Current News

Tuesday, July 15, 2014 -

This announcement is also available online at:

http://www.uphs.upenn.edu/news/News_Releases/2014/07/zaret/

PHILADELPHIA — Kenneth S. Zaret, PhD, a nationally recognized leader in the fields of developmental and stem cell biology, has been named the new director of the Penn Institute for Regenerative Medicine (IRM). Zaret, who was the IRM associate director, is also the co-director of the Epigenetics Program in the Perelman School of Medicine at the University of Pennsylvania.

Established in 2006, IRM is a locus for interdisciplinary research involving faculty from more than 25 departments in five schools to advance the field of regenerative medicine. As IRM associate director, Zaret worked with John Gearhart, PhD, first director of the IRM, and Ed Morrisey, PhD, IRM scientific director, to establish IRM as a national leader in the field.

“I am confident that Dr. Zaret will bring his solid knowledge and experience in developmental and stem cell biology, as well as epigenetics, to lead the Institute for Regenerative Medicine into its next chapter of research, education, and clinical advances,” said J. Larry Jameson, MD, PhD, dean of the Perelman School of Medicine and executive vice president of the University of Pennsylvania for the Health System.

“In the next phase of the Institute, I aim to coalesce new discoveries, technologies, and ethical perspectives to create important scientific and clinical advances, especially in the areas of digestive tissue regeneration, cancer diagnosis and targeting, and skin repair, with additional focus on musculoskeletal, nervous system, and cardiovascular repair,” said Zaret.

He earned his PhD degree from the University of Rochester Medical School and completed his postdoctoral training in the Department of Biochemistry at the University of California, San Francisco. Before joining Penn in 2009 as the Joseph Leidy Professor in the Department of Cell and Developmental Biology, he was a Senior Member of the Cell and Developmental Biology Program at the Fox Chase Cancer Center, where he held the W. W. Smith Chair. Prior to that, Zaret was on the faculty of the Brown University Medical School.

The goal of his research program has been to understand how genes are activated to specify different cell types during embryonic development. Zaret’s lab discovered a basis for the normal path of development in different tissue types by identifying pioneer transcription factors that engage target genes in progenitor cells, early in the development process. He established the use of mammalian embryonic endoderm cells as an experimental system and used them to discover signals that induce liver and pancreas tissue in the embryo. These discoveries are now used by others in regenerative medicine to identify specific types of stem cells for therapies and research.

His lab discovered that endothelial cells possess a direct signaling role in promoting liver and pancreas development, a finding that colleagues use to enhance artificial organ development. While investigating the basis by which cells resist being reprogrammed, the Zaret lab also found large areas on chromosomes that physically block the binding of regulatory factors, which must be overcome to allow cell reprogramming. 

Recently, his lab used stem-cell technology to reprogram human pancreatic cancer cells to develop an experimental model to recreate and study early stages of the disease.

Zaret has written or cowritten nearly 100 peer-reviewed research articles, as well as numerous book chapters. He has been an editor of the journals Molecular and Cellular Biology and Development; chaired international scientific meetings; and served on numerous scientific advisory boards for academia, biotech/pharma, and the National Institutes of Health, including the National Institute of General Medical Sciences (NIGMS) Council.

Among numerous professional accolades, he has received a MERIT award from NIGMS, the Hans Popper Basic Science Award from the American Association for the Study of Liver Diseases and the American Liver Foundation, and is a Fellow of the American Association for the Advancement of Science.

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Penn Medicine is one of the world's leading academic medical centers, dedicated to the related missions of medical education, biomedical research, and excellence in patient care. Penn Medicine consists of the Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania (founded in 1765 as the nation's first medical school) and the University of Pennsylvania Health System, which together form a $4.3 billion enterprise.

The Perelman School of Medicine has been ranked among the top five medical schools in the United States for the past 17 years, according to U.S. News & World Report's survey of research-oriented medical schools. The School is consistently among the nation's top recipients of funding from the National Institutes of Health, with $392 million awarded in the 2013 fiscal year.

The University of Pennsylvania Health System's patient care facilities include: The Hospital of the University of Pennsylvania -- recognized as one of the nation's top "Honor Roll" hospitals by U.S. News & World Report; Penn Presbyterian Medical Center; Chester County Hospital; Penn Wissahickon Hospice; and Pennsylvania Hospital -- the nation's first hospital, founded in 1751. Additional affiliated inpatient care facilities and services throughout the Philadelphia region include Chestnut Hill Hospital and Good Shepherd Penn Partners, a partnership between Good Shepherd Rehabilitation Network and Penn Medicine.

Penn Medicine is committed to improving lives and health through a variety of community-based programs and activities. In fiscal year 2013, Penn Medicine provided $814 million to benefit our community.

Thursday, June 19, 2014 -

This article is available online at:

http://www.uphs.upenn.edu/news/News_Releases/2014/06/morrisey/

Penn study points to new mechanisms of tissue development and origins of congenital lung disorders

PHILADELPHIA — It’s a long way from DNA to RNA to protein, and only about two percent of a person’s genome is eventually converted into proteins. In contrast, a much higher percentage of the genome is transcribed into RNA. What these non-protein-coding RNAs do is still relatively unknown. However, given their vast numbers in the human genome, researchers believe that they likely play important roles in normal human development and response to disease.

Large-scale sequencing has allowed investigators to identify thousands of non-coding RNAs. Small non-coding RNAs, including microRNAs, are known to be important players in regulating gene expression in many contexts, including tissue development. On the other hand, the function of long non-coding RNAs (lncRNAs) is less well understood.

