More Stem Cell News

Since the last time I wrote about stem cells, several things of note have occurred. Among these was the announcement that the Japanese researcher Haruko Obokata has resigned from the RIKEN Center for Developmental Biology, because the finding from her paper (Obokata et al. (2014)) – that she could induce a stem cell state by treating differentiated cells with acid – could not be reproduced. An investigation by the RIKEN Center has found that the supposedly reprogrammed cell cultures were likely contaminated by embryonic stem cell lines, but it is still unclear whether that was accidental or deliberate.

On a more positive note (assuming that these results are true), Irie et al. (2014) have been able to demonstrate the reprogramming of differentiated human epithelial cells into induced pluripotent stem cells (iPSC), which they then re-differentiated into primordial germ cells (PGC), the precursors of germ cells (egg and sperm cells). In particular, they found that the transcription factor SOX17 is a main regulator of this cell state in humans, whereas it is a different transcription factor, BLIMP1, in mice. The implications of this work are potentially vast (see the Nature blog comment here). For instance, when the PGCs generated from differentiated mouse cells were transplanted into mouse testes or ovaries they developed normally into sperm or egg cells, respectively, and were then amenable to in vitro fertilisation. Potentially, therefore, this recent advancement in human cells may be a step towards treating infertility, or enabling (male) homosexual couples to have their own biological children. However, there are biological, technical and ethical hurdles to be overcome if these findings are to be applied. The following figure summarises their findings and is copied directly from their graphical abstract:

Irie et al., Graphical abstract-final5_wt

The full text of Irie et al. can be viewed here as an open access text. And this is because the research and publication costs were covered by the Wellcome Trust, a “global charitable foundation dedicated to achieving extraordinary improvements in human and animal health”, which supports “public engagement, education and the application of research to improve health”. Many funding bodies, including the Wellcome Trust, are increasingly imposing the restriction that any of the research funded with their money must be published open access, including the sharing of raw data.

As one would say in German, I wish you “a good slip into the New Year”!

References:

Irie N, Weinberger L, Tang WW, Kobayashi T, Viukov S, Manor YS, Dietmann S, Hanna JH, Surani MA (2014) SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate. Cell

Obokata H, Wakayama T, Sasai Y, Kojima K, Vacanti MP, Niwa H, Yamato M, Vacanti CA (2014) Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature 505: 641-647

PhD interviews – Round 2

NHNN

The time difference between Vienna and London is only an hour, but still I had to make sure at least three times that I had really converted 10.15 (GMT) into the appropriate time here “on the continent”. The picture above is of the Leonard Wolfson Experimental Neurology Centre in London; it is part of UCL and closely affiliated with the National Hospital for Neurology and Neurosurgery.

The PhD interview I was invited to attend for the Wolfson Centre had to be conducted via Skype since I had already flown home, and it was a significantly different experience from the first interviews I had had two weeks previously.

Firstly, the interview panel this time consisted of five group leaders (compared to four), including Nicholas Wood, the professor who runs the programme, Anthony Schapira, the head of the Department of Clinical Neurosciences, and Linda Greensmith, a professor of neuroscience who researches motor neuron disorders. Secondly, since the Skype connection was not perfect it was extremely difficult to see all of them at once, let alone discern their facial expressions. I certainly did not manage to make them laugh once during the 15-minute grilling. Thirdly, and possibly most importantly, there was no paper we had to read beforehand or any presentation we needed to give. This, combined with the fact that I know almost nothing about neuroscience, caused me to be a lot less sure of my abilities. Fourthly, some of the questions they asked were really quite hard. Apart from the more obvious, “Why do you want to join this programme?”, there was also, “What do you think is the role of industry in science?”. To answer the latter question I rambled on a bit about pharmaceutical companies and cancer combination therapies, which is probably not what they really wanted to hear. And then there was also, “What do you consider the most important advancement in biology in the last ten years?”. Luckily, this is something I had thought about during the course of exam preparations in previous years, and so I answered “fluorescent proteins” with quite some confidence and then went on to say that I didn’t think I’d recently read a molecular/cell biology paper that did not utilise fluorescent proteins. Lastly, they understandably also wanted to know what field of neuroscience/neurodegenerative disease research I was particularly interested in. Given that I have never taken a dedicated neuroscience course this was particularly tricky to answer. Thankfully, a lot of the group leaders’ research at UCL focuses on various aspects of mitochondrial (dys)function and so I tried to argue that it would be interesting to find out more about the differences and similarities between mitochondrial functions in various neurodegenerative disorders, such as Parkinson’s and Alzheimer’s diseases.

