Antitumor effects of Cypaliuruside F from Cyclocarya paliurus on HepG2 cells.

An undescribed dammarane triterpenoid saponin Cypaliuruside F was isolated from the leaves of Cyclocarya paliurus in our preliminary study. The MTT assay, flow cytometry, cell scratch, and DAPI staining were used to detect the antitumor effects of Cypaliuruside F on HepG2 cells. Subsequently, network pharmacology and molecular docking analysis were used to analyse the key targets of Cypaliuruside F against HCC. In addition, a Western blot was performed to determine the effects of Cypaliuruside F on the expression of key proteins in HepG2 cells. The experimental results indicated that the damarane triterpenoid saponin Cypaliuruside F from Cyclocarya paliurus inhibits the proliferation of HepG2 cells by inducing apoptosis and cell cycle arrest. These changes may promote the apoptosis of HepG2 cells by inhibiting the expression of mTOR, STAT3, and Bcl-2 while activating Bax.

Postsurgical Analgesic Effectiveness of Ultrasound-Guided Parasternal Block After Auricular Reconstruction Using Autologous Costal Cartilage in Pediatric Patients: A Randomized Controlled Trial.

OBJECTIVE: To study the efficacy of ultrasound-guided parasternal block (US-PSI) in pediatric patients undergoing auricular reconstruction surgery. METHODS: For this study, the authors recruited 60 children between the ages of 5 and 12 years who underwent auricular reconstruction with autologous costal cartilage (ACC) to correct microtia. They were randomized to receive either ultrasound-guided modified parasternal block or periprostatic local infiltration anesthesia (PLIA), with 30 cases in each group. Ultrasound-guided parasternal block was administered following anesthesia induction, whereas PLIA was administered after ACC harvest. Lastly, following surgery, all children were provided with patient-controlled intravenous analgesia with sufentanil, and the numeric pain rating scale (NRS) was used to assess the intensity of pain. Our primary outcomes were the resting NRS pain scores and the NRS scores upon coughing at 1, 6, 12, 24, and 48 hours postsurgery. Sufentanil consumption within the first 24 hours of surgery, the mean duration to first ambulation, and the usage of rescue analgesics were our secondary outcomes. The authors also recorded the occurrence of undesirable side effects as well as more serious side effects like pneumothorax. RESULTS: Pediatric patients who were administered US-PSI showed significantly reduced NRS chest pain scores at 6 and 12 hours postsurgery compared to those who received PLIA (P<0.05). In addition, sufentanil consumption within the first 24 hours postsurgery, duration to first ambulation, and use of rescue analgesics were significantly lower among patients in the US-PSI group when compared to those in the PLIA group (P<0.05). CONCLUSIONS: This study found that US-PSI was a highly efficacious and safe technique for postsurgical analgesia following auricular reconstruction with ACC in pediatric patients. LEVEL OF EVIDENCE: Level II, therapeutic study.

Cadmium binding by the F-box domain induces p97-mediated SCF complex disassembly to activate stress response programs.

The F-box domain is a highly conserved structural motif that defines the largest class of ubiquitin ligases, Skp1/Cullin1/F-box protein (SCF) complexes. The only known function of the F-box motif is to form the protein interaction surface with Skp1. Here we show that the F-box domain can function as an environmental sensor. We demonstrate that the F-box domain of Met30 is a cadmium sensor that blocks the activity of the SCFMet30 ubiquitin ligase during cadmium stress. Several highly conserved cysteine residues within the Met30 F-box contribute to binding of cadmium with a KD of 8 µM. Binding induces a conformational change that allows for Met30 autoubiquitylation, which in turn leads to recruitment of the segregase Cdc48/p97/VCP followed by active SCFMet30 disassembly. The resulting inactivation of SCFMet30 protects cells from cadmium stress. Our results show that F-box domains participate in regulation of SCF ligases beyond formation of the Skp1 binding interface.

SUMOylation of annexin A6 retards cell migration and tumor growth by suppressing RHOU/AKT1-involved EMT in hepatocellular carcinoma.

