Review
Biochemistry & Molecular Biology
Montse Baldan-Martin, Maria Chaparro, Javier P. Gisbert
Summary: Inflammatory bowel diseases (IBDs) are chronic and inflammatory conditions affecting the gastrointestinal tract. Despite endoscopy being the gold standard test for assessing IBD, it is invasive and uncomfortable for patients. Therefore, non-invasive biomarkers for IBD diagnosis are urgently needed. This review summarizes proteomics and metabolomics studies in animals and humans, identifying urinary biomarkers for IBD diagnosis. Large-scale multi-omics studies with collaboration between clinicians, researchers, and industry are necessary for the development of sensitive and specific diagnostic biomarkers for personalized medicine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Gastroenterology & Hepatology
Monica State, Lucian Negreanu, Theodor Voiosu, Andrei Voiosu, Paul Balanescu, Radu Bogdan Mateescu
Summary: This study summarized the performance of noninvasive biomarkers in assessing MH in IBD patients. Fecal markers were the main focus, with fecal calprotectin being the most investigated marker, while among serum markers, the endoscopic healing index showed the best performance.
WORLD JOURNAL OF GASTROENTEROLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ondrej Fabian, Lukas Bajer, Pavel Drastich, Karel Harant, Eva Sticova, Nikola Daskova, Istvan Modos, Filip Tichanek, Monika Cahova
Summary: Inflammatory bowel diseases (IBD) are systemic immune-mediated conditions that primarily affect the gastrointestinal tract. Despite advancements in research, the exact causes of IBD remain largely unknown, leading to limited success in achieving remission and the development of severe complications. The use of proteomics, which analyzes a wide range of proteins in tissues, may provide valuable insights into the identification of new biomarkers for IBD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Pharmacology & Pharmacy
Sara Salvador-Martin, Alejandra Melgarejo-Ortuno, Luis A. Lopez-Fernandez
Summary: The use of biological drugs in pediatric inflammatory bowel disease has shown significant improvements, and predicting response to these drugs is particularly valuable in children. Clinical, biochemical, and genetic parameters can potentially predict response to biological drugs in children with IBD.
Article
Gastroenterology & Hepatology
Montserrat Baldan-Martin, Maria Chaparro, Javier P. Gisbert
Summary: Inflammatory bowel disease is a global disease with challenges in understanding its complex pathogenesis and progression, leading to limited progress in diagnosis and treatment. Future studies are needed to comprehensively characterize the disease biology for early detection and monitoring of clinical outcomes.
INFLAMMATORY BOWEL DISEASES
(2021)
Review
Pediatrics
Marleen Bouhuys, Willem S. Lexmond, Patrick F. van Rheenen
Summary: Inflammatory bowel diseases (IBDs) are chronic, immune-mediated disorders that include Crohn's disease and ulcerative colitis. Pediatric onset of the disease occurs in about 10% of cases. The management of pediatric IBD has evolved, with anti-tumor necrosis factor therapy being used upfront for patients at high risk for complications. Biochemical or endoscopic remission is the therapeutic goal, and pediatric IBD comes with unique challenges such as growth impairment and psychological issues. General pediatricians play a crucial role in integrating these challenges in the clinical care of patients with IBD and optimizing their outcomes.
Article
Nutrition & Dietetics
Arno R. Bourgonje, Laura A. Bolte, Lianne L. C. Vranckx, Lieke M. Spekhorst, Ranko Gacesa, Shixian Hu, Hendrik M. van Dullemen, Marijn C. Visschedijk, Eleonora A. M. Festen, Janneke N. Samsom, Gerard Dijkstra, Rinse K. Weersma, Marjo J. E. Campmans-Kuijpers
Summary: This study aimed to investigate the association between dietary patterns and circulating inflammatory proteins in patients with inflammatory bowel disease (IBD). The results showed that a high-sugar diet was inversely associated with fibroblast growth factor-19 (FGF-19), while a Mediterranean-style diet was associated with higher FGF-19 levels. A diet characterized by high alcohol and coffee intake was positively associated with CCL11 levels and lower levels of IL-12B.
Article
Gastroenterology & Hepatology
Lorenza Putignani, Salvatore Oliva, Sara Isoldi, Federica Del Chierico, Claudia Carissimi, Ilaria Laudadio, Salvatore Cucchiara, Laura Stronati
Summary: The study showed significant alterations in gut microbiota profile in pediatric IBD patients, with an abundance of species with proinflammatory mucosal activity clearly detected. Analysis of gut microbiota could play a role in designing personalized IBD treatment scenarios in the future.
