Sohn Conference: Accelerating Translation of Pediatric Cancer Research

Although there were exciting strides in reducing death and disease from pediatric cancer between the early 1970s and early 2000s, progress has largely stagnated in the last 15 years. “We have a system that is not working fast enough,” said Richard Gilbertson, of Cancer Research UK Cambridge Institute. Gilbertson delivered the keynote address to open the 2.5-day conference held by the Sohn Conference Foundation and the New York Academy of Sciences in London from February 26 to February 28, 2018.

In some ways, it is becoming even more difficult to improve care for childhood cancer patients. “We do not have enough drugs and we do not have enough knowledge,” Gilbertson continued. In the last 20 years, only three drugs have been developed specifically for pediatric cancer. Moreover, he added, because molecular studies are dividing cancer types into smaller and smaller subtypes, we do not have enough patients for randomized controlled clinical trials.

The treatments that do exist for pediatric cancers are mired in challenges. Gilbertson pointed out that approximately 95% of children being treated for cancer will develop long-term health problems as a result, and about a third of these side effects will be severe, leading to premature death. Another underappreciated issue, he said, is that “we are creating a world of inequality” in caring for pediatric cancer patients. In Africa, Asia, and Latin America, there are both more cases of childhood cancer and children are more likely to die from their cancer.

Gilbertson challenged conference attendees to be disruptive on multiple levels — in how they screen for and manage disease and in how they collaborate. Early detection of cancer is “probably the biggest area of excitement in adult oncology at the moment,” he noted. Five-year survival rates are much higher for adult patients diagnosed when their cancer is in early stages as opposed to late stages. Gilbertson described technology being developed in Cambridge, UK, to allow earlier detection of adult cancers, such as a test that detects biomarkers of cancer in a person’s breath. A noninvasive “breathalyzer” type of test could be administered as part of routine checkups in the pediatric population.

The pediatric oncology community is remarkably galvanized and has enormous potential to collaborate, perhaps because pediatric cancers are so rare, Gilbertson said. He urged scientists to work together and in particular, to include clinicians in their work. But more than that, researchers must look for collaborators beyond the people they know. “We should have in this room physicists, chemists, engineers, mathematicians, people who have never thought about children’s cancer,” Gilbertson said. “They are the people that we need to disrupt the approaches to make things better.”

Gilbertson discussed new research ventures calling upon diverse groups of experts to spur drug discovery and optimize treatment decisions. The Cancer Research UK Brain Tumour Centre of Excellence, which Gilbertson leads, launched in February 2018. It includes oncologists, surgeons, and statisticians, who meet monthly and work together to design drugs. Another example is the Cambridge Centre for Integrated Cancer Medicine, which brings together statisticians, physicists, engineers, and other experts to interpret various types of patient data to assess treatment response.

Progress in reducing death and disease from childhood cancers has stagnated in the last 15 years.

Li-Fraumeni Syndrome: The Molecular Basis of Cancer Predisposition, Early Detection and Prevention

Inherited cancer syndromes share certain aspects of their biology and clinical management with cancers that arise from somatic DNA mutations. Li-Fraumeni Syndrome (LFS), an autosomal dominant, inherited disorder associated with early onset of various cancer types, may shed light on other types of pediatric cancer, as David Malkin, from the Hospital for Sick Children, discussed in his presentation. It is not possible to predict the age of cancer onset or response to therapy in patients with LFS-associated tumors, similar to other types of pediatric cancer. Nevertheless, work by Malkin’s group and others suggests there are correlations between the age of tumor onset along with survival outcomes and the type of mutation in the p53 tumor suppressor gene— the only gene so far identified in which pathogenic variants are definitively associated with LFS, with at least 70% of individuals diagnosed clinically with LFS harboring detectable germline p53 mutations.

Li-Fraumeni Syndrome is associated with very early onset of cancer and a wide variety of cancer types.

Malkin’s group found that surveilling individuals in families with LFS who carry germline p53 mutations, using a protocol they developed that involves blood, urine, and imaging tests, was associated with earlier tumor detection and improved survival. “It is the first attempt at using screening in a pediatric context for early tumor detection,” Malkin said. The group is now focusing on developing clinical tests to determine the most appropriate age to start surveillance. Early data suggest DNA methylation profiles of circulating tumor DNA can predict whether a young child will develop cancer by the age of six with a false negative rate of about 11%, which is within the error rate of existing clinical lab tests. As such, methylation profiles may allow clinicians to identify for whom surveillance should begin before the age of six, Malkin said.

Malkin’s group developed a clinical surveillance protocol for individuals from families with Li-Fraumeni Syndrome that is associated with improvements in long-term survival.

Highlights

• Neuroblastoma-derived cells are dependent on transcription factors, which form a core regulatory circuit, and may represent new druggable targets.
• The EWS-FLI1 fusion oncoprotein in Ewing sarcoma may cause epigenetic changes in genomic regulatory regions that contribute to the disease’s clinical heterogeneity.