BACKGROUND: The protein annexin A6 (AnxA6) is involved in numerous membrane-related biological processes including cell migration and invasion by interacting with other proteins. The dysfunction of AnxA6, including protein expression abundance change and imbalance of post-translational modification, is tightly related to multiple cancers. Herein we focus on the biological function of AnxA6 SUMOylation in hepatocellular carcinoma (HCC) progression. METHODS: The modification sites of AnxA6 SUMOylation were identified by LC-MS/MS and amino acid site mutation. AnxA6 expression was assessed by immunohistochemistry and immunofluorescence. HCC cells were induced into the epithelial-mesenchymal transition (EMT)-featured cells by 100 ng/mL 12-O-tetradecanoylphorbol-13-acetate exposure. The ability of cell migration was evaluated under AnxA6 overexpression by transwell assay. The SUMO1 modified AnxA6 proteins were enriched from total cellular proteins by immunoprecipitation with anti-SUMO1 antibody, then the SUMOylated AnxA6 was detected by Western blot using anti-AnxA6 antibody. The nude mouse xenograft and orthotopic hepatoma models were established to determine HCC growth and tumorigenicity in vivo. The HCC patient's overall survival versus AnxA6 expression level was evaluated by the Kaplan-Meier method. RESULTS: Lys579 is a major SUMO1 modification site of AnxA6 in HCC cells, and SUMOylation protects AnxA6 from degradation via the ubiquitin-proteasome pathway. Compared to the wild-type AnxA6, its SUMO site mutant AnxA6K579R leads to disassociation of the binding of AnxA6 with RHOU, subsequently RHOU-mediated p-AKT1ser473 is upregulated to facilitate cell migration and EMT progression in HCC. Moreover, the SENP1 deSUMOylates AnxA6, and AnxA6 expression is negatively correlated with SENP1 protein expression level in HCC tissues, and a high gene expression ratio of ANXA6/SENP1 indicates a poor overall survival of patients. CONCLUSIONS: AnxA6 deSUMOylation contributes to HCC progression and EMT phenotype, and the combination of AnxA6 and SENP1 is a better tumor biomarker for diagnosis of HCC grade malignancy and prognosis.

Research and implementation of multi-disease diagnosis on chest X-ray based on vision transformer.

Background: Disease diagnosis in chest X-ray images has predominantly relied on convolutional neural networks (CNNs). However, Vision Transformer (ViT) offers several advantages over CNNs, as it excels at capturing long-term dependencies, exploring correlations, and extracting features with richer semantic information. Methods: We adapted ViT for chest X-ray image analysis by making the following three key improvements: (I) employing a sliding window approach in the image sequence feature extraction module to divide the input image into blocks to identify small and difficult-to-detect lesion areas; (II) introducing an attention region selection module in the encoder layer of the ViT model to enhance the model's ability to focus on relevant regions; and (III) constructing a parallel patient metadata feature extraction network on top of the image feature extraction network to integrate multi-modal input data, enabling the model to synergistically learn and expand image-semantic information. Results: The experimental results showed the effectiveness of our proposed model, which had an average area under the curve value of 0.831 in diagnosing 14 common chest diseases. The metadata feature network module effectively integrated patient metadata, further enhancing the model's accuracy in diagnosis. Our ViT-based model had a sensitivity of 0.863, a specificity of 0.821, and an accuracy of 0.834 in diagnosing these common chest diseases. Conclusions: Our model has good general applicability and shows promise in chest X-ray image analysis, effectively integrating patient metadata and enhancing diagnostic capabilities.

What Factors Can Affect the Occurrence of Vertigo in Patients After Craniofacial Surgery in China?

