Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma

Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.

Neuroinflammatory Disease Responsive to MEK-Inhibitor

Objective

Illustrate that some neuroinflammatory diseases may respond best to antiproliferative therapies rather than immunomodulatory therapies.

Background

Genomics are increasingly employed in the diagnostic armamentarium of refractory neuro-inflammatory diseases. Metagenomic next-generation sequencing is used to detect pathogens and germline genetic testing is used to detect inborn errors of the immune system. Genetic testing of tissue can identify somatic mutations for targeted treatment. MEK-inhibitors are an emerging treatment for RAS/MAPK pathway mutated diseases which include some neuro-inflammatory mimics like neuro-histiocytoses.

Design/Methods

NA.

Results

Previously healthy 12-year-old girl presented with 1 month of diplopia and headaches. Her brother has clinically diagnosed NF1 (café-au-lait macules, cutaneous neurofibromas). Exam notable for right third nerve palsy. MRI showed T2/FLAIR hyperintense lesions of the right temporal lobe, basal ganglia, and cervical through thoracic cord, nodular leptomeningeal enhancement along the entire spinal cord, and right middle cerebral artery vessel wall enhancement. CSF: WBC 6/mm3(62% lymphocytes 37% monocytes), protein 133 mg/dL. She improved with pulse methylprednisolone and maintenance steroids. At 5 months, she developed malignant elevated intracranial pressure with CSF OP >50 cm water, bradycardia, and encephalopathy requiring weekly LPs. Brain biopsy showed astrocytic and microglial activation without significant inflammation. No histiocytes were noted. There was no evidence of neoplasia or infection. She was tried on anakinra. At 6 months, she developed left third nerve palsy and seizures. For weeks, she required daily LPs for intracranial hypertension despite placement of ventriculoperitoneal shunt. Additional treatments included infliximab, steroids, and siltuximab. NGS from brain biopsy identified 2 NF1 mutations (nonsense, splicing). Allele fractions: 6% and 9%. Her mental status and need for frequent LP improved dramatically with trametinib.

Conclusions

This case illustrates the importance of considering somatic genomic testing of neural tissue even when the neuropathology is not suggestive of a malignancy or histiocytosis as this can inform newer molecularly targeted therapeutic options.

Deep learning-based electrocardiogram analysis detecting paroxysmal atrial fibrillation during sinus rhythm in patients with cryptogenic stroke: validation study using implantable cardiac monitoring

Background

Atrial fibrillation (AF) is the most cause of cardioembolic source causing cryptogenic stroke. In these, anticoagulation therapy could reduce recurrence of stroke. However, paroxysmal AF would not be detected even by 24 hours Holter monitoring. Deep learning-based electrocardiogram (ECG) analysis models were recently developed to detect AF during sinus rhythm.

Purpose

We aimed to develop a deep learning algorithm (DLA) to detect AF during sinus rhythm and validate the model in patients with cryptogenic stroke who underwent implantable cardiac monitoring (ICM) to diagnose paroxysmal AF.

Methods

This cohort study involved three hospitals (A, B, and C). We developed a DLA to detect AF using sinus rhythm 10 s 12-lead ECG. We included adult patients aged ≥18 years from hospital A and B. We used development data from AF adult patients who had at least one atrial fibrillation rhythm in the study period (Jan 2016 to Dec 2021) and non-AF patients who had no reference to AF in the ECG and electronic medical record. DLA was based on convolutional neural network (CNN) using 10 s 12-lead. For external validation, the ECGs from 217 patients (hospital C) with cryptogenic stroke who underwent ICM were analyzed by using the DLA for validating the accuracy in the real-world clinical situations.

Results

We included 10,605 AF adult patients and 50,522 non-AF patients as development data. During the internal validation, the area under the curve (AUC) of the final DLA based on CNN was 0.793 (95% Confidence interval 0.778–0.807). In external validation data from cryptogenic stroke patients, the mean ICM duration was 15.1 months, and AF >5 mins was detected in 32 patients (14.5%). The diagnostic accuracy of DLA was 0.793 to detect AF during sinus rhythm, and AUC was 0.824. The sensitivity, specificity, positive predictive value, and negative predictive value of the model were 0.844, 0.784, 0.403, and 0.967, respectively, which outperformed other conventional predictive methods based on clinical factors, such as CHARGE-AF, C2hest, and HATCH.

Conclusions

In this study, DLA accurately detected paroxysmal AF using 12-leads normal sinus rhythm ECG in patients with cryptogenic stroke and outperformed the conventional models. The DLA could be used as a screening tool to identify the cause of stroke in the future.

Funding Acknowledgement

Type of funding sources: None.

AAV-vector based gene therapy for mitochondrial disease: progress and future perspectives

Mitochondrial diseases are a group of rare, heterogeneous diseases caused by gene mutations in both nuclear and mitochondrial genomes that result in defects in mitochondrial function. They are responsible for significant morbidity and mortality as they affect multiple organ systems and particularly those with high energy-utilizing tissues, such as the nervous system, skeletal muscle, and cardiac muscle. Virtually no effective treatments exist for these patients, despite the urgent need. As the majority of these conditions are monogenic and caused by mutations in nuclear genes, gene replacement is a highly attractive therapeutic strategy. Adeno-associated virus (AAV) is a well-characterized gene replacement vector, and its safety profile and ability to transduce quiescent cells nominates it as a potential gene therapy vehicle for several mitochondrial diseases. Indeed, AAV vector-based gene replacement is currently being explored in clinical trials for one mitochondrial disease (Leber hereditary optic neuropathy) and preclinical studies have been published investigating this strategy in other mitochondrial diseases. This review summarizes the preclinical findings of AAV vector-based gene replacement therapy for mitochondrial diseases including Leigh syndrome, Barth syndrome, ethylmalonic encephalopathy, and others.

