Bio Business November/December 2015 by Dovetail Communications

Agri-based Industrial Bioproducts Driving innovation 6

Big Data

Small companies unlock its potential 10

Bioprinting

The birth of bioprinting leads to a Canadian lab 23

november/december 2015

Championing the Business of Biotechnology in Canada

Multi-disciplinary research will impact clinical practice soon

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inside

feature

big data

The life sciences and information technology industries are working together to manage all of the data we create and put it to good use.

3d bioprinting

Championing the Business of Biotechnology in Canada

Printing functional 3D human tissue is no longer science fiction, but there are still challenges to overcome.

The Birth of Bioprinting

Canadian lab paved the way for the advancements we see in 3D bioprinting today.

agri-BaseD inDustrial BioproDucts driving innovation 6

Big Data

Small companies unlock its potential 10

Bioprinting

The birth of bioprinting leads to a Canadian lab 23

noveMBer/deCeMBer 2015

DaviD Suzuki Magnificent mushrooms

Championing the Business of Biotechnology in Canada

Multi-disciplinary research will impact clinical practice soon

Healing Power The DefiniTive Source for Lab ProDucTS, newS anD DeveLoPmenTS

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November/December 2015

Harnessing the body’s own process

Arthur B. McDonald

Canada’s newest Nobel laureate helps solve a mystery

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standard Editor’s note 5 canadian news 6 worldwide news 8 moments in time 23

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Publisher & CEO Christopher J. Forbes cforbes@jesmar.com Executive Editor Theresa Rogers trogers@jesmar.com staff writerS Hermione Wilson hwilson@jesmar.com Doug Wintemute dwintemute@dvtail.com art director Katrina Teimourabadi kteimo@jesmar.com Secretary/ Treasurer Susan A. Browne marketing Stephanie Wilson manager swilson@jesmar.com vp of production Roberta Dick robertad@jesmar.com production Crystal Himes MANAGER chimes@jesmar.com account manager Mike Forbes mforbes@jesmar.com

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Big Data I

n research, experts often spend a lot of time and money trying to answer a question or solve a problem. What eventually happens to all of that information? And how can we best utilize it? As Doug Wintemute writes in our computing story on p. 10, the potential of Big Data is unknown. As technology advances, so too does the promise of what we can achieve with such a vast collection of information. The reality of high costs, restricted availability and limited usability means it’s not that simple, but the benefits can be big. Last November, Newfoundland’s Memorial University, in partnership with IBM, the federal government, and the government of Newfoundland and Labrador, announced the launch of the Translational and Personalized Medicine Initiative (TPMI), which aims to understand the influence of familial relationships on diseasecausing genetic mutations, as well as provide more efficient and cost-effective delivery of healthcare in Newfoundland and Labrador, a province known for having some of the highest rates of heritable diseases in the world. Today, with the help of IBM, Memorial is using analytics to create innovative treatments designed specifically for the individual physiology of high-risk patients. Rapid testing using high-performance computing and analytics capabilities allows physicians to prescribe more precise treatments that can begin earlier – improving efficacy, and providing speed turnaround time for critical testing and results by more than 83 per cent – from one year to less than 12 weeks. Physicians are no longer bound by a one-size-fits-all approach to diagnosing illness. By supporting them with greater insight to determine which tests align with individuals’ genetic signatures, the solution eliminates unnecessary and costly testing. The $50-million partnership has allowed TPMI to assemble research teams, and in the process, fund 12 graduate students at the masters, PhD and post-doc levels. TPMI built a large and fast computing system, now housed at Memorial in the Faculty of Medicine and used by researchers across campus. An on-site IBM architect is located within the Centre for Health Informatics and Analytics (CHIA) and is instrumental in the design and flow of current research projects. In Ontario, the Southern Ontario Smart Computing Innovation Platform (SOSCIP) was formed with various Ontario universities and again, IBM as the technology partner. SOSCIP is a research and development consortium that pairs small and medium-sized enterprises and academic researchers from southern Ontario with advanced computing tools. By providing advanced computing solutions for researchers and companies working with Big Data, SOSCIP has become a matchmaker of sorts, helping find the best and most profitable pairing for the stakeholders involved. SOSCIP can provide companies with academic expertise and research expertise to help their business, but also the computing platforms and tech support to figure out how to use the platforms to the best of their abilities to solve business problems. Theresa Rogers It feels like we’re barely scratching the surface, but executive Editor it’s a start.

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Championing the Business of Biotechnology in Canada

editor’s note

canadian news

Targeting Immuno-oncology Therapies

New Program will Grow Agri-based Industrial Bioproduct Development

A team at the IRCM led by Dr. André Veillette, identified the mechanism of action for a new target for novel immuneoncology treatments. The researchers study natural killer (NK) cells, which are crucial to the immune system and protect the body by destroying cancer cells, specifically a protein called DNAM-1 that plays a key role in the elimination of cancer cells. Their discovery is published in the print edition of the scientific journal The Journal of Experimental Medicine.

