The combination of breast cancer PDO and mini-PDX platform for drug screening and individualized treatment.

The majority of advanced breast cancers exhibit strong aggressiveness, heterogeneity, and drug resistance, and currently, the lack of effective treatment strategies is one of the main challenges that cancer research must face. Therefore, developing a feasible preclinical model to explore tailored treatments for refractory breast cancer is urgently needed. We established organoid biobanks from 17 patients with breast cancer and characterized them by immunohistochemistry (IHC) and next generation sequencing (NGS). In addition, we in the first combination of patient-derived organoids (PDOs) with mini-patient-derived xenografts (Mini-PDXs) for the rapid and precise screening of drug sensitivity. We confirmed that breast cancer organoids are a high-fidelity three-dimension (3D) model in vitro that recapitulates the original tumour's histological and genetic features. In addition, for a heavily pretreated patient with advanced drug-resistant breast cancer, we combined PDO and Mini-PDX models to identify potentially effective combinations of therapeutic agents for this patient who were alpelisib + fulvestrant. In the drug sensitivity experiment of organoids, we observed changes in the PI3K/AKT/mTOR signalling axis and oestrogen receptor (ER) protein expression levels, which further verified the reliability of the screening results. Our study demonstrates that the PDO combined with mini-PDX model offers a rapid and precise drug screening platform that holds promise for personalized medicine, improving patient outcomes and addressing the urgent need for effective therapies in advanced breast cancer.

A systematic mutation analysis of 13 major SARS-CoV-2 variants.

SARS-CoV-2 evolves constantly with various novel mutations. Due to their enhanced infectivity, transmissibility and immune evasion, a comprehensive understanding of the association between these mutations and the respective functional changes is crucial. However, previous mutation studies of major SARS-CoV-2 variants remain limited. Here, we performed systematic analyses of full-length amino acids mutation, phylogenetic features, protein physicochemical properties, molecular dynamics and immune escape as well as pseudotype virus infection assays among thirteen major SARS-CoV-2 variants. We found that Omicron exhibited the most abundant and complex mutation sites, higher indices of hydrophobicity and flexibility than other variants. The results of molecular dynamics simulation suggest that Omicron has the highest number of hydrogen bonds and strongest binding free energy between the S protein and ACE2 receptor. Furthermore, we revealed 10 immune escape sites in 13 major variants, some of them were reported previously, but four of which (i.e. 339/373/477/496) are first reported to be specific to Omicron, whereas 462 is specific to Epslion. The infectivity of these variants was confirmed by the pseudotype virus infection assays. Our findings may help us understand the functional consequences of the mutations within various variants and the underlying mechanisms of the immune escapes conferred by the S proteins.

Epigenetic silencing of LDHB promotes hepatocellular carcinoma by remodeling the tumor microenvironment.

Lactate dehydrogenase B (LDHB) reversibly catalyzes the conversion of pyruvate to lactate or lactate to pyruvate and expressed in various malignancies. However, the role of LDHB in modulating immune responses against hepatocellular carcinoma (HCC) remains largely unknown. Here, we found that down-regulation of lactate dehydrogenase B (LDHB) was coupled with the promoter hypermethylation and knocking down the DNA methyltransferase 3A (DNMT 3A) restored LDHB expression levels in HCC cell lines. Bioinformatics analysis of the HCC cohort from The Cancer Genome Atlas revealed a significant positive correlation between LDHB expression and immune regulatory signaling pathways and immune cell infiltrations. Moreover, immune checkpoint inhibitors (ICIs) have shown considerable promise for HCC treatment and patients with higher LDHB expression responded better to ICIs. Finally, we found that overexpression of LDHB suppressed HCC growth in immunocompetent but not in immunodeficient mice, suggesting that the host immune system was involved in the LDHB-medicated tumor suppression. Our findings indicate that DNMT3A-mediated epigenetic silencing of LDHB may contribute to HCC progression through remodeling the tumor immune microenvironment, and LDHB may become a potential prognostic biomarker and therapeutic target for HCC immunotherapy.

