Unified cross-modality integration and analysis of T cell receptors and T cell transcriptomes by low-resource-aware representation learning.

Single-cell RNA sequencing (scRNA-seq) and T cell receptor sequencing (TCR-seq) are pivotal for investigating T cell heterogeneity. Integrating these modalities, which is expected to uncover profound insights in immunology that might otherwise go unnoticed with a single modality, faces computational challenges due to the low-resource characteristics of the multimodal data. Herein, we present UniTCR, a novel low-resource-aware multimodal representation learning framework designed for the unified cross-modality integration, enabling comprehensive T cell analysis. By designing a dual-modality contrastive learning module and a single-modality preservation module to effectively embed each modality into a common latent space, UniTCR demonstrates versatility in connecting TCR sequences with T cell transcriptomes across various tasks, including single-modality analysis, modality gap analysis, epitope-TCR binding prediction, and TCR profile cross-modality generation, in a low-resource-aware way. Extensive evaluations conducted on multiple scRNA-seq/TCR-seq paired datasets showed the superior performance of UniTCR, exhibiting the ability of exploring the complexity of immune system.

PAD4-dependent citrullination of nuclear translocation of GSK3ß promotes colorectal cancer progression via the degradation of nuclear CDKN1A.

Peptidylarginine deiminase 4 (PAD4), a Ca2+-dependent enzyme, catalyzes the conversion of arginine to citrulline and has been strongly associated with many malignant tumors. However, the molecular mechanisms of PAD4 in the development and progression of colorectal cancer (CRC) remain unclearly defined. In our study, PAD4 expression was increased in CRC tissues and cells, and was closely related to tumor size, lymph node metastasis. Moreover, the transcription factor KLF9 directly bound to PADI4 gene promoter, leading to overexpression of PAD4 in CRC cells, which augmented cell growth and migration. We revealed that PAD4 interacted with and citrullinated glycogen synthase kinase-3ß (GSK3ß) in CRC cells, and GSK3ß Arg-344 was the dominating PAD4-citrullination site. Furthermore, IgL2 and catalytic domains of PAD4 directly bound to the kinase domain of GSK3ß in CRC cells. Mechanistically, PAD4 promoted the transport of GSK3ß from the cytoplasm to the nucleus, thereby increasing the ubiquitin-dependent proteasome degradation of nuclear cyclin-dependent kinase inhibitor 1 (CDKN1A). Our study is the first to reveal the details of a critical PAD4/GSK3ß/CDKN1A signaling axis for CRC progression, and provides evidence that PAD4 is a potential diagnosis biomarker and therapeutic target in CRC.

The Impact of Atorvastatin on RANKL Expression in Rats during the Retention Stage after Orthodontic Tooth Movement.

Objective: To probe into the impact of atorvastatin on RANKL expression in rats during the retention stage after orthodontic tooth movement and its associated molecular mechanisms. Methods: After establishing an orthodontic tooth movement model, the left teeth of the retention-stage rats were the maintained side, and the right teeth were the nonmaintained side, which were given physiological saline or atorvastatin dosing at 7d, 14d, and 21d, respectively, by tube feeding, in order to keep the rats as a control group at the beginning of the retention stage. A model of the rat's upper jaw gypsum in each group was made at various time points to measure the distance at which the teeth relapsed. The pathological slices of the upper jaw arch were taken separately for TRAP staining observation. Results: Compared to the physiological saline group, the recurrence distance of rats in the atorvastatin group was visually lower (p < 0.05), and the number of bone-breaking cells was signally lower (p < 0.05); P-5b, PTH, VitD3, GC, IL-1, and IL-17 expressions (p < 0.05) were visually decreased, while IL-11 expression was elevated (p < 0.05). Conclusion: The atorvastatin given to rats during the retention stage after orthodontic tooth movement inhibits RANKL expression and may function through OPG/RANKL/RANK system.

Enhanced autophagy suppresses inflammation-mediated bone loss through ROCK1 signaling in bone marrow mesenchymal stem cells.

