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1.
Exp Cell Res ; 434(1): 113857, 2024 01 01.
Article in English | MEDLINE | ID: mdl-38008278

ABSTRACT

Genetic factors coordinate with environmental factors to drive the pathogenesis of prostate adenocarcinoma (PRAD). SPOP is one of the most mutated genes and LRP5 mediates lipid metabolism that is abnormally altered in PRAD. Here, we investigated the potential cross-talk between SPOP and LRP5 in PRAD. We find a negative correlation between SPOP and LRP5 proteins in PRAD. SPOP knockdown increased LRP5 protein while SPOP overexpression resulted in LRP5 reduction that was fully rescued by proteasome inhibitors. LRP5 intracellular tail has SPOP binding site and the direct interaction between LRP5 and SPOP was confirmed by Co-IP and GST-pulldown. Moreover, LRP5 competed with Daxx for SPOP-mediated degradation, establishing a dynamic balance among SPOP, LRP5 and Daxx. Overexpression of LRP5 tail could shift this balance to enhance Daxx-mediated transcriptional inhibition, and inhibit T cell activity in a co-culture system. Further, we generated human and mouse prostate cancer cell lines expressing SPOP variants (F133V, A227V, R368H). SPOP-F133V and SPOP-A227V have specific effects in up-regulating the protein levels of PD-1 and PD-L1. Consistently, SPOP-F133V and SPOP-A227V show robust inhibitory effects on T cells compared to WT SPOP in co-culture. This is further supported by the mouse syngeneic model showing that SPOP-F133V and SPOP-A227V enhance tumorigenesis of prostate cancer in in-vivo condition. Taken together, our study provides evidence that SPOP-LRP5 crosstalk plays an essential role, and the genetic variants of SPOP differentially modulate the expression and activity of immune checkpoints in prostate cancer.


Subject(s)
Prostatic Neoplasms , Repressor Proteins , Male , Animals , Mice , Humans , Repressor Proteins/genetics , Repressor Proteins/metabolism , B7-H1 Antigen/genetics , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Prostatic Neoplasms/pathology , Carcinogenesis/genetics , Cell Transformation, Neoplastic , Mutation , Low Density Lipoprotein Receptor-Related Protein-5/genetics , Molecular Chaperones/genetics , Co-Repressor Proteins/genetics
2.
Proc Natl Acad Sci U S A ; 119(11): e2109667119, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35275791

ABSTRACT

SignificanceYersinia pestis, the etiologic agent of plague, has been responsible for high mortality in several epidemics throughout human history. This plague bacillus has been used as a biological weapon during human history and is currently one of the deadliest biological threats. Currently, no licensed plague vaccines are available in the Western world. Since an array of immunogens are enclosed in outer membrane vesicles (OMVs), immune responses elicited by OMVs against a diverse range of antigens may reduce the likelihood of antigen circumvention. Therefore, self-adjuvanting OMVs from a remodeled Yersinia pseudotuberculosis strain as a type of plague vaccine could diversify prophylactic choices and solve current vaccine limitations.


Subject(s)
Antigens, Bacterial , Lipid A , Plague Vaccine , Plague , Pore Forming Cytotoxic Proteins , Yersinia pseudotuberculosis , Animals , Antibodies, Bacterial/blood , Antigens, Bacterial/genetics , Antigens, Bacterial/immunology , Lethal Dose 50 , Lipid A/genetics , Lipid A/immunology , Mice , Plague/prevention & control , Plague Vaccine/administration & dosage , Plague Vaccine/genetics , Plague Vaccine/immunology , Plasmids/genetics , Pore Forming Cytotoxic Proteins/genetics , Pore Forming Cytotoxic Proteins/immunology , Yersinia pseudotuberculosis/genetics , Yersinia pseudotuberculosis/immunology
3.
J Proteome Res ; 23(7): 2441-2451, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38833655

