bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryopreservation and current legal problems: seeking and selling immortality
Authors: Mullock Alexandra , Romanis Elizabeth Chloe 
Published: November 2023

Abstract
Cryonics, the ‘freezing’ of the human body after death in the hope of reanimation in the future, remains a remote possibility, and yet it is becoming a more popular choice. There has been much academic discussion of the ethics of cryopreservation; however, the legal problems have received little attention. There are, however, several potential current conflicts that might arise, as was illustrated by the case of JS in England, in which a 14-year-old girl who sought cryopreservation against her father’s wishes. In the USA, there have been disputes within families about cryonic preservation, and between cryonics organizations and loved ones of the deceased when there is negligent preservation. Cryopreservation raises questions concerning the law on death and posthumous interests, property in the body, contract law, and (potentially) negligence. We argue that, in the absence of proper regulation, cryonics organizations may be able to exploit the dying and dead. The potential legal problems that we have identified in relation to the law in England and Wales demonstrate that the law is ill-equipped to protect the interests of the dead and their next of kin.
ANGI-04. IKIP SUPPRESSES MIGRATION AND INVASION OF GLIOBLASTOMA BY DOWNREGULATING THBS1/FAK SIGNALING
Authors: Liu Hao , Hu Yanjia , Zhu Zhaoying 
Published: November 2023

Abstract

BACKGROUND
The role of the inhibitor of NF-κB kinase-interacting protein (IKIP) in glioblastoma (GBM) migration and invasion remains poorly understood, despite its known involvement in the negative regulation of NF-κB signaling and inflammation. This study aimed to investigate the impact of IKIP on GBM metastasis and elucidate the underlying molecular mechanisms.

METHODS
Expression levels of IKIP were analyzed in gliomas and normal brain tissues using bioinformatic analysis of public databases and immunohistochemical staining of clinical samples. Transwell and wound healing assays were employed to assess the migration and invasion of GBM cell lines. RNA sequencing was conducted to unravel the molecular pathways involved.

RESULTS
Bioinformatic analysis revealed a significantly higher expression of IKIP in GBM compared to normal brain tissues, and its upregulation was associated with a poor prognosis in glioma patients. However, immunohistochemical and immunofluorescent staining demonstrated the downregulation of IKIP in GBM. Furthermore, functional assays demonstrated that IKIP overexpression suppressed the migratory and invasive capabilities of GBM cell lines, whereas IKIP knockdown enhanced migration and invasion. Mechanistically, IKIP overexpression downregulated THBS1 at the transcriptional level, resulting in the inhibition of THBS1/FAK signaling.

CONCLUSIONS
This study provides evidence for the first time that IKIP exerts inhibitory effects on GBM migration and invasion by downregulating THBS1/FAK signaling. These findings shed light on the complex mechanisms underlying GBM progression and identify IKIP as a potential therapeutic target for GBM invasion.
BIOM-03. LACK OF CORRELATION OF MR-DETERMINED WHITE MATTER INJURY(WMI)WITH NEUROCOGNITIVE FUNCTION (NCF)6 MONTHS FOLLOWING WBRT+/-HIPPOCAMPAL AVOIDANCE(HA)+MEMANTINE:SECONDARY ANALYSIS OF NRG ONCOLOGY NRGCC001
Authors: Bovi Joseph , Pugh Stephanie , Brown Paul , Gondi Vinai , Robinson Clifford , Wefel Jeffrey , Sabsevitz David , Sprenger Markus , Kundapur Vijayananda , Roberge David , Devisetty Kiran , Shah Sunjay , Usuki Kenneth , Stea Baldassarre , Yoon Harold , Donnelly Eric , Laack Nadia , Baschnagel Andrew , Paulus Rebecca , Kachnic Lisa 
Published: November 2023

Abstract

PURPOSE
Previous analysis of NRG-CC001 suggested pre-treatment WMI volume was a significant imaging-biomarker predictor of post-treatment neurocognitive decline at 4-and 12-months following HA-WBRT+Memantine. This suggested patients with greater pre-treatment WMI were more susceptible to neurocognitive decline, specifically when undergoing HA-WBRT, but not standard-WBRT. The current analysis examined the relationship between changes in MR-determined WMI and NCF 6-months following WBRT+memantine+/-HA.

