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Last Updated: 10/10/18

Developmental and HyperActive Ras Tumor (DHART) SPORE

Indiana University

Principal Investigators:
D. Wade Clapp, M.D., Contact PI, Indiana University School of Medicine
Kevin M. Shannon, M.D., Multi-PI, University of California, San Francisco

PRINCIPAL INVESTIGATOR CONTACT INFORMATION

D. Wade Clapp, MD
Richard L. Schreiner Professor and Chairman
Department of Pediatrics
Indiana University School of Medicine
Riley Hospital for Children at Indiana University Health
705 Riley Hospital Dr., 5900
Indianapolis, IN 46202
Tel: (317) 944-7810
Fax: (317) 944-4471
Email: dclapp@iu.edu

Kevin M. Shannon, MD
Professor, Department of Pediatrics
School of Medicine
University of California, San Francisco
1450 3rd Street
San Francisco, CA 94143-3112
Tel: 415 476-7932
Fax: (415) 514-4996
Email: ShannonK@peds.ucsf.edu

OVERALL ABSTRACT

The Developmental and HyperActive Ras Tumor (DHART) SPORE is a national collaborative effort that harnesses the expertise of researchers at Pediatric Branch of the National Cancer Institute (NCI) and eight leading academic institutions. Our overall goal is to implement effective new targeted treatments for tumors characterized by mutations of the NF1 tumor suppressor gene. The collaborating researchers are pursuing this goal by conducting integrated, mechanistically based translational research. In contrast to most other SPORE efforts supported by the NCI, the DHART SPORE does not focus on a particular type of cancer. Instead, we are working to implement new treatments for tumors that develop in different tissues due to NF1 mutations.

A unique attribute of the DHART SPORE is the focus on tumors that develop in patients with neurofibromatosis type 1 (NF1). NF1 is a both a disorder in which the development of multiple different tissues is abnormal and the most common inherited cancer predisposition syndrome. Persons with NF1 have a markedly increased incidence of developing specific tumors, which are frequently diagnosed in children, adolescents, and young adults. NF1 is also the founding member of a group of developmental disorders called the “Rasopathies” that also includes Noonan, Legius, Costello, and cardiofaciocutaneous syndromes. A unifying molecular feature of the Rasopathies is that they are caused by inherited mutations that aberrantly “turn on” Ras proteins or activate proteins that are regulated by Ras.

This multi-disciplinary and multi-institutional SPORE is pursuing innovative strategies to address the fundamental challenge of accelerating new therapies for uncommon (“orphan”) cancers as exemplified by tumors in patients with Rasopathy disorders. First, we are “re-purposing” drugs that are being developed to block the biochemical effects of RAS gene mutations, which are found in about 1/3rd of all cancers. Pharmaceutical and biotechnology companies have made enormous investments toward developing inhibitors of Ras and Ras-regulated proteins. Because the protein made by the NF1 gene interacts directly with Ras and controls its activity, drugs that are being tested in cancers with RAS gene mutations should also be systematically evaluated in malignancies driven by NF1 inactivation. This SPORE addresses this important translational gap. Second, the very nature of orphan cancers means that they affect limited numbers of patients and it is therefore not feasible to accrue large numbers to clinical trials. To address this bottleneck, the participating researchers collaboratively developed and characterized a series of genetically engineered mouse models of NF1-associated tumors, and pioneered using them to test promising anti-cancer agents in preclinical trials. Using these advanced systems facilitates moving only the most promising drugs for into clinical trials, which will be conducted by SPORE investigators. Finally, building a team of experts from across the country with complementary basic science and clinical trials expertise allows the DHART SPORE to bring the most accomplished researchers together to develop better treatments for these orphan cancers.

While the focus of this SPORE is on testing rational, mechanism-based treatments for tumors that develop in patients with NF1, this research has broad relevance for improving the treatment of the large number of cancers arising in patients without NF1 that carry mutations in NF1 or in RAS genes. These common cancers include glioblastoma, lung cancer, melanoma, and leukemia. In addition, molecular and epidemiologic studies within the DHART SPORE address the role of radiation and chemotherapy in causing secondary malignancies, with is a fundamental problem in the growing population of cancer survivors worldwide. Given the central importance of aberrant Ras/GAP function in human cancer and the emerging role of somatic NF1 mutations in common sporadic malignancies, achieving the goals of this SPORE will broadly advance translational cancer research and stimulate the development of “next generation” treatments.

