Phylogenomic reconstruction of Cryptosporidium spp. captured directly from clinical samples reveals extensive genetic diversity

Cryptosporidium is a leading cause of severe diarrhea and mortality in young children and infants in Africa and southern Asia. More than twenty Cryptosporidium species infect humans, of which C. parvum and C. hominis are the major agents causing moderate to severe diarrhea. Relatively few genetic markers are typically applied to genotype and/or diagnose Cryptosporidium. Most infections produce limited oocysts making it difficult to perform whole genome sequencing (WGS) directly from stool samples. Hence, there is an immediate need to apply WGS strategies to 1) develop high-resolution genetic markers to genotype these parasites more precisely, 2) to investigate endemic regions and detect the prevalence of different genotypes, and the role of mixed infections in generating genetic diversity, and 3) to investigate zoonotic transmission and evolution. To understand Cryptosporidium global population genetic structure, we applied Capture Enrichment Sequencing (CES-Seq) using 74,973 RNA-based 120 nucleotide baits that cover ~92% of the genome of C. parvum. CES-Seq is sensitive and successfully sequenced Cryptosporidium genomic DNA diluted up to 0.005% in human stool DNA. It also resolved mixed strain infections and captured new species of Cryptosporidium directly from clinical/field samples to promote genome-wide phylogenomic analyses and prospective GWAS studies.

Secondary cerebro-cerebellar and intracerebellar dysfunction in cerebellar mutism syndrome

BACKGROUND

Cerebellar mutism syndrome (CMS) is characterized by deficits of speech, movement, and affect that can occur following tumor removal from the posterior fossa. The role of cerebrocerebellar tract injuries in the etiology of CMS remains unclear, with recent studies suggesting that cerebrocerebellar dysfunction may be related to chronic, rather than transient, symptomatology.

METHODS

We measured functional connectivity between the cerebellar cortex and functional nodes throughout the brain using fMRI acquired after tumor removal but prior to adjuvant therapy in a cohort of 70 patients diagnosed with medulloblastoma. Surgical lesions were mapped to the infratentorial anatomy, and connectivity with cerebral cortex was tested for statistical dependence on extent of cerebellar outflow pathway injury.

RESULTS

CMS diagnosis was associated with an increase in connectivity between the right cerebellar and left cerebral hemisphere, maximally between cerebellum and ventromedial prefrontal cortex (VM-PFC). Connectivity dependence on cerebellar outflow was significant for some speech nodes but not for VM-PFC, suggesting altered input to the cerebellum. Connectivity between posterior regions of cerebellar cortex and ipsilateral dentate nuclei was abnormal in CMS participants, maximally within the right cerebellar hemisphere.

CONCLUSIONS

The functional abnormalities we identified are notably upstream of where causal surgical injury is thought to occur, indicating a secondary phenomenon. The VM-PFC is involved in several functions that may be relevant to the symptomatology of CMS, including emotional control and motor learning. We hypothesize that these abnormalities may reflect maladaptive learning within the cerebellum consequent to disordered motor and limbic function by the periaqueductal grey and other critical midbrain targets.

WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp

Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.

Population pharmacokinetics of methotrexate and 7-hydroxymethotrexate and delayed excretion in infants and young children with brain tumors

PURPOSE

The objectives of this study were to develop a population pharmacokinetic model of methotrexate (MTX) and its primary metabolite 7-hydroxymethotrexate (7OHMTX) in children with brain tumors, to identify the sources of pharmacokinetic variability, and to assess whether MTX and 7OHMTX systemic exposures were related to toxicity.

METHODS

Patients received 2.5 or 5 g/m2 MTX as a 24-hour infusion and serial samples were analyzed for MTX and 7OHMTX by an LC-MS/MS method. Pharmacokinetic parameters were estimated using nonlinear mixed-effects modeling. Demographics, laboratory values, and genetic polymorphisms were considered as potential covariates to explain the pharmacokinetic variability. Association between MTX and 7OHMTX systemic exposures and MTX-related toxicities were explored using random intercept logistic regression models.

RESULTS

The population pharmacokinetics of MTX and 7OHMTX were adequately characterized using two-compartment models in 142 patients (median 1.91 y; age range 0.09 to 4.94 y) in 513 courses. The MTX and 7OHMTX population clearance values were 4.6 and 3.0 l/h/m2, respectively. Baseline body surface area and estimated glomerular filtration rate were significant covariates on both MTX and 7OHMTX plasma disposition. Pharmacogenetic genotypes were associated with MTX pharmacokinetic parameters but had only modest influence. No significant association was observed between MTX or 7OHMTX exposure and MTX-related toxicity.

CONCLUSIONS

MTX and 7OHMTX plasma disposition were characterized for the first time in young children with brain tumors. No exposure-toxicity relationship was identified in this study, presumably due to aggressive clinical management which led to a low MTX-related toxicity rate.

Cerebellar mutism is linked to midbrain volatility and desynchronization from speech cortices

Cerebellar mutism syndrome is a disorder of speech, movement and affect that can occur after tumour removal from the posterior fossa. Projections from the fastigial nuclei to the periaqueductal grey area were recently implicated in its pathogenesis, but the functional consequences of damaging these projections remain poorly understood. Here, we examine functional MRI data from patients treated for medulloblastoma to identify functional changes in key brain areas that comprise the motor system for speech, which occur along the timeline of acute speech impairment in cerebellar mutism syndrome. One hundred and twenty-four participants, all with medulloblastoma, contributed to the study: 45 with cerebellar mutism syndrome, 11 patients with severe postoperative deficits other than mutism, and 68 without either (asymptomatic). We first performed a data-driven parcellation to spatially define functional nodes relevant to the cohort that align with brain regions critical for the motor control of speech. We then estimated functional connectivity between these nodes during the initial postoperative imaging sessions to identify functional deficits associated with the acute phase of the disorder. We further analysed how functional connectivity changed over time within a subset of participants that had suitable imaging acquired over the course of recovery. Signal dispersion was also measured in the periaqueductal grey area and red nuclei to estimate activity in midbrain regions considered key targets of the cerebellum with suspected involvement in cerebellar mutism pathogenesis. We found evidence of periaqueductal grey dysfunction in the acute phase of the disorder, with abnormal volatility and desynchronization with neocortical language nodes. Functional connectivity with periaqueductal grey was restored in imaging sessions that occurred after speech recovery and was further shown to be increased with left dorsolateral prefrontal cortex. The amygdalae were also broadly hyperconnected with neocortical nodes in the acute phase. Stable connectivity differences between groups were broadly present throughout the cerebrum, and one of the most substantial differences-between Broca's area and the supplementary motor area-was found to be inversely related to cerebellar outflow pathway damage in the mutism group. These results reveal systemic changes in the speech motor system of patients with mutism, centred on limbic areas tasked with the control of phonation. These findings provide further support for the hypothesis that periaqueductal grey dysfunction (following cerebellar surgical injury) contributes to the transient postoperative non-verbal episode commonly observed in cerebellar mutism syndrome but highlights a potential role of intact cerebellocortical projections in chronic features of the disorder.

Mapping pediatric brain tumors to their origins in the developing cerebellum

BACKGROUND

Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas.

METHODS

We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques.

RESULTS

We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study.

CONCLUSION

Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar "lineage of origin."

Outcomes of Infants and Young Children With Relapsed Medulloblastoma After Initial Craniospinal Irradiation-Sparing Approaches: An International Cohort Study

PURPOSE

Infant and young childhood medulloblastoma (iMB) is usually treated without craniospinal irradiation (CSI) to avoid neurocognitive late effects. Unfortunately, many children relapse. The purpose of this study was to assess salvage strategies and prognostic features of patients with iMB who relapse after CSI-sparing therapy.

METHODS

We assembled a large international cohort of 380 patients with relapsed iMB, age younger than 6 years, and initially treated without CSI. Univariable and multivariable Cox models of postrelapse survival (PRS) were conducted for those treated with curative intent using propensity score analyses to account for confounding factors.

RESULTS

The 3-year PRS, for 294 patients treated with curative intent, was 52.4% (95% CI, 46.4 to 58.3) with a median time to relapse from diagnosis of 11 months. Molecular subgrouping was available for 150 patients treated with curative intent, and 3-year PRS for sonic hedgehog (SHH), group 4, and group 3 were 60%, 84%, and 18% (P = .0187), respectively. In multivariable analysis, localized relapse (P = .0073), SHH molecular subgroup (P = .0103), CSI use after relapse (P = .0161), and age ≥ 36 months at initial diagnosis (P = .0494) were associated with improved survival. Most patients (73%) received salvage CSI, and although salvage chemotherapy was not significant in multivariable analysis, its use might be beneficial for a subset of children receiving salvage CSI < 35 Gy (P = .007).

CONCLUSION

A substantial proportion of patients with relapsed iMB are salvaged after initial CSI-sparing approaches. Patients with SHH subgroup, localized relapse, older age at initial diagnosis, and those receiving salvage CSI show improved PRS. Future prospective studies should investigate optimal CSI doses and the role of salvage chemotherapy in this population.

Fastigial nuclei surgical damage and focal midbrain disruption implicate PAG survival circuits in cerebellar mutism syndrome

BACKGROUND

Pediatric postoperative cerebellar mutism syndrome (CMS) is a rare but well-known complication of medulloblastoma (Mb) resection with devastating effects on expressive language, mobility, cognition, and emotional regulation that diminishes quality of life for many Mb survivors. The specific anatomical and neuronal basis of CMS remains obscure. We address this issue by identifying patterns of surgical damage and secondary axonal degeneration in Mb survivors with CMS.

METHODS

Children with Mb deemed high risk for CMS based on intraventricular location of the tumor had T1 images analyzed for location(s) of surgical damage using a specially developed algorithm. We used three complementary methods of spatial analysis to identify surgical damage linked to CMS diagnosis. Magnetization transfer ratio (MTR) images were analyzed for evidence of demyelination in anatomic regions downstream of the cerebellum, indicating neuronal dysfunction.

RESULTS

Spatial analyses highlighted damage to the fastigial nuclei and their associated cerebellar cortices as the strongest predictors of CMS. CMS-related MTR decrease was greatest in the ventral periaqueductal gray (PAG) area and highly consistent in the left red nucleus.

CONCLUSION

Our evidence points to disruption of output from the fastigial nuclei as a likely causal trigger for CMS. We propose that core CMS symptoms result from a disruption in the triggering of survival behaviors regulated by the PAG, including the gating of vocalization and volitional movement. The fastigial nuclei provide the densest output to the PAG from the cerebellum, thus sparing these structures may provide a greater likelihood of CMS prevention.

MEDB-49. Relapsed SHH medulloblastomas in young children. Are there alternatives to full-dose craniospinal irradiation?

