bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPCO-17. METHYLATION ANALYSIS OF MATCHED PRIMARY AND RECURRENT IDHmt ASTROCYTOMA; AN UPDATE FROM THE GLIOMA LONGITUDINAL ANALYSIS NL (GLASS-NL) CONSORTIUM
Authors: Vallentgoed Wies , Niers Anneke , van  Garderen Karin , van den Bent Martin , Draaisma Kaspar , de Heer Iris , Kouwenhoven Mathilde , Kros Johan , Martin Ivonne , Robe Pierre , Smits Marion , Tesileanu Mircea , van Thuijl Hinke , Verhaak Roel , Westerman Bart , van de Wiel Mark , Ylstra Bauke , de Leng Wendy , Wesseling Pieter , French Pim 
Published: November 2021

Abstract
The GLASS-NL consortium, was initiated to gain insight into the molecular mechanisms underlying glioma evolution and to identify markers of progression in IDH-mutant astrocytomas. Here, we present the first results of genome-wide DNA-methylation profiling of GLASS-NL samples. 110 adult patients were identified with an IDH-mutant astrocytoma at first diagnosis. All patients underwent a surgical resection of the tumor at least twice, separated by at least 6 months (median 40.9 months (IQR: 24.0, 64.7). In 37% and 18% of the cases, patients were treated with radiotherapy or chemotherapy respectively, before surgical resection of the recurrent tumor. DNA-methylation profiling was done on 235 samples from 103 patients (102 1st, 101 2nd, 29 3rd, and 3 4th resection). Copy number variations were also extracted from these data. Methylation classes were determined according to Capper et al. Overall survival (OS) was measured from date of first surgery. Of all primary tumors, the methylation-classifier assigned 85 (87%) to the low grade subclass and 10 (10%) to the high grade subclass. The relative proportion of high grade tumors increased ~three-fold at tumor recurrence (32/101, 32%) and even further in the second recurrence (15/29, 52%). Methylation classes were prognostic, both in primary and recurrent tumors. The overall DNA-methylation levels of recurrent samples was lower than that of primary samples. This difference is explained by the increased number of high grade samples at recurrence, since near identical DNA-methylation levels were observed in samples that remained low grade. In an unsupervised analysis, DNA-methylation data derived from primary and first recurrence samples of individual patients mostly (79%) cluster together. Recurrent samples that do not cluster with their primary tumor, form a separate group with relatively low genome-wide DNA-methylation. Our data demonstrate that methylation profiling identifies a shift towards a higher grade at tumor progression coinciding with reduced genome-wide DNA-methylation levels.
EPCO-29. GENOMIC PROFILING OF SPORADIC MULTIPLE MENINGIOMAS
Authors: Erson-Omay Zeynep , Barak Tanyeri , Vetsa Shaurey , Nadar Arushii , Miyagishima Danielle , Yalcin Kanat , Aguilera Stephanie , Mishra-Gorur Ketu , McGuone Declan , Fulbright Robert , Gunel Murat , Moliterno-Gunel Jennifer 
Published: November 2021

Abstract

INTRODUCTION
In rare cases, sporadic meningiomas can occur as multiple tumors in the same patient without a known germline mutation. While the underlying mechanism that leads to the formation of these multiple lesions has been hypothesized to be monoclonal or independent, the genomic profiles to support these theories remain understudied.

METHODS
Patients with an absence of family history of meningioma and prior radiation history with multiple metachronous meningiomas were included. All tissue underwent whole exome sequencing and analysis of somatic single nucleotide variations (SNV), small insertion/deletion (INDEL) events together with copy number variations (CNV) was performed. The genomic findings were correlated with clinical data.

