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3 years, 6 months ago

Changing the code of life

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Changing the code of life



Congratulations!
 
On 7 October,  the Royal Swedish Academy of Sciences announced that it had awarded the 2020 Nobel Prize for Chemistry to two women scientists: Emmanuelle Charpentier (L), a French microbiologist, geneticist and biochemist,  who is now the director of the Max Planck Unit for the Science of Pathogens in Berlin, Germany, and Jennifer Doudna (R), an American biochemist  who is a professor of chemistry, biochemistry and molecular biology at UC Berkeley.

The scientists developed a simple, cheap, yet powerful, and precise technique for editing DNA, which is called CRISPR-Cas9 (an acronym for Clustered Regularly Interspaced Short Palindromic Repeats) and popularly referred to as a pair of ‘genetic-scissors’. The technology endows science and scientists with extraordinary powers to manipulate genes to cure genetic diseases, improve crops to withstand drought, mould and pests, and affect climate change, and is considered to be the most important discovery in the history of biology. The Nobel citation refers to Charpentier’s and Doudna’s scientific contribution as a, “tool for rewriting the code of life”, which has “a revolutionary impact on the life sciences, by contributing to new cancer therapies and may make the dream of curing inherited diseases come true”.

For more than four years HealthPad has been following and publishing Commentaries on the scientists’ work. Our Commentaries have a large and growing global following of leading physicians, scientists, policy makers, journalists and students. The Commentaries listed below about CRISPR techniques, which we re-publish to celebrate Charpentier’s and Doudna’s Nobel Prize, have had more than 120,000 views.
 
Gene editing positioned to revolutionise medicine
1 Feb 2017
 
Gene editing battles
15 Mar 2017
 
Who should lead MedTech?
18 Jul 18
Base-editing next-generation genome editor with delivery challenges
17 oct 2018
CRISPR-Cas9 genome editing a 2-edged sword
31 Oct 2018
Will China become a world leader in health life sciences and usurp the US?
27 Feb 2019
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4 years, 5 months ago

For better or worse we all now live in CRISPR’s world

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  • Prime editing devised by researchers at the Broad Institute led by David Liu is a significant advance of the original CRISPR gene editing tool discovered in 2012
  • CRISPR can cut and edit your DNA to correct defects inside your body’s cells to prevent and heal a range of incurable diseases and has revolutionized biomedicine
  • The original CRISPR is fraught with inaccuracies referred to as off target effects
  • Prime editing substantially reduces CRISPR’s off target effects and has the potential to correct up to 89% of known disease-causing genetic variations
  • CRISPR also has the capacity to edit genes in an embryo in such a way that the change is heritable
  • In 2018 Chinese researcher He Jiankui “created” the world’s first CRISPR babies
  • This triggered international criticism from scientists and bioethicists
  • A principal concern is that CRISPR is easy-to-use, cheap, regularly used in thousands of laboratories throughout the world and there is no internationally agreed and enforceable regulatory framework for its use
 
For better or worse we all now live in CRISPR’s world
 
In 2012 the world of biomedicine changed when a revolutionary gene editing technology known as CRISPR-Cas9 (an acronym for Clustered Regularly Interspaced Short Palindromic Repeats) was discovered. The technology harnesses your body’s naturally occurring immune system that bacteria use to fight-off viruses and has the potential to forever change the fundamental nature of humanity. Since its discovery CRISPR has been developing at lightning speed primarily because it is simple and affordable and today is used in thousands of laboratories throughout the world.
 
In this Commentary
 
In this Commentary we describe prime editing, which is the latest advance of the CRISPR's tool box, devised bya team of researchers, led by Andrew Anzalone, a Jane Coffin Childs postdoctoral fellow from the Broad Institute of MIT and Harvard and published in the October 2019 edition of Nature. Prime editing is significant because it provides a means to eliminate the unintentional consequences of CRISPR and therefore bring the technique closer for use in clinics. But this is still a long way off.
 
We also review a case where an ambitious scientist “created” the first CRISPR babies. This immediately triggered international criticism and a call for tighter regulatory control of the technology. Scientists and bioethicists are concerned that CRISPR can easily be used to create heritable DNA changes, which ultimately could lead to ‘designer babies’.
 
These two accounts of CRISPR might seem “opposites” and not sit well together in a single Commentary. Notwithstanding, what prompted putting them together was John Travis, the News Managing Editor of the well-known scientific journal Science, who soon after CRISPR’s discovery in 2012  said, “For better or worse we all now live in CRISPR’s world”. 
 
CRISPR and your DNA

CRISPR is different to traditional gene therapy, which uses viruses to insert new genes into cells to try and treat diseases and has caused some safety challenges. CRISPR, which avoids the use of viruses, was conceived in 2007 when a yogurt company identified an unexpected defence mechanism that its bacteria used to fight off viruses. Subsequent research made a surprising observation that bacteria could remember viruses. CRISPR has been likened to a pair of microscopic scissors that can cut and edit your DNA to correct defects inside your body’s cells to prevent and heal a range of intractable diseases. The standard picture of DNA is a double helix, which looks similar to a ladder that has been twisted. The steps in this twisted ladder are DNA base pairs. The fundamental building blocks of DNA are the four bases adenine (A), cytosine (C), guanine (G) and thymine (T). They are commonly known by their respective letters, A, C, G and T. Three billion of these letters form the complete manual for building and maintaining  your body, but tiny errors can cause disease.  For example, a mutation that turned one specific A into a T results in the most common form of sickle cell disease.
 
The original CRISPR
 
The original CRISPR tool, which is the first and most popular gene editing system, uses a guide RNA (principally a messenger carrying instructions from your DNA for controlling the synthesis of proteins) to locate a mutated gene plus an enzyme, like Cas9, to cut the double-stranded gene helix and create space for functioning genes to be inserted. However, a concern about CRISPR is that the editing could go awry and cause unintended changes in DNA that could trigger health problems. Findings of a study published in the July 2018 edition of  the journal Nature Biotechnology found that such inaccuracies, referred to as off-target effects, were substantially higher than originally reported and some were thought to silence genes that should be active and activate genes that should be silent. These off-target effects, such as random insertions, deletions, translocations, or other base-to-base conversions, pose significant challenges for developing policy associated with the technology.

Subsequently however, the paper was retracted, and an error correction was posted on a scientific website. Contrary to their original findings, the authors of the Nature Biotechnology paper restated that the CRISPR-Cas9 gene editing approach, "can precisely edit the genome at the organismal level and may not introduce numerous, unintended, off-target mutations".
 
Base editing

Notwithstanding, researchers remained concerned about CRISPR’s off target effects and several devised a technique, referred to as base editing, to reduce these. Base editing is described in three research papers published in 2017: one in the November edition of the journal ‘Protein and Cell’, another in the October edition of ‘Science’ the and a third by researchers from the Broad Institute, in the October edition of the journal ‘Nature’. Base editing takes the original CRISPR-Cas9 and fuses it to proteins that can make four precise DNA changes: it can change the letters C-to-T, T-to-C, A-to-G and G-to-A. The technique genetically transforms base pairs at a target position in the genome of living cells with more than 50% efficiency and virtually no detectable off-target effects. Despite its success, there remained  other types of point mutations that scientists wanted to target for diseases.

 

Prime editing
 
Prime editing is different to previous gene editing systems in that it uses RNA to direct the insertion of new DNA sequences in human cells. According to David Liu,  the senior author of the 2019 Nature paper and a world renowned authority on genetics and next-generation therapeutics, “a major aspiration in the molecular life sciences is the ability to precisely make any change to the genome in any location. We think prime editing brings us closer to that goal”.  Because prime editing provides a means to be more precise and more efficient in editing human cells in a versatile way, which eliminates many of CRISPR’s unintentional errors, it significantly expands the scope of gene editing for biological and therapeutic research.
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CRISPR-Cas9 genome editing a 2-edged sword
There are around 75,000 different mutations that can cause disease in people and prime editing has the potential to correct up to 89% of known disease-causing genetic variations. According to Liu, "Prime editing is the beginning, rather than the end, of a long-standing aspiration in the molecular life-sciences to be able to make any DNA change in any position of a living cell or organism, including potentially human patients with genetic diseases". Liu’s team at the Broad Institute intends to continue optimizing prime editing. In their October 2019 Nature paper researchers reported that they can precisely correct mutant genes, which cause sickle cell anaemia and Tay Sachs disease.
 
Sickle cell anaemia and Tay Sachs
 
Sickle cell anaemia is an inherited form of anaemia. This is when there are not enough healthy red blood cells  (haemoglobin) to carry adequate oxygen throughout your body. The condition is the most common inherited blood disorder in the US, affecting 70,000 to 80,000 and further it is estimated  each year some 300,000 babies are born with the disorder worldwide. Tay-Sachs disease is a rare and fatal nerve condition often caused by the addition of four extra letters of code.  Although anyone can be a carrier of  the disease it is much more common among people of Ashkenazi (Eastern European) Jewish descent. In the Ashkenazi Jewish population, the disease incidence is about 1 in every 3,500 new-borns and the carrier frequency is 1 in every 29 individuals.
 
Some moral and ethical implications of CRISPR
 
Being able to modify your DNA with CRISPR tools has transformed scientific research and is revolutionising medicine although it will be some time before the technology is regularly used in clinics. In addition to its potential benefits there are significant moral and ethical challenges associated with the technology, especially when it is used for germline engineering, which is the process by which your genome is edited in such a way that the change is heritable. Inappropriate use of germline editing could dent the progress of the CRISPR technology.
 
The first CRISPR babies
 
One well publicized  inappropriate use of CRISPR is a team in China, led by He Jiankui of the Southern University of Science and Technology in Shenzhen, which in November 2018 “created” the first gene edited twins, known by their pseudonyms Lulu and Nana. He edited the twins’ cells to be immune to HIV infection when they were embryos, therefore ensuring that every cell in their bodies were changed, including their reproductive ones, which means their edited genomes can be passed on to their children and grandchildren, despite the fact that scientists cannot be sure what the long term effects of such lasting modifications might be. The twins are the first CRISPR babies and the first humans to have every cell in their body genetically modified using the technology.
 
In 2015 Chinese researchers were the first to edit the genes of a human embryo in a laboratory dish. Although the embryos did not go to term, the experiment triggered an international outcry from bioethicists, who argued that CRISPR should not be used to make babies. Notwithstanding, He Jiankui did just this.
 
He  employed CRISPR to alter a gene in IVF embryos to disable the production of an immune cell surface protein, CCR5, which HIV uses to establish an infection before insemination. CCR5 is a well-studied genetic mutation, and there is scientific and medical value in understanding how CRISPR can be used to disable and prevent HIV/AIDS. He believed that the use of CRISPR technology was medically appropriate and expected his experiment, “to produce an IVF baby naturally immunized against AIDS”. But more contentiously, He created twins who could pass the protective mutation to future generations. It is CRISPR’s ability to easily and cheaply edit human embryos, eggs, or sperm in order to create irrevocable changes and the potential for designer babies, which raises concerns.  
 
He defended his work at a Hong Kong genomics conference in late November 2018, but there was immediate and significant international criticism about the scientific and ethical legitimacy of his experiments, which broached China’s guidelines as well as international ethical and regulatory norms. A Chinese government investigation found He to have violated state law in pursuit of “personal fame and fortune”.  His endeavours cost him his university position and the leadership of a biotech company he founded, which had successfully raised US$43m start-up capital and was advised by Craig Mello, professor  of the University of Massachusetts Medical School and Nobel Laureate for medicine in 2006 for his genetics research.
 