Neoadjuvant tislelizumab plus stereotactic body radiotherapy and adjuvant tislelizumab in early-stage resectable hepatocellular carcinoma: the Notable-HCC phase 1b trial.

Notable-HCC (NCT05185531) is a phase 1b trial, aiming to evaluate the safety and preliminary effectiveness of neoadjuvant PD-1 blockade plus stereotactic body radiotherapy (SBRT) in early-stage resectable hepatocellular carcinoma (HCC). Twenty patients with HCC of BCLC stage 0-A received 3 × Gy SBRT and two cycles of tislelizumab, an anti-PD-1 monoclonal antibody before the curative HCC resection. Primary endpoints were the surgery delay, radiographic and pathological tumor response after the neoadjuvant therapy, safety and tolerability. During the neoadjuvant therapy, treatment-related adverse events (TRAEs) of grade 1-2 occurred in all 20 patients (100%), eight patients (40%) had grade 3 TRAEs, no grade 4 to 5 TRAE occurred, and all resolved without corticosteroids treatment. Per mRECIST, the objective response rate was 63.2% (12/19), with 3 complete response; the disease control rate was 100%. Two (10.5%) patients achieved complete pathological response. No surgery delay occurred. The neoadjuvant therapy did not increase the surgical difficulty or the incidence of complications. Secondary endpoints of disease-free survival and overall survival were not mature at the time of the analysis. Our pilot trial shows that neoadjuvant therapy with anti-PD-1 + SBRT is safe and promotes tumor responses in early-stage resectable HCC.

Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress.

The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.

A Smart Pesticide-Controlled Release Platform with Dual Stimuli-Responsive Functions for Enhanced Treatment of Plant Black Shank.

Realizing controllable input of botanical pesticides is conducive to improving pesticide utilization, reducing pesticide residues, and avoiding environmental pollution but is extremely challenging. Herein, we constructed a smart pesticide-controlled release platform (namely, SCRP) for enhanced treatment of tobacco black shank based on encapsulating honokiol (HON) with mesoporous hollow structured silica nanospheres covered with pectin and chitosan oligosaccharide (COS). The SCRP has a loading capacity of 12.64% for HON and could effectively protect HON from photolysis. Owing to the pH- and pectinase-sensitive property of the pectin, the SCRP could smartly release HON in response to a low pH or a rich pectinase environment in the black shank-affected area. Consequently, the SCRP effectively inhibits the infection of P. nicotianae on tobacco with a controlled rate for tobacco black shank of up to 87.50%, which is mainly due to the SCRP's capability in accumulating ROS, changing cell membrane permeability, and affecting energy metabolism. In addition, SCRP is biocompatible, and the COS layer enables SCRP to show a significant growth-promoting effect on tobacco. These results indicate that the development of a stimuli-responsive controlled pesticide release system for plant disease control is of great potential and value for practical agriculture production.

Integrated transcriptome and metabolome analysis revealed that HaMYB1 modulates anthocyanin accumulation to deepen sunflower flower color.

KEY MESSAGE: HanMYB1 was found to play positive roles in the modulation of anthocyanins metabolism based on the integrative analysis of different color cultivars and the related molecular genetic analyses. As a high value ornamental and edible crop with various colors, sunflowers (Helianthus annuus L.) provide an ideal system to understand the formation of flower color. Anthocyanins are major pigments in higher plants, which is associated with development of flower colors and ability of oxidation resistance. Here, we performed an integrative analysis of the transcriptome and flavonoid metabolome in five sunflower cultivars with different flower colors. According to differentially expressed genes and differentially accumulated flavonoids, these cultivars could be grouped into yellow and red. The results showed that more anthocyanins were accumulated in the red group flowers, especially the chrysanthemin. Some anthocyanins biosynthesis-related genes like UFGT (UDP-glycose flavonoid glycosyltransferase) also expressed more in the red group flowers. A MYB transcriptional factor, HanMYB1, was found to play vital positive roles in the modulation of anthocyanins metabolism by the integrative analysis. Overexpressed HanMYB1 in tobacco could deepen the flower color, increase the accumulation of anthocyanins and directly active the express of UFGT genes. Our findings indicated that the MYB transcriptional factors provide new insight into the dynamic regulation of the anthocyanin biosynthesis in facilitating sunflower color formation and anthocyanin accumulation.

