tbuckley/cabot-search huggingface dataset:
INVESTIGATING CUDC-101 EFFECT AND MECHANISM OF ACTION AGAINST GLIOBLASTOMA IN VITRO
Authors: Ms Rebecca Chandler, Dr Jane Alder, Dr Roshini Mathews, Dr Izabela Stasik
Journal: Neuro-Oncology (2024)

Abstract AIMS Glioblastoma (GB) has complex pathophysiology, diﬃcult treatment and resultant poor prognosis. Its median survival rate is approximately 15 months. The aggressive nature of GB results in rapid disease progression in 60-70% patients often within 12 weeks. Limited treatment options include maximal safe surgical resection, followed by radiotherapy and temozolomide (TMZ). The blood brain barrier restricts chemotherapeutic entry and increases dosage leading to increased side effects and decreased treatment tolerance. Furthermore, signiﬁcant disease heterogeneity means reoccurrence is expected in most cases, for which there are no standard treatment routes. This coupled with ineﬃcient treatment with temozolomide (TMZ) due to the blood brain barrier, highlights the requirement for novel treatments. METHOD Histone deacetylases (HDAC) and endothelial growth factor receptor (EGFR) are mutated and upregulated in GB allowing tumour inﬁltration and proliferation. CUDC-101 is known to target both HDAC and EGFR in other cancers making it a promising therapeutic to trial in GB. Cell viability of U251, T98G and U87MG human cells was measured post-CUDC-101 administration at 24, 48 and 72hrs. SVGp19 embryonic non-cancerous human glial cells were used as a control to establish CUDC-101 preliminary speciﬁcity. Targeting another major hallmark of GB, wound healing assays were performed to assess CUDC-101 capacity to inhibit migration. In addition to this, long-term cellular resistance was investigated through clonogenic assays. Western blotting was then used to identify non-/treated expression levels of activated EGFR and acetylated histone H3. Expression levels in non/-treated cells were then visualised with ﬂuorescent microscopy. In addition, ﬂow cytometry was utilised to observe cell cycle changes. RESULTS Overall, results indicate CUDC-101 has a dose-dependent effect on cell viability (long-term and short-term) and migration. Additionally, ﬂuorescent images show treatment does increase histone acetylation and decrease total EGFR. CONCLUSION Future work will solidify these datasets and show changes in activated EGFR and acetylated histone H3 using western blotting.
AN EX-VIVO SPECTRAL AND LIFETIME-DECAY ANALYSIS OF 5-ALA DERIVED PPIX ﬂUORESCENCE: OBJECTIVE ﬂUORESCENCE MAPPING IN GLIOMA SURGERY
Authors: Mr Matthew Elliot, Dr Silvere Segaud, Mr Oscar MacCormac, Ms Sabina Patel, Dr Zita Reisz, Mr Jose Lavrador, Mr Francesco Vergani, Mr Ranjeev Bhangoo, Prof Keyoumars Ashkan, Prof Safa Al-Sarraj, Dr Graeme Stasiuk, Dr Yijing Xie, Prof Tom Vercauteren, Mr Jonathan Shapey
Journal: Neuro-Oncology (2024)

Abstract AIMS 5ALA/Protoporphyrin IX (PpIX) ﬂuorescence guided surgery (FGS) in high-grade glioma has been shown to increase resection and survival, despite this beneﬁts are limited in low-grade glioma by low emission and subjective interpretation. Quantitative ﬂuorescence could address these issues, however is challenging due to photobleaching and variations in tissue induced distortion and PpIX photochemical state that are poorly understood. Lifetime-decay measures intrinsic ﬂuorophore properties and is not inﬂuenced by these factors, but is diﬃcult to measure intra-operatively. We used paired optical and ﬂuorescence spectroscopy with lifetime decay mapping to characterise PpIX emission within the glioma tissue microenvironment. METHOD Biopsies were collected from 20 patients undergoing glioma FGS, along with 4 controls from partial temporal lobectomies. Paired measurements of emission and lifetime were matched with optical property readings. Lifetime and emission ratios at 635 and 620nm were calculated (PpIX635/620), corresponding to the primary emission peak for the photochemical states of PpIX in tissue. Raw and optically corrected emission was correlated with lifetime decay. RESULTS 205 specimens were analysed by WHO grade (56 Grade4, 66 Grade3, 37 Grade2, 20 control). PpIX635/620 emission was 0.93 in control (CI 0.91-0.95), 1.03 in grade 2 tumours (CI 0.95-1.26), 1.56 in grade 3 (CI 1.22-1.91) and 6.99 (CI 5.78-8.20) in grade 4. PpIX635/620 lifetime correlated with emission (R2 =0.98, range 0.94-1.57). Correlation of emission with lifetime readings improved signiﬁcantly following optical correction at 635nm (raw R2 =0.81, corrected R2 =0.90) and 620nm (raw R2 =0.44, corrected R2 =0.86). CONCLUSION PpIX620 and PpIX635 photochemical states are present in human glioma, with an increase in PpIX635/620 suggesting increased WHO grade. The ability to distinguish these forms holds the potential to provide real-time data for tumour differentiation and pathology. Accurate characterisation and correction of tissue induced distortion signiﬁcantly improves the ability to detect, characterise and quantify PpIX intra-operatively.
TARGETING RESIDUAL CANCER FROM THE INVASIVE MARGIN OF GLIOBLASTOMA USING COMPUTATIONAL TOOLKITS
Authors: Ms Maria Shah, Dr Stuart Smith, Dr Emyr Bakker, Dr Ruman Rahman
Journal: Neuro-Oncology (2024)