Opacity and scientific competition
 
Some scientists are reluctant to be critical of He and suggest his studies, which resulted in the first CRISPR babies,  simply signal the “next chapter in the technology’s story”. He Jiankui appears to be an ambitious scientist desperate to become the first to conduct the gene editing experiment on humans, but who made some significant errors of judgement by initiating his study prematurely and by withholding information from regulatory authorities and his university. A generous interpretation might suggest that He was motivated by science and humanity. Through a Beijing-based organization, which helps Chinese people with HIV, he recruited couples for his experiment where only the fathers were living with HIV infections, which they managed by antiviral drugs. Eight couples agreed to participate, although one subsequently withdrew.
 
Since He’s statement at the Hong Kong conference he has disappeared, but the background to his studies has been well documented. In late 2017, He, who specialized in sequencing DNA, began his efforts to produce human babies from gene edited embryos and before and during his study it is reported that he sought advice from international experts in the field and communicated openly with international colleagues about his plans. Notwithstanding, it is alleged that He faked a blood test for one of the fathers in the study, aware that in China the HIV status of the father would disqualify him from participating in fertility treatments. Also, He failed to appropriately inform the hospital where the twins were edited and implanted of the status of his experiments.

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Fierce competition among scientists is not uncommon and competition fuels opacity among scientists in their battle to become the first to make a discovery. Indeed, it is not uncommon for scientists to shield their ideas and research. This does not condone He’s actions, but it might help to explain them. Generally speaking, scientific opacity is not created by ambitious scientists alone, but it is partly created by scientific funding bodies and research institutions. Such opacity is a significant obstacle to open collaboration. In addition to wanting to be the first, He’s intentions might also have been an attempt to spare children of parents with HIV/AIDS  from inheriting the disease.
CRISPR is not yet safe
 
Be that as it may, many scientists agree that CRISPR is not yet safe and precise enough to be used in human embryos. In the March 2019 edition of Nature a group of 18 prominent CRISPR scientists and bioethicists from seven countries called for a global moratorium on heritable genome editing until the establishment of an international framework that would compel countries to establish both scientific safety and broad societal agreement before allowing the technology to progress.  "We call for a global moratorium on all clinical uses of human germline editing; that is, changing heritable DNA (in sperm, eggs or embryos) to make genetically modified children" , the scientists wrote.

Opposition to germline editing is mixed
 
However, opposition to germline editing is mixed. In February 2017 the US National Academies of Sciences, Engineering, and Medicine (NASEM) published a report, which did not call for an international ban of germline editing, but instead suggested that it "might be permitted" if strict criteria were met. In July 2018, the UK’s Nuffield Council of Bioethics published a report on heritable genome editing and suggested that under certain circumstances it could be morally permissible, even in cases of human enhancement. 

Given that CRISPR is cheap, easy-to-use and already an effective tool in thousands of laboratories throughout the world, it seems reasonable to assume that standards and laws are unlikely to prevent a determined scientist and desperate patients from using the technology prematurely. Indeed, science and medicine have a history of researchers attracting public criticism for undertaking experiments prematurely only to have those experiments become common medical practices: in-vitro fertilization  (IVF) is one such example. Although IVF has a chequered history today it accounts for millions of births worldwide and  1% to 3% of all births every year in the US and Europe.
 
Germline engineering and somatic genetic modification
 
Here we describe the difference between germline and somatic adjustments. The former uses CRISPR to modify DNA in such a way that the change is heritable. The latter uses CRISPR to modify the DNA of people with incurable diseases in a way that such modifications are limited to the people treated and not passed on to future generations. Broadly speaking, your body has two kinds of cells: somatic and germ cells. The vast majority are somatic. These cells make up your body and are responsible for forming all your familiar structures: such as your skin, blood, muscles and organs etc. Your somatic cells die when you die so there is no chance of them creating a new organism. However, germ cells are different. Early in your development your germ cells  are sequestered: they divide more slowly and under restricted circumstances. Germ cells cannot become a physical feature such as an ear or a finger, but they do make the only bits of you, which can form a new person: your eggs and your sperm. Every cell in your body holds your DNA in an unbroken lineage stretching back millions of years and thousands of generations, but only the germline has a chance to go forward. Human germline modification means deliberately changing the genes passed on to children and future generations and thereby creating genetically modified people. Somatic genetic modification is different. It adds, cuts, or changes the genes in some of your cells, typically to alleviate a medical condition. The use of human genome editing to make edits in somatic cells for purposes of treating genetically inherited diseases is already in clinical studies. If perfected, somatic gene editing (gene therapy) holds promise for helping people who are sick, affecting only an individual consenting patient. With the exception of He’s studies, human clinical studies with CRISPR have been limited to somatic cells. In effect, this renders CRISPR no more consequential than any other experimental drug or treatment. Any CRISPR-made somatic cell changes are a genetic dead-end and are not heritable. However, germline cells have the possibility of immortality, with the potential to affect thousands of people over the course of several generations. Tampering with germline cells is therefore a much more serious proposition.
 
Clinical studies of gene therapies
 
Gene therapy is primarily available in a research setting. The US Food and Drug Administration (FDA) has approved only a limited number of gene therapy products for sale in the US.According to the US National Institutes of Health, which serves as a clearinghouse for biomedical research worldwide, there are over 800 clinical studies currently underway to test gene therapy as a treatment for genetic conditions. The list includes a relatively small number of CRISPR studies as a treatment for cancers of the lung, bladder, cervix and prostate, the majority of which are in China where doctors appear to be leading the race to treat cancer by editing genes. For the past two decades China has been investing heavily in biomedicine. It is one way that China is able to compete with the West and demonstrate its technological prowess in the 21st century. Also, it is important for China to keep its vast population healthy in the 21st century. Given the somewhat ambiguous state of CRISPR technology it seems reasonable to assume that the first therapeutic applications of CRISPR will be in diseases where cells can be taken out of your body, edited, checked to ensure they are safe and then reintroduced. This suggests blood disorders such as sickle cell or thalassemia.
 
Takeaways
 
Bioethicist Henry T (Hank) Greely, professor at Stanford University, California, US, compares CRISPR to the Model T Ford, which was not the first automobile, but because of its simplicity of production, dependability and affordability it transformed society. CRISPR is not the first gene editing technology, but it is cheap and easy to use and is on the cusp of transforming biomedicine. A significant challenge is getting CRISPR tools, which are capable of performing gene edits, into the right place and to ensure they are safe. Prime editing is a smart, innovative and a substantial step forward in achieving this. Indeed, David Liu and his colleagues from the Broad Institute  have expanded the gene editing toolbox to facilitate ever-more precise editing ability and efficiency. Significantly, the overwhelming majority of human genetic disorders are due to the types of mutation that prime editing is able to correct, which stands the technique in good stead to be useful in therapies for intractable diseases. Notwithstanding, it is one thing to cut out sequences of DNA that cause genetic diseases and another to make genetic changes that are passed down to all later generations. Because CRISPR is cheap, easy-to-use, in the hands of scientists throughout the world, and already has been used to create babies with heritable traits, the technology provokes deep ethical and societal debate about what is, and what is not acceptable in efforts to prevent disease. Given that CRISPR has the potential to change the nature of humanity, it is incumbent on all citizens, not just scientists, bioethicists and regulators, to call for open and inclusive processes associated with all aspects of CRISPR.
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5 years, 6 months ago

Base-editing next-generation genome editor with delivery challenges

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  • ‘Base editing’ is a more efficient version of CRISPR Cas-9 technology
  • CRISPR Cas-9 is a ground-breaking gene editing technology that was discovered in 2012
  • CRISPR Cas-9 operates like molecular scissors to cut and remove mutant strands of DNA and creates space for functioning genes to be inserted
  • CRISPR technologies raise hope for new therapies to replace traditional medicines and provide a one-time procedure to cure devastating inherited disorders that have no cure or few treatment options
  • Recent studies suggest that CRISPR Cas-9 is not as accurate as initially thought and can introduce thousands of unintended ‘off-target’ mutations into the genome
  • Base editing significantly reduces ‘off-target’ mutations because it does not cut the DNA but uses a chemical process to convert just one letter (base) of DNA into another
  • 66% of genetic illnesses involve mutations where there is a change in a single letter of DNA
  • A significant challenge for base editing is in the delivery of the technique
 
Base-editing next-generation genome editor with delivery challenges

Since the first human genome was sequenced in 2003 there has been a revolution in human genomics, which has transformed the way we think about diseases and their causes and has paved the way for the development of therapies that target both the illness and the patient. It has also led to the introduction of the genome-editing tool CRISPR Cas-9 in 2012. This transformed gene editing from a devilishly difficult task to an easy and inexpensive “day-to-day” laboratory technology, which allows scientists to cut-out and change sections of DNA at specific sites in an organism or cell. CRISPR technology revolutionized genetic research and raised hope that it could provide a powerful therapeutic tool for millions of people living with inherited debilitating diseases for which there are either no cures or few treatment options. Recently, next-generation gene-editing technologies have been developed, which have reignited the hope that gene therapies could eventually replace traditional medicines and be used by physicians in clinics as a one-time procedure to cure some of the most devastating inherited disorders. Notwithstanding, scientists have cautioned that the therapeutic use of CRISPR technologies have significant technical, safety, regulatory, ethical and delivery obstacles to overcome before they can be used as therapies.
 
In this Commentary
 
This Commentary describes a new and expanded gene editing technology called base editing or chemical surgery, which compliments CRISPR Cas-9, but instead of cutting strands of DNA it provides a more accurate and predictable means to rewrite single letters (bases) of DNA and RNA. This enables scientists to make more targeted and precise alterations to DNA and RNA with less unintended consequences, referred to as “off-target” effects.  Base editing has significant therapeutic potential for thousands of human disorders known to be caused by a single genetic error and range from sickle-cell anaemia to metabolic disorders to cystic fibrosis, which currently lack options. The new base editing techniques are described in three research papers, which appeared in scientific journals in late 2017. One was published in the November 2017 edition of the journal ‘Protein and Cell’, another in the October 2017 edition of the ‘Nature’ and a third in the October 2017 edition of the journal ‘Science’. Research reported in these papers represents an important advance in our ability to alter single letters (bases) in peoples’ DNA and RNA. Notwithstanding, scientists caution that before base editing techniques become standard clinical practice the technology will require more research, extensive clinical studies and significant advances in delivery methods.
 
CRISPR and intellectual property battles

Base editing is a development of CRISPR Cas-9 technology, which was developed by a group of researchers from University College Berkeley, the Max-Plank Institute, Harvard University and The Massachusetts Institute of Technology (MIT) and others. The Broad Institute, a non-profit disease research facility established jointly by Harvard University and MIT, obtained the basic US patents on CRISPR Cas-9 in February 2017 after a heated patent dispute between two of the technology’s originators. On one side Jennifer Doudna of University College Berkeley and Emmanuelle Charpentier of the Max-Planck Institute in Berlin. On the other side Feng Zhang of the Broad Institute. While the Broad Institute has been considered the winning party in the US, the European intellectual property landscape is a different story.  Due to technical errors associated with listed CRISPR inventions and claimed priority dates, the European patents filed by the Broad Institute have been revoked. 

The Broad Institute is expected to appeal the decision and the gene-editing intellectual property battles continue. Notwithstanding, this has not slowed the development and commercialization of the technology.
 
