bluuebunny/crossref_metadata_2025_split huggingface dataset:
CSIG-02. SHH PATHWAY ACTIVATION DRIVES NEURAL CREST CELL SIGNATURE IN A SUBGROUP OF MPNSTS
Authors: Suppiah Suganth , Liu Jeffrey , Li Mira , Heidari Mohsen , Yakubov Rebeca , Bunda Severa , Zadeh Gelareh 
Published: November 2023

Abstract

INTRODUCTION
Neurofibromatosis Type 1 is hereditary tumor predisposition syndrome that results in the development of innumerable nerve sheath tumors that fall within the spectrum of benign, premalignant and malignant lesions. Our previous work has demonstrated that SHH pathway activation drives malignant transformation in a subset of malignant peripheral nerve sheath tumors (MPNSTs). Here, we demonstrate that SHH pathway activation induces a neural crest cell-like state in a subset of MPNSTs.

METHODS
We performed single nuclear RNA sequencing on 6 tumors (5 MPNSTS and 1 atypical neurofibroma). We performed in vitro experiments to assess the correlation between SHH pathway activation and neural crest signatures. We inhibited SHH pathway with sonidegib, a SMO inhibitor, in MPNST cell lines and performed RT-PCR to assess markers of neural crest cell signatures. In addition, we assessed cellular viability with treatment.

RESULTS
We observed that cells that express SMO at high levels, with SHH pathway activation, express neural crest cell makers. Single cell trajectory analysis further demonstrates a pseudotemporal continuum from atypical neurofibromas (Schwann cells), MPNSTs (Schwann cell precursor cells) and other MPNSTs (neural crest cells), which supports that these tumors fall along the developmental trajectory of neural crest cell lineage. SHH pathway activity was high in S462TY MPNST cell line and low in STS-26T MPNST cell line. S462TY also demonstrated prominent elevation in expression of neural crest cell markers TWIST1, SOX9, SNAI2, OTX2, PAX4 and PAX6 . We found that treatment with sonidegib treatment attenuates the expression of neural crest cell signatures. Finally, inhibiting SHH pathway activation reduced cellular viability in MPNST cell lines.

CONCLUSION
SHH pathway activation drives dedifferentiation into a neural crest cell-like state in a subset of MPNSTs. We confirm that inhibiting SHH pathway activity in a subset of MPNSTS prevent growth and malignant progression, providing a rational for future clinical trials.
CSIG-05. A FIRST COMPREHENSIVE ANALYSIS OF TRANSCRIBED ULTRA CONSERVED REGIONS UNCOVERS IMPORTANT REGULATORY FUNCTIONS OF NOVEL NON-CODING TRANSCRIPTS IN GLIOMAS
Authors: Gibert Myron , Saha Shekhar , Zhang Ying , Marcinkiewicz Pawel Pawel , Chagari Bilhan , Roig-Laboy Christian , Sarkar Aditya , Dube Collin , Hudson Kadie , Sun Yunan , Kefas Benjamin , Abounader Roger 
Published: November 2023

