The 4th Canadian Conference on Epigenetics: “Mechanisms of Disease” happened November 26-29th 2017 in beautiful Whistler, British Columbia, Canada. It boasted 190 attendees, 88 of which were trainees. This meeting encouraged presentation of new data, collaboration, and discussion between researchers. The snow was flying, and the smoked salmon was devoured at every meal. If you missed it, the 5th Canadian Conference on Epigenetics will be occurring from September 30th-October 3rd, 2018 at Esterel Resort in Esterel, Quebec, Canada.
After a touching tribute to contributions made by the late Denise Barlow to the lncRNA field, keynote speaker Anne Ferguson Smith introduced the BLUEPRINT Epigenome Project. BLUEPRINT uses multiple mouse strains, cell types and sexes to compare RNA-Seq, WGBS, oxWGBS, CHIP-Seq histone methylation and acetylation datasets focused on the Hematopoietic System. It aims to integrate single-cell epigenome data with transcriptome and proteome datasets.
High-throughput epigenome mapping
Shyam Prabhakar from the Genome Institute of Singapore shared ongoing work using CHIP-Seq in a histone acetylation-wide association study of autism. In collaboration with Jonathan Mill for RNA-Seq data and Daniel H. Gerschwind for DNA methylation data, they have found over 5000 different histone acetylation peaks in prefrontal and temporal cortex in frozen post-mortem brain samples. Dr. Prabhakar also shared work on a tuberculosis cohort, where a novel association with expression and histone acetylation of an unspecified ion channel has been found.
Next, Jordana Bell from King’s College London, England shared her work on DNA methylation in twins using the Illumina 450K and EPIC array. She found approximately 10% of the methylome is highly heritable. Enhancer and insulator methylation are more heritable, while promoter methylation is the least heritable.
Maxwell Libbrecht from Simon Fraser University (Burnaby, BC, Canada) introduced the Segway encyclopedia of human regulatory elements. Their group has developed a pattern discovery algorithm and applied it to 1615 genome-wide assays from 164 human cell types from the ENCODE project to predict genomic regions without any a priori annotations. As such, it has the potential to identify currently unknown genomic elements. The encyclopedia annotates inactive regions, constitutive heterochromatin with permanently silent regions marked by H3K9me3, facultative heterochromatin with cell-type specific repression marked by H3K27me3, transcribed regions, promoters, enhancers, permissive regions with weak activity such as H3K4me1, bivalent regions with both activation and repression marks, and other low confidence regions. Dr. Libbrecht’s work is also available as an article preprint.
Eric Campos from The Hospital for Sick Children (Toronto, ON, Canada) shared his work on how histones marks are maintained through the cell cycle. Dr. Campos discussed how new histones without modifications are chaperoned by ASF1 and CAF-1 at the replication fork, while older histones are segregated between leading and lagging strands, although the exact mechanism remains unknown. He suggested that the eukaryotic replicative helicase, CMG, may be mediating this with a histone binding domain and the FACT histone chaperone, although more work needs to be done.
Developmental epigenome regulation
Wendy Robinson from the University of British Columbia (Vancouver, BC, Canada) emphasized the importance of the placenta as a mediator of pregnancy complications resulting from various genetic and environmental factors. Dr. Robinson likened placental DNA methylation more to cancer than typical somatic cells with characteristic global hypomethylation, hypermethylation of tumor suppressors, and hypomethylation of oncogenes. Yet, she notes that lots of placental variability still supports healthy fetal development. Additionally, cell-free placental DNA is found in maternal blood. Dr. Robinson has found 48 differentially methylated regions associated with decreased gene expression, but has her sights set on integrating with multi-omic data to identify subtypes and associated markers with the goal of healthier mothers and babies.
Jacquetta Trasler from McGIll University (Montreal, QC, Canada) described her work on DNA methylation and paternal folate. Low levels of paternal folate result in altered sperm epigenome with increased negative pregnancy outcomes. Even a minor change in methylation may have severe consequences. Typically, the sperm methylome is very stable between individuals and over time. Of interest is MTHFR in the folate pathway – a common polymorphism is associated with decreased sperm activity and some infertility. Using a mouse model, Dr. Trasler and her team have observed DNA hypomethylation following folate supplementation in wildtype and Mthfr deficient mice. Over generations, there were lower numbers of sperm in F1 mice, with F2 mortality.
Richard Pilsner from University of Massachusetts Amherst shared his work on advanced paternal age. Dr. Pilsner’s lab addresses how paternal age may be associated with development and DNA methylation in sperm. To do this, he launched the Sperm Environmental Epigenetics and Development Study (SEEDS). Through this study, Dr. Pilsner found increases in age correlated with decreased fertility and decreased embryo quality. There is increased DNA methylation with age, and Richard suggests that just 10 CpGs could explain up to 94% of the variance with age, while 20 CpG sites are sufficient to accurately predict age.
Serge McGraw from Université de Montréal (Montreal, QC, Canada) explained his work on early embryonic alcohol exposure. With ethanol injection at just the 8-cell stage, Dr. McGraw was able to see lasting changes in DNA methylation via RRBS in the forebrain and placenta at embryonic day 10.5. By embryonic day 18.5, even more damage has accumulated in a sex-specific manner.
Cellular signalling through the histone code
Tatiana Kutateladze from the University of Colorado discussed the massive number of epigenetic readers of histone modifications. Specifically, she focused on PHD fingers that bind to specific histone modifications. She unravelled some of the complexity of binding, with multiple sequential reader domains required or combinatorial bivalent interactions that her lab has described.