Research led by Ed Morrisey, PhD, professor of Medicine and Cell and Developmental Biology in the Perelman School of Medicine, University of Pennsylvania and scientific director of the Penn Institute for Regenerative Medicine, has identified hundreds of these lncRNAs, sometimes called the “genomic dark matter,” that are expressed in developing and adult lungs. Their findings, described in and featured on the cover of the current issue of Genes and Development, reveal that many of these lncRNAs in the lung regulate gene expression by opening and closing the DNA scaffolding on neighboring genes.

The team identified 363 long non-coding RNAs in the lung of the embryonic and adult mouse. They show that these lncRNAs are often located near transcription factors in the genome of lung cell lineages. “We have defined a new association of long non-coding RNAs with proteins called transcription factors that bind to specific DNA sequences and control cell identity and function,” Morrisey says. “This association is important for lung development in mouse embryos, and at least for one of these long non-coding RNAs, important for human lung function.”

Critical Pathways for Development, Disease

The team identified a lncRNA, called NANCI, that regulates the critical transcription factor Nkx2.1. This factor is the first lung molecular marker during mouse and human development and is essential for lungs to mature properly in an embryo.

NANCI appears to act upstream of Nkx2.1, but down-stream of Wnt signaling, a critical pathway for specifying cell type later in lung tissue development. Knockdown of NANCI expression during lung development leads to decreased Nkx2.1 expression and mimics the defects due to loss of a single copy of the Nkx2.1 gene, including decreased expression of surfactant proteins. These proteins aid in marking bacteria invading the lung for destruction by the immune system.

Importantly, patients with mutations in a single copy of NKX2.1 often have Brain-Lung-Thyroid Syndrome, which is characterized by respiratory distress after birth and accompanied by decreased surfactant protein expression. “There is also a report of a patient with a deletion in NANCI but not NKX2.1 who has Brain-Lung-Thyroid Syndrome, suggesting that mutations in NANCI and other lncRNAs can underlie human diseases,” explains Morrisey.

In addition to NANCI, the team identified another lncRNA, which they named LL34, that regulates retinoic acid signaling, another important pathway for early lung development. LL34 is highly expressed in the early developing foregut, a region of the embryo that generates multiple tissue types, including lung, thyroid, and liver. Knockdown of LL34 expression leads to decreased retinoic acid signaling, suggesting that this lncRNA may play an early role in the development of the lung, as well as other tissues controlled by this pathway.

While other lncRNAs expressed in the lung, such as MALAT1, may primarily play a role in cancer progression, the data generated by the Morrisey lab provides unique insight into lncRNAs that regulate lung development. “We are hopeful that these new data provide the foundation for a better understanding of how the non-coding transcriptome regulates tissue development and also maintenance of adult tissues,” says Morrisey.

Future work will be directed towards understanding how these lncRNAs control lung development, as well as adult lung regeneration using both mouse and human model systems.

Additional coauthors are Michael J. Herriges, Michael P. Morley, Komal S. Rathi, Tien Peng, and Kathleen M. Stewart, all from Penn and Daniel T. Swarr, from The Children’s Hospital of Philadelphia.  

Studies in the Morrisey lab were supported by funding from the National Heart, Lung and Blood Institute (HL100405, HL110942).

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Penn Medicine is one of the world's leading academic medical centers, dedicated to the related missions of medical education, biomedical research, and excellence in patient care. Penn Medicine consists of the Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania (founded in 1765 as the nation's first medical school) and the University of Pennsylvania Health System, which together form a $4.3 billion enterprise.

The Perelman School of Medicine has been ranked among the top five medical schools in the United States for the past 17 years, according to U.S. News & World Report's survey of research-oriented medical schools. The School is consistently among the nation's top recipients of funding from the National Institutes of Health, with $392 million awarded in the 2013 fiscal year.

The University of Pennsylvania Health System's patient care facilities include: The Hospital of the University of Pennsylvania -- recognized as one of the nation's top "Honor Roll" hospitals by U.S. News & World Report; Penn Presbyterian Medical Center; Chester County Hospital; Penn Wissahickon Hospice; and Pennsylvania Hospital -- the nation's first hospital, founded in 1751. Additional affiliated inpatient care facilities and services throughout the Philadelphia region include Chestnut Hill Hospital and Good Shepherd Penn Partners, a partnership between Good Shepherd Rehabilitation Network and Penn Medicine.

Penn Medicine is committed to improving lives and health through a variety of community-based programs and activities. In fiscal year 2013, Penn Medicine provided $814 million to benefit our community.

Friday, April 11, 2014 -

On April 11, 2014 the Institute hosted a Symposium on Cellular Reprograming honoring John Gurdon, the 2012 Nobel Laureate in Physiology and Medicine.

Dean J. Larry Jameson opened the conference and John Gurdon presented the Keynote Address on Past, Present and Future Prospects for Nuclear Reprogramming by Amphibian Eggs and Oocytes.

Kathrin Plath (UCLA) and Ken Zaret presented studies on the mechanisms and steps involved in the programming and reprogramming of pluripotency; Nancy Speck illustrated lessons from the embryo through her work on hematopoietic stem cell formation and Jim Eberwine emphasized the importance of gene expression variability with his studies of functional single cell genomics.  Young investigators Kilang Yanger and Russ Addis presented their research on reprogramming in the adult liver and forced transdifferentiaton of fibroblasts to cardiomyocytes, respectively.  George Cotsarelis presented the final talk on the basic science of stem cells in the hair bulb and the progress to the clinic.

Nicholas Wade, a science journalist with the New York Times, provided the audience with an objective and practical perspective on the coverage of the stem cell story (which he had covered since the ‘90’s) emphasizing the need for circumspection on claims and the importance of strategies for informing the public on science.

Click here to view symposium photos.     

