scholarly journals ADAMTS1 Supports Endothelial Plasticity of Glioblastoma Cells with Relevance for Glioma Progression

Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 44
Author(s):  
Orlando Serrano-Garrido ◽  
Carlos Peris-Torres ◽  
Silvia Redondo-García ◽  
Helena G. Asenjo ◽  
María del Carmen Plaza-Calonge ◽  
...  
Keyword(s):  
Basic Knowledge ◽  
Sequencing Data ◽  
Extracellular Proteases ◽  
Human Gliomas ◽  
Primary Glioblastoma ◽  
Current Availability ◽  
Massive Sequencing ◽  
The Central Nervous System ◽  
Endothelial Plasticity ◽  
Cell Subpopulations

Gliomas in general and the more advanced glioblastomas (GBM) in particular are the most usual tumors of the central nervous system with poor prognosis. GBM patients develop resistance to distinct therapies, in part due to the existence of tumor cell subpopulations with stem-like properties that participate in trans-differentiation events. Within the complex tumor microenvironment, the involvement of extracellular proteases remains poorly understood. The extracellular protease ADAMTS1 has already been reported to contribute to the plasticity of cancer cells. Accordingly, this basic knowledge and the current availability of massive sequencing data from human gliomas, reinforced the development of this work. We first performed an in silico study of ADAMTS1 and endothelial markers in human gliomas, providing the basis to further assess these molecules in several primary glioblastoma-initiating cells and established GBM cells with the ability to acquire an endothelial-like phenotype. Using a co-culture approach of endothelial and GBM cells, we noticed a relevant function of ADAMTS1 in GBM cells leading the organization of endothelial-like networks and, even more significantly, we found a blockade of the formation of tumor-spheres and a deficient response to hypoxia in the absence of ADAMTS1. Our data support a chief role of this protease modulating the phenotypic plasticity of GBM.

scholarly journals IMMU-35. TRANSCRIPTIONALLY DEFINED IMMUNE CONTEXTURE IN HUMAN GLIOMAS AT SINGLE-CELL RESOLUTION

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii112-ii112
Author(s):  
Pravesh Gupta ◽  
Minghao Dang ◽  
Krishna Bojja ◽  
Tuan Tran M ◽  
Huma Shehwana ◽  
...  
Keyword(s):  
Dendritic Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Wild Type ◽  
Sequencing Data ◽  
Human Gliomas ◽  
Cell Clusters ◽  
Recurrent Gliomas ◽  
Antigen Presenting

Abstract The brain tumor immune microenvironment (TIME) continuously evolves during glioma progression and a comprehensive understanding of the glioma-centric immune cell repertoire beyond a priori cell types and/or states is uncharted. Consequently, we performed single-cell RNA-sequencing on ~123,000 tumor-derived immune cells from 17-pathologically stratified, IDH (isocitrate dehydrogenase)-differential primary, recurrent human gliomas, and non-glioma brains. Our analysis delineated predominant 34-myeloid cell clusters (~75%) over 28-lymphoid cell clusters (~25%) reflecting enormous heterogeneity within and across gliomas. The glioma immune diversity spanned functionally imprinted phagocytic, antigen-presenting, hypoxia, angiogenesis and, tumoricidal myeloid to classical cytotoxic lymphoid subpopulations. Specifically, IDH-mutant gliomas were enriched for brain-resident microglial subpopulations in contrast to enhanced bone barrow-derived infiltrates in IDH-wild type, especially in a recurrent setting. Microglia attrition in IDH-wild type -primary and -recurrent gliomas were concomitant with invading monocyte-derived cells with semblance to dendritic cell and macrophage/microglia like transcriptomic features. Additionally, microglial functional diversification was noted with disease severity and mostly converged to inflammatory states in IDH-wild type recurrent gliomas. Beyond dendritic cells, multiple antigen-presenting cellular states expanded with glioma severity especially in IDH-wild type primary and recurrent- gliomas. Furthermore, we noted differential microglia and dendritic cell inherent antigen presentation axis viz, osteopontin, and classical HLAs in IDH subtypes and, glioma-wide non-PD1 checkpoints associations in T cells like Galectin9 and Tim-3. As a general utility, our immune cell deconvolution approach with single-cell-matched bulk RNA sequencing data faithfully resolved 58-cell states which provides glioma specific immune reference for digital cytometry application to genomics datasets. Resultantly, we identified prognosticator immune cell-signatures from TCGA cohorts as one of many potential immune responsiveness applications of the curated signatures for basic and translational immune-genomics efforts. Thus, we not only provide an unprecedented insight of glioma TIME but also present an immune data resource that can be exploited to guide pragmatic glioma immunotherapy designs.