EUROPEAN JOURNAL OF GASTROENTEROLOGY & HEPATOLOGY
(2021)
Review
Pediatrics
So Yoon Choi, Ben Kang
Summary: The introduction of biological agents, particularly anti-TNF agents, has significantly improved the long-term prognosis of patients with inflammatory bowel disease (IBD). In pediatric populations, only two biological agents, infliximab (IFX) and adalimumab (ADL), have been approved for use. ADL has shown efficacy in achieving mucosal healing (MH) and histological remission in both naive patients and those who have previously received biologic treatment. Therapeutic drug monitoring may further enhance the effectiveness of ADL treatment and reduce treatment failure.
FRONTIERS IN PEDIATRICS
(2022)
Article
Gastroenterology & Hepatology
Markus F. Neurath, Michael Vieth
Summary: Mucosal healing is an important prognostic factor in the management of patients with inflammatory bowel disease. It can predict clinical remission and resection-free survival. There are two levels of mucosal healing: endoscopic healing and histological healing. Drug therapies and new techniques can have an impact on mucosal healing, but cannot provide a definitive cure.
Article
Gastroenterology & Hepatology
Ayano Kondo, Siyuan Ma, Michelle Y. Y. Lee, Vivian Ortiz, Daniel Traum, Jonathan Schug, Benjamin Wilkins, Natalie A. Terry, Hongzhe Lee, Klaus H. Kaestner
Summary: This study used imaging mass cytometry platform to analyze multiple imaging of IBD and healthy intestinal tissues, revealing increased proliferation and HLA-DR expression in intestinal epithelia of IBD patients, positively correlated with inflammation severity. Neighborhood analysis showed enrichment of regulatory T cell interactions with macrophages, T cells, and plasma cells in IBD.
Review
Microbiology
Sean L. Carlson, Liya Mathew, Michael Savage, Klaartje Kok, James O. Lindsay, Carol A. Munro, Neil E. Mccarthy
Summary: The gut microbiome, consisting of bacteria, viruses, and fungi, plays a crucial role in the development of inflammatory bowel disease. Candida albicans, a common gut commensal and pathogenic fungus, has been extensively studied for its impact on the pathophysiology of IBD.
Article
Gastroenterology & Hepatology
Lorenzo Bertani, Brigida Barberio, Marco Fornili, Luca Antonioli, Federico Zanzi, Cesare Casadei, Laura Benvenuti, Sonia Facchin, Vanessa D'Antongiovanni, Greta Lorenzon, Linda Ceccarelli, Laura Baglietto, Nicola de Bortoli, Massimo Bellini, Francesco Costa, Edoardo Vincenzo Savarino, Matteo Fornai
Summary: This study suggests that serum oncostatin M is a drug-specific biomarker that can be used to predict therapeutic effectiveness in anti-TNF treatment. These results emphasize the utility of serum oncostatin M measurement in patients treated with anti-TNF.
DIGESTIVE AND LIVER DISEASE
(2022)
Review
Biochemistry & Molecular Biology
Vibeke Andersen, Tue B. Bennike, Corinna Bang, John D. Rioux, Isabelle Hebert-Milette, Toshiro Sato, Axel K. Hansen, Ole H. Nielsen
Summary: Inflammatory bowel diseases (IBD) are challenging to manage due to the diversity between patients and the lack of reliable biomarkers. Diet, gut microbiota, genetics, and patient factors are all crucial for disease occurrence and progression. Recent research has identified potential biomarkers for IBD management, but further evaluation is needed. This review provides an update on cutting-edge research in IBD to improve disease management and patient quality of life.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Gastroenterology & Hepatology
Esther Orlanski-Meyer, Martine Aardoom, Amanda Ricciuto, Dan Navon, Nicholas Carman, Marina Aloi, Jiri Bronsky, Jan Daebritz, Marla Dubinsky, Seamus Hussey, Peter Lewindon, Javier Martin De Carpi, Victor Manuel Navas-Lopez, Marina Orsi, Frank M. Ruemmele, Richard K. Russell, Gabor Veres, Thomas D. Walters, David C. Wilson, Thomas Kaiser, Lissy de Ridder, Anne Griffiths, Dan Turner
Summary: By surveying experts and conducting systematic reviews, key predictors for pediatric UC outcomes, including colectomy, acute severe colitis, and cancer, were identified. These predictions can be used for personalized treatment approaches, improving outcomes for pediatric UC patients.
