EpiGenie | Epigenetics, Stem Cell, and Synthetic Biology News http://epigenie.com Scientific News, Technology, and Product Information Mon, 16 Apr 2018 17:30:40 +0000 en-US hourly 1 https://wordpress.org/?v=4.9.5 dmrseq Powers-Up Whole-Genome Bisulfite Sequencing Analysis http://epigenie.com/dmrseq-powers-whole-genome-bisulfite-sequencing-analysis/ http://epigenie.com/dmrseq-powers-whole-genome-bisulfite-sequencing-analysis/#respond Mon, 16 Apr 2018 17:24:34 +0000 http://epigenie.com/?p=26974 In our modern world, power is everything. Whether it be political, social, or even statistical, humankind always thirsts for more. While political and social power may be a little beyond our scope, a new bioinformatic package has come forth to power up your ability to detect differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS) data.

The identification of DMRs by WGBS is no easy task; the high cost of sequencing leads to low sample sizes with low coverage and thus the requirement for complex statistical inference. Further complications arise from the correlated nature of CpG sites, which makes controlling the false discovery rate (FDR) challenging. However, as the price of sequencing continues to plummet, WGBS has emerged as a truly genome-wide method that can be applied to complex experimental designs.

To tackle the challenges of identifying DMRs from WGBS data, the lab of Rafael Irizarry at Harvard University (USA) has brought forth dmrseq. dmrseq builds on the data structure of the popular bsseq (BSmooth) package, which was also developed in the Irizarry lab, but offers a very different approach.

The identification DMR employs two critical steps:

  1. DMR Detection: The differences in CpG methylation for the effect of interest are pooled and smoothed to give CpG sites with higher coverage a higher weight, and candidate DMRs are assembled
  2. Statistical Analysis: A region statistic for each DMR, which is comparable across the genome, is estimated via the application of a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest. Then, permutation testing of a pooled null distribution enables the identification of significant DMRs
    • This approach accounts for both inter-individual and inter-CpG variability across the entire genome

Notably, by performing the statistical testing on DMRs and not CpGs, dmrseq offers accurate FDR control. This approach also allows the direct adjustment of covariates in the model, an ideal situation for covariates that are continuous or contain two or more groups. Covariates can also be incorporated by balancing the permutations, which is ideal for two group covariates such as sex. Finally, dmrseq also allows for multi-group comparisons and can identify DMRs with a sample size as low as two per group.

By comparing dmrseq to bsseq, DSS, and Metilene, and examining the differences in DMR identification in data from the human epigenome roadmap, mouse models, or simulations, the talented team demonstrated the powerful capabilities of dmrseq in identifying DMRs.

Get your hands on the package over at Bioconductor and check out the full article in Biostatistics, February 2018.

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If You Snooze, You Lose: DNA Methylation Loss at Late Replicating Regions Tracks Cellular Aging http://epigenie.com/snooze-lose-dna-methylation-loss-late-replicating-regions-tracks-cellular-aging/ http://epigenie.com/snooze-lose-dna-methylation-loss-late-replicating-regions-tracks-cellular-aging/#respond Sat, 14 Apr 2018 07:39:18 +0000 http://epigenie.com/?p=26968 “Early to bed and early to rise makes a man healthy, wealthy, and wise!” While many night owls happily ignore this sage advice and enjoy a few extra hours in bed in the mornings, a new study regarding DNA methylation dynamics in normal and cancer cells gives credence to the old axiom “If you snooze, you lose!” and may provide a means to track cellular aging!

More precisely, the bright eyed and bushy tailed researchers from the labs of Hui Shen, Peter W. Laird (Van Andel Research Institute), and Benjamin P. Berman (Cedars-Sinai Medical Center) have studied DNA methylation loss or hypomethylation at “lazier” regions of the genome, actually known as late-replicating regions. Previous studies have linked lamina-associated, late-replicating regions, otherwise known as partially methylated domains (PMDs), to various types of cancer and one study employed PMDs to trace the evolution of gene regulation in mammalian placentas. Fascinatingly, the author’s new findings establish that DNA methylation loss at late-replicating regions occurs progressively in most cells, beginning from even the earliest stages of development, and accurately tracks the number of cellular divisions made.