METHODS
NCF-testing was performed at baseline, 2, 4, 6, and 12 months post-WBRT, and included Hopkins Verbal Learning Test–Revised (HVLT-R), Trail Making Test (TMT) Parts A and B, and Controlled Oral Word Association (COWA). Pre-treatment WMI was measured by FLAIR-volume corrected for whole brain volume and corrected for the FLAIR volume associated with metastases (met vol) (FLAIR-volume/(whole brain volume–met-vol). Pearson correlation coefficients were used to assess the correlation between pre-treatment WMI and change from baseline to 6-months for each standardized NCF score.

RESULTS
Of the 518 randomized patients, 443 (217 patients WBRT+Memantine and 226 HA-WBRT+Memantine) had WMI data available at baseline, and of those, 162 patients (89 patients WBRT+Memantine and 73 HA-WBRT+Memantine) had both baseline and 6-month imaging available. For these patients, there was only a trend toward significance for change in corrected FLAIR-volume from baseline to 6-months (p = 0.174) but no significant change in met-vol (p = 0.438) or whole brain volume (p = 0.977). The change in standardized TMT Part A and B and the change in composite 6-month change scores were moderately correlated with change in corrected FLAIR volume adjusted for met-vol but only in the WBRT+Memantine arm (rho=-0.35, -0.34, -0.39 and p-value = 0.003, 0.006, 0.001).

CONCLUSIONS
Despite an increase in post-WBRT MR-WMI at 6-months, analysis did not show strong correlation between NCF and MR-WMI as determined by FLAIR-volume change between baseline and 6-months. Similar analyses are underway for the NRG-CC003 imaging data.
BIOM-05. FIRST-IN-HUMAN PROSPECTIVE TRIAL OF SONOBIOPSY IN GLIOBLASTOMA PATIENTS USING NEURONAVIGATION-GUIDED FOCUSED ULTRASOUND
Authors: Yuan Jinyun , Xu Lu , Chien Chih-Yen , Yang Yaoheng , Yue Yimei , Fadera Siaka , Stark Andrew H , Schwetye Katherine , Nazeri Arash , Desai Rupen , Athiraman Umeshkumar , Chaudhuri Aadel , Chen Hong , Leuthardt Eric 
Published: November 2023

Abstract

INTRODUCTION
Blood-based liquid biopsy for brain cancer offers a noninvasive alternative to invasive surgical biopsies. However, the presence of the blood-brain barrier (BBB) limits the release of brain tumor-derived molecular biomarkers into the bloodstream for sensitive diagnosis. Focused ultrasound (FUS)-enabled blood-based liquid biopsy (sonobiopsy) locally disrupts the BBB and releases tumor-derived biomarkers into blood circulation. Our previous studies have demonstrated that sonobiopsy improved the detection sensitivity of glioblastoma (GBM)-specific cirulating tumor DNA (ctDNA) in animal models of GBM. This study aimed to evaluate the feasibility and safety of sonobiopsy in enriching circulating tumor biomarkers in a first-in-human, prospective clinical trial.

METHODS
Five GBM patients (G01-05) were enrolled in the initial study. The sonobiopy procedures were performed prior to tumor resection, using a nimble FUS device integrated with a clinical neuronavigation system. The plasma level of glial fibrillary acidic protein (GFAP) was quantified using ultrasensitive single-molecule array (Simoa), while the cell-free DNA (cfDNA) levels were quantified using Bioanalyzer. Patient-specific tumor variants were comprehensively analyzed using a personalized tumor-informed ctDNA assay (Invitae Personalized Cancer Monitoring assay). Additionally, the two most common GBM-specific tumor variants were analyzed using customized ddPCR assays.