BACKGROUND/RATIONAL: Following initial irradiation sparing therapy, many young children with relapsed medulloblastoma can be salvaged with craniospinal irradiation (CSI). However, the interval to relapse is short and neurocognitive sequelae remain a major concern. The contribution of molecular subgrouping may help refine indications and modalities of salvage strategies in this population. METHOD: From a cohort of 151 young children with molecularly characterized relapsed medulloblastoma, subset analysis of the SHH medulloblastoma was conducted to describe the practice of salvage radiotherapy and associated post-relapse survival (PRS). RESULTS: Sixty-seven SHH medulloblastoma patients (46 M0; 54 GTR; 11 non-ND/MBEN) received salvage therapy with curative intent. Before relapse, 54 (80.6%) received conventional chemotherapy (CC), 13 (19.4%) high-dose chemotherapy (HDC), while seven had additional focal radiotherapy (fRT). Median time to relapse was 11.1 months (range 3.8-41.0) and 43.3% were localized. Thirty patients (16 localized relapse) underwent surgery. Forty-seven (71.2%) received salvage radiotherapy (20 with CC; 10 with HDC; 15 alone, two unknown). CSI and fRT accounted for 82% and 18% respectively. CSI median dose was 36Gy (range 18-39Gy). Ten patients (eight with localized relapse) received CSI doses ≤23.4Gy. Nineteen patients (28.8%) did not receive any radiotherapy (nine HDC; 10 CC only). Radiotherapy was associated with better 3-year PRS (73.0% versus 36.1%; p=0.001). All patients treated with CSI ≤ 23.4Gy were alive at median follow-up of 69 months(24-142). Six of nine patients treated with HDC without irradiation were alive at last follow-up. Sixty-three percent of patients received reduced dose CSI(≤23.4Gy), fRT, or no radiotherapy, and their PRS did not significantly differ from those who received CSI ≥ 30.6Gy (p = 0.54). CONCLUSION: While salvage CSI provided PRS benefit in this SHH medulloblastoma cohort, we report the use of reduced salvage radiotherapy and irradiation avoidance in 63% of the patients, with 60% alive at last follow-up.

MEDB-74. Serial assessment of measurable residual disease in medulloblastoma liquid biopsies

Nearly one-third of children with medulloblastoma, a malignant embryonal tumor of the cerebellum, succumb to their disease. Conventional response monitoring by imaging and cerebrospinal fluid (CSF) cytology remains challenging and a marker for measurable residual disease (MRD) is lacking. Here, we show the clinical utility of CSF-derived cell-free DNA (cfDNA) as a biomarker of MRD in serial samples collected from children with medulloblastoma (123 patients, 476 samples) enrolled on a prospective trial. Using low-coverage whole-genome sequencing, tumor-associated copy-number variations (CNVs) in CSF-derived cfDNA are investigated as an MRD surrogate. MRD is detected at baseline in 85% and 54% of patients with metastatic and localized disease, respectively. The number of MRD-positive patients decline with therapy, yet those with persistent MRD have significantly higher risk of progression. Importantly, MRD detection precedes radiographic progression in half who relapse. Our findings advocate for the prospective assessment of CSF-derived liquid biopsies in future trials for medulloblastoma.

MEDB-29. Application of Rotterdam Post-Operative Cerebellar Mutism Syndrome Prediction Model to Patients Operated for Medulloblastoma in a Single Institution

BACKGROUND: Post-operative cerebellar mutism syndrome (CMS) develops in up to 30% of children. The Rotterdam model (RM) predicts a 66% risk of CMS in patients with a score ≥100. However, our findings suggested that surgical experience contributes to CMS risk. The aim of this study was to retrospectively apply the RM and report incidence of CMS in high-risk patients from our institution. METHODS: Participants had to have first tumor resection at our institution and be enrolled on SJMB12 protocol (NCT01878617). All participants got structured serial neurologic evaluations. CMS, when present, was categorized into type 1 (complete mutism) and type 2 (paucity of speech with an inability to string 3-word sentence). Rotterdam score is calculated based on pre-operative imaging parameters and study neurologist (RBK) obtained it while blinded to CMS status. RESULTS: Of the 40 (14 female, 26 male) study participants, 4 (10%) had CMS (3 CMS1, 1 CMS2). Median age at tumor resection was 11.7 years (range 3.5-17.8). Tumor location was midline in 30 (75%), right lateral 6 (15%) and left lateral 4 (10%). Median Evans index was 0.3 (0.2-0.4) and 34 (85%) were ≥0.3 (indicative of hydrocephalus); 5 participants needed ventricular shunt. Median tumor volume was 50 cm3 (2-180.6). Gross total resection was achieved in 35 (87.5%), near total in 4 (10%) and subtotal in 1. Twelve tumors were SHH, 7 WNT, and 29 NWNS. Median RM score was 90 (25 – 145). Eighteen participants had a score of ≥100 and 16.7% of these (n=3) had CMS. Scores for the 4 with CMS were 85, 125, 145 and 145. CONCLUSION: At our institution, the incidence of CMS in those that had RM of ≥100 was much lower than reported risk of 66%. This data supports our hypothesis that neurosurgical experience remains a significant risk factor in the development of CMS.

EPCT-01. Pediatric Brain Tumor Consortium (PBTC)-055: A phase I study of trametinib and hydroxychloroquine (HCQ) for BRAF-fusion or Neurofibromatosis type-1 (NF1)-associated pediatric gliomas

INTRODUCTION: Autophagy is a highly conserved process by which intracellular components are degraded and recycled promoting cell survival. Preclinically, autophagy has been implicated as a resistance mechanism in BRAF-mutant glioma cells treated with MAPK-pathway inhibitors. HCQ, an oral autophagy inhibitor, has been evaluated preclinically and clinically to overcome resistance. METHODS: PBTC-055 (NCT04201457) is a phase I/II trial of HCQ combined with trametinib (BRAF-fusion or NF1-associated gliomas) or trametinib and dabrafenib (BRAFV600E gliomas) in patients &lt; 30 years with progressive glioma. Prior treatment with RAF and/or MEK inhibitor with sub-optimal response (no response or response followed by progression on therapy) was required. Here, we present phase I data combining trametinib with HCQ utilizing a rolling-6 design. HCQ was administered at escalating dose levels (8, 15, or 20 mg/kg/day divided BID) in combination with standard pediatric trametinib dosing. All patients received prior MEK inhibitor therapy; 5/18 (28%) exhibited no response and 13/18 (72%) progressed on active therapy. RESULTS: Eighteen eligible/evaluable subjects were enrolled. Median age was 9.6 years (2.5-20.4 years); 10 were male. There were 2 dose-limiting toxicities (both grade 3 rash one each at DL1 and DL3). The highest dose level of HCQ (20 mg/kg/day divided BID) was declared the RP2D. Grade 3 adverse events possibly related to therapy included skin infection, rash, cardiac ejection fraction decrease, weight loss, and anorexia. There were no grade 4 or 5 attributable toxicities. Preliminarily, combination pharmacokinetic assessment revealed similar metabolism of trametinib to that reported as a single agent; HCQ demonstrated more rapid clearance compared to adults. Pharmacodynamic assessments are ongoing. CONCLUSIONS: The combination of trametinib and HCQ is safe with a RP2D of HCQ of 20 mg/kg/day divided BID. Currently, subjects are enrolling on the phase II portion evaluating the efficacy of this novel combination.

MEDB-42. GermlineElp1 deficiency promotes genomic instability and survival of granule neuron progenitors primed for SHH medulloblastoma pathogenesis

Germline loss-of-function (LOF) mutations in Elongator complex protein 1 (ELP1) are found in 15-20% of childhood SHH medulloblastoma (MB) and are exceedingly rare in non-SHH-MB or other cancers. ELP1 germline carriers that develop SHH-MB harbor frequent somatic PTCH1 mutations and universally sustain loss-of-heterozygosity of the remaining ELP1 allele through chromosome 9q deletion. ELP1 functions as a scaffolding subunit of the Elongator complex that is required for posttranscriptional modification of tRNAs and maintenance of efficient translational elongation and protein homeostasis. However, the molecular, biochemical, and cellular mechanisms by which ELP1/Elongator LOF contribute to SHH-MB tumorigenesis remain largely unknown. Herein, we report that mice harboring germline Elp1 monoallelic loss (i.e., Elp1^+/-) exhibit hallmark features of malignant predisposition in developing cerebellar granule neuron progenitors (GNPs), the lineage-of-origin for SHH-MB. Elp1^+/- GNPs are characterized by increased replication stress-induced DNA damage, upregulation of the homologous recombination repair pathway, aberrant cell cycle, and attenuation of p53-dependent apoptosis. CRISPR/Cas9-mediated Elp1 and Ptch1 gene targeting in mouse GNPs reproduces highly penetrant SHH-MB tumors recapitulating the molecular and phenotypic features of patient tumors. Reactivation of the p53 pathway through MDM2 and PAK4 inhibitors promotes selective cell death in patient-derived xenograft tumors (PDX) harboring deleterious ELP1 mutations. Together, our findings reveal that germline Elp1 deficiency heightens genomic instability and survival in GNPs, providing a mechanistic model for the subgroup-restricted pattern of predisposition and malignancy associated with pathogenic ELP1 germline carriers. These results provide rationale for further preclinical studies evaluating drugs that overcome p53 pathway inhibition in ELP1-associated SHH-MB and a renewed outlook for improving treatment options for affected children and their families.*, # Contributed equally

MEDB-78. Unified rhombic lip origins of Group 3 and Group 4 medulloblastoma

Identification and characterization of lineage-specific beginnings of distinct medulloblastoma (MB) subgroups is a fundamental challenge in the field. Genetically engineered mouse models and cross-species transcriptomics have provided mounting evidence of discrete, subgroup-specific developmental origins. Likewise, murine single-cell transcriptional atlases of cerebellar development have recently provided further clues into MB subgroup origins, particularly for poorly defined Group 3 and Group 4-MB. However, initial studies were underpowered to characterize rare populations and lacked robust validation, resulting in incomplete findings. Herein, we leveraged a large harmonized murine cerebellar atlas, targeted lineage enrichment, and integrative multi-omic strategies to deeply dissect MB origins. Isolation of spatially and temporally discrete developmental trajectories of key glutamatergic lineages born out of the murine upper rhombic lip provided an enhanced reference for mapping MB subgroup origins, especially for Group 3 and Group 4-MB. However, human-specific anatomic and cellular complexity, particularly within the rhombic lip germinal zone complicated murine-derived inferences. Further tumor-normal integrations using a novel single-cell atlas of the human fetal cerebellum, companioned with laser-capture micro-dissected transcriptional and epigenetic datasets, reinforced developmental insights extracted from candidate murine cerebellar lineages. Characterization of compartment-specific transcriptional signatures identified in the human upper rhombic lip implicated convergent cellular correlates of Group 3 and Group 4-MB, suggestive of a common developmental trajectory underlying their ancestry. Systematic imaging review and 3D summarization of a large clinical trial series of patient tumors, coupled with our advanced insights into developmental signatures, substantiated subgroup-specific tumor location patterns observed at diagnosis. Together, our results strongly implicate a common lineage trajectory of the upper rhombic lip as the probable origin of Group 3 and Group 4-MB. These important findings provide unprecedented opportunities to explore context-dependent mechanisms of MB pathogenesis and will foster generation of improved preclinical models that more faithfully recapitulate tumor biology.

