Epigenomics and Synthetic Biology: 2015 in Review

Despite how slow it feels doing it, every year science propels at a startling rate. Here are some paradigm shifts that really impacted my perceptions. Some are a selection of my contributions to EpiGenie and Epibeat, while the rest are written by others from places such as The Scientist and MIT Tech Review.

Epigenomics and Synthetic Biology Breakthroughs:

  1. The labs of Alexander Meissner, J. Keith Joung, and John Rinn brought the non-controversial paper: CRISPR used in human embryonic stem cells to show fundamental difference between mice and men.
  2. Michael Skinner shows that Epigenetics drives genetics straight into evolution
  3. Sperm miRNA Drives Intergenerational Stress Response
  4. A ‘new’ epigenetic mark: 6mA Makes the Grade as a Eukaryotic Epigenetic Mark
  5. DNA Methylation Helps Muscles Remember
  6. The Brain’s Circular RNAs
  7. Epigenome Editing with CRISPR-dCas9, TALEs, and Zinc Fingers
  8. Obesity Alters Sperm Epigenome
  9. CRISPR Gets Creative with Histone Acetylation
  10. Antidepressant Exerts Epigenetic Changes
  11. Move over Optogenetics, here comes Magnetogenetics: Discovery of long-sought biological compass claimed
  12. 5fC is Stable in Mammalian Brains
  13. CRISPR Inversion Untangles How CTCF Controls Chromatin Looping
  14. Epigenetic Clock Goes from Analog to iWatch
  15. New Biotech?! Viral Elements Horizontally Transfer Parasite’s Genes into Non-Standard Host Genomes
  16. RNAi pesticide: ‘Deep inside its labs, Monsanto is learning how to modify crops by spraying them with RNA rather than tinkering with their genes
  17. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function at Protocadherins
  18. CRISPR-Display: For the lncRNA Enthusiast that has Everything
  19. CTCF Tucks Genes Into Their Lamina Associated Beds
  20. Reversal of phenotypes in MECP2 duplication mice using genetic rescue or antisense oligonucleotides
  21. A DNMT1 (protein) and miRNA complex inactivating the catalytic region
  22. For that question you hear a million times: RNA doesn’t correlate with protein? Huh?
  23. Using Synbio to make narcotics: Brewing Bad
  24. Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model
  25. Spray Your Way Free of Cystic Fibrosis with a Gene Editing Nasal Spray
  26. Sex On the Brain: DNA Methylation Defines Gender
  27. New Insights into Puzzling Placental DNA Methylation Domains
  28. 5hmC: a Helping Hand in Drug Addiction
  29. Optogenetic CRISPR/Cas9
  30. Evolving a bigger brain with human DNA
  31. Computed Chromatin Conformation Verfied by CRISPR [Awesome Video]
  32. A Reporter System to Trace Dynamic Changes of DNA Methylation at Single-Cell Resolution

Epigenomic Controversy

Sometimes big ideas need pilots. These pilots need more verification before public exposure but aren’t always uninterpretable, however they should be read with caution in regards to over-interpreting. Small sample sizes aren’t always applicable to a diverse general population and could be noisy but these experiments may start some interesting thoughts and still reveal underlying biology. But sometimes press releases aren’t handled properly.

  1. A paper on Intergenerational Holocaust Effects on Stress Signalling lead to this popular press and then this interesting response.
  2. A talk at ASHG about Epigenomics of Homosexuality got made into popular press and was followed by this critique and subsequent rebuttal.

CRISPR Craze & Crisis

There was  a gene editing summit that called together the leaders of the field. Interestingly it represented a wide variety of the thought spectrum. They came to a conclusion I think most can get behind: don’t start engineering babies clinically, but let the basic research into editing embryos (that don’t go to term) go strong.

Also of interest was the tweeting and blogging of Paul Knoepfler via IPSCell that showed off some of the academic communicative power of social media.

Gene drives have caught my attention as well since they can hijack evolution. They have a lot of potential for disease, with Malaria being the trailblazer. However, they also conjure up images of a dystopia where there’s a new bioterrorism tool in town, capable of specific genocide with just a few genome edited agents needed to ‘infiltrate’ the population.