RESULTS
Analysis of plasmas collected before and after FUS sonication showed sonobiopsy enhanced plasma circulating tumor biomarker levels, including a maximum increase of 1.3-fold for GFAP, 1.6-fold for the concentration of mono-nucleosomal cfDNA fragment (120–280 bp), 1.9-fold increase in patient-specific tumor variant levels, and 5.6-fold increase in the TERT mutation level. Histological analysis of surgically resected tumors confirmed the safety of the procedure. Transcriptome analysis of sonicated and nonsonicated tumor tissues found that FUS sonication mainly modulated cell physical structure-related genes.

CONCLUSIONS
These feasibility and safety data support the continued investigation of sonobiopsy for noninvasive molecular diagnosis of brain diseases.
BIOM-06. LONGITUDINAL CEREBROSPINAL FLUID LIQUID BIOPSY IN PHASE 0/2 TRIAL OF NIRAPARIB FOR NEWLY-DIAGNOSED GLIOBLASTOMA
Authors: Furey Charuta , DeSantis Anita , White Connor , Tien An-Chi , Mehta Shwetal , Sanai Nader 
Published: November 2023

Abstract

INTRODUCTION
Effective drug development in glioblastoma (GBM) requires visualization of tumor evolution in response to experimental therapy. Today, genetic and epigenetic mechanisms of tumor resistance are undetected in clinical trials. Here, we establish the feasibility of a liquid biopsy paradigm in tracking tumor evolution in response to a novel therapeutic using an intra-cavitary reservoir for serial cerebrospinal fluid (CSF) collection.

METHODS
We conducted a Phase 0/2 clinical trial of niraparib, a potent PARP1/2 inhibitor, in newly-diagnosed GBM patients (NCT05076513). Intra-cavitary reservoirs were placed in select patients following tumor resection. Monthly outpatient CSF samples were collected to longitudinally examine cell-free tumor DNA (cfDNA) using a 293-gene amplicon-based next-generation sequencing (NGS) panel and circulating tumor cells using single cell RNA-sequencing (scRNA-seq). Concordance analysis was performed using paired tumor tissue samples against multiple liquid biopsies.

RESULTS
Tumor-derived cfDNA and circulating tumor cells were successfully isolated from intra-cavitary reservoirs at regular intervals for the duration of the clinical trial. Twelve patients so far have been implanted with the reservoirs for CSF collection. Among 55 CSF samples, 53 (94%) has detectable cfDNA. Radiographic tumor burden is associated with concentration of cfDNA (ng/ml, p&lt; 0.01). No adverse events were observed during liquid biopsy acquisition. CSF sequencing data was highly concordant with NGS analyses of tumor tissue. cfDNA and single-cell analyses from serial CSF samples reflected the disparate evolution of GBM patient tumors in the face of PARP1/2 inhibition.

CONCLUSION
This is the first reported experience of serial CSF liquid biopsy to monitor DNA- and RNA-based tumor evolution in the context of an experimental therapy. Our data demonstrate the feasibility of cfDNA NGS and scRNA-seq using longitudinal CSF sampling of clinical trial patients. This new strategy for serial tumor profiling will be an important component of future drug development efforts targeting the moving biology of glioblastoma.
BIOM-07. NON-TUMOR PLASMA EXTRACELLULAR VESICLES PREDICT THE OCCURRENCE OF GBM: A MACHINE LEARNING ANALYSIS
Authors: Aibaidula Abudumijiti (Zack) , Ghaith Abdul Karim , Bydon Mohamad , Parney Ian 
Published: November 2023

Abstract

INTRODUCTION
Glioblastoma (GBM) is the most common primary malignant brain tumor and has a poor clinical outcome. Extracellular vesicles (EVs) are promising biomarkers to assist the differential diagnosis between pseudoprogression and true tumor progression. We aimed to identify non-tumor plasma EV markers that predicted GBM occurrence using trained multiple tree-based machine learning algorithms.

