Modern peer review, science communication and this week’s science news

Modern peer review

At the time of writing this blog post, I am enjoying the lunch provided by the organisers of a workshop on “How to get the most out of modern peer review?” (it is being filmed so you can benefit from it, too!). I have learned a lot, and some things are worth sharing. The first presentation by Wei Mun Chan, Editorial Manager at eLife, offered valuable insight into consultative peer review where reviewers engage in a discussion with each other and feed back to the editors. The final decision letter and the author feedback is also openly accessible to promote greater transparency. This is just one example of a great initiative to promote faster peer reviews, less bias during the process and increased transparency. On to the second presentation, Dr Sabina Alam from F1000 introduced their open-science publishing platform where the paper/data comes first, followed by a transparent peer review process. The whole life-cycle of the paper can be followed openly by the readers who are also invited to comment and review the paper publicly. F1000 allows the publication of multiple types of data, including single findings, as long as it is reported correctly and meets scientific standards. So if you have old reagents gathering dust in the lab and projects that were terminated prematurely, why not share it with the rest of the world? Someone might be able to take it up and build on your efforts. You will get recognition for it, too! In the same vein, F1000 promotes the dissemination of scientific posters and PowerPoint slides; these do not undergo peer review, but are assigned a DOI and are therefore citable – GREAT!

Next we heard from Dr Laurent Gatto from the Proteomics Research Unit here at Cambridge. He gave us some tips for good reviewing, and you can view those online as Dr Gatto shares his material openly. In summary, make sure that the data is always there, that the names and numbers match up, that the metadata is available and the science reproducible!

The final talk before lunch was given by Tom Culley, Marketing Director at Publons. This is my first encounter with Publons, and I am impressed. What a great initiative to give scientists recognition for their peer review work! This can only improve the quality of the published science because reviewers have an incentive to do well and will be recognised for it. Publons creates a complete track record of all your reviews and you can even add past reviews to obtain the deserved credit for them. Another great initiative to foster trust and integrity in research!

I am looking forward to the last sessions and a workshop by Dr Varsha Khodiyar, Data Curation Editor at Scientific Data!

Writing for non-scientists

I have recently had to write a grant application which forced me to think carefully about wording when describing my research to the general public. I quickly realised that I will need much more trial-and-error experience to become as good as my supervisor (who has the added benefit of being a clinician who talks science to non-scientists all the time!). Luckily, there are many good guides available on the internet, and I have just come across a very useful collection provided by eLife on how to write plain language summaries! Looking forward to putting these into practice as I will be writing a guest blog for the Biochemical Society which is quite exciting.. Also, if I have time, I would really like to have a go at writing a story for the Biochemical Society’s Science Communication Competition!

Finally, a bit from the research world…

I haven’t had a chance to look at these in detail yet, but here are some papers that caught my attention this week. Fingers crossed for solid data reporting!

Phosphorylation of the exocyst protein Exo84 by TBK1 promotes insulin-stimulated GLUT4 trafficking (http://stke.sciencemag.org/content/10/471/eaah5085)

Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states (https://elifesciences.org/content/6/e20487)

Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions (http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3834.html)

Lysosomal cholesterol activates mTORC1 via an SLC38A9–Niemann-Pick C1 signaling complex (http://science.sciencemag.org/content/355/6331/1306)

Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells (http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3805.html)

The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue (http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.4297.html)

Some recent reads.. So much new science!

Metabolism and physiology

An adipo-biliary-uridine axis that regulates energy homeostasis (Deng et al. 2017 Science Signaling)

Copied lay description: “The nucleoside uridine is well known for its role in critical cellular functions such as nucleic acid synthesis. Its role in whole-animal physiology has received comparatively little attention. In mammals, plasma uridine levels are tightly regulated, but the underlying mechanisms are unclear. Studying mouse models, Deng et al. show that plasma uridine levels are controlled by feeding behavior (see the Perspective by Jastroch and Tschöp). Fasting causes an adipocyte-mediated rise in plasma uridine, which triggers a lowering of body temperature. Feeding causes a bile-mediated drop in plasma uridine, which enhances insulin sensitivity in a leptin-dependent manner. Thus, uridine is part of a complex regulatory loop that affects energy balance and potentially contributes to metabolic disease.” – read through it briefly, and it is quite interesting!

Pik3r1 is required for glucocorticoid-induced perilipin 1 phosphorylation in lipid dropled for adipocyte lipolysis (in press in Diabetes; by Kuo et al.)

  • Not read in detail, but claims to demonstrate a role of p85a independent of its regulatory function as class IA PI3K components.. Would be worth reading in detail as I can imagine multiple confounding factors given the deinhibition of the catalytic p110 subunit in the absence of p85a.

