Proteomic Analysis of Caco-2 Cells Disrupted by EcN 1917-Derived OMVs Reveals Molecular Information on Bacteria-Mediated Cancer Cell Migration.

Escherichia coli Nissle 1917 (EcN 1917) exhibits distinct tumor-targeting activity, and early studies demonstrated that outer membrane vesicles (OMVs) mediate bacteria-host interactions. To decipher the molecular mechanism underlying the interaction between EcN 1917 and host cells via OMV-mediated communication, we investigated the phenotypic changes in Caco-2 cells perturbed by EcN 1917-derived OMVs and constructed proteomic maps of the EcN 1917-derived OMV components and OMV-perturbed host cells. Our findings revealed that the size of the EcN 1917-derived OMV proteome increased 4-fold. Treatment with EcN 1917-derived OMVs altered the proteomic and phosphoproteomic profiles of host cells. Importantly, for the first time, we found that treatment with EcN 1917-derived OMVs inhibited cancer cell migration by suppressing the expression of ANXA9. In addition, phosphoproteomic data suggested that the ErbB pathway may be involved in OMV-mediated cell migration. Taken together, our study provides valuable data for further investigations of OMV-mediated bacteria-host interactions and offers great insights into the underlying mechanism of probiotic-assisted colorectal cancer therapy.

Profiling of the Proteins Interacting with Amyloid Beta Peptides in Clinical Samples by PACTS-TPP.

The accumulation of amyloid beta (Aß1-42) results in neurotoxicity and is strongly related to neurodegenerative disorders, especially Alzheimer's disease (AD), but the underlying molecular mechanism is still poorly understood. Therefore, there is an urgent need for researchers to discover the proteins that interact with Aß1-42 to determine the molecular basis. Previously, we developed peptide-ligand-induced changes in the abundance of proTeinS (PACTS)-assisted thermal proteome profiling (TPP) to identify proteins that interact with peptide ligands. In the present study, we applied this technique to analyze clinical samples to identify Aß1-42-interacting proteins. We detected 115 proteins that interact with Aß1-42 in human frontal lobe tissue. Pathway enrichment analysis revealed that the differentially expressed proteins were involved mainly in neurodegenerative diseases. Further orthogonal validation revealed that Aß1-42 interacted with the AD-associated protein mitogen-activated protein kinase 3 (MAPK3), and knockdown of the Aß1-42 amyloid precursor protein (APP) inhibited the MAPK signaling pathway, suggesting potential functional roles for Aß1-42 in interacting with MAPK3. Overall, this study demonstrated the application of the PACTS-TPP in clinical samples and provided a valuable data source for research on neurodegenerative diseases.

Structural insights into the activation and inhibition of CXC chemokine receptor 3.

The chemotaxis of CD4+ type 1 helper cells and CD8+ cytotoxic lymphocytes, guided by interferon-inducible CXC chemokine 9-11 (CXCL9-11) and CXC chemokine receptor 3 (CXCR3), plays a critical role in type 1 immunity. Here we determined the structures of human CXCR3-DNGi complexes activated by chemokine CXCL11, peptidomimetic agonist PS372424 and biaryl-type agonist VUF11222, and the structure of inactive CXCR3 bound to noncompetitive antagonist SCH546738. Structural analysis revealed that PS372424 shares a similar orthosteric binding pocket to the N terminus of CXCL11, while VUF11222 buries deeper and activates the receptor in a distinct manner. We showed an allosteric binding site between TM5 and TM6, accommodating SCH546738 in the inactive CXCR3. SCH546738 may restrain the receptor at an inactive state by preventing the repacking of TM5 and TM6. By revealing the binding patterns and the pharmacological properties of the four modulators, we present the activation mechanisms of CXCR3 and provide insights for future drug development.

Importance of aspartic acid side chain carboxylate-arginine interaction in substrate selection of arginine 2,3-aminomutase BlsG.