Rx&D Honours Mark Lievonen

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The Board of Directors of Canada’s Research-Based Pharmaceutical Companies (Rx&D) has conferred a Honourary Life Achievement designation to Mark Lievonen, President of Sanofi Pasteur Limited, for his service and leadership in the innovative pharmaceutical industry in Canada. This designation recognizes Lievonen’s leadership, outstanding achievements in the pharmaceutical industry and unwavering dedication to sustainable healthcare in Canada, as an outward reflection of Rx&D’s spirit of innovation. The award was given at a ceremony at the Making Canada Better 2015 Conference.

Biotechs on Canada’s Top 100 Employer Listing

Novo Nordisk Canada and Sanofi Canada have been included in the “Canada’s Top 100 Employers” listing for 2016 as announced in a special magazine copublished in the national edition of The Globe and Mail. Novo Nordisk has a corporate culture that helps employees excel in their area of expertise, a culture where they have the freedom to manage their careers. Sanofi Canada brings value, health and hope to Canadians through a range of innovative healthcare solutions.

Ontario Centres of Excellence (OCE) and the Agricultural Adaptation Council (AAC) are fostering innovation in the province’s growing agri-based industrial bioproducts sector. Through the $3 million Agri-Based Industrial Bioproducts (ABIB) R&D Challenge, OCE and AAC will partner with the National Science and Agri-based industrial bioproducts are any Engineering Research Council (NSERC), academia and the commercial product derived from agricultural bioproducts industry to fund sources such as plant fibres, plant and approximately 10 projects. The vegetable oils, plant-based protein and sugar/ program encourages for-profit starch crops. businesses with innovative industrial bioproduct ideas to collaborate with academic research institutions to foster innovation and drive commercialization. “We are excited to be working with all of our partners on this challenge,” says Dr. Tom Corr, President and CEO of OCE. “OCE is already working with several companies who have seen success with bioproducts and biopharmaceuticals and this challenge will help even more companies succeed.” Agri-based industrial bioproducts are any commercial product derived from agricultural sources such as plant fibres, plant and vegetable oils, plant-based protein and sugar/starch crops. Anticipated projects will include the development of biocomposite materials to replace petrochemical-derived plastics, renewable plant-based oils to create bio-based polymers, and plant-based proteins as an alternative to petroleum-based plastics. “The ABIB R&D Challenge will further support Ontario’s developing agri-based products industry value chains from farm field to industrial bioproducts,” says Judy Dirksen, AAC Chair. “The use and interest in agri-based products is growing, and it is imperative that the development of these innovative products and technologies continue to be supported.” Ultimately, it is expected the resulting projects will provide significant economic benefits to Ontario in the form of jobs and prosperity through the development of the next generation of agri-based industrial bioproducts. The province of Ontario has identified the development of bioproducts as having potential for significant economic, environmental and health benefits. Bioproducts typically come in three varieties: bioenergy (liquid fuels such as ethanol and biodiesel, and combustible biomass), biomaterials (plastic, foam, rubber) and biochemicals (lubricants, pharmaceuticals and cosmetics).

canadian news

PM Announces Funds for Stem Cell Research

Removing Micropollutants from Wastewater

A U.S. patent was recently awarded jointly to Centre de recherche industrielle du Québec (CRIQ) and Institut national de recherche scientifique (INRS) for a system and a process that remove emerging micropollutants from industrial wastewater. In preliminary studies, the patented membrane bioreactor system eliminated 99% of BPA and other compounds in heavily contaminated wastewater. The system is designed for installation at factory outlets to treat wastewater at the source and can also be incorporated into wastewater treatment plants.

National Microbiology Lab Awarded

Quick Facts • The project, which has a total cost The government says this will be the first of $43.8 million, has the potential cell therapy development facility in the to make Ontario a global hub for world to use a collaborative approach – the cell therapy industry. between research institutions and industry • Federal funding will be used to – to solve cell therapy manufacturing support improvements to the challenges. new facility and the purchase of specialized equipment. Funding will support the development of at least five new patent applications, the commercialization of 30 new products or processes, and the creation or maintenance of 389 high-quality jobs by project completion in December 2018.

Canadian R&D-to-Sales Ratio for Brand-Name Drug Companies Sets Historic Low

Brand-name drug companies’ R&D spending as a percentage of sales in Canada has dropped to new historic lows according to the most recent annual report from the federal government’s Patented Medicine Price Review Board (PMPRB). The latest annual reports shows that in 2014 member companies of Canada’s ResearchBased Pharmaceutical Companies (Rx&D) spent only 5% of their Canadian revenues on R&D in Canada. This is the lowest level since the PMPRB began tracking in 1988. The figure is short of 10% of domestic sales brand-name drug companies promised to spend when their periods of market exclusivity were increased in 1987. This marks the 12th consecutive year they have failed to meet the threshold.

