Fibrolamellar received minimal research attention prior to the founding of FCF. Since 2010 FCF has invested nearly $6 million in research, with the goal to accelerate the road to curative therapies. Research has been both in traditional and non-traditional approaches, led by respected M.D.’s and PhD’s who focus on clinical trials, translational, and basic research.
The projects listed below are in chronological order from the most recent.
University of California San Francisco
Harvard University, Cambridge, MA
2016 – 2018
Flipping the switch on PKA: synthetic lethal approaches to block PKA-driven tumor growth in fibrolamellar liver cancer
Principal Investigators: John Gordan. M.D., Ph.D, Clinical Instructor, University of California San Francisco; Nabeel Bardeesy, Ph.D, Associate Professor, Harvard University
The discovery of a genetic change in the protein kinase A (PKA) gene in most cases of fibrolamellar liver cancer (FLC) creates hope that targeted therapy against PKA will have potent effects for FLC patients. However, progress is impeded by the relative scarcity of established model systems and the current lack of an effective anti-PKA drug. PKA is a component of the G protein-coupled receptor (GPCR) pathway, which is thought to play a role in many other cancer types. However, little is known about how this pathway makes tumors grow, and if it creates any specific liabilities in tumor cells that can be effectively targeted even when PKA is still active. We hypothesize that common mechanisms support the growth of different cancers where PKA is abnormally activated and that deciphering these mechanisms will lead to new treatment strategies for FLC.
In this project, we will apply cutting-edge proteomic methods to comprehensively map biochemical processes controlled by GPCRs and PKA across a number of cancer cell lines. We will complement these efforts with genetic approaches to identify other genes that are essential for PKA-driven cancer growth. Finally, we will use newly developed FLC models to test key targets identified with our screening techniques.
By identifying and rigorously testing the importance of the mediators of PKA signaling in FLC, we will be positioned to repurpose existing drugs to accelerate progress in the treatment of patients with FLC.
University of Washington, Seattle, WA
T cell immunotherapy in fibrolamellar cancer
Principal Investigator: Kevin M. Sullivan, M.D., General Surgery
Immunotherapy is a form of cancer treatment that harnesses the patient’s own immune system to fight the disease. The immune system can precisely target cancer cells, while also minimizing damage to the remainder of the body’s normal cells. In this project, we will investigate a well-established method of using the immune system, successful in treating other cancers such as melanoma, as a treatment for fibrolamellar. We will start by using a variety of techniques to look at which types of immune cells reside within the fibrolamellar tumors. One type of immune cell, called the T cell, is of particular interest because it can specifically recognize and destroy cancer cells. In preliminary work, our group has confirmed that T cells are found within a fibrolamellar tumor. In this project, we will gain a detailed understanding of the characteristics of the T cells that are active within fibrolamellar tumors. We then plan to grow and activate these T cells and test their ability to fight cancer cells in cell cultures and slices of fibrolamellar tumor grown in the laboratory. Ultimately, our project will provide the basis for making this type of T cell as a treatment against fibrolamellar a reality.
University of Wisconsin, Madison, WI
Role of the innate immune system in Fibrolamellar Hepatocellular Carcinoma (FL-HCC) using zebrafish as a model system
Principal Investigator: Sofia de Oliveira, Ph.D., EMBO Postdoctoral Fellow Huttenlocher Lab
About 80% of FHC cases are characterized by the presence of an activated form of a protein called Protein Kinase A (PKA). The mechanism of how active PKA leads to disease remains unclear. Normal PKA is involved in complex signaling pathways that among other processes control innate immune response. A better understanding of the mechanisms triggered by this active PKA and how it modulates innate immune response is crucial to develop more efficient drug therapies and increase the survival rate of fibrolamellar patients. Up to now, there are limited animal models to study FHC, which hampers our knowledge about the disease. This research proposes to take advantage of the outstanding characteristics of zebrafish and develop a FHC model. Zebrafish has proven to be an extremely useful tool to study innate immunity and cancer biology. Additionally, it has been used to study liver development, conventional hepatocellular carcinoma and several other liver disorders, displaying remarkable similarities and sharing genetic signatures with human diseases. More over zebrafish is the only vertebrate model with high homology with humans that allows visualization of cellular and molecular interactions in a whole organism context without the need to use invasive imaging methods since the larvae are transparent.
