Regio- and diastereoselective synthesis of diverse spirocyclic indenes by cyclization with indene-dienes as two carbon building blocks.

We report a base-promoted cyclization with indene-dienes as two carbon building blocks toward diverse spirocyclic indene scaffolds including hexacyclic spiroindenes bearing benzo pyran motifs and pentacyclic spiroindenes containing oxindole units in high yields with excellent diastereoselectivities.

Characterization of tumor-associated reactive astrocytes in gliomas by single-cell and bulk tumor sequencing.

Objective: Astrocytes constitute approximately 30% of cells in gliomas and play important roles in synapse construction and survival. Recently, JAK/STAT pathway activation associated with a new type of astrocyte was reported. However, the implications of these tumor-associated reactive astrocytes (TARAs) in glioma are not known. Methods: We comprehensively assessed TARAs in gliomas, both in single cells and at the bulk tumor level, by analyzing five independent datasets. First, we analyzed two single-cell RNA sequencing datasets of 35,563 cells from 23 patients to estimate the infiltration level of TARAs in gliomas. Second, we collected clinical information and genomic and transcriptomic data of 1,379 diffuse astrocytoma and glioblastoma samples from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas datasets to evaluate the genomic, transcriptomic and clinical characteristics of TARA infiltration. Third, we downloaded expression profiles of recurrent glioblastoma samples from patients receiving PD-1 inhibitors to analyze the predictive value of TARAs for immune checkpoint inhibition. Results: Single-cell RNA sequencing data showed TARAs were abundant in the glioma micro-environment (15.7% in the CGGA dataset and 9.1% in the Gene Expression Omnibus GSE141383 dataset, respectively). Bulk tumor sequencing data showed that the extent of TARA infiltration was highly associated with major clinical and molecular features of astrocytic gliomas. Patients with more TARA infiltration were more likely to have MUC16, FLG, and PICK3A mutations, chromosome 9p21.3, 10q23.3, and 13q14.2 deletions and 7p11.2 amplification. Gene Ontology analysis revealed that the high level of astrocyte infiltration was characterized by immune and oncogenic pathways, such as the inflammatory response, positive regulation of the JAK-STAT cascade, positive regulation of NIK/NF-kappa B signaling and the tumor necrosis factor biosynthetic process. Patients with greater TARA infiltration showed inferior prognosis. Meanwhile, the extent of reactive astrocyte infiltration exhibited a predictive value for recurrent glioblastoma patients undergoing anti-PD-1 immune therapy. Conclusion: TARA infiltration might promote glioma tumor progression and can be used as a diagnostic, predictive and prognostic marker in gliomas. Prevention of TARA infiltration might be a new therapeutic strategy for glioma.

A regioselective [3 + 2] cycloaddition reaction of 2-benzylidene-1-indenones with functional olefins to access indanone-fused 2D/3D skeletons.

The regioselective [3 + 2] cycloaddition reaction of 2-benzylidene-1-indenones with functional olefins was established with DABCO as a base under mild conditions. Using this approach, a series of diversely substituted indanone-fused cyclopentane polycycles with highly crowded multiple substituents were synthesized in high yields.

Construction of an Axially Chiral Fluorene Nitrile-Based Framework via Benzannulation of Indene Diene with Benzoylacetonitrile.

The methodology for the synthesis of fluorene-based atropisomers was developed via the strategy of aromatic ring formation. By this strategy, an efficient benzannulation of indene-based diene with benzoylacetonitrile divergently promoted by DABCO and a chiral organocatalyst was established, and various atropisomeric fluorene-based skeletons were generated in good yields, which not only provide a new strategy for the construction of atropisomeric biaryls but also offer a new member to the atropisomeric family.

Divergent Metal-Free [4 + 2] Cascade Reaction of 1-Indanylidenemalononitrile with 3-Benzylidenebenzofuran-2(3H)-one: Access to Spiro-dihydrofluorene-benzofuranone and Axially Chiral Fluorenylamine-phenol Derivatives.

An efficient cascade reaction of 1-indanylidenemalononitrile with 3-benzylidenebenzofuran-2(3H)-one divergently promoted by DABCO or chiral organocatalyst was developed under mild reaction conditions, and various spiro-dihydrofluorene-benzofuranones were produced in gratifying results, respectively. It is worth noting that both the spiro and axially chiral products can be obtained by tuning the reaction conditions. The mechanism of the transformation was also studied by quantum chemical calculations.