ETMR-14. The single-cell landscape of pineoblastoma identifies developmental origins and exposes novel therapeutic vulnerabilities

Pineoblastoma (PB) is a rare and aggressive childhood brain tumor with highly variable age and treatment-associated outcomes. Our recent bulk tumor analyses of DNA methylation and mutational landscapes uncovered four discrete PB molecular subgroups (PB-miRNA1, PB-miRNA2, PB-MYC/FOXR2, and PB-RB), providing a major advance in our understanding of biological and clinical heterogeneity. However, developmental origins of PB subgroup heterogeneity and mechanisms governing how specific genetic alterations promote malignancy remain unknown. To resolve the cellular origins of PB, we assembled a large single-nucleus RNA-sequencing cohort (n=32) of primary PB tumors, including representatives from each subgroup. Transcriptomic analysis identified subgroup-specific gene expression programs driving intra-tumoral heterogeneity. In addition, we discovered substantial differences in the expression of miRNA biogenesis genes between the PB-miRNA1 and PB-miRNA2 subgroups, providing mechanistic support for their distinct subgroup identities despite overlapping driver events. The MYC/FOXR2 subgroup was characterized by over-expression of the FOXR2 proto-oncogene in bulk RNA-seq, which we validated in single-nuclei and identified co-expressed downstream target genes. To map PB subgroups to their putative developmental beginnings, we created a single-cell transcriptional atlas of the murine pineal gland across 11 developmental stages (E11-P21). Trajectory inference within the developing pineal gland revealed a differentiation continuum of early, mid, and mature alpha-/beta pinealocytes. Cross-species correlation and deconvolution identified significant associations between multiple PB subgroups and specific differentiation states of the pinealocyte lineage, suggestive of developmental origins. Characterization of pinealocyte development informed generation of biologically faithful disease models, including a novel genetically engineered mouse model of the PB-RB subgroup. PB-Rb1 mouse tumors were histologically and molecularly validated for their fidelity to human tumor counterparts, exhibiting up-regulation of key pinealocyte lineage markers that are diagnostic in patients. Finally, high-throughput drug screening identified several promising pharmacological candidates that may attenuate consequences of Rb1 deficiency in affected children.

POS0460 METABOLOMICS ACROSS AGE IDENTIFIES UNIQUE CHANGES IN THE SERUM METABOLIC PROFILE IN PATIENTS WITH SLE

Background

Cardiovascular disease (CVD) is a leading cause of mortality in patients with systemic lupus erythematosus (SLE, female:male ratio of 9:1) through accelerated atherosclerosis, the build-up of lipids and inflammation in the major artery walls, compared to age and sex matched healthy individuals. This is due to chronic inflammation, dyslipidaemia and other cardiometabolic defects that exacerbate with age (1). SLE in women aged of 35-44 increases the risk of coronary artery disease by 50 times and there is a 100-300-fold increased CVD-related mortality risk in young patients that develop SLE before the age of 18. Investigating metabolic defects in young patients and how they progress with age could help us understand the progressive mechanisms of atherosclerosis in SLE.

Objectives

This study investigated detailed changes in the metabolomic profile of female patients with SLE and matched healthy controls across age.

Methods

Serum NMR metabolomics (>250 metabolites, Nightingale) covering glycolysis metabolites, amino acids and 130 lipid measures was performed on serum from a cohort of female SLE patients (n=164, 13-72 years of age, median 35) and matched healthy controls (HCs, n=120, 15-76 years of age, median 36) and analysed by linear regression and Venn analysis. Multiple t-tests (corrected for multiple comparisons by false discovery rate) were used to assess unique metabolic changes by age group between SLE patients and HCs (≤25, n=62/43; 26-49, n=50/46; ≥50, n=52/31) and dysregulated metabolic pathways were assessed using metaboanalyst software. The metabolic impact of disease activity measures and treatments was assessed by Spearman correlations and unpaired t-tests respectively.

Results

Twenty-five metabolites were significantly altered in all SLE age groups compared to HCs, dominated by atheroprotective high density lipoprotein (HDL) subsets and their surface-bound peptide, apolipoprotein(Apo)A1, all of which were significantly decreased in SLE compared to HCs (p<0.0001 in ages combined). In addition, the concentration of glycoprotein acetyls (GlycA, inflammatory biomarker) was increased in SLE in all age groups compared to HCs (p<0.0001 in ages combined). Importantly, ApoA1 correlated negatively with disease activity measures (SLEDAI, p=0.005; BILAG, p=0.0009; dsDNA, p=0.003; ESR, p=0.0006) and positively with lymphocyte count (p=0.0005), whilst GlycA correlated positively with ESR (p<0.0001) and CRP (p<0.0001). Alternatively, metabolites unique to specific age groups in SLE compared to HCs included reduced amino acid subsets in the ≤25 age group, increased atherogenic very low density lipoproteins and reduced polyunsaturated fatty acids in the 26-49 age group, and increased atherogenic low density lipoproteins in the ≥50 age group.

Separately, metabolites associated with the glycolysis pathway (p=0.004, metaboanalyist), including acetone, citrate, creatinine, glycerol, lactate and pyruvate, had significant positive correlations with age in SLE patients, but not in HCs. These metabolites were not significantly associated with disease activity measures. However, pyruvate (p=0.01) and lactate (p=0.009) were significantly upregulated in prednisolone treated patients, whilst citrate (p=0.002) and creatinine (p= 0.005) were downregulated in hydroxychloroquine treated patients.

Conclusion

Increasing HDL (ApoA1) levels whilst maintaining low disease activity in patients with SLE from a young age could improve cardiometabolic risk outcomes. This could be achieved through improved nutrition, lipid targeted therapies and better treatment strategies. Focusing on understanding and monitoring biomarkers of the glycolytic pathway could aid treatment decisions and help avoid adverse metabolic effects of current anti-inflammatory therapies in SLE (1).

References

[1]Robinson G.A, Pineda-Torra I, Ciurtin C, Jury E.C. Lipid metabolism in autoimmune rheumatic disease: implications for modern and conventional therapies. J Clin Invest. 2022;132(2):e148552. https://doi.org/10.1172/JCI148552.

Acknowledgements

The authors would like to thank all of the patients and healthy blood donors, as well as Prof. Arne Akbar and Dr. Chris Wincup for additional patient and healthy donor samples.

Disclosure of Interests

None declared.

POS0039 MONOCYTE TRANSCRIPTOMICS AND TARGETED PROTEOMICS DEFINE HETEROGENEOUS SUBGROUPS IN WOMEN WITH SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) AND SUBCLINICAL ATHEROSCLEROSIS

Background

Systemic lupus erythematosus (SLE), a chronic, inflammatory autoimmune disease, predominantly affects women with a 9:1 female:male incidence. Cardiovascular disease (CVD) is a leading cause of mortality in SLE via accelerated atherosclerosis: the build-up of cells and lipids in the vascular wall and the main pathology underlying CVD.

Objectives

To define molecular profiles of SLE with subclinical atherosclerosis using multi-omics data analysis and clinical data in a well-characterised cohort of CVD-free SLE women.

Methods

Multi-omics analyses were conducted to explore the molecular signatures of SLE patients with (SLE-P) and without (SLE-NP) subclinical atherosclerosis defined by non-invasive ultrasound scanning of the carotid and femoral arteries. SLE blood CD14+ monocyte transcriptomes were investigated by bulk RNA-sequencing (SLE-P N=13, SLE-NP N=8), and targeted serum cardiometabolic and cardiovascular proteomics (OLINK) were used to explore matched protein expression (SLE-P N=17, SLE-NP N=20) (no difference in disease activity between groups). Bioinformatics approaches, including pathway and disease module enrichment analyses and extended protein-protein interaction networks, further defined molecular profiles of SLE patients with atherosclerosis from patients that remained plaque free. Gene signature-derived interferon (IFN) scores were applied to investigate heterogeneous subgroups within the cohort as a measure of inflammation.

Results

Distinct monocyte gene and protein expression profiles were identified in SLE and enriched in biological pathways relating to extracellular mechanisms, including purinergic and cytokine signalling. Lipid regulatory mechanisms were enriched in SLE-P, whereas SLE-NP patient’s transcriptome and proteome profiles were defined by pathways relating to inflammation. Specifically, the type-I IFN pathway was exclusively reduced in SLE-P compared to SLE-NP. IFN scores derived from published IFN-responsive gene expression signatures stratified patients into significantly distinct subgroups (high versus low IFN-response, p=0.0001) with 66% (N=14) of patients showing high IFN expression across multiple signatures not associated with age, ethnicity, or disease activity. However, IFN scores did not predict the presence of sub-clinical atherosclerosis and further heterogeneity was revealed with 46% of SLE-P patients showing a low IFN response (N=6). Further, a measure of plaque lipid content (echogenicity) was inversely correlated with IFN score (grey scale median, p=0.03, r=-0.8) which may reflect distinct plaque phenotypes between these subgroups relating to clinical presentation and risk of cardiovascular events.

Conclusion

Lipid dysregulation is a key mechanism that drives atherosclerosis pathology and genes and proteins relating to lipid metabolism distinguished SLE patients with and without subclinical atherosclerosis. Differences in levels of interferons and other inflammatory molecules may contribute to unique patterns of gene expression between SLE patients. A distinct subset of SLE-P patients showed low interferon expression, which may be suggestive of a dampened immune response in early subclinical CVD. Further elucidating the complexity of lipid dysregulation, inflammation and immune function in atherosclerosis in SLE will help improve patient stratification towards investigating the efficacy of anti-atherosclerotic therapies.

Disclosure of Interests

None declared

Diagnostic accuracy of an automated artificial intelligence derived right ventricular to left ventricular diameter ratio tool on CT pulmonary angiography to predict pulmonary hypertension at right heart catheterisation

AIM

To determine the diagnostic accuracy of an automated artificial intelligence derived right ventricle/left ventricle diameter ratio (RV/LV) computed tomography pulmonary angiography (CTPA) analysis tool to detect pulmonary hypertension (PH) in patients with suspected PH referred to a specialist centre.