Technologies to edit the genetic code and some ethical challenges

CRISPR Cas-9, discovered in 2012, is a particularly versatile and inexpensive gene editing technology. Since its discovery it has been used extensively by scientists throughout the world in an attempt to further their understanding of the role played by genes in disease. The technology works by slicing through the two strands of bases that spiral to create DNA’s famous double-helix and is especially useful when the goal is to insert or delete DNA bases. CRISPR acts like a genetic GSP: a guide molecule made of RNA that allows a specific site of interest on the DNA double helix to be targeted. The RNA molecule is attached to a bacterial enzyme called Cas-9 that works like a pair of “molecular scissors”, which can cut out strands of DNA at an exact point. This allows scientists to target and remove faulty genetic material and create space for functioning genes to be inserted in a similar way a word processor allows you to correct and enhance documents. Although CRISPR Cas-9 is increasingly being used in studies of genetic disorders, it has been challenging for the technology to fix a point mutation, caused by a change in a single DNA letter in a given gene. Further the technology’s cutting mechanism can result in “off-target” activity, which either can make changes to a gene you do not want changed or fail to change a gene that you do. This represents a significant challenge for scientists, and a major concern for the technology’s therapeutic applications.

For example, research published in the July 2018 edition of  the journal Nature Biotechnology discovered unintended deletions of thousands of DNA bases, including at spots far from the edit. Another study reported in the May 2017 edition the journal Nature Methods found that CRISPR Cas-9 introduced hundreds of unintended mutations into the genome. And a third study published in December 2017 in the Proceedings of the US National Academy of Sciences suggested that genetic variation between patients may affect the efficacy and safety of CRISPR-based treatments enough to warrant custom treatments. In addition to these technical concerns, ethical concerns about the technique also have been raised. In the March 2015 edition of the journal Nature, Michael Werner, the executive director of the Washington DC based Alliance for Regenerative Medicine suggested that ethical and safety issues should put germline editing research (a process by which every cell in the human body could be altered in such a way that the change is heritable) off limits because, “It’s still a little premature to say that we’ve resolved all these safety issues now,” says Werner. Notwithstanding, in July 2018 the UK’s Nuffield Council on Bioethics suggested that germline editing is “morally permissibly” under certain circumstances.
 
CRISPR triggers intense commercial activity

Despite safety and ethical concerns about CRISPR, genome editing has rapidly become a large fast-growing global market. In late 2012, Charpentier  suggested to a few colleagues, including Doudna, Zhang and George Church, professor of genetics at Harvard University Medical School who is credited with developing the first direct genomic sequencing method in 1984, that they should start a company to accelerate the gene editing technology into clinics.  They did not, but later the same scientists and others started separate genome editing companies. Four have become publicly traded companies and have successfully raised billions. For example, in 2013 Charpentier founded Crispr Therapeutics. Based in Switzerland, the company has become a US$2bn Nasdaq traded company. The other three, all based in the US are: Editas Medicine, which has a market cap of US$1.3bn and was founded by Zhang, Church and David Liu, Professor of Chemistry at Harvard University, a core member of the Broad Institute, and the first to describe base editing in research published in the May 2016 edition of the journal Nature. Doudna is  a founding member of Intellia Therapeutics, which today has a market cap of US$1bn,  and Juno Therapeutics, which has a market cap of US$10bn was founded in 2013 through a collaboration of the Fred Hutchinson Cancer Research Center, Memorial Sloan-Kettering Cancer Center and the Seattle Children’s Research Institute.

Since their inceptions, big pharma companies have been competing to invest in them. In January 2018 Celgene, which already owned 9.7% of Juno agreed to acquire the rest of its stock for US$9bn in cash in order to gain access to Juno's pipeline of CAR-T cancer drugs. This technology entails extracting blood cells from patients, then using CRISPR to edit T cells (immune cells) outside the body - ex vivo gene therapy - in order to transform the cells into enhanced cancer fighters before reintroducing them back into the patient’s blood stream. Earlier Bayer, a German pharmaceutical company, acquired a US$35m equity stake in Crispr Therapeutics, which it increased in January 2018. In 2016 Bayer invested US$335m over 5-years in a joint venture with Crispr Therapeutics called Casebia, with the intention to discover, develop and commercialize new breakthrough therapeutics to cure blood disorders, blindness, and congenital heart disease. Casebia also expects to develop new delivery mechanisms for CRISPR technologies, which will be critical to future drugs meant to target cells in the human body. Crispr Therapeutics retains a 50% interest in the joint venture, and also gains access to Bayer’s state-of-the-art delivery technologies and protein engineering knowhow.
According to market analysis the global genome editing market is expected to grow at a CAGR of 14.5% to reach US$6.3bn by 2022. Market drivers include rising government funding and the growth in the number of genomic projects, high and increasing prevalence of debilitating and often fatal diseases, technological advancements, increasing production of genetically modified crops, and growing application areas of genomics.
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Tens of thousands of devastating diseases are the result of a single minute error in one letter the human genome
 
While big pharma competes to commercialize CRISPR Cas-9 technologies, scientists compete to develop ever-more versatile and efficient versions of the technology. One result of the competition among scientists is “base editing”, which is predicated upon the same basic mechanism as the standard CRISPR technology but differs because it does not require the DNA to be physically cut. Instead, base editing uses a chemical process to directly convert a single base (letter) of DNA to another without deleting and inserting random bases in the process.  Think of base editing as similar to changing one letter in a vast WORD document. The technique allows scientists to edit the body’s genes one letter at a time with exquisite precision.  Base editing rewrites single errors in the genetic code instead of cutting and replacing whole strands of DNA. The technique is not a replacement for CRISPR, but a complementary technology for altering the genome in an attempt to correct disease. Converting one letter to another may not sound significant until you consider that there are billions of letters in the human genome, and tens of thousands of diseases can be traced to a single minute error in just one letter in the human genome. Indeed, of more than 50,000 genetic changes currently known to be associated with disease in humans, 32,000 are caused by the simple substitution of one base letter for another. Base editing is significantly more efficient than standard CRISPR systems at making single base substitutions.
 
DNA molecules as a sequence of letters

Your genes are an instruction manual for your body. Hidden inside every cell in your body is a chemical called DNA. Genes are short sections of DNA, which are the biological templates your body uses to make the structural proteins and enzymes needed to build and maintain your tissues and organs. Genes influence how you look on the outside and how you function on the inside. The DNA that makes up all genomes is composed of four related chemicals called nucleic acids: (i) adenine ‘A’, (ii) guanine ’G’, (iii) cytosine ‘C’, and (iv) thymine ‘T’.  A sequence of DNA is a string of these nucleic acids (also called “bases” or “base pairs”). These bases connect in a specific way: ‘A’ always pairs with ‘T’, and ‘C’ always pairs with ‘G’. The letters represent the “alphabet” scientists use to write genetic code. The principal biological function of a base is to bond nucleic acids together. Nucleic acids are complex organic substances present in living cells, especially DNA or RNA. There are some 24,000 genes in the human genome, which are bundled into 23 pairs of chromosomes all coiled up in the nucleus of every one of your cells. There are about 37trn cells in the human body. Only about 1.5% of your genetic code, or genome, is made up of your genes. Another 10% regulates your genes to ensure that they turn on and off in the right cells at the right time.
 
The November 2017 Protein and Cell study

In the April 2015 edition of the journal Protein and Cell, scientists led by Junjiu Huang from Sun Yat-sen University in Guangzhou, China, reported research where he and his colleagues used CRISPR Cas-9 to correct abnormal β-thalassemia genes in human embryos without much success. Researchers suggested, “our work highlights the pressing need to further improve the fidelity and specificity of the CRISPR Cas-9 platform, a prerequisite for any clinical applications of CRISPR Cas-9-mediated editing”. In the November 2017 edition of Protein and Cell Huang and colleagues demonstrated that they had enhanced the fidelity of CRISPR and used the new base editing technique for the first time in human embryos to repair a faulty gene that gives rise to β-thalassemia. They suggested that, “their study demonstrated the feasibility of curing genetic disease in human somatic cells and embryos by a base editor system”.
 
Β-thalassemia

Β-thalassemia is a serious blood disorder, common in China and southeast Asia, which can be caused by a single mutation in the DNA code. The disorder reduces the production of haemoglobin, which is an iron-containing protein in red blood cells that carries oxygen to cells throughout the body. Without treatment, patients with a severe type of β-thalassemia, usually die before age 5. Correcting this mutation in human embryos may cure people with the disorder and also prevent the disease being passed on to future generations.

Innovative approach

Humans carry two copies of every gene, and in many cases both versions have to be “healthy” to avoid disease. Because it is challenging for researchers to find a lot of embryos, which all have a rare double mutation, Huang’s team created a batch of cloned embryos, then took skin cells from patients with β-thalassemia, removed their DNA-containing nuclei, and introduced them into donor eggs that had their own nuclei removed. The eggs then developed into early stage embryos, which carried the β-thalassemia mutation. Despite the study’s success to effectively edit the embryos and repair the mutations it was only about 20% efficient. Huang noted that the base editing technique he and his colleagues used was not uniform across all cells in the embryos, and their endeavours only sometimes repaired one faulty gene instead of 2. This created what is called “mosaic embryos”, which have both normal and mutant cells and result in a patchwork of cells with different genetic make-up and is potentially dangerous. 

Huang concluded that more research is required to improve the safety of the study’s base editing approach. Notwithstanding, scientists believe Huang’s research represents a significant advance, and that base editing techniques hold out the potential to treat and prevent a number of serious and debilitating inherited human diseases, which are more common than some people realise. For example, 1 in 25 children are born with some genetic disorder, which includes β-thalassemia, cystic fibrosis, genetic blindness, sickle cell anaemia, muscular dystrophy, and Tay-Sachs disease.
 
The October 2017 Nature study

In October 2017, David Liu, and colleagues from the Broad Institute published a paper describing their latest and improved base editing research in the journal Nature. Liu's group genetically transformed base pairs at a target position in the genome of living cells with more than 50% efficiency, with virtually no detectable ‘off-target’ effects such as random insertions, deletions, translocations, or other base-to-base conversions. The work of Liu and his team is significant because it, “introduced point mutations more efficiently and cleanly, and with less off-target genome modification than a current Cas-9 nuclease-based method, and can install disease-correcting or disease-suppressing mutations in human cells”. This clears the path for scientists to use base editing to address many more single-letter mutations than was previously possible. “What we’ve developed is a base editor, a molecular machine, that is a programmable, irreversible, efficient, and an extremely clean way to correct mutations in the genome of living cells,” says Liu.
 
Delivery is the challenge

Notwithstanding, Liu suggests that the status of base editing is like Amazon without UPS, its principal delivery agent, “Creating a machine that makes the genetic change you need to treat a disease is an important step forward, but it’s only one part of what’s needed to treat a patient. We still have to deliver that machine”, says Liu, and further, “We have to test its safety, we have to assess its beneficial effects in animals and patients and weigh them against any side-effects. We need to do many more things. But having the machine is a good start.” Liu is hopeful that base editing of DNA and RNA could be used as complementary approaches for a “broad set of potential therapeutic applications.” He and his colleagues are exploring base editing to fix blood and neurological disorders as well as hereditary deafness and blindness.
 
The October 2017 Science study and the advantages of editing RNA
 
In a paper published in the October 2017 edition of the journal Science, Feng Zhang, of the Broad Institute who is one of the original architects of CRISPR, and senior author describes a variant of base editing, which acts on RNA in human cells instead of DNA. RNA acts as a temporary genetic messenger within cells and naturally degrades in the body. This means that editing RNA instead of DNA does not result in a permanent change to a person’s genome, and therefore has significant potential as a tool for both research and disease treatment. Zhang’s base editing technique makes a temporary correction of a disease-causing mutation without permanent alteration to the genome. According to Zhang, editing DNA is, “permanent and very difficult to reverse, which poses a safety concern, while editing RNA is not.” Zhang’s approach is a potentially safer option when it comes to gene-fixing therapeutics, although any treatment using the technique would need to be administered repeatedly. But Zhang believes repetition could be an advantage because it allows for a therapy to be “upgraded” as scientific knowledge increases and provides a better understanding of specific disease states. The system can change single RNA nucleotides in mammalian cells in a programmable and precise fashion and has the ability to reverse disease-causing mutations at the RNA level, as well as other potential therapeutic and basic science applications.
 
