ABSTRACT
In eukaryotic cells, organelles and the cytoskeleton undergo highly dynamic yet organized interactions capable of orchestrating complex cellular functions. Visualizing these interactions requires noninvasive, long-duration imaging of the intracellular environment at high spatiotemporal resolution and low background. To achieve these normally opposing goals, we developed grazing incidence structured illumination microscopy (GI-SIM) that is capable of imaging dynamic events near the basal cell cortex at 97-nm resolution and 266 frames/s over thousands of time points. We employed multi-color GI-SIM to characterize the fast dynamic interactions of diverse organelles and the cytoskeleton, shedding new light on the complex behaviors of these structures. Precise measurements of microtubule growth or shrinkage events helped distinguish among models of microtubule dynamic instability. Analysis of endoplasmic reticulum (ER) interactions with other organelles or microtubules uncovered new ER remodeling mechanisms, such as hitchhiking of the ER on motile organelles. Finally, ER-mitochondria contact sites were found to promote both mitochondrial fission and fusion.
Subject(s)
Endoplasmic Reticulum/metabolism , Microtubules/metabolism , Mitochondria/metabolism , Mitochondrial Dynamics , Animals , COS Cells , Cell Line, Tumor , Chlorocebus aethiops , Humans , Microscopy, FluorescenceABSTRACT
SNX32 is a member of the evolutionarily conserved Phox (PX) homology domain- and Bin/Amphiphysin/Rvs (BAR) domain- containing sorting nexin (SNX-BAR) family of proteins, which play important roles in sorting and membrane trafficking of endosomal cargoes. Although SNX32 shares the highest amino acid sequence homology with SNX6, and has been believed to function redundantly with SNX5 and SNX6 in retrieval of the cation-independent mannose-6-phosphate receptor (CI-MPR) from endosomes to the trans-Golgi network (TGN), its role(s) in intracellular protein trafficking remains largely unexplored. Here, we report that it functions in parallel with SNX1 in mediating epidermal growth factor (EGF)-stimulated postendocytic trafficking of the epidermal growth factor receptor (EGFR). Moreover, SNX32 interacts directly with EGFR, and recruits SNX5 to promote sorting of EGF-EGFR into multivesicular bodies (MVBs) for lysosomal degradation. Thus, SNX32 functions distinctively from other SNX-BAR proteins to mediate signaling-coupled endolysosomal trafficking of EGFR.
Subject(s)
Epidermal Growth Factor , ErbB Receptors , Lysosomes , Protein Transport , Sorting Nexins , Sorting Nexins/metabolism , Sorting Nexins/genetics , ErbB Receptors/metabolism , Lysosomes/metabolism , Humans , Protein Transport/physiology , Epidermal Growth Factor/metabolism , HeLa Cells , Endosomes/metabolism , trans-Golgi Network/metabolism , Multivesicular Bodies/metabolismABSTRACT
Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing the generation of oncogenic proteins involved in cancer hallmarks. In this study, we investigated the genes that encode RNA-binding proteins and identified potential splicing factors that contribute to the aberrant splicing applying a random forest classification model. The result suggested 56 splicing factors were related to the prognosis of 13 cancers, two SF complexes in liver hepatocellular carcinoma, and one SF complex in esophageal carcinoma. Further systematic bioinformatics studies on these cancer prognostic splicing factors and their related alternative splicing events revealed the potential regulations in a cancer-specific manner. Our analysis found high ILF2-ILF3 expression correlates with poor prognosis in LIHC through alternative splicing. These findings emphasize the importance of SFs as potential indicators for prognosis or targets for therapeutic interventions. Their roles in cancer exhibit complexity and are contingent upon the specific context in which they operate. This recognition further underscores the need for a comprehensive understanding and exploration of the role of SFs in different types of cancer, paving the way for their potential utilization in prognostic assessments and the development of targeted therapies.
