Front Plant Sci. 2023 Feb 16;14:1093358. doi: 10.3389/fpls.2023.1093358. eCollection 2023.

ABSTRACT

Research strategies that combine molecular data from multiple levels of genome expression (i.e., multi-omics data), often referred to as a systems biology strategy, has been advocated as a route to discovering gene functions. In this study we conducted an evaluation of this strategy by combining lipidomics, metabolite mass-spectral imaging and transcriptomics data from leaves and roots in response to mutations in two AuTophaGy-related (ATG) genes of Arabidopsis. Autophagy is an essential cellular process that degrades and recycles macromolecules and organelles, and this process is blocked in the atg7 and atg9 mutants that were the focus of this study. Specifically, we quantified abundances of ~100 lipids and imaged the cellular locations of ~15 lipid molecular species and the relative abundance of ~26,000 transcripts from leaf and root tissues of WT, atg7 and atg9 mutant plants, grown either in normal (nitrogen-replete) and autophagy-inducing conditions (nitrogen-deficient). The multi-omics data enabled detailed molecular depiction of the effect of each mutation, and a comprehensive physiological model to explain the consequence of these genetic and environmental changes in autophagy is greatly facilitated by the a priori knowledge of the exact biochemical function of the ATG7 and ATG9 proteins.

PMID:36875559 | PMC:PMC9978356 | DOI:10.3389/fpls.2023.1093358

Front Cell Infect Microbiol. 2023 Feb 15;13:1013809. doi: 10.3389/fcimb.2023.1013809. eCollection 2023.

ABSTRACT

BACKGROUND: Differences in bronchial microbiota composition have been found to be associated with asthma; however, it is still unclear whether these findings can be applied to recurrent wheezing in infants especially with aeroallergen sensitization.

OBJECTIVES: To determine the pathogenesis of atopic wheezing in infants and to identify diagnostic biomarkers, we analyzed the bronchial bacterial microbiota of infants with recurrent wheezing and with or without atopic diseases using a systems biology approach.

METHODS: Bacterial communities in bronchoalveolar lavage samples from 15 atopic wheezing infants, 15 non-atopic wheezing infants, and 18 foreign body aspiration control infants were characterized using 16S rRNA gene sequencing. The bacterial composition and community-level functions inferred from between-group differences from sequence profiles were analyzed.

RESULTS: Both α- and β-diversity differed significantly between the groups. Compared to non-atopic wheezing infants, atopic wheezing infants showed a significantly higher abundance in two phyla (Deinococcota and unidentified bacteria) and one genus (Haemophilus) and a significantly lower abundance in one phylum (Actinobacteria). The random forest predictive model of 10 genera based on OTU-based features suggested that airway microbiota has diagnostic value for distinguishing atopic wheezing infants from non-atopic wheezing infants. PICRUSt2 based on KEGG hierarchy (level 3) revealed that atopic wheezing-associated differences in predicted bacterial functions included cytoskeleton proteins, glutamatergic synapses, and porphyrin and chlorophyll metabolism pathways.

CONCLUSION: The differential candidate biomarkers identified by microbiome analysis in our work may have reference value for the diagnosis of wheezing in infants with atopy. To confirm that, airway microbiome combined with metabolomics analysis should be further investigated in the future.

PMID:36875523 | PMC:PMC9975506 | DOI:10.3389/fcimb.2023.1013809

Front Immunol. 2023 Feb 17;14:1127358. doi: 10.3389/fimmu.2023.1127358. eCollection 2023.

ABSTRACT

Coronavirus disease 2019 (COVID-19) is a severe respiratory disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that affects the lower and upper respiratory tract in humans. SARS-CoV-2 infection is associated with the induction of a cascade of uncontrolled inflammatory responses in the host, ultimately leading to hyperinflammation or cytokine storm. Indeed, cytokine storm is a hallmark of SARS-CoV-2 immunopathogenesis, directly related to the severity of the disease and mortality in COVID-19 patients. Considering the lack of any definitive treatment for COVID-19, targeting key inflammatory factors to regulate the inflammatory response in COVID-19 patients could be a fundamental step to developing effective therapeutic strategies against SARS-CoV-2 infection. Currently, in addition to well-defined metabolic actions, especially lipid metabolism and glucose utilization, there is growing evidence of a central role of the ligand-dependent nuclear receptors and peroxisome proliferator-activated receptors (PPARs) including PPARα, PPARβ/δ, and PPARγ in the control of inflammatory signals in various human inflammatory diseases. This makes them attractive targets for developing therapeutic approaches to control/suppress the hyperinflammatory response in patients with severe COVID-19. In this review, we (1) investigate the anti-inflammatory mechanisms mediated by PPARs and their ligands during SARS-CoV-2 infection, and (2) on the basis of the recent literature, highlight the importance of PPAR subtypes for the development of promising therapeutic approaches against the cytokine storm in severe COVID-19 patients.

