Literature Watch

Diagnosis of Oral Cancer With Deep Learning. A Comparative Test Accuracy Systematic Review

Deep learning - Mon, 2025-03-31 06:00

Oral Dis. 2025 Mar 31. doi: 10.1111/odi.15330. Online ahead of print.

ABSTRACT

OBJECTIVE: To directly compare the diagnostic accuracy of deep learning models with human experts and other diagnostic methods used for the clinical detection of oral cancer.

METHODS: Comparative diagnostic studies involving patients with photographic images of oral mucosal lesions (cancer or non-cancer) were included. Only studies using deep learning methods were eligible. Medline, EMBASE, Scopus, Google Scholar, and ClinicalTrials.gov were searched until September 2024. QUADAS-C assessed the risk of bias. A Bayesian meta-analysis compared diagnostic test accuracy.

RESULTS: Eight studies were included, none of which had a low risk of bias. Three studies compared deep learning versus human experts. The difference in sensitivity favored deep learning by 0.024 (95% CI: -0.093, 0.206), while the difference in specificity favored human experts by -0.041 (95% CI: -0.218, 0.038). Two studies compared deep learning versus postgraduate medical students. The differences in sensitivity and specificity favored deep learning by 0.108 (95% CI: -0.038, 0.324) and by 0.010 (95% CI: -0.119, 0.111), respectively. Both comparisons provided low-level evidence.

CONCLUSIONS: Deep learning models showed comparable sensitivity and specificity to human experts. These models outperformed postgraduate medical students in terms of sensitivity. Prospective clinical trials are needed to evaluate the real-world performance of deep learning models.

PMID:40163741 | DOI:10.1111/odi.15330

Categories: Literature Watch

Childhood muscle growth: Reference curves for lower leg muscle volumes and their clinical application in cerebral palsy

Deep learning - Mon, 2025-03-31 06:00

Proc Natl Acad Sci U S A. 2025 Apr 8;122(14):e2416660122. doi: 10.1073/pnas.2416660122. Epub 2025 Mar 31.

ABSTRACT

Skeletal muscles grow substantially during childhood. However, quantitative information about the size of typically developing children's muscles is sparse. Here, the objective was to construct muscle-specific reference curves for lower leg muscle volumes in children aged 5 to 15 y. Volumes of 10 lower leg muscles were measured from magnetic resonance images of 208 typically developing children and 78 ambulant children with cerebral palsy. Deep learning was used to automatically segment the images. Reference curves for typical childhood muscle volumes were constructed with quantile regression. The median total leg muscle volume of a 15-y-old child is nearly five times that of a 5-y-old child. Between the ages of 5 and 15, boys typically have larger muscles than girls, both in absolute terms (medians are greater by 5 to 20%) and per unit of body weight (1 to 13%). Muscle volumes vary widely between children of a particular age: the range of volumes for the central 80% of the distribution (i.e., between the 10th and 90th centiles) is more than 40% of the median volume. Reference curves for individual muscle volumes have a similar shape to reference curves for total lower leg muscle volume. Confidence bands about the centile curves were wide, especially at the youngest and oldest ages. Nonetheless, the reference curves can be used with confidence to identify small-for-age muscles (centile < 10). We show that 56% of children with cerebral palsy in our cohort had total lower leg muscle volumes that were small-for-age and that 80% had at least one lower leg muscle that was small-for-age.

PMID:40163724 | DOI:10.1073/pnas.2416660122

Categories: Literature Watch

Artificial Intelligence for Classification of Endoscopic Severity of Inflammatory Bowel Disease: A Systematic Review and Critical Appraisal

Deep learning - Mon, 2025-03-31 06:00

Inflamm Bowel Dis. 2025 Mar 31:izaf050. doi: 10.1093/ibd/izaf050. Online ahead of print.

ABSTRACT

BACKGROUND: Endoscopic scoring indices for ulcerative colitis and Crohn's disease are subject to inter-endoscopist variability. There is increasing interest in the development of deep learning models to standardize endoscopic assessment of intestinal diseases. Here, we summarize and critically appraise the literature on artificial intelligence-assisted endoscopic characterization of inflammatory bowel disease severity.