Zhang and colleagues made one RNA-editing enzyme into a programmable gene-editing tool. “There are 12 possible base changes you can do,” says Omar Abudayyeh, a researcher at the Broad Institute and one of the paper’s authors. Having edited one, “we’re now thinking about the ways to do the other eleven.” By operating on RNA, Zhang and his colleagues avoid ‘off-target’ effects. “With RNA, you have to think about ‘off-targets’ a little differently.” says Abudayyeh. “If some of the RNA gets edited incorrectly the cell will have at least some amount of the right protein. If things go really wrong, the edit is reversible. You can always remove the system and the RNA will eventually degrade and recycle and revert back to normal,” says Abudayyeh. Liu and his team call their new creation REPAIR. They tested it on human cells growing in dishes and edited up to about 27% of the RNAs of two genes. The researchers did not find any ’off-target’ effects and suggest, “REPAIR presents a promising RNA editing platform with broad applicability for research, therapeutics, and biotechnology.”
 
Delivery challenges

Liu and other medical researchers have stressed the significant challenges associated with delivering CRISPR technologies, which have yet to be resolved before gene editing techniques become viable therapies. The conundrum researchers face is that your body’s biological barriers, which protect you from diseases are the same barriers that create significant obstacles for the delivery of genetic editors. Let us explain. Your DNA is like Fort Knox gold in that it is extremely well protected. For a harmful agent to access your DNA it first has to get under your skin and into your bloodstream. It then has to travel through your bloodstream without being detected by your immune system, which is comprised of networks of cells, tissues, and organs that work together to protect your body. One of the important cells involved in your immune system are white blood cells, also called leukocytes, which come in two basic types that combine to seek out and destroy disease-causing agents. Assuming the harmful agent successfully gets past all these biological barriers, it then has to penetrate your cell membrane and find a way to the nucleus of the cell. These biological defences help to keep you healthy by preventing harmful agents penetrating and transforming your cells into disease-making entities. But, they are the same obstacles that prevent scientists getting gene editors to the right place at the right time in the right quantity. Although delivery technologies are improving, Crispr Therapeutics, Editas Medicine, and Intellia Therapeutics, as well as, Casebia are all investing in delivery mechanisms, which remain significant challenges to overcome before gene editing becomes a regular therapy.  This is not only a concern for private companies, but also for the public sector. In January 2018 the US National Institutes of Health announced it will be awarding US$190m in research grants over the next six years, in part to “remove barriers that slow the adoption of genome editing for treating patients”.
 
Takeaways

Researchers have made substantial scientific advances in embryo gene editing technologies, which have significant potential for next-generation therapeutics. Base editing, described in this Commentary, is one advance, which has the potential to provide effective therapies for a range of disorders known to be caused by the mutation of a single letter in a gene, which currently have either little or no means of a cure. This is important because about 66% of genetic illnesses in humans involve mutations where there is a change in a single letter (or base). Notwithstanding, before such technologies become regular therapies in clinics there are major technical challenges, which need to be overcome in the delivery mechanism for these gene editors.
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6 years, 2 months ago

CRISPR positioned to eliminate human papilloma viruses that cause cervical cancer

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cervical cancer
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gynaecological cancers
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Human Papilloma Virus
  • A 2018 clinical study in China is the first to use CRISPR to edit cells inside the human body in an attempt to eliminate the human papilloma virus (HPV) and is hugely significant for millions of women
  • Nearly all sexually active people get an HPV virus at some point in their lives and persistent high-risk HPV infections are the main cause of cervical cancer
  • Respectively 34,800 and 256,000 women in the UK and US live with cervical cancer and each year about 3,200 and 12,200 new cases of cervical cancer are diagnosed in the UK and US respectively nearly all related to HPV
  • Cervical cancer is increasing in older women not eligible for the HPV vaccine and not availing themselves of Pap test screening programs
  • A new study suggests that cervical cancer mortality among older women could increase by 150% in the next 20 years

CRISPR positioned to eliminate human papilloma viruses that cause cervical cancer

January 2018 marked the beginning of the first CRISPR clinical study to attempt to edit cells while they are in the body of women in the hope to eliminate the human papilloma virus (HPV), which is the main cause of cervical cancer. The study, led by Zheng Hu of the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China, is the first to edit human cells while inside the body. Zheng Hu will apply a gel that carries the necessary DNA coding for the CRISPR machinery to the cervixes of 60 women between the ages of 18 and 50. The study’s aim is to prevent cervical cancers by targeting and destroying the HPV genes that cause tumor growth while leaving the DNA of normal cells untouched. Current estimates suggest that every year 527,624 women are diagnosed with cervical cancer and 265,672 die from the disease. Zheng Hu’s study is expected to be completed by November 2018 and findings reported in January 2019.
 
In this Commentary

This Commentary describes the Chinese CRISPR study and the etiology and epidemiology of cervical cancer. It also describes the current cervical cancer vaccination possibilities and the challenges they face. Further, the significance of the Chinese study is demonstrated by an English study, published in December 2017 in the Lancet Public Health, which warns that although HPV vaccination programs have significantly reduced the incidence of cervical cancer among young women, the incidence of the disease is increasing significantly among older women who do not qualify for the cervical cancer vaccine, and fail to avail themselves of regular Pap tests (A Pap test is a simple, quick and essentially painless screening procedure for cancer or precancer of the uterine cervix). The latter part of the Commentary describes advances that CRISPR technology has made over the past decade as well as describing its main ethical and technical challenges.
 
Human papilloma virus (HPV)

There are over 200 different types of HPV related viruses. Viruses are the etiological agents of approximately 15% of human cancers worldwide, and high-risk HPVs are responsible for nearly 5% of cancers worldwide. It is estimated that about 75% of the reproductive-age population has been infected with 1 or 2 types of genital HPV. About 79m Americans are currently infected with HPV, and about 14m people become newly infected each year. The American Centers for Disease Control and Prevention estimates that more than 90 and 80% of sexually active American men and women respectively will be infected with at least one type of HPV at some point in their lives. Most HPV infections are harmless, they last no more than 1 to 2 years, and usually the body clears the infections on its own. More than 40 HPV types can be easily spread by anal, oral and vaginal sex. About 12 HPV types are high risk, and it is estimated these persist in only about 1% of women. However, a central component of the association between HPV and cervical carcinogenesis is the ability of HPV to persist in the lower genital tract for long periods without being cleared. These persistent high-risk types of HPV can lead to cell changes, which if untreated, may progress to cancer. Other HPV types are responsible for genital warts, which are not sexually transmitted.
 
Etiology of cervical cancer
 
 “The way that the HPV causes cancer informs us about how cancer occurs in other settings. Virus particles insert foreign DNA into a person’s normal cells. This virus then turns off the “off-switch” and allows the oncogenes [Genes that can transform a cell into a tumor cell] to progress unchecked and create an oncogenic virus. So, in this case the 'insult' is known: it’s an HPV virus. However, in many circumstances we’re not sure what that initial switch is that upsets the balance between a tumor suppressor and an oncogene,” says Whitfield Growdon, of the Massachusetts General Hospital and Professor of Obstetrics, Gynecology and Reproductive Biology at the Harvard University Medical School: see video below:
 
 
HPV and cervical cancer

The association of risk with sexual behavior has been suggested since the mid-19th century, but the central causal role of HPV infection was identified just 40 years ago. HPV infection is the main etiologic agent of cervical cancer. 99% of cervical cancer cases are linked to genital infection with HPV and it is the most common viral infection of the reproductive tract. HPV types 16 and 18 are responsible for about 70% of all cervical cancer cases worldwide. Further, there is growing evidence to suggest that HPV also is a relevant factor in other anogenital cancers (anus, penis, vagina and vulva) as well as head and neck cancers. The importance of prevention and cervical cytological screening was established in the second half of the 20th century, which preceded and even advanced etiologic understanding.
 
Epidemiology of cervical cancer
 
Cervical cancer is one of the most common types of gynecological malignancies worldwide. It ranks as the 4th most frequent cancer among women in the World, and the 2nd most common female cancer in women between 15 and 44. According to the World Health Organization there were some 630m cases of HPV infections in 2012, and 190m of these led to over 0.5m new diagnoses of cervical cancer. The World has a population of some 2,784m women aged 15 and older who are at risk of developing cervical cancer. Each year about 3,200 and 12,200 new cases of cervical cancer are diagnosed in the UK and US respectively; nearly all related to HPV. There is estimated to be 34,800 and 256,000 women in the UK and US respectively living with cervical cancer. Each year some 890 and 4,200 women die from cervical in the UK and US respectively.
 
HPV vaccines
 
HPV vaccines, which prevent certain types of HPV infections, are now available to females up to the age of 26, and have the potential to reduce the incidence of cervical and other anogenital cancers. “Vaccinations work by using your own immune system against foreign pathogens such as viruses and bacteria. Vaccination against some high risk sub-types of cancer-causing HPV viruses is one of the most meaningful interventions we’ve had since the development of the Pap test,” says Growdon: see video below.
 
 
Gardasil and Cervarix

Gardasil, an HPV vaccine developed by Merck & Co., and licenced by the US Food and Drug Administration (FDA) in 2006, was the first HPV vaccine recommended for girls before their 15th birthday, and can also be used for boys. In 2008 Cervarix, an HPV vaccine manufactured by GlaxoSmithKline,  was introduced into the UK’s national immunization program for girls between 12 and 13. Both vaccines have very high efficacy and are equally effective to immunise against HPV types 16 and 18, which are estimated to cause 70% of cervical cancer cases. Both vaccines significantly improve the outlook for cervical cancer among women living in countries where it is routinely administered to girls before they become sexually active. “Both Gardasil and Cervarix vaccines have been shown to be incredibly effective at preventing the development of high-grade dysplasia, which we know, if left unchecked, would turn into cervical cancer,” says Growdon: see video above.

Gardasil also protects against HPV types 6 and 11, which can cause genital warts in both men and women. Second-generation vaccines are under development to broaden protection against HPV. In 2014 the FDA approved Gardasil 9, an enhanced vaccine, which adds protection against an additional 5 HPV types that cause approximately 20% of cervical cancers.
Global challenge

Despite the availability of prophylactic vaccines, HPVs remain a major global health challenge due to inadequate vaccine availability and vaccination coverage. Despite the promise, vaccine uptake has been variable in developed nations, and limited in developing nations, which are most in need. The available vaccines are expensive, require a cold chain to protect their quality, and are administered in 2 to 3 doses spanning several months. Thus, for a variety of practical and societal reasons (e.g., opposition to vaccination of young girls against a sexually transmitted agent, fear of vaccination), coverage, particularly in the US has been lower than would be optimal from a public health perspective.
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Gene editing battles
Success among young women

Notwithstanding, a study referred to above and published in the Lancet Public Health suggests cervical cancer cases are expected to fall by 75% among young women for whom vaccination is now the norm. Death from cervical cancer among the generation who were 17 or younger in 2008 when the UK vaccination program was introduced is expected to virtually disappear.
 
Challenges for older women

Notwithstanding the success of HPV vaccines for young women, there are continuing challenges for older women who, because of their age, do not qualify for HPV vaccines, and do not attend their Pap screening test when invited. “Pap tests involve scraping the cervix on the outside for cells, which then udergo microscopic examination. Today this is carried out by a computer. Further examination is carried out by a cytopathologist who determines status . . . . . . . . . . Pap tests do not diagnose cancer, but tell you whether you are at high risk of either having pre-cancerous or cancerous cells. Actual diagnosis of cervical cancer involves a colposcopy. This is a simple procedure, which uses a specific type of microscope called a colposcope to look directly into the cervix, magnify its appearance, and helps to take biopsies of abnormal areas,” says Growdon: see videos below.
 