Vertigo is a complication of craniomaxillofacial contour plastic surgery characterized by dizziness from hypovolemia in the cerebral hemispheres and brainstem. The authors analyzed the current status and influencing factors of postoperative vertigo in patients who undergo craniomaxillofacial contouring and discussed improvements in nursing strategies. The authors investigated 418 patients admitted to the authors' hospital who underwent craniomaxillofacial contouring between November 2020 and October 2023 and divided them into asymptomatic and symptomatic groups based on syncopal precursors or vertigo. The authors screened the current status of vertigo in patients after craniomaxillofacial contouring and the factors affecting vertigo and determined nursing improvement strategies. After craniomaxillofacial contouring, 125 patients had vertigo symptoms. Postcraniomaxillofacial contouring syncope or vertigo was associated with age, patient vertigo history, family history, depression, weight loss, blood pressure at admission, feeding before getting out of bed, and the level of intraoperative hemorrhage Multifactorial logistic regression analysis revealed the association between postcraniomaxillofacial contouring syncope or vertigo and vertigo history, depression, weight loss, feeding before getting out of bed, and intraoperative bleeding volume. Vertigo precursor incidence after craniomaxillofacial contouring surgery is 29.90%. Its influencing factors are complex, suggesting that nurses need to improve the perioperative health education of craniomaxillofacial contouring surgery and optimize the nursing care, encourage patients to have a reasonable diet or provide parenteral nutritional support preoperatively, help patients get out of bed early postoperatively, encourage them to have multiple meals in little quantity before getting out of bed, and control the intraoperative bleeding, to ensure patient safety postoperatively.

DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples.

Protein-protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes are the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for defining endogenous PPIs of cellular networks. While proteome-wide studies have been performed in cell lysates, intact cells and tissues, applications of XL-MS in clinical samples have not been reported. In this study, we adopted a DSBSO-based in vivo XL-MS platform to map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As a result, we have generated a PDX interaction network comprising 2,557 human proteins and identified interactions unique to breast cancer subtypes. Interestingly, most of the observed differences in PPIs correlated well with protein abundance changes determined by TMT-based proteome quantitation. Collectively, this work has demonstrated the feasibility of XL-MS analysis in clinical samples, and established an analytical workflow for tissue cross-linking that can be generalized for mapping PPIs from patient samples in the future to dissect disease-relevant cellular networks.

Novel inhibitors targeting the PGK1 metabolic enzyme in glycolysis exhibit effective antitumor activity against kidney renal clear cell carcinoma in vitro and in vivo.

Our previous research has revealed phosphoglycerate kinase 1 (PGK1) enhances tumorigenesis and sorafenib resistance of kidney renal clear cell carcinoma (KIRC) by regulating glycolysis, so that PGK1 is a promising drug target. Herein we performed structure-based virtual screening and series of anticancer pharmaceutical experiments in vitro and in vivo to identify novel small-molecule PGK1-targeted compounds. As results, the compounds CHR-6494 and Z57346765 were screened and confirmed to specifically bind to PGK1 and significantly reduced the metabolic enzyme activity of PGK1 in glycolysis, which inhibited KIRC cell proliferation in a dose-dependent manner. While CHR-6494 showed greater anti-KIRC efficacy and fewer side effects than Z57346765 on nude mouse xenograft model. Mechanistically, CHR-9464 impeded glycolysis by decreasing the metabolic enzyme activity of PGK1 and suppressed histone H3T3 phosphorylation to inhibit KIRC cell proliferation. Z57346765 induced expression changes of genes related to cell metabolism, DNA replication and cell cycle. Overall, we screened two novel PGK1 inhibitors, CHR-6494 and Z57346765, for the first time and discovered their potent anti-KIRC effects by suppressing PGK1 metabolic enzyme activity in glycolysis.

Comparing the Analgesic Effects Between the Pre- and Post-costal Cartilage Harvest Cohorts Using Ultrasound-Guided Deep Serratus Anterior Plane Block in Children with Microtia Undergoing Auricular Reconstruction: A Randomized Clinical Trial.

