Hybrid classical and quantum computing for enhanced glioma tumor classification using TCGA data.

Deep Neural Networks for Radiographic Risk Stratification of Gliomas

Objective: To investigate the perfusion characteristics of arterial spin labeling (ASL) in intracranial tumor and its application value in classification. Methods: The clinical, pathological and imaging data of 44 patients with gliomas confirmed by pathology were analyzed retrospectively, including 9 low grade gliomas, 15 high grade gliomas, 11 cases of meningiomas, 6 cases of neurilemmoma, 3 cases of metastatic tumors.Conventional plain scan, 3D- ASL and MRI dynamic enhanced imaging (DSC-MRI) were performed.The mean maximal cerebral blood flow (CBF) of the solid component of tumor was obtained based on the region of interest.Immunohistochemical staining was performed in 24 patients with glioma.The differences of cerebral blood flow map (CBF) and relative cerebral blood flow (rCBF) in 44 patients with intracranial tumors were compared. The results of paired t test between the tumor area and the contralateral mirror area were measured by the two methods. Results: Taken the normal control-lateral grey matter(GM) as reference to normalize the CBF of tumor, three normalized tumor blood flow (nTBF) acquired by ASL showed statistical difference between low grade and high grade gliomas respectively (P<0.05). While taken the mirror region (M) and normal control-lateral white matter (WM) as reference to normalize the CBF of tumor, it showed no statistical difference (P>0.05). There was no 1p deletion in the cases of ASL perfusion in low-grade glioma group.In the case of 1p deletion in high grade glioma group, ASL was low perfusion, and there was no 1p deletion in the cases of ASL perfusion. Conclusion: 3D ASL can be used to identify high-grade and low-grade gliomas which has important reference value in the qualitative diagnosis of brain tumors and preoperative grading of gliomas.A separate use of 3D-ASL might cause over-or underestimation of tumor diagnosis, therefore a comprehensive analysis is needed.

BACKGROUND: Phospholipase C beta 1 (PLCβ1) expresses in glioma tissue and cultured glial cells, but barely detectable in normal glial cells. Whether PLCβ1 gene expression plays a pathological role in glioma has not been studied. METHODS: We analyzed data from Gene Expression Omnibus (GEO-GDSxxx), The Cancer Genome Atlas (TCGA), and the Repository for Molecular Brain Neoplasia Data (REMBRANDT) to investigate the potential role of PLCβ1 in high-grade glioma (HGG). RESULTS: In GDS1815, PLCβ1 expression correlates with known proneural (PN) signature genes; its expression level from PN subtype (n = 15) is significantly higher than that from mesenchymal (Mes) subtype (n = 33) HGG (p < 0.001). Furthermore, PLCβ1 expression is significantly higher in grade III than in grade IV gliomas from GDS1815 (n = 24 vs. 76), GDS1962 (n = 19 vs. 81), and GDS1975 (n = 26 vs. 59); ultimately, p < 0.05 for all. In GDS1962, the PLCβ1 expression is highest in non-tumor brain tissue (n = 23) and is significantly higher than that in grade II astrocytomas (n = 7) and oligodendrogliomas (n = 37; p < 0.05 for both. PLCβ1 expression is also higher in low-grade (n = 8) than in high-grade astrocytomas (n = 6) in GDS2853 (p < 0.001). A Kaplan-Meier survival plot from a REMBRANDT cohort demonstrates that astrocytoma and glioma patients with intermediate levels of PLCβ1 expression (n = 45 and 103, respectively) survived significantly longer than down-regulated (2X) PLCβ1 groups (n = 57 and 226, respectively; p < 0.001). From TCGA data, PLCβ1 RNA-Seq signal inversely correlates with the pathological grades and higher levels of PLCβ1 expression in PN (n = 8) than in Mes (n = 8) subtypes of glioblastoma (p < 0.05). The top 50% of PLCβ1 expression subgroup (n = 294) of glioma cases (grade II to IV merged) survived significantly longer time than the low 50%-ile of the PLCβ1 expression subgroup (n = 293; p < 0.001). CONCLUSIONS: PLCβ1 is a candidate signature gene for PN subtype HGG, its expression inversely correlates with glioma pathological grade and is a potential prognosis factor.