PMID:36875108 | PMC:PMC9981974 | DOI:10.3389/fimmu.2023.1127358

JACC Adv. 2023 Jan;2(1):100169. doi: 10.1016/j.jacadv.2022.100169. Epub 2023 Jan 27.

ABSTRACT

BACKGROUND: Infants with SVHD experience morbidity related to pulmonary vascular inadequacy. Metabolomic analysis involves a systems biology approach to identifying novel biomarkers and pathways in complex diseases. The metabolome of infants with SVHD is not well understood and no prior study has evaluated the relationship between serum metabolite patterns and pulmonary vascular readiness for staged SVHD palliation.

OBJECTIVES: The purpose of this study was to evaluate the circulating metabolome of interstage infants with single ventricle heart disease (SVHD) and determine whether metabolite levels were associated with pulmonary vascular inadequacy.

METHODS: This was a prospective cohort study of 52 infants with SVHD undergoing Stage 2 palliation and 48 healthy infants. Targeted metabolomic phenotyping (175 metabolites) was performed by tandem mass spectrometry on SVHD pre-Stage 2, post-Stage 2, and control serum samples. Clinical variables were extracted from the medical record.

RESULTS: Random forest analysis readily distinguished between cases and controls and preoperative and postoperative samples. Seventy-four of 175 metabolites differed between SVHD and controls. Twenty-seven of 39 metabolic pathways were altered including pentose phosphate and arginine metabolism. Seventy-one metabolites differed in SVHD patients between timepoints. Thirty-three of 39 pathways were altered postoperatively including arginine and tryptophan metabolism. We found trends toward increased preoperative methionine metabolites in patients with higher pulmonary vascular resistance and higher postoperative tryptophan metabolites in patients with greater postoperative hypoxemia.

CONCLUSIONS: The circulating metabolome of interstage SVHD infants differs significantly from controls and is further disrupted after Stage 2. Several metabolites showed trends toward association with adverse outcomes. Metabolic dysregulation may be an important factor in early SVHD pathobiology.

PMID:36875009 | PMC:PMC9979841 | DOI:10.1016/j.jacadv.2022.100169

Bioinform Adv. 2023 Feb 22;3(1):vbad014. doi: 10.1093/bioadv/vbad014. eCollection 2023.

ABSTRACT

MOTIVATION: Here, we performed a benchmarking analysis of five tools for microbe sequence detection using transcriptomics data (Kraken2, MetaPhlAn2, PathSeq, DRAC and Pandora). We built a synthetic database mimicking real-world structure with tuned conditions accounting for microbe species prevalence, base calling quality and sequence length. Sensitivity and positive predictive value (PPV) parameters, as well as computational requirements, were used for tool ranking.

RESULTS: GATK PathSeq showed the highest sensitivity on average and across all scenarios considered. However, the main drawback of this tool was its slowness. Kraken2 was the fastest tool and displayed the second-best sensitivity, though with large variance depending on the species to be classified. There was no significant difference for the other three algorithms sensitivity. The sensitivity of MetaPhlAn2 and Pandora was affected by sequence number and DRAC by sequence quality and length. Results from this study support the use of Kraken2 for routine microbiome profiling based on its competitive sensitivity and runtime performance. Nonetheless, we strongly endorse to complement it by combining with MetaPhlAn2 for thorough taxonomic analyses.

AVAILABILITY AND IMPLEMENTATION: https://github.com/fjuradorueda/MIME/ and https://github.com/lola4/DRAC/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.

PMID:36874954 | PMC:PMC9976984 | DOI:10.1093/bioadv/vbad014

Synth Syst Biotechnol. 2022 Nov 18;8(1):176-185. doi: 10.1016/j.synbio.2022.11.001. eCollection 2023 Mar.

