bluuebunny/crossref_metadata_2025_split huggingface dataset:
BIOM-35. CLINICALLY TRACTABLE OUTCOME PREDICTION OF GROUP 3/4 MEDULLOBLASTOMA BASED ON TPD52 IMMUNOHISTOCHEMISTRY: A MULTICOHORT STUDY
Authors: Delaidelli Alberto , Dunham Christopher , Santi Mariarita , Negri Gian Luca , von Deimling Andreas , Pfister Stefan , Kool Marcel , Ramaswamy Vijay , Korshunov Andrey , Taylor Michael , Sorensen Poul 
Published: November 2021

Abstract

BACKGROUND
International consensus and the 2021 WHO classification recognize eight molecular subgroups among Group 3/4 medulloblastoma (representing ~60% of tumors). However, very few clinical centers worldwide possess the technical capabilities to determine DNA-methylation patterns or other molecular parameters of high-risk for Group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an immunohistochemistry (IHC) marker as a clinically tractable method for improved medulloblastoma risk-stratification.

PATIENTS AND METHODS
We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three Group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. Risk stratification and prediction capability were computed utilizing uni- and multivariate survival analysis. Newly developed risk classifiers including TPD52 IHC were compared to state-of-the-art risk stratification schemes in terms of prediction error, area under the time-dependent receiver operating characteristic (ROC) curves and C-statistic. Biomarker-driven prognostic stratification models identified were cross validated in different cohorts.

RESULTS
TPD52 IHC positivity represents a significant independent predictor of early relapse and death for Group 3/4 medulloblastoma (HRs between 3.67-26.7 [95% CIs between 1.00-706.23], p = 0.05, 0.017 and 0.0058). Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing disease risk-stratification schemes, and reclassified ~50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity is a predictive indicator of poor response to chemotherapy (HR 12.66 [95% CI 3.53-45.40], p &lt; 0.0001), suggesting important implication for therapeutic choices.

CONCLUSION
The current study redefines the approach to risk-stratification in Group 3/4 medulloblastoma. Integration of TPD52 IHC in classification algorithms significantly improves outcome prediction and can be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
BIOM-38. THE PROGNOSTIC ROLE OF THE IMMUNOHISTOCHEMICAL MARKERS H3K27me3, SSTR1-5 AND BAP1 IN MENINGIOMA
Authors: Behling Felix , Fodi Christina , Renovanz Mirjam , Paulsen Frank , Skardelly Marco , Honegger Jürgen , Tatagiba Marcos , Schittenhelm Jens , Tabatabai Ghazaleh 
Published: November 2021

Abstract
Meningiomas are the most common primary tumors of the nervous system. These slow growing tumors arise from the meninges. Most patients can be cured by surgical excision. Yet, approximately 20% of patients suffer tumor recurrence. Prognostic markers are warranted to facilitate the identification of patients with an increased risk of tumor recurrence. Immunohistochemical markers are very interesting candidates in this regard and could be integrated into the routine clinical workflow as an inexpensive tool for prognostication and risk stratification. We analyzed the prognostic impact of the immunohistochemical expression of H3K27me3, somatostatin receptors 1-5 and BAP1 in the Tübingen meningioma cohort including &gt; 1200 meningiomas. We identified an independent negative prognostic impact of the loss of H3K27me3. An increased expression score for SSTR2A was associated with a shorter progression-free survival. Higher expression of SSTR5 indicated a more favorable prognosis. The loss of BAP1 expression in meningioma cells was a negative prognostic factor with a shorter progression-free survival. Taken together, we present potential candidate prognostic markers that could be further investigated in prospective cohorts to determine their clinical utility.
STEM-02. THERAPEUTIC INTERVENTION OF LUNG-, BREAST-, AND MELANOMA-BRAIN METASTASIS
Authors: Kieliszek Agata , Bassey-Archibong Blessing , Venugopal Chitra , Singh Sheila K 
Published: November 2021

Abstract

BACKGROUND
The incidence of brain metastases (BM) is tenfold higher than that of primary brain tumours. BM predominantly originate from primary lung, breast, and melanoma tumours with a 90% mortality rate within one year of diagnosis, posing a large unmet clinical need to identify novel therapies against BM.This unmet clinical need is largely attributed to a small population of cancer stem cells (CSCs), termed BM-initiating cells (BMICs), that are able to escape a primary tumour, drive metastasis and facilitate the formation of a secondary tumour in the brain.

METHODS
Using a large in-house biobank of patient-derived BMIC lines, the Singh Lab has generated murine orthotopic patient-derived xenograft models of BM and captured a “premetastatic” population of BMICs that have just seeded the brains of mice before forming clinically detectable tumours: a cell population that is impossible to detect in human patients but represents a therapeutic window wherein metastasizing cells can be targeted and eradicated before establishing clinically detectable tumours.

RESULTS
RNA sequencing of pre-metastatic BMICs from all three primary tumour models with subsequent Connectivity Map analysis identified a lead compound that exhibits selective anti-BM activity in vitro. Preliminary in vivo work has shown that this lead compound reduces the tumor burden of treated mice compared to vehicle control while providing a significant survival advantage. Ongoing mechanistic investigations aim to delineate the protein target of this compound in the context of the observed selective anti-BMIC phenotype.

CONCLUSION
Identification of novel small molecules that target premetastatic BM cells could prevent the formation of BM and dramatically improve the prognosis of at-risk cancer patients.
STEM-12. THE SMALL MOLECULE DRUG CBL0137 INCREASES THE LEVEL OF DNA DAMAGE AND THE EFFICACY OF RADIOTHERAPY FOR GLIOBLASTOMA
Authors: Tallman Miranda , Zalenski Abby , Deighen Amanda , Grubb Treg , Schrock Morgan , Mortach Sherry , Kastury Preetham , Huntoon Kristin , Summers Matthew , Venere Monica 
Published: November 2021

Abstract
Glioblastoma (GBM) is a fatal and incurable brain tumor, with an average life expectancy after diagnosis of only 12-15 months. A main reason for the lethality of GBM is inevitable recurrence, caused by a small population of the tumor cells, called cancer stem cells (CSCs). These cells are aggressive, infiltrative, and resistant to current GBM treatments of chemotherapy and radiotherapy. We use a small molecule drug, CBL0137, which inhibits the FACT (facilitates chromatin transcription) complex leading to cancer cell specific cytotoxicity. Here, we show that CBL0137 sensitized GBM CSCs to radiotherapy and hence lead to increased CSC death and prolonged survival in preclinical models. Clonogenic assays were used to show that CSCs were radiosensitized after CBL0137 treatment. We saw increased DNA damage when GBM CSCs were treated with CBL0137, as well as a decrease in foci resolution over time, when CBL0137 was combined with irradiation. In order to elucidate if the increase in DNA damage was directly due to the inhibition of the FACT complex, we depleted the level of FACT in our GBM CSCs. FACT depletion also led to increased DNA damage, and even more so when combined with irradiation. To validate whether combination therapy sensitized CSCs to radiotherapy in vivo, we used a subcutaneous mouse model and showed combination treatment decreased CSCs frequency in these tumors as well as decreased tumor volume. With an orthotopic model of GBM, we showed that CBL0137 treatment followed by radiotherapy significantly increased survival of mice bearing tumors over either treatment alone. Together, this work establishes a new treatment paradigm for GBM, which sensitizes radio-resistant GBM CSCs to irradiation, a critical component of patient care. Radio-sensitizing agents, including CBL0137, pose an exciting new therapeutic capable of increasing the efficacy of irradiation, by inclusively targeting CSCs.
STEM-16. TRYPTOPHANYL tRNA SYNTHETASE (trpRS) FUNCTIONS AS A PRO-STEMNESS CYTOKINE DURING CHEMOTHERAPY IN GLIOBLASTOMA
Authors: Nandoliya Khizar , Budhiraja Shreya , Shireman Jack , Zolp Andrew , Lin Peiyu , Perrault Ella , Park Cheol , Baisiwala Shivani , Pott Sebastian , Basu Anindita , Ahmed Atique 
Published: November 2021

Abstract
Glioblastoma (GBM) is the most common adult malignant brain tumor. Despite an aggressive standard of care involving surgical resection, radiation therapy, and temozolomide (TMZ)-based chemotherapy, GBM remains a fatal disease due to a 100% recurrence rate. Tumor heterogeneity and cell plasticity are the main contributors to GBM recurrence after treatment, and thus it is essential to study the mechanisms of therapy-induced cellular plasticity. To identify these mechanisms, we performed in vivo single-cell analysis of primary (no therapy), during therapy, and post-therapy recurrent model patient-derived xenograft model of GBM. The analysis revealed a higher transcription of tryptophanyl-tRNA synthetase (trpRS) during TMZ therapy (p &lt; 0.0001). Across multiple datasets, elevated trpRS was shown to correlate significantly with shorter GBM patient survival times (p = 0.0069). TrpRS has been noted to have non-canonical functions, including the ability to be secreted and act as a cytokine in response to injury, often to upregulate stemness pathways to promote healing and regeneration. Based on this observation, we hypothesized that during TMZ treatment, trpRS secretion promotes stemness in neighboring GBM cells via activation of the phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) pathway. This study shows that in response to TMZ treatment, secreted trpRS levels are significantly elevated compared to control in multiple GBM cell lines as analyzed by western blotting. Additionally, expression of trpRS is elevated in TMZ-resistant GBM6R cells compared to TMZ-sensitive GBM6. Furthermore, phosphorylated Akt levels, indicative of the activation of the pro-stemness PI3K/Akt pathway, correlate positively with trpRS. This study, one of the few to examine genetic changes during therapy, sheds light on a novel therapeutic target for GBM.
STEM-25. ADENO-ASSOCIATED VIRUS INTRAVENTRICULAR INJECTION ALLOWS THE RESTRICTED TRANSDUCTION OF GLIOBLASTOMA CELLS NESTED IN THE PERI- AND SUB-VENTRICULAR ZONE IN A PATIENT-DERIVED ORTHOTOPIC XENOGRAFT MODEL
Authors: Lombard Arnaud , Valentin Emmanuel Di , Neirincx Virginie , Martin Didier , Rogister Bernard 
Published: November 2021

Abstract
INTRODUCTION: Glioblastoma (GBM) seems to arise from cells nested in the subventricular zone (SVZ), a neurogenic zone in the adult brain. After striatal engraftment of patient-derived GBM cells in mice, we showed that some tumor cells escape the tumor mass to colonize the SVZ. We aimed to determine if the SVZ-nested GBM cells could be highlighted by the intraventricular injection of a viral vector. MATERIALS AND METHODS: We determined the optimal Adeno-Associated Virus (AAV) serotype to transduce patient-derived GBM cells cultured in 3D (GB1). We studied the spreading of the virus 4 weeks after intraventricular injection in mice. We realized striatal engraftment with GB1 cells, previously transfected with a lentiviral construction in order to express the Red-Fluorescent-Protein (RFP) spontaneously, while they express Green-Fluorescent-Protein (eGFP) only in presence of Cre-recombinase. 10 weeks after engraftment, an AAV expressing Cre-Recombinase was injected in the lateral ventricle and mice were perfused at 14 weeks. RESULTS: AAV serotype DJ (AAVDJ) efficiently transduced GB1 cells. 4 weeks after intraventricular injection, the AAVDJ transduced cells in the SVZ and the medial part of the caudoputamen (mCP). The median of the longest distance between the right ventricle and the transduced cells in the mCP was 293.8µm [245 – 376.5]. In 5 mice, the median of the shortest distance between RFP-positive GBM cells and right ventricle was 580.1µm [535 – 785.1]. SVZ was not colonized and eGFP signal was not found. In the 4 other mice, SVZ was invaded and eGFP signal was detected. The median of the longest distance between the right ventricle and eGFP-positive tumor cells was 240.5µm [195.7 – 372.5]. The median of the eGFP volume was 9 499 404µm3. CONCLUSION: It is possible to transduce GBM cells nested in the peri- and sub-ventricular zone thanks to AAV intraventricular injection.
STEM-27. A PERIVASCULAR STEM CELL UNDERLIES VERTEBRATE MENINGEAL TUMORIGENESIS
Authors: Choudhury Abrar , Cady Martha , Lucas Calixto , Palikuqi Brisa , Klein Ophir , Hervey-Jumper Shawn , Phillips Joanna , Dickinson Peter , Magill Stephen , Bhaduri Aparna , Crouch Elizabeth , Raleigh David 
Published: November 2021

Abstract

BACKGROUND
Meningiomas are the most common primary intracranial tumors in humans and dogs, but biologic drivers and cell types underlying meningeal tumorigenesis are incompletely understood. Here we integrate meningioma single-cell RNA sequencing with stem cell approaches to define a perivascular stem cell underlying vertebrate meningeal tumorigenesis.

METHODS
Single-cell RNA sequencing was performed on 57,114 cells from 8 human meningiomas, 54,607 cells from 3 dog meningiomas, and human meningioma xenografts in mice. Results were validated using immunofluorescence (IF), immunohistochemistry (IHC), and deconvolution of bulk RNA sequencing of 200 human meningiomas. Mechanistic and functional studies were performed using clonogenic and limiting dilution assays, xenografts, and genetically engineered mouse models.

RESULTS
Copy number variant identification from human meningioma single cells distinguished tumor cells with loss of chr22q from non-tumor cells with intact chr22q. A single cluster distinguished by expression of Notch3 and other cancer stem cell genes had an intermediate level of loss of chr22q, suggesting this cluster may represent meningioma stem cells. In support of this hypothesis, pseudotime trajectory analysis demonstrated transcriptomic progression starting from Notch3+ cells and encompassing all other meningioma cell types. Notch3+ meningioma cells had transcriptomic concordance to mural pericytes, and IF/IHC of prenatal and adult human meninges, as well as lineage tracing using a Notch3-CreERT2 allele in mice, confirmed Notch3+ cells were restricted to the perivascular stem cell niche in mammalian meningeal development and homeostasis. Integrating human and dog meningioma single cells revealed Notch3+ cells in tumor and non-tumor clusters in dog meningiomas. Notch3 IF/IHC and cell-type deconvolution of bulk RNA sequencing showed Notch3+ cells were enriched in high-grade human meningiomas. Notch3 overexpression in human meningioma cells increased clonogenic growth in vitro, and increased tumorigenesis and tumor growth in vivo, decreasing overall survival.

CONCLUSIONS
Notch3+ stem cells in the perivascular niche underlie vertebrate meningeal tumorigenesis.
CBIO-12. KAT5 ACTIVITY CONTROLS GLIOBLASTOMA CELL CYCLE DYNAMICS AND TUMOR GROWTH
Authors: Mihalas Anca , Feldman Heather , Arora Sonali , Bassett John , Patel Anoop , Paddison Patrick 
Published: November 2021

Abstract
Current standard of care therapy for glioblastoma (GB) includes cytoreduction followed by ablative therapies that target rapidly dividing cell types. However, non-cycling, quiescent-like states (G0 phase cells) are present in both normal tissue and tumors and play important roles in maintaining heterogeneity and cellular hierarchies. The presence of quiescent-like/G0 states therefore represents a natural reservoir of tumor cells that are resistant to current treatments. Quiescence or G0 phase is a reversible state of “stasis” cells enter in response to developmental or environmental cues. However, it remains largely unclear to what degree or by what mechanisms tumor cells enter into or exit from quiescent-like states. To gain insight into how GB cells might regulate G0-like states, we performed a genome-wide CRISPR-Cas9 screen in patient-derived GB stem-like cells (GSCs) harboring a G0 reporter construct, which is stabilized when cells enter a G0-like state. Among the top screen hits were members of the Tip60/KAT5 histone acetyltransferase complex, including KAT5 itself. Remarkably, we show that knockout of KAT5 in vitro and in vivo dramatically increases G0 subpopulations in GSC cultures and GSC-induced tumors. Using genetically engineered GSC harboring KAT5 under the control of a Doxycyclin-titratable promoter, we establish that incrementally down regulating KAT5 activity is sufficient to slow cell cycle dynamics causing a build-up G0-like cells; and that partial inhibition of KAT5 leads to extended (mouse) patient survival. Further, in primary tumors, cell-based KAT5 activity assays revealed that high grade tumors harbor larger cell subpopulations with higher KAT5 activity than lower grade tumors. In summary, our results suggest that Tip60/KAT5 activity plays key roles in G0 ingress/egress for GBM tumors, may contribute to tumor progression, and may provide novel therapeutic opportunities.
CBIO-13. THOC1 DRIVES GBM AGGRESSION THROUGH MODULATION OF R-LOOPS AND GENOMIC STABILITY
Authors: Budhiraja Shreya , Baisiwala Shivani , Nandoliya Khizar , Chen Li , Dmello Crismita , Perrault Ella , Park Cheol , Zolp Andrew , Dara Gabriel , Sonabend Adam , Ahmed Atique 
Published: November 2021

Abstract
Glioblastoma (GBM) is the most aggressive and common type of adult malignant brain tumor, with a median survival of only 21 months. To identify which genes drive its highly aggressive phenotype, we performed a genome-wide CRISPR-Cas9 knockout screen. Results showed substantial enrichment of ~160 novel essential oncogenic driver genes and pathways, including a previously unstudied gene THOC1—involved in RNA processing—that showed significant elevations in expression at RNA and protein levels (p&lt; 0.05) in GBM, as well as a significant survival benefit in patient datasets when downregulated (p&lt; 0.05). Knocking out THOC1 resulted in cell death in multiple GBM patient-derived xenograft (PDX) lines and extended survival compared to the controls (p&lt; 0.01) in vivo. Overexpression of THOC1 in neural stem cells resulted in transformation to a cancerous phenotype, as evidenced by sphere formation in a soft agar assay (p&lt; 0.01) and in vivo tumor engraftment assays. Further investigation of THOC1 through immunoprecipitation in neural stem cells and multiple GBM lines showed significant interaction in GBM with histone deacetylase complex SIN3A, involved in recruiting major histone deacetylases in order to close the DNA and prevent the accumulation of R-loops, RNA:DNA hybrids that pose a threat to genomic stability. Additional investigation revealed that THOC1-knockdowns in vitro induced R-loop formation and DNA damage, while THOC1-overexpression in vitro resulted in an untenable decrease in R-loops and DNA damage, suggesting that the THOC1-SIN3A axis is elevated in GBM in order to prevent the accumulation of genotoxic R-loops. Additionally, histone deacetylase activity was shown to be elevated in THOC1-overexpression conditions and reduced in THOC1-knockdown conditions, confirming that the THOC1-SIN3A axis functions to prevent R-loop accumulation through the epigenetic regulation. In summary, our whole-genome CRISPR-Cas9 knockout screen has identified a promising therapeutic target for GBM—a disease desperately in need of therapeutic innovations.
CBIO-18. TP53-MUTANT OLIGODENDROGLIOMA: A SINGLE INSTITUTION CASE SERIES
Authors: Webb Mason , Kizilbash Sani , Kollmeyer Thomas , Jenkins Robert , Sung Sarah , Raghunathan Aditya , Giannini Caterina , Fung Kar-Ming , Bouffard John-Paul , Ida Cristiane 
Published: November 2021

Abstract
TP53 mutations are frequent in IDH-mutant astrocytomas but unusual in oligodendroglioma and the clinical significance of TP53 mutations in oligodendroglioma are not well characterized. We reviewed genetically defined oligodendroglioma (i.e., IDH-mutant, whole-arm 1p/19q-codeleted diffuse glioma) cases that were molecularly profiled (2017-2020) at our institution and identified 7 cases with TP53 mutation (9%; n=76). Molecular testing was performed using targeted neuro-oncology NGS panel (50-gene mutation and/or 187-gene mutation/rearrangement) and OncoScan™ microarray. Four (of 7) patients were female. Median age at diagnosis was 43 years (range, 23-63). Most common presenting symptom was seizures (3 of 7). All tumors were supratentorial. Histologically, 3 tumors were WHO grade II and 4 were WHO grade III. Two (of 3) patients with a WHO grade II tumor underwent biopsy and radiotherapy at diagnosis followed by temozolomide at recurrence (progression at 67 and 157 months after diagnosis; overall survival of 124 and 201 months). Three (of 4) patients with a WHO grade III tumor were diagnosed within the last two years and are currently progression-free after standard therapy. Molecularly, in addition to TP53 mutation(s), all cases had an IDH1 and TERT promoter mutation as well as other gene mutation(s) including FUBP1 (n=5), SETD2 (n=4), PIK3R1 (n=4), PIK3CA (n=3), NF1 (n=3) and CIC (n=3). In 3 (of 7) cases, the mutational profile with high mutation count enriched for C &gt;T/G &gt;A transitions was highly suggestive of a hypermutation phenotype (2 cases were recurrent tumors treated with temozolomide; a recurrent and a treatment-naïve tumor had mismatch repair gene mutation). Five (of 7) cases, including the 3 hypermutant cases, lacked functional TP53 (1 case with 2 mutations, 2 cases with 1 mutation plus loss of other copy, 2 cases with 1 mutation plus copy neutral loss-of-heterozygosity). TP53 mutations are uncommon in oligodendroglioma and appear enriched in hypermutant tumors.
CBIO-20. HIGH LEVELS OF TERT CONFER SENSITIVITY TO THE DNA HYPOMETHYLATING AGENT DECITABINE (DAC) IN GLIOMAS
Authors: Park Jong-Whi , Sahm Felix , Steffl Bianca , Arrillaga-Romany Isabel , Cahill Daniel , Monje Michelle , Herold-Mende Christel , Wick Wolfgang , Turcan Sevin 
Published: November 2021

Abstract

BACKGROUND
Decitabine (DAC)-incorporated DNA binds DNMT1 enzyme and subsequently triggers DNMT1 degradation. Previously, we showed that DAC can mediate the anti-tumor effect in a preclinical model of IDH-mutant gliomas. Here, we further investigate molecular determinants of response to DAC in gliomas.

METHODS
DAC response was assessed by soft agar anchorage independent growth assays and cell proliferation measurements. Patient-derived IDH-mutant chromosome 1p/19q codeleted (codel) and non-codel glioma lines upon vehicle and DAC treatment were used for RNA sequencing and Gene Set Enrichment Analysis (GSEA).

RESULTS
We found that DAC treatment is effective in high TERT-expressing gliomas including IDH-mutant and IDH-wildtype glioma lines. In contrast, pharmacological inhibition of TERT reduces DAC response in glioma lines. Interestingly, transcriptomic profiling showed that DAC reduces the expression of TERT, along with increased CDKN1A/p21 expression. We experimentally validated that TERT expression depends on CDKN1A/p21. Furthermore, p53 is required for DAC-mediated CDKN1A/p21 induction. Importantly, DAC-mediated proliferation defects in TERT-proficient glioma cells are abolished by DNMT1 knockdown, indicative of an expected DAC mechanism.

CONCLUSIONS
DAC could elicit the pronounced anti-tumor response in IDH-mutant codel oligodendroglioma and IDH-wildtype glioblastoma with TERT activating mutations.