ABSTRACT

Global profiling of single-cell proteomes can reveal cellular heterogeneity, thus benefiting precision medicine. However, current mass spectrometry (MS)-based single-cell proteomic sample processing still faces technical challenges associated with processing efficiency and protein recovery. Herein, we present an innovative sample processing platform based on a picoliter single-cell reactor (picoSCR) for single-cell proteome profiling, which involves in situ protein immobilization and sample transfer. PicoSCR helped minimize surface adsorptive losses by downscaling the processing volume to 400 pL with a contact area of less than 0.4 mm2. Besides, picoSCR reached highly efficient cell lysis and digestion within 30 min, benefiting from optimal reagent and high reactant concentrations. Using the picoSCR-nanoLC-MS system, over 1400 proteins were identified from an individual HeLa cell using data-dependent acquisition mode. Proteins with copy number below 1000 were identified, demonstrating this system with a detection limit of 1.7 zmol. Furthermore, we profiled the proteome of circulating tumor cells (CTCs). Data are available via ProteomeXchange with the identifier PXD051468. Proteins associated with epithelial-mesenchymal transition and neutrophil extracellular traps formation (which are both related to tumor metastasis) were observed in all CTCs. The cellular heterogeneity was revealed by differences in signaling pathways within individual cells. These results highlighted the potential of the picoSCR platform to help discover new biomarkers and explore differences in biological processes between cells.


Subject(s)
Proteome , Proteomics , Single-Cell Analysis , Humans , Single-Cell Analysis/methods , HeLa Cells , Proteome/analysis , Proteome/metabolism , Proteomics/methods , Epithelial-Mesenchymal Transition , Bioreactors
4.
Anal Chem ; 96(24): 9849-9858, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38836774

ABSTRACT

The scarcity and dynamic nature of phosphotyrosine (pTyr)-modified proteins pose a challenge for researching protein complexes with pTyr modification, which are assembled through multiple protein-protein interactions. We developed an integrated complex-centric platform for large-scale quantitative profiling of pTyr signaling complexes based on cofractionation/mass spectrometry (CoFrac-MS) and a complex-centric algorithm. We initially constructed a trifunctional probe based on pTyr superbinder (SH2-S) for specifically binding and isolation of intact pTyr protein complexes. Then, the CoFrac-MS strategy was employed for the identification of pTyr protein complexes by integrating ion exchange chromatography in conjunction with data independent acquisition mass spectrometry. Furthermore, we developed a novel complex-centric algorithm for quantifying protein complexes based on the protein complex elution curve. Utilizing this algorithm, we effectively quantified 216 putative protein complexes. We further screened 21 regulated pTyr protein complexes related to the epidermal growth factor signal. Our study engenders a comprehensive framework for the intricate examination of pTyr protein complexes and presents, for the foremost occasion, a quantitative landscape delineating the composition of pTyr protein complexes in HeLa cells.


Subject(s)
Algorithms , Mass Spectrometry , Phosphotyrosine , Signal Transduction , Phosphotyrosine/metabolism , Phosphotyrosine/analysis , Phosphotyrosine/chemistry , Humans , HeLa Cells , Chromatography, Ion Exchange/methods
5.
Small ; : e2400941, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38529737

ABSTRACT

Multidimensional metabolic analysis has become a new trend in establishing efficient disease monitoring systems, as the constraints associated with relying solely on a single dimension in refined monitoring are increasingly pronounced. Here, coordination polymers are employed as derivative precursors to create multishell hollow hybrids, developing an integrated metabolic monitoring system. Briefly, metabolic fingerprints are extracted from hundreds of serum samples and urine samples, encompassing not only membranous nephropathy but also related diseases, using high-throughput mass spectrometry. With optimized algorithm and initial feature selection, the established combined panel demonstrates enhanced accuracy in both subtype differentiation (over 98.1%) and prognostic monitoring (over 95.6%), even during double blind test. This surpasses the serum biomarker panel (≈90.7% for subtyping, ≈89.7% for prognosis) and urine biomarker panel (≈94.4% for subtyping, ≈76.5% for prognosis). Moreover, after attempting to further refine the marker panel, the blind test maintains equal sensitivity, specificity, and accuracy, showcasing a comprehensive improvement over the single-fluid approach. This underscores the remarkable effectiveness and superiority of the integrated strategy in discriminating between MN and other groups. This work has the potential to significantly advance diagnostic medicine, leading to the establishment of more effective strategies for patient management.

6.
Anal Bioanal Chem ; 416(7): 1589-1597, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38289356

ABSTRACT

Uric acid (UA) is an important biomarker, as a high concentration in blood can lead to gout and further renal syndrome. Although several point-of-care testing (POCT) devices have been reported to detect UA, there are some limitations such as the requirement for uricase and the complicated pretreatment of serum/plasma samples, which restricts their use at home or in undeveloped areas. In this work, we developed an approach by applying Zn2+ to precipitate proteins and cells in whole blood to avoid interference with the chromogenic reaction. We used carboxymethylcellulose (CMC) to immobilize tetramethylbenzidine (TMB) on a nitrocellulose membrane for colorimetric detection. Using the oxidization properties of H2O2, which turns TMB into oxidized tetramethylbenzidine (TMBox) in the presence of catalyst gold nanoparticles (AuNPs), we successfully constructed an enzyme-free paper-based POCT device using the reduction reaction of UA and TMBox for simple, speedy, and cheap colorimetric detection of UA, achieving a detection time of 8 min, a linear range of 0-150 µg/mL, and an LOD of 25.79 µg/mL. The UA concentration in whole blood samples was further measured and correlated well with the clinical value (R2 = 0.8212). Thus, the proposed assay has the potential for POCT diagnosis, monitoring, and prognosis of diseases related to UA.