METHODS
We included plasma samples of 40 GBM and 40 non-GBM (20 brain metastasis, 20 normal donors). Spectral flow cytometry was performed to determine plasma EV subpopulation frequency based on CD9,CD81,CD63,CD11b,CD45,CD31, and CD41a expression. Multiparametric t-SNE and FlowSOM analysis clustered plasma EVs based on these markers. Decision trees and random forest classifiers were trained and tested to predict the disease status (GBM vs non-GBM) based on plasma EV subpopulations.

RESULTS
Compared to non-GBM, GBM had increased frequency of CD9+ EVs (64.52% vs 40.69%, p&lt; 0.0001), CD9+CD63-CD81- EVs (54.45% vs 37.26%, p&lt; 0.0001) and myeloid-derived EVs (CD9+CD11b+ EVs, 20.77% vs 12.48%, p = 0.0241). In the decision tree analysis, low frequency of CD9+ EVs was found in 44% of all cases and represented a chance of 75% to be classified as non-GBM cases. An algorithm based on random forest analysis (n = 500 trees) using these markers had a sensitivity of 85.71% and specificity of 77.8% with an overall accuracy of 81.25% for identifying GBM. The frequencies of CD9+, CD9+CD63-CD81-, and CD9+CD63+CD81+ were the most critical factors in predicting GBM diagnosis. FlowSOM analysis identified 20 plasma EV subpopulations but had a lower accuracy (62.5%) when combined with our machine learning algorithm.

CONCLUSIONS
Non-tumor plasma EV expression profile combined with tree-based machine learning demonstrated high accuracy in predicting patient disease status. CD9+ EV frequency was one of the most promising biomarkers to assist in this diagnosis. We will continue to test our established algorithm and further validate our findings in a larger cohort.
BIOM-08. SINGLE-MOLECULE SYSTEMS FOR DETECTION OF PLASMA CIRCULATING ONCOPROTEINS IN DIFFUSE MIDLINE GLIOMA
Authors: Erez Nir , Furth Noa , Fedyuk Vadim , Wadden Jack , Aittaleb Rayan , Schwark Kallen , Miclea Madeline , Venneti Sriram , Koschmann Carl , Shema Efrat 
Published: November 2023

Abstract
Diffuse midline glioma (DMG) is a high-risk pediatric brain tumor that has primarily been diagnosed and monitored via medical imaging (MRI) due to risks associated with re-biopsying midline brain structures. Recent advances in molecular diagnostics have improved classification and molecular characterization of DMG; these tumors are in dire need of non-invasive, molecular-based diagnostic tools to supplement serial assessments of radiographic response. Our group recently developed a single-molecule imaging platform, Epigenetics of Plasma Isolated Nucleosomes (EPINUC), to profile histone modification patterns in cell-free tumor DNA (ctDNA) from plasma of cancer patients. We developed a novel strategy for single-molecule detection of the histone mutation H3K27M, a key DMG genetic driver, by capturing mutant nucleosomes on a PEG-streptavidin coated surface and detecting them with fluorescently labeled antibodies targeting histone modifications enriched on these mutant nucleosomes. We applied this method to 46 H3K27M and 10 H3 wildtype DMG samples and found significantly higher signal in K27M samples. Using this data, we generated a predictive model of H3 status with an AUC of 0.81, sensitivity 90%, specificity 71%, and precision 73%. This test was found to be highly reproducible and rapid (60 minutes) and required less than 100 uL of plasma. We also analyzed mutant p53 protein in plasma samples from 11 p53-mutant and 4 p53-wildtype DMG patients, seeing significant separation between the two groups. We overlayed H3K27M and p53 cell-free protein results with H3.3K27M and TP53 ctDNA variant allele fraction (VAF) by digital droplet PCR (ddPCR) in serial plasma samples from n = 3 DMG patients undergoing experimental therapy. These data highlighted unique patterns of disease response by (1) MRI, (2) plasma tumor protein, and (3) plasma ctDNA. Overall, these results demonstrate the clinical potential of our platform for non-invasive and accurate detection and monitoring of levels of key oncoproteins in plasma of DMG patients.
BIOM-09. OPPOSING EFFECTS OF LINKED CX3CR1 GERMLINE VARIANTS ON SURVIVAL AND IMMUNE ACTIVATION IN GLIOMA
Authors: Khan Abdul Basit , McDonald Malcolm , Curry Rachel , Yang Yuhui , Khatri Latha , Deneen Benjamin , Serin-Harmanci Akdes , Rao Ganesh 
Published: November 2023