I’ve also been thinking alot about the designer baby CRISPR CRISIS, it seems that enough of prominet researchers in genomics dismiss the notion of it, since single genes rule very few traits, but I’m still quite worried about myostatin. The condition works in humans, is famous in cows, and has been done in pigssheep, and dogs. It’s just a single gene that can easily make your child athlete of the century or a soldier in a superhuman army. And of course, something about this old Spiderman comic strip reflects on the Stan Lee’s judgement of the current designer baby CRISPR CRISIS:

CVbG-8hWsAA4i4f.jpg-large

 

Advertisements

Two New FASD Papers

The journal Epigenetics & Chromatin just put out two interesting new papers about the epigenetics of FASD. The first is by Veazey et al. They found significant alterations to histone mods (H3K9me2, H3K9ac, and H3K27me3) at days 7 and 17 that are dose dependent and correlate to severity of phenotype. They also found changes to homeobox and histone genes, two things we saw in our own earlier mouse model but had not pursued. They also noticed that in this model, the profiles were different after a 4 day recovery period, something we’ve also seen when examining the short and long term transcriptional changes across a wider window but have not examined at the epigenetic level. Another similarity was that the chromatin mods don’t usually line up with current transcription, which is also in line with our developmental footprint idea. This observation was also complemented by finding altered transcription in a number of epigenetic writers. I also imagine some of the differences between models here relate to stem cell models and ontogeny.

The second paper is by Zhang et al. and deals with the discovery of a glutamate transporter that shows age and sex dependent alterations to expression. The transcriptional increase appears to be driven by decreased DNA methylation and an increase in activating H3K4me3. Also of interest was that while the mRNA levels were increased the protein levels were decreased, which appears to be an increase in an imprinted miRNA, from a cluster we’ve previously identified, which was functionally confirmed to bind. Interestingly, there was also a correlation between this miRNA in the brain and levels of it in the serum. While it is a mouse specific cluster, it hints that the other clusters shared with humans may leave the same clues.

In terms of caveats, both papers have a bit of a bias in that they were not scanning the genome but rather pre-picked players, but that is also just my omic bias talking. Overall, these papers continue to provide evidence for the consensus idea that FASD is in part maintained by an initial alteration combined with recovery response that may one day be narrowed down to certain drivers of phenotype. The targets arising from these groups, and our own, would make excellent candidates for epigenome editing, which we just published a review on in the very same journal.

Early Prenatal Alcohol Exposure and the Hippocampus

Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model” comes from the lab of Dr. Nina Kaminen-Ahola at the University of Helsinki in Finland. For those of you not caught in the niche of FASD epigenomics, while working with Dr. Emma Whitelaw and Dr. Suyinn Chong, she brought forth the first and founding wave of evidence that FASD is an epigenetic disease. My favourite of the papers is from the Agouti FASD mouse model, which paved the way for our understanding of Gene x Environment interaction by offering a model of the non-genetic inheritance of a trait being altered by the environment.

Now in her latest and as a PI, they continue on with their next model: ‘wild-type’ C57BL/6J mice., which is quite similar to our (Singh Lab’s) earlier model of the long-term effects of moderate prenatal alcohol exposure. The main difference is that this models timing is restricted to only the earlier stages of pregnancy and produces some powerful evidence for “no safe time, no safe amount”. They top it off with focusing in on the hippocampus, showing some interesting ethanol induced volume changes via MRI.

At the molecular level, they scanned the transcriptome using expression arrays and then followed up with qPCR confirmations and bisulfite sequencing of the candidate genes across a number of tissues. It’s interesting to see them so focused on a transriptomic approach that lead to their focus on rather different candidates. We’ve always found the epigenomic approach most informative in deciphering the transcriptional mess. However, that might also explain their choice of further investigation into histone variants and is also worth noting that buried in the supplementary (array database) of our epigenomic paper is altered methylation in the histone clusters.

Also of personal interest, was the confirmation of the genes very closely related to what we found in our transcriptomic approach of whole brain, which was interesting to see so faithfully replicated from a shorter exposure window and in a single brain region. The references and comparison to our past work is an honour, as their work has been so fundamental to ours. It’s great to see the science come full circle. And speaking of that, it has a nice press release as well, which drew my attention to their human epiFASD project.

Genome Editing Human Embryos

It seems that the ethical buzz was coming from a paper by a unknown Chinese group not involved with any of the genome editing pioneers. They took the unviable leftovers from In Vitro Fertilization (IVF) and then genome edited these human ’embyros’.