PURPOSE: Pain following costal cartilage harvest surgery is the most common complaint of auricular reconstruction (AR). Anesthesiologists are continuously searching for an effective postoperative pain control method. METHODS: This study was conducted from 10 April 2022 to 10 June 2022. Sixty children undergoing AR using costal cartilage were randomly assigned to either a serratus anterior plane block performed before costal cartilage harvest (SAPB-pre-cohort; n = 30) or the SAPB-post-cohort (Post-costal cartilage Harvest Cohort: n = 30). The primary endpoint measures were the Numerical Rating Scale (NRS) scores of the chest and ear pain degrees recorded at 1-, 6-, 12-, 24-, and 48-h after surgery. Intraoperative anesthetic and analgesic dosages, sufentanil consumption and rescue analgesia consumption during the first 24 h post-operation, cough score during extubation, extubation agitation score, length of stay, the extubation time, first ambulatory time, analgesia duration, and opioid-related adverse effects and SAPB-related adverse effects were the secondary endpoints. RESULTS: The rest and coughing NRS scores were significantly reduced in the SAPB-pre-cohort 6 and 12 h post-operation in comparison with the SAPB-post-cohort (rest 6 h p = 0.002, others p < 0.001). No significant difference in the NRS ear scores existed between the two cohorts (p > 0.05). The use of propofol and remifentanil for general anesthesia during the SAPB-pre-procedure was significantly reduced compared to the SAPB-post-group, with statistical significance (p < 0.001). Sufentanil consumption and rescue analgesia consumption were significantly reduced in the SAPB-pre-cohort (p = 0.001, p = 0.033). The extubation time and first ambulatory time were markedly shorter in the SAPB-pre-cohort (all p < 0.001). Analgesia duration was markedly longer in the SAPB-pre-cohort (p < 0.001). No significant differences were noted in the cough score during extubation, extubation agitation score, length of stay between the two cohorts (all p > 0.05). Opioid-related adverse effects occurred more in the SAPB-post-cohort, while there was no statistical significance (16.7 vs. 36.7%; p = 0.082). There were no blockade-related complications observed in either cohort. CONCLUSION: The analgesic effect of the SAPB-pre-cohort was better than the SAPB-post-cohort suggesting both efficacy and feasibility of preemptive analgesia. LEVEL OF EVIDENCE II: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Prokaryotic Expression and Affinity Purification of DDX3 Protein.

BACKGROUND: DDX3 is a protein with RNA helicase activity that is involved in a variety of biological processes, and it is an important protein target for the development of broad-spectrum antiviral drugs, multiple cancers and chronic inflammation. OBJECTIVE: The objective of this study is to establish a simple and efficient method to express and purify DDX3 protein in E. coli, and the recombinant DDX3 should maintain helicase activity for further tailor-made screening and biochemical function validation. METHODS: DDX3 cDNA was simultaneously cloned into pET28a-TEV and pNIC28-Bsa4 vectors and transfected into E. coli BL21 (DE3) to compare one suitable prokaryotic expression system. The 6×His-tag was fused to the C-terminus of DDX3 to form a His-tagging DDX3 fusion protein for subsequent purification. Protein dissolution buffer and purification washing conditions were optimized. The His-tagged DDX3 protein would bind with the Ni-NTA agarose by chelation and collected by affinity purification. The 6×His-tag fused with N-terminal DDX3 was eliminated from DDX3 by TEV digestion. A fine purification of DDX3 was performed by gel filtration chromatography. RESULTS: The recombinant plasmid pNIC28-DDX3, which contained a 6×His-tag and one TEV cleavage site at the N terminal of DDX3 sequence, was constructed for DDX3 prokaryotic expression and affinity purification based on considering the good solubility of the recombinant His-tagging DDX3, especially under 0.5 mM IPTG incubation at 18 °C for 18 h to obtain more soluble DDX3 protein. Finally, the exogenous recombinant DDX3 protein was obtained with more than 95% purity by affinity purification on the Ni-NTA column and removal of miscellaneous through gel filtration chromatography. The finely-purified DDX3 still retained its ATPase activity. CONCLUSION: A prokaryotic expression pNIC28-DDX3 system is constructed for efficient expression and affinity purification of bioactive DDX3 protein in E. coli BL21(DE3), which provides an important high-throughput screening and validation of drugs targeting DDX3.

Heterocyclic-Modified Imidazoquinoline Derivatives: Selective TLR7 Agonist Regulates Tumor Microenvironment against Melanoma.