Friday, March 21, 2014 -

By John George, Philadelphia Business Journal

Dr. John Gearhart

Dr. John Gearhart, director of the University of Pennsylvania Institute for Regenerative Medicine in the lab with Jamie Ifkovits, Ph.D.

Wednesday, January 29, 2014 -
Wednesday, January 8, 2014 -

Inside Life Science

Sharon Reynolds
Posted January 8, 2014

This article is available online at:

http://publications.nigms.nih.gov/insidelifescience/learning-about-cancer.html

Normally, when a cell becomes damaged or doesn’t divide properly, the body’s natural recycling process breaks it down and it dies. Sometimes, though, the damage is to the genes that control a cell, and the result is out-of-control division. When this happens, a cancer cell is born.

New insights into how cancer cells arise and develop into tumors have come from researchers funded by the National Institutes of Health. Some of them are exploring the process by studying stem cells.

Modeling Early Pancreatic Cancer

Pancreatic cancer cells grown in culture. Credit: Anne Weston, London Research Institute, CRUK
Pancreatic cancer cells grown in culture. Credit: Anne Weston, London Research Institute, CRUK (image available under a Creative Commons Attribution, Non-Commercial, No Derivatives License Link to external Web site). Click for larger image

Despite decades of progress in the detection, treatment and prevention of many types of cancer, the long-term survival rate for pancreatic cancer remains very low. One reason is that pancreatic cancer rarely produces symptoms until it has spread in the body.

The late stage at diagnosis also poses problems for researchers who want to study the early development of pancreatic cancer, according to Kenneth Zaret of the University of Pennsylvania School of Medicine. That’s because pancreatic cancer cells taken from people and then used to form tumors in animal models immediately produce the aggressive, advanced cancers from which they were derived.

Zaret’s lab has focused on understanding how transcription factors—proteins that control which genes in a cell are expressed—work in stem cells. His team recently explored the idea of reprogramming cancer cells so they act like embryonic stem cells, which can become just about any type of cell in the body. Because transcription factors in embryonic stem cells guide early organ development, the researchers thought that forcing cancer cells back to an embryonic state might allow the transcription factors to reproduce the early stages of cancer. This could then provide a model for studying the early development of pancreatic cancer.

Using tumor tissue from people with pancreatic cancer, Zaret and his colleagues succeeded in turning a sample of cancer cells back to an early, stem cell-like state. When used to create tumors in mice, these so-called induced pluripotent stem (iPS) cells formed early stage tumors and slowly progressed to invasive disease.

The human tumors grown in mice also secreted a wide range of proteins that are indicative of cell networks known to drive pancreatic cancer progression, as well as some not previously known to be associated with the disease. “We’re setting up collaborations to test these markers for their utility in screening human blood samples and see if they function as markers for detecting or predicting pancreatic cancer in humans,” said Zaret.

Scientists are also interested in using the iPS cells to screen new anticancer compounds and determine whether drugs under development might have the potential to help treat early stage pancreatic cancer.

Unraveling Cause and Effect in a Precursor to Esophageal Cancer

Stem cells (green) and epithelial cells (blue) in the adult fruit fly gastrointestinal tract. Credit: Lucy O'Brien and David Bilder, University of California, Berkeley.
Stem cells (green) and epithelial cells (blue) in the adult fruit fly gastrointestinal tract. Credit: Lucy O'Brien and David Bilder, University of California, Berkeley. Click for larger image

Like pancreatic cancer, esophageal cancer, which can begin anywhere in the muscular tube that runs from the throat to the stomach, has a low long-term survival rate. But unlike pancreatic cancer, research has produced insights into how to reduce the risk of developing esophageal cancer, including quitting smoking, reducing alcohol consumption and monitoring a potential precursor condition called Barrett’s esophagus.

In Barrett’s esophagus, the cells that line the lower esophagus, called epithelial cells, slowly change to resemble abnormal stomach or intestinal cells. The condition eventually progresses to esophageal cancer in up to 10 percent of cases. Scientists want to better understand the cellular mechanisms driving Barrett’s esophagus to find ways to help treat it or prevent it from occurring and progressing to cancer.

The most common explanation for how Barrett’s esophagus begins is that an excess of stomach acid, produced by conditions such as acid reflux (heartburn), washes up into the esophagus and causes tissue damage that leads to the production of the abnormal cells seen in the disease. Consequently, acid-reducing drugs are often prescribed to people with Barrett’s esophagus to help slow its progression. However, new research from the lab of Heinrich Jasper at the Buck Institute for Research on Aging suggests an alternative explanation for the cellular changes seen in Barrett’s esophagus.

Jasper’s lab explores how stressful conditions affect the function of adult stem cells, which can become specialized tissue or organ cells. While looking at how stem cells control the regeneration of the gastrointestinal tract in a type of fruit fly, Jasper made an unexpected discovery: When a cell-signaling pathway driven by a protein called Dpp goes awry, it causes the stem cells that normally create the lining of the esophagus (the esophageal epithelium) to instead produce acid-generating stomach cells within the esophagus.

“What happens in Barrett’s esophagus is really quite similar to what we observed [in fruit flies], which was a transformation of esophageal epithelium into something more like gastric epithelium,” said Jasper. In other words, cellular changes in the esophagus may actually drive the excess production of acid rather than the other way around.

Jasper’s lab is now working with collaborators at the University of Rochester to investigate this process in a mouse model of Barrett’s esophagus. If something similar occurs in people, an understanding of errors in stem cell signaling might lead to the development of new treatments for Barrett’s esophagus and the prevention of esophageal cancer.