New Vulnerabilities in Pediatric Cancer

Many of the molecular events that drive the development of pediatric cancers involve transcription factors, fusion oncoproteins, and epigenetic regulators, all of which are unfortunately difficult to target. To find new druggable targets, Kimberly Stegmaier, of the Dana-Farber Cancer Institute and Boston Children’s Hospital, and her collaborators carried out a genome-scale CRISPR-Cas9 loss-of-function screen in 80 pediatric cancer cell lines representing a range of cancer types. They made perturbations in genes across the genomes of these cells using the CRISPR-Cas9 system, which Stegmaier called a “disruptive” technology with the Broad Institute’s AVANA library that has about 70,000 CRISPR sequences. Genomic DNA of cell lines transduced with the Avana library and passaged for three weeks was analyzed for the enrichment or depletion of guide CRISPR sequences. CRISPR sequences that were depleted reflect gene dependency and the ones enriched represent candidate suppressor genes. Data from these maps will be made publicly available on a quarterly basis, Stegmaier said.

In neuroblastoma cell lines, there are strong dependencies on genes encoding transcription factors, such as HAND2 and ISL1, compared with cell lines derived from other cancer types. Further experiments revealed that the set of transcription factors form a core regulatory circuit, in which circuit members regulate each other’s expression. Stegmaier and her collaborators found that a bromodomain inhibitor, in combination with a cyclin-dependent kinase CDK7 inhibitor, turns off the core regulatory circuit in cell culture and has antitumor activity in a mouse model of MYCN amplified neuroblastoma.

“Now we are quite interested in taking the dependency map data, Stegmaier said, “and looking at other diseases and asking: do all pediatric cancers have core regulatory circuits?”

CRISPR-Cas9 screening of neuroblastoma-derived cell lines revealed dependencies on a set of transcription factors that form a core regulatory circuit and that may represent new drug targets.

Ewing Sarcoma: An Enhancer Disease with Widespread Epigenetic Heterogeneity

Like many types of pediatric cancer, Ewing sarcoma (ES) has a quiet genome other than the EWS-FLI1 fusion oncogene, which is a diagnostic marker for the cancer. However, ES is phenotypically heterogeneous in terms of the primary site of presentation, age of diagnosis, and response to treatment. In her presentation, Eleni Tomazou, of the Children’s Cancer Research Institute (CCRI) in Austria, discussed data suggesting that epigenetic deregulation contributes to this heterogeneity and that DNA methylation in particular could be a tool for studying the clinical variability.

Ewing sarcoma is characterized by a quiet genome, marked by the EWS-FLI1 fusion protein, but has a wide range of clinical presentations.

Tomazou’s research team mapped the epigenome, including histone acetylation, DNA methylation, and RNA expression levels, in an ES cell line with an inducible small hairpin RNA (shRNA) that silenced EWS-FLI1 expression. They found that H3K27 acetylation was the epigenetic mark most strongly affected by knockdown of EWS-FLI1, with H3K27 levels either correlated or anticorrelated with EWS-FLI1 expression, and acetylation tended to occur in enhancer elements. The team compiled a list of thousands of these EWS-FLI1-regulated enhancers that are specific to ES cell lines and also present in patient samples. The team is considering whether all enhancers are equal or if there are drivers among them that are important for tumorigenesis.

To understand clinical variability in ES, Tomazou’s group carried out genome-wide DNA methylation profiling, based on bisulfite sequencing, for 140 ES patients. There was a high degree of between-patient heterogeneity in the level of DNA methylation, particularly in two types of regulatory regions, which, as Tomazou explained, suggests a two-dimensional epigenetic disease spectrum. In one dimension, DNA methylation in ES-specific enhancers was associated with degree of epigenome reprogramming by EWS-FLI. In the other dimension, DNA methylation in EWS-FLI anti-correlated enhancers reflects the differentiation state of the tumor cell of origin, where the more stem cell-like signature is associated with a more metastatic clinical presentation. “My big question now is how we can exploit this novel concept toward precision medicine,” Tomazou said.

DNA methylation profiles in two Ewing sarcoma-relevant regulatory regions reflect the extent of epigenome reprogramming and cell of origin of the tumor.

Highlight

• Cell surface proteins that are differentially expressed on cancer cells could represent new immunotherapy targets for pediatric cancers.

Pediatric Cancer Immunotherapy: Not a Trickle Down from Medical Oncology

Although there has been a surge in new immunotherapy drugs for adult cancers, there are only two such therapies approved by the U.S. Food and Drug Administration (FDA) for pediatric cancer. One of them is tisagenlecleucel, approved in 2017 for children with B-cell precursor acute lymphoblastic leukemia (ALL). It is a “game changer,” curing previously incurable patients, said John Maris, from the Children’s Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania. However, he noted that the other FDA-approved immunotherapy, dinutuximab, for children with high-risk neuroblastoma, represents only an incremental improvement.

