Genetic Engineering & Biotechnology News

DEC 2018

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D community with critical information on the tools, technologies, and trends that drive the biotech industry.

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GENengnews.com | Genetic Engineering & Biotechnology News | DECEMBER 2018 | 9 clinicians aren't trained for it like computa- tional biologists." The workshop aims to help clinicians un- derstand how systems biology can be used to analyze patient data. Attendees were given simulated immune-cell data and encour- aged to perform some of the analyses that Dr. Pandit carries out in his lab. "We want to expose them to a systems perspective, such as how genes interact with each other, so they understand the concept of intercon- nected networks," he said. "From there, they can discover the differences between healthy controls and simulated patients." Dr. Pandit works on developing compu- tational tools for studying heterogeneity— what makes immune cells differ between patients with, and without, autoimmune dis- ease. "These areas are in their infancy," he admitted. "Most of things we're doing are quite novel so, to analyze these types of data, we need to design our own methods." He designs novel tools for a variety of projects, including deconvolution and bench- marking approaches to studying immune cells. "Most studies do bulk sequencing of tissue, including skin cells, so if you decon- volute data into different cells, you can see which cell type is most important to focus upon," he explained. He's also applying computational ap- proaches to stem cells, to understand how immune cells form and how the environ- ment affects the types of cells produced. "Our goal is to understand autoimmunity," he concluded. "One of the main things is the potential [for stem cells] to specialize into different immune cells has been mainly discovered in mouse models or in human models in homeostasis, but in an autoim- mune disease there is inflammation inside the patient, and that affects the potential of different cells." Understanding the Environment Another aspect to systems medicine is studying the patient as a whole, including the effect of their environment, or exposome. "There is not much known about how en- vironmental factors affect wellbeing, and in systems medicine people's focus is mostly on developing personalized medicine and the molecular pathways that contribute to dis- ease," said Tjitske Bezema, Ph.D., chair of Immunowell and founder of Hidden Health Solutions. She is leading a grassroots initiative to understand how lifestyle and other envi- ronment factors affect the health of patients with two autoimmune intestinal diseases— Crohn's disease and ulcerative colitis. Working in coordination with research- ers from the Amsterdam Medical Centre, Utrecht University, and VU University Medi- cal Centre in Amsterdam, Dr. Bezema is pi- loting a study of what makes patients enter remission using a technique called Participa- tory Narrative Inquiry (PNI). "It's a normal well-used technique in social science, but is not used in this context, so we got together a team of researchers interested in trying it," she explained. Recruiting from patient groups on Face- book and by leaving flyers with clinicians, Dr. Bezema had patients write down the story of a time when they felt better. This was accompanied by semi-quantitative and quantitative questions, such as whether their medicine had changed, how much their symptoms improved (on a scale of 1 to 10), and which symptoms got better. "By collecting experiences from patients in a structured way, and analyzing them, you can see if there are patterns emerging from what people have in common," she noted. So far, Dr. Bezema and collaborators have collected 65 stories, and from her pre- liminary analysis she thinks stress and self- esteem might be important topics, as well as exercise and diet. She's planning to hold a sense-making session in January 2019, with doctors, researchers, and patients, to make a more thorough analysis of the data. Dr. Bezema also hopes to engage research- ers in her project with the aim, in the future, of investigating other co-morbid autoim- mune disease and to spark interest in further researchers. "If stress is an important fac- tor," she suggested, "we can find out what sort of stress may call for what sort of stress management techniques. Then, perhaps, we can see if we can develop interventions that work alongside medicine." Drug Discovery

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