When Dr. Yamile López-Hernández learned in early 2020 that the National Council of Science and Technology of Mexico (CONACYT) had issued a call for proposals for COVID-19-related research, one of the first people she reached out to was TMIC co-director Dr. David Wishart.
While a guest at TMIC’s Research Hotel during the summer of 2019, Dr. López-Hernández, a researcher at the Autonomous University of Zacatecas, had spent time in Dr. Wishart’s lab. When she spoke with him in early 2020, they discussed ways to use metabolomics to identify how COVID-19 changes a person’s metabolic profile and how that information could be used to better predict the course of a person’s illness.
The resulting paper, “Targeted Metabolomics Identifies High Performing Diagnostic and Prognostic Biomarkers for Covid-19” was published July 19, 2021, in Scientific Reports. Among its important findings were that plasma metabolites could be used to accurately (~95%) distinguish individuals who were COVID-19 negative but had COVID-19-like symptoms from those who were COVID-19 positive and had COVID-19-like symptoms. Furthermore, plasma metabolites could be used to accurately (~98%) predict the severity of the disease and outcomes (no hospitalization, hospitalization, intubation) in COVID-19 infected patients.
When Dr. López-Hernández applied for the grant in April 2020, only one paper had been published about the metabolic profiles of COVID-19. It focused on Chinese patients and contained little evidence about metabolic changes provoked by the virus.
In early 2020, owing to a lack of ventilators and ICU beds in Mexico, one of the questions Dr. López-Hernández wanted to answer was how to predict which patients would be hospitalized and, more important, which would require intubations and which were most likely to die.
Working with her own university as well as the Mexican Institute of Social Security and the Christus Muguerza Hospital in Chihuahua, Dr. López-Hernández assembled a team of physicians, nurses, laboratory analysts, PhD students and researchers. They collected blood samples from more than 1000 patients between March and November 2020, of which a sample of 161, from patients between the ages of 35 and 70, was analyzed.
“It wouldn’t have been possible without TMIC participation,” Dr. López-Hernández said via email shortly after the paper was published, explaining what a challenge she and her team in Mexico faced: in addition to collecting biological samples at a time of heightened biosecurity, there was the difficulty of seeing patients dying—40 percent died before the study ended. There was also a risk to those who were conducting the study, some of whom became infected with COVID-19.
Dr. López-Hernández praised Dr. Rupasri Mandal for her help coordinating the shipment of samples, which were analyzed within a month. The quick turnover allowed the scientists in Mexico and Edmonton to get to work on data analysis, interpretation, manuscript writing, and discussion.
The paper was submitted at the end of February. Dr. López-Hernández and her team in Mexico continued to analyze their data, looking at cytokine/chemokine measurements that could be used to identify an immuno-metabolic signature for COVID-19. Those results have been submitted to PLOS-ONE and are under review.
“The collaboration continues, and this alliance strengthens the scientific capabilities in the region,” Dr. López-Hernández wrote in that same email. “The results are quite satisfactory. We think that at least, with this, we have contributed in a small way in the fight against the disease.”
The Metabolomics Society is excited to introduce Metabolomics 2021 Online, the second virtual conference that will take place from June 22-24, 2021.
The conference will follow the general format that was instituted for Metabolomics 2020 Online, with the conference taking place in all time zones, enabling it to continue as a truly international event. Day 1 will offer workshops on special interest topics. Days 2 and 3 will feature scientific sessions that will begin with a keynote speaker followed by talks selected from submitted abstracts.
A new study from Lawson Health Research Institute, Western University and University of Alberta suggests that COVID-19 affects the human body’s blood concentration levels of specific metabolites – small molecules broken down in the human body through the process of metabolism. Three specific metabolites identified in this study could act as biomarkers and one day be measured through an inexpensive blood test to quickly screen patients for the disease and predict which patients will become most critically ill. The team also suspects those metabolites depleted by the virus could be delivered to patients as dietary supplements, acting as a secondary therapy. Published in Critical Care Explorations, the early findings add to the research team’s growing body of evidence on the bodily changes caused by the SARS-CoV-2 virus.
The article was released through Lawson Health Research Institute.
The paper, published in Critical Care Explorations, can be found here.
BioAlberta and The Metabolomics Innovation Center are bringing you a unique four-part webinar series during May 2021!
On May 4, 2:00-3:00 PM MDT, Dr. David Wishart will be presenting on how metabolomics can move your discoveries towards translation.
This presentation will introduce attendees to the field of metabolomics and explain how metabolomics works, why it’s being used and what it can do. Dr. David Wishart will explain how Alberta has become a world leader in metabolomics and give a brief history of The Metabolomics Innovation Center (TMIC). TMIC is Canada’s national metabolomics facility and based right here in Alberta. A virtual tour of TMIC will be provided and examples will be given of how metabolomics is allowing discoveries to be translated into practice.
