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Since genome instability can drive cancer initiation and progression, cells have evolved highly effective and ubiquitous DNA Damage Response (DDR) programs. However, some cells, in skin for example, are normally exposed to high levels of DNA damaging agents. Whether such high-risk cells possess lineage-specific mechanisms that tailor DNA repair to the tissue remains largely unknown. Here we show, using melanoma as a model, that the microphthalmia-associated transcription factor MITF, a lineage addition oncogene that coordinates many aspects of melanocyte and melanoma biology, plays a non-transcriptional role in shaping the DDR. On exposure to DNA damaging agents, MITF is phosphorylated by ATM/DNA-PKcs, and unexpectedly its interactome is dramatically remodelled; most transcription (co)factors dissociate, and instead MITF interacts with the MRE11-RAD50-NBS1 (MRN) complex. Consequently, cells with high MITF levels accumulate stalled replication forks, and display defects in homologous recombination-mediated repair associated with impaired MRN recruitment to DNA damage. In agreement, high MITF levels are associated with increased SNV burden in melanoma. Significantly, the SUMOylation-defective MITF-E318K melanoma predisposition mutation recapitulates the effects of ATM/DNA-PKcs-phosphorylated MITF. Our data suggest that a non-transcriptional function of a lineage-restricted transcription factor contributes to a tissue-specialised modulation of the DDR that can impact cancer initiation.

DNA methylation (DNAm) has pervasive effects on gene expression and associations with ageing-related traits. Here we describe monocyte DNAm responses to inflammatory stimuli across 192 individuals. We find that, unlike the similarly widespread changes in gene expression elicited by LPS and IFNγ, DNAm is markedly more sensitive to LPS. Exposure to LPS caused differential methylation at 20,858 immune-modulated CpGs (imCpGs) which display distinct genomic localisation and transcription factor usage, dependent upon whether methylation is lost or gained. Demethylated imCpGs are profoundly enriched for enhancers, and are over-represented by genes implicated in human diseases, most notably cancer. We find LPS-induced demethylation follows hydroxymethylation and for most sites the degree of demethylation correlates with baseline signal. Notably, we find LPS exposure triggers gain in epigenetic age by approximately 6 months, identifying a potential cause of accelerated epigentic aging which has diverse negative health associations. Finally, we explore the effect of genetic variation on LPS-induced changes in DNAm, identifying 209 imCpGs under genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of human disease associated loci that also modulate imCpG formation.In summary, our findings suggest innate immune activity continually remodels DNAm in a highly punctate, enhancerenriched fashion that is under tight genetic control and predominantly involves genes commonly mutated in cancer.

Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.

Bisulfite sequencing has been the gold standard for mapping DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) for decades1–4. However, this harsh chemical treatment degrades the majority of the DNA and generates sequencing libraries with low complexity2,5,6. Here, we present a bisulfite-free and base-level-resolution sequencing method, TET-assisted pyridine borane sequencing (TAPS), for detection of 5mC and 5hmC. TAPS combines ten-eleven translocation (TET) oxidation of 5mC and 5hmC to 5-carboxylcytosine (5caC) with pyridine borane reduction of 5caC to dihydrouracil (DHU). Subsequent PCR converts DHU to thymine, enabling a C-to-T transition of 5mC and 5hmC. TAPS detects modifications directly with high sensitivity and specificity, without affecting unmodified cytosines. This method is nondestructive, preserving DNA fragments over 10 kilobases long. We applied TAPS to the whole-genome mapping of 5mC and 5hmC in mouse embryonic stem cells and show that, compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing costs, thus enabling higher quality, more comprehensive and cheaper methylome analyses. A new method using mild chemical reactions and enzymatic oxidation allows nondestructive sequencing of 5-methylcytosine and 5-hydroxymethylcytosine with base-level resolution.