METHODS: A systematic search of Ovid MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, and IEEE Xplore was performed to identify reports of AI systems used for endoscopic severity classification of IBD. Selected studies were critically appraised for methodological and reporting quality using APPRAISE-AI.

RESULTS: Thirty-one studies published between 2019 and 2024 were included. Of 31 studies, 28 studies examined endoscopic classification of ulcerative colitis and 3 examined Crohn's disease. Researchers sought to accomplish a wide range of classification tasks, including binary and multilevel classification, based on still images or full-length colonoscopy videos. Overall scores for study quality ranged from 41 (moderate quality) to 64 (high quality) out of 100, with 28 out of 31 studies within the moderate quality range. The highest-scoring domains were clinical relevance and reporting quality, while the lowest-scoring domains were robustness of results and reproducibility.

CONCLUSIONS: Multiple AI models have demonstrated the potential for clinical translation for ulcerative colitis. Research concerning the endoscopic severity assessment of Crohn's disease is limited and should be further explored. More rigorous external validation of AI models and increased transparency of data and codes are needed to improve the quality of AI studies.

PMID:40163659 | DOI:10.1093/ibd/izaf050

Categories: Literature Watch

A Systematic Review of Advances in Infant Cry Paralinguistic Classification: Methods, Implementation, and Applications

Deep learning - Mon, 2025-03-31 06:00

JMIR Rehabil Assist Technol. 2025 Feb 18. doi: 10.2196/69457. Online ahead of print.

ABSTRACT

BACKGROUND: Effective communication is essential for human interaction, yet infants can only express their needs through various types of suggestive cries. Traditional approaches of interpreting infant cries are often subjective, inconsistent, and slow leaving gaps in timely, precise caregiving responses. A precise interpretation of infant cries can potentially provide valuable insights into the infant's health, needs, and well-being, enabling prompt medical or caregiving actions.

OBJECTIVE: This study seeks to systematically review the advancements in methods, coverage, deployment schemes, and applications of infant cry classification over the last 24 years. The review focuses on the different infant cry classification techniques, feature extraction methods, and the practical applications. Furthermore, we aimed to identify recent trends and directions in the field of infant cry signal processing to address both academic and practical needs.

METHODS: A systematic literature review was conducted by using nine electronic databases: Cochrane Database of Systematic Reviews, JSTOR, Web of Science Core Collection, Scopus, PubMed, ACM, MEDLINE, IEEE Xplore, and Google Scholar. A total of 5904 search results were initially retrieved, with 126 studies meeting the eligibility criteria after screening by two independent reviewers. The methodological quality of the studies was assessed using the Cochrane risk-of-bias tool version 2 (RoB2), with 92% (n=116) of the studies indicating a low risk of bias and 8% (n=10) of the studies showing some concerns regarding bias. The overall quality assessment was performed using the TRIPOD (Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis) guidelines. The data analysis was conducted using R version 3.64.

RESULTS: Notable advancements in infant cry classification methods were realized, particularly from 2019 onwards employing machine learning, deep learning, and hybrid approaches. Common audio features included Mel-frequency cepstral coefficients (MFCCs), spectrograms, pitch, duration, intensity, formants, zero-crossing rate and chroma. Deployment methods included mobile applications and web-based platforms for real-time analysis with 90% (n=113) of the remaining models remained undeployed to real world applications. Denoising techniques and federated learning were limitedly employed to enhance model robustness and ensure data confidentiality from 5% (n=6) of the studies. Some of the practical applications spanned healthcare monitoring, diagnostics, and caregiver support.

CONCLUSIONS: The evolution of infant cry classification methods has progressed from traditional classical statistical methods to machine learning models but with minimal considerations of data privacy, confidentiality, and ultimate deployment to the practical use. Further research is thus proposed to develop standardized foundational audio multimodal approaches, incorporating a broader range of audio features and ensuring data confidentiality through methods such as federated learning. Furthermore, a preliminary layer is proposed for denoising the cry signal before the feature extractions stage. These improvements will enhance the accuracy, generalizability, and practical applicability of infant cry classification models in diverse healthcare settings.

