Traditional Chinese medicine for functional gastrointestinal disorders and inflammatory bowel disease: narrative review of the evidence and potential mechanisms involving the brain-gut axis.

Functional gastrointestinal disorders (FGIDs) and inflammatory bowel disease (IBD) are common clinical disorders characterized by recurrent diarrhea and abdominal pain. Although their pathogenesis has not been fully clarified, disruptions in intestinal motility and immune function are widely accepted as contributing factors to both conditions, and the brain-gut axis plays a key role in these processes. Traditional Chinese Medicine (TCM) employs a holistic approach to treatment, considers spleen and stomach impairments and liver abnormality the main pathogenesis of these two diseases, and offers a unique therapeutic strategy that targets these interconnected pathways. Clinical evidence shows the great potential of TCM in treating FGIDs and IBD. This study presents a systematic description of the pathological mechanisms of FGIDs and IBD in the context of the brain-gut axis, discusses clinical and preclinical studies on TCM and acupuncture for the treatment of these diseases, and summarizes TCM targets and pathways for the treatment of FGIDs and IBD, integrating ancient wisdom with contemporary biomedical insights. The alleviating effects of TCM on FGID and IBD symptoms are mainly mediated through the modulation of intestinal immunity and inflammation, sensory transmission, neuroendocrine-immune network, and microbiota and their metabolism through brain-gut axis mechanisms. TCM may be a promising treatment option in controlling FGIDs and IBD; however, further high-quality research is required. This review provides a reference for an in-depth exploration of the interventional effects and mechanisms of TCM in FGIDs and IBD, underscoring TCM's potential to recalibrate the dysregulated brain-gut axis in FGIDs and IBD.

xQTLatlas: a comprehensive resource for human cellular-resolution multi-omics genetic regulatory landscape.

Understanding how genetic variants influence molecular phenotypes in different cellular contexts is crucial for elucidating the molecular and cellular mechanisms behind complex traits, which in turn has spurred significant advances in research into molecular quantitative trait locus (xQTL) at the cellular level. With the rapid proliferation of data, there is a critical need for a comprehensive and accessible platform to integrate this information. To meet this need, we developed xQTLatlas (http://www.hitxqtl.org.cn/), a database that provides a multi-omics genetic regulatory landscape at cellular resolution. xQTLatlas compiles xQTL summary statistics from 151 cell types and 339 cell states across 55 human tissues. It organizes these data into 20 xQTL types, based on four distinct discovery strategies, and spans 13 molecular phenotypes. Each entry in xQTLatlas is meticulously annotated with comprehensive metadata, including the origin of the tissue, cell type, cell state and the QTL discovery strategies utilized. Additionally, xQTLatlas features multiscale data exploration tools and a suite of interactive visualizations, facilitating in-depth analysis of cell-level xQTL. xQTLatlas provides a valuable resource for deepening our understanding of the impact of functional variants on molecular phenotypes in different cellular environments, thereby facilitating extensive research efforts.

Targeting RAC1 reactivates pyroptosis to reverse paclitaxel resistance in ovarian cancer by suppressing P21-activated kinase 4.

Pyroptosis may play an important role in the resistance of ovarian cancer (OC) to chemotherapy. However, the mechanism by which pyroptosis modulation can attenuate chemotherapy resistance has not been comprehensively studied in OC. Here, we demonstrated that RAS-associated C3 botulinum toxin substrate 1 (RAC1) is highly expressed in OC and is negatively correlated with patient outcomes. Through cell function tests and in vivo tumor formation tests, we found that RAC1 can promote tumor growth by mediating paclitaxel (PTX) resistance. RAC1 can mediate OC progression by inhibiting pyroptosis, as evidenced by high-throughput automated confocal imaging, the release of lactate dehydrogenase (LDH), the expression of the inflammatory cytokines IL-1ß/IL-18 and the nucleotide oligomerization domain-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome. Mechanically, RNA-seq, gene set enrichment analysis (GSEA), coimmunoprecipitation (Co-IP), mass spectrometry (MS), and ubiquitination tests further confirmed that RAC1 inhibits caspase-1/gasdermin D (GSDMD)-mediated canonical pyroptosis through the P21-activated kinase 4 (PAK4)/mitogen-activated protein kinase (MAPK) pathway, thereby promoting PTX resistance in OC cells. Finally, the whole molecular pathway was verified by the results of in vivo drug combination tests, clinical specimen detection and the prognosis. In summary, our results suggest that the combination of RAC1 inhibitors with PTX can reverse PTX resistance by inducing pyroptosis through the PAK4/MAPK pathway.