RESULTS
A cohort of 13 meningiomas and one dural specimen, from five individuals was studied. The majority (9/13 tumors) of tumors had NF2 mutation/Chr22 loss. Four out of 5 cases had a monoclonal origination, whereas one case displayed an independent clonal formation. The somatic profile of dura was unrevealing. In contrast to the current understanding, we found monoclonal formation of multiple meningiomas is not exclusive to NF2 driven cases, as non-NF2 mutated meningiomas can too display a monoclonal etiology. Moreover, multiple monoclonal-originating lesions did not always display a homogenous profile, but rather exhibited heterogeneity through branching evolution, where some lesions acquired genomic alterations associated with aggressive behavior. The histological characterization of multiple meningioma cases does not necessarily overlap with the genomic clustering.

CONCLUSION
To our knowledge, this is the first study to use unbiased comprehensive genomic methods to reveal the heterogeneity of multiple meningioma genomic profiles. Our extensive genomic characterization of this cohort revealed that monoclonal formation can be observed both in NF2 and non-NF2 mutant meningiomas and can introduce heterogeneity. Therefore, in order to understand the full scope of each individual’s disease, detailed genomic profiling of all lesions, when possible, should be performed.
EPCO-32. IDENTIFICATION OF PROGNOSTIC CHORDOMA SUBGROUPS USING DNA METHYLATION SIGNATURES IN TISSUE AND PLASMA
Authors: Zuccato Jeffrey , Patil Vikas , Mansouri Sheila , Liu Jeffrey , Nassiri Farshad , Mamatjan Yasin , Chakravarthy Ankur , Karimi Shirin , Almeida Joao Paulo , Bernat Anne-Laure , Hasen Mohammed , Khan Shahbaz , Kislinger Thomas , Sinha Namita , Froelich Sébastien , Adle-Biassette Homa , Aldape Kenneth , De Carvalho Daniel , Zadeh Gelareh 
Published: November 2021

Abstract

BACKGROUND
Chordomas are malignant bone cancers arising from the skull-base and spine that are rare but cause devastating central nervous system morbidities. Survival is highly variable despite surgery and radiotherapy as 10% live under 1 year and 30-35% survive over 20 years. There are currently no reliable prognostic factors and this limits our ability to tailor patient treatment to their risk. Accordingly, this work identifies epigenetic prognostic chordoma subgroups that are detectable non-invasively through plasma methylomes to guide treatment.

METHODS
A total of 68 chordoma surgical specimens resected between 1996-2018 across three international centres underwent DNA methylation profiling. Cell-free methylated tumor DNA immunoprecipitation and high-throughput sequencing was performed on available matched plasma samples.

RESULTS
Two stable tumor clusters were identified through consensus clustering of tissue methylation data. Clusters had statistically significantly different disease-specific survivals (log-rank p=0.0062) independent of clinical factors in a multivariable Cox analysis (HR=16.5, 95%CI: 2.8-96, p=0.0018). The poorer-performing “Immune-infiltrated” cluster had genes hypomethylated at promoters, typically resulting in transcription, within immune-related pathways and higher immune cell abundance within tumors. The better-performing “Cellular” cluster showed higher tumor cellularity plus cell-to-cell interaction and extracellular matrix pathway hypomethylation. Fifty chordoma-versus-other binomial generalized linear models built using plasma methylome data distinguished chordomas from meningiomas and spinal metastases, as representative clinical differential diagnoses, in random left-out 20% testing sets (mean AUROC=0.84, 95%CI: 0.52-1.00). Plasma-based methylation signatures were highly correlated with tissue-based signals within both poor-performing (median r=0.69, 95%CI: 0.66-0.72) and better-performing cluster tumors (median r=0.67, 95%CI: 0.62-0.72).

