Publications

Vitamins etc, appear to slow down epigenetic aging and reduce inflammation–March 2024(opens in a new tab)

Lisa Schmunk · Dani Martin-Herranz, PhD — with Kirsty C McGee, Jack Sullivan, Jon Hazeldine, Thomas Jackson, Janet M Lord

vitamindwiki.com

A scalable multimodal framework for unbiased risk biomarker discovery across multiple cancer types(opens in a new tab)

Constantin Petrescu · Jack Monahan · Abbas Salami · Lisa Schmunk · Tom Stubbs, PhD

Cancer Research 86 (7_Supplement): Abstract 1116 · 2026 · aacrjournals.org

A novel framework to build saliva-based DNA methylation biomarkers: quantifying systemic chronic inflammation as a case study(opens in a new tab)

Lisa Schmunk · Toby Call · Hira Javaid · Vanja Jovicevic · Drago Kojadinovic · Natacha Tomkinson · Emma Stone · Milos Gavrilov · Rob Thompson · Tom Stubbs, PhD · Dani Martin-Herranz, PhD — with Daniel L McCartney, Waylon J Hastings, Eliska Zlamalova, Kirsty C McGee, Jack Sullivan, Archie Campbell, Andrew M McIntosh, Veronika Óvári, Karl Wishart, Christian E Behrens, Thomas Jackson, Janet M Lord

Accessible and non-invasive biomarkers that measure human ageing processes and the risk of developing age-related disease are paramount in preventative healthcare. Here, we describe a novel framework to train saliva-based DNA methylation (DNAm) biomarkers that are reproducible and biologically interpretable. By leveraging a reliability dataset with replicates across tissues, we demonstrate that it is possible to transfer knowledge from blood DNAm to saliva DNAm data using DNAm proxies of blood proteins (EpiScores). We apply these methods to create a new saliva-based epigenetic clock (InflammAge) that quantifies systemic chronic inflammation (SCI) in humans. Using a large blood DNAm human cohort with linked electronic health records and over 18,000 individuals (Generation Scotland), we demonstrate that InflammAge significantly associates with all-cause mortality, disease outcomes, lifestyle factors, and immunosenescence; in many cases outperforming the widely used SCI biomarker C-reactive protein (CRP). We propose that our biomarker discovery framework and InflammAge will be useful to improve understanding of the molecular mechanisms underpinning human ageing and to assess the impact of gero-protective interventions.

2025 · bioRxiv

A combination nutritional supplement reduces DNA methylation age only in older adults with a raised epigenetic age(opens in a new tab)

Lisa Schmunk · Dani Martin-Herranz, PhD

An increase in systemic inflammation (inflammaging) is one of the hallmarks of aging. Epigenetic (DNA methylation) clocks can quantify the degree of biological aging and this can be reversed by lifestyle and pharmacological intervention. We aimed to investigate whether a multi-component nutritional supplement could reduce systemic inflammation and epigenetic age in healthy older adults.We recruited 80 healthy older participants (mean age ± SD: 71.85 ± 6.23; males = 31, females = 49). Blood and saliva were obtained pre and post a 12-week course of a multi-component supplement, containing: Vitamin B3, Vitamin C, Vitamin D, Omega 3 fish oils, Resveratrol, Olive fruit phenols and Astaxanthin. Plasma GDF-15 and C-reactive protein (CRP) concentrations were quantified as markers of biological aging and inflammation respectively. DNA methylation was assessed in whole blood and saliva and used to derive epigenetic age using various clock algorithms.No difference between the epigenetic and chronological ages of participants was observed pre- and post-treatment by the blood-based Horvath or Hannum clocks, or the saliva-based InflammAge clock. However, in those with epigenetic age acceleration of ≥ 2 years at baseline, a significant reduction in epigenetic age (p = 0.015) and epigenetic age acceleration (p = 0.0058) was observed post-treatment using the saliva-based InflammAge clock. No differences were observed pre- and post-treatment in plasma GDF-15 and CRP, though participants with CRP indicative of an elevated cardiovascular disease risk (hsCRP ≥ 3µg/ml), had a reduction in CRP post-supplementation (p = 0.0195).Our data suggest a possible benefit of combined nutritional supplementation in individuals with an accelerated epigenetic age and inflammaging.