Immune Checkpoint Inhibition as Single Therapy for Synchronous Cancers Exhibiting Hypermutation: An IRRDC Study

Two targets with one arrow: #Immunotherapy as single treatment for synchronous RRD #glioblastoma and #metastatic cancers.

Mechanisms of targeted therapy resistance in a pediatric glioma driven by ETV6-NTRK3 fusion

Chromosomal rearrangements of the NTRK genes generate kinase fusions that are targetable oncogenic drivers in diverse adult and pediatric malignancies. Despite robust clinical response to targeted NTRK inhibition, the emergence of therapeutic resistance poses a formidable clinical challenge. Here we report the characterization of an ETV6-NTRK3 fusion-driven pediatric glioma that progressed through NTRK-targeted treatments with entrectinib and selitrectinib. Genetic analysis of multifocal recurrent/resistant lesions identified a previously uncharacterized NTRK3 p.G623A and a known p.G623E resistance mutation, in addition to other alterations of potential pathogenic impact. Functional studies using heterologous reconstitution model systems and patient-derived tumor cell lines establish that NTRK3^G623A and NTRK3^G623E mutated kinases exhibit reduced sensitivity to entrectinib and selitrectinib, as well as other NTRK inhibitors tested herein. In summary, this genetic analysis of multifocal recurrent/resistant glioma driven by ETV6-NTRK3 fusion captured a cross section of resistance-associated alterations that, based on in vitro analysis, likely contributed to resistance to targeted therapy and disease progression.

Clinical Outcomes and Patient-Matched Molecular Composition of Relapsed Medulloblastoma

We sought to investigate clinical outcomes of relapsed medulloblastoma and to compare molecular features between patient-matched diagnostic and relapsed tumors.

IMMU-14. IMMUNE CHECKPOINT INHIBITOR THERAPY FOR TREATMENT OF SYNCHRONOUS CANCERS IN PAEDIATRIC PATIENTS WITH CONSTITUTIONAL MISMATCH REPAIR DEFICIENCY

Constitutional mismatch repair deficiency (CMMRD) is an autosomal recessive condition in which affected patients carry biallelic germline mutations in the MMR genes. This highly penetrant syndrome results in nearly universal development of malignant neoplasms at a young age, most commonly pediatric brain tumors. Importantly, in addition to brain tumors, patients frequently develop multiple metachronous or even synchronous tumors making it impossible to treat these cancers with current chemotherapeutic approaches due to the complexity of different chemoradiation regimens required, resulting in excess toxicity and lack of efficacy. We first, assessed the metachronous (defined here as serial tumors diagnosed >1 year apart or after completion of definitive treatment for the initial tumor) or synchronous cancers (defined here as tumors diagnosed within a year of each other or during the definitive treatment for the initial tumor) in all patients within the consortium. Strikingly, 47% developed synchronous and/or metachronous cancers leading to patient demise. Molecular analysis revealed that all synchronous tumors (n=26) harbored a hypermutational burden accompanied by high genomic microsatellite instability and the relevant signatures. We therefore treated two patients with glioblastomas who had synchronous solid tumors with checkpoint inhibitors. In both patients, objective tumor response was associated with clinical benefit and prolonged survival. Biomarker analysis revealed increased tumor mutational burden, microsatellite instability and immune cell infiltration. These cases highlight the role of universal, mechanism based and tumor-agnostic approach to treat patients with brain tumors with additional synchronous cancers in the setting of cancer predisposition.

Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma

Medulloblastoma is among the most common malignant brain tumors in children. Recent studies have identified at least four subgroups of the disease that differ in terms of molecular characteristics and patient outcomes. Despite this heterogeneity, most patients with medulloblastoma receive similar therapies, including surgery, radiation, and intensive chemotherapy. Although these treatments prolong survival, many patients still die from the disease and survivors suffer severe long-term side effects from therapy. We hypothesize that each patient with medulloblastoma is sensitive to different therapies and that tailoring therapy based on the molecular and cellular characteristics of patients' tumors will improve outcomes. To test this, we assembled a panel of orthotopic patient-derived xenografts (PDX) and subjected them to DNA sequencing, gene expression profiling, and high-throughput drug screening. Analysis of DNA sequencing revealed that most medulloblastomas do not have actionable mutations that point to effective therapies. In contrast, gene expression and drug response data provided valuable information about potential therapies for every tumor. For example, drug screening demonstrated that actinomycin D, which is used for treatment of sarcoma but rarely for medulloblastoma, was active against PDXs representing Group 3 medulloblastoma, the most aggressive form of the disease. Functional analysis of tumor cells was successfully used in a clinical setting to identify more treatment options than sequencing alone. These studies suggest that it should be possible to move away from a one-size-fits-all approach and begin to treat each patient with therapies that are effective against their specific tumor. SIGNIFICANCE: These findings show that high-throughput drug screening identifies therapies for medulloblastoma that cannot be predicted by genomic or transcriptomic analysis.

Abstract IA11: Overcoming immune evasion in pediatric brain tumors

Many immunotherapies act by enhancing T-cell killing of tumor cells. Cytotoxic T cells recognize antigens presented by class I major histocompatibility complex (MHC-I) proteins on tumor cells. Our studies suggest that medulloblastomas and high-grade gliomas lacking the p53 tumor suppressor do not express surface MHC-I and are therefore resistant to immune rejection. Mechanistically, this is because p53 regulates expression of the peptide transporter Tap1 and the aminopeptidase Erap1, which are required for MHC-I trafficking to the cell surface. Treatment with tumor necrosis factor or lymphotoxin beta receptor agonist rescues expression of Erap1, Tap1, and MHC-I on p53 mutant tumor cells. In vivo, TNF treatment prolongs survival and markedly augments the efficacy of the immune checkpoint inhibitor anti-PD-1. These studies identify p53 as a key regulator of immune evasion in vivo and suggest that TNF could be used to enhance sensitivity of p53-mutant tumors to immunotherapy.

