for them.

Moreover, by enabling researchers and patients, clinicians, to interact directly and jointly determine research priorities, such as the selection specific studies to support, PCORnet aims to advance the shift in clinical research from investigator-driven to patient-centered studies.

“The Children’s Hospital of Philadelphia is thrilled to lend its efforts to PCORnet,” said Philip R. Johnson, MD, chief scientific officer and executive vice president of the CHOP Research Institute. “Multidisciplinary collaborations like this, that help researchers share findings and speed investigations, will help move innovative research from the bench to bedside and improve the care of children and families worldwide.”

Over the next 18 months, the CHOP-led network will use PCORI funds to expand and improve its systems, work to standardize its data, and be part of the process to develop policies governing data sharing and security and protection of patient privacy.

“We are pleased that PEDSnet will be part of this exciting initiative to build the data structures needed to significantly enhance the speed and efficiency of patient-centered comparative effectiveness research,” said PCORI Executive Director Joe Selby. “The process to select the awardees was very competitive and PEDSnet demonstrated it has the expertise, resources, and commitment to engaging patients and other stakeholders to be an excellent fit in PCORnet.”

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How Can Common Organisms Cause Disease?


The human body is a crowded place. In addition to the many human cells — which number approximately 37.2 trillion, according to a recent Annals of Human Biology paper — there are many, many more microbial cells that live in our bodies. Indeed, the NIH’s Human Microbiome Project notes “microbial cells are estimated to outnumber human cells ten to one,” including many that are commensal and live in perfect harmony with our own cells.

But sometimes these commensal microbes can cause disease, in particular when they leave their normal environment — such as the gut or pharynx — and spread to other sites. One Children’s Hospital researcher, Joseph W. St. Geme, III, MD, has spent much of his career working to better understand how this transition can happen. CHOP’s Physician-in-Chief and Chair of the Department of Pediatrics at the University of Pennsylvania, Dr. St. Geme has two NIH awards to support a pair of bacterial studies.

In addition to working as a clinician, Dr. St. Geme has worked for many years examining host-pathogen interactions, with a particular focus on the bacterium Haemophilus influenzae. Despite its somewhat misleading name, H. influenzae does not cause influenza, but is instead associated with invasive infections and localized respiratory tract disease. More recently, Dr. St. Geme has initiated studies of Kingella kingae, an emerging cause of bone and joint infections in young children.

Both H. influenzae and K. kingae are members of the normal bacterial flora, H. influenzae in the nasopharynx and K. kingae in the posterior pharynx. Dr. St. Geme said that “up to 70 percent or so of children in their first few years of life are colonized at some point with each of these organisms.”

The NIH awards, one from the National Institute of Allergy and Infectious Disease (NIAID) and the other from the National Institute on Deafness and Other Communication Disorders  (NIDCD), are supporting his investigations of K. kingae and H. influenzae, respectively. Dr. St. Geme has received ongoing support from the NIH to support his H. influenzae work since 1995 and has had the NIAID award to support his K. kingae work since September of 2013.

“In many ways the thrusts of the two projects, the general themes of the projects, are similar,” Dr. St. Geme said. Both projects are “investigations of host-pathogen interactions and focus on understanding how bacteria that are common, commensal organisms, usually not associated with disease, in some circumstances produce disease.”

Despite the fact that K. kingae is common in young children, the bacterium has only been appreciated as an important pathogen within the last fifteen years and is a leading cause of bone and joint infections in children younger than 3 or 4 years of age, Dr. St. Geme noted. Though K. kingae is a “fastidious organism” that has been historically difficult to grow in the lab, “improved cultivation techniques and molecular diagnostics have led to a surge of interest in this organism,” he said.

Last year Dr. St. Geme led a study that was published in Journal of Bacteriology and examined calcium binding in two K. kingae-associated adhesive proteins called PilC1 and PilC2. He also led a study that was published in PLoS One in September 2013 and elucidated K. kingae’s production of a polysaccharide capsule.

The NIAID award will allow Dr. St. Geme to build on his earlier K. kingae research, with investigations that he hopes will lead to “an improved understanding of the pathogenesis of disease … and will lay the foundation for developing a capsule-based vaccine.” In addition to Dr. St. Geme, CHOP researchers Katherine Rempe, Brad Kern, and Eric Porsch (who all moved to CHOP from Duke with Dr. St. Geme), as well as Duke’s Sue Grass, with whom Dr. St. Geme has been working since 1994, Jessica McCann, and Kim Starr have contributed to the H. influenzae and K. kingae projects.