PMID:40163619 | DOI:10.2196/69457

Categories: Literature Watch

Deep Learning with Reflection High-Energy Electron Diffraction Images to Predict Cation Ratio in Sr(2x)Ti(2(1-x))O(3) Thin Films

Deep learning - Mon, 2025-03-31 06:00

Nano Lett. 2025 Mar 31. doi: 10.1021/acs.nanolett.5c00787. Online ahead of print.

ABSTRACT

Machine learning (ML) with in-situ diagnostics offers a transformative approach to accelerate, understand, and control thin film synthesis by uncovering relationships between synthesis conditions and material properties. In this study, we demonstrate the application of deep learning to predict the stoichiometry of Sr2xTi2(1-x)O3 thin films using reflection high-energy electron diffraction images acquired during pulsed laser deposition. A gated convolutional neural network trained for regression of the Sr atomic fraction achieved accurate predictions with a small dataset of 31 samples. Explainable AI techniques revealed a previously unknown correlation between diffraction streak features and cation stoichiometry in Sr2xTi2(1-x)O3 thin films. Our results demonstrate how ML can be used to transform a ubiquitous in-situ diagnostic tool, that is usually limited to qualitative assessments, into a quantitative surrogate measurement of continuously valued thin film properties. Such methods are critically needed to enable real-time control, autonomous workflows, and accelerate traditional synthesis approaches.

PMID:40163590 | DOI:10.1021/acs.nanolett.5c00787

Categories: Literature Watch

Anticancer drug response prediction integrating multi-omics pathway-based difference features and multiple deep learning techniques

Deep learning - Mon, 2025-03-31 06:00

PLoS Comput Biol. 2025 Mar 31;21(3):e1012905. doi: 10.1371/journal.pcbi.1012905. Online ahead of print.

ABSTRACT

Individualized prediction of cancer drug sensitivity is of vital importance in precision medicine. While numerous predictive methodologies for cancer drug response have been proposed, the precise prediction of an individual patient's response to drug and a thorough understanding of differences in drug responses among individuals continue to pose significant challenges. This study introduced a deep learning model PASO, which integrated transformer encoder, multi-scale convolutional networks and attention mechanisms to predict the sensitivity of cell lines to anticancer drugs, based on the omics data of cell lines and the SMILES representations of drug molecules. First, we use statistical methods to compute the differences in gene expression, gene mutation, and gene copy number variations between within and outside biological pathways, and utilized these pathway difference values as cell line features, combined with the drugs' SMILES chemical structure information as inputs to the model. Then the model integrates various deep learning technologies multi-scale convolutional networks and transformer encoder to extract the properties of drug molecules from different perspectives, while an attention network is devoted to learning complex interactions between the omics features of cell lines and the aforementioned properties of drug molecules. Finally, a multilayer perceptron (MLP) outputs the final predictions of drug response. Our model exhibits higher accuracy in predicting the sensitivity to anticancer drugs comparing with other methods proposed recently. It is found that PARP inhibitors, and Topoisomerase I inhibitors were particularly sensitive to SCLC when analyzing the drug response predictions for lung cancer cell lines. Additionally, the model is capable of highlighting biological pathways related to cancer and accurately capturing critical parts of the drug's chemical structure. We also validated the model's clinical utility using clinical data from The Cancer Genome Atlas. In summary, the PASO model suggests potential as a robust support in individualized cancer treatment. Our methods are implemented in Python and are freely available from GitHub (https://github.com/queryang/PASO).

PMID:40163555 | DOI:10.1371/journal.pcbi.1012905

Categories: Literature Watch

Model interpretability on private-safe oriented student dropout prediction

Deep learning - Mon, 2025-03-31 06:00

PLoS One. 2025 Mar 31;20(3):e0317726. doi: 10.1371/journal.pone.0317726. eCollection 2025.