GeroScience · 2024 · doi.org/10.1007/s11357-024-01138-8

Ratiometric gibberellin biosensors for the analysis of signaling dynamics and metabolism in plant protoplasts(opens in a new tab)

Lisa Schmunk — with Jennifer Andres, Federico Grau‐Enguix, Justine Braguy, Sophia L Samodelov, Tim Blomeier, Rocio Ochoa‐Fernandez, Wilfried Weber, Salim Al‐Babili, David Alabadí, Miguel A Blázquez, Matias D Zurbriggen

Gibberellins (GAs) are major regulators of developmental and growth processes in plants. Using the degradation-based signaling mechanism of GAs, we have built transcriptional regulator (DELLA)-based, genetically encoded ratiometric biosensors as proxies for hormone quantification at high temporal resolution and sensitivity that allow dynamic, rapid and simple analysis in a plant cell system, i.e. Arabidopsis protoplasts. These ratiometric biosensors incorporate a DELLA protein as a degradation target fused to a firefly luciferase connected via a 2A peptide to a renilla luciferase as a co-expressed normalization element. We have implemented these biosensors for all five Arabidopsis DELLA proteins, GA-INSENSITIVE, GAI; REPRESSOR-of-ga1-3, RGA; RGA-like1, RGL1; RGL2 and RGL3, by applying a modular design. The sensors are highly sensitive (in the low pm range), specific and dynamic. As a proof of concept, we have tested the applicability in three domains: the study of substrate specificity and activity of putative GA-oxidases, the characterization of GA transporters, and the use as a discrimination platform coupled to a GA agonists' chemical screening. This work demonstrates the development of a genetically encoded quantitative biosensor complementary to existing tools that allow the visualization of GA in planta.

2024 · onlinelibrary.wiley.com

Genomic discovery and functional validation of MRP1 as a novel fetal hemoglobin modulator and potential therapeutic target in sickle cell disease(opens in a new tab)

Lisa Schmunk — with Yannis Hara, Emily Kawabata, Viktor T Lemgart, Paola G Bronson, Alexandra Hicks, Robert Peters, Sriram Krishnamoorthy, Jean-Antoine Ribeil, Jennifer Eglinton, Nicholas A Watkins, David J Roberts, Emanuele Di Angelantonio, John Danesh, William J Astle, Dirk S Paul, Samuel Lessard, Adam S Butterworth

ABSTRACT Sickle cell disease (SCD) remains a major health burden with limited treatment options. Despite promising gene-editing clinical trials, there is an unmet need for cost-effective therapies. As induction of fetal hemoglobin (HbF) is an established therapeutic strategy for SCD, we conducted a genome-wide association study of circulating HbF levels in ~11,000 participants to identify further HbF modulators. We identified associations in 11 genomic regions, including eight novel loci such as ABCC1 (encoding multidrug resistance-associated protein 1, MRP1). Using gene-editing and pharmacological approaches, we showed that inhibition of MRP1 increases HbF, intracellular glutathione levels, and reduces sickling in erythroid cells from SCD patients. Overall, our findings identify several novel genetically-validated potential therapeutic targets for SCD, including promising proof-of-principle results from small molecule inhibition of MRP1.

2023 · medrxiv.org

Single cell DNA methylation ageing in mouse blood(opens in a new tab)