Abstract AIMS Inﬁltrative margin GBM, as a proxy for residual disease post-surgery, can be identiﬁed by 5-aminolevulininc acid (5ALA) to facilitate the discovery of uniquely expressed or upregulated molecular pathways. Complementary bioinformatics approaches offer reproducible ways to enable interoperability of heterogenous data sources towards identiﬁcation of therapeutic targets associated with GBM inﬁltration. METHOD RNA-seq primary tumour data was ﬁrst categorised as: 5ALA+ (inﬁltrative margin) vs tumour core and 5ALA+ vs 5ALA- (reactive brain). Two levels of ﬁltration (genes with adjusted p-value &amp;lt;0.05; degree of fold change with log2&amp;gt;1.5) were applied to genes, creating two separate gene lists. Cross-referencing gene lists identiﬁed transcripts upregulated in both 5ALA+ vs core and 5ALA+ vs 5ALA-. This candidate gene list was inputted into STRING to generate an uncurated protein-protein interaction (PPI) network, which returned a signiﬁcant PPI enrichment p-value to conﬁrm network connectivity, and next inputted into Metascape to elucidate biological processes associated with tumour inﬁltration. RESULTS Of 141 upregulated 5ALA+ genes TCP10L3, HELT, MGAM, ALOX5 and FOXI1 exhibited the greatest fold change. The most prevalent 5ALA+ biological processes were primitive streak formation, disaccharide metabolic process and sodium ion transmembrane transport. LOC157273, LINC00200, LINC00656, LOC285626 and LINC01568 were identiﬁed as long non-coding RNAs (lncRNA) most abundant in the inﬁltrative margin of GBM relative to tumour core and reactive brain. Regulatory associations between candidate 5ALA+ lncRNA and genes, and in silico drug repurposing via molecular docking, are being investigated. CONCLUSION The plasticity of GBM warrants analysis of the GBM inﬁltrative margin via computational toolkits to enhance understanding of upregulated molecular pathways, functionally associated with an invasive phenotype.
GLIOMA MONITORING VIA LONGITUDINAL INTRACRANIAL CSF CELL-FREE DNA: ONE PATIENT AT A TIME
Authors: Ms Cecile Riviere-Cazaux, Dr Xiaoxi Dong, Dr Wei Mo, Dr Chao Dai, Dr Jian Campian, Dr Michael Ruff, Dr Jeanette Eckel-Passow, Dr Timothy Kaufmann, Dr Sani Kizilbash, Dr Arthur Warrington, Dr Robert Jenkins, Dr Pan Du, Dr Shidong Jia, Dr Terry Burns
Journal: Neuro-Oncology (2024)