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Prime Minister Justin Trudeau announced the Centre for Commercialization of Regenerative Medicine (CCRM) will receive $20 million – under the Advanced Manufacturing Fund (AMF) – to establish and operate the Centre for Advanced Therapeutic Cell Technologies. The government says this will be the first cell therapy development facility in the world to use a collaborative approach – between research institutions and industry – to solve cell therapy manufacturing challenges. Regenerative medicine has emerged as a promising approach to disease prevention and treatment, harnessing the power of stem cells to repair, regenerate, or replace damaged cells, tissues, and organs affected by disease. The CCRM, in collaboration with GE Healthcare and other industry partners, will establish a centre that will accelerate the development and adoption of cell manufacturing technologies. “We are pleased the federal government is investing in the new advanced therapeutic cell technologies centre at MaRS,” says Reza Moridi, Ontario Minister of Research and Innovation. “Ontario provided seed funding for the Centre for the Commercialization of Regenerative Medicine to support research and commercialization in regenerative medicine, which we know will continue to be a key driver in the province’s life sciences sector. [The] announcement will further grow Ontario’s reputation as a global leader in this field, which offers incredible potential for continued growth in the future.”

The Public Health Agency of Canada acknowledged the National Microbiology Lab’s Dr. Kobinger and his Special Pathogens team in Winnipeg as recipients of the Manitoba Order of the Buffalo Hunt for 2016. The Order of the Buffalo Hunt is one of the highest honours the province of Manitoba can bestow on individuals and is awarded for excellence in leadership, service, sports and community commitment. Kobinger is being recognized on behalf of his team, for their work and commitment to combat the Ebola virus.

worldwide news

Biosensor Chips in Drug Development

Pierre Fabre Médicament (PFM) and the Swiss Federal Institute of Technology in Lausanne (EPFL) have agreed to a scientific collaboration on the use of biosensor chips developed by the EPFL in clinical studies conducted by PFM. The biosensor chips developed by the EFPL’s scientists are able to assess the homeostasis of individuals (pH, temperature, blood glucose level, etc.) and measure more accurately than traditional methods the concentration in the body of an active agent coming from an administered drug.

2015 “Site Selection for Life Sciences Companies in Europe” Report INTERNATIONAL CORPORATE TAX

Site Selection for Life Sciences Companies in Europe 2015

Epigenetics Research into Crickets Limb Regeneration

A team out of Okayama University has been researching the mechanisms behind cricket limb regeneration. Their latest research identifies key genes and proteins involved in these epigenetic changes that allow regeneration to occur. Following the loss of a leg, the cricket develops assemblies of cells that can differentiate into various different types to restore the lost part of the leg. It is understood that epigenetic changes are responsible for the processes in regeneration. Epigenetic changes can occur through chemical modifications of amino acids, which can repress or promote gene expression. bio business n ov e m b e r / d e c e m b e r 2 01 5

RNA-based Drugs Give More Control Over Gene Editing

In the past, researchers have found a way to use a bacterial system known as CRISPR/ Cas9 to inactivate or correct specific genes in any organism. CRISPR/Cas9 gene editing activity runs continuously, though, leading to risk of additional editing at unwanted sites. Now, researchers at University of California, San Diego School of Medicine, Ludwig Cancer Research and Isis Pharmaceuticals, demonstrate a commercially feasible way to use RNA to turn the CRISPR-Cas9 system on and off as desired – permanently editing a gene, but only temporarily activating CRISPR-Cas9.

In association with

4 | Site Selection for Life Sciences Companies

Site Selection for Life Sciences Companies | 5

Scope of the report

This report provides senior executives of Life Sciences (LS) businesses (Pharmaceutical, Biotechnology and Medical Devices) and investors with information on the various LS clusters in Europe, including their capacity to host crucial value drivers. It summarizes the European LS landscape and its regional strengths such as in Distribution, Research & Development (R&D), Manufacturing and regional headquarters / shared services activities. It compares in detail Belgium, France, Germany, Ireland, the Netherlands, Switzerland and the UK. These countries have been selected as they are the leading recipients of LS investments in Europe. There remain more countries in Europe with dynamic LS industries and attractive offerings. The report takes account of this by also providing data on their respective LS clusters. In order to develop new capabilities for coping with the changing LS environment, LS companies need to strengthen collaboration with peers, universities and suppliers. Marketing internal assets and expertise to outside parties is a growing strategy among LS companies. The first section of the report therefore focuses on clusters of LS companies, providing insights into such as the number, size and specialization of the LS industry in the given countries. This analysis also includes detailed overviews of product pipelines as well as sharing insights into existing regional and global headquarters (HQs). This part of the report is based on data from the global Biotechgate database (www.biotechgate.com). The second section of the report deals with the general business environment in the covered countries with regard to the speed and sustainability of business transformation. In particular, it keeps in mind the prospect