Tom Stubbs, PhD

ABSTRACT Ageing is the accumulation of changes and overall decline of the function of cells, organs and organisms over time. At the molecular and cellular level, the concept of biological age has been established and biomarkers of biological age have been identified, notably epigenetic DNA-methylation based clocks. With the emergence of single-cell DNA methylation profiling methods, the possibility to study biological age of individual cells has been proposed, and a first proof-of-concept study, based on limited single cell datasets mostly from early developmental origin, indicated the feasibility and relevance of this approach to better understand organismal changes and cellular ageing heterogeneity. Here we generated a large single-cell DNA methylation and matched transcriptome dataset from mouse peripheral blood samples, spanning a broad range of ages (10-101 weeks of age). We observed that the number of genes expressed increased at older ages, but gene specific changes were small. We next developed a robust single cell DNA methylation age predictor (scEpiAge), which can accurately predict age in a broad range of publicly available datasets, including very sparse data and it also predicts age in single cells. Interestingly, the DNA methylation age distribution is wider than technically expected in 19% of single cells, suggesting that epigenetic age heterogeneity is present in vivo and may relate to functional differences between cells. In addition, we observe differences in epigenetic ageing between the major blood cell types. Our work provides a foundation for better single-cell and sparse data epigenetic age predictors and highlights the significance of cellular heterogeneity during ageing. Highlights - Model to estimate DNA methylation age in single cells - Large multi-omics dataset of single cells from murine blood - Epigenetic age deviations from chronological age are greater than technical expected from technical variability - Number of genes expressed increases with chronological and epigenetic age

bioRxiv (preprint) · 2023 · doi.org/10.1101/2023.01.30.526343

Multi-omic rejuvenation of human cells by maturation phase transient reprogramming(opens in a new tab)

Tom Stubbs, PhD

Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of somatic cell reprogramming, which suggests full reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first "maturation phase transient reprogramming" (MPTR) method, where reprogramming factors are selectively expressed until this rejuvenation point then withdrawn. Applying MPTR to dermal fibroblasts from middle-aged donors, we found that cells temporarily lose and then reacquire their fibroblast identity, possibly as a result of epigenetic memory at enhancers and/or persistent expression of some fibroblast genes. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome was rejuvenated to a similar extent, including H3K9me3 levels and the DNA methylation ageing clock. The magnitude of rejuvenation instigated by MPTR appears substantially greater than that achieved in previous transient reprogramming protocols. In addition, MPTR fibroblasts produced youthful levels of collagen proteins, and showed partial functional rejuvenation of their migration speed. Finally, our work suggests that optimal time windows exist for rejuvenating the transcriptome and the epigenome. Overall, we demonstrate that it is possible to separate rejuvenation from complete pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.

eLife · 2022 · doi.org/10.7554/eLife.71624

Multi‐omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming(opens in a new tab)

Dani Martin-Herranz, PhD — with Dafni Chondronasiou, Diljeet Gill, Lluc Mosteiro, Rocio G Urdinguio, Antonio Berenguer‐Llergo, Mònica Aguilera, Sylvere Durand, Fanny Aprahamian, Nitharsshini Nirmalathasan, Maria Abad, Camille Stephan‐Otto Attolini, Neus Prats, Guido Kroemer, Mario F Fraga, Wolf Reik, Manuel Serrano

The expression of the pluripotency factors OCT4, SOX2, KLF4, and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, partial and reversible reprogramming does not change cell identity but can reverse markers of aging in cells, improve the capacity of aged mice to repair tissue injuries, and extend longevity in progeroid mice. However, little is known about the mechanisms involved. Here, we have studied changes in the DNA methylome, transcriptome, and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen, and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites and biomarkers altered with aging were also restored to young levels upon transient reprogramming. These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic, and metabolomic changes toward a younger configuration in multiple tissues and in the serum.

2022 · onlinelibrary.wiley.com

The CADENCE pilot trial – Promoting physical activity in bladder cancer survivors: A protocol paper(opens in a new tab)

Adam Abbs — with Lee Smith, Anne Marie Carrie, Mark A Tully, Yvonne Barnett, Laurie T Butler, Claire Gillvray, Rosie Lindsay, Mike Trott, Olawale Olanrewaju, Lin Yang, Cristian P Ilie

Background Participation in physical activity has been found to be beneficial for mental and physical health outcomes among cancer survivors. However, to date no intervention exists specifically to promote physical activity among bladder cancer survivors. In light of this knowledge a home-based exercise intervention was co-created for those recently diagnosed with bladder cancer. Aim The aim of the present study, financially supported by Action Bladder Cancer UK [1], is to pilot the home-based exercise intervention tailored specifically for bladder cancer survivors (i.e. from the point of diagnosis) to improve physical and mental health outcomes (during treatment and beyond) in this population. Methods This study will use a randomised controlled trial design. Arm one will consists of the 14 week home-based exercise intervention and arm two usual care (15 participants will be randomised to each arm). Baseline data collection will take place shortly after clinical diagnosis of bladder cancer, and follow-up approximately 7 weeks and then again approximately 14 weeks after commencement of the intervention. At each data collection point data will be collected from participants relating to demographics, physical and mental health. Participants will aslo be asked to wear an Actigraph Accelerometer at each data collection point for seven consecutive days. Immediately after baseline data collection participants in the intervention arm will be given the home-based exercise booklet. Ethics and dissemination Ethical approval was obtained for the present study via The London- City and East Research Ethics Committee (ID:291676). Results of this study will be disseminated through peer-reviewed publications and scientific presentations.

