Biliary Atresia Clinical Care Program

Basic Biliary Atresia Research

The basic science initiatives at the Fred & Suzanne Biesecker Pediatric Liver Center focus on understanding liver biology and pathology in children. Our research programs aim to:

The branches of the Basic Science Research Program are:

Liver Repair and Regeneration

Studies of liver regeneration focus on the molecular mechanisms of injury and repair following transplantation. These processes are key to the overall success of liver transplantation and in transplantation of partial liver grafts and living-donor liver transplantation.

Liver Center researchers have demonstrated the critical importance of specific cytokines, chemokines and growth factors in the process of regeneration and recovery from injury and demonstrated patterns of gene expression in human livers after transplantation.

Current investigations involve both basic science studies and human translational research with a focus on ischemic injury and regeneration after liver transplantation as outlined below:

Animal studies

Human studies

These lines of investigation are funded by NIH grants and The Fred & Suzanne Biesecker Pediatric Liver Center at The Children's Hospital of Philadelphia. The laboratory personnel have published in top-ranked journals such as Nature Medicine, Hepatology and Transplantation.

Liver Transplant and Immunology

Transplantation provides a potential cure for end-stage disease affecting various organs and tissues, including end-stage liver disease. However, while the results of organ transplantation are commonly life-saving, resulting in a return to a normal or near-normal lifestyle and development, this typically entails long-term maintenance immunosuppression. Recognizing that any maintenance drug therapy, especially involving powerful agents like those used for immunosuppression, carries certain risks, our research is focused on understanding the mechanisms of induction and persistence of transplant tolerance, so ultimately transplant recipients will require little or no ongoing drug therapy.

The researchers involved in the transplantation and immunobiology group undertake multifaceted investigations into the mechanisms of graft rejection and tolerance induction, using clinical samples and various experimental transplant models. The strength of this research lies in the use of in vivo models in which specific genes of interest are either deleted or over-expressed to determine their importance in the overall regulation of host responses post-transplant.

Ongoing studies involve:

Additional research initiatives of this group focus on the molecular and immunologic approaches to dissect fundamental steps in T-cell regulation, activation and function, in the hopes of identifying new targets for immunoregulation. Ongoing studies involve cell-cycle regulation, novel transcription factors and regulation of key genes involved in T-cell anergy and tolerance, including Foxp3 and its various homologs; and human immune monitoring pre- and post-transplant.


The research of the following investigators’ focuses on transplant immunobiology:

Wayne W. Hancock, MBBS, PhD, FRCPA

Dr. Wayne Hancock is a professor of pathology and laboratory medicine at The Perelman School of Medicine at the University of Pennsylvania. He leads a multidisciplinary team focused on improving the outcomes of organ transplantation.

Dr. Hancock's group undertakes both clinical and basic science studies, and has expertise in multiple areas of transplant immunobiology. They are currently undertaking studies of the effects of standard immunosuppression on regulatory T cells in liver transplant recipients, and are developing approaches involving histone deacetylase inhibitors to stabilize and boost the function of these Treg cells in transplant recipients.

Andrew D. Wells, PhD

Dr. Andrew Wells completed his BA in microbiology in 1991 from Miami University, and his PhD in medical microbiology and immunology in 1996 from the University of Wisconsin-Madison. He joined the Immunobiology of Normal and Neoplastic Lymphocytes training program as a postdoctoral fellow at the University of Pennsylvania, where he studied the cellular and molecular mechanisms by which co-stimulation promotes T lymphocyte function and opposes tolerance. Dr. Wells became as an assistant professor in the Department of Pathology and Laboratory Medicine at the University of Pennsylvania and The Children’s Hospital of Philadelphia in 2002, and was promoted to associate professor with tenure in 2010.

Dr. Wells’ research interests include the regulation of gene expression, DNA methylation, and chromatin structure during T lymphocyte immune responses, and the impact these processes have on the balance between immunity and tolerance. Over the past several years, the Wells laboratory has uncovered several mechanisms by which transcriptional silencing of pro-inflammatory cytokine genes occurs during tolerance, primarily in models of organ transplant tolerance.

