Meningiomas are the most common primary intracranial tumour in adults
. Patients with symptoms are generally treated with surgery as there are no effective medical therapies. The World Health ...Organization histopathological grade of the tumour and the extent of resection at surgery (Simpson grade) are associated with the recurrence of disease; however, they do not accurately reflect the clinical behaviour of all meningiomas
. Molecular classifications of meningioma that reliably reflect tumour behaviour and inform on therapies are required. Here we introduce four consensus molecular groups of meningioma by combining DNA somatic copy-number aberrations, DNA somatic point mutations, DNA methylation and messenger RNA abundance in a unified analysis. These molecular groups more accurately predicted clinical outcomes compared with existing classification schemes. Each molecular group showed distinctive and prototypical biology (immunogenic, benign NF2 wild-type, hypermetabolic and proliferative) that informed therapeutic options. Proteogenomic characterization reinforced the robustness of the newly defined molecular groups and uncovered highly abundant and group-specific protein targets that we validated using immunohistochemistry. Single-cell RNA sequencing revealed inter-individual variations in meningioma as well as variations in intrinsic expression programs in neoplastic cells that mirrored the biology of the molecular groups identified.
Hip fractures at the femoral neck are a major cause of morbidity and mortality, but aside from biomechanical strength testing, little is known about femoral neck architecture in mice. Procedures were ...optimized to analyze high-resolution (6 μm voxel size) microCT scans of the mouse femoral neck to provide bone mass and architectural information. Similar to histomorphometric observations in rats, the boundary between cortical and trabecular bone is difficult to identify in the mouse femoral mid-neck and these compartments were not analyzed separately. Analyses included total area, mineralized bone area, and bone volume fraction (BV/TV). Femoral neck architecture varies in C57BL/6J, 129/SvEv and BALB/c mouse strains. Bone cross sectional area and BV/TV were low in Lrp5 but elevated in Sost gene knockout mice. Sfrp4 gene knockout resulted in high total area, normal bone area, low BV/TV and, as indicated by BS/BV values, greater trabecularization. Femoral neck BV/TV declined with age and ovariectomy, but increased with teriparatide treatment. These findings demonstrate that the architecture of the mouse femoral neck mimics phenotypes and treatment effects observed at other skeletal sites and is a relevant bone site for translational studies examining osteoporosis therapies.
We use NMR spectra to determine protein–protein contact sites by observing differences in amide proton hydrogen–deuterium exchange in the complex compared to the free protein in solution. Aprotic ...organic solvents are used to preserve H/D labeling patterns that would be scrambled in water solutions. The binding site between the mammalian co-chaperone Aha1 with the middle domain of the chaperone Hsp90 obtained by our H/D exchange method corresponds well with that in the X-ray crystal structure of the homologous complex from yeast, even to the observation of a secondary binding site. This method can potentially provide data for complexes with unknown structure and for large or dynamic complexes inaccessible via NMR and X-ray methods.
INTRODUCTION: Mutations in isocitrate dehydrogenase (IDH) enzymes are recognised to drive the molecular footprint of diffuse gliomas through the accumulation of oncometabolite R-2-hydroxyglutarate ...which drives the widespread restructuring of the DNA methylome; however, beyond R-2-hydroxyglutarate, a comprehensive metabologenomic characterization of IDH-mutant gliomas has yet to be performed. METHODS: Glioma samples from a cohort of 154 patients underwent multiplatform molecular analysis, including metabolomic studies, genome-wide DNA methylation profiling and bulk RNA sequencing. A integrative analysis was performed, including hierarchical clustering and principal component analysis of identified metabolites, differentially methylated probes, copy number alteration and bulk mRNA data. Survival analysis as well as multivariable hazard ratios for clinical variables were calculated by fitting Cox Proportional Hazards Models. RESULTS: We discovered a group of IDH-mutant gliomas whose metabolic profile highly resembled IDH wildtype tumors. Notably, these IDH-mutant gliomas with dysregulated metabolism were distinguished from their IDH-mutant counterparts by significantly shorter overall survival (median OS 118.9 months vs 173.6 months, p=0.048). The IDH-mutant tumors with dysregulated metabolism harbored distinct epigenetic alterations that converged to drive proliferative and stem-like transcriptional profiles. The prognostic relevance of dysregulated metabolism complements, but was not wholly explained by canonically recognized prognostic classifications in IDH-mutant gliomas including 1p/19q codeletion, glioma CpG Island Hypermethylator (GCIMP) status and CDKN2A homozygous deletion. CONCLUSIONS: Utilizing a cross-platform analysis we have uncovered a novel subtyping of IDH-mutant gliomas with dysregulated cellular metabolism with similar survival to IDH-wildtype tumors. The metabolic profile provides unique information on glioma phenotypes, which may facilitate a more comprehensive understanding of glioma biology, and provide a window to target novel dependencies.
Abstract
INTRODUCTION
Brain metastases, the most common form of intracranial neoplasms, carry a poor survival rate, mostly attributed to their high recurrence rates. Currently there are no reliable ...methods to determine which patients will progress. DNA methylation profiling (DNAmp) has become a useful tool in the diagnosis and stratification of intracranial neoplasms, and has the potential to provide clues on the epigenetic mechanisms that govern tumor behavior.