Transcriptomics integrated with metabolomics reveal the competitive relationship between co-cultured Trichoderma asperellum HG1 and Bacillus subtilis Tpb55.

Microbial co-culture has proven to be an effective way to improve the ability of microorganisms to biocontrol. However, the interactive mechanisms of co-cultural microbes, especially between fungi and bacteria, have rarely been studied. By comparative analysis of morphology, transcriptomics and metabolomics, the interactive mechanisms of a sequential co-culture system of Trichoderma asperellum HG1 and Bacillus subtilis Tpb55 was explored in this study. The results revealed that co- culture has no significant effect on the growth and cell morphology of the two strains, but lead to mycelium wrinkling of HG1. RNA-seq analysis showed that co-culture significantly upregulated the HG1 genes concerning amino acid degradation and metabolism, proteolysis, resisting environmental stress, cell homeostasis, glycolysis, the glyoxylate cycle, and the citric acid (TCA) cycle, while Tpb55 genes related to cell homeostasis, spore formation and membrane fluidization were significantly upregulated, but genes associating to TCA, glycolytic cycles and fatty acid ß-oxidation were significantly downregulated. Metabolomic results revealed that some amino acids related to energy metabolism were significantly altered in HG1, whereas palmitic acid, which is related to cell membrane functions, was upregulated in Tpb55. These results indicated that HG1 could interfere with carbon metabolism and cell membrane fluidity, but accelerate spore formation of Tpb55. Biophysical assays further convinced that co-culture could decrease ATP content and inhibit ATPase activity in HG1, and could promote spore formation and reduce the cell membrane fluidity of Tpb55. In addition, co-culture also accelerated the production of intracellular anti-oomycete compound octhilinone. The above results indicate that HG1 and Tpb55 are mainly in a competitive relationship in the co culture system. These findings provide new insights for understanding the interaction mechanism between co cultured microbes.

USP29 activation mediated by FUBP1 promotes AURKB stability and oncogenic functions in gastric cancer.

BACKGROUND: Gastric cancer is a highly prevalent cancer type and the underlying molecular mechanisms are not fully understood. Ubiquitin-specific peptidase (USP) 29 has been suggested to regulate cell fate in several types of cancer, but its potential role in gastric carcinogenesis remains unclear. METHODS: The expression of USP29 in normal and gastric cancer tissues was analyzed by bioinformatics analysis, immunohistochemistry and immunoblot. Gene overexpression, CRISPR-Cas9 technology, RNAi, and Usp29 knockout mice were used to investigate the roles of USP29 in cell culture, xenograft, and benzo[a]pyrene (BaP)-induced gastric carcinogenesis models. We then delineated the underlying mechanisms using mass spectrometry, co-immunoprecipitation (Co-IP), immunoblot, ubiquitination assay, chromatin immunoprecipitation (ChIP), quantitative real-time PCR (qRT-PCR), and luciferase assays. RESULTS: In this study, we found that USP29 expression was significantly upregulated in gastric cancers and associated with poor patient survival. Ectopic expression of USP29 promoted, while depletion suppressed the tumor growth in vitro and in vivo mouse model. Mechanistically, transcription factor far upstream element binding protein 1 (FUBP1) directly activates USP29 gene transcription, which then interacts with and stabilizes aurora kinase B (AURKB) by suppressing K48-linked polyubiquitination, constituting a FUBP1-USP29-AURKB regulatory axis that medicates the oncogenic role of USP29. Importantly, systemic knockout of Usp29 in mice not only significantly decreased the BaP-induced carcinogenesis but also suppressed the Aurkb level in forestomach tissues. CONCLUSIONS: These findings uncovered a novel FUBP1-USP29-AURKB regulatory axis that may play important roles in gastric carcinogenesis and tumor progression, and suggested that USP29 may become a promising drug target for cancer therapy.