Citation Format: Alexandra Garancher, Hiromichi Suzuki, Svasti Haricharan, Meher B. Masihi, Jessica M. Rusert, Paula S. Norris, Florent Carrette, Megan M. Romero, Sorana A. Morrissy, Patryk Skowron, Florence M.G. Cavalli, Hamza Farooq, Vijay Ramaswamy, Alaide Morcavallo, Jacob J. Henderson, James M. Olson, Yoon-Jae Cho, Xiao-Nan Li, Louis Chesler, Marco A. Marra, Oren J. Becher, Linda M. Bradley, Carl F. Ware, Michael D. Taylor, Robert J. Wechsler-Reya. Overcoming immune evasion in pediatric brain tumors [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr IA11.

Tumor necrosis factor overcomes immune evasion in p53-mutant medulloblastoma

Many immunotherapies act by enhancing the ability of cytotoxic T cells to kill tumor cells. Killing depends on T cell recognition of antigens presented by class I major histocompatibility complex (MHC-I) proteins on tumor cells. In this study, we showed that medulloblastomas lacking the p53 tumor suppressor do not express surface MHC-I and are therefore resistant to immune rejection. Mechanistically, this is because p53 regulates expression of the peptide transporter Tap1 and the aminopeptidase Erap1, which are required for MHC-I trafficking to the cell surface. In vitro, tumor necrosis factor (TNF) or lymphotoxin-β receptor agonist can rescue expression of Erap1, Tap1 and MHC-I on p53-mutant tumor cells. In vivo, low doses of TNF prolong survival and synergize with immune checkpoint inhibitors to promote tumor rejection. These studies identified p53 as a key regulator of immune evasion and suggest that TNF could be used to enhance sensitivity of tumors to immunotherapy.

Comparison of a 1064-nm neodymium-doped yttrium aluminum garnet picosecond laser using a diffractive optical element vs. a nonablative 1550-nm erbium-glass laser for the treatment of facial acne scarring in Asian patients: a 17-week prospective, randomized, split-face, controlled trial

BACKGROUND

Novel picosecond lasers using a diffractive optical element (P-DOE) have been available for skin resurfacing with distinct mechanisms. However, there are limited data directly comparing P-DOE and conventional fractional lasers for the treatment of atrophic acne scarring.

OBJECTIVES

We sought to compare the efficacy and safety of a 1064-nm neodymium-doped yttrium aluminium garnet P-DOE and a non-ablative fractional laser (NAFL) in the treatment of acne scarring.

METHODS

A prospective, randomized, split-face, controlled trial was performed. One randomly assigned half-side of each patient's face (n = 25) was treated with four consecutive sessions of P-DOE at 3-week intervals and the other side with NAFL, with subsequent follow-up for 8 weeks after the final sessions. The efficacy and safety of the two lasers were determined by the Echelle d'Evaluation Clinique des Cicatrices d'acné (Scale of Clinical Evaluation of Acne Scars; ECCA) grading scale, Investigator's Global Assessment (IGA) score and patients' reports at the final visit. Histologic analysis was also performed.

RESULTS

The P-DOE-treated side achieved a significantly better improvement in acne appearance (ECCA per cent reduction: 55% vs. 42%) with less severe pain (4.3 vs. 5.6) (P < 0.05). The IGA score and subjective satisfaction were consistent with ECCA score results. Occurrences of treatment-related side-effects were also lower in the group treated with P-DOE (P < 0.05). Histologic analysis revealed elongation and increased density of neocollagen fibres, elastic fibres and mucin throughout the dermis from both sides.

CONCLUSIONS

Compared with NAFL, P-DOE afforded better clinical outcomes and fewer side-effects in the treatment of acne scarring in Asian patients.

P3429A novel prediction model for mortality after cardiac surgery using institutional case volume

Purpose

A number of risk prediction models have been developed to identify short term mortality after cardiovascular surgery. Most models include patient characteristics, laboratory data, and type of surgery, but no consideration for the amount of surgical experience. With numerous reports on the impact of case volume on patient outcome after high risk procedures, we attempted to develop a risk prediction models for in-hospital and 1-year mortality that takes institutional case volume into account.

Methods

We identified adult patients who underwent cardiac surgery from January 2008 to December 2017 from the National Health Insurance Service (NHIS) database by searching for patients with procedure codes of coronary artery bypass grafting, valve surgery, and surgery on thoracic aorta during the hospitalization. Study subjects were randomly assigned to either the derivation cohort or the validation cohort. In-hospital mortality and 1-year mortality data were collected using the NHIS database. Risk prediction models were developed from the derivation cohort using Cox proportional hazards regression. The prediction performances of models were evaluated in the validation cohort.

Results

The models developed in this study demonstrated fair discrimination for derivation cohort (N=22,004, c-statistics, 0.75 for in-hospital mortality; 0.73 for 1-year mortality) and acceptable calibration in the validation cohort. (N=22,003, Hosmer-Lemeshow χ2-test, P=0.08 and 0.16, respectively). Case volume was the key factor of mortality prediction models after cardiac surgery. (50≤ x <100 case per year. 100≤ x <200 case per year, ≥200 case per year are correlated with OR 3.29, 2.49, 1.85 in in-hospital mortality, 2.76, 1.99, 1.69 in 1-year mortality respectively, P value <0.001.)

Annual case volume as risk factor Variables In-hospital mortality 1-year mortality OR (95% CI) p-value OR (95% CI) p-value Annual case-volume (reference: ≥200) – – 100–200 1.69 (1.48, 1.93) <0.001 1.85 (1.58, 2.18) <0.001 50–100 1.99 (1.75, 2.25) <0.001 2.49 (2.15, 2.89) <0.001 <50 2.76 (2.44, 3.11) <0.001 3.29 (2.85, 3.79) <0.001 OR: Odds ratio; CI: confidence interval; Ref: Reference.