ABSTRACT

Environmental sustainability is an increasingly important issue in industry. As an environmentally friendly and sustainable way, constructing microbial cell factories to produce all kinds of valuable products has attracted more and more attention. In the process of constructing microbial cell factories, systems biology plays a crucial role. This review summarizes the recent applications of systems biology in the design and construction of microbial cell factories from four perspectives, including functional genes/enzymes discovery, bottleneck pathways identification, strains tolerance improvement and design and construction of synthetic microbial consortia. Systems biology tools can be employed to identify functional genes/enzymes involved in the biosynthetic pathways of products. These discovered genes are introduced into appropriate chassis strains to build engineering microorganisms capable of producing products. Subsequently, systems biology tools are used to identify bottleneck pathways, improve strains tolerance and guide design and construction of synthetic microbial consortia, resulting in increasing the yield of engineered strains and constructing microbial cell factories successfully.

PMID:36874510 | PMC:PMC9979088 | DOI:10.1016/j.synbio.2022.11.001

Front Oncol. 2023 Feb 17;13:1087644. doi: 10.3389/fonc.2023.1087644. eCollection 2023.

ABSTRACT

INTRODUCTION: Colorectal cancer (CRC) remains a significant cause of cancer related mortality. Fat mass and obesity-associated protein (FTO) is a m6A mRNA demethylase that plays an oncogenic role in various malignancies. In this study we evaluated the role of FTO in CRC tumorigenesis.

METHODS: Cell proliferation assays were conducted in 6 CRC cell lines with the FTO inhibitor CS1 (50-3200 nM) (± 5-FU 5-80 mM) and after lentivirus mediated FTO knockdown. Cell cycle and apoptosis assays were conducted in HCT116 cells (24 h and 48 h, 290 nM CS1). Western blot and m6A dot plot assays were performed to assess CS1 inhibition of cell cycle proteins and FTO demethylase activity. Migration and invasion assays of shFTO cells and CS1 treated cells were performed. An in vivo heterotopic model of HCT116 cells treated with CS1 or with FTO knockdown cells was performed. RNA-seq was performed on shFTO cells to assess which molecular and metabolic pathways were impacted. RT-PCR was conducted on select genes down-regulated by FTO knockdown.

RESULTS: We found that the FTO inhibitor, CS1 suppressed CRC cell proliferation in 6 colorectal cancer cell lines and in the 5-Fluorouracil resistant cell line (HCT116-5FUR). CS1 induced cell cycle arrest in the G2/M phase by down regulation of CDC25C and promoted apoptosis of HCT116 cells. CS1 suppressed in vivo tumor growth in the HCT116 heterotopic model (p< 0.05). Lentivirus knockdown of FTO in HCT116 cells (shFTO) mitigated in vivo tumor proliferation and in vitro demethylase activity, cell growth, migration and invasion compared to shScr controls (p< 0.01). RNA-seq of shFTO cells compared to shScr demonstrated down-regulation of pathways related to oxidative phosphorylation, MYC and Akt/ mTOR signaling pathways.

DISCUSSION: Further work exploring the targeted pathways will elucidate precise downstream mechanisms that can potentially translate these findings to clinical trials.

PMID:36874096 | PMC:PMC9981948 | DOI:10.3389/fonc.2023.1087644

Res Pharm Sci. 2023 Jan 19;18(2):159-176. doi: 10.4103/1735-5362.367795. eCollection 2023 Apr.

ABSTRACT

BACKGROUND AND PURPOSE: Recently, the use of immunotoxins for targeted cancer therapy has been proposed, to find new anticancer drugs with high efficacy on tumor cells with minimal side effects on normal cells. we designed and compared several arazyme (AraA)-based fusion proteins with different ligands to choose the best-targeted therapy for interleukin 13 receptor alpha 2 (IL13Rα2)-overexpressed cancer cells. For this purpose, IL13Rα2 was selected as a receptor and IL13 and IL13.E13K were evaluated as native and mutant ligands, respectively. In addition, Pep-1 and A2b11 were chosen as the peptide ligands for targeted cancer therapy.

EXPERIMENTAL APPROACH: Several bioinformatics servers were used for designing constructs and optimization. The structures of the chimeric proteins were predicted and verified by I-TASSER, Q-Mean, ProSA, Ramachandran plot, and Verify3D program. Physicochemical properties, toxicity, and antigenicity were predicted by ProtParam, ToxinPred, and VaxiJen. HawkDock, LigPlot+, and GROMACS software were used for docking and molecular dynamics simulation of the ligand-receptor interaction.