What is a Pap smear test?


Diagnostic tests for cervical cancer
 
Older women and Pap tests

Pap tests, which are offered by NHS England to women between 25 and 64, is the most effective way of preventing cervical cancer; yet data show that in 2016 there was a significant drop in Pap test screening as women’s age increased. If such screening covered 85% of women, it is estimated that it would reduce deaths from cervical cancer by 27% in 5 years, and the diagnosis of new cases of cervical cancer by 14% in 1 year. According to the authors of the 2017 Lancet study, “The risk of acquiring an HPV infection that will progress to cancer has increased in unvaccinated individuals born since 1960, suggesting that current screening coverage is not sufficient to maintain – much less reduce – cervical cancer incidence in the next 20 years.”
 
Cervical cancer projected to increase in older women

Over the next 2 decades, diagnoses of cervical cancer in women between 50 and 64 are projected to increase by 62%, which could increase mortality from the disease by nearly 150%. “The main reason for this is that the population is ageing and women currently 25-40 will not benefit from vaccination – and they are in the age range where the likelihood of getting an HPV infection is quite high,” saidAlejandra Castanon one of the authors of the Lancet study.
 
Chinese study extends CRISPR technology

The Chinese study mentioned above to eliminate the HPV virus employs an innovative extension of CRISPR, which is a ‘game-changing’ technology. Over the past decade CRISPR has become a significant tool for genetic manipulation in biomedical research and biotechnology.  
 
CRISPR and genome editing

CRISPR is a complex system that can recognize and cut DNA sequences in order to provide organisms a strong defence against attacks and make them immune from further assaults. CRISPR has been adapted for both in vitro and in vivo use in eukaryotic cells to perform highly selective gene silencing or editing. Eukaryotic cells are those that contain a nucleus surrounded by a membrane and whose DNA is bound together by proteins into chromosomes.  CRISPRs are specialized stretches of DNA, and "CRISPR-Cas9" provides a powerful tool for precision editing due to its highly efficient targeting of specific DNA sequences in a genome, and has become the standard for genetic editing. Cas9 protein is an enzyme that acts like a pair of molecular scissors capable of cutting strands of DNA. The genomes of organisms encode messages and instructions within their DNA sequences. Genome editing involves changing those sequences, thereby changing the messages. This is achieved by making a break in the DNA, and tricking a cell's natural DNA repair mechanisms to make desired changes; CRISPR-Cas9 provides a means to do this. The technology’s ease of use and low cost have made it popular among the scientific community, and the possibility of its use as a clinical treatment in several genetically derived pathologies has rapidly spread its significance worldwide.
 
Changing ethical concerns

Despite CRISPRS promise there have been significant ethical concerns to genome editing, which center around human germline editing. This is because germline editing entails deliberately changing the genes passed on to children and future generations; in other words, creating genetically modified people. The debate about genome editing is not a new one, but has regained attention following the discovery that CRISPR has the potential to make such editing more accurate and even "easy" in comparison to older technologies. As of 2014, there were about 40 countries that discouraged or banned research on germline editing, including 15 nations in Western Europe. There is also an international effort, launched in December 2015 at the International Summit on Human Gene Editing and led by the US, UK, and China, to harmonize regulation of the application of genome editing technologies. 
 
After initially being opposed to using CRISPR in humans, in June 2016, the US National Institutes of Health advisory panel approved the technology for a study designed to target three types of cancer and funded by the Parker Institute for Cancer Immunotherapy at the University of Pennsylvania. In 2017 the UK approved the use of CRISPR for research in healthy human embryos. 
 
Off-target effects

Soon after scientists reported that CRISPR can edit DNA in 2012, experts raised concerns about “off-target effects,” meaning either CRISPR changes a gene scientist did not want changed or it fails to change a gene that they do. Although CRISPR-Cas9 is known for its precision a study, published in 2017 in the journal Nature Methods, raised concerns that because of the potential for “off-target effects” testing CRISPR in humans may be premature. Non-intended consequenes can happen because one molecule in the CRISPR system acts like a “molecular bloodhound”, searching the genome until it finds a match to its own sequence of  genetic letters; but there are 6bn genetic letters of the human genome, which suggests that there may be more than one match. Scientists anticipate and plan for this by using a computer algorithm to predict where such flaws might occur, then they search those areas to see if such off-target effects did occur. Notwithstanding such procedures and despite CRISPR’s precision, substantial efforts still are required to make the technology a common device safe for human clinical treatments.
 
Advances using CRISPR
 
The first clinical study using CRISPR began in October 2016 at the West China Hospital in Chengdu. Researchers, led by oncologist Lu You from Sichuan University, removed immune cells from the blood of a person with lung cancer, used CRISPR to disable a gene called PD-1, and then returned the cells to the body. This study is part of a much larger CRISPR genome editing revolution. Today, there are about 20 human clinical studies taking place using CRISPR technology most of which are in China. Different studies focus on different cancers including, breast, bladder, oesophageal, kidney, and prostate cancers. Further, a 2017 paper published in the journal Cell describes a number of innovative ways CRISPR being used; including editing cells while inside the body.
 
Takeaways
 
Despite the efficacy of HPV vaccines, immunization against cervical cancer still has significant challenges. Vaccines only target young people before they become sexually active, and are not recommended for slightly older and sexually active women. There is an urgent and growing concern about older women therefore who were not eligible for HPV vaccination, and are not availing themselves of regular Pap tests, and in whom the incidence of cervical cancer is increasing significantly. This makes Zheng Hu’s clinical study extremely important because it holds out the potential to substantially dent this large and rapidly increasing burden of cervical cancer.
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6 years, 2 months ago

Huntington’s disease and gene silencing

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Huntington’s Chorea
Huntington's disease
neurodegenerative disorders
  • For the first time in medical history scientists have corrected the cause of Huntington’s disease (HD)
  • HD is a fatal congenital neurodegenerative disorder that causes uncontrolled movements, emotional challenges, and loss of cognition
  • Current treatments only help symptoms rather than slow the progression of the disease
  • Researchers from University College London (UCL)havesafely lowered the levels of toxic proteins in the brain that cause HD
  • Experts say this is the biggest breakthrough in neurodegenerative research for 50 years
  • Earlier, an American animal study successfully used a similar technique to “silence” the mutant huntingtin gene in mice brains
  • Gene silencing stops the gene from making any mutant protein but does not eradicate the mutant HD gene
  • More studies are necessary to show whether the UCL study will effectively change the course of HD
  • Gene editing is a game-changer in biomedical research, but it faces significant technical and ethical challenges

Huntington’s disease and gene silencing
 
In December 2017, scientists completed the first human genetic engineering study that targeted the cause of Huntington’s disease (HD) (also known as Huntington’s Chorea), and successfully lowered the level of the harmful huntingtin protein that irreversibly damages the brains of patients suffering from this incurable degenerative condition. Current treatments for HD only help with symptoms, rather than slow the disease’s progression. The study’s leader, Professor Sarah Tabrizi, director of the Huntington’s Disease Centre at University College (UCL) London’s Institute of Neurology, says, “The results of this trial are of ground-breaking importance for Huntington’s disease patients and families”. Tabrizi’s research followed an earlier American study, which successfully used a similar technique to “silence” the mutant huntingtin gene in mice brains.
 
This Commentary describes Huntington’s disease, the 2 studies to silence the huntingtin gene, and also the gene silencing technology, which underlies both studies.
 
Huntington's disease
 
Huntington’s disease (HD) is a fatal congenital neurodegenerative disorder caused by a mutation in the gene of a protein called huntingtin, which triggers the degeneration of cells in the motor control regions of the brain, as well as other areas. HD is one of the most devastating neurodegenerative diseases, which some patients describe as Parkinson’s, Alzheimer’s and Motor Neurone disease rolled into one. HD leads to loss of muscle co-ordination; behavioural abnormalities and cognitive decline. Generally if one parent has HD then each child has a 50% chance of inheriting the disease. HD affects both sexes and about 12 people in 100,000, but appears to be less common in people of Japanese, Chinese, and African descent. If a child does not inherit the huntingtin gene, s/he will not develop the disease and generally cannot pass it to subsequent generations. Although there is a wide variation in its onset age, the majority of HD patients are diagnosed in middle age. Currently there is no cure for the disorder: although drugs exist, which help manage some symptoms they do not influence the progression of the disease.
 
 Signs and symptoms
 
The characteristic symptoms of HD include, cognitive impairment, mood shifts, irritability, depression and behavioural changes. As the disease develops symptoms get progressively worse and include uncontrolled movements, cognitive difficulties and issues with speech and swallowing. HD typically begins between the ages of 30 and 50. An earlier onset form called juvenile HD occurs in people under 20.  Symptoms of juvenile HD differ somewhat from adult onset HD and include unsteadiness, rigidity, difficulties at school, and seizures.  
 
Diagnoses
 
A genetic test, together with a medical history and neurological and laboratory tests, support doctors in their diagnosis of HD. Genetic testing, which costs between US$250 and US$350, is both cost-effective and diagnostically precise, and is important to establish whether HD is present in a family because some other illnesses may be misdiagnosed as HD. The disorder is a model for genetic testing because HD is relatively common, its etiology is understood, and there is significant experience with its management. There are 3 main types ofHD genetic testing: (i) to confirm or rule out the disorder, (ii) pre-symptomatic testing, and (iii) prenatal testing. Persons at risk of HD often seek pre-symptomatic testing to assist in making decisions about marriage, having children, and career. Positive results can evoke significant adverse emotional reactions, so appropriate pre- and post-test counselling is important.
  
Treatment
 
Current treatments can only alleviate the symptoms of HD, and do not delay the onset or slow the progression of the disease. Until the findings of the Tabrizi study there was no treatment that could stop or reverse the course of the disorder. Tetrabenazine and deuterabenazine are drugs prescribed for treating the chorea associated with HD.  Antipsychotic drugs may also help to alleviate chorea and can be used to help control hallucinations, delusions, and violent outbursts associated with the disease. Drugs may be prescribed to treat depression and anxiety, which are relatively common among HD sufferers. Drugs used to treat HD may have side effects such as fatigue, sedation, decreased concentration, restlessness, or hyper-excitability, and only should be used when symptoms create problems for the individual.
 
The Emory Study

In June 2017 scientists from the Emory University School of Medicine in Atlanta, USA, published findings of an animal study in the Journal of Clinical Investigation, which used the gene editing technique CRISPR-Cas9 to “silence” the mutate huntingtin gene (mHTT) in mice brains.

Study leader Xiao-Jiang Li, professor and expert in molecular mechanisms of inherited neuro-degeneration, used adult mice engineered to have the same mutant Huntington's-causing gene as humans, and were already showing signs of the disease. Using CRISPR-Cas9 Xiao-Jiang introduced genetic changes in an afflicted region of the brain that prevented further production of the faulty huntingtin gene. After 3 weeks, researchers noted that the brain region where the vector was applied, the mice brains showed that the aggregated proteins had almost disappeared, and there was a concomitant improvement in their physical functions; although not to the levels of the control mice.

The Emory research team’s findings showed that CRISPR-Cas9 successfully silenced part of a gene that produces toxic protein aggregates in the brains of mice, and demonstrated that the technique holds out the possibility of a one-time solution for HD.
 