Discrimination and calibration

Conclusion

We developed and validated new risk prediction models for in-hospital and 1-year mortality after cardiac surgery using the NHIS database. These models may provide useful guides to predict mortality risks of patients with basic information and without laboratory findings.

TNF superfamily cytokines overcome immune evasion in medulloblastoma

Many immunotherapies act by enhancing T cell killing of tumor cells. CD8+ cytotoxic T cells recognize antigens presented by class I major histocompatibility complex (MHC-I) proteins on tumor cells. Here we show that medulloblastomas lacking the p53 tumor suppressor do not express surface MHC-I and are therefore resistant to immune rejection. Mechanistically, this is because p53 regulates expression of the peptide transporter Tap1 and the aminopeptidase Erap1, which are required for MHC-I trafficking to the cell surface. Treatment with tumor necrosis factor (TNF) or lymphotoxin beta receptor agonist (LTβRag) rescues expression of Erap1, Tap1 and MHC-I on p53-mutant tumor cells. In vivo, TNF treatment prolongs survival and markedly augments the efficacy of the immune checkpoint inhibitor anti-PD-1. These studies identify p53 as a key regulator of immune evasion in vivo, and suggest that TNF could be used to enhance sensitivity of p53-mutant tumors to immunotherapy.

A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases

While the preponderance of morbidity and mortality in medulloblastoma patients are due to metastatic disease, most research focuses on the primary tumor due to a dearth of metastatic tissue samples and model systems. Medulloblastoma metastases are found almost exclusively on the leptomeningeal surface of the brain and spinal cord; dissemination is therefore thought to occur through shedding of primary tumor cells into the cerebrospinal fluid followed by distal re-implantation on the leptomeninges. We present evidence for medulloblastoma circulating tumor cells (CTCs) in therapy-naive patients and demonstrate in vivo, through flank xenografting and parabiosis, that medulloblastoma CTCs can spread through the blood to the leptomeningeal space to form leptomeningeal metastases. Medulloblastoma leptomeningeal metastases express high levels of the chemokine CCL2, and expression of CCL2 in medulloblastoma in vivo is sufficient to drive leptomeningeal dissemination. Hematogenous dissemination of medulloblastoma offers a new opportunity to diagnose and treat lethal disseminated medulloblastoma.

MR Imaging-Based Radiomic Signatures of Distinct Molecular Subgroups of Medulloblastoma

BACKGROUND AND PURPOSE

Distinct molecular subgroups of pediatric medulloblastoma confer important differences in prognosis and therapy. Currently, tissue sampling is the only method to obtain information for classification. Our goal was to develop and validate radiomic and machine learning approaches for predicting molecular subgroups of pediatric medulloblastoma.

MATERIALS AND METHODS

In this multi-institutional retrospective study, we evaluated MR imaging datasets of 109 pediatric patients with medulloblastoma from 3 children's hospitals from January 2001 to January 2014. A computational framework was developed to extract MR imaging-based radiomic features from tumor segmentations, and we tested 2 predictive models: a double 10-fold cross-validation using a combined dataset consisting of all 3 patient cohorts and a 3-dataset cross-validation, in which training was performed on 2 cohorts and testing was performed on the third independent cohort. We used the Wilcoxon rank sum test for feature selection with assessment of area under the receiver operating characteristic curve to evaluate model performance.

RESULTS

Of 590 MR imaging-derived radiomic features, including intensity-based histograms, tumor edge-sharpness, Gabor features, and local area integral invariant features, extracted from imaging-derived tumor segmentations, tumor edge-sharpness was most useful for predicting sonic hedgehog and group 4 tumors. Receiver operating characteristic analysis revealed superior performance of the double 10-fold cross-validation model for predicting sonic hedgehog, group 3, and group 4 tumors when using combined T1- and T2-weighted images (area under the curve = 0.79, 0.70, and 0.83, respectively). With the independent 3-dataset cross-validation strategy, select radiomic features were predictive of sonic hedgehog (area under the curve = 0.70-0.73) and group 4 (area under the curve = 0.76-0.80) medulloblastoma.

CONCLUSIONS

This study provides proof-of-concept results for the application of radiomic and machine learning approaches to a multi-institutional dataset for the prediction of medulloblastoma subgroups.

Publisher Correction: Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma

The original version of this Article omitted Suzana A. Kahn, Siddhartha S. Mitra & Samuel H. Cheshier as jointly supervising authors. This has now been corrected in both the PDF and HTML versions of the Article.

Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma

Medulloblastoma is the most common malignant brain tumor of childhood. Group 3 medulloblastoma, the most aggressive molecular subtype, frequently disseminates through the leptomeningeal cerebral spinal fluid (CSF) spaces in the brain and spinal cord. The mechanism of dissemination through the CSF remains poorly understood, and the molecular pathways involved in medulloblastoma metastasis and self-renewal are largely unknown. Here we show that NOTCH1 signaling pathway regulates both the initiation of metastasis and the self-renewal of medulloblastoma. We identify a mechanism in which NOTCH1 activates BMI1 through the activation of TWIST1. NOTCH1 expression and activity are directly related to medulloblastoma metastasis and decreased survival rate of tumor-bearing mice. Finally, medulloblastoma-bearing mice intrathecally treated with anti-NRR1, a NOTCH1 blocking antibody, present lower frequency of spinal metastasis and higher survival rate. These findings identify NOTCH1 as a pivotal driver of Group 3 medulloblastoma metastasis and self-renewal, supporting the development of therapies targeting this pathway.