CONCLUSIONS
The first identification of two distinct prognostic epigenetic chordoma subgroups is shown here with “Immune-infiltrated” tumors having a poorer prognosis than “Cellular” tumors. Plasma methylomes can be utilized for non-invasive chordoma diagnosis and subtyping. This work may transform chordoma treatment decision-making by guiding surgical planning in advance to match resection aggressiveness with patient prognosis.
EPCO-33. CELL-TYPE PROPORTION DECONVOLUTION OF PEDIATRIC CENTRAL NERVOUS SYSTEM TUMORS FROM SINGLE NUCLEI RNA-seq UNCOVERS UNDERLYING TRANSCRIPTOMIC CHANGES FROM BULK TUMOR RNA-seq COMPARED TO NORMAL BRAIN
Authors: Lee Min Kyung , Azizgolshani Nasim , Kolling Fred , Nguyen Lananh , Zanazzi George , Christensen Brock 
Published: November 2021

Abstract
Identifying transcriptomic alterations in pediatric central nervous system (pCNS) tumors often relies on transcriptomic profiles from bulk tissue RNA-sequencing that can be confounded by varying cell type proportions across tumor and normal brain tissues. We utilized single nuclei RNA-sequencing (snRNA-seq) and bulk RNA-seq in 33 pCNS tumors and 3 non-diseased pediatric brain tissue samples collected from the Norris Cotton Cancer Center to identify variation in gene expression in bulk tissue attributed to overrepresentation of specific cell-type populations when determining differentially expressed genes comparing pCNS tumors to normal pediatric brain tissues. snRNA-seq of 43,515 nuclei (mean = 1,209 nuclei/sample) revealed large proportions of astrocytes (median = 0.45, range = 0.24–0.93) and oligodendrocytes (median = 0.37, range = 0.00–0.66) in pCNS tumors. Compared to normal pediatric brain, proportions of astrocytes were significantly higher (P = 9.2E-03) and neurons were significantly lower (P = 9.4E-03) in pCNS tumors. Differential expression analyses comparing bulk RNA-sequencing data from pCNS tumors to normal pediatric brain identified 902 additional differentially expressed genes (# DE genes = 1,802) when adjusting for astrocyte and neuron proportions compared with unadjusted analysis (# DE genes = 900). In cell-type proportion unadjusted analysis, top DE genes included astrocyte-specific markers, GFAP and CIITA, both of which were found to be not significantly differentially expressed in cell-type proportion adjusted analysis. Indeed, pathways enrichment analysis revealed DE genes in unadjusted models were associated with processes of the neurons and astrocytes such as interferon signaling and postsynaptic signal transmission. After adjustment for astrocyte and neuron proportions, DE genes were associated with defensins and DNA replication-related processes. Our results highlight new potential biological pathways essential in pCNS tumors and indicate the significance of the distribution of varying cell types in tissue samples when conducting studies to investigate transcriptomic alterations in bulk tissue of pCNS tumors.
BIOM-12. DEVELOPMENT OF 5-ALA BASED LIQUID BIOPSY FOR THE NON-INVASIVE DIAGNOSIS OF GLIOBLASTOMA
Authors: Yekula Anudeep , Hsia Tiffaney , Balaj Leonora , Carter Bob 
Published: November 2021

Abstract

INTRODUCTION
Tumor specificity of 5-aminolevulinic acid (5-ALA) induced protoporphyrin IX (PpIX) fluorescence is widely applied for fluorescence-guided surgery (FGS) in gliomas. We recently showed the feasibility of detecting tumour-specific fluorescent PpIX extracellular vesicles (EVs) derived from the plasma of glioblastoma (GBM) patients undergoing 5-ALA based fluorescence-guided surgery. Here, we further develop methods to characterize, sort and study fluorescent PpIX EVs in plasma of patients with glioma.

METHODS
We used imaging flow cytometry and Astrios EQ nanoFACS to characterize and sort PpIX EVs, respectively. Downstream RNA analysis utilized transcriptome sequencing analysis and droplet digital PCR (EGFRvIII mRNA).

