Multiomics approach showing genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric brain tumors

Gene ◽  
2016 ◽  
Vol 576 (2) ◽  
pp. 734-742 ◽  
Author(s):  
Neetu Singh ◽  
Dinesh Kumar Sahu ◽  
Archana Mishra ◽  
Preeti Agarwal ◽  
Madhu Mati Goel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brain Tumors ◽  
Copy Number ◽  
Indian Pediatric ◽  
Pediatric Brain Tumors ◽  
Copy Number Alterations ◽  
Genome Wide ◽  
Different Types ◽  
Differential Gene ◽  
Pediatric Brain

scholarly journals Changes in the Expression of Pre-Replicative Complex Genes in hTERT and ALT Pediatric Brain Tumors

Cancers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 1028 ◽  
Author(s):  
Aurora Irene Idilli ◽  
Francesca Pagani ◽  
Emanuela Kerschbamer ◽  
Francesco Berardinelli ◽  
Manuel Bernabé ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brain Tumors ◽  
Cancer Cells ◽  
Pediatric Brain Tumors ◽  
Telomere Maintenance ◽  
Telomeric Dna ◽  
Maintenance Mechanism ◽  
Alternative Lengthening ◽  
Differential Gene ◽  
Pediatric Brain

Background: The up-regulation of a telomere maintenance mechanism (TMM) is a common feature of cancer cells and a hallmark of cancer. Routine methods for detecting TMMs in tumor samples are still missing, whereas telomerase targeting treatments are becoming available. In paediatric cancers, alternative lengthening of telomeres (ALT) is found in a subset of sarcomas and malignant brain tumors. ALT is a non-canonical mechanism of telomere maintenance developed by cancer cells with no-functional telomerase. Methods: To identify drivers and/or markers of ALT, we performed a differential gene expression analysis between two zebrafish models of juvenile brain tumors, that differ only for the telomere maintenance mechanism adopted by tumor cells: one is ALT while the other is telomerase-dependent. Results: Comparative analysis of gene expression identified five genes of the pre-replicative complex, ORC4, ORC6, MCM2, CDC45 and RPA3 as upregulated in ALT. We searched for a correlation between telomerase levels and expression of the pre-replicative complex genes in a cohort of paediatric brain cancers and identified a counter-correlation between telomerase expression and the genes of the pre-replicative complex. Moreover, the analysis of ALT markers in a group of 20 patients confirmed the association between ALT and increased RPA and decreased H3K9me3 localization at telomeres. Conclusions: Our study suggests that telomere maintenance mechanisms may act as a driver of telomeric DNA replication and chromatin status in brain cancers and identifies markers of ALT that could be exploited for precise prognostic and therapeutic purposes.

scholarly journals Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors

2017 ◽  
pp. now294 ◽  
Author(s):  
Shakti H. Ramkissoon ◽  
Pratiti Bandopadhayay ◽  
Jaeho Hwang ◽  
Lori A. Ramkissoon ◽  
Noah F. Greenwald ◽  
...  
Keyword(s):  
Brain Tumors ◽  
Precision Medicine ◽  
Copy Number ◽  
Pediatric Brain Tumors ◽  
Genome Wide ◽  
Medicine Analysis ◽  
Pediatric Brain

scholarly journals Ras, TrkB, and ShcA Protein Expression Patterns in Pediatric Brain Tumors

2021 ◽  
Vol 10 (10) ◽  
pp. 2219
Author(s):  
Monika Prill ◽  
Agnieszka Karkucinska-Wieckowska ◽  
Magdalena Lebiedzinska-Arciszewska ◽  
Giampaolo Morciano ◽  
Agata Charzynska ◽  
...  
Keyword(s):  
Brain Tumors ◽  
Expression Patterns ◽  
Pediatric Brain Tumors ◽  
Astrocytic Tumors ◽  
Embryonal Tumors ◽  
Altered Expression ◽  
Malignancy Grade ◽  
Oligodendroglial Tumors ◽  
Different Types ◽  
Pediatric Brain

Numerous papers have reported altered expression patterns of Ras and/or ShcA proteins in different types of cancers. Their level can be potentially associated with oncogenic processes. We analyzed samples of pediatric brain tumors reflecting different groups such as choroid plexus tumors, diffuse astrocytic and oligodendroglial tumors, embryonal tumors, ependymal tumors, and other astrocytic tumors as well as tumor malignancy grade, in order to characterize the expression profile of Ras, TrkB, and three isoforms of ShcA, namely, p66Shc, p52Shc, and p46Shc proteins. The main aim of our study was to evaluate the potential correlation between the type of pediatric brain tumors, tumor malignancy grade, and the expression patterns of the investigated proteins.

scholarly journals Integrated Analysis of Genome-Wide Copy Number Alterations and Gene Expression Profiling of Lung Cancer in Xuanwei, China

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0169098 ◽  
Author(s):  
Yanliang Zhang ◽  
Qiuyue Xue ◽  
Guoqing Pan ◽  
Qing H. Meng ◽  
Xiaoyu Tuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Copy Number ◽  
Integrated Analysis ◽  
Copy Number Alterations ◽  
Genome Wide