Stem cell and developmental biology

Autophagy maintains the metabolism and function of young and old stem cells (Ho et al. 2017 Nature)

  • Aim of study: to identify how autophagy controls hematopoietic stem cell function, and how changes in autophagy levels control HSC ageing.
  • Results: autophagy plays a critical role in preserving HSC functionality by clearing aged mitochondria. This maintains HSC quiescience and stemness. Decreased autophagy with age, resulting in lower regeneration potential.

Human haematopoietic stem cell lineage commitment is a continuous process (Velten et al. Nature 2017)

  • This is an interesting topic, particularly because I recently attended a talk by Dr Ana Cvejic who talked about the current debate about the accuracy of the current haematopoietic lineage tree. Are there distinct intermediate steps from a multipotent stem cell to a unipotent cell? Or does the transition occur directly? This confusion largely stems from the reliance on cell surface markers to identify distinct cell populations. Instead, a call was made to incorporate single-cell transcriptional analyses as part of future studies.
  • This is exactly what this study has done and it describes that the tree-like structure of haematopoiesis is incorrect as haematopoietic stem cells appear to acquire differentiation biases in a gradual manner without passing through discrete intermediate states.

 PI3K/AKT/mTORC signalling pathway

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide (Matsumoto et al. Nature 2017) – from January but only got around to looking at it now. The second long non-coding RNA that seems to play a role in regulating this signalling pathway (see Lin et al. Nature Cell Biology 2017 for another example). What’s special about this one is that its regulatory role depends not on its non-coding properties, but on a hidden protein-coding sequence. The peptide that is produced by LINC00961 is expressed in a tissue-specific manner and restricts mTORC1 activation in response to amino acids.  It is demonstrated that this mechanism has a functional importance in muscle regeneration in mouse model organisms.

 PARK2 depletion connects energy and oxidative stress to PI3K/Akt activation via PTEN S-Nitrosylation (Gupta et al. Molecular Cell 2017; Lewis Cantley one of the last authors)

  • PARK2 is commonly deleted in cancer, and this paper demonstrates a novel regulatory mechanism that involves indirect PARK2-induced activation (via decreased removal of damaged mitochondria) of eNOS. Activation of eNOS in this setting promotes S-nitrosylation of PTEN and its subsequent Ubiquitin-dependent degradation. This mechanism was demonstrated in specific cancer cell lines and other immortalised cell models. Supporting its pathological importance, PARK2 and PTEN loss occur together in many cancers – if one PTEN allele is lost, the protein product of the remaining allele will suffer increased degradation upon concomitant PARK2 The only thing that is missing from this paper is a clear statement of the number of independent experimental replicates that they produced!

Amino acid – insensitive mTORC1 regulation enables nutritional stress resilience in hematopoietic stem cells (Kalaitzidis et al. 2017 JCI; Sabatini as one of the last authors)

  • Interesting paper because of increasing evidence in the stem cell worls that mTORC signalling is carefully regulated, partly to maintain low protein synthesis rate.
  • The authors suggest that a nutrient-insensitive mTORC1 in HSCs is part of a protective mechanism against variable nutrient availability and oncogenes due to excess nutrient stimulation.

A key leading edge review from Sabatini: mTOR signalling in growth and disease (Cell 2017)

 

 Technical

GuideScan software for improved single and paired CRISPR guide RNA design (Perez et al. 2017 Nat Biotechnology)

  • For the CRISPR users out there, the Ventura lab offer a new and superior tool for CRISPR gRNA design with improved specificity compared to commonly used competitor tools. Utility demonstrated for non-coding DNA regions.

Optimized labeling of membrane proteins for applications to super-resolution imaging in confined cellular environments using monomeric streptavidin (Chamma et al. 2017 Nature Protocols)

  • This seems quite cool and relevant if you want to perform cell imaging experiments with the aim to define target-specific trafficking events. The monomeric streptavidin labelling method has the advantage that the tag is very small, hence the fluorescent probe will be right in the vicinity what you want to study which is important for reliable superresolution results. The tag is only 15 aa big.

I came across an “older” paper from 2015 on CRISPR sgRNA designs by Farboud, B. and Meyer, B. (Genetics 2015); they describe improved targeting efficiency if the sgRNAs have a 3’ GG motif in addition to the 3’ terminal NGG PAM site. Worth a read..

Diet/exercise and other interesting bits and pieces

Went back to read Raubenheimer and Simpson’s review in Annual Rev Nutr 2016 which describes their nutritional geometry framework that advocates a holistic approach to nutrition science. Instead of focusing on the effects of a single nutrient in isolation, we should explore how different food components interact and how an animal’s behaviour, including foraging, is dependent on multiple environmental variables that are often left out in reductionist-type nutrient science. It is also worth having a look at the same authors’ Cell Metabolism paper from 2014: The Ratio of Macronutrients, Not Caloric Intake, Dictates Cardiometabolic Health, Aging, and Longevity in Ad Libitum-Fed Mice.

 Dieting, independent of genetic factors, has been shown to result in long-term weight gain – by yet another study (International Journal of Obesity, Pietiläinen et al. Does dieting make you fat? A Twin Study).

