tbuckley/cabot-search huggingface dataset:
RADT-14. COMPARISON OF MACHINE LEARNING ALGORITHMS IN DISTINGUISHING RADIATION NECROSIS FROM PROGRESSION OF BRAIN METASTASES TREATED WITH STEREOTACTIC RADIOSURGERY (SRS)
Authors: Xuguang Chen, Vishwa Parekh, Luke peng, Michael Chan, Michael Soike, Emory McTyre, Michael Jacobs, Lawrence Kleinberg
Journal: Neuro-Oncology (2020)

Abstract PURPOSE To test the effectiveness of machine learning algorithms in distinguishing radiation necrosis (RN) from tumor progression (TP) using MRI radiomic features. METHODS Brain metastases were treated with SRS to a median dose of 18Gy. Lesions that showed evidence of progression on follow-up MRI were sampled surgically, and diagnoses confirmed by histopathology. Cases from 2 institutions were combined and randomly assigned for training (70%) and testing (30%). T1 post-contrast (T1c) and T2 fluid attenuated inversion recovery (T2 FLAIR) MRI were used for radiomic feature extraction (50 features each). Three subsets of radiomic features were obtained and tested: Signature #1 included 10 previously published features that correlated with diagnosis on T test; signature #2 and #3 included 5 and 12 features obtained through recursive elimination using random forest (RF) and support vector machine (SVM), respectively. Supervised machine learning models were trained using RF, SVM (radial kernel) and regularized discriminant analysis (RDA) algorithms based on all three radiomics signatures. Receiver operator characteristics (ROC) were compared between signatures and algorithms. RESULTS A total of 135 individual lesions (37 RN and 98 TP) were included. Signature #3 demonstrated the highest area under the curve in the training set (average AUC=0.98, vs 0.95 and 0.92 for signature #1 and #2), as well as the testing set (average AUC=0.83, vs 0.74 and 0.79 for signature #1 and #2). RF and SVM demonstrated similar performance in both training (average AUC 0.99-1) and testing datasets (average AUC 0.79-0.80) among all three signatures. Both RF and SVM were superior to RDA in performance (average training AUC 0.83, testing AUC 0.77). The greatest sensitivity (83%) and specificity (100%) in the testing set were achieved using signature #3 and SVM. CONCLUSION RF and SVM are effective in distinguishing RN from TP in a multi-institution dataset using radiomic signatures.
CSIG-15. INNOVATIVE COMPUTATIONAL PLATFORM ADDRESSES PROSTAGLANDIN E RECEPTOR 3 AS THE MASTER REGULATOR MEDIATING RESISTANCE TO TUMOR TREATING FIELDS IN GLIOBLASTOMA CELLS
Authors: Dongjiang Chen, Son Le, Tarun Hutchinson, David Tran
Journal: Neuro-Oncology (2020)