Functional status of immune cells in patients with long-lasting type 2 diabetes mellitus

Although patients with diabetes contract infectious diseases at higher frequencies, and in more severe forms, compared to non-diabetics, the underlying defects of the immune function have not been defined clearly. To address this, we designed an immune monitoring protocol and analysed the functional status of various immune cells. Peripheral blood mononuclear cells (PBMCs) were stimulated with the proper ligands and the functional reactivity of each lineage of cells was subsequently measured. Patients with type 2 diabetes mellitus (T2DM) had PBMC composition ratios comparable to healthy controls, except for a higher frequency of B cell and effector T cell fractions. The capacity of myeloid cells to secrete proinflammatory cytokines was not diminished in terms of the sensitivity and magnitude of the response. Furthermore, cytolytic activity and interferon (IFN)-γ production of natural killer (NK) cells and CD8⁺ T cells were not decreased in T2DM patients. Phenotypical maturation of dendritic cells, indicated by the up-regulation of major histocompatibility complex (MHC) proteins and co-stimulatory molecules in response to lipopolysaccharide (LPS), was slightly enhanced in T2DM patients. Finally, the functional differentiation profiles of CD4⁺ T cells did not differ between T2DM patients and the control group. These data indicate that patients with long-lasting T2DM do not have any gross functional defects in immune cells, at least in circulating monocytes, dendritic cells, NK cells and T lymphocytes.

Developmental phosphoproteomics identifies the kinase CK2 as a driver of Hedgehog signaling and a therapeutic target in medulloblastoma

A major limitation of targeted cancer therapy is the rapid emergence of drug resistance, which often arises through mutations at or downstream of the drug target or through intrinsic resistance of subpopulations of tumor cells. Medulloblastoma (MB), the most common pediatric brain tumor, is no exception, and MBs that are driven by sonic hedgehog (SHH) signaling are particularly aggressive and drug-resistant. To find new drug targets and therapeutics for MB that may be less susceptible to common resistance mechanisms, we used a developmental phosphoproteomics approach in murine granule neuron precursors (GNPs), the developmental cell of origin of MB. The protein kinase CK2 emerged as a driver of hundreds of phosphorylation events during the proliferative, MB-like stage of GNP growth, including the phosphorylation of three of the eight proteins commonly amplified in MB. CK2 was critical to the stabilization and activity of the transcription factor GLI2, a late downstream effector in SHH signaling. CK2 inhibitors decreased the viability of primary SHH-type MB patient cells in culture and blocked the growth of murine MB tumors that were resistant to currently available Hh inhibitors, thereby extending the survival of tumor-bearing mice. Because of structural interactions, one CK2 inhibitor (CX-4945) inhibited both wild-type and mutant CK2, indicating that this drug may avoid at least one common mode of acquired resistance. These findings suggest that CK2 inhibitors may be effective for treating patients with MB and show how phosphoproteomics may be used to gain insight into developmental biology and pathology.

Abstract LB-322: Casein kinase 2 is a major regulator of medulloblastoma growth

Medulloblastoma (MB) is the most common malignant pediatric brain tumor, accounting for about 20% of all cases. While surgery, craniospinal irradiation, and chemotherapy have resulted in a cure rate of 70%, the surviving patients are afflicted with neurocognitive impairment, endocrine dysfunction, and a severe decrease in quality of life. Consequently, better and more effective treatments are needed to treat these young patients. Casein kinase 2 (CK2) is an intriguing therapeutic target for MB because it is dysregulated in all the MB molecular subgroups and patients with high CK2 expression have a significantly worse prognosis. To elucidate the role of CK2 in MB we transduced multiple MB cell lines with CK2 isoforms. We discovered that a CK2 isoform, CK2a, increased tumorigenesis in both the Sonic Hedgehog and Group 3 MB subgroups, while knocking down expression ameliorated MB growth. Through these transduced cell lines we also determined that CK2 can regulate MB tumorigenesis through b-catenin and potentially GLI1. Moreover, mice orthotopically injected with MB cells over-expressing CK2a or CK2b displayed a reduced survival compared to control. We extended our analysis to a CK2 inhibitor, CX-4945, which is currently undergoing phase I/II clinical trials for toxicity and safety. Treatment with CX-4945 reduced MB cell growth and also reduced expression of MGMT, a well-known regulator of temozolomide (TMZ) efficacy. Our findings were corroborated when we screened 4,000 FDA approved compounds to identify molecules that work synergistically with CX-4945. TMZ was one of the major compounds that were identified in the screen, suggesting that CX-4945 treatment can sensitize MB cells to TMZ by dysregulating MGMT. Combinatorial treatment with CX-4945 and TMZ had a synergistic effect on reducing MB tumor growth. Together, our findings suggest that CK2 is a novel therapeutic target for MB and that combining CX-4945 and TMZ can lead to a promising new MB therapy.

Citation Format: Ryan Nitta, Sara Matilda Bolin, Ginikachi Nwagbo, Teresa Purzner, Suzana Kahn, Yoon-Jae Cho, Gordon Li. Casein kinase 2 is a major regulator of medulloblastoma growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-322.

Dielectric function, critical points, and Rydberg exciton series of WSe2 monolayer

The complex dielectric function ([Formula: see text]) of WSe₂ monolayer grown by atomic layer deposition is investigated using spectroscopic ellipsometry. Band structure parameters are obtained by standard line-shape analysis of the second-energy-derivative of [Formula: see text] spectra. The fundamental band gap is observed at 2.26 eV, corresponds to transition between valence band (VB) maximum at the K point and conduction band (CB) minimum at Q point in the Brillouin zone (BZ). Two strong so-called A and B excitonic peaks in [Formula: see text] spectra originate from vertical transitions from spin-orbit split (0.43 eV) VB to CB at K point of the BZ. Binding energies of A and B exactions are 0.71 and 0.28 eV, respectively. Well resolved five excited excitons states has been detected within the spectral region between A and B. Energy profile of the Rydberg series shows significant deviation from the hydrogenic behavior, discussed in connection with the 2D hydrogen model. Results presented here will improve our understanding about the optical response of 2D materials and will help to design better optoelectronic applications and validate theoretical considerations.