MATERIALS AND METHODS

The present study was a retrospective analysis of a prospectively maintained database of 202 consecutive patients with suspected PH, who underwent CTPA within 12 months of right heart catheterisation (RHC). Automated ventricular segmentation and RV/LV calculation (Imbio LLC, Minneapolis, MN, USA) was undertaken on the CTPA images. PH diagnosis was made using the RHC reference standard.

RESULTS

The automated RV/LV correlated more strongly with RHC metrics than main pulmonary artery (MPA) diameter and MPA to ascending aorta diameter ratio (MPA/AA) measured manually (mean pulmonary arterial pressure [mPAP] r=0.535, R² = 0.287 p<0.001; pulmonary vascular resistance [PVR] r=0.607, R² = 0.369 p<0.001). In the derivation cohort (n=100), the area under the receiver-operating curve for automated RV/LV discriminating PH was 0.752 (95% confidence interval [CI] 0.677-0.827, p<0.001). Using an optimised Youden's Index of ≥1.12 classified from derivation, automated RV/LV ratio analysis was more sensitive for the detection of PH with higher positive predictive value (PPV) when compared with manual MPA and MPA/AA in the validation cohort (n=102). Automated RV/LV compromise (1.12) and specific (1.335) thresholds were strongly predictive of mortality (log-rank 7.401, p=0.007 and log-rank 16.075, p<0.001 respectively).

CONCLUSION

In suspected PH, automated RV/LV diameter thresholds have high sensitivity for PH, outperform manual MPA and MPA/AA and can predict survival.

Pretreatment Normal WM Magnetization Transfer Ratio Predicts Risk of Radiation Necrosis in Patients with Medulloblastoma

BACKGROUND AND PURPOSE

Radiation necrosis, for which abnormal WM enhancement is a hallmark, is an uncommon complication of craniospinal irradiation in children with medulloblastoma. The magnetization transfer ratio measures macromolecular content, dominated by myelin in the WM. We investigated whether the pretreatment supratentorial (nonsurgical) WM magnetization transfer ratio could predict patients at risk for radiation necrosis after radiation therapy for medulloblastoma.

MATERIALS AND METHODS

Ninety-five eligible patients with medulloblastoma (41% female; mean age, 11.0 [SD, 5.4]  years) had baseline balanced steady-state free precession MR imaging before proton or photon radiation therapy. Associations among baseline supratentorial magnetization transfer ratio, radiation necrosis (spontaneously resolving/improving parenchymal enhancement within the radiation field)³, age, and the presence of visible brain metastases were explored by logistic regression and parametric/nonparametric techniques as appropriate.

RESULTS

Twenty-three of 95 (24.2%) children (44% female; mean age, 10.7 [SD, 6.7] years) developed radiation necrosis after radiation therapy (19 infratentorial, 1 supratentorial, 3 both). The mean pretreatment supratentorial WM magnetization transfer ratio was significantly lower in these children (43.18 versus 43.50, P = .03). There was no association between the supratentorial WM magnetization transfer ratio and age, sex, risk/treatment stratum, or the presence of visible brain metastases.

CONCLUSIONS

A lower baseline supratentorial WM magnetization transfer ratio may indicate underlying structural WM susceptibility to radiation necrosis and may identify children at risk for developing radiation necrosis after craniospinal irradiation for medulloblastoma.

BIOM-36. SERIAL ASSESSMENT OF MEASURABLE RESIDUAL DISEASE IN MEDULLOBLASTOMA LIQUID BIOPSIES

Medulloblastoma is the most common malignant brain tumor in children. Despite the use of contemporary multi-modal therapy, up to one-third of patients will succumb to disease progression. Conventional response monitoring is based on magnetic resonance imaging and cerebrospinal fluid (CSF) cytology and a marker for measurable residual disease (MRD) is lacking. In this study, we show the clinical utility of profiling CSF-derived cell-free DNA (cfDNA) as a biomarker of MRD based on a sizable cohort of children with medulloblastoma enrolled on a prospective, multi-center, risk-adapted trial (SJMB03; NCT00085202). A total of 476 CSF samples were serially collected from 123 patients by lumbar puncture at post-operative baseline, during therapy, and at regular surveillance after completion of therapy. Using low-coverage whole-genome sequencing (lcWGS), tumor-associated copy-number alterations in CSF-derived cfDNA were investigated as an MRD surrogate for correlation with clinical features and outcomes. MRD was detected in post-operative baseline CSF samples for 85% and 54% of patients with metastatic and localized disease, respectively. The number of MRD-positive patients declined with therapy, yet those with persistent MRD detected at the end of therapy (20 of 68 CSFs at this timepoint) had significantly higher risk of disease progression (hazard ratio 8.94, 95%CI 4.10-19.49; log-rank p&lt; 0.0001). Importantly, MRD-positivity from routine surveillance samples often preceded radiographic progression by more than 3 months. Comparative analyses of copy-number variations obtained from serial CSF samples enabled identification of relapse-specific alterations and early detection of relapse-dominant clones. Overall, our findings advocate for the routine incorporation of CSF-derived liquid biopsies in future medulloblastoma trials.

EPCO-26. INTEGRATIVE MULTI-OMICS IDENTIFIES CONVERGING DEVELOPMENTAL ORIGINS OF DISTINCT MEDULLOBLASTOMA SUBGROUPS

Understanding the interplay between normal development and tumorigenesis, including the identification and characterization of lineage-specific origins of MB, is a fundamental challenge in the field. Recent studies have highlighted novel associations between biologically distinct MB subgroups and diverse murine cerebellar lineages via cross-species single-cell transcriptomics. Specifically, Group 4-MB correlated with the unipolar brush cell lineage and Group 3-MB resembled Nestin+ stem cells of the early cerebellum. However, these analyses were hampered by low resolution due to the sparsity of pertinent cerebellar cell types and the cross-species nature of the approach. Herein, we profoundly expand the depth of these rare developmental populations in the murine cerebellum using a combination of lineage tracing and integrative multi-omics. Isolation and enrichment of spatially and temporally unique developmental trajectories of key rhombic lip-derived glutamatergic lineages provided an enhanced reference for mapping MB subgroups based on molecular overlap, especially for poorly defined Group 3- and Group 4-MB. Further comparisons to a novel single-cell atlas of the human fetal cerebellum, companioned with laser-capture microdissected transcriptional and epigenetic datasets, reinforced developmental insights extracted from the mouse. Characterization of compartment-specific transcriptional programs and co-expression networks identified in the human upper rhombic lip implicated convergent cellular correlates of Group 3- and Group 4-MB, suggestive of a common developmental link. Together, our results strongly implicate developmental lineages of the upper rhombic lip as the probable origins of poorly defined Group 3- and Group 4-MB. These important findings will shape future efforts to accurately model the biological heterogeneity underlying these subgroups and provide unprecedented opportunities to explore their cellular and mechanistic basis.

Chemotherapy strategies for young children newly diagnosed with desmoplastic/extensive nodular medulloblastoma up to the era of molecular profiling – a comparative outcomes analysis of prospective multi-center European and North American trials

Aims

Survival has been poor in several multi-center/national trials since the 1980s, either delaying, avoiding or minimizing brain irradiation in young children with medulloblastoma. The introduction of German regimens supplementing “standard” chemotherapy with both intravenous high-dose (HD-MTX) and intraventricular (IVENT-MTX) methotrexate, and North American regimens incorporating marrow-ablative chemotherapy with autologous hematopoietic cell rescue (HDCx+AuHCR), have reported encouraging outcomes. We performed a comparative outcomes analysis of these differing strategies for young children with desmoplastic/extensive nodular medulloblastoma.

Method

Data from 12 trials reported between 2005 and 2020 for children &lt;six-years-old with desmoplastic/extensive nodular medulloblastoma were reviewed; event-free (EFS) survival+/-standard errors were compared.

Results

The German HIT-SKK’92 and HIT-SKK’00 trials incorporating HD-MTX and IVENT-MTX reported 85+/-8% and 95+/-5% 5-10-year EFS respectively; a third trial (ACNS1221) incorporating HIT-SKK therapy but without IVENT-MTX reported only 49+/-10% EFS. Three trials (Head Start I and II combined and CCG-99703) employing induction chemotherapy without HD-MTX, followed by one or three HDCx+AuHCR cycles, reported 3-5-year EFS of 67+/-16% and 79+/-11%. Two trials employing HD-MTX-containing induction chemotherapy (Head Start III and ACNS0334), followed by one or three HDCx+AuHCR cycles, reported 3-5-year EFS of 89+/-6% and 100%, respectively. Finally, four trials utilizing neither IVENT-MTX nor HDCx+AuHCR (UK-CNS-9204, CCG-9921, COG-P9934 and SJYC07) reported 2-5 year EFS of 35+/-11%, 77+/-9%, 58+/-8% and 53+/-9% respectively.

Conclusion

A trend towards better EFS for young children with desmoplastic/extensive nodular medulloblastoma is observed in trials including eitherHD-MTX and IVENT-MTX or including HD-MTX-containing induction chemotherapy and HDCx+AuHCR. Trials excluding HD-MTX, IVENT-MTX and HDCx+AuHCR have poorer outcomes.

Accuracy of echocardiographic doppler measures of pulmonary hypertension compared with right heart catheterisation in a real world population referred to a specialist centre

Introduction

Right heart catheterisation (RHC) is the gold standard investigation for the diagnosis of pulmonary hypertension (PH). Transthoracic echocardiography (TTE) allows non-invasive screening for PH. This retrospective audit sought to compare the accuracy of non-invasive Doppler estimates of pulmonary artery pressure and pulmonary vascular resistance (PVR) compared to RHC in a real world cohort referred to a shared care PH centre.

Method

Between 2010 and 2019, a total of 310 patients referred for initial assessment of PH underwent TTE followed by RHC (mean interval 31±30 days). Bland-Altman analysis was used to retrospectively investigate the accuracy of Doppler estimates of Pulmonary Artery Systolic Pressure (PASP), mean Pulmonary Artery Pressure (mPAP), Right Atrial Pressure (RAP) and PVR compared to RHC. TTE mPAP estimates were made using the pulmonary regurgitation velocity at the beginning of diastole (mPAP = 4(PRVBD)2 + RAP). TTE PVR estimates were calculated using the equation 10(TRV / RVOTVTI) + 0.16.

Results

Seventy-six percent of the cohort (n=235) had RHC diagnosed PH (average mPAP 42.8±11.7mmHg). The peak tricuspid regurgitation velocity (TRV) was measurable in 87% (n=269) and was unmeasurable in 8% (n=19) of those with confirmed RHC PH. Ten percent (n=30) had inadequate IVC imaging. TTE estimates of PASP (n=239) had a good correlation to RHC PASP (rs=0.82, 95% CI 0.75–0.84). TTE PASP estimates tended to underestimate RHC PASP (bias −3.7±15.2mmHg) with wide limits of agreement (95% limits of agreement −33.5–26.1mmHg) (figure 1); highlighting the imprecision of Doppler estimates alone. Only 44% of TTE PASP estimates were within 10mmHg of RHC PASP readings. Underestimation occurred more frequently accounting for 66% of inaccurate TTE PASP estimates. TTE RAP estimates (n=292) were weakly correlated to RHC RAP (rs=0.38, 95% CI 0.27–0.48).