Abstract OBJECTIVES Tumor Treating Fields (TTFields) are approved in combination with temozolomide for newly diagnosed glioblastoma (GBM). TTFields are low-intensity alternating electric fields that are thought to disturb mitotic macromolecules’ assembly. The addition of TTFields resulted in a significant improvement in overall survival. However, most GBM patients eventually develop resistance to TTFields and the mechanism remains unexplored. METHODS Multiple GBM cell lines were treated continuously at clinically approved frequency of 200 kHz using an in vitro TTFields system until cells with relative resistance to the cytotoxic effects of TTFields. A systems approach aided by innovative network ranking computational algorithms were utilized to analyze global gene expression profiles and identify resistance pathways, which were subsequently validated experimentally. RESULTS TTFields-induced chromosomal instability is preserved in resistant cells, indicating that TTFields resistance is mediated through a non-biophysical mechanism. This acquired TTFields resistance phenotype is associated with a transition of GBM cells to a stem-like state as determined by a neurosphere assay, stemness markers such as CD44 and increased tumorigenesis when implanted into mouse brain. Using an innovative computational platform-NETZEN, we methodically dissected this stemness program in resistant cells. 3 networks were found disrupted and all play critical roles in GBM stemness. Mechanistically, Prostaglandin E Receptor 3 (PTGER3) is the top ranked regulator responsible for resistance. PTGER3 is rapidly upregulated both in vitro and in vivo upon exposure to TTFields and further increases with prolonged treatment as resistance sets in. Immunofluorescence staining shows PTGER3’s nuclear translocation along with Lamin A/C disruption in response to TTFields. Pharmacological inhibition of PTGER3 using aspirin or PTGER3-specific inhibitors resensitized or prevent cells becoming resistance to TTFields. CONCLUSIONS We have identified a novel regulator PTGER3 at the apex that plays a critical role in TTFields resistance. This is a potential therapeutic target to reduce resistance to TTFields therapy in GBM.
IMG-15. PEDIATRIC GLIOBLASTOMAS CONTRAST ENHANCEMENT PATTERN IS PREDICTIVE OF SURVIVAL
Authors: Zsila Sadighi, Halyna Pokhylevych, Maria Gule-Monroe, Melissa Chen, Greg Fuller, Stephen Gruschkus, David Sandberg, Susan McGovern, Mary Frances McAleer, Wafik Zaky, Soumen Khatua, Jason Johnson
Journal: Neuro-Oncology (2020)

Abstract BACKGROUND Pediatric GBMs are rare, accounting for 3% of all pediatric CNS tumors. Despite advances in treatment, the outcomes for pediatric glioblastomas (GBM) have not significantly improved. Research suggests a link between enhancement patterns and survival in adult patients with glial tumors. We sought to study this relationship in a cohort of pediatric GBMs. METHODS A radiology database was searched for cases &amp;lt; 22 years, pathology proven brain glioblastoma, and pre-surgical MR imaging available for review. Based on pre-treatment, T1-contrast enhanced MR images, size, and contrast enhancement patterns were characterized as focal, diffuse, or ring-like. The extent of resection was assessed by comparing pre- and post-surgery T2 hyperintensity and contrast enhancement. RESULTS 64 eligible patients (age 2-21y, 14.6 + 5.4) were identified. The majority of lesions demonstrated enhancement on gadolinium-enhanced T1 imaging. (n=58/64; 90%). The lesions were categorized into six (9.4%) cases with focal enhancement, 37 (57.8%) cases with diffuse enhancement, and 15 (23.4%) with ring-like enhancement. Patients who received GTR/subtotal resection (STR) and had focal-enhanced GBMs had a significantly longer progression-free survival (PFS) – 14.1 months (p = 0.0308), comparing to diffuse and ring-like enhancing glioblastomas which had respectively 13.9 and 5.5 months of PFS. DISCUSSION Our data suggests that the contrast enhancement pattern is a significant prognostic factor for survival in pediatric GBM. Patients with GTR/STR who had focal-enhancing GBMs had a significantly longer progression-free survival (p=0.03) comparing to other enhancement patterns.
Neuropsychiatric symptoms are early indicators of an upcoming metabolic decline in Alzheimer’s disease
Authors: Kok Pin Ng, Tharick A. Pascoal, Sulantha Mathotaarachchi, Yiong Huak Chan, Lai Jiang, Joseph Therriault, Andrea L. Benedet, Monica Shin, Nagaendran Kandiah, Celia M. T. Greenwood, Pedro Rosa-Neto, Serge Gauthier
Journal: Translational Neurodegeneration (2021)