This program encompasses four highly integrated projects and three cores. Across all four projects, genome-wide analysis of clinical specimens and murine cancers will elucidate molecular mechanisms of tumorigenesis in primary and second malignancies. The main projects are:

Project 1: Molecular, Developmental, and Genetic Evaluation of Plexiform Neurofibromas to Inform Clinical Trials.

Project 2: Targeted Therapies for Malignant Peripheral Nerve Sheath Tumors (MPNST)

Project 3: A High Content Clinical Trial of the MEK Inhibitor Trametinib in Juvenile Myelomonocytic Leukemia (JMML).

Project 4: Subsequent Malignant Neoplasms (SMNs) Among NF1 Cancer Survivors.

The cores provide support for the main research projects, developmental research projects, and career development investigators to facilitate and expand translational research for the SPORE research efforts. The Administrative Core (Core 1) provides scientific and fiscal oversight for the program as well as coordination of the development of an integrated SPORE database in which all preclinical and clinical trial data will be stored and shared by all investigators. All data, including data generated and analyzed by the following research cores will be delivered and integrated into the database.

There are two state-of-the-art research core facilities. The Biospecimen/Pathology Core (Core 3) will receive human and mouse samples from all four SPORE projects. This core will also perform pathological review of all samples and will make these data available to SPORE investigators and the broader research community. The Omics Core (Core 2) will provide a unique set of proteomic and genomic platforms for performing RNAseq and whole exome sequencing analysis combined with comprehensive kinome activation measurements.

OVERALL APPROACH

The goal of this DHART SPORE is to implement more effective therapeutic strategies for tumors arising in patients with NF1 by performing collaborative translational research. These studies also address the fundamental problem of hyperactive Ras signaling in cancer. Here we introduce the four research projects and three core components of this SPORE. Innovative aspects of the DHART SPORE include: (1) a focus on advancing the science and care of patients with orphan diseases; (2) a strong emphasis on tumors arising in children, adolescents, and young adults; (3) studies of diverse tumor types that share a common driver mutation; and, (4) an investigative team drawn from 9 leading research centers across the nation.

PROJECT 1: Molecular and Genetic Features across Mouse and Human Plexiform Neurofibromas to Inform Clinical Trials

D. Wade Clapp, MD, Basic Science Co-Leader (Indiana University School of Medicine)
Jaishri Blakeley, MD, Clinical Science Co-Leader (Johns Hopkins University)
Brigitte Widemann, MD, Clinical Science Co-Leader (National Institute of Health)
Lu Le, MD, PhD, Basic Science Co-Leader (University of Texas, Southwestern)
Kent Robertson, MD, Ph.D. Co-Investigator (Indiana University School of Medicine)

Plexiform neurofibromas (PNs) PNs are complex nerve and soft tissue tumors that affect 25-50% of people with NF1, cause serious lifelong morbidity and mortality due to organ compression, and progress to malignant peripheral nerve sheath tumors (MPNST) in ~8-13% of patients. Collaborative studies performed by Drs. Clapp and Luis Parada in a genetically engineered mouse (GEM) model of PNs unexpectedly demonstrated a central role of infiltrating Nf1 haploinsufficient bone marrow-derived mast cells in promoting the growth of PN lesions in vivo. These novel data led to a clinical trial administering imatinib mesylate to target aberrant stem cell factor (SCF)/c-kit signaling in the tumor microenvironment, which induced objective clinical responses in a subset of patients. Based on the observation that young children with head, neck, and airway tumors were most likely to have partial tumor regression, Drs. Robertson, Blakeley, Widemann and Michael Fisher are pursuing a registration trial in this patient population. More recently, studies in GEM models informed successful clinical trials of MEK inhibitors to directly inhibit aberrant Ras/Raf/MEK/ERK signaling in PN cells. The objective of Project 1 is to extend these promising data to investigate the developmental, molecular, and pharmacokinetic effects of c-kit and MEK inhibition alone and in combination. Our investigative team will characterize the adaptive responses of PNs to these kinase inhibitors in GEM models and in parallel studies in patients. The aims of Project 1 are:

Aim 1: Evaluate tumor and circulating markers before and after treatment with the MEK inhibitor selumetinib in pediatric and adult patients with NF1 associated plexiform neurofibromas.

