scholarly journals Recurrent structural variations of lncRNA gene CCDC26 in diffuse intrinsic pontine glioma

2021 ◽  
Author(s):  
Lihua Zou
Keyword(s):  
Brain Cancer ◽  
Noncoding Rna ◽  
Diffuse Intrinsic Pontine Glioma ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Pontine Glioma ◽  
Structural Variations ◽  
Lncrna Gene ◽  
Elevated Expression ◽  
Pediatric Brain

AbstractWe report recurrent somatic structural variations (SVs) involving long noncoding RNA (lncRNA) CCDC26 in 13% of Diffuse Intrinsic Pontine Glioma (DIPG) patients. We validate our findings using whole genome sequencing data from two independent patient cohorts. CCDC26 SVs cause increased expression of CCDC26 gene in patients. In addition, CCDC26 expression is associated with elevated expression of MYC and proliferation signature. Our findings identify CCDC26 as a novel significantly mutated gene in DIPG and highlight the importance of structural variations in pediatric brain cancer.

scholarly journals Genes encoding histone proteins are differentially expressed between men and women with diffuse intrinsic pontine glioma and their expression correlates with survival.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Brain Cancer ◽  
Diffuse Intrinsic Pontine Glioma ◽  
Histone Genes ◽  
Histone H4 ◽  
Pontine Glioma ◽  
Histone H2b ◽  
Men And Women ◽  
Genes Encoding ◽  
Pediatric Brain ◽  
Median Survival Rate

Diffuse intrinsic pontine glioma is a pediatric brain cancer and has the lowest median survival rate of all cancers known to man (1). 99% of patients diagnosed with DIPG will expire within 5 years (1). Understanding the transcriptional behavior of tumors in DIPG is critical for the development of novel therapies. In this study, I compared the transcriptomes of tumors from men with DIPG versus that of tumors from women diagnosed with DIPG using a published dataset (2). I found that three histone genes, including HIST1H4C, HIST1H2BD, and HIST1H3D, which encode Histone H4, Histone H2B Type 1D, and Histone H3.1 were among the genes whose expression was most different between the DIPG tumors of men and women. Importantly, the expression level of two of these genes significantly correlated in a linear fashion with the amount of time the patient survived. It has previously been reported that 78% of DIPG tumors contain a mutation in Histone H3.1 (HIST1H3B) (3). This is the first report of differential expression of histone genes in tumors of patients with DIPG.

scholarly journals In diffuse intrinsic pontine gliomas, non-coding RNA expression is significantly varied dependent on overall survival

2021 ◽  
Author(s):  
Rucha ◽  
Vijay S
Keyword(s):  
Overall Survival ◽  
Brain Cancer ◽  
Transcriptional Activity ◽  
Diffuse Intrinsic Pontine Glioma ◽  
Rna Expression ◽  
Pontine Glioma ◽  
Non Coding Rna ◽  
Diffuse Intrinsic Pontine Gliomas ◽  
New Treatments ◽  
Pediatric Brain

Abstract Diffuse intrinsic pontine glioma is a kind of pediatric brain cancer that kills 99 percent of patients within five years and for which there are no conventional chemotherapies. It is crucial for new treatments to comprehend the cancer's transcriptional activity. Using a published dataset, we compared the transcriptomes of tumors from patients who lived longer or less than six months. Among the genes whose expression changed most, we observed that numerous microRNAs and snoRNAs were present. The publication's findings are the first evidence of variable levels of non-coding RNA expression in diffuse intrinsic pontine glioma.

scholarly journals Non-coding RNA are differentially expressed in diffuse intrinsic pontine gliomas based on overall survival.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Brain Cancer ◽  
Expression Profiling ◽  
Diffuse Intrinsic Pontine Glioma ◽  
Novel Therapies ◽  
Pontine Glioma ◽  
Non Coding Rna ◽  
Differential Gene ◽  
Diffuse Intrinsic Pontine Gliomas ◽  
Pediatric Brain