Dr. Wells has received five NIH grants, has authored more than 50 journal articles, is an associate editor at the Journal of Immunology, and a full member of the Tolerance, Transplantation and Tumor Immunity NIH study section. He teaches multiple graduate level courses and has served on multiple committees in the Immunology (IGG) and the Cell and Molecular Biology (CAMB) graduate groups at the University of Pennsylvania. Dr. Wells hopes the discoveries in his laboratory will eventually lead to new therapies for the treatment of autoimmune disease and organ transplant rejection.

Liver Fibrosis

Liver fibrosis and cirrhosis, characterized by the excessive production and decreased degradation of abnormal extracellular matrix, are a major cause of morbidity and mortality in biliary atresia. Although adequate bile drainage can be achieved in many patients through a Kasai hepatoportoenterostomy, fibrosis generally progresses and is notable for being among the most rapidly progressive forms of liver fibrosis known. The etiology of biliary atresia and the mechanism for the unusually rapid fibrosis are not well understood.

Most of the fibrogenic cells in the liver are a-smooth muscle actin-expressing myofibroblasts and most are derived from the transdifferentiation of hepatic stellate cells. It has recently been recognized, however, that other cells, including fibroblasts and bone marrow-derived stem cells, may also contribute. In particular, portal fibroblasts are believed to play a significant role in early biliary fibrosis.

Through the use of isolated cells in culture, animal model systems and banked human tissue, researchers in the Pediatric Liver Center at CHOP are studying the major populations of fibrogenic cells in biliary atresia and are identifying the factors (some specific to this disease) that induce these cells to secrete abnormal and excess matrix. By understanding the process of fibrogenesis in biliary atresia, investigators hope they will be able to develop rational therapies.


The following investigator's research focuses on fibrosis:

Rebecca G. Wells, MD

Dr. Rebecca Wells is a gastroenterologist and associate professor of medicine, pathology and laboratory medicine at the Perelman School of Medicine at the University of Pennsylvania. Her lab studies mechanisms of liver fibrosis and she is particularly interested in pediatric liver disease. 

Liver and Bile Duct Disease and Development

The liver and bile duct disease and development group is working to understand the molecular basis of normal and abnormal bile duct development, as it applies to human disease. The group consists of a collaborative and interactive group of labs, working in different organisms. The research labs study the biology of human disease states, work on mouse models to define and analyze genes important in bile duct development, and work in the zebrafish model to identify genes important in bile duct development and understand their functioning.

One of the areas of interest for the bile duct development group is the role of Notch signaling in bile duct and liver development. This work illustrates the power of the constellation of investigators in our group. The Notch Signaling Pathway gene Jagged1 was found to be the cause of a disorder of bile duct development (Alagille syndrome) in 1997 by the Spinner lab. In addition to Jagged1, mutations in another gene in the Notch signaling pathway, Notch2, has been shown to cause bile duct paucity and other features of Alagille syndrome, providing additional support for the role of Notch signaling. Since this time, the localization and timing of expression of Notch signaling genes have been extensively studied in mice and researchers have discovered the Jagged-Notch pathway also regulates biliary development in zebrafish.

This work is being followed up to more fully define the abnormalities caused by Jagged1 or Notch2 deficiency and the mechanism by which bile duct paucity occurs in humans. Liver Center investigators have been working on human tissue to more clearly define the abnormalities of Jagged1 and Notch2 in diseased livers. Work on Notch signaling is therefore taking place in humans cells, the mouse and zebrafish, providing an outstanding opportunity to utilize the benefits of each of these systems.

An important area of research is the identification of additional genes involved in bile duct development. Liver Center investigators are actively working to define the genetic players in this process in the zebrafish and mouse respectively. We anticipate that genes identified will be found to play a role in human diseases of the biliary system, and we will have an outstanding opportunity to study this, using human samples that we are banking at the hospital.


