Investigating genome-environment interactions in diabetes

Type 1 diabetes is a disease in which the pancreas does not produce insulin, resulting in glucose accumulation in the blood instead of being used for energy.

The Challenge

Type 1 Diabetes (T1D) is a complex disease often arising in childhood in which the immune system destroys the insulin producing cells of the pancreas. Insulin is a crucial hormone in sugar and fat metabolism. Despite insulin therapy, T1D greatly increases the probability of heart attack, stroke, blindness and limb amputation, as well as shortened life expectancy.

  • Canada has the third largest incidence of T1D in the world, affecting some 200,000 Canadians, including 45,000 – 90,000 Ontarians
  • Ontario spends $5 billion a year on diabetes and associated conditions

The Research Solution

T1D is caused by multiple genetic risk factors and currently unknown environmental factors. Now an innovative research project is investigating the interactions of genetic risks and environmental factors underlying T1D.

Dr. Jayne Danska, Senior Scientist at Toronto’s Hospital for Sick Children and Professor in the Faculty of Medicine at the University of Toronto, and Dr. Andrew Macpherson, Canada Research Chair in mucosal immunology at McMaster University, are involved in a project that aims to understand how genetics can be used to control T1D in humans and rodent models. They will also study how exposure to common intestinal bacteria affects the development of the immune system and how such exposures affect the probability that people at genetic risk of T1D will develop the disease.

This project is expected to discover new genetic markers and identify environmental exposures that increase T1D risk, with the long-term aim of reducing disease risks through therapeutic intervention.

Successes to date

Several genes involved in diabetes have been discovered in tests carried out with mice. These tests have identified potential ways to help improve the immune systems in people with diabetes

The tests with mice has led to the building of a unique germ-free mouse facility in Toronto – one of only two in North America – that enables genomic analysis of animals with specific bacterial exposures under controlled conditions. This facility with its state-of-the-art technology will speed up research into diabetes and help discoveries be made quicker

This research is making great leaps towards reaching the ultimate goal of understanding how T1D is affected by environmental conditions, and armed with this understanding, researchers will be able to predict the body’s immune systems reaction to various treatments and environments, and even manipulate environmental factors to block or stop the development of the condition.

Associated Integrated GE3LS Research Project: Attitudes of Adults and Adolescents to Predictive Genetic Testing for Diabetes

Cleaning up contaminated water

Challenge
Water contaminants can lead to debilitating and deadly diseases such as dengue fever, cholera, dysentery, and diarrhea. More than a billion people worldwide have no access to a decent water supply. As a result, unsafe water, poor sanitation and hygiene are the leading causes of death in the developing world. In fact, the majority of illnesses in developing countries are caused by poor water and sanitation conditions.

Genomics solution
DNA-based technologies can quickly and accurately detect pathogens in a water supply, identifying unsafe water before it can make people sick. KB-1 is a value-recovery tool for contaminated groundwater. KB-1 can be injected into an area contaminated with trichloroethene (TCE) next to a river. Within 6 months, 98% of the estimated TCE mass was removed. It is the most widely used bioaugmentation culture used in the world for dechlorination. These versatile technologies can be adapted to identify a variety of contaminants, and are suitable for the unique conditions of developing countries.

Impact
Cleaning up contaminated water has an impact on human health. The rapid increases in population in developing countries & major urban centers will influence major investments for water and wastewater treatment needs and will drive water recycling and re-use.
KB-1 is currently being marketed and sold by SiREM. It has been translated from lab to marketplace.

KB-1 was discovered by Dr. Elizabeth Edwards (University of Toronto) and is now marketed and sold by SiREM. Dr. Edwards also leads the BEEM project, which aims to accelerate discovery and characterization of microbial consortia (KB-1 and others).

GAPP project description – Scale-up of bioaugmentation cultures and development of delivery strategies and monitoring tools for anaerobic benzene and alkylbenzene bioremediation

Making every species count

DNA barcoding is the use of short stretches if DNA to identify species. Making reliable and rapid species identification is essential to combating many of the threats facing our environment.