Transcriptome analysis reveals how cadmium promotes root development and accumulates in Apocynum venetum, a promising plant for greening cadmium-contaminated soil.

Cadmium (Cd) contamination poses a substantial threat the environment, necessitating effective remediation strategies. Phytoremediation emerges as a cost-efficient and eco-friendly approach for reducing Cd levels in the soil. In this study, the suitability of A. venetum for ameliorating Cd-contaminated soils was evaluated. Mild Cd stress promoted seedling and root growth, with the root being identified as the primary tissue for Cd accumulation. The Cd content of roots ranged from 0.35 to 0.55 mg/g under treatment with 10-50 µM CdCl2·2.5 H2O, and the bioaccumulation factor ranged from 28.78 to 84.43. Transcriptome sequencing revealed 20,292 unigenes, and 7507 nonredundant differentially expressed genes (DEGs) were identified across five comparison groups. DEGs belonging to the "MAPK signaling pathway-plant," "monoterpenoid biosynthesis," and "flavonoid biosynthesis pathway" exhibited higher expression levels in roots compared to stems and leaves. In addition, cytokinin-related DEGs, ROS scavenger genes, such as P450, glutathione-S-transferase (GST), and superoxide dismutase (SOD), and the cell wall biosynthesis-related genes, CSLG and D-GRL, were also upregulated in the root tissue, suggesting that Cd promotes root development. Conversely, certain ABC transporter genes, (e.g, NRAMP5), and some vacuolar iron transporters, predominantly expressed in the roots, displayed a strong correlation with Cd content, revealing the mechanism underlying the compartmentalized storage of Cd in the roots. KEGG enrichment analysis of DEGs showed that the pathways associated with the biosynthesis of flavonoids, lignin, and some terpenoids were significantly enriched in the roots under Cd stress, underscoring the pivotal role of these pathways in Cd detoxification. Our study suggests A. venetum as a potential Cd-contaminated phytoremediation plant and provides insights into the molecular-level mechanisms of root development promotion and accumulation mechanism in response to Cd stress.

Cattle manure hydrochar posed a higher efficiency in elevating tomato productivity and decreasing greenhouse gas emissions than plant straw hydrochar in a coastal soil.

Rehabilitation of degraded soil health using high-performance and sustainable measures are urgently required for restoring soil primary productivity and mitigating greenhouse gas (GHG) emission of coastal ecosystems. However, the effect of livestock manure derived hydrochar on GHG emission and plant productivity in the coastal salt-affected soils, one of blue carbon (C) ecosystems, was poorly understood. Therefore, a cattle manure hydrochar (CHC) produced at 220 °C was prepared to explore its effects and mechanisms on CH4 and N2O emissions and tomato growth and fruit quality in a coastal soil in comparison with corresponding hydrochars derived from plant straws, i.e., sesbania straw hydrochars (SHC) and reed straw hydrochars (RHC) using a 63-day soil column experiment. The results showed that CHC posed a greater efficiency in reducing the global warming potential (GWP, 54.6 % (36.7 g/m2) vs. 45.5-45.6 % (22.2-30.6 g/m2)) than those of RHC and SHC. For the plant growth, three hydrochars at 3 % (w/w) significantly increased dry biomass of tomato shoot and fruit by 12.4-49.5 % and 48.6-165 %, respectively. Moreover, CHC showed the highest promotion effect on shoot and fruit dry biomass of tomato, followed by SHC ≈ RHC. Application of SHC, CHC and RHC significantly elevated the tomato sweetness compared with CK, with the order of CHC (54.4 %) > RHC (35.6 %) > SHC (22.1 %). Structural equation models revealed that CHC-depressed denitrification and methanogen mainly contributed to decreased GHG emissions. Increased soil phosphorus availability due to labile phosphorus supply from CHC dominantly accounted for elevated tomato growth and fruit production. Comparably, SHC-altered soil properties (e.g., decreased pH and increased total carbon content) determined variations of GHG emission and tomato growth. The findings provide the high-performance strategies to enhance soil primary productivity and mitigate GHG emissions in the blue C ecosystems.

Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere.

The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.

Integrin αvß1 facilitates ACE2-mediated entry of SARS-CoV-2.

Integrins have been suggested to be involved in SARS-CoV-2 infection, but the underlying mechanisms remain largely unclear. This study aimed to investigate how integrins facilitate the ACE2-mediated cellular entry of SARS-CoV-2. We first tested the susceptibility of a panel of human cell lines to SARS-CoV-2 infection using the spike protein pseudotyped virus assay and examined the expression levels of integrins in these cell lines by qPCR, western blot and flow cytometry. We found that integrin αvß1 was highly enriched in the SARS-CoV-2 susceptible cell lines. Additional studies demonstrated that RGD (403-405)→AAA mutant was defective in binding to integrin αvß1 compared to its wild type counterpart, and anti-αvß1 integrin antibodies significantly inhibited the entry of SARS-CoV-2 into the cells. Further studies using mouse NIH3T3 cells expressing human ACE2, integrin αv, integrin ß1, and/or integrin αvß1 suggest that integrin αvß1 was unable to function as an independent receptor but could significantly facilitate the cellular entry of SASR-CoV-2. Finally, we observed that the Omicron exhibited a significant increase in the ACE2-mediated viral entry. Our findings may enhance our understanding of the pathogenesis of SARS-CoV-2 infection and offer potential therapeutic target for COVID-19.

Ensifer sp. GMS14 enhances soybean salt tolerance for potential application in saline soil reclamation.

Rhizosphere microbiomes play an important role in enhancing plant salt tolerance and are also commonly employed as bio-inoculants in soil remediation processes. Cultivated soybean (Glycine max) is one of the major oilseed crops with moderate salt tolerance. However, the response of rhizosphere microbes me to salt stress in soybean, as well as their potential application in saline soil reclamation, has been rarely reported. In this study, we first investigated the microbial communities of salt-treated and non-salt-treated soybean by 16S rRNA gene amplicon sequencing. Then, the potential mechanism of rhizosphere microbes in enhancing the salt tolerance of soybean was explored based on physiological analyses and transcriptomic sequencing. Our results suggested that Ensifer and Novosphingobium were biomarkers in salt-stressed soybean. One corresponding strain, Ensifer sp. GMS14, showed remarkable growth promoting characteristics. Pot experiments showed that GMS14 significantly improved the growth performance of soybean in saline soils. Strain GMS14 alleviated sodium ions (Na+) toxicity by maintaining low a Na+/K+ ratio and promoted nitrogen (N) and phosphorus (P) uptake by soybean in nutrient-deficient saline soils. Transcriptome analyses indicated that GMS14 improved plant salt tolerance mainly by ameliorating salt stress-mediated oxidative stress. Interestingly, GMS14 was evidenced to specifically suppress hydrogen peroxide (H2O2) production to maintain reactive oxygen species (ROS) homeostasis in plants under salt stress. Field experiments with GMS14 applications showed its great potential in saline soil reclamation, as evidenced by the increased biomass and nodulation capacity of GMS14-inoculated soybean. Overall, our findings provided valuable insights into the mechanisms underlying plant-microbes interactions, and highlighted the importance of microorganisms recruited by salt-stressed plant in the saline soil reclamation.

Phytotoxic and Antimicrobial Terrein Derivatives and Butenolides Isolated from the Endophytic Fungus Aspergillus terreus HT5.