Corpus callosum involvement is associated with poorer survival in high grade glioma (HGG), but the prognostic value in low grade glioma (LGG) is unclear. To determine the prognostic impact of corpus callosum involvement on progression free survival (PFS) and overall survival (OS) in HGG and LGG, the records of 233 glioma patients treated from 2008 to 2011 were retrospectively reviewed. Preoperative magnetic resonance (MR) images were used to identify corpus callosum involvement. Age, sex, preoperative Karnofsky performance scale, postoperative Eastern Cooperative Oncology Group (ECOG) score and extent of resection (EOR) were evaluated with respect to PFS and OS. The incidence of corpus callosum involvement was similar among HGG (14%) and LGG (14.5%). Univariate analysis revealed that PFS and OS were significantly shorter in both WHO grade II and grade IV glioma with corpus callosum involvement (both, p<0.05). Multivariate analysis showed that grade II glioma with corpus callosum involvement have shorter PFS (p=0.03), while EOR, instead of corpus callosum involvement (p=0.16), was an independent factor associated with PFS in grade IV glioma (p<0.05). Corpus callosum involvement was no longer significantly associated with OS after adjusting age, gender, EOR, preoperative and postoperative performance status (p=0.16, 0.17 and 0.56 in grade II, III and IV gliomas, respectively). Corpus callosum involvement happened in both LGG and HGG, and is associated with lower EOR and higher postoperative ECOG score both in LGG and HGG. Corpus callosum involvement tends to be an independent prognostic factor for PFS in LGG, but not for OS in LGG or in HGG.

(1) Background: The elevation of glucose metabolism is linked to high-grade gliomas such as glioblastoma multiforme (GBM). The high glycolytic phenotype is associated with cellular proliferation and resistance to treatment with chemotherapeutic agents in GBM. MicroRNA-542-3p (miR-542-3p) has been implicated in several tumors including gliomas. However, the role of miR-542-3p in glucose metabolism in human gliomas remains unclear; (2) Methods: We measured the levels of cellular proliferation in human glioma cells. We measured the glycolytic activity in miR-542-3p knockdown and over-expressed human glioma cells. We measured the levels of miR-542-3p and HK2 in glioma tissues from patients with low- and high-grade gliomas using imaging analysis; (3) Results: We show that knockdown of miR-542-3p significantly suppressed cellular proliferation in human glioma cells. Knockdown of miR-542-3p suppressed HK2-induced glycolytic activity in human glioma cells. Consistently, over-expression of miR-542-3p increased HK2-induced glycolytic activity in human glioma cells. The levels of miR-542-3p and HK2 were significantly elevated in glioma tissues of patients with high-grade gliomas relative to that in low-grade gliomas. The elevation of HK2 levels in patients with high-grade gliomas were positively correlated with the high levels of miR-542-3p in GBM and low-grade gliomas (LGG) based on the datasets from the Cancer Genome Atlas (TCGA) database. Moreover, the high levels of miR-542-3p were associated with poor survival rate in the TCGA database; (4) Conclusions: miR-542-3p contributes to the HK2-mediated high glycolytic phenotype in human glioma cells.