Immunotherapy targeting the toll-like receptor 7 (TLR7) is a promising strategy for cancer treatment. Herein, we describe the design and synthesis of a series of imidazoquinoline-based TLR7 agonists and assess NF-κB pathway activation using HEK-Blue hTLR7 cells to identify the most potent small-molecule TLR7 agonist, SMU-L11 (EC50 = 0.024 ± 0.002 µM). In vitro experiments demonstrated that SMU-L11 specifically activated TLR7, resulting in recruitment of the MyD88 adaptor protein and activation of the NF-κB and MAPK signaling pathways. Moreover, SMU-L11 was found to exert immune-enhancing effects by significantly inducing the secretion of proinflammatory cytokines in murine dendritic cells, macrophages, and human peripheral blood mononuclear cells while promoting M1 macrophage polarization. In vivo studies using a B16-F10 mouse tumor model showed that SMU-L11 significantly enhanced immune cell activation and augmented CD4+ T and CD8+ T-cell proliferation, directly killing tumor cells and inhibiting tumor growth.

Effect of norepinephrine, vasopressin, and dopamine for survivals of the elderly with sepsis and pre-existing heart failure.

Our study focused on evaluating the effect of three common vasoactive drugs on the prognosis of elderly patients with sepsis and pre-existing heart failure. The Medical Information Mart for Intensive Care III database, Version 1.4, was used. Our study included critically ill older patients (aged ≥ 65 years) with sepsis and heart failure treated with vasoactive drugs. Patients were divided into norepinephrine group, norepinephrine combined with vasopressin group, and dopamine group. The baseline characteristics, primary outcome, and secondary outcome measures were compared among the three groups. In total, 1357 elderly patients were included (766 in norepinephrine group, 250 in norepinephrine combined with vasopressin group, and 341 in dopamine group). After propensity score matching, statistically significant differences in 28-d and 90-d mortality (P = 0.046, P = 0.031) were observed; meanwhile, there was a significant difference in the incidence of mechanical ventilation, AKI, and malignant arrhythmias. Cox regression analysis revealed that norepinephrine combined with vasopressin decreased 5-year survival statistically(P = 0.001). Multiple linear regression analysis indicated dopamine as an independent risk factor in reducing ICU and hospital length of stay (P = 0.001, P = 0.017). Logistic regression analysis showed dopamine was an independent risk factor for new-onset arrhythmias (P < 0.001), while norepinephrine combined with vasopressin was an independent risk factor for new-onset malignant arrhythmias (P < 0.001). Norepinephrine in combination with vasopressin decreased survival and increased the incidence of malignant arrhythmias in elderly sepsis patients with pre-existing heart failure. Dopamine alone reduces ICU and hospital length of stay but increases the new-onset arrhythmias.

2.5D transfer deep learning model for segmentation of contrast-enhancing lesions on brain magnetic resonance imaging of multiple sclerosis and neuromyelitis optica spectrum disorder.

Background: Multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD) are the two mimic autoimmune diseases of the central nervous system, which are rare in East Asia. Quantitative detection of contrast-enhancing lesions (CELs) on contrast-enhancing T1-weighted magnetic resonance (MR) images is of great significance for assessing the disease activity of MS and NMOSD. However, it is challenging to develop automatic segmentation algorithms due to the lack of data. In this work, we present an automatic segmentation model of CELs based on Fully Convolutional with Attention DenseNet (FCA-DenseNet) and transfer learning strategy to address the challenge of CEL quantification in small-scale datasets. Methods: A transfer learning approach was employed in this study, whereby pretraining was conducted using 77 MS subjects from the open access datasets (MICCAI 2016, MICCAI 2017, ISBI 2015) for white matter hyperintensity segmentation, followed by fine-tuning using 24 MS and NMOSD subjects from the local dataset for CEL segmentation. The proposed FCA-DenseNet combined the Fully Convolutional DenseNet and Convolutional Block Attention Module in order to improve the learning capability. A 2.5D data slicing strategy was used to process complex 3D MR images. U-Net, ResUNet, TransUNet, and Attention-UNet are used as comparison models to FCA-DenseNet. Dice similarity coefficient (DSC), positive predictive value (PPV), true positive rate (TPR), and volume difference (VD) are used as evaluation metrics to evaluate the performances of different models. Results: FCA-DenseNet outperforms all other models in terms of all evaluation metrics, with a DSC of 0.661±0.187, PPV of 0.719±0.201, TPR of 0.680±0.254, and VD of 0.388±0.334. Transfer learning strategy has achieved success in building segmentation models on a small-scale local dataset where traditional deep learning approaches fail to train effectively. Conclusions: The improved FCA-DenseNet, combined with transfer learning strategy and 2.5D data slicing strategy, has successfully addressed the challenges in constructing deep learning models on small-scale datasets, making it conducive to clinical quantification of brain CELs and diagnosis of MS and NMOSD.