Abstract Background Neuropsychiatric symptoms (NPS) are increasingly recognized as early non-cognitive manifestations in the Alzheimer’s disease (AD) continuum. However, the role of NPS as an early marker of pathophysiological progression in AD remains unclear. Dominantly inherited AD (DIAD) mutation carriers are young individuals who are destined to develop AD in future due to the full penetrance of the genetic mutation. Hence, the study of DIAD mutation carriers enables the evaluation of the associations between pure AD pathophysiology and metabolic correlates of NPS without the confounding effects of co-existing pathologies. In this longitudinal study, we aimed to identify regional brain metabolic dysfunctions associated with NPS in cognitively intact DIAD mutation carriers. Methods We stratified 221 cognitively intact participants from the Dominantly Inherited Alzheimer’s Network according to their mutation carrier status. The interactions of NPS measured by the Neuropsychiatric Inventory-Questionnaire (NPI-Q), age, and estimated years to symptom onset (EYO) as a function of metabolism measured by [ 18 F]flurodeoxyglucose ([ 18 F]FDG) positron emission tomography, were evaluated by the mixed-effects regression model with family-level random effects in DIAD mutation carriers and non-carriers. Exploratory factor analysis was performed to identify the neuropsychiatric subsyndromes in DIAD mutation carriers using the NPI-Q sub-components. Then the effects of interactions between specific neuropsychiatric subsyndromes and EYO on metabolism were evaluated with the mixed-effects regression model. Results A total of 119 mutation carriers and 102 non-carriers were studied. The interaction of higher NPI-Q and shorter EYO was associated with more rapid declines of global and regional [ 18 F]FDG uptake in the posterior cingulate and ventromedial prefrontal cortices, the bilateral parietal lobes and the right insula in DIAD mutation carriers. The neuropsychiatric subsyndromes of agitation, disinhibition, irritability and depression interacted with the EYO to drive the [ 18 F]FDG uptake decline in the DIAD mutation carriers. The interaction of NPI and EYO was not associated with [ 18 F]FDG uptake in DIAD mutation non-carriers. Conclusions The NPS in cognitively intact DIAD mutation carriers may be a clinical indicator of subsequent metabolic decline in brain networks vulnerable to AD, which supports the emerging conceptual framework that NPS represent early manifestations of neuronal injury in AD. Further studies using different methodological approaches to identify NPS in preclinical AD are needed to validate our findings.
Secondary transmission of COVID-19 in preschool and school settings in northern Italy after their reopening in September 2020: a population-based study
Authors: Elisabetta Larosa, Olivera Djuric, Mariateresa Cassinadri, Silvia Cilloni, Eufemia Bisaccia, Massimo Vicentini, Francesco Venturelli, Paolo Giorgi Rossi, Patrizio Pezzotti, Emanuela Bedeschi
Journal: Eurosurveillance (2020)

We report epidemiological investigations of transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 41 classes of 36 schools in Reggio Emilia province, northern Italy, from their reopening on 1 September to 15 October 2020. The overall secondary case attack rate was 3.2%, reaching 6.6% in middle and high schools. More timely isolation and testing of classmates could be effective in reducing virus transmission in this setting.
NCOG-73. EFFECT OF TIME TO DIAGNOSIS IN CHILDREN WITH MALIGNANT CENTRAL NERVOUS SYSTEM TUMORS ON SURVIVAL OUTCOMES AND DISEASE-ASSOCIATED MORBIDITY: AN INSTITUTIONAL COHORT STUDY
Authors: Rebecca Ronsley, Mike Irvine, Mehima Kang, Ran Goldman, Sylvia Cheng
Journal: Neuro-Oncology (2020)