Subject(s)
Metal Nanoparticles , Uric Acid , Gold , Colorimetry , Hydrogen Peroxide , Zinc
7.
Neuroradiology ; 66(1): 135-144, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38001311

ABSTRACT

PURPOSE: Prader-Willi syndrome (PWS) suffers from brain functional reorganization and developmental delays during childhood, but the underlying neurodevelopmental mechanism is unclear. This paper aims to investigate the intra- and internetwork functional connectivity (FC) changes, and their relationships with developmental delays in PWS children. METHODS: Resting-state functional magnetic resonance imaging datasets of PWS children and healthy controls (HCs) were acquired. Independent component analysis was used to acquire core resting-state networks (RSNs). The intra- and internetwork FC patterns were then investigated. RESULTS: In terms of intranetwork FC, children with PWS had lower FC in the dorsal attention network, the auditory network, the medial visual network (VN) and the sensorimotor network (SMN) than HCs (FWE-corrected, p < 0.05). In terms of internetwork FC, PWS children had decreased FC between the following pairs of regions: posterior default mode network (DMN) and anterior DMN; posterior DMN and SMN; SMN and posterior VN and salience network and medial VN (FDR-corrected, p < 0.05). Partial correlation analyses revealed that the intranetwork FC patterns were positively correlated with developmental quotients in PWS children, while the internetwork FC patterns were completely opposite (p < 0.05). Intranetwork FC patterns showed an area under the receiver operating characteristic curve of 0.947, with a sensitivity of 96.15% and a specificity of 81.25% for differentiating between PWS and HCs. CONCLUSION: Impaired intra- and internetwork FC patterns in PWS children are associated with developmental delays, which may result from neural pathway dysfunctions. Intranetwork FC reorganization patterns can discriminate PWS children from HCs. REGISTRATION NUMBER ON THE CHINESE CLINICAL TRAIL REGISTRY: ChiCTR2100046551.


Subject(s)
Prader-Willi Syndrome , Child , Humans , Prader-Willi Syndrome/diagnostic imaging , Prader-Willi Syndrome/pathology , Brain Mapping , Magnetic Resonance Imaging/methods , Nerve Net/diagnostic imaging , Brain/pathology
8.
Int J Mol Sci ; 25(11)2024 May 28.
Article in English | MEDLINE | ID: mdl-38892048

ABSTRACT

The Roquin family is a recognized RNA-binding protein family that plays vital roles in regulating the expression of pro-inflammatory target gene mRNA during the immune process in mammals. However, the evolutionary status of the Roquin family across metazoans remains elusive, and limited studies are found in fish species. In this study, we discovered that the RC3H genes underwent a single round of gene duplication from a primitive ancestor during evolution from invertebrates to vertebrates. Furthermore, there were instances of species-specific gene loss events or teleost lineage-specific gene duplications throughout evolution. Domain/motif organization and selective pressure analysis revealed that Roquins exhibit high homology both within members of the family within the same species and across species. The three rc3h genes in zebrafish displayed similar expression patterns in early embryos and adult tissues, with rc3h1b showing the most prominent expression among them. Additionally, the promoter regions of the zebrafish rc3h genes contained numerous transcription factor binding sites similar to those of mammalian homologs. Moreover, the interaction protein network of Roquin and the potential binding motif in the 3'-UTR of putative target genes analysis both indicated that Roquins have the potential to degrade target mRNA through mechanisms similar to those of mammalian homologs. These findings shed light on the evolutionary history of Roquin among metazoans and hypothesized their role in the immune systems of zebrafish.