METHODS
A cohort of 58 BM tumor samples were selected for analysis. The cohort was composed of three groups: N=21 primary metastatic tumors (PMT), N=21 matched paired recurrent tumors (RMT), and a cohort of N= 16 primary metastatic tumors without any evidence of recurrence (NRMT). All tumor samples underwent DNAmp on the Illumina Infinium EPIC array to determine their methylation status at 850,000 CpG sites. Tumors were profiled via unsupervised hierarchical clustering, pathway enrichment analysis, and cell deconvolution analysis.
RESULTS
Differential methylation analysis revealed over 32617 differentially methylated CpG sites between grouped PMT and RMT samples, and 835424 sites between PMT and NRMT samples. When comparing PMT with NRMT samples, we revealed a distinct DNAmp that was upheld upon hierarchical clustering analysis. NRMT samples show a significant downregulation of pathways involved in DNA-binding and transcriptional regulation. Paired analysis of PMT and RMT revealed a relative paucity of differentially methylated CpG sites shared across paired samples: a total of 257 probes were differentially methylated across 14/19 samples. These probes however showed enrichment primarily for DNA-binding and transcription factor regulation, in reverse from the non-recurrent samples.
CONCLUSION
Our data suggests that DNAmp may be capable of differentiating tumors destined to progress from those with less aggressive features, and that DNAmp appear to remain stable through to recurrence. This work demonstrates the potential for DNA methylation to be utilized to uncover pathways associated with BM recurrence.
Immune-mediated anti-tumoral responses, elicited by oncolytic viruses and augmented with checkpoint inhibition, may be an effective treatment approach for glioblastoma. Here in this multicenter phase ...1/2 study we evaluated the combination of intratumoral delivery of oncolytic virus DNX-2401 followed by intravenous anti-PD-1 antibody pembrolizumab in recurrent glioblastoma, first in a dose-escalation and then in a dose-expansion phase, in 49 patients. The primary endpoints were overall safety and objective response rate. The primary safety endpoint was met, whereas the primary efficacy endpoint was not met. There were no dose-limiting toxicities, and full dose combined treatment was well tolerated. The objective response rate was 10.4% (90% confidence interval (CI) 4.2-20.7%), which was not statistically greater than the prespecified control rate of 5%. The secondary endpoint of overall survival at 12 months was 52.7% (95% CI 40.1-69.2%), which was statistically greater than the prespecified control rate of 20%. Median overall survival was 12.5 months (10.7-13.5 months). Objective responses led to longer survival (hazard ratio 0.20, 95% CI 0.05-0.87). A total of 56.2% (95% CI 41.1-70.5%) of patients had a clinical benefit defined as stable disease or better. Three patients completed treatment with durable responses and remain alive at 45, 48 and 60 months. Exploratory mutational, gene-expression and immunophenotypic analyses revealed that the balance between immune cell infiltration and expression of checkpoint inhibitors may potentially inform on response to treatment and mechanisms of resistance. Overall, the combination of intratumoral DNX-2401 followed by pembrolizumab was safe with notable survival benefit in select patients (ClinicalTrials.gov registration: NCT02798406).
Abstract
Using next generation sequencing (NGS) with a noise reduction mechanism to detect somatic variants of 0.1% minor allele frequency or lower has attracted increasing interest for cancer ...research and diagnostics. Molecular barcoding is a technology that aims to reduce the noise and errors caused by PCR and sequencing artifacts, and improves mutation detection accuracy. Here, we report a novel multiplex PCR-based, ultra-sensitive molecular barcoding technology that drastically reduces false positive calls, additionally, barcoded sequencing reads can be assigned back to both the forward and reverse strands of the original DNA fragment, thus further remove variant call noise. While providing a simple and fast workflow, this technology does not have the base bias associated with capture hybridization. It achieves an error rate of 4 X 10-7 nucleotides, and detects allele frequencies at 0.1%.
Citation Format: Li Jacey Zhang, Lucie Siu Lee, Yang Lily Liu, Jeff Liu, Tao Chen, Guoying Liu, Zhitong Liu. Detecting low allele frequency somatic mutations using targeted amplicon sequencing and a novel double strand molecular barcoding scheme abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1564.
Management of clinically aggressive meningiomas is a considerable challenge. PD-L1 induced immune suppression has increasingly gained attention in clinical management of cancer; however, to date, the ...clinical significance and regulatory mechanisms of PD-L1 in meningioma is not yet fully characterized. We sought to characterize PD-L1 expression in meningioma and elucidate its regulatory mechanisms. Immunohistochemical staining of PD-L1 expression in meningiomas showed 43% positivity in both tumor and immune cells and we observed intra and inter tumoral heterogeneity. Univariate and multivariate analyses confirmed that PD-L1 protein expression is an independent prognostic marker for worse recurrence free survival in meningioma. Furthermore, our transcriptomic analysis revealed a strong association between PD-L1 expression and that of NFKB2 and carbonic anhydrase 9 (CA9). We also demonstrated that both of these markers, when co-expressed with PD-L1, predict tumor progression. Our studies on several meningioma cell lines cultured in hypoxic conditions validated the association of CA9 and PD-L1 expression. Here we show the clinical significance of PD-L1 in meningioma as a marker that can predict tumor recurrence. We also show an association PD-L1 expression with NFKB2 expression and its induction under hypoxic conditions. These findings may open new avenues of molecular investigation in pathogenesis of meningioma.
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