Abstract
Linkage-disequilibrium connects CX3CR1 V249I and T280M single-nucleotide polymorphisms; V249I occurs as a single-variant (SV) and T280M exclusively as a double-variant (DV) concurrent with V249I. In low-grade gliomas (LGG), we found improved median overall-survival (mOS) in SV (n = 14, mOS 21.03yrs), compared to WT (n = 45, mOS 9.41yrs) and DV (n = 31, mOS 10.49yrs; p = 0.037 Log-rank). In TCGA glioblastoma (GBM), SV (n = 69, mOS 15.65mo) improved survival over DV (n = 106, mOS 11.74mo; p = 0.044 Log-rank). In a separate GBM cohort, bulk RNA-sequencing revealed MMP9 over-expression in DV (n = 15) compared to SV (n = 10; log2FC 2.87, p-adj 0.079). On a single-gene basis, MMP9 expression was decreased in SV compared to DV and WT (n = 33; p = 0.044, Kruskal-Wallis). MMP9 promotes tumor angiogenesis and invasion. SV showed SPP1 over-expression compared to DV (log2FC -1.75, p-adj 0.026), with decreased SPP1 expression in both WT and DV compared to SV (p = 0.004, Kruskal-Wallis). SPP1 is a pro-inflammatory cytokine enriched in glioma-associated macrophages. Gene Ontology revealed enrichment of biological processes: neutrophil migration, granulocyte chemotaxis, and neutrophil chemotaxis in SV (p&lt; 0.05). We single-cell RNA-sequenced IDH mutant gliomas (51777 cells). We subset and re-clustered myeloid-derived cells (microglia/macrophages, 8944 cells), identifying thirteen clusters. Myeloid-derived cells clustered by CX3CR1 status, with 50.8% of SV cells in cluster five and 85.3% of DV cells in clusters six or seven. Cluster five over-expressed IL1B (average-log2FC 3.23), a tumor-suppressive M1 macrophage marker. Clusters six and seven were characterized by IFIT genes – immunomodulatory in myeloid-derived cells (IFIT3 average-log2FC 2.65 and 2.06). Assessing CX3CR1 status in normal population – 74.2% are WT, 10.0% SV, and 15.7% DV. In glioma patients, we identify 59.9% WT, 14.9% SV, and 25.2% DV – an increase of 49% in SV and 61% in DV (p = 1.95e-6, Chi-square). Our findings demonstrate opposing effects of linked CX3CR1 germline variants on glioma survival and indicate enhanced immune activation in SV.
BIOM-10. KI-67 IS ASSOCIATED WITH PROGRESSION-FREE SURVIVAL IN PATIENTS WITH GLIOBLASTOMA
Authors: Bergman Drew , Anand Sumyuktha , Gill Gobind , Harris Brent , Fadul Camilo , Havrda Matthew , Pointer Kelli 
Published: November 2023

