bluuebunny/crossref_metadata_2025_split huggingface dataset:
BIOM-05. CIRCULATING TUMOR CELLS (CTC) IN CEREBROSPINAL FLUID (CSF) AS A PREDICTOR OF SURVIVAL IN CNS METASTASES
Authors: Diaz Maria , Singh Priya , Kotchetkov Ivan , Skakodub Anna , Reiner Anne , Panageas Katherine , Ramanathan Lakshmi , Pentsova Elena 
Published: December 2020

Abstract

BACKGROUND
CSF-CTC testing using the CellSearch® platform is a validated diagnostic tool for leptomeningeal metastases (LM) from solid tumors. CSF-CTCs can also be detected in patients with brain metastases (BM), but their significance is unclear. Our objective was to evaluate the utility of CSF-CTC quantification in predicting outcomes in CNS metastases.

METHODS
We retrospectively reviewed charts of patients with solid tumors who underwent CSF-CTC measurement between 2016–2019 at Memorial Sloan Kettering Cancer Center. Information on neuroaxis imaging, CSF results, systemic cancer status, tumor molecular profile and survival was collected. LM was diagnosed by MRI and/or CSF cytology. Survival analyses were performed using Cox proportional hazards modeling, and CSF-CTC splits associated with survival were identified through recursive partitioning analysis (RPA).

RESULTS
A total of 407 patients (38% lung primary, 34% breast, 28% other tumor types) were included; of these, 144 had LM and 233 had BM diagnosed before or around the time of CSF tests (97 had both). For a subgroup of 101 patients with LM diagnosed within 30 days of CSF sampling, mean CSF-CTCs were 127.3/3ml, compared to 44.6/3ml in the overall cohort. CSF-CTCs predicted survival in these patients, with optimal cutoff at 61 CSF-CTCs/3ml, above which the risk of death doubled (HR=2.09, 95% CI: 1.13–3.87, p=0.02). For 53 patients with BM diagnosed 1–6 months prior to CSF tests, CSF-CTCs (mean 54.1/3ml) also determined higher risk of death when above the optimal cutoff of 94 (HR=5.15, 95% CI: 2.08–12.78, p=0.004). For both groups, positive/suspicious cytology was associated with higher risk of death as well, but these results were not statistically significant (LM group: HR=1.79, 95% CI: 0.95–3.35, p=0.07; BM group: HR=1.86, 95%CI: 0.82–4.22, p=0.14).

CONCLUSION
In newly diagnosed LM and BM, quantification of CSF-CTCs predicts survival. CSF-CTC analysis can be used as a prognostic tool in patients with CNS metastases.
BIOM-06. CLINICAL AND PROGNOSTIC SIGNIFICANCE OF KRAS MUTATIONS FOR BRAIN METASTASES FROM COLORECTAL ADENOCARCINOMA IN THE UNITED STATES
Authors: Lamba Nayan , Smith Timothy , Iorgulescu Bryan 
Published: December 2020

Abstract

BACKGROUND
KRAS mutations in colorectal adenocarcinomas have been associated with metastatic involvement of the brain (BM); and predict a lack of benefit to EGFR-targeted antibodies. Herein we leverage national data to evaluate the prevalence and impact of KRAS mutations on colorectal BMs.

METHODS
Newly-diagnosed patients with stage 4 colorectal adenocarcinoma were identified from the National Cancer Database, comprising &gt;70% of newly-diagnosed cases in the U.S. from 2010–2016. Multivariable logistic regression was used to evaluate predictors of brain involvement, including KRAS mutation status. Overall survival (OS) was estimated with Kaplan-Meier techniques, and compared by logrank test and multivariable Cox regression.