Jean-Francois Couture from the University of Ottawa (Ottawa, ON, Canada) introduced his work on posttranslational modification of histones – specifically the SET1 family of lysine methyltransferases. With many disease associations, particularly cancer, with complex associated with SET1 (COMPASS), Dr. Couture has found that catalytic activity of SET 1 requires various COMPASS support proteins essential for histone methylation activity.
Simone Sidoli from Benjamin Garcia’s lab at the University of Pennsylvania shared their work on overlapping proteomic and metabolomics data for histone modification analysis. Dr. Sidoli discussed “bottom-up” mass spectrometry for histones to find rare posttranslational modifications. Additionally, Dr. Sidoli mentioned the ability to overlap ChIP-Seq and ATAC-seq data as a robust method to characterize histone modifications.
Mechanisms of epigenomic perturbation in disease
Rosanna Weksberg from The Hospital for Sick Children (Toronto, ON, Canada) introduced her pioneering work in DNA methylation and mendelian disorders. She described a range of intellectual disability syndromes linked to epigenes. Many genes associated with neurodevelopmental syndromes are genes involved with epigenetic regulation. For example, Sotos syndrome following NSD1 methyltransferase mutations. As a result, these patients see a massive loss of DNA methylation. Using methylation signatures from the 450K array, variants of unknown significance are confidently called as Sotos syndrome. Weaver syndrome is clinically like Sotos, but the Weksberg lab has been able to distinguish them based on the Sotos NSD1 signature, and a specific methylation signature in Weaver syndrome patients at EZH2, a histone lysine methyltransferase. Similarly, Kabuki and CHARGE syndromes have high clinical overlap, but have unique DNA methylations profiles, particularly KMTZD, a histone lysine methyltransferase, for Kabuki syndrome and CHD7, a chromodomain helicase DNA-binding protein, for CHARGE syndrome. Dr. Weksberg invited collaboration through patient data submissions to further characterize epigene mutations that require known pathogenic mutations and reliable phenotypic data.
Jennifer Mitchell from the University of Toronto (Toronto, ON, Canada) described her work on enhancer mutations and disease, whereby even a single nucleotide difference is sufficient for negative phenotypes. She has used associations with transcription factors to predict enhancers from known promoter regions. Specifically, Dr. Mitchell found an enhancer cluster about 100 kb downstream from Sox2 that was heavily associated with transcription factors, in what is now referred to as a super enhancer. Her work now focuses on the redundancy and potency of these locations through targeted deletions using the CRISPR/Cas9 system.
Epigenetics in Cancer
Talks throughout the conference converged on how epigenetics plays a role in cancer. First, Joe Costello from University of California San Francisco introduced his work on IDH1 mutant glioma brain tumors. These mutations create inhibitory substrates of the citric acid cycle, known as oncometabolites. IDH1 produces alphaketoglutarate that acts as a TET protein substrate, the disruption of which leads to accumulation of DNA methylation. Often there is an accumulation of mutations from the initial IDH1 that leads to epigenetic and metabolic reprogramming, followed by additional p53 and ATRX mutations. Even with later changes in IDH1 mutation status, the initial methylation changes are stable with cells perpetuating the methylation profile.
Jacek Majewski from McGill University (Montreal, QC, Canada) extended Joe Costello’s investigation into adult gliomas to those occurring in children. For Dr. Majewski, there seems to be a primary mutation in histone subunit H3, with lots of histone modifying genes identified. Through Dr. Majewski’s research, he’s found that H3K36me3 seems to be a silencing mark in gene bodies where it recruits DNA methylation.
Mathieu Lupien from the University of Toronto (Toronto, ON, Canada) outlined three specifics of his research. First, his lab addressed how epi alterations are shaping cancer development. Second, Dr. Lupien and his team investigate how epigenetics overlap with the genetic findings in cancer. Finally, Dr. Lupien wonders how tumor metabolism changes the epigenome. The focus for the Lupien lab has been on DNA and histone methylations since in tumors a metabolic adaptation results in altered SAM, the universal methyl donor. Dr. Lupien has found large organized chromatin lysine domains (LOCKs) where H3K27me3 signals accumulate in mutant populations resistant to paclitaxel, a chemotherapy drug. LOCKs where also associated with decreased DNA methylations and enriched for repeat elements, not genes. Dr. Lupien suggests that as SAM drops at these repeat elements, the cell can survive by adding histone LOCKs to keep these regions repressed.
Marco Gallo from the University of Calgary (Calgary, AB, Canada) discussed his patient-derived models of glioblastomas. The Gallo lab works to understand how histone variants play a role in the hierarchy or tumorigenic potential and what role the 3D genome architecture has as well. Compared to other available datasets, Dr. Gallo finds lower expression of H2A2 messenger RNA. Additionally, increased H2A2 transcripts antagonize the self-renewal of glioblastomas. Knockdowns of H2A2 lead to nuclear expansions from condensed chromatin. Using Hi-C combined with Chip-Seq examining H3K27ac, The Gallo lab has been able to find super enhancers on the arm of other chromosomes, and other important organizational changes in glioblastomas.
Martin Krzywinski from Canada’s Michael Smith Genome Sciences Centre (Vancouver, BC, Canada) hosted a workshop about data visualization that delivered a punch. He circled the posters on display, finding figures that he presented his own improvements on. This educational for everyone, and a little humiliating for some also. Martin explained Gestalt principles, emphasizing that we see tone over space over shape when we look at figures. He explained how we could isolate the essence of what our figures were showing, and minimize excess information. Martin recommended using Brewer palettes for colour schemes that are more appealing to human eyes than default RBG schemes. He also recommended using UpSet visualization in place of Venn diagrams when overlapping multiple datasets.
Thanks to Bonnie Alberry for writing this summary