Abstract OBJECTIVE To determine the impact of time to diagnosis on disease related morbidity and mortality. METHODS This is a retrospective review of all diagnoses of malignant CNS tumors in children presenting to BC Children’s Hospital (BCCH) from 2000-2019. Analyses were conducted to assess the relationship between time to diagnosis and overall survival as well as long-term morbidity; stratified by tumor type, age and presence of metastatic disease. RESULTS From 2000-2019, there were 116 children diagnosed with malignant CNS tumors at BCCH (mean age 9.5 years, 67% male). Tumors included medulloblastoma (27, 23.3%), ependymoma (14, 12.1%), high grade gliomas (19, 16.4%), CNS germ cell tumors (40, 34.4%), and other embryonal CNS tumors (16, 13.8%). Median time to diagnosis from first symptom onset was 63 days (IQR 26.5 – 237.5 days). 18% had metastatic disease. Within this cohort, 3-year EFS was 57%, and 5-year overall survival was 78.4%. 64% of patients were alive with no evidence of disease at median follow up from treatment completion of 4.31 years (IQR 1.77 – 6.15 years). Long-term morbidity included panhypopituitarism (20.7%), vision loss(22.4%), hearing loss(30.2%), learning disability(17.2%) and cognitive impairment (19.8%). In a cox proportional hazards model, overall survival was associated with time to diagnosis(estimate 0.0271;SE=1.6500;p=0.028), high grade glioma(estimate 8.3200; SE=0.6650; p=0.001), age at diagnosis(estimate 0.8590; SE=0.0532; p=0.004), relapse (estimate 4.9600; SE=0.6100; p=0.009) and metastatic disease (estimate 9.1700; SE=0.5660; p&amp;lt; 0.001). Vision loss was also significantly correlated with time to diagnosis (estimate 0.542; SE=0.2940; p=0.038). CONCLUSION Median time to diagnosis is associated with overall survival and long-term morbidity in pediatric patients treated for malignant CNS tumors. These data highlight that knowledge translation to the public, primary care and emergency room professionals should be a priority in order to promote early connection with medical care and mitigate morbidity and mortality in those with pediatric CNS tumors.
High Prevalence of Pulmonary Sequelae at 3 Months after Hospital Discharge in Mechanically Ventilated Survivors of COVID-19
Authors: Rob J. J. van Gassel, Julia L. M. Bels, Anne Raafs, Bas C. T. van Bussel, Marcel C. G. van de Poll, Sami O. Simons, Lieke W. L. van der Meer, Hester A. Gietema, Rein Posthuma, Susanne van Santen
Journal: American Journal of Respiratory and Critical Care Medicine (2020)
CSIG-06. PLATELET DERIVED GROWTH FACTOR RECEPTOR ALPHA AS AN ONCOGENIC DRIVER IN GLIOBLASTOMA
Authors: Artem Berezovsky, Susan Irtenkauf, Andrea Transou, Laura Hasselbach, Tom Mikkelsen, Ana de Carvalho
Journal: Neuro-Oncology (2020)

Abstract Activated platelet derived growth factor receptor alpha (PDGFRα) is essential for the maintenance of oligodendrocyte progenitors. Differential signaling results from phosphorylation of specific tyrosine residues in the kinase insert (KI) domain present in most RTKs in variable length. Our goal is to identify the molecular contexts in which PDGFRA activation is an essential driver for maintenance of the malignant phenotype in glioblastoma. RNA sequencing was conducted on 13 glioblastoma mouse orthotopic PDXs (n=3/line). PDGFRA mRNA overexpression was observed for 3 glioblastomas: one carrying PDGFRA extrachromosomal (ecDNA) amplification (HF3253) and two non-amplified (Tukey p=0.41, 0.19). Corresponding PDGFRα KI activation (pY754) was observed only for HF3253. To assess activation as an adaptation to microenvironmental pressures, pY754 was quantified by reverse phase protein array on 4 growth conditions (normal, -growth factors, two serum concentrations) for 8 neurospheres. PDGFRɑ activation was highest in growth factor-depleted conditions in the absence of exogenous ligand (Tukey p=0.02). Taking advantage of genomic heterogeneity in HF3253, we isolated cellular lineages with divergent frequencies of PDGFRA ecDNA. PDGFRA copy number (TaqMan) decreased longitudinally. PDX tumors from higher passage had slower tumor growth due to strong selection for initial low frequency PDGFRA ecDNA-amplified clones. IHC showed that the tumors had comparably high total and activated PDGFRα to low passage tumors. Further exploiting intra-tumoral heterogeneity, we have isolated single cell clones. Tumor growth was reduced in 2 ecDNA(-) tumors compared to parental ecDNA(+) (log-rank test p= 3e-3, 1e-3). In contrast to parental, ecDNA(-) tumors demonstrated diffuse tumor morphology and weak PDGFRα activation. The staining index (mean intensity x area) for the ecDNA(-) clones was significantly lower than the ecDNA(+) (1-wayANOVA p=2e-16). We established dependency on PDGFRα signaling in a patient-derived glioblastoma model. Our data demonstrates that detection of ecDNA-amplified PDGFRA has the potential to be a predictive biomarker of future PDGFRɑ-targeted therapies.
LINC-06. OBSERVATION ONLY IN A PATIENT WITH SUSPECTED LOW GRADE GLIOMA. SHOULD NEUROSURGERY ALWAYS BE THE FIRST STEP IN LOW AND MIDDLE INCOME COUNTRIES?
Authors: Carlos Leal - Cavazos, Jose Arenas-Ruiz, Oscar Vidal-Gutierrez
Journal: Neuro-Oncology (2020)