TTE estimates of mPAP were only measurable in 81 patients and demonstrated moderate correlation to RHC mPAP (rs=0.58, 95% CI 0.4–0.71). TTE estimates tended to underestimate RHC mPAP (bias of −10±10.9mmHg) with wide limits of agreement (95% limits of agreement −31.3–11.3mmHg) (figure 1) suggesting poor accuracy and precision. Only 51% of TTE estimates were within 10mmHg of RHC mPAP with 93% of inaccuracies due to an underestimation of RHC mPAP. TTE PVR estimates (n=238) correlated well with RHC PVR measures (rs=0.68, 95% CI 0.6–0.74). However, Bland-Altman analysis (figure 2) demonstrated bias of −2.2±3.1WU with wide limits of agreement (95% limits of agreement −8.2–3.8WU), highlighting significant inaccuracy.

Conclusion

Doppler TTE measures to assess PH lack accuracy when compared with the gold standard RHC. Furthermore, the peak TRV was unmeasurable in 8% of those with confirmed RHC diagnosed PH. These findings further support the use of a multi parameter TTE approach for screening of PH.

Funding Acknowledgement

Type of funding sources: None.

Genomes for Kids: The scope of pathogenic mutations in pediatric cancer revealed by comprehensive DNA and RNA sequencing

Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole genome (WGS), exome, and RNA sequencing, to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically-relevant (25%), and/or cancer predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors) and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor-normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers.

Small-molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma

Medulloblastoma (MB) consists of four core molecular subgroups with distinct clinical features and prognoses. Treatment consists of surgery, followed by radiotherapy and cytotoxic chemotherapy. Despite this intensive approach, outcome remains dismal for patients with certain subtypes of MB, namely, MYC-amplified Group 3 and TP53-mutated SHH. Using high-throughput assays, six human MB cell lines were screened against a library of 3208 unique compounds. We identified 45 effective compounds from the screen and found that cell cycle checkpoint kinase (CHK1/2) inhibition synergistically enhanced the cytotoxic activity of clinically used chemotherapeutics cyclophosphamide, cisplatin, and gemcitabine. To identify the best-in-class inhibitor, multiple CHK1/2 inhibitors were assessed in mice bearing intracranial MB. When combined with DNA-damaging chemotherapeutics, CHK1/2 inhibition reduced tumor burden and increased survival of animals with high-risk MB, across multiple different models. In total, we tested 14 different models, representing distinct MB subgroups, and data were validated in three independent laboratories. Pharmacodynamics studies confirmed central nervous system penetration. In mice, combination treatment significantly increased DNA damage and apoptosis compared to chemotherapy alone, and studies with cultured cells showed that CHK inhibition disrupted chemotherapy-induced cell cycle arrest. Our findings indicated CHK1/2 inhibition, specifically with LY2606368 (prexasertib), has strong chemosensitizing activity in MB that warrants further clinical investigation. Moreover, these data demonstrated that we developed a robust and collaborative preclinical assessment platform that can be used to identify potentially effective new therapies for clinical evaluation for pediatric MB.

Abstract 642: Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in pediatric cancer

Clinical genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. In the Genomes for Kids study (NCT02530658) we used a three-platform sequencing approach, including whole genome (WGS), whole exome (WES) and RNA sequencing, to examine tumor and paired germline genomes from prospectively identified children with cancer. The goal of the study was to assess the potential of comprehensive next generation sequencing to elucidate the molecular mechanisms underlying tumor formation and investigate the potential of this information to influence clinical decision-making.The cohort, with a median age of 6 yrs, range 0 - 26 yrs, included 301 patients with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type or stage. Patients with hematologic malignancies accounted for 41% of cases, 31% had CNS tumors, and 28% had other non-CNS solid tumors. This cohort also included 18 patients with very rare tumor types, defined here as occurring in less than 2 cases per million person per year.Two hundred fifty three patients (84%) had sufficient tumor for three-platform sequencing and all 301 had adequate paired germline samples. Following analysis, 86% of patients harbored diagnostic (53%), prognostic (57%), therapeutically relevant (25%), and/or cancer predisposing (18%) variants. The inclusion of WGS enabled detection of oncogenic gene fusions, as well as 22 cases in which oncogenes were activated through enhancer hijacking, a particularly frequent occurrence in hematologic malignancies. In addition, WGS effectively detected clinically relevant small intragenic deletions (15% of tumors) and a variety of mutational signatures, which were not detectable through analysis of whole exome data. Evaluation of 56 pathogenic germline variants in the context of paired tumor sequence data helped establish the disease relevance of several genes that are not typically associated with the cancer type in question, providing critical insights on a case-by-case basis. Examples include a pathogenic germline variant in MUTYH in a patient with retinoblastoma whose tumor exhibited a mutation signature associated with reactive oxygen species indicative of loss of MUTYH function; and conversely, a likely pathogenic variant in PMS2 in a rare brain cancer, which did not exhibit a mutation signature associated with microsatellite instability. This study successfully demonstrated the power of this three-platform approach to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers. As a result of these findings, we have incorporated this three-platform approach into our routine real-time clinical service at St. Jude Children's Hospital.

Citation Format: David A. Wheeler, Scott Newman, Joy Nakitandwe, Chimene A. Kesserwan, Elizabeth M. Azzato, Michael C. Rusch, Sheila Shurtleff, Armita Bahrami, Brent Orr, Jeffery M. Klco, Dale J. Hedges, Kayla V. Hamilton, Scott G. Foy, Michael N. Edmonson, Andrew Thrasher, Jiali Gu, Lynn W. Harrison, Lu Wang, Roya Mostafavi, Manish Kubal, Jamie Maciaszek, Michael Clay, Annastasia Ouma, Antonina Silkov, Yanling Liu, Zhaojie Zhang, Yu Liu, Samuel W. Brady, Xin Zhou, Mark Wilkinson, Delaram Rahbarinia, Jay Knight, Jian Wang, Charles G. Mullighan, Rose B. McGee, Emily A. Quinn, Elsie L. Gerhardt, Leslie M. Taylor, Regina Nuccio, Jessica M. Valdez, Stacy J. Hines-Dowell, Alberto Pappo, Giles Robinson, Liza-Marie Johnson, Ching-Hon Pui, David W. Ellison, James R. Downing, Jinghui Zhang, Kim E. Nichols. Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 642.

POS0174 IMMUNOPHENOTYPE OF SJÖGREN´S SYNDROME AND SYSTEMIC LUPUS ERYTHEMATOSUS PATIENTS IDENTIFIED TWO ENDOTYPES WITH POTENTIAL THERAPEUTIC IMPLICATIONS

Background:

Primary Sjögren’s syndrome (pSS) and systemic lupus erythematosus (SLE) are chronic autoimmune rheumatic diseases (ARDs) that share a strong female gender bias, as well as genetic, clinical and serological characteristics.Although significant progress has been made in improving treatment and patient related outcomes in pSS and SLE, there is a need for improved early diagnosis, adequate therapy monitoring, treatment of refractory manifestations and strategies to address co-morbidities.However, the results of many clinical trials are disappointing, and nobiologic treatments are licensedin pSS, while few are available for SLE patients with refractory disease.

Objectives:

Identifying shared immunological features between patients with pSS and SLE that could lead to better treatment selection using a stratification approach.

Methods:

Immune-phenotyping of 29 immune-cell subsets in peripheral blood from patients with pSS (n=45), SLE (n=29) and secondary SS associated with SLE (SLE/SS) (n=14) with low disease activity or in clinical remission, and sex-matched healthy controls (n=31), was performed using flow cytometry. Data were analysed using logistic regression and multiple t-tests andsupervised machine learning (balanced random forest-BRF, sparse partial least squares discriminant analysis-sPLS-DA). Patients were stratified by k-means clustering. Clinical trajectories were analysed over 5 year follow-up.

Results:

Comparing the immune profile of pSS and SLE patients using a variety of statistical and machine learning (ML) approaches, identified very few statistically significant differences between the two cohorts despite patients having a different clinical presentation and diagnosis. Thus, we hypothesised that immune-based subtypes could be shared between pSS, SLE and SLE/SS patients. Unsupervised k-means clustering was applied to the immunological features of the combined patient cohorts and two distinct patient endotypes, were identified: Group-1 (n=49; pSS=24, SLE=19, SLE/SS=6) and Group-2 (n=39; pSS=21, SLE=10, SLE/SS=8). Significant differences in immune-cell phenotypes across B-cell and T-cell subsets were identified by logistic regression, BRF (AUC=0.9942, assessed by 10-fold cross-validation) and sPLS-DA analysis. Comparison of the multiple analysis approaches identified eight common immune-cell subsets, including total and memory CD4+ and CD8+ T-cell subsets but no B-cell subsets. Using this common immune-signature the stratification between the groups was maintained and slightly improved (AUC=0.9979 and accuracy 96.16%). Interestingly, patients in Group-2 had elevated disease activity measures at baseline and over a 5-year trajectory compared to Group-1. Finally, correlation analysis identifed correlations between disease activity markers and the top ranked immune features from the ML models.

Conclusion:

The identified immune-cell signatures could reflect the underlying disease pathogenesis that spans diagnositc criteria and could be used to select patients for targeted therapeutic approaches.

Acknowledgements:

LM-G is supported by a project grant from The Dunhill Medical Trust (RPGF1902\117); JP is supported by Versus Arthritis (21226). GAR is supported by Lupus UK, The Rosetrees Trust (M409) and Versus Arthritis (21593). MN is supported by NIHR UCLH Biomedical Research Centre (BRC525/III/CC/191350). HP has a Versus Arthritis PhD studentship (22203). This work was performed within the Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH supported by grants from Versus Arthritis (21593 and 20164), GOSCC, and the NIHR-Biomedical Research Centres at both GOSH and UCLH.

We would like to thank Mr Jamie Evans for expert support with flow cytometry analysis and Ms Eve McLoughlin for support with patient recruitment.

