42 research outputs found
The interaction between cytosine methylation and processes of DNA replication and repair shape the mutational landscape of cancer genomes
© The Author(s) 2017. Methylated cytosines (5mCs) are frequently mutated in the genome. However, no studies have yet comprehensively analysed mutation-methylation associations across cancer types. Here we analyse 916 cancer genomes, together with tissue type-specific methylation and replication timing data. We describe a strong mutation-methylation association across colorectal cancer subtypes, most interestingly in samples with microsatellite instability (MSI) or Polymerase epsilon (POLE) exonuclease domain mutations. By analysing genomic regions with differential mismatch repair (MMR) efficiency, we suggest a possible role for MMR in the correction of 5mC deamination events, potentially accounting for the high rate of 5mC mutation accumulation in MSI tumours. Additionally, we propose that mutant POLE asserts a mutator phenotype specifically at 5mCs, and we find coding mutation hotspots in POLE-mutant cancers at highly-methylated CpGs in the tumour-suppressor genes APC and TP53. Finally, using multivariable regression models, we demonstrate that different cancers exhibit distinct mutation-methylation associations, with DNA repair influencing such associations in certain cancer genomes. Taken together, we find differential associations with methylation that are vital for accurately predicting expected mutation loads across cancer types. Our findings reveal links between methylation and common mutation and repair processes, with these mechanisms defining a key part of the mutational landscape of cancer genomes.Link_to_subscribed_fulltex
Bioinformatics analysis reveals biophysical and evolutionary insights into the 3-nitrotyrosine post-translational modification in the human proteome
Protein 3-nitrotyrosine is a post-translational modification that commonly arises from the nitration of tyrosine residues. This modification has been detected under a wide range of pathological conditions and has been shown to alter protein function. Whether 3-nitrotyrosine is important in normal cellular processes or is likely to affect specific biological pathways remains unclear. Using GPS-YNO2, a recently described 3-nitrotyrosine prediction algorithm, a set of predictions for nitrated residues in the human proteome was generated. In total, 9.27 per cent of the proteome was predicted to be nitratable (27 922/301 091). By matching the predictions against a set of curated and experimentally validated 3-nitrotyrosine sites in human proteins, it was found that GPS-YNO2 is able to predict 73.1 per cent (404/553) of these sites. Furthermore, of these sites, 42 have been shown to be nitrated endogenously, with 85.7 per cent (36/42) of these predicted to be nitrated. This demonstrates the feasibility of using the predicted dataset for a whole proteome analysis. A comprehensive bioinformatics analysis was subsequently performed on predicted and all experimentally validated nitrated tyrosine. This found mild but specific biophysical constraints that affect the susceptibility of tyrosine to nitration, and these may play a role in increasing the likelihood of 3-nitrotyrosine to affect processes, including phosphorylation and DNA binding. Furthermore, examining the evolutionary conservation of predicted 3-nitrotyrosine showed that, relative to non-nitrated tyrosine residues, 3-nitrotyrosine residues are generally less conserved. This suggests that, at least in the majority of cases, 3-nitrotyrosine is likely to have a deleterious effect on protein function and less likely to be important in normal cellular function. © 2013 The Authors.Link_to_subscribed_fulltex
Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples
© Ma et al. Massively parallel DNA sequencing enables the detection of thousands of germline and somatic single nucleotide variants (SNVs) in cancer samples. The functional analysis of these mutations is often carried out through in silico predictions, with further downstream experimental validation rarely performed. Here, we examine the potential of using mass spectrometry-based proteomics data to further annotate the function of SNVs in cancer samples. RNA-seq and whole genome sequencing (WGS) data from Jurkat cells were used to construct a custom database of single amino acid variant (SAAV) containing peptides and identified over 1,000 such peptides in two Jurkat proteomics datasets. The analysis enabled the detection of a truncated form of splicing regulator YTHDC1 at the protein level. To extend the functional annotation further, a Jurkat phosphoproteomics dataset was analysed, identifying 463 SAAV containing phosphopeptides. Of these phosphopeptides, 24 SAAVs were found to directly impact the phosphorylation event through the creation of either a phosphorylation site or a kinase recognition motif. We identified a novel phosphorylation site created by a SAAV in splicing factor SF3B1, a protein that is frequently mutated in leukaemia. To our knowledge, this is the first study to use phosphoproteomics data to directly identify novel phosphorylation events arising from the creation of phosphorylation sites by SAAVs. Our study reveals multiple functional mutations impacting the splicing pathway in Jurkat cells and demonstrates potential benefits of an integrative proteogenomics analysis for high-throughput functional annotation of SNVs in cancer.Link_to_subscribed_fulltex