Abstract AIMS Methods for disease monitoring in glioma are currently limited. Liquid biopsies are of increasing interest within the ﬁeld but have been challenging due to the blood-brain barrier. To bypass this challenge, we aimed to assess the technical and clinical feasibility of obtaining intracranial cerebrospinal ﬂuid (CSF) for disease monitoring via cell-free DNA (cfDNA). METHOD Adults with gliomas were recruited for longitudinal intracranial CSF collection via CSF access devices, including Ommaya reservoirs in four patients and an existing VP shunt in one patient. cfDNA was then extracted and analyzed using two sequencing platforms, PredicineCARE for cancer variant proﬁling and PredicineSCORE for low-pass whole genome sequencing (LP-WGS). This analysis generated genomic aberration proﬁles and genome wide copy number burden (CNB) score. RESULTS Across ﬁve patients, thirty-ﬁve CSF samples were obtained (median volume: 3.80 mL; 0.5-5 mL), with 30 samples (85.7%) yielding suﬃcient cfDNA. Tumor fraction increased by 6.28x and 2.87x in two patients with radiographic disease progression and decreased by 0.08x and 0.04x in another two after chemoradiation. In another patient with pseudoprogression, tumor fraction decreased from 0.26 after resection to unmeasurable levels. Patient speciﬁc tumor-associated variant allelic frequencies (VAFs), including TP53, PTEN, and TERT, decreased within individual patients after resection and chemoradiation. In two patients with IDH-mutant gliomas, IDH1 VAF after resection correlated with decreased CSF D-2-hydroxyglutarate (D-2-HG) levels (0.64x and 0.62x, respectively, for the ﬁrst patient, and 0.01x and 0.07x for the other patient). Both IDH1 VAF and D-2-HG increased in a patient with radiographic progression (2.56x and 9.21x, respectively). CNB decreased below the limit of quantiﬁcation during treatment and increased above the limit at progression. CONCLUSION Longitudinal CSF cfDNA can feasibly be obtained via CSF access devices in patients with gliomas during their disease course. Further sample collection and analysis are ongoing to determine the thresholds of change indicative of treatment response and progression.
INVESTIGATING GLIOBLASTOMA STEM CELL DIFFERENTIATION IN HUMAN BRAIN 3D ORGANOID CO-CULTURES
Authors: Dr Roberta Azzarelli, Dr Laura Morcom, Prof David Rowitch, Prof Anna Philpott
Journal: Neuro-Oncology (2024)

Abstract AIMS Glioblastoma (GBM) recurrence is rooted in the ability of residual stem cells to survive treatment and drive relapse. One way to eradicate glioblastoma stem cells (GSCs) is to differentiate them into post-mitotic, non-tumorigenic cell types. Here we aim to differentiate GSCs via genetic manipulation, and test how their response differs in 2D and 3D cultures. METHOD We generated a co-culture model to grow GSC lines with iPSC-derived 3D human brain organoids. Before co-culture, the GSC lines were genetically engineered to overexpress a Doxycycline (Dox) inducible form of the proneural transcription factor ASCL1 (wild type and phosphorylation defective). Live imaging and immunochemistry were performed to analyse tumor composition. RESULTS Our data show that activation of the proneural factor ASCL1 in GSCs when co-cultured with 3D human brain organoids drives reduction in tumor growth and that inhibition of ASCL1 phosphorylation only slightly improves this effect. In comparison to data in 2D cultures, the effect of ASCL1 activation seems enhanced in 3D organoids. At day 7 and 14 of ASCL1 induction, there are only few cancer cells left in the organoids, while, in 2D, wildtype ASCL1-expressing cells continue to grow, even if at a slower rate than control GSCs. CONCLUSION Our data show that cancer stem cells embedded in 3D human brain organoids behave differently than when in 2D culture on plastic and respond more effectively to differentiation treatments. Our model provides a platform to test novel treatments for GBM.
MULTI-AGENCY DEVELOPMENT OF A NEW INFORMATION RESOURCE FOR PATIENTS WITH BRAIN METASTASES
Authors: Ms Rhona Watson, Ms Gemma Austin, Dr Helen Bulbeck
Journal: Neuro-Oncology (2024)

