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Background: Engineered cells provide versatile tools for precise, tunable drug delivery, especially when synthetic stimulus-responsive gene circuits are incorporated. In many complex disease conditions, endogenous pathologic signals such as inflammation can vary dynamically over different time scales. For example, in autoimmune conditions such as rheumatoid arthritis or juvenile idiopathic arthritis, local (joint) and systemic inflammatory signals fluctuate daily, peaking in the early morning, but can also persist over long periods of time, triggering flare-ups that can last weeks to months. However, treatment with disease-modifying anti-rheumatic drugs is typically provided at continuous high doses, regardless of disease activity and without consideration for levels of inflammatory signals. In previous studies, we have developed cell-based drug delivery systems that can automatically address the different scales of flares using either chronogenetic circuits (i.e., clock gene-responsive elements) that can be tuned for optimal drug delivery to dampen circadian variations in inflammatory levels or inflammation-responsive circuits (i.e., NF-κB-sensitive elements) that can respond to sustained arthritis flares on demand with proportional synthesis of drug. The goal of this study was to develop a novel dual-responsive synthetic gene circuit that responds to both circadian and inflammatory inputs using OR-gate logic for both daily timed therapeutic output and enhanced therapeutic output during chronic inflammatory conditions.
Results: We developed a synthetic gene circuit driven by tandem inflammatory NF-κB and circadian E'-box response elements. When engineered into induced pluripotent stem cells that were chondrogenically differentiated, the gene circuit demonstrated basal-level circadian output with enhanced stimulus-responsive output during an inflammatory challenge shown by bioluminescence monitoring. Similarly, this system exhibited enhanced therapeutic levels of biologic drug interleukin-1 receptor antagonist (IL-1Ra) during an inflammatory challenge in differentiated cartilage pellets. This dual-responsive therapeutic gene circuit mitigated both the inflammatory response as measured by bioluminescence reporter output and tissue-level degradation during conditions mimicking an arthritic flare.
Conclusions: The dual-responsive synthetic gene circuit developed herein responds to input cues from two key homeostatic transcriptional networks, enabling dynamic and tunable output. This proof-of-concept approach has the potential to match drug delivery to disease activity for optimal outcomes that addresses the complex environment of inflammatory arthritis.
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http://dx.doi.org/10.1101/2025.03.20.644403 | DOI Listing |
Genome Biol
September 2025
Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, Plön, Germany.
Background: Most RNA-seq datasets harbor genes with extreme expression levels in some samples. Such extreme outliers are usually treated as technical errors and are removed from the data before further statistical analysis. Here we focus on the patterns of such outlier gene expression to investigate whether they provide insights into the underlying biology.
View Article and Find Full Text PDFSci China Life Sci
September 2025
State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
Diurnal floret opening and closure (DFOC) is essential for rice reproductive development and hybrid breeding, yet transcriptional dynamics and underlying regulatory networks remain poorly characterized. Here, we conducted high-temporal-resolution transcriptomic analyses of lodicules to dissect DFOC regulatory networks in two japonica rice cultivars. Analysis of differentially expressed genes (DEGs) uncovered core genes shared by both cultivars, primarily associated with jasmonic acid (JA) signaling and cell wall remodeling.
View Article and Find Full Text PDFJ Theor Biol
September 2025
Department of Bioengineering, Indian Institute of Science, Bengaluru 560012, India. Electronic address:
Several computational models are available for representing the gene expression process, with each having their advantages and disadvantages. Phenomenological models are widely used as they make appropriate simplifications that aim to find a middle ground between accuracy and complexity. The existing phenomenological models compete in terms of how the transcription initiation process is approximated, to achieve high accuracy while having the lowest complexity possible.
View Article and Find Full Text PDFPlant J
September 2025
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
Genome imbalance, resulting from varying the dosage of individual chromosomes (aneuploidy), has a more detrimental effect than changes in complete sets of chromosomes (haploidy/polyploidy). This imbalance is likely due to disruptions in stoichiometry and interactions among macromolecular assemblies. Previous research has shown that aneuploidy causes global modulation of protein-coding genes (PCGs), microRNAs, and transposable elements (TEs), affecting both the varied chromosome (cis-located) and unvaried genome regions (trans-located) across various taxa.
View Article and Find Full Text PDFAm J Reprod Immunol
September 2025
Department of Laboratory Animal Science, Kunming Medical University, Kunming, China.
Objective: To explore B cell infiltration-related genes in endometriosis (EM) and investigate their potential as diagnostic biomarkers.
Methods: Gene expression data from the GSE51981 dataset, containing 77 endometriosis and 34 control samples, were analyzed to detect differentially expressed genes (DEGs). The xCell algorithm was applied to estimate the infiltration levels of 64 immune and stromal cell types, focusing on B cells and naive B cells.