To identify new targets for immune-based therapies, Maris’ group looked for genes highly expressed in neuroblastoma but not normal tissue, and selected those that were computationally predicted to encode cell surface proteins.  Of the nine candidate genes, the group chose to study GPC2, which codes for a protein belonging to a family of six glypican signaling co-receptors. They found that MYCN drives expression of GPC2, and neuroblastoma cell lines are dependent on GPC2 such that silencing GPC2 leads to apoptosis. Maris’ group developed a GPC2-directed antibody-drug conjugate (ADC) that binds cell surface GPC2 and gets internalized, where the drug, DNA-damaging pyrrolobenzodiazepine (PBD) dimers, causes cell death. The molecule shrank tumors in patient-derived xenograft (PDX) mouse models of neuroblastoma.

To find new immunotherapy targets for pediatric cancers, Maris and his research team looked for genes differentially expressed in cancer cell lines that were computationally predicted to be on the cell surface.

“There are a fair number of pediatric cancers that have high GPC2 expression,” Maris said. Those cancers include retinoblastoma, medulloblastoma, and small-cell lung cancer “That is why we have been able to partner with a company who is now making this in GLP (good laboratory practice) conditions for us,” he continued, “and we hope to have this in the clinic in the next couple of years.”

Maris’s group found that the ADC they developed shrank tumors in mouse patient-derived xenograft (PDX) models of neuroblastoma (NBL).

Maris also described an unpublished project spearheaded by a graduate student in his lab to develop T-cell receptor-type therapies against neuroblastoma. The student found peptides differentially present in neuroblastoma cells, and for a subset of them, developed MHC-based dextramers to detect antigen-specific T-cells. He is currently attempting to engineer these T-cells and test their antitumor activity in mice.

Highlight

• Small molecules that inhibit binding partners of fusion oncoproteins have antitumor activity but may have to be used in combination to avoid resistance.

Targeting Chromatin Complexes in Pediatric Cancer

Scott Armstrong, of the Dana-Farber Cancer Institute, returned to the role fusion proteins play in the development of pediatric cancer with a focus on developing targeted therapies. He discussed the encouraging results, and caveats, of a Phase I clinical trial of a DOT1L inhibitor against acute myeloid leukemia (AML). The human MLL gene is associated with the development of a subset of aggressive pediatric acute leukemias with limited treatment options. MLL encodes a transcriptional regulator that is oncogenic when fused to one of 70-80 proteins. Dr. Armstrong’s group and others have shown that the histone methyltransferase DOT1L is required for the development and maintenance of MLL-rearranged leukemia in model systems. MLL fusion proteins bind and recruit DOT1L to MLL target genes, leading to aberrant gene expression and subsequent. In the clinical trial of DOT1L inhibitor, there was indication of biological activity in about 25% of the adult and pediatric patients with AML. However, it required treatment for at least two months. In addition, there is evidence of resistance to the DOT1L inhibitor, which appears to involve different mechanisms than resistance to kinase inhibitors.

Small molecules that inhibit binding partners of the MLL fusion oncoprotein in acute myeloid leukemia may have to be used in combination with other therapies to reduce the risk of drug resistance.

Armstrong’s group is collaborating with Syndax (and previously with Vitae Pharmaceuticals) to develop potential combination therapies. They found that a small molecule, VTP-50469, that blocks the interaction between the MLL fusion protein and a protein called Menin is a potent inhibitor of proliferation in leukemia cell lines. VTP-50469 leads to loss of Menin chromatin binding and loss of expression of transcription factors, including HOX and MEIS1, which are critical for MLL fusion-driven leukemia. In a PDX mouse model of leukemia, VTP-50469 is associated with eradication of cancer in the bone marrow.

In another study, Armstrong’s lab is also using a CRISPR-Cas9 screening approach to target various domain-level dependency rather than entire gene dependency of cancer cells, to home in on areas to target with small molecules. They found that synovial sarcoma cell lines are dependent on the bromodomain of BRD9, which is part of the BAF chromatin remodeling complex that is hijacked by synovial sarcoma fusion protein SS18-SSX. The group also found that a BRD9 degrader molecule, comprised of a BRD9 inhibitor linked to an E3 ligase that directs the protein to degradation complexes, inhibits proliferation of synovial sarcoma cell lines. Degrading targets rather than just binding them is “a new approach to drug development that is quite exciting,” Armstrong said.

Highlights

• Controlling translation messenger RNA (mRNA) may allow cancer cells to adjust to new environments during metastasis.
• Medulloblastoma can be divided into 12 subtypes based on molecular profiling, which could help researchers study these tumors.
• There is little survival benefit associated with gross total resection of primary medullobastoma tumors compared with subtotal resection.
• Clinicians can ask pharmaceutical companies for compassionate use to give therapies to children with non-responsive tumors.
• Adult clinical trial studies should include individuals at 12 years of age because adolescents have adult physiology.

Stress-mediated Translational Control of Sarcoma Metastasis

Cancer cells face numerous challenges in order to metastasize, including adjusting to new environments. Epigenetic changes, such as histone and DNA methylation, are probably too protracted to allow cancer cells to rapidly adapt to meet these challenges, as Poul Sorensen, of the British Columbia Cancer Research Centre and the University of British Columbia, posited in his presentation. Instead, translation of messenger RNA (mRNA) occurs very quickly, and selective translation of a subset of mRNAs “seems to be a pretty interesting way for cells to respond to stress,” Sorensen said.