2021 · ResearchGate

Freshwater monitoring by nanopore sequencing(opens in a new tab)

Dani Martin-Herranz, PhD

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.

eLife · 2021 · doi.org/10.7554/eLife.61504

Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation(opens in a new tab)

Tom Stubbs, PhD

Adult skeletal muscles are maintained during homeostasis and regenerated upon injury by muscle stem cells (MuSCs). A heterogeneity in self-renewal, differentiation and regeneration properties has been reported for MuSCs based on their anatomical location. Although MuSCs derived from extraocular muscles (EOM) have a higher regenerative capacity than those derived from limb muscles, the molecular determinants that govern these differences remain undefined. Here we show that EOM and limb MuSCs have distinct DNA methylation signatures associated with enhancers of location-specific genes, and that the EOM transcriptome is reprogrammed following transplantation into a limb muscle environment. Notably, EOM MuSCs expressed host-site specific positional Hox codes after engraftment and self-renewal within the host muscle. However, about 10% of EOM-specific genes showed engraftment-resistant expression, pointing to cell-intrinsic molecular determinants of the higher engraftment potential of EOM MuSCs. Our results underscore the molecular diversity of distinct MuSC populations and molecularly define their plasticity in response to microenvironmental cues. These findings provide insights into strategies designed to improve the functional capacity of MuSCs in the context of regenerative medicine.

PLOS Genetics · 2020 · doi.org/10.1371/journal.pgen.1009022

Human Immunodeficiency Virus Infection and Diverse Physical Health Outcomes: An Umbrella Review of Meta-analyses of Observational Studies(opens in a new tab)

Adam Abbs — with Igor Grabovac, Nicola Veronese, Sinisa Grabovac, Sandra Haider, Sarah E Jackson, Ai Koyanagi, Michael Meilinger, Brendon Stubbs, Joseph Firth, Pinar Soysal, Francesco Di Gennaro, Jacopo Demurtas, Daragh T. Mcdermott, Lin Yang, Lee Smith

Background Our aim was to assess both the credibility and strength of evidence arising from systematic reviews with meta-analyses of observational studies and physical health outcomes associated with human immunodeficiency virus (HIV) but not acquired immunodeficiency syndrome. Methods We performed an umbrella review of observational studies. Evidence was graded as convincing, highly suggestive, suggestive, weak, or nonsignificant. Results From 3413 studies returned, 20 were included, covering 55 health outcomes. Median number of participants was 18 743 (range 403-225 000 000). Overall, 45 (81.8%) of the 55 unique outcomes reported nominally significant summary results (P Conclusions Results show highly suggestive and suggestive evidence for HIV and the presence of a cough, COPD, ischemic heart disease, pregnancy-related mortality, maternal sepsis, and bone fractures. Public health policies should reflect and accommodate these changes, especially in light of the increases in the life expectancy and the incidence of comorbidities in this population.

2020 · ResearchGate

Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells(opens in a new tab)

Tom Stubbs, PhD

Age-related tissue alterations have been associated with a decline in stem cell number and function. Although increased cell-to-cell variability in transcription or epigenetic marks has been proposed to be a major hallmark of ageing, little is known about the molecular diversity of stem cells during ageing. Here we present a single cell multi-omics study of mouse muscle stem cells, combining single-cell transcriptome and DNA methylome profiling. Aged cells show a global increase of uncoordinated transcriptional heterogeneity biased towards genes regulating cell-niche interactions. We find context-dependent alterations of DNA methylation in aged stem cells. Importantly, promoters with increased methylation heterogeneity are associated with increased transcriptional heterogeneity of the genes they drive. These results indicate that epigenetic drift, by accumulation of stochastic DNA methylation changes in promoters, is associated with the degradation of coherent transcriptional networks during stem cell ageing. Furthermore, our observations also shed light on the mechanisms underlying the DNA methylation clock.