RESULTS
Of 86,719 patients newly presenting with stage 4 colorectal adenocarcinoma, 1.5% (n=1,318) had BMs. 39.7% of BM cases had KRAS mutation testing, in which 57.9% (n=361) of BM cases were KRAS-mutant, as opposed to only 45.6% (n=13,259) of non-BM cases (p&lt; 0.001). Mutant KRAS persisted as independently associated with BMs (OR 1.37, 95%CI: 1.09–1.72, p=0.006) following adjustment for age at diagnosis, sex, AJCC cT and cN status, and metastatic lung, liver, or bone involvement. Overall, BM patients displayed a median OS of 5.3 months (95%CI: 4.6–6.1): 7.5 months (95%CI: 5.7–10.6) if KRAS-wildtype vs. 12.0 months (95%CI: 10.4–15.4) if KRAS-mutant (p=0.01). The improved OS associated with KRAS-mutant BMs also persisted (HR 0.63, 95%CI: 0.47–0.84, p=0.001) after adjusting for the aforementioned clinical variables, in addition to comorbidity index, chemoradiotherapy, metastasectomy, and treating hospital type.

CONCLUSIONS
Nationally, testing colorectal BM patients for KRAS mutation status—a predictive biomarker for EGFR-mab therapy—remains underutilized. KRAS-mutant colorectal adenocarcinomas were more likely to have metastatic brain involvement, with KRAS-wildtype BMs demonstrating significantly worse OS than KRAS-mutant BMs. Our data suggest that KRAS mutation testing is underutilized in colorectal BM patients and provides useful prognostic information.
BIOM-08. TARGETSELECTORTM CEREBROSPINAL FLUID (CSF) CIRCULATING TUMOR CELLS AND BIOMARKER ANALYSIS: IMPROVING SENSITIVITY AND TARGETED TREATMENT OPTIONS IN BREAST AND NSCLC CANCER PATIENTS WITH CNS INVOLVEMENT
Authors: Singh Veena , Fisher Deanna , Schultz Robbie , Mayer Julie , Boorgula Smitha , Gill Jaya , Nguyen Minhdan , Troung Judy , Dobrawa Lucia , Carrillo Jose , Wagle Naveed , Kesari Santosh 
Published: December 2020

Abstract

BACKGROUND
Liquid biopsy has emerged as a minimally invasive and cost-effective strategy to assess cancer biomarkers without the risk of complications associated with biopsies. Once a tumor has metastasized to the brain, circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) can be found in the cerebrospinal fluid (CSF). We analyzed CSF samples from patients(pts) with primary lung or breast cancer with either brain (BM) or leptomeningeal disease (LMD). Here we report the analytical and clinical validation of Target Selector™ CSF assays.

METHODS
CSF was collected prospectively from pts with a prior solid tumor diagnosis and confirmed or clinical/ radiological suspicion of BM or LMD. CTCs were captured in microfluidic channel and classified as either CK+ or CK-. Cell-free total nucleic acids (cfTNA) was extracted from CSF supernatant and underwent both Target Selector™ single gene and next-generation sequencing (NGS) NSCLC and breast multi-gene testing. For NGS, data analysis was performed using Torrent Suite with annotation and curation by Ion Reporter and Oncomine Knowledgebase Reporter software.

RESULTS
The Target Selector™ CTC platform assays performed on clinical samples (n = 89) resulted in clinical sensitivity = 80.0%, clinical specificity = 96.6%, positive predictive value (PPV) = 98%, negative predictive value (NPV) = 70.0% at a limit of detection of 2 CTCs. For molecular analyses, Target Selector™ platform assays resulted in clinical sensitivity = 85.2%, clinical specificity = 88.3%, PPV = 76.7%, and NPV = 93.0%.