Subject(s)
Computational Biology , Evolution, Molecular , Phylogeny , Zebrafish , Animals , Zebrafish/genetics , Computational Biology/methods , Humans , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Immune System/metabolism , Zebrafish Proteins/genetics , Zebrafish Proteins/metabolism , Gene Duplication , Multigene Family , Promoter Regions, Genetic , Ubiquitin-Protein Ligases
9.
Anal Chem ; 95(35): 13113-13122, 2023 09 05.
Article in English | MEDLINE | ID: mdl-37609888

ABSTRACT

From metabolic waste to biological mediators, exosomes have emerged as the key player in a variety of pathological processes, particularly in oncogenesis. The exosome-mediated communication network involves nearly every step of cancer progression, promoting the proliferation and immune escape of cancer cells. Therefore, the removal of cancer-derived exosomes has profound clinical significance. Current methods for exosome separation and enrichment are either for large-scale samples or require complex pretreatment processes, lacking effective methods for trace-volume exosome capture in situ. Herein, we have developed an in situ exosome capturing and counting device based on the antibody-functionalized capillary. Specific antibodies targeting exosome biomarkers were immobilized to the inner wall of the capillary via biotin-streptavidin interaction for direct cancer exosome capturing. Subsequent exosome staining enabled imaging and enumeration. Acceptable linearity and reproducibility were achieved with our device, with the capturing and detective range between 3.3 × 104 and 3.3 × 108 particles, surpassing the nanoparticle tracking analysis by 2 orders of magnitude while requiring merely 30 µL sample. We demonstrated that MCF-7-derived exosomes induced epithelial-mesenchymal transition of epithelial cells MCF-10A, and our method was able to completely or partially reverse the transition by complete depletion or specific depletion of cancer exosomes without any preprocessing. Moreover, both whole exosomes and cancer-specific exosomes alone from mimic blood samples were successfully captured and counted, without obvious non-specific adsorption. In all, our approach realized the in situ depletion and number-counting of cancer-derived exosomes directly from the complex humoral environment, having the potential to provide a comprehensive tumor therapeutic and prognosis evaluation tool by targeted hemodialysis and counting of tumor-derived exosomes.


Subject(s)
Exosomes , Neoplasms , Humans , Reproducibility of Results , Carcinogenesis , Adsorption , Antibodies
10.
Anal Chem ; 95(27): 10196-10203, 2023 07 11.
Article in English | MEDLINE | ID: mdl-37368911

ABSTRACT

Pancreatic cancer (PC) has a high mortality, with a fairly low five-year survival rate, because of its delayed diagnosis. Recently, liquid biopsy, especially based on exosomes, has attracted vast attention, thanks to its low invasiveness. Herein, we constructed a protocol for pancreatic cancer related Glypican 1 (GPC1) exosome quantification, based on in situ mass spectrometry signal amplification, by utilizing mass tag molecules on gold nanoparticles (AuNPs). Exosomes were extracted and purified by size-exclusion chromatography (SEC), captured by TiO2 modified magnetic nanoparticles, and then targeted specifically by anti-GPC1 antibody modified on AuNPs. With matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), the signal of PC biomarker, GPC1, was converted to a mass tag signal and amplified. With addition of a certain amount of internal standard molecules modified on AuNPs, the relative intensity ratio of mass tag to internal standard was proportional to the concentration of GPC1(+) exosomes derived from pancreatic cancer cell lines, PANC-1, with good linearity (R2 = 0.9945) in a wide dynamic range from 7.1 × 10 to 7.1 × 106 particles/µL. This method was further applied to plasma samples from healthy control (HC) and pancreatic cancer patients with different tumor load, and exhibited a great potential in discriminating diagnosed PC patients from HC, and has the monitoring potential in PC progression.


Subject(s)
Exosomes , Metal Nanoparticles , Pancreatic Neoplasms , Humans , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Glypicans , Gold/chemistry , Exosomes/metabolism , Metal Nanoparticles/chemistry , Pancreatic Neoplasms/pathology , Biomarkers, Tumor/metabolism , Pancreatic Neoplasms
11.
Anal Chem ; 95(12): 5232-5239, 2023 03 28.
Article in English | MEDLINE | ID: mdl-36913664

ABSTRACT

Circulating tumor cells (CTCs) are crucial in tumor progression and metastasis, but the knowledge of their roles grows slowly at single-cell levels. Characterizing the rarity and fragility of CTCs by nature, highly stable and efficient single-CTC sampling methods are still lacking, which impedes the development of single-CTC analysis. Herein, an improved, capillary-based single-cell sampling (SiCS) method, the so-called bubble-glue single-cell sampling (bubble-glue SiCS), is introduced. Benefiting from the characteristic that the cells tend to adhere to air bubbles in the solution, single cells can be sampled with bubbles as low as 20 pL with a self-designed microbubble-volume-controlled system. Benefiting from the excellent maneuverability, single CTCs are sampled directly from 10 µL volume of real blood samples after fluorescent labeling. Meanwhile, over 90% of the CTCs obtained survived and well proliferated after the bubble-glue SiCS process, which showed considerable superiority for downstream single-CTC profiling. Furthermore, a highly metastatic breast cancer model of the 4T1 cell line in vivo was employed for the real blood sample analysis. Increases in CTC numbers were observed during the tumor progression process, and significant heterogeneities among individual CTCs were discovered. In all, we propose a novel avenue for target SiCS and provide an alternative technique route for CTC separation and analysis.