Abstract
Most glioma research has focused on protein-coding genes and much less on non-coding RNAs (ncRNAs). Transcribed Ultra-Conserved Regions (TUCRs) represent a severely understudied class of ncRNAs that are highly conserved across multiple species, including 100% conservation in mouse and rat genomes. These 481 transcripts are highly resistant to variation and are commonly deregulated in cancer, which suggests regulatory and functional importance when considered along with their high degree of conservation. We performed the first-ever analysis of TUCRs in glioblastoma (GBM) and low-grade gliomas (LGG). We first annotated all TUCRs in gliomas and described their genomic locations. We then showed that numerous TUCRs are highly expressed and deregulated in gliomas, and that this deregulation is associated with clinical outcomes. We then used a WGCNA pipeline to predict the functions for all TUCRs in gliomas by compiling gene ontology (GO) terms for coregulated genes. These data were used to identify several TUCRs that are potentially relevant to glioma initiation and progression. Of these, we investigated the most highly upregulated intergenic TUCR, uc.110, in vitro and in vivo in GBM. Knockdown of uc.110 in vitro reduced GBM cell accumulation and invasion and knockdown in vivo inhibited GBM xenograft growth and increased animal survival. We then performed mechanistic analyses of uc.110 and found that it regulates the expression of a Wnt pathway member, membrane frizzled-related protein (MFRP). We discovered that uc.110 sponges the tumor suppressor microRNA miR-544, which targets and inhibits MFRP, thus increasing the bioavailability of MFRP in GBM. This study is the first of its kind in gliomas. It shows important regulatory roles for TUCRs in gliomas and outlines novel methods for studying TUCRs in any disease context.
CSIG-08. GAIN-OF-FUNCTION MUTANT P53 REGULATES LONG-NONCODING RNAS TO CONTROL HIF1Α TRANSCRIPTION IN GLIOBLASTOMA
Authors: Zhang Ying , Yuan Ying , Grello Cassandra , Reon Brian , Gibert Myron , Dube Collin , Yang Yanzhi , Hudson Kadie , Kefas Benjamin , Dutta Anindya , Abounader Roger 
Published: November 2023

Abstract
P53 is mutated in a large subset of glioblastoma (GBM). Most hot-spot p53 mutants are gain-of-function (with only partially understood mechanisms). To investigate the role of gain-of-function mutant p53 (GOF-Mut-p53), we performed ChIP-seq analysis of GOF-Mut-p53 R273H, the most common p53 mutation in GBM. We identified and verified numerous GOF-Mut-p53 targets that differed from those of wildtype p53. Among the 2,830 targets of GOF-Mut-p53 were 535 long non-coding RNAs (lncRNAs), the majority of which we also found enriched in Mut-p53 human tumors and deregulated in the TCGA database. LncRNAs play important regulatory roles in cancer. One of the most highly enriched lncRNAs was LINC00643. We first performed ChIP confirmation of GOF-Mut-p53 binding to the promoter of LINC00643. We then showed that GOF-Mut-p53 inhibits LINC00643 expression. Furthermore, we found that LINC00643 is deregulated in human GBM and LGG and correlated with patient survival. Overexpression of LINC00643 led to a significant inhibition of GBM cell proliferation, migration, invasion and in vivo xenograft growth. Co-expression of human LINC00643 or its mouse homologue with PDGF and Cre in RCAS transgenic mice (N/tv-a; Ink4a-arf-/-; Pten-fl/fl) reduced tumor growth and improved animal survival. These data show that GOF-Mut-p53 exerts oncogenic effects in GBM by downregulating LINC00643. To elucidate the mechanisms of action of LINC00643, we performed Chromatin Isolation by RNA purification high-throughput sequencing (CHIRP-seq) to identify its binding targets. We found that LINC00643 binds to the HIF1α enhancer region. Overexpression of LINC00643 and knockdown of GOF-Mut-p53 in GBM cells under hypoxia growth conditions reduced HIF1α mRNA and protein expression. LINC00643 also regulated the expression of numerous hypoxia-regulating genes downstream of HIF1α. Our study shows for the first time that GOF-Mut-p53 transcriptionally regulates a subset of lncRNAs and that GOF-Mut-p53-regulated LINC00643 regulates hypoxia in GBM.
CSIG-09. RADIOTHERAPY WITH CONCURRENT INHIBITION OF CHEK2 ACTIVATES STING IN GLIOMAS
Authors: Chen Li , McManus Graysen , Arrieta Victor , Kim Kwang-Soo , Habashy Karl , Silvers Caylee , Najem Hinda , Gould Andrew , Ahmed Atique , Lukas Rimas , Heimberger Amy , Lee-Chang Catalina , Sonabend Adam , Dmello Crismita 
Published: November 2023

