Article
Chemistry, Medicinal
Sumaiah J. Alarfaj, Sally Abdallah Mostafa, Walaa A. Negm, Thanaa A. El-Masry, Marwa Kamal, Mohamed Elsaeed, Ahmed Mohamed El Nakib
Summary: Individual differences exist in the severity, behavior, progression, and therapy response of IBD patients. The evaluation of mucosal gene expression is crucial in understanding IBD, as it is initiated by a break in the intestinal epithelial barrier. Molecular analysis of biomarkers in intestinal biopsies provides a reliable means of assessing localized inflammation. This investigation aimed to identify changes in gene expression in the inflamed mucosa of IBD patients undergoing treatment with 5-aminosalicylic acid (5ASA) or anti-TNF drugs.
Article
Cell Biology
Lili Ye, Yongwei Lin, Xing-di Fan, Yaoming Chen, Zengli Deng, Qian Yang, Xiaotian Lei, Jizong Mao, Chunhui Cui
Summary: The number of patients with Inflammatory bowel disease (IBD) is increasing globally. Researchers identified IBD-related genes using a SVM-based method based on disease similarities and gene interactions, achieving good results. The study highlights the importance of genetic factors in the occurrence of IBD.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Engineering, Biomedical
Yingzheng Zhao, Pengpeng Xue, Gaolong Lin, Mengqi Tong, Jiaojiao Yang, Yingying Zhang, Kunjie Ran, Deli Zhuge, Qing Yao, Helin Xu
Summary: In this study, a double-network hydrogel (PMSP) was developed for the targeted therapy of ulcerative colitis (UC). PMSP showed specific adhesion to the inflamed mucosa and exhibited good mechanical strength and bio-adhesive force. The treatment with PMSP-KPV improved colitis symptoms, promoted the recovery of the colonic epithelial barrier, and modulated the gut flora.
ACTA BIOMATERIALIA
(2022)
Article
Medicine, General & Internal
Ruben Y. Gabriels, Arno R. Bourgonje, Julius Z. H. von Martels, Tjasso Blokzijl, Rinse K. Weersma, Kevin Galinsky, Julius Juarez, Klaas Nico Faber, Gursah Kats-Ugurlu, Gerard Dijkstra
Summary: This study aimed to explore the predictive value of mucosal eosinophils and serum eotaxin-1 regarding response to vedolizumab induction therapy in patients with inflammatory bowel disease (IBD). The results showed that mucosal eosinophil abundance in non-inflamed colonic tissue and baseline serum eotaxin-1 levels were associated with response to vedolizumab treatment. However, the predictive capacity of baseline serum eotaxin-1 levels could not be validated in another study cohort.
JOURNAL OF CLINICAL MEDICINE
(2022)
Review
Immunology
Ying Wang, Ningning Xue, Ziyuan Wang, Xin Zeng, Ning Ji, Qianming Chen
Summary: With improving quality of life, the pressure on oral health is increasing. Common oral mucosal diseases, such as oral lichen planus and gingivitis, are related to the destruction of the oral immune barrier. T-helper 17 (Th17) cells and their cytokines play vital roles in maintaining oral immune homeostasis. An excessive Th17/IL-17 response can lead to autoimmune damage, highlighting the importance of understanding the role of Th17 cells in oral mucosa and their potential as therapeutic targets for oral mucosal diseases.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Medicine, Research & Experimental
Anna Onody, Apor Veres-Szekely, Domonkos Pap, Reka Rokonay, Beata Szebeni, Erna Sziksz, Franz Oswald, Gabor Veres, Aron Cseh, Attila J. Szabo, Adam Vannay
Summary: The study demonstrates increased IL-24 expression in serum and colon samples of children with IBD and DSS treated mice. Inflammatory factors such as IL-1 beta, LPS, and H2O2 can increase IL24 expression in PBMCs and LPMCs. IL-24 treatment promotes the expression of TGF-beta and PDGF-B in HT-29 cells, as well as enhances ECM-related gene expression and motility in CCD-18Co cells.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Review
Medicine, Research & Experimental
Yaoyao Chang, Lixiang Zhai, Jiao Peng, Haiqiang Wu, Zhaoxiang Bian, Haitao Xiao
Summary: IBD is a chronic inflammatory intestinal disorder with limited treatment options, and correcting the imbalance of Th17/Treg has been shown to be effective in preventing and treating IBD. Phytochemicals derived from natural products have been recognized as potent regulators of Th17/Treg and may offer protective benefits against colonic inflammation, showing great potential for the development of new drugs for IBD treatment.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Review
Gastroenterology & Hepatology
Eduardo J. Villablanca, Katja Selin, Charlotte R. H. Hedin
Summary: Current treatments for inflammatory bowel disease (IBD) mainly focus on inhibiting inflammation, but the use of immunosuppressive therapy can lead to infectious and neoplastic diseases. Therefore, finding a way to achieve mucosal healing without immunosuppression is important. The lack of treatments that directly promote mucosal healing and regeneration in IBD may be due to a lack of understanding of the underlying pathways. Stem cells, growth factors, and organoid culture and stem cell therapy are potential novel mechanisms to restore barrier function in IBD.
NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY
(2022)
Article
Medicine, General & Internal
Writaja Halder, Faidon-Marios Laskaratos, Hanan El-Mileik, Sergio Coda, Stevan Fox, Saswata Banerjee, Owen Epstein
Summary: The COVID-19 pandemic has heavily impacted healthcare services for patients with chronic diseases. This review explores the use of colon capsule endoscopy as a method for assessing and treating inflammatory bowel disease. Despite its limitations, there is increasing evidence to support the use of the second-generation colon capsule.
Review
Biochemistry & Molecular Biology
Marcello Candelli, Laura Franza, Giulia Pignataro, Veronica Ojetti, Marcello Covino, Andrea Piccioni, Antonio Gasbarrini, Francesco Franceschi
Summary: The article discusses the interaction between lipopolysaccharides (LPS), gut microbiota (GM), and gut-associated lymphoid tissue (GALT), indicating that the inflammatory reactions caused by LPS can directly impact the gut microbiota and immune system, leading to chronic inflammation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Pediatrics
Asia Smith, Shweta Namjoshi, John A. Kerner, James C. Y. Dunn
Summary: This study retrospectively reviewed the clinical data of 51 children with short bowel syndrome and found that small bowel length and type of remnant intestine were associated with the duration of parenteral nutrition use. Children with longer small bowel length achieved enteral autonomy faster. The presence of ileocecal valve and ileum enhanced the ability to wean from parenteral nutrition. Patients with the entire colon achieved enteral autonomy sooner than those with partial colon.
JOURNAL OF PEDIATRIC SURGERY
(2023)
Review
Biochemistry & Molecular Biology
Michelle Temby, Theresa L. Boye, Jacqueline Hoang, Ole H. Nielsen, John Gubatan
Summary: This article reviews the role of kinase signaling pathways in colitis-associated colon cancer, including MAPK, CDK, autophagy-activated kinases, JAK-STAT, and other kinases. It also discusses the involvement of JAK-STAT signaling in the pathogenesis of inflammatory bowel disease (IBD) and the potential use of JAK inhibitors for treating 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
Cell Biology
Yongyu Chen, Jing Lei, Song He
Summary: Evidence suggests a connection between m(6)A modification and immune infiltration in IBD. The study identified decreased expression of IGF2BP1 and IGF2BP2 in CD tissues, and decreased expression of IGF2BP2 in UC tissues. It also found associations between different m(6)A clusters and specific immune cell types in the intestinal mucosa.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Miha Jerala, Nina Hauptman, Nika Kojc, Nina Zidar
Summary: By comparing gene expression data of liver and kidney fibrosis, we identified several genes that are important for fibrosis in inflammatory bowel diseases. These genes showed similar expression changes as in fibrosis of other organs, suggesting common mechanisms of fibrosis in different organ diseases. In addition, some genes were already active in patients with inflammatory bowel diseases even without fibrosis, indicating early activation of profibrotic pathways or overlapping functions between fibrosis and inflammation.