Subject(s)
Alternative Splicing , Computational Biology , Gene Expression Regulation, Neoplastic , Machine Learning , Neoplasms , RNA Splicing Factors , Humans , RNA Splicing Factors/genetics , RNA Splicing Factors/metabolism , Prognosis , Alternative Splicing/genetics , Neoplasms/genetics , Computational Biology/methods , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , RNA Splicing/genetics , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Liver Neoplasms/genetics , Carcinoma, Hepatocellular/geneticsABSTRACT
Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in DRMref are browsable and searchable, with detailed annotations provided. Meanwhile, DRMref includes analyses of cellular composition, intratumoral heterogeneity, epithelial-mesenchymal transition, cell-cell interaction and differentially expressed genes in resistant cells. Notably, DRMref investigates the drug resistance mechanisms (e.g. Aberration of Drug's Therapeutic Target, Drug Inactivation by Structure Modification, etc.) in resistant cells. Additional enrichment analysis of hallmark/KEGG (Kyoto Encyclopedia of Genes and Genomes)/GO (Gene Ontology) pathways, as well as the identification of microRNA, motif and transcription factors involved in resistant cells, is provided in DRMref for user's exploration. Overall, DRMref serves as a unique single-cell-based resource for studying drug resistance, drug combination therapy and discovering novel drug targets.
Subject(s)
Databases, Factual , Drug Resistance , MicroRNAs , Neoplasms , Humans , Drug Resistance/genetics , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , MicroRNAs/genetics , Neoplasms/drug therapy , Neoplasms/genetics , InternetABSTRACT
Microhomology-mediated end joining (MMEJ), an error-prone DNA damage repair mechanism, frequently leads to chromosomal rearrangements due to its ability to engage in promiscuous end joining of genomic instability and also leads to increasing mutational load at the sequences flanking the breakpoints (BPs). In this study, we systematically investigated the homology sequences around the genomic breakpoint area of human fusion genes, which were formed by the chromosomal rearrangements initiated by DNA double-strand breakage. Since the RNA-seq data is the typical data set to check the fusion genes, for the known exon junction fusion breakpoints identified from RNA-seq data, we have to infer the high chance of genomic breakpoint regions. For this, we utilized the high feature importance score area calculated from our recently developed fusion BP prediction model, FusionAI and identified 151 K microhomologies among ~24 K fusion BPs in 20 K fusion genes. From our multiple bioinformatics studies, we found a relationship between sequence homologies and the immune system. This in-silico study will provide novel knowledge on the sequence homologies around the coded structural variants.
Subject(s)
Computational Biology , Neoplasms , Humans , Genomics , Neoplasms/genetics , Exons , Genomic InstabilityABSTRACT
Rapid visualization of latent fingerprints, preferably at their point of origin, is essential for effective crime scene evaluation. Here, we present a new class of green fluorescent protein chromophore-based fluorescent dyes (LFP-Yellow and LFP-Red) that can be used for real-time visualization of LFPs within 10 s. Compared with traditional chemical reagents for LFPs, these fluorescent dyes are completely water-soluble, exhibit low cytotoxicity, and are harmless to users. Level 1-3 details of the LFPs could be clearly revealed through "off-on" fluorescence signal readout. Additionally, the fluorescent dyes were constructed based on an imidazolinone core and so do not contain pyridine groups or metal ions, which ensures that the DNA is not contaminated during extraction and identification after the LFPs are treated with the dyes. Combined with our as-developed portable system for capturing LFPs, LFP-Yellow and LFP-Red enabled the rapid capture of LFPs. Therefore, these green fluorescent protein chromophore-based probes provide an approach for the rapid identification of individuals who were present at a crime scene.
