Showing posts with label cautionary tale. Show all posts
Showing posts with label cautionary tale. Show all posts

Friday, October 19, 2018

√ Seeing Isn’T Always Believing: A Cautionary Tale On Gfp Transfer When Trying To Restore Vision

s usually because one of the wires has come unplugged √ Seeing isn’t always believing: a cautionary tale on GFP transfer when trying to restore vision
Dr. Valerie Wallace, presenting her research, at the annual Till & McCulloch Meetings in Mont Tremblant, on Nov 6th.

By Samantha Yammine


When our TV stops working, it’s usually because one of the wires has come unplugged. We begrudgingly huff and puff over to the back of the TV, track down the loose culprit, plug it back in, and boom: back to Netflix.


If you multiply all those wires in the back of your TV by several billion, that will approximate what the wiring in your central nervous system is like. Your eyes, brain and spinal cord are made up of different types of cells that are connected together in a way that lets you see, think and move.


With many diseases and injuries, some of the cells in this interconnected web become damaged and no longer function properly. So why can’t we just plug new cells in like we do our TVs and move on with it already?


While a network of cells a billion times more complicated than your TV is certainly harder to fix, this is not as impossible a task as it may seem.


And it’s one that Canadian stem cell researcher Dr. Valerie Wallace, along with her lab, wanted to tackle in the context of vision loss. She reported on her team’s work at this year’s Till & McCulloch Meeting and this post is a summary of the key points of the presentation. Her lab asked whether it is possible to restore vision by transplanting new light-sensing photoreceptors into the retina – the dark sheet at the back of our eyes whose cells receive light and enable us to see.


The researchers tested this question in the expected manner: they took cells from a healthy mouse that were labeled with a green fluorescent protein (GFP) and transplanted them carefully into intact retinas that were not fluorescent. With only the donor cells marked green, they reasoned that any green cells found integrated into the host retina would be indicative of successfully integrated transplanted cells.


Three weeks after they injected the green donor cells, they checked under the microscope and saw some beautifully connected photoreceptors in the retina fluorescing green! An exciting and promising result you’d probably want to write home about…


…but it wasn’t what they had hoped. In fact, the more they tested this the more they realized that the GFP+ cells fluorescing green were not actually the cells they had transplanted, but rather the result of the host cells taking up GFP from the donor cells!


It is very common, in fact it is critical for our survival, for cells to signal to one another by transmitting proteins. But the transmission of a fluorescent protein like the one used in this study was definitely a surprise that had big implications on how the researchers interpreted their results.


To better test what was happening, they cleverly tried labeling the DNA of their donor cells instead. Proteins float around in the cell’s cytoplasm and so are transferred a bit more easily, but DNA doesn’t leave a cell unless the cell is dividing. Since none of theirs were thought to be dividing they assumed this would be a much more stable way to do their experiment.


Unfortunately, but interestingly, this confirmed their suspicions: they no longer saw labeled cells integrated in the retina when they fluorescently-labeled DNA instead of proteins. Their transplanted cells were not effectively integrating into the host retina, but just sharing their fluorescent contents with cells that were already intact in the circuitry.


They looked back at other reports where researchers had suggested they could get their transplanted cells to integrate and found that if you looked closely enough, the old results were not that different from their own. Dr. Wallace cautioned that we must be careful how we interpret older data for this reason, and be more clever with how we design controls for future experiments.


This strange transfer of cell materials remains elusive to study; it doesn’t seem to happen to cells in a dish that are a lot easier to observe, and so far they’ve only seen it happening between photoreceptor cells. Whether it may be a cause of false positive transplant results in other parts of the body remains to be seen, and will easily go unnoticed unless scientists do their experiments by labeling proteins as well as the DNA of the cells they’re transplanting.


It’s not all bad news though – in fact, it’s quite interesting. See many transplant studies, including those in other parts of the body, show that transplanting new cells can have a beneficial effect just by offering support to their host cells. These are called “paracrine” effects, and studying this type of protein transfer could improve our understanding of these indirect beneficial effects seen in the eye and other systems.


But for now, Dr. Wallace cautions: “Just because you see marked cells integrating after your transplant, doesn’t mean the cells you transplanted have successfully integrated!” Seeing isn’t always believing and it’s important we keep our minds open to new interpretations for the things we think we see.


An eye-opening talk. #punintended #sorrynotsorry


To read more, see the recently published paper here.