Key findings

of enhancing agility to react quickly to changes arising from variations in demand, achieving shorter supply cycles, and rapidly recalibrating plans in the face of volatility of markets, prices and supply. Countries are therefore compared to show how easy it is to transform business in light of the labor force, flexibility of labor law, legal requirements and other key considerations. How a country sets its tax planning and incentive models can greatly impact the value of an investment in that country. This is especially true for IP-driven industries such as LS. The third section of the report therefore provides an overview of the tax environment and incentives of each country. Critical in this regard are current changes in international tax planning as required by the OECD’s “BEPS” initiative. As most countries that appeal to LS tend to offer attractive tax planning models, it is important to analyze how governments are responding to these new requirements vis-à-vis existing and new investments from abroad. The report should assist executives and their advisors in initially shortlisting potential target countries for building or shifting key value drivers in Europe. Further detailed analysis will be necessary to reach a final decision. It is important to note that many aspects discussed can also be used for other knowledge-driven industries such as ICT, MEMS (Microelectronic and Mechanical Systems), Nutrition and Food, Aerospace and Chemicals, among others. The report ends with an introduction to business transformation and value chain management as an efficient tool to identify key value drivers in the LS industry and to help determine the vital site selection factors that influence productivity.

A business environment that allows companies to be agile when adjusting business models amid rapidly evolving technologies and markets is essential when seeking fast and sustainable growth. The factors that influence this flexibility – as well as enabling greater productivity and sustainability – vary greatly between the seven countries (Belgium, France, Germany, Ireland, Netherlands, Switzerland, UK) covered in detail in this report. To reach the right decision in site selection involves a careful balancing of each prospective location’s pros and cons and how these might impact a given company’s circumstances and objectives. We set out below some of the key factors to consider: • Rankings from leading organizations in assessing competiveness and economic freedom place Switzerland as the most competitive country in Europe. Globally, the UK, Ireland and Germany are also ranked in the top 10 in one or more league tables from the World Economics Global Competiveness report, the Heritage Foundation’s Index of Economic Freedom and the IMD’s World Competitiveness Yearbook. • Strong macroeconomic data in Germany and Switzerland are complemented by exceptionally strong labor productivity. Germany has the highest labor productivity in Europe, followed by Switzerland. • Ireland’s macroeconomic situation has improved, enabling the country to considerably lower its unemployment rate to below 10% and achieve a positive current account balance. This helps improve future economic stability. • France, Germany and Belgium offer competitive salaries. The Netherlands, the UK and Ireland are in the mid-range, while Switzerland has the highest average salaries. • Annual wage growth over the next five years is expected to be highest in the UK, Germany and Ireland, medium in the Netherlands, France and Belgium and lowest in Switzerland. • Switzerland, the UK and Ireland have the most businessfriendly labor markets and labor regulations, particularly with regard to hiring and firing practices. • The UK has by far the most universities (9) in the top 100 globally, followed by France, Germany, Switzerland and the Netherlands (4 each)

• All countries covered in the report have at least one international airport with good to excellent direct flight connections to other major international LS clusters. London tops the list as having the airport with the most connections. In terms of air transportation infrastructure (quality/reliability of services), the Netherlands leads the group. Excellent high-speed train connections in continental Europe and the UK are also widely available. • For standard of living, Germany and Switzerland have the most cities in the top 40. In terms of environmental protection, Germany, the Netherlands, the UK and Switzerland are particularly well positioned. • London, Zurich and Geneva are among the most expensive cities in the world, whereas the cost of living is much lower in Belgium, the Netherlands, Germany and France. However, inhabitants of Switzerland, France and Belgium have a much higher purchasing power than those in the other countries. • Attracting, retaining and developing talent is essential for a successful business location. Switzerland, the UK, Netherlands and Germany are especially strong in putting in place educational systems that meet the needs of industry. Switzerland and the UK are the biggest magnet for foreign workers. Collaborations with suppliers, peers and/or academic institutions is a key factor LS companies to expand their capabilities along the value chain from R&D to manufacturing to distribution. There are significant differences between the various LS clusters (size, workforce, specialization, etc.) in countries covered in this report. The number of products in development may also be an important consideration for site selection decisions, as well as the ease of raising capital and tax benefits and incentives. Belgium • Many LS companies have regional HQs covering the Benelux countries • Fewest number of LS companies performing R&D, but the highest involved in manufacturing • High density of Pharma companies • Rather weak early stage product pipeline