The UCL study
 
What the Emory study achieved in mice the UCL study achieved in humans. The UCL study of the huntingtin-lowering drug Ionis-HTTRx led by Tabrizi and sponsored by Ionis Pharmaceuticals, a US$6bn NASDAQ traded company based in Carlsbad, California, used a similar technique as the Emory study to “silence” the mutated huntingtin gene. The study, which had been in pre-clinical development for over a decade, enrolled 46 human patients with early HD in 9 study centers in the UK, Germany and Canada. Each patient received 4 doses of either Ionis-HTTRx or a placebo, which were given one month apart by injection into the spinal fluid to enable the drug to reach the brain. As the study progressed, the dose of Ionis-HTTRx was increased several times according to the ascending-dose study design.
Orphan drug

Ionis-HTTRx is a so-called antisense drug, which means that it inhibits the expression of the huntingtin gene and therefore reduces the production of the mutant huntingtin protein (mHTT) in patients with HD.  In January 2016 Ionis-HTTRx received orphan drug designation from the US Food and Drug Administration (FDA), and the European Medicines Agency. This is a special status given to drugs that are not developed by the pharmaceutical industry for economic reasons but which respond to public health need.
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UCL study extended

Ionis-HTTRx was found to reduce the amounts of the mutant huntingtin gene that caused HD in the patients tested. It was also found to have an acceptable safety and tolerability profile.  It is too early to call Tabrizi and her colleagues’ findings a “cure” for HD, as the study was too small and not long enough to demonstrate whether patients’ clinical symptoms improve over time. Long-term data are necessary to show whether lowering the mHTT will effectively change the course of the disease. Notwithstanding the study’s findings point to the prospect of effective future treatments.
 
As a result of the study’s success, Ionis’s partner, Roche, a Swiss multinational healthcare company, has exercised its option and paid US$45m to license Ionis-HTTRx and assume responsibility for its further development, regulatory activities and commercialization. A future open-label extension study is expected to assess the effect of Ionis-HTTRx on the progression of HD, and Ionis Phamaceuticals announced that all patients in the completed study would be offered a place in the extension study.
 
Gene silencing

Gene silencing, the technique used in the both the UCL and Emory studies, relies on the fact that cells do not directly copy DNA into protein, but instead make a rough copy from a chemical called RNA, which acts as a “messenger” carrying instructions from DNA that control proteins. Gene silencing techniques target the RNA message: cutting it up, and thereby stopping the cell from making the mutant protein. However, even if gene silencing works to reduce the level of the harmful huntingtin gene, as it did in both the UCL and Emory studies, it does not change the DNA, and a HD mutation carrier still has the mutant HD gene. The “silencing” simply stops the gene making any mutant protein. Rather than silencing the mutant huntingtin gene it would be more efficacious if scientists could cut out the extra copies of the mutation that causes the disease.
 
CRISPR

CRISPR allows scientists to easily and inexpensively find and alter virtually any piece of DNA in any species. The technology potentially offers a cure for a number of incurable diseases, but its use in humans is not only ethically controversial, but also challenged by a need to find efficacious ways to deliver gene editing techniques inside the human body. Notwithstanding, there is a global race to push the technique to its limits.
 
Despite the potential of gene editing technology, scientists have encountered significant delivery challenges in using CRISPR techniques in humans for HD. Because CRISPR therapies are based on big protein molecules, they cannot be taken as a pill, but have to be delivered into the brain using injections, packaged into viruses, or similar technology. This presents delivery challenges, and the efficacy of gene editing therapies for neurodegenerative disorders is predicated upon effective delivery.
 
Takeaways

The UCL study significantly reduced the relevant protein levels in the cerebrospinal fluid of patients with Huntington’s. CRISPR’s success with HD raises the possibility that the technique might work for other neurodegenerative disorders such as Alzheimer’s. However, the genetic causes of Alzheimer’s and other neurodegenerative disorders are less well understood and more complex than Huntington’s, which makes them potentially more challenging. Further there are still significant scientific and ethical challenges to be overcome before gene-editing technology becomes common practice.
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6 years, 3 months ago

A cure for hemophilia?

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Directory:
Haematology
Tags:
blood clotting disorder
commentary
cryoprecipitate plasma
excessive bleeding
fresh frozen plasma (FFP
gene editing
hemophilia
hemophilia A
hemophilia B
tainted blood scandal
  • A new gene editing study is poised on the cusp of medical history because it holds out the prospect of providing a cure for hemophilia
  • Hemophilia is a rare incurable life-threatening blood disorder
  • People with hemophilia have little or no protein needed for normal blood clotting
  • Severe forms of the disorder may result in spontaneous and excessive bleeding
  • In recent history many people with hemophilia died before they reached adulthood because of the dearth of effective treatments
  • A breakthrough therapy in the 1980s was contaminated with deadly viruses
 
A cure for hemophilia?

A study led by researchers from Barts Health NHS Trust and Queen Mary University London and published in a 2017 edition of the New England Journal of Medicine has made a significant step forward towards finding a cure for hemophilia A, a rare incurable life threatening-blood disorder, which is caused by the failure to produce certain proteins required for blood clotting. In recent history only a few people with hemophilia survived into adulthood. This was because of the dearth of effective treatments and any small cut or internal hemorrhaging after even a minor bruise was often fatal.
 
The royal disease

There are 2 main types of hemophilia: A and B.  Both are rare congenital bleeding disorders sometimes referred to as “the royal disease,” because in the 19th and 20th centuries hemophilia affected European royal families. Queen Victoria of England is believed to have been a carrier of hemophilia B, a rarer condition than hemophilia A. 2 of Victoria’s 5 daughters (Alice and Beatrice) were also carriers.  Through marriage they passed on the mutation to various royal houses across Europe including those of Germany, Russia and Spain. Victoria’s son Prince Leopold was diagnosed with hemophilia A when he was a child. He died at 31 and throughout his life had a constant staff of doctors around him.
 
Epidemiology

The worldwide incidence of hemophilia A is about 1 in 5,000 males, with approximately 33% of affected individuals not having a family history of the disorder, which in their cases result from a new mutation or an acquired immunologic process. Only 25% of people with hemophilia receive adequate treatment; most of these are in developed nations. In 2016 there were some 7,700 people diagnosed with the condition in the UK, 2,000 of whom had a severe form with virtually no blood clotting protein. In the US there are some 20,000 people living with the disorder. Morbidity and death from hemophilia are primarily the result of haemorrhage, although HIV and hepatitis infections became prominent in patients who received therapies with contaminated blood products prior to the mid-1980s: see below.
 
Etiology
Hemophilia A and B are similar disorders. Both are caused by an inherited or acquired genetic mutation, which reduces or eliminates the coagulation genes referred to as factor VIII for hemophilia A, and factor IX for hemophilia B. Factors VIII and IX are essential blood clotting proteins, which work with platelets to stop or control bleeding. The amount of the protein present in your blood and its activity determines the severity of symptoms, which range from mild to severe. Factors VIII and IX deficiencies are the best-known and most common types of hemophilia, but other clotting factor deficiencies also exist. Factors VIII and IX are encoded in genes and located on the X chromosomes, which come in pairs. Females have 2 X chromosomes, while males have 1 X and 1 Y chromosome. Only the X chromosome carries the genes related to clotting factors. A male who has a hemophilia gene on his X chromosome will have hemophilia. Since females have 2 X chromosomes, a mutation must be present in both copies of the gene to cause the hemophilia. When a female has a hemophilia gene on only 1 of her X chromosomes, she is a "carrier” of the disorder and can pass the gene to her children. Sometimes carriers have low levels of a clotting factor and therefore have symptoms of hemophilia, including bleeding.

 

Hemophilia A and B

Hemophilia A and B affect all races and ethnic groups equally. Hemophilia B is the second most common type of hemophilia and is less common than factor VIII deficiency. Notwithstanding, the result is the same for people with hemophilia A and B: they both bleed more easily and for a longer time than usual. The differences between hemophilia A and B are in the factor that is either missing or at a low level. The treatments to replace factors A and B are different. Hemophilia A needs to be treated with factor VIII, and hemophilia B with factor IX. Giving factor VIII to someone with hemophilia B will not help to stop the bleeding.
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Mild to severe hemophilia

People with mild hemophilia have few symptoms on a day-to-day basis, but may bleed excessively for example during surgery, whilst those with a severe form of the disorder may have spontaneous bleeds. Severe hemophilia tends to be diagnosed in childhood or as part of screening in families known to have bleeding disorders. People who do not have hemophilia have a factor VIII activity of 100%, whereas people who have severe hemophilia A have a factor VIII activity of less than 1%. In severe forms, even the slightest injury can result in excessive bleeding as well as spontaneous internal bleeding, which can be life threatening. Also, the pressure of massive bleeding into joints and muscles make hemophilia one of the most painful diseases known to medicine. Without adequate treatment, many people with hemophilia die before they reach adulthood. However, with effective replacement therapy, life expectancy is about 10 years less than that of males without hemophilia, and children can look forward to a normal life expectancy. Replacement therapy entails concentrates of clotting factor VIII (for haemophilia A) or clotting factor IX (for haemophilia B) being slowly dripped or injected into a vein to help replace the clotting factors that are missing or low.
 
Brief history of treatments

In the 1950s and 60s fresh frozen plasma (FFP) was the principal therapy for hemophilia A and B. However, because each bag of FFP contained only very small amounts of the clotting agents, large amounts of plasma had to be transfused to stop bleeding episodes and people with the conditions had to be hospitalized. In some countries FFP is still the only product available for treating hemophilia.
 
In the mid-1960s Judith Pool, an American scientist, made a significant advance in haemophilia therapy when she discovered that the sludge, which sank to the bottom of thawing plasma was rich in factor VIII (but not IX) and could be frozen and stored as “cryoprecipitate plasma”. This more concentrated clotting factor VIII became the preferred treatment for severe hemophilia A as it required smaller volumes and patients could receive treatment as outpatients. Notwithstanding cryoprecipitate is less safe from viral contamination than concentrates and is harder to store and administer.
 
The tainted blood scandal

In the early 1970s drug companies found they could take the clotting factors VIII and IX out of blood plasma and freeze-dry them into a powder. This quickly became the treatment of choice as it could be used to treat hemophilia at home. There was a huge demand for the new freeze-dried product, and drug companies distilled the plasma of large groups of donors, sometimes as many as 25,000, to meet the demand. This led companies seeking substantial supplies of blood to pay prisoners and others to give blood. Some donors were addicted to drugs and infected with the HIV virus and hepatitis C. By the early 1980s, human blood, plasma and plasma-derived products used in therapies for hemophilia were discovered to be transmitting potentially deadly blood-borne viruses, including hepatitis viruses and HIV. So the same advanced substance being used to treat people with hemophilia was also responsible for causing sufferers prolonged illnesses and premature death.
 
Infected hemophilia treatments in the UK

A report published in 2015 by a UK All Party Parliamentary Group on Haemophilia found that 7,500 people in Britain with the disorder were infected with the contaminated blood products. According to Tainted Blood, a group set up in 2006 to campaign on behalf of people with hemophilia, 4,800 people were infected with hepatitis C, a virus that causes liver damage and can be fatal. Of these, 1,200 were also infected with HIV, which can cause AIDS, and some 2,400 sufferers died prematurely.
 
A 2017 UK official enquiry
 
In 1991 the UK government made ex-gratia payments to hemophilia patients infected with HIV, averaging £60,000 each, on condition that they dropped further legal claims. The extent of infection with hepatitis C was not discovered until years later. Campaigners unearthed evidence suggesting that UK officials in the Department of Health knew or suspected that the imported factor concentrates were risky as early as 1983. Notwithstanding, NHS England is said to have continued to administer the contaminated concentrates to patients with hemophilia. In 2017 the UK government set up an inquiry into the NHS contaminated blood scandal.  
 