Innate immune cells, such as neutrophils and macrophages are important players in cancer development. Their presence in the tumor microenvironment might be beneficial or detrimental to cancer progression, depending on the type of cancer. This study will leverage the zebrafish models to study the role of different innate immune cells in FHC, and assess the potential role of neutrophils and macrophages as therapeutic targets for FHC.
University of California San Francisco
Pre-clinical studies of the interactions of the immune system with FL-HCC
Principal Investigator: Kevin Barry, Ph.D., Postdoctoral Scholar
All sequenced human fibrolamellar hepatocellular carcinoma (FL-HCC) samples contain a mutation that leads to a fusion of the proteins DNAJB1 and PRKACA. The mutant DNAJB1-PRKACA protein is thought to drive the development of FL-HCC. There is a clear need to further understand the mechanism of FL-HCC tumorigenesis and to develop novel treatments.
Cancer immunotherapies harness the power of the immune system to kill tumors. Checkpoint blockade immunotherapies are an exciting class of cancer immunotherapies that remove the brakes from the immune system by targeting molecules that inhibit tumor-directed responses by immune cells called T cells. T cells are important for protecting patients from tumors as these cells directly kill tumor cells and modulate the global immune response towards tumors. Immunotherapies targeting T cells have been remarkably effective in treating cohorts of non FL-HCC cancer patients, leading to tumor regression and immune memory which offers long-term protection; effectively providing a cure to cancer in some patients. However, very little is known about how the immune system interacts with FL-HCC or if immunotherapy would be an effective treatment for FL-HCC. The study of the efficacy of immunotherapy in the treatment of FL-HCC is hampered by the fact that the current pre-clinical animal model of FL-HCC utilizes the transplantation of human tumor into immune compromised animals, making it impossible to study the interactions between the immune system and FL-HCC in a tractable system.
This research, in collaboration with Dr. Julien Sage’s group and Stanford University, will generate a pre-clinical animal model of FL-HCC in mice with fully functional immune systems and will undertake the initial studies of how the immune system interacts with FL-HCC. These studies represent the first step in moving towards treating FL-HCC patients with immunotherapy in the clinic.
Johns Hopkins University, Baltimore, MD
2016 – 2019
Investigating immune checkpoint biomarkers in tissue and peripheral blood of
patients with fibrolamellar hepatocellular carcinoma
Principal investigator: Amy K. Kim, M.D., Assistant Professor
The understanding of immune checkpoint molecules that suppress host immune response against tumor cells and the discovery of drugs that block these immune checkpoints have revolutionized current cancer treatment. Anti-PD1 (programmed cell death protein 1) immunotherapy has shown benefit in many cancer types, but certain cancers have also shown strong resistance to this immunotherapy. It is unclear how fibrolamellar cancer would respond to different immune checkpoint blockade, including anti-PD1 therapy. In addition, there is a need to investigate how circulating tumor cells (CTCs) in the blood that have disseminated from the primary tumor site induce anti-tumor immune response outside the tumor environment. This project will address these issues by pursuing the following specific aims: 1) to define the dominant immune checkpoint pathway in fibrolamellar cancer and its interaction with the patient’s immune response in the tumor, and; 2) to determine how immune checkpoint markers are associated with circulating tumor cells in the peripheral blood, in comparison to the primary tumor site. Understanding the immune checkpoint expressions in fibrolamellar cancers will guide in the future selection of immunotherapy and studying the role of circulating tumor cells and tumor-associated immune cells can reveal a novel way to predict cancer treatment response that does not require an invasive procedure for tumor tissue from the patients.
Rockefeller University, New York, New York
2016 – 2018
Developing Therapeutics for Fibrolamellar Hepatocellular Carcinoma
Principal Investigator: Sandy Simon, Ph.D., Professor
Investigator Collaboration: Barbara A. Lyons, Ph.D., Professor, New Mexico State University
The goal of this work is to develop a therapeutic for fibrolamellar hepatocellular carcinoma (FLHCC). These are three different two-year projects, with independent synergistic strategies, to identify small molecules to treat fibrolamellar. The strategy is based on this laboratory’s published work that there is a single alteration in the DNA that is found in all fibrolamellar tumors: a deletion of 400kB that results in a fusion gene, a chimera of the heat shock protein DNAJB1 and the catalytic subunit of protein kinase A, PRKACA and on this laboratory’s unpublished work that the chimera with an active kinase is sufficient to cause fibrolamellar.