Epigenetic DNA modifications are essential for normal cell function in vertebrates, but they can also be hotspots of mutagenesis. Methylcytosine in particular has long been known to be less stable than other nucleotides and spontaneously deaminates to thymine. Beyond this well-established phenomenon, however, the influence of epigenetic marks on mutagenesis has recently become an active field of investigation. In this review, we summarize current knowledge of the interactions between different DNA modifications and other mutagenic processes. External mutagens, such as UV light or smoking carcinogens, affect modified cytosines differently from unmodified ones, and modified cytosine can in some cases be protective rather than mutagenic. Notably, cell-intrinsic processes, such as DNA replication, also appear to influence the mutagenesis of modified cytosines. Altogether, evidence is accumulating to show that epigenetic changes have a profound influence on tissue-specific mutation accumulation.

OBJECTIVE The patients after Mustard and Senning corrections of transposition of the great arteries (TGA) are at an increased risk of unexpected death. The aim of this study was to identify markers allowing risk stratification of patients after atrial switch correction of TGA to provide them with optimum care. METHODS AND RESULTS In this study, 87 patients were retrospectively evaluated after atrial switch correction of TGA followed-up between 2005 and 2015. The mortality during the follow-up was 9% (8 cardiac deaths). Markers significantly predictive of death using univariable Cox proportional hazard ratio survival analysis were: N-terminal pro-B-type natriuretic peptide (NT-proBNP), ejection fraction and end-diastolic dimension of the systemic right ventricle, mitral E, e', and s'. Surprisingly, the Doppler parameters of mitral valve in subpulmonary ventricle were more important for prognosis than those of systemic tricuspid valve. In multivariable analysis, the only independent predictors of mortality were NT-proBNP (P = .00048; AUC 0.97) and the velocity of early diastolic filling (mitral E) in subpulmonary ventricle (P = .01815; AUC 0.81). According to Kaplan-Meier survival analysis, patients with NT-proBNP > 1000 pg/ml are at high risk of death. Patients with mitral E

The raw data is available on Mendeley at https://data.mendeley.com/datasets/hfpbctm7tg/draft?a=1c91e494-cadc-4be0-a8ff-91d8736a28e7 © The Author(s) 2019. Expression of the mismatch repair gene MutL homolog 1 (MLH1) is silenced in a clinically important subgroup of sporadic colorectal cancers. These cancers exhibit hypermutability with microsatellite instability (MSI) and differ from microsatellite-stable (MSS) colorectal cancers in both prognosis and response to therapies. Loss of MLH1 is usually due to epigenetic silencing with associated promoter methylation; coding somatic mutations rarely occur. Here we use the presence of a colorectal cancer (CRC) risk variant (rs1800734) within the MLH1 promoter to investigate the poorly understood mechanisms of MLH1 promoter methylation and loss of expression. We confirm the association of rs1800734 with MSI+ but not MSS cancer risk in our own data and by meta-analysis. Using sensitive allele-specific detection methods, we demonstrate that MLH1 is the target gene for rs1800734 mediated cancer risk. In normal colon tissue, small allele-specific differences exist only in MLH1 promoter methylation, but not gene expression. In contrast, allele-specific differences in both MLH1 methylation and expression are present in MSI+ cancers. We show that MLH1 transcriptional repression is dependent on DNA methylation and can be reversed by a methylation inhibitor. The rs1800734 allele influences the rate of methylation loss and amount of re-expression. The transcription factor TFAP4 binds to the rs1800734 region but with much weaker binding to the risk than the protective allele. TFAP4 binding is absent on both alleles when promoter methylation is present. Thus we propose that TFAP4 binding shields the protective rs1800734 allele of the MLH1 promoter from BRAF induced DNA methylation more effectively than the risk allele. Funding was provided by a Medical Research Council New Investigator Research Grant (MR/P000738/1). Core funding to the Wellcome Trust Centre for Human Genetics was provided by the Wellcome Trust (090532/Z/09/Z). D.T., N.S. and D.F. were supported by the EPIGENOMICS FLAGSHIP PROJECT- EPIGEN (project number 08934412) and by University of Insubria. M.T. and S.K. were funded by Ludwig Cancer Research.