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.

Metabolism

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.

Signalling:

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)

Reading nuggets from this week (for scientists)

My favourite occupation is to read scientific papers and here is a biassed list of what I have come across recently.. Unfortunately, it would require technical knowledge, so probably most appropriate for scientists themselves.

My favourites because they are relevant for my stuff: 

A very important contribution in Nature Cell Biology by Liu et al.: G1 cyclins link proliferation, pluripotency and differentiation of embryonic stem cells. Demonstration that multiple cells are actually capable of proliferating in the absence of any of the G1 cyclins (D + E) – contrary to the prevailing model; however, pluripotent stem cells lose their pluripotent proficiency and acquire a trophectodermal cell fate (as well as a propensity to generate neural tissue in chimerism studies). The underlying mechanism comprises G1 Cyclin/CDK-mediated phosphorylation of the core transcription factors NANOG, OCT4 and SOX2. This is suggested as a potential contributing mechanism to the acquisition of pluripotency traits in malignant cells. Very interesting given the link between PI3K/AKT activation and Cyclin D + CDK2 upregulation. Note that individual loss of either Cyclin D or E doesn’t result in pluripotency loss. Also, the studies are performed in MEFs isolated from genetically engineered mice of the right genotype.

Review in Nature Communication by Dejana et al.: The molecular basis of endothelial cell plasticity. Covers early endothelial development, and the remarkable cell fate plasticity exhibited by endothelial cells. Essentially, all aspects of endothelial cell commitment and their ability to transition into haematopoietic stem cells or cardiac mesenchyme are dependent on the same set of pathways, which include VEGFR1/VEGFR2 and c-KIT signalling, i.e. PI3K activation.

A Stem Cell paper from Harding et al.: Highly Efficient Differentiation of Endothelial Cells from Pluripotent Stem Cells Requires the MAPK and the PI3K Pathways. The most useful bit of this paper is the development of an efficient endothelial cell differentiation protocol from human pluripotent stem cells that doesn’t require cell sorting. As of the claim that PI3K and MAPK pathways are essential, I would like to see more detailed evidence beyond the use of broad-spectrum inhibitors.

Signalling studies and molecular biology

The Yudushkin lab (same guy who recently published a nice Molecular Cell paper PIP3-dependent restriction of AKT activity to cell membranes) have contributed a paper to JCB, examining the localisation of mTORC2 activity (Ebner et al. 2017: Localization of mTORC2 activity inside cells). The starting question was how growth factors couple to mTORC2 in order to induce downstream phosphorylation of AKT. Previous studies had provided some evidence that mTORC2 associates with mitochondria, ribosomes, endosomal compartments and the plasma membrane. However, not much known regarding which of these membranes link to mTORC2 activity in a cellular context and whether there are pool-specific contributions to AKT activation. One outcome of the current study is, therefore, the development of a tool that allows tracking of mTORC2 enzymatic activity towards AKT within the cell. Important findings from this paper include: PM-associated mTORC2 is constitutively active towards AKT; hence neither growth factors nor PI3K inhibition has an effect on mTORC2 activity at this cellular site – however, PI3K activity is required for mTORC2 activity at early and late endosomes. Studies performed in HEK293s, so will be interesting to see if this is replicated in additional cell types in the future.

Metabolism, T2D, obesity incl. adipocyte studies 

Nature paper by Wong et al. The role of fatty acid β-oxidation in lymphangiogenesis. Haven’t read beyond abstract and discussion, but interesting concept! Turns out that β-oxidation, as expected, contributed to energy generation and nucleotide synthesis, as well as epigenetic regulation through Acetyl-CoA-dependent p300-mediated histone acetylation of the PROX1 gene, which is important for VEC to LEC differentiation. Multiple reports out recently that elegantly demonstrate the integration of metabolism and cell fate commitment.

Cell Metabolism paper by Mauro et al. 2017 (K. Okkenhaug is a co-author): Obesity-Induced Metabolic Stress Leads to Biased Effector Memory CD4+ T Cell Differentiation via PI3K p110δ-Akt-Mediated Signals. Haven’t read it in detail, but this is the summary provided by the journal (seems relevant!): “Lymphocyte infiltration of non-lymphoid tissues, including adipose and vascular tissues, is a prominent feature of chronic inflammation in diet obesity. Mauro et al. find that the saturated fatty-acid palmitate activates a PI3K p110δ-Akt pathway leading to CD4+ T cell differentiation into effector memory-like T cells upon priming in obese mice and humans.”