Aim 2: Evaluate the molecular adaptive responses, PK/PD and clinical response of plexiform neurofibromas in genetically engineered mice (GEM) with selumetinib alone, and in combination with imatinib mesylate.

Aim 3: Utilize GEM models to identify the optimal therapeutic window(s) of c-kit (SCF) inhibition at distinct embryonic and adult stages of PN formation utilizing Nf1flox/- and Nf1flox/-;Scf flox/flox mice under the transcriptional control of a PLP tamoxifen + Cre transgene.

The translational impact of this project involves: (1) defining therapeutic window(s) for c-kit inhibition at distinct embryonic and adult stages of PN formation; (2) investigating a rational approach to combinatorial therapy based on simultaneously interfering with paracrine growth signals emanating from the tumor microenvironment while also targeting aberrant Raf/MEK/ERK pathway activation in tumor cells; and (3) defining novel biomarkers by analyzing tumor specimens and blood obtained both prior to and after treatment.

PROJECT 2: Targeted Therapies for Malignant Peripheral Nerve Sheath Tumors

Luis Parada, PhD, Basic Science Co-Leader (Memorial Sloan Kettering Cancer Center)
Stephen X. Skapek, MD, Clinical Science Co-Leader (University of Texas, Southwestern)
Ted Laetsch, MD, Co-Investigator (University of Texas, Southwestern)
Noelle Williams, PhD, Co-Investigator (University of Texas, Southwestern)
Xiankai Sun, PhD, Co-Investigator (University of Texas, Southwestern)
Guiyang Hao, PhD, Co-Investigator (University of Texas, Southwestern)

Malignant peripheral nerve sheath tumors (MPNST) evolve from pre-existing plexiform neurofibromas, and we therefore hypothesize that these aggressive sarcomas continue to express some of the transcriptional programs present in the initiating fetal precursor population. This, in turn, might create novel synthetic lethal dependencies that can be exploited therapeutically. Indeed, Dr. Parada recently identified CXCR4 and CDK4/6 as key drivers of MPNST cell proliferation and tumor progression in GEM models. The major goals of Project 2 are to translate these provocative preclinical data and to harness functional imaging to develop better markers of early response in MPNST. The aims of Project 2 are:

Aim 1. To optimize CXCR4 and Cyclin D1-associated CDK4/6 inhibition in MPNST

Aim 2. To optimize functional imaging for early response assessment in MPNST

Aim 3. To conduct pilot, “Phase 0” studies of GEM-guided, molecularly-targeted therapy in MPNST

The translational impact of these studies encompasses the development of a biomarker profile to identify early markers of MPNST progression and evaluate efficacy of CXCR4 and CDK4/6 inhibitors in clinical trials.

PROJECT 3: Efficacy of MEK Inhibition in Juvenile Myelomonocytic Leukemia

Kevin Shannon, MD, Basic Science Co-Leader (University of California, San Francisco)
Mignon Loh, MD, Clinical Science Co-Leader (University of California, San Francisco)
Benjamin Braun, MD, PhD, Co-Investigator (University of California, San Francisco)
Elliot Stieglitz, MD, Co-Investigator (University of California, San Francisco)

Children with NF1 are predisposed to juvenile myelomonocytic leukemia (JMML), an aggressive myeloproliferative neoplasm (MPN) that responds poorly to chemotherapy. Hematopoietic stem cell transplantation (HSCT) cures ~50% of patients. Our studies of JMML specimens proved that NF1 functions as a tumor suppressor gene in hematopoietic cells, and provided the first direct evidence of deregulated Ras signaling in primary cancer cells from NF1 patients. These studies support the role of hyperactive Ras signaling in JMML pathogenesis, and our group and other researchers subsequently discovered mutations in NRAS, KRAS, PTPN11, and CBL in JMML patient specimens. Overall, >85% of JMML cases have mutations in one of these genes, including 15-20% with clinical NF1 or mutations in the NF1 gene. Despite the routine use of HSCT, up to 30% of JMML patients progress to acute myeloid leukemia (AML). Consistent with the molecular genetics of JMML, using the Mx1-Cre transgene to inactivate the conditional mutant Nf1flox allele generated by the Parada lab or to express oncogenic KrasG12D or NrasG12D in the hematopoietic compartment induces a JMML-like MPN in mice. Preclinical trials in these accurate GEM models revealed remarkable efficacy of MEK inhibitors. Importantly, however, this, treatment does not eradicate mutant bone marrow cells, but modulates their proliferation and differentiation in vivo. The overall goals of Project 3 are to translate these promising preclinical data in JMML patients though an innovative clinical trial that includes deep molecular analysis. The aims of Project 3 are:

Aim 1. To conduct a national A national phase II trial investigator initiated trial of the MEK inhibitor trametinib in JMML and other refractory pediatric leukemias, and to interrogate molecular mechanisms of response and resistance. This trial will be executed in collaboration with the National Cancer Institute’s Cancer Therapy Evaluation Program (CTEP) and the Developmental Therapeutics Consortium (DVL) of the Children’s Oncology Group (COG).