Uvod: Zajistěni dobre kvality života je důležitý cil lecby pacientů s komplexni cyanotickou vrozenou srdecni vadou (VSV). V literatuře vsak neexistuje shoda o kvalitě života těchto pacientů. Cilem nasi studie bylo zhodnoceni kvality života a výskytu depresi u dospělých s původně komplexni cyanotickou VSV v dlouhodobem odstupu od operace. Metody: Vysetřili jsme celkem 212 dospělých po operaci komplexni cyanoticke VSV a 86 zdravých kontrol pomoci dotazniku hodnoceni kvality života SF-36 a Zungova dotazniku hodnoceni deprese. Vsichni pacienti byli dale dotazani na subjektivni hodnoceni vlivu VSV na jejich život, na fyzicke aktivity, funkcni třidu NYHA, vzdělani, zaměstnani, pocet děti a vsichni podstoupili echokardiograficke vysetřeni. Výsledky byly srovnany se skupinou 32 neoperovaných pacientů s komplexni cyanotickou VSV, jejichž výsledky jsme publikovali v minulosti. Výsledky: Výskyt deprese se významně nelisil mezi skupinou operovaných s VSV a zdravými kontrolami. Těžka deprese byla u 8,5 % pacientů s operovanou komplexni cyanotickou VSV a u 7 % zdravých kontrol (p = 0,816). Mezi neoperovanými pacienty s perzistujici cyanozou byl výskyt těžke deprese významně vyssi (28,1 %) oproti operovaným (p = 0,003). Kvalita života hodnocena pomoci dotazniku SF-36 se významně nelisila mezi pacienty s operovanými komplexnimi VSV a kontrolami, kromě horsiho vnimani obecneho zdravi, hodnoceni fyzických funkci a fyzickeho omezeni cinnosti. Zavěr: Pacienti s operovanou komplexni cyanotickou VSV maji v dospělosti dobrou kvalitu života, srovnatelnou s kontrolni skupinou zdravých jedinců, zatimco neoperovani pacienti s perzistujici cyanozou u komplexni VSV maji významně vyssi pocet depresi. © 2019, CKS.

V poslednich deseti letech bylo na Kardiochirurgickem odděleni v Nemocnici Na Homolce (NNH) provedeno celkem 844 operaci u 805 dospělých s vrozenou srdecni vadou (VSV). Median věku operovaných byl 37 let (mezikvartilove rozpěti 25-49, celkove rozpěti 16-81 let). Operace komplexnich a vzacných VSV tvořily 47 %. Ve 44 % (u 354 pacientů) se jednalo o reoperaci po předchozi operaci v dětstvi ci dospělosti, ve 14 % (113 pacientů) se jednalo o opakovanou reoperaci. Kombinovane výkony byly provedeny v 70 % připadů.Celkova 30denni mortalita cinila v celem souboru 1,36 %; hospitalizacni mortalita 1,7 %. Průměrne pětilete přeživani po operaci VSV v NNH cinilo 97 %.Mezi významne rizikove faktory casneho i pozdniho umrti po operaci VSV patřily symptomy ve třidě NYHA III-IV (p < 0,0001; OR 30,8), anamneza městnaveho srdecni selhani (p = 0,001; OR 6,7), cyanoza (p < 0,0001; OR 60,5), pocet předchozich operaci (p = 0,00033), přitomnost mechanicke chlopenni protezy (p = 0,0032; OR 3,7) a univentrikularni cirkulace (p = 0,0276; OR 5,4). Statisticke významnosti pro riziko umrti nedosahly arytmie (p = 0,078), plicni hypertenze (p = 0,072), věk v době operace (p = 0,372) a pohlavi (p = 0,48).Centralizace pece o dospěle s VSV do center s vysokým poctem výkonů a zkusenostmi přinasi velmi dobre chirurgicke výsledky s nizkou casnou i pozdni mortalitou.Důležita je vcasna indikace operace a odstraněni vsech rezidualnich nalezů kombinovaným výkonem. Přitomnost dětskeho kardiochirurga je nezbytna u operaci komplexnich VSV.