- May 12, 2:00 – 3:00 PM - Metabolomics and Precision Medicine
- May 19, 2:00 - 3:00 PM - Metabolomics and Agri-Food
- May 27, 3:30 - 4:30 PM - Metabolomics and the Environment
Dr. Anas Abdel Rahman and his research group at King Faisal Specialist Hospital and Center (KFSHRC) in Saudi Arabia, working with the TMIC Li-node team, have identified a group of metabolites that potentially segregates patients with hyper IgE syndrome (HIES) from severe atopic dermatitis (AD). This pattern was identified in a group of HIES patients with Dedicator of cytokinesis 8 (DOCK8) genetic deficiency and AD. The identified metabolites were further studied to keep the ones related to the genetic deficiency, and exclude the others related to the secondary phenotypes. This group of metabolites has a great potential to replace the tedious genetics testing that is hard to interpret, and could be used efficiently for newborn screening and follow up evaluation.
Dr. Philip Britz-McKibbin, one of TMIC's lead scientists, as well as a group of researchers at McMaster have identified several metabolites, detectable in blood and urine, that can accurately measure dietary intake, potentially offering a new tool for physicians, dietitians and researchers to assess eating habits, measure the value of fad diets and develop health policies. The research, published in the journal Nutrients, addresses a major challenge in assessing diets: studies in nutrition largely rely on participants to record their own food intake, which is subject to human error, forgetfulness or omission. Scientists set out to determine if they could identify chemical signatures, or metabolites, that reflect changes in dietary intake, measure those markers and then compare the data with the foods study participants were provided and then reported they had eaten. With the aid of metabolomics technologies they were able to detect short-term changes in dietary patterns which could be measured objectively.
Britz-McKibbin cautions that food chemistry is highly complex. Our diets are composed of thousands of different kinds of chemicals, he says, and researchers don’t know what role they all may play in overall health. In future, he hopes to broaden this work by examining a larger cohort of participants over a longer period of time. His team is also exploring several ways to assess maternal nutrition during crucial stages of fetal development and its impact on obesity and metabolic syndrome risk in children.
This article was originally posted on McMaster's Brighter World by Michelle Donovan.
The paper, published in Nutrients, can be found on the MDPI website.
Phenylketonuria, also called PKU, is a rare metabolic disorder that causes a severe buildup of the amino acid phenylalanine in circulation. If left untreated, PKU can lead to intellectual disability, seizures, behavioral problems, and mental disorders. Management of PKU requires the lifelong restriction of protein intake using specialized medical foods. This poses a challenge to patients wanting to maintain their diet while ensuring adequate nutrition. A unique collaboration between TMIC's own Dr. Britz-McKibbin and McMaster Children's Hospital has developed a non-invasive approach for better treatment monitoring of patients with PKU. Through metabolomic profiling, they identified new biomarkers in urine that yield much more accurate information regarding patient dietary adherence when compared to self-reported diet records. Moreover, the study paves the way to designing novel therapies that will help PKU patients adhere to specific diets without nutritional deficiencies.
To find out more, the article is available here.
The Milk Composition Database (MCDB) is a freely available online resource containing detailed information about small molecule metabolites found in cow’s milk. Developed by TMIC’s Wishart Research Group, MCDB contains a complete list of metabolite names, structures, level of verification, reference spectra and citations for all of the milk compounds that have ever been identified, quantified or reported in either this database or existing scientific literature.
MCDB currently contains 2,355 metabolite entries, including water and lipid-soluble metabolites as well as metabolites that would be regarded as either abundant (>1 uM) or relatively rare (<1 nM). Each metabolite entry contains more than 90 data fields, and many of them are hyperlinked to other databases (including PubChem and DrugBank, among others) as well as a variety of structure and pathway viewing applets. In addition, MCDB is fully searchable and supports text, mass, spectral and structure searches.
In a recent interview with the Edmonton Journal, TMIC’s own Dr. Liang Li and University of Alberta psychology professor Dr. Roger Dixon discussed their latest research into the early detection of Alzheimer’s disease. Taking a non-invasive approach, Li and Dixon examined the saliva samples of 109 patients who were grouped according to whether they had Alzheimer’s disease, mild cognitive impairment, or neither.
After analyzing over 6,000 metabolites in the samples using mass spectrometry, Li and Dixon were able to identify three of these compounds as biomarkers. These biomarkers can not only help doctors identify which individuals have a higher risk of developing Alzheimer’s, but also assist in the development of effective preventative measures for patients to use.
A recent video in the Journal of Visualized Experiments (JoVE) from one of TMIC’s project leaders, Dr. Michael Overduin, and Dr. Alastair Barr (University of Westminster) evaluates the merits and limitations of several techniques studying protein-protein interactions (PPIs). PPIs are fundamental to the generation of biological effects, with many PPIs being intimately linked with disease and used as targets for drug action.