Computational Approaches for Transcriptome Assembly Based on Sequencing Technologies

2020 ◽  
Vol 15 (1) ◽  
pp. 2-16
Author(s):  
Yuwen Luo ◽  
Xingyu Liao ◽  
Fang-Xiang Wu ◽  
Jianxin Wang
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Critical Role ◽  
High Sensitivity ◽  
Biological Properties ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Massive Sequencing ◽  
Generation Sequencing

Transcriptome assembly plays a critical role in studying biological properties and examining the expression levels of genomes in specific cells. It is also the basis of many downstream analyses. With the increase of speed and the decrease in cost, massive sequencing data continues to accumulate. A large number of assembly strategies based on different computational methods and experiments have been developed. How to efficiently perform transcriptome assembly with high sensitivity and accuracy becomes a key issue. In this work, the issues with transcriptome assembly are explored based on different sequencing technologies. Specifically, transcriptome assemblies with next-generation sequencing reads are divided into reference-based assemblies and de novo assemblies. The examples of different species are used to illustrate that long reads produced by the third-generation sequencing technologies can cover fulllength transcripts without assemblies. In addition, different transcriptome assemblies using the Hybrid-seq methods and other tools are also summarized. Finally, we discuss the future directions of transcriptome assemblies.

scholarly journals Extracellular proteases and their inhibitors ingenetic diseases of the central nervous system

2003 ◽  
Vol 12 (suppl 2) ◽  
pp. R195-R200 ◽  
Author(s):  
F. Molinari ◽  
V. Meskanaite ◽  
A. Munnich ◽  
P. Sonderegger ◽  
L. Colleaux
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Extracellular Proteases ◽  
The Central Nervous System

The 2016 revision of the WHO classification of tumours of the central nervous system

2017 ◽  
Author(s):  
Paul Kleihues ◽  
Elisabeth Rushing ◽  
Hiroko Ohgaki
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Who Classification ◽  
De Novo ◽  
Genetic Profiling ◽  
Primary Glioblastoma ◽  
System P ◽  
Significant Step ◽  
The Central Nervous System

The revised fourth edition of the WHO classification of Tumours of the Central Nervous System, published in 2016, comprises several newly recognized tumour entities, and a significant restructuring of the classification, mainly based on genetic profiling. Glioblastomas are now classified into two major types. Isocitrate dehydrogenase (IDH)-wildtype glioblastoma (primary glioblastoma IDH-wildtype) develops rapidly de novo without a recognizable precursor lesion. IDH-mutant glioblastoma (secondary glioblastoma IDH-mutant) develops more slowly through malignant progression from diffuse or anaplastic astrocytoma. Medulloblastomas are now defined by combining histological patterns (classic, desmoplastic/nodular, extensive nodularity, anaplastic) and genetic hallmarks (WNT-activated; SHH-activated, TP53-mutant; SHH-activated, TP53-wildtype; non-WNT/non-SHH). Other newly recognized tumour entities include diffuse midline glioma, H3 K27M-mutant; ependymoma, RELA fusion-positive; and embryonal tumour with multilayered rosettes. The new classification is a significant step forward and will facilitate the development of novel targeted therapies of brain tumours.

scholarly journals Disorders of Neuronal Migration

1987 ◽  
Vol 14 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Peter G. Barth
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Neuronal Migration ◽  
Brain Regions ◽  
Distinct Pattern ◽  
Basic Knowledge ◽  
Detailed Knowledge ◽  
Important Process ◽  
The Central Nervous System ◽  
Environmental Causes

Abstract:Neuronal migration constitutes one of the major processes by which the central nervous system takes shape. Detailed knowledge about this important process now exists for different brain regions in rodent and monkey models as well as in the human. In the human, distinct genetic, chromosomal and environmental causes are known that affect neuronal migration, often in a morphologically distinct pattern, but the underlying pathological mechanisms are largely unknown. This review is intended to integrate our basic knowledge of the field with the accumulated intelligence on a large number of disorders and syndromes that represent the human part of the story.

scholarly journals Phenotype-guided subpopulation identification from single-cell sequencing data

2020 ◽  
Author(s):  
Duanchen Sun ◽  
Xiangnan Guan ◽  
Amy E. Moran ◽  
David Z. Qian ◽  
Pepper Schedin ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Single Cell ◽  
Clinical Information ◽  
Single Step ◽  
Cell Subpopulation ◽  
Clustering Methods ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Cell Subpopulations ◽  
Cell Data