Abstract AIMS Based in a large neuro-oncology centre which provides specialist care for hundreds of patients with BM per year, the authors identiﬁed a need for relevant, non-disease speciﬁc, technically accurate and holistically focussed patient information material. This project aimed to develop a comprehensive and patient-focussed information resource for patients with BM. METHOD A scoping exercise of twenty UK-based cancer charity websites was carried out. Generic cancer charity sites and sites of charities supporting the four main primary cancer groups which metastasize to the brain were targeted. Information pertaining to BM was collated and reviewed by a multidisciplinary group to assess for scope and quality of information provided. Particular attention was paid to identifying information which was technically accurate and speciﬁcally addressed the holistic needs of this patient group. RESULTS Information found was primary disease-speciﬁc, technically inaccurate and did not acknowledge the holistic needs of the patient. This exercise highlighted the need for comprehensive and relevant patient-focussed information material. A working group consisting of health professionals and BrainsTrust charity staff was formed to create an effective patient information resource. Existing BrainsTrust information templates were used to structure the new resource. Evidence-based clinical information was provided by the healthcare professionals involved and holistic information was created collaboratively with charity input. A patient reviewer was enlisted to provide feedback on draft versions. CONCLUSION This project resulted in production of a patient-focussed and comprehensive information resource on BM. Patient and healthcare professional feedback to date has been positive.
EXPLORING MOLECULAR LINKS IN BRAIN TUMOUR BIOPSY TISSUES AND ALZHEIMER’S DISEASE
Authors: Ms Kristy Montalbo, Dr Izabela Stasik, Dr Emyr Bakker, Dr Christopher George Severin Smith
Journal: Neuro-Oncology (2024)

Abstract AIMS Generate and identify putative targets in the SORL1-network by mining online databases. Analyse 21 FFPE human brain tumour biopsy tissues through transcriptome sequencing performed by CeGaT (Tübingen, Germany) to explore differentially expressed genes. These biopsy samples are from consenting patients in association with Brain Tumour North West (BTNW) and the Royal Preston Hospital. METHOD Group comparisons are performed with the control and cancerous sample groups (low-grade glioma staying low, low-grade glioma becoming high and high-grade staying high). Further analysis involves comparing section and resection from the same patient for each cancer tissue group. Samples are explored on four different bioinformatic levels and sequenced on the Illumina platform. In Level 1 the data is demultiplexed and trimmed and in Level 2 trimmed reads are additionally mapped. Level 3 provides insights into the cell’s metabolic state and Level 4 performs several group comparisons. RESULTS Gain insights into differentially expressed genes’ presence in biopsy tissues from different stages of brain cancer, expression levels and links to clinical characteristics. Bioinformatic analysis provides data on quality control of the starting material, library preparation, sequencing parameters, and the Q30 value of the sequencing. CONCLUSION The analysis demonstrates molecular links in the SORL1-network in tissue from section and resection from a patient cohort to better understand disease recurrent and progression. Prospective bioinformatic work would explore interactions between signiﬁcant targets identiﬁed to create a curated network that could predict druggable targets in gliomas.
INTEGRATING TRANSCRIPTOMICS WITH SPATIAL RADIOGRAPHIC ATLASES FOR GLIOMA ANALYSIS
Authors: Mr Yonghao Li, Mr Yizhou Wan, Prof Stephen Price
Journal: Neuro-Oncology (2024)

Abstract AIMS The localization of gliomas in the brain is a critical prognostic factor, reﬂecting the genetic makeup of their originating cells. Variations in transcriptomic proﬁles across different regions and subtypes may further shed light on the mechanisms driving tumor development. Our research delves into the complex interplay between glioma locations and their transcriptomic signatures, seeking to dissect the spatial and genetic intricacies contributing to glioma diversity. METHOD In this study, we conducted a comprehensive analysis of preoperative anatomical MRI and transcriptomic data from 242 glioma patients to investigate the relationship between spatial distribution and tumor transcriptomic proﬁles. The MRI data were standardized by registration to the MNI-152 brain space. Tumors were segmented, and the brain was partitioned into 84 discrete subregions for detailed examination. Transcriptomic data underwent preprocessing, with principal component analysis employed to reduce dimensionality. Statistical analyses were used to assess the relationship between glioma description across different subtypes and PCA results. Additionally, we identify differentially expressed genes and common genes across regions for various glioma subtypes. Comparative analyses with the Allen Brain Atlas (divided into 84 subregions with expression data) were also performed to discern transcriptional differences between healthy individuals and glioma patients, further enhancing our understanding of glioma biology at the molecular level. RESULTS We generated 21 frequency maps detailing regional glioma occurrences, categorized by biomarkers, subtypes, and grades. Notably, some of these maps showed signiﬁcant correlations with expression principal component analyses (PCAs). Our ﬁndings include a set of genes consistently expressed across subregions, alongside region speciﬁc differentially expressed genes. Additionally, we identiﬁed distinct gene expression patterns when comparing glioma patients to healthy controls in the Allen Brain Atlas, highlighting potential molecular underpinnings of glioma heterogeneity. CONCLUSION Our analysis revealed notable correlations between glioma subtype locations and transcriptomic proﬁles, underscoring the role of transcriptomic signatures in explaining regional variations in glioma incidence.
UNVEILING THE MECHANISTIC INSIGHTS OF ARGININE DEPRIVATION COMBINED WITH RADIOTHERAPY FOR THE TREATMENT OF GLIOBLASTOMA
Authors: Dr Maria Chatziathanasiadou, Mr Jake Symington, Mr Huan Huang, Dr Tom Thorne, Mr Kevin O’Neill, Dr Nelofer Syed
Journal: Neuro-Oncology (2024)