CONCLUSIONS
Target Selector™ is a viable and sensitive platform for CTC detection and molecular analysis of CSF samples from patients with NSCLC or breast cancer with CNS metastases compared to the current standard of care (CSF cytology) and when imaging findings are equivocal. Identifying CTCs and actionable biomarkers can help to confirm CNS involvement when clinically suspected, guide targeted therapy selection and potentially monitor treatment response.
BIOM-10. PREVALENCE OF NF1 MISSENSE MUTATIONS AND CANDIDATE MODIFIER GENES IN SPINAL NEUROFIBROMATOSIS PATIENTS
Authors: Riva Paola , Bianchessi Donata , Mangano Eleonora , Cesaretti Claudia , Bettinaglio Paola , Bordoni Roberta , Tritto Viviana , Battaglia Cristina , Cagnoli Giulia , Saletti Veronica , Melone Marina , Schettino Carla , Natacci Federica , Finocchiaro Gaetano , Eoli Marica 
Published: December 2020

Abstract

INTRODUCTION
Spinal Neurofibromatosis (SNF), a distinct clinical entity of NF1, characterized by bilateral neurofibromas involving all spinal roots and a few, if any, cutaneous manifestations, entails greater morbidity than the classical form of disease. Nevertheless, there are no reliable patterns to sort out patients at risk for developing SNF.

MATERIALS AND METHODS
We investigated 19 NF1 families with at least one SNF member, 37 sporadic SNF patient and 100 NF1 patients with classical form of disease. We applied Targeted NGS using a panel consisting of 139 genes encoding RAS pathway effectors, neurofibromin interactors and genes mapping at 17q11.2 region.

RESULTS
In SNF patients we found a higher percentage of missense (21% versus 8%, p=0 0.016, OR 3.13 (95% CI 01.1 -8.2) and a lower percentage of nonsense NF1 mutations (12.5% versus 28%,, p= 0.026, OR 0.36 (95% CI 0.14–0.9) than in classical NF1 cases. Furthermore, we evaluated rare variants with damaging potential predictors in genes of the RAS pathway and in neurofibromin interactors. In more than one sporadic case possible pathogenic variants were found in LIMK2 (neurofibromin interactor), RASAL1, RASAL3, SOS1, A2ML1, MAP3K1 (RAS pathway effectors), while in more than one SNF family were detected RASAL1, RASAL3, MAP3K1 genes variations.

CONCLUSIONS
Our results confirm the correlation between NF1 genotype and SNF phenotype as previously reported (Ruggieri, 2015), suggesting that neurofibromin gain-of-functions mutations are associated to SNF. In some patients, the co-occurrence of potential pathogenic variants in NF1 related genes with severe phenotypes was detected supporting their role as modifier genes and promising therapeutic targets.
BIOM-14. METHODS FOR SCREENING AND MONITORING BY GBM MASTER REGULATORY GENE MARKERS IN LIQUID BIOPSY
Authors: Liu Tianyi , Le Son , Tran David 
Published: December 2020

Abstract

BACKGROUND
Current liquid-based cancer screening relies on massive deep NGS to detect rare cancer cell-derived genetic materials - a costly method fraught with high false-negative and false-positive rates. We aim to develop a non-NGS-centered, AI-directed liquid-based detection of GBM stem-like cells (GSC).

METHODS
Utilized a robust AI suite, NETZEN, we defined a common master regulatory gene network (MRGN) in GSC. Since master regulators (MR) in MRGN are developmentally restricted, their chromosomal loci are accessible in GSC but not in normal cells. Downstream factors in MRGN are massively overexpressed in GSC compared to normal cells. Thus, we measured 1) accessibility of MR genes using transposase/transposons carrying unique barcodes that can be detected after insertion into the MR’s predetermined accessible locations, and 2) expression of downstream factors using nested qRT-PCR, in PBMC from healthy controls spiked with known quantities of GSC or patients with GBM.

RESULTS
We characterized 10 MR genes in GSC with ≥1 GC-rich promoter region that is hypomethylated and accessible (ATACseq) in GBM/GSC per GSE70175/92460/52271 (19 samples) and GSE67633/96088 (14 samples), and hypermethylated and inaccessible in lymphocytes/PBMC per GSE98837 (6) and GSE74912 (13), respectively. Using barcoded transposons, we specifically disrupted 4 MR’s accessible regions only in GSC, not in PBMC. We also characterized 50 upregulated downstream factors with the top 20 having 3 to 5-orders-of-magnitude higher mean expression in GSC compared to PBMC (GSE79362/86884, 451 samples). Currently our method has a detection limit of 0.2–1 GSC in 106 PBMC. Using the first iteration, we detected GSC’s MRGN in blood samples of 14/14 GBM patients before resection, compared to in none of 15 healthy donors.