Aim 2. To use genetically accurate mouse models of MPN and acute myeloid leukemia (AML) characterized by Nf1 inactivation to investigate the efficacy and mechanisms of action of “second generation” therapies, and to functionally validate candidate mechanisms of drug resistance.

The translational impact of these studies involves rigorously testing a novel therapeutic strategy for an aggressive pediatric cancer with deep molecular analysis of primary leukemia cells to ascertain mechanisms of response and resistance.

PROJECT 4: Secondary Cancers among NF1 Cancer Survivors Outcome

Smita Bhatia, MD, Clinical Science Co-Leader (University of Alabama, Birmingham)
Jean L. Nakamura, MD, Basic Science Co-Leader (University of California, San Francisco)
Michael Fisher, MD, Co-Investigator (Children’s Hospital of Philadelphia)
Lennie Wong, PhD, Co-Investigator (City of Hope)

Subsequent malignant neoplasms (SMNs) are histologically distinct cancers that develop months to years after patients receive radiation and/or chemotherapy to cure a primary malignancy. SMNs are a fundamental problem in cancer survivors. Compelling data generated by Drs. Nakamura and Shannon in GEM mice demonstrated that irradiation cooperates strongly with heterozygous Nf1 inactivation in the development of a spectrum of SMNs that recapitulate common SMNs in human patients with and without NF1. Project 4 will translate these novel data and will systematically assess the incidence of SMNs in NF1 patients and examine associated risk factors such as age at diagnosis, anatomic site of the primary tumor, and dose and duration of prior treatment. Data compiled by the NCI-funded Childhood Cancer Survivor Study (CCSS) will play an integral role in Project 4. The aims of Project 4 are:

Aim 1. To describe the magnitude of risk of second malignant neoplasms (SMNs) in individuals with NF1.

Aim 2. To perform comparative oncogenomics to identify genetic alterations associated with radiation-induced tumorigenesis in individuals with NF1.

Aim 3. To validate in model systems the biologic importance of candidate pathways in radiation-induced tumorigenesis and to determine whether radiotherapy promotes transformation of plexiform neurofibromas to MPNSTs in vivo.

The translational impact of this work involves informing current clinical practice in the treatment of tumors arising in NF1 patients to reduce the risk of SMN and generating insights into the underlying biology of SMN that will lead to new therapies for these common, aggressive, and largely refractory cancers.

CORE 1: Administrative Core

D. Wade Clapp, MD, Co-Core Director (Indiana University School of Medicine)
Kevin Shannon, MD, Co-Core Director (University of California, San Francisco)
Lang Li, PhD, Co-Investigator and Bioinformatics Data Integration Leader (Indiana University School of Medicine

The Administrative Core coordinates research within the SPORE and oversight by the program’s advisory boards. SPORE components include the four translational research projects summarized above as well as a Developmental Research Program (DRP), a Career Development Program (CDP), and specialized core resources (Biospecimen/Pathology Core and Omics Core). Members of the External and Internal Advisory Boards are listed in the Figure.

CORE 2: Omics Core

Gary L Johnson, PhD, Core Director (University of North Carolina)
David Eberhard, MD, PhD, Co-Investigator (University of North Carolina)
Shawn Gomez, Co-Investigator (University of North Carolina)
Piotr Mieczkowski, PhD, Co-Investigator (University of North Carolina)
Joel Parker, PhD, Co-Investigator (University of North Carolina)

The Omics Core will advance the scientific goals of Projects 1-4 by providing proteomic and genomic platforms for performing RNAseq and whole exome sequencing analysis combined with comprehensive kinome activation measurements. This core will be led and coordinated by Dr. Gary Johnson (UNC). Dr. Johnson is Director of the Human Genome RNAi Screening Facility that provides automated genome-wide RNAi screens. This core has extensive next-generation sequencing and informatics experience with the TCGA and will provide a comprehensive infrastructure for the four SPORE projects by providing state-of-the-art services for exome and transcriptome (RNA) sequencing. The Omics Core will also provide additional innovative chemical proteomic methods that allow assay en masse of the activation state of 75-80% of the expressed kinome in tumor cells. The Administrative Core, coordinated by the IU biostatistician and bioinformaticist Dr. Li, will have primary responsibility for performing biostatistical and bioinformatic analyses.