Background DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures—each representing a mutagenic process—derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions. Results We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication. The properties of these associations are distinct for different signatures and shed new light on several mutagenic processes. For example, our results suggest that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. Conclusions Together, our results indicate an interaction between DNA replication, the associated damage repair, and most mutagenic processes. Electronic supplementary material The online version of this article (10.1186/s13059-018-1509-y) contains supplementary material, which is available to authorized users.

Bisulfite sequencing has been the gold standard for mapping DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) for decades

The deamination of unmodified cytosine to uracil by treatment with bisulfite has for decades been the gold standard for sequencing epigenetic DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). However, this harsh chemical reaction degrades the majority of the DNA and generates sequencing libraries with low complexity. Here, we present a novel bisulfite-free and base-resolution sequencing method, TET Assisted Pic-borane Sequencing (TAPS), for detection of 5mC and 5hmC. TAPS relies on mild reactions, detects modifications directly without affecting unmodified cytosines and can be adopted to detect other cytosine modifications. Compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing costs, enabling higher quality, more comprehensive and cheaper methylome analyses.One Sentence SummaryA bisulfite-free and base-resolution method to directly sequence epigenetically modified cytosine.

Table S1. Overview of the used whole-genome sequencing samples. (PDF 211 kb)

Table S2. Overview of the strand asymmetry and correlation with replication timing in mutational signatures. (PDF 205 kb)

Review history. (DOCX 64 kb)

Figures S1â S33. Supplementary figures. (PDF 6116 kb)

Transitions of cytosine to thymine in CpG dinucleotides are the most frequent type of mutations observed in cancer. This increased mutability is commonly explained by the presence of 5-methylcytosine (5mC) and its spontaneous hydrolytic deamination into thymine. Here, we describe observations that question whether spontaneous deamination alone causes the elevated mutagenicity of 5mC. Tumours with somatic mutations in DNA mismatch-repair genes or in the proofreading domain of DNA polymerase ε (Pol ε) exhibit more 5mC to T transitions than would be expected, given the kinetics of hydrolytic deamination. This enrichment is asymmetrical around replication origins with a preference for the leading strand template, in particular in methylated cytosines flanked by guanines (GCG). Notably, GCG to GTG mutations also exhibit strand asymmetry in mismatch-repair and Pol ε wild-type tumours. Together, these findings suggest that mis-incorporation of A opposite 5mC during replication of the leading strand might be a contributing factor in the mutagenesis of methylated cytosine.