Bone marrow mesenchymal stem cells (BMSCs) have strong proliferative ability and multi-directional differentiation potential. Osteoarthritis is a degenerative joint disease that is closely related to the loss of osteogenic differentiation function of BMSCs. Autophagy, plays a crucial role in the maintenance of cellular functions, but its regulatory mechanism during the osteogenic differentiation of BMSCs remains unclear. In this study, we analyzed the differential gene networks and pathways during BMSC osteogenesis using bioinformatics, and further validated the regulatory roles of autophagy during the osteogenic differentiation of BMSCs in inflammatory condition in vitro. We found that Tumor necrosis factor alpha (TNF-α) treatment led to actin cytoskeleton rearrangements and inhibited osteogenic differentiation in BMSCs. In addition, TNF-α enhanced Rho-associated protein kinase 1 (ROCK1) expression and decreased autophagy activation. ROCK1 knockdown reduced Endoplasmic Reticulum stress (ER stress) and promoted autophagy, resulting reversion of osteogenic differentiation in BMSCs under inflammatory condition. Rapamycin reversed the TNF-α-induced decrease in osteogenesis of BMSCs, assessed by alkaline phosphatase (ALP) activity and Alizarin staining. Autophagy treated with inhibitor 3-Methyladenine (3-MA) further increased TNF-α-induced osteogenesis inhibition of BMSCs. Collectively, these results indicate that ER stress and dysfunction of autophagy promote inflammation-induced bone loss through the activation of ROCK1 signaling in BMSCs.

MiRNA-20b/SUFU/Wnt axis accelerates gastric cancer cell proliferation, migration and EMT.

Previous research has found that miRNA-20b is highly expressed in gastric cancer (GC), however, its function and underlying mechanism are not clear. Wnt signaling pathway, implicated in tumorigeneisis, is activated in more than 30% of GC. We would like to characterize the biological behavior of miRNA-20b in terms of modulating Wnt/ß-catenin signaling and EMT. We showed that miRNA-20b inhibitors suppressed Topflash/Fopflash dependent luciferase activity and the ß-catenin nuclear translocation, resulting in inhibition of Wnt pathway activity and EMT. SUFU, negatively regulating Wnt and Hedgehog signaling pathway, was proved to be targeted by miRNA-20b. Moreover, additional knockdown of SUFU alleviated the inhibitory effect on Wnt pathway activity, EMT, cell proliferation/migration and colony formation caused by miRNA-20b inhibition. In summary, miRNA-20b is an oncogenic miRNA and promoted cell proliferation, migration and EMT in GC partially by activating Wnt pathway via targeting SUFU.

Circ-LRP6 mediates epithelial-mesenchymal transition and autophagy in oral squamous cell carcinomas.

BACKGROUND: Tumor metastasis seriously affects the therapeutic effect and prognosis of cancer patients. Here, we studied the role of has_circ_0000378 (circ-LRP6) in oral squamous cell carcinoma (OSCC) metastasis to explore new ideas and schemes for clinical treatment. METHODS: The expressions of circ-LRP6 in OSCC and normal tissues from matched controls were measured by real-time PCR (RT-PCR). Levels of epithelial-mesenchymal transition (EMT) transcription factors, P62 and LC3B, were determined by Western blot analysis and immunofluorescence (IF) assay. Furthermore, we evaluated the effects of circ-LRP6 downregulation on migration, invasion, and autophagy using CCK8, transwell assays, transmission electron microscopy (TEM), and immunofluorescence (IF) assay. RESULTS: The expression of circ-LRP6 in OSCC tissues was high. Downregulation of circ-LRP6 reduced the EMT process of SCC-15 cells, as evidenced by increased E-cadherin and decreased vimentin and Zeb1 levels. Downregulation of circ-LRP6 also decreased autophagy as shown by increased levels of P62 and decreased LC3B in SCC-15 cells. Autophagy revulsant rapamycin (RAPA) rescued the inhibitory effect of circ-LRP6 on LC3B, vimentin, and Zeb1. CONCLUSIONS: circ-LRP6 promoted EMT and autophagy of OSCC and increased autophagy could rescue EMT in OSCC cells inhibited by circ-LRP6 siRNA.

iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak.

