Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs

Cardon, Tristan; Fournier, Isabelle; Salzet, Michel

doi:10.3389/fcell.2021.703583

Cited by 7 publications

(6 citation statements)

References 87 publications

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“…Table 2). Taken together, we identified several AltProts issued from ncRNA (~57%) which is in line with our previous work on a glioma cell line (NCH82) (Cardon et al, 2020b and(Cardon et al, 2021)).…”

Section: Identification Of Alternative Proteinssupporting

confidence: 91%

Spatial reference and alternative proteome analysis of glioblastoma reveals molecular signatures and associates survival with specific markers

Duhamel

Drelich

Wisztorski

et al. 2022

Preprint

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Molecular heterogeneity is a key feature of glioblastoma pathology impeding patient’s stratification and leading to high discrepancies between patients mean survivals. We performed a spatial proteomics analysis on a cohort of 96 glioblastoma patients with survival varying from few months to more than 4 years. 46 tumors were analyzed by spatially-resolved high resolution mass spectrometry proteomics. Integrative analysis of protein expression and clinical information allowed us to identify three molecular regions associated with immune, neurogenesis and tumorigenesis signatures. Several of these molecular signatures can be enriched within the same tumor sample leading to high intra-tumoral heterogeneity. Nevertheless, a set of proteins was found statistically significant based on patient’s survival times, 10 of which stem from alternative AltORF or non-coding RNA. From these proteins, 5 were selected as survival markers. Classification of patients based on the expression of these 5 proteins leads to a clear difference in survival. The expression of these 5 proteins was validated by immunofluorescence on an external cohort of 50 glioblastoma patients, with a similar correlation with their survival. Taken together, our work has enabled the characterization of new molecular regions within glioblastoma tissues based on protein expression which can help to guide glioblastoma prognosis and to improve the current glioblastoma classification.

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Section: Identification Of Alternative Proteinssupporting

confidence: 91%

Spatial reference and alternative proteome analysis of glioblastoma reveals molecular signatures and associates survival with specific markers

Duhamel

Drelich

Wisztorski

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…These pseudogenes, for which no protein has been observed yet, express their transcripts in glioma cell lines (Expression Atlas). Interestingly, the last one IP_079312, from the mRNA encoding EDARADD was correlated with a low survival rate in ovarian cancer patients 53 . Recently it has been demonstrated that pseudogenes can also be used as signatures for glioma prognosis.…”

Section: Discussionmentioning

confidence: 97%

Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival

et al. 2022

Self Cite

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Molecular heterogeneity is a key feature of glioblastoma that impedes patient stratification and leads to large discrepancies in mean patient survival. Here, we analyze a cohort of 96 glioblastoma patients with survival ranging from a few months to over 4 years. 46 tumors are analyzed by mass spectrometry-based spatially-resolved proteomics guided by mass spectrometry imaging. Integration of protein expression and clinical information highlights three molecular groups associated with immune, neurogenesis, and tumorigenesis signatures with high intra-tumoral heterogeneity. Furthermore, a set of proteins originating from reference and alternative ORFs is found to be statistically significant based on patient survival times. Among these proteins, a 5-protein signature is associated with survival. The expression of these 5 proteins is validated by immunofluorescence on an additional cohort of 50 patients. Overall, our work characterizes distinct molecular regions within glioblastoma tissues based on protein expression, which may help guide glioblastoma prognosis and improve current glioblastoma classification.

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“…However, its therapeutic benefits are frequently limited with the development of radiotherapy resistance. LncRNAs emerged as regulators in radioresistance ( Cardon et al, 2021 ). Our previous study suggested that high expression of KCNQ1OT1 was observed in stereotactic body radiotherapy-resistant cells and tissues, positively correlated with advanced clinical stage, and lower response rate to concurrent therapy.…”

Section: Significance Of Lncrnas In Gbm Malignant Phenotypesmentioning

confidence: 99%

Evolving Insights Into the Biological Function and Clinical Significance of Long Noncoding RNA in Glioblastoma

Liu

Chen

Wang

et al. 2022

Front. Cell Dev. Biol.

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Glioblastoma (GBM) is one of the most prevalent and aggressive cancers worldwide. The overall survival period of GBM patients is only 15 months even with standard combination therapy. The absence of validated biomarkers for early diagnosis mainly accounts for worse clinical outcomes of GBM patients. Thus, there is an urgent requirement to characterize more biomarkers for the early diagnosis of GBM patients. In addition, the detailed molecular basis during GBM pathogenesis and oncogenesis is not fully understood, highlighting that it is of great significance to elucidate the molecular mechanisms of GBM initiation and development. Recently, accumulated pieces of evidence have revealed the central roles of long noncoding RNAs (lncRNAs) in the tumorigenesis and progression of GBM by binding with DNA, RNA, or protein. Targeting those oncogenic lncRNAs in GBM may be promising to develop more effective therapeutics. Furthermore, a better understanding of the biological function and underlying molecular basis of dysregulated lncRNAs in GBM initiation and development will offer new insights into GBM early diagnosis and develop novel treatments for GBM patients. Herein, this review builds on previous studies to summarize the dysregulated lncRNAs in GBM and their unique biological functions during GBM tumorigenesis and progression. In addition, new insights and challenges of lncRNA-based diagnostic and therapeutic potentials for GBM patients were also introduced.

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Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs

Cited by 7 publications

References 87 publications

Spatial reference and alternative proteome analysis of glioblastoma reveals molecular signatures and associates survival with specific markers

Spatial reference and alternative proteome analysis of glioblastoma reveals molecular signatures and associates survival with specific markers

Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival

Evolving Insights Into the Biological Function and Clinical Significance of Long Noncoding RNA in Glioblastoma

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