Targeted gene-expression analysis during malignant transformation in primary and secondary malignant meningioma

Abstract BACKGROUND Malignant meningiomas comprise 2–5% of all meningiomas. The process of malignant transformation when benign meningiomas (WHO grade I-II) become malignant (WHO grade III) has not previously been investigated in sequential tumour surgeries. Upregulation of FOXM1 expression and DREAM-complex repression have shown phenotypical subgroups correlating with WHO grade and aggressiveness. We investigated the RNA expression of 30 genes central to meningioma biology and 770 genes involved in neuroinflammatory pathways in primary and secondary malignant meningioma patients who underwent one to several operations. MATERIALS AND METHODS We identified a cohort of consecutive malignant meningioma patients treated at Rigshospitalet, Copenhagen from 2000–2020 (n=51) and gathered their malignant tumours and previous WHO grade I/II tumours. The malignant cohort (MC) was counter matched with a benign cohort (BC) where patients had no recurrences during follow-up. RNA expression signatures from 140 samples from the MC and 51 samples from the BC were analysed with the Nanostring Neuroinflammation panel customized with 30 genes known to be relevant in meningioma phenotypes. RESULTS 49% of MC patients had a previous grade I/II meningioma making them secondary malignant meningioma patients. Progression-free survival calculated from first malignant surgery to first recurrence or death showed no significant difference in the primary vs. secondary patients. Preliminary results of single-gene analysis of MC tumours showed FOXM1, MYBL2, TOP2A, BIRC5 expression was higher in WHO grade III samples. Gene-expression signatures in the individual patients and gene ontology enrichment analyses are in process. CONCLUSIONS FOXM1, MYBL2, TOP2A, BIRC5 RNA expression levels seem to rise during malignant progression across patients. Gene-expression analysis using the Nanostring technology is feasible and a potentially powerful tool to distinguish meningiomas prone to malignant transformation from truly benign meningiomas.

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OTEH-3. Targeted Gene-Expression analysis during malignant transformation in primary and secondary malignant meningioma

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab070.042 ◽

2021 ◽

Vol 3 (Supplement_2) ◽

pp. ii10-ii11

Author(s):

Andrea Daniela Maier ◽

Alessandra Meddis ◽

Jeppe Haslund-Vinding ◽

Christian Mirian ◽

Ausrine Areskeviciute ◽

...

Keyword(s):

Gene Expression ◽

Malignant Transformation ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Rna Expression ◽

Malignant Meningioma ◽

Who Grade ◽

Significant Difference ◽

Who Grade Iii ◽

Grade Iii

Abstract Background Malignant meningiomas comprise 2–5% of all meningiomas. The process of malignant transformation when benign meningiomas (WHO grade I-II) become malignant (WHO grade III) has not previously been investigated in sequential tumour surgeries. Upregulation of FOXM1 expression and DREAM-complex repression have shown phenotypical subgroups correlating with WHO grade and aggressiveness. We investigated the RNA expression of 30 genes central to meningioma biology and 770 genes involved in neuroinflammatory pathways in primary and secondary malignant meningioma patients who underwent one to several operations. Methods We identified a cohort of consecutive malignant meningioma patients treated at Rigshospitalet, Copenhagen from 2000–2020 (n=51) and gathered their malignant tumours and previous WHO grade I/II tumours. The malignant cohort (MC) was counter matched with a benign cohort (BC) where patients had no recurrences during follow-up. RNA expression signatures from 140 samples from the MC and 51 samples from the BC were analysed with the Nanostring Neuroinflammation panel customized with 30 genes known to be relevant in meningioma phenotypes. Results 49% of MC patients had a previous grade I/II meningioma making them secondary malignant meningioma patients. Progression-free survival calculated from first malignant surgery to first recurrence or death showed no significant difference in the primary vs. secondary patients. Preliminary results of single-gene analysis of MC tumours showed FOXM1, MYBL2, TOP2A, BIRC5 expression was higher in WHO grade III samples. Gene-expression signatures in the individual patients and gene ontology enrichment analyses are in process. Conclusions FOXM1, MYBL2, TOP2A, BIRC5 RNA expression levels seem to rise during malignant progression across patients. Gene-expression analysis using the Nanostring technology is feasible and a potentially powerful tool to distinguish meningiomas prone to malignant transformation from truly benign meningiomas.

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Proteomics, bioinformatics and targeted gene expression analysis reveals up-regulation of cochlin and identifies other potential biomarkers in the mouse model for deafness in usher syndrome type 1F

Human Molecular Genetics ◽

10.1093/hmg/ddq025 ◽

2010 ◽

Vol 19 (8) ◽

pp. 1515-1527 ◽

Cited By ~ 14

Author(s):

Mark R. Chance ◽

Jinsook Chang ◽

Shuqing Liu ◽

Giridharan Gokulrangan ◽

Daniel H.-C. Chen ◽

...

Keyword(s):

Gene Expression ◽

Mouse Model ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Usher Syndrome ◽

Syndrome Type ◽

Targeted Gene Expression ◽

Potential Biomarkers ◽

Usher Syndrome Type

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Targeted gene expression analysis of human deep veins

Journal of Vascular Surgery Venous and Lymphatic Disorders ◽

10.1016/j.jvsv.2020.08.025 ◽

2020 ◽

Author(s):

Maxim E. Shaydakov ◽

Jose A. Diaz ◽

Anthony J. Comerota ◽

Fedor Lurie

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Targeted Gene Expression

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Textile Hemp vs. Salinity: Insights from a Targeted Gene Expression Analysis

Genes ◽

10.3390/genes8100242 ◽

2017 ◽

Vol 8 (10) ◽

pp. 242 ◽

Cited By ~ 7

Author(s):

Gea Guerriero ◽

Marc Behr ◽

Jean-Francois Hausman ◽

Sylvain Legay

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Targeted Gene Expression

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Leveraging Transcriptome Data for Enhanced Gene Expression Analysis in Apple

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04424-18 ◽

2018 ◽

Vol 143 (5) ◽

pp. 333-346 ◽

Cited By ~ 1

Author(s):

Heidi Hargarten ◽

Sumyya Waliullah ◽

Lee Kalcsits ◽

Loren A. Honaas

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Gene Sequence ◽

Primer Design ◽

Specific Gene ◽

Transcriptome Data ◽

Rna Seq ◽

Polymerase Chain ◽

Targeted Gene Expression

Complex changes in gene expression occur during postharvest storage of apple (Malus ×domestica) and often precede or accompany changes in ripening and disorder development. Targeted gene expression analysis fundamentally relies on previous knowledge of the targeted gene. Minimally, a substantial fragment of the gene sequence must be known with high accuracy so that primers and probes, which bind to their targets in a complimentary fashion, are highly specific. Here, we describe a workflow that leverages publicly available transcriptome data to discover apple cultivar–specific gene sequences to guide primer design for quantitative real-time polymerase chain reaction (qPCR). We find that problematic polymorphisms occur frequently in ‘Granny Smith’ and ‘Honeycrisp’ apple when candidate primer binding sites were selected using the ‘Golden Delicious’ genome. We attempted to validate qPCR-based gene expression measurements with RNA sequencing (RNA-Seq) analysis of the same RNA samples. However, we found that agreement between the two technologies was highly variable and positively correlated with the similarity between cultivar-specific genes and RNA-Seq reference genes. Thus, we offer insight that 1) improves the accuracy and efficiency of qPCR primer design in cultivars that lack sufficient sequence resources and 2) better guides the essential step of validation of RNA-Seq data with a subset of genes of interest examined via qPCR.

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