Emerging viral infections seriously threaten human health globally. Several challenges exist in identifying effective compounds against viral infections: (1) at the initial stage of a new virus outbreak, little information, except for its genome information, may be available; (2) although the identified compounds may be effective, they may be toxic in vivo and (3) cytokine release syndrome (CRS) triggered by viral infections is the primary cause of mortality. Currently, an integrative tool that takes all those aspects into consideration for identifying effective compounds to prevent viral infections is absent. In this study, we developed iDMer, as an integrative and mechanism-driven response system for addressing these challenges during the sudden virus outbreaks. iDMer comprises three mechanism-driven compound identification modules, that is, a virus-host interaction-oriented module, an autophagy-oriented module and a CRS-oriented module. As a one-stop integrative platform, iDMer incorporates compound toxicity evaluation and compound combination identification for virus treatment with clear mechanisms. iDMer was successfully tested on five viruses, including the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our results indicated that, for all five tested viruses, compounds that were reported in the literature or experimentally validated for virus treatment were enriched at the top, demonstrating the generalized effectiveness of iDMer. Finally, we demonstrated that combinations of the individual modules successfully identified combinations of compounds effective for virus intervention with clear mechanisms.

Benchmarking and integrating genome-wide CRISPR off-target detection and prediction.

Systematic evaluation of genome-wide Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) off-target profiles is a fundamental step for the successful application of the CRISPR system to clinical therapies. Many experimental techniques and in silico tools have been proposed for detecting and predicting genome-wide CRISPR off-target profiles. These techniques and tools, however, have not been systematically benchmarked. A comprehensive benchmark study and an integrated strategy that takes advantage of the currently available tools to improve predictions of genome-wide CRISPR off-target profiles are needed. We focused on the specificity of the traditional CRISPR SpCas9 system for gene knockout. First, we benchmarked 10 available genome-wide off-target cleavage site (OTS) detection techniques with the published OTS detection datasets. Second, taking the datasets generated from OTS detection techniques as the benchmark datasets, we benchmarked 17 available in silico genome-wide OTS prediction tools to evaluate their genome-wide CRISPR off-target prediction performances. Finally, we present the first one-stop integrated Genome-Wide Off-target cleavage Search platform (iGWOS) that was specifically designed for the optimal genome-wide OTS prediction by integrating the available OTS prediction algorithms with an AdaBoost ensemble framework.

Histone methyltransferase SET8 is regulated by miR-192/215 and induces oncogene-induced senescence via p53-dependent DNA damage in human gastric carcinoma cells.

Gastric cancer (GC) is the most common cancer throughout the world. Despite advances of the treatments, detailed oncogenic mechanisms are largely unknown. In our previous study, we investigated microRNA (miR) expression profiles in human GC using miR microarrays. We found miR-192/215 were upregulated in GC tissues. Then gene microarray was implemented to discover the targets of miR-192/215. We compared the expression profile of BGC823 cells transfected with miR-192/215 inhibitors, and HFE145 cells transfected with miR-192/-215 mimics, respectively. SET8 was identified as a proposed target based on the expression change of more than twofold. SET8 belongs to the SET domain-containing methyltransferase family and specifically catalyzes monomethylation of H4K20me. It is involved in diverse functions in tumorigenesis and metastasis. Therefore, we focused on the contributions of miR-192/215/SET8 axis to the development of GC. In this study, we observe that functionally, SET8 regulated by miR-192/215 is involved in GC-related biological activities. SET8 is also found to trigger oncogene-induced senescence (OIS) in GC in vivo and in vitro, which is dependent on the DDR (DNA damage response) and p53. Our findings reveal that SET8 functions as a negative regulator of metastasis via the OIS-signaling pathway. Taken together, we investigated the functional significance, molecular mechanisms, and clinical impact of miR-192/215/SET8/p53 in GC.

Data imbalance in CRISPR off-target prediction.

For genome-wide CRISPR off-target cleavage sites (OTS) prediction, an important issue is data imbalance-the number of true OTS recognized by whole-genome off-target detection techniques is much smaller than that of all possible nucleotide mismatch loci, making the training of machine learning model very challenging. Therefore, computational models proposed for OTS prediction and scoring should be carefully designed and properly evaluated in order to avoid bias. In our study, two tools are taken as examples to further emphasize the data imbalance issue in CRISPR off-target prediction to achieve better sensitivity and specificity for optimized CRISPR gene editing. We would like to indicate that (1) the benchmark of CRISPR off-target prediction should be properly evaluated and not overestimated by considering data imbalance issue; (2) incorporation of efficient computational techniques (including ensemble learning and data synthesis techniques) can help to address the data imbalance issue and improve the performance of CRISPR off-target prediction. Taking together, we call for more efforts to address the data imbalance issue in CRISPR off-target prediction to facilitate clinical utility of CRISPR-based gene editing techniques.