FINDINGS/RESULTS: The in silico results showed AraA-A2b11 has higher values of confidence score and Q-mean score was obtained for high-resolution crystal structures. All chimeric proteins were stable, non-toxic, and non-antigenic. AraA-(A(EAAAK)4ALEA(EAAAK)4A)2-IL13 retained its natural structure and based on ligand-receptor docking and molecular dynamic analysis, the binding ability of AraA-(A(EAAAK)4ALEA(EAAAK)4A)2-IL13 to IL13Rα2 was sufficiently strong.

CONCLUSION AND IMPLICATIONS: Based on the bioinformatics result AraA-(A(EAAAK)4ALEA(EAAAK)4A)2-IL13 was a stable fusion protein with two separate domains and high affinity with the IL13Rα2 receptor. Therefore, AraA-(A(EAAAK)4ALEA(EAAAK)4A)2-IL13 fusion protein could be a new potent candidate for target cancer therapy.

PMID:36873271 | PMC:PMC9976060 | DOI:10.4103/1735-5362.367795

J Nutr Biochem. 2023 Mar 3:109309. doi: 10.1016/j.jnutbio.2023.109309. Online ahead of print.

ABSTRACT

Fish oil or its major constituents, namely omega-3 poly-unsaturated fatty acid (n3-PUFA), are popular supplements to improve neurogenesis, neuroprotection, and overall brain functions. Our objective was to probe the implications of fat enriched diet with variable PUFAs supplements in ameliorating social stress (SS). We fed mice on either of the three diet types, namely the n-3 PUFA-enriched diet (ERD, n3:n6= 7:1), a balanced diet (BLD, n3:n6= 1:1) or a standard lab diet (STD, n3:n6= 1:6). With respect to the gross fat contents, the customized special diets, namely ERD and BLD were extreme diet, not reflecting the typical human dietary composition. Aggressor-exposed SS (Agg-E SS) model triggered behavioral deficiencies that lingered for 6 weeks (6w) post-stress in mice on STD. ERD and BLD elevated bodyweights but potentially helped in building the behavioral resilience to SS. STD adversely affected the gene networks of brain transcriptomics associated with the cell mortality, energy homeostasis and neurodevelopment disorder. Diverging from the ERD's influences on these networks, BLD showed potential long-term benefits in combatting Agg-E SS. The gene networks linked to cell mortality and energy homeostasis, and their subfamilies, such as cerebral disorder and obesity remained at the baseline level of Agg-E SS mice on BLD 6w post-stress. Moreover, neurodevelopment disorder network and its subfamilies like behavioral deficits remained inhibited in the cohort fed on BLD 6w post Agg-E SS.

PMID:36871836 | DOI:10.1016/j.jnutbio.2023.109309

Philos Trans R Soc Lond B Biol Sci. 2023 Apr 24;378(1875):20210477. doi: 10.1098/rstb.2021.0477. Epub 2023 Mar 6.

ABSTRACT

Rhythmic patterns in interactive contexts characterize human behaviours such as conversational turn-taking. These timed patterns are also present in other animals, and often described as rhythm. Understanding fine-grained temporal adjustments in interaction requires complementary quantitative methodologies. Here, we showcase how vocal interactive rhythmicity in a non-human animal can be quantified using a multi-method approach. We record vocal interactions in harbour seal pups (Phoca vitulina) under controlled conditions. We analyse these data by combining analytical approaches, namely categorical rhythm analysis, circular statistics and time series analyses. We test whether pups' vocal rhythmicity varies across behavioural contexts depending on the absence or presence of a calling partner. Four research questions illustrate which analytical approaches are complementary versus orthogonal. For our data, circular statistics and categorical rhythms suggest that a calling partner affects a pup's call timing. Granger causality suggests that pups predictively adjust their call timing when interacting with a real partner. Lastly, the ADaptation and Anticipation Model estimates statistical parameters for a potential mechanism of temporal adaptation and anticipation. Our analytical complementary approach constitutes a proof of concept; it shows feasibility in applying typically unrelated techniques to seals to quantify vocal rhythmic interactivity across behavioural contexts. This article is part of a discussion meeting issue 'Face2face: advancing the science of social interaction'.