Disclosure of Interests:

None declared

OP0013 SEX DIFFERENCES IN AUTOIMMUNE DISEASE SUSCEPTIBILITY; A MULTI-OMIC APPROACH

Background:

Males and females have altered immune responses resulting in variation in autoimmune and cardiovascular disease risk (CVR). Recently, these differences have played a role in the inflammatory response to COVID-19. Sex differences exist in the frequency and activity of immune-cell subsets but mechanisms underlying sexual dimorphism remain unknown. Juvenile-onset systemic lupus erythematosus (JSLE) is an autoimmune disorder that commonly emerges during puberty, has a strong female prevalence (female:male ratio, 4.5:1) and results in an increased CVR. JSLE is characterised by chronic inflammation and dyslipidaemia, where cardiovascular disease is a leading cause of mortality for patients. Our previous work identified a link between immune cell function and lipid metabolism in adult-onset SLE. We hypothesised that sex hormones could influence both lipid metabolism and immune cell function and this could determine sex-specific susceptibility to JSLE and associated CVR.

Objectives:

We investigated the role of sex hormones in modifying systemic lipid metabolism and inflammation.

Methods:

Nuclear magnetic resonance spectroscopy based serum metabolomics measuring over 130 lipoproteins (14-subsets with lipid compositions), flow cytometry measuring immune-cells, and RNA-sequencing were used to assess the metabolic and immune profile in young, pre/post-pubertal males (n=10/17) and females (n=10/23) and in individuals with gender-dysphoria (GD) under cross-hormone treatment (trans-male/female, n=26/25). This analysis was also performed on a cohort of post-pubertal male (n=12) and female (n=23) JSLE patients. Data was analysed by logistic regression, balanced random forest machine learning (BRF-ML), differential gene expression (DEG) and pathway analysis.

Results:

Post-pubertal males had significantly reduced cardio-protective high-density lipoprotein (HDL) subsets (p<0.0001) and increased cardio-pathogenic very-low-density lipoprotein subsets (p<0.0001) compared to females. These differences were not observed pre-puberty and were reversed significantly by cross-hormone treatment in GD individuals, suggesting that sex hormones regulate lipid metabolism in-vivo.

BRF-ML (28 immune-cell subsets) identified an increased frequency of anti-inflammatory regulatory T-cells (Tregs) in post-pubertal males compared to females (p=0.0097). These Tregs were also more suppressive in males compared to females. Differences in Treg frequency were seen pre-puberty and were not altered by sex hormone treatment in GD individuals. However, Treg DEGs and functional transcriptomic pathways altered between post-pubertal males and females, including those involved in inflammatory signalling, overlapped with those altered by hormones in GD, suggesting hormones may also drive Treg functional changes. In addition, HDL metabolites modified by hormones showed differential associations with Treg phenotypes between post-pubertal males and females.

Strikingly, sex differences in lipoproteins and Tregs were lost in JSLE, suggesting hormone signalling could be dysregulated in the pathogenesis of autoimmunity and could increase CVR for patients.

Conclusion:

Sex hormones drive altered lipoprotein metabolism and functional transcriptomic pathways in Tregs. Males have a lipoprotein profile associated with increased CVR, but a more anti-inflammatory immune profile compared to females. Together, this could explain sex differences in inflammatory disease susceptibilities and inform future sex-specific therapeutic strategies for the management of both JSLE and CVR.

Acknowledgements:

Lupus UK

Rosetrees Trust

Versus Arthritis

NIHR UCLH Biomedical Research Centre

Disclosure of Interests:

None declared

A phase I trial of the CDK 4/6 inhibitor palbociclib in pediatric patients with progressive brain tumors: A Pediatric Brain Tumor Consortium study (PBTC-042)

BACKGROUND

Disruption of cell-cycle regulators is a potential therapeutic target for brain tumors in children and adolescents. The aim of this study was to determine the maximum tolerated dose (MTD) and describe toxicities related to palbociclib, a selective cyclin-dependent kinase 4/6 (CDK4/6) inhibitor in pediatric patients with progressive/refractory brain tumors with intact retinoblastoma protein.

METHODS

Palbociclib was administered orally starting at 50 mg/m² daily for the first 21 days of a 28-day course. Dose escalation was according to the Rolling-6 statistical design in less heavily (stratum I) and heavily pretreated (stratum II) patients, and MTD was determined separately for each group. Pharmacokinetic studies were performed during the first course, and pharmacodynamic studies were conducted to evaluate relationships between drug levels and toxicities.

RESULTS

A total of 21 patients were enrolled on stratum I and 14 patients on stratum II. The MTD for both strata was 75 mg/m² . Palbociclib absorption (mean T_max between 4.9 and 6.6 h) and elimination (mean half-life between 11.3 and 19.5 h) were assessed. The most common toxicity was myelosuppression. Higher palbociclib exposure was associated with grade 3/4 neutropenia and leukopenia. Dose limiting toxicities included grade 4 neutropenia and grade 3 thrombocytopenia and dehydration. No patients had an objective response to palbociclib therapy.

CONCLUSIONS

Palbociclib was safely administered to children and adolescents at a dosage of 75 mg/m² for 21 consecutive days followed by seven days of rest in both strata. Future studies will establish its optimal utilization in pediatric patients with brain tumors.

Analysis of Cryptosporidium spp. from clinical samples by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

AIM

To purify Cryptosporidium spp. oocysts from clinical stool samples and evaluate using an up-to-date mass spectrometry protocol producing high-quality reference spectra.

METHODS AND RESULTS

A refined purification protocol was developed for oocysts from stools, involving salt flotation and potassium bromide density centrifugation. Purified oocysts were prepared for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) by formic acid extraction, and the extracts analysed using the Bruker MALDI Biotyper system. Individual spectral markers were identified by their specific mass peaks. Cryptosporidium parvum oocysts (Iowa strain) propagated in vivo, and C.  parvum (n = 2) and Cryptosporidium hominis (n = 1) oocysts from clinical stool samples produced distinct spectra that were considered specific to Cryptosporidium spp. with no evidence of contamination.

CONCLUSIONS

The production of distinct spectra demonstrated the utility of the purification method for oocysts from clinical stool samples and provided reference spectra.

SIGNIFICANCE AND IMPACT OF THE STUDY

The use of MALDI-TOF MS and other mass spectrometry techniques has been limited previously to C.  parvum oocysts propagated in vivo. Appropriate purification of oocysts can achieve sufficient biomass, enabling analysis by MALDI-TOF MS and potentially other mass spectrometry platforms, facilitating peptide and protein discovery and identification of biomarkers from a much wider range of Cryptosporidium spp. from natural infections.

COVID-19: looking beyond the peak. Challenges and tips for radiologists in follow-up of a novel patient cohort

As the coronavirus pandemic evolves, the focus of radiology departments has begun to change. The acute phase of imaging a new disease entity whilst rationalising radiology services in the face of lockdown has passed. Radiologists are now becoming familiar with the complications of COVID-19, particularly the lung parenchymal and pulmonary vascular sequelae and are considering the impact follow-up imaging may have on departments already struggling with a backlog of suspended imaging in the face of reduced capacity. This review from the British Society of Thoracic Imaging explores both the thoracic and extra-thoracic complications of COVID-19, recognising the importance of a holistic approach to patient follow-up. The British Thoracic Society guidelines for respiratory follow-up of COVID-19 will be discussed, together with newly developed reporting templates, which aim to provide consistency for clinicians as well as an opportunity for longer-term data collection.

MBCL-26. FACTORS ASSOCIATED WITH LONGER SURVIVAL AFTER FIRST RECURRENCE IN MEDULLOBLASTOMA BY MOLECULAR SUBGROUP AFTER RISK-BASED INITIAL THERAPY

OBJECTIVE

To evaluate differences in time to recurrence among molecular subgroups of medulloblastoma treated on a single protocol and to identify factors associated with survival after first recurrence.

METHODS

Time to recurrence following SJMB03 treatment was compared across methylation subgroups among relapsed patients. Therapies received subsequent to relapse were noted. Kaplan-Meier methods and log-rank tests were used for statistical analyses.

RESULTS

74 of 330 medulloblastoma patients developed recurrence after initial therapy. (38 Standard-Risk; 36 High-Risk). The 2- and 5-year survival after first recurrence was 30.4% and 14.6% respectively. DNA methylation-based subgroups from initial diagnosis were SHH (n=14), Group 3 (n=24), Group 4 (n=26), and unclassified (n=8). None of the pts with WNT MB had recurrent disease. Median time to first recurrence was 1.23, 0.91, and 3.09 years in SHH, Group3, and Group 4 respectively. Group 4 patients had longer post-recurrence survival than others (p-value=0.0169). Clinical risk at diagnosis (p-value=0.337), anaplasia (p-value=0.4032), TP53 (p-value=0.1969), MYC (p-value=0.8967), and MYCN (p value = 0.9404) abnormalities were not associated with post progression survival. Patients who received any therapeutic modality (chemotherapy, re-radiation and second surgery) had longer survival and those who had all three (n=10) had the best outcome (p-value<0.0001).

CONCLUSION

Outcome after recurrence in medulloblastoma is dismal, however, association with subgroups is still present. Group 4 patients had a longer time to recurrence and post progression survival. No other prognostic factor at initial diagnosis was associated with outcome after recurrence. Patients who received all 3 types of conventional therapy had better survival.

MBCL-19. CHEMOTHERAPY STRATEGIES FOR YOUNG CHILDREN NEWLY DIAGNOSED WITH DESMOPLASTIC/EXTENSIVE NODULAR MEDULLOBLASTOMA UP TO THE ERA OF MOLECULAR PROFILING – A COMPARATIVE OUTCOMES ANALYSIS OF PROSPECTIVE MULTI-CENTER EUROPEAN AND NORTH AMERICAN TRIALS

BACKGROUND/OBJECTIVE

Survival has been poor in several multi-center/national trials since the 1980s, either delaying, avoiding or minimizing brain irradiation in young children with medulloblastoma. The introduction of German regimens incorporating both intravenous high-dose (HD-MTX) and intraventricular (IVENT-MTX) methotrexate, and North American regimens utilizing marrow-ablative chemotherapy with autologous hematopoietic cell rescue (HDCx+AuHCR), have reported encouraging outcomes. We performed a comparative outcomes analysis of these strategies for young children with desmoplastic/extensive nodular medulloblastoma (D/ENMB).

DESIGN/METHODS

Data from 12 trials reported between 2005 and 2019 for children &lt;six-years-old with D/ENMB were reviewed; event-free (EFS) with standard errors were compared.

RESULTS

The German HIT-SKK’92 and HIT-SKK’00 trials incorporating HD-MTX and IVENT-MTX reported 85+/-8% and 95+/-5% 5-10-year EFS respectively; a third trial (ACNS1221) incorporating HIT-SKK therapy but without IVENT-MTX reported 49+/-10% EFS. Three trials (Head Start I/II combined and CCG-99703) employing induction chemotherapy without HD-MTX, followed by 1/3 HDCx+AuHCR cycles, reported 3-5-year EFS of 67+/-16% and 79+/-11%. Two trials employing HD-MTX-containing induction chemotherapy (Head Start III and ACNS0334), followed by 1/3 HDCx+AuHCR cycles, reported 3-5-year EFS of 89+/-6% and 100%, respectively. Finally, four trials utilizing neither IVENT-MTX nor HDCx+AuHCR (UK-CNS-9204, CCG-9921, COG-P9934 and SJYC07) reported 2-5-year EFS of 35+/-11%, 77+/-9%, 58+/-8% and 53+/-9%.