SLCO4A1, as a novel prognostic biomarker of non­small cell lung cancer, promotes cell proliferation and migration.

Solute carrier organic anion transporter family member 4A1 (SLCO4A1) is a membrane transporter protein. The role of this molecule in non­small cell lung cancer (NSCLC) remains unclear. Bulk sequencing was carried out using early­stage NSCLC tissues with lymph node metastasis to identify SLCO4A1 that influences NSCLC cell proliferation, metastasis and prognosis. The in vitro functional assays carried out included the following: Cell Counting Kit­8, plate colony formation, Transwell and wound healing assays. The molecular techniques used included reverse transcription­quantitative PCR, western blotting and immunohistochemistry. The present study revealed the role of SLCO4A in NSCLC. SLCO4A1 was found to be expressed at high levels in NSCLC tissues and cells, and promotes cell proliferation, migration and invasion. Kaplan­Meier survival analysis indicated that patients with NSCLC and high expression of SLCO4A1 had a poor prognosis. SLCO4A was revealed to regulate the expression of the proliferation­related proteins Ki­67 and PCNA, and that of the extracellular matrix proteins vimentin and E­cadherin. Mechanistically, SLCO4A1 may affect the MAPK signaling pathway to promote NSCLC cell proliferation, migration and invasion. In addition, bioinformatics analysis demonstrated a strong association between SLCO4A1 and tumor infiltrating immune cells, highlighting its critical role in immune therapies such as immune checkpoint inhibitor treatment of patients with NSCLC.

Metabolomics reveals that chronic restraint stress alleviates carbon tetrachloride-induced hepatic fibrosis through the INSR/PI3K/AKT/AMPK pathway.

Hepatic fibrosis (HF) could be developed into liver cirrhosis or even hepatocellular carcinoma. Stress has an important role in the occurrence and development of various considerable diseases. However, the effect of a certain degree stress on HF is still controversial. In our study, stress was simulated with regular chronic restraint stress (CRS) and HF model was induced with CCl4 in mice. We found that CRS was able to attenuate CCl4-induced liver injury and fibrosis in mice. Surprisingly, behavioral analysis showed that the mice in the HF group exhibited depression-like behavior. Further, the metabolomic analysis revealed that 119 metabolites and 20 metabolic pathways were altered in mice liver, especially the betaine metabolism pathway. Combined with the results of Ingenuity Pathway Analysis (IPA), the key proteins INSR, PI3K, AKT, and p-AMPK were identified and verified, and the results showed that CRS could upregulate the protein levels and mRNA expression of INSR, PI3K, AKT, and p-AMPK in liver tissues of HF mice. It suggested that CRS alleviated CCl4-induced liver fibrosis in mice through upregulation of the INSR/PI3K/AKT/AMPK pathway. Proper stress might be a potential therapeutic strategy for the treatment of chronic liver disease, which provided new insights into the treatment of HF. KEY MESSAGES: Chronic restraint stress mitigated CCl4-induced liver injury and hepatic fibrosis. CCl4-induced liver fibrosis could cause depression-like behavior. Chronic restraint stress altered metabolomic profiles in hepatic fibrosis mice, especially the betaine metabolism pathway. Chronic restraint stress increased betaine levels in liver tissue. Chronic restraint stress regulated the INSR/PI3K/AKT/AMPK signaling pathway in hepatic fibrosis mice.