Abstract BACKGROUND Low grade gliomas (LGGs) are the most frequent pediatric brain tumor and they comprise a variety of histologies. Complete surgery is curative but sometimes its location makes it difficult. Recent publications highlight the excellent long-term outcomes of patients with LGGs with complete and incomplete resected tumors. Current strategies are focused on reducing risks of treatment related sequelae. METHOD We describe a patient with a suspected LGG managed by close observation. We describe the case of a 6 year old female with 5 months history of focal onset seizures. During this time a brain MRI was requested and tumor was evidenced. After “tumor diagnosis” was made family visited a handful of private neurosurgeons with a uniformly dismal prognosis and high risk morbidity from procedures offered. When first seen at our Hospital, the clinical history seemed compatible with a LGG and seizures well controlled with antiepileptic drugs. Neurological examination was completely normal. MRI showed a large tumor (7x5x5 cm) hypointense on T1, hyperintense on T2, without contrast enhancement, involving the right temporal lobe white matter, insula, internal capsule, hipoccampus, thalamus and mesencephalus with middle cerebral artery encasement. Interval imaging was proposed and after 4.5 years since diagnosis the tumor has been stable and patient clinically excellent. CONCLUSION Overall survival in pediatric LGGs is excellent and risk of sequelae should always be part of multidisciplinary team considerations. In centers with significant neurosurgical morbidity, biopsy of large tumors that are compatible with LGG may not be required in selected cases.
4-1BB co-stimulation further enhances anti-PD-1-mediated reinvigoration of exhausted CD39<sup>+</sup>CD8 T cells from primary and metastatic sites of epithelial ovarian cancers
Authors: Galam Leem, Junsik Park, Minwoo Jeon, Eui-Soon Kim, Sang Wun Kim, Yong Jae Lee, Seong Jin Choi, Baekgyu Choi, Seongyeol Park, Young Seok Ju, Inkyung Jung, Sunghoon Kim, Eui-Cheol Shin, Jung Yun Lee, Su-Hyung Park
Journal: Journal for ImmunoTherapy of Cancer (2020)