BioTechgate has released the 2015 edition of the Site Selection for Life Sciences Companies in Europe report. Published by KPMG in association with Venture Valuation, the report analyzes the structure of the European life sciences landscape and looks at the strength of the biotech, medtech and pharma industry in 14 countries. The 2015 edition of the report was The 2015 edition of the report was created utilizing the data within the created utilizing the data within the global Biotechgate database which has global Biotechgate database which has more than 37,000 companies more than 37,000 companies listed, listed, including a comparison of the including a comparison of the following following countries: Austria, Belgium, countries: Austria, Belgium, Denmark, Denmark, France, Finland, Germany, France, Finland, Germany, Ireland, Italy, Ireland, Italy, Netherlands, Norway, Netherlands, Norway, Spain, Sweden, Spain, Sweden, Switzerland and the United Kingdom. Switzerland and the United Kingdom. The report provides senior executives of Life Sciences (LS) businesses (Pharmaceutical, Biotechnology and Medical Devices) and investors with information on the various LS clusters in Europe, including their capacity to host crucial value drivers. It summarizes the European LS landscape and its regional strengths such as in distribution, R&D, manufacturing and regional headquarters/shared services activities. It compares in detail Belgium, France, Germany, Ireland, the Netherlands, Switzerland and the UK, which were selected as they are the leading recipients of LS investments in Europe. The report should assist executives and their advisors in initially shortlisting potential target countries for building or shifting key value drivers in Europe. Many aspects discussed can also be used for other knowledge-driven industries such as ICT, MEMS (microelectronic and mechanical systems), nutrition and food, aerospace and chemicals, among others.

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“Celebrating 20 Years”

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Small Companies

Big Data with

D i sc o v e r i n g t h e p r o m i s e i n b i g d ata a n a ly s i s

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By Doug Wintemute

he rise of supercomputers has given humans the indirect ability to process vast and varied amounts of information remotely and in real-time. With this borrowed skill, researchers and companies are now exploring new ways of understanding our world and even ourselves a little better. In 1997, computer scientist Michael Lesk wrote that by the year 2000, humans would be able to save everything but most of that information would never even be seen by humans. Today, nearly two decades after Leskâ&#x20AC;&#x2122;s prediction, data management has truly become a matter of great concern. While we may not actually save everything, the ability to record and store incredible amounts of data has created the dizzying problem of deciding not only what data to save but also what data to see.

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Managing big data

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The true potential of Big Data is unfolding more and more each day. As the technology advances so too does the promise of what we can achieve with such a vast collection of information. However, even though the technology exists, the reality of high costs, restricted availability and limited usability has led to a small percentage of people actually utilizing it, a problem that some have felt compelled to address. In 2011, Elissa Strome, now the Executive Director of the Southern Ontario Smart Computing Innovation Platform (SOSCIP), and some colleagues from various Ontario universities, recognized that Big Data had the potential to drive economic growth for business, but there were roadblocks. “Big Data was starting to become a big issue,” she says. “We saw that the universities were starting to get a lot of expertise, and Big Data and advanced computing were emerging technologies that could really drive business and drive the economy of the future. But there wasn’t a lot of transfer of that knowledge of the technologies to companies, and the companies didn’t have good or affordable access to those kinds of technologies.” Knowing the opportunity and the problem, Strome and her colleagues set out to find an industrial partner that had both the technology and the knowhow to provide a solution, and IBM answered the call. In offering a strong R&D background as well as access to the most powerful advanced computing platforms in Canada, such as the Blue Gene/Q supercomputer, IBM showed itself to be the ideal partner for this type of collaboration.

The Artemis Project is a platform for real-time analysis of data pulled from hospital monitors to detect various conditions such as neonatal apnea. Identifying and tracking patterns in data allow the platform to alert physicians and improve outcomes.

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Hope in hospital monitors

Big Data is seen as pure opportunity for those who work with consumer patterns. Optimized customer offerings, targeted advertising and market predictions are all areas that Big Data can help illuminate, but when Carolyn McGregor, PhD, brought her expertise in data mining and pattern recognition to a neonatal intensive care unit in 1999, she saw a different kind of opportunity. Technology, McGregor, paired with IBM, started the Artemis Project, a marketable platform for the real-time analysis of data streams pulled from hospital monitors to plot, classify and detect significant health outcomes, such as neonatal apnea, particularly in premature children. McGregor and her team have demonstrated that with this platform they can dramatically improve detection rates of several conditions. For instance, by identifying and tracking the patterns of change in a baby succumbing to infection, the Artemis project can spot problems in real-time and alert the physicians, an ability they wish to pass along to the doctors so that they can utilize these same metrics and incorporate them into the care process. Furthermore, this can all be done remotely and indicators can be sent and received from virtually anywhere, limiting both the amount of space used and the amount of people dedicated. “With SOSCIP, we wanted to show that we can run these types of platforms in a cloud computing setting rather than having the infrastructure in a hospital,” says McGregor. “This type of thing is very important when we want to provide support for critical care patients in rural and remote areas. We want to make it so doctors can work with multiple streams, multiple patients, and multiple conditions and do it in multiple locations.” For McGregor and the Artemis Project, it was more than simply

