More papers.. :-)

As always, the world of science never sleeps, and hundreds of papers are published each week. Here is a list of what I found interesting this week, including a couple of reviews. Again, just my notes as I have been reading, but perhaps some of it is useful to others, too..

Stem cells (incl. gene editing):

Favourite because  it is simply cool! – Harrison et al. (Science 2017): Assembly of embryonic and extra-embryonic stem cells to mimic embryogenesis in vitro. It is almost like science fiction except that it is real. Cambridge researchers succeed in mimicking early embryogenesis in vitro by fostering close interaction between mouse embryonic and extramebryonic cells in a 3D Matrigel scaffold and specialised medium allowing co-development of such cells. The ESCs and TSCs self-assemble into a structure that faithfully mimics the natural embryo. Several developmental processes demonstrated (cavitation, early specification of endoderm and mesoderm, formation of primordial germ cells), including the underlying signalling mechanisms. This is crucial as it will allow future modelling of developmental process in vitro, reducing the requirement for animal studies.

Guénantin et al. (Diabetes, 2017): Functional human beige adipocytes from induced pluripotent stem cells. Very unfortunate not to have access to this; I have not actually come across a protocol for beige adipocytes from iPSCs before, so this would seem to be particularly novel and relevant. According to abstract, no overexpression of exogenous factors required and cells are functional upon engraftment in mice.

Mitzelfelt et al. (Stem Cell Reports, 2017): Efficient precision genome editing in iPSCs via genetic co-targeting with selection. Adding to the pile of papers dealing with improving the efficiency of CRISPR/Cas9-mediated gene editing in stem cells. Particularly relevant for disease modelling in the research lab. Note that this method doesn’t allow subsequent removal of the co-targeted antibiotic resistance gene which is incorporated into the safe-harbour AAVS1 locus. Interestingly, another group simultaneously published a similar approach in JBC, but their method relies on a transposable HDR reporter that can be used to enrich successfully edited cells (demonstrated in immortalised and immortalised cell lines; NB – not in stem cells, though). It is an elegant approach and worth keeping in mind. Importantly, the HDR reporter can be removed following successful knockins by adding Piggybac transposase to the cells. Paper details: Wen et al. JBC 2017 – A stable but reversible integrated surrogate reporter for assaying CRISPR/Cas9-stimulated homology-directed repair).

Araki et al. (Stem Cells, 2017): The number of point mutations in iPS cells and ntES cells depends ont he method and somatic cell type employed for their generation. Need to read properly, but would appear to be useful for people considering the use of iPSCs for disease modelling. It seems to suggest that point mutations are intrinsic to the process of reprogramming and are not a Yamanaka-specific phenomenon. The extent of point mutations during reprogramming might be reduced by careful optimisation of various reprogramming conditions, including consideration of the age of the parental line used for reprogramming.


Pappalardo et al. (Diabetes, 2017): A Whole Genome RNA Interference Screen Reveals a Role for Spry2 in Insulin Transcription and the Unfolded Protein Response. Unfortunately, no access but appears to be interesting in that Spry2 is a known GWAS hit for T2D, yet no previous connections to metabolic phenotypes. Mechanistic studies in cells and in mice according to the abstract.

Robinson et al. (Cell Metabolism, 2017): Enhanced protein translation underlies improved metabolic and physical adaptations to different exercise training models in yound and old humans. Although not scrutinised in detail, it is very interesting. This group sets out to assess the effect of different exercise modalities on skeletal muscle adaptations in young vs  old adults. Although n-numbers are modest, several significant effects emerge, and there are important insights into the molecular transducers of exercise adaptations. Mitochondrial proteins are, perhaps not surprisingly, topping the list. Ultimately, the study concludes that supervised HIIT appears to be an effective recommendation to improve cardiometabolic health in ageing adults.

Suzuki et al. (Cell Reports, 2017): ER Stress Protein CHOP Mediates Insulin Resistance by Modulating Adipose Tissue Macrophage Polarity. Haven’t read, but potentially relevant.


Barilari et al. (The EMBO Journal, 2017): ZRF1 is a novel S6 kinase substrate that drives the senescence programme. Decent paper and relevant for understanding the signalling mechanisms underlying oncogene-induced senescence (OIS); the protective mechanisms employed by cells against malignant transformation in response to hyperactivation of growth pathways such as PI3K/AKT. Hyperactivation of mTOR in vivo and in vitro leads to senescence in the absence of concomitant p53 mutations. This group demonstrates that the increase in p16 (cell cycle inhibitor involved in triggering OIS) is dependent on ZRF1  phosphorylation by S6K.

In the context of oncogene-induced senescence, it is interesting to note a Previews article in Cell Stem Cell covering a publication from last week that demonstrates an intricate link between senescence and cellular plasticity, whereby senescence-induced secretory factors trigger dedifferentiation in neighbouring cells – in a physiological context, this would enhance tissue regeneration, but it is easy to envisage how such a mechanism can be hijacked in cancer. Preview details: Taguchi & Yamada (Cell Stem Cell, 2017): Unveiling the role of senescence-induced cellular plasticity. Another paper that deals with this topic, published earlier this year: Ritschka et al. The senescence-associated secretory phenotype induces cellular plasticity and tissue regeneration (Genes & Development 2017).

Mitochondrial homeostasis in adipose tissue remodelling (Svetlana Altshuler-Keylin and Shingo Kajimura): pertinent review given the need for research into the relationship between mitophagy and energy metabolism. The authors outline the balance between mitochondrial generation and degradation (via global autophagy or selective autophagy, i.e. mitophagy). Mitochondrial damage = major physiological trigger for mitophagy. Such mechanisms are important in mitochondria-enriched cells, incl. brown and beige adipocytes. Mitophagy occurs through two different mechanisms: adapter-mediated (ubiquitin-dependent) and adapter-independent (ubiquitin-independent). The review highlights the need for controlled Cre line usage to elucidate the role of autophagy/mitophagy in defined cell types, such as preadipocytes and differentiated adipocytes. Previous genetic autophagy-deficient animal models have yielded inconsistent results due to use of multiple Cre lines with temporal differences in induction and affected cell type. Physiologically, autophagy regulation is tightly coupled to nutrient sensing via mTOR signalling. Another physiologically relevant pathway: PKA downstream of beta3-AR signalling, which is a known mediator of beige adipocyte biogenesis in response to cold exposure. PKA directly phosphorylates mTOR and its binding partner RAPTOR, activating the complex and thereby promoting autophagy inhibition. Mitophagy has to be activated when during beige-to-white adipocyte conversion. Mechanism under investigation. Dysregulation in obesity and metabolic diseases; autophagy blocks beige adipocyte development. Mitochondria are also critically important in the pancreas – for glucose-stimulated insulin secretion; on the other hand, autophagy maintains β-cell homeostasis by removing damaged mitochondria and/or ER. Autophagy is also important in liver metabolic control – here it prevents diet-induced liver steatosis. The review ends by listing methodologies that can be used for detecting mitophagy in adipocytes.

Other bits and pieces: 

GuideScan – new software to design single and paired CRISPR guide RNAs (Perez et al. Nature Biotechnology 2017)

Highly efficient RNA-guided base editing in mouse embryos (Kim et al. Nature Biotechnology 2017)


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