Nature Communications · 2019 · doi.org/10.1038/s41467-019-12293-4

DNA methylation clocks in aging: categories, causes, and consequences(opens in a new tab)

Age-associated changes to the mammalian DNA methylome are well documented and thought to promote diseases of aging, such as cancer. Recent studies have identified collections of individual methylation sites whose aggregate methylation status measures chronological age, referred to as the DNA methylation clock. DNA methylation may also have value as a biomarker of healthy versus unhealthy aging and disease risk; in other words, a biological clock. Here we consider the relationship between the chronological and biological clocks, their underlying mechanisms, potential consequences, and their utility as biomarkers and as targets for intervention to promote healthy aging and longevity.

Molecular Cell · 2019 · doi.org/10.1016/j.molcel.2019.06.026

Telomere length and health outcomes: An umbrella review of systematic reviews and meta-analyses of observational studies(opens in a new tab)

Adam Abbs — with Lee Smith, Claudio Luchini, Jacopo Demurtas, Pinar Soysal, Brendon Stubbs, Mark Hamer, Alessia Nottegar, Rita T. Lawlor, Guillermo Felipe López-Sánchez, Joseph Firth, Ai Koyanagi, Justin D. Roberts, Peter Willeit, Thomas Waldhör, Mike Loosemore, James A Johnstone, Lin Yang, Nicola Veronese

The aim of the present study was to map and grade evidence for the relationships between telomere length with a diverse range of health outcomes, using an umbrella review of systematic reviews with meta-analyses. We searched for meta-analyses of observational studies reporting on the association of telomere length with any health outcome (clinical disease outcomes and intermediate traits). For each association, random-effects summary effect size, 95% confidence interval (CI), and 95% prediction interval were calculated. To evaluate the credibility of the identified evidence, we assessed also heterogeneity, evidence for small-study effect and evidence for excess significance bias. Twenty-one relevant meta-analyses were identified reporting on 50 different outcomes. The level of evidence was high only for the association of short telomeres with higher risk of gastric cancer in the general population (relative risk, RR = 1.95, 95%CI: 1.68-2.26), and moderate for the association of shorter telomeres with diabetes or with Alzheimer's disease, even if limited to meta-analyses of case-control studies. There was weak evidence for twenty outcomes and not significant association for 27 health outcomes. The present umbrella review demonstrates that shorter telomere length may have an important role in incidence gastric cancer and, probably, diabetes and Alzheimer's disease. At the same time, conversely to general assumptions, it does not find strong evidence supporting the notion that shorter telomere length plays an important role in many health outcomes that have been studied thus far.

2019 · ResearchGate

Screening for genes that accelerate the epigenetic ageing clock in humans reveals a role for the H3K36 methyltransferase NSD1(opens in a new tab)

Dani Martin-Herranz, PhD · Tom Stubbs, PhD

ABSTRACT Background Epigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data, and which have emerged in the last few years as the most accurate biomarkers of the ageing process. However, little is known about the molecular mechanisms that control the rate of such clocks. Here, we have examined the human epigenetic clock in patients with a variety of developmental disorders, harbouring mutations in proteins of the epigenetic machinery. Results Using the Horvath epigenetic clock, we performed an unbiased screen for epigenetic age acceleration (EAA) in the blood of these patients. We demonstrate that loss-of-function mutations in the H3K36 histone methyltransferase NSD1, which cause Sotos syndrome, substantially accelerate epigenetic ageing. Furthermore, we show that the normal ageing process and Sotos syndrome share methylation changes and the genomic context in which they occur. Finally, we found that the Horvath clock CpG sites are characterised by a higher Shannon methylation entropy when compared with the rest of the genome, which is dramatically decreased in Sotos syndrome patients. Conclusions These results suggest that the H3K36 methylation machinery is a key component of the epigenetic maintenance system in humans, which controls the rate of epigenetic ageing, and this role seems to be conserved in model organisms. Our observations provide novel insights into the mechanisms behind the epigenetic ageing clock and we expect will shed light on the different processes that erode the human epigenetic landscape during ageing.