Diffuse intrinsic pontine glioma is a pediatric brain cancer; 99% of patients diagnosed with this disease will expire within 5 years (1) and there are no standard chemotherapies available for it (2). Understanding the transcriptional behavior of this cancer is critical for the development of novel therapies. We performed global differential gene expression profiling of tumors from patients with DIPG by comparing the transcriptomes of tumors from those who survived greater or less than six months using a published dataset (3). We found that multiple microRNAs and snoRNAs were among the genes whose expression was most different between those who survived greater or less than six months. This is the first report of outcome-associated differential expression of non-coding RNA in diffuse intrinsic pontine glioma.

scholarly journals In diffuse intrinsic pontine gliomas, non-coding RNA expression is significantly varied dependent on overall survival

2021 ◽  
Author(s):  
Henley Castillo ◽  
Kenzie Mellor ◽  
Amelia-Mae Marks ◽  
Willard L
Keyword(s):  
Overall Survival ◽  
Brain Cancer ◽  
Transcriptional Activity ◽  
Diffuse Intrinsic Pontine Glioma ◽  
Rna Expression ◽  
Pontine Glioma ◽  
Non Coding Rna ◽  
Diffuse Intrinsic Pontine Gliomas ◽  
New Treatments ◽  
Pediatric Brain

Abstract Diffuse intrinsic pontine glioma is a kind of pediatric brain cancer that kills 99 percent of patients within five years and for which there are no conventional chemotherapies. It is crucial for new treatments to comprehend the cancer's transcriptional activity. Using a published dataset, we compared the transcriptomes of tumors from patients who lived longer or less than six months. Among the genes whose expression changed most, we observed that numerous microRNAs and snoRNAs were present. The publication's findings are the first evidence of variable levels of non-coding RNA expression in diffuse intrinsic pontine glioma.

scholarly journals Receptor-driven invasion profiles in diffuse intrinsic pontine glioma (DIPG)

2021 ◽  
Author(s):  
Anju Karki ◽  
Noah E Berlow ◽  
Jin-Ah Kim ◽  
Esther Hulleman ◽  
Qianqian Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Growth Factor ◽  
Protein Expression ◽  
Cell Viability ◽  
Rna Sequencing ◽  
Cell Invasion ◽  
Growth Factor Receptor ◽  
Diffuse Intrinsic Pontine Glioma ◽  
Sequencing Data ◽  
Pontine Glioma

Abstract Background Diffuse intrinsic pontine glioma (DIPG) is a devastating pediatric cancer with unmet clinical need. DIPG is invasive in nature, where tumor cells interweave into the fiber nerve tracts of the pons making the tumor unresectable. Accordingly, novel approaches in combating the disease is of utmost importance and receptor-driven cell invasion in the context of DIPG is under-researched area. Here we investigated the impact on cell invasion mediated by PLEXINB1, PLEXINB2, platelet growth factor receptor (PDGFR)α, PDGFRβ, epithelial growth factor receptor (EGFR), activin receptor 1 (ACVR1), chemokine receptor 4 (CXCR4) and NOTCH1. Methods We used previously published RNA-sequencing data to measure gene expression of selected receptors in DIPG tumor tissue versus matched normal tissue controls (n=18). We assessed protein expression of the corresponding genes using DIPG cell culture models. Then, we performed cell viability and cell invasion assays of DIPG cells stimulated with chemoattractants/ligands. Results RNA-sequencing data showed increased gene expression of receptor genes such as PLEXINB2, PDGFRα, EGFR, ACVR1, CXCR4 and NOTCH1 in DIPG tumors compared to the control tissues. Representative DIPG cell lines demonstrated correspondingly increased protein expression levels of these genes. Cell viability assays showed minimal effects of growth factors/chemokines on tumor cell growth in most instances. Recombinant SEMA4C, SEM4D, PDGF-AA, PDGF-BB, ACVA, CXCL12 and DLL4 ligand stimulation altered invasion in DIPG cells. Conclusions We show that no single growth factor-ligand pair universally induces DIPG cell invasion. However, our results reveal a potential to create a composite of cytokines or anti-cytokines to modulate DIPG cell invasion.

scholarly journals Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1444
Author(s):  
Nazeefa Fatima ◽  
Anna Petri ◽  
Ulf Gyllensten ◽  
Lars Feuk ◽  
Adam Ameur
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Single Molecule ◽  
Large Scale ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Structural Variations ◽  
Single Molecule Sequencing ◽  
Human Samples

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies.

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