AbstractSingle-cell sequencing yields novel discoveries by distinguishing cell types, states and lineages within the context of heterogeneous tissues. However, interpreting complex single-cell data from highly heterogeneous cell populations remains challenging. Currently, most existing single-cell data analyses focus on cell type clusters defined by unsupervised clustering methods, which cannot directly link cell clusters with specific biological and clinical phenotypes. Here we present Scissor, a novel approach that utilizes disease phenotypes to identify cell subpopulations from single-cell data that most highly correlate with a given phenotype. This “phenotype-to-cell within a single step” strategy enables the utilization of a large amount of clinical information that has been collected for bulk assays to identify the most highly phenotype-associated cell subpopulations. When applied to a lung cancer single-cell RNA-seq (scRNA-seq) dataset, Scissor identified a subset of cells exhibiting high hypoxia activities, which predicted worse survival outcomes in lung cancer patients. Furthermore, in a melanoma scRNA-seq dataset, Scissor discerned a T cell subpopulation with low PDCD1/CTLA4 and high TCF7 expressions, which is associated with a favorable immunotherapy response. Thus, Scissor provides a novel framework to identify the biologically and clinically relevant cell subpopulations from single-cell assays by leveraging the wealth of phenotypes and bulk-omics datasets.

scholarly journals Features of alternative splicing in stomach adenocarcinoma and their clinical implication: A research based on massive sequencing data

2020 ◽  
Author(s):  
Yuanyuan Zhang ◽  
Shengling Ma ◽  
Qian Niu ◽  
Yun Han ◽  
Xingyu Liu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Operating Characteristic ◽  
High Efficiency ◽  
Area Under The Curve ◽  
Regulation Mechanism ◽  
Sequencing Data ◽  
Molecular Events ◽  
Massive Sequencing ◽  
Stomach Adenocarcinoma ◽  
Prognostic Prediction

Abstract Background: Alternative splicing (AS) offers a main mechanism to form protein polymorphism. A growing body of evidence indicates the correlation between splicing disorders and carcinoma. Nevertheless, an overall analysis of AS signatures in stomach adenocarcinoma (STAD) is absent and urgently needed.Results: 2042 splicing events were confirmed as prognostic molecular events. Furthermore, the final prognostic signature constructed by 10 AS events gave good result with an area under the curve (AUC) of receiver operating characteristic (ROC) curve up to 0.902 for 5 years, showing high potency in predicting patient outcome. We built the splicing regulatory network to show the internal regulation mechanism of splicing events in STAD. QKI may play a significant part in the prognosis induced by splicing events.Conclusions: In our study, a high-efficiency prognostic prediction model was built for STAD patients, and the results showed that AS events could become potential prognostic biomarkers for STAD. Meanwhile, QKI may become an important target for drug design in the future.

Imbalances in T-cell subpopulations and survival in human gliomas

1991 ◽  
Vol 35 ◽  
pp. 95
Author(s):  
G. Rosoklija ◽  
I. Dzonov ◽  
P. Kolevski ◽  
T. Kuzmanovski ◽  
M. Mirčevski
Keyword(s):  
T Cell ◽  
Human Gliomas ◽  
Cell Subpopulations ◽  
T Cell Subpopulations

scholarly journals T Helper Cells: The Modulators of Inflammation in Multiple Sclerosis

Cells ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 482 ◽  
Author(s):  
Martina Kunkl ◽  
Simone Frascolla ◽  
Carola Amormino ◽  
Elisabetta Volpe ◽  
Loretta Tuosto
Keyword(s):  
Multiple Sclerosis ◽  
Inflammatory Responses ◽  
Clinical Symptoms ◽  
Inflammatory Disorder ◽  
T Helper ◽  
Th Cells ◽  
Cytokines And Chemokines ◽  
Th Cell ◽  
The Central Nervous System ◽  
Cell Subpopulations

Multiple sclerosis (MS) is a chronic neurodegenerative disease characterized by the progressive loss of axonal myelin in several areas of the central nervous system (CNS) that is responsible for clinical symptoms such as muscle spasms, optic neuritis, and paralysis. The progress made in more than one decade of research in animal models of MS for clarifying the pathophysiology of MS disease validated the concept that MS is an autoimmune inflammatory disorder caused by the recruitment in the CNS of self-reactive lymphocytes, mainly CD4+ T cells. Indeed, high levels of T helper (Th) cells and related cytokines and chemokines have been found in CNS lesions and in cerebrospinal fluid (CSF) of MS patients, thus contributing to the breakdown of the blood–brain barrier (BBB), the activation of resident astrocytes and microglia, and finally the outcome of neuroinflammation. To date, several types of Th cells have been discovered and designated according to the secreted lineage-defining cytokines. Interestingly, Th1, Th17, Th1-like Th17, Th9, and Th22 have been associated with MS. In this review, we discuss the role and interplay of different Th cell subpopulations and their lineage-defining cytokines in modulating the inflammatory responses in MS and the approved as well as the novel therapeutic approaches targeting T lymphocytes in the treatment of the disease.

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