bioRxiv (preprint) · 2019 · doi.org/10.1101/545830

On the epigenetic ageing clock in humans(opens in a new tab)

Dani Martin-Herranz, PhD

Epigenetic clocks are mathematical models that predict the biological age of an organism using DNA methylation data, and which have emerged in the last few years as the most accurate biomarkers of the ageing process. However, little is known about the molecular mechanisms that control the rate of such clocks. In this thesis I focus on the study of the epigenetic ageing clock in humans. First, I review and benchmark statistical and computational tools required for the analysis of DNA methylation data in the context of human ageing. Next, I validate the performance of the Horvath epigenetic clock, the most widely used multi-tissue epigenetic clock in humans, in a control blood dataset and test its behaviour in patients with a variety of developmental disorders, which harbour mutations in proteins of the epigenetic machinery. I demonstrate that loss-of-function mutations in the H3K36 methyltransferase NSD1, which cause Sotos syndrome, substantially accelerate epigenetic ageing. Furthermore, I show that the normal ageing process and Sotos syndrome share methylation changes and the genomic context in which they happen. These results suggest that the H3K36 methylation machinery is a key component of the epigenetic ... (continues)

2019 · repository.cam.ac.uk

The origins and vulnerabilities of two transmissible cancers in Tasmanian devils(opens in a new tab)

Dani Martin-Herranz, PhD — with Maximilian R Stammnitz, Tim HH Coorens, Kevin C Gori, Dane Hayes, Beiyuan Fu, Jinhong Wang, Ludmil B Alexandrov, Adrian Baez-Ortega, Syd Barthorpe, Alexandra Beck, Francesca Giordano, Graeme W Knowles, Young Mi Kwon, George Hall, Stacey Price, Ruth J Pye, Jose MC Tubio, Hannah VT Siddle, Sukhwinder Singh Sohal, Gregory M Woods, Ultan McDermott, Fengtang Yang, Mathew J Garnett, Zemin Ning, Elizabeth P Murchison

Transmissible cancers are clonal lineages that spread through populations via contagious cancer cells. Although rare in nature, two facial tumor clones affect Tasmanian devils. Here we perform comparative genetic and functional characterization of these lineages. The two cancers have similar patterns of mutation and show no evidence of exposure to exogenous mutagens or viruses. Genes encoding PDGF receptors have copy number gains and are present on extrachromosomal double minutes. Drug screening indicates causative roles for receptor tyrosine kinases and sensitivity to inhibitors of DNA repair. Y chromosome loss from a male clone infecting a female host suggests immunoediting. These results imply that Tasmanian devils may have inherent susceptibility to transmissible cancers and present a suite of therapeutic compounds for use in conservation.

2018 · scholar.google.com

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.(opens in a new tab)

Tom Stubbs, PhD — with Clark SJ, Argelaguet R, Kapourani CA, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W

Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.

2018 · Europe PMC

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches(opens in a new tab)

Dani Martin-Herranz, PhD · Tom Stubbs, PhD

DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome. Herein, we present customised Reduced Representation Bisulfite Sequencing (cuRRBS), a novel and easy-to-use computational method that solves this problem. By computing the optimal enzymatic digestions and size selection steps required, cuRRBS generalises the traditional MspI-based Reduced Representation Bisulfite Sequencing (RRBS) protocol to all restriction enzyme combinations. In addition, cuRRBS estimates the fold-reduction in sequencing costs and provides a robustness value for the personalised RRBS protocol, allowing users to tailor the protocol to their experimental needs. Moreover, we show in silico that cuRRBS-defined restriction enzymes consistently out-perform MspI digestion in many biological systems, considering both CpG and CHG contexts. Finally, we have validated the accuracy of cuRRBS predictions for single and double enzyme digestions using two independent experimental datasets.