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Together, they formed SOSCIP, a research and development consortium that pairs small and medium-sized enterprises (SMEs) and academic researchers from southern Ontario with advanced computing tools to bridge the innovation gap. By providing advanced computing solutions for researchers and companies working with Big Data, SOSCIP has become a matchmaker of sorts, helping find the best and most profitable pairing for the stakeholders involved. SOSCIP can provide companies with academic expertise and research expertise to help their business, but also the computing platforms and the tech support to figure out how to use the platforms to the best of their abilities to solve business problems. “If an academic has got a great idea but they don't know exactly what company to partner with to pilot it, or test a prototype, or contribute to the research, then we help them,” says Strome. “But we also have a collection of projects that come directly from the companies. We have companies that have identified that they are Big Data-focused, or they need advanced analytics, or they have a need for high performance computing.”

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gaining access to advanced computing. In order to continue and even further the research, the project needed to find solutions that could be brought to market, a complex stage that SOSCIP eases by pairing researchers with industry partners who complement each other, allowing each party to focus on their own strengths but work toward a common goal. “In Canada, we have great opportunity and great success in academic research,” says Strome. “But there is a gap between that and innovation and driving those ideas, inventions and technologies out of the universities and into the companies where they are commercialized and reaching market. We’re starting to bridge that gap.”

Finding relevance in genetic variants

Carolyn McGregor

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“I wanted to create a platform that had the ability to ingest all of those raw numbers and actually associate them better with behaviours that were looking for certain related conditions.” – Carolyn McGregor, Canada Research Chair in Health Informatics at the University of Ontario Institute of Technology

For the team at Cytognomix, a London, ON-based biotechnology company and SOSCIP collaborator, it was the demand for timely interpretation of Big Data in the field of clinical genomics that led to the development and commercialization of the Mutation Forecaster, software that aids in the interpretation, analysis and management of genetic variant data. “When you hear about next generation sequencing, they talk about the $1,000 genome and the $10,000 interpretation,” says Peter Rogan, Founder of Cytognomix and Professor in the Department of Biochemistry at Western University. “Part of the reason why the interpretation is so expensive is because it takes so long. Right now, when you sequence a person’s genome or their exome, a typical exome will have 30,000 variants that are novel, that pass filters. These are 30,000 variants that tend to be in different genes. So you have an enormous amount of variants to look up to decide what is relevant to the patient’s phenotype.” When dealing with mutated genes, clinicians need to not only search if that mutation has been found before, but they also need to determine how and if that gene causes disease and what literature supports the involvement of that gene in causing certain symptoms and disease. The Mutation Forecaster scours the

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Big dreams

The different companies involved with SOSCIP are all connected by their vision of and for Big Data, the idea that within the all of this information lay clues to understanding ourselves better, solutions hidden in plain sight. The search is on for new ways to use our incredible technological advances to our advantage. But, as Lesk predicted, our ability to save everything has us led to the interesting paradox of the more we record, the more truths are likely to be revealed, but the more we record, the more we camouflage those truths. While small steps are continually made toward unlocking the true potential of Big Data, we are likely only barely scratching the surface. Until Big Data and its timely analysis is accessible for all companies, organizations like SOSCIP will have a place. Until that time, both the problems of and the hopes for Big Data will persist. Humans will continue to create data, technology will continue to improve on its ability to save and store it, and great minds will continue to dream up new ways of using that data to make human lives easier and better. Until that time arrives, SMEs will rely on SOSCIP and others like it to make the waters a little easier to navigate as they seek to uncover what hidden mysteries might be found in Big Data. BB

SOSCIP ADVANCED COMPUTING PLATFORMS IBM BLUE GENE/Q: Canada’s fastest supercomputer is suited for largescale, distributed applications that require massively parallel processing power. CLOUD ANALYTICS: Canada’s first research-dedicated cloud environment hosts a broad array of IBM software tools for application development and data analytics. The Cloud Analytics platform is ideal for complex data analysis, streaming and managing large data volumes, and data mining applications. AGILE COMPUTING: Canada’s first multi-platform agile research environment uses Field-Programmable Gate Array (FPGA) technology to accelerate hardware performance. FPGA cards can accomplish numerically complex tasks more efficiently and at lower cost than a traditional CPU could do alone.

LARGE MEMORY SYSTEM: The LMS platform is a single 64-core virtual system with 4.5 TB of RAM. Outfitted with the latest IBM analytics software, the LMS is ideal for data-intensive projects with huge active memory requirements.