Subject(s)
Fluorescent Dyes , Humans , Green Fluorescent Proteins , FluorescenceABSTRACT
The phytohormone auxin controls plant growth and development via TIR1-dependent protein degradation of canonical AUX/IAA proteins, which normally repress the activity of auxin response transcription factors (ARFs). IAA33 is a non-canonical AUX/IAA protein lacking a TIR1-binding domain, and its role in auxin signaling and plant development is not well understood. Here, we show that IAA33 maintains root distal stem cell identity and negatively regulates auxin signaling by interacting with ARF10 and ARF16. IAA33 competes with the canonical AUX/IAA repressor IAA5 for binding to ARF10/16 to protect them from IAA5-mediated inhibition. In contrast to auxin-dependent degradation of canonical AUX/IAA proteins, auxin stabilizes IAA33 protein via MITOGEN-ACTIVATED PROTEIN KINASE 14 (MPK14) and does not affect IAA33 gene expression. Taken together, this study provides insight into the molecular functions of non-canonical AUX/IAA proteins in auxin signaling transduction.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , DNA-Binding Proteins/metabolism , Gene Expression Regulation, Plant/drug effects , Indoleacetic Acids/pharmacology , Nuclear Proteins/metabolism , Plants, Genetically Modified/metabolism , Arabidopsis/drug effects , Arabidopsis/growth & development , Arabidopsis Proteins/genetics , DNA-Binding Proteins/genetics , Nuclear Proteins/genetics , Phosphorylation , Plant Growth Regulators/pharmacology , Plants, Genetically Modified/drug effects , Plants, Genetically Modified/growth & development , Proteolysis , Signal TransductionABSTRACT
Biomolecule-functionalized nanoparticles represent a type of promising biomaterials in biomedical applications owing to their excellent biocompatibility and versatility. DNA-based reactions on nanoparticles have enabled emerging applications including intelligent biosensors, drug delivery, and biomimetic devices. Among the reactions, strand hybridization is the critical step to control the sensitivity and specificity of biosensing, and the efficiency of drug delivery. However, a comprehensive understanding of DNA hybridization on nanoparticles is still lacking, which may differ from the process in homogeneous solutions. To address this limitation, coarse-grained model-based molecular dynamic simulation is harnessed to disclose the critical factors involved in intermolecular hybridization. Based on simulation guidance, DNA walker-based smart theranostic platform (DWTP) based on "on-particle" hybridization is developed, showing excellent consistency with simulation. DWTP is successfully applied for highly sensitive miRNA 21 detection and tumor-specific miRNA 21 imaging, driven by tumor-endogenous APE 1 enzyme. It enables the precise release of antisense oligonucleotide triggered by tumor-endogenous dual-switch miRNA 21 and APE 1, facilitating effective gene silencing therapy with high biosafety. The simulation of "on-particle" DNA hybridization has improved the corresponding biosensing performance and the release efficiency of therapeutic agents, representing a conceptually new approach for DNA-based device design.
Subject(s)
DNA , MicroRNAs , Theranostic Nanomedicine , DNA/chemistry , Theranostic Nanomedicine/methods , Humans , Nucleic Acid Hybridization , Nanoparticles/chemistry , Molecular Dynamics Simulation , Biosensing Techniques/methodsABSTRACT
The polar auxin transport is required for proper plant growth and development. D6 PROTEIN KINASE (D6PK) is required for the phosphorylation of PIN-FORMED (PIN) auxin efflux carriers to regulate auxin transport, while the regulation of D6PK stabilization is still poorly understood. Here, we found that Cytosolic ABA Receptor Kinases (CARKs) redundantly interact with D6PK, and the interactions are dependent on CARKs' kinase activities. Similarly, CARK3 also could interact with paralogs of D6PK, including D6PKL1, D6PKL2, and D6PKL3. The genetic analysis shows that D6PK acts the downstream of CARKs to regulate Arabidopsis growth, including hypocotyl, leaf area, vein formation, and the length of silique. Loss-of-function of CARK3 in overexpressing GFP-D6PK plants leads to reduce the level of D6PK protein, thereby rescues plant growth. In addition, the cell-free degradation assays indicate that D6PK is degraded through 26 S proteasome pathway, while the phosphorylation by CARK3 represses this process in cells. In summary, D6PK stabilization by the CARK family is required for auxin-mediated plant growth and development.
Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/growth & development , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis/enzymology , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/genetics , Phosphorylation , Indoleacetic Acids/metabolism , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/genetics , Cytosol/metabolism , Abscisic Acid/metabolism , Gene Expression Regulation, Plant , Protein Kinases/metabolism , Protein Kinases/genetics , Proteasome Endopeptidase Complex/metabolism , Plants, Genetically ModifiedABSTRACT
A novel series of 1,8-naphthalimide piperazinamide based benzenesulfonamides derivatives were designed and synthesized as carbonic anhydrase IX (CA IX) inhibitors and ferroptosis inducers for the treatment of triple-negative breast cancer (TNBC). The representative compound 9o exhibited more potent inhibitory activity and selective against CA IX over off-target CA II, compared with positive control SLC-0111. Molecular docking study was also performed to gain insights into the binding interactions of 9o in the binding pocket of CAIX. Moreover, compound 9o exhibited superior antitumor activities against breast cancer cells under hypoxia than that of normoxia conditions. Mechanism studies revealed that compound 9o could act as DNA intercalator and effectively suppressed cell migration, arrested the cell cycle at G1/S phase and induced apoptosis in MDA-MB-231 cells, while inducing ferroptosis accompanied by the dissipation of MMP and the elevation intracellular levels of ROS. Notably, in vivo studies demonstrated that 9o effectively inhibited tumor growth and metastasis in a highly metastatic murine breast cancer 4 T1 xenograft model. Taken together, this study suggests that compound 9o represents a potent and selective CA IX inhibitor and ferroptosis inducer for the treatment of TNBC.
Subject(s)
Antineoplastic Agents , Benzenesulfonamides , Carbonic Anhydrase IX , Carbonic Anhydrase Inhibitors , Cell Proliferation , Dose-Response Relationship, Drug , Drug Screening Assays, Antitumor , Ferroptosis , Naphthalimides , Sulfonamides , Triple Negative Breast Neoplasms , Humans , Carbonic Anhydrase IX/antagonists & inhibitors , Carbonic Anhydrase IX/metabolism , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/pathology , Triple Negative Breast Neoplasms/metabolism , Carbonic Anhydrase Inhibitors/pharmacology , Carbonic Anhydrase Inhibitors/chemistry , Carbonic Anhydrase Inhibitors/chemical synthesis , Ferroptosis/drug effects , Sulfonamides/pharmacology , Sulfonamides/chemistry , Sulfonamides/chemical synthesis , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Antineoplastic Agents/chemical synthesis , Animals , Molecular Structure , Cell Proliferation/drug effects , Structure-Activity Relationship , Mice , Female , Naphthalimides/chemistry , Naphthalimides/pharmacology , Naphthalimides/chemical synthesis , Drug Discovery , Apoptosis/drug effects , Molecular Docking Simulation , Piperazines/pharmacology , Piperazines/chemistry , Piperazines/chemical synthesis , Cell Line, Tumor , Antigens, NeoplasmABSTRACT
The proliferation of nitrile mixtures has significantly exacerbated environmental pollution. This study employed metagenomic analysis to investigate the short-term effects of nitrile mixtures on soil microbial communities and their metabolic functions. It also examined the responses of indigenous microorganisms and their functional metabolic genes across various land use types to different nitrile stressors. The nitrile compound treatments in this study resulted in an increase in the abundance of Proteobacteria, Actinobacteria, and Firmicutes, while simultaneously reducing overall microbial diversity. The key genes involved in the denitrification process, namely, nirK, nosZ, and hao, were down-regulated, and NO3--N, NO2--N, and NH4+-N concentrations decreased by 7.7%-12.3%, 11.1%-21.3%, and 11.3%-30.9%, respectively. Notably, pond sludge samples exhibited a significant increase in the abundance of nitrogen fixation-related genes nifH, vnfK, vnfH, and vnfG following exposure to nitrile compounds. Furthermore, the fumarase gene fumD, which is responsible for catalyzing fumaric acid into malic acid in the tricarboxylic acid cycle, showed a substantial increase of 7.2-10.6-fold upon nitrile addition. Enzyme genes associated with the catechol pathway, including benB-xylY, dmpB, dmpC, dmpH, and mhpD, displayed increased abundance, whereas genes related to the benzoyl-coenzyme A pathway, such as bcrA, dch, had, oah, and gcdA, were notably reduced. In summary, complex nitrile compounds were found to significantly reduce the species diversity of soil microorganisms. Nitrile-tolerant microorganisms demonstrated the ability to degrade and adapt to nitrile pollutants by enhancing functional enzymes involved in the catechol pathway and fenugreek conversion pathway. This study offers insights into the specific responses of microorganisms to compound nitrile contamination, as well as valuable information for screening nitrile-degrading microorganisms and identifying nitrile metabolic enzymes.
