February 27

Lgr5 liver stem cells and Hepatic organoids

Meritxell Huch1,2

1Gurdon Institute, Wellcome Trust/ Cancer Research UK, 2Department of Physiology, Developmental Biology and Neuroscience, University of Cambridge, UK

 

Despite the enormous replication potential of the liver, there are currently no culture systems available that sustain hepatocyte replication in vitro. Hepatocytes can be maintained in culture for a few days. However, they lose their hepatocyte phenotype and function almost immediately, thus precluding its application for cell therapy treatments. Liver stem cells have the potential to self-renew and differentiate into functional hepatic lineages. We have recently described that, upon liver damage, the intestinal stem cell marker Lgr5 becomes highly expressed in the stem/progenitor cells that contribute to liver regeneration via de-novo generation of hepatocytes and ductal cells. Mouse liver stem cells can be indefinitely expanded in vitro (for >1 year), into "liver organoids", in our novel liver stem cell culture system, in the absence of a mesenchymal niche. The cultured cells express ductal markers and differentiate into functional hepatocytes in vitro and in vivo. We have now further developed our culture system to study human liver stem cells and human liver disease. We describe a culture system that allows the long-term expansion of adult human liver stem cells (>3 months) from donor biopsies while maintaining their differentiation potential towards functional hepatocytes in vitro. The expanded cells are highly stable at the chromosome and structural level, while single base changes occur at very low rates. The cells can readily be converted into functional hepatocytes in vitro and upon transplantation in vivo. Organoids from α1-antitrypsin deficiency and Alagille Syndrome patients mirror the in vivo pathology. Clonal long-term expansion of primary adult liver stem cells opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine and gene therapy.

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March 10

Epigenetic inheritance and reprogramming in the mammalian germline

Jamie Hackett1

1Gurdon Institute, Wellcome Trust

 

Epigenetic mechanisms act to define and restrict cellular identity. In mammals, primordial germ cells (PGC), the precursors to sperm and oocytes, undergo unprecedented reprogramming including global erasure of DNA methylation and genomic imprints. This process resets the epigenome to enable the acquisition of totipotency – the capacity to form all cell types – in the zygote. We have been investigating the mechanism that drives comprehensive epigenome resetting in PGCs and find a key role for TET-mediated 5-hydroxymethylation. We also find rare loci that escape from epigenetic reprogramming in PGCs. The epigenetic states at these genomic sites may represent a mechanism for transgenerational epigenetic inheritance, which may be sensitive to environmental perturbations

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March 26

The 1000 Genomes Project and Beyond

Laura Clarke1

11000 Genome Project Consortium, EMBL-EBI, Wellcome Trust Sanger Institute

 

The 1000 Genomes Project provides an essential reference catalog of human variation with more than 60 million variant sites ranging from single nucleotide polymorphisms to structural variant events including inversions and duplications. Also provided are global allele frequencies and genotypes for 2535 individuals from 26 different populations across Europe, Africa, East and South Asia and the Americas, which enable many other projects to better interpret their results. Primary uses for the 1000 Genomes data sets include imputation panels to create whole genome variant sets from exome or array-based genotypes; as filters of “normal” or shared variation in rare disease or cancer sequencing projects; and to explore demography and selection in human populations.

 

The 1000 Genomes Project is now drawing to a close. Here we describe plans to maintain the resource in order to ensure it remains the valuable data set it is today by providing long-term support for the 1000 Genomes Project resource. We will continue to host both the FTP site (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp) and the project website (http://www.1000genomes.org) to ensure the community can access both the raw data and the documentation about the project. There will also be a stable version of the 1000 Genomes Browser (browser.1000genomes.org) based on the project's final date release. This project specific Ensembl-based browser displays all of the 1000 Genomes variants as soon as possible and will use the GRCh37 assembly of the human reference genome.

 

We will also maintain the existing tools and incorporate new ones as appropriate to enable users to easily access the data they desire. Our most popular tools are the Data Slicer—that allows users to select genomic subsections of our alignment (BAM) and variant (VCF) files and thus download just the piece of the file they need—and the Variation Pattern Finder, which allows users to discover patterns of shared variation in a specific region of the genome. Other tools include the VCF to PED converter, which allows users to generated PLINK format files from remotely hosted VCF files and the recently introduced the Allele Frequency Calculator that will calculate allele frequencies in bulk for specific sub populations from our VCF files.

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April  16

Super-resolution imaging - Getting and understanding, microscopy images with more details

Martin O. Lenz1

1Cambridge Advanced Imaging Centre, Department of Physiology, Development and Neuroscience 

 

Recently the Nobel prize in Chemistry has been awarded ‘for the development of super-resolved fluorescence microscopy’. The field is still comparatively young and the set of these techniques can be utilised in many different ways. They were developed over the last decade and allow to visualise processes of interest with much finer structure than what is possible with conventional microscopy. In order to visualise specimen at the nm-­scale some methods rely heavily on complex optical implementations while others are based on sophisticated image processing techniques. I will be presenting an overview of various super-resolution techniques for light microscopy including their respective advantages & disadvantages.