Sorensen’s group demonstrated that stress granules, which are cellular bodies where mRNAs can be rerouted under stressful conditions and preserved for later translation, are essential for Ewing sarcoma (ES) cell metastasis. Short interfering RNA against G3BP1, a protein required for stress granule formation, causes tumors to lose their local invasive capacity in a renal capsule mouse model of ES. More recently, the group identified MS-275, a class I histone deacetylase (HDAC) inhibitor, from a drug screen for inhibitors of stress granule formation in an ES cell line. MS-275 acetylates the RNA-binding protein YB-1, blocking its ability to activate translation of G3BP1, and, similar to G3BP1 knockdown, inhibits metastasis in the renal capsule ES mouse model.

Sorensen also presented unpublished data suggesting that stress granule formation is important for ES cells because it increases their plasticity and adaptability. Sarcomas tend to be hypoxic and under a high degree of oxidative stress. HIF1α and NRF2, which control cellular responses to hypoxia and oxidative stress respectively, appear to be translational targets of YB-1. Binding of HIF 1-alpha and NRF2 mRNAs to YB-1 could prevent them from being shunted to stress granules, allowing “tumor cells to survive and go on and induce metastatic capacity,” Sorensen said.

Preventing formation of stress granules, which could help tumor cells respond to stress, by silencing G3BP1 reduces metastasis in a mouse model of Ewing sarcoma.

Heterogeneity through Space and Time Drive the Clinical Behavior of Childhood Brain Cancers

To better understand the tumor biology of medulloblastoma, Michael D. Taylor, of The Hospital for Sick Children, led research to characterize tumor subgroups. Based on gene expression and DNA methylation profiling of 700-800 medulloblastomas from around the world, he proposed a “dirty dozen” model involving 12 subtypes within four recognized subgroups (WNT, sonic hedgehog, groups 3 and 4): two WNT subtypes, four SHH (sonic hedgehog) subtypes, and three subtypes in both groups 3 and 4. This model is of “great benefit to those of us doing mouse modeling [and] looking for cells of origin,” Taylor said. But it is not very informative clinically, other than to single out the SHHb and group 3g subtypes, which are associated with poorer outcomes, he added.

Michael D. Taylor’s research suggests there are 12 subtypes of medulloblastoma based on gene expression and DNA methylation data.

Taylor presented other sets of data with direct clinical implications. Firstly, based on deep exome sequencing of multiple biopsy samples across a single tumor, medulloblastoma tumors are not clonal but rather are heterogeneous. “Whenever we are doing guided therapies, we need to be doing probably three or four biopsies per patient to make sure [mutations] are ubiquitous throughout the tumor,” Taylor explained. In addition, an analysis of a very large data set indicated there is little survival advantage to performing gross total resection of primary medullobastoma tumors, as compared with near-total or subtotal resection. As such, neurosurgeons should avoid gross total resection if it puts the patient at risk of cranial nerve deficits, Taylor said.

Finally, he discussed evidence from patient samples and mouse studies suggesting that medulloblastoma tumors do not metastasize via the cerebrospinal fluid, as Taylor and colleagues had assumed, but through the blood. In one set of experiments, they surgically attached two sister mice to each other such that they shared blood vessels, and implanted a brain tumor in one mouse. They found the partner mouse developed leptomeningeal metastatic disease, indicating that the tumor metastasize through the blood from one mouse to the other. Further, they found that the chemokine CCL2 and its receptor CCR2 appear to be drivers of metastasis.

vers of metastasis.

Medulloblastoma may metastasize through the blood rather than the cerebrospinal fluid. In experiments in parabiotic mice, a brain tumor in one mouse spreads via blood vessels to the leptomeninges of the surgically attached mouse.

Patient-driven Discovery in Pediatric Oncology

Despite important advances in using genome sequencing to diagnose cancer and identify molecular drivers, fewer than 10% of patients that harbor a potentially actionable alteration actually receive a drug matched to that alteration. In his presentation, Andrew Kung, from Memorial Sloan Kettering Cancer Center (MSKCC), explained the approach of the Pediatrics Translational Medicine Program (PTMP), which he and his colleagues established at his institute to try to address some of these deficiencies.

The Pediatrics Translational Medicine Program (PTMP) at the Memorial Sloan Kettering Cancer Center is comprised of disease groups dedicated to specific cancer types along with a translational platform that treats all patients with molecularly informed therapies.

PTMP uses cutting-edge diagnostic techniques to identify potentially targetable mutations in patients, such as the IMPACT test developed at MSKCC, which is based on next-generation sequencing of important cancer genes, and the Archer test, which characterizes gene fusions. Moreover, the program is pushing to expand the portfolio of molecularly informed therapies for patients. “We very aggressively started opening early phase clinical trials of agents available to the pediatric population,” said Kung, and now there are more agents against commonly occurring alterations. In addition, to increase the options available to pediatric cancer patients, the center now only conducts Phase I adult clinical trials if they include individuals starting at age 12, because 12-year-olds are adult-sized and have adult physiology. When data exist in teenagers, it becomes easier to ask drug companies for compassionate use of the drug in even younger patients, Kung said.