ABSTRACT
The intentional binding effect refers to the phenomenon where the perceived temporal interval between a voluntary action and its sensory consequence is subjectively compressed. Prior research revealed the importance of tactile feedback from the keyboard on this effect. Here we examined the necessity of such tactile feedback by utilizing a touch-free key-press device without haptic feedback, and explored how initial/outcome sensory modalities (visual/auditory/tactile) and their consistency influence the intentional binding effect. Participants estimated three delay lengths (250, 550, or 850 ms) between the initial and outcome stimuli. Results showed that regardless of the combinations of sensory modalities between the initial and the outcome stimuli (i.e., modal consistency), the intentional binding effect was only observed in the 250 ms delay condition. This findings indicate a stable intentional binding effect both within and across sensory modalities, supporting the existence of a shared mechanism underlying the binding effect in touch-free voluntary actions.
Subject(s)
Feedback, Sensory , Intention , Psychomotor Performance , Touch Perception , Humans , Male , Female , Young Adult , Adult , Touch Perception/physiology , Feedback, Sensory/physiology , Psychomotor Performance/physiology , Visual Perception/physiology , Time Perception/physiology , Auditory Perception/physiology , Volition/physiologyABSTRACT
BACKGROUND: With the improvements in laparoscopic or robotic surgical techniques and instruments, a growing number of surgeons have attempted to complete all digestive tract reconstruction intracorporeally; these procedures include totally robotic gastrectomy (TRG) and totally laparoscopic gastrectomy (TLG). This study aimed to evaluate the safety and feasibility of the TRG and compare the short-term outcomes of the TRG and TLG in patients with gastric cancer. METHODS: Between January 2018 and June 2023, 346 consecutive patients who underwent TRG or TLG at a high-volume academic gastric cancer specialty center were included. 1:1 propensity score matching (PSM) was performed to reduce confounding bias. The surgical outcomes, postoperative morbidity, and surgical burden were compared in PSM cohort. RESULTS: After PSM, a well-balanced cohort of 194 patients (97 in each group) was included in the analysis. The total operation time of the TRG group was significantly longer than that of the TLG group (244.9 vs. 213.0 min, P < 0.001). There was no significant difference in the effective operation time between the 2 groups (217.8 vs. 207.2 min, P = 0.059). The digestive tract reconstruction time of the TRG group was significantly shorter than that of the TLG group (39.4 vs. 46.7 min, P < 0.001). The mean blood loss in the TRG group was less than that in the TLG group (101.1 vs. 126.8 mL, P = 0.014). The TRG group had more retrieved lymph nodes in the suprapancreatic area than that in the TLG group (16.6 vs 14.2, P = 0.002). The TRG group had a lower surgery task load index (38.9 vs. 43.1, P < 0.001) than the TLG group. No significant difference was found in terms of postoperative morbidity between the 2 groups (14.4% vs. 16.5%, P = 0.691). CONCLUSION: This study demonstrated that TRG is a safe and feasible procedure, and is preferable to TLG in terms of invasion and ergonomics. The TRG may maximize the superiority of robotic surgical systems and embodies the theory of minimally invasive surgery.
