bluuebunny/crossref_metadata_2025_split huggingface dataset:
BIOM-40. ANALYSIS OF SERUM MIRNA IN GLIOBLASTOMA PATIENTS: TARGETED ENRICHMENT OF EXTRACELLULAR VESICLES ENHANCES SPECIFICITY FOR PROGNOSTIC SIGNATURE
Authors: Tzaridis Theophilos , Weller Johannes , Bachurski Daniel , Schäfer Niklas , Schaub Christina , Hallek Michael , Scheffler Björn , Glas Martin , Hartmann Gunther , Herrlinger Ulrich , Wild Stefan , Coch Christoph , Reiners Katrin 
Published: December 2020

Abstract
Glioblastoma is a devastating disease, for which biomarkers allowing a prediction of prognosis are urgently needed. microRNAs have been described as potentially valuable biomarkers in cancer. Here, we studied a panel of microRNAs in extracellular vesicles (EV) from the serum of glioblastoma patients and also in total serum without prior EV separation, and evaluated their correlation with the survival of these patients. Our study included 55 patients in total, 26 (47.3%) of which were treated within the multicenter Phase III CeTeG/NOA-09 trial and 29 (52.7%) in the Division of Clinical Neurooncology of the University Hospital of Bonn, as well as 10 healthy volunteers (HV). Blood was drawn from patients during the adjuvant chemotherapeutic treatment. A panel of 15 microRNAs was studied by quantitative real-time PCR in EV that were separated by size-exclusion chromatography, followed by CDxx* immunoprecipitation (SEC+CDxx*), and compared with those from total serum of glioblastoma patients and HV. Comparing SEC+CDxx* to total serum, we found evidence for enrichment of miR-21-3p and miR-106a-5p and, conversely, lower levels of miR-15b-3p in SEC+CDxx* EV. miR-15b-3p and miR-21-3p were upregulated in serum of glioblastoma patients compared to healthy subjects. Significant correlation with survival of the patients was found for levels of miR-15b-3p in total serum and miR-15b-3p, miR-21-3p, miR-106a-5p and miR-328-3p in SEC+CDxx* EV. Combining miR-15b-3p in serum or miR-106a-5p in SEC+CDxx* EV with any one of the other three microRNAs in SEC+CDxx* EV allowed for a prognostic stratification of glioblastoma patients. We have thus identified four microRNAs whose levels, in combination, can predict the prognosis for these patients. *=Cluster of Differentiation xx (CDxx); Molecule cannot be specifically mentioned due to pending patent.
BIOM-41. GENETIC MARKERS CORRELATED WITH PROGRESSION-FREE SURVIVAL TIMES IN GLIOBLASTOMA PATIENTS UNDERGOING TREATMENT WITH TUMOR TREATING FIELDS
Authors: Monson Caitlin , Tipps Megan , Jackson Kelsey , Tierney Meghan , Banerji Nilanjana , Trusheim John 
Published: December 2020

Abstract

INTRODUCTION
Despite advances in surgical approaches, followed by chemo-radiotherapy protocols, the overall prognosis for patients with glioblastoma remains poor. Clinical trials have demonstrated that the use of low intensity alternating electric fields, known as Tumor Treating Fields (TTFields), via the Optune™ device extends overall survival times when combined with standard chemotherapy. However, the response to TTFields varies across patients, and it is currently unclear why some patients show increased time to tumor progression with TTFields treatment while others do not. One possible answer lies in the biological diversity of the tumors themselves. Genetic alterations are known to impact survival times and chemotherapy sensitivity in glioblastoma, suggesting that certain markers may also predict responsiveness to TTFields. Here, we compare the genetic profile of primary glioblastoma tumors with progression times in patients receiving TTFields treatment.

METHODS
Patients with primary glioblastoma who chose treatment with the Optune™ device were prospectively enrolled and a sample from their primary tumor resection was sent for FoundationONE CDx™ testing. Genetic alteration results, including mutation burden and copy number alterations, were then compared with clinical data and tumor progression times.

RESULTS
Mutations and/or copy number changes in genes that regulate cell growth/proliferation, apoptosis, and interactions with DNA were among the most common alterations observed in our cohort. For patients that recurred within 12 months, we found a common pattern of alterations that includes CDKN2A/2B co-deletion, MTAP deletion, and PIK3 mutations. This pattern was not observed in patients that recurred after 12 months.