Background Responses to immunotherapy vary between different cancer types and sites. Here, we aimed to investigate features of exhaustion and activation in tumor-infiltrating CD8 T cells at both the primary and metastatic sites in epithelial ovarian cancer. Methods Tumor tissues and peripheral blood were obtained from 65 patients with ovarian cancer. From these samples, we isolated tumor-infiltrating lymphocytes (TILs) and peripheral blood mononuclear cells. These cells were used for immunophenotype using multicolor flow cytometry, gene expression profile using RNA sequencing and ex vivo functional restoration assays. Results We found that CD39 + CD8 TILs were enriched with tumor-specific CD8 TILs, and that the activation status of these cells was determined by the differential programmed cell death protein 1 (PD-1) expression level. CD39 + CD8 TILs with high PD-1 expression (PD-1 high ) exhibited features of highly tumor-reactive and terminally exhausted phenotypes. Notably, PD-1 high CD39 + CD8 TILs showed similar characteristics in terms of T-cell exhaustion and activation between the primary and metastatic sites. Among co-stimulatory receptors, 4-1BB was exclusively overexpressed in CD39 + CD8 TILs, especially on PD-1 high cells, and 4-1BB-expressing cells displayed immunophenotypes indicating higher degrees of T-cell activation and proliferation, and less exhaustion, compared with cells not expressing 4-1BB. Importantly, 4-1BB agonistic antibodies further enhanced the anti-PD-1-mediated reinvigoration of exhausted CD8 TILs from both primary and metastatic sites. Conclusion Severely exhausted PD-1 high CD39 + CD8 TILs displayed a distinctly heterogeneous exhaustion and activation status determined by differential 4-1BB expression levels, providing rationale and evidence for immunotherapies targeting co-stimulatory receptor 4-1BB in ovarian cancers.
GCT-66. FINAL REPORT OF THE PROSPECTIVE NEXT/CNS-GCT-4 CONSORTIUM TRIAL (GemPOx FOLLOWED BY MARROW-ABLATIVE CHEMOTHERAPY) IN PATIENTS WITH REFRACTORY/RECURRENT CNS GERM CELL TUMORS
Authors: Margaret Shatara, Megan Blue, Joseph R Stanek, Allison Y Liu, Diana S Osorio, Mohamed S AbdelBaki, Daniel Prevedello, Vinay Puduvalli, Pierre Giglio, Sharon Gardner, Jeffrey Allen, Kenneth E Wong, Girish Dhall, Jonathan L Finlay
Journal: Neuro-Oncology (2020)

Abstract BACKGROUND We report the responses, toxicities and long-term outcomes of gemcitabine, paclitaxel and oxaliplatin (GemPOx) regimen administered, in responsive patients, prior to single cycle marrow-ablative chemotherapy (thiotepa, etoposide and carboplatin) with autologous hematopoietic progenitor cell rescue (HDCx+AuHPCR). METHODS Since December 2009, 11 recurrent/refractory patients (10 MMGCT, 1 germinoma; 10 males; mean age 16.5 years, range 7–46 years) have been treated with up to four cycles of gemcitabine (800mg/M2), paclitaxel (170mg/M2) and oxaliplatin (100mg/M2) administered on one day at 14 days intervals. RESULTS All 11 patients were enrolled on a prospective multi-center trial, which was closed in October 2019. Three patients achieved complete remissions (tumor marker and/or imaging studies), five achieved partial remissions, two developed disease progression (PD), and one was withdrawn after one cycle for severe paclitaxel neurotoxicity followed by rapid tumor progression and death. One patient with PD after one cycle had pathologically-confirmed metastatic transformation to pure embryonal rhabdomyosarcoma, and rapidly expired. A second patient, with pure pineal choriocarcinoma, progressed after the second GemPOx cycle, ultimately died of tumor progression. Eight of the 11 responsive patients subsequently underwent HDCx+AuHPCR; five of these received some form of radiotherapy. Seven patients (six MMGCT, one germinoma) are alive and disease-free without recurrence for a mean of 94 months (range 74–118 months) since completion of therapy. CONCLUSION GemPOx is an effective re-induction regimen for patient with recurrent CNS germ cell tumors, with acceptable toxicities; when followed by marrow-ablative chemotherapy and subsequent irradiation/re-irradiation, the regimen produces encouraging long-term disease-free survival.
Abstract 12042: Genetic Disruption of Histone Deacetylase 6 Protects the Heart by Preserving Mitochondrial Complex I During Ischemia/reperfusion Injury in Diabetes
Authors: Zhi-Dong Ge, Shelley L Baumgardt, Yanan Liu, Shigang Qiao, Zeljko J Bosnjak, Judy Kersten, Joseph M Forbess
Journal: Circulation (2019)

Introduction: Diabetes exacerbates myocardial ischemia/reperfusion injury (IRI) and impairs mitochondrial function. The inhibitors of histone deacetylase (HDAC) are recently shown to attenuate myoc...