Genome Engineering
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Genome Engineering
Genome engineering is progressing from the single-gene fix to the multiple gene targeting: with genome sequencing, we have the ability to read genomes; with the improved sequence-targeting techniques I'm collecting here, we have the capacity to write and re-write whole genomes - see also 'synthetic biology.' Note that genome engineering is not to be confused with gene therapy, which is mostly about using genes as therapeutic agents than it is about fixing defective genes.
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This video perfectly explains why CRISPR really will change the world forever

This video perfectly explains why CRISPR really will change the world forever | Genome Engineering | Scoop.it
No, seriously.
Clem Stanyon's insight:
Great video on the CRISPR system and the implications of its application.
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China's about to rewrite human DNA using a revolutionary tool for the first time

China's about to rewrite human DNA using a revolutionary tool for the first time | Genome Engineering | Scoop.it

Here we go...

Clem Stanyon's insight:
The Chinese, once again, proving how quickly they can adopt new technology, and beating the US to essentially the same application. The IP is still in the balance; see my next post for more on that.
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Autism isn’t just a brain disease, new evidence suggests

Autism isn’t just a brain disease, new evidence suggests | Genome Engineering | Scoop.it
This changes everything!
Clem Stanyon's insight:
So, in this case, the mice were engineered to lack the implicated proteins only in their peripheral nervous system. That means that, in theory, people who experience hyper-stimulation like this could have their peripheral nervous system neurones genetically engineered to have the necessary proteins. Imagine that: a cream or a bacterial emulsion that could be applied to the skin, that would contain the necessary DNA or protein species needed to change the genome to restore or create the proteins needed...
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We can now 'cut and paste' RNA in addition to DNA, and it could disable viruses

We can now 'cut and paste' RNA in addition to DNA, and it could disable viruses | Genome Engineering | Scoop.it
Science gets smarter.
Clem Stanyon's insight:
This should come as no surprise; once you can imagine it, there is probably something like, somewhere it in the biological world. As for disabling viruses, sure, but most viruses – even RNA viruses like HIV – still require a DNA template to replicate, so, while their RNA form could be suppressed, to kill a virus will still require a head-shot to their DNA.
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93% of leukaemia patients in remission after an experimental T cell therapy

93% of leukaemia patients in remission after an experimental T cell therapy | Genome Engineering | Scoop.it
It's early days, but results are promising.
Clem Stanyon's insight:
Great application of Genome Engineering to create T-cells capable of targeting cancer.
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Scientists have removed HIV from human immune cells using a new gene-editing technique

Scientists have removed HIV from human immune cells using a new gene-editing technique | Genome Engineering | Scoop.it
And they can permanently shut down its replication.
Clem Stanyon's insight:
About time this happened! HIV is just the start, for sure; there are a few incurable viral infections that the CRISPR biotechnology could be used to kill.

Also, the permanent protection is significant; the T-cells are genetically modified to continue expressing the two system components, yet suffer no ill effects, indicating that the system is very specific, a concern when dealing with long-lived organisms like humans (as opposed to bacteria, from where the system was derived): the abstract reads...

"We employed an RNA-guided CRISPR/Cas9 DNA editing system to precisely remove the entire HIV-1 genome spanning between 5′ and 3′ LTRs of integrated HIV-1 proviral DNA copies from latently infected human CD4+ T-cells. Comprehensive assessment of whole-genome sequencing of HIV-1 eradicated cells ruled out any off-target effects by our CRISPR/Cas9 technology that might compromise the integrity of the host genome and further showed no effect on several cell health indices including viability, cell cycle and apoptosis. Persistent co-expression of Cas9 and the specific targeting guide RNAs in HIV-1-eradicated T-cells protected them against new infection by HIV-1. Lentivirus-delivered CRISPR/Cas9 significantly diminished HIV-1 replication in infected primary CD4+ T-cell cultures and drastically reduced viral load in ex vivo culture of CD4+ T-cells obtained from HIV-1 infected patients. Thus, gene editing using CRISPR/Cas9 may provide a new therapeutic path for eliminating HIV-1 DNA from CD4+ T-cells and potentially serve as a novel and effective platform toward curing AIDS."
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We could be just weeks away from the first genetically modified human embryos in Britain

We could be just weeks away from the first genetically modified human embryos in Britain | Genome Engineering | Scoop.it
Clem Stanyon's insight:

Yup. It's getting that close. First will come the diseases, then the 'designer babies' - as if that isn't already achieved through more mundane means. Cas9/CRISPR system, based on nucleic acid targeting rather than protein, has become the number one in the world in only 3 short years, overtaking over a decade of use of various forms of sequence-targeting proteins.