CONCLUSION
The identification of genetic markers that predict treatment responsiveness may help direct patients toward optimal treatment options. Ongoing work is aimed at expanding our sample size, correlating these genetic markers with overall patient survival, and determining if this pattern of expression is specifically related to TTFields treatment response.
BIOM-44. GENOMIC PREDICTORS OF ADVERSE EVENTS IN NEWLY DIAGNOSED IDH-WILDTYPE GLIOBLASTOMA
Authors: Jane Lim-Fat Mary , Rahman Rifaquat , Muzikansky Alona , Woodward Eleanor , Whorral Sydney , Allen Marie , Touat Mehdi , Iorgulescu Bryan , Youssef Gilbert , Chukwueke Ugonma , Mcfaline-Figueroa Jose , Nayak Lakshmi , Lee Eudocia , Reardon David , Huang Raymond , Beroukhim Rameen , Bi Wenya Linda , Ligon Keith , Wen Patrick 
Published: December 2020

Abstract

BACKGROUND
Adverse outcomes including lymphopenia, thromboembolism (VTE), pseudoprogression and seizures cause significant morbidity in glioblastoma (GBM) patients. The association between genomic biomarkers and adverse outcomes in IDH-wildtype (IDH-wt) GBM needs to be further validated.

METHODS
We identified 1,011 consecutive adult patients with histologically confirmed GBM with OncoPanel testing (capture-based next-generation sequencing of 447 cancer-associated genes) at Dana-Farber Cancer Institute from 2013–2019. IDH-mutant patients and those without consistent follow-up at DFCI were excluded. Seizure at presentation, lymphopenia (absolute lymphocyte count &lt; 1.0x109/L) at the beginning and end of chemoradiation, VTE, radiographic pseudoprogression (&lt; 6 months of RT end) and early progression (&lt; 6 months since completing RT) were identified retrospectively as adverse events. Single nucleotide variants and indels of relevant genes (Tier 1 or 2 mutations) and copy number analysis were derived. Variables were compared using Wilcoxon rank-sum test or Fisher’s Exact test with p&lt; 0.05 indicating statistical significance.

RESULTS
Among 557 patients included, 198/508 (39%) had MGMT-methylated GBMs. Seizure at presentation occurred in 176/542 (32%) and was more common in TP53- or RB1-mutant GBM. Pre-RT 83/338 (25%), but not post-RT lymphopenia (249/367, 68%), was associated with PIK3CA mutation. VTE was detected in 74/509 (15%) during follow-up and was associated with mutations in PIK3CA and POLE. Pseudoprogression was noted in 43/457 (9%) of patients and was not associated with MGMT status or genomic alterations. Early progressive disease occurred in 33% of patients and was associated with unmethylated MGMT, PIK3CA, STAG2 and PTPN11 mutations. Median overall survival for the entire cohort was 17.5 months.

CONCLUSION
PIK3CA mutations were associated with baseline lymphopenia, risk of VTE and early progression in this cohort. Genomic biomarkers may help identify patients at higher risk of select adverse events in IDH-wt GBM. This could benefit patients through tailoring of supportive care and prophylactic therapies.
BIOM-54. A RAPID GENOTYPING PANEL FOR SENSITIVE AND SPECIFIC SEGREGATION OF CNS PATHOLOGIES
Authors: Gupta Mihir , Burns Evan , Georgantas Nicholas , Thierauf Julia , Nayyar Naema , Burns Ryan , Velarde Jose , Brastianos Priscilla , Dietrich Jorg , Marble Hetal , Lennerz Jochen , Romero Javier , Tateishi Kensuke , Cahill Daniel , Shankar Ganesh 
Published: December 2020