ABSTRACT

Student dropout is a significant social issue with extensive implications for individuals and society, including reduced employability and economic downturns, which, in turn, drastically influence social sustainable development. Identifying students at high risk of dropping out is a major challenge for sustainable education. While existing machine learning and deep learning models can effectively predict dropout risks, they often rely on real student data, raising ethical concerns and the risk of information leakage. Additionally, the poor interpretability of these models complicates their use in educational management, as it is difficult to justify identifying a student as high-risk based on an opaque model. To address these two issues, we introduced for the first time a modified Preprocessed Kernel Inducing Points data distillation technique (PP-KIPDD), specializing in distilling tabular structured dataset, and innovatively employed the PP-KIPDD to reconstruct new samples that serve as qualified training sets simulating student information distributions, thereby preventing student privacy information leakage, which showed better performance and efficiency compared to traditional data synthesis techniques such as the Conditional Generative Adversarial Networks. Furthermore, we empower the classifiers credibility by enhancing model interpretability utilized SHAP (SHapley Additive exPlanations) values and elucidated the significance of selected features from an educational management perspective. With well-explained features from both quantitative and qualitative aspects, our approach enhances the feasibility and reasonableness of dropout predictions using machine learning techniques. We believe our approach represents a novel end-to-end framework of artificial intelligence application in the field of sustainable education management from the view of decision-makers, as it addresses privacy leakage protection and enhances model credibility for practical management implementations.

PMID:40163446 | DOI:10.1371/journal.pone.0317726

Categories: Literature Watch

Putting computational models of immunity to the test-An invited challenge to predict B.pertussis vaccination responses

Systems Biology - Mon, 2025-03-31 06:00

PLoS Comput Biol. 2025 Mar 31;21(3):e1012927. doi: 10.1371/journal.pcbi.1012927. Online ahead of print.

ABSTRACT

Systems vaccinology studies have been used to build computational models that predict individual vaccine responses and identify the factors contributing to differences in outcome. Comparing such models is challenging due to variability in study designs. To address this, we established a community resource to compare models predicting B. pertussis booster responses and generate experimental data for the explicit purpose of model evaluation. We here describe our second computational prediction challenge using this resource, where we benchmarked 49 algorithms from 53 scientists. We found that the most successful models stood out in their handling of nonlinearities, reducing large feature sets to representative subsets, and advanced data preprocessing. In contrast, we found that models adopted from literature that were developed to predict vaccine antibody responses in other settings performed poorly, reinforcing the need for purpose-built models. Overall, this demonstrates the value of purpose-generated datasets for rigorous and open model evaluations to identify features that improve the reliability and applicability of computational models in vaccine response prediction.

PMID:40163550 | DOI:10.1371/journal.pcbi.1012927

Categories: Literature Watch

Automated and High-throughput Microbial Monoclonal Cultivation and Picking Using The Single-cell Microliter-droplet Culture Omics System

Systems Biology - Mon, 2025-03-31 06:00

J Vis Exp. 2025 Mar 14;(217). doi: 10.3791/67925.

ABSTRACT

Pure bacterial cultures are essential for the study of microbial culturomics. Traditional methods based on solid plates, well plates, and micro-reactors are hindered by cumbersome procedures and low throughput, impeding the rapid progress of microbial culturomics research. To address these challenges, we had successfully developed the Single-cell Microliter-droplet Culture Omics System (MISS cell), an automated high-throughput platform that utilizes droplet microfluidic technology for microbial monoclonal isolation, cultivation, and screening. This system can generate a large number of single-cell droplets and cultivate, screen, and collect monoclonal colonies in a short time, facilitating an integrated process from microbial isolation to picking. In this protocol, we demonstrated its application using the isolation and cultivation of human gut microbiota as an example and compared the microbial isolation efficiency, monoclonal culture performance, and screening throughput using the solid-plate culture method. The experimental workflow was simple, and reagent consumption was very low. Compared to solid-plate culture methods, the MISS cell could cultivate a greater diversity of gut microbiota species, offering significant potential and value for microbial culturomics research.

PMID:40163395 | DOI:10.3791/67925

Categories: Literature Watch

Deep Learning-Enhanced Hand-Driven Microfluidic Chip for Multiplexed Nucleic Acid Detection Based on RPA/CRISPR

Systems Biology - Mon, 2025-03-31 06:00

Adv Sci (Weinh). 2025 Mar 31:e2414918. doi: 10.1002/advs.202414918. Online ahead of print.