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Algae has been engineered to kill cancer cells and leave healthy cells unharmed

Algae has been engineered to kill cancer cells and leave healthy cells unharmed | Genome Engineering | Scoop.it
Scientists have genetically engineered tiny algae to kill up to 90 percent of cancer cells in the lab, while leaving healthy ones unharmed, and the treatment has also been shown to effectively treat tumours in mice without doing damage to the rest...
Clem Stanyon's insight:

The connection: if algae can be engineered to target cancer cells for chemotherapeutic delivery, they can also be engineered to target cells for the delivery of genome modifying DNA, RNA, protein, etc...

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New device can immediately target and destroy deadly blood clots

New device can immediately target and destroy deadly blood clots | Genome Engineering | Scoop.it
Australian researchers have developed a nano-sized capsule that can be delivered to a patient intravenously to immediately target and break down the blot clots that cause heart attacks and strokes. No only does the minuscule device start working...
Clem Stanyon's insight:

Why is this about genome engineering? Simple. It's all about targeting. Imagine that, instead of an anti-blood clot medication being delivered by antibodies recognising an activated platelet-specific antigen, the antibodies recognised another molecular marker... Every type of blood vessel has it's own molecular signature, too, so one could target different tissues in this way, potentially addressing the genetic basis for connective-tissue problems that cause aneurisms, for example.

Then, imagine that there are a great many sub-clinical and clinical conditions that involve similar mechanisms of clotting within the lumen of blood vessels: this targeted treatment could impact those, too.

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The Hypermobile Dancer » 4dancers

The Hypermobile Dancer » 4dancers | Genome Engineering | Scoop.it

Everyone knows that dancers need to be flexible. You can work hard to achieve flexibility but while this is not easy or comfortable it is achievable to a certain extent. However, there are those dancers who do not have to work for flexibility – they can already do the splits every which way, often have swayback knees, a very flexible spine and ‘amazing’ feet. These dancers have an inherited joint flexibility. This means the connective tissue, at cellular level, which binds the body together – joint capsule, fascia, ligaments, tendon, and skin – is not as tightly or evenly knit together compared to other bodies.

Clem Stanyon's insight:

How does this relate to Genome Engineering? Not so much, directly, but if you look up "Marfan's Syndrome" you might get a better idea. This is more about the protein interaction networks of the extracellular matrix, the best-known of which is collagen, than about genetic networks per se. However, dominant disorders or dysfunctions are a challenge for genetic engineering, where the majority of the cells in a tissue must be modified in situ; no short-cut from modifying stem cells here.

I've known I was hypermobile since I was quite young, inherited as a dominant condition from my mother, who is also hypermobile. I've learned to recognise the morphological signs in the bodies of others, which include disproportionate body/appendage lengths, elongated & extended dimensions in men & women, which also includes size of eyes and fullness of lips; it also includes curly hair in caucasians. One of the common effects of the more extreme forms of the condition is internal organ failure: stroke from artery aneurism rupture is one example.
 

Being flexible has it's advantages, for sure, even to those who are merely social dancers, but after spraining one's ankle for the nth time, it gets to be a bit of a drag; I even changed my way of walking (think more like English Tango: knees always bent when I place my foot on the ground) to deal with it. Then, there is the whole muscle strength issue. I played field sports (soccer & Lacrosse) for years, suffered hugely every weekend without understanding that sprinting was ripping my muscles apart at the cellular level much more than most people; only after starting cycling routinely to and from work did my legs start to gain substantial strength. Similarly, swimming was a great way to develop strength: resistance exercise, not high-impact, is the way to go until science develops something to boost connective tissue strength, and probably even then...