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress

DDX3X encodes a DEAD-box family RNA helicase (DDX3) commonly mutated in medulloblastoma, a highly aggressive cerebellar tumor affecting both children and adults. Despite being implicated in several facets of RNA metabolism, the nature and scope of DDX3′s interactions with RNA remain unclear. Here, we show DDX3 collaborates extensively with the translation initiation machinery through direct binding to 5′UTRs of nearly all coding RNAs, specific sites on the 18S rRNA, and multiple components of the translation initiation complex. Impairment of translation initiation is also evident in primary medulloblastomas harboring mutations in DDX3X, further highlighting DDX3′s role in this process. Arsenite-induced stress shifts DDX3 binding from the 5′UTR into the coding region of mRNAs concomitant with a general reduction of translation, and both the shift of DDX3 on mRNA and decreased translation are blunted by expression of a catalytically-impaired, medulloblastoma-associated DDX3^R534H variant. Furthermore, despite the global repression of translation induced by arsenite, translation is preserved on select genes involved in chromatin organization in DDX3^R534H-expressing cells. Thus, DDX3 interacts extensively with RNA and ribosomal machinery to help remodel the translation landscape in response to stress, while cancer-related DDX3 variants adapt this response to selectively preserve translation.

Disrupting the CD47-SIRPα anti-phagocytic axis by a humanized anti-CD47 antibody is an efficacious treatment for malignant pediatric brain tumors

Morbidity and mortality associated with pediatric malignant primary brain tumors remain high in the absence of effective therapies. Macrophage-mediated phagocytosis of tumor cells via blockade of the anti-phagocytic CD47-SIRPα interaction using anti-CD47 antibodies has shown promise in preclinical xenografts of various human malignancies. We demonstrate the effect of a humanized anti-CD47 antibody, Hu5F9-G4, on five aggressive and etiologically distinct pediatric brain tumors: group 3 medulloblastoma (primary and metastatic), atypical teratoid rhabdoid tumor, primitive neuroectodermal tumor, pediatric glioblastoma, and diffuse intrinsic pontine glioma. Hu5F9-G4 demonstrated therapeutic efficacy in vitro and in vivo in patient-derived orthotopic xenograft models. Intraventricular administration of Hu5F9-G4 further enhanced its activity against disseminated medulloblastoma leptomeningeal disease. Notably, Hu5F9-G4 showed minimal activity against normal human neural cells in vitro and in vivo, a phenomenon reiterated in an immunocompetent allograft glioma model. Thus, Hu5F9-G4 is a potentially safe and effective therapeutic agent for managing multiple pediatric central nervous system malignancies.

The whole-genome landscape of medulloblastoma subtypes

Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and ‘enhancer hijacking’ events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma.

Genomic analysis of 491 medulloblastoma samples, including methylation profiling of 1,256 cases, effectively assigns candidate drivers to most tumours across all molecular subgroups.

Medulloblastomas are highly malignant brain tumours that develop during childhood. Paul Northcott and colleagues analysed the whole-genome sequences of 491 medulloblastomas in order to characterize the genomic landscape across tumours and identify new drivers and mutational signatures. Their integrative genomic analyses, including methylation profiling of 1,256 medulloblastomas, identifies subgroup-specific driver mutations and suggests additional tumour subtypes. The authors assign driver mutations to a high proportion of the less well characterized Group 3 and Group 4, which together contribute to more than 60% of all medulloblastomas.

Functional validation of the oncogenic cooperativity and targeting potential of tuberous sclerosis mutation in medulloblastoma using a MYC-amplified model cell line

Medulloblastoma is the most common malignant brain tumor of childhood. To identify targetable vulnerabilities, we employed inhibitor screening that revealed mTOR inhibitor hypersensitivity in the MYC-overexpressing medulloblastoma cell line, D341. Concomitant exome sequencing unveiled an uncharacterized missense mutation, TSC2^A415V , in these cells. We biochemically demonstrate that the TSC2^A415V mutation is functionally deleterious, leading to shortened half-life and proteasome-mediated protein degradation. These data suggest that MYC cooperates with activated kinase pathways, enabling pharmacologic intervention in these treatment refractory tumors. We propose that identification of activated kinase pathways may allow for tailoring targeted therapy to improve survival and treatment-related morbidity in medulloblastoma.

Pediatric high-grade glioma: biologically and clinically in need of new thinking

High-grade gliomas in children are different from those that arise in adults. Recent collaborative molecular analyses of these rare cancers have revealed previously unappreciated connections among chromatin regulation, developmental signaling, and tumorigenesis. As we begin to unravel the unique developmental origins and distinct biological drivers of this heterogeneous group of tumors, clinical trials need to keep pace. It is important to avoid therapeutic strategies developed purely using data obtained from studies on adult glioblastoma. This approach has resulted in repetitive trials and ineffective treatments being applied to these children, with limited improvement in clinical outcome. The authors of this perspective, comprising biology and clinical expertise in the disease, recently convened to discuss the most effective ways to translate the emerging molecular insights into patient benefit. This article reviews our current understanding of pediatric high-grade glioma and suggests approaches for innovative clinical management.

Performance of the Minto model for the target-controlled infusion of remifentanil during cardiopulmonary bypass

We studied the predictive performance of the Minto pharmacokinetic model during cardiopulmonary bypass in patients undergoing cardiac surgery. Patients received remifentanil target-controlled infusion using the Minto model during total intravenous anaesthesia with propofol. From 56 patients, 275 arterial blood samples were drawn before, during and after bypass to determine the plasma concentration of remifentanil, and the predicted concentrations were recorded at each time. For pooled data, the median prediction error and median absolute prediction error were 21.3% and 21.8%, respectively, and 22.1% and 22.3% during bypass. Both were 148.4% during hypothermic circulatory arrest and measured concentrations were more than three times greater than predicted (26.9 (17.0) vs. 7.1 (1.6) ng.ml^-1 ). The Minto model showed considerable bias but overall acceptable precision during bypass. The target concentration of remifentanil should be reduced when using the Minto model during hypothermic circulatory arrest.