About the Author: Samantha Yammine is a PhD Candidate studying neural stem cell biology in Dr. Derek van der Kooy’s lab at the University of Toronto. Her research focuses on neural stem cell hierarchies in the developing mammalian brain, and activation of quiescent stem cells in the 4dukt brain. She is also an avid science communicator on social media and can be found @SamanthaZY on Twitter and @Science.Sam on Instagram sharing the science we all love in new ways everyday.


Shared with permission from Signals Blog



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Saturday, September 1, 2018

√ Mulling Over Latest Crispr Tumult, This One From Nat Biot Pub On Dna Lesions

CRISPR human genetic modification dart board √ Mulling over latest CRISPR tumult, this one from Nat Biot pub on DNA lesionsIf it seems to you like dramatic cautionary tales about CRISPR accompanied by all sorts of media are coming at us more frequently, it’s not your imagination. In the latest yesterday, it was reported in a new paper led by Allan Bradley that CRISPR-Cas9 results in sometimes large-scale chromosomal lesions at or even away from the sasaran locus.


The media have really sunk their teeth into this one, just as in past situations where CRISPR has reportedly encountered anything from bumps in the road to supposed landmines. For instance, here and here are a couple of media stories on the latest CRISPR challenge.


It was just about a month ago that some panicked at a claimed CRISPR-cancer connection, which I wrote about on The Niche. When issues with gene editing are reported, we should pay close attention, but think about them logically rather than emotionally. Here’s what I wrote about some past reports of CRISPR hurdles:


“The initial gene editing “don’t panic” moment came when first one and then another paper came out indicating that the human body may have, to put it simply, some immunity to the key CRISPR protein component for standard gene editing, the nuclease Cas9. This is a real, sizable issue, but there are possible workarounds and in a way that news brought a needed taste of reality to the gene editing arena. The path ahead is not a smooth, linear one, but that’s OK.


Now two new research papers in Nature Medicine (here and here) are being portrayed as being some big new “bad news” connection between CRISPR and cancer. The first paper is “CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response”, by a Swedish-UK team led by Jussi Taipale. The second paper is, “p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells” from a team led by Ajamete Kaykas at Novartis.”


Ok, so what’s the deal with the latest CRISPR tech challenge?


CRISPR-Cas9 in a couple different cell types and with targeting of distinct loci, sometimes didn’t do what it was supposed to and the results of that misbehavior were striking. In fact, the authors report a surprisingly high rate of mistakes that sometimes are quite large in nature. I’d recommend reading the media posts above and especially that one by Julianna LeMieux for a good sense of just how wide the range of reactions to this paper has turned out to be, from basically this is probably no big deal to it being big trouble. The authors themselves suggest potential pathogenic consequences.




On Twitter there has also been a range of discussion. I found Gaetan Burgio’s thread on this (see tweet above, then scroll down once on Twitter)) to be valuable and notably he also indicates that additional data on this kind of dilema is coming soon without going into details.


I also directly asked Gaetan as an expert for his take on this situation and he kindly provided this quote:


“In short my take home message of this paper is it an important contribution demonstrating we still have a lot to learn on the effect of Cas9 in cells before implementing the technology into the clinics.”


Clearly, overall we need to take this seriously, particularly in the translational bench-to-bedside context, but more broadly it should be on our radar screens too. This report is from a pioneering gene targeting lab and it sounds like the Nature Biotechnology editors were very demanding, probably appropriately so, before the pub could see the light of day.


Final note: this paper has some resonance for the Ma, et al. paper from the Mitalipov lab that reported supposed interhomolog repair for apparent CRISPR gene editing in human embryos, but was then challenged by an Egli, et al preprint. The authors of that preprint, including Allan Bradley (probably not by coincidence) raised some simple explanations for how the Ma, et al. paper’s main conclusions may have been wrong including for example the production of Indels (rather than corrected alleles) that make PCR amplification of alleles impossible, and so in turn skewing results to make it seem like all alleles present are WT. These hypothesized deletions could be like some of the genomic lesions mentioned in the new paper. Other cellular or technical events could also make the cells seem WT (presumed in the Ma paper to be due to gene editing-based mutant allele correction) in artifactual ways.


Remarkably, the Ma, et al. paper’s key points on CRISPR in human embryos remain in limbo, without having been recapitulated and if anything in more doubt at this point, but nothing further has been published to direct address it.



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