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Jennifer Doudna, a Pioneer Who Helped Simplify Genome Editing

Jennifer Doudna, a Pioneer Who Helped Simplify Genome Editing | Genome Engineering | Scoop.it
The biochemist at the University of California, Berkeley, helped make a monumental discovery: a relatively simple way to alter any organism’s DNA. But she is stuck in a patent fight over it.
Clem Stanyon's insight:

This article is interesting for two reasons: first, it gives the seldom-heard back-story of how a scientific break-through was achieved, in this case the Cas9/CRISPR system of bacterial restriction of bacterial virus proliferation. Second, it highlights the toxic effects of the patent system, which is most effective at excluding individuals and smaller companies from the innovation field; they can't afford the legal team to navigate the patent minefield. More on that anon.

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Scientists find possible cause of asthma, and how to prevent an attack

Scientists find possible cause of asthma, and how to prevent an attack | Genome Engineering | Scoop.it
For the first time, researchers in the UK have discovered that a particular protein is playing a key role in the development of asthma, and knowing this, they’ve found a class of drugs that can effectively treat its most harrowing symptoms. Working...
Clem Stanyon's insight:

This is interesting; the basis of cystic fibrosis, (CF), from memory, is to do with calcium channels or similar. CF presents as lungs filling with fluid... which always sounded a lot like asthma to me.

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Synthetic nucleases for genome engineering in plants: prospects for a bright future - Plant J.

Synthetic nucleases for genome engineering in plants: prospects for a bright future - Plant J. | Genome Engineering | Scoop.it

Puchta & Fauser, 2013

By inducing double-strand breaks (DSB), it is possible to initiate DNA recombination. For a long time, it was not possible to use DSB induction for efficient genome engineering due to the lack of a way to target DSBs to specific sites. With the development of modified meganucleases and synthetic DNA binding domains, this limitation was overcome. Domains derived from zinc finger transcription factors or transcription activator-like effectors can be designed to recognise almost any DNA sequence. By fusing these domains to the endonuclease domains of a class II restriction enzyme, an active endonuclease dimer can be formed that introduces a site-specific DSB. Recent studies demonstrate that gene knock-outs via nonhomologous end joining or gene modification via homologous recombination are becoming routine in many plant species. By setting a single genomic DSB, the complete knock-out of a gene, the sequence-specific integration of foreign DNA, or the subtle modification of individual amino acids in a specific protein domain can be achieved. The induction of two or more DSBs allows for complex genomic rearrangements such as deletions, inversions, or the exchange of chromosome arms. The potential of controlled genome engineering in plants is tremendous. The recently discovered RNA-based CRISPR/Cas9 system as new tool to induce multiple DSBs or sophisticated technical applications, such as the in planta gene targeting system, are further steps in this development. At the moment, the focus still lies on the engineering of single genes; in the future, the engineering of whole genomes will become an option.


Via dromius
Clem Stanyon's insight:

I've just recently started working in the field (no pun intended) of plant genetic engineering and things are not quite so rosy as this makes out; plants are far more likely to repair dsDNA damage by a process called non-homologous end joining (NHEJ) than by homologous recombination (HR); the former process just sticks broken ends together, virtually willy-nilly, while the latter substitutes like-for-like, as determined by DNA sequence homology.

The ratio between NHEJ and HR in yeast, which does HR very effectively by all estimates, is probably about 1:1 - 50% of events are by HR. In plants, the ratio is more like 100:1 - ~1% of events are repaired by HR. The dreaded and annoying off-target effects in plants, therefore, are a far, far higher proportion of the total, so even a highly effective and very specifically targeting dsDNA break promoter like the Cas9/CRISPR system won't be able to prevent NHEJ from swamping the HR events. All is not lost, however, as there are ways to make the proetome of any organism dance to one's own tune, if one has the right instrument...

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The CRISPR Clash: Who owns this groundbreaking, DNA altering technique? - IPWatchdog.com | Patents & Patent Law

The CRISPR Clash: Who owns this groundbreaking, DNA altering technique? - IPWatchdog.com | Patents & Patent Law | Genome Engineering | Scoop.it
If the PTO decides Broad does not own the core CRISPR technology, Zhang and his team may be stripped of other CRISPR patents as well. This decisio
Clem Stanyon's insight:
Interesting battle over CRISPR IP; the bottom line is that it's still not clear who will own it, mainly as the universities concerned are fighting for the millions in revenue that *exclusive* license granting will bring. Bast case scenario for corporations, possibly for everyone, is that both parties will be given rights, so that more companies can use the technology and move it further, faster. 

Yet another example of how IP is being used to block innovation, rather than enhance it, all for money. At least universities and non-profits can use it, either way.
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A federal panel just gave the green light to use gene editing on humans

A federal panel just gave the green light to use gene editing on humans | Genome Engineering | Scoop.it
Sharing the science that matters.
Clem Stanyon's insight:
CRISPR system comes to T-cell manipulation, to create more vigorous anti-cancer T-cells. A space worth watching!
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Scientists have performed the first trials of a 'universal cancer vaccine'

Scientists have performed the first trials of a 'universal cancer vaccine' | Genome Engineering | Scoop.it
It's really happening.
Clem Stanyon's insight:
This is not genome engineering, per se, but given the link to using GE to combat viral infections, there is some common interest; in theory, the 'RNA darts' used to inoculate the immune system against cancer types could also be used to target cells infected with viruses, which are also frequently involved in cellular transformation to cancerous phenotypes. This might prove particularly important for people with chronic infections, like papilloma viruses or Hepatitis C, that are not the focus of major research efforts like those against HIV.
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Gene therapy reverses sight loss and is long-lasting - BBC News

Gene therapy reverses sight loss and is long-lasting - BBC News | Genome Engineering | Scoop.it
A genetic therapy improves the vision of some patients who would otherwise have gone blind.
Clem Stanyon's insight:
Sight; you wouldn't get far without it. Never forget that there is a very human side to the potential benefit of gene therapy like this. Retinal cells are just the start; muscle degeneration – hereditary or age-related – could be similarly dealt with, for starters...
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First Gene Therapy Successful Against Human Ageing

First Gene Therapy Successful Against Human Ageing | Genome Engineering | Scoop.it
Elizabeth Parrish, CEO of Bioviva USA Inc. has become the first human being to be successfully rejuvenated by gene therapy, after her own company’s experimental therapies reversed 20 years of normal telomere shortening.
Clem Stanyon's insight:
Very scant on details, in particular what approach was used to modify the lymphycyte genomes to lengthen telomeres. The most likely method would seem to be telomerase protein administration; that would lengthen the telomeres in a single cell cycle, without leaving behind dangerous nucleic acid expression constructs that could result in leukaemia, if incorporated into the genome and expressed constitutively. Combined with cell-penetrating peptides, such an approach could be very effective without side-effects; even muscle cells could be targeted in situ, using an appropriate delivery mode such as magnetic particles coated with the protein.

A better article on the subject is here:

https://www.technologyreview.com/s/542371/a-tale-of-do-it-yourself-gene-therapy/
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Researchers kill drug-resistant cancer in the lab using 50 times less chemo

Researchers kill drug-resistant cancer in the lab using 50 times less chemo | Genome Engineering | Scoop.it
Awesome news.
Clem Stanyon's insight:

So, why is this important for genome engineering? Well, in this study, exosomes were used as a delivery vehicle for drugs. Substitute DNA and protein and you have a gene-targeting approach. Imagine what could be done to destroy viruses, rectify dysfunctional genes...

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World’s largest cloning factory in China set to produce cattle, racehorses and sniffer dogs

World’s largest cloning factory in China set to produce cattle, racehorses and sniffer dogs | Genome Engineering | Scoop.it
China is no stranger to the commercial opportunities of genetic editing , but its latest ambition applies the controversial techniques on a much grander scale. The nation is currently building the world’s largest cloning factory in a...
Clem Stanyon's insight:

All they need, really, is artificial wombs in which to grow the foetuses; that would take care of the deficit of stock in short order.