Don’t ask me how, but I managed to convince them to let me visit the institute in January so that we can have a proper conversation and more in-depth discussion of the available research projects.

To end on a festive and fluorescent note, here is a picture (taken from the website of Roger Tsien’s lab) of glowing bacteria producing red and green proteins – merry Christmas!

IMAGE - Wreath 2001

Michaelmas Term Round-Up

This past Michaelmas term – the first term at several British universities including Cambridge and Oxford, which runs between late September/early October to Christmas – was an exceedingly exciting time.

The master’s thesis project I am working on progressed from being an unmanageably complex undertaking to a concise and interesting project. At this stage, the melanoma model I have constructed includes not only the most basic cellular phenotypes (e.g. proliferation and cell death) as readouts, but also an indication of motility/metastatic potential. This addition seemed important to us, because in the case of melanoma the metastases cause mortality. The model accurately recapitulates a range of data from the available literature and can now be used to make simple predictions about the phenotypic readouts when the starting conditions are altered. Next term (Lent term here in Cambridge, but Hilary term in Oxford) I will actually get to test some of these new hypotheses in the lab. For example, I will be carrying out immunohistochemistry staining of tumour samples from mice with genetically different melanoma lesions and checking whether the differential activity of various signalling pathways predicted by the model actually occurs in vivo. Additionally, we will perform analyses on a cell line (from Girotti et al. (2013)) that has become resistant to vemurafenib (the drug described here) and try to confirm the mechanism(s) of resistance as predicted by the model.

Apart from the project the biochemistry course also consists of taught elements, including lectures and weekly workshops. The lecture module I took was entitled “cell fate”; we learnt about stem cells, somatic cell reprogramming, neurodegenerative disorders and cellular ageing and cell death. I’m not sure what this says about me, but one of the things I look forward to most during the upcoming holidays is being able to sit down with a cup of tea and (re)consolidate the content of these lectures, and also tackle some essay questions, such as, “Is it accurate to describe embryonic stem cells as stem cells? In what ways do they differ from adult stem cells?”

Interestingly, I think the combination of starting to use Twitter, blogging and learning more and more about the latest experiments and scientific discoveries in a particular area has made me much more aware of the current scientific literature. A particularly helpful resource is the Nature News & Views section, which provides short commentary articles from where one can follow up by reading the actual papers. For example, just a couple of days ago this led me to read about a new type of pluripotent stem cell (Tonge et al. (2014)) termed the F-class cell (F stands for “fuzzy” because of their morphological appearance). The authors conducted various experiments, including in vitro differentiation tests and teratoma formation assays, to show that the F cells truly are pluripotent. On the one hand, unlike embryonic stem cells (ESCs), they cannot form part of a chimaeric embryo when injected into the blastocyst (early stage of embryo developments). On the other hand, however, due to their morphology and decreased adherence to each other and the Petri dish they may be more suited to being grown in stirred suspension culture. And this may be useful for the testing of new drugs or in clinical applications which require reprogramming of large quantities of patients’ somatic cells. (This might be an interesting development worth mentioning in the essay I will write once I stop procrastinating by blogging.) Tonge et al. summarise their findings in this diagram (copied from the paper):

Screen Shot 2014-12-14 at 14.01.26

Lastly, this term also marked the beginning of the quest for a PhD position starting next year. Since the last update about this I have been offered a place to study type 2 diabetes at the MRC Clinical Sciences Centre! Another meeting with the supervisor in January will hopefully shed more light on the precise project to be undertaken and also help in the decision-making process.

All in all, despite (or maybe precisely because?) the differences between this term and the previous years here I feel like I’ve had a successful and worthwhile last Michaelmas.