CONCLUSIONS

A trend towards better EFS for young children with D/ENMB is observed in trials including either HD-MTX as well as IVENT-MTX or including HD-MTX-containing induction chemotherapy and HDCx+AuHCR. Trials excluding HD-MTX, IVENT-MTX and HDCx+AuHCR have poorer outcomes.

HGG-01. ENTRECTINIB IN RECURRENT OR REFRACTORY SOLID TUMORS INCLUDING PRIMARY CNS TUMORS: UPDATED DATA IN CHILDREN AND ADOLESCENTS

STARTRK-NG (phase 1/2) is evaluating entrectinib, a CNS-penetrant oral, TRK/ROS1/ALK tyrosine kinase inhibitor, in patients <21 years with recurrent/refractory solid tumors, including primary CNS tumors. After determining the recommended dose, 550mg/m²/day, in all-comers, expansion cohorts with gene-fusion-positive CNS/solid tumors (NTRK1/2/3, ROS1) are being enrolled. As of 5Nov2019 (data cut-off), 39 patients (4.9m–20y; median 7y) have been evaluated for response, classified as complete (CR) or partial response (PR), stable (SD) or progressive disease (PD) using RANO (CNS), RECIST (solid tumors), or Curie score (neuroblastoma). Responses in patients with fusion-positive tumors were Investigator-assessed (BICR assessments are ongoing) and occurred at doses ≥400mg/m². Best responses in fusion-positive CNS tumors (n=14) were: 4 CR (GKAP1-NTRK2, ETV6-NTRK3 [n=2], EML1-NTRK2); 5 PR (KANK1-NTRK2, GOPC-ROS1, ETV6-NTRK3, TPR-NTRK1, EEF1G-ROS1); 3 SD (BCR-NTRK2, ARHGEF2-NTRK1, KIF21B-NTRK1); 2 PD (PARP6-NTRK3, EML4-ALK); and in fusion-positive solid tumors (n=8) were: 3 CR (ETV6-NTRK3 [n=2], DCTN1-ALK); 5 PR (EML4-NTRK3, TFG-ROS1 [n=3], KIF5B-ALK). Responses (Investigator-assessed) in non-fusion tumors (n=17) were: 1 CR (ALK F1174L mutation), 3 SD, 10 PD, 3 no data/unevaluable. The objective response rate (CR+PR/total) in patients with fusion-positive tumors was 77% (17/22) versus 6% (1/17) in those with non-fusion tumors. All 39 patients experienced ≥1 adverse event (AE); the most frequent AEs included weight gain and anemia (both 48.7%); increased ALT, increased AST, cough and pyrexia (all 46.2%); increased creatinine and vomiting (both 43.6%); and bone fractures (n=10, in 9 patients). Entrectinib has produced striking, rapid, and durable responses in solid tumors with target gene fusions, especially high-grade CNS neoplasms.

MBCL-37. CHEMOTHERAPY STRATEGIES FOR YOUNG CHILDREN NEWLY DIAGNOSED WITH CLASSIC (CLMB) OR ANAPLASTIC/LARGE CELL (A/LCMB) MEDULLOBLASTOMA UP TO THE ERA OF MOLECULAR PROFILING – A COMPARATIVE OUTCOMES ANALYSIS

BACKGROUND/OBJECTIVE

The introduction of German regimens, supplementing “standard” chemotherapy with both intravenous high-dose (HD-MTX) and intraventricular (IVENT-MTX) methotrexate, and North American regimens incorporating marrow-ablative chemotherapy with autologous hematopoietic cell rescue (HDCx+AuHCR), report encouraging outcomes for young children with medulloblastoma. We performed a comparative outcomes analysis of treatment strategies for young children with ClMB or A/LCMB. DESIGN/

METHODS

Data from 12 prospective multi-center trials published between 2005 and 2019 for children <six-years-old with ClMB or A/LCMB were reviewed; survivals were compared.

RESULTS

COG-9921, UKCCSG-CNS9204, COG-P9934 and SJYCO7 employing standard chemotherapy with either no or risk-based irradiation, reported 3-5-year event-free survival (EFS) of 17+/-5%, 33+/-28% (ClMB), 14+/-7% and 13.8+/-9% (ClMB) respectively, with reported EFS of 0% for A/LCMB in UKCCSG-CNS9204 and SJYCO7. HIT-SKK’87, HIT-SKK’92 and HIT-SKK’00 incorporating HD-MTX and IVENT-MTX reported 2-10-year EFS of 30–34+/-10–11% for ClMB and 33+/-27% (HIT-SSK’00) for A/LCMB. Head Start HS-I-II combined, CCG-99703 and HS-III employing induction chemotherapy, with or without HD-MTX, followed by single or tandem HDCx+AuHCR reported 3-5-year EFS of 42+/-14%, 50+/-11% and 27+/-6% for ClMB, with EFS for A/LCMB of 38+/-13% (HS-III). Finally, 5-year overall survivals for ACNS0334, without or with induction HD-MTX, are 39% and 69% respectively for ClMB and A/LCMB combined.

CONCLUSIONS

A trend towards better outcomes for young children with ClMB and A/LCMB is observed in trials including either HD-MTX and IVENT-MTX or including HD-MTX-containing induction chemotherapy and HDCx+AuHCR. Trials excluding HD-MTX, IVENT-MTX and HDCx+AuHCR have poorer outcomes.

MBCL-08. INTEGRATIVE MOLECULAR ANALYSIS OF PATIENT-MATCHED DIAGNOSTIC AND RELAPSED MEDULLOBLASTOMAS

INTRODUCTION

The next generation of clinical trials for relapsed medulloblastoma demands a thorough understanding of the clinical behavior of relapsed tumors as well as the molecular relationship to their diagnostic counterparts.

METHODS

A multi-institutional molecular cohort of patient-matched (n=126 patients) diagnostic MBs and relapses/subsequent malignancies was profiled by DNA methylation array. Entity, subgroup classification, and genome-wide copy-number aberrations were assigned while parallel next-generation (whole-exome or targeted panel) sequencing on the majority of the cohort facilitated inference of somatic driver mutations.

RESULTS

Comprised of WNT (2%), SHH (41%), Group 3 (18%), Group 4 (39%), primary tumors retained subgroup affiliation at relapse with the notable exception of 10% of cases. The majority (8/13) of discrepant classifications were determined to be secondary glioblastomas. Additionally, rare (n=3) subgroup-switching events of Group 4 primary tumors to Group 3 relapses were identified coincident with MYC/MYCN pathway alterations. Amongst truly relapsing MBs, copy-number analyses suggest somatic clonal divergence between primary MBs and their respective relapses with Group 3 (55% of alterations shared) and Group 4 tumors (63% alterations shared) sharing a larger proportion of cytogenetic alterations compared to SHH tumors (42% alterations shared; Chi-square p-value &lt; 0.001). Subgroup- and gene-specific patterns of conservation and divergence amongst putative driver genes were also observed.

CONCLUSION

Integrated molecular analysis of relapsed MB discloses potential mechanisms underlying treatment failure and disease recurrence while motivating rational implementation of relapse-specific therapies. The degree of genetic divergence between primary and relapsed MBs varied by subgroup but suggested considerably higher conservation than prior estimates.

RARE-21. CANCER SPECTRUM IN GERMLINE SUFU MUTATION CARRIERS: A COLLABORATIVE PROJECT OF THE SIOPE HOST GENOME WORKING GROUP

BACKGROUND

Little is known about cancer risk associated with pathogenic germline SUFU variants.

METHODS

Data of all previously published and 25 still unpublished patients with a pathogenic germline SUFU mutation were compiled.

RESULTS

124 patients in 67 families were identified, most of them ascertained after the occurrence of a medulloblastoma (MB) or as part of Gorlin syndrome cohorts. Overall, 30 patients were healthy carriers and 94 patients developed a total of 129 tumors (up to 4 tumors/patient): 68 MBs, always as first tumor (median age at diagnosis: 1.5yr [0.1–5]), 22 patients with at least 1 basal cell carcinoma (BCC) (median 10/patient) (median age at first BCC: 43yr, [17–52]), 15 meningiomas (median age 43yr, [13–72]), 7 ovarian stromal/fibrous tumors (median age 12yr [5–34]), and 17 other tumors including 5 sarcomas (median age: 50yr [7–79]). Median age at last follow-up was 30yr. Nineteen patients died, including 11 from MB. Second malignancies were diagnosed in 21 patients including 13 in MB survivors. Mutations were inherited in 58/66 (88%) of cases in which inheritance could be tested and de novo in 8. In 6/67 families (9%), >2 children were diagnosed with a MB.

CONCLUSION

In this large cohort of germline SUFU mutation carriers, MB in infants is the most frequent tumor but the spectrum also includes typical Gorlin syndrome tumors (BCC, meningiomas, and ovarian stromal/fibrous tumors) either as first tumors or as second malignancies. This broad tumor spectrum and the high risk of second malignancies justify the implementation of specific cancer surveillance programs.

EPCT-05. A PHASE I TRIAL OF THE CDK 4/6 INHIBITOR PALBOCICLIB IN PEDIATRIC PATIENTS WITH PROGRESSIVE OR REFRACTORY CNS TUMORS: A PEDIATRIC BRAIN TUMOR CONSORTIUM (PBTC) STUDY

PBTC-042 was a phase I trial of palbociclib to determine the maximum tolerated dose (MTD) and describe toxicities in children. Palbociclib is an oral, selective cyclin dependent kinase 4/6 inhibitor. METHODS: A rolling-6 design was utilized. Eligible patients were children ≥4 and ≤21 years-old with a progressive/refractory CNS tumor with intact retinoblastoma protein, measurable disease, and ability to swallow capsules. Pharmacokinetic studies were performed during the first course. Here, we report on the heavily pretreated stratum, which included patients who received >4 prior treatment regimens (either chemotherapy or biologic agent), and/or craniospinal irradiation, and/or myeloablative chemotherapy plus stem cell rescue. Palbociclib was initiated at 50 mg/m²/day for 21 consecutive days of a 28-day course. This was one dosage level below the MTD for the less heavily pretreated stratum (75 mg/m²). RESULTS: Fourteen eligible patients were enrolled (median age 12.8 years; male 79%). Eleven patients (79%) had either ependymoma or medulloblastoma. Four eligible and evaluable patients were enrolled at 50 mg/m² with no DLTs. This prompted a dosage increase to 75 mg/m². Ten eligible subjects were enrolled and 7 were evaluable for DLT assessment. One of 7 evaluable patients experienced a DLT (grade 3 thrombocytopenia). This established 75 mg/m² as the MTD for more heavily pretreated patients. Mean ± SD palbociclib apparent oral clearance was 34.6 ± 18.4 L/h/m2. CONCLUSION: The MTD for palbociclib on a 3 week on/1 week off schedule in children with brain tumors is 75 mg/m² and does not appear to be influenced by the degree of prior therapy.