The research of the following investigators’ focuses on liver and bile duct disease and development:

Joshua R. Friedman, MD, PhD

Dr. Josh Friedman studies ways in which the appropriate genes are turned on (and off) in the liver, because this control of gene expression is the most important determinant of liver formation, function and disease. Specifically, his research is focused on a form of gene regulation that was only recently discovered, known as microRNA.

Dr. Friedman’s laboratory was the first to demonstrate that microRNAs regulate development of the bile ducts and that microRNA is required for the survival of liver cells after birth. He has undertaken projects dedicated to discovering the function of microRNA in an important disease of young infants known as biliary atresia.

Using samples from an NIH-sponsored, national multicenter project, he is performing the first studies of microRNA in biliary atresia.

Dr. Friedman’s lab has pioneered the use of microRNA levels in the bloodstream as blood tests for inflammatory bowel disease in children, and his group is pursuing a similar approach in biliary atresia. His laboratory has discovered several microRNAs that are elevated in the blood of infants with biliary atresia. Because infants with biliary atresia do better the earlier they are diagnosed, this type of test can have a major impact on children with the disease.

Finally, Dr. Friedman’s lab has performed the first studies of microRNA function in the liver that is suffering from jaundice, with the discovery of several microRNAs that regulate the production of bile by the liver. His goal is to apply these discoveries to novel microRNA-based treatments for a range of liver disorders that are associated with jaundice.

Linda E. Greenbaum, MD

Dr. Linda Greenbaum received her subspecialty training in Gastroenterology at the University of Pennsylvania and served on the faculty at the University of Pennsylvania as assistant professor in the Department of Medicine from 1999-2009. During her period on faculty at the University of Pennsylvania, Dr. Greenbaum first identified the forkhead factor Foxl1 as a marker of liver progenitor cells and Foxl1 protein as an important regulator of bile duct recovery in mouse models of liver injury.

In her current position as associate professor of cancer, biology and medicine at Thomas Jefferson University, Dr. Greenbaum continues to investigate the role of Foxl1 for expansion of liver progenitor cells and is using genetic approaches in mouse injury models and cell culture studies to investigate selected signaling pathways that are responsible for progenitor cell expansion and differentiation of these cells to become mature bile ductular cells (cholangiocytes) and hepatocytes.

The goal of these studies is to understand key questions that have impeded progress in understanding the biology of hepatic progenitor cells in vivo during liver injury and identify new therapies to prevent and treat liver fibrosis and cirrhosis.

Kathleen M. Loomes, MD

Dr. Kathleen Loomes is an attending physician in the Division of Gastroenterology, Hepatology and Nutrition at The Children's Hospital of Philadelphia and an associate professor of pediatrics at the Perelman School of Medicine at the University of Pennsylvania. She is also the Director of Fellows’ Research Training in the GI Division. Dr. Loomes completed her pediatric residency at the Johns Hopkins Hospital in Baltimore, MD. She received her subspecialty training in pediatric gastroenterology and nutrition at The Children's Hospital of Philadelphia.

Dr. Loomes is actively engaged in both basic and clinical research related to hepatology. The work in her laboratory focuses on investigating the role of Jagged1 and the Notch signaling pathway in liver and bile duct development. Recently, Dr. Loomes has investigated the role of the Jag1 gene in bone development. Additional interests include clinical manifestations of Alagille syndrome, especially predisposition to bone disease and pathologic fractures.

Dr. Loomes is also involved in clinical research related to Alagille syndrome, viral hepatitis and causes of acute liver failure in children.

Randolph P. Matthews, MD, PhD

Dr. Randy Matthews is a pediatric gastroenterologist and assistant professor of pediatrics at The Perelman School of Medicine of The University of Pennsylvania. His laboratory is interested in studying genetic and epigenetic influences on pediatric hepatobiliary disease, in particular biliary atresia.