A nice Cell Metabolism review on ketogenesis and alternative functions of ketone bodies; Puchalska, P. & Crawford, P. 2017: Multi-dimensional Roles of Ketone Bodies in Fuel Metabolism, Signaling, and Therapeutics

A paper in Diabetes (Ehrlund et al. 2017: Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution), published a few a weeks ago, explores the transcriptional dynamics of adipocytes subjected to differentiation in vitro. Unfortunately, I can’t get access to the paper even when I login. From the abstract, however, I gather that it might be relevant as the study profiles the expressional changes of genes, enhancers, and long noncoding RNAs and demonstrates that enhancers expressed during adipogenesis overlap with SNPs associated with white adipose tissue distribution. The paper should contain useful time courses with important distinctions between downregulated, transient and late-induced transcripts, such as relationships to hypertrophy and insulin sensitivity.

Another report in Diabetes by Ralph de Fronzo (big name in the field I believe; Gastaldelli et al. 2017: Role of Adipose Tissue Insulin Resistance in the Natural History of T2DM: Results from the San Antonio Metabolism Study) investigates the role of adipose tissue insulin resistance in the natural progression to Type 2 Diabetes in humans. Specifically, they recruited 302 subjects varying glucose tolerance (normal, impaired, Type 2 Diabetes), subjected them to an OGTT (oral glucose tolerance test) and an euglycaemic insulin clamp and profiled their insulin sensitivity alongside plasma free-fatty acids (FFAs). A progressive decline in insulin sensitivity was accompanied by impaired FFA suppression, but overt hyperglycaemia was only established with the progression to T2D. Results are kind of expected in light of the burgeoning mouse literature on the topic as well as epidemiological studies, but I suppose it had not been formally demonstrated in human beings.

PIK3CD papers that might be relevant

Compagno et al. Phosphatidylinositol 3-kinase δ blockade increases genomic instability in B cells (Nature 2017); mechanism relies on the ability of PIK3CD to suppress activation-induced cytidine deaminase (AID) in B cells, where this enzyme promotes class switching of immunoglobulin genes.

 

 

Just out of interest…

The Biochemical Society’s recent Biochemist issue focussed on Gender Medicine. All too often, the variable “sex” is ignored in biomedical research, and that needs to change. Personally, I can see why it can be difficult to always include XX and XY in your research – after all, this doubles the resources required for your study. I suppose funders need to be more supportive in this respect! The issue also contains additional interesting reads on science policy and outreach, so have a look if you can gain access to it via the following link (not sure if you are not a member): http://www.biochemistry.org/Portals/0/Biochemist/February2017Biochemist-smaller2.pdf?utm_medium=email&utm_campaign=Biochemist%20Online%20-%20February%202017&utm_content=Biochemist%20Online%20-%20February%202017+CID_4dbf76701bce671026dc91550506090f&utm_source=Campaign%20Monitor&utm_term=pdf

One step closer to understanding consciousness? A group in the U.S. discovered the existence of mouse neurons that seem to wrap around the whole brain; the group believes that this might underlie the mechanism of consciousness as the three neurons seemed to connect to most or all of the outer parts of the brain that take in sensory  information and control behaviour. Furthermore, the Read the Nature News & Views here: http://www.nature.com/news/a-giant-neuron-found-wrapped-around-entire-mouse-brain-1.21539?WT.ec_id=NEWS-20170302&spMailingID=53538106&spUserID=MTExMDUzNjM3NTkxS0&spJobID=1120320868&spReportId=MTEyMDMyMDg2OAS2

 

 

Interesting papers, week 8

I realise that week 8 was last week, but I thought I would share the regular paper digest that I send out to people in my lab each week. I love papers and reading about exciting, new science. Sometimes, I also come across publications, even high-impact ones, that are actually flawed in some way or other, and I think it is important to evaluate all new findings critically and highlight potential misinformation.

So join the discussion and add to this list of papers if you have come across something that excited you recently, or perhaps a paper that should be highlighted as problematic!

In future posts, I will try to be more detailed as this is taken straight from an email sent out to the lab!

Transcriptional activation of lipogenesis by insulin requires phosphorylation of MED17 by CK2 (Science Signaling)
Report on how MED17 is phosphorylated by CK2 in response to insulin, but only if it hasn’t been phosphorylated by p38 – something that happens during fasting. MED17 interacts with USF1 in order to be recruited to the FASN promoter. Mechanism demonstrated in liver in vivo and in hepatocytes in vitro. MED17 is a core component of the Mediator complex, by the way. The Mediator complex recruits RNA pol II to active promoters and initiates gene transcription. Lots of biochemical stuff in this paper, too – seems decent.
Pentraxin-3 is a PI3K signaling target that promotes stem cell – like traits in basal-like breast cancers (Science Signaling)
The role of PTX3 appears to be dependent on the particular tumours, but in basal-like breast cancers it seems to enhance PI3K-dependent hyperactivation of key cancer phenotypes. Stem cell-like properties not investigated directly – inferred by observation that PTX3 is highly enriched in mesenchymal / mesenchymal stem cell-like breast cancers.
 
Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras (Cell)
It is not directly related to what we do, but good inspiration for what is possible in the future if you want to get a step closer to personalised medicine; i.e. analyse gene essentiality relationship in mutant iPSCs subjected to a CRISPR screen and identify specific liabilities that can guide potential future treatment. Also good discussion on synthetic lethality in cancer and how it may differ for oncogenes compared to mutations in “caretaker” genes.
Two back-to-back Nature papers on GATORs and mTORC1 regulation in relation to nutrient sensing (haven’t read in detail, but seem interesting, and apparently the identified components have been identified in neurological disorders that lead to mTORC1 hyperactivation!): 
 
KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1 (Sabatini lab)
SZT2 dictates GATOR control of mTORC1 signalling (Quite impressive with only 3 authors: Min Peng, Na Yin, Ming Li)
The LINK-A lncRNA interacts with PtdIns ( 3 , 4 , 5 ) P 3 to hyperactivate AKT and confer resistance to AKT inhibitors (Lin et al. Nature)
Seems cool, but not read in detail yet as it has A LOT of complex biochemistry so don’t read if your brain is mushy!
Lipid transport by TMEM24 at ER–plasma membrane contacts regulates pulsatile insulin secretion (Lees et al., Science)
Same as above.

A high-throughput, image-based screen to identify kinases involved in brown adipocyte development (Perdikari et al., Science Signaling)

Also not read properly. Using two orthogonal approaches – lentivirus-mediated shRNAs to knockdown kinases (the whole mouse kinome actually!) as well as kinase-specific inhibitors. Apparently, they see that knockdown of the insulin receptor results in improved BAT differentiation!

DNA damage is a major cause of sequencing errors, directly confounding variant identification. (Science)
Seems quite important for the sequencing crew.. Not read beyond abstract, but it suggests that DNA damage during the preparatory stage of DNA for sequencing leads to spurious findings of low-frequency variants, i.e. false-positives. This has implications for the identification of true somatic variants.
Adipose-derived circulating miRNAs regulate gene expression in other tissues (Nature)
I do believe the demonstration that adipose tissue is an important source of miRNAs and that these are likely to regulate other tissues, in an adipose tissue-specific and receptor tissue-specific manner; I will believe the miR-99b story outlined in this paper upon further validation as the stats are not great and n-numbers are low.
Labeling proteins inside living cells using external fluorophores for microscopy. (eLife)
Teng et al. optimise the use of the pore-forming bacterial toxin streptolysin O (SLO) to create small pores in cell membranes in order to facilitate the labelling of intracellular proteins with membrane-impermeant probes, allowing the study of the targeted proteins in live cells. Probes range in size from 2 kDa to 150 kDa; optimised for labelling of cytoplasmic or nuclear proteins, transfected or non-transfected (hence possibly to avoid overexpression artefacts). Cells retain intact membrane structures following recovery. Relevant following our discussion of click chemistry and the issues relating to intracellular labelling of proteins. Also relevant for super resolution imaging applications. Notably, labelling with probes <2 kDa results in background-free labelling because the unbound probe is able to diffuse out through the formed pores during the recovery phase.

 

New Year, new blogpost, new language: my project in Danish!

For friends and family in Denmark (+ any other interested Danish readers), finally a description of what I spend most of my wake hours doing. I hope it makes sense!

Hver gang jeg kommer hjem til Danmark, bliver jeg mødt af velmente spørgsmål og bemærkninger vedrørende min forskning:

”Hvad er det præcist, du laver?”

”Er det ikke diabetes, du forsker i?”

”Du finder vel sikkert kuren mod kræft!”

”Ej, det lyder godt nok specifikt og komplekst.”

Det er skønt, at folk er oprigtigt interesserede i mit arbejde! Og det er på tide, at jeg takker for interessen ved at trylle mystikken væk og give jer alle en (forhåbentligt) forståelig beskrivelse af, hvad jeg bruger de fleste af mine vågne timer på.

Tænk dig først tilbage til den tid, hvor du lå gemt i din mors mave. Er det ikke utroligt, at sammensmeltningen af en ægcelle og en sædcelle på 9 måneder kan føre til fødslen af en oftest velskabt menneskebaby? Utallige komplekse processer finder sted i løbet af denne udvikling, hvor en enkelt celle bliver til en hel organisme bestående af op mod 10000000000000 celler organiseret på en helt bestemt måde. Hvad er op og ned, venstre og højre? Hvor skal de forskellige organer placeres, og hvor store skal de være?

Vores tidlige udvikling er derfor et godt eksempel på, hvorfor det er vigtigt, at vækst er nøje reguleret helt nede på cellulært niveau. Modsat er kræft et eksempel på, hvor galt det kan gå, når cellers vækst pludselig ikke kan holdes i skak. Typisk sker det, fordi vores celler med alderen akkumulerer flere og flere fejl i sit DNA (”computerkoden”), hvorved diverse vækstregulerende mekanismer går tabt, mens andre bliver forstærket. Det kan kun ende i en katastrofe, når bremserne ikke virker, og speederen er i bund.