The first project is a high-throughput screen for molecules that directly block the chimera. This is an agnostic screen, which presumes no advanced knowledge about the chimera, with the goal of blocking its kinase activity. The screen will cover millions of compounds with no prior assumptions about what might work.
The second project is a screen to identify the molecules that are directly phosphorylated by the chimera (in contrast to identifying downstream elements that change as a consequence of the activity of the chimera).
The third project is an analysis of the structural dynamics of the chimera using a molecular dynamics simulation. This project is based on to-date-unpublished x-ray and NMR data on the structure of the chimera, together with molecular dynamics simulations, to identify sites on the chimera that would be appropriate for targeting therapeutics. Unlike the first project, which is an agnostic screen, this project is based on the hope that domains can be identified that are critical to the chimera’s.
Stanford University, Palo Alto, CA
Developing pre-clinical models for fibrolamellar FL-HCC:Therapeutic target identification and testing
Principal Investigator: Dr. Julien Sage, Ph.D., Associate Professor, Department of Pediatrics and Genetics
Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare but lethal form of liver cancer for which few therapeutic options are available. Major barriers hampering the development of better therapies for FL-HCC patients include the rarity of the disease and the fact that many of these patients are children, limiting the implementation of clinical trials. One solution to this problem can come from the development of accurate pre-clinical models of FLHCC; such models can be used both to investigate the basic mechanisms of FL-HCC development, which may help identify new therapeutic targets, and to test novel therapeutic strategies. Here we propose to generate a mouse model for FL-HCC. We and others have analyzed the sequence of FL-HCC patients and identified a distinct genetic alteration resulting in the fusion of two proteins (a small piece of “DnaJ” and a larger piece of “PKA” are fused together). This DnaJ-PKA fusion is present in all the FL-HCC tumors sequenced so far and we showed it has pro-tumorigenic effects in cells.
Based on the pattern of development of FL-HCC, mostly in children and young adults, we hypothesize that the expression of the DnaJ-PKA fusion initiates cancer in specific liver stem/progenito cell populations during liver development. We have introduced the DnaJ-PKA DNA fusion into the genome of mice but the fusion protein can only be expressed upon activation of an activating enzyme (named “Cre”). To test our hypothesis, we will introduce the Cre enzyme at specific stages of liver development using genetic tools in mice.
If tumors develop, this will conclusively demonstrate that expression of the DnaJ-PKA fusion is an essential step in FL-HCC development, providing novel insights into the mechanisms of FL-HCC development. In addition, the generation of mice developing FL-HCC tumors resembling human tumors would provide a pre-clinical platform to test new therapeutic strategies.
For additional details see the article published by Stanford on FCF’s grant and collaboration.
Mayo Clinic, Rochester, MN
Kinase fusion function investigation
Principal Investigator: Dr. Yi Guo, Ph.D, Associate Consultant – Asst Professor, Dept of Biochemistry and Molecular Biology
A recurring chromosomal deletion on human chromosome 19 was detected in at least 80% of FL-HCC cases, resulting a novel kinase fusion of DNAJB1-PRKACA (Cornella et al., 2015; Honeyman et al., 2014; Xu et al., 2015). While this novel fusion is identified as a potential oncogenic factor, the establishment of the causal and mechanistic relationship between the DNAJB1-PRKACA fusion and FL-HCC is critical for developing targeted cancer therapy.
This study aims to investigate the function of DNAJB1-PRKACA fusion in FL-HCC oncogenesis using both Drosophila and mice models. We established a DNAJB1-PRKACA transgenic Drosophila model and discovered abnormal phenotype affecting both proliferation and differentiation of Drosophila eyes. We also exploited CRISPR/Cas9 genome-engineering technology in murine cultured hepatocytes to recreate the endogenous chromosomal deletion as found in FL-HCC patients. For this Research Grant application, we proposed to 1) characterize the oncogenic and fibrogenic activities of genetic engineered murine hepatocytes in vitro and in vivo; and 2) screen potent therapeutics using the human DNABJ1-PRKACA over-expression model in Drosophila menalogaster. This study will provide essential resources and knowledge for fighting this aggressive hepatocellular carcinoma.