Correction to "Monitoring the Hierarchical Evolution from a Double-Stranded Helix to a Well-Defined Microscopic Morphology Based on a Turbine-like Aromatic Molecule".

[This corrects the article DOI: 10.1021/acsomega.0c01443.].

Correction: Metal-free [3+3] benzannulation of 1-indanylidene-malononitrile with Morita-Baylis-Hillman carbonates: direct access to functionalized fluorene and fluorenone derivatives.

Correction for 'Metal-free [3+3] benzannulation of 1-indanylidene-malononitrile with Morita-Baylis-Hillman carbonates: direct access to functionalized fluorene and fluorenone derivatives' by Ya-Sa Xie et al., Chem. Commun., 2020, 56, 1948-1951, DOI: 10.1039/D0CC00143K.

Characterization and prognostic significance of alternative splicing events in lower-grade diffuse gliomas.

Alternative splicing (AS) is assumed to play important roles in the progression and prognosis of cancer. Currently, the comprehensive analysis and clinical relevance of AS in lower-grade diffuse gliomas have not been systematically addressed. Here, we gathered alternative splicing data of lower-grade diffuse gliomas from SpliceSeq. Based on the Percent Spliced In (PSI) values of 515 lower-grade diffuse glioma patients from the Cancer Genome Atlas (TCGA), we performed subtype-differential AS analysis and consensus clustering to determine robust clusters of patients. A total of 48 050 AS events in 10 787 genes in lower-grade diffuse gliomas were profiled. Subtype-differential splicing analysis and functional annotation revealed that spliced genes were significantly enriched in numerous cancer-related biological phenotypes and signalling pathways. Consensus clustering using AS events identified three robust clusters of patients with distinguished pathological and prognostic features. Moreover, each cluster was also associated with distinct genomic alterations. Finally, we developed and validated an AS-related signature with Cox proportional hazards model. The signature, significantly associated with clinical and molecular features, could serve as an independent prognostic factor for lower-grade diffuse gliomas. Thus, our results indicated that AS events could discriminate molecular subtypes and have prognostic impact in lower-grade diffuse gliomas.

Whole-transcriptome sequencing profiling identifies functional and prognostic signatures in patients with PTPRZ1-MET fusion-negative secondary glioblastoma multiforme.

Gliomas are the most common type of primary brain tumor in adults with a high mortality rate. Low-grade gliomas progress to glioblastoma multiforme (GBM) in the majority of cases, forming secondary GBM (sGBM), followed by rapid fatal clinical outcomes. Protein tyrosine phosphatase receptor type Z1 (PTPRZ1)-MET proto-oncogene receptor tyrosine kinase (MET) (ZM) fusion has been identified as a biomarker for sGBM that is involved in glioma progression, but the mechanism of gliomagenesis and pathology of ZM-negative sGBM has remained to be fully elucidated. A whole-transcriptome signature is thus required to improve the outcome prediction for patients with sGBM without ZM fusion. In the present study, whole-transcriptome sequencing on 42 sGBM samples with or without ZM fusion from the Chinese Glioma Genome Atlas database identified mRNAs with differential expression between patients with and without ZM fusion and the most significant survival-associated genes were identified. A 6-gene signature was identified as a novel prognostic model reflecting survival probability in patients with ZM-negative sGBM. Clinical characteristics in patients with a high or low risk score value were analyzed with the Kaplan-Meier method and a two-sided log-rank test. In addition, ZM-negative sGBM patients with a high risk score exhibited an increase in immune cells, NF-κB-induced pathway activation and a decrease in endothelial cells compared with those with a low risk score. The present study demonstrated the potential use of a next-generation sequencing-based cancer gene signature in patients with ZM-negative sGBM, indicating possible clinical therapeutic strategies for further treatment of such patients.

Ferroptosis-Related Gene Signature Predicts Glioma Cell Death and Glioma Patient Progression.

Glioma is a fatal brain tumor characterized by rapid proliferation and treatment resistance. Ferroptosis is a newly discovered programmed cell death and plays a crucial role in the occurrence and progression of tumors. In this study, we identified ferroptosis specific markers to reveal the relationship between ferroptosis-related genes and glioma by analyzing whole transcriptome data from Chinese Glioma Genome Atlas, The Cancer Genome Atlas dataset, GSE16011 dataset, and the Repository of Molecular Brain Neoplasia Data dataset. Nineteen ferroptosis-related genes with clinical and pathological features of glioma were identified as highly correlated. Functional assays in glioma cell lines indicated the association of ferroptosis with temozolomide resistance, autophagy, and glioma cell migration. Therefore, the identified ferroptosis-related genes were significantly correlated with glioma progression.