Throughout the country, NIH-funded researchers continue to explore how our cells work normally and how they malfunction in disease. What scientists learn using stem cells, model organisms and a wealth of other approaches could help promote health as well as the diagnosis, treatment and prevention of diseases like cancer.

Monday, December 16, 2013 -
CONTACT:
Karen Kreeger
(215) 349-5658
karen.kreeger@uphs.penn.edu

This release is available online at:

Manipulation of the Wnt/β-catenin Signaling Pathway Could Provide Therapeutic Targets for Hair Loss, Unwanted Hair Growth and Skin Cancer

PHILADELPHIA — A pathway known for its role in regulating adult stem cells has been shown to be important for hair follicle proliferation, but contrary to previous studies, is not required within hair follicle stem cells for their survival, according to researchers with the Perelman School of Medicine at the University of Pennsylvania. A new study, published in Cell Stem Cell, identifies a molecular pathway that can be activated to prompt hair growth of dormant hair follicles, or blocked to prevent growth of unwanted hair.

The team examined the functions of Wnt proteins, which are small molecular messengers that convey information between cells and activate signaling via the intracellular molecule β-catenin. By disrupting Wnt signaling in an animal model with an inhibitor Dkk1, the team found that hair growth was prevented. However, stem cells were still maintained within the dormant hair follicles. When Dkk1 was removed, the Wnt/β-catenin pathway resumed normal function, the stem cells were activated, and hair growth was restored.

The team also unexpectedly found that the Wnt/β-catenin pathway is normally active in non-hairy regions, such as on the palms of hands, soles of feet and the tongue, as well as between hair follicles on the surface of the skin. This finding is consistent with previous results showing that removing β-catenin prevents growth of skin tumors.

"While more research is needed to improve our understanding of this pathway, our results suggest that therapeutics capable of decreasing levels of Wnt/β-catenin signaling in the skin could potentially be used to block growth of unwanted hair, and/or to treat certain skin tumors. Conversely, if delivered in a limited, safe and controlled way, agents that activate Wnt signaling might be used to promote hair growth in dormant hair follicles in conditions such as male pattern baldness,” said senior author Sarah Millar, PhD, professor in the departments of Dermatology and of Cell and Developmental Biology.
  
Researchers aim to better understand the key components and functions of the Wnt/β-catenin pathway. Important areas of focus for future work will include developing effective means of safely targeting therapeutics to the skin for clinical and cosmetic applications.

The research team includes co-corresponding author Edward E. Morrisey, PhD, professor of Medicine, along with co-first authors Yeon Sook Choi and Yuhang Zhang, and Mingang Xu, Mayumi Ito, Thomas Andl, and George Cotsarelis from Penn's department of Dermatology; Tien Peng and Zheng Cio from Penn Cardiology; and colleagues from the University of Cincinnati, Cincinnati Children's Hospital Medical Center, Mount Sinai Hospital in Toronto, and Sloan Kettering Institute in New York.

The research was funded by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (R37 AR47709 and P30 AR057217).

Monday, July 22, 2013 -
CONTACT:
Karen Kreeger
(215) 349-5658
karen.kreeger@uphs.penn.edu

This release is available online at:

http://www.uphs.upenn.edu/news/News_Releases/2013/07/morrisey/

PHILADELPHIA – The evolution of adaptations for life on land have long puzzled biologists – are feathers descendents of dinosaur scales, how did arms and legs evolve from fins, and from what ancient fish organ did the lung evolve?

Biologists have known that the co-development of the cardiovascular and pulmonary systems is a recent evolutionary adaption to life outside of water, coupling the function of the heart with the gas exchange function of the lung. And, the lung is one of the most recent organs to have evolved in mammals and is arguably the most vital for terrestrial life.

The coordinated maturation of the cells of these two systems is illustrated during embryonic development, when the primitive lung progenitor cells protrude into the primitive cardiac progenitor cells as the two organs develop in parallel to form the cardiopulmonary circulation. However, little is known about the molecular cues guiding this simultaneous development, and how a common progenitor cell for both organs may influence the pathology of such related diseases as pulmonary hypertension.

In a new paper published this week online in Nature, a team from the Perelman School of Medicine, University of Pennsylvania, shows that the pulmonary vasculature, the blood vessels that connect the heart to the lung, develops even in the absence of the lung. Mice in which lung development is inhibited still have pulmonary blood vessels, which revealed to the researchers that cardiac progenitors, or stem cells, are essential for cardiopulmonary co-development.

The Penn team, led by  Edward E. Morrisey, PhD, professor of Medicine and Cell and Developmental Biology and scientific director of the Penn Institute for Regenerative Medicine, identified a population of multi-potent CardioPulmonary mesoderm Progenitor cells they named CPPs. The CPPs can be distinguished from many other early embryonic cells by the expression of a well-studied signaling molecule Wnt2.

“We asked if these progenitor cells are capable of generating both heart and lung derivatives,” says Morrisey. “Our data show that Wnt2-positive cells exist prior to lung development and help coordinate lung and heart co-development by generating cell types in both tissues.”

The issue of how the lung develops and connects to the cardiovascular system has intrigued the Morrisey lab for many years. “It’s pretty obvious to anyone who has looked at the anatomy of most terrestrial animals that the heart and lung are intimately linked. This is even reflected in clinical medicine where in many places, including the Perelman School of Medicine, the Division of Cardiovascular Medicine was once referred to as the Division of Cardiopulmonary Medicine,” notes Morrisey.  

The Morrisey lab began with a couple of simple questions: how do the lung and heart co-develop and what are the critical signals that regulate this process? The breakthrough in this work occurred when the team characterized the expression pattern of the Wnt2 gene.
“Wnt2 is expressed in a unique place in the early embryo -- exactly in between the early heart and foregut tube, where the lung will arise from.” This allowed the researchers to create a model system in mice, whose cardiopulmonary anatomy is very similar to humans, and ask whether Wnt2-positive cells could coordinate heart and lung co-development.

