Pseudogenes: Four Decades of Discovery

Salmena, Leonardo

doi:10.1007/978-1-0716-1503-4_1

Cited by 10 publications

(12 citation statements)

References 106 publications

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“…Pseudogenes, characteristic by high sequence similarity to functional parent genes, have long been regarded as “junk DNA” due to the presence of a variety of disabling mutations (e.g., insertions, deletions, and stop codons) that result in loss of function [ 20 ]. The advent of large-scale, pan-cancer studies has prompted many to reexamine the function of pseudogenes, highlighting their multifaceted roles in cancer biology [ 3 – 5 ]. Integrative analysis of multiomics data showed that pseduogenes can be transcribed and translated, and that pseudogenic RNA and protein can regulate the function of key cancer genes, including their parent genes [ 3 – 5 ].…”

Section: Discussionmentioning

confidence: 99%

“…Compelling data have linked pseudogene alterations with glioma biology and response to treatment [ 3 – 5 ]. DNA methylation is a critical layer of control for the pseudogene transcriptome [ 6 ] and has long been regarded as an ideal cancer biomarker [ 7 ]; therefore, the identification of clinical relevant alterations in DNA methylation of pseudogenes is of great importance.…”

Section: Introductionmentioning

confidence: 99%

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A Novel Pseudogene Methylation Signature to Predict Temozolomide Outcome in Non-G-CIMP Glioblastomas

Wang

Liu

et al. 2022

Journal of Oncology

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Objective. Alterations in the methylation state of pseudogenes may serve as clinically useful biomarkers of glioblastomas (GBMs) that do not have glioma-CpG island methylator phenotype (G-CIMP). Methods. Non-G-CIMP GBM datasets were included for evaluation, and a RISK-score signature was determined from the methylation state of pseudogene loci. Both bioinformatic and experimental analyses were performed for biological validation. Results. By integrating clinical information with DNA methylation microarray data, we screened a panel of eight CpGs from discovery cohorts of non-G-CIMP GBMs. Each CpG could accurately and independently predict the prognosis of patients under a treatment regime that combined radiotherapy (RT) and temozolomide (TMZ). The 8-CpG signature appeared to show opposite prognostic correlations between patients treated with RT/TMZ and those treated with RT monotherapy. The analyses further indicated that this signature had predictive value for TMZ efficacy because different survival benefits between RT/TMZ and RT therapies were observed in each risk subgroup. The incorporation of other risk factors, such as age and O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status, with our pseudogene methylation signature could provide precise risk classification. In vitro experimental data revealed that two locus-specific pseudogenes (ZNF767P and CLEC4GP1) may modulate TMZ resistance via distinct mechanisms in GBM cells. Conclusion. The biologically and clinically relevant RISK-score signature, based on pseudogene methylation loci, may offer information for predicting TMZ responses of non-G-CIMP GBMs, that is independent from, but complementary to, MGMT-based approaches.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Novel Pseudogene Methylation Signature to Predict Temozolomide Outcome in Non-G-CIMP Glioblastomas

Wang

Liu

et al. 2022

Journal of Oncology

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“…Such intersections suggest goals for the research program proposed here. The investigation of pseudo-genes was a successful example of such research [ 13 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 ]. In the future, a number of further in silico-testable hypotheses about the nature of genes could be included.…”

Section: The Virtual Gene Concept Can Define a Practical Research Pro...mentioning

confidence: 99%

“…Or are they more commonly a type of biological noise that results from open chromatin in transcriptionally active chromosomal domains? There are already many known examples of functional antisense [ 87 , 88 , 89 ], functional expressed pseudo-genes, and functional long non-coding RNAs [ 67 , 69 , 71 , 73 ]. The quantification of genome-wide trends is needed, now.…”