Abstract
Primary central nervous system lymphoma (PCNSL) remains challenging to diagnose due to nonspecific clinical and radiologic features and low diagnostic yields of cerebrospinal fluid (CSF) studies. We sought to characterize the diagnostic approach of suspected PCNSL, in order to improve clinical workflow. We first reviewed 1,007 new brain lesions of unknown etiology that included PCNSL in the radiologic differential diagnosis. The most common final diagnoses included high-grade glioma (28.2%) and PCNSL (14.6%). Diagnostic biopsies were frequently performed for high-grade glioma (100%) and PCNSL (94.4%), while CSF was frequently sampled for PCNSL (78.7%). We next identified 159 patients with an established new diagnosis of PCNSL. CSF studies were non-diagnostic in 86.7% of cases, whereas biopsy was positive in 93%. However, intraoperative histopathology was inconclusive for PNCSL in 54.5%, likely contributing to 22% of patients undergoing surgical resection. These challenges resulted in 12 days median time to treatment initiation, and readmission for further workup or treatment initiation in 27% of patients. These results indicated the need for a rapid, sensitive and specific platform to segregate PCNSL and glioma using CSF and tissue samples. We developed a qPCR-based assay to genotype the MYD88 L265P hotspot mutation from CSF and plasma within 80 minutes of sample acquisition. Results were concordant with orthogonal DNA sequencing in extracts from 87 archived specimens, with detection limits of 490pg of input genomic DNA and 0.15% mutant allele frequency. When performed simultaneously with assays for TERT promoter, IDH1/2, H3F3A and BRAF point mutations, the resulting panel accurately segregated PCNSL and adult diffuse glioma molecular diagnoses in 87 archived specimens and 19 prospective liquid biopsies, including cases of lymphoma and glioma. We propose that inclusion of targeted analysis of these mutually exclusive recurrent molecular alterations characterizing gliomas and PCNSL will facilitate rapid, sensitive diagnosis from solid and liquid biopsies.
BIOM-56. THE INTEGRATION OF A LIQUID BIOPSY PROGRAM INTO THE CARE OF PEDIATRIC BRAIN TUMOR PATIENTS
Authors: Miller Alexandra , Szalontay Luca , Ahmad Hamza , Bouvier Nancy , Rodriguez-Sanchez Irene , Bale Tejus , Benayed Ryma , Arcila Maria , Donzelli Maria , Dunkel Ira , Gilheeney Stephen , Khakoo Yasmin , Kramer Kim , Sait Sameer Farouk , Souweidane Mark , Mellinghoff Ingo , Karajannis Matthias 
Published: December 2020

Abstract
Pediatric CNS tumors remain the leading cause of cancer-related death in children and adolescents. Safe sampling of tumor tissue for diagnostic purposes may be difficult if not impossible. Detection of minimal residual or recurrent disease prior to definitive clinical or radiographic progression may allow earlier initiation of novel therapies and ultimately improve overall survival. Given the rarity of serial sampling of tumor tissue, our understanding of molecular evolution in response to therapy remains limited. Recent technological advances have led to the development of “liquid biopsy” assays, which detect cell-free DNA (cfDNA) in blood, cerebrospinal fluid (CSF) or other bodily fluids. Here, we report our initial clinical experience with the recently established MSK Kids pediatric neuro-oncology liquid-biopsy program at Memorial Sloan Kettering Cancer Center (MSKCC) using MSK-IMPACT, which is clinically validated by the New York State Department of Health for CSF cell-free DNA (cfDNA)vprofiling. All CSF samples were collected as part of clinical care, and results reported to both clinicians and patients/families. Samples from 29 unique patients were sequenced. Histopathology included high-grade glioma (5); low-grade glioma (2); medulloblastoma (8); pineoblastoma (3); retinoblastoma (4); other (7). CSF cfDNA could be detected in 18/42 samples (43%) and 12/29 patients (34%). CSF cfDNA was more commonly detected in higher-grade, disseminated tumors such as high-grade glioma (60%), medulloblastoma (38%), and pineoblastoma (100%). Low-grade lesions without leptomeningeal involvement did not result in detectable CSF cfDNA shedding (86% were negative). In a subset of patients, MSK-IMPACT identified previously unrecognized molecular actionable targets (e.g. BRAF-KIAA1549 fusion); or the detection of “minimal residual disease” prior to the detection of tumor recurrence by conventional diagnostics, impacting clinical care decisions. Future directions include integration of CSF cfDNA into prospective clinical trials as a correlative biomarker.
BIOM-61. FUNCTIONAL DIAGNOSTIC TESTING OF LIVE-CELL DRUG RESPONSE USING 3D PATIENT DERIVED GLIOBLASTOMA SPHEROIDS ON THE INCUCYTE PLATFORM
Authors: Malinowski Seth , Touat Mehdi , Stockslager Max , Giglio Ross , Geduldig Jack , Sinai Claire , Pelton Kristine , Reardon David , Wen Patrick , Chow Kin Hoe , Manalis Scott , Ligon Keith 
Published: December 2020