UNC School of Medicine, Chapel Hill, NC
RNA validation and evaluation of FLC, including therapeutic targets
Principal Investigator: Dr. Praveen Sethupathy, Ph.D. Assistant Professor of Genetics
Our research is focused on: (1) validating UNC’s RNA signature of FLC in an independent set of FLC, HCC, and CCA samples (collaboration with Dr. Michael Torbenson); (2) evaluating the expression and function of these RNAs in the first ever FLC transplantable tumor line- TU-2010 (collaboration with Dr. Lola Reid); and (3) identifying candidate therapeutic targets of FLC for future clinical development. For example, effective small molecule inhibitors are already available for some of the proteins of interest, such as CA12, and these could be tested immediately if our findings suggest that CA12 is a critical driver of FLC progression. Additionally, it may be possible to identify early diagnostic markers, which is critical for survival outcome. CA12 was previously detected in the sera of patients with specific lung tumors and microRNA-10b was reported as a candidate biomarker of breast cancer. UNC hypothesizes that CA12 and microRNA-10b are present at high levels in the sera of FLC patients as well. In order to test this hypothesis, UNC requires access to FLC sera. If findings in the serum samples validate the hypothesis, these genes could serve as early diagnostic biomarkers for FLC. The proposed research is groundbreaking because it is focused on defining the molecular landscape of FLCs and identifying biomarkers and pathogenic drivers of FLCs. The successful completion of these aims will chart a clear path for subsequent efforts to develop novel early diagnostic tools and therapeutic strategies for FLCs.
Johns Hopkins University, Baltimore, MD
BLT: Sequential Partial Liver Transplant with Bone Marrow Transplantation
Principal Investigator: Dr. Ephraim Fuchs, MD, MBA, Professor of Oncology and Immunology
FCF and the Johns Hopkins University School of Medicine are sponsoring a trial of sequential partial liver transplantation followed by bone marrow transplantation from the same living related donor. This treatment applies to patients whose cancer remains confined to the liver but is too widespread to be removed by surgery or treated by a liver transplant from a deceased donor. The purpose of this combined treatment is to reduce the risk of the cancer coming back after the liver transplant The bone marrow transplant may reduce the risk of the cancer coming back in two ways. First, patients who have combined bone marrow and solid organ transplants may be able to get off all anti-rejection drugs, which inhibit the immune system from destroying cancer cells. Second, the donor’s bone marrow contains cells of the immune system, which can attack any cancer cells that remain after the liver transplant. More information is available through clinicaltrials.gov
University of North Carolina, Chapel Hill
2010 to present
Principal Investigator: Lola Reid, PhD, Professor, University of North Carolina, Chapel Hill
Dr.Reid is working with FCF Founder Tucker Davis’ cancer cells to determine where these cells start within the stem cells of the biliary tree. Dr. Reid has found a way to culture Tucker’s cells and grow them to provide more cells for other labs’ research. She is presently giving Tucker’s cancer cells to immunosuppresed mice with the hope that a specific treatment option will result from her work. Dr. Reid has shared Tucker’s cells with the National Institute of Health and Dr. Malcolm Moore at MSKCC.
The following initiatives were funded since 2010 and are listed in reverse order of funding. Research is no longer continuing on these grants.
Yale School of Medicine, New Haven, CT
Iodine Transporter Research: FCF funded Dr. Nancy Carrasco at Yale School of Medicine to analyze FLC cells to discover whether they could be effectively targeted by radioactive iodine. Radioactive iodine has a long history as a safe and effective treatment for thyroid cancer. Research had indicated that fibrolamellar cells might have pathways similar to those of thyroid cancer cells. Use of radioactive iodine on several patients did not confirm this theory and the project was terminated.
Johns Hopkins University, Baltimore, MD
Harvard University, Cambridge, MA
Dr. Michael Torbenson while at Johns Hopkins (he is now at Mayo Clinic in Rochester, MN) wrote the first paper on blood markers for fibrolamellar which was published in the journal, Modern Pathology, in late 2010. The article recognized FCF for their financial support. While at Johns Hopkins Dr. Torbenson was studying the microRNA of fibrolamellar cells and his laboratory was working on a genetic sequencing study of fibrolamellar to determine if there are genetic mutations unique to fibrolamellar cells.
Rockefeller University, New York, NY
FCF funding to Rockefeller University resulted in a potentially game-changing discovery of a unique genetic mutation common to all fibrolamellar tissues studied, a chimera. This research was conducted at the Tucker Davis Research Facility at Rockefeller University. Dr. Sandy Simon is head of that facility and his daughter Elana, who is a fibrolamellar patient, was a lead researcher. The results were published in the preeminent medical journal, Science and reported in The Wall Street Journal, US News and World Report, AP, The Today Show, NBC Nightly News, and presented to President Obama.