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Gene editing has saved the life of a girl with "incurable" leukaemia

Gene editing has saved the life of a girl with "incurable" leukaemia | Genome Engineering | Scoop.it
Researchers in the UK have successfully treated Layla, a baby girl with leukaemia, using a gene-editing therapy that had previously only been trialled in mice. Doctors say it's too soon to declare her cured, but she's now living healthily and...
Clem Stanyon's insight:

Science FTW, once again. Why is she the first? Because 'traditional' approaches had *all* failed and she was dying. Seems like an overly high bar, when the traditional approaches are mostly about poisoning the body...

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Ancient Viruses Resurrected To Improve Gene Therapy

Ancient Viruses Resurrected To Improve Gene Therapy | Genome Engineering | Scoop.it
Researchers are turning to the past to help better improve gene therapy with the hope of curing modern diseases. Ancient viruses were resurrected to effectively deliver gene therapy to the liver, muscle and retina. These viruses were not only safer, but were more potent than therapies currently available.
Clem Stanyon's insight:

It's all about delivery, these days; the targeting side – how to integrate DNA at a target locus – has been mostly resolved. AAV has been around for a good while and host resistance can be dealt with by using ancient viral coat proteins: it's not the virus but its raiment that has been resurrected.

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World-first cystic fibrosis treatment could be available within 5 years

World-first cystic fibrosis treatment could be available within 5 years | Genome Engineering | Scoop.it
For the first time, gene therapy has been shown to significantly improve lung function in patients with cystic fibrosis in phase 2 trials in the UK. The researchers admit that the results were modest and inconsistent, but they demonstrate that the...
Clem Stanyon's insight:

Note: broad-spectrum treatment *by 2020* . . . That would be ~50 years since the start of DNA manipulation science, molecular biology, and 30 years since the single gene dysfunction was elucidated. Don't despair, though; advances in science tend to be very organic in nature: they accelerate, so what took 10 years the first time, will take 5 years the second, 2 years the third, and by the tenth time, almost no time at all. 

Just last week, I was looking at a reference with a colleague, who had come across it randomly while looking into improving DNA delivery. In this in vitro approach, micelles were used to punch holes in cells by simple centrifugation. Very mechanical. Also very effective. Can't centrifuge a human, though, so magnetic oscillation might be more effective...

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World's first genetically modified human embryo raises ethical concerns

World's first genetically modified human embryo raises ethical concerns | Genome Engineering | Scoop.it
The first case of genetically engineering a human embryo to cure a congenital disease is a technical breakthrough but raises troubling ethical questions.
Clem Stanyon's insight:

This demonstrates the power of the Cas9/CRISPR technique, but also the capacity to advance science where researchers are not hamstrung by a religious lobby. A friend of mine who had a stroke at 30 returned home to China where, as a result of there not having been a moratorium on stem cell research for a decade or so as there was in the US leading up to that time, stem cell research had advanced enough to create a treatment that resulted in her recovery from the stroke to a substantial degree.

Science works, bitches, and so much better when religion keeps out of it.

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New mitochondrial DNA editing technique prevents genetic diseases in mice

New mitochondrial DNA editing technique prevents genetic diseases in mice | Genome Engineering | Scoop.it
A new technique to edit mitochondrial DNA has been tested on mice, and if replicable in humans, could help prevent mothers living with certain incurable disease from passing them onto their children, researchers say. Mitochondria are tiny...
Clem Stanyon's insight:

From the original paper abstract, the authors report that they "selectively prevented [mtDNA haplotype] germline transmission using either mitochondria-targeted restriction endonucleases or TALENs." 

While this is indeed impressive in a model system – the mouse –germline manipulations are a lot more problematic than somatic modifications. However, as the researchers rightly point out, you don't need to correct the mistakes in all mtDNA, just enough of them to alleviate the disease. The same applies in adult humans: modification of mtDNA in aged or defective stem cells as part of a larger, whole-body rejuvenation program, could substantially impact the health of recipients; the body is an ecosystem, so putting healthier, genetically modified cells in it will see them overtake the unhealthy resident competitors.

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