The Challenge

  • Climate change, invasive species migration and globalization of trade threaten ecosystems and biodiversity around the world
  • Pest damage to agricultural crops costs farmers the equivalent of billions of dollars each year, and leads to food shortage

The Research Solution

  • Dr. Paul Hebert’s International Barcode of Life (iBOL) project is working towards cataloging the world’s biodiversity by building a DNA barcode database
  • With research teams in 25 countries across the globe, Dr. Hebert is aiming to build a public resource with DNA barcodes from five million speciments representing at least 500,000 species over five years

How DNA barcoding will impact our world

New practical applications are constantly emerging, indicating limitless potential for iBOL’s growing digital reference library of DNA barcodes to impact on the way we live and interact with the world around us:

  • The ability to identify mosquitoes will help public health authorities to control the spread of diseases like the West Nile virus, malaria and yellow fever
  • Border control officials will be able to spot invasive species and fight the trade in endangered plants and animals
  • Early identification and control of invasive species will save the forestry and agricultural industries billions in lost production
  • Health care workers will be able to identify and control the organisms that make us sick as well as the vectors that spread disease
  • Animal feed will be tested for banned substances such as those that cause diseases like BSE
  • Water authorities will be able to monitor the health of our oceans, lakes and rivers, and the quality of our drinking water
  • Consumers will be able to check fish and other food products to ensure that what they are buying is what is advertised

Successes to date

  • Nearly ¾ of a million DNA barcodes sequenced worldwide to date
  • Dr. Hebert and his team at the Biodiversity Institute of Ontario are recognized as world-leaders in DNA barcoding

To read more about this research visit: www.ibol.org

To read more about barcoding, visit http://dna-barcoding.blogspot.ca/

Autism: Genomes to outcomes

Autism is a developmental disorder that appears in the first three years of life, and affects the brain\’s normal development of social and communication skills.

The Challenge

  • Autism is one of the world’s most urgent public health challenges
  • Around one in 120 newborns is likely to have autism spectrum disorder (ASD), making it more common than type 1 diabetes, childhood cancer and cystic fibroses combined
  • The cost of treating autism is some $35 billion annually worldwide
  • Genes are the most likely culprit in causing autism, whether directly or indirectly, in upwards of 80-90% of individuals with ASD

The Research Solution

  • Drs. Stephen Scherer, Peter Szatmari and their team at The Hospital for Sick Children are using a $9.9 million LSARP award to help discover and characterize all of the genes involved in autism
  • This ground-breaking work will mark Canada’s contribution to an ambitious international initiative that aims to sequence and analyze the genomes of 10,000 people with autism spectrum disorder.
  • This work will help to facilitate early diagnoses, better medical management and individualize approaches to ASD treatment
  • By discovering all the autism rick genes, studies of environmental influences in ASD will be possible

Successes 

  • Numerous disease susceptibility genes have already been discovered and other genetic factors underlying autism have been defined
  • Recently, Dr. Scherer and his team discovered that a number of autism cases are linked to a gene found on the X chromosome, helping to explain why boys are four times more likely than girls to develop ASD
  • Current thinking is that there is over 100 different genes involved in autism, with 15% of those identified to date
  • The hope is that this information will help the development of drugs to treat autism

For more information on autism, visit: www.autismspeaks.ca

 

Finding the cause of rare diseases

The Challenge

Genetic diseases, while often rare, have, in aggregate, an enormous impact on the well-being of Canadian families, affecting the lives of approximately 500,000 children. The majority of genes causing these conditions are still unknown. These parents go through cycles of treatment and cost the health care system an inordinate amount of money considering the percentage of people affected. There is often no cure or any therapeutic treatment because the causes are unknown.

Genomics solution

Dr. Kym Boycott and collaborators used DNA sequencing to determine the causes of rare diseases that were put forward to the consortium by physicians across the country who deal with patients. The determination of the gene causing the diseases will then lead to a screening test for those particular disorders and also potential therapy options should the gene be identified in a well-known cellular pathway that drugs may have been designed for.

77 disorders were identified and four novel therapies were determined from this work. On a broader scale it showed the utility of these new genomic technologies to the clinical and to providing personalized care. While the economic modelling has not been done, the ability to know what gene causes a particular disorder and whether there is any therapy, will reduce the repeat visits to the clinic for the patients. In terms of quality of life, it is clearly of great benefit to the patients to get this information.

More information

Three OG seeded companies get additional funding

InDanio Bioscience, Encycle Therapeautics made new research partnerships for research and drug development and RNA Diagnostics received angel investment.