目的：肝癌是消化系统常见恶性肿瘤，是全世界第三位死亡原因和中国第二位死亡原因。肿瘤基因组图谱(TCGA)计划利用大规模测序为主的基因组分析技术，通过广泛的合作，理解癌症的分子机制，本研究利用TCGA数据库深入挖掘肝癌发生关键基因。材料方法：根据标准流程对TCGA数据进行处理、整合，对数据类型及水平进行评估，用R语言(3.1.1版本)中自带的DESeq和edgeR程序包进行分析，结果以热图(pheatmap)、韦恩图(VennDiagram)、hist、PlotMA等表示。差异基因的判断标准：1，表达量在2倍以上或者0.5倍以下，2，P Objective: Hepatocellular carcinoma (HCC) is a common cancer of the digestive system, is the third cause of death worldwide and the second cause of death in China. The Cancer Genome Atlas (TCGA) aims to better understand the molecular mechanisms of cancer by using a large-scale genome se-quencing-based analysis techniques and extensive cooperation. This study introduces TCGA data-base to find key genes of HCC events. Materials and Methods: The data from TCGA were processed, integrated according to the standard procedure of TCGA, data types and levels were carefully as-sessed. Bioinformatics analysis was done using the DESeq and edgeR package of R language (3.1.1 version). Results were showed as pheatmap, VennDiagram, hist, PlotMA etc. Differences were de-fined as follows: expression increased more than two folds; P <0.05; gene ranked in the top 10%. Results: 17 mRNA chips of HCC and 9 mRNA chips of normal tissue were collected from TCGA data- base. Hist figure reflected the number of different gene was large. PLotMA map showed the distribu-tion of gene expression, suggesting most genes of different expression were increased. 719 diffe-rentially expressed genes were found by DESeq, while 4413 by edger, among which 713 were com-mon different genes. Conclusion: Compared to conventional microarray, TCGA method has its own advantages such as larger number of samples, less cost and easier for analyzing, offering opportuni-ty for large-scale genomic studies of HCC and subsequent functional genomics-based research.

Background:Differentiation of high-grade gliomas (HGGs) and low-grade gliomas (LGGs) is an important clinical problem because treatment strategies vary greatly. This study was performed to investigate the potential diagnostic value of incoherent intravoxel motion imaging (IVIM) to distinguish HGG from LGG by meta-analysis.Methods:A computerized search of the literature was performed using the free-access PubMed database, Web of Science, and Chinese biomedical database, and relevant articles until September 18, 2018 that used IVIM to distinguish HGG from LGG were included. All analyses were performed using Review Manager 5.3 and Stata. Mean difference (MD) at 95% confidence interval (CI) of the apparent diffusion coefficient (ADC), diffusion coefficient value (D), perfusion fraction value (f), and perfusion coefficient value (D∗) were summarized.Results:Nine studies were used for general data pooling. In the tumor parenchyma (TP) regions, subgroup analysis revealed D∗ in HGG is higher than in LGG (MD = 1.19, P = .002), and D in HGG is lower than in LGG (MD = −1.06, P = .001). However, no significant difference in f (MD = 0.89, P = .056) was detected between HGG and LGG. In the white matter regions, HGG had higher D∗ (MD = 0.76, P = .04) compared with LGG, while no marked differences between the D value (P = .07) and f (P = .09) values.Conclusion:The present meta-analysis shows that the ADC, D, and D∗ values derived from IVIM may be useful in differentiating HGG from LGG. Considering the small sample of this study, we need to be cautious when interpreting the results of this study. Other prospective and large-sample randomized controlled trials were needed to establish the value of IVIM in differentiating HGG from LGG.