Using cell lineage tracing analysis, they showed that Wnt2 cells generate single clones that, in turn, generate both heart and lung tissue, including cardiomyocytes and blood vessel cells such as vascular smooth muscle. Indeed, CPPs are capable of generating the vast majority of early embryonic cell types in the heart and lung. These studies also showed that the different cell lineages within the lung are related. For example, vascular smooth muscle and airway smooth muscle share a common progenitor cell in the lung.

The development of CPPs is regulated by the expression of another well-known protein called hedgehog, which is required for proper connection of the pulmonary vasculature to the heart.  These studies show that hedgehog, which is also expressed by early lung progenitor cells, helps to promote CPPs to differentiate into the smooth muscle component of the pulmonary vasculature.

Together, these studies identify a novel population of multi-potent cardiopulmonary progenitors that coordinate heart and lung co-development, which is required for adaptation to terrestrial existence. 

The finding that CPPs coordinate lung and heart co-development also has important implications for diseases that affect both organs, such as pulmonary hypertension. It is unclear whether pulmonary hypertension is primarily a lung disease or whether there are also intrinsic defects in the heart or cardiovascular system.  The identification of CPPs could provide important insight into pulmonary hypertension and other diseases by identifying a common progenitor cell for both organs. Future studies will focus on whether CPPs exist in the adult cardiopulmonary system and whether they play a role in the response of the lung and heart to injury or disease.

Co-authors are Tien Peng, Ying Tian, Cornelis J. Boogerd, Min Min Lu, Rachel S. Kadzik, Kathleen M. Stewart, all from Penn, and Sylvia M. Evans, University of California, San Diego.

This work was funded by the Heart, Lung and Blood Institute (HL110942, HL100405, HL087825, HL117649) and the American Heart Association Jon DeHaan Myogenesis Center.

Thursday, June 20, 2013 -
CONTACT:
Karen Kreeger
(215) 349-5658
karen.kreeger@uphs.penn.edu

This release is available online at:

http://www.uphs.upenn.edu/news/News_Releases/2013/06/zaret/

Markers Discovered in Initial Stages of Disease Could be Used for Early Detection, Treatment, Prognosis

PHILADELPHIA — Pancreatic cancer carries a dismal prognosis. According to the National Cancer Institute, the overall five-year relative survival for 2003-2009 was 6 percent.

Still, researchers and clinicians don’t have a non-invasive way to even detect early cells that portent later disease. ‘There’s no PSA test for pancreatic cancer,’ they say, and that’s one of the main reasons why pancreatic cancer is detected so late in its course.  

They have been searching for a human-cell model of early-disease progression. Now, Perelman School of Medicine, University of Pennsylvania scientists have used stem-cell technology to create a research cell line from a patient with advanced pancreatic ductal adenocarcinoma (PDAC).

This first-of-its-kind human-cell model of pancreatic cancer progression was published this week in Cell Reports from the lab of Ken Zaret, PhD, professor of Cell and Developmental Biology.

“It is the first example using induced pluripotent stem [iPS] cells to model cancer progression directly from a solid tumor, and the first human cell line that can model pancreatic cancer progression from early to invasive stages,” says Zaret, also the associate director of the Penn Institute for Regenerative Medicine.

“We were able to predict the appearance of cellular features and protein markers in the intermediate stages of pancreatic cancer that are not evident in the terminal stages. This has given us new perspectives into what this deadly type of cancer looks like – something no one has seen before in human cells. Our analysis revealed known molecular networks that are activated during PDAC progression, as well as a new molecular network that is activated during the intermediate stages. This could provide a fresh outlook on biomarkers for early stages of the disease.”

A Leap of Faith

Zaret and first author Jungsun Kim, PhD, a postdoctoral associate in the Zaret lab, hypothesized that if human PDAC cells were reprogrammed back to pluripotent cells and then allowed to re-differentiate into pancreatic tissue, they might undergo the early stages of cancer. To do this, they created the PDAC pluripotent cells and indeed found that they recapitulated the early to intermediate stages of pancreatic cancer.  They then isolated the cells at the early stage, cultured the cells in vitro, and identified the secreted and released proteins that might serve as early-stage biomarkers of disease progression.

There’s one caveat, though, says Zaret. “Using the iPS method, we could only get a cancer cell line from one patient to reprogram, meaning this work is representative of one individual’s cancer,” noting that his close collaboration with John Hoffman, a surgeon from the Fox Chase Cancer Center (FCCC) was key in order to get fresh cancer cells for the reprogramming. They tried this method with cells from nine human tumors in total. However, as Zaret points out, there are many examples of where a single human cell line has served as a highly useful model for human disease.  

“Our iPS-like cells exhibited pluripotency, like other stem cells, but when they differentiated after we injected them into the immunodeficient mice, they preferentially developed into early-stage pancreatic cancer cells,” says Zaret. He explains that the approach is another example of using iPS cells from human patients to model disease, by capturing the genome of an affected individual. However, this is a first in solid tumor cancers, whereas many other labs have developed these types of cell lines for neurological and cardiovascular disorders.

The visual characteristics of these cancer cells -- as they progress from early- to late-stage cancer -- are typical of what is seen in cells analyzed from cancer patients in the clinic now. In the early stage, pancreatic ducts have lesions with cells of an abnormal shape, and express characteristic proteins as measured by stains. Over time, some of these aberrant cells may grow excessively, lose their ductal characteristics, and become invasive.