DNA Methylation Loss at Late Replicating Regions Tracks Cellular Aging

Here’s what the team discovered after applying advanced bioinformatics analysis to an extensive range of normal and cancerous mouse and human whole-genome bisulfite sequencing (WGBS) datasets, including tumor and adjacent normal data from eight common cancer types:

  • A WCGW motif (where W = A or T) without neighboring CpGs (solo) represented the most hypomethylation-prone motif within late-replicating sequences
  • A search for solo-WCGWs discovered previously undetected hypomethylation in the vast majority of healthy tissue types
    • DNA methylation loss starts from embryonic development and progressively increases with chronological age
  • solo-WCGW motif analysis in cancer cells demonstrated that higher mutation density and increased expression of proliferation-associated genes correlated to increased DNA methylation loss within late-replicating sequences
  • Therefore, the authors propose that the loss of DNA methylation at solo-WCGWs within these regions tracks the accumulation of cell divisions and can precisely establish cellular age, which may be different to the chronological age of the host

Conclusions: The View from the Early Risers

Let’s finish with the thoughts of the three study leaders, who surely get up very early in the morning:

“Our cellular clock starts ticking the moment our cells begin dividing,” Laird said. “This method allows us to track the history of these past divisions and measure age-related changes to the genetic code that may contribute to both normal aging and dysfunction.”

“What is striking about the results from our new method is that they push back the start of this process to the earliest stages of in utero development,” Berman said. “That was completely surprising, given the current assumption that the process begins relatively late on the path to cancer. This finding also suggests that it may play a functional role relatively early in the formation of tumors.”

“Tissues with higher turnover rates are typically more susceptible to cancer development simply because there are more opportunities for errors to accumulate and force the change from a normal cell to a malignant one,” Shen said. “What we’re seeing is a normal process — cellular aging — augmented and accelerated once a cell becomes cancerous. The cumulative effect is akin to a runaway freight train.”

Quit your snoozing and be the early bird who catches the scientific worm at Nature Genetics, April 2018.

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Classification Conundrums: DNA Methylation and Central Nervous System Tumors http://epigenie.com/classification-conundrums-dna-methylation-central-nervous-system-tumors/ http://epigenie.com/classification-conundrums-dna-methylation-central-nervous-system-tumors/#respond Fri, 13 Apr 2018 22:49:58 +0000 http://epigenie.com/?p=26963 It’s human nature to categorize the world around us. From the earliest taxonomic classification defining us as Homo sapiens, we’ve grouped dogs by breed (pugs, bulldogs, retrievers), wines by grape (merlots, chardonnays, pinot noirs), and of course, cancers by origin (gliomas, melanomas, sarcomas). You can order a DNA test for your dog, or ask the sommelier about your wine, but how can we ensure the right tumor classification?

Currently, the World Health Organization (WHO) primarily classifies central nervous system (CNS) tumors based on histological methods. This is subject to the pathologist’s interpretation, which inevitably introduces variability and error. Alternatively, in-depth molecular profiling is needed. Given that the consequences for misclassifying a tumor are much higher than ordering the wrong wine, researchers out of the German Cancer Research Center and University Hospital Heidelberg (Heidelberg, Germany) developed an unbiased CNS tumor classification system based on tumor DNA methylation profiles. Here’s how they did it:

  • First, they established a reference cohort using the 450k BeadChip Array to acquire genome-wide methylation data for ~2,800 tumor samples. The samples were derived from nearly all current WHO classifications, as well as a variety of tumor microenvironments
    • Unsupervised iterative clustering gives rise to 82 classes of CNS tumors based on unique methylation patterns
  • They used the reference cohort to develop a diagnostic tool to sort and classify 1,104 patient samples; 977 of the samples successfully matched to a methylation class
    • 86% of matches are in agreement between the histopathological approach and the methylation approach
    • In 171 of these, a specific molecular subgroup could be identified, which is not possible using histology only
  • For 139 samples, the identified DNA methylation class is not in agreement with histopathological diagnosis. These samples were further evaluated with in-depth molecular diagnostics
    • In 129 of 139 cases, the histopathological diagnosis is incorrect, and was resolved in favor of DNA methylation class
    • In 71% of the revised diagnoses there was also a change in the WHO grading (a measure of tumor malignancy)

This work holds promise as a more accurate system for the diagnosis of CNS tumors, which could in turn improve treatment plans and patient outcomes.