Tautomerism and bioactivities of curcumenol, a common sesquiterpenoid widely existing in edible plants.

Curcumenol was firstly revealed as a pair of hemiacetal-ketone tautomers in solutions by using temperature variation 1H-NMR experiments, 2D NMR, and chemical methods. Quantum chemical calculation allowed the explanation of its spectroscopic behavior. An antioxidative SAR study on its derivatives verified the tautomeric bio-significance. Curcumenol also remarkably enhanced myogenic differentiation and mitochondrial function.

κ-Carrageenan Enhances Lipopolysaccharide-Induced Interleukin-8 Secretion by Stimulating the Bcl10-NF-κB Pathway in HT-29 Cells and Aggravates C. freundii-Induced Inflammation in Mice.

Background. The dietary usage of carrageenan as common food additive has increased observably over the last 50 years. But there is substantial controversy about its safety. Methods. We investigated whether the κ-carrageenan could enhance lipopolysaccharide-induced IL-8 expression by studying its actions on the TLR4-NF-κB pathway. The aggravating effect of κ-carrageenan on Citrobacter freundii DBS100-induced intestinal inflammation was also investigated in a mouse model. Results. Our data show that κ-carrageenan pretreatment promoted LPS-induced IL-8 expression in HT-29 cells. Although CD14, MD-2, and TLR4 were upregulated, the binding of LPS was not enhanced. However, the pathway of Bcl10-NF-κB was triggered. Interestingly, κ-carrageenan competitively blocked the binding of FITC-LPS. Furthermore, pretreatment with κ-carrageenan for one week previous to gavage with C. freundii DBS100 markedly aggravated weight loss, mortality, and colonic damage. The secretion of cytokines was unbalanced and the ratio of Tregs was decreased significantly. In addition, κ-carrageenan, together with C. freundii DBS100, enhanced the transcription and secretion of TLR4 and NF-κB. Conclusions. κ-Carrageenan can synergistically activate LPS-induced inflammatory through the Bcl10-NF-κB pathway, as indicated by its aggravation of C. freundii DBS100-induced colitis in mice. General Significance. Our results suggest that κ-carrageenan serves as a potential inflammatory agent that magnifies existing intestinal inflammation.

Left atrial function examination of healthy individuals with 2D speckle-tracking imaging.

The aim of the present study was to determine the left atrial (LA) function of healthy individuals of various ages by examining their LA strain and time-to-peak (TP) using 2D speckle-tracking imaging (2DSTI). In addition, the study investigated the potential value of STI in clinical applications. The 142 volunteers were divided into three age groups, namely, young adult, middle-aged and elderly. Images were obtained from examining the volunteers via echocardiography, 2D apical four-chamber, apical two-chamber and apical left ventricular longitudinal views. Following the examinations, an STI technique was applied to acquire the strain curves of the LA wall, which determined the strains and TPs. LA strains of the three age groups showed that the strain of the inferior segment was higher compared with that of the central segment, whereas the central segment was higher than that of the superior segment. The inferior segment of the strain of the elderly group decreased as age increased compared with the young adult and middle-aged groups. The central segment of the elderly group was lower than the young adult and middle-aged groups. As age increased, the TP of the inferior segment showed longer duration in the elderly group compared with the other two groups. The elderly and the middle-aged groups showed a longer central TP compared with the young adult group. No statistical significance was observed between the elderly and middle-aged groups. STI demonstrated objective and accurate examination results of the LA function, which provide a novel approach for the early monitoring of potential subclinical diseases in LA function.

The response of type 2 quorum sensing in Klebsiella pneumoniae to a fluctuating culture environment.