The fungicide nucleoside blasticidin S features a ß-arginine, a moiety seldom revealed in the structure of natural products. BlsG, a radical SAM arginine-2,3-aminomutase from the blasticidin S biosynthetic pathway, displayed promiscuous activity to three basic amino acids. Here in this study, we demonstrated that BlsG showed high preference toward its natural substrate arginine. The combined structural modeling, steady-state kinetics, and mutational analyses lead to the detailed understanding of the substrate recognition of BlsG. A single mutation of T340D changed the substrate preference of BlsG leading to a little more preference to lysine than arginine. On the basis of our understanding of the substrate selection of BlsG and bioinformatic analysis, we propose that the D…D motif locationally corresponding to D293 and D330 of KAM is characteristic of lysine 2,3-aminomutase while the corresponding D…T motif is characteristic of arginine 2,3-aminomutase. The study may provide a simple way to discern the arginine 2,3-aminomutase and thus lead to the discovery of new natural compounds with ß-arginine moiety.

A Novel Her2/VEGFR2/CD3 trispecific antibody with an optimal structural design showed improved T-cell-redirecting antitumor efficacy.

Rationale: T-cell-redirecting bispecific antibodies (bsAbs) and trispecific antibodies (tsAbs) designed to recognize different epitopes or antigens have emerged as promising cancer therapies. Current approaches are all designed to include another antibody specific to the site of the primary antibody, and the molecular structures are generally established. However, the dimensions of target molecule and epitope location play a key role in the efficiency of the immunological synapse (IS) formation and subsequent T-cell-redirecting activities, therefore the connection flexibility of these antibodies determines the geometries of different formats of these molecules and will have a major impact on the efficacy. Methods: We describe a novel recombination strategy using various linker designs to site-specifically fuse anti-Her2 (2Rs15) or anti-VEGFR2 (3VGR19) nanobodies to different positions of the anti-CD3 antibody fragment (Fab, SP34). Based on the comparison among the various antigen-specific bsAbs, we could determine the desired fusion site of each nanobody to SP34, and further ensure the optimal structure of tsAbs with synergistic dual-antigen enhanced T-cell-redirecting activities. Results: This approach allows precise control of the formation of IS between Her2- and/or VEGFR2-expressing cancer cells and T cells, to obtain the optimal structure of the Her2/VEGFR2/CD3 tsAb without the need to map antibody-binding epitopes. Optimization of Her2/VEGFR2/CD3 tsAb results in enhanced T-cell-redirecting in vitro and in vivo antitumor efficacy compared with the corresponding bsAbs alone or in combination, and the potency to overcome tumor relapse due to antigen escape or resistance to Herceptin and Cyramza therapy. Conclusion: The novel design strategy for developing tsAbs using a site-specific recombination approach represents a promising platform for immuno-oncology and in applications other than cancer therapy.

Structural basis for recognition of N-formyl peptides as pathogen-associated molecular patterns.

The formyl peptide receptor 1 (FPR1) is primarily responsible for detection of short peptides bearing N-formylated methionine (fMet) that are characteristic of protein synthesis in bacteria and mitochondria. As a result, FPR1 is critical to phagocyte migration and activation in bacterial infection, tissue injury and inflammation. How FPR1 distinguishes between formyl peptides and non-formyl peptides remains elusive. Here we report cryo-EM structures of human FPR1-Gi protein complex bound to S. aureus-derived peptide fMet-Ile-Phe-Leu (fMIFL) and E. coli-derived peptide fMet-Leu-Phe (fMLF). Both structures of FPR1 adopt an active conformation and exhibit a binding pocket containing the R2015.38XXXR2055.42 (RGIIR) motif for formyl group interaction and receptor activation. This motif works together with D1063.33 for hydrogen bond formation with the N-formyl group and with fMet, a model supported by MD simulation and functional assays of mutant receptors with key residues for recognition substituted by alanine. The cryo-EM model of agonist-bound FPR1 provides a structural basis for recognition of bacteria-derived chemotactic peptides with potential applications in developing FPR1-targeting agents.

A trifunctional peptide broadly inhibits SARS-CoV-2 Delta and Omicron variants in hamsters.