To get the details on how they developed this methylation-based classification system, click over to the online classifier tool and check out Nature, March 2018

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Don’t Blame Mom, Thank Her! Extra Maternal Care Creates a Stress Resilient Epigenomic Profile in the Developing Brain http://epigenie.com/dont-blame-mom-thank-extra-maternal-care-creates-stress-resilient-epigenomic-profile-developing-brain/ http://epigenie.com/dont-blame-mom-thank-extra-maternal-care-creates-stress-resilient-epigenomic-profile-developing-brain/#respond Tue, 10 Apr 2018 20:52:32 +0000 http://epigenie.com/?p=26955 Stress is something we are all too familiar with. When it comes down to a stressful situation, it seems that there are almost two types of people: those stricken by anxiety and depression, and those who keep on walking on as if nothing has happened. But what shapes such a distinction between people? One contributing factor is early-life maternal care. With over five decades of evidence, rodent models have served as an important proxy for humans, where licking and grooming of a pup by their mother mirrors the contact that a human mother provides to her baby.

While much of the research into maternal care has focused on risk factors for anxiety and depression, the protective factors that shape resilience to stress remain underexplored. Furthermore, maternal care studies have primarily focused on a few select genes. Now, new findings from the lab of Janine LaSalle at the University of California, Davis, demonstrate for the first time that pups receiving extra maternal care exhibit genome-wide differences in DNA methylation as well as microRNA (miRNA) and gene expression in the stress center of the brain (the hypothalamus).

To gain an integrative genome-wide perspective, the team employed whole-genome bisulfite sequencing (WGBS), a genome-wide miRNA assay, and RNA-seq to analyze the hypothalamus of male rat pups (post-natal day 9) that received extra maternal care and compared this data to matched controls receiving standard levels of maternal care. Here’s what they uncovered:

  • 9,439 differentially methylated regions (DMRs), which are enriched for CTCF binding sites, and map to genes related to stress response and neurodevelopment
  • 2,464 differentially expressed genes that are enriched for the mTOR signaling pathway, including binding sites for the Elk1 transcription factor
  • While the study discovered only five differentially expressed miRNAs, bioinformatic prediction suggests that these miRNAs target 127 of the 2,464 differentially expressed genes
  • Furthermore, a non-coding isoform of Ube3a, which functions as a miRNA sponge, becomes down-regulated, while a predicted target miRNA (mir-542-5p) becomes up-regulated
  • Integration of the three diverse data sets revealed a suite of 20 genes displaying differences on all three levels
    • While some genes have been previously implicated in stress responses, most represent novel finds and relate to diverse functions that can potentially shape resilience to stress

Overall, this exploratory study represents the first genome-wide analysis of DNA methylation following extra maternal care, where it uncovers a genome-wide profile of differences. Additionally, the in-depth analysis provides multiple novel candidates for future functional experimentation.

Senior Author Dag Yasui concludes with his outlook that, “If nothing else, our findings illustrate how important maternal care is with genome-wide alterations affecting a range of cellular processes in the augmented newborn. Most importantly, can new therapies based on the protective modifications we have identified be employed in people who are suffering from anxiety and depression? If so the benefits to society are enormous as it is estimated that one in five people experience mental health disorders in a given year.”

To see why you should appreciate the care provided by your mother, head over to Epigenetics, April 2018.