When the human PDAC iPS cells are grown as lesions in the mouse, they secrete or release proteins corresponding to protein networks expressed during the progression of human pancreatic cancer, namely molecules centered on a trio of key proteins: HNF4, integrin, and TGFbeta.

“We propose to look in the blood of potential pancreatic cancer patients or relatively early-stage patients for the biomarkers we found downstream of these molecular networks, to see if they are present in people,” says Zaret.

The Making of a Model

This approach allows human cells to be studied directly, as opposed to examining characteristics of pancreatic cancer progression in an animal model and then having to assess whether the findings apply to humans. The cells harvested from the cancer patient were reprogrammed using the four Yamanaka factors carried in a lentivirus, which was adapted by the Zaret lab.

To see what the reprogramming did at a genetic level, the team compared the genomic structure of the early iPS pancreatic cancer cell line to original tumor cells from which the cell line was isolated. They found 23 chromosomal aberrations in the primary tumor cells as compared to 20 of the same chromosomal aberrations in the PDAC iPS line, demonstrating that the PDAC iPS line was derived from the original tumor cells.

By contrast, no chromosomal abberations were seen in cells taken from the margin of the tumor in a cancer-free part of the pancreas from the patient, as well as from an iPS line that the Zaret group made from the margin cells.  

These sets of comparisons allowed the team to directly observe the changes in the pancreatic cancer cell line versus a normal cell line derived from the same human genetic background.

“We understand that the pancreatic cancer field has been dogged by searching for unique markers in the blood that detect disease early, and we hope that this live-cell progression approach will gives us a new way to see early molecular markers for pancreatic cancer,” says Zaret.

“Since we can detect released protein markers of at least three different networks from the early-stage human lesions in our model, we think that looking for blood markers of the simultaneous activation the three pathways, instead of a single marker, could provide better leverage in detection. The new model could also be used to test drugs that block the intermediate stages of the disease. We would also like to know how we got lucky with this one cell line, so that the iPS technology can be adapted to model other human cancers.”

The research was funded by the National Institute for General Medical Sciences through an NIH Merit award (R37GM36477)

Other co-authors are R. Katherine Alpaugh, Andrew D. Rhim, Maximilian Reichert, Ben Z. Stanger, Emma E. Furth, Antonia R. Sepulveda, Chao-Xing Yuan, Kyoung-Jae Won, Greg Donahue, and Jessica Sands, all from Penn, and Andrew A. Gumbs, from FCCC.

Wednesday, May 15, 2013 -

By David Brown, The Washington Post

Read the full article.

Wednesday, May 15, 2013 -

By Robb Stein and Michaeleen Doucleff, NPR

Read the full article.

Sunday, May 12, 2013 -
CONTACT:
Karen Kreeger
(215) 349-5658
karen.kreeger@uphs.penn.edu

This release is available online at:

http://www.uphs.upenn.edu/news/News_Releases/2013/05/epstein/

Mutation Causing Wrong-Way Plumbing Explains One Type of Blue-Baby Syndrome

PHILADELPHIA — Total anomalous pulmonary venous connection (TAPVC), one type of “blue baby” syndrome, is a potentially deadly congenital disorder that occurs when pulmonary veins don’t connect normally to the left atrium of the heart. This results in poorly oxygenated blood throughout the body, and TAPVC babies are born cyanotic — blue-colored — from lack of oxygen.

TAPVC is usually detected in newborns when babies are blue despite breathing normally. Life-threatening forms of the disorder are rare – about 1 in 15,000 live births. A closely related, but milder disorder, partial anomalous pulmonary venous connection (PAPVC), in which only some of the pulmonary veins go awry, is found in as many as 1 in 150 individuals.

Now, researchers have found that a mutation in a key molecule active during embryonic development makes the plumbing between the immature heart and lungs short-circuit, disrupting the delivery of oxygenated blood to the brain and other organs. The mutation ultimately causes blood to flow in circles from the lungs to the heart’s right side and back to the lungs.

Senior author Jonathan A. Epstein, MD, chair of the Department of Cell and Developmental Biology, at the Perelman School of Medicine, University of Pennsylvania, and colleagues from The Children’s Hospital of Philadelphia, describe in Nature Medicine, that a molecule called Semaphorin 3d (Sema3d) guides the development of endothelial cells and is crucial for normal development of pulmonary veins. It is mutations in Sema3d that cause embryonic blood vessels to hook up in the wrong way.

Epstein is also the William Wikoff Smith professor and scientific director of the Penn Cardiovascular Institute. Karl Degenhardt, MD, PhD, assistant professor at The Children’s Hospital of Philadelphia; Manvendra K. Singh, PhD, an instructor of Cell and Developmental Biology at Penn; and Haig Aghajanian, a graduate student in Cell and Molecular Biology at Penn are the co-first authors on the paper.

Physicians thought that TAPVC occurred when the precursor cells of the pulmonary vein failed to form at the proper location on the embryonic heart atrium. However, analysis of Sema3d mutant embryos showed that TAPVC occurs despite normal formation of embryonic precursor veins. 

In these embryos, the maturing pulmonary venous plexus, a tangle of vessels, does not connect just with properly formed precursor veins. In the absence of the Sema3d guiding signal, endothelial tubes form in a region that is not normally full of vessels, resulting in aberrant connections. Normally, Sema3d provides a repulsive cue to endothelial cells in this area, establishing a boundary.

Sequencing of Sema3d in individuals affected with anomalous pulmonary veins identified a point mutation that adversely affects Sema3d function in humans. The mutation causes Sema3d to lose its normal ability to repel certain types of cells to be able to guide other cells to grow in the correct place. When Sema3d can’t keep developing veins in their proper space, the plumbing goes haywire.