Article
Gastroenterology & Hepatology
Natasha Bollegala, Melanie Barwick, Nancy Fu, Anne M. Griffiths, Laurie Keefer, Sara Ahola Kohut, Karen I. Kroeker, Sally Lawrence, Kate Lee, David R. Mack, Thomas D. Walters, Jacqueline de Guzman, Claudia Tersigni, Ashleigh Miatello, Eric I. Benchimol
Summary: The study is a multi-center randomized controlled trial to evaluate the clinical effectiveness of a multimodal intervention for adolescents and young adults with IBD in Canada. The intervention program includes individualized assessment, transition navigator, virtual patient skills-building, and a virtual structured education program. The control group will receive standard-of-care defined by each center.
BMC GASTROENTEROLOGY
(2022)
Letter
Gastroenterology & Hepatology
Joshua Quan, Christopher Ma, Remo Panaccione, Lindsay Hracs, Nastaran Sharifi, Michelle Herauf, Ante Makovinovic, Stephanie Coward, Joseph W. Windsor, Lea Caplan, Richard J. M. Ingram, Jamil N. Kanji, Graham Tipples, Jessalyn K. Holodinsky, Charles N. Bernstein, Douglas J. Mahoney, Sasha Bernatsky, Eric Benchimol, Gilaad G. Kaplan
Article
Health Care Sciences & Services
Aman K. Dheri, M. Ellen Kuenzig, David R. Mack, Sanjay K. Murthy, Gilaad G. Kaplan, Jessy Donelle, Glenys Smith, Eric Benchimol
Summary: This study showed that there were no significant differences between meta-analysis in a distributed network and individual-level analysis in assessing time trends of health services utilization with health administrative data.
JOURNAL OF CLINICAL EPIDEMIOLOGY
(2022)
Review
Nutrition & Dietetics
Kendra Hodgkinson, Faiha El Abbar, Peter Dobranowski, Juliana Manoogian, James Butcher, Daniel Figeys, David Mack, Alain Stintzi
Summary: Butyrate, produced by gut microbiota through fermentation of dietary fiber, serves as a key energy source for colonocytes. It has important roles in gastrointestinal health, impacting both host and microbial functions. Maintaining optimal butyrate levels improves gastrointestinal health by supporting colonocyte function, decreasing inflammation, maintaining the gut barrier, and promoting a healthy microbiome. However, increasing butyrate levels in humans and reversing negative outcomes have yielded mixed results, despite its protective actions in intestinal diseases.
CLINICAL NUTRITION
(2023)
Article
Public, Environmental & Occupational Health
Shirley Wang, Anton Pottegard, William Crown, Peter Arlett, Darren M. Ashcroft, Eric Benchimol, Marc L. Berger, Gracy Crane, Wim Goettsch, Wei Hua, Shaum Kabadi, David M. Kern, Xavier Kurz, Sinead Langan, Takahiro Nonaka, Lucinda Orsini, Susana Perez-Gutthann, Simone Pinheiro, Nicole Pratt, Sebastian Schneeweiss, Massoud Toussi, Rebecca J. Williams
Summary: Problem ambiguity in communication of key study parameters hinders the use of real-world evidence studies in healthcare decision-making. Clear communication about data provenance, design, analysis, and implementation is essential for reproducibility and assessing potential biases.
PHARMACOEPIDEMIOLOGY AND DRUG SAFETY
(2023)
Article
Gastroenterology & Hepatology
Michelle J. Gould, Margaret A. Marcon, Geoffrey C. Nguyen, Eric Benchimol, Rahim Moineddin, Sarah Swayze, Alexander Kopp, Elyanne M. Ratcliffe, Neil Merritt, Jacob Davidson, Jacob C. Langer, Niraj Mistry, Armando J. Lorenzo, Michael Temple, Catharine M. Walsh
Summary: This study aimed to assess the impact of antegrade enema initiation on healthcare utilization. The results showed no significant differences in the rate of hospitalizations, outpatient visits, or same-day surgical procedures between the intervention group and the control group. However, the intervention group had an increased rate of emergency department visits, primarily due to device-related complications.