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available resources on MEDLINE and PubMed, narrowing down the results to only the most relevant, effectively eliminating the burden of manually sorting through the more than 30 million abstracts available. “It doesn’t replace interpretation, but it certainly facilitates it,” says Rogan. “Typically, what happens in next generation sequencing is you throw away all of the variants that are common in the population because the basic idea is that, if it’s common, it’s not likely to cause disease. Yet even after you’re done with that, you still have an overwhelming number of genes and variants. Now imagine you’re running a business or a clinical lab and you have 50 or 100 patients to do this for. It’s simply impossible.”

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HOT feature story

PRESS OFF THE

feature storY

By hermione wilson

printing seems at first glance to be fantastically futuristic, akin Instead of T hree-dimensional to Star Trek’s replicator technology. Just press a button and out pops a piece of art, a household object, maybe even a whole building. Of course, the process is much more than that, but the possibilities of this technology are seemingly endless. ink on paper, complicated There is no domain – be it artistic, mechanical, or medical – where 3D printing is not and has not already made a major impact. scientists are applicable When it comes to 3D bioprinting, an even greater layer of complexity is added. To a plastic construct is one thing, but when the ink being used is comprised of printing cells print human tissue cells, the building blocks of life itself, that is something else altogether. In the quest to repair and regenerate our bodies, life science research has turned recent innovations like 3D bioprinting for answers. Also known as additive and tissues tomanufacturing, 3D printing technology has made it possible to rehabilitate damaged body parts such as joints, skin and other important components. destined to the bio in 3D bioprinting repair the ItPutting is important to make the distinction between 3D printing and 3D bioprinting. 3D printing, which has led, in the context of medical research and clinical practice, to innovations as life-size medical models and custom-fitted prosthetics, involves human body such synthetic materials. 3D bioprinting, on the other hand, involves living cells and tissues.

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“[Bioprinting] refers to spatially organizing biomaterials in physiologically meaningful ways that mimic intact tissues,” says Dr. Axel Guenther. His research team, at the University of Toronto’s Institute of Biomaterials and Biomedical Engineering, has developed a novel 3D bioprinting platform called the PrintAlive Bioprinter. The device has been specifically designed to produce readily handleable skin grafts used for treating burn injuries. The Guenther Research Group’s specialty is microfluidic systems, which is why their bioprinter differs somewhat from other models. Unlike other 3D bioprinters that are like an inkjet printer, the PrintAlive uses a micro-fabricated printer cartridge that extrudes a liquid biopolymer in an organized pattern that mimics the structure of organic tissue. The team is currently focused on printing skin and is collaborating with Dr. Marc Jeschke, who heads the Sunnybrook Hospital burn unit. Not only is the PrintAlive device considerably smaller than other 3D printers (less than a foot wide and weighing about one pound), it works much faster. “The rate limiting step is not the printing anymore,” Guenther says. “We can form a squaremetre’s worth of [printed tissue] within an hour or two.” The process slows down at the stage where they populate the printed tissue with biological cells. “We’re quite convinced that [the PrintAlive device] could be applicable to quite a variety of different researchers, as well ultimately clinicians because it’s so simple,” Guenther says.

Vascularisation

Skin today, custom-made organs tomorrow? There are some road blocks to overcome before major internal organs like the heart and kidneys can be grown for transplantation, says Dr. Ibrahim Ozbolat, Associate Professor at Pennsylvania State University’s Engineering Science and Mechanics department.

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feature story

Top: Rita Kandel holds a model of a human joint. Photo credit: Mount Sinai Hospital. Bottom: A printed tissue scaffold. Photo credit: University of Iowa.

feature storY

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Technically organs can be printed, Ozbolat says, whose expertise is in bioprinting, biofabrication and tissue engineering. 3D bioprinting technology has already accomplished the engineering of organs that don’t have a great need for blood supply, like cartilage, or that are thin and/or cylindrical and hollow in shape (like skin and blood vessels). But when it comes to “large-scale highly active metabolic organs” like the heart, kidney and pancreas, their size, the thickness of the tissues they are compromised of and their overall complexity may prove prohibitive, Ozbolat says. “Organs are too complicated,” he says. It’s not that Ozbolat is a pessimist, but as the technology now stands, he doesn’t think we have the ability to surmount big challenges like maturation, immune rejection, structural integrity, fusion of tissue, and vascularisation with organs of this size. “There are things we can print and there are things we cannot print,” Ozbolat says. “In my opinion, we won’t be able to print the entire organ.” That being said, Ozbolat is finding ways to work around those problems. One focus of his research is solving the vascularisation problem and figuring out how to incorporate blood, capillaries and larger vessels into printed tissues. Taking inspiration from miniaturized organs that are engineered for drug testing purposes, Ozbolat is working on printing a small vascularised pancreas model – about 2x2 cm in size. The tiny organ will be a simplified version of a pancreas, with a large blood vessel running through its middle that splits into smaller vessels, and eventually capillaries. “The goal here is figuring out how to create capillaries in the tissue and how to connect those capillaries into bioprinted blood vessels,” Ozbolat says. “Those are some major impediments right now.” Another project Ozbolat has underway is the development of organs that do not exist in nature. For example, he is exploring the possibility of an electrogenic organ, something akin to the electronic organ of an electric eel (which can generate up to 700 volts) that could act as a biological battery in the human body, perhaps powering devices like pacemakers or prosthetic devices. Ozbolat is also exploring the idea that we may not need to replace whole organs, just augment their function. “Do we really need to make the same as what you have or [can] you make something that functions enough to restore the function of the failed organ?” he asks. “If I can make an organ that can secrete insulin that is glucose-sensitive, which means it produces more insulin when the glucose level is high, then will that be enough for… the patient that suffers from Type 1 Diabetes?”