CONCLUSIONS
Chromosomal accessibility of MR and signal amplification in MRGN of GSC provide powerful substrates for a non-NGS, low-cost, liquid-based GBM detection system with potentially high sensitivity and specificity. Further testing and optimization are ongoing.
BIOM-16. IMMUNOMIC ANALYSIS OF GLIOBLASTOMA (GBM) USING GENE EXPRESSION PROFILING
Authors: Castro Michael , Badra-Azar Nilofar , Kessler Thomas , Schütte Moritz , Lange Bodo , Yaspo Marie-Laure 
Published: December 2020

Abstract

BACKGROUND
Despite the success of immunotherapy across the spectrum of human cancer, a successful strategy has not emerged for GBM. While PD-L1 IHC and TMB have demonstrated some utility as predictors of immunotherapy benefit, responsiveness is complexly determined by factors affecting T cell trafficking, antigen presentation, other immune checkpoints, and mediators of immune exhaustion. Thus, we set out to to characterize mediators of immune resistance and their diversity in a population of GBM patients utilizing quantitative gene expression.

METHODS
A set of 54 immunotherapy and checkpoint relevant genes and seven genes related to immune failure were selected from the literature. RNA gene counts for TCGA glioblastoma multiforme samples (N=163) were downloaded from https://portal.gdc.cancer.gov/. Annotation on subtypes and PFS values were obtained from PMID: 24120142. Gene expression normalization as FPKM, hierarchical clustering and box-plots were performed using R-3.6.0. Statistical differences of gene expression between subtypes were quantified using a TurkeyHSD test.

RESULTS
A heatmap with hierarchical clustering for immune related genes for the TCGA GBM cohort was generated including colored annotation for the subtype and progression free survival. The graph shows a rough separation into two groups, where one group of the genes is tentatively associated with mesenchymal subtype and shorter survival and showing higher expression for most immune evasion genes. However, a heterogeneity of immune evasion signatures was identified within and across subtypes. Transcripts related to antigen presentation, EZH2, and LDHA varied significantly between GBM subtypes (p &lt; 0.05).

CONCLUSION
Gene expression analysis has utility to identify specific mediators of immune evasion and to inform the selection of combination therapies for discrete subsets of patients. A Bayesian approach to patient selection for specific immunotherapy strategies may enhance the likelihood of successful implementation of immunotherapy in the clinic.
BIOM-19. METABOLIC ALTERATION INDUCED BY SELECTIVE KNOCK DOWN OF GABPB1L IN U251 CELLS
Authors: Minami Noriaki , Ayyappan Vinay , Stevers Nick , Molloy Abigail , Batsios Georgios , Hong Donghyun , Gillespie Anne Marie , Subramani Elavarasan , Radoul Marina , Costello Joseph , Viswanath Pavithra , Ronen Sabrina 
Published: December 2020

Abstract

BACKGROUND
TERT promoter mutations that result in TERT expression are observed in over 80% of GBM and upstream inhibition of TERT expression by targeting GABPB1L is currently under investigation. In that context, non-invasive reliable biomarkers that can help detect TERT expression are needed. The aim of this research was to assess the value of magnetic resonance spectroscopy (MRS)-detectable metabolic changes as biomarkers of TERT expression in GBM.

METHODS
GABPB1L knock down clones (GABPB1LKD) were established by introducing Crispr Cas9 plasmid vector targeting GABPB1L into U251 cells. Two representative clones with different knock down efficiency were chosen and compared to control cells. Tumor forming capacity was evaluated by colony formation assay and magnetic resonance imaging of orthotopically implanted tumors in mice. Cells were extracted using the dual phase extraction method and 1H-MRS data of cell extracts acquired using a Bruker 500 scanner. The data was analyzed using Mnova software. Multivariate analysis was performed using the SIMCA software.