Bacterial cells communicate with one another using chemical signaling molecules. This phenomenon is termed quorum sensing (QS). QS in Klebsiella pneumoniae is mediated by the synthesis of interspecies autoinducer 2 (AI-2), a furanosyl borate diester molecule. The response of Type 2 QS to environmental cues such as carbon sources, the initial pH of the medium, and boracic acid was investigated in the present study using a Vibrio harveyi BB170 reporter assay and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis. The results show that glucose can affect AI-2 synthesis to the greatest extent, and 3.0% glucose can stimulate K. pneumoniae to produce more AI-2, with a four times increase in activity compared with that of the control culture. According to our previous research, Type 2 QS in K. pneumoniae is luxS dependent. Therefore, the close relationship between glucose concentration and luxS transcription level was confirmed with qRT-PCR technology. The results show that the response of QS to a fluctuating glucose concentration was observed as a change in the amount of luxS RNA transcripts. A maximum of luxS transcription appeared during the exponential growth phase when the glucose concentration was 30.0 g/L. At the same time, AI-2 production was also slightly impacted by the low initial pH. It is noteworthy that the addition of boracic acid at microdosage (0.1 g/L) can also induce AI-2 synthesis. Presumably, in K. pneumoniae, the 4,5-dihydroxy-2,3-pentanedione cyclizes by the addition of borate and loss of water, is hydrated, and is converted to the final AI-2 signaling molecule.

A luxS-dependent transcript profile of cell-to-cell communication in Klebsiella pneumoniae.

Bacterial cells communicate with one another using chemical signaling molecules. The phenomenon is termed quorum sensing. The quorum sensing bacterium Klebsiella pneumoniae secretes a non-homoserine lactone autoinducer in the exponential phase of growth as detected by a Vibrio harveyi reporter assay for autoinducer 2 (AI-2). To further investigate regulation of AI-2 production in K. pneumoniae, the pfs and luxS promoter fusions to an operon luxCDABE reporter were constructed in a low copy number vector, which is derived from pBR322 and pET28a((+)) and allows an examination of transcription of the genes in the pathway for signal synthesis. In this study, comparisons were performed on the cell densities of wild-type and recombinant K. pneumoniae, on the transcription activity of pfs and luxS promoters, and on the synthesis of AI-2 as a function of culture time. The results show that luxS expression is constitutive and the transcription of luxS is tightly correlated to AI-2 production in K. pneumoniae because the peaks of AI-2 production and transcriptional level of luxS appear at the same time point. The close relation of the profiles of luxS transcription and AI-2 production was also confirmed with quantitative reverse transcription-PCR technology. These facts support the idea that the quorum sensing in K. pneumoniae is luxS dependent.

Constructing distributed Hippocratic video databases for privacy-preserving online patient training and counseling.

Digital video now plays an important role in supporting more profitable online patient training and counseling, and integration of patient training videos from multiple competitive organizations in the health care network will result in better offerings for patients. However, privacy concerns often prevent multiple competitive organizations from sharing and integrating their patient training videos. In addition, patients with infectious or chronic diseases may not want the online patient training organizations to identify who they are or even which video clips they are interested in. Thus, there is an urgent need to develop more effective techniques to protect both video content privacy and access privacy . In this paper, we have developed a new approach to construct a distributed Hippocratic video database system for supporting more profitable online patient training and counseling. First, a new database modeling approach is developed to support concept-oriented video database organization and assign a degree of privacy of the video content for each database level automatically. Second, a new algorithm is developed to protect the video content privacy at the level of individual video clip by filtering out the privacy-sensitive human objects automatically. In order to integrate the patient training videos from multiple competitive organizations for constructing a centralized video database indexing structure, a privacy-preserving video sharing scheme is developed to support privacy-preserving distributed classifier training and prevent the statistical inferences from the videos that are shared for cross-validation of video classifiers. Our experiments on large-scale video databases have also provided very convincing results.

Integrating concept ontology and multitask learning to achieve more effective classifier training for multilevel image annotation.

In this paper, we have developed a new scheme for achieving multilevel annotations of large-scale images automatically. To achieve more sufficient representation of various visual properties of the images, both the global visual features and the local visual features are extracted for image content representation. To tackle the problem of huge intraconcept visual diversity, multiple types of kernels are integrated to characterize the diverse visual similarity relationships between the images more precisely, and a multiple kernel learning algorithm is developed for SVM image classifier training. To address the problem of huge interconcept visual similarity, a novel multitask learning algorithm is developed to learn the correlated classifiers for the sibling image concepts under the same parent concept and enhance their discrimination and adaptation power significantly. To tackle the problem of huge intraconcept visual diversity for the image concepts at the higher levels of the concept ontology, a novel hierarchical boosting algorithm is developed to learn their ensemble classifiers hierarchically. In order to assist users on selecting more effective hypotheses for image classifier training, we have developed a novel hyperbolic framework for large-scale image visualization and interactive hypotheses assessment. Our experiments on large-scale image collections have also obtained very positive results.