The Foundation granted Dr. Sandy Simon funds to study immunotherapy and fibrolamellar. Rockefeller University has put their full support behind Dr. Simon and charges no administrative fees for this research. Rockefeller University has provided Dr. Simon with a dedicated space exclusively for fibrolamellar research, The Tucker Davis Fibrolamellar Research Facility. FCF provided a freezer for fibrolamellar tissue samples. Dr. Simon’s goal is finding a cure – total eradication from the body. He feels this path is through the immune system using the patients’ own antibodies to track and kill the cancer cells. His research also includes melanoma and breast cancer cells.
Dr. Simon has already discovered a way to extract antibodies from a patient, mark them, and re-introduce them into the body. The marked antibodies can attach to the smallest of cancer cells which will help surgeons and pathologists determine, during surgery, whether all the cancer has been removed.
Memorial Sloan Kettering Cancer Center, New York, NY
FCF funded the first clinical trial of drugs aimed specifically at fibrolamellar liver cancer. This trial was coordinated by Dr. Ghassan Abou-Alfa at Memorial Sloan Kettering Cancer Center (MSKCC). The trial was also at other consortium members, the University of California San Francisco, Johns Hopkins, and Dana Farber. Two major pharmaceutical companies are donating the drugs. While the trial is ongoing for exisiting patients no new patients are being accepted.
MSKCC is sequencing the exome of the fibrolamellar genome.
MSKCC is the coordinator of the Fibrolamellar Consortium.
British Columbia Cancer Center, Canada
Dr. Y.Z. Wang published his findings on the microRNA research he is doing on cancer. He has thanked FCF for supporting his effort. His findings will help other microRNA researchers who are studying other cancers, ie. Dr. Torbenson at Johns Hopkins University who is studying microRNA of fibrolamellar. Dr. Wang’s paper sets an important precedent in cancer research in that it reports discrete molecular (microRNA) differences between tumors which metastasize and perfectly matched tumors that do not. These findings may have diagnostic, prognostic and most important of all, therapeutic implications.
FCF has funded the creation of The Fibrolamellar Consortium in 2011. This is a collaborative effort by Memorial Sloan- Kettering (NYC), Johns Hopkins (Baltimore), University of California/San Francisco, University of Texas Southwestern Medical Center, Dallas, Texas, and Dana Farber (Boston). The consortium’s mission is to:
- promote awareness about FLC within the oncology community
- develop new therapies for FLC
- pool information on FLC patients in order to document trends in diagnosis, treatment and survival.
The consortium conducted a clinical trial, now closed, which tested a novel treatment designed specifically for FLC. This was the first clinical trial dedicated to patients with advanced FLC that cannot be treated with surgery.
The Consortium meets twice a year at the ASCO (American Society of Clinical Oncology) converntions. The Consortium had a poster presentation at the ASCO convention in Chicago, June 2011. This generated a lot of interest and queries about fibrolamellar research.
FIBROLAMELLAR SCIENTIFIC CONFERENCE
In an effort to bring the best medical and scientific minds together who are involved in studying and treating fibrolamellar, the Foundation hosted the first ever scientific conference to focus exclusively on this disease in April 2014. There were over 40 people in attendance, including fibrolamellar researchers and clinicians who treat fibrolamellar patients including representatives from major cancer centers in the U.S., Canada and Israel including Memorial Sloan-Kettering, Dana Farber, Johns Hopkins, Mayo Clinic, MD Anderson, Seattle Cancer Center, UCSF, British Columbia Cancer Center, Vanderbilt Ingram and the International Center for Cell Therapy and Cancer Immunology. There were scientists from Yale, Rockefeller, Columbia, Johns Hopkins, University of North Carolina and the NIH. The retired pathologist who gave this cancer its name, FCF Board member Dr. John Craig, was also present.
Over the course of the day there were multiple presentations with opportunities for questions. Recent significant findings were reported by several of the scientists some of which could be the foundation for future treatments. There were fascinating discussions about psychiatric symptoms and other previously unrecognized commonalities amongst some fibrolamellar patients. While much of the research is preliminary it presents interesting and hopeful avenues to pursue.
A second conference is being planned for Fall 2017.