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A Long non-coding RNA Superhero is GUARDIN our Genome from DNA Damage! http://epigenie.com/long-non-coding-rna-superhero-guardin-genome-dna-damage/ http://epigenie.com/long-non-coding-rna-superhero-guardin-genome-dna-damage/#respond Wed, 04 Apr 2018 13:31:21 +0000 http://epigenie.com/?p=26951 Batman swoops through Gotham, Supergirl flies over National City, and the Black Panther keeps his keen eyes on Wakanda; every superhero acts as a guardian of the beloved place they call home, protecting from any number of devious and dastardly threats. Now, researchers from the laboratory of Xu Dong Zhang and Mian Wu (Henan Provincial People’s Hospital, Zhengzhou, China) have revealed that a superhero also protects our genome and maintains DNA integrity: the long non-coding RNA (lncRNA) we now know as GUARDIN!

In brief, the authors set out to identify additional lncRNAs induced by the tumor suppressor and DNA damage repair facilitator p53 that help to maintain genome integrity. p53 plays multiple roles in response to threats to genome integrity, including the promotion of cell cycle arrest to allow DNA damage repair or signaling for the apoptosis of cells with severely damaged DNA.

So what fantastical deeds by GUARDIN did the authors discover?

  • Employing p53-null human lung adenocarcinoma cells carrying an inducible wild-type p53 expression system, the authors aimed to uncover new p53-responsive lncRNAs
    • This approach highlighted the accumulation of the longest isoform of the RP3-510D11.2 lncRNA, which the authors named GUARDIN
  • Wild-type p53 expression in several cancer cell lines increases GUARDIN expression via direct binding to the GUARDIN promoter
  • Activation of the DNA damage response leads to GUARDIN upregulation both in cancer and normal human cells
  • Detailed analysis suggested that GUARDIN promotes survival and proliferation by protecting against the constitutive cellular stresses present in cells, as well as exogenous genotoxic stress, by employing two primary mechanisms:
    1. miRNA Sponge: GUARDIN prevents the activation of the DNA damage response at telomere ends by sequestering microRNA-23a and thereby promoting the accumulation of its target, the telomeric repeat-binding factor 2 (TRF2), a critical component of the shelterin complex that protects telomere ends
    2. RNA Scaffold: GUARDIN enhances DNA damage repair by acting as an RNA scaffold to promote the heterodimerization of breast cancer 1 (BRCA1) and BRCA1-associated RING domain protein 1 (BARD1), thereby promoting BRCA1 stability and function
  • GUARDIN silencing triggered apoptosis and senescence, but also enhanced the cytotoxicity of exogenous genotoxic stress and inhibited cancer xenograft growth
    • Small molecules that block the interaction of GUARDIN with miRNA-23a and BRCA1 may represent a means to improve cancer treatment

What the talented team discovered in this new p53-based study may permit the design of new and more effective anti-cancer therapies, with our new superhero GUARDIN playing the central role.

For more on the heroic deeds of the lncRNA GUARDIN and p53 in defense of our genome, see the accompanying News and Views article, or go straight to the original study at Nature Cell Biology, March 2018.

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Hemimethylated CpGs: Paradox or Paradigm?! http://epigenie.com/hemimethylated-cpgs-paradox-paradigm/ http://epigenie.com/hemimethylated-cpgs-paradox-paradigm/#respond Wed, 28 Mar 2018 16:59:01 +0000 http://epigenie.com/?p=26946 Science is full of paradoxes, and while we humble epigeneticists have yet to come across a cat that is both alive and dead, we have discovered a mysterious states of DNA methylation! For instance, some CpG sites can be both methylated and unmethylated at the same time, depending on which strand it is located on.

During DNA replication, DNA strands split, and the methylation profile is not written at the same time; rather, a complex containing the maintenance DNA methyltransferase DNMT1 later recognizes the hemimethylated CpG (hemiCpG) site and methylates the nascent strand. But does it always? Exciting new findings from the lab of Victor Corces at Emory University (Atlanta, USA) demonstrate that hemiCpGs actually hang around for multiple cell divisions and have functional roles that involve CTCF.