Two new terrein derivatives, aspergilethers A and B (1 and 2), two known analogues (3 and 4), and three known butenolides (5-7) were isolated from the endophyte Aspergillus terreus HT5. Their structures were determined by spectroscopic analysis and ECD and NMR calculations. Interestingly, 1 and 2 had unpresented medium aliphatic side chains in terrein derivatives, with different absolute configurations at C-7, which was very scarce. (+)-Terrein (3) exhibited potent postemergence phytotoxicity toward Amaranthaceae, Portulacaceae, and Fabaceae, with MIC values of 250-1000 µg/mL. Transcriptome analysis and qRT-PCR suggested that (+)-terrein induced the transcriptional expression of aging-related genes to accelerate organ senescence and stimulated plant detoxification response. The conjugated system between keto carbonyl and double bonds in the cyclopentenone ring and side chain, and the configurations of C-2 and C-3, played critical roles in the phytotoxicity of terrein derivatives. Meanwhile, 3 was first reported to display moderate antioomycetes activity toward Phytophthora nicotiana.

Recombinant outer membrane vesicles delivering eukaryotic expression plasmid of cytokines act as enhanced adjuvants against Helicobacter pylori infection in mice.

The widespread prevalence of Helicobacter pylori (H. pylori) infection remains a great challenge to human health. The existing vaccines are not ideal for preventing H. pylori infection; thus, exploring highly effective adjuvants may improve the immunoprotective efficacy of H. pylori vaccines. In a previous study, we found that the outer membrane vesicles (OMVs), a type of nanoscale particle spontaneously produced by Gram-negative bacteria, could act as adjuvants to boost the immune responses to vaccine antigens. In this study, we explored the potential application of OMVs as delivery vectors for adjuvant development. We constructed recombinant OMVs containing eukaryotic expression plasmid of cytokines, including interleukin 17A or interferon-γ, and evaluated their function as adjuvants in combination with inactivated whole-cell vaccine (WCV) or UreB as vaccine antigens. Our results showed that recombinant OMVs as adjuvants could induce stronger humoral and mucosal immune responses in mice than wild-type H. pylori OMVs and the cholera toxin (CT) adjuvant. Additionally, the recombinant OMVs significantly promoted Th1/Th2/Th17-type immune responses. Furthermore, the recombinant OMV adjuvant induced more potent clearance of H. pylori than CT and wild-type OMVs. Our findings suggest that the recombinant OMVs coupled with cytokines may become potent adjuvants for the development of novel and effective vaccines against H. pylori infection.

TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing.

Single-molecule Real-time Isoform Sequencing (Iso-seq) of transcriptomes by PacBio can generate very long and accurate reads, thus providing an ideal platform for full-length transcriptome analysis. We present an integrated computational toolkit named TAGET for Iso-seq full-length transcript data analyses, including transcript alignment, annotation, gene fusion detection, and quantification analyses such as differential expression gene analysis and differential isoform usage analysis. We evaluate the performance of TAGET using a public Iso-seq dataset and newly sequenced Iso-seq datasets from tumor patients. TAGET gives significantly more precise novel splice site prediction and enables more accurate novel isoform and gene fusion discoveries, as validated by experimental validations and comparisons with RNA-seq data. We identify and experimentally validate a differential isoform usage gene ECM1, and further show that its isoform ECM1b may be a tumor-suppressor in laryngocarcinoma. Our results demonstrate that TAGET provides a valuable computational toolkit and can be applied to many full-length transcriptome studies.

Lipid alternations in the plasma of COVID-19 patients with various clinical presentations.