Subject(s)
Gastrectomy , Laparoscopy , Operative Time , Propensity Score , Robotic Surgical Procedures , Stomach Neoplasms , Humans , Stomach Neoplasms/surgery , Gastrectomy/methods , Robotic Surgical Procedures/methods , Laparoscopy/methods , Male , Female , Middle Aged , Aged , Retrospective Studies , Feasibility Studies , Treatment Outcome , Postoperative Complications/epidemiology , Postoperative Complications/etiologyABSTRACT
Cervical cancer (CC) is a gynaecological malignancy tumour that seriously threatens women's health. Recent evidence has identified that interferon regulatory factor 5 (IRF5), a nucleoplasm shuttling protein, is a pivotal transcription factor regulating the growth and metastasis of various human tumours. This study aimed to investigate the function and molecular basis of IRF5 in CC development. IRF5, protein phosphatase 6 catalytic subunit (PPP6C) and methyltransferase-like 3 (METTL3) mRNA levels were evaluated by quantitative real-time (qRT)-polymerase chain reaction (PCR). IRF5, PPP6C, METTL3, B-cell lymphoma 2 and Bax protein levels were detected using western blot. Cell proliferation, migration, invasion, angiogenesis and apoptosis were determined by using colony formation, 5-ethynyl-2'-deoxyuridine (EdU), transwell, tube formation assay and flow cytometry assay, respectively. Glucose uptake and lactate production were measured using commercial kits. Xenograft tumour assay in vivo was used to explore the role of IRF5. After JASPAR predication, binding between IRF5 and PPP6C promoter was verified using chromatin immunoprecipitation and dual-luciferase reporter assays. Moreover, the interaction between METTL3 and IRF5 was verified using methylated RNA immunoprecipitation (MeRIP). IRF5, PPP6C and METTL3 were highly expressed in CC tissues and cells. IRF5 silencing significantly inhibited cell proliferation, migration, invasion, angiogenesis and glycolytic metabolism in CC cells, while induced cell apoptosis. Furthermore, the absence of IRF5 hindered tumour growth in vivo. At the molecular level, IRF5 might bind with PPP6C to positively regulate the expression of PPP6C mRNA. Meanwhile, IRF5 was identified as a downstream target of METTL3-mediated m6A modification. METTL3-mediated m6A modification of mRNA might promote CC malignant progression by regulating PPP6C, which might provide a promising therapeutic target for CC treatment.
Subject(s)
Cell Proliferation , Interferon Regulatory Factors , Methyltransferases , Phosphoprotein Phosphatases , Up-Regulation , Uterine Cervical Neoplasms , Animals , Female , Humans , Mice , Apoptosis/genetics , Cell Line, Tumor , Cell Movement/genetics , Cell Proliferation/genetics , Disease Progression , Gene Expression Regulation, Neoplastic , Interferon Regulatory Factors/genetics , Interferon Regulatory Factors/metabolism , Methyltransferases/genetics , Methyltransferases/metabolism , Mice, Nude , Neoplasm Invasiveness , Neovascularization, Pathologic/genetics , Neovascularization, Pathologic/pathology , Neovascularization, Pathologic/metabolism , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/metabolism , Phosphoprotein Phosphatases/genetics , Phosphoprotein Phosphatases/metabolismABSTRACT
Pseudotime analysis from scRNA-seq data enables to characterize the continuous progression of various biological processes, such as the cell cycle. Cell cycle plays an important role in cell fate decisions and differentiation and is often regarded as a confounder in scRNA-seq data analysis when analyzing the role of other factors. Therefore, accurate prediction of cell cycle pseudotime and identification of cell cycle stages are important steps for characterizing the development-related biological processes. Here, we develop CCPE, a novel cell cycle pseudotime estimation method to characterize cell cycle timing and identify cell cycle phases from scRNA-seq data. CCPE uses a discriminative helix to characterize the circular process of the cell cycle and estimates each cell's pseudotime along the cell cycle. We evaluated the performance of CCPE based on a variety of simulated and real scRNA-seq datasets. Our results indicate that CCPE is an effective method for cell cycle estimation and competitive in various applications compared with other existing methods. CCPE successfully identified cell cycle marker genes and is robust to dropout events in scRNA-seq data. Accurate prediction of the cell cycle using CCPE can also effectively facilitate the removal of cell cycle effects across cell types or conditions.