CellContrast: Reconstructing spatial relationships in single-cell RNA sequencing data via deep contrastive learning.

A vast amount of single-cell RNA sequencing (SC) data have been accumulated via various studies and consortiums, but the lack of spatial information limits its analysis of complex biological activities. To bridge this gap, we introduce CellContrast, a computational method for reconstructing spatial relationships among SC cells from spatial transcriptomics (ST) reference. By adopting a contrastive learning framework and training with ST data, CellContrast projects gene expressions into a hidden space where proximate cells share similar representation values. We performed extensive benchmarking on diverse platforms, including SeqFISH, Stereo-seq, 10X Visium, and MERSCOPE, on mouse embryo and human breast cells. The results reveal that CellContrast substantially outperforms other related methods, facilitating accurate spatial reconstruction of SC. We further demonstrate CellContrast's utility by applying it to cell-type co-localization and cell-cell communication analysis with real-world SC samples, proving the recovered cell locations empower more discoveries and mitigate potential false positives.

A Recombinant Mosaic HAs Influenza Vaccine Elicits Broad-Spectrum Immune Response and Protection of Influenza a Viruses.

The annual co-circulation of two influenza A subtypes, H1N1 and H3N2, viruses in humans poses significant public health threats worldwide. However, the continuous antigenic drift and shift of influenza viruses limited the effectiveness of current seasonal influenza vaccines, necessitating the development of new vaccines against both seasonal and pandemic viruses. One potential solution to this challenge is to improve inactivated vaccines by including multiple T-cell epitopes. In this study, we designed stabilized trimeric recombinant mosaic HA proteins named HAm, which contain the most potential HA T-cell epitopes of seasonal influenza A virus. We further evaluated the antigenicity, hemagglutinin activity, and structural integrity of HAm and compared its immunogenicity and efficacy to a commercial quadrivalent inactivated influenza vaccine (QIV) in mice. Our results demonstrated that the HAm vaccine was able to induce broadly cross-reactive antibodies and T-cell responses against homologous, heterologous, and heterosubtypic influenza-naive mice. Additionally, the HAm antigens outperformed QIV vaccine antigens by eliciting protective antibodies against panels of antigenically drifted influenza vaccine strains from 2009 to 2024 and protecting against ancestral viruses' lethal challenge. These results suggest that the HAm vaccine is a promising potential candidate for future universal seasonal and pandemic influenza vaccine development.

SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers.

Non-coding RNAs (ncRNAs) participate in multiple biological processes associated with cancers as tumor suppressors or oncogenic drivers. Due to their high stability in plasma, urine, and many other fluids, ncRNAs have the potential to serve as key biomarkers for early diagnosis and screening of cancers. During cancer progression, tumor heterogeneity plays a crucial role, and it is particularly important to understand the gene expression patterns of individual cells. With the development of single-cell RNA sequencing (scRNA-seq) technologies, uncovering gene expression in different cell types for human cancers has become feasible by profiling transcriptomes at the cellular level. However, a well-organized and comprehensive online resource that provides access to the expression of genes corresponding to ncRNA biomarkers in different cell types at the single-cell level is not available yet. Therefore, we developed the SCancerRNA database to summarize experimentally supported data on long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA biomarkers, as well as data on their differential expression at the cellular level. Furthermore, we collected biological functions and clinical applications of biomarkers to facilitate the application of ncRNA biomarkers to cancer diagnosis, as well as the monitoring of progression and targeted therapies. SCancerRNA also allows users to explore interaction networks of different types of ncRNAs, and build computational models in the future. SCancerRNA is freely accessible at http://www.scancerrna.com/BioMarker.

Full-scale polymer relaxation induced by single-chain confinement enhances mechanical stability of nanocomposites.

Polymer nanocomposites with tuning functions are exciting candidates for various applications, and most current research has focused on static mechanical reinforcement. Actually, under service conditions of complex dynamic interference, stable dynamic mechanical properties with high energy dissipation become more critical. However, nanocomposites often exhibit a trade-off between static and dynamic mechanics, because of their contradictory underlying physics between chain crosslinking and chain relaxation. Here, we report a general strategy for constructing ultra-stable dynamic mechanical complex fluid nanocomposites with high energy dissipation by infusing complex fluids into the nanoconfined space. The key is to tailor full-scale polymer dynamics across an exceptionally broad timescale by single-chain confinement. These materials exhibit stable storage modulus (100 ~ 102 MPa) with high energy dissipation (loss factor > 0.4) over a broad frequency range (10-1 ~ 107 Hz)/temperature range (-35 ~ 85°C). In the loss factor > 0.4 region, their dynamic mechanical stability (rate of modulus change versus temperature (k)) is 10 times higher than that of conventional polymer nanocomposites.

