Pan-Cancer Repository of Validated Natural and Cryptic mRNA Splicing Mutations

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 351,423 of these validated mutations, the majority of which (69.1%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 117,951 unique mutations which weaken or abolish natural splice sites, and 244,415 mutations which strengthen cryptic splice sites (10,943 affect both simultaneously). 27,803 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon “Validated Splicing Mutations” either separately or in aggregate alongside other Beacons through the public Beacon Network (http://www.beacon-network.org/#/search?beacon=cytognomix), as well as through our website (https://validsplicemut.cytognomix.com/).

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Pan-cancer repository of validated natural and cryptic mRNA splicing mutations

F1000Research ◽

10.12688/f1000research.17204.2 ◽

2019 ◽

Vol 7 ◽

pp. 1908 ◽

Cited By ~ 1

Author(s):

Ben C. Shirley ◽

Eliseos J. Mucaki ◽

Peter K. Rogan

Keyword(s):

Splice Junction ◽

Cancer Genome ◽

Mrna Splicing ◽

The Cancer Genome Atlas ◽

Splice Sites ◽

Global Alliance ◽

Multiple Tumor ◽

Link Type ◽

Splicing Mutations ◽

Single Nucleotide Polymorphism Database

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon “Validated Splicing Mutations” either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website.

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Pan-cancer repository of validated natural and cryptic mRNA splicing mutations

F1000Research ◽

10.12688/f1000research.17204.3 ◽

2019 ◽

Vol 7 ◽

pp. 1908 ◽

Cited By ~ 3

Author(s):

Ben C. Shirley ◽

Eliseos J. Mucaki ◽

Peter K. Rogan

Keyword(s):

Gene Expression ◽

Cancer Genome ◽

Mrna Splicing ◽

The Cancer Genome Atlas ◽

Splice Sites ◽

Global Alliance ◽

Multiple Tumor ◽

Link Type ◽

Splicing Mutations ◽

Molecular Phenotypes

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. An algorithm was developed to classify variants into splicing molecular phenotypes that integrates germline heterozygosity, degree of information change and impact on expression. The classification thresholds were calibrated against the ClinVar clinical database phenotypic assignments. Variants are partitioned into allele-specific alternative splicing, likely aberrant and aberrant splicing phenotypes. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon “Validated Splicing Mutations” either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website. The website provides additional information, such as a visual representation of supporting RNAseq results, gene expression in the corresponding normal tissues, and splicing molecular phenotypes.

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Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis

F1000Research ◽

10.12688/f1000research.5654.1 ◽

2014 ◽

Vol 3 ◽

pp. 282 ◽

Cited By ~ 47

Author(s):

Natasha G. Caminsky ◽

Eliseos J. Mucaki ◽

Peter K. Rogan

Keyword(s):

Splice Site ◽

Genetic Disease ◽

Mrna Splicing ◽

Regulatory Sequences ◽

Splice Sites ◽

Review Of The Literature ◽

Cryptic Splice Site ◽

Broad Perspective ◽

Genomic Variants ◽

Splicing Mutations

The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.

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Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis

F1000Research ◽

10.12688/f1000research.5654.2 ◽

2015 ◽

Vol 3 ◽

pp. 282 ◽

Cited By ~ 5

Author(s):

Natasha G. Caminsky ◽

Eliseos J. Mucaki ◽

Peter K. Rogan

Keyword(s):

Splice Site ◽

Genetic Disease ◽

Mrna Splicing ◽

Regulatory Sequences ◽

Splice Sites ◽

Review Of The Literature ◽

Cryptic Splice Site ◽

Broad Perspective ◽

Genomic Variants ◽

Splicing Mutations

The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.

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U1 small nuclear RNAs with altered specificity can be stably expressed in mammalian cells and promote permanent changes in pre-mRNA splicing.

Molecular and Cellular Biology ◽

10.1128/mcb.13.5.2666 ◽

1993 ◽

Vol 13 (5) ◽

pp. 2666-2676 ◽

Cited By ~ 14

Author(s):

J B Cohen ◽

S D Broz ◽

A D Levinson

Keyword(s):

Splice Site ◽

Mammalian Cells ◽

Mrna Processing ◽

Mrna Splicing ◽

Small Nuclear Rna ◽

Splice Sites ◽

Gene Complementation ◽

Small Nuclear Rnas ◽

Nuclear Rna ◽

Mutant Genes

Pre-mRNA 5' splice site activity depends, at least in part, on base complementarity to U1 small nuclear RNA. In transient coexpression assays, defective 5' splice sites can regain activity in the presence of U1 carrying compensatory changes, but it is unclear whether such mutant U1 RNAs can be permanently expressed in mammalian cells. We have explored this issue to determine whether U1 small nuclear RNAs with altered specificity may be of value to rescue targeted mutant genes or alter pre-mRNA processing profiles. This effort was initiated following our observation that U1 with specificity for a splice site associated with an alternative H-ras exon substantially reduced the synthesis of the potentially oncogenic p21ras protein in transient assays. We describe the development of a mammalian complementation system that selects for removal of a splicing-defective intron placed within a drug resistance gene. Complementation was observed in proportion to the degree of complementarity between transfected mutant U1 genes and different defective splice sites, and all cells selected in this manner were found to express mutant U1 RNA. In addition, these cells showed specific activation of defective splice sites presented by an unlinked reporter gene. We discuss the prospects of this approach to permanently alter the expression of targeted genes in mammalian cells.