By using nascent DNA bisulfite sequencing (nasBS-seq) to probe human embryonic stem cells (hESCs) they found:

  • The methylation status of almost all CpG sites, and even CpH sites, is faithfully maintained 20 minutes after division
  • However, some 2467 hemiCpGs are inherited across multiple cell divisions
    • The methylation level of most hemiCpGs is conserved in pluripotent cells but not non-pluripotent cells
  • Profiling of the methyltransferases (DNMT1, DNMT3A, DNMT3B) by chromatin immunoprecipitation on nascent chromatin followed by bisulfite sequencing (nasChIP-BS-seq) revealed the details of how the maintenance and de novo methyltransferases transiently bind hemiCpGs that later become fully methylated
    • Interestingly, some DNMT3A bound sites remain hemimethylated after multiple cell divisions, suggesting that DNMT3A regulates loci-specific hemiCpGs, while the other de novo methyltransferase (DNMT3B) does not
  • nasCHIP-BS-seq of CTCF revealed enrichment of hemiCpGs at regions flanking CTCF binding sites in human and mouse pluripotent cells, which along with the computational analysis of MeCP2 binding, suggests a functional role for hemiCpGs in chromatin architecture

Overall, these findings enable an unprecedented resolution of the dynamics of DNA methylation maintenance while also providing crucial evidence for a functional role of hemiCpGs in chromatin architecture. However, these findings leave us eager to find out all the details of the how hemiCpG sites are chosen in a locus-specific manner as well all their functional consequences during embryonic development and beyond!

Catch the perspective and the rest of this paradoxical paradigm over at Science, March 2018.

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CRISPR Live-cell Imaging Captures CLINGing Chromosomes http://epigenie.com/crispr-live-cell-imaging-captures-clinging-chromosomes/ http://epigenie.com/crispr-live-cell-imaging-captures-clinging-chromosomes/#respond Wed, 28 Mar 2018 11:12:09 +0000 http://epigenie.com/?p=26943 An old teddy bear with an eye missing, a dog-eared children’s book, or a ragged musty-smelling blanket; we all “cling” on to certain treasured objects, although we usually wish to keep them secret from the world! However, this isn’t the case for researchers from the laboratory of John Rinn (Harvard University, Cambridge, USA), who have employed an exciting new CRISPR-based approach to show all and sundry how specific regions on different chromosomes CLING to each other over time and coordinate gene regulation.

In this context, CLING stands for CRISPR live-cell imaging, and the talented team applied this novel technique to study the dynamic genome contacts made between non-homologous chromosomes over time. As an example, non-homologous contacts occur between chromosome A and chromosome B (interchromosomal), while homologous contacts arise between sister chromatids of chromosome A (intrachromosomal). While highly useful, current techniques employed to assess genome organization, including conventional imaging-based techniques and genome-wide chromosome conformation capture (Hi-C), present drawbacks that do not permit the assessment of locus-specific chromosomal contacts over time.

So how does CLING work? Simply put, the technique employs dCas9 and two pools of single-guide RNAs (sgRNAs); one sgRNA pool targets one chromosomal locus and contains a specific RNA-aptamer motif fused to a fluorescent label, while another sgRNA pool targets the interacting chromosomal locus and contains the required RNA-binding protein fused to a different fluorescent label. When applied to a single mammalian cell, the group simply recorded the movements of the fluorescent-labelled regions to describe the dynamics and the frequency of non-homologous chromosomal contacts (NHCCs).

What did the authors discover with this clingy new CRISPR-based technique?

  • CLING and Hi-C techniques readily detect similar homologous chromosomal contacts (HCCs)
    • Examples include interactions between the FIRRE locus and the DXZ4 macrosatellite repeat or the inactive-X CTCF-binding contact element (ICCE)
  • Interestingly, NHCCs occur at a similar frequency to HCCs and display similar levels of stability
    • NHCC examples include interactions of the FIRRE locus with YPEL4 or ATF4 loci or the interaction of the CISTR-ACT locus with the SOX9 locus
  • NHCCs occur in the majority of the mouse and human cells assessed and exhibit three-dimensional conservation
  • However, NHCCs occur over more considerable distances compared to HCCs and, therefore, may be missed by Hi-C analysis
    • The group suggest that this proves the advantage of live-cell imaging in assessing chromosomal contacts

The authors hope that the spatiotemporal dimension of live-cell imaging afforded by CLING will help to develop our understanding of how both short distance HCCs and long distance NHCCs control gene expression.