BRAF alterations are common in pediatric low-grade gliomas (LGG) and a subset of high-grade gliomas (HGG) in adults and children. BRAF-targeted therapy can be effective at preventing tumor growth, though resistance commonly emerges in HGG. Recently, tovorafenib was FDA approved for recurrent or refractory LGG with BRAFV600 alterations or BRAF rearrangements. While the trial showed it is effective for children with LGG previously treated with BRAF or MEK inhibitors, the safety in adults and efficacy in HGG is unknown. A cohort of appropriate patients was identified through routine clinical care. This research was conducted in accordance with IRB regulations with a waiver of written consent. Seven adults (5 HGG, 2 LGG) who received tovorafenib were identified. All patients had received prior BRAF-targeted therapy, and all patients with HGG had received prior radiation and temozolomide as well. Three individuals (2 HGG, 1 LGG) experienced stable disease or better for 4 or more months. Median duration of treatment was 8 weeks (range 3 weeks to 10 months). Two individuals experienced CTCAE grade 4 intratumoral hemorrhage (1 HGG, 1 LGG). Two patients remain on therapy at 4 and 10 months of treatment (1 HGG, 1 LGG). Our experience with tovorafenib indicates some limited efficacy in HGG in combination with other standard treatments. These observations demonstrate the need for further clinical trials in patients with HGG to understand potential clinical utility, either earlier in the disease course or in combination with other therapies.

Sphere formation is an indicator of tumor aggressiveness independent of the tumor grade; however, its relation to progression-free survival (PFS) is less known. This study was designed to assess the neurosphere forming ability among low grade glioma (LGG) and high-grade glioma (HGG), its stem cell marker expression, and correlation to PFS. Tumor samples of 140 patients, including (LGG; n = 67) and (HGG; n = 73) were analyzed. We used sphere forming assay, immunofluorescence, and immunohistochemistry to characterize the tumors. Our study shows that, irrespective of the pathological sub type, both LGG and HGG formed neurospheres in vitro under conventional sphere forming conditions. However, the number of neurospheres formed from tumor tissues were significantly higher in HGG compared to LGG (P < 0.0001). Different grades of glioma were further characterized for the expression of stem cell marker proteins and lineage markers. When neurospheres were analyzed, CD133 positive cells were identified in addition to CD15 and nestin positive cells in both LGG and HGG. When these neurospheres were subjected to differentiation, cells positive for GFAP and β-tubulin III were observed. Expression of stem cell markers and β-tubulin III were prominent in HGG compared to LGG, whereas GFAP expression was higher in LGG than in HGG. Kaplan-Meier survival analysis demonstrated that neurosphere forming ability was significantly associated with shorter PFS (P < 0.05) in both LGG and HGG. Our results supports earlier studies that neurosphere formation may serve as a definitive indicator of stem cell population within the tumor and thus a better predictor of PFS than the tumor grades alone. © 2018 IUBMB Life, 71(1):244-253, 2019.

P52a: Multiplex analysis of 27 cytokines produced by low-grade and high-grade glioma cells

Despite the improved prognostic relevance of the 2016 WHO molecular-based classification of lower-grade gliomas, variability in clinical outcome persists within existing molecular subtypes. Our aim was to determine prognostically significant metrics on preoperative MR imaging for lower-grade gliomas within currently defined molecular categories. We undertook a retrospective analysis of 306 patients with lower-grade gliomas accrued from an institutional data base and The Cancer Genome Atlas. Two neuroradiologists in consensus analyzed preoperative MRIs of each lower-grade glioma to determine the following: tumor size, tumor location, number of involved lobes, corpus callosum involvement, hydrocephalus, midline shift, eloquent cortex involvement, ependymal extension, margins, contrast enhancement, and necrosis. Adjusted hazard ratios determined the association between MR imaging metrics and overall survival per molecular subtype, after adjustment for patient age, patient sex, World Health Organization grade, and surgical resection status. For isocitrate dehydrogenase (IDH) wild-type lower-grade gliomas, tumor size (hazard ratio, 3.82; 95% CI, 1.94-7.75; P < .001), number of involved lobes (hazard ratio, 1.70; 95% CI, 1.28-2.27; P < .001), hydrocephalus (hazard ratio, 4.43; 95% CI, 1.12-17.54; P = .034), midline shift (hazard ratio, 1.16; 95% CI, 1.03-1.30; P = .013), margins (P = .031), and contrast enhancement (hazard ratio, 0.34; 95% CI, 0.13-0.90; P = .030) were associated with overall survival. For IDH-mutant 1p/19q-codeleted lower-grade gliomas, tumor size (hazard ratio, 2.85; 95% CI, 1.06-7.70; P = .039) and ependymal extension (hazard ratio, 6.34; 95% CI, 1.07-37.59; P = .042) were associated with overall survival. MR imaging metrics offers prognostic information for patients with lower-grade gliomas within molecularly defined classes, with the greatest prognostic value for IDH wild-type lower-grade gliomas.