NEUROGASTROENTEROLOGY AND MOTILITY
(2023)
Article
Biochemical Research Methods
Marybeth Creskey, Leyuan Li, Zhibin Ning, Emily E. F. Fekete, Janice Mayne, Krystal Walker, Anna Ampaw, Robert Ben, Xu Zhang, Daniel Figeys
Summary: This study demonstrates that the TMT labeling procedures can be simplified by using pre-aliquoted dry TMT reagents, which achieve high labeling efficiency in both microbiome and mammalian cell line samples. The workflow was successfully applied to analyze 97 samples and consistently revealed microbiome responses. This study supports the use of pre-aliquoted, dried, and stored TMT reagents for robust quantitative proteomics and metaproteomics in high throughput applications.
Article
Multidisciplinary Sciences
Leyuan Li, Tong Wang, Zhibin Ning, Xu Zhang, James Butcher, Joeselle M. M. Serrana, Caitlin M. A. Simopoulos, Janice Mayne, Alain Stintzi, David R. R. Mack, Yang-Yu Liu, Daniel Figeys
Summary: Functional redundancy is a crucial ecosystem property in which different species contribute to the ecosystem in similar ways through redundant functions. This study quantifies the proteome-level functional redundancy (FRp) in the human gut microbiome using metaproteomics. The research reveals high proteome-level functional redundancy and nestedness in the human gut proteomic content networks. The findings show that proteomic content networks' nested topology and small functional distances between taxa contribute to high FRp. FRp outperforms diversity indices in detecting significant microbiome responses to various environmental factors.
NATURE COMMUNICATIONS
(2023)
Article
Gastroenterology & Hepatology
Emily Ef Fekete, Daniel Figeys, Xu Zhang
Summary: Mounting evidence suggests that the gut microbiome plays a causative or correlative role in various diseases, such as gastrointestinal diseases, metabolic diseases, neurological disorders, and cancers. Therefore, there have been efforts to develop and apply therapies that target the gut microbiota for disease treatment and wellness maintenance. This review summarizes the current development of gut microbiota-directed therapeutics, emphasizes the importance of advanced -omics approaches for evaluating microbiota-type therapies, and discusses the clinical and regulatory challenges. It also explores the development and potential application of ex vivo microbiome assays and in vitro intestinal cellular models. Overall, this review provides a comprehensive view of the promises and challenges in the emerging field of microbiome-directed human healthcare.
Article
Biochemical Research Methods
Kai Cheng, Zhibin Ning, Leyuan Li, Xu Zhang, Joeselle M. Serrana, Janice Mayne, Daniel Figeys
Summary: The research on microbial communities has gained attention in agriculture, environment, and human health. Metaproteomics has become a powerful tool to understand the roles of microbes through analyzing their expressed proteins. However, analyzing metaproteomic data at genome resolution is challenging due to the lack of efficient bioinformatics tools. Here, we introduce MetaLab-MAG, a specialized tool for microbiome characterization from metagenome-assembled genomes databases. MetaLab-MAG performs well compared to directly searching the gene catalog protein database, allowing quantification of genome-level microbiota compositions and supporting different quantification strategies. It overcomes the obstacles in metaproteomic data analysis and provides comprehensive information from microbiomes to researchers.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Zhongzhi Sun, Zhibin Ning, Kai Cheng, Haonan Duan, Qing Wu, Janice Mayne, Daniel Figeys
Summary: Metaproteomics studies functional changes in the human gut microbiome and peptide identification is a crucial step in this research. However, the large search space complicates peptide identification methods. This study constructed MetaPep, a core peptide database, and demonstrated its importance for human gut metaproteomics research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Meeting Abstract
Gastroenterology & Hepatology
Michelle Gould, Margaret A. Marcon, Geoffrey C. Nguyen, Eric I. Benchimol, Rahim Moineddin, Jacob Langer, Armando Lorenzo, Niraj Mistry, Michael Temple, Sarah Swayze, Alexander Kopp, Elyanne M. Ratcliffe, Neil H. Merritt, Jacob Davidson, Catharine M. Walsh
Meeting Abstract
Gastroenterology & Hepatology
Michelle Gould, Margaret A. Marcon, Geoffrey C. Nguyen, Eric I. Benchimol, Rahim Moineddin, Jacob Langer, Armando Lorenzo, Niraj Mistry, Michael Temple, Sarah Swayze, Alexander Kopp, Elyanne M. Ratcliffe, Neil H. Merritt, Jacob Davidson, Catharine M. Walsh