Kung presented two cases of difficult-to-treat pediatric cancers in which the PTMP accelerated experimental drug access for the patients, skipping laboratory-based studies of their cancers that often take several years. In both examples, the clinical team identified gene fusions for which inhibitors were available. They were able to get permission from the drug companies to give these drugs as compassionate use, and in both cases, they achieved dramatic tumor response. At the same time, PTMP has a pipeline to develop cell lines, patient-derived xenograft (PDX) animal models, and do whole-genome sequencing of patients’ cancers to further characterize their cancers' mechanisms, as well as understand treatment response, resistance and plan follow-up care.

The MSKCC Pediatrics Translational Medicine Program aims to fast track experimental drugs to children with difficult-to-treat cancers. They also develop post clinical models, such patient-derived xenograft mouse models, to understand treatment resistance.

Highlights

• Juvenile myelomonocytic leukemia (JMML), a rare blood cancer with early age of onset, is the result of hyperactive Ras-MAPK signaling, although mutations in other genes affect aggressiveness of the cancer.
• Last year, Loh and collaborators started a Phase II trial of a MEK inhibitor in children with JMML, a trial that took six years to develop.
• DNA hypermethylation is associated with lower rates of 4-year survival.
• Loh hopes to work with international colleagues to carry out molecular analyses of JMML to improve treatment.

Juvenile myelomonocytic leukemia (JMML) is a rare form of blood cancer that has clinical and biological similarities with chronic myeloid leukemia (CML) and chronic myelomonocytic leukemia (CMML), but its median age of onset is 1.7 years and it predominantly affects boys. Survival rates following conventional chemotherapy are dismal, and even after hematopoietic stem cell (HSC) transplantation, relapse can occur. In her keynote address, Mignon Lee-Cheun Loh, of Benioff Children’s Hospital and the Helen Diller Family Cancer Center, discussed decades of research showing that JMML is caused by hyperactive Ras-MAPK signaling, and the strategy to therapeutically target the RAS pathway. Because it is difficult to target Ras directly, Loh and colleagues decided instead to pursue inhibitors of MEK, a downstream effector of Ras signaling.

In September 2017, Loh and her collaborators opened a Phase II clinical trial to test trametinib, a MEK inhibitor, in 24 children (ages 2 to 21 years) with relapsed or refractory JMML following chemotherapy and other treatments. Loh said that she was confident in giving trametinib to children based on data from cell, mouse, and preclinical studies, including an adult Phase II trial of patients with Ras-mutated CMML, acute myeloid leukemia (AML), or myelodysplastic neoplasms (MDS), in which the drug achieved 20% objective response rate. However, Loh pointed out that it took six years to develop their clinical trial, underscoring the need “to push industry and our government into doing this faster because there is no reason why this should have taken so long.”

Genetic alterations that result in hyperactive Ras signaling are thought to drive juvenile myelomonocytic leukemia.

While Ras-MAPK signaling is important in JMML, mutations in genes outside the Ras signaling networks can also contribute to the aggressiveness of the disease. Loh and her collaborators carried out a research that involved exome, RNA sequence, methylation, and targeted capture array (TCA) analysis of patient samples and identified mutations in ten other genes with roles in signaling, epigenetic regulation, and other cellular processes. A mutation in one of these genes in combination with an alteration in the Ras pathway is associated with poorer outcomes. Loh presented data from her colleague, Ben Braun, at the University of California, San Francisco, showing that mice null for both Nf1, a gene important in the Ras pathway, and SH2B3, which encodes the LNK protein involved in Jak signaling, have a higher white count, reduced survival, and higher percentage of hematopoietic stem cells compared to Lnk^-/^- or Nf1^Δ/ ^Δ, supporting the hypothesis that these combinatory lesions are going to make the hematopoiesis even more disordered for these patients.

Loh and her collaborators are currently testing induced pluripotent stem cells (iPSCs) derived from JMML patient samples with various drug inhibitors. They have also established isogenic iPSC lines and will use them to study the genetic dependencies of combinations of mutations, such as in PTNP11, which encodes the Ras pathway protein SHP-2, and SETBP1, a gene they found in their research that is implicated in adult myeloid malignancies.

JMML can sometimes spontaneously resolve, but this is difficult to predict. In the last section of her presentation, Loh discussed efforts to identify factors to predict whether leukemia in JMML patients will resolve spontaneously. JMML in patients with alterations in CBL, a protein implicated in Ras pathway activation, generally resolves, whereas patients with an Nf1 mutation need HSC transplantation, and for patients with PTNP11 mutations, it depends. “It can be very confusing for clinicians,” Loh said. She and her collaborators performed methylation studies on their UCSF patient cohort and a German cohort and found that certain DNA hypermethylation patterns predict a much more aggressive disease with worse four-year survival. In fact, multivariate analysis of patient characteristics suggests that the two factors associated with poor outcome are hypermethylation status and high number of somatic mutations.