A First-in-Class TWIST1 Inhibitor with Activity in Oncogene-Driven Lung Cancer

TWIST1, an epithelial-mesenchymal transition (EMT) transcription factor, is critical for oncogene-driven non-small cell lung cancer (NSCLC) tumorigenesis. Given the potential of TWIST1 as a therapeutic target, a chemical-bioinformatic approach using connectivity mapping (CMAP) analysis was used to identify TWIST1 inhibitors. Characterization of the top ranked candidates from the unbiased screen revealed that harmine, a harmala alkaloid, inhibited multiple TWIST1 functions, including single-cell dissemination, suppression of normal branching in 3D epithelial culture, and proliferation of oncogene driver-defined NSCLC cells. Harmine treatment phenocopied genetic loss of TWIST1 by inducing oncogene-induced senescence or apoptosis. Mechanistic investigation revealed that harmine targeted the TWIST1 pathway through its promotion of TWIST1 protein degradation. As dimerization is critical for TWIST1 function and stability, the effect of harmine on specific TWIST1 dimers was examined. TWIST1 and its dimer partners, the E2A proteins, which were found to be required for TWIST1-mediated functions, regulated the stability of the other heterodimeric partner posttranslationally. Harmine preferentially promoted degradation of the TWIST1-E2A heterodimer compared with the TWIST-TWIST1 homodimer, and targeting the TWIST1-E2A heterodimer was required for harmine cytotoxicity. Finally, harmine had activity in both transgenic and patient-derived xenograft mouse models of KRAS-mutant NSCLC. These studies identified harmine as a first-in-class TWIST1 inhibitor with marked anti-tumor activity in oncogene-driven NSCLC including EGFR mutant, KRAS mutant and MET altered NSCLC.Implications: TWIST1 is required for oncogene-driven NSCLC tumorigenesis and EMT; thus, harmine and its analogues/derivatives represent a novel therapeutic strategy to treat oncogene-driven NSCLC as well as other solid tumor malignancies. Mol Cancer Res; 15(12); 1764-76. ©2017 AACR.

Pediatric oncology enters an era of precision medicine

With the use of high-throughput molecular profiling technologies, precision medicine trials are ongoing for adults with cancer. Similarly, there is an interest in how these techniques can be applied to tumors in children and adolescents to expand our understanding of the biology of pediatric cancers and evaluate the clinical implications of genomic testing for these patients. This article reviews the early studies in pediatric oncology showing the feasibility of this approach, describe the future plans to evaluate the clinical implications in a multicenter clinical trial and identify the challenges of applying genomics in this patient population.

FBW7 suppression leads to SOX9 stabilization and increased malignancy in medulloblastoma

SOX9 is a master transcription factor that regulates development and stem cell programs. However, its potential oncogenic activity and regulatory mechanisms that control SOX9 protein stability are poorly understood. Here, we show that SOX9 is a substrate of FBW7, a tumor suppressor, and a SCF (SKP1/CUL1/F‐box)‐type ubiquitin ligase. FBW7 recognizes a conserved degron surrounding threonine 236 (T236) in SOX9 that is phosphorylated by GSK3 kinase and consequently degraded by SCF^FBW7α. Failure to degrade SOX9 promotes migration, metastasis, and treatment resistance in medulloblastoma, one of the most common childhood brain tumors. FBW7 is either mutated or downregulated in medulloblastoma, and in cases where FBW7 mRNA levels are low, SOX9 protein is significantly elevated and this phenotype is associated with metastasis at diagnosis and poor patient outcome. Transcriptional profiling of medulloblastoma cells expressing a degradation‐resistant SOX9 mutant reveals activation of pro‐metastatic genes and genes linked to cisplatin resistance. Finally, we show that pharmacological inhibition of PI3K/AKT/mTOR pathway activity destabilizes SOX9 in a GSK3/FBW7‐dependent manner, rendering medulloblastoma cells sensitive to cytostatic treatment.

Abstract B37: Chemi-genomic analysis of patient-derived xenografts to identify personalized therapies for medulloblastoma

Medulloblastoma (MB) is the most common malignant brain tumor in children. Even with an intensive regimen of surgery, radiation and chemotherapy, one-third of patients still die from their disease. Moreover, survivors suffer devastating side effects including cognitive deficits, endocrine disorders and an increased incidence of secondary cancers later in life. Thus, more effective and less toxic therapies are desperately needed. Recent genomic analyses have identified 4 major subgroups of MB—WNT, SHH, Group 3 and Group 4—that differ in terms of mutations, gene expression profiles and patient outcomes. Despite this heterogeneity, all MB patients currently receive the same therapy. To identify novel therapies for each subgroup of MB, we have assembled a diverse panel of patient-derived xenograft (PDX) lines. These lines, established by orthotopic transplantation of tumor cells obtained from surgery, recapitulate the properties of patients' tumors more accurately than cultured cell lines. We are using these PDX lines to screen small molecule libraries and identify compounds that can inhibit tumor growth and survival. To date we have completed screening of 18 lines, including 10 representing Group 3 MB, the most aggressive and lethal form of the disease. Among the ~7800 compounds tested, we have found 20 that are effective against the majority of Group 3 PDX lines. Ongoing studies are focused on validating the activity of these compounds against additional Group 3 lines and moving the most promising ones forward into in vivo efficacy studies. Similar approaches will be pursued for each of the other subgroups of MB. Drug response data will also be compared with genomic and epigenomic data (whole exome and low coverage whole genome DNA sequencing, DNA methylation analysis, and gene expression profiling) to identify biomarkers of drug responsiveness and key pathways that may be exploited for therapy. Based on these studies, we hope to move away from a one-size-fits-all approach, and begin to treat each patient with therapies that are likely to be effective against their tumor.