Abstract AIMS Glioblastoma is a lethal form of primary brain tumour in adults. Despite surgery, radiation and chemotherapy, life expectancy is short rendering the need for novel therapeutic approaches. Metabolic therapies provide a multifaceted effect in the heterogeneous glioblastoma microenvironment as they target its reprogrammed metabolism while overcoming therapeutic obstacles such as the blood brain barrier. We have shown that arginine deprivation combined with radiation eliminates the tumours in vivo, however, the exact mechanism of action is yet unknown. Here, using spatial transcriptomics we explore the effects of arginine deprivation and radiation, alone and combined, on the glioblastoma microenvironment. METHOD Brains collected from CT2A immunocompetent mice 6 days after treatment with ADI-PEG20 (5 IU) for arginine depletion, radiation (8 Gy) or their combination were analysed by 10X Genomics Spatial Transcriptomics. Bioinformatic analysis was performed using the R package Seurat and the Ingenuity Pathway Analysis (Qiagen). RESULTS The induction of innate immune response was observed with all treatments, however, it was the prevailing element only in the combination treatment. Upregulated pathways in all treatments involved the activation of antigen presentation cells. The pro-inﬂammatory cascades included key molecules of an immune response such as Type I IFNs, IFN-γ, STAT1, ISG15 and IRFs. Protein translation pathways indicating resistance to treatment dominated the changes caused by the two monotherapies, while they were absent in the combination group. The upregulation of CXCL10 and CCL5 signiﬁed the transition to adaptive immune response. Cytosolic DNA sensing by the cGAS-STING was enriched in the radiation and combination groups providing a possible trigger for the innate immune response. Pyroptosis and extracellular matrix remodelling were uniquely presented in the combination group. CONCLUSION Our analysis indicates that arginine deprivation and radiation when combined enhance each other’s effect leading to a fortiﬁed immune response that is possibly initiated by cytosolic DNA sensing.
QUALITY OF LIFE IN PATIENTS WITH SKULL BASE CHORDOMA AND CHONDROSARCOMA TREATED WITH PENCIL BEAM SCANNING PROTON THERAPY
Authors: Dr Katarina Bryjova, Dr Paul-Henry Mackeprang, Prof Damien Charles Weber
Journal: Neuro-Oncology (2024)

Abstract AIMS The objective of this study is to assess the health-related quality of life (HRQoL) of skull base chor- doma/chondrosarcoma patients treated with proton therapy (PT). METHOD Seventy seven adult patients with skull base chordoma/chondrosarcoma completed the EORTC-QLQ-C30 and the BN20 Questionnaires prior to PT, Clinical outcome and therapy related acute and late toxicities have been recorded in course of the follow-up. The data was collected, categorized and analyzed, comparing the posttreatment scores to each patient’s baseline. In order to assess the impact of the clinical outcome and toxicities on HRQoL, the scores were correlated to collected clinical outcomes. RESULTS Median follow-up was 51 months. 6-year overall survival and local failure free survival rates observed were 85.1% and 80.3%. One G3 brain radiation necrosis and one G4 optic nerve disorder were documented during FU. HRQL deteriorated after the completion of proton therapy and returned to baseline values one year thereafter. After the second and third year, we observed further decrease in HRQL. This development was unrelated to tumor relapse. However, comparing the whole cohort over time, global QoL did not change substantially over the course of follow-up. GTR was correlated to better QoL at all time points. Disease progression was correlated with overall worse QoL and higher neurological symptoms already before PT, and higher symptom burden one year thereafter. Males had better QoL before and one year after PT than females. CONCLUSION PT achieves an excellent local and distant control in patients with skull base chordoma/chondrosarcoma. The HRQoL in these patients decreases immediately after the treatment completion, returns to the baseline from one year thereafter, and tends to deteriorate again with longer FU. The observed changes in global HRQoL were however not substantial in the whole cohort over the course of follow-up.