Det viser sig, at der på verdensplan findes sjældne individer med fejl i dette vækstprogram – fejl, som har fundet sted meget tidligt i fosterudviklingen. Disse mennesker har ikke kræft, men er ved fødslen kendetegnet ved abnorm vækst, som fortsætter livet igennem. Det var et gennembrud, da min vejleder og hans team in 2011 opdagede, at en af de mest hyppige programmeringsfejl i kræft også er årsagen til disse sjældne vækstsygdomme. Det drejer sig om en genetisk mutation – en stavefejl i DNA’et – i lige netop den del, der koder for proteinet PIK3CA (de fleste gener koder for proteiner, og proteiner udfører de fleste funktioner i vores celler).

PIK3CA er ikke et tilfældigt protein. Det fungerer som tænd-knappen for cellens vækst, stofskifte, deling og bevægelse. De omtalte genetiske ”stavefejl” fører til, at PIK3CA er aktivt hele tiden, eller med andre ord: tænd-knappen sidder fast. Konsekvenserne er til at få øje på. Den første patient, som blev diagnosticeret med denne mutation, har to ben, der hver især vejer over 50 kg. Til sammenligning er hendes overkrop overraskende tynd. Som følge af, at den genetiske fejl opstår under udviklingen, er der altså ingen garanti for, at det er hele kroppen, der kommer til at lide af abnorm vækst. Vi har derfor at gøre med et helt spektrum af sjældne patienter, hvor nogle kun har en enkelt finger, der er for stor, mens andre kæmper med alvorlige misdannelser omfattende hjerne og blodkar.

Formålet med mit projekt er at forstå, hvorledes de forskellige genetiske ”stavefejl” i PIK3CA omprogrammerer en celles udvikling og vækst. For at komme så tæt på den tidlige udvikling som muligt bruger jeg pluripotente stamceller, dvs. celler med potentiale til at blive til enhver anden celle i menneskekroppen. For at få stamceller med de rette genetiske fejl, kan man benytte sig af to forskellige teknikker. Den ene er at få en vævsprøve fra patienten og omprogrammere hudceller tilbage til stamceller – en metode, der førte til udgivelsen af en Nobelpris! Den anden teknik benytter sig af nutidens biologis mest revolutionerende redskab (en kommende Nobelpris): CRISPR. CRISPR kan sammenlignes med en saks, der er i stand til at klippe meget præcist i DNA’et i lige netop dét gen, man ønsker at ændre. Man lapper derefter DNA-bruddet og indsætter samtidigt den ønskede ”stavefejl”. Voilá – jeg har de celler, jeg skal bruge! (Helt så let er det heller ikke, og det tog mig et helt år at nå dertil!)

Min forskning er betydningsfuld, fordi den nye viden potentielt kan føre til udviklingen af nye behandlingsmetoder for sjældne patienter med abnorm vækst. I bredere forstand vil vi lære noget fundamentalt om udviklings- og vækstkontrol på cellulært niveau. Sidst men ikke mindst vil denne viden bidrage til en bedre forståelse af individuelle kræftgeners virkningsmekanismer.

Mange, der kender mig, tænker sikkert: ”Det har godt nok ingenting med diabetes at gøre.”

Og så alligevel – det har i den grad noget med det at gøre. Den hyppigste form for diabetes, Type 2, er en stofskiftesygdom karakteriseret ved manglende evne til at fjerne sukker fra blodet, fordi bugspytkirtlen ikke er i stand til at producere nok af hormonet insulin og den smule, der stadig bliver lavet, er ikke længere i stand til at virke på de muskel- og fedtceller, der skal optage sukkeret. PIK3CA er et af nøgleproteinerne, der gør en celle i stand til at respondere på insulin: ved at optage sukker og vokse. PIK3CA orkestrerer derfor cellens stofskifte, og mit projekt giver mig den unikke mulighed for at få et indblik i de underliggende mekanismer.

Det er vildt spændende. Og krævende! Dog er jeg taknemmelig for at kunne sige, at jeg bliver betalt for at lave noget, som jeg elsker, som er sjovt, og som har en mening – for mig personligt, og også for de patienter, der bliver berørt af det.

Wow, n=3 independent experiments finally makes sense…

3 December – really??! Where did this year go? I don’t know the answer to this question, but I certainly look forward to Christmas. It has been an extremely busy but exciting year. My PhD project seems to have gained momentum, the models I investigate are more or less established, and I enjoy what I am doing. Can’t help the feeling of insecurity even when I am writing this; the recurrent question: “What if it goes wrong just because you state that it currently goes well?” Rubbish thought, dismiss it. Need to believe in myself, but it has proven more difficult than anticipated..

One of my main discoveries this past year is that n=3 independent experiments really matters. Let me explain. In biomedical science, particular in experiments involving cells, you usually repeat something at least 3 times on different days – ideally also on different cells.. This way, if you observe the same result with every repeat, you can be more confident that your findings are robust. We tend to laugh at this because from a statistical point of view n=3 is by no means a magical number.. Although scientists love to perform statistical tests on n=3, from a statistical point of view it doesn’t make much sense. So when I first entered the field, I thought that n=3 was quite a peculiar idea because it remains statistically irrelevant.