ABSTRACT

The early detection of high-risk human papillomavirus (HR-HPV) is crucial for the assessment and improvement of prognosis in cervical cancer. However, existing PCR-based screening methods suffer from inadequate accessibility, which dampens the enthusiasm for screening among grassroots populations, especially in resource-limited areas, and contributes to the persistently high mortality rate of cervical cancer. Here, a portable system is proposed for multiplexed nucleic acid detection, termed R-CHIP, that integrates Recombinase polymerase amplification (RPA), CRISPR detection, Hand-driven microfluidics, and an artificial Intelligence Platform. The system can go from sample pre-processing to results readout in less than an hour with simple manual operation. Optimized for sensitivity of 10-17 M for HPV-16 and 10-18 M for HPV-18, R-CHIP has an accuracy of over 95% in 300 tests on clinical samples. In addition, a smartphone microimaging system combined with the ResNet-18 deep learning model is used to improve the readout efficiency and convenience of the detection system, with initial prediction accuracies of 96.0% and 98.0% for HPV-16 and HPV-18, respectively. R-CHIP, as a user-friendly and intelligent detection platform, has great potential for community-level HR-HPV screening in resource-constrained settings, and contributes to the prevention and early diagnosis of other diseases.

PMID:40163382 | DOI:10.1002/advs.202414918

Categories: Literature Watch

Twisted Sister1: an agravitropic mutant of bread wheat (Triticum aestivum) with altered root and shoot architectures

Systems Biology - Mon, 2025-03-31 06:00

Plant J. 2025 Apr;122(1):e70122. doi: 10.1111/tpj.70122.

ABSTRACT

We identified a mutant of hexaploid wheat (Triticum aestivum) with impaired responses to gravity. The mutant, named Twisted Sister1 (TS1), had agravitropic roots that were often twisted along with altered shoot phenotypes. Roots of TS1 were insensitive to externally applied auxin, with the genetics and physiology suggestive of a mutated AUX/IAA transcription factor gene. Hexaploid wheat possesses over 80 AUX/IAA genes, and sequence information did not identify an obvious candidate. Bulked segregant analysis of an F2 population mapped the mutation to chromosome 5A, and subsequent mapping located the mutation to a 41 Mbp region. RNA-seq identified the TraesCS5A03G0149800 gene encoding a TaAUX/IAA protein to be mutated in the highly conserved domain II motif. We confirmed TraesCS5A03G0149800 as underlying the mutant phenotype by generating transgenic Arabidopsis thaliana. Analysis of RNA-seq data suggested broad similarities between Arabidopsis and wheat for the role of AUX/IAA genes in gravity responses, although there were marked differences. Here we show that the sequenced wheat genome, along with previous knowledge of the physiology of gravity responses from other plant species, gene mapping, RNA-seq, and expression in Arabidopsis have enabled the cloning of a key wheat gene that defines plant architecture.

PMID:40162979 | DOI:10.1111/tpj.70122

Categories: Literature Watch

FGF19 is a biomarker associated with prognosis and immunity in colorectal cancer

Systems Biology - Mon, 2025-03-31 06:00

Int J Immunopathol Pharmacol. 2025 Jan-Dec;39:3946320251324401. doi: 10.1177/03946320251324401. Epub 2025 Mar 31.

ABSTRACT

OBJECTIVE: This study aimed to investigate the relationship between fibroblast growth factor 19 (FGF19) and the prognosis and immune infiltration of colorectal cancer (CRC) and identify the related genes and pathways influencing the onset and progression of CRC.

INTRODUCTION: The potential of FGF19 to guide the prognosis of CRC and inform immunotherapeutic strategies warrants further investigation.

METHODS: We performed Quantitative Real-Time PCR to assess the expression of FGF19 and conducted a bioinformatics analysis to evaluate the impact of FGF19 expression on the clinical prognosis of CRC. We also analyzed the association between FGF19 expression and immune cell infiltration in CRC, and explored the related genes and pathways through which FGF19 influences CRC development.