CTNI-27. FIRST-IN-PEDIATRICS PHASE I STUDY OF GDC-0084 (PAXALISIB), A CNS-PENETRANT PI3K/mTOR INHIBITOR, IN NEWLY DIAGNOSED DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG) OR OTHER DIFFUSE MIDLINE GLIOMA (DMG)

BACKGROUND

GDC-0084 is an oral, highly selective and potent inhibitor of class I PI3K and moderate inhibitor of mTOR, with an established adult maximum tolerated dose (MTD) of 60 mg/day and evidence of brain tumor penetration in adult recurrent glioblastoma.

METHODS

We used a rolling-6 design to evaluate the safety and pharmacokinetic (PK) properties and establish the pediatric MTD of once-daily GDC-0084 administered after focal RT in children with newly diagnosed DIPG and histone H3 K27M-mutant DMG. Non-compartmental plasma PK analyses were performed using samples collected on cycle 1 days 1–3 after single-dose and day 28 at steady-state.

RESULTS

Twenty-five patients have been enrolled, 16 of whom were treated at study dosage levels of 27 mg/m2 (n=11) and 35 mg/m2 (n=5). Two dose limiting toxicities (DLTs) observed at 35 mg/m2 were grade 3 mucositis and grade 3 rash. Grade 3 hyperglycemia was the only DLT at 27 mg/m2. The most frequent grade 3 or 4 adverse events attributed to GDC-0084 were rash (5 patients), neutropenia (4), and hyperglycemia (2). After single-dose, GDC-0084 exposures (AUC0-48h) at 27 and 35 mg/m2 were 3399±1301 and 4462±2868 hr·ng/mL, respectively. Mean GDC-0084 half-life was 20.6±9.1 hr, comparable to that observed in adults.

CONCLUSIONS

The dosage of 27 mg/m2 has been established as the pediatric MTD of GDC-0084, which is approximately equivalent to 80% of the adult MTD. At 27 mg/m2, GDC-0084 is well tolerated in children where the spectrum of toxicities is similar to those observed in adults and consistent with this class of agents.

OP0287 A MACHINE LEARNING APPROACH FOR PRECISION STRATIFICATION OF JUVENILE-ONSET SLE

Background:

Juvenile-onset systemic lupus erythematosus (JSLE) is a complex and heterogeneous disease characterised by diagnosis and treatment delays. An unmet need exists to better characterise the immunological profile of JSLE patients and investigate its links with the disease trajectory over time.

Objectives:

A machine learning (ML) approach was applied to explore new diagnostic signatures for JSLE based on immune-phenotyping data and stratify patients by specific immune characteristics to investigate longitudinal clinical outcome.

Methods:

Immune-phenotyping of 28 T-cell, B-cell and myeloid-cell subsets in 67 age and sex-matched JSLE patients and 39 healthy controls (HCs) was performed by flow cytometry. A balanced random forest (BRF) ML predictive model was developed (10,000 decision trees). 10-fold cross validation, Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) and logistic regression was used to validate the model. Longitudinal clinical data were related to the immunological features identified by ML analysis.

Results:

The BRF-model discriminated JSLE patients from healthy controls with 91% prediction accuracy suggesting that JSLE patients could be distinguished from HCs with high confidence using immunological parameters. The top-ranked immunological features from the BRF-model were confirmed using sPLS-DA and logistic regression and included CD19+ unswitched memory B-cells, naïve B-cells, CD14+monocytes and total CD4+, CD8+and memory T-cell subsets.

K-mean clustering was applied to stratify patients using the validated signature. Four groups were identified, each with a distinct immune and clinical profile. Notably, CD8+T-cell subsets were important in driving patient stratification while B-cell markers were similarly expressed across the JSLE cohort. JSLE patients with elevated effector memory CD8+T-cell frequencies had more persistently active disease over time, and this was associated with increased treatment burden and prevalence of lupus nephritis. Finally, network analysis identified specific clinical features associated with each of the top JSLE immune-signature variables.

Conclusion:

Using a combined ML approach, a distinct immune signature was identified that discriminated between JSLE patients and HCs and further stratified patients. This signature could have diagnostic and therapeutic implications. Further immunological association studies are warranted to develop data-driven personalised medicine approaches for JSLE.

Acknowledgments:

Lupus UK, Rosetrees Trust, Versus Arthritis

Disclosure of Interests:

George Robinson: None declared, Junjie Peng: None declared, Pierre Dönnes: None declared, Leda Coelewij: None declared, Meena Naja: None declared, Anna Radziszewska: None declared, Chris Wincup: None declared, Hannah Peckham: None declared, David Isenberg Consultant of: Study Investigator and Consultant to Genentech, Yiannis Ioannou: None declared, Ines Pineda Torra: None declared, Coziana Ciurtin Grant/research support from: Pfizer, Consultant of: Roche, Modern Biosciences, Elizabeth Jury: None declared

OP0006 ABNORMAL IRON METABOLISM AND MITOCHONDRIAL DYSFUNCTION: INVESTIGATING A NOVEL PATHOLOGICAL MECHANISM IN SYSTEMIC LUPUS ERYTHEMATOSUS

Background:

Iron is vital for numerous essential physiological processes including erythropoiesis and energy metabolism (as iron is found in the mitochondrial electron transport chain, the central site of ATP production). Iron homeostasis is tightly controlled by a number of regulators including; 1. Hepcidin, which prevents iron release from stores (under the influence of IL6 and IL1β); 2. Ferritin, an iron storage protein; 3. Lipocalin-2 (LCN2), which is released upon innate immune activation that induces iron sequestration; 4. Transferrin, which binds circulating iron and enables its transport to effector cell targets; 5. Haptoglobin, which binds free haemoglobin and assisting iron recycling; 6. Erythropoietin (EPO), which stimulates erythropoiesis as a result of hypoxia.

Chronic inflammation may result in dysregulation of iron metabolism and in turn impair mitochondrial function yet little is known regarding how these processes change in systemic lupus erythematosus (SLE).

Objectives:

In this study, we investigated how dysregulation of iron metabolism may occur in SLE and subsequently sought to identify how a lack of iron may ultimately induce abnormal mitochondrial function.

Methods:

1. Investigating abnormal iron metabolism in SLE.Serum samples from patients with SLE (n=39) and healthy controls (HC, n=17) were assessed hepcidin, IL-1ß, IL-6, ferritin, LCN2, EPO, haptoglobin and transferrin levels by ELISA. Hierarchical cluster analysis of normalised data (converted to Z-scores) was performed using MeV software in order to characterise patient groups based upon iron metabolism profile. Anti-dsDNA antibody titres, complement C3 levels and SLEDAI-2K were excluded to limit the influence of these variables on cluster analysis. Results were presented as a heatmap.

2. Studying mitochondrial function in iron deficiency and SLE. Peripheral blood mononuclear cells (PBMCs) from HCs and patients with SLE were analysed using Seahorse Respirometry, which measures mitochondrial oxygen consumption rate (a measure of energy metabolism dependent upon oxidative phosphorylation). To assess differences between health, iron deficiency and SLE 3 groups were assessed; 1. PBMCs derived from HCs; 2. PBMCs from patients with SLE; 3. Healthy PBMCs cultured in iron deficient condition, in which cells were treated with the potent iron chelator, Deferiprone.

Results:

Figure 1a demonstrates that four groups were identified following cluster analysis. In spite of excluding markers of disease activity, these groups showed significant differences in SLEDAI-2K (shown in Figure 1b). In summary, patients with more active disease (Groups C and D) showed higher levels of hepcidin (which prevents the release of iron from stores, under the influence of IL-1ß and IL-6) and reduced transferrin thus suggesting that iron is inefficiently transported when compared with those with less active disease (in Groups A and B).

Figure 2a demonstrates that basal mitochondrial respiration is significantly reduced in PBMCs derived from healthy controls when grown in iron deficiency conditions (following treatment with Deferiprone and is lower still in those with SLE. Figure 2b shows that PBMCs from patients with SLE have reduced maximal mitochondrial respiration capacity that is comparable to the levels seen in iron deficient healthy PBMCs.

Conclusion:

Patients with SLE demonstrate abnormalities in iron metabolism that results in cellular iron deficiency as iron is not released from stores, nor adequately transported at the rate required to meet physiological demands. Furthermore, PBMCs derived from patients with SLE who impaired basal and maximal respiration that is comparable with healthy PBMCs treated potent iron chelation. This suggests that abnormal iron metabolism may in turn limit mitochondrial energy metabolism in SLE and represents a potential future therapeutic target.

References:

Nil

Acknowledgments:

Versus Arthritis (Grant No 594143) and LUPUS UK

Disclosure of Interests:

None declared

Phase I study of vemurafenib in children with recurrent or progressive BRAFV600E mutant brain tumors: Pacific Pediatric Neuro-Oncology Consortium study (PNOC-002)

Background: BRAFV600E mutation is present in a subset of pediatric brain tumors. Vemurafenib is an oral, selective ATP-competitive inhibitor of BRAFV600E kinase. The goal of this multi-center study conducted through the Pacific Pediatric Neuro-Oncology Consortium (PNOC) was to determine the recommended phase 2 dose (RP2D) and dose limiting toxicities (DLTs) in children < 18 years with recurrent or progressive BRAFV600E mutant brain tumors. Results: Nineteen eligible patients were enrolled. Eleven patients had received three or more prior therapies. Data reported are from the start of treatment for the first patient (April 30 2014) through August 31 2019. The RP2D was defined as 550 mg/m2 twice daily after DLT criteria adjustment for rash. Related grade ≥ 3 adverse events included secondary keratoacanthoma (n = 1); rash (n =16); and fever (n = 5). Subjects received a median of 23 cycles (range 3-63). Four patients remain on treatment. Centrally reviewed best radiographic responses included 1 complete response, 5 partial responses, and 13 stable disease. The steady-state area under the curve (AUC0-∞median) was 604 mg*h/L (range 329-1052). Methods: Vemurafenib was given starting at 550 mg/m2, twice daily which corresponds to the adult RP2D. Adverse events were graded using the NIH Common Terminology Criteria for Adverse Events (CTCAE) version 4.0. Central imaging review was performed. Pharmacokinetic sampling was performed. Conclusions: Vemurafenib has promising anti-tumor activity in recurrent BRAF V600E-positive brain tumors with manageable toxicity. A phase 2 study is ongoing (NCT01748149).