Monitoring the Hierarchical Evolution from a Double-Stranded Helix to a Well-Defined Microscopic Morphology Based on a Turbine-like Aromatic Molecule.

1H-Indazolo[1,2-b]phthalazine-5,10-dione IPDD with an approximate turbine-like spatial structure, primary assembled double-stranded helices at the first level, was predicted by quantum chemical calculations and confirmed by atomic force microscopy. The higher-dimensional hierarchical architectures including fibrils, helical fibers, spherical shells, and porous prismatic structures were observed in sequence by the scanning electron microscopy technique. The final porous prismatic structures sensitive to NH3 vapors have the potential to be applied in gas sensing and absorbing materials.

Metal-free [3+3] benzannulation of 1-indanylidene-malononitrile with Morita-Baylis-Hillman carbonates: direct access to functionalized fluorene and fluorenone derivatives.

An efficient [3+3] benzannulation of Morita-Baylis-Hillman carbonates with 1-indanylidenemalononitrile was achieved under metal-free reaction conditions selectively delivering a wide range of functional multi-substituted fluorene or fluorenone compounds in high yields, respectively (up to 86% yield). Moreover, experiments and quantum chemical calculations were also performed to study the mechanism of the transformation.

Coumarin-3-formylpyrazoles as 3-carbon synthons in cyclocondensation for the synthesis of spiro-fused pentacyclic spirooxindoles.

Coumarin-3-formylpyrazoles have been synthesized and applied as 3-carbon synthons in reaction with 3-hydroxyoxindoles by using DABCO as the catalyst. A range of structurally diverse spiro-fused pentacyclic spirooxindoles, bearing a spirooxindole-γ-lactone and a 3,4-dihydrocoumarin substructure, could be smoothly obtained in good to excellent yields (up to 99%) with excellent diastereoselectivities (all cases >20 : 1 dr). The asymmetric version of this tandem reaction was preliminarily investigated by using chiral organocatalysts.

Immune Cytolytic Activity Is Associated With Genetic and Clinical Properties of Glioma.

Background: Immunotherapy provided unprecedented advances in the treatment of several previously untreated cancers. However, these immunomodulatory maneuvers showed limited response to patients with glioma in clinical trials. Our aim was to depict the immune characteristics of glioma with immune cytolytic activity at genetic and transcriptome levels. Methods: In total, 325 gliomas from CGGA dataset as training cohort and 699 gliomas from TCGA dataset as validation cohort were enrolled in our analysis. We calculated the immune cytolytic activity for 1,000 of gliomas. The characteristics of immune cytolytic activity in gliomas were interpreted by the corresponding clinical, molecular genetics and radiological information. Results: We found that immune cytolytic activity was highly associated with molecular, clinical, and edema extent. High cytolytic activity gliomas were more likely to be diagnosed as glioblastoma and might be a potential marker of mesenchymal subtype. Moreover, those gliomas exhibited significantly increased copy number alterations including recurrent focal amplifications of PDGFA and EGFR, as well as recurrent deletions of CDKN2A/B. Subsequent biological function analysis revealed that the immune response and immune checkpoints expression were significantly correlated with the cytolytic activity of gliomas. Immune cytolytic activity was significantly positively associated with the extent of peri-tumor edema and was independently correlated with reduced survival time. Conclusion: Our results highlighted the immunoregulatory mechanism heterogeneity of gliomas. Cytolytic activity, indirectly reflected by the extent of peri-tumor edema, may provide a potential index to evaluate the status of immune microenvironment and immune checkpoints in glioma, which should be fully valued for precision classification and immunotherapy.

Peripheral blood test provides a practical method for glioma evaluation and prognosis prediction.