PMID:36871583 | DOI:10.1098/rstb.2021.0477

Nat Commun. 2023 Mar 4;14(1):1239. doi: 10.1038/s41467-023-36932-z.

ABSTRACT

Exosomes and extracellular vesicles (EV) are increasingly being explored as circulating biomarkers, but their heterogenous composition will likely mandate the development of multiplexed EV technologies. Iteratively multiplexed analyses of near single EVs have been challenging to implement beyond a few colors during spectral sensing. Here we developed a multiplexed analysis of EV technique (MASEV) to interrogate thousands of individual EVs during 5 cycles of multi-channel fluorescence staining for 15 EV biomarkers. Contrary to the common belief, we show that: several markers proposed to be ubiquitous are less prevalent than believed; multiple biomarkers concur in single vesicles but only in small fractions; affinity purification can lead to loss of rare EV subtypes; and deep profiling allows detailed analysis of EV, potentially improving the diagnostic content. These findings establish the potential of MASEV for uncovering fundamental EV biology and heterogeneity and increasing diagnostic specificity.

PMID:36870999 | DOI:10.1038/s41467-023-36932-z

Cardiovasc Diabetol. 2023 Mar 4;22(1):44. doi: 10.1186/s12933-023-01774-y.

ABSTRACT

BACKGROUND: Obesity is a negative chronic metabolic health condition that represents an additional risk for the development of multiple pathologies. Epidemiological studies have shown how maternal obesity or gestational diabetes mellitus during pregnancy constitute serious risk factors in relation to the appearance of cardiometabolic diseases in the offspring. Furthermore, epigenetic remodelling may help explain the molecular mechanisms that underlie these epidemiological findings. Thus, in this study we explored the DNA methylation landscape of children born to mothers with obesity and gestational diabetes during their first year of life.

METHODS: We used Illumina Infinium MethylationEPIC BeadChip arrays to profile more than 770,000 genome-wide CpG sites in blood samples from a paediatric longitudinal cohort consisting of 26 children born to mothers who suffered from obesity or obesity with gestational diabetes mellitus during pregnancy and 13 healthy controls (measurements taken at 0, 6 and 12 month; total N = 90). We carried out cross-sectional and longitudinal analyses to derive DNA methylation alterations associated with developmental and pathology-related epigenomics.

RESULTS: We identified abundant DNA methylation changes during child development from birth to 6 months and, to a lesser extent, up to 12 months of age. Using cross-sectional analyses, we discovered DNA methylation biomarkers maintained across the first year of life that could discriminate children born to mothers who suffered from obesity or obesity with gestational diabetes. Importantly, enrichment analyses suggested that these alterations constitute epigenetic signatures that affect genes and pathways involved in the metabolism of fatty acids, postnatal developmental processes and mitochondrial bioenergetics, such as CPT1B, SLC38A4, SLC35F3 and FN3K. Finally, we observed evidence of an interaction between developmental DNA methylation changes and maternal metabolic condition alterations.

CONCLUSIONS: Our observations highlight the first six months of development as being the most crucial for epigenetic remodelling. Furthermore, our results support the existence of systemic intrauterine foetal programming linked to obesity and gestational diabetes that affects the childhood methylome beyond birth, which involves alterations related to metabolic pathways, and which may interact with ordinary postnatal development programmes.

PMID:36870961 | DOI:10.1186/s12933-023-01774-y

J Biol Chem. 2023 Mar 2:104575. doi: 10.1016/j.jbc.2023.104575. Online ahead of print.

ABSTRACT

Endosomal Sorting Complex Required for Transport (ESCRT) proteins assemble on the cytoplasmic leaflet of membranes and remodel them. ESCRT is involved in biological processes where membranes are bent away from the cytosol, constricted, and finally severed, such as in multi-vesicular body formation (in the endosomal pathway for protein sorting) or abscission during cell division. The ESCRT system is hijacked by enveloped viruses to allow buds of nascent virions to be constricted, severed and released. ESCRT-III proteins, the most downstream components of the ESCRT system, are monomeric and cytosolic in their autoinhibited conformation. They share a common architecture, a four-helix bundle with a fifth helix that interacts with this bundle to prevent polymerizing. Upon binding to negatively charged membranes, the ESCRT-III components adopt an activated state that allows them to polymerize into filaments and spirals, and to interact with the AAA-ATPase Vps4 for polymer remodeling. ESCRT-III has been studied with electron microscopy (EM) and fluorescence microscopy (FM); these methods provided invaluable information about ESCRT assembly structures or their dynamics, respectively, but neither approach provides detailed insights into both aspects simultaneously. High-speed atomic force microscopy (HS-AFM) has overcome this shortcoming, providing movies at high spatio-temporal resolution of biomolecular processes, significantly increasing our understanding of ESCRT-III structure and dynamics. Here, we review the contributions of HS-AFM in the analysis of ESCRT-III, focusing on recent developments of non-planar and deformable HS-AFM supports. We divide the HS-AFM observations into four sequential steps in the ESCRT-III lifecycle: 1) polymerization, 2) morphology, 3) dynamics, and 4) depolymerization.