The video covers several methods for studying PPIs, including widely used techniques such as coimmunoprecipitation and affinity purification, as well as narrower techniques specific to certain protein structures. While Dr. Overduin and Dr. Barr conclude that no one technique is best due to the wide diversity of PPIs, they do highlight the emerging technique of spatial proteomics, which has been successfully harnessed as a discovery tool to unravel complex disease mechanisms.
Published in Analytica Chimica Acta, Dr. James Harynuk’s latest publication looks at optimizing the design and development of new two-dimensional gas chromatography (GCxGC) methods using secondary columns. The inclusion of these columns can enhance the separation power over one-dimensional GC methods and improve ultimate separation quality. However, the choices of stationary phase chemistries, geometries and configurations must also be assessed before changing the instrument design.
Previously, these choices were made using educated guesses, literature searches, or trial and error. In this article, Dr. Harynuk proposes a new thermodynamic model for GC separations which uses characteristic thermodynamic parameters to create retention maps. These maps provide a fast and easy way of acquiring information that can inform choices of column chemistries, phase ratios and configurations.
Dr. Harynuk also points out that although these retention maps were used to evaluate two-dimensional GC separations, they can be easily extended to evaluate three-dimensional (GCxGCxGC) separations as well.
Featured on the back cover of Proteomics – Clinical Applications, Dr. Christoph Borchers’ newest publication focuses on the identification of biomarkers specific to coronary artery disease (CAD). Along with a group of BC scientists, including researchers from the University of Victoria and University of British Columbia, Dr. Borchers helped develop an LC-ESI-MS based assay that can measure 107 stable isotope labeled peptide standards and native peptides in tryptic digests of plasma.
After extensive computational and statistical analysis of samples from subjects with and without angiographic evidence of CAD, the assay revealed six plasma proteins associated with the disease. If the results of the study are externally validated, the assay and identified biomarkers can improve CAD risk stratification in patients.
A recent study by TMIC’s Britz-McKibbin Research Group at McMaster University has identified new biomarkers for Irritable Bowel Syndrome (IBS) after comparing the metabolite profiles of urine samples from a cohort of IBS patients to a control group of healthy adults.
Speaking on the study’s findings, lead author Dr. Philip Britz-McKibbin commented, “We were interested in finding if there is a better way to detect and monitor IBS that avoids invasive colonoscopy procedures while also giving us better insights into its underlying mechanisms.”
In addition to the study, the Britz-McKibbin Research Group is currently expanding its research to discover new biomarkers in urine that can differentiate Crohn’s disease from ulcerative colitis in children. The group aims to avoid future colonoscopies altogether, and hopes that their research may allow for rapid screening of various chronic gut disorders more accurately and at a lower cost.
Dr. Britz-McKibbin, one of TMICs core-scientists, and his team at McMaster University have discovered several new biomarkers from a single drop of blood that could allow earlier and more definitive detection of cystic fibrosis (CF), a genetic disease which strikes both children and adults, causing chronic problems with the digestive system and the lungs.
The findings, published online in the Journal of Proteome Research are significant because current newborn screening methods are not accurate enough to identify the disorder in the population, which can manifest itself in many different ways, requiring additional testing and causing further stress for anxious parents.
Click here to read the full article!
Dr. David Wishart’s ground-breaking contributions to the scientific community, his dedication to education, and his positive influence as a mentor have not gone unnoticed. The University of Alberta has awarded Dr. Wishart the title of Distinguished University Professor and the Alumni Award. TMIC congratulates Dr. Wishart on these accomplishments.
The title of Distinguished University Professor recognizes exceptional faculty members who are globally recognized leaders and whose exemplary teaching, research and citizenship have made them leaders in their disciplines internationally. They serve as senior advisors to the University Community, and act as mentors and exemplars to other professors.
The University of Alberta Alumni Awards recognize the professional achievements, community service and innovation of graduates around the globe — people who uphold the promise to use their education “for the public good.”
TMIC has just finished its first competition for a stay at its Research Hotel. The competition is currently closed and applications are under review. Applicants will be notified by the end of October.
The hotel, which has been gaining popularity since the program began in 2011, gives visiting scientists, students and postdoctoral fellows office and bench space at TMIC’s central facility at the University of Alberta in Edmonton. They conduct their own experiments, expand their knowledge of metabolomics, receive one-on-one mentoring, and share in-person in the TMIC experience. Keep an eye on our website for future competitions and announcements!
To find out more about the Research Hotel, click here.
Lorna Shaw lost her entire family to cancer. To honour their legacy, she has decided to donate into research which furthers studies into disease prevention.