Abstract
Three-dimensional patient derived cultures hold great potential for use as personalized functional diagnostics, enabling more accurate preclinical evaluations of drug treatments compared to conventional cell lines. Optical imaging of live cells allows for continuous, time lapsed measurements, and can provide drug response data based on rich phenotypic changes of cell cultures. However, current imaging techniques based on 2D microscopy evaluation aren’t readily adaptable to evaluate the drug response of intact spheroids, which may better represent the in vivo environment and retain critical cellular interactions within the tumor microenvironment. Using the IncuCyte live cell imaging platform, we successfully imaged a large cohort (n = 77) of patient derived glioblastoma spheroid cultures and evaluated whether changes in sphere volume could be used as a direct measure of treatment response. Improving on the default Incucyte analysis software, we developed an R data processing pipeline better suited for spheroid measurements, which quantified the heterogeneity in GBM baseline spheroid growth, and calculated a drug response score based on spheroid changes in response to DNA damaging agents (TMZ as an example). Compared to conventional viability measurements, this novel 3D drug response score was found to accurately identify both drug sensitive and resistant spheroids and showed robust concordance with genomic biomarkers of response (NGS and MGMT promoter methylation) and patient outcomes. Additionally, we coupled the 3D drug score with known genetic data to explore other key pathways and genes involved in TMZ response. We provide here novel analysis methods and public code (Github) to advance the use of IncuCyte spheroid measurements, and deconvolute 3D spheroid drug response into a quantifiable statistic. These methods are adaptable to freshly isolated patient cells for rapid evaluation of treatment response in GBM patients while remaining widely applicable to other cancers such as pancreatic, colon, and non-cancer organoids/spheroids with 3D growth.
CBIO-02. COMPREHENSIVE ANALYSIS OF MECHANISMS AND MOLECULAR TARGETS FOR BREAST CANCER LEPTOMENINGEAL METASTASIS
Authors: Kijima Noriyuki , Achiha Takamune , Nakagawa Tomoyoshi , Hirayama Ryuichi , Kinoshita Manabu , Kagawa Naoki , Kishima Haruhiko 
Published: December 2020

Abstract
Leptomeningeal metastasis from solid cancer is a devastating state for cancer patients. Leptomeningeal metastasis is diagnosed either by cerebrospinal fluid cytology and/or magnetic resonance imaging (MRI). However, it remains unclear as to whether tumor cells attached to leptomeninges are the same from floating tumor cells in cerebrospinal fluid (CSF). In this study, we aim to analyze the differences between tumor cells attached to leptomeninges and floating cells in CSF by xenograft models. We used breast cancer cell line, MDA-MB-231, labelled with green fluorescent protein (GFP) and luciferase. We injected those cells into right lateral ventricle of NOD/Shi-scid IL2Rγ KO mice. When the mice got any signs of tumor, we dissected spinal cord and got CSF from mice. We sorted tumor cells by flow cytometry and extracted RNA from the sorted tumor cells from spinal cord and CSF, respectively. We analyzed transcriptome differences between tumor cells from spinal cord and CSF by RNA sequencing. We found that extracellular matrix related proteins were highly upregulated while cell growth related proteins were downregulated in tumor cells from spinal cord compared with those from CSF. These results suggest that tumor cells attached to leptomeninges have different transcriptome profiles from floating tumor cells in CSF and extracellular matrix related proteins could be therapeutic targets for breast cancer leptomeningeal metastasis.
CBIO-08. ASTROCYTE SENESCENCE CONTRIBUTES TO SEX DIFFERENCES IN GLIOBLASTOMA INCIDENCE AND OUTCOME
Authors: Broestl Lauren , Rhee Gina , Grandison Lucia , Sponagel Jasmin , Kfoury Najla , Hill Cameron , Rubin Joshua 
Published: December 2020

Abstract
Sex differences in incidence and outcome are consistently observed in cancer, including in the most common malignant brain tumor – glioblastoma (GBM). Women are less likely to develop GBM and have a survival advantage compared to men. Previous research from our lab identified the proteins Rb, p16, and p21 as key mediators of female protection against cellular transformation. Strikingly, these proteins are all primary components of the senescence response, a potent cell-intrinsic anti-cancer mechanism that results in permanent cell cycle arrest, preventing proliferation of damaged cells. We hypothesized that sex differences in GBM incidence and outcome are mediated by differences in senescence induction after DNA damage in male and female cells. Using both wildtype astrocytes and a GBM model, we found that females have a lower threshold for senescence induction in response to oxidative stress, telomere shortening, and treatment with chemotherapy or radiation. Following irradiation, female GBM model cells had higher levels of p21 expression, and p21 levels correlated with the percentage of senescent cells. Knocking out p21 eliminated sex differences in the senescence response following irradiation. Achieving a better understanding of mechanisms of senescence and how they differ in male and female cells could advance development of senescence-directed therapies and potentially improve treatment for brain tumors.
CBIO-10. REDUCED IRON EXPORT FUNCTIONS IN A CELL INTRINSIC MANNER TO DRIVE GLIOBLASTOMA GROWTH
Authors: Troike Katie , Mulkearns-Hubert Erin , Silver Daniel , Connor James , Lathia Justin 
Published: December 2020