Statistically irrelevant doesn’t mean biologically irrelevant, though. Science is expensive, so performing the same experiment n=10 is unlikely to happen because your finances will suffer. Nonetheless, performing it minimum 3 times really is a good idea as I have discovered following endless worries that I might have messed something up. Perhaps a consequence of my pathological perfectionism, I often myself doubting every single thing I do and whether I might have messed something up without noticing? It doesn’t help that I spend most of my wake hours culturing cells, which at some point becomes quite automated so you just do stuff; yet, what if my autopilot has failed me without me noticing? Is everything I do wrong? Disaster. Rubbish thought, dismiss again. You see how easy it is to enter a vicious cycle of worries and self-doubt? Thankfully, I need to repeat it anyway, right? So hopefully, even if my autopilot might have failed me at some point, it won’t do so in a subsequent repeat. So if n=2 is different from n=1, n=3 surely will either conform to n=2 or n=1, if not – go for n=4 and n=5!

I wonder if others come across similar doubts and worries? Do share your comments if that’s the case. It usually helps to discover that you are not alone! Just remember, n=3 is there for a reason..

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Fighting your sweet tooth

kidandcake

If you are anything like me, you love chocolate, cake, biscuits, anything sugary and fatty! You know that it is bad for you, yet it is difficult to resist the temptations lurking around the corners. At my work place, cakes and sweets find their way at bigger seminars, at  group meetings, at birthdays, leaving dos, the last Friday of the month, the monthly Student Cake Club… Whatever the reason, the sugar bombs will be accessible on a daily basis, inviting you to try them as were each time the last to ever have a cake experience.

I have often wondered if my brain’s appetite circuit is failing completely as I am remarkably limited in my ability to resist the aforementioned temptations. It is scary as I have all the necessary knowledge to resist, yet it is so hard to turn my back to the moist and tasty chocolate brownie appearing in the Institute’s social room on a regular afternoon.

Right until a good friend and colleague of mine and I joined forces and declared a war on those sugary treats. Here is what we are doing: we stick to eating sugary food once a week only; for every 6/7 sugar-free days, we collect £20 from each other and save those in a “reward” jar towards a trip to Copenhagen. There is also an additional £10 bonus for every 7 bouts of exercise, and our goal is to reach a total of £500 each to cover flights, accommodation and pocket money for the trip. The whole process is rather addictive and incredibly motivating.

The key aspect here is reward and positive feedback. Rather than establishing a punishment system against failure, we reward ourselves for being strong. We sustain a positive feedback through a shared calendar to log our exercises as well as a spreadsheet detailing our savings so far. We have also decided that breaking the rules even once requires all money to be donated to a charity organisation and the Copenhagen trip to be cancelled. Thus, a failure by one will take away a good experience from the other, so rather than only doing it from a “selfish” perspective, we are actually also doing it for each other.

This is just an example of one scheme, and similar approaches can be adopted by others willing to limit their daily consumption of unhealthy food. Find a reward cycle that suits you  and your fellow cake fighters – plan trips to the cinema, spoil each other  with useful little presents or something completely different that does not require you to spend money at all. You will be surprised at how good your brain becomes at resisting the temptations when you are all in it together.

Bottom line: you can make the right dietary choices with the right support network and incentives in place. So find your partner in anti-cake crime, establish your favourite reward scheme, share a calendar or spreadsheet to track your progress and start fighting that sweet tooth now!

Taking the pulse of biomedical science: reproducibility, racing and speaking out loud

Last night, my college (Clare Hall) hosted the termly fellow-student interaction dinner, and I happened to sit next to a renowned scientist and group leader at the MRC Laboratory of Molecular Biology (LMB) in Cambridge. He did not seem interested in discussing molecular biology; instead, we entered a brief, yet insightful, conversation on a worrying development in scientific culture. My thoughts on this development have been brewing for a long time, and yesterday’s conversation has now triggered their release.

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CRISPR: using, not abusing

dna_methylationWhat if your child suffers from an untreatable and fatal genetic disease that could be reversed by a novel “search-cut-copy-pasting” gene-editing technology? Welcome CRISPR, the “crispy” name given to a bacterial mechanism to fight invading viruses, which has been adapted in a revolutionising gene-editing technology, once again sparking ongoing discussions about the ethics of tinkering with the code of life itself. The debates reached a new high earlier this year when researchers from Sun Yat-sen University in China used  CRISPR to edit the genes of unviable human embryos; although, the latter had lost the ability to develop into human beings, the study highlighted the potential of this powerful technology to generate permanent genetic changes that could ultimately affect the course of evolution if applied to viable offspring. Yet, the predicted benefits of CRISPR are hard to ignore.