Computational Characterization of Undifferentially Expressed Genes with Altered Transcription Regulation in Lung Cancer.

A transcriptome profiles the expression levels of genes in cells and has accumulated a huge amount of public data. Most of the existing biomarker-related studies investigated the differential expression of individual transcriptomic features under the assumption of inter-feature independence. Many transcriptomic features without differential expression were ignored from the biomarker lists. This study proposed a computational analysis protocol (mqTrans) to analyze transcriptomes from the view of high-dimensional inter-feature correlations. The mqTrans protocol trained a regression model to predict the expression of an mRNA feature from those of the transcription factors (TFs). The difference between the predicted and real expression of an mRNA feature in a query sample was defined as the mqTrans feature. The new mqTrans view facilitated the detection of thirteen transcriptomic features with differentially expressed mqTrans features, but without differential expression in the original transcriptomic values in three independent datasets of lung cancer. These features were called dark biomarkers because they would have been ignored in a conventional differential analysis. The detailed discussion of one dark biomarker, GBP5, and additional validation experiments suggested that the overlapping long non-coding RNAs might have contributed to this interesting phenomenon. In summary, this study aimed to find undifferentially expressed genes with significantly changed mqTrans values in lung cancer. These genes were usually ignored in most biomarker detection studies of undifferential expression. However, their differentially expressed mqTrans values in three independent datasets suggested their strong associations with lung cancer.

Transcriptomic Analysis of the Reduction in Seed Oil Content through Increased Nitrogen Application Rate in Rapeseed (Brassica napus L.).

Nitrogen is essential for improving the seed oil yield of rapeseed (Brassica napus L.). However, the molecular mechanism by which increased nitrogen rates impact seed oil content is largely unknown. Therefore, a field experiment was conducted to determine how three nitrogen application rates (120, 240, and 360 kg ha-1) regulated seed oil content via transcriptomic analysis. The results showed that the seed yield and the protein and total N contents increased from N1 to N3, with average increases of 57.2%, 16.9%, and 79.5%, respectively. However, the seed oil content significantly decreased from N1 to N3, with an average decrease of 8.6%. These results were repeated over a number of years. The quantity of oil protein bodies observed under a transmission electron microscope was in accordance with the ultimate seed oil and protein contents. As the nitrogen application rate increased, a substantial number of genes involved in the photosynthesis, glycolysis, and phenylpropanoid biosynthesis pathways were up-regulated, as were TF families, such as AP2/ERF, MYB, and NAC. The newly identified genes were mainly involved in carbohydrate, lipid, and amino acid metabolism. Metabolic flux analysis showed that most of the genes involved in glycolysis and fatty acid biosynthesis had higher transcript levels in the early development stages. Our results provide new insights into the molecular regulation of rapeseed seed oil content through increased nitrogen application rates.

Lipid-anchored proteasomes control membrane protein homeostasis.

Protein degradation in eukaryotic cells is mainly carried out by the 26S proteasome, a macromolecular complex not only present in the cytosol and nucleus but also associated with various membranes. How proteasomes are anchored to the membrane and the biological meaning thereof have been largely unknown in higher organisms. Here, we show that N-myristoylation of the Rpt2 subunit is a general mechanism for proteasome-membrane interaction. Loss of this modification in the Rpt2-G2A mutant cells leads to profound changes in the membrane-associated proteome, perturbs the endomembrane system, and undermines critical cellular processes such as cell adhesion, endoplasmic reticulum-associated degradation and membrane protein trafficking. Rpt2G2A/G2A homozygous mutation is embryonic lethal in mice and is sufficient to abolish tumor growth in a nude mice xenograft model. These findings have defined an evolutionarily conserved mechanism for maintaining membrane protein homeostasis and underscored the significance of compartmentalized protein degradation by myristoyl-anchored proteasomes in health and disease.