Since it’s already known that semaphorins guide blood vessels and axons to grow properly, the authors surmise that Sema3d could be used for anti-angiogenesis therapies for cancer, to treat diabetic retinopathy, or to help to grow new blood vessels to repair damaged hearts or other organs.

Daniele Massera, Qiaohong Wang, Jun Li, Li Li, Connie Choi, Amanda D. Yzaguirre, Lauren J. Francey, Emily Gallant, Ian D. Krantz, and Peter J. Gruber are co-authors.

This work was supported by the National Institutes of Health (NIH 5K12HD043245-07, NIH T32 GM07229, and NIH UO1 HL100405).

Monday, February 25, 2013 -
CONTACT:
Karen Kreeger
(215) 349-5658
karen.kreeger@uphs.penn.edu

Tweaking Gene Expression to Repair Lungs

PHILADELPHIA — Lung diseases such as asthma and chronic obstructive pulmonary disease (COPD) are on the rise, according to the American Lung Association and the National Institutes of Health.

“A healthy lung has some capacity to regenerate itself like the liver,” notes Ed Morrisey, Ph.D., professor of Medicine and Cell and Developmental Biology and the scientific director of the Penn Institute for Regenerative Medicine in the Perelman School of Medicine, University of Pennsylvania. “In COPD, these reparative mechanisms fail.”

Morrisey is looking at how epigenetics controls lung repair and regeneration. Epigenetics involves chemical modifications to DNA and its supporting proteins that affect gene expression. Previous studies found that smokers with COPD had the most significant decrease in one of the enzymes controlling these modifications, called HDAC2.

“HDAC therapies may be useful for COPD, as well as other airway diseases,” he explains. “The levels of HDAC2 expression and its activity are greatly reduced in COPD patients. We believe that decreased HDAC activity may impair the ability of the lung epithelium to regenerate.”

Using genetic and pharmacological approaches, they showed that development of progenitor cells in the lung is specifically regulated by the combined function of two highly related HDACs, HDAC/1 and /2. Morrisey and colleagues published their findings in this week’s issue of Developmental Cell.

By studying how HDAC activity, as well as other epigenetic regulators, controls lung development and regeneration, they hope to develop new therapies to alleviate the unmet needs of patients with asthma and COPD.

HDAC1/2 deficiency leads to a loss of expression of the key transcription factor, a protein called Sox2, which in turn leads to a block in airway epithelial cell development. This is affected in part by deactivating a repressor of expression (derepressing) of two other proteins, Bmp4 and the tumor suppressor Rb1 - targets of HDAC1/2.

In the adult lung, loss of HDAC1/2 leads primarily to increased expression of inhibitors of cell proliferation including the proteins Rb1, p16, and p21. This results in decreased epithelial proliferation in lung injury and inhibition of regeneration.

Together, these data support a critical role for HDAC-mediated mechanisms in regulating both development and regeneration of lung tissue. Since HDAC inhibitors and activators are currently in clinical trials for other diseases, including cancer, such compounds could be tested in the future for efficacy in COPD, acute lung injury, and other lung diseases that involve defective repair and regeneration, says Morrisey.

This work was funded by the National Heart, Lung and Blood Institute (HL071589, HL087825, HL100405, HL110942) and the Lung Repair and Regeneration consortium, funded by the NHLBI.

Monday, November 26, 2012 -

By studying the first 48 hours of stem cell reprogramming—in which adult somatic cells are converted into induced pluripotent stem cells (iPSCs)—researchers have identified some barriers to the process and one potential way to boost speed and efficiency early on. For now, the process is not very efficient: Only about one out of every 1000 human somatic cells wind up becoming iPSCs, and the process of conversion can take about a month. “[The finding] was thrilling, and we didn’t expect it at all,” said lead investigator Kenneth Zaret, PhD, associate director of the Penn Institute for Regenerative Medicine and Professor of cell and development, in BioTechniques NewsClick here for full article.

Friday, November 16, 2012 -

CONTACT:
Karen Kreeger
215-349-5658
karen.kreeger@uphs.upenn.edu

 

This release is available online at
http://www.uphs.upenn.edu/news/News_Releases/2012/11/zaret/

Penn Study Decodes Molecular Mechanisms Underlying Stem Cell Reprogramming

PHILADELPHIA — Fifty years ago, UK researcher John Gurdon demonstrated that genetic material from non-reproductive cells could be reprogrammed into an embryonic state when transferred into an egg. In 2006, Kyoto University researcher Shinya Yamanaka expanded on those findings by expressing four proteins in mouse somatic cells to rewind their genetic clocks, converting them into embryonic-like stem cells called induced pluripotent stem cells, or iPS cells.

In early October, Gurdon and Yamanaka were awarded the 2012 Nobel Prize in Physiology or Medicine for their discoveries. Now, thanks to some careful detective work by a team of scientists led by Kenneth Zaret, PhD, at the Perelman School of Medicine, University of Pennsylvania, researchers can better understand just how iPS cells form – and why the Yamanaka process is so inefficient, an important step to work out for regenerative medicine. Zaret is associate director of the Penn Institute for Regenerative Medicine and professor of Cell and Developmental Biology.

The findings, which appear in the Nov. 22 issue of the journal Cell, uncover cellular impediments to iPS cell development that, if overcome, could dramatically improve the efficiency and speed of iPS cell generation.

“These studies provide detailed insights into how reprogramming factors interact with the chromatin of differentiated cells and start them down the path toward becoming stem cells,” said Susan Haynes, PhD, National Institute of General Medical Sciences, which partially funded the work. “Dr. Zaret’s work also identified a major structural roadblock in the chromatin that the factors must overcome in order to bind DNA. This knowledge will help improve the efficiency of reprogramming, which is important for any future therapeutic applications.”