Abstract
Identifying predictive and prognostic markers for glioblastoma (GBM) is an area of intense investigation. The objective of this study was to evaluate OLIG2 and Ki-67 as prognostic biomarkers. A tissue microarray with clinical data was created for 70 patients diagnosed with GBM between 2002-2007 at a single institution. Immunohistochemistry was performed to evaluate expression of OLIG2 and Ki-67. Overall survival and progression free survival (PFS) were calculated using the Kaplan-Meier method. Univariable (UVA) and multivariable (MVA) analysis was performed using Cox proportional hazards modeling. The median age of diagnosis was 63, 66% of patients were male, 80% had a KPS ≥70, 64% had a subtotal resection or biopsy, and 36% had a gross total resection. Median OS and PFS were 13.3 months and 9.5 months respectively. For patients who received resection plus chemoradiation, median OS and PFS were 16.7 months and 9.5 months respectively. 36.4% of patient samples had Ki-67 expression fraction &gt; 20%. 18.0% had heavy OLIG2 staining. On MVA, lower KPS was associated with shorter OS and radiation therapy was associated with longer OS. OLIG2 was not associated with OS or PFS. Patients who had a Ki-67 &lt; 20% had a shorter PFS, but not OS on MVA. Our data demonstrate higher Ki-67 levels correlate with improved PFS without an OS benefit. This association persisted for patients receiving standard of care treatment. OLIG2 levels did not correlate with PFS or OS in either cohort. Our study indicates that further investigation is needed to determine whether Ki-67 is useful in predicting recurrence risk and potentially changing treatment strategies for these patients, as well as the mechanism behind the associated improvement seen with higher Ki-67 levels. These data are currently limited by lack of IDH and MGMT status but suggest Ki-67 should be further investigated as a biomarker for progression.
BIOM-12. ULTRA-DEEP WHOLE GENOME SEQUENCING UNCOVERS A HIGH PREVALENCE OF GLIOBLASTOMA-DERIVED CELL-FREE DNA IN PLASMA
Authors: Underhill Hunter , Farrell Andrew , Dean Charlie , Harrison Brion , Bronner Mary , Colman Howard , Jensen Randy 
Published: November 2023

Abstract
The detection of glioblastoma-derived circulating cell-free DNA (ccfDNA) has proven formidable because tumor-specific mutations are hidden among the abundance of ccfDNA from healthy cells. While capture-enrichment panels provide the necessary read depth to detect low-frequency variants, searches are constrained to a narrow range of targets and largely limited to single nucleotide variants (SNVs). Here, we use ultra-deep whole genome sequencing (WGS) to broaden the search for somatic mutations across the entire genome. In addition, a kmer-based reference-free variant caller, which mitigates the bias and errors that accrue during alignment, is used to extend the mutation search beyond SNVs to include insertions/deletions (INDELS) and structural variants (SVs) such as large INDELS ( &gt;20 bp) and tandem duplications. In tumor DNA and ccfDNA, we achieve a WGS (GRCh38) mean read depth of 263X and 225X, respectively. WGS of matched buffy coat DNA and sequencing reads from the 1000 Genome Database were used to eliminate germline polymorphisms, sequencing artifacts, and common variants. We detected 20,488 somatic mutations in tumor DNA of which 17.3% affected a coding sequence, 31.9% were INDELS, 91 were large INDELs, and 18 were tandem duplications. A tumor-informed search identified 489 of these somatic mutations in ccfDNA which included a large INDEL and a similar portion of mutations affecting a coding sequence. Using an unguided search for glioblastoma-derived ccfDNA uncovered an additional 8,794 somatic mutations of which 16.6% involved a coding sequence, 60.7% were INDELS, 30 were large INDELS, and 3 were tandem duplications. The high prevalence of somatic mutations discovered in ccfDNA using an unbiased approach highlights the low yield of tumor-informed searches in spatially genetically heterogeneous cancers like glioblastoma. Our findings demonstrate that ultra-deep WGS detects glioblastoma-derived ccfDNA by broadening the search for variants across the entire genome and through the inclusion of INDELS and SVs.