PMID:36870686 | DOI:10.1016/j.jbc.2023.104575

Antiviral Res. 2023 Mar 2:105576. doi: 10.1016/j.antiviral.2023.105576. Online ahead of print.

ABSTRACT

Rapid emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prompted an urgent need for the development of broadly applicable and potently neutralizing antibody platform against the SARS-CoV-2, which can be used for combatting the coronavirus disease 2019 (COVID-19). In this study, based on a noncompeting pair of phage display-derived human monoclonal antibodies (mAbs) specific to the receptor-binding domain (RBD) of SARS-CoV-2 isolated from human synthetic antibody library, we generated K202.B, a novel engineered bispecific antibody with an immunoglobulin G4-single-chain variable fragment design, with sub- or low nanomolar antigen-binding avidity. Compared with the parental mAbs or mAb cocktail, the K202.B antibody showed superior neutralizing potential against a variety of SARS-CoV-2 variants in vitro. Furthermore, structural analysis of bispecific antibody-antigen complexes using cryo-electron microscopy revealed the mode of action of K202.B complexed with a fully open three-RBD-up conformation of SARS-CoV-2 trimeric spike proteins by simultaneously interconnecting two independent epitopes of the SARS-CoV-2 RBD via inter-protomer interactions. Intravenous monotherapy using K202.B exhibited potent neutralizing activity in SARS-CoV-2 wild-type- and B.1.617.2 variant-infected mouse models, without significant toxicity in vivo. The results indicate that this novel approach of development of immunoglobulin G4-based bispecific antibody from an established human recombinant antibody library is likely to be an effective strategy for the rapid development of bispecific antibodies, and timely management against fast-evolving SARS-CoV-2 variants.

PMID:36870394 | DOI:10.1016/j.antiviral.2023.105576

Free Radic Biol Med. 2023 Mar 2:S0891-5849(23)00098-9. doi: 10.1016/j.freeradbiomed.2023.02.025. Online ahead of print.

ABSTRACT

Alternative splicing is a key posttranscriptional gene regulatory process, acting in diverse adaptive and basal plant processes. Splicing of precursor-messenger RNA (pre-mRNA) is catalyzed by a dynamic ribonucleoprotein complex, designated the spliceosome. In a suppressor screen, we identified a nonsense mutation in the Smith (Sm) antigen protein SME1 to alleviate photorespiratory H2O2-dependent cell death in catalase deficient plants. Similar attenuation of cell death was observed upon chemical inhibition of the spliceosome, suggesting pre-mRNA splicing inhibition to be responsible for the observed cell death alleviation. Furthermore, the sme1-2 mutants showed increased tolerance to the reactive oxygen species inducing herbicide methyl viologen. Both an mRNA-seq and shotgun proteomic analysis in sme1-2 mutants displayed a constitutive molecular stress response, together with extensive alterations in pre-mRNA splicing of transcripts encoding metabolic enzymes and RNA binding proteins, even under unstressed conditions. Using SME1 as a bait to identify protein interactors, we provide experimental evidence for almost 50 homologs of mammalian spliceosome-associated protein to reside in the Arabidopsis thaliana spliceosome complexes and propose roles in pre-mRNA splicing for four uncharacterized plant proteins. Furthermore, like in sme1-2, a mutant in the Sm core assembly protein ICLN resulted in a decreased sensitivity to methyl viologen. Taken together, these data show that both a perturbed Sm core composition and assembly results in the activation of a defense response and enhanced resilience to oxidative stress.

PMID:36870374 | DOI:10.1016/j.freeradbiomed.2023.02.025

Protein Cell. 2023 Mar 4:pwad010. doi: 10.1093/procel/pwad010. Online ahead of print.