His laboratory uses the zebrafish as a model organism, but frequently utilizes patient samples to perform translational studies based on findings in zebrafish, and also uses studies in patients to inform studies in zebrafish.

Dr. Michael A. Pack, MD

Dr. Michael Pack is an adult gastroenterologist and associate professor of medicine and cell and developmental biology at The Perelman School of Medicine at The University of Pennsylvania. The focus of Dr. Pack’s research is on the development of the intestine, liver and pancreas. His lab works exclusively with the zebrafish, an animal model system that is uniquely suited to genetic analyses.

Dr. Pack’s laboratory has generated zebrafish models of heritable diseases affecting the human biliary system, such as the Alagille syndrome, the arthrogryposis renal dysfunction and cholestasis syndrome and the Indian childhood cirrhosis syndrome. Dr. Pack’s laboratory has also generated zebrafish models in which the function of developmental genes that control formation of the biliary system have been disrupted.

These models have enabled Dr. Pack to conduct mechanistic studies that are not feasible using other animal models, such as the mouse and rat, or that can be performed using cells derived from the human liver.

Matthew J. Ryan, MD

Dr. Matt Ryan trained at The Children’s Hospital of Philadelphia from 2003 through 2006. He was appointed assistant professor at The Perelman School of Medicine at the University of Pennsylvania in 2007. His research interests focus on bile duct development and remodeling.

Dr. Ryan's team uses mouse models to identify genetic modifiers affecting biliary phenotypes. Furthermore, they utilize a murine cholangiocyte cell culture system to examine Notch glycosylation and downstream effects on bile duct development.

His research includes novel techniques to isolate biliary cells within the liver as well as three-dimensional imaging of the biliary and vascular trees in the liver.

The goals of Dr. Ryan’s laboratory are to understand the developmental relationship of vascular and biliary structures in various cholestatic diseases and to elucidate the role of genetic modifiers in bile duct growth and remodeling.

Nancy B. Spinner, PhD

Dr. Nancy Spinner’s laboratory is interested in the identification and understanding of genes causing pediatric developmental and neonatal disorders. In particular, the laboratory has a long-standing interest in genetic disorders affecting the liver, including Alagille syndrome and biliary atresia. The laboratory has studied Alagille syndrome (a dominant disorder affecting the liver, heart, skeleton, eye, kidney and vasculature) since 1992, and identified the two disease genes for this disorder (Jagged1 and Notch2).

Currently, we are searching for genetic modifiers of the severity of the liver disease in Alagille syndrome. We are also working to identify genetic susceptibility factors for biliary atresia. This project is being carried out in collaboration with the International ChiLDREN consortium, and we are using Next Generation Sequencing and Genome-wide Association Analysis for gene identification.

Through the years, we have built outstanding and productive collaborations with the Division of Gastroenterology and the Center for Applied Genomics at our institution and the present work builds on our previous accomplishments and relationships. The laboratory is also working on identifying the molecular etiology of the Ring Chromosome 20 syndrome, a disorder caused by a unique ring chromosome abnormality, that is associated with intractable seizures.

Dr. Spinner is also the director of the Clinical CytoGenomics Laboratory at CHOP, and she is currently part of a multi-investigator project to investigate the utility of Whole Genome sequencing for diagnosis.

Benjamin Stanger, MD, PhD

Dr. Ben Stanger received his MD and PhD degrees from Harvard Medical School and did his clinical training in internal medicine and adult gastroenterology at University of California, San Francisco, and Massachusetts General Hospital.

His laboratory at the University of Pennsylvania is interested in mechanisms of liver development and regeneration, with a particular emphasis on how bile ducts form and the role that cellular plasticity — the interconversion of one liver cell type into another — may play during physiologic organ regeneration. 

For more information

To learn about clinical and collaborative studies or basic research opportunities at the Biesecker Pediatric Liver Center or any of its affiliates, please contact us at 215-590-2525.

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