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Enolase 1 Correlated With Cancer Progression and Immune-Infiltrating in Multiple Cancer Types: A Pan-Cancer Analysis

Frontiers in Oncology ◽

10.3389/fonc.2020.593706 ◽

2021 ◽

Vol 10 ◽

Author(s):

Wenhua Xu ◽

Wenna Yang ◽

Chunfeng Wu ◽

Xiaocong Ma ◽

Haoyu Li ◽

...

Keyword(s):

Cancer Progression ◽

Stress Protein ◽

Enrichment Analysis ◽

Tumor Stage ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Multiple Cancer ◽

Clinical Prognosis ◽

Multiple Tumor ◽

Normal Tissues

Enolase 1 (ENO1) is an oxidative stress protein expressed in endothelial cells. This study aimed to investigate the correlation of ENO1 with prognosis, tumor stage, and levels of tumor-infiltrating immune cells in multiple cancers. ENO1 expression and its influence on tumor stage and clinical prognosis were analyzed by UCSC Xena browser, Gene Expression Profiling Interactive Analysis (GEPIA), The Cancer Genome Atlas (TCGA), and GTEx Portal. The ENO1 mutation analysis was performed by cBio Portal, and demonstrated ENO1 mutation (1.8%) did not impact on tumor prognosis. The relationship between ENO1 expression and tumor immunity was analyzed by Tumor Immune Estimation Resource (TIMER) and GEPIA. The potential functions of ENO1 in pathways were investigated by Gene Set Enrichment Analysis. ENO1 expression was significantly different in tumor and corresponding normal tissues. ENO1 expression in multiple tumor tissues correlated with prognosis and stage. ENO1 showed correlation with immune infiltrates including B cells, CD8+ and CD4+ T cells, macrophages, neutrophils, and dendritic cells, and tumor purity. ENO1 was proved to be involved in DNA replication, cell cycle, apoptosis, glycolysis process, and other processes. These findings indicate that ENO1 is a potential prognostic biomarker that correlates with cancer progression immune infiltration.

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Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants

10.21203/rs.2.12748/v2 ◽

2019 ◽

Author(s):

Raphael Leman ◽

Hélène Tubeuf ◽

Sabine Raad ◽

Isabelle Tournier ◽

Céline Derambure ◽

...

Keyword(s):

Branch Point ◽

Mrna Splicing ◽

Large Set ◽

Branch Points ◽

Splice Sites ◽

Prediction Tools ◽

Mature Mrna ◽

Bioinformatics Tools ◽

The Impact

Abstract Background: Branch points (BPs) map within short motifs upstream of acceptor splice sites (3’ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3’ss. Results: We used a large set of constitutive and alternative human 3’ss collected from Ensembl (n = 264,787 3’ss) and from in-house RNAseq experiments (n = 51,986 3’ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3’ss (99.48 % and 65.84 % accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17 %. Conclusions: Our investigations revealed that Branchpointer was optimal to detect BPs upstream of 3’ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area. Keywords: Branch Point, Prediction, RNA, Benchmark, HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR, RNABPS, Variants

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Spontaneous splicing mutations at the dihydrofolate reductase locus in Chinese hamster ovary cells

Molecular and Cellular Biology ◽

10.1128/mcb.6.6.1926-1935.1986 ◽

1986 ◽

Vol 6 (6) ◽

pp. 1926-1935

Author(s):

P J Mitchell ◽

G Urlaub ◽

L Chasin

Keyword(s):

Amino Acid ◽

Dihydrofolate Reductase ◽

Splice Site ◽

Chinese Hamster Ovary ◽

Chinese Hamster Ovary Cells ◽

Chinese Hamster ◽

Splice Sites ◽

Ovary Cells ◽

Splicing Mutations ◽

Intron 4

We isolated and characterized three spontaneous mutants of Chinese hamster ovary cells that were deficient in dihydrofolate reductase activity. All three mutants contained no detectable enzyme activity and produced dihydrofolate reductase mRNA species that were shorter than those of the wild type by about 120 bases. Six exons are normally represented in this mRNA; exon 5 was missing in all three mutant mRNAs. Nuclease S1 analysis of the three mutants indicated that during the processing of the mutant RNA, exon 4 was spliced to exon 6. The three mutant genes were cloned, and the regions around exons 4 and 5 were sequenced. In one mutant, the GT dinucleotide at the 5' end of intron 5 had changed to CT. In a second mutant, the first base in exon 5 had changed from G to T. In a revertant of this mutant, this base was further mutated to A, a return to a purine. Approximately 25% of the mRNA molecules in the revertant were spliced correctly to produce an enzyme with one presumed amino acid change. In the third mutant, the AG at the 3' end of intron 4 had changed to AA. A mutation that partially reversed the mutant phenotype had changed the dinucleotide at the 5' end of intron 4 from GT to AT. The splicing pattern in this revertant was consistent with the use of cryptic donor and acceptor splice sites close to the original sites to produce an mRNA with three base changes and a protein with two amino acid changes. These mutations argue against a scanning model for the selection of splice site pairs and suggest that only a single splice site need be inactivated to bring about efficient exon skipping (a regulatory mechanism for some genes). The fact that all three mutants analyzed exhibited exon 5 splicing mutations indicates that these splice sites are hot spots for spontaneous mutation.

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Mechanisms for selecting 5′ splice sites in mammalian pre-mRNA splicing

Trends in Genetics ◽

10.1016/0168-9525(94)90233-x ◽

1994 ◽

Vol 10 (3) ◽

pp. 100-106 ◽

Cited By ~ 129

Author(s):

David S. Horowitz ◽

Adrian R. Krainer

Keyword(s):

Mrna Splicing ◽

Splice Sites

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