A new scientific era

In the early 1980s, soon after HIV was identified, another significant breakthrough occurred in the treatment of hemophilia when manufacturers used genetically engineered cells that carry a human factor gene (called recombinant products). Today, all commercially prepared factor concentrates are treated to remove or inactivate blood-borne viruses. Also, scientists have a better understanding of the etiology of the disease and are able to detect and measure its inhibitors and know how to eliminate them by manipulating the immune system.
 
A cure for haemophilia A

Researchers, led by John Pasi, Director of the Haemophilia Centre at Barts Health NHS Trust and Professor of Haemostasis and Thrombosis at Queen Mary University London, have successfully carried out the first gene editing study for hemophilia A. The study enrolled 13 patients across England and injected them with a copy of their missing gene, which allows their cells to produce the essential blood-clotting agent factor VIII. Researchers followed participants for up to 19 months, and findings showed that 85% had normal or near normal levels of the previously missing factor VIII clotting agent and all participants were able to stop their previously regular haemophilia A treatment: they were effectively cured.
 
Gene editing
Gene editing is particularly relevant for diseases such as hemophilia A where, until the recent UK study reported in this Commentary, there was no cure. Gene editing allows doctors to prevent and treat a disorder by inserting a healthy gene into a patient’s cells to replace a mutated or missing gene that causes the disease. The technique has risks and is still under consideration to ensure that it is safe and effective. In 2015, a group of Chinese scientists edited the genomes of human embryos in an attempt to modify the gene responsible for β-thalassemia, another potentially fatal blood disorder.
 
Expanding the study

According to Pasi, "We have seen mind-blowing results, which have far exceeded our expectations. When we started out we thought it would be a huge achievement to show a 5% improvement, so to actually be seeing normal or near normal factor levels with dramatic reduction in bleeding is quite simply amazing. We really now have the potential to transform care for people with haemophilia using a single treatment for people who at the moment must inject themselves as often as every other day." Pasi and his colleagues are expected to undertake further studies with participants from the USA, Europe, Africa and South America.
 
Takeaway

Hemophilia is a life-changing, often painful and debilitating disorder. In recent history there was a dearth of effective therapies and people with the disorder barely survived into adulthood.  More recent scientific advances that used concentrated blood products to improve treatment were contaminated with deadly viruses, which further destroyed the lives of sufferers, and in many cases led to their premature death. The study, undertaken by Pasi and his colleagues, is on the cusp of medical history because it has the potential to provide a cure for what has been an incurable life-changing disease. Notwithstanding, it is worth bearing in mind that scientific discovery is rarely quick and rarely proceeds in a straight line.
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7 years, 1 month ago

Gene editing battles

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Medical Technology
Tags:
cancer genetics
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gene biology
gene editing
genetics
genome research
genomics
human genome
immunotherapy
  • Competition is intensifying among scientists to develop and use gene editing and immunotherapy to defeat intractable diseases
  • Chinese scientists were the first to inject people with cells modified by the CRISPR–Cas9 gene-editing technique
  • Several studies have extracted a patient’s own immune cells, modified them using gene-editing techniques, and re-infused them into the patient to seek and destroy cancer cells
  • A new prêt à l'emploi gene editing treatment disables the gene that causes donor immune cells to attack their host
  • The technique harvests immune cells from a donor, modifies and multiplies them so that they may be used quickly, easily and cheaply on different patients
  • Commercial, technical, regulatory and ethical barriers to gene editing differ in different geographies 

Gene editing battles

Gene editing and immunotherapy are developing at a pace. They have been innovative and effective in the fight against melanoma, lung cancer, lymphomas and some leukaemias, and promise much more. Somatic gene therapy changes, fixes and replaces genes at the tissue or cellular levels to treat a patient, and the changes are not passed on to the patient’s offspring. Germ line gene therapy inserts genes into reproductive cells and embryos to correct genetic defects that could be passed on to future generations.  Although there are still many unanswered clinical, commercial and ethical questions surrounding gene therapy, its future is assured and will be shaped by unexpected new market entrants and competition between Chinese and Western scientists, which is gaining momentum.
  
14 February 2017

On the 14th February 2017 an influential US science advisory group formed by the National Academy of Sciences and the National Academy of Medicine gave support to the modification of human embryos to prevent “serious diseases and disabilities” in cases where there are no other “reasonable alternatives”. This is one step closer to making the once unthinkable heritable changes in the human genome. The Report, however, insisted that before humanity intervenes in its own evolution, there should be a wide-ranging public debate, since the technology is associated with a number of unresolved ethical challenges. The French oppose gene editing, the Dutch and the Swedes support it, and a recent Nature editorial suggested that the EU is, “habitually paralysed whenever genetic modification is discussed”. In the meantime, clinical studies, which involve gene-editing are advancing at a pace in China, while the rest of the world appears to be embroiled in intellectual property and ethical debates, and playing catch-up.
 
15 February 2017

On the 15th February 2017, after a long, high-profile, heated and costly intellectual property action, judges at the US Patent and Trademark Office ruled in favor of Professor Feng Zhang and the Broad Institute of MIT and Harvard, over patents issued to them associated with the ownership of the gene-editing technology CRISPR-Cas9: a cheap and easy-to-use, all-purpose gene-editing tool, with huge therapeutic and commercial potential.
 
The proceedings were brought by University College Berkeley who claimed that the CRISPR technology had been invented by Professor Jennifer Doudna of the University, and Professor Emmanuelle Charpentier, now at the Max Planck Institute for Infection Biology in Berlin, and described in a paper they published in the journal Science in 2012. Berkeley argued that after the 2012 publication, an “obvious” development of the technology was to edit eukaryotic cells, which Berkeley claimed is all that Zhang did, and therefore his patents are without merit.

The Broad Institute countered, suggesting that Zhang made a significant inventive leap in applying CRISPR knowledge to edit complex organisms such as human cells, that there was no overlap with the University of California’s research outcomes, and that the patents were therefore deserved. The judges agreed, and ruled that the 10 CRISPR-Cas9 patents awarded to Zhang and the Broad Institute are sufficiently different from patents applied for by Berkeley, so that they can stand. 
 
The scientific community

Interestingly, before the 15th February 2017 ruling, the scientific community had appeared to side with Berkeley. In 2015 Doudna, and Charpentier were awarded US$3m and US$0.5m respectively for the prestigious Breakthrough Prize in life sciences and the Gruber Genetics Prize. In 2017 they were awarded the Japan Prize of US$0.45m for, “extending the boundaries of life sciences”. Doudna and Charpentier have each founded companies to commercially exploit their discovery: respectively Intellia Therapeutic, and CRISPR Therapeutics.
 
16 February 2017

A day after the patent ruling, Doudna said: “The Broad Institute is happy that their patent didn’t get thrown out, but we are pleased that our patent based on earlier work can now proceed to be issued”. According to Doudna, her patents are applicable to all cells, whereas Zhang’s patents are much more narrowly indicated. “They (Zhang and the Broad Institute) will have patents on green tennis balls. We will get patents on all tennis balls,” says Doudna.
 
Gene biology

Gene therapy has evolved from the science of genetics, which is an understanding of how heredity works. According to scientists life begins in a cell that is the basic building block of all multicellular organisms, which are made up of trillions of cells, each performing a specific function. Pairs of chromosomes comprising a single molecule of DNA reside in a cell’s nucleus. These contain the blueprint of life: genes, which determine inherited characteristics. Each gene has millions of sequences organised into segments of the chromosome and DNA. These contain hereditary information, which determine an organism’s growth and characteristics, and genes produce proteins that are responsible for most of the body’s chemical functions and biological reactions.

Roger Kornberg, an American structural biologist who won the 2006 Nobel Prize in Chemistry "for his studies of the molecular basis of eukaryotic transcription", describes the Impact of human genome determination on pharmaceuticals:
 
 
China’s first
 
While American scientists were fighting over intellectual property associated with CRISPR-Cas9, and American national scientific and medical academies were making lukewarm pronouncements about gene editing, Chinese scientists  had edited the genomes of human embryos in an attempt to modify the gene responsible for β-thalassemia and HIV, and are planning further clinical studies. In October 2016, Nature reported that a team of scientists, led by oncologist Lu You, at Ghengdu’s Sichuan University in China established a world first by using CRISPR-Cas9 technology to genetically modify a human patient’s immune cells, and re-infused them into the patient with aggressive lung cancer, with the expectation that the edited cells would seek, attack and destroy the cancer. Lu is recruiting more lung cancer patients to treat in this way, and he is planning further clinical studies that use similar ex vivo CRISPR-Cas9 approaches to treat bladder, kidney and prostate cancers
 
The Parker Institute for Cancer Immunotherapy
 
Conscious of the Chinese scientists’ achievements, Carl June, Professor of Pathology and Laboratory Medicine at the University of Pennsylvania and director of the new Parker Institute for Cancer Immunotherapy, believes America has the scientific infrastructure and support to accelerate gene editing and immunotherapies. Gene editing was first used therapeutically in humans at the University of Pennsylvania in 2014, when scientists modified the CCR5 gene (a co-receptor for HIV entry) on T-cells, which were injected in patients with AIDS to tackle HIV replication. Twelve patients with chronic HIV infection received autologous cells carrying a modified CCR5 gene, and HIV DNA levels were decreased in most patients.
 
Medical science and the music industry

The Parker Institute was founded in 2016 with a US$250m donation from Sean Parker, founder of Napster, an online music site, and former chairman of Facebook. This represents the largest single contribution ever made to the field of immunotherapy. The Institute unites 6 American medical schools and cancer centres with the aim of accelerating cures for cancer through immunotherapy approaches. 

Parker, who is 37, believes that medical research could learn from the music industry, which has been transformed by music sharing services such as Spotify. According to Parker, more scientists sharing intellectual property might transform immunotherapy research. He also suggests that T-cells, which have had significant success as a treatment for leukaemia, are similar to computers because they can be re-programed to become more effective at fighting certain cancers. The studies proposed by June and colleagues focus on removing T-cells, from a patient’s blood, modifying them in a laboratory to express chemeric antigen receptors that will attack cancer cells, and then re-infusing them into the patient to destroy cancer. This approach, however, is expensive, and in very young children it is not always possible to extract enough immune cells for the technique to work.
 
Prêt à l'emploi therapy

Waseem Qasim, Professor of Cell & Gene Therapy at University College London and Consultant in Paediatric immunology at Great Ormond Street Hospital, has overcome some of the challenges raised by June and his research. In 2015 Qasim and his team successfully used a prêt à l'emploi gene editing technique on a very young leukaemia patient. The technique, developed by the Paris-based pharmaceutical company Cellectis, disables the gene that causes donor-immune cells to attack their host. This was a world-first to treat leukaemia with genetically engineered immune cells from another person. Today, the young leukaemia patient is in remission. A second child, treated similarly by Qasim in December 2015, also shows no signs of the leukaemia returning. The cases were reported in 2017 in the journal Science Translational Medicine.
 
Universal cells to treat anyone cost effectively

The principal attraction of the prêt à l'emploi gene editing technique is that it can be used to create batches of cells to treat anyone. Blood is collected from a donor, and then turned into “hundreds” of doses that can then be stored frozen. At a later point in time the modified cells can be taken out of storage, and easily re-infused into different patients to become exemplars of a new generation of “living drugs” that seek and destroy specific cancer cells. The cost to manufacture a batch of prêt à l'emploi cells is estimated to be about US$4,000 compared to some US$50,000 using the more conventional method of altering a patient’s cells and returning them to the same patient. Qasim’s clinical successes raise the possibility of relatively cheap cellular therapy using supplies of universal cells that could be dripped into patients' veins on a moment’s notice.
 