Interestingly, the success was quite poor. There was:

  • A Low Editing Rate
  • Toxicity
  • Rampant Off-Target effects

This in stark contrast to the use of CRISPR/Cas9 in dozens of animals ranging the entire tree of life. Ultimately, it doesn’t appear to be human limitation, as mammals including monkeys have been done much more successfully, but rather a result of poor experimental design, as these effects can be almost entirely attenuated by good guide RNA design and it seems that they didn’t considers the different chromatin states of embroynic stem cells that would influence off-target effects.

This was probably due to rushing the design in order to claim to be the first to alter human embryos, as opposed to the much more informative, well done, and ethically appeasing altering of Human Embryonic Stem Cells (HESCs) that showed off human CRISPR/Cas9 genome editing can be done properly in germ-line cells, with all its perks, and lead to breakthrough at the basic level in addition to all the clinical potential of genome editing technologies.

This speculation is apparent as there was a large outcry when the Chinese authors tried the ‘high impact’ journals and it seems they settled on a much lesser known open access that has additional concerns with the peer review process, mainly that it took one day, instead of 6 months to a year of the purgatory that is usually is.

Ultimately, it seems this was rushed for fame of unknown researchers and unknown journal, rather than science. But it’s still a Pubmed indexed journal with an impact factor and published by Springer. It is a bit of a shame as the Pandora’s box of CRISPR in human embryos needed to be opened quite slowly and carefully. The parts are all relatively easily accessible and not restricted, which is what has lead to spectacular pace of CRISPR/Cas9 genome editing development. While the field has its leaders developing CRISPR for the clinic the proper way, the technology it is now at the place where it can be picked up by many more who may not just be interested in the somatic line. But here we are now, waiting to see if genome editing technology will change the world, by curing inherited human disease or being used to design sci-fi nightmares. Either way, human inheritance has entered the designer era.

Sources:

  1. The Primary Publication
  2. Nature News
  3. Stem Cell Assays

The Paper We’ve Been Waiting For? CRISPR/Cas9 in Human Embryonic Stem Cells

Well it seems it has been done, the paper showing off the stuff science fiction has come out. CRISPR/Cas9 was used in human embryonic stem cells by the Meissner group at Harvard featuring J. Keith Joung and John Rinn.

“Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells”

Nature Genetics

Abstract: “DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Here we inactivated all three catalytically active DNA methyltransferases (DNMTs) in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing to further investigate the roles and genomic targets of these enzymes. Disruption of DNMT3Aor DNMT3B individually as well as of both enzymes in tandem results in viable, pluripotent cell lines with distinct effects on the DNA methylation landscape, as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to findings in mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome this immediate lethality, we generated a doxycycline-responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1-mutant lines. However, doxycycline-mediated repression of exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death. Our data provide a comprehensive characterization of DNMT-mutant ESCs, including single-base genome-wide maps of the targets of these enzymes.”

A Scientific Landmark: Inherited and Efficient Genome Editing of Human Embryos

With scientists a buzz, it seems that the dreams of sci-fi have become sic-fact. Apparently, papers are circulating where human embryos have been edited (but not taken to term):

“There are also suspicions that scientists have already created human embryos with edited genomes. Several researchers who do not want to be named told Nature’s news team that papers describing such work are being considered for publication.”

Source: Nature News

My suspicions of the players involved in the work or bringing it to public attention are some of the big 4 of (epi)genome editing: Feng Zhang, Jennifer Doudna, J. Keith Joung, and George Church. I think there is a good chance that George Church and army were involved somehow based on this recent interview with the MIT Technology Review.

It seems like the community doesn’t know what to think of the possibility as it came much early then most would have dreamed. The ability to alter simple Mendelian traits would have tremendous implications for inherited disease. Although, the off-target effects have been greatly improved from previous technologies, they are still there and concerning, but it may not be enough to stop some. Sure we’ve been able to create mutations before, but never with such accuracy, ease, precision, and potential for successful pregnancy with in vitro fertilization in a HUMAN. If it happens, I don’t think anyone would be able to consider the initial experimental optimization ethical.

Then again, this all just rumours and buzz with a bit conjecture. I’m quite curious to see the actual work and the levels of success achieved in the editing of embryos.