RESULTS: CRC patients with higher FGF19 expression exhibited a poorer prognosis. In terms of the Receiver Operating Characteristic (ROC), FGF19 achieved an area under the curve (AUC) of 0.904. FGF19 expression correlated with the N stage, M stage, and pathological stage in patients with CRC. Functional enrichment analysis revealed significant enrichment of FGF19 in pathways associated with tumor development. ssGSEA and Spearman correlation analysis demonstrated that FGF19 expression was linked to tumor immune cells. We discovered that FGF19 is closely related to neutrophil extracellular traps (NETs), which play a significant role in the immune microenvironment.

CONCLUSION: FGF19 is a key gene associated with immunity and prognosis in CRC patients. Our findings suggest that FGF19 may influence CRC progression by promoting NETs expression, which leads to suppression of immune cells.

PMID:40162957 | DOI:10.1177/03946320251324401

Categories: Literature Watch

Copper Nanoparticle Decorated Multilayer Nanocoatings for Controlled Nitric Oxide Release and Antimicrobial Performance with Biosafety

Systems Biology - Mon, 2025-03-31 06:00

Biomacromolecules. 2025 Mar 31. doi: 10.1021/acs.biomac.4c01798. Online ahead of print.

ABSTRACT

Biomedical device-related bacterial infections are a leading cause of mortality, and traditional antibiotics contribute to resistance. Various surface modification strategies have been explored, but effective clinical solutions remain limited. This study introduces a novel antibacterial nanocoating with copper nanoparticles (CuNPs) that triggers localized nitric oxide (NO) release. The multilayered nanocoating is created using branched polyethylenimine (BPEI) and poly(acrylic acid) (PAA) via a Layer-by-Layer assembly method. CuNP-decorated nanocoatings are formed by reducing copper ions coordinated with amine/carboxylic acid groups. In a physiological environment, CuNPs oxidize to Cu(I), promoting NO release from endogenous NO donors. The nanocoating's thickness is adjustable to regulate amount of CuNPs and NO flux. The optimal thickness for effective NO release against Staphylococcus aureus and Pseudomonas aeruginosa is identified, preventing microbial adhesion and biofilm formation. Importantly, the coating remains cytocompatible due to minimal CuNPs, physiological NO levels, and stable coating properties under physiological conditions.

PMID:40162566 | DOI:10.1021/acs.biomac.4c01798

Categories: Literature Watch

Analyzing the brain's dynamic response to targeted stimulation using generative modeling

Systems Biology - Mon, 2025-03-31 06:00

Netw Neurosci. 2025 Mar 5;9(1):237-258. doi: 10.1162/netn_a_00433. eCollection 2025.

ABSTRACT

Generative models of brain activity have been instrumental in testing hypothesized mechanisms underlying brain dynamics against experimental datasets. Beyond capturing the key mechanisms underlying spontaneous brain dynamics, these models hold an exciting potential for understanding the mechanisms underlying the dynamics evoked by targeted brain stimulation techniques. This paper delves into this emerging application, using concepts from dynamical systems theory to argue that the stimulus-evoked dynamics in such experiments may be shaped by new types of mechanisms distinct from those that dominate spontaneous dynamics. We review and discuss (a) the targeted experimental techniques across spatial scales that can both perturb the brain to novel states and resolve its relaxation trajectory back to spontaneous dynamics and (b) how we can understand these dynamics in terms of mechanisms using physiological, phenomenological, and data-driven models. A tight integration of targeted stimulation experiments with generative quantitative modeling provides an important opportunity to uncover novel mechanisms of brain dynamics that are difficult to detect in spontaneous settings.

PMID:40161996 | PMC:PMC11949581 | DOI:10.1162/netn_a_00433

Categories: Literature Watch

Neural network embedding of functional microconnectome

Systems Biology - Mon, 2025-03-31 06:00

Netw Neurosci. 2025 Mar 5;9(1):159-180. doi: 10.1162/netn_a_00424. eCollection 2025.