The emergence of highly transmissible SARS-CoV-2 variants has led to the waves of the resurgence of COVID-19 cases. Effective antivirals against variants are required. Here we demonstrate that a human-derived peptide 4H30 has broad antiviral activity against the ancestral virus and four Variants of Concern (VOCs) in vitro. Mechanistically, 4H30 can inhibit three distinct steps of the SARS-CoV-2 life cycle. Specifically, 4H30 blocks viral entry by clustering SARS-CoV-2 virions; prevents membrane fusion by inhibiting endosomal acidification; and inhibits the release of virions by cross-linking SARS-CoV-2 with cellular glycosaminoglycans. In vivo studies show that 4H30 significantly reduces the lung viral titers in hamsters, with a more potent reduction for the Omicron variant than the Delta variant. This is likely because the entry of the Omicron variant mainly relies on the endocytic pathway which is targeted by 4H30. Moreover, 4H30 reduces syncytia formation in infected hamster lungs. These findings provide a proof of concept that a single antiviral can inhibit viral entry, fusion, and release.

PACTS-Assisted Thermal Proteome Profiling for Use in Identifying Peptide-Interacting Proteins.

Bioactive peptides play important roles in various biological processes. However, the traditional methods for profiling the peptide-interacting proteins require modifications to the peptide molecules, often leading to false identifications. We found that the interaction between peptide ligands and protein receptors induced significant changes in the abundance of the interacting proteins, which is a signature indicating the interaction and providing complementary information for use in the classical thermal proteome profiling (TPP) technique. Herein, we developed a novel Peptide-ligand-induced Abundance Change of proTeinS (PACTS)-assisted TPP strategy for the identification of peptide-interacting proteins based on the peptide-ligand-induced change in protein abundance. The utility and efficacy of this approach were demonstrated by the identification of the interaction of the protein 3-phosphoinositide-dependent protein kinase 1 (PDPK1) and PDPK1-interacting fragment (PIF) pair and by large-scale profiling of the interacting proteins of PIF. The PACTS-assisted TPP approach was applied to describe the interactome of amyloid beta (Aß) 1-42 in THP-1 cells and resulted in the identification of 103 interacting proteins. Validation experiments indicated that Aß1-42 interacted directly with fatty acid synthase and inhibited its enzymatic activity, providing insights into fatty acid metabolic disorders in Alzheimer's disease (AD). Overall, PACTS-assisted TPP is an efficient approach, and the newly identified Aß-interacting proteins provide rich resources for the research on AD.

A [3Fe-4S] cluster and tRNA-dependent aminoacyltransferase BlsK in the biosynthesis of Blasticidin S.

Blasticidin S is a peptidyl nucleoside antibiotic. Its biosynthesis involves a cryptic leucylation and two leucylated intermediates, LDBS and LBS, have been found in previous studies. Leucylation has been proposed to be a new self-resistance mechanism during blasticidin S biosynthesis, and the leucyl group was found to be important for the methylation of ß-amino group of the arginine side chain. However, the responsible enzyme and its associated mechanism of the leucyl transfer process remain to be elucidated. Here, we report results investigating the leucyl transfer step forming the intermediate LDBS in blasticidin biosynthesis. A hypothetical protein, BlsK, has been characterized by genetic and in vitro biochemical experiments. This enzyme catalyzes the leucyl transfer from leucyl-transfer RNA (leucyl-tRNA) to the ß-amino group on the arginine side chain of DBS. Furthermore, BlsK was found to contain an iron-sulfur cluster that is necessary for activity. These findings provide an example of an iron-sulfur protein that catalyzes an aminoacyl-tRNA (aa-tRNA)-dependent amide bond formation in a natural product biosynthetic pathway.

Hierarchical registration of laser point clouds between airborne and vehicle-borne data considering building eave attributes.