RESULTS
All GBM cell lines (Gli36vIII, U87, Gli36 WT) dosed with 5-ALA demonstrated PpIX fluorescence, and released PpIX positive EVs. There was a high correlation between fluorescence in cells and the number of PpIX EVs released (r2=0.9). We sorted 100,000 PpIX EVs from Gli36vIII cells dosed with 5-ALA and detected 65 copies and 24 copies of mutant EGFRvIII mRNA and wildtype EGFR mRNA per 100,000 EVs, respectively. RNAseq analysis of the sorted PpIX EVs showed expression patterns reflective of parent cells. Furthermore, 100,000 sorted PpIX EVs from the plasma of a patient with EGFRvIII glioma yielded 22 copies of EGFRvIII mRNA while &lt; 5 copies were detected in 1ml of plasma and healthy control plasma, demonstrating the tumor-specific nature of PpIX EVs. Finally, we performed transcriptome analysis on 250,000 PpIX EVs each from 8 patients undergoing 5-ALA based FGS. We identified several mRNAs including Gli3, STAG2, ELF3, PHLPP1 which play an important role in cancer.

CONCLUSION
The ability to sort and characterize tumor specific PpIX EVs following 5-ALA administration opens new avenues for liquid biopsy-based glioma diagnosis.
BIOM-15. SERUM AMYLOID-β42 AS A NONINVASIVE BIOMARKER FOR PROGNOSIS AND HISTOLOGIC FEATURES OF GLIOMA
Authors: Hwang Kihwan , Noh Minhee , Park Jay , Ji So Young , Han Jung Ho , Ahn Kwang Sung , Kim Chae-Yong 
Published: November 2021

Abstract

INTRODUCTION
Glioma is the most common primary tumor in central nervous system and is often refractory. Histopathologic examination is essential to establish initial diagnosis, and multiple imaging studies are conducted to assess for treatment response. However, those conventional approaches usually accompanies high risks and costs during treatment. The purpose of this study is to find a novel candidate of noninvasive biomarker for histologic prediction and prognostic assessment of glioma.

METHODS
Serum was prepared from blood samples collected preoperatively from 65 patients with WHO grade II–IV glioma from October 2004 to December 2017 in a single tertiary-level institution. Concentration of amyloid beta-42 (Aβ42) was measured by SMCxPRO (Merck) immunoassay. Clinical characteristics and histologic features of the patients including the molecular subtype were reviewed. Progression-free survival has been evaluated for the primary outcome.

RESULTS
The mean age of the patients was 53.7±12.2 years. 37 (56.9%) patients were males and 21 (32.3%) cases were primary tumors. In Kaplan-Meier survival analysis, higher serum Aβ42 (&gt;5.7 pg/ml) group showed poor outcome with a statistical significance (p=0.014). In multivariate regression analysis, the concentration of serum Aβ42 showed a significant association with EGFR expression, or Ki-67 labeling index. The higher concentration of serum Aβ42 was associated with EGFR wild type (odds ratio 0.237, p=0.022), high cell proliferation (β=0.339, p=0.007) and poor outcome (hazard ratio 0.339, p=0.046).

CONCLUSION
Serum Aβ42 level is a possible good candidate of noninvasive biomarkers for prediction of histologic features and prognosis in glioma patients. Further studies with large cohorts might be mandatory for the clinical use of Aβ42.
BIOM-23. A PILOT STUDY OF WHOLE GENOME SEQUENCING (WGS) OF PLASMA CELL-FREE DNA (cfDNA) FOR ULTRASENSITIVE DETECTION OF TUMOR DNA IN PATIENTS WITH GLIOBLASTOMA (GBM)
Authors: Bagley Stephen J , Till Jacob , Abdalla Aseel , Nasrallah MacLean , Lauterman Tomer , Tavassoly Iman , Oklander Boris , Zviran Asaf , Carpenter Erica 
Published: November 2021

Abstract

BACKGROUND
Plasma circulating tumor DNA (ctDNA) is rarely detectable by traditional methods in patients with GBM. As a result, unlike in lung and other cancers, serial next generation sequencing of ctDNA for monitoring GBM tumor burden has been challenging. In light of the low tumor fraction (TF) of DNA fragments in GBM patient plasma and the urgent need to improve upon MRI for tracking GBM tumor burden, we conducted a pilot study in patients with newly diagnosed GBM using the C2 intelligence platform (C2i Genomics), which leverages genome-wide mutational integration for highly sensitive ctDNA detection.

