FCF Research Projects


Fibrolamellar received minimal research attention prior to the founding of FCF. Since 2010 FCF has invested nearly $7 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.


Micro RNAs and long non-coding RNAs role in fibrolamellar and evaluation of RNA-based therapeutics

Principal Investigators: Praveen Sethupathy Associate Professor Department of Biomedical Sciences, Cornell University, College of Veterinary Medicine

Fibrolamellar carcinoma (FLC) is a rare liver cancer that is characterized by multi-drug resistance, early onset, and high metastatic capacity.  We are leveraging genome-scale approaches to discover the most critical molecular factors that promote and maintain these key features of FLC.  Specifically, we are: (1) identifying microRNAs and long, non-coding RNAs (lncRNAs) that facilitate FLC tumor formation and/or invasion and evaluating the potential of RNA-based therapeutics; (2) mapping the chromatin activity patterns in FLC to identify master transcriptional regulators; (3) defining the super enhancer landscape in FLC to identify the regulatory elements and genes most critical for driving tumor behavior; and (4) integrating different types of large-scale datasets, including metabolomics data, to identify critical druggable pathways.  We are actively engaged in collaborative ventures that bring together researchers with a shared commitment to tackle this devastating disease and bring relief and hope for patients.  For a description of some of our recently published work, we encourage you to visit here<https://www.cmghjournal.org/article/S2352-345X(19)30010-4/fulltext> and here<http://news.cornell.edu/stories/2019/02/key-rare-aggressive-liver-cancer-found-rna-molecule>.



Hedgehog and YAP signaling in fibrolamellar carcinoma: Tumor-stroma crosstalk and the
cancer stem cell niche

Principal Investigators: Cynthia Guy, MD, Associate Professor of Pathology; Anna Mae Diehl, MD, Florence McAlister Professor of Medicine, Duke University School of Medicine

Fibrolamellar carcinoma has a unique appearance; it is made up of large tumor cells surrounded by thick fibrous bands (the stroma). We believe that the cancers growth may result from deregulated communications signals between the tumor cells and cells that produce the stroma.

The major producers of stroma in the liver are called hepatic stellate cells (HSCs). Evidence from our laboratory has shown that in many different types of liver disease, HSCs promote repair of damaged livers by producing stroma and sending out signals that help surviving liver cells to regenerate. When repair is effective, stroma transiently accumulates and then regresses as healthy liver tissue is regenerated. However, when repair becomes dysregulated, excessive stroma (a.k.a., scar) accumulates and regeneration stalls before recovery of healthy liver tissue is accomplished. Our research revealed that HSCs regulate repair by controlling the activity of the Hedgehog (Hh) signaling pathway. We have demonstrated that while Hh signaling is helpful during normal liver development and repair, if it becomes deregulated, it can result in lead to pathologic processes. These processes include fibrosis (scarring) and the activation of a downstream signaling pathway that leads to the activation of Yap, a factor that can make liver cells become more primitive (and in many ways like cancer stem cells). Thus, dysregulation of Hh and Yap results in accumulation of stroma (scar) and primitive stem-like cells and as such, resembles key features of fibrolamellar carcinoma (FLC).

Given this background, we will evaluate evidence for and against the concept that Hh and Yap signaling between the tumor cells and the stroma is important for FLC growth, and for the perpetuation of cancer stem cells. This possibility is supported by a recent publication by a FCF- sponsored investigator, Lola Reid, PhD, who showed that malignant fibrolamellar cells produce Hh protein. Furthermore, there is growing evidence that Hh and Yap interact to control liver growth. However, to date, neither pathway has been formally studied in FLC, or considered as a possible diagnostic or therapeutic target in this cancer. Our project is the first to explore this possibility and offers the promise of novel interventions to prevent and treat this devastating disease. We will examine human fibrolamellar carcinoma samples to look for evidence of Hh and Yap signaling in the tumor cells and stroma. In addition, we will grow cells in culture with and without different types of HSCs to find the best cell-cell signals to target for anti-cancer therapy.



Characterizing enzyme inhibition of the DnaJPKAc chimeric protein derived from fibrolamellar hepatocellular carcinomas


Principal Investigator: Hibba tul Rehman, M.D., University of Vermont

Scientists have identified a unique fusion protein, DnaJ-PKAc, which causes this cancer. When overexpressed, this protein causes havoc in the downstream signaling pathways that are involved in cell growth and metabolism and is thought to be the key driver for cancer growth. Based on the 100% presence of the chimeric DnaJ-PKAc protein in FL-HCC patients, we are proposing a two pronged approach towards the regulation of the cancer cells. First, we will screen a previously developed peptide library to test the substrates against purified wild-type vs. the chimeric DnaJ-PKAc in vitro. Second, we propose to develop a library of inhibitory peptides that would preferentially inhibit DnaJ-PKAc. The studies suggested here should allow us to develop inhibitors that regulate the function of the chimeric enzyme without affecting the wild- type enzyme, thus selectively targeting cancer cells without affecting healthy tissue.


University of California San Francisco


Harvard University, Cambridge, MA


2016 – 2019     

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.

This grant is one of four awarded in partnership with the Cancer Research Institute.



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.

This grant is one of four awarded in partnership with the Cancer Research Institute.


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.

This grant is one of four awarded in partnership with the Cancer Research Institute.

 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.

This grant is one of four awarded in partnership with the Cancer Research Institute.


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-Logo-black_blue_original8Mayo 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 logoUNC 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.

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.


Rockefeller University, New York, New York

2016 – 2017

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.


yale logo 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 medicine logoJohns Hopkins University, Baltimore, MD

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 logoRockefeller 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.



MSKCC_logo 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 univ logoBritish 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.



In an effort to bring the best medical and scientific minds together who are involved in studying and treating fibrolamellar, the Foundation has hosted two scientific conference to focus exclusively on this disease. Attendees included fibrolamellar researchers and clinicians who treat fibrolamellar patients including representatives from major cancer centers in the U.S., Canada, Denmark, leading academic institutions, the NHI/NCI, the pharmaceutical industry and other cancer foundations. The Journal of Hepatology published an article of findings from the 2017 conference entitled “Road Map for Fibrolamellar Carcinoma: progress and goals of a diversified approach.”

FCF’s next summit is planned for November 2019.