Replacement parts and team efforts

“When I think of bioprinting, I think of materials and cells together to develop a biological tissue,” says Dr. Rita Kandel, Chief of Pathology and Laboratory Medicine at Mount Sinai Hospital. “We’re using 3D printing. We are printing a material and using that to grow tissues on. The end result is the same, we get a biological structure, but the way of getting there is slightly different.” Kandel’s research team at Mount Sinai’s Lunenfeld-Tanenbaum Research Institute has been focusing on printing custom-fitted joint replacements made from a calcium and phosphates-based biomaterial that acts as a substitute for bone. Using the biomaterial as a base, the team uses a patient’s own cells to grow tissue that will mimic the surface of a natural joint. The idea is that the replacement joint will support healing of the patient’s damaged bone and eventually degrade once the normal regenerative process has replaced it with actual bone. The challenge is “trying to get a material that resembles bone,” Kandel says. The calcium-phosphate amalgam she is currently working with is just the beginning of that search, and trumps the plastic and metal surgeons were using previously.

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feature story

Top: Vascularized tissue constructed created using bioprinting. Photo credit: University of Iowa. Bottom: A tissue strand constructed using bioink. Photo credit: University of Iowa.

in the spotlight

“[The joint replacements] would be made in two or three sizes and the surgeon would be forced to use it as best they could,” Kandel says. “This way we can create the right shape and size for that particular individual.” The joint project is the collaborative effort of the Bioengineering of Skeletal Tissues Team, an interdisciplinary group of investigators from all over Ontario that Kandel heads. The team is also looking into printing replacements for intervertebral discs, the part of the body that is to blame for most back pain. That collaborative spirit has characterized the application of 3D printing technology to biomedical research. The work requires knowledge in such diverse specialties as engineering, cell biology and clinical practice, meaning one discipline cannot work independent of the other. “A lot of this innovation happens at the interface between people that specialize in sophisticated microsystems, designing them, characterizing them, biomaterials, worrying about properties materials should have if one wants to use them for engineered tissues, different types of cells, getting them from human sources, having an understanding of their characterization, their function,” Guenther says. “It’s a very multi-faceted field.”

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By putting their heads together, researchers are sure that this technology will have a major impact on clinical practice in the near future. “I’m pretty sure that whatever you can think about, 3D printing will likely contribute in some way. I wouldn’t be surprised,” Kandel says. BB

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moments in time

The Birth of

Bioprinting

Artificial blood vessel (From, “A completely biological tissueengineered human blood vessel”, 1998)

his summer California biotech Organovo unveiled its bioprinted human liver tissue model, a tiny version of the organ for use in pre-clinical drug-testing trials. The company will launch its human kidney tissue model sometime in 2016. The next logical step seems to be bioprinting full-size human organs, constructed with a patient’s own cells, for rejectionproof transplantation. There are many moments that led to this innovative period of bioengineering history. Moments such as the invention of stereolithography in 1984, a printing process that allowed tangible 3D objects to be created from digital data, which laid the groundwork for the 3D printing technology we know today. Equally significant to bioprinting was when researchers at the Universities of Minnesota and Michigan Technological University demonstrated that lasers could direct the deposition of cells in two dimensions in 1999. Another such breakthrough took place in Canada in 1998 which contributed to our ability to construct 3D tissue. A group of researchers from Quebec’s Laboratoire d’Angiogénèse Expérimentale (LOEX) developed a novel way to tissue-engineer blood vessels. Without using any synthetic or exogenous biomaterials, they created a cellular sheet, made from cultured human vascular smooth muscle cells, and wrapped it around a tubular support. Another sheet, this one made of human fibroblasts, was added in a second layer. Once the tissue went through a period of maturation, the tubular support was removed and the inside of the structure was seeded with endothelial cells. Thus, the first completely biological tissueengineered blood vessel to display a burst strength comparable to that of human vessels was born in a Canadian lab, paving the way for the incredible advancements in 3D bioprinting we see today. BB

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