Clinical Application of Whole Genome Array Improves the Diagnosis of Pediatric Brain Tumors

2017 ◽  
Vol 25 (8) ◽  
pp. 688-695 ◽  
Author(s):  
Lina Shao ◽  
Sue Miller ◽  
Carl Koschmann ◽  
Sandra Camelo-Piragua
Keyword(s):  
High Resolution ◽  
Brain Tumors ◽  
Copy Number ◽  
Essential Role ◽  
Pediatric Brain Tumors ◽  
Whole Genome ◽  
Diagnosis And Prognosis ◽  
Genetic Abnormalities ◽  
Genome Array ◽  
Pediatric Brain

Pediatric brain tumors are the leading cause of childhood cancer mortality. Recurring genetic abnormalities play an essential role in the diagnosis and prognosis of pediatric brain tumors. However, clinical workup has not routinely included whole genome assessment. Here, we present high resolution whole genome array results in 11 pediatric brain tumors. Array identified clinically relevant abnormalities in all samples. Copy number aberrations with targeted therapy implication, GOPC-ROS1 fusion, CDK4 amplification, and NF1 deletion, were detected in 3 cases. In addition, array detected recurring genetic abnormalities, including KIAA1549-BRAF fusion, 19q13.42 amplification, i(17q), and monosomy 6, which assisted accurate histological diagnosis in pediatric brain tumors. In conclusion, our results show that whole genome high-resolution array detects diagnostic and treatment-relevant copy number abnormalities in pediatric brain tumors.

scholarly journals Selective cancer-germline gene expression in pediatric brain tumors

2008 ◽  
Vol 88 (3) ◽  
pp. 273-280 ◽  
Author(s):  
Joannes F. M. Jacobs ◽  
Oliver M. Grauer ◽  
Francis Brasseur ◽  
Peter M. Hoogerbrugge ◽  
Pieter Wesseling ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brain Tumors ◽  
Pediatric Brain Tumors ◽  
Germline Gene ◽  
Pediatric Brain ◽  
Cancer Germline

Genome‐wide analysis of DNA copy number alterations and gene expression in gastric cancer

2008 ◽  
Vol 216 (4) ◽  
pp. 471-482 ◽  
Author(s):  
Y Tsukamoto ◽  
T Uchida ◽  
S Karnan ◽  
T Noguchi ◽  
LT Nguyen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Copy Number ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Dna Copy Number Alterations

scholarly journals Magnetic resonance–guided laser interstitial thermal therapy: report of a series of pediatric brain tumors

2016 ◽  
Vol 17 (6) ◽  
pp. 723-733 ◽  
Author(s):  
Zulma Tovar-Spinoza ◽  
Hoon Choi
Keyword(s):  
Magnetic Resonance ◽  
Brain Tumors ◽  
Pediatric Brain Tumors ◽  
Thermal Therapy ◽  
Laser Interstitial Thermal Therapy ◽  
Children's Hospital ◽  
Different Types ◽  
Children’S Hospital ◽  
The Mean ◽  
Pediatric Brain

OBJECTIVE Magnetic resonance–guided laser interstitial thermal therapy (MRgLITT) is a novel, minimally invasive treatment that has multiple advantages in pediatric use and broad applicability for different types of lesions. Here, the authors report the preliminary results of the first series of pediatric brain tumors treated with MRgLITT at Golisano Children's Hospital in Syracuse, New York. METHODS Pediatric brain tumors treated with MRgLITT between February 2012 and August 2014 at Golisano Children's Hospital were evaluated retrospectively. Medical records, radiological findings, surgical data, complications, and results of tumor volumetric analyses were reviewed. The Visualase thermal laser system (Medtronic) was used in all MRgLITT procedures. RESULTS This series included 11 patients with 12 tumors (pilocytic astrocytoma, ependymoma, medulloblastoma, choroid plexus xanthogranuloma, subependymal giant cell astrocytoma, and ganglioglioma). A single laser and multiple overlapping ablations were used for all procedures. The mean laser dose was 10.23 W, and the mean total ablation time was 68.95 seconds. The mean initial target volume was 6.79 cm3, and the mean immediate post-ablation volume was 7.86 cm3. The mean hospital stay was 3.25 days, and the mean follow-up time was 24.5 months. Tumor volume decreased in the first 3 months after surgery (n = 11; p = 0.007) and continued to decrease by the 4- to 6-month followup (n = 11; mean volume 2.61 cm3; p = 0.009). Two patients experienced post-ablation complications: transient right leg weakness in one patient, and transient hemiparesis, akinetic mutism, and eye movement disorder in the other. CONCLUSIONS Magnetic resonance–guided laser interstitial thermal therapy is an effective first- or second-line treatment for select pediatric brain tumors. Larger multiinstitutional clinical trials are necessary to evaluate its use for different types of lesions to further standardize practices.

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