Subject(s)
Breast Neoplasms , Neoplastic Cells, Circulating , Humans , Female , Neoplastic Cells, Circulating/pathology , Breast Neoplasms/pathology , Neoplasm Metastasis , Single-Cell Analysis/methods , Biomarkers, Tumor
12.
Anal Chem ; 95(20): 8011-8019, 2023 05 23.
Article in English | MEDLINE | ID: mdl-37154434

ABSTRACT

Traditional lateral flow assay (LFA) is restricted to providing qualitative or semi-quantitative results and often requires special equipment for obtaining quantitative results. Herein, we proposed a naked-eye readout distance quantitative lateral flow assay based on the permeability changes in enzyme-catalyzed hydrogelation, which not only has the advantages of being simple, immediate, of high efficiency and low cost, and accurate in quantification but also avoids the use of special equipment. The developed LFA method includes three principal components of a nitrocellulose (NC) membrane containing a control line (C line) loading goat anti-rabbit (GAR) antibodies and a test line (T line) loading specific antibodies, alginate-tyramine conjugates forming a hydrogel in the presence of hydrogen peroxide (H2O2) and horseradish peroxidase (HRP), and the HRP-AuNPs-Ab probe only labeling targets captured on the T line. Hemoglobin A1c (HbA1c) was chosen as a representative example to demonstrate the feasibility of our method. Under the optimal conditions, the developed LFA method shows excellent performance in standard samples and real human blood samples where the results of real human blood samples show a high linear correlation with the clinical data obtained by ion exchange chromatography (R2 = 0.9929) and the margin of recovery is only 3.8%. All results demonstrated that our developed LFA method not only has enormous potential in the quantitative detection of HbA1c in clinical complex samples but also can serve as a versatile method for highly efficient detection of other target biomolecules due to the fungibility of antibodies.


Subject(s)
Hydrogen Peroxide , Metal Nanoparticles , Animals , Humans , Rabbits , Glycated Hemoglobin , Hydrogen Peroxide/chemistry , Gold/chemistry , Metal Nanoparticles/chemistry , Antibodies , Permeability , Catalysis
13.
Anal Chem ; 95(27): 10231-10240, 2023 07 11.
Article in English | MEDLINE | ID: mdl-37322584

ABSTRACT

Due to the highly heterogeneous nature of hepatocellular carcinoma (HCC), the accurate diagnosis of HCC during the early phase of development is still a challenging task. Therefore, the further development of novel diagnostic methods by discovering new biomarkers is required to improve the rate of HCC diagnosis in the early phase. In this work, an oxygen-modified three-dimensional interconnected porous carbon probe is designed and fabricated to profile the differences of N-glycans in human serum from health controls (H) and patients with hepatic dysfunction (HD) and HCC for the discovery of new biomarkers with HCC development. Excitingly, we discovered that the expression levels of 12 serum N-glycans were gradually increased from H to patients with HD and eventually to patients with HCC. Moreover, two machine learning models established based on these 12 serum N-glycans reached a satisfactory accuracy for predicting HCC development where the receiver operating characteristic curve arrived above 0.95 for distinguishing healthy controls and patients with liver diseases (HD or HCC) and the ROC curve arrived at 0.85 for distinguishing HD and HCC. Our work not only developed a new method for the large-scale characterization of serum N-glycans but also provided valuable guidance for accurate and highly sensitive diagnosis of early liver cancer development in a non-invasive manner.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Humans , Liver Neoplasms/diagnosis , Porosity , Biomarkers, Tumor , Biomarkers , ROC Curve , Polysaccharides
14.
J Virol ; 96(24): e0121022, 2022 12 21.
Article in English | MEDLINE | ID: mdl-36448796