ABSTRACT

Our brains operate as a complex network of interconnected neurons. To gain a deeper understanding of this network architecture, it is essential to extract simple rules from its intricate structure. This study aimed to compress and simplify the architecture, with a particular focus on interpreting patterns of functional connectivity in 2.5 hr of electrical activity from a vast number of neurons in acutely sliced mouse brains. Here, we combined two distinct methods together: automatic compression and network analysis. Firstly, for automatic compression, we trained an artificial neural network named NNE (neural network embedding). This allowed us to reduce the connectivity to features, be represented only by 13% of the original neuron count. Secondly, to decipher the topology, we concentrated on the variability among the compressed features and compared them with 15 distinct network metrics. Specifically, we introduced new metrics that had not previously existed, termed as indirect-adjacent degree and neighbor hub ratio. Our results conclusively demonstrated that these new metrics could better explain approximately 40%-45% of the features. This finding highlighted the critical role of NNE in facilitating the development of innovative metrics, because some of the features extracted by NNE were not captured by the currently existed network metrics.

PMID:40161994 | PMC:PMC11949542 | DOI:10.1162/netn_a_00424

Categories: Literature Watch

A pooled CRISPR screen identifies the Tα2 enhancer element as a driver of <em>TRA</em> expression in a subset of mature human T lymphocytes

Systems Biology - Mon, 2025-03-31 06:00

Front Immunol. 2025 Mar 14;16:1536003. doi: 10.3389/fimmu.2025.1536003. eCollection 2025.

ABSTRACT

The T cell receptor (TCR) is crucial for immune responses and represents a pivotal therapeutic target for CAR T cell therapies. However, which enhancer elements drive the constitutive expression of the TCRα chain in mature, peripheral T cells has not been well defined. Earlier work has suggested that enhancer alpha is inactive in mature peripheral T cells and that an alternative enhancer element in the 5' J region was driving TRA expression, while more recent findings indicated the opposite. Here, we applied a pooled CRISPR screen to probe a large genomic region proximal to the human TRA gene for the presence of regulatory elements. Interestingly, no sgRNA targeting the 5' J region was identified that influenced TRA expression. In contrast, several sgRNAs targeting enhancer alpha element Tα2, were identified that compromised the expression of the TCRα chain in Jurkat E6.1, as well as in a subset of human primary T cells. Our results provide new insights into the regulation of TRA in human peripheral T cells, advancing our understanding of how constitutive TRA expression is driven and regulated.

PMID:40160815 | PMC:PMC11949936 | DOI:10.3389/fimmu.2025.1536003

Categories: Literature Watch

Protein-constrained models pinpoints the role of underground metabolism in robustness of metabolic phenotypes

Systems Biology - Mon, 2025-03-31 06:00

iScience. 2025 Feb 28;28(3):112126. doi: 10.1016/j.isci.2025.112126. eCollection 2025 Mar 21.

ABSTRACT

Integrating enzyme parameters into constraint-based models have significantly improved the prediction of physiological and molecular traits. To further improve these models, we integrated promiscuous enzyme activities that jointly comprise the so-called underground metabolism by developing the CORAL toolbox, which increases the resolution of modeled enzyme resource allocation. Applying CORAL to a protein-constrained model of Escherichia coli revealed that underground metabolism resulted in larger flexibility of metabolic fluxes and enzyme usage. Simulating metabolic defects where the main activity of a promiscuous enzyme was blocked but promiscuous activities remained functional showed a small enzyme redistribution to the side activities. Further, blocking pairs of main activities showed that non-promiscuous enzymes exhibited larger impact on growth than promiscuous enzymes. These simulations showed that promiscuous enzymes can compensate for these defects, in line with experimental evidence. Together, our results indicated that promiscuous enzyme activities are vital to maintain robust metabolic function and growth.

PMID:40160425 | PMC:PMC11951047 | DOI:10.1016/j.isci.2025.112126

Categories: Literature Watch

Dynamic Plasma Membrane Topography Linked With Arp2/3 Actin Network Induction During Cell Shape Change

Systems Biology - Mon, 2025-03-31 06:00

Bioessays. 2025 Mar 31:e70004. doi: 10.1002/bies.70004. Online ahead of print.