NO ABSTRACT

PMID:36869814 | DOI:10.1093/procel/pwad010

Biol Res. 2023 Mar 3;56(1):8. doi: 10.1186/s40659-023-00419-4.

ABSTRACT

BACKGROUND: Sepsis is an uncontrolled inflammatory response against a systemic infection that results in elevated mortality, mainly induced by bacterial products known as endotoxins, producing endotoxemia. Disseminated intravascular coagulation (DIC) is frequently observed in septic patients and is associated with organ failure and death. Sepsis activates endothelial cells (ECs), promoting a prothrombotic phenotype contributing to DIC. Ion channel-mediated calcium permeability participates in coagulation. The transient reception potential melastatin 7 (TRPM7) non-selective divalent cation channel that also contains an α-kinase domain, which is permeable to divalent cations including Ca2+, regulates endotoxin-stimulated calcium permeability in ECs and is associated with increased mortality in septic patients. However, whether endothelial TRPM7 mediates endotoxemia-induced coagulation is not known. Therefore, our aim was to examine if TRPM7 mediates coagulation during endotoxemia.

RESULTS: The results showed that TRPM7 regulated endotoxin-induced platelet and neutrophil adhesion to ECs, dependent on the TRPM7 ion channel activity and by the α-kinase function. Endotoxic animals showed that TRPM7 mediated neutrophil rolling on blood vessels and intravascular coagulation. TRPM7 mediated the increased expression of the adhesion proteins, von Willebrand factor (vWF), intercellular adhesion molecule 1 (ICAM-1), and P-selectin, which were also mediated by the TRPM7 α-kinase function. Notably, endotoxin-induced expression of vWF, ICAM-1 and P-selectin were required for endotoxin-induced platelet and neutrophil adhesion to ECs. Endotoxemic rats showed increased endothelial TRPM7 expression associated with a procoagulant phenotype, liver and kidney dysfunction, increased death events and an increased relative risk of death. Interestingly, circulating ECs (CECs) from septic shock patients (SSPs) showed increased TRPM7 expression associated with increased DIC scores and decreased survival times. Additionally, SSPs with a high expression of TRPM7 in CECs showed increased mortality and relative risk of death. Notably, CECs from SSPs showed significant results from the AUROC analyses for predicting mortality in SSPs that were better than the Acute Physiology and Chronic Health Evaluation II (APACHE II) and the Sequential Organ Failure Assessment (SOFA) scores.

CONCLUSIONS: Our study demonstrates that sepsis-induced DIC is mediated by TRPM7 in ECs. TRPM7 ion channel activity and α-kinase function are required by DIC-mediated sepsis-induced organ dysfunction and its expression are associated with increased mortality during sepsis. TRPM7 appears as a new prognostic biomarker to predict mortality associated to DIC in SSPs, and as a novel target for drug development against DIC during infectious inflammatory diseases.

PMID:36869357 | DOI:10.1186/s40659-023-00419-4

Sci Rep. 2023 Mar 3;13(1):3626. doi: 10.1038/s41598-023-30536-9.

ABSTRACT

Circulating tumor cells (CTC) have been studied in various solid tumors but clinical utility of CTC in small cell lung cancer (SCLC) remains unclear. The aim of the CTC-CPC study was to develop an EpCAM-independent CTC isolation method allowing isolation of a broader range of living CTC from SCLC and decipher their genomic and biological characteristics. CTC-CPC is a monocentric prospective non-interventional study including treatment-naïve newly diagnosed SCLC. CD56+ CTC were isolated from whole blood samples, at diagnosis and relapse after first-line treatment and submitted to whole-exome-sequencing (WES). Phenotypic study confirms tumor lineage and tumorigenic properties of isolated cells for the 4 patients analyzed with WES. WES of CD56+ CTC and matched tumor biopsy reveal genomic alteration frequently impaired in SCLC. At diagnosis CD56+ CTC were characterized by a high mutation load, a distinct mutational profile and a unique genomic signature, compared to match tumors biopsies. In addition to classical pathways altered in SCLC, we found new biological processes specifically affected in CD56+ CTC at diagnosis. High numeration of CD56+ CTC (> 7/ml) at diagnosis was associated with ES-SCLC. Comparing CD56+ CTC isolated at diagnosis and relapse, we identify differentially altered oncogenic pathways (e.g. DLL3 or MