Tagged: genome research

  • 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.
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.
view in full page
  • 16% of Mexico’s population has type-2 diabetes (T2DM) and each year it kills 70,000
  • Mexican mothers feed their children sugary beverages from birth and create soda addicts
  • In 2014 a national sugar tax on fizzy drinks was introduced, but sales on untaxed sugary beverages increased
  • The Carlos Slim Foundation (CSF) takes fundamental action to dent Mexico’s T2DM epidemic
  • The CSF collaborates with MIT’s Broad Institute to conduct the largest and most comprehensive genomic study on T2DM in Mexican populations
  • Three years later CSF announces the discovery of the first common genetic variant shown to predispose Mexicans to T2DM
  • Findings could lead to improved diagnostics and new therapies for T2DM, say experts
  • The Broad Institute and the CSF make their genomic studies and other data freely available to scientists worldwide
  • Organizations with bureaucratic walls that restrict the free-flow and sharing of knowhow and information significantly impede the advancement of our understanding and management of globally important chronic conditions such as T2DM
Slim lessons in diabetes understanding and management

What can a self-made 77-year-old son of Catholic Lebanese immigrants to Mexico contribute to our understanding and management of T2DM?
77-year-old Carlos Slim built a business empire, which today is worth the equivalent to 6% of Mexico’s GDP. His company Grupo Carso is influential in every sector of the Mexican economy, and he is currently the chairman and CEO of telecom giants Telmex and América Móvil. Slim believes that businessmen should do more than just give‍ money, and says they "should participate in solving problems".

An important aspect of reducing the significant burden of chronic health conditions such as T2DM, is to reduce the bureaucracies of key organizations, which impede the sharing of important knowhow that help our understanding and management of these globally important disease.
Slim has turned his attention to Mexico’s vast and escalating diabetes epidemic, which devastates the lives of millions, and significantly dents the Mexican economy. Recently, the Carlos Slim Foundation (CSF) started applying the knowhow and skills used to build world-class companies to tackle the Mexican diabetes burden, and in less than three years, discovered a gene, which contributes to the significantly higher incidence rate of T2DM in Latin Americans. The CSF intends to build on this to develop new treatments.

Diabetes in Mexico

Each year, T2DM related complications kill 70,000 Mexicans. In 2015, there were 11m people with diabetes in Mexico - almost 12% of its adult population - projected to rise to some 16m by 2035. Mexico has one of the world’s highest rates of childhood obesity, a significant contributory risk factor of T2DM. The prevalence of overweight or obese children and adolescents between 5 and 19 years is 35%. This is believed to be the result of mother’s feeding their babies sugary drinks: partly because of the lack of clean water, and partly cultural since many Mexicans consider chubby babies to be good. According to Dr. Salvador Villalpando, a childhood obesity specialist at the Federico Gomez Children's Hospital in Mexico City, “about 10% of Mexican children are fed soda from birth to six months, and by the time they reach two it's about 80%." Mexico has become the No. 1 per capita consumer of sugary beverages, with the average person drinking more than 46 gallons per year: nearly 50% more than the average American.
Over the last 20 years, the prevalence of T2DM in Mexico, a country with a population of 122 million, has increased rapidly. The Mexican health system is struggling to effectively adapt to the diabetes burden facing the nation. Healthcare spending represents approximately 6% of GDP and is divided near equally between the public and private sectors. The former, supports mostly low-income non-salaried workers, accounting for about 60% of those in work: some 30m. The latter, is an employer-based scheme linked to salaried workers.

Sugar tax

So acute is the problem of T2DM in Mexico that in January 2014, the government introduced a 10% tax on sugar-sweetened beverages. Research published in the British Medical Journal in 2016 suggests that the tax resulted in a 6% reduction in the purchases of taxed beverages in the first year, increasing to 12% by the end of the second year. The study also reported increases in purchases of untaxed beverages. Findings are disputed by the drinks industry. “Fizzy drinks only account for 5.6% of Mexico's average calorie consumption so can only be a small part of the solution to obesity and diabetes,” says Jorge Terrazas of Anprac; Mexico's bottled drinks industry body.
Carlos Slim Foundation and diabetes