RESULTS
TERT expression was significantly reduced in GABPB1LKD compared to control cells depending on the GABPB1L knock down efficiency. Colony forming capacity was impaired in GABPB1LKD compared to control cells. In vivo MRI data showed significantly smaller tumor volumes in GABPB1LKD compared to control. Unbiased PCA analysis of 1H-MRS data showed separation of GABPB1LKD and control extracts and VIP scores derived from the OPLS-DA analysis, demonstrated that the common metabolites leading to separation of GABPB1LKD and control cells were aspartate, glutathione, glycerophosphocholine, glutamine, NAD(P)+, AXP. This data was confirmed by univariate analysis that revealed that aspartate, glutathione, glutamine, NAD(P)+, AXP level was significantly reduced in GABPB1LKD.

CONCLUSIONS
GABPB1L knock down cells that show reduced TERT expression demonstrate MRS-detectable metabolic changes. These could be translated into clinical applications, improve the monitoring of GBM patients and advance precision medicine.
BIOM-25. IDENTIFYING EXTRACELLULAR VESICLES FROM GLIOBLASTOMA OR NON-NEOPLASTIC CELLS VIA IMAGING FLOW CYTOMETRY
Authors: Milbeth Cumba Garcia Luz , Aibaidula Abudumijiti , Kazemi Nazanin Yeganeh , Jung Miyeon , Lucien-Matteoni Fabrice , Markovic Svetomir , Parney Ian 
Published: December 2020

Abstract
Patients with glioblastoma (GBM) have a median survival of 15 months despite aggressive treatment. Immunosuppressive monocytes are heavily infiltrated in these tumors and in patients’ circulation. Treatment-related pseudo-progression confounds outcome assessment by MRI. Thus, there is a need for additional non-invasive methods to assess treatment response. Extracellular vesicles (EVs) contain tumor-specific microRNA (miRNA) cargo that could serve as a liquid biopsy to distinguish true progression from treatment-related pseudo-progression. We had found significant differences in plasma EVs molecular profile (i.e. miRNA signatures) between GBM patients and healthy donors. Our overall hypothesis is that these differences reflect the EVs cell of origin. Our goal in this project was to develop a fluorescent staining paradigm by flow cytometry to distinguish EVs from different cells in vitro and determine differences in EV miRNA expression profile between GBM and monocytic cell-derived EVs. Gleolan (5-ALA) is an FDA-approved orally available agent for fluorescence-guided resection of GBM tumors. It is metabolized to protoporphyrin IX (PpIX) in GBM cells but not in non-neoplastic cells and has been reported to aid in the detection of GBM-derived EVs by flow cytometry. However, distinguishing between GBM-derived EVs and EVs from other cells of origin has not been described. We co-cultured human GBM cells (dBT114 or dBT116) and CD14+ monocytes for 72 hours in the presence or absence of 5-ALA. EVs were isolated by ultracentrifugation and stained for CD11b (myeloid cell marker). ImageStream Imaging Flow Cytometry was performed showing clear differentiation between PpIX+ EVs from GBM cells and CD11b+ EVs from monocytes. Interestingly, a small number of double-positive EVs (presumably representing monocyte-derived EVs that had taken up PpIX after phagocytizing GBM cells) were also present. Taken together, we were able to optimize a technique to distinguish EVs originating from GBM and monocytes for further characterization by short non-coding RNA sequencing.
BIOM-28. IDENTIFICATION OF SOLUBLE AXL AS A POTENTIAL NON-INVASIVE SERUM BIOMARKER FOR GLIOBLASTOMA
Authors: Akhtar Parvez , Raymond Daniel , Fukui Melanie , Zwernik Samuel , Winn Robert , LaCrosse Amber , Last Brittany , Polinske Natalie , Rovin Richard 
Published: December 2020