Takeaways
 
CRISPR-Cas9 provides a relatively cheap and easy-to-use means to get an all-purpose gene-editing technology into clinics throughout the world. Clinical studies using the technology have shown a lot of promise especially in blood cancers. These studies are accelerating, and prêt à l'emploi gene editing techniques as an immunotherapy suggest a new and efficacious therapeutic pathway. Notwithstanding the clinical successes, there remain significant clinical, commercial and ethical challenges, but expect these to be approached differently in different parts of the world. And expect these differences to impact on the outcome of the scientific race, which is gaining momentum.
 
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7 years, 2 months ago

Gene editing positioned to revolutionise medicine

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Medical Technology
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commentary
DNA
DNA sequencing
embryo
gene editing
human embryo
human genome
intractable diseases
  • Chinese scientists lead the world in editing genomes of human embryos in order to develop new therapies for intractable diseases
  • US and UK regulators have given permission to edit the genes of human embryos
  • CRISPR-Cas9 has become the most common gene editing platform, which acts like is a pair of molecular scissors
  • CRISPR technology has the potential to revolutionize medicine, but critics say it could create a two-tiered society with elite citizens, and an underclass and have called for a worldwide moratorium on gene editing
  • Roger Kornberg, professor of medicine at Stanford University and 2006 Nobel Prize winner for Chemistry explains the science, which underpins gene-editing technology
  
Gene editing positioned to revolutionise medicine
 
It is a world first for China.
 
In 2015, a group of Chinese scientists edited the genomes of human embryos in an attempt to modify the gene responsible for β-thalassemia, a potentially fatal blood disorder. Researchers, led by Junjiu Huang from Sun Yat-sen University in Guangzhou, published their findings in the journal Protein & Cell.
 
In April 2016, another team of Chinese scientists reported a second experiment, which used the same gene editing procedure to alter a gene associated with resistance to the HIV virus. The research, led by Yong Fan, from Guangzhou Medical University, was published in the Journal of Assisted Reproduction and Genetics. At least two other groups in China are pursuing gene-editing research in human embryos, and thousands of scientists throughout the world are increasingly using a gene-editing technique called CRISPR-Cas9.
 
 
CRISPR-Cas9

Almost all cells in any living organism contain DNA, a type of molecule, which is passed on from one generation to the next. The genome is the entire sequence of DNA or an organism. Gene editing is the deliberate alteration of a selected DNA sequence in a living cell. CRISPR-Cas9 is a cheap and powerful technology that makes it possible to precisely “cut and paste” DNA, and has become the most common tool to create genetically modified organisms. Using CRISPR-Cas9, scientists can target specific sections of DNA, delete them, and if necessary, insert new genetic sequences. In its most basic form, CRISPR-Cas9 consists of a small piece of RNA, a genetic molecule closely related to DNA, and an enzyme protein called Cas9. The CRISPR component is the programmable molecular machinery that aligns the gene-editing tool at exactly the correct position on the DNA molecule. Then Cas9, a bacterial enzyme, cuts through the strands of DNA like a pair of molecular scissors. Gene editing differs from gene therapy, which is the introduction of normal genes into cells in place of missing or defective ones in order to correct genetic disorders.
 
Ground-breaking discovery 

The ground-breaking discovery of how CRISPR-Cas9 could be used in genome editing was first described by Jennifer Doudna, Professor of Chemistry and Cell Biology at the University of California, Berkeley, and Emmanuelle Charpentier, a geneticist and microbiologist, now at the Max Plank Institute for Infections in Berlin, and published in the journal Science in 2012.

In 2011 Feng Zhang, a bioengineer at the Broad Institute, MIT and Harvard, learned about CRISPR and began to work adapting CRISPR for use in human cells. His findings were published in 2013, and demonstrated how CRISPR-Cas9 can be used to edit the human genome in living cells.  

Subsequently, there has been a battle, which is on-going, between the scientists and their respective institution over the actual discovery of CRISPR’s use in human embryos, and who is entitled to the technology’s patents.
 
Gene editing research gathers pace worldwide: a few western examples

In 2016 a US federal biosafety and ethics panel licensed scientists at the University of Pennsylvania’s new Parker Institute of Cancer Immunotherapy to undertake the first human study to endow T-cells with the ability to attack specific cancers. Patients in the study will become the first people in the world to be treated with T-cells that have been genetically modified.

T-cells are designed to fight disease, but puzzlingly they are almost useless at fighting cancer. Carl June, the Parker Institute’s director and his team of researchers, will alter three genes in the T-cells of 18 cancer patients, essentially transforming the cells into super fighters. The patients will then be re-infused with the cancer-fighting T-cells to see if they will seek and destroy cancerous tumors.

Also in 2016, the UK’s Human Fertilisation and Embryology Authority (HFEA), which regulates fertility clinics and research, granted permission to a team of scientists led by Kathy Niakan at the Francis Crick Institute in London to edit the genes of human IVF embryos in order to investigate the causes of miscarriage. Out of every 100 fertilized eggs, fewer than 50 reach the early blastocyst stage, 25 implant into the womb, and only 13 develop beyond three months.
 
Frederick Lander, a development biologist at the Karolinska Institute Stockholm, is also using gene editing in an endeavour to discover new ways to treat infertility and prevent miscarriages. Lander is the first researcher to modify the DNA of healthy human embryos in order to learn more about how the genes regulate early embryonic development. Lander, like other scientists using gene-editing techniques on human embryos, is meticulous in not allowing them to result in a live birth. Lander only studies the modified embryos for the first seven days of their growth, and he never lets them develop past 14 days. “The potential benefits could be enormous”, he says.
 
Gene editing cures in a single treatment

Doctors at IVF clinics can already test embryos for genetic diseases, and pick the healthiest ones to implant into women. An advantage of gene editing is that potentially it could be used to correct genetic faults in embryos instead of picking those that happen to be healthy. This is why the two Chinese research papers represent a significant turning point. The gene editing technology they used has the potential to revolutionize the whole fight against devastating diseases, and to do many other things besides. The main benefit of gene editing therapy is that it provides potential cures for intractable diseases with a single treatment, rather than multiple treatments with possible side-effects.
 
The promise of gene editing for fatal and debilitating diseases
 
Among other things, gene editing holds out promise for people with fatal or debilitating inherited diseases. There are over 4,000 known inherited single gene conditions, affecting about 1% of births worldwide. These include the following:- cystic fibrosis, which each year affects about 70,000 people worldwide, 30,000 in the US, and about 10,000 in the UK; Tay-Sachs disease, which results in spasticity and death in childhood. The BRCA1 and BRCA2 inherited genes predispose women with a significantly greater chance of developing breast or ovarian cancer. Sickle-cell anaemia, in which inheriting the sickle cell gene from both parents causes the red blood cells to spontaneously “sickle” during a stress crisis; heart disease, of which many types are passed on genetically; haemophilia, a bleeding disorder caused by the absence of genetic clotting agent and. Huntington disease, a genetic condition which slowly kills victims by affecting cognitive functions and neurological status. Further, genomics play a significant role in mortality from chronic conditions such as cancer, diabetes and heart disease.
 
A world first

Huang and his colleagues set out to see if they could replace a gene in a single-cell fertilized human embryo. In principle, all cells produced as the embryo develops would then have the replaced gene. The embryos used by Huang were obtained from fertility clinics, but had an extra set of chromosomes, which prevented them from resulting in a live birth, though they did undergo the first stages of development. The technique used by Huang’s team involved injecting embryos with the enzyme complex CRISPR-Cas9, which, as described above, acts like is a pair of molecular scissors that can be designed to find and remove a specific strand of DNA inside a cell, and then replace it with a new piece of genetic material.
 
The science underpinning gene editing

In the two videos below Roger Kornberg, professor of medicine at Stanford University and 2006 Nobel Prize winner for Chemistry for his work on “transcription”, the process by which DNA is converted into RNA, explains the science, which underpins gene-editing technology:
 
How biological information, encoded in the genome, is accessed for all human activity

 
 
Impact of human genome determination on pharmaceuticals
 
An immature technology
 
Huang’s team injected 86 embryos, and then waited 48 hours; enough time for the CRISPR-Cas9 system, and the molecules that replace the missing DNA to act, and for the embryos to grow to about eight cells each. Of the 71 embryos that survived, 54 were genetically tested. Only 28 were successfully spliced, and only a fraction of those contained the replacement genetic material.
 
Therapy to cure HIV
 
Fan, the Chinese scientist who used CRISPR in an endeavor to discover a therapy for HIV/Aids, collected 213 fertilized human eggs, donated by 87 patients, which like embryos used by Huang, were unsuitable for implantation, as part of in vitro fertility therapy. Fan used CRISPR–Cas9 to introduce into some of the embryos a mutation that cripples an immune-cell gene called CCR5. Some humans who naturally carry this mutation are resistant to HIV, because the mutation alters the CCR5 protein in a way that prevents the virus from entering the T-cells it tries to infect. Fan’s analysis showed that only 4 of the 26 human embryos targeted were successfully modified.
 
Deleting and altering genes not targeted
 
In 2012, soon after scientists reported that CRISPR could edit DNA, experts raised concerns about “off-target effects,” where CRISPR inadvertently deletes or alters genes not targeted by the scientists. This can happen because one molecule in CRISPR acts like a bloodhound, and sniffs around the genome until it finds a match to its own specific sequence. Unfortunately, the human genome has billions of potential matches, which raises the possibility that the procedure might result in more than one match. 
 
Huang is considering ways to decrease the number of “off-target” mutations by tweaking the enzymes to guide them more precisely to a desired spot, introducing the enzymes in a different format in order to try to regulate their lifespans, allowing enzymes to be shut down before mutations accumulate; and varying the concentrations of the introduced enzymes and repair molecules. He is also, considering using other gene-editing techniques, such as LATENT.
 
The slippery slope to eugenics

Despite the potential therapeutic benefits from gene editing, critics suggest that genetic changes to embryos, known as germline modifications, are the start of a “slippery slope” that could eventually lead to the creation of a two-tiered society, with elite citizens, genetically engineered to be smarter, healthier and to live longer, and an underclass of biologically run-of-the-mill humans.
 
Some people believe that the work of Huang, Fan and others crosses a significant ethical line: because germline modifications are heritable, they therefore could have an unpredictable effect on future generations. Few people would argue against using CRISPR to treat terminal cancer patients, but what about treating chronic diseases or disabilities? If cystic fibrosis can be corrected with CRISPR, should obesity, which is associated with many life-threatening conditions? Who decides where the line is drawn?
 
40 countries have banned CRISPR in human embryos. Two prominent journals, Nature and Science, rejected Huang’s 2012 research paper on ethical grounds, and subsequently, Nature published a note calling for a global moratorium on the genetic modification of human embryos, suggesting that there are “grave concerns” about the ethics and safety of the technology.
 
A 2016 report from the Nuffield Council on Bioethics suggests that because of the steep rise in genetic technology, and the general availability of cheap, simple-to-use gene-editing kits, which make it relatively straightforward for enthusiasts outside laboratories to perform experiments, there needs to be internationally agreed ethical codes before the technology develops further.
 
Recently, the novelist Kazuo Ishiguro, among others, joined the debate, arguing that social changes unleashed by gene editing technologies could undermine core human values. “We’re coming close to the point where we can, objectively in some sense, create people who are superior to others,” says Ishiguro.
 
Takeaways

CRISPR has been described as the “Model T of genetics”.  Just as the Model T was the first motor vehicle to be successfully mass-produced, and made driving cheap and accessible to the masses, so CRISPR has made a complex process to alter any piece of DNA in any species easy, cheap and reliable, and accessible to scientists throughout the world. Although CRISPR still faces some technical challenges, and notwithstanding that it has ignited significant protests on ethical grounds, there is now a global race to push the boundaries of its capabilities well beyond its present limits.
 
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