Patterns of low DNA methylation are associated with spontaneous resolution and higher four-year survival rates.

The hope, Loh said, is to work with colleagues in Germany, England, and Japan to carry out genotype and methylation analysis, as well as HLA typing, in an international trial to learn more about how to risk stratify patients and select the most appropriate treatment.

Highlights

• Innovative Therapies for Children with Cancer (ITCC) creates complete molecular profiles of children with relapsed cancer and offers at least one appropriate clinical trial in which they can participate.
• Regulatory agencies are shifting to require pharmaceutical companies to study a drug in children if it targets a mechanism involved in pediatric cancer.
• Incentives such as 6-month patent extension are probably not enough to motivate industry to study cancer drugs in children.
• Progress is being made in improving children’s access to cancer drugs, but we still have a long way to go.

Innovative Designs and Strategy to Accelerate Translation of Pediatric Cancer Research into New Effective Therapies

It is estimated that only 10%–15% of children in Europe with relapsed cancer have access to innovative oncologic drugs. To improve this situation, we must apply what we know about the biological determinants of pediatric malignancies to identify adult drugs that could be relevant. We must also develop new drugs for pediatric-specific targets, said Gilles Vassal, from the Gustave Roussy Institute, and give children better access to clinical trials. Toward these goals, the Innovative Therapies for Children with Cancer (ITCC) organization, of which Vassal is president, created the Precision Cancer Medicine Program. The strategy is to generate a complete molecular profile of children’s tumors at the time of relapse, and offer every child the opportunity to participate in a Phase I or II clinical trial of treatments that best match their molecular profiles. Vassal pointed out studies around Europe using this strategy, including MAPPYACTS and INFORM, as well as ITHER and SM-PAED, which have yet to launch. The goal is to sequence at least 3,000 exomes of children with malignant solid tumors and leukemia at the time of relapse by 2019.

However, “what matters in precision medicine is not the molecular profile of the tumor, it is access to drugs for patients,” Vassal said. He shared examples of ITCC initiatives to expedite trials. The organization is collaborating on the AcSe eSMART trial, which launched in August 2016, to look at the effectiveness of at least ten new drugs developed for children with relapsed or refractory malignancies not targeted by existing drugs. Vassal stressed the importance of bringing various stakeholders together. In 2013, the ITCC, along with the European Society for Paediatric Oncology (SIOPE) and Cancer Drug Development Forum (CDDF), created the ACCELERATE platform. It brings together representatives from academia, industry, parent organizations, and government agencies to create initiatives to address major challenges in pediatric oncology.

Several European studies, including MAPPYACTS, use the Innovative Therapies for Children with Cancer (ITCC) strategy of connecting every child with relapsed cancer to a clinical trial.

Innovative Clinical Trials and New Drug Development: A Pharmaceutical Industry Perspective

It costs $1–$2 billion (USD) to release a new drug on the market and candidate drugs have high attrition rates. Developing a cancer drug for children is even more difficult because there are fewer pediatric patients to study. On top of that, pharmaceutical companies that want to study a drug that they are developing for adults in children, must get authority from regulatory agencies such as the US Food and Drug Administration (FDA) and European Medicines Agency (EMA) early in the development timeline when the likelihood of the drug succeeding is less clear.

Pharmaceutical companies developing cancer drugs for children face a number of challenges, including the need to discuss pediatric investigative plans with health authorities after early phase clinical studies of the drug in adults.

Raphaël Rousseau, of Gritstone Oncology, Inc., discussed these issues as well as possible solutions. As a result of the myriad challenges, companies typically do not develop drugs for children unless they are required to, such as when the adult indication has an equivalent disease in children, which is rare in oncology, Rousseau said.  Fortunately, regulatory agencies in the US and Europe are shifting to require companies to investigate drugs for pediatric populations with mechanism of action-based plans. Regulatory agencies offer incentives to companies developing cancer drugs for children, such as priority review vouchers in the US and 6-month patent extensions, but they “are usually not considered very interesting by companies,” said Rousseau.

There are a number of steps required to improve children’s access to cancer drugs. In the short-term, strides are being made, such as ensuring drugs with pediatric rationale are available for this population. We also need to improve the business valuation of repurposing adult drugs for children and increase funding for early clinical trials. In the long-term, the industry needs academic researchers to identify new pediatric-specific druggable targets. Rousseau ended his talk by mentioning CureSearch, a nonprofit designed to advance the search for cures for pediatric cancer; it can be a resource for academic researchers who want to find pediatric oncologists, such as himself, working in industry.

Highlights

• Circulating tumor cells and cell-free tumor DNA could help clinicians predict recurrence and treatment response in children with osteosarcoma.
• Structural changes such as amplifications and translocations could be detectable in cell-free tumor DNA samples from children with sarcomas.