Human iPS cells are generated by expressing four DNA-binding proteins – Oct4, Sox2, Klf4, and c-Myc (O, S, K, and M) – in human non-reproductive, or somatic cells, such as skin cells. These factors have generated intense interest in the stem cell and medical communities, not least because they offer the promise of embryonic stem cells with none of the messy ethical and moral dilemmas. Just as significantly, patient-specific iPS cells from individuals with genetic disorders can be used to study disease origin and to develop drugs for a range of conditions such as Huntington’s and Parkinson’s diseases.

Yet, the process of generating iPS cells is highly inefficient. It can take a month to fully reprogram somatic cells into iPS cells, and as few as one in 10,000 cells that take up the four factors will successfully convert. What’s more, some studies indicate that, for all their plasticity, iPS cells are not precisely equivalent to embryonic stem cells. Zaret, with Penn postdoctoral fellow Abdenous Soufi, PhD, and bioinformatician Greg Donahue, PhD, decided to find out why.

Destination Determination

The team analyzed the destination in the human genome of the four reprogramming factors 48 hours after the initiation of iPS cell reprogramming and compared those locations to four cell types: the starting cell population; the fully reprogrammed iPS cells; cells nearing the end of the reprogramming process (pre-iPS); and embryonic stem cells.

They found that at 48 hours the factors tended to bind gene regulatory elements called enhancers, far removed from the genes they regulate, rather than the target genes themselves. That suggests that O, S, and K serve as “pioneer factors” that open closed chromatin structures on the DNA itself, facilitating the reprogramming process by making target sections of the genome available to be read by messenger RNA.

The team also found large regions of the genome that were “refractory” to the binding of reprogramming factors at 48 hours, but which were eventually activated in, and are in fact required, for the formation of iPS cells.

“Basically, large chunks of the human genome were physically resisting these factors from entering,” Zaret explained. “That provided some understanding that you’ve got to overcome the binding impediment to get these factors to their final destination.”

These refractory sequences tended to be chemically marked with a histone modification called H3K9me3. When the team blocked the enzymes that create that modification, they “significantly accelerated” the reprogramming process.

According to Zaret, these findings reveal genetic roadblocks that slow and impede the iPS cell reprogramming process, as well as factors that may underlie the subtle differences between iPS and embryonic stem cells. They also suggest a potential workaround to these issues, by adding inhibitors of H3K9me3.

But the findings also reveal a normal cellular mechanism that cells may be using to repress genes that are contrary to the cell’s biology, Zaret said. “We went into this thinking we were going to learn something about the mechanism of conversion to pluripotency, but at the end of the day we ended up discovering new ways that cells control gene expression by shutting down parts of their genome.”

The study was supported by the NIGMS (Grants R37GM36477 and P01GM099134).

Friday, July 27, 2012 -

IRM Outreach Director, Dr. Jamie Shuda describes in the Penn Current, her new course in stem cell ethics and education.  “Stem Cell Science in Schools: History, Ethics, and Education,” will give undergraduate students a better understanding what stem cells are and how they apply to their lives. 

For full details, visit the Penn Current (click here).

Wednesday, March 7, 2012 -
March 6, 2012

CONTACT: Karen Kreeger
215-349-5658
karen.kreeger@uphs.upenn.edu
 

This release is available online at
http://www.uphs.upenn.edu/news/News_Releases/2012/03/shuda/

Penn Medicine Science Educator Recognized by Society for Developmental Biology

PHILADELPHIA — Jamie Shuda, EdD, director of life science outreach at the University of Pennsylvania's Institute for Regenerative Medicine (IRM), and coordinator of life science education at the Netter Center for Community Partnerships also at Penn, along with Steve Farber, PhD, Investigator, Embryology Department, Carnegie Institution for Science, Baltimore, have been awarded the Hamburger Outstanding Educator Prize from the Society for Developmental Biology (SBD).

Shuda and Farber run Project BioEYES, a K-12 science education program that provides classroom-based, hands-on learning using live zebrafish to teach about how cells and animals develop. The program is located within the Perelman School of Medicine, Penn; the Carnegie Institution; Notre Dame University in South Bend, IN; and Monash University in Melbourne, Australia, among others, and reaches over 9,000 students per year.

"I am honored that the Society for Developmental Biology has chosen me and Dr. Farber as the 2012 recipients of the Viktor Hamburger prize," says Shuda. "Project BioEYES exemplifies how scientists and educators can come together to teach cutting edge, exciting science to students of all ages. Collaboration across disciplines is greatly supported by Penn and the IRM and it is wonderful that the university is being recognized for their public engagement. Viktor Hamburger was a pioneer in both science and teaching and I hope our education programs inspire more scientists just like him."

With over 10 years of experience in public education, Dr. Shuda has worked with teachers, students, and university staff to develop innovative science curricula. Her research focuses on the role informal science education plays in developing an effective science curriculum in K-12 schools and the characteristics of successful university and community partnerships to enhance science education at the undergraduate level. At the University of Pennsylvania, Dr. Shuda teaches Stem Cell Science in Schools: History, Ethics, and Education, which provides university and high school students with the opportunity to learn the science of stem cells while becoming deeply engaged with social and ethical issues relevant to everyday life. Dr. Shuda holds an MS.Ed and teaching certification from Drexel University and an Ed.D in education policy from Temple University.

Established in 2002 by the SDB Board of Directors in honor of Dr. Viktor Hamburger and sponsored by the Professional Development and Education Committee, this Hamburger award recognizes individuals who have made outstanding contributions to developmental biology education. The recipients deliver a lecture at the Education Symposium of the SDB Annual Meetings.