Abstract
Using an in vivo CRISPR screen approach, we demonstrated the contribution of glioma cell intrinsic checkpoint kinase 2 (Chek2) in the evasion of tumor cells from CD8+ T cell recognition. Genetic depletion or pharmacological inhibition of Chek2 with blood-brain-barrier permeable drugs that are being evaluated in clinical trials, in combination with standard of care radiotherapy and PD-1/PD-L1 blockade, led to survival benefit in multiple preclinical glioma models. Moreover, we observed that Chek2 inhibition or depletion is associated with activation of cytosolic DNA-sensing STING pathway in the glioma cells. A positive correlation was identified between STING pathway activity and T cell infiltration in the TCGA glioblastoma dataset. STING activation has been shown to promote robust immune response in glioblastoma. Building upon these results, we evaluated the impact of radiotherapy on Chek2 and STING signaling. After applying 2 Gy radiotherapy, a 20 fold increase of Chek2 activation was observed within the first hour in the in vitro grown glioblastoma patient derived cells, specifically GBM6 and GBM43 cells. Chek2 activation levels returned to the baseline within 6 hours in these cells. However, STING activation was moderate to absent at different time intervals within the first 48 hours post 2 Gy radiotherapy. Interestingly, when the in vitro-grown GBM6 cells were pretreated with Chek1/2 inhibitor prexasertib for 48 hours prior to the 2 Gy radiotherapy exposure, there was 10 fold reduction in the activation of Chek2 as compared to the radiotherapy alone group. Concomitantly, a 2-fold increase in the activation of STING was noted for up to 48 h in the pretreated group, as compared to the radiotherapy alone group. Our in vitro findings suggest an inverse relationship between the activation of Chek2 and STING. In conclusion, radiotherapy with concurrent inhibition of Chek2 offers a novel therapeutic combination to modulate STING activation in gliomas.
CSIG-10. SEX-DIFFERENCES IN NF-ΚB SIGNALING DRIVE SEX-BIASED RESPONSES TOWARDS SENESCENCE AND INFLAMMATION IN GLIOBLASTOMA
Authors: Wong Jason P , Tripp Lloyd , Reinhold Nicholas , Broestl Lauren , Luo Jingqin , Mitra Robi D , Rubin Joshua B 
Published: November 2023

Abstract
Male glioblastoma (GBM) patients have a higher incidence rate and worse median survival in comparison to females. The molecular mechanisms that drive these sex differences in incidence and survival are not well understood. Using a murine in vitro GBM model, we identified that male and female cells tend to segregate into two unique groups based on differential gene expression. Male-enriched processes included myc, E2F and G2-M checkpoint signaling. Female-enriched processes included epithelial-mesenchymal transition, interferon responses and TNF-α signaling by NF-κB. Reports from human GBM patients corroborate an increased enrichment for inflammatory and innate immune responses in females. Since the NF-κB pathway regulates senescence and its associated inflammatory response, the senescence-associated secretory phenotype, we examined if there are sex differences in NF-κB signaling as we have reported that female GBM cells undergo senescence more readily. We found that low levels of NF-κB activity were correlated with higher levels of senescence, and that cells from the female-enriched group correspondingly had lower levels of NF-κB activity. Interestingly, p-p65 S536 expression (a marker of increased NF-κB transcriptional activity) was negatively correlated with NF-κB activity in cells within the female-enriched group. Furthermore, female cells with low NF-κB activity responded more readily to TNF-α treatment. These results suggest that female cells can more readily modulate the NF-κB pathway in response to stimuli, thereby poising them towards a pro-inflammatory state. Since inflammation and senescence regulate therapeutic responses in GBM, and we have previously reported that female GBM cells undergo senescence more readily following radiation, these results suggest that further studies to understand the sex differences in NF-κB signaling may improve patient response to radiation and chemotherapy treatment.
CSIG-11. LIN28B EXPRESSION IN DIFFUSE MIDLINE GLIOMA
Authors: Knowles Truman , An Shejuan , Huang Tina , Qi Jin , Saratsis Amanda 
Published: November 2023

Abstract

INTRODUCTION
Diffuse midline glioma (DMG) is the most lethal of all childhood cancers. LIN28B is a RNA binding protein expressed in a variety of cancers, which suppresses the let-7 family of microRNAs, which in turn suppresses a plethora of oncogenes. However, the role of LIN28B in DMG has not yet been explored. Therefore, we sought to determine the pattern of expression and potential function of LIN28B in DMG using rare DMG cell lines.

METHODS
All studies were performed on DMG cell lines (n = 6) and controls (normal human astrocytes n = 1, human neural stem cells n = 1). RNA-Seq was performed using single-read sequencing at 50bp on the Illumina NextSeq 500 Sequencing System. Cells were then treated with DMSO or the LIN28B inhibitor, LI71, and submitted to functional in vitro studies, as well as RNA-Seq and Western Blot analysis. Functional pathways analysis was subsequently performed on resulting gene expression values with Ingenuity Pathways Analysis (Qiagen).

RESULTS
Differential LIN28B expression was demonstrated across cell lines, with DMG cells expressing greater LIN28B gene and protein levels compared to controls. LIN28B inhibition with small molecule inhibitor LI71 resulted in decreased cell proliferation and migration, in vitro. A total of 946 differentially expressed genes were identified between treatment groups (FC&gt;2 or &lt;-2, p&lt; 0.05). Functional pathways analysis of differentially expressed genes implicated Cancer and Neurological Disease as the top disease processes, with Cellular Movement as the top molecular process in cell lines expressing LIN28B. Further, inactivation of Myc signaling was implicated in cells treated with LI71.

CONCLUSIONS
Our data demonstrates increased LIN28B expression in DMG cell lines compared with controls, with oncogenic effects on cell proliferation and migration. Further investigation of the LIN28B-let7 signaling axis is warranted in order to further explore LIN28B as a novel therapeutic target in DMG.
CSIG-12. GLIOMA MICROENVIRONMENT: FUNCTIONS, MOLECULAR MECHANISMS, AND THERAPEUTIC IMPLICATIONS
Authors: Bao Zhaoshi , Zhang Ying , Wang Peng , Zheng Chengjun , Wang Zhiliang , Fan Wenhua 
Published: November 2023

Abstract
Abstract Gliomas are the most common intracranial tumors in adults. The high mortality and disability rates place a heavy burden on society and the families of patients. The median survival of patients who have primary grade 4 glioma at the World Health Organization is only 14.6 months. Unlike primary glioblastoma (WHO grade 4, pGBM) which usually occurs in older adults, secondary glioblastoma (WHO grade 4, sGBM) with isotrate dehydrogenase (IDH) mutations typically progresses from low to high grades within 5-10 years of diagnosis. Although surgery, radiotherapy, and chemotherapy have almost become the standard treatment for gliomas, the prognosis of patients is still poor. In recent years, the immune microenvironment has gradually become a possible direction for tumor treatment, and treatment methods such as PD1/PDL1 inhibitors and tumor vaccines have emerged. Owing to the microenvironment around the intracranial tumor cells and the body tumor being different, the microenvironment cells have their specific characteristics, and there is a blood-brain barrier, immunotherapy for the glioma microenvironment has encountered a bottleneck. Here, we summarize the current tumor-associated microenvironment and the interactions between tumor and immune cells and introduce the current status of glioma-specific microenvironment and immunotherapy for glioma. Finally, we mentioned several recent microenvironment-related research advances by our team and looked forward to future glioma microenvironmental research.
CSIG-15. PTN-PTPRZ1 SIGNALING MEDIATES TUMOR-NORMAL CROSSTALK IN GLIOBLASTOMA
Authors: Kan Ryan , Ge Weihong , Yilgor Can , Bayley Nicholas , Tse Christopher , Tum Andrew , Patel Kunal , Nathanson David , Bhaduri Aparna 
Published: November 2023

Abstract
Glioblastoma (GBM) is the most devastating form of brain cancer with poor patient prognosis and high recurrence. An increasing body of literature suggests crosstalk between tumor and its surroundings, both molding the immune microenvironment and forming functional synapses with neighboring normal cells. Despite the high intra-tumoral and inter-patient heterogeneity, we have discovered PTN-PTPRZ1 signaling as the most significant and preserved communication pathway between GBM cells and their immediate neighboring cells. Through a novel tumor transplantation protocol onto cortical organoids, which are human embryonic stem cell-derived aggregates that faithfully mimic the human brain, we have seen evidence of tumor-normal crosstalk where PTN-PTPRZ1 is a key signaling axis. We hypothesize that PTN-PTPRZ1 signaling is pivotal to tumor growth and invasion, which ultimately leads to recurrence. Modulating PTN and/or PTPRZ1 levels on the cortical organoids via shRNA affects PTN and/or PTPRZ1 expression on the tumors, suggesting dynamic communication between tumor and normal cells via PTN-PTPRZ1 signaling. During the process of generating PTN knockdown cortical organoids, we have additionally discovered a pivotal role for PTN in the very early stages of cortical development. PTN and PTPRZ1 are signature markers of the outer radial glia in the developing human brain, which are absent in mouse models where the majority of PTN biology has been studied. By supplementing exogenous PTN to PTN knockdown organoids and withdrawing it at various timepoints, we have identified drastic phenotypes of neuron and radial glia survival and cell fate specification. With cortical organoids, we can interrogate the role of PTN in the early stages of neurodevelopment via a human-derived system.
CSIG-17. NICOTINAMIDE N-METHYLTRANSFERASE (NNMT) AS A POTENTIAL THERAPEUTIC TARGET FOR EGFRVIII-DRIVEN GLIOBLASTOMA
Authors: Li Ming , Chen Clark 
Published: November 2023

Abstract
Nicotinamide N-methyltransferase (NNMT) is an enzymatic catalyst involved in converting methyl groups from S-adenosyl-L-methionine (SAM) to nicotinamide (NAM), generating S-adenosine hyperblastoids (SAH) and 1-methylnicotinamide (MNA). Increased NNMT expression is frequently observed in various cancers and is associated with tumor progression, metastasis, unfavorable clinical outcomes, and drug resistance. Notably, NNMT stands out as one of the most up-regulated metabolism-related genes in glioblastoma, although the underlying mechanism for its overexpression remains elusive. Glioblastoma commonly exhibits genetic lesions in the epidermal growth factor receptor (EGFR) gene, including amplification or mutation, with EGFRvIII being the predominant mutant contributing to glioblastoma cell proliferation, invasion, therapeutic resistance, metastasis, and stemness. In this study, we demonstrate that activation of wild-type EGFR by EGF or the constitutively active mutant EGFRvIII promotes NNMT expression and enzyme activity in established glioblastoma cell lines and glioblastoma stem-like cells via the p38 mitogen-activated protein kinase pathway. Additionally, we identify STAT1 as a downstream transcription factor essential for EGFR/EGFRvIII-induced NNMT upregulation. RNA interference-mediated knockdown of NNMT in glioblastoma cells significantly inhibits EGFRvIII-promoted invasion and proliferation in vitro. Targeting NNMT effectively suppresses EGFRvIII-driven glioblastoma tumorigenicity and prolongs the survival of tumor-bearing mice. Clinically, NNMT is highly expressed and positively correlated with EGFR expression in human glioblastoma tumors. Collectively, these findings establish NNMT as a previously unrecognized downstream target gene of EGFR/EGFRvIII expression and highlight its potential as a therapeutic target for inhibiting EGFRvIII-driven glioblastoma.
CSIG-18. WNT SIGNALING MODULATES TUMORIGENIC FEATURES AND CELLULAR IDENTITY IN A MODEL OF LOW-GRADE GLIOMAGENESIS
Authors: Koch Marilin , Deo Minh , Hoetker Michael , Herold-Mende Christel , Wick Wolfgang , Turcan Sevin 
Published: November 2023