OBJECTIVE: To investigate the relationship between tumor characteristics and the preoperative counts of immune cells in peripheral blood test in glioma patients. METHODS: We included 260 WHO grades II-IV patients who had preoperative peripheral blood test result from Sanbo hospital as training set. The 66 patients from Tiantan hospital was obtained for validation. RNA sequencing data from CGGA and TCGA datasets were used to evaluate the features of neutrophil subtype and lymphocyte subtype in glioma. RESULTS: We revealed that the count of preoperative lymphocytes, eosinophils and neutrophils were associated with glioma grades. Neutrophil-to-lymphocyte ratio (NLR) <3.2 was associated with better prognosis, whereas increased NLR was strongly corresponding with a poor prognosis. Lymphocyte type glioma patients demonstrated a positive correlation with isocitrate dehydrogenase (IDH) mutation and lower grade. IDH mutant glioma contained a higher proportion of tumor-infiltrating lymphocytes than IDH wild-type glioma. The immune subtype (neutrophil subtype and lymphocyte subtype) was an independent prognostic factor in glioma. CONCLUSION: Our data demonstrated that NLR was an important prognostic factor in glioma. We classified that the immune subtype of glioma may contribute to a better understanding of disease pathogenesis and lead to the identification of new therapeutic targets for glioma patients.

Predicting chromosome 1p/19q codeletion by RNA expression profile: a comparison of current prediction models.

BACKGROUND: Chromosome 1p/19q codeletion is increasingly being recognized as the crucial genetic marker for glioma patients and have been included in WHO classification of glioma in 2016. Fluorescent in situ hybridization, a widely used method in detecting 1p/19q status, has some methodological limitations which might influence the clinical management for doctors. Here, we attempted to explore an RNA sequencing computational method to detect 1p/19q status. METHODS: We included 692 samples with 1p/19q status information from TCGA cohort as training set and 222 samples with 1p/19q status information from REMBRANDT cohort as validation set. We reviewed and compared five tools: TSPairs, GSVA, PAM, Caret, smoother, with respect to their accuracy, sensitivity and specificity. RESULTS: In TCGA cohort, the GSVA method showed the highest accuracy (98.4%) in predicting 1p/19q status (sensitivity=95.5%, specificity=99.6%) and smoother method showed the second-highest accuracy (accuracy=97.8%, sensitivity=96.4%, specificity=98.3%). While in REMBRANDT cohort, smoother method exhibited the highest accuracy (98.6%) (sensitivity= 96.7%, specificity=98.9%) in 1p/19q status prediction. CONCLUSIONS: Our independent assessment of five tools revealed that smoother method was selected as the most stable and accurate method in predicting 1p/19q status. This method could be regarded as a potential alternative method for clinical practice in future.

PD-L2 expression is correlated with the molecular and clinical features of glioma, and acts as an unfavorable prognostic factor.

Background: Gliomas are aggressive tumors with various molecular and clinical characteristics and exhibit strongly resistance to radio-chemotherapy. Programmed cell death 1 ligand 2 (PD-L2) is a cell surface protein, which was reported in many cancers, modulating cancer-associated immune responses, while the role of PD-L2 in gliomas remained unclear. Herein, we aimed to investigate the biological behaviors and clinical prognostic values of PD-L2 in gliomas. Methods: Totally, we enrolled RNA sequencing data of 325 glioma samples from Chinese Glioma Genome Atlas (CGGA) as training cohort and RNA expression data of 1032 samples from The Cancer Genome Atlas (TCGA) dataset as validation cohort in this research. Then, the clinical and molecular characteristics, and the prognostic value of PD-L2 were analyzed. Results: We found that PD-L2 expression level was significantly upregulated in higher grade glioma and IDH wild-type glioma. Receiver Operating Characteristic (ROC) analysis revealed that PD-L2 was a potential indicator of mesenchymal subtype. PD-L2 exhibited tight relationship with immune response and immune-modulating process in glioma. Moreover, PD-L2 expression level could predict unfavorable prognoses of patients independent of age, grade, IDH status and 1p/19q status. Conclusions: Our study revealed that PD-L2 was closely related with inflammation and immune response. Patients with lower PD-L2 expression level tended to experience improved survival. Targeting PD-L2 may become a valuable approach for the treatment of gliomas in clinical practice.

Inductively Coupled Plasma Mass Spectrometry as a Reference Method to Evaluate Serum Calcium Measurement Bias and the Commutability of Processed Materials during Routine Measurements.