Article
Engineering, Environmental
Kristel Mijnendonckx, Tom Rogiers, Francisco J. Gimenez del Rey, Mohamed L. Merroun, Adam Williamson, Md Muntasir Ali, Daniel Charlier, Natalie Leys, Nico Boon, Rob Van Houdt
Summary: Uranium contamination is a widespread issue caused by natural and human activities. However, the molecular mechanisms underlying uranium resistance in bacteria are still not well understood. This study investigated the resistance mechanisms of Cupriavidus metallidurans NA4 to toxic uranium concentrations. Through the increased expression of a specific small periplasmic protein, PrsQ2, the bacteria were able to form periplasmic uranium-phosphate precipitates, thus improving their resistance to uranium.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Medicine, Research & Experimental
Philippe Decruyenaere, Kimberly Verniers, Franco Poma-Soto, Jo Van Dorpe, Fritz Offner, Jo Vandesompele
Summary: This study compared the impact of three RNA extraction methods on yield, quality, and sequencing-based gene expression results in FFPE samples. The results showed that methods B and C outperformed method A, resulting in higher fractions of uniquely mapped reads, an increased number of detectable genes, a lower fraction of duplicated reads, and better representation of the B-cell receptor repertoire. Caution should be applied when comparing and interpreting results obtained using different methods.
LABORATORY INVESTIGATION
(2023)
Article
Biochemical Research Methods
Celine Everaert, Jasper Verwilt, Kimberly Verniers, Niels Vandamme, Alvaro Marcos Rubio, Jo Vandesompele, Pieter Mestdagh
Summary: RNA sequencing is widely used for transcriptome analysis, but quantification of low-abundant transcripts remains challenging. Researchers have developed a strategy using high-affinity RNA-binding oligonucleotides to reduce the abundance of specific RNA transcripts in sequencing libraries. This method is efficient, reproducible, and can be easily integrated into existing RNA sequencing protocols, improving transcriptome coverage and complexity.
BIOLOGICAL PROCEDURES ONLINE
(2023)
Article
Environmental Sciences
Kankana Kundu, Josefien Van Landuyt, Valerie Mattelin, Bram Martin, Marijke Neyts, Koen Parmentier, Nico Boon
Summary: This study found that the microbiome in sediment near a World War I munition dumpsite in the Belgian part of the North Sea can degrade 2,4,6-trinitrotoluene (TNT). The degradation of TNT was enhanced by adding methanol and several enriched genera, such as Colwellia, Thalossospira, and Methylophaga, were identified as TNT-utilizing bacteria.
MARINE POLLUTION BULLETIN
(2023)
Review
Biochemistry & Molecular Biology
Jasper Verwilt, Pieter Mestdagh, Jo Vandesompele
Summary: RNA sequencing has become influential in various research fields. However, the reverse transcription reaction in most protocols often leads to biases and artifacts in the resulting cDNA pool, which are overlooked in the literature. This review discusses these issues and provides solutions and good practices for RNA sequencing experiments, aiming to contribute to scientifically sound RNA studies.
Article
Polymer Science
Valerie Mattelin, Lennert Verfaille, Kankana Kundu, Stefaan De Wildeman, Nico Boon
Summary: With the accumulation of plastic waste in both controlled waste management settings and natural settings, there is a need for solutions in the field of biodegradation. However, determining the biodegradability of plastics in natural environments remains challenging due to low biodegradation rates. This study validates a colorimetric test using carbon nanodots to screen the biodegradation of plastics in natural environments. The results indicate that this method is a good alternative, but a combination of different methods provides the most information.
Review
Medical Laboratory Technology
Matthijs Vynck, Yao Chen, David Gleerup, Jo Vandesompele, Wim Trypsteen, Antoon Lievens, Olivier Thas, Ward De Spiegelaere
Summary: Background partition classification is essential in digital PCR data analysis. This review provides an overview of available methods and their challenges, serving as a guide for practitioners. Strengths, weaknesses, and application gaps are discussed, stimulating method development.
CLINICAL CHEMISTRY
(2023)
Article
Engineering, Environmental
Kevin Sabbe, Liese D'Haen, Nico Boon, Ramon Ganigu
Summary: As part of the circular bio-economy paradigm shift, waste management has shifted focus towards producing added-value compounds. The use of mixed culture bioprocesses for converting waste to platform chemicals has gained interest, but these processes often lack microbiological diversity and are prone to disturbances. To address this, flow cytometry was used to monitor a lactic acid chain elongation process for caproic acid production, allowing for qualitative and quantitative assessment. Specific community types were identified and correlated to functionality and genotypic diversity, and machine-learning algorithms showed high accuracy in predicting production rates.