The search for cis-regulatory driver mutations in cancer genomes
With the advent of high-throughput and relatively inexpensive whole-genome sequencing technology, the focus of cancer research has begun to shift toward analyses of somatic mutations in non-coding cis-regulatory elements of the cancer genome. Cis-regulatory elements play an important role in gene regulation, with mutations in these elements potentially resulting in changes to the expression of linked genes. The recent discoveries of recurrent TERT promoter mutations in melanoma, and recurrent mutations that create a super-enhancer regulating TAL1 expression in T-cell acute lymphoblastic leukaemia (T-ALL), have sparked significant interest in the search for other somatic cis-regulatory mutations driving cancer development. In this review, we look more closely at the TERT promoter and TAL1 enhancer alterations and use these examples to ask whether other cis-regulatory mutations may play a role in cancer susceptibility. In doing so, we make observations from the data emerging from recent research in this field, and describe the experimental and analytical approaches which could be adopted in the hope of better uncovering the true functional significance of somatic cis-regulatory mutations in cancer.Link_to_subscribed_fulltex
Functional Mutations Form at CTCF-Cohesin Binding Sites in Melanoma Due to Uneven Nucleotide Excision Repair across the Motif
© 2016 The Author(s) CTCF binding sites are frequently mutated in cancer, but how these mutations accumulate and whether they broadly perturb CTCF binding are not well understood. Here, we report that skin cancers exhibit a highly specific asymmetric mutation pattern within CTCF motifs attributable to ultraviolet irradiation and differential nucleotide excision repair (NER). CTCF binding site mutations form independently of replication timing and are enriched at sites of CTCF/cohesin complex binding, suggesting a role for cohesin in stabilizing CTCF-DNA binding and impairing NER. Performing CTCF ChIP-seq in a melanoma cell line, we show CTCF binding site mutations to be functional by demonstrating allele-specific reduction of CTCF binding to mutant alleles. While topologically associating domains with mutated CTCF anchors in melanoma contain differentially expressed cancer-associated genes, CTCF motif mutations appear generally under neutral selection. However, the frequency and potential functional impact of such mutations in melanoma highlights the need to consider their impact on cellular phenotype in individual genomes.Link_to_subscribed_fulltex
Restoration ecophysiology: an ecophysiological approach to improve restoration strategies and outcomes in severely disturbed landscapes
As human activities destroy and degrade the world's ecosystems at unprecedented scales, there is a growing need for evidence-based methods for ecological restoration if we are to preserve biodiversity and ecosystem services. Mining represents one of the most severe anthropogenic disturbances, often necessitating intensive intervention to restore the most basic attributes of native ecosystems. Despite examples of successful mine-site restoration, re-establishing native vegetation in these degraded landscapes remains a significant challenge. Plant ecophysiology-the study of the interactions between plants and the environment-can provide a useful framework for evaluating and guiding mine-site restoration. By understanding the physiological mechanisms that allow plants to establish and persist in these highly disturbed environments, practitioners may be able to improve restoration outcomes. Specifically, methods in plant ecophysiology can inform site preparation and the selection of plant material for restoration projects, aid in monitoring restoration progress by providing additional insight into plant performance, and ultimately improve our ability to predict restoration trajectories. Here, we review the challenges and benefits of integrating an ecophysiological perspective to mine-site restoration in Western Australia, a global hotspot of biodiversity and mining operations. Using case studies and examples from the region's diverse ecosystems, we illustrate how an ecophysiological approach can guide the restoration of some of the world's most severely disturbed landscapes. With careful selection of study species and traits and consideration of the specific environmental conditions and stressors within a site, the restoration ecophysiology framework outlined here has the potential to inform restoration strategies across ecosystems
