Relationship between the Biological Clock and Inflammatory Bowel Disease

Giebfried, Jonathan; Lorentz, Axel

doi:10.3390/clockssleep5020021

Cited by 10 publications

(4 citation statements)

References 127 publications

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“…TRIM40 drives IBD pathogenesis by targeting cell-cell junctions in the mucosal epithelial barrier and promoting inflammation in the gut ( Noguchi et al 2011 , Kang et al 2023 ). Disturbances in the circadian rhythm are also linked to IBD manifestations ( Giebfried and Lorentz 2023 ); for instance, CLOCK expression is disrupted in IBD patients ( Weintraub et al 2020 , Giebfried and Lorentz 2023 ). Interestingly, BoostDiff identifies an edge between CLOCK and STAT3 , which could point to a candidate regulatory mechanism where the circadian clock influences STAT3 , a known driver of the CD phenotype.…”

Section: Resultsmentioning

confidence: 99%

Inference of differential gene regulatory networks using boosted differential trees

Galindez,

List,

Baumbach

et al. 2024

Bioinformatics Advances

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Diseases can be caused by molecular perturbations that induce specific changes in regulatory interactions and their coordinated expression, also referred to as network rewiring. However, the detection of complex changes in regulatory connections remains a challenging task and would benefit from the development of novel non-parametric approaches. We develop a new ensemble method called BoostDiff (boosted differential regression trees) to infer a differential network discriminating between two conditions. BoostDiff builds an adaptively boosted (AdaBoost) ensemble of differential trees with respect to a target condition. To build the differential trees, we propose differential variance improvement as a novel splitting criterion. Variable importance measures derived from the resulting models are used to reflect changes in gene expression predictability and to build the output differential networks. BoostDiff outperforms existing differential network methods on simulated data evaluated in four different complexity settings. We then demonstrate the power of our approach when applied to real transcriptomics data in COVID-19, Crohn’s disease, breast cancer, prostate adenocarcinoma, and stress response in Bacillus subtilis. BoostDiff identifies context-specific networks that are enriched with genes of known disease-relevant pathways and complements standard differential expression analyses. BoostDiff is available at https://github.com/scibiome/boostdiff_inference.

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Section: Resultsmentioning

confidence: 99%

Inference of differential gene regulatory networks using boosted differential trees

Galindez,

List,

Baumbach

et al. 2024

Bioinformatics Advances

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“…In ulcerative colitis, 50 genes were expressed differentially, and 27 were upregulated. It was observed that the clock genes Arntl2 and RorA were upregulated, while Csnk2B , Npas2 , Per1 , and Per3 were downregulated [ 38 , 39 ]. This could be related to the manifestation of these pathologies in subjects exposed to conditions of desynchronization such as shift work or jet lag [ 40 , 41 ].…”

Section: Circadian Rhythms In the Enteral Systemmentioning

confidence: 99%

Chronodisruption and Gut Microbiota: Triggering Glycemic Imbalance in People with Type 2 Diabetes

Moreno-Cortés,

Meza-Alvarado,

García-Mena

et al. 2024

Nutrients

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The desynchronization of physiological and behavioral mechanisms influences the gut microbiota and eating behavior in mammals, as shown in both rodents and humans, leading to the development of pathologies such as Type 2 diabetes (T2D), obesity, and metabolic syndrome. Recent studies propose resynchronization as a key input controlling metabolic cycles and contributing to reducing the risk of suffering some chronic diseases such as diabetes, obesity, or metabolic syndrome. In this analytical review, we present an overview of how desynchronization and its implications for the gut microbiome make people vulnerable to intestinal dysbiosis and consequent chronic diseases. In particular, we explore the eubiosis–dysbiosis phenomenon and, finally, propose some topics aimed at addressing chronotherapy as a key strategy in the prevention of chronic diseases.

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“…Cholesterol levels are said to be lowest between 2 and 6 p. m. and highest at 6 am. [51,52]. For hypercholesterolemia, chronotherapy can be performed by scheduling the medicine following the circadian cycle.…”

Section: Diseasementioning

confidence: 99%

Pulsatile Drug Delivery Systems the Novel Approach

BODKE,

TEKADE,

BADEKAR

et al. 2024

Int J Pharm Pharm Sci

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Oral pulsatile drug delivery systems (PDDS) are intended to induce programmable lag phases before a quick and quantifiable, repeated, or prolonged medication release. As a result, they are gaining popularity due to their inherent suitability for achieving chronotherapeutic goals, which have just been highlighted concerning several prevalent chronic illnesses characterized by typical night or early-morning recurring symptoms (e. g. bronchial asthma, heart attack, rheumatoid arthritis, early-morningawakening). Furthermore, time-based colonic release is possible when pulsatile delivery devices are correctly modified to overcome unexpected gastric emptying and give delay periods that roughly match the small intestine transit time. Oral pulsatile administration is accomplished using several release platforms, including reservoir, capsular, and osmotic devices. The current review article addressed the topics that followed: the reason pulsatile drug delivery systems have been invented; diseases for which pulsatile release is necessary; classification, advantages and disadvantages; methods used in the current systems; the situation nowadays and its potential for the future; recent advancements, and especially, the previous five to ten years of research on pulsatile drug delivery conducted by researchers using a variety of drugs for a variety of diseases.

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Relationship between the Biological Clock and Inflammatory Bowel Disease

Cited by 10 publications

References 127 publications

Inference of differential gene regulatory networks using boosted differential trees

Inference of differential gene regulatory networks using boosted differential trees

Chronodisruption and Gut Microbiota: Triggering Glycemic Imbalance in People with Type 2 Diabetes

Pulsatile Drug Delivery Systems the Novel Approach

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