CORE 3: Biospecimen/Pathology Core

Tatiana M. Foroud, PhD, Co-Core Director, Biospecimen (Indiana University School of Medicine)
Andrew E. Horvai, MD, PhD, Co-Core Director, Pathology (University of California, San Francisco)
Scott Kogan, MD, Co-Core Director, Pathology (University of California, San Francisco)

The Biospecimen/Pathology Core brings together a team with expertise in pathology and sample banking. This Core will be co-led by Drs. Tatiana Foroud (IU), Scott Kogan (UCSF), and Andrew Horvai (UCSF).

A key function of the Biospecimen/Pathology Core will be to serve as the central site to track and store samples and pathological data from the human and mouse biospecimens collected as part of the four SPORE projects. This core will perform pathological review of all samples and will make these data available to SPORE investigators and the broader research community. The biospecimens will be banked in this core and then distributed to the Omics Core for deep molecular analysis. In addition, the Biospecimen/Pathology Core will maintain an electronic catalog which will link the specimens and tissue to the pathological reports as well as data generated in the projects for each study subject. The project investigators will use this electronic catalog to select the samples needed for analyses.

SPORE Leadership

D. Wade Clapp, MD, Multi-Principal Investigator, Indiana University School of Medicine

D. Wade Clapp, MD

Dr. Clapp is the Richard L. Schreiner Professor and Chairman, Department of Pediatrics and Professor of Microbiology at Indiana University, and a member in the Tumor Microenvironment and Metastasis Program in the NCI sponsored Cancer Center at IU (The Indiana University Simon Cancer Center). He was formerly the Director of the IU MSTP and the pediatric physician-scientist development program at IU.

A major effort in his laboratory is understanding the genetic, biochemical and cell-cell interactions that lead to the genesis and progression of plexiform neurofibromas that are often congenital in origin and become clinically apparent in babies and young children. Given the intractability of targeting Ras directly, the laboratory has focused on genetically disrupting components of the Ras pathway, both using mouse genetics and subsequently by pharmacologic inhibition. Molecular targets that have been identified in the lab as having a significant therapeutic effect are then moved forward into phase 1 and phase 2 clinical trials He has prior experience in leading large, multi-institutional grants (DOD, Children’s Tumor Foundation, P50, UO1). Dr. Clapp is also a PI in both neurofibromatosis focused preclinical and clinical consortiums that will facilitate collaborations with the translational research goals involved in this program.

Kevin M. Shannon, MD, Multi-Principal Investigator, University of California, San Francisco

Kevin M. Shannon, MD

Dr. Shannon is a pediatric hematologist/oncologist and the Auerback Distinguished Professor of Molecular Oncology in the UCSF Department of Pediatrics. He is an American Cancer Society Research Professor. Dr. Shannon has held numerous leadership positions at UCSF, including Interim Chair of Pediatrics and Director of the UCSF MSTP. He is currently Director of the UCSF Physician Scientist Scholar Program.

Dr. Shannon has conducted basic and translational research in normal and leukemic hematopoiesis for the past three decades. His laboratory was the first to show that NF1 functions as tumor suppressor gene in human cancer by negatively regulating Ras signaling, and subsequently identified somatic NRAS, KRAS, and PTPN11 mutations in JMML. The Shannon lab discovered germ line KRAS mutations as a cause of Noonan syndrome, another common Rasopathy. His group has engineered mouse models of early stage and advanced human hematologic cancers driven by Nf1 inactivation or by endogenous oncogenic Kras and Nras expression, which they have utilized to perform biologic and translational preclinical trials focusing on elucidating mechanisms of response and resistance to conventional and targeted anti-cancer agents. Like Dr. Clapp, Dr. Shannon leads a component of an ongoing neurofibromatosis focused preclinical consortium that will facilitate collaborations with the translational research goals involved in this program. Dr. Shannon oversees the DRP and CDP components of the DHART SPORE.