Subject(s)
Cell Cycle/genetics , Computational Biology/methods , Gene Expression Profiling/methods , RNA-Seq , Single-Cell Analysis , Algorithms , Databases, Genetic , Gene Expression Regulation , RNA-Seq/methods , Single-Cell Analysis/methodsABSTRACT
The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. Our intensive studies of lncRNAs provide diverse potential mechanisms of lncRNAs that regulate gene expression through binding enhancers and 3'-UTRs of genes, competing for miRNA binding sites with mRNAs, recruiting the transcription factors to gene promoters. Furthermore, we investigated lncRNAs that potentially affect the alternative splicing events through interacting with RNA binding Proteins. We also performed multiple functional annotations including cancer stage-associated lncRNAs, RNA A-to-I editing event-associated lncRNAs, and lncRNA expression quantitative trait loci. lncRNAfunc is a unique resource for cancer research communities to help better understand potential lncRNA regulations and therapeutic lncRNA targets.
Subject(s)
Databases, Genetic , Knowledge Bases , Neoplasms/genetics , RNA, Long Noncoding/genetics , Alternative Splicing/genetics , Humans , Neoplasms/classification , RNA, Long Noncoding/classification , RNA, Messenger/geneticsABSTRACT
A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies. FusionGDB is a unique functional annotation database of human fusion genes and has been widely used for studies with diverse aims. In this study, we report fusion gene annotation updates aided by deep learning (FusionGDB 2.0) available at https://compbio.uth.edu/FusionGDB2/. FusionGDB 2.0 has substantial updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with 44 human genomic features across five cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of the protein feature retention of individual fusion partner genes in the protein level. Among â¼102k fusion genes, about 15k kept their ORF as In-frames, which is two times compared to the previous version, FusionGDB. FusionGDB 2.0 will be used as the reference knowledgebase of fusion gene annotations. FusionGDB 2.0 provides eight categories of annotations and it will be helpful for diverse human genomic studies.
Subject(s)
Databases, Genetic , Gene Fusion/genetics , Genome, Human/genetics , Genomics , Amino Acid Sequence/genetics , Deep Learning , Humans , Knowledge Bases , Molecular Sequence AnnotationABSTRACT
BACKGROUND: Since May 2022, mpox outbreaks have been occurring in non-mpox endemic areas, with the main population affected being men who have sex with men (MSM). Outbreak prevention and control depend not only on the effectiveness of vaccines but also on people's willingness to receive these vaccines. Currently, there is lack of synthesis on the overall rates and influence factors of MSMs' willingness to vaccinate against mpox. Therefore, we systematically reviewed studies that assessed the willingness of MSM to receive mpox vaccine. METHODS: Studies reporting mpox vaccination intentions among MSM were included by searching five databases (PubMed, Web of Science, EMBASE, CINAHL, and SCOPUS) from inception to May 12, 2024. The quality of the included literature was assessed using Joanna Briggs Institute's critical appraisal tool. The data analysis software is Stata17. The systematic review has been registered with Prospero (registration ID: CRD42023452357). RESULTS: Twenty cross-sectional studies were included in the review. Meta-analysis results showed that the pooled willingness rate of vaccinate against mpox was 77.0% (95% CI: 73-81%, I2 = 99.4%). According to subgroup analysis, study countries (P = 0.002), research sample size (P = 0.001), and whether participants were infected with HIV (P = 0.002) may be sources of heterogeneity. The results of the meta-analysis of influencing factors showed that more number of sexual partners (OR: 2.24, 95%CI: 1.86-2.69), pre-exposure prophylaxis use (OR: 6.04, 95%CI: 4.80-7.61), history of sexually transmitted infections (OR: 2.96, 95%CI: 2.33-3.76), confidence in the vaccine's effectiveness (OR: 2.79, 95%CI: 2.04-3.80) and safety (OR: 10.89, 95%CI: 5.22-22.72), fear of mpox infection (OR: 2.47, 95%CI: 2.11-2.89) and epidemics (OR: 2.87, 95%CI: 2.22-3.70), high mpox knowledge (OR: 2.35, 95%CI: 1.51-3.66), and the belief that people at high risk should be prioritized for vaccination (OR: 3.09, 95%CI: 1.40-6.84) were the facilitators of vaccine willingness. In addition, as a secondary outcome, meta-analysis results showed a pooled unwillingness rate of 16% (95% CI: 13-20%, I2 = 98.1%, 9 studies). CONCLUSION: Willingness to vaccinate mpox was high among MSM, but some participants still had negative attitudes towards vaccination. Therefore, the Ministry of Public Health should develop targeted and effective strategies against those influencing factors to prevent and manage mpox outbreaks.