ABSTRACT

All lentiviruses encode a post-transcriptional transactivator, Rev, which mediates the export of viral mRNA from the nucleus to the cytoplasm and which is required for viral gene expression and viral replication. In the current study, we demonstrate that equine infectious anemia virus (EIAV), an equine lentivirus, encodes a second post-transcriptional transactivator that we designate Grev. Grev is encoded by a novel transcript with a single splicing event that was identified using reverse transcription-PCR (RT-PCR) and RNA-seq in EIAV-infected horse tissues and cells. Grev is about 18 kDa in size, comprises the first 18 amino acids (aa) of Gag protein together with the last 82 aa of Rev, and was detected in EIAV-infected cells. Similar to Rev, Grev is localized to the nucleus, and both are able to mediate the expression of Mat (a recently identified viral protein of unknown function from EIAV), but Rev can mediate the expression of EIAV Gag/Pol, while Grev cannot. We also demonstrate that Grev, similar to Rev, specifically binds to rev-responsive element 2 (RRE-2, located in the first exon of mat mRNAs) to promote nuclear export of mat mRNA via the chromosome region maintenance 1 (CRM1) pathway. However, unlike Rev, whose function depends on its multimerization, we could not detect multimerization of Grev using coimmunoprecipitation (co-IP) or bimolecular fluorescence complementation (BiFC) assays. Together, these data suggest that EIAV encodes two post-transcriptional transactivators, Rev and Grev, with similar, but not identical, functions. IMPORTANCE Nuclear export of viral transcripts is a crucial step for viral gene expression and viral replication in lentiviruses, and this export is regulated by a post-transcriptional transactivator, Rev, that is shared by all lentiviruses. Here, we report that the equine infectious anemia virus (EIAV) encodes a novel viral protein, Grev, and demonstrated that Grev, like Rev, mediates the expression of the viral protein Mat by binding to the first exon of mat mRNAs via the chromosome region maintenance 1 (CRM1) pathway. Grev is encoded by a single-spliced transcript containing two exons, whereas Rev is encoded by a multiple-spliced transcript containing four exons. Moreover, Rev is able to mediate EIAV Gag/Pol expression by binding to rev-responsive element (RRE) located within the Env-coding region, while Grev cannot. Therefore, the present study demonstrates that EIAV encodes two post-transcriptional regulators, Grev and Rev, suggesting that post-transcriptional regulation patterns in lentivirus are diverse and complex.


Subject(s)
Equine Infectious Anemia , Infectious Anemia Virus, Equine , Trans-Activators , Animals , Equine Infectious Anemia/virology , Exons , Gene Products, rev/genetics , Horses/genetics , Infectious Anemia Virus, Equine/genetics , Infectious Anemia Virus, Equine/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Trans-Activators/genetics , Trans-Activators/metabolism , Gene Expression Regulation, Viral/genetics
15.
J Virol ; 96(18): e0098622, 2022 09 28.
Article in English | MEDLINE | ID: mdl-36069548

ABSTRACT

All lentiviruses encode the accessory protein Rev, whose main biological function is to mediate the nuclear export of unspliced and incompletely spliced viral transcripts by binding to a viral cis-acting element (termed the Rev-responsive element, RRE) within the env-encoding region. Equine infectious anemia virus (EIAV) is a member of the lentivirus genus in the Retroviridae family and is considered an important model for the study of lentivirus pathogenesis. Here, we identified a novel transcript from the EIAV genome that encoded a viral protein, named Mat, with an unknown function. The transcript mat was fully spliced and comprised parts of the coding regions of MA and TM. Interestingly, the expression of Mat depended on Rev and the chromosome region maintenance 1 (CRM1) pathway. Rev could specifically bind to Mat mRNA to promote its nuclear export. We further identified that the first exon of Mat mRNA, which was located within the Gag-encoding region, acted as an unreported RRE. Altogether, we identified a novel fully spliced transcript mat with an unusual RRE, which interacted with Rev for nuclear export through the CRM1 pathway. These findings updated the EIAV genome structure, highlighted the diversification of posttranscriptional regulation patterns in EIAV, and may help to expand the understanding of gene transcription and expression of lentivirus. IMPORTANCE In lentiviruses, the nuclear export of viral transcripts is an important step in controlling viral gene expression. Generally, the unspliced and incompletely spliced transcripts are exported via the CRM1-dependent export pathway in a process mediated by the viral Rev protein by binding to the Rev-responsive element (RRE) located within the Env-coding region. However, the completely spliced transcripts are exported via an endogenous cellular pathway, which was Rev independent. Here, we identified a novel fully spliced transcript from EIAV and demonstrated that it encoded a viral protein, termed Mat. Interestingly, we determined that the expression of Mat depended on Rev and identified that the first exon of Mat mRNA could specifically bind to Rev and be exported to the cytoplasm, which suggested that the first exon of Mat mRNA was a second RRE of EIAV. These findings provided important insights into the Rev-dependent nuclear export of completely spliced transcripts in lentiviruses.