Development of Liquid Biopsies/cfDNA in Osteosarcoma: An Unmet Need

No predictive markers exist to help clinicians identify the 35% of children with localized osteosarcoma that are likely to have disease recurrence after treatment. Lee Helman, of the Children’s Hospital of Los Angeles, discussed “rapidly evolving” technologies using circulating tumor cells (CTCs) and cell-free tumor DNA (ctDNA) present in patient blood, which studies suggest could become predictive markers in osteosarcoma. It is critical to find less invasive ways to predict recurrence and monitor treatment response in children because it is difficult to biopsy kids, Helman said.

The Children’s Oncology Group (COG) as well as Helman’s group have started to analyze ctDNA as a predictive marker of outcome in pediatric osteosarcoma patients. It is not clear yet whether CTCs or ctDNA could be more useful, as they both have advantages and disadvantages, Helman said. Reports have found increased level of CTCs in liquid biopsies from patients with osteosarcoma correlates with poorer progression-free survival and distant metastases. CTCs allow researchers to do in vitro experiments with live cells but may underestimate tumor genetic heterogeneity, whereas ctDNA may better reflect heterogeneity. Both CTCs and ctDNA have to be distinguished from normal cells such as blood cells or circulating DNA shed from normal cells, respectively. Helman described a recent study that found only about 10% of the total cell-free DNA (cfDNA) has to be tumor DNA in order to be analyzed by whole-exome sequencing.

Pediatric osteosarcoma and other sarcomas are marked by structural changes such as copy number variations and translocations, whereas adult sarcomas typically have single nucleotide variations.

Certain structural changes could be detectable in cell-free DNA assays, according to Lee Helman. In adult cancer patients, many studies have demonstrated that tumor-associated mutations in cfDNA predict recurrence and therapy resistance. However, pediatric cancers are marked by structural changes, such as copy number alterations in osteosarcoma, rather than single-nucleotide mutations. Nevertheless, there are changes in pediatric osteosarcoma, particularly 8q amplification and p53 translocations, which should be detectable in cfDNA, Helman said. Likewise, the EWS-FLI1 fusion could be detected in Ewing sarcoma patient samples, he added.

Highlights

• Cancer treatments can have numerous long-term complications, such as congestive heart failure following anthracycline chemotherapy.
• Additional factors such as genetic predisposition and lifestyle exposures mediate the risk of long-term complications among childhood cancer survivors.
• Bhatia and colleagues are conducting an ongoing clinical study to determine whether carvedilol, a beta-blocker, can reduce the risk of anthracycline-related heart disease.

Increased mortality risk among childhood cancer survivors continues 25 years after diagnosis. Various cancer treatments carry numerous health risks, such as congestive heart failure following anthracycline chemotherapy and secondary cancers due to alkylating agents and radiation. However genetic predisposition, lifestyle exposures, and other factors mediate these risks, and should be considered in identifying individuals most likely to develop complications, said Smita Bhatia, of the University of Alabama at Birmingham. Bhatia has been leading a Children’s Oncology Group study since 2004 following childhood cancer survivors to understand why some of them have adverse events.

Bhatia focused her talk on the increased risk of congestive heart failure among patients who received anthracycline, particularly those who got high doses of the chemotherapy (greater than 250 mg per meter squared). Patients are at increased risk of anthracycline-related heart disease if they received chest radiation, are female, and less than 5 years old at the time of treatment. In order to define the genetic factors mediating risk, Bhatia and her colleagues used an array of single nucleotide polymorphisms (SNPs) in 2,100 genes linked to de novo cardiovascular disease. They found a polymorphism in the HAS3 gene, which was associated with 9-fold increased risk of cardiomyopathy among individuals who got high-dose anthracycline. The HAS3 gene product makes hyaluronan, a component of the extracellular matrix that could help heart muscle recover after anthracycline-induced damage.

A subset of childhood cancer survivors do not develop cardiomyopathy despite receiving high doses of anthracycline (red dots above the red line in the right-hand graph), whereas others develop heart disease even after getting low doses of the chemotherapy (green dots below the red line in left-hand graph), suggesting that genetic factors could play a role in modifying cardiomyopathy risk.

Bhatia and colleagues found additional gene variants associated with increased risk of cardiomyopathy after anthracycline treatment by taking a candidate gene approach, looking at genes involved in cellular anthracycline metabolism, and performing a genome-wide association study (GWAS). Along with colleagues, Bhatia developed a model based on clinical characteristics and 16 genes involved in anthracycline-related processes that together could predict development of congestive heart failure in 80% of cancer survivors.

Bhatia and colleagues are conducting a clinical trial to determine if the beta-blocker carvedilol can reduce heart failure risk among childhood cancer survivors who received high doses of anthracycline.

To mitigate the risk of heart failure, Bhatia and colleagues are using carvedilol, a beta-blocker that is well tolerated in children. They give the medication before patients have a decrease in ejection fraction (EF), a measure of the heart’s contractility. If EF is already decreased, “it is too late because they all go into heart failure,” Bhatia said. She and her colleagues are conducting a randomized, placebo-controlled trial to test whether carvedilol reduces heart failure risk, based on measures such as EF, in childhood cancer survivors who received high-dose anthracycline.