Gastric and esophageal adenocarcinomas (G/EAC) exhibit a characteristic pattern of somatic variants, known as signature 17. Signature 17 associates with high mutation burden, elevated neoantigen levels and a potential sensitivity to cell cycle inhibitors. Signature 17 correlates with poor survival, and is increased in cancer patients with a history of the common pre-malignant lesion called Barrett’s esophagus. We recently showed that oxidative damage during DNA replication is a likely source of signature 17; however this hypothesis remains to be validated. Intriguingly, we observe signature 17 arising in clonally expanded primary mouse cells (Hupki MEF) and in mouse models of liver cancer. Here, we aim to identify the mechanisms underlying signature 17 by mining TCGA and ICGC data, as well as generating genome-wide molecular profiles of relevant experimental cell systems. Mutational signatures were extracted from exome and whole-genome sequencing (WGS) data of over 460 G/EAC tumors. Pathway analysis of RNA-seq data from matching samples was performed using NIH DAVID. Exposure to signature 17 was next assessed with regards to clinico-pathologic data. Lastly, we compared the asymmetry of signature 17 mutations around replication origins and early/late replicating regions in WGS data from MEF cells and G/EAC cancers. Comparing the transcriptomes of signature 17-high and -low tumors implicated cell proliferation, regulation of apoptosis, DNA damage response and repair, oxidoreductase activity and gastric acid secretion as relevant pathways. We found positive associations between signature 17 intensity and Barrett’s esophagus history, poorer survival, and microsatellite instability. MEF WGS data revealed signature 17 enrichment in late-replicating genomic regions and on the lagging strand, analogous to observations in human tumors. Importantly, in all cultured MEF clones as well as in most EAC genomes, signature 17 co-occurred with signature 18 which is likely linked to oxidative damage of DNA, supporting the hypothesis that inflammation-driven oxidative DNA damage leads to these human cancers. The replication strand and timing asymmetries were significant in both signature 17 and signature 18 in EAC genomes, while the Hupki MEF clones exhibited significant strand asymmetry in signature 17 but not in signature 18, and showed significant correlation with replication timing in signature 18. Collectively, our results elucidate new features of a modifiable mutagenic activity underlying signature 17 in cancers of the esophagus, stomach, and in model systems. We have also identified novel clinical and molecular associations with signature 17. Investigations using the reported innovative cell-based models will help to identify the precise mechanistic basis of signature 17, with potential implications for primary and secondary cancer prevention and personalized therapy. Citation Format: Marketa Tomkova, Claire Renard, Lara Urban, Souad Kolli, Maude Ardin, Manuraj Pandey, Maria Zhivagui, Hana Huskova, Magali Olivier, Hiroyuki Marusawa, Benjamin Schuster-Böckler, Jiri Zavadil. Deciphering the causes of the COSMIC mutational signature 17 by combining pan-cancer data with experimental mouse models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4661.

Aberrant DNA methylation changes are powerful prognostic and predictive biomarkers in cancer diagnosis and treatment. For decades bisulfite sequencing has been the gold standard for DNA methylation analysis. However, this method relies on harsh deamination reaction of unmodified cytosine to uracil which degrades the majority of DNA and generates sequencing libraries with low complexity. Those drawbacks limit the applications on low-input samples and lead to poor sequencing quality, low mapping rates, uneven genome coverage and increased sequencing cost. Here, we present a novel bisulfite-free and base-resolution sequencing method, TET Assisted Pyridine borane Sequencing (TAPS), for direct detection of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) without affecting unmodified cytosine. We utilised TET enzymes to readily oxidize 5mC and 5hmC to 5-carboxylcytosine (5caC), which was then converted to dihydrouracil by pyridine borane via a previously unknown reductive decarboxylation/deamination reaction. This non-destructive method enables high-throughput sequencing with nanoscale input materials (genomic DNA and cell-free DNA) and preserve DNA up to 10 kbs long which could allow long read sequencing. We demonstrated that TAPS could directly replace bisulfite sequencing with higher mapping rates, more even coverage and lower sequencing costs, and enable more comprehensive, cheaper and faster methylome analyses. This would be a revolutionary tool for epigenetic study and facilitate both academic research and clinical diagnostics. Citation Format: Yibin Liu, Paulina Siejka, Gergana Velikova, Ying Bi, Marketa Tomkova, Benjamin Schuster-Boeckler, Chun-Xiao Song. TAPS: A bisulfite-free, base-resolution and quantitative sequencing method for cytosine modifications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 825.

DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures – each representing a mutagenic process – derived from 3056 patients spanning 19 cancer types to quantify the asymmetry of mutational signatures around replication origins and between early and late replicating regions. We observe that 22 out of 29 mutational signatures are significantly impacted by DNA replication. The distinct associations of different signatures with replication timing and direction around origins shed new light on several mutagenic processes, for example suggesting that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. Together, our results indicate an involvement of DNA replication and associated damage repair in most mutagenic processes.