Laser point cloud registration is a key step in multisource laser scanning data fusion and application. Aimed at the problems of fewer overlapping regional features and the influence of building eaves on registration accuracy, a hierarchical registration algorithm of laser point clouds that considers building eave attributes is proposed in this paper. After extracting the building feature points of airborne and vehicle-borne light detection and ranging data, the similarity measurement model is constructed to carry out coarse registration based on pseudo-conjugate points. To obtain the feature points of the potential eaves (FPPE), the building contour lines of the vehicle-borne data are extended using the direction prediction algorithm. The FPPE data are regarded as the search set, in which the iterative closest point (ICP) algorithm is employed to match the true conjugate points between the airborne laser scanning data and vehicle-borne laser scanning data. The ICP algorithm is used again to complete the fine registration. To evaluate the registration performance, the developed method was applied to the data processing near Shandong University of Science and Technology, Qingdao, China. The experimental results showed that the FPPE dataset can effectively address the coarse registration accuracy effects on the convergence of the iterative ICP. Before considering eave attributes, the mean registration errors (MREs) of the proposed method in the xoz plane, yoz plane, and xoy plane are 0.318, 0.96, and 0.786 m, respectively. After considering eave attributes, the MREs decrease to 0.129, 0.187, and 0.169 m, respectively. The developed method can effectively improve the registration accuracy of the laser point clouds, which not only solves the problem of matching true conjugate points under the effects of the eaves but also avoids converging to a local minimum due to ICP's poor coarse registration.

Clinical features and corresponding immune function status of recurrent viral polymerase chain reaction positivity in patients with COVID-19 : A meta- analysis and systematic review.

INTRODUCTION: Coronavirus disease 2019 (COVID-19) was declared a global pandemic in March 2020. Since then, several studies have found COVID-19 patients with recurrent viral polymerase chain reaction (PCR) positivity. METHODS: On May 6, 2021, an exhaustive literature search of the Web of Science, PubMed, Cochrane Library, Chinese National Knowledge Infrastructure databases, Embase, Wan Fang Data, VIP database, Sinomed database, BioRxiv, MedRxiv, and Research Square was conducted to find describing the laboratory indicators of recurrent and non-recurrent viral PCR positivity in patients with COVID-19. The data were statistically analyzed using STATA version 15.0. RESULTS: In total, 22 studies-comprising 5154 laboratory-confirmed COVID-19 cases-were included in the analyses. Patients with less severe COVID-19 illness (i.e. those clinically classified as mild or common-type) seemed to exhibit recurrent PCR positivity more commonly than patients with more severe illness (i.e. those classified as severe or critical). There were also significant differences between the two groups in terms of the rates of headaches and dizziness, in addition to the levels of aspartate aminotransferase, C reactive protein, interleukin-6, and lactate dehydrogenase. Further, there were variations in the ratio of CD4+ T cells/CD8+ T cells on admission to the hospital. CONCLUSION: In comparison to COVID-19 patients with non-recurrent viral PCR positivity, patients with recurrent virus PCR positivity seem to experience more severe immune function suppression upon hospital admission.

Reactivation of SARS-CoV-2 infection following recovery from COVID-19.

INTRODUCTION: Many individuals test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA after recovering from the coronavirus disease (COVID-19), but the incidence of reactivation is unknown. We, therefore, estimated the incidence of reactivation among individuals who had recovered from COVID-19 and determined its predictors. METHODS: In this retrospective cohort study, patients with COVID-19 were followed up for at least 14 days after two consecutive negative SARS-CoV-2 polymerase chain reaction test results obtained ≥24 h apart, and the frequency of SARS-CoV-2 reactivation was assessed. RESULTS: Of the 109 patients, 29 (27%) experienced reactivation, and seven (24%) of these were symptomatic. The mean period for the real-time PCR tests for SARS-CoV-2 from negative to positive results was 17 days. Compared with patients without reactivation, those with reactivation were significantly younger and more likely to have a lymphocyte count of <1500/µL (odds ratio [OR]: 0.34, 95% confidence interval [CI]: 0.12-0.94) and two or fewer symptoms (OR: 0.20, 95% CI: 0.07-0.55) during the initial episode. CONCLUSION: Risk-stratified surveillance should be conducted among patients who have recovered from COVID-19.

The predictive effect of the platelet-to-lymphocyte ratio (PLR) and the neutrophil-to-lymphocyte ratio (NLR) on the risk of death in patients with severe fever with thrombocytopenia syndrome (SFTS): a multi-center study in China.