Highlights

• More pediatric oncologists need to work in pharmaceutical companies to help bridge the gap between academia and industry.
• The cost of cancer drugs could be lowered several ways, such as through academic-industry collaborations and reducing the regulatory burden associated with clinical trials.
• Parent and advocacy groups can help accelerate drug development through fundraising, forming working groups, and pushing authorities to make regulatory improvements.

The panel discussion brought together speakers from academia, industry, and parent groups to explore ways to accelerate drug development for pediatric cancer. Kathy Pritchard Jones, of the University College London, opened the discussion by noting how the pediatric drug development landscape used to be a desert, in which biological insights into childhood cancers, access to new drugs, and interest among pharmaceutical companies were all lacking. Now there is a wealth of data about disease mechanisms, but as Jones said, “how do we translate that information into knowledge…and ultimately therapies?”

Panel speaker Paul Workman, of the Institute of Cancer Research, London, stressed the importance of academic and industry groups, healthcare systems, and patient and other funding groups, working together to bring compounds to clinical trials. Academia plays a key role in drug discovery because there are no shareholders and venture capitalists in this setting. “We can take out much of the risk that way,” Workman said. However, he noted that early data can have reproducibility and robustness problems; academic labs need to be rigorous about validating targets, such as through CRISPR, RNAi, and addiction screens. During the question and answer period, John Maris, of the Children’s Hospital of Philadelphia, pointed out that the issue with data reproducibility occurs in both academia and industry.

Maris also commented that there are important differences between big pharmaceutical companies and start-up companies. Big pharmaceutical companies are generally interested in hearing from academic researchers about a target compound’s mechanism of action and mechanism of resistance. “We can think with them about combinatorial approaches and what they have in the pipeline,” Maris said. “Those collaborations have been very exciting.” On the other hand, a small biotech company with one drug in their portfolio may be more interested in model systems that academic labs develop to demonstrate proof of concept.

Louis Chesler, of the Institute of Cancer Research, posed a question to the panel about how academic labs can streamline the process of getting access to companies’ target compounds and mouse model systems to validate compounds. Panelist Raphaël Rousseau, of Gritstone Oncology, Inc., recommended academic labs establish a master agreement, where they have access to the company’s portfolio, and master collaboration. Beyond providing the drug, Rousseau said, industry insiders would also like to “provide you with additional expertise so that we jointly work on a project and we jointly publish.”

Facilitating those collaborations is one of many reasons why it is important to bring more pediatric oncologists into industry, Rousseau said. He also noted that numerous companies organize fellowships so pediatricians can spend one to two years learning about drug development. During the question and answer period, Mignon Lee-Cheun Loh, of the University of California, San Francisco, discussed the resources that her institution puts into training their faculty.

An audience member challenged the panel to consider ways to lower the cost of drugs. Panelist Stefan Burdach, of the Technical University of Munich, argued that it’s possible to reduce the cost of clinical trials by reducing unnecessary paperwork. “We all want safe drugs, but I want to posit that the equipoise between safety gain and regulatory volume has been lost,” Burdach said. He suggested that researchers talk with regulatory authorities about reducing drug development costs, and encouraged parent and advocacy groups to push politicians who fund regulatory authorities to ease the regulatory burden.

The fourth panelist, Patricia Blanc, of Imagine for Margo and Unite2Cure, represented the parent perspective. Blanc talked about creating Imagine for Margo, a French foundation, six years ago after her daughter Margaux died of an aggressive brain tumor for which there were no innovative treatments or even clinical trials. She proposed three areas where parents can help improve access to innovative drugs for children: fundraising so researchers can start trials earlier and enroll more children; cooperating with other shareholders to form working groups that tackle barriers to drug access; and advocating on a national and European level for regulatory improvements, which she does with Unite2Cure, a European network of parents and patients organizations.

• What contributes to clinical heterogeneity in pediatric cancer when the cancers are genetically homogeneous and harbor few mutations?

• How can scientists develop compounds that modify the activity of fusion oncoproteins, transcription factors, and other molecular drivers of pediatric cancers when these targets are difficult to drug pharmacologically?

• How do cancer cells rapidly adapt to new environments to metastasize when epigenetic changes occur on a protracted timeline?

• What are the best ways to connect pediatric cancer patients who have aggressive and difficult-to-treat diseases with innovative treatments and clinical trials?

• How can we increase the number of pediatric cancer patients who receive treatments that match their molecular alteration?

• How can regulatory authorities incentivize pharmaceutical companies to develop drugs for pediatric cancer?

• How can the various shareholders, academic and industry scientists, parents, advocates, and regulatory authorities work together to accelerate the development of drugs for pediatric cancer?

• What are feasible ways to lower the cost of drug development?

• What are the genetic factors and lifestyle exposures that mediate the risk of childhood cancer survivors developing serious long-term complications following treatment?