Recent Progress in Polyion Complex Nanoparticles with Enhanced Stability for Drug Delivery.

Polyion complex (PIC) nanoparticles, including PIC micelles and PICsomes, are typically composed of poly(ethylene glycol) block copolymers coupled with oppositely charged polyelectrolytes or therapeutic agents via electrostatic interaction. Due to a simple and rapid preparation process with high drug-loading efficiency, PIC nanoparticles are beneficial to maintaining the chemical integrity and high biological activity of the loaded drugs. However, the stability of PIC nanoparticles can be disrupted in high-ionic-strength solutions because electrostatic interaction is the DRIVING force; these disruptions can thus impair drug delivery. Herein, we summarize the advances in the use of PIC nanoparticles for delivery of charged drugs, focusing on the different chemical and physical strategies employed to enhance their stability, including enhancing the charge density, crosslinking, increasing hydrophobic interactions, forming hydrogen bonds, and the development of PIC-based gels. In particular, we describe the use of PIC nanoparticles to load peptide antibiotics targeting antibiotic-resistant and biofilm-related diseases and the use of nanoparticles that load chemotherapeutics and gaseous donors for cancer treatment. Furthermore, the application of PIC nanoparticles as magnetic resonance imaging contrast agents is summarized for the first time. Therefore, this review is of great significance for advances in the use of polymeric nanoparticles for functional drug delivery.

Large-Area Layered Membranes with Precisely Controlled Nano-Confined Channels.

Two-dimensional (2D) nanosheets-based membranes, which have controlled 2D nano-confined channels, are highly desirable for molecular/ionic sieving and confined reactions. However, it is still difficult to develop an efficient method to prepare large-area membranes with high stability, high orientation, and accurately adjustable interlayer spacing. Here, we present a strategy to produce metal ion cross-linked membranes with precisely controlled 2D nano-confined channels and high stability in different solutions using superspreading shear-flow-induced assembly strategy. For example, membranes based on graphene oxide (GO) exhibit interlayer spacing ranging from 8.0±0.1 Što 10.3±0.2 Å, with a precision of down to 1 Å. At the same time, the value of the orientation order parameter (f) of GO membranes is up to 0.95 and GO membranes exhibit superb stability in different solutions. The strategy we present, which can be generalized to the preparation of 2D nano-confined channels based on a variety of 2D materials, will expand the application scope and provide better performances of membranes.

Responses of colonization and development of periphytic biofilms to three typical tire wear particles with or without incubation-aging in migrating aqueous phases.

Understanding the behavior of tire wear particles (TWPs) and their impact on aquatic environments after aging is essential. This study explored the characteristics of TWPs generated using different methods (rolling friction, sliding friction, and cryogenic milling) and their transformation after exposure to environmental conditions mimicking runoff and sewage, focusing on their effects on river water and periphytic biofilms. Laboratory experiments indicate that at low exposure levels (0.1 mg/L), TWPs promoted biofilm growth, likely due to zinc release acting as a nutrient and the aggregation of particles serving as biofilm scaffolds. However, at higher concentrations (100 mg/L), TWPs inhibited biofilm development. This inhibition is linked to toxic byproducts like N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone and environmentally persistent free radicals, which reduce biofilm biomass, alter algal diversity, and decrease the production of essential biofilm components such as proteins and polysaccharides, consistent with the inhibitory behavior of TWPs on bis-(3'-5')-cyclic diguanosine monophosphate and quorum sensing signals, including acyl-homoserine lactone and autoinducer-2. Aging processes, particularly after simulated sewage treatment, further affect ecological impacts of TWPs, reducing the benefits observed at low concentrations and intensifying the negative effects at high concentrations. Contribution of here lies in systematically revealing the impact of TWPs on the development of aquatic biofilms, emphasizing the logical relationship between their aging characteristics, environmental behavior, and ecological risks. It assesses not only the release effects of typical additives and conventional size effects but also highlights the emerging photochemical toxicity (persistent free radicals), thus providing valuable insights into the aquatic ecological risk assessment of TWPs.