CpG dinucleotides are the main mutational hot-spot in most cancers. The characteristic elevated C>T mutation rate in CpG sites has been related to 5-methylcytosine (5mC), an epigenetically modified base which resides in CpGs and plays a role in transcription silencing. In brain nearly a third of 5mCs have recently been found to exist in the form of 5-hydroxymethylcytosine (5hmC), yet the effect of 5hmC on mutational processes is still poorly understood. Here we show that 5hmC is associated with an up to 53% decrease in the frequency of C>T mutations in a CpG context compared to 5mC. Tissue specific 5hmC patterns in brain, kidney and blood correlate with lower regional CpG>T mutation frequency in cancers originating in the respective tissues. Together our data reveal global and opposing effects of the two most common cytosine modifications on the frequency of cancer causing somatic mutations in different cell types. DOI: http://dx.doi.org/10.7554/eLife.17082.001, eLife digest A molecule called DNA encodes genetic information inside our cells. Random changes to the DNA sequence, known as mutations, can occur in any cell. Most mutations are harmless, but some can lead to disease – most prominently cancer. Like how car accidents can happen more often on some roads than others, mutations are more frequent in some parts of the DNA. Cytosine, one of the four letters of the genetic code, usually accumulates more mutations than the other three letters. Cytosine can be decorated with distinct ‘marks’ to form either methyl-cytosine or hydroxymethyl-cytosine. Methyl-cytosine is known to mutate relatively easily, and is the most common type of mutation observed in most cancers. However, little was known about how easily hydroxymethyl-cytosine mutates. Modifications of cytosine are distributed differently in cells from different tissues. To test whether hydroxymethyl-cytosine mutates more or less often than methyl-cytosine in human cells, Tomkova et al. used the cytosine mutations measured in human brain, kidney and blood cancer samples. Comparing these mutations to maps of cytosine modifications from healthy tissues of the same type revealed that in all tissues, hydroxymethyl-cytosine appears to mutate less often than methyl-cytosine. There are several possible explanations for the difference in mutation frequency between methyl-cytosine and hydroxymethyl-cytosine. Tomkova et al. plan to investigate these possibilities further in an effort to fully understand the underlying mechanisms that drive cytosine to mutate. DOI: http://dx.doi.org/10.7554/eLife.17082.002

Introduction Understanding the mechanisms of mutagenesis in cancer is important for the prevention and treatment of the disease. While it is well known that environmental carcinogens such as tobacco smoke substantially increase disease incidence, other studies have suggested that the number of replicative cycles a cell undergoes is the biggest risk factor for cancer. To reconcile these divergent observations, it is critical to understand of and how DNA replication influences distinct mechanisms of mutagenesis. Material and methods Here, we developed a methodology to identify replication-strand and timing asymmetry of mutational signatures, representing different mutagenic mechanisms. Results and discussions Applying this computational framework to whole-genome sequencing data from over 3000 patients, spanning 19 cancer types, reveals a significant impact of DNA replication in 22 out of 29 mutational signatures. This includes some well-known examples, such as the APOBEC class of enzymes that preferentially attack cytosine residues on the lagging strand. Notably, however, we find that most exogenous mutagens, such as UV light or tobacco smoke, also exhibit significant replication strand and timing asymmetry. Even more surprisingly, mutations of epigenetically methylated cytosine residues show clear replication strand asymmetry in cancers deficient of different error correction mechanisms. Finally, our results shed light on the potential mechanisms underlying several unknown mutagenic signatures, such as Signature 17 which is associated with gastric and oesophageal cancers. We show that this process is likely to involve reactive oxygen species altering the composition of the dNTP pool, leading to replication-associated mutations. Conclusion Our findings demonstrate that DNA replication and the associated repair have a bigger influence on the fixation of DNA damage into somatic mutations than previously acknowledged. In some cases, such as for Signature 17 or methylated cytosine, our results point towards a direct causal role of the replicative machinery in the formation of mutations. In summary, our discoveries shed new light onto the link between tissue regeneration, mutagenesis and cancer.