Nucleic Acids Research · 2017 · doi.org/10.1093/nar/gkx814

Multi-tissue DNA methylation age predictor in mouse.(opens in a new tab)

Tom Stubbs, PhD — with Bonder MJ, Stark AK, Krueger F; BI Ageing Clock Team; von Meyenn F, Stegle O, Reik W.

Background DNA methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an underlying ageing process. It has also not been shown whether this epigenetic clock is unique to humans or conserved in the more experimentally tractable mouse. Results We have generated a comprehensive set of genome-scale base-resolution methylation maps from multiple mouse tissues spanning a wide range of ages. Many CpG sites show significant tissue-independent correlations with age which allowed us to develop a multi-tissue predictor of age in the mouse. Our model, which estimates age based on DNA methylation at 329 unique CpG sites, has a median absolute error of 3.33 weeks and has similar properties to the recently described human epigenetic clock. Using publicly available datasets, we find that the mouse clock is accurate enough to measure effects on biological age, including in the context of interventions. While females and males show no significant differences in predicted DNA methylation age, ovariectomy results in significant age acceleration in females. Furthermore, we identify significant differences in age-acceleration dependent on the lipid content of the diet. Conclusions Here we identify and characterise an epigenetic predictor of age in mice, the mouse epigenetic clock. This clock will be instrumental for understanding the biology of ageing and will allow modulation of its ticking rate and resetting the clock in vivo to study the impact on biological age.

2017 · Europe PMC

Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism.(opens in a new tab)

Tom Stubbs, PhD — with Hahn O, Grönke S, Ficz G, Hendrich O, Krueger F, Andrews S, Zhang Q, Wakelam MJ, Beyer A, Reik W, Partridge L.

Background Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan in diverse species, including rodents. However, the mechanisms by which DR interacts with the aging process to improve health in old age are poorly understood. DNA methylation could play an important role in mediating the effects of DR because it is sensitive to the effects of nutrition and can affect gene expression memory over time. Results Here, we profile genome-wide changes in DNA methylation, gene expression and lipidomics in response to DR and aging in female mouse liver. DR is generally strongly protective against age-related changes in DNA methylation. During aging with DR, DNA methylation becomes targeted to gene bodies and is associated with reduced gene expression, particularly of genes involved in lipid metabolism. The lipid profile of the livers of DR mice is correspondingly shifted towards lowered triglyceride content and shorter chain length of triglyceride-associated fatty acids, and these effects become more pronounced with age. Conclusions Our results indicate that DR remodels genome-wide patterns of DNA methylation so that age-related changes are profoundly delayed, while changes at loci involved in lipid metabolism affect gene expression and the resulting lipid profile.

2017 · Europe PMC

Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming.(opens in a new tab)

Tom Stubbs, PhD — with Milagre I, King MR, Spindel J, Santos F, Krueger F, Bachman M, Segonds-Pichon A, Balasubramanian S, Andrews SR, Dean W, Reik W.

Global DNA demethylation is an integral part of reprogramming processes in vivo and in vitro, but whether it occurs in the derivation of induced pluripotent stem cells (iPSCs) is not known. Here, we show that iPSC reprogramming involves both global and targeted demethylation, which are separable mechanistically and by their biological outcomes. Cells at intermediate-late stages of reprogramming undergo transient genome-wide demethylation, which is more pronounced in female cells. Global demethylation requires activation-induced cytidine deaminase (AID)-mediated downregulation of UHRF1 protein, and abolishing demethylation leaves thousands of hypermethylated regions in the iPSC genome. Independently of AID and global demethylation, regulatory regions, particularly ESC enhancers and super-enhancers, are specifically targeted for hypomethylation in association with transcription of the pluripotency network. Our results show that global and targeted DNA demethylation are conserved and distinct reprogramming processes, presumably because of their respective roles in epigenetic memory erasure and in the establishment of cell identity.