Subject(s)
Gene Products, rev , Infectious Anemia Virus, Equine , Lentiviruses, Equine , Animals , Gene Products, rev/genetics , Horses , Infectious Anemia Virus, Equine/metabolism , RNA Splicing , RNA, Messenger/genetics , RNA, Viral/genetics
16.
Anal Bioanal Chem ; 415(26): 6411-6420, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37644324

ABSTRACT

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease which leads to the formation of immune complex deposits in multiple organs and has heterogeneous clinical manifestations. Currently, exosomes for liquid biopsy have been applied in diagnosis and monitoring of diseases, whereas SLE discrimination based on exosomes at the metabolic level is rarely reported. Herein, we constructed a protocol for metabolomic study of urinary exosomes from SLE patients and healthy controls (HCs) with high efficiency and throughput. Exosomes were first obtained by high-performance liquid size-exclusion chromatography (HPL-SEC), and then metabolic fingerprints of urinary exosomes were extracted by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with high throughput and high efficency. With the statistical analysis by orthogonal partial least-squares discriminant analysis (OPLS-DA) model, SLE patients were efficiently distinguished from HCs, the area under the curve (AUC) of the receiver characteristic curve (ROC) was 1.00, and the accuracy of the unsupervised clustering heatmap was 90.32%. In addition, potential biomarkers and related metabolic pathways were analyzed. This method, with the characteristics of high throughput, high efficiency, and high accuracy, will provide the broad prospect of exosome-driven precision medicine and large-scale screening in clinical applications.

17.
World J Surg Oncol ; 21(1): 30, 2023 Jan 31.
Article in English | MEDLINE | ID: mdl-36721264

ABSTRACT

OBJECTIVE: According to the different characteristics of patients and cervical lymph node metastasis of oral and oropharyngeal cancer, the marginal mandibular branches of facial nerves were treated by different surgical procedures, and the safety and protective effects of different surgical procedures were investigated. METHODS: One hundred ninety-seven patients with oral and oropharyngeal cancer satisfying the inclusion criteria were selected. According to the different characteristics of patients and cervical metastatic lymph nodes, three different surgical procedures were used to treat the marginal mandibular branches of the facial nerve: finding and exposing the marginal mandibular branches of the facial nerves at the mandibular angles of the platysma flaps, finding and exposing the marginal mandibular branches of facial nerves at the intersections of the distal ends of facial arteries and veins with the mandible, and not exposing the marginal mandibular branches of the facial nerves. The anatomical position, injury, and complications of the marginal mandibular branches of the facial nerves were observed. RESULTS: The marginal mandibular branches of the facial nerves were found and exposed at the mandibular angles of the platysma flaps in 102 patients; the marginal mandibular branches of facial nerves were found and exposed at the intersections of the distal ends of the facial arteries and veins with the mandibles in 64 patients; the marginal mandibular branches of facial nerves were not exposed in 31 patients; among them, four patients had permanent injury of the marginal mandibular branches of the facial nerves, and temporary injury occurred in seven patients. There were statistically significant differences in the protection of the mandibular marginal branch of the facial nerve among the three different surgical methods (P = 0.0184). The best protective effect was to find and expose the mandibular marginal branch of the facial nerve at the mandibular angle of the platysma muscle flap, and the injury rate was only 2.94%. CONCLUSION: The three different surgical procedures were all safe and effective in treating the marginal mandibular branches of the facial nerves, the best protective effect was to find and expose the mandibular marginal branch of the facial nerve at the mandibular angle of the platysma muscle flap.


Subject(s)
Facial Nerve , Oropharyngeal Neoplasms , Humans , Lymph Node Excision , Oropharyngeal Neoplasms/surgery , Lymph Nodes/surgery , Lymphatic Metastasis
18.
BMC Surg ; 23(1): 297, 2023 Sep 30.
Article in English | MEDLINE | ID: mdl-37775750