METHODS
Plasma was collected pre- and post-operatively in patients with newly diagnosed GBM undergoing surgical resection/biopsy. cfDNA was extracted, quantified, and analyzed for fragment size. Genomic DNA (gDNA) was extracted from matched tumor tissue. Whole genome sequencing (WGS) was performed on both gDNA and cfDNA. A specific copy number alteration (CNA) compendium was created for each patient to generate a readout of TF (Zviran, Nat Medicine 2020). We assessed the association between TF at post-operative day 1 (a surrogate for residual disease) and OS, adjusting for other prognostic factors using Cox regression.

RESULTS
37 patients were enrolled. For samples with high tumor fraction (n=5), a statistically significant (p&lt; 1e-4) correlation between CNA profiles of tumor tissue and plasma samples was observed. Post-operative TF above the median value was associated with inferior OS (median 7.7 vs. 19.3 months, p=0.019). This association persisted after adjusting for age, O6-methylguanine-DNA methyltransferase methylation status, extent of resection, and performance status (adjusted HR 2.5, 95% CI 1.1-5.6, p=0.03).

CONCLUSION
Genome-wide mutational integration enables ultra-sensitive detection of ctDNA in GBM patient plasma. Post-operative TF measured by the C2i test is independently associated with OS in newly diagnosed GBM, providing the foundation to evaluate this technology for personalized prognostication and disease monitoring.
BIOM-32. ENDOPLASMIC RETICULUM PROTEIN SSR3 DETERMINES AND PREDICTS RESPONSE TO PACLITAXEL IN BREAST CANCER AND GLIOBLASTOMA
Authors: Dmello Crismita , Sonabend Aarón , Arrieta Víctor , Zhang Daniel , Kanojia Deepak , Chen Li , Gould Andrew , Kane J Robert , Zhang Jiangshan , Kang Seong , Winter Jan , Horbinski Craig , Győrffy Balázs , Cordero Alex , Chang Catalina , Castro Brandyn , Hsu Patrick , Ahmed Atique , Lesniak Maciej , Stupp Roger , Sonabend Adam M 
Published: November 2021

Abstract
Paclitaxel (PTX) is one the most potent and commonly used chemotherapies for breast and pancreatic cancer. Given the potency of this drug for glioblastomas (GBM) several ongoing clinical trials are investigating means of enhancing delivery of PTX across the blood-brain barrier for this disease. In spite of the efficacy of PTX, individual tumors exhibit variable susceptibility to this drug, with response rate in the range of 30%-60%. To identify predictive biomarkers for response to PTX, we performed a genome-wide CRISPR knock-out screen using human glioma cells. The most enriched genes in the CRISPR screen underwent further selection based on their correlation with survival in the breast cancer patient cohorts treated with PTX and not in patients treated with other chemotherapies, a finding that was validated on a second independent patient cohort. This led to the discovery of endoplasmic reticulum (ER) protein SSR3 as a putative predictive biomarker for PTX. SSR3 protein levels showed positive correlation with response to PTX in breast cancer cells, glioma cells, in multiple intracranial glioma xenografts and in GBM patient derived explant cultures. Knockout of SSR3 turned the cells resistant to PTX while its overexpression sensitized the cells to PTX. In gliomas, SSR3-mediated susceptibility to PTX relates to modulation of phosphorylation of ER stress sensor IRE1α. Thus, by using genome-wide screen combined with patient response data, we discovered a biomarker that demonstrates causal and correlative relationship with response to PTX in breast cancer and GBM. Prospective validation of this biomarker is warranted for its broad implementation for precision oncology.
BIOM-41. LIVE-CELL IMAGING SHOWS UNEVEN SEGREGATION OF EXTRACHROMOSOMAL DNA ELEMENTS AND TRANSCRIPTIONALLY ACTIVE EXTRACHROMOSOMAL DNA CLUSTERS IN CANCER
Authors: Yi Eunhee , Gujar Amit , Guthrie Molly , Kim Hoon , Zhao Dacheng , Johnson Kevin , Amin Samirkumar , Das Sunit , Jillette Nathaniel , Clow patricia , Cheng Albert , Verhaak Roel 
Published: November 2021