So don’t get too attached to old methodologies when it comes to chromatin contacts; instead CLING on to something new at Molecular Cell, March 2018.

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Transgenerational Epigenetic Inheritance of a Trio of Epigenomic Changes Induced by DDT http://epigenie.com/transgenerational-epigenetic-inheritance-trio-epigenomic-changes-induced-ddt/ http://epigenie.com/transgenerational-epigenetic-inheritance-trio-epigenomic-changes-induced-ddt/#respond Tue, 27 Mar 2018 21:56:26 +0000 http://epigenie.com/?p=26941 DNA methylation has long been the shining star of transgenerational epigenetic inheritance work, with other mechanisms signing backup. But now, the solo act has now become a trio, with histone modifications and non-coding (ncRNA) stepping into the limelight. For an in utero exposure to be truly transgenerational, and not an intergenerational effect, it must impact the F3 generation which was not directly exposed as a fetus (F1) or as germ cells (F2). Environmentally induced transgenerational epigenetic inheritance has been shown for numerous toxins as well as poor maternal nutrition. Studies have found changes in DNA methylation and non-coding RNA in F3 sperm, though no study has examined histone modifications nor multiple marks in mammals.

The laboratory of Michael Skinner at Washington State University has been a leader in transgenerational research. The group commonly uses DDT as an exposure to model transgenerational epigenetic inheritance. DDT was a common pesticide from the 1940s-70s, but persists in the environment after being banned. It causes endocrine and developmental abnormalities. Previous work from this group found that DDT induces transgenerational inheritance of testis, ovary, kidney and prostate disease up to the F3 generation. The group has examined the epigenetic changes in the sperm of each generation that may underlie these diseases. They exposed gestating female rats to DDT from pregnancy day 8 to 14. Each generation was aged to 90 days for mating, and then sperm collected at 120 up to the F3 generation. They looked for DNA methylation, ncRNA, and histone modification changes in the sperm of each generation.

Here’s what they found:

  • Using MeDIP-seq, they discovered that the F1 sperm has the fewest differentially methylated regions (DMRs), while the F2 have the most, and there is little overlap between generation
    • On average, the DMRs are associated with CpG deserts with a size range of 1-5kb
  • Using RNA-seq on small non-coding RNA (sncRNA) and long non-coding RNA (lncRNA) samples, they found 10 times more lncRNAs are differentially expressed in response to DDT in each generation
    • There were many more dysregulated lncRNAs in the F1 vs. F2 & F3, and many more sncRNAs dysregulated in F3 vs. F1 & F2
  • From the small number of histones that are known to be retained by sperm, there is differential retention in the F3 generation that is not present in the F1/F2
    • H3K27me3 changes were also examined in the F3, and found to not be as abundant as the differential histone retention
  • About 20% of the DNA methylation, ncRNA, and histone changes occur near genes that are involved in metabolism, transcription, signaling, and receptor functions
    • These functions are similar across generations even though the individual genes are not

These data show for the first time that a broad range of epigenetic changes accompany transgenerational disease inheritance. The transgenerational sperm “epimutations” are present in regions with similar genomic features, but their localization is distinct. The fact that different epimutations are found in directly exposed (F1 & F2) vs. indirectly (F3) generations suggests a complex mechanism of transmission that is not yet clear. So, move over DNA methylation and welcome ncRNA and histone; the solo act is now a trio.

Tune into the transgenerational trio over at Epigenetics & Chromatin, February 2018

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Embrace Your Age! Age-related H4K16ac Gains Protect Your Brain from Developing Alzheimer’s Disease http://epigenie.com/embrace-age-age-related-h4k16ac-gains-protect-brain-developing-alzheimers-disease/ http://epigenie.com/embrace-age-age-related-h4k16ac-gains-protect-brain-developing-alzheimers-disease/#respond Mon, 19 Mar 2018 18:19:28 +0000 http://epigenie.com/?p=26932 In our quest for the fountain of youth, we often find ourselves attracted to anything that will fight off the signs of aging. But now, the first genome-wide analysis of a specific histone modification in the brains of human patients affected by Alzheimer’s disease (AD) demonstrates that we should embrace the epigenetic changes that come with healthy aging since they can help protect us from disease development.