Abstract
AXL, a member of the TAM family of tyrosine kinases, engages cellular pathways that promote a cancer phenotype. In glioblastoma, increasing AXL expression is associated with worse prognosis. The extracellular domain of AXL is cleaved by the sheddases ADAM10 and ADAM17, releasing soluble AXL (sAXL), which is detectable in blood and tumor related fluid collections. In this study we use ELISA to measure serum sAXL levels in 23 patients with newly diagnosed GBM pre- and post- operatively and every 3 months during treatment. Relative AXL expression was assessed in tumor tissue obtained from 13 patients via western blotting. Additionally, we used T1-weighted MRI scans to interpolate pre-operative tumor volume for all patients enrolled in the study. We found that serum sAXL concentrations were elevated in 84 GBM serum samples (35.77 ±1.25 ng/mL) compared to 40 healthy volunteer samples (30.16 ±1.88 ng/mL). When normalized to total serum albumin the difference between GBM and healthy controls was statistically significant (t(df)=5.647(122), p= 0.0132). In the 19 patients with paired samples, the pre- and post- operative sAXL levels were not significantly different. Using the Pearson method, we did not find a significant correlation between tumor volume and sAXL level. However, in patients with sAXL levels above the healthy population average, there was a moderate negative correlation between sAXL and pre-operative tumor volume (r= -0.58; p= 0.23). Interestingly, there was a strong correlation between sAXL level and tumor expression of AXL in patients with high preoperative sAXL levels (r= 0.85; p= 0.03). Though sAXL shed from brain tumors is detectable in the serum of GBM patients, in this small series of patients, it does not correlate with tumor volume. That said, we feel a larger study correlating sAXL level with improved volumetric MRI determination of viable GBM is warranted.
BIOM-42. ASSOCIATION OF NEUTROPHIL-LYMPHOCYTE RATIO WITH GLIOMA GRADING AND SURVIVAL
Authors: Ghazali Malueka Rusdy , Dwianingsih Ery Kus , Alethea Maria , Argo Ibnu Widya , Ramadhani Aulia Fitri , Saleh Sabillal , Wicaksono Adiguno Suryo , Dananjoyo Kusumo , Asmedi Ahmad , Hartanto Rachmat Andi 
Published: December 2020

Abstract

INTRODUCTION
Gliomas are the most common primary central nervous system tumor. Inflammatory responses are thought to play an important role in cancer progression. Neutrophil-lymphocyte ratio (NLR) is a simple, low cost and easy to measure inflammation marker that has been shown to be a poor prognostic factor in many solid tumors. The preoperative NLR has been shown to be associated with histopathological grading of glioblastoma. This study aimed to find the association of NLR with glioma grading and overall survival in Indonesian patients.

METHODS
The patients were enrolled from Dr. Sardjito General Hospital, Yogyakarta Province, Indonesia. Neutrophil and lymphocyte counts were extracted from the complete blood count test before surgery. NLR was calculated as neutrophil count divided by lymphocyte count using standard units. Detailed demographic and clinical data were collected from medical records.

RESULT
A total of 79 patients were included in this study, consisting of 48 (60.8%) males and 31(39.2%) females. Most patients were diagnosed as WHO grade IV gliomas (43%), followed by grade II (26%), grade III (13%), and grade I (7.6%). In multivariate analysis, NLR ≥ 5.01 was significantly associated with high grade glioma (HR 5.50, 95%CI 1.96–15.44, p=0.001). We also found that patients with NLR ≥ 10.5 have significantly shorter median overall survival compared with patients with NLR &lt; 10.5 (4.6 months and 27.2 months respectively, HR 2.13, 95%CI 1.03–4.40, p=0.041). Multivariate analysis using Cox Regression method showed that higher NLR (≥ 10.5) and IDH1 wild type were independent predictors for worse outcome.

CONCLUSION
In conclusion, NLR is associated with grading and overall survival of glioma patients in Indonesia.