Abstract
RATIONALE: Isocitrate dehydrogenase (IDH)-1/2 mutations are known driver mutations for the development of low-grade gliomas (LGGs). However, secondary drivers are needed for tumor growth, and it remains unclear which co-factors and pathways are necessary to develop the LGG tumor phenotype. To identify additional players in IDH mutant-mediated oncogenesis, we investigated the effects of disrupting glioma-associated pathways in a tractable in vitro system of IDH-mutant malignant transformation. METHODS: A doxycycline-inducible IDHR132H expressing normal human astrocyte cell line was concomitantly treated with either a Wnt-activator/inhibitor (CHIR99021/IWP-2), TGF-β inhibitor (Repsox) or Notch inhibitor (YO-01027). IDH-associated CD171 marker expression changes were assessed with Flow cytometry, followed by transcriptional and proteomic analysis with RNA-Seq and mass spectrometry. Functional characterization entailed cell viability and clonogenic assays as well as cell cycle analyses. RESULTS: We observed significant IDH-related CD171 expression changes upon treatment with CHIR99021, Repsox and YO-01027. Wnt activation with CHIR99021 profoundly affected the IDH mutant-induced transcriptional landscape, leading to differential usage of LGG and stemness programs including altered expression of SOX4 and SOX11. On the protein level, Wnt activation additionally impacted pathways relevant for cellular architecture, specifically Rho-Rac-CDC42 signaling. This was also reflected by an altered cell morphology with small, rounded up cells, augmented clonal proliferation capacity and increased proportions of cell in S-phase. CONCLUSION: Wnt activation in a IDHR132H model system modulated LGG development, leading to differential expression of key LGG and stemness associated profiles, morphologic cell changes and increased replication capacity. While aberrant Wnt signaling is a common feature in glioblastoma, our data point to an effect also on low-grade gliomagenesis, therefore requiring further investigation.
CSIG-21. TITLE: INTEGRATIVE TRANSCRIPTOME PROFILING OF EXOSOME AND TISSUE IDENTIFIES PROGNOSTIC GENES AS THERAPEUTIC TARGETS OF GLIOBLASTOMA
Authors: Goel Pallavi , Roy Vijay Laxmi , Sadasivam Subhashini , Ghanekar Yashoda , Kaur Inderjeet , Sreegiriraju Vijay , Prathapa Kiran , Madiraju Surya , Ray Amit , Group Exsegen Neurosurgery 
Published: November 2023

Abstract
For glioma, molecular genetic analysis has grown in significant amounts for disease diagnosis and pathogenesis research. Due to limitations of tissue samples, liquid biopsy is being considered as a substitute for tissue biopsy which can be developed as a diagnostic technique. Studies have demonstrated that exosome-carrying molecules can foster a milieu that is favorable to cancer growth and therapy resistance. METHODS: In the present study the tumor tissue and serum of the same 80 patients were collected with a confirmed diagnosis of glioma with prior consent. Demographic details, pathology reports and survival data were also collected. RNA-seq analysis was performed in both tumor tissue and exosomal RNA. Fastq file with 100bp paired end reads were generated. Raw reads were trimmed using Trimmomatic (Version 0.39) to remove adapter sequences and low-quality reads. Reads mapping to ribosomal RNA were removed using SortMeRNA tool. Trimmed reads were then mapped to the human reference genome GRCh38.d1.vd1.fa using a two-pass method with STAR (2.7.10a). Differential gene expression was performed using DESeq2. The gene ontology and pathway analysis were performed using open source tool PANTHER. RESULTS: The differentially expressed genes shared between tumour tissue RNA and exosomal RNA experiments were selected for further analysis. Genes such as EGFR (tissue: Fold change (FC)[6.1], exosome: FC[7.2]; p-value&lt; 0.001), PDFGRA (tissue: FC[3.7], exosome: FC[5.2]; p-value&lt; 0.001), TTN (tissue: FC[12.6], exosome: FC[11.3]; p-value&lt; 0.001) were found to be differentially regulated and were prominently associated with Integrin signaling pathway, Synaptic vesicle trafficking pathway, Wnt signaling and cellular proliferation. As per literature and clustering analysis, we found that these pathways and genes play an important role in the progression of tumors which can be further integrated into diagnostic platforms. CONCLUSION: This study will provide a reliable and effective way of diagnosis and management of glioma in patients with minimal invasion.