Review
Microbiology
Fabian Mermans, Valerie Mattelin, Ruben van den Eeckhoudt, Cristina Garcia-Timermans, Josefien Van Landuyt, Yuting Guo, Irene Taurino, Filip Tavernier, Michael Kraft, Hira Khan, Nico Boon
Summary: New techniques in single-cell research have revolutionized our ability to study microbes at unprecedented scales and depths. This review focuses on the state-of-the-art technologies in single-cell analysis in microbial ecology applications, particularly highlighting optical tools like flow cytometry and Raman spectroscopy, as well as emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches, discussing successful applications, exploring emerging techniques, and promoting the integration of established and novel approaches in research.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Thomas Pluym, Cristina Garcia-Timermans, Sander Vervloet, Riet Cornelissen, Nico Boon, Bart De Gusseme
Summary: The use of advanced membrane processes, such as reverse osmosis (RO), is crucial for producing process water and drinking water that meet microbiological standards. However, bacterial breakthrough and the passage of ultra-small species of bacteria can occur in reverse osmosis systems. Currently, microbiological and breakthrough monitoring is done through plating methods and conductivity monitoring, but this case study demonstrates the added value of using on-line flow cytometry for monitoring membrane integrity and microbial quality.
ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Thomas Van den Berghe, Danilo Babin, Min Chen, Martijn Callens, Denim Brack, Helena Maes, Jan Lievens, Marie Lammens, Maxime Van Sumere, Lieve Morbee, Simon Hautekeete, Stijn Schatteman, Tom Jacobs, Willem-Jan Thooft, Nele Herregods, Wouter Huysse, Jacob L. Jaremko, Robert Lambert, Walter Maksymowych, Frederiek Laloo, Xenofon Baraliakos, Ann-Sophie De Craemer, Philippe Carron, Filip van den Bosch, Dirk Elewaut, Lennart Jans
Summary: This study aimed to evaluate the feasibility and diagnostic accuracy of a deep learning network for detection of structural lesions of sacroiliitis on multicenter pelvic CT scans. The results showed that the optimized deep learning pipeline, including an explainability analysis, can detect structural lesions of sacroiliitis on pelvic CT scans with excellent statistical performance on a slice-by-slice and patient level.
EUROPEAN RADIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alan Van Goethem, Jill Deleu, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, Sanjeev A. Vasudevan, Fjoralba Zeka, Fleur Demuynck, Eveline Barbieri, Frank Speleman, Pieter Mestdagh, Jason Shohet, Jo Vandesompele, Tom Van Maerken
Summary: In this study, we evaluated whether circulating miRNAs can be used to monitor neuroblastoma tumor burden and treatment-induced changes in the tumor. We performed small RNA sequencing on serum samples from mice with neuroblastoma xenografts treated with idasanutlin or temsirolimus. We identified serum miRNAs that correlated with tumor tissue expression and tumor volume, as well as miRNAs that responded to p53 activation following idasanutlin treatment.
Article
Immunology
Koen Venken, Tine Decruy, Tim Sparwasser, Dirk Elewaut
Summary: Regulatory T cells (Tregs) and invariant natural killer T (iNKT) cells play a crucial role in controlling autoimmune diseases. The study reveals that Treg depletion enhances iNKT cell responses and leads to severe liver and gut pathology in preclinical models of autoimmunity.
Article
Environmental Sciences
Paula Alejandra Lamprea Pineda, Kristof Demeestere, Jose Joaquin Gonzalez-Cortes, Allan A. Alvarado-Alvarado, Nico Boon, Frank Devlieghere, Herman Van Langenhove, Christophe Walgraeve
Summary: This study investigated the removal of difficult-to-degrade VOC mixtures using biofiltration and the impact of operational conditions. The results showed that the type of inoculum and packing material influenced the removal efficiency, and different microbial populations dominated in the biofilters.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemical Research Methods
Ruben Van den Eeckhoudt, An-Sofie Christiaens, Frederik Ceyssens, Vasileios Vangalis, Kevin J. Verstrepen, Nico Boon, Filip Tavernier, Michael Kraft, Irene Taurino
Summary: This paper introduces a microfluidic device for full-electric cell capturing, analyzing, and selectively releasing single cells. The device was experimentally demonstrated on Saccharomyces cerevisiae, showing potential for small-scale, high-throughput single-cell analysis and sorting.