Two SMEs, InDanio Bioscience and Encycle Therapeautics will partner with Toronto researchers and provide in-kind contributions to the $1.5M funding by CQDM and CIHR, through its institutes of Cancer Research, Genetics and Infection and Immunity medicine, for two translational projects in personalized medicine to accelerate drug discovery and drug development. In addition, RNA Diagnostics, a Sudbury-based medical diagnostic company, has successfully closed an additional round of angel investment with support of the NORCAT Innovation Mill Angel group. The Ontario Genomics Institute\’s Pre-commercialization Business Development Fund (PBDF) funded RNA Diagnostics in 2012, InDanio Bioscience in 2010.

More Canadians to benefit from personalized cancer treatment

Personalized cancer treatment requires complex clinical laboratory testing to determine a tumour’s genetic profile. The Princess Margaret Cancer Centre, a leader in providing this testing for its patients, and LifeLabs Medical Laboratory Services have begun working together to expand this testing capacity to more Canadians.

The Princess Margaret Cancer Centre (PMCC) has teamed up with Ontario-based LifeLabs Medical Laboratory Services (LifeLabs) to expand the availability of cancer genome profiling across Canada, with funding from Genome Canada. This will improve access to personalized cancer treatment for patients across the country.

Cancer genome profiling is emerging as an essential step in modern cancer care. The percentage of patients whose tumours were driven by genetic mutations that could be targets for tailored cancer therapeutics range from 21% (head and neck tumours) up to 73% (melanoma), according to a Personalized Medicine Coalition report. In fact, tumour classification is changing from being based on the tissue of origin to being based on the underlying genomic alterations, making it critical that patients across the country have equal and timely access to appropriate testing. And as discussed in an accompanying article “Can personalized cancer care be cost-effective?” this type of testing can lead to better outcomes as well as save healthcare dollars.

Major treatment centres such as the PMCC have been at the forefront of developing and applying new tumour genetic profiling tests for their patients. However, access to these tests outside such major cancer centres is difficult due to the complexity of the tests.

For this project, Dr. Suzanne Kamel-Reid at the PMCC and team will combine their expertise in next-generation sequencing for clinical tumour profiling with LifeLabs’ expertise in specimen collection, their transportation network and logistics capabilities. They will also develop a secure cloud-based cancer genome analysis infrastructure to be able to store and share information between the two groups. The combined expertise and resources will expand the availability of such tests across Canada including rural areas and community hospitals.

By: Kathryn Deuchars, Director, Ontario Personalized Medicine Network

Rising prices for new targeted therapeutics threatens their own success

One cancer drug alone could wipe out Canada’s total budget of $12B for prescription drugs. Can this last?

Drug companies bringing out new targeted therapies for rare disorders are asking, and getting, eye-popping prices. Examples include Kalydeco® for one type of Cystic Fibrosis, reported to cost CAD$300,000 per year, or the recently marketed Solaris® for which Alexion tried to get CAD$700,000 per year for Canadian patients (even higher than it was charging U.S. patients). Drug companies argue that these costs are justified because the drugs are showing dramatic results for patients. But because these are for a very small number of patients, and only a few have been marketed so far, our healthcare system may be able to absorb the cost – there are only 90 patients in Canada that might benefit from Solaris, for example. But this won’t always be the case – there are 7,000 rare disorders that may be amenable to drug treatment, and treatments are typically needed life-long.

What really brings it home are the escalating prices for some new targeted therapies for cancer.

Prominent oncologist Dr. Leornard Saltz of the Memorial Sloan Kettering Cancer Center took aim at these at the recent American Society of Clinical Oncology (ASCO) meeting. At the plenary speech, Dr. Saltz focused on the expected high cost of new combination treatment for metastatic melanoma from Bristol-Myers Squibb Co. Although he welcomed the arrival of a “truly, truly remarkable” new therapy, “he said that combining the drugs would cost around $295,000 a patient over nearly one year, which he called unsustainable. If all U.S. patients with metastatic cancer took drugs priced at $295,000 a year, it would cost $174 billion to treat them all for just one year” reports the Wall Street Journal.

Given that Canada’s total public spend on prescription drugs is about $12B, and adjusting for Canada’s population size, that would pretty much wipe out Canada’s total budget for prescription drugs.