Abstract
Glioblastoma (GBM), the most common primary malignant brain tumor in adults, is characterized by invasive growth and poor prognosis. Iron is a critical regulator of many cellular processes, and GBM tumor cells have been shown to modulate expression of iron-associated proteins to enhance iron uptake from the surrounding microenvironment, driving tumor initiation and growth. While iron uptake has been the central focus of previous investigations, additional mechanisms of iron regulation, such as compensatory iron efflux, have not been explored in the context of GBM. The hemochromatosis (HFE) gene encodes a transmembrane glycoprotein that aids in iron homeostasis by limiting cellular iron release, resulting in a sequestration phenotype. We find that HFE is upregulated in GBM tumors compared to non-tumor brain and that expression of HFE increases with tumor grade. Furthermore, HFE mRNA expression is associated with significantly reduced survival specifically in female patients with GBM. Based on these findings, we hypothesize that GBM tumor cells upregulate HFE expression to augment cellular iron loading and drive proliferation, ultimately leading to reduced survival of female patients. To test this hypothesis, we generated Hfe knockdown and overexpressing mouse glioma cell lines. We observed significant alterations in the expression of several iron handling genes with Hfe knockdown or overexpression, suggesting global disruption of iron homeostasis. Additionally, we show that knockdown of Hfe in these cells increases apoptosis and leads to a significant impairment of tumor growth in vivo. These findings support the hypothesis that Hfe is a critical regulator of cellular iron status and contributes to tumor aggression. Future work will include further exploration of the mechanisms that contribute to these phenotypes as well as interactions with the tumor microenvironment. Elucidating the mechanisms by which iron effulx contributes to GBM may inform the development of next-generation targeted therapies.
CBIO-13. EPIGENETIC DEREGULATION OF NUCLEAR TRANSLOCATION - A NOVEL MECHANISM FOR TREATMENT RESISTANCE IN GLIOBLASTOMA
Authors: Nguyen Thi Tham , Rajakannu Premnath , Pham Minh Diêu Thanh , Weman Leo , Jucht Alexander , Van Dommelen Kristof , Hegi Monika 
Published: December 2020

Abstract
In a genome-wide DNA methylation analysis of glioblastoma we identified aberrant methylation of the HIV-1 Tat interactive protein 2 (HTATIP2) gene promotor. This was strongly correlated with downregulation of HTATIP2 gene expression, suggesting a potential tumor suppressor function in glioblastoma. HTATIP2 has been shown to inhibit nuclear translocation through interaction with β-importins. We hypothesize that deregulation of HTATIP2 expression inhibits nuclear entry of cancer-relevant proteins, thereby disturbing their specific function in the nucleus. We identified N-Methylpurine-DNA Glycosylase (MPG) as a potential cancer relevant candidate with the observation of nuclear and/or cytoplasmic localization in glioblastoma. MPG is a DNA repair protein that recognizes DNA lesions (N7-meG, N3-meA) and initiates base excision repair. We have shown that nuclear MPG expression contributes to resistance of glioblastoma to treatment with the alkylating agent temozolomide. Here we investigated the effect of HTATIP2 on cellular localization of MPG using (i) an inducible system (TET-ON) to express HTATIP2 in non-expressing glioblastoma cells, and (ii) HTATIP2-targeting siRNAs to knock down HTATIP2 in cells with endogenous expression. Results from confocal microscopy or Imagestream analyses showed a significant cytoplasmic retention of MPG in presence of HTATIP2, while knock-down of HTATIP2 resulted in nuclear MPG localization. Cytoplasmic retention of MPG in the presence of HTATIP2 was associated with a significant increase in γ-H2Ax signal after treatment with the alkylating agent: methyl methanesulfonate (MMS), suggesting increase in DNA damage. Mechanistically, we found that HTATIP2 co-localizes with importin β1, and excludes MPG localization. Furthermore, HTATIP2 displayed a similar effect on cytoplasmic retention of MPG as pharmacologic inhibition of Importin β 1. Taken together, these results suggest that epigenetic silencing of HTATIP2 may increase nuclear localization of MPG, thereby increasing the capacity of the tumor cells to repair treatment related lesions and thereby contributing to treatment resistance.