BACKGROUND: Severe fever with thrombocytopenia syndrome is caused by infection with the severe fever with thrombocytopenia syndrome virus. METHODS: Between April 2011 and December 2019, data on consecutive patients who were diagnosed with severe fever with thrombocytopenia syndrome were prospectively collected from five medical centers in China. The score of the death risk model was correlated with the platelet-to-lymphocyte ratio and the neutrophil-to-lymphocyte ratio. Multivariable Cox analyses were used to identify the independent factors associated with mortality. RESULTS: During the study period, 763 patients were diagnosed with severe fever with thrombocytopenia syndrome; 415 of these patients were enrolled in our study. We found that the neutrophil-to-lymphocyte ratio of the group that died was significantly higher on admission (P=0.007) than that of the group that survived, and the neutrophil-to-lymphocyte ratio showed a positive correlation with the score of the death risk model. Multivariate Cox regression suggested that a neutrophil-to-lymphocyte ratio greater than 5.4 was an independent risk factor for survival time (HR=6.767, P=0.011). Platelet-to-lymphocyte ratio did not show a special role in this study. CONCLUSIONS: A neutrophil-to-lymphocyte ratio greater than 5.4 can increase the risk of death and decrease the survival time of patients. In summary, the neutrophil-to-lymphocyte ratio provides a supplementary means for effectively managing severe fever with thrombocytopenia syndrome (SFTS).

Hydroa Vacciniforme-like Lymphoproliferative disorder in an adult invades the liver and bone marrow with clear pathological evidence: a case report and literature review.

BACKGROUND: Hydroa Vacciniforme-like Lymphoproliferative Disorder (HV-LPD) is the name given to a group of Epstein-Barr virus (EBV)-associated diseases. It resembles hydroa vacciniforme (HV), the rarest form of photosensitivity, and is a T-cell disorder associated with an Epstein-Barr virus infection. The majority of diagnosed cases occur in East Asia and South America. It is rare in the United States and Europe. Multiple studies have revealed the clinical manifestation of an enlarged liver, but no gold standard such as pathology has yet supported this as a clinical sign of HV-LPD. CASE PRESENTATION: Here, we report a case of a 34-year-old Asian female with definite liver invasion. The patient had complained of a recurring facial rash for many years. The patient was admitted to the hospital because of an enlarged liver. After hospitalization, she was given an EB virus nucleic acid test. The EB virus nucleic acid test was positive, and pathological examination suggested that HV-LPD had invaded the skin, bone marrow, and liver. After being given antiviral treatment, the patient's symptoms were mitigated. CONCLUSIONS: Our case confirms the liver damage was caused by HV-LPD and the effectiveness of antiviral treatment.

Clinical manifestations of death with severe fever and thrombocytopenia syndrome: A meta-analysis and systematic review.

Severe hemorrhagic fever disease is caused by severe fever with thrombocytopenia syndrome virus (SFTSV) infection, which belongs to the Phlebovirus genus in the Bunyaviridae family. A comprehensive literature search of PubMed, Web of Science, Embase, Cochrane Library, Chinese National Knowledge Infrastructure databases, Wan Fang Data, Sinomed Database, and VIP database was conducted for articles which have described the clinical manifestation of deceased patients. Data from selected studies were pooled by using STATA VERSION 15.0 software. Finally, 29 articles comprising 4717 laboratory-confirmed SFTSV cases were included in this analysis. We found there were significant differences between the two groups for fatigue, headache, underlying disease, vomiting, diarrhea, skin bleeding, neurological symptoms, arrhythmia, diffuse intravascular coagulation, and multiple organ failure. There were some significant differences between the fatal and nonfatal groups, and we need to pay more attention to the above symptoms to distinguish between fatal and nonfatal patients.

Improved progressive triangular irregular network densification filtering algorithm for airborne LiDAR data based on a multiscale cylindrical neighborhood.