Background: COVID-19 is a highly infectious respiratory disease that can manifest in various clinical presentations. Although many studies have reported the lipidomic signature of COVID-19, the molecular changes in asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals remain elusive. Methods: This study combined a comprehensive lipidomic analysis of 220 plasma samples from 166 subjects: 62 healthy controls, 16 asymptomatic infections, and 88 COVID-19 patients. We quantified 732 lipids separately in this cohort. We performed a difference analysis, validated with machine learning models, and also performed GO and KEGG pathway enrichment analysis using differential lipids from different control groups. Results: We found 175 differentially expressed lipids associated with SASR-CoV-2 infection, disease severity, and viral persistence in patients with COVID-19. PC (O-20:1/20:1), PC (O-20:1/20:0), and PC (O-18:0/18:1) better distinguished asymptomatic infected individuals from normal individuals. Furthermore, some patients tested positive for SARS-CoV-2 nucleic acid by RT-PCR but did not become negative for a longer period of time (≥60 days, designated here as long-term nucleic acid test positive, LTNP), whereas other patients became negative for viral nucleic acid in a shorter period of time (≤45 days, designated as short-term nucleic acid test positive, STNP). We have found that TG (14:1/14:1/18:2) and FFA (4:0) were differentially expressed in LTNP and STNP. Conclusion: In summary, the integration of lipid information can help us discover novel biomarkers to identify asymptomatic individuals and further deepen our understanding of the molecular pathogenesis of COVID-19.

SMiT: symmetric mask transformer for disease severity detection.

PURPOSE: The application of deep learning methods to the intelligent diagnosis of diseases has been the focus of intelligent medical research. When dealing with image classification tasks, if the lesion area is small and uneven, the background image involved in the training will affect the ultimate accuracy in determining the extent of the lesion. We did not follow the traditional approach of building an intelligent system to assist physicians in diagnosis from the perspective of CNN models, but instead proposed a pure transformer framework that can be used for diagnostic grading of pathological images. METHODS: We propose a Symmetric Mask Pre-Training vision Transformer SMiT model for grading pathological cancer images. SMiT performs a symmetrically identical high probability sparsification of the input image token sequence at the first and last encoder layer positions to pre-train visual transformers, and the parameters of the baseline model are fine-tuned after loading the pre-training weights, allowing the model to concentrate more on extracting detailed features in the lesion region, effectively getting rid of the potential feature dependency problem. RESULTS: SMiT achieved 92.8% classification accuracy on 4500 histopathological images of colorectal cancer processed by Gaussian filter denoising. We validated the effectiveness and generalizability of this study's methodology on the publicly available diabetic retinopathy dataset APTOS2019 from Kaggle and achieved quadratic Cohen Kappa, accuracy and F1-score of 91.9%, 86.91% and 72.85%, respectively, which were 1-2% better than previous studies based on CNN models. CONCLUSION: SMiT uses a simpler strategy to achieve better results to assist physicians in making accurate clinical decisions, which can be an inspiration for making good use of the visual transformers in the field of medical imaging.

Effect of planting salt-tolerant legumes on coastal saline soil nutrient availability and microbial communities.

Soil salinization is a serious global environmental problem affecting sustainable development of agriculture. Legumes are excellent candidates for the phytoremediation of saline soils; however, how soil microbes mediate the amelioration of coastal saline ecosystems is unknown. In this study, two salt-tolerant legumes, Glycine soja and Sesbania cannabina were planted in coastal saline soil for three years. Soil nutrient availability and microbiota structure (including bacteria, fungi, and diazotrophs) were compared between the phytoremediated soils and control soil (barren land). Planting legumes reduced soil salinity, and increased total carbon, total nitrogen, and NO3--N contents. Among the soil microbiota, some nitrogen-fixing bacteria (e.g., Azotobacter) were enriched in legumes, which were probably responsible for soil nitrogen accumulation. The complexity of the bacterial, fungal, and diazotrophic networks increased significantly from the control to the phytoremediated soils, suggesting that the soil microbial community formed closer ecological interactions during remediation. Furthermore, the dominant microbial functions were chemoheterotrophy (24.75%) and aerobic chemoheterotrophy (21.97%) involved in the carbon cycle, followed by nitrification (13.68%) and aerobic ammonia oxidation (13.34%) involved in the nitrogen cycle. Overall, our findings suggested that G. soja and S. cannabina legumes were suitable for ameliorating saline soils as they decreased soil salinity and increased soil nutrient content, with microorganisms especially nitrogen-fixing bacteria, playing an important role in this remediation process.