The International Society for Stem Cell Research (ISSCR) Annual Meeting was held June 16-19, 2010 in San Francisco, CA. Luckily for us Rutgers University Graduate Fellow, and EpiGenie friend, Jonathon Davila was there to soak in all the latest research he could find. Check out some of the event’s highlights from his report below:
I arrived in San Francisco after a long journey across the country wanting only to head straight to the hotel for a nap. But there was no time for that, so off to the meeting I went. I had heard the quote by Mark Twain stating that the coldest winter he experienced was a summer in San Francisco. I thought it was a symbolic statement because I had no idea how cold it could get in this town during the summer. But things warmed up once I arrived at the convention center as I was exposed to some of the hottest research topics in stem cell biology.
Chromatin Remodeling And Epigenetic Plasticity In Development
Joanna Wysocka, Stanford University
Joanna Wysocka was awarded the “Outstanding Young Investigator Award” at the meeting, which isn’t surprising after watching her talk. Her studies focused on chromatin remodeling and epigenetic plasticity during development. She combined hESCs and epigenomics to discover human cell type specific enhancers in specific cell types. Her focus was on neural crest lineage cells (NCLC). She did chip-seq with anti-p300 for ESC, NSC, NCLC cultures. She “rediscovered” known neural crest-specific enhancers such as SOX9, SOX10. Using GREAT, a novel tool to analyze functional significance of cis-regulatory regions (McLean Nature Biotech, 2010, Bejerano lab), she discovered over 2500 regions bound in NCLC but not the other stages. These were mostly distal, over 10 Kb away from TSS. The top 22 enriched categories given by the software were mostly related to facial morphology. She also chip-seq’d CHD7, an ATP dependent chromatin remodeler, in NCLCs. CHD7 is another player (in addition to p300) at enhancers.
She found this protein bound, for example, SOX9. Mutations in CHD7 have been previously associated to CHARGE syndrome, a sporadic disease which affects facial and cranial malformations. In order to test phenotypic relevance, she infected hESC with dox-inducible, RFP-linked shRNA and showed that CHD7 shRNA result in complete loss of migratory population from neural rosettes in cultures during a neural differentiation protocol. She then tested this in an in vivo Xenopus system, where knockdown or overexpression of a dominant negative mutant for CHD7 abolishes migratory cells in embryo. This recapitulates CHARGE disease. CHD7 is required for expression of Sox9, Twist, Slug, all associated with neural crest specification. In her model, CHD7 regulates transcription after binding enhancers distal to TSS by remodeling chromatin (K4me1, K27ac). This was an excellent talk because she merged development, epigenetics and diseases in one coherent story. It really showed a functional aspect to epigenetic studies.
Repression Of Let-7 MicroRNA By Lin-28 And Tut4 In Embryonic Stem Cells
V. Narry Kim, Seoul National University
V. Narry Kim described a beautiful mircoRNA regulatory pathway. In the past her lab and others had shown that the processing of certain pre-let-7 family members by Dicer was regulated by Lin-28. In this talk she demonstrated that Tutase 4 (Tut4) is a crucial component to this regulatory pathway. Narry showed that Tut4 serves to urydilate pre-let-7 in a Lin-28 manner. In ESCs, when Lin-28 is present, Tut4 will add a chain of U’s to the 3’ end of the Let-7 precursor. This addition of multiple U’s to the precursor is what inhibits Dicer from cleaving the precursor into the mature let-7 form. Furthermore, when Lin-28 is absent, Tut4 can add only one U to the Let-7 precursor. This single addition of one U increases the Dicer procesivity of pre-Let-7. Interestingly she also found in HeLa cells that multiple precursors are urydilated in the absence of Lin-28 suggesting that there are other pathways regulating the maturation of microRNAs after their transcription as primary transcripts. This microRNA story just gets more interesting every time something new comes out.
MicroRNA Stabilization Of The Switch Between ESC Self-Renewal And Differentiation
Robert Blelloch, UCSF
Robert Blelloch started his talk by giving a nice review on the biogenesis of microRNAs. He then began to explain their role in ESCs as regulatory switches between self-renewal and activators of differentiation. Using mouse DGCR8 KO ESCs he was able to show that different families of microRNAs have opposing roles in ESC maintenance. DGCR8 KO ESCs can self-renew but lack the ability to differentiate or to lose pluripotent markers. To test if individual microRNAs could rescue this phenotype he screened approximately 300 microRNAs and identified 9 that could clearly silence the self-renewal capacity of these cells. Amongst these 9 were members of the let-7 family. Interestingly, exogenous expression of let-7 family members in WT mouse ESCs was not sufficient to stop self-renewal. This supported the idea that there are microRNAs with opposing functions being expressed in the WT cells. He then described very nicely a model in which Let-7 and mir-294 serve opposing roles in ESC maintanace by regulating myc pathways. He finished his talk showing some early data that indicates that Dicer dependent endo-siRNAs are important in meiosis but microRNAs are not.
Directing And Redirecting Cell Fates
George Daly, Children’s Hospital in Boston
George Daly suggested that current IPS cells retain some kind of epigenetic memory from their original cellular phenotype. He first compared methylation states of IPS cells to true ESCs using the CHARM methylation method. Looking at all CpG islands in the genome, they observed that the IPS cells genome showed more hypermethylated locations than ESCs. He also stated that it was easier to differentiate IPS cells to blood cells if they were originally derived from blood cells rather than bone cells. He also saw the opposite with the bone derived IPS cells; these were able to differentiate towards bone cells more readily than blood derived IPS cells. These observations are critical because if the scientific community intends to harness the power of IPS cells for clinical or just purely investigative applications, we must learn to optimize the reprogramming of the cells. This includes removing any trace of the original cellular phenotype, be it cellular markers, mRNAs, non-coding RNAs, epigenetic markings, etc… In other words we must learn to strip these cells down to a clean slate before we begin to try to direct their differentiation.
Neuronal Plasticity And Diversity
Fred “Rusty” Gage, Salk Institute
One of the coolest talks was given by the keynote speaker, Rusty Gage. I must confess that his talk was so high-level that I am still trying to grasp the full implications of his observations. He started his talk with his normal intro about adult neurogenesis and the factors that regulate it (enriched environment, exercise, stroke, etc…). Then all of a sudden, he began to talk about L1 retrotransposomes and LINE elements. His lab had developed a L1-GFP reporter system that could track transposition events. Interestingly, they only saw the transposition events in mouse neural progenitor cells. When they searched for the genomic locations of these insertions, they found that over 50% of them landed in neuronal genes.
One of the events was mapped to Psd-93 and it caused the gene to be differentially expressed and cause a neuronal phenotype to arise. He then used his L1-GFP reporter to measure L1 transposition activity in human ESCs differentiating towards neurons and saw the major activity to occur during the early differentiation steps. He also quantified the transposable events by qPCR in different autopsied human tissues. He found that there were ~1000-10000 more copies in brain tissues than in liver or heart, and was able to estimate that there must be 80-300 insertions per neuronal cell. He finished up providing some data to support a model in which MeCP2 could regulate L1 expression in progenitor cells. Furthermore, he linked this to Rhett Syndrome in humans. The implications of these studies are incredible because if he is correct, practically every neuron in the brain could have a unique genome. By altering genomic sequences in cis, neuronal cells would be able to exponentially expand their potential of neural plasticity.
**EpiGenie would like to thank Jonathon Davila from the Stem Cell Research Center at Rutgers University for providing this conference coverage.