"I felt that this is the kind of research that needs to be done... I know from my experience working in research many years ago that it takes a long time for results to come to fruition, but I gave to research, not treatment, because that is where real, long-term change can occur." - Lorna Shaw
Lorna Shaw's gift to TMIC has opened new and exciting research opportunities. Her unrestricted donation has allowed our lab to purchase a QTRAP 5500 mass spectrometer which will further enhance our ability to conduct critical research. This addition will not only benefit the scientific community but will pave the way for better health-care through early detection and improved cure rates.
"Making data and ideas available for other scientists moves our whole field forward faster. With this tool, we’re helping patients and we’re changing lives for the better. We’re incredibly grateful for Lorna’s support." - David Wishart, TMIC Lead
Dr. Wishart was featured in an article during the University of Alberta's Changing Lives Week, a collection of donor-inspired stories which highlights how donors change lives. To read the entire article click here.
TMIC is looking forward to welcoming talented visiting researchers from all over the world again this year. On April 1, TMIC will launch its first competition for a stay at its Research Hotel. Applications will be accepted from researchers seeking a chance to land one of the coveted spots at the Hotel.
TMIC’s Research Hotel has been gaining popularity since the program began in 2011. The hotel gives visiting scientists, students and postdoctoral fellows office and bench space at TMIC’s central facility at the University of Alberta in Edmonton. They conduct their own experiments, expand their knowledge of metabolomics, receive one-on-one mentoring, and share in-person in the TMIC experience.
Applicants will be chosen based on the proposal they submit. Keep an eye on our website as we will be posting the application form here soon.
To find out more about the Research Hotel click here.
On January 9, 2017, the Canada Foundation for Innovation (CFI) announced an investment of $328 million in 17 national research facilities. The Metabolomics Innovation Centre (TMIC) received $6 million in funding through CFI's Major Science Initiatives (MSI) Fund thus ensuring its continued status as a cutting edge, world-class facility.
"This new funding will give TMIC the long-term stability it needs to make both Alberta and Canada a real leader in metabolomics research and development. ...it will allow hundreds of scientists from across Canada to come train and conduct research at TMIC and to make metabolomics an integral part of their research program. It will also foster the growth of Canada’s emerging metabolomics industry, where made-in-Canada ideas and technologies can be used in precision medicine, precision farming, and environmental monitoring.” - David Wishart
With the support of CFI, the field of metabolomics research will continue to grow strong... and TMIC will be at the forefront of this exciting field of science.
Visit CFI's website for more information.
The Metabolomics in Personalized Medicine: From Theory to Practice workshop will be held on June 8th, 2017 in Toronto at Mount Sinai Hospital. This free one-day event will headline talented presenters from diverse disciplines and should not be missed. Organizers are Dr. David Wishart at The Metabolomics Innovation Centre (TMIC) at the University of Alberta, and Biocrates Life Sciences phenotyping company.
For registration, please email your name, affiliation, and areas of research interest to email@example.com.
Our very own Lu Deng, postdoctoral fellow with University of Alberta’s Department of Computing Science and Department of Biological Sciences, has been rewarded for her achievements. She has won the Mitacs & National Research Council-IRAP Award for Commercialization 2016.
Lu’s research was conducted during her Mitacs Elevate fellowship with Edmonton-based Metabolomic Technologies Inc. (MTI). She developed PolypDx, an inexpensive urine test used to screen for polyps, the precursor to colon cancer.
Previous screening had to be done on cost-prohibitive highly specialized equipment. With the development of PolypDx, medical laboratories in Canada and the U.S. can now proceed using pre-existing mass-spectrometer technology. The product was launched in the spring and has already been in use for months in labs across the U.S.
Lu has completed her Mitacs fellowship and has moved on to a full-time senior scientist position at MTI. We wish her well.
$3 million of new federal funding – that’s how much the Canadian government values the cutting-edge metabolomics research being done at Genome Alberta and the University of Alberta, world leaders in the emerging metabolomics market.
The money will buy a 700 MHz Nuclear Magnetic Resonance machine and a Quadrupole-Time of Flight Mass Spectrometer. This equipment will enable scientists to speed up the process of commercializing their discoveries in biomarker research. The goal is to devise medical testing procedures that are less invasive, more accurate, and cheaper to use.
A new research and development medium will also be born, dubbed The Metabolomics Technology Demonstration Centre. Dr. David Wishart, professor at the departments of Biological Sciences and Computing Science, University of Alberta and one of the lead researchers in the project, had this to say: "The Metabolomics Technology Demonstration Centre will provide Canadian researchers with cutting-edge infrastructure and technical expertise to support translation of innovative biomarker discoveries into real life applications. We are very excited to work with our collaborators to develop prototype tools and products that will be implemented and commercialized through industry partnerships."
The government’s research agency, the National Institute of Nanotechnology, is not the only sponsor of this research. Other investors include Alberta Innovates Health Solutions, Metabolomics Technologies Inc. (MTI), and Genome Canada.