Abstract
Oncogenic extrachromosomal DNA elements (ecDNAs) promote intratumoral heterogeneity, creating a barrier for successful cancer treatments. The underlying mechanisms are poorly understood and studies are hampered in part by a lack of adequate tools enabling studies of ecDNA behavior. Here, we show that single-cell ecDNA copy numbers greatly vary between tumor cells, both in vitro and in patient glioblastoma specimens, suggesting uneven ecDNA segregation during mitosis. We established a CRISPR-based approach which leverages unique ecDNA breakpoint sequences to tag ecDNA with fluorescent markers in living cells. Applying this method during mitosis revealed disjointed ecDNA inheritance patterns, providing an explanation for rapid ecDNA accumulation in cancer. Post-mitosis, ecDNAs tended to cluster and clustered ecDNAs colocalized with RNA polymerase II, promoting transcription of cargo oncogenes. Our observations provide direct evidence for uneven segregation of ecDNA and sheds new light on mechanisms through which ecDNAs contribute to oncogenesis.
BIOM-45. CHARACTERIZATION OF EVs RELEASED FROM 5-ALA DOSED GLIAL AND EXTRA-AXIAL TUMORS
Authors: Hsia Tiffaney , Yekula Anudeep , Carter Bob , Balaj Leonora 
Published: November 2021

Abstract

INTRODUCTION
The administration of 5-Aminolevunlinic acid (5-ALA) in the context of fluorescence-guided surgery is contingent on the highly selective accumulation of PpIX in tumor cells. PpIX is a precursor in the heme pathway that naturally exhibits fluorescent and phototoxic properties upon excitation. We have previously reported evidence of PpIX fluorescence in tumor-specific extracellular vesicles (EVs). Here, we explore the implications of exogenous 5-ALA on cellular function, EV characteristics, and gene expression.

METHODS
We have characterized a range of glioblastoma, meningioma, and healthy cell lines (Gli36 EGFRvIII, Gli36 EGFR WT, U87, CH-157, IOMM-Lee, and HBMVEC). At equal confluency, cells were dosed with 0.8 mM 5-ALA or mock dosed. Media was collected and processed to eliminate debris after 24 hours. Analysis of cells and EVs was conducted using Amnis ImageStream (IFC) and Nanoparticle Tracking Analysis. EV subpopulations were analyzed with IFC following antibody staining. RNA was extracted using Qiagen exoRNeasy and RNeasy. Libraries were prepared via Qiagen UPX 3’ Transcriptome kit and sequenced using Illumina MiSeq. Data analysis was carried out via GeneGlobe, CLC workbench, and MATLAB.

RESULTS
Following 5-ALA dosing, all tumor cells and their derived EVs exhibit significant levels of fluorescence. Analysis of EV subpopulations demonstrated a general decrease in tetraspanin-positive EVs following 5-ALA dosing. At 24 hours, Gli36 cell lines exhibited increased EV release post 5-ALA whereas U87 and meningioma lines resulted in a decreased EV release rate. This clustering is also reflected in EV size distributions and in cellular and EV differential gene expression analysis. Gene ontology analysis of common genes from mock and dosed EVs demonstrated high counts of genes controlling biological regulation as well as cellular and metabolic processes.

CONCLUSION
Collection and characterization of cancer specific EVs may be advantageous to liquid biopsy development.