Laser point cloud filtering is a fundamental step in various applications of light detection and ranging (LiDAR) data. The progressive triangulated irregular network (TIN) densification (PTD) filtering algorithm is a classic method and is widely used due to its robustness and effectiveness. However, the performance of the PTD filtering algorithm depends on the quality of the initial TIN-based digital terrain model (DTM). The filtering effect is also limited by the tuning of a number of parameters to cope with various terrains. Therefore, an improved PTD filtering algorithm based on a multiscale cylindrical neighborhood (PTD-MSCN) is proposed and implemented to enhance the filtering effect in complex terrains. In the PTD-MSCN algorithm, the multiscale cylindrical neighborhood is used to obtain and densify ground seed points to create a high-quality DTM. By linearly decreasing the radius of the cylindrical neighborhood and the distance threshold, the PTD-MSCN algorithm iteratively finds ground seed points and removes object points. To evaluate the performance of the proposed PTD-MSCN algorithm, it was applied to 15 benchmark LiDAR datasets provided by the International Society for Photogrammetry and Remote Sensing (ISPRS) commission. The experimental results indicated that the average total error can be decreased from 5.31% when using the same parameter set to 3.32% when optimized. Compared with five other publicized PTD filtering algorithms, the proposed PTD-MSCN algorithm is not only superior in accuracy but also more robust.

Functional mosaic organization of neuroligins in neuronal circuits.

Complex brain circuitry with feedforward and feedback systems regulates neuronal activity, enabling neural networks to process and drive the entire spectrum of cognitive, behavioral, sensory, and motor functions. Simultaneous orchestration of distinct cells and interconnected neural circuits is underpinned by hundreds of synaptic adhesion molecules that span synaptic junctions. Dysfunction of a single molecule or molecular interaction at synapses can lead to disrupted circuit activity and brain disorders. Neuroligins, a family of cell adhesion molecules, were first identified as postsynaptic-binding partners of presynaptic neurexins and are essential for synapse specification and maturation. Here, we review recent advances in our understanding of how this family of adhesion molecules controls neuronal circuit assembly by acting in a synapse-specific manner.

Guanidine N-methylation by BlsL Is Dependent on Acylation of Beta-amine Arginine in the Biosynthesis of Blasticidin S.

The peptidyl nucleoside blasticidin S (BS) produced by Streptomyces griseochromogenes was the first non-mercurial fungicide used to prevent rice blast and increasingly used as a selection reagent in transgenic study. Acylation by addition of a leucine residue at the beta amine group of arginine side chain of demethylblasticidin S (DBS) has been proposed as a novel self-resistance to the cytotoxic biosynthetic intermediate. But the resultant product leucyldemethylblasticidin S (LDBS) has not been isolated as a metabolite, and LDBS synthetase activity remained to be demonstrated in S. griseochromogenes. In this study, we isolated LDBS in a BS heterologous producer S. lividans WJ2 upon the deletion of blsL, which encodes a S-Adenosyl methionine-dependent methyltransferase. Purified BlsL efficiently methylated LDBS at the delta N of beta-arginine to generate the ultimate intermediate LBS, but nearly didn't methylate DBS to final product BS. Above experiments demonstrated that LDBS is indeed an intermediate in BS biosynthetic pathway, and acylation of beta-amino group of arginine side chain is prerequisite for efficient guanidine N-methylation in addition to being a self-resistance mechanism.

[Factors Associated with Successful Submucosal Tunneling Endoscopic Resection Treatment for Upper Gastrointestinal Submucosal Tumors].

OBJECTIVE: To determine the influence of location, depth and size of upper gastrointestinal (GI) submucosal tumors (SMTs) on the success of submucosal tunneling endoscopic resection (STER). METHODS: Patient records of 31 cases with upper GI SMTs who had STER between Jan. 1, 2014 and June 30, 2015 in West China Hospital of Sichuan University were retrieved. The success of STER was determined by its efficiency, complete resection rate, and incidence of complications. RESULTS: Of the 31 cases, 29 were treated successfully, with an average of (13.76 +/- 9.70) min and (32.00 +/- 27.35) min for tunnel formation of esophageal and stomach mucosal tumors respectively (P = 0.045). The 2 unsuccessful cases were gastric tumors. SMTs resection for mucous layer and muscularis propria took (17.50 +/- 9.06) min and (36.24 +/- 15.68) min, respectively (P=0.004). SMTs resection for tumors diameter < 2.0 cm and > or = 2.0 cm took (25.78 +/- 12.13) min and (39.73 +/- 19.23) min, respectively (P=0.023). Six cases of gastric tumors from muscularis propria had complications (19.4%) during or after surgery. CONCLUSION: Location, depth and size of upper GI SMTs has implications on duration of different STER stages, which may determine complete resection rate and incidence of complications.