The H4K16ac modification not only associates with active enhancers and promoters, but also with senescence in mammalian cell culture and aging in model organisms. This intriguing age-related association prompted the labs of labs of Shelley Berger, Nancy Bonini, and Brad Johnson from the University of Pennsylvania to investigate the role of H4K16ac in AD. To tackle this feat, the talented team employed H4K16ac ChIP-seq of a brain region affected early in AD development, the lateral temporal lobe, and compared their results with younger (~52 years old) and elderly (~62 years old) cognitively normal control samples. Notably, the group quantified neurons by flow cytometry to mask ChIP-seq peaks associated with neuronal loss.

Here’s what they discovered:

  • While all groupings exhibit losses and gains of H4K16ac peaks that correlate with gene expression, H4K16ac levels preferentially decrease in AD patients and increase in older patient samples
    • Intriguingly, the gains observed during normal aging negatively correlate with AD losses, suggesting that AD represents a deregulated aging process
    • Transcription factor motif analysis revealed an enrichment for the HIC ZBTB Transcriptional Repressor 1 (HIC1) binding motif at regions of H4K16ac gained during aging and lost during AD
  • There are 3 types of H4K16ac changes that occur with AD: age-regulated, age-deregulated, and disease-specific
  • The differential H4K16ac peaks associated with AD are enriched for expression quantitative trait loci (eQTLs) and SNPs identified by AD genome-wide association studies (GWAS)

First author Raffaella Nativio shares, “These analyses point to a new model of Alzheimer’s disease. Specifically it appears that AD is not simply an advanced state of normal aging, but rather dysregulated aging that may induce disease-specific changes to the structure of chromatin”. Taken together, these findings demonstrate that not all age related epigenetic changes should be thought of as undesirable.

Take a detour from the fountain of youth over at Nature Neuroscience, March 2018

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Cutting Through the Epigenetic Complexities Linking Aging and Tumorigenesis http://epigenie.com/cutting-epigenetic-complexities-linking-aging-tumorigenesis/ http://epigenie.com/cutting-epigenetic-complexities-linking-aging-tumorigenesis/#comments Fri, 16 Mar 2018 14:40:07 +0000 http://epigenie.com/?p=26927 Writing your first grant proposal? Optimizing that tricky Western blot? Programming an old PCR machine? Only a few things are more complex than our current understanding of the epigenetic links between aging and tumorigenesis, but this has not stopped a few valiant labs from doubling down and busting a few paradigms while they are at it!

In general, aging is the most important risk factor for cancer development; the older you are, the more likely you are to suffer from this often-devastating disease. But why? One hypothesis states that the accumulation of epigenetic alterations over time predisposes our cells to go rogue, but quite how they do it is open to interpretation. In a related hypothesis, the epigenetic profile of the senescent cells that accumulate in the aging body may foster tumorigenicity if cells can escape the senescent state. Furthermore, we also know that focal DNA hypermethylation and global DNA hypomethylation occur in both tumorigenesis and aging/senescence, suggesting an epigenetic link between the two processes.

Now, two studies from laboratories from opposite sides of the Atlantic have cut through some of the epigenetic complexity surrounding the link between aging and tumorigenesis to provide fresh insight into this highly complicated relationship.

Same Old DNA Hypomethylation, Different Chromatin Context!

Our first study from the labs of Agustín F. Fernández and Mario F. Fraga (Universidad de Oviedo, Spain) aimed to fill a few knowledge gaps concerning DNA hypomethylation during aging and tumorigenesis. Previous studies have discerned a robust link between the chromatin patterns of DNA hypermethylation sites in tumorigenesis and aging, although few have reported on the chromatin context of DNA hypomethylation. This prompted the authors to integrate 450K array data generated by The Cancer Genome Atlas consortium from 2,311 healthy and tumoral samples obtained from differentially aged individuals with histone, chromatin state, and transcription factor binding site data from the NIH Roadmap Epigenomics and ENCODE projects.