Subject(s)
Homosexuality, Male , Humans , Male , Homosexuality, Male/psychology , Homosexuality, Male/statistics & numerical data , Patient Acceptance of Health Care/statistics & numerical data , Patient Acceptance of Health Care/psychologyABSTRACT
Background: Deep vein thrombosis is a common complication after surgery, particularly in cancer patients, necessitating efficient diagnostic methods for timely intervention. Objective: This study aimed to investigate the potential of combining C-reactive protein (CRP) and interleukin-6 (IL-6) tests in diagnosing deep vein thrombosis (DVT) following endometrial cancer surgery. Methods: A cohort of 60 patients who developed DVT post-endometrial cancer surgery and were admitted to the First Hospital of Hebei Medical University between March 2018 and March 2022 constituted the DVT group. Additionally, 60 patients who underwent endometrial cancer surgery during the same period but did not develop DVT formed the non-DVT group. Serum levels of CRP and IL-6 were quantified and compared between the two groups using reliable laboratory techniques. Subsequently, the diagnostic accuracy of single-parameter testing (CRP or IL-6 alone) versus combined testing (CRP and IL-6) for postoperative DVT was assessed. Results: Analysis revealed significantly elevated levels of CRP and IL-6 in the serum of patients in the DVT group compared to those in the non-DVT group (P < .05). Furthermore, combined testing of CRP and IL-6 exhibited heightened sensitivity (0.85%), specificity (0.917%), and area under the curve (AUC) (0.952) compared to single-parameter testing alone, indicating its superiority in diagnosing postoperative DVT. Conclusions: The combination of CRP and IL-6 testing presents a promising diagnostic strategy for identifying postoperative DVT in endometrial cancer patients. Implementing this approach in clinical practice could facilitate early detection and prompt management of DVT, thereby potentially reducing associated morbidity and mortality.
ABSTRACT
Objective: Investigating the application effectiveness of using loop-mediated isothermal amplification (LAMP) on a microfluidic chip to detect the pathogens associated with ventilator-associated pneumonia (VAP). Methods: Eighty samples of bronchoalveolar lavage fluid from patients with ventilator-associated pneumonia (VAP) were collected at The First Hospital of Hebei Medical University from July 2022 to July 2023. The bacterial culture technique and the LAMP method were used to detect the nucleic acid of the pathogens in the patient samples. The positivity rates of bacterial culture and LAMP method in detecting VAP pathogens were analyzed. Results: A total of 80 specimens were examined, with 73 positive specimens detected using the LAMP method (positivity rate of 91.25%) and 60 positive specimens detected using bacterial culture (positivity rate of 75.00%). The LAMP method exhibited a higher number of positive detections compared to bacterial culture. Both methods showed a high level of concordance and were virtually identical in detecting methicillin-resistant Staphylococcus aureus, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Enterobacter aerogenes, Haemophilus influenzae, and Streptococcus pneumoniae. Conclusion: The LAMP method demonstrates significantly improved performance in the detection of pathogens for VAP, with a higher pathogen positivity rate compared to bacterial culture. This method holds promising prospects for clinical application.