Not all new drug pricing seems so far out of line. Although the recently released Hepatitis C drug Harvoni® costs over $1,000 per pill, and a complete course of treatment costs approximately CAD$85,000, this is a one-time treatment with near 100% cure rate for a potentially lethal disease with a very high cost burden (see our July 2015 article about this new treatment). And as outlined in an accompanying article, “Can personalized cancer care be cost-effective?” selecting the best targeted treatment for a patient’s cancer by genetic analysis of their tumour has been shown to be both cost effective and to give better outcomes.

The focus needs to be on how to appropriately price new drugs. The CBC looked into the Solaris story, pointing out that the cost of such drugs has little to do with the development and manufacturing costs. The CBC article also pointed out that much of the basic discovery costs came out of the public purse in the form of academic research funding, which drug companies do not factor into their pricing. Barry Werth of the MIT Technology Review looked into the high prices for two new drugs, Kalydeco® and Zaltrap®, and cites veteran drug maker and former Genzyme CEO Henri Termeer as saying “In determining the price for a drug, companies ask themselves questions that have next to nothing to do with the drugs’ costs. It is not a science […] It is a feel.”

Two efforts underway in Canada should help realign drug pricing. Ontario’s MaRS EXCITE program helps companies develop the evidentiary bundle, including an economic analysis, that a company can bring to the bargaining table to provide a more rational approach to drug pricing. The project “PACE-‘Omics,” led by Alberta’s Drs. Christopher McCabe and Tania Bubela, funded by Genome Canada, aims to develop better decision-making tools “to give policymakers and investors the tools they need to make the right investment decisions on technology development, regulatory pathways, cost-effectiveness and benefit to the Canadian healthcare system.” Together these approaches should help bring a better informed approach to establishing sustainable prices for new drugs.

By: Kathryn Deuchars, Director, Ontario Personalized Medicine Network

Can personalized cancer care be cost-effective?

A study of personalized cancer care in action found that this approach not only saved money but resulted in better outcomes. Such personalized cancer treatment is available here in Ontario.

A small study by Intermountain Healthcare, in Salt Lake City, compared the costs of using personalized medicine in cancer patients with late stage, metastatic disease. Patients whose therapy selection was based on next-generation tumour profiling testing rather than using standard chemotherapy options have lower costs per week and longer progression-free survival.

Personalized approaches to cancer treatment are being tested at many centers, including Ontario’s Princess Margaret Cancer Centre, which launched the “IMPACT” trial (for “Integrated Molecular Profiling in Advanced Cancer Trial”) in March, 2012. This trial is described as “the first Canadian comprehensive molecular profiling program that seeks to provide doctors with specific cancer gene information so that each patient’s treatment can be tailored to his/her specific form of the disease” and aims to test 1,000 patients.

Intermountain Healthcare has been offering a similar type of test, a 98-gene cancer panel test for genes commonly altered in solid tumours. The test involves sequencing over 1200 regions of these 98 genes. The results can be used to identify the appropriate targeted therapeutic specific to the genetic profile of a patient’s tumour. In a retrospective matched cohort study of 72 patients with metastatic cancer, patients at Intermountain Healthcare that received the gene panel test had an average progression-free survival of 22.9 weeks compared to 12 weeks for the group that received standard chemotherapy treatment. The respective costs per week were slightly lower in the gene panel group, at US$3,204 vs. US$3,501. The $6,000 price of the test was included in the cost analysis.

The key contributors to the costs in chemotherapy arm “were more and longer hospital stays and emergency room visits.” In addition to avoiding such hospital visits, “targeted therapies offer other benefits. Many of the targeted drugs are oral agents, which allow patients to take them at home or work, while continuing to be productive at work and go about their daily life. They don\’t have to take time off work to go into the hospital for chemotherapy treatment” according to the authors of the study. These ancillary benefits were not factored into the above cost analysis, suggesting that the overall cost benefit is even higher.

Full details of the Intermountain Healthcare study are yet to be released (the work was presented in abstract form in conjunction with the recent annual meeting of the American Society of Clinical Oncology). Yet they suggest that the promise of personalized medicine of reducing costs while improving care can be realized. A key influencer of this, however, will be the cost of targeted therapeutics. As discussed in the accompanying article “Rising prices for new targeted therapeutics threatens their own success” new approaches are needed to ensure that high costs don’t derail the potential of personalized medicine.

By: Kathryn Deuchars, Director, Ontario Personalized Medicine Network