After the computational processing winded down and the dust settled, Pérez and colleagues discovered:

  • Hyper- and hypo-methylated changes display a similar distribution throughout the genome but also exhibit some tissue-independent alterations
    • Bidirectional changes in DNA methylation occur during tumorigenesis, while hypermethylation predominates during aging
    • Interestingly, the authors identified common DNA methylation signature that occurred across all tumors, and, separately, a common DNA methylation signature in many aged tissues
    • Most tumor types do not exhibit age-associated DNA methylation changes, which is in agreement with the reprogramming of the epigenetic clock in cancer cells
  • As expected, hypermethylated regions associate with both aging and tumorigenesis display chromatin modifications characteristic of bivalent chromatin domains
    • Hypermethylation changes tend to occur in CpG-dense regions, associated with binding of the EZH2 and SUZ12 polycomb components, and affect developmentally-associated genes
  • However, hypomethylated DNA sequences associate with different chromatin contexts during aging and tumorigenesis
    • During aging, DNA hypomethylated sequences occur at enhancers with the activating H3K4me1 modification
    • During tumorigenesis, DNA hypomethylation arises at heterochromatic sites displaying the repressive H3K9me3 modification
    • While hypomethylated regions in tumorigenesis affect genes associated with cellular signaling, the study observed no strong correlations for aging

What does this all mean? The data gathered here suggests that while the story may appear straightforward for DNA hypermethylation, DNA hypomethylation occurs in different chromatin contexts during tumorigenesis and aging, suggesting that different mechanisms may be at play.

DNA Methylation Profiling: Busting Cancer Paradigms and Tracking Cancer Risks

Our second study from the labs of Stephen B. Baylin and Hariharan Easwaran (Johns Hopkins University, Baltimore, USA) employed DNA methylation profiling to investigate the hypotheses that tumor-promoting epigenetic states arise in the senescent cells that accumulate in the aging body. Xie and colleagues compared DNA methylation alterations during the tumorigenic transformation of engineered fibroblasts and replicative senescence of unmodified fibroblasts with the 450K array.

Their new work not only busts a cancer paradigm, but may also provide a new means to stratify cancer patients into risk categories:

  • While DNA methylation patterns during tumorigenesis and senescence appear globally similar, transformation induces a significantly different DNA methylation state when compared to senescence
  • Senescence-associated promoter hypermethylation events mainly involve the silencing of biosynthesis- and metabolism-associated genes in cells unlikely to undergo transformation
    • The shutdown of biosynthetic processes via DNA methylation likely inhibits tumor development, thereby representing an epigenetic contribution to the Hayflick phenomenon
  • Methylation changes during transformation arise stochastically at pro-survival and developmental gene promoters and occur independently of senescence-associated changes
    • Many of these genes display promoter hypermethylation in primary tumors
  • Of note, the study discovered a subset of self-renewal and cell survival genes commonly methylated during tumorigenic transformation and senescence
    • These genes represent hotspots for DNA hypermethylation in primary tumors and aging tissues and, perhaps, a crucial means to track cancer risk

Overall, these new findings do not support a role for senescence-associated methylation in tumorigenesis but do support a role for the random DNA hypermethylation events that accumulate during normal aging; specifically, patients who accrue DNA methylation at select gene promoters may present with an increased likelihood of tumorigenesis.

Conclusions: Complexity Cut?

As with many good studies, cutting through the epigenetic complexities has redefined some of our basic assumptions regarding the links between aging and cancer and provided further engaging questions moving forward. Future research may uncover the different mechanisms controlling DNA hypomethylation in during aging/tumorigenesis and refine the use of DNA methylation analysis as a potent means to define cancer risk.

For more on the complexities of DNA hypomethylation events during tumorigenesis and aging, see Aging Cell, March 2018, and for the low down on DNA methylation and cancer risk, head on over to Cancer Cell, February 2018.

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