ABSTRACT

Recent studies show the importance of mesoscale changes to plasma membrane (PM) topography during cell shape change. Local folding and flattening of the cell surface is mechanosensitive, changing in response to both microenvironment structural elements and intracellular cytoskeletal activities. These topography changes elicit local mechanical signaling events that act in conjunction with molecular signal transduction pathways to remodel the cell cortex. Experimental manipulations of local PM curvature show its sufficiency for recruiting Arp2/3 actin network induction pathways. Additionally, studies of diverse cell shape changes-ranging from neutrophil migration to early Drosophila embryo cleavage to neural stem cell asymmetric division-show that local generation of PM folding is linked with local Arp2/3 actin network induction, which then remodels the PM topography during dynamic control of cell structure. These examples are reviewed in detail, together with known and potential causes of PM topography changes, downstream effects, and higher-order feedback.

PMID:40159841 | DOI:10.1002/bies.70004

Categories: Literature Watch

An Open-Label, Single and Multiple Dose Study to Evaluate the Pharmacokinetics and Safety of Fezolinetant in Healthy Chinese Female Subjects

Drug-induced Adverse Events - Mon, 2025-03-31 06:00

Drug Des Devel Ther. 2025 Mar 26;19:2243-2252. doi: 10.2147/DDDT.S486562. eCollection 2025.

ABSTRACT

PURPOSE: To evaluate pharmacokinetics (PK) and safety of fezolinetant after single-dose and multiple-dose administration of 15, 30, and 60 mg in healthy Chinese women.

PATIENTS AND METHODS: This was a fixed-sequence crossover study in 16 healthy Chinese female subjects, 18-45 years old. All received single doses of fezolinetant 15 mg, 30 mg or 60 mg with a 3-day washout. From Day 10, subjects received multiple doses of 30 mg fezolinetant once-daily for 7 days. PK parameters were obtained during the single- and multiple-dose periods. Safety assessments were based on adverse events, vital signs, and laboratory tests.

RESULTS: Fezolinetant exhibited rapid absorption, with median time of the maximum concentration (tmax) 1.50 to 1.75 hours after single-dose administration of fezolinetant tablets in the fasted state, followed by a decline in plasma levels, with a mean t1/2 of 6.12-7.69 hours at dose levels of 15, 30 and 60 mg. There was a dose-proportional increase in maximum concentration and total exposure for fezolinetant across the doses studied. Mean peak concentration (Cmax) values were 221, 439 and 834 ng/mL, for the 15, 30, and 60 mg doses, respectively. The drug exposure parameters had a low-to-moderate variability (21.1-39.7%). Minimum accumulation was observed after multiple doses. Metabolite ES259564 showed rapid formation following a single dose of fezolinetant, with a median tmax of 1.50-2.00 hours. Plasma levels then declined, with mean t1/2 ranging from 5.72-6.31 hours. Dose-proportional increases in Cmax and AUCinf were observed following single-doses of fezolinetant. Steady state was achieved on the second day after starting multiple-dose administration. In total, 3 (18.8%) subjects experienced 4 drug-related treatment-emergent adverse events; all mild in severity.

CONCLUSION: Linear PK was confirmed within the dose range of 15 to 60 mg in healthy Chinese women.

PMID:40160966 | PMC:PMC11955179 | DOI:10.2147/DDDT.S486562

Categories: Literature Watch

Anastrozole-induced interstitial lung disease followed by tamoxifen-induced agranulocytosis in a patient with breast cancer

Drug-induced Adverse Events - Mon, 2025-03-31 06:00

Int Cancer Conf J. 2024 Dec 28;14(2):91-96. doi: 10.1007/s13691-024-00742-x. eCollection 2025 Apr.

ABSTRACT

A 70-year-old woman with the breast cancer exhibited interstitial lung disease 20 months after the administration with anastrozole, which was performed as the post-operative adjuvant therapy. The drug-induced lymphocyte stimulation test revealed that anastrozole was responsible for the development of interstitial lung disease in this patient. The interstitial lung disease was effectively treated by prednisolone. Then, tamoxifen was used as an alternative therapy, resulting in the occurrence of agranulocytosis 24 days after the administration with tamoxifen. Both anastrozole and tamoxifen are widely used and are highly effective drugs for the treatment of breast cancer. However, the current patient shows that both drugs could cause, albeit very rare, serious side effects in some patients.

PMID:40160876 | PMC:PMC11950607 | DOI:10.1007/s13691-024-00742-x

Categories: Literature Watch

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