Intraoperative Magnetic Resonance Imaging for Low-Grade and High-Grade Gliomas: What Is the Evidence? A Meta-Analysis

Purpose/Objective(s): Pancreatic ductal adenocarcinoma (PDAC) is characterized by an unusually high degree of hypoxia in the tumor microenvironment, which activates hypoxic signaling pathways orchestrated by hypoxia-inducible factor 1α (HIF1α). It has been shown previously that HIF1α significantly increases PDAC radioresistance and growth, though its mechanism of action is unknown. Here, we test the hypothesis that HIF1α confers these traits in PDAC through involvement in DNA damage repair and KRAS signaling in vitro. Materials/Methods: We performed studies with the KPC cell line (KrasLSL-G12D/+;TP53LSL-R172H/+). We used CRISPR-Cas9, a genome editing tool, to generate a HIF1α knockout (KO) cell line. Hypoxic microenvironments were induced using 100uM of the oxygen scavenger CoCl2. Radioresistance and double-strand DNA damage was evaluated and compared between wild-type (WT) and KO cells after treatment with increasing doses of ionizing radiation using neutral comet assays. Tumor signaling pathways were mapped and analyzed using western blot and co-immunoprecipitation. The KRASG12D inhibitor, BI-2852, was obtained from Boehringer-Ingelheim. Cancer cells were evaluated for growth and migration using cell proliferation assays and scratch wound assays following treatment with 50 uM BI-2852. Bioinformatic analysis was conducted using TCGA (The Cancer Genome Atlas) data; high and low expression were defined as samples with mRNA expression z-scores ≥ 1 and ≤ -1, respectively, Results: HIF1α KO cells demonstrated significantly increased radioresistance compared to WT cells following 8 and 10 Gy of radiation in hypoxic conditions (t-test, P&amp;lt;0.05). The olive moment of KO cells treated with the IC50 radiation dose (4 Gy) was significantly higher than that of WT cells (t-test, P&amp;lt;0.0001), suggesting that the DNA damage repair was upregulated by HIF1α. In addition, WT cells demonstrated higher tumor proliferation (t-test, P&amp;lt;0.01) and migration (t-test, P&amp;lt;0.05) compared to KO cells under hypoxia, suggesting HIF1α promoted tumor growth. WT cells treated with BI-2852 demonstrated significantly lower levels of TP53; using coimmunoprecipitation, we show that TP53 was likely degraded through Mdm2. HIF1α KO was necessary to induce high levels of apoptosis in cells treated with BI-2852. Our results suggest that HIF1α may act synergistically with KRAS to promote tumor survival through anti-apoptotic pathways that target TP53 for degradation. TCGA data also suggest that tumors with high expression of HIF1α is are associated with significantly poorer prognosis coimpared to tumors with low expression of HIF1α (Logrank test, P=0.003). Conclusion: Overall, this study demonstrates that HIF1α promotes DNA damage repair in PDAC and reveals a HIF1α/KRAS/p53 signaling axis. Future studies will test anti-HIF1α and anti-KRAS combination therapies in PDAC mouse models. Citation Format: Kevin J. Tu, Sanjit K. Roy, Amit Sawant, Hem D. Shukla. HIF1α is involved in radiation-induced DNA damage repair and anti-apoptotic pathways in pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4810.