ABSTRACT

OBJECTIVE: This study aimed to assess the effects of surgical timing and approach on operative duration, postoperative suture removal time, and postoperative recurrence rate in the management of preauricular fistula. A 12-year single-center clinical observation was conducted to analyze the potential effects of different surgical strategies on these critical outcomes. METHODS: The clinical data from 576 (782 ears) patients who underwent surgical resection for preauricular fistulas were examined in this retrospective study. The patients were classified into various groups based on differences in operative duration, surgical techniques and the use of intraoperative magnifying equipment. Furthermore, the specific data on operative duration, postoperative suture removal time, and postoperative recurrence rate were also recorded. RESULTS: The average operative duration for 782 ears and the average time required for postoperative suture removal were determined to be (34.57 ± 4.25) min and (3.62 ± 0.76) days, respectively. Among the cases examined, recurrence occurred in 13 ears, but all of them were cured after a second surgery, resulting in a recurrence rate of 1.67% (13/782). Interestingly, the operative and postoperative suture removal time was prolonged during the infection period (P < 0.05). The postoperative recurrence rate was significantly higher in the absence of magnifying equipment, as compared to those with the use of a microscope with 2.5× magnification (P < 0.05). No statistically significant differences were noted in the recurrence rate when comparing different anesthesia methods and types of surgical incisions, as well as the intraoperative use of methylene blue, and partial removal of cartilage of the pedicle (P > 0.05). CONCLUSION: The use of methylene blue, partial removal of the cartilage of the pedicle, and surgical incision during preauricular fistula resection did not affect the operative duration, postoperative suture removal time, and postoperative recurrence rate. Therefore, surgeons can select their preferred approaches based on their individual practices and patient-specific situations. However, the use of magnifying equipment during surgery is associated with a reduced risk of recurrence.


Subject(s)
Fistula , Methylene Blue , Humans , Retrospective Studies , Treatment Outcome , Ear, External/surgery , Recurrence
19.
Anal Chem ; 94(34): 11925-11933, 2022 08 30.
Article in English | MEDLINE | ID: mdl-35980697

ABSTRACT

Ultra-low-copy number proteins play a crucial role in exploring cellular heterogeneity and the insight of protein biomarkers in a single cell. However, counting ultra-low-copy number target proteins in a single cell remains a grand challenge. Herein, we developed a so-called single-cell picoliter liquid operating technology for counting target proteins in a single cell. An ingenious volume-controllable sampling technique was employed to capture a single cell for subsequent analysis. Remarkably, 50 pL of sample volume was employed for sample preparation, single-cell capture, in-droplet lysis, and target protein immobilization on a functionalized coverslip in a monolayer. Then, target protein antibodies coupled with quantum dots were added and incubated to label those immobilized proteins. After clean-up, a single-view image under 100× objective was taken, and the 80 × 80 µm2 view image was then applied to count the precise copy number of the target proteins in the single cell. Furthermore, good linearity and repeatability were achieved for ultra-low-copy number proteins, ranging from 1 to 1500. Finally, the expression level of human epidermal growth factor receptor 2 in single cells from both MCF-7 and MDA-MB-231 cell lines was also analyzed. In a word, this work stimulated the development of capillary-based single-cell analysis and updated the connotation of counting ultra-low-copy number proteins.


Subject(s)
Quantum Dots , Antibodies , Humans , Proteins/analysis , Single-Cell Analysis , Technology
20.
Anal Chem ; 94(3): 1831-1839, 2022 01 25.
Article in English | MEDLINE | ID: mdl-35025210

ABSTRACT

Plasma exosomes have shown great potential for liquid biopsy in clinical cancer diagnosis. Herein, we present an integrated strategy for isolating and analyzing exosomes from human plasma rapidly and then discriminating different cancers excellently based on deep learning fingerprints of plasma exosomes. Sequential size-exclusion chromatography (SSEC) was developed efficiently for separating exosomes from human plasma. SSEC isolated plasma exosomes, taking as less as 2 h for a single sample with high purity such that the discard rates of high-density lipoproteins and low/very low-density lipoproteins were 93 and 85%, respectively. Benefitting from the rapid and high-purity isolation, the contents encapsulated in exosomes, covered by plasma proteins, were well profiled by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS). We further analyzed 220 clinical samples, including 79 breast cancer patients, 57 pancreatic cancer patients, and 84 healthy controls. After MS data pre-processing and feature selection, the extracted MS feature peaks were utilized as inputs for constructing a multi-classifier artificial neural network (denoted as Exo-ANN) model. The optimized model avoided overfitting and performed well in both training cohorts and test cohorts. For the samples in the independent test cohort, it realized a diagnosed accuracy of 80.0% with an area under the curve of 0.91 for the whole group. These results suggest that our integrated pipeline may become a generic tool for liquid biopsy based on the analysis of plasma exosomes in clinics.


Subject(s)
Deep Learning , Exosomes , Neoplasms , Exosomes/chemistry , Humans , Plasma , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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