2017 · Europe PMC

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs(opens in a new tab)

Tom Stubbs, PhD — with Mélanie A. Eckersley-Maslin, Valentine Svensson, Christel Krueger, Pascal Giehr, Felix Krueger, Ricardo J. Miragaia, Charalampos Kyriakopoulos, Rebecca V. Berrens, Inês Milagre, Jörn Walter, Sarah A. Teichmann, Wolf Reik

Mouse embryonic stem cells are dynamic and heterogeneous. For example, rare cells cycle through a state characterized by decondensed chromatin and expression of transcripts, including the Zscan4 cluster and MERVL endogenous retrovirus, which are usually restricted to preimplantation embryos. Here, we further characterize the dynamics and consequences of this transient cell state. Single-cell transcriptomics identified the earliest upregulated transcripts as cells enter the MERVL/Zscan4 state. The MERVL/Zscan4 transcriptional network was also upregulated during induced pluripotent stem cell reprogramming. Genome-wide DNA methylation and chromatin analyses revealed global DNA hypomethylation accompanying increased chromatin accessibility. This transient DNA demethylation was driven by a loss of DNA methyltransferase proteins in the cells and occurred genome-wide. While methylation levels were restored once cells exit this state, genomic imprints remained hypomethylated, demonstrating a potential global and enduring influence of endogenous retroviral activation on the epigenome.

2016 · Cell Press

Modularized CRISPR/dCas9 effector toolkit for target-specific gene regulation(opens in a new tab)

Lisa Schmunk — with Michael Agne, Ilona Blank, Alica J Emhardt, Christoph G Gäbelein, Fenja Gawlas, Nadine Gillich, Patrick Gonschorek, Thomas J Juretschke, Stefan D Krämer, Natalie Louis, Anne Müller, Alina Rudorf, Manuel C Scheidmann, Philipp M Schwenk, Maximilian R Stammnitz, Philipp M Warmer, Wilfried Weber, Adrian Fischer, Beate Kaufmann, Hanna J Wagner, Gerald Radziwill

The ability to control mammalian genes in a synergistic mode using synthetic transcription factors is highly desirable in fields of tissue engineering, stem cell reprogramming and fundamental research. In this study, we developed a standardized toolkit utilizing an engineered CRISPR/Cas9 system that enables customizable gene regulation in mammalian cells. The RNA-guided dCas9 protein was implemented as a programmable transcriptional activator or repressor device, including targeting of endogenous loci. For facile assembly of single or multiple CRISPR RNAs, our toolkit comprises a modular RNAimer plasmid, which encodes the required noncoding RNA components.

2014 · pubs.acs.org

The RNA-dependent RNA polymerase of the influenza A virus.(opens in a new tab)

Tom Stubbs, PhD — with Te Velthuis AJ

The influenza A virus causes a highly contagious respiratory disease that significantly impacts our economy and health. Its replication and transcription is catalyzed by the viral RNA polymerase. This enzyme is also crucial for the virus, because it is involved in the adaptation of zoonotic strains. It is thus of major interest for the development of antiviral therapies and is being intensively studied. In this article, we will discuss recent advances that have improved our knowledge of the structure of the RNA polymerase and how mutations in the polymerase help the virus to spread effectively among new hosts.

2014 · Europe PMC

Insight into the Family of Na+/Ca2+ Exchangers of Caenorhabditis elegans(opens in a new tab)

Dani Martin-Herranz, PhD — with Vishal Sharma, Chao He, Julian Sacca-Schaeffer, Eric Brzozowski, Zelda Mendelowitz, David A Fitzpatrick, Damien M O’Halloran

Here we provide the first genome-wide in vivo analysis of the Na+/Ca2+ exchanger family in the model system Caenorhabditis elegans. We source all members of this family within the Caenorhabditis genus and reconstruct their phylogeny across humans and Drosophila melanogaster. Next, we provide a description of the expression pattern for each exchanger gene in C. elegans, revealing a wide expression in a number of tissues and cell types including sensory neurons, interneurons, motor neurons, muscle cells, and intestinal tissue. Finally, we conduct a series of behavioral and functional analyses through mutant characterization in C. elegans. From these data we demonstrate that, similar to mammalian systems, the expression of Na+/Ca2+ exchangers in C. elegans is skewed toward excitable cells, and we propose that C. elegans may be an ideal model system for the study of Na+/Ca2+ exchangers.

2013 · Oxford Academic

Listeria rhomboencephalitis(opens in a new tab)

Adam Abbs — with Tp Nandakumar, Dalila Mooraby, Pyari Bose

2012 · ResearchGate