Gliomas are the most prevalent primary brain tumors with immense clinical heterogeneity, poor prognosis and survival. The nucleotide-binding domain, and leucine-rich repeat containing receptors (NLRs) and absent-in-melanoma 2 (AIM2) are innate immune receptors crucial for initiation and progression of several cancers. There is a dearth of reports linking NLRs and AIM2 to glioma pathology. NLRs are expressed by cells of innate immunity, including monocytes, macrophages, dendritic cells, endothelial cells, and neutrophils, as well as cells of the adaptive immune system. NLRs are critical regulators of major inflammation, cell death, immune and cancer-associated pathways. We used a data-driven approach to identify NLRs, AIM2 and NLR-associated gene expression and methylation patterns in low grade glioma and glioblastoma, using The Cancer Genome Atlas (TCGA) patient datasets. Since TCGA data is obtained from tumor tissue, comprising of multiple cell populations including glioma cells, endothelial cells and tumor-associated microglia/macrophages we have used multiple cell lines and human brain tissues to identify cell-specific effects. TCGA data mining showed significant differential NLR regulation and strong correlation with survival in different grades of glioma. We report differential expression and methylation of NLRs in glioma, followed by NLRP12 identification as a candidate prognostic marker for glioma progression. We found that Nlrp12 deficient microglia show increased colony formation while Nlrp12 deficient glioma cells show decreased cellular proliferation. Immunohistochemistry of human glioma tissue shows increased NLRP12 expression. Interestingly, microglia show reduced migration towards Nlrp12 deficient glioma cells.

Purpose: This study was conducted in order to analyze the prognostic effects of epidermal growth factor receptor (EGFR) and CDKN2A alterations and determine the prognostic significance of EGFR and CDKN2A alterations on regulated genes in patients with glioblastoma (GBM) or lower grade glioma (LGG).Methods: The alteration frequencies of EGFR and CDKN2A across 32 tumor types were derived from cBioPortal based on The Cancer Genome Atlas (TCGA) datasets. The Kaplan–Meier analysis was used to determine the prognostic significance of EGFR and CDKN2A alterations. EGFR and CDKN2A alterations on regulated expression signatures were identified from RNA-seq data in the TCGA GBM datasets. The prognostic significance of EGFR and CDKN2A alterations on regulated genes in patients with glioma was determined using the TCGA and the Chinese Glioma Genome Atlas (CGGA) datasets.Results: Compared with the other 31 tumor types, EGFR amplification and CDKN2A deletion particularly occurred in patients with GBM. GBM patients with EGFR amplification or CDKN2A deletion demonstrated poor prognosis. Statistical analysis showed the coexistence of EGFR alteration and CDKN2A deletion in GBM patients. We identified 864 genes which were commonly regulated by EGFR amplification and CDKN2A deletion, and those genes were highly expressed in brain tissues and associated with the cell cycle, EBRR2, and MAPK signaling pathways. Spermatogenesis-associated serine-rich 2-like gene (SPATS2L) was upregulated in GBM patients with EGFR amplification or CDKN2A alteration. Higher expression levels of SPATS2L were associated with worse prognosis in patients with GBM in both TCGA and CGGA datasets. Moreover, the expression levels of SPATS2L were higher in patients with a mesenchymal subtype of GBM. Statistical analysis also showed that the coexistence of EGFR alteration and CDKN2A deletion was significant in patients with LGG. SPATS2L was upregulated in LGG patients with EGFR amplification or CDKN2A alteration. Furthermore, higher expression levels of SPATS2L were associated with worse prognosis in patients with LGG in both TCGA and CGGA datasets. The expression levels of SPATS2L were higher in patients with an astrocytoma subtype of LGG. Finally, the coexistence and unfavorable prognostic effects of EGFR amplification and CDKN2A alteration were validated using the Memorial Sloan Kettering Cancer Center (MSKCC) glioma datasets.Conclusions: EGFR amplification and CDKN2A deletion of the regulated gene SPATS2L have significant prognostic effects in patients with GBM or LGG.