The obesity epidemic, aging population and escalating health costs have increasingly strained resources and exacerbated Mexico’s diabetes burden, which the CSF is intent to reduce. In 2010 the Foundation formed an association with MIT’s Broad Institute. With an investment of US$74m it formed the Slim Initiative in Genomic Medicine for the Americas (SIGMA). It was a natural fit because Slim knows just how big data strategies transformed retail businesses and also cancer research and therapies; and the Broad Institute specialises in developing big genomic data sets and making them available to molecular scientists in premier research centres throughout world in order to transform medicine. From its inception SIGMA set out to systematically identify genes underlying diabetes.
The development of T2DM depends on complex inheritance-environment interactions along with certain lifestyle behaviors. Previous HealthPad Commentaries have described such complexities. One described the lifetime research endeavors of Professor Sir Steve Bloom, Head of Diabetes, Endocrinology and Metabolism at Imperial College London, on obesity and the gut-brain relationship.
SIGMA believed that having access to genomic research undertaken by a network of world class scientists holds out the possibility of discovering fundamental aspects of the biological mechanisms linked to T2DM. And this could form the basis for more effective diagnostics and new and improved therapies for the condition. Until recently, only a select group of specialists had full access to such data. The CSF was also mindful that their relationship with the Broad Institute would help build Mexico’s capacity in genomic medicine.
T2DM risk gene found in Latin Americans

A major focus of SIGMA’s 2010 research agenda was to identify the genetic risk factors that contribute to the significantly higher incidence rate of T2DM in Mexico compared with the rest of the world. SIGMA conducted the largest and most comprehensive genomic study to date on T2DM in Mexican populations, which involved scientists at 125 institutions in 40 countries, and resulted in the discovery of the first common genetic variant shown to predispose Latin American’s to T2DM.

Findings show that people who carry the higher risk version of the gene are 25% more likely to have diabetes than those who do not. People who inherit copies of the gene from both parents are 50% more likely to have diabetes. The higher risk-form of the gene is present in half of the people with recent Native American ancestry, including Latin Americans. The elevated frequency of this risk gene in Latin Americans could account for, as much as 20% of the populations’ increased prevalence of T2DM. The gene variant also is found in about 20% of East Asians, but is rare in populations from Europe and Africa.

Doing science with one eye closed

"Most genomic research has focused on European or European-derived populations, which is like doing science with one eye closed,” says Eric Lander, Professor of Biology at MIT and President and Founding Director of the Broad Institute, who went on to say, “There are many discoveries that can only be made by studying non-European populations." José Florez, a principal investigator of the SIGMA study adds, “By expanding our search to include samples from Mexico and Latin America, we’ve found one of the strongest genetic risk factors discovered to date, which could illuminate new pathways to target with drugs and a deeper understanding of T2DM.”
The impact of evolutionary science on healthcare systems

Roger Kornberg, Professor of Medicine at Stanford University who won the 2006 Nobel Prize in chemistry, "for his studies of the molecular basis of eukaryotic transcription", describes how human genome sequencing and genomic research fundamentally changed the way healthcare is organized and delivered. “Genomic sequencing enables us to identify every component of the body responsible for all life processes. In particular, it enables the identification of components, which are either defective or whose activity we may wish to edit in order to improve a medical condition,” says Kornberg.
Website helps translating genomic discoveries into therapies

Three years following their discoveries; the CSF launched SIGMA 2 with a mandate to complete its genetic analysis of T2DM, improve diagnostics, and develop therapeutic roadmaps to guide the development of new treatments. SIGMA 2 also planned to ramp up scientific capabilities in both the US, and Mexico by developing a unique resource. In 2016 SIGMA 2 created a website of open-access genetic data on T2DM. The site contains data available from all the SIGMA studies, plus information on major international data networks, including more than 100,000 DNA samples, and the complete results of 28 large genome association studies. Scientists throughout the world have free access to these data.
The importance of the open exchange of information

The new web portal represents a breakthrough, because it allows scientists throughout the world access to genetic information, and this is expected to accelerate progress of our understanding and treating diabetes. “The open exchange of information is essential for scientific progress, but it is not always easily achievable. This site not only helps us to overcome this barrier – by allowing access to patient data from around the world – but also will allow directing scientists to the most prevalent genetic risk factors among the populations of Latin America and others who have been underrepresented in large-scale genomic studies,” says Lander who believes that, "It is essential that the benefits of the genomic revolution are accessible to people throughout the Americas and the world."

The SIGMA project has been a story of total success. Our extraordinary partners, both in Mexico and the US, have made it possible to make historic advances in the understanding of the basic causes of T2DM. We hope that through our contributions we will be able to improve the ways in which the disease is detected, prevented and treated,” says Roberto Tapia-Conyer, CEO of the CSF.

So, for an investment of US$25m a year for three years SIGMA made a significant discovery, which could beneficially affect the diagnostics and treatment of T2DM, and it also enhanced Mexico’s capacity for genomic research. Such success was due, in part, to the leadership of a 77-year-old Mexican businessman intent on solving problems, who thought globally, partnered with world-class institutions, understood and supported the potential of big data strategies and genomic research, and stood shoulder-to-shoulder with Eric Lander against healthcare organizations, which build and defend bureaucratic walls that significantly restrict the open access of knowhow and data.
view in full page