What I have read of interesting papers this week

Some useful reviews

One in Nature Medicine “Refining strategies to translate genome editing to the clinic” (Cornu et al. 2017). It covers some of the recent gene editing clinical trials and outlines key standardisations required to translate CRISPR and similar techniques into effective therapeutic strategies.

Brendand Manning and Alex Toker have written a comprehensive Cell review “AKT/PKB Signaling: Navigating the Network”. Looking forward to giving it a proper read!

Insulin signalling

Key paper in Cell: The Ubiquitin Ligase CHIP Integrates Proteostasis and Aging by Regulation of Insulin Receptor Turnover (Tawo et al. 2017)

Apparently, previous studies have shown that although CHIP-null mice exhibit normal embryonic development, lack of CHIP (ubiquitin ligase, key for cellular protein quality control) accelerates ageing. Also, the livers of these mice develop insulin resistance. Using C. elegans and D. melanogaster, this study demonstrates that under non-stress conditions, CHIP ubiquitylates INSR and targets it for endocytic (not proteasomal) degradation; however, under proteotoxic stress, CHIP is “busy” sorting out other damaged proteins and this results in increased INSR levels and enhanced downstream activation of PI3K/AKT signalling. Interestingly, they make a link to severe INSR due to mutations in the receptor by mentioning K1095E; apparently, they have identified this residue to be ubiquitylated. So the findings are extrapolated to speculations about the effects of metabolic insults on INSR degradation and therefore glucose homeostasis.

Metabolic

Chad Cowan and co. on “Activation of IRF1 in Human Adipocytes Leads to Phenotypes Associated with Metabolic Disease” (Friesen et al. 2017, Stem Cell Reports)

From Jens Brüning’s lab on IL-6: IL-6 improves energy and glucose homeostasis in obesity via enhanced central IL-6 trans-signaling (Timper et al. 2017 Cell Reports) – not read in detail, but abstract suggests that similar to leptin, central IL-6 signalling suppresses feeding and improves glucose tolerance, but its actions are actually enhanced upon challenging mice with HFD. And the mechanism of signalling is interesting – the soluble IL-6R complexes with gp130 on the target cell surface, hence why they call this trans-signalling.

Obesity-induced hepatic steatosis is mediated by endoplasmic reticulum stress in the subfornical organ of the brain (Horwath et al. 2017, JCI Insight) – not read beyond abstract, but might be of relevance. Apparently reporting an uncoupling of hepatic steatosis from other obesity-linked conditions – i.e. reducing brain stress can reverse NAFLD, but without altering body weight, food intake, adiposity, or hypertension.

β-Klotho deficiency protects against obesity through a crosstalk between liver, microbiota, and brown adipose tissue (Somm et al. JCI Insight) – also only given this one a brief skim of the abstract and the introduction.

Some “old” stem cell signalling knowledge

An 10-year-old paper, but nonetheless interesting for me…

Self-renewal of human embryonic stem cells requires insulin-like growth factor-1 receptor and ERBB2 receptor signaling (Wang et al. 2007, Blood)

The abstract of this paper rightly starts out by stating that little is known about the cell-surface receptors (and implicit signalling pathways) that are activated under conditions that support stem cell self-renewal – despite improvements in developing defined conditions. Advances have been made in the past 10 years, but I would still argue that a lot remains to be learned.

The hESCs used in this study are maintained in MEF-conditioned medium on Matrigel or in defined medium supplemented with Heregulin-1B, Activin A, IGF1 & FGF2. Following various stimulations, the cell lysates are profiled with RTK arrays (42 human RTKs) to identify activated receptors. Hits are subsequently validated with inhibitor studies.

There is a strong phosphorylation of IGF1R and IR upon addition of conditioned medium, and the study then goes on to determine that it is IGF1R specifically that maintains self-renewal and prevents differentiation in stem cell maintenance conditions. Interestingly, they find that the stem cells express high levels of IGF1R (flow cytometry) and very low expression of insulin receptor (IR), which is consistent with my observations of absence of a response to insulin stimulation, but a clear activation of PI3K/AKT signalling in response to IGF1 stimulation. Looks quite solid and they also show a requirement for ERBB2/3 signalling. One thing that surprises me, though, is that they perform GF-depletion studies (DMEM/F12 + 0.5 % BSA) overnight which is really harsh for stem cells – mine start to day after 3h.

Another study was published in Nature at the same time as this paper, supporting the notion that IGF1R signalling in stem cells is essential for their self-renewal potential (Bendall et al. 2007, Nature).

Delayed Accumulation of H3K27me3 on Nascent DNA Is Essential for Recruitment of Transcription Factors at Early Stages of StemCell Differentiation (Petruk et al. 2017a, Molecular Cell) – there is an accompanying paper by the same group Petruk et al. 2017b in Cell Reports as well.

This is quite cool, by the group who originally developed a chromatin assembly assay relying on PLA (proximity ligation assay) to study the structure of nascent chromatin. Here, they show that immediately following DNA replication in stem cells, there is a delay in H3K27me3 deposition on the DNA, which allows transcription factors induced by differentiation signals to bind to their target sites. This is a very finely tuned time window that allows for exquisite control of differentiation only when the right transcription factors are induced and when the chromatin is open. Because the time window is limited, it also prevents spurious binding of other transcription factors later on, essentially allowing the cell to reconfigure itself in the process of differentiation once the primary transcription factors have done their job. There is an accompanying news and views as well: A Determined “Hesitation” on H3K27me3 Empowers Stem Cells to Differentiate (Huang and Wang 2017, Molecular Cell). In the Cell Reports paper, which I haven’t read, they apparently show that the same is true for HSCs.

Of general interest

Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity (Saleheen et al. 2017, Nature)

Moving beyond non-human models to understand the complete  loss of certain genes in human. This is possible due to large scale sequencing of inbred populations that are likely to harbour two copies of rare mutations that result in complete loss of function for a particular gene. Really interesting and a more comprehensive catalogue of possible human knockouts is soon to come out. In this study, the authors link the discovered gene knockouts to more than 200 phenotypic traits, providing a detailed functional analysis. Interesting to go back and link the phenotypes to those observed in mice engineered to lack some of the same genes – you might be surprised at some of the discrepancies, cautioning us against thinking of mice as mini-humans. An accompanying news and views is also available at Nature.

 

Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency (Yang et al. 2017, Cell)

This is quite ground-breaking in the developmental world (if it stands the test of independent replication). The study reports the first ever derivation of pluripotent stem cells (both mouse and human) with both extraembryonic (i.e. can generate placenta etc.) and embryonic capacity, terms extended pluripotent stem (EPS) cells.

Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation (Slobodin et al. 2017, Cell)

Quite cool both on the biological and techy side of things. Very, very nice approach to screen for differential promoter effects by using a barcoded reporter, essentially designing a new technique “Barcoded polysomal profiling” (BPP). Biologically, the study reports that mA6 of RNA is an epigenetic mechanism that determines the future activity and fate of the transcribed mRNA, thereby indirectly coupling transcription and translation.

Not read in detail, but this sounds a bit cool (apparently, you can change the sex of C. elegans with fatty acids): Fatty Acids Regulate Germline Sex Determination through ACS-4-Dependent Myristoylation (Tang et al. Cell 2017 quite impressive with only 2 authors!).

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a (Swarts et al. 2017, Molecular Cell –  from the Jinek lab) – just one of those papers that are good to have; Cas12a = Cpf1, the cousin of Cas9, also used for gene editing. Different from Cas9 by being able to process its own guide RNAs + different PAM requirement + Cpf1 generates staggered cuts.

 

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