“If we understand the bacterial determinants of the initial stages of infection, which are fundamental to the development of disease, we can use this information to develop new vaccines to prevent disease” Dr. St. Geme said. “Alternatively, we can use this information to develop novel antimicrobials that target bacterial factors required for infection.”

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CHOP, Drexel Consortium to Boost Pediatric Medical Device Pipeline


For medical devices, as with many medicines, the market for children is a small fraction of the adult market, and there are far fewer child-sized devices. But the need for pediatric medical devices exists, even if proper devices may not.

“It’s not simply a matter of scaling down adult equipment for pediatric use,” said Children’s Hospital bioengineer Matthew Maltese, PhD. “Pediatricians have long known that children are not just small adults, and adults are not just big children.”

Dr. Maltese is the principal investigator of the Philadelphia Regional Pediatric Medical Device Consortium (PPDC), which brings engineers and biomedical researchers from CHOP, Drexel University, and the University of Pennsylvania to address the shortage of medical devices designed for children. The PPDC recently received a $1.5 million, five-year grant from the U.S. Food and Drug Administration (FDA).

One of only seven pediatric device consortia nationwide recently funded by the FDA, the consortium will provide clinical, business, and regulatory expertise, as well as seed funding, to help translate innovative ideas into commercial devices for use in young patients.

Robert Levy, MD, who holds William J. Rashkind Endowed Chair in Pediatric Cardiology at CHOP and is a co-principal investigator of the PPDC, sees opportunities to help children, saying that the consortium “will help to address unmet needs for pediatric medical devices.” Dr. Levy’s medical device experience is reflected in his 35 issued U.S. patents that have led to extensive licensing activities, both to established medical device companies and to start-ups. One such example is the CHOP spinout firm, Vascular Magnetics, which is developing magnetically guided devices to precisely deliver drugs to injured arteries in children and adults.

As the center of the nation’s largest pediatric care network, CHOP offers a large, diverse pool of pediatric patients, allowing for carefully regulated clinical trials to test potential medical devices.

In addition, the PPDC will benefit from Dr. Maltese’s own experience adapting medical devices for children in his position in Critical Care Medicine at CHOP. The Hospital is currently collaborating with industry partners to develop pediatric versions of existing FDA-approved cardiopulmonary resuscitation (CPR) quality feedback tools developed for adults. These smartphone-sized devices measure motion and force on a patient’s chest during CPR to rapidly produce sound and visual prompts that improve the quality of CPR and save lives.

“For a variety of reasons, it is difficult to advance pediatric medical devices beyond the idea stage,” said Dr. Maltese. The PPDC provides “innovators with the support they need to transform concepts into practical and available medical devices that benefit children,” he added.

To read more about the PPDC, see the full press release.

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Junior Investigator Grant Proposals Now Being Accepted


The Clinical and Translational Research Center is now accepting research proposals to be considered for the Junior Investigator Preliminary/Feasibility Grant Program. The primary goal of the Clinical Translational Research Center Junior Investigator Preliminary/Feasibility Grant Program is to encourage junior investigators to develop clinical research projects that will ultimately lead to extramural NIH funding.

The awards are designed to allow junior faculty members, clinical fellows and MD, PhD, or DMD post-doctoral trainees with appropriate mentors to obtain funds for pilot projects that are investigator-initiated, human-based, CTRC studies that will enable an applicant to obtain preliminary data for an NIH K or R grant submission.

It is anticipated that the award will lead to a competitive extramural grant application and to a career in Clinical Translational Research Center-focused clinical investigation.

The grants will be available at each institution effective July 1, 2014.


Please see the full announcement on the Research Intranet for eligibility criteria, proposal instructions, and additional details.

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Share Your Story!


The success stories from CHOP Research are incredible. They have the power to connect investigators who can combine unique approaches for enhanced success, inspire donors to contribute the resources necessary to take a project to its next step, and provide hope for families struggling with childhood disease. Sharing your story is essential so that we can spread the word about the amazing, groundbreaking work accomplished every day at CHOP Research.

We want to know your story, your news, your success. Many steps in the research process are newsworthy. Some of the things we are interested in include:

The Research Institute benefits from a spirit of collaboration that extends beyond the workbench. We encourage you to share not only your news, but also the news of your CHOP Research colleagues.

Please share your news with us by contacting Jennifer Long, director of Research Communications, at

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