Cancer-Associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression
© 2017 The Author(s). Cancer is a multifactorial disease driven by a combination of genetic and environmental factors. Many cancer driver mutations have been characterised in protein-coding regions of the genome. However, mutations in noncoding regions associated with cancer have been less investigated. G-quadruplex (G4) nucleic acids are four-stranded secondary structures formed in guanine-rich sequences and prevalent in the regulatory regions. In this study, we used published whole cancer genome sequence data to find mutations in cancer patients that overlap potential RNA G4-forming sequences in 5ⲠUTRs. Using RNAfold, we assessed the effect of these mutations on the thermodynamic stability of predicted RNA G4s in the context of full-length 5ⲠUTRs. Of the 217 identified mutations, we found that 33 are predicted to destabilise and 21 predicted to stabilise potential RNA G4s. We experimentally validated the effect of destabilising mutations in the 5ⲠUTRs of BCL2 and CXCL14 and one stabilising mutation in the 5ⲠUTR of TAOK2. These mutations resulted in an increase or a decrease in translation of these mRNAs, respectively. These findings suggest that mutations that modulate the G4 stability in the noncoding regions could act as cancer driver mutations, which present an opportunity for early cancer diagnosis using individual sequencing information.Link_to_subscribed_fulltex
Lynch Syndrome Associated with Two MLH1 Promoter Variants and Allelic Imbalance of MLH1 Expression
© 2015 The Authors. **Human Mutation published by Wiley Periodicals, Inc. Lynch syndrome is a hereditary cancer syndrome caused by a constitutional mutation in one of the mismatch repair genes. The implementation of predictive testing and targeted preventative surveillance is hindered by the frequent finding of sequence variants of uncertain significance in these genes. We aimed to determine the pathogenicity of previously reported variants (c.-28A > G and c.-7C > T) within the MLH1 5â²untranslated region (UTR) in two individuals from unrelated suspected Lynch syndrome families. We investigated whether these variants were associated with other pathogenic alterations using targeted high-throughput sequencing of the MLH1 locus. We also determined their relationship to gene expr ession and epigenetic alterations at the promoter. Sequencing revealed that the c.-28A > G and c.-7C > T variants were the only potentially pathogenic alterations within the MLH1 gene. In both individuals, the levels of transcription from the variant allele were reduced to 50% compared with the wild-type allele. Partial loss of expression occurred in the absence of constitutional epigenetic alterations within the MLH1 promoter. We propose that these variants may be pathogenic due to constitutional partial loss of MLH1 expression, and that this may be associated with intermediate penetrance of a Lynch syndrome phenotype. Our findings provide further evidence of the potential importance of noncoding variants in the MLH1 5â²UTR in the pathogenesis of Lynch syndrome.Link_to_subscribed_fulltex
Microbial inoculation to improve plant performance in mine-waste substrates: A test using pigeon pea (Cajanus cajan)
Mining activities alter soil physicochemical and biological properties that are critical for plant establishment. Revitalisation of soil biological properties via microbial inoculations can potentially be adopted to improve vegetation restoration. Here, we evaluate the feasibility of using beneficial microorganisms in the form of commercially available inoculants to enhance plant performance in a non-toxic and infertile mine-waste substrate, using pigeon pea [Cajanus cajan (L) Millsp.] as a test plant. Six treatments were established to investigate the effects of inoculants (Bradyrhizobium spp., microbial mix and uninoculated controls) and water availability (low and moderate) in a factorial design over 6 months. Plant performance was determined by physiological parameters (leaf gas exchange, leaf carbon, nitrogen and stable isotopes) and growth (height and biomass). Plant xylem sap phytohormones were measured to determine the plants' physiological status and effects of inoculation treatments. Results revealed that water had a greater effect on plant growth than inoculation treatments. Inoculation treatments, however, improved some physiological parameters. This study suggests that physical conditions such as soil moisture and nutrient availability may occlude more subtle (direct or interactive) effects of beneficial soil microbes on plant growth and plant condition. Prior knowledge on the biological and physicochemical properties of the soil to be amended, and on plant species-specific responses, would be needed to customise microbial inoculants for maximum benefits to ecological restoration, to support future adoption of this practice