Section: The Virtual Gene Concept Can Define a Practical Research Pro...mentioning

confidence: 99%

Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science

Huminiecki

2021

Entropy

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Mendel proposed an experimentally verifiable paradigm of particle-based heredity that has been influential for over 150 years. The historical arguments have been reflected in the near past as Mendel’s concept has been diversified by new types of omics data. As an effect of the accumulation of omics data, a virtual gene concept forms, giving rise to genetical data science. The concept integrates genetical, functional, and molecular features of the Mendelian paradigm. I argue that the virtual gene concept should be deployed pragmatically. Indeed, the concept has already inspired a practical research program related to systems genetics. The program includes questions about functionality of structural and categorical gene variants, about regulation of gene expression, and about roles of epigenetic modifications. The methodology of the program includes bioinformatics, machine learning, and deep learning. Education, funding, careers, standards, benchmarks, and tools to monitor research progress should be provided to support the research program.

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“…Pseudogenes were considered nonfunctional genes because of loss of protein coding ability or without expression in cells ( 23 ). However, recent studies have found that some of them might deal an important role in regulating parental genes, and even some pseudogenes could be transcribed into RNA ( 24 , 25 ). Some pseudogenes are now considered a potential tumor suppressor gene or oncogene and played a crucial role in the occurrence and development of many pathophysiological processes ( 22 , 23 ).…”

Section: Introductionmentioning

confidence: 99%

ANXA2P2: A Potential Immunological and Prognostic Signature in Ovarian Serous Cystadenocarcinoma via Pan-Carcinoma Synthesis

Zhang

Chen

2022

Front. Oncol.

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BackgroundAlthough the effect of pseudogene ANXA2P2 on some tumors has been reported in a few literatures, the therapeutic potential and prognostic value of ANXA2P2 in ovarian serous cystadenocarcinoma (OV) have not been elucidated.MethodsThe correlation for ANXA2P2 expression patterns to prognostic characteristics, tumor immune microenvironment, immune cell infiltration level, tumor mutation burden (TMB), tumor microsatellite instability (MSI), drug sensitivity, and pathway function enrichment were investigated in pan-carcinoma via TCGA and GTEx databases. Subsequently, the role of ANXA2P2 expression levels in the pathway enrichments and prognosis prediction in OV were further explored using weighted correlation network analysis (WGCNA) analysis, gene mutation analysis, and risk-independent prognostic analysis.ResultsANXA2P2 was frequently overexpressed in a variety of tumors compared with normal tissues. The correlation analysis for prognostic characteristics, tumor immune microenvironment, immune cell infiltration level, TMB, MSI, drug sensitivity, and pathway function enrichment revealed that ANXA2P2 expression patterns might deal a significant impact on the pathogenesis, development, and prognosis of various tumors. Then, GSVA, GSEA, WGCNA, gene mutation, and independent prognostic analysis for OV have indicated that high expression in ANXA2P2 could be mostly enriched in TNF-α signaling-via-NF-κB, epithelial-mesenchymal transition, apical junction, IL-6-JAK STAT3 signaling, etc., which were also proved to act as crucial factors on tumorigenesis, development, invasion, and metastasis. The mutation of TP53 (94%), TTN (24%), and CSMD3 (9%) in the biological process of tumor had been confirmed by relevant studies. Finally, the independent prognostic analysis demonstrated that ANXA2P2 expression in OV contributes greatly to the dependability of 3- and 5-year survival prediction.ConclusionIn summary, our findings might provide a helpful foundation for prospective explorative researches, afford new strategies for the clinical treatment, deal prognosis prediction, and give new hope for OV patients.

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Pseudogenes: Four Decades of Discovery

Cited by 10 publications

References 106 publications

A Novel Pseudogene Methylation Signature to Predict Temozolomide Outcome in Non-G-CIMP Glioblastomas

A Novel Pseudogene Methylation Signature to Predict Temozolomide Outcome in Non-G-CIMP Glioblastomas

Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science

ANXA2P2: A Potential Immunological and Prognostic Signature in Ovarian Serous Cystadenocarcinoma via Pan-Carcinoma Synthesis

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