Citation Format: Jessica M. Rusert, Alexandra Garancher, Yoko T. Udaka, Sebastian Brabetz, Lourdes A. Esparza, Huriye Seker-Cin, Lin Qi, Mari Kogiso, Simone Schubert, Till Milde, Yoon-Jae Cho, Xiao-Nan Li, James M. Olson, John R. Crawford, Michael L. Levy, Marcel Kool, Stefan M. Pfister, Robert J. Wechsler-Reya. Chemi-genomic analysis of patient-derived xenografts to identify personalized therapies for medulloblastoma. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B37.

Abstract 2475: Bmi1 is a therapeutic target in recurrent medulloblastoma

We describe the epigenetic regulator Bmi1 as a novel therapeutic target for the treatment of recurrent human Group 3 medulloblastoma, a childhood brain tumor for which there is virtually no treatment option beyond palliation. Through comparative profiling of primary and recurrent medulloblastoma, we show that Bmi1 defines a treatment-refractory cell population that is uniquely targetable by a novel class of small molecule inhibitors. When administered to mice xenografted with patient tumors, we observed significant reduction in tumor burden and increased mouse survival, without neurotoxicity. As Group 3 medulloblastoma is often metastatic and uniformly fatal at recurrence, with no current or planned trials of targeted therapy, an efficacious targeted agent would be rapidly transitioned to clinical trials.

Current clinical trials for recurrent medulloblastoma patients who no longer respond to risk-adapted therapy are based on genomic profiles of primary, treatment-naïve tumors. These approaches will provide limited clinical benefit for patients since recurrent metastatic Group 3 medulloblastomas are highly genetically divergent from their primary tumor. Our experimental approach defines a tractable target, the epigenetic regulator Bmi1, which characterizes not only recurrent medulloblastoma, but many other metastatic and treatment-resistant cancers. As future clinical oncology trials will most likely begin with relapsed patients, therapeutic targets from comparative analyses in primary and matched-recurrent tumors offer the greatest clinical yield and may be readily translated to the patient bedside.

Citation Format: Sheila K. Singh, Neha Garg, Branavan Manornajan, David Bakhshinyan, Chitra Venugopal, Robin Hallett, Kevin Xin Wang, Vijay Ramaswamy, Yoon-Jae Cho, Siddhartha Mitra, David Kaplan, Thomas Davis, Michael Taylor. Bmi1 is a therapeutic target in recurrent medulloblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2475.

Abstract 2473: Combined BET-bromodomain and CDK2 inhibition in MYC-driven medulloblastoma

Misexpression of MYC genes (MYC and MYCN) occurs commonly in medulloblastoma (MB), the most frequent malignant childhood brain tumor. We previously showed that tumors are addicted to MYCN and that MYCN stabilization is required for MB development in mice (Swartling et al, Genes & Dev, 2010; Cancer Cell, 2012). Targeted MYCN suppression completely depleted MYCN-driven MB cells in vivo. Immediate transcriptional changes from such MYCN blockade were found by RNA-Seq and showed similarities to changes that occurred after CDK2 suppression or when inhibiting BET bromodomains. CDK2 and BET inhibitors both inhibited MYC protein expression and effectively induced cell cycle arrest or apoptosis. Compared with either agent alone a sustained combination treatment over 7-10 days displayed synergy and effectively abolished tumor cell proliferation in vitro. The combined treatment further reduced tumor growth in orthotopical MB transplants and significantly prolonged survival as compared to single agent therapy. Our data suggest that dual inhibition of CDK2 and BET Bromodomains could be a novel treatment approach in suppressing medulloblastoma by targeting MYC proteins.

Citation Format: Sara Bolin, Anna Borgenvik, Camilla Persson, Gabriela Rosén, Anders Sundström, Jun Qi, James E. Bradner, William A. Weiss, Yoon-Jae Cho, Holger Weishaupt, Fredrik J. Swartling. Combined BET-bromodomain and CDK2 inhibition in MYC-driven medulloblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2473.

Proteomic profiling of high risk medulloblastoma reveals functional biology

Genomic characterization of medulloblastoma has improved molecular risk classification but struggles to define functional biological processes, particularly for the most aggressive subgroups. We present here a novel proteomic approach to this problem using a reference library of stable isotope labeled medulloblastoma-specific proteins as a spike-in standard for accurate quantification of the tumor proteome. Utilizing high-resolution mass spectrometry, we quantified the tumor proteome of group 3 medulloblastoma cells and demonstrate that high-risk MYC amplified tumors can be segregated based on protein expression patterns. We cross-validated the differentially expressed protein candidates using an independent transcriptomic data set and further confirmed them in a separate cohort of medulloblastoma tissue samples to identify the most robust proteogenomic differences. Interestingly, highly expressed proteins associated with MYC-amplified tumors were significantly related to glycolytic metabolic pathways via alternative splicing of pyruvate kinase (PKM) by heterogeneous ribonucleoproteins (HNRNPs). Furthermore, when maintained under hypoxic conditions, these MYC-amplified tumors demonstrated increased viability compared to non-amplified tumors within the same subgroup. Taken together, these findings highlight the power of proteomics as an integrative platform to help prioritize genetic and molecular drivers of cancer biology and behavior.

Medulloblastoma Genotype Dictates Blood Brain Barrier Phenotype

The childhood brain tumor, medulloblastoma, includes four subtypes with very different prognoses. Here, we show that paracrine signals driven by mutant β-catenin in WNT-medulloblastoma, an essentially curable form of the disease, induce an aberrant fenestrated vasculature that permits the accumulation of high levels of intra-tumoral chemotherapy and a robust therapeutic response. In contrast, SHH-medulloblastoma, a less curable disease subtype, contains an intact blood brain barrier, rendering this tumor impermeable and resistant to chemotherapy. The medulloblastoma-endothelial cell paracrine axis can be manipulated in vivo, altering chemotherapy permeability and clinical response. Thus, medulloblastoma genotype dictates tumor vessel phenotype, explaining in part the disparate prognoses among medulloblastoma subtypes and suggesting an approach to enhance the chemoresponsiveness of other brain tumors.