References:

Girotti MR, Pedersen M, Sanchez-Laorden B, Viros A, Turajlic S, Niculescu-Duvaz D, Zambon A, Sinclair J, Hayes A, Gore M, Lorigan P, Springer C, Larkin J, Jorgensen C, Marais R (2013) Inhibiting EGF Receptor or SRC Family Kinase Signaling Overcomes BRAF Inhibitor Resistance in Melanoma. Cancer Discovery 3: 158-167

Tonge PD, Corso AJ, Monetti C, Hussein SMI, Puri MC, Michael IP, Li M, Lee D-S, Mar JC, Cloonan N, Wood DL, Gauthier ME, Korn O, Clancy JL, Preiss T, Grimmond SM, Shin J-Y, Seo J-S, Wells CA, Rogers IM, Nagy A (2014) Divergent reprogramming routes lead to alternative stem-cell states. Nature 516: 192-197

PhD interviews – Round 1

You’re sitting in front of a panel of four principal investigators (PIs)/group leaders and they start by asking you to simply summarise the paper you were assigned a week in advance (Radford et al. (2014)). You had read the paper carefully, analysed the figures and written down the main things you liked about it, the few things you thought could have been improved, and importantly, what future experiments you would want to do. Simply summarising the paper should have been simple, but was in fact surprisingly tricky. However, after some rambling you do manage to relay the gist of the article.

Next, they start asking about previous research experience and when you mention CRISPR as a genome-editing tool one of the PIs immediately starts questioning you about where it originally came from and what its purpose is. Luckily, having read about the subject, thought about it a fair amount and written about it, those questions did not pose any difficulty.

The toughest question during the panel interview was undoubtedly, “which biological question would you like to answer?”. I thought honesty would be the best policy and so I said that I wasn’t sure since my research interests are still broad. There are probably better ways of phrasing this though. All in all, the panel interview was far less painful than I had anticipated and somehow I even managed to make all four of them laugh.

The next stage involved speaking to potential supervisors in one-on-one meetings, half an hour each. At the end of these we were required to submit our top three choices:

1. Jean-Baptiste Vannier

telomere-rep-stability-360x360-1405607617

His group works on telomeres (the DNA stretches that protect the end of each of the 46 chromosomes in your cells) and how their maintenance is impaired in various medical conditions, ranging from cancers to dyskeratosis congenita. The PhD project would involve mainly in vitro work in mouse cell lines with a lot of fluorescence microscopy and hopefully the use of CRISPR to knock-out various factors that normally protect telomeres. His own post-doc work is summarised in Vannier et al. (2014).

2. Mathieu Latreille

Cellular-Identity-and-Metabolism-Mathieu-Latreille-360x360-1406799926

Mathieu has made type 2 diabetes his research topic. In particular he studies how the dysregulated expression of certain microRNAs (short RNAs that regulate the translation of messenger RNAs into proteins) affect beta cell function in the pancreas. His PhD project, for which the foundation work was laid in Latreille et al. (2014), would be a combination of in vitro experimentation and modelling the disease in mouse models.

3. Simona Parrinello

Simona_P-360x360

Lastly, and this is a testimony to the fact that I really do find a lot of biological problems intriguing, Simona’s group studies the interactions between neural stem cells and endothelial cells, the cells that make up blood vessels. Their most recent paper is Ottone et al. (2014). In particular, the PhD project would investigate how this “vascular niche” influences neurons’ responses to injury. Probably the hardest question she asked was, “if I offered you the position would you accept?”. Again, I thought honesty would be best and I said that I had also applied at other institutes (probably like all the other candidates as well) and that this set of interviews at the MRC Clinical Sciences Centre was the first. They will let us know of the outcome next week…

And on that note, best to end with this cheery bit of news: I’ve been invited to the PhD interviews for the Crick/London Research Institute (LRI). At the moment the LRI is situated in central London at Lincoln’s Inn Fields, but will be moving into the new Francis Crick Institute just behind King’s Cross, and they focus exclusively on cancer research.

References:

Latreille M, Hausser J, Stutzer I, Zhang Q, Hastoy B, Gargani S, Kerr-Conte J, Pattou F, Zavolan M, Esguerra JLS, Eliasson L, Rulicke T, Rorsman P, Stoffel M (2014) MicroRNA-7a regulates pancreatic beta cell function. Journal of Clinical Investigation 124: 2722-2735

Ottone C, Krusche B, Whitby A, Clements M, Quadrato G, Pitulescu ME, Adams RH, Parrinello S (2014) Direct cell-cell contact with the vascular niche maintains quiescent neural stem cells. Nature Cell Biology 16: 1045

Radford EJ, Ito M, Shi H, Corish JA, Yamazawa K, Isganaitis E, Seisenberger S, Hore TA, Reik W, Erkek S, Peters A, Patti ME, Ferguson-Smith AC (2014) In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism. Science 345: 785-785

Vannier JB, Sarek G, Boulton SJ (2014) RTEL1: functions of a disease-associated helicase. Trends in cell biology 24: 416-425