Recently, CRISPR’s co-inventor, Jennifer Doudna, wrote in a Nature Comment: “Who besides the scientists using the technique would be able to lead an open conversation about its repercussions?” So here is my contribution to the conversation, highlighting what the fuss is all about and how to use, but not abuse, this incredible technology. Praised as the scientific “Breakthrough of the Year” and a “game-changer” in molecular biology, CRISPR to me compares to the industrial revolution, the latter comprising the modernisation of basic tools and the introduction of modern manufacturing. Molecular components capable of snapping the DNA open have been available since the 70’s, and refined tools to engineer precise genetic changes were introduced once at the beginning of the century and again ten years later. Nonetheless, the toolbox was too complex, to rigid and available to few expert laboratories. Think of the first computers in history and their modern-day counterparts. CRISPR belongs to the latter, and here comes why.

Search-cut-copy-and-paste

That’s all there is to CRISPR. Exactly, it is dead-easy to do! As a result, the technique has been adopted by thousands of laboratories worldwide soon after its use as a gene editing tool was described back in 2012. Our genes are coded by the letters A, G, C, T – and there are 6 billion (!) letters in every single diploid human cell (i.e. a cell with a set of DNA from your dad and another set from your mum). Even a single typo in the sequence, when part of an essential gene, may prove to be fatal. Such point mutations underlie monogenic diseases like cystic fibrosis and the severe overgrowth disorders that my PhD project focusses on. CRISPR consists of two basic components that enable precise cutting of the DNA at the site of a mutation and correction of the latter.  The so-called guide RNA is like “velcro” – it is designed to match the region of the DNA that you want to correct. It searches the DNA and guides the second component, a molecular scissor named Cas9, to the matching region. In the split of a second, Cas9 cuts the DNA open at the exact position specified by the guide, and if a copy of the correct DNA code has been provided, the cell can now amend the break by pasting the correct sequence, potentially getting rid of a devastating disease. Other uses of this technology involve the introduction of mutations to create herbicide-resistant plants, malaria-resistant mosquitoes, pigs that can grow human organs for transplant, and hypoallergenic peanuts, to name just a few. In short, a versatile molecular version of a Swiss army knife has been developed.

Fear and regulations

With third-graders using CRISPR to manipulate the DNA of yeast for less than $100, it is no surprise that concerns have been raised over the potential (ab)use of CRISPR by the wrong hands, including those of terrorists. Perhaps the technique should be banned, the reagents destroyed and forgotten?! Unlikely to be effective. After all, gene editing has been possible years before CRISPR, and a ban of the latter is unlikely to be the solution. Similarly, few people would agree to banning the manufacturing of weapons altogether to prevent them from being used by terrorist groups. Having said that, the CRISPR “craze” has urged (and rightly so!) world leaders in biology, genetics, ethics and policymaking to debate future regulations aimed at stipulating how research and applications of genome engineering might be pursued responsibly. Partly because the technique is not fail-proof and fears of such “off-target” effects – the introduction of unwanted mutations – continue to haunt the scientists using it. Consequently, in their most recent three-day meeting, leaders in this field concluded that gene editing should not be applied in the clinic to alter viable human embryos until “(i) the relevant safety and efficacy issues have been resolved … and (ii) there is broad societal consensus about the appropriateness of the proposed application.”

CRISPR and me

As alluded to above, the power of CRISPR makes it possible to correct or replicate the genetic defect causing a particular human disorder. That’s exactly what I have been up to in the past two months. I feel lucky that the discovery of CRISPR (for gene editing) was made only 3 years ago, in time for my PhD. Previously, my supervisor’s team has been limited to studying cells isolated from the skin of our patients, and these cells constitute a very poor  disease model, hampering our attempts at understanding the molecular mechanisms underlying PROS (“PIK3CA-related overgrowth spectrum”; for more on my PhD project, click here). Thanks to CRISPR and stem cell technology, this is now history. I can introduce the specific mutation that I want to scrutinise in stem cells in less than a month, and use these stem cells to generate the exact cell type that is most relevant to the disease I want to study. The insight gleaned from such studies may ultimately drive the development of new therapies for a disease that is currently untreatable. Not to mention, the importance of a better understanding of the protein encoded by PIK3CA, p110a, which plays a key role in cancer and a cell’s response to insulin.

The above is my personal example of how to use – and not abuse – CRISPR. Clearly, the latter will have major effects on society as a whole, and it is imperative that its implications are communicated to ordinary people before they are offered gene-edited pets or the life-saving reversal of a fatal mutation.

Here are some links if you want to know more:

A video by MIT researchers, explaining the CRISPR method for gene-editing

A New Yorker article on CRISPR, which I personally find very interesting and accessible: “The Gene Hackers”

CRISPR in agriculture

A summary of the recent gene-editing summit in Washington

An ethical perspective: “Editing life: Scientists can, but should they?”

Jennifer Doudna on embryo editing