BACKGROUND: Measuring total serum calcium is important for the diagnosis of diseases. Currently, results from commercial kits for calcium measurement are variable. Generally, the performance of serum calcium measurements is monitored by external quality assessment (EQA) or proficiency testing schemes. However, the commutability of the EQA samples and calibrators is often unknown, which limits the effectiveness of EQA schemes. The aim of this study was to evaluate the bias of serum calcium measurements and the commutability of processed materials. METHODS: Inductively coupled plasma mass spectrometry was applied as a comparative method, and 14 routine methods were chosen as test methods. Forty-eight serum samples from individual patients and 25 processed materials were quantified. A scatter plot was generated from patient samples, and 95% prediction intervals were calculated to evaluate the commutability of the processed materials and measurement bias at three concentration levels was used to determine the accuracy of routine assays. RESULTS: All assays showed high precision (total coefficient of variation [CV] <2.26%) and correlation coefficients (r > 0.99). For all assays, the mean bias for the 48 patient samples ranged from -0.13 mmol/L to 0.00 mmol/L (-5.61-0.01%), and the ranges for the three concentrations were -0.10-0.04 mmol/L (-5.71-2.35%), -0.14--0.01 mmol/L (-5.80--0.30%), and -0.19-0.04 mmol/L (-6.24-1.22%). The EQA samples, calibrators, and animal sera exhibited matrix effects in some assays; human serum pools were commutable in all assays; certificate reference materials were commutable in most assays, and only GBW09152 exhibited a matrix effect in one assay; and aqueous reference materials exhibited matrix effects in most assays. CONCLUSIONS: Biases for most assays were within the acceptable range, although the accuracy of some assays needs improvement. Human serum pools prepared from patient samples were commutable, and the other tested materials exhibited a matrix effect.

Molecular and clinical characterization of PTPN2 expression from RNA-seq data of 996 brain gliomas.

BACKGROUND: Immune checkpoint inhibitors have been shown to promote antitumor immunity and achieve durable tumor remissions. However, certain tumors are refractory to current immunotherapy. These negative results encouraged us to uncover other therapeutic targets and strategies. PTPN2 (protein tyrosine phosphatase, non-receptor type 2) has been newly identified as an immunotherapy target. Loss of PTPN2 sensitizes the tumor to immunotherapy via IFNγ signaling. METHODS: Here, we investigated the relationship between PTPN2 mRNA levels and clinical characteristics in gliomas. RNA-seq data of a cohort of 325 patients with glioma were available from the Chinese Glioma Genome Atlas and 671 from The Cancer Genome Atlas. R language, GraphPad Prism 5, and SPSS 22.0 were used to analyze data and draw figures. RESULTS: PTPN2 transcript levels increased significantly with higher grades of glioma and in isocitrate dehydrogenase (IDH) wild-type and mesenchymal subtype gliomas. A comprehensive biological analysis was conducted, which indicated a crucial role of PTPN2 in the immune and inflammation responses in gliomas. Specifically, PTPN2 was positively associated with HCK, LCK, MHC II, and STAT1 but negatively related to IgG and interferon. Moreover, canonical correlation analysis showed a positive correlation of PTPN2 with infiltrating immune cells, such as macrophages, neutrophils, and CD8+ T cells. Clinically, higher levels of PTPN2 were associated with a worse overall survival both in patients with gliomas and glioblastomas. CONCLUSION: PTPN2 expression level was increased in glioblastomas and associated with gliomas of the IDH wild-type and mesenchymal subtype. There was a close correlation between PTPN2 and the immune response and inflammatory activity in gliomas. Our results show that PTPN2 is a promising immunotherapy target and may provide additional treatment strategies.

MiR-134, epigenetically silenced in gliomas, could mitigate the malignant phenotype by targeting KRAS.

Gliomas are characterized by a malignant phenotype with proliferation, cell cycle arrest and invasion. To explore the biological consequences of epigenetically regulated miRNAs, we performed a microarray-based screening (whose expression was affected by 5-AZA treatment) followed by bisulfite sequencing validation. We found that miR-134 as an epigenetically regulated suppressor gene with prognostic value in gliomas. MicroRNA-134 was downregulated in high-grade gliomas, especially in GBM samples. Functional studies in vitro and in vivo in mouse models showed that overexpression of miR-134 was sufficient to reduce cell cycle arrest, cell proliferation and invasion. Target analysis and functional assays correlated the malignant phenotype with miR-134 target gene KRAS, an established upstream regulator of ERK and AKT pathways. Overall, our results highlighted a role for miR-134 in explaining the malignant phenotype of gliomas and suggested its relevance as a target to develop for early diagnostics and therapy.