Summary Isocitrate dehydrogenase 1 mutations drive human gliomagenesis, probably through neomorphic enzyme activity that produces D-2-hydroxyglutarate. To model this disease, we conditionally expressed Idh1R132H in the subventricular zone (SVZ) of the adult mouse brain. The mice developed hydrocephalus and grossly dilated lateral ventricles, with accumulation of 2-hydroxyglutarate and reduced α-ketoglutarate. Stem and transit amplifying/progenitor cell populations were expanded, and proliferation increased. Cells expressing SVZ markers infiltrated surrounding brain regions. SVZ cells also gave rise to proliferative subventricular nodules. DNA methylation was globally increased, while hydroxymethylation was decreased. Mutant SVZ cells overexpressed Wnt, cell-cycle and stem cell genes, and shared an expression signature with human gliomas. Idh1R132H mutation in the major adult neurogenic stem cell niche causes a phenotype resembling gliomagenesis., Graphical Abstract, Highlights • Idh1R132H knockin in the mouse brain SVZ recapitulates features of gliomagenesis • Self-renewal and proliferation of neural stem cells and progenitors increase • SVZ cells proliferate ectopically, infiltrate the brain parenchyma, and form nodules • Increases occur in 2HG levels, Wnt and telomere pathway activity, and DNA methylation, Bardella et al. report that expression of IDH1R132H in the subventricular zone of the adult mouse brain causes features of gliomagenesis, including increased numbers of neural stem cells, cellular infiltration into surrounding brain regions, and a gene expression profile overlapping that of human gliomas.

There is ample experimental evidence describing changes of tonotopic organisation in the auditory cortex due to environmental factors. In order to uncover the underlying mechanisms, we designed a large-scale computational model of the auditory cortex. The model has up to 100 000 Izhikevich's spiking neurons of 17 different types, almost 21 million synapses, which are evolved according to Spike-Timing-Dependent Plasticity (STDP) and have an architecture akin to existing observations. Validation of the model revealed alternating synchronised/desynchronised states and different modes of oscillatory activity. We provide insight into these phenomena via analysing the activity of neuronal subtypes and testing different causal interventions into the simulation. Our model is able to produce experimental predictions on a cell type basis. To study the influence of environmental factors on the tonotopy, different types of auditory stimulations during the evolution of the network were modelled and compared. We found that strong white noise resulted in completely disrupted tonotopy, which is consistent with in vivo experimental observations. Stimulation with pure tones or spontaneous activity led to a similar degree of tonotopy as in the initial state of the network. Interestingly, weak white noise led to a substantial increase in tonotopy. As the STDP was the only mechanism of plasticity in our model, our results suggest that STDP is a sufficient condition for the emergence and disruption of tonotopy under various types of stimuli. The presented large-scale model of the auditory cortex and the core simulator, SUSNOIMAC, have been made publicly available.

Natriuretic peptides are often elevated in congenital heart disease (CHD); however, the clinical impact on mortality is unclear. The aim of our study was to evaluate the prognostic value of N-terminal pro-brain natriuretic peptide (NT-proBNP) in the prediction of all-cause mortality in adults with different CHD. In this prospective longitudinal mortality study, we evaluated NT-proBNP in 1,242 blood samples from 646 outpatient adults with stable CHD (mean age 35 ± 12 years; 345 women). Patients were followed up for 6 ± 3 (1 to 10) years. The mortality rate was 5% (35 patients, mean age 40 ± 14 years, 17 women). Median NT-proBNP (pg/ml) was 220 in the whole cohort, 203 in survivors, and 1,548 in deceased patients. The best discrimination value for mortality prediction was 630 pg/ml with 74% sensitivity and 84% specificity. During the follow-up, the survival rate was 65% for those with median NT-proBNP ≥630 pg/ml and 94% for NT-proBNP 1,548 pg/ml. Even the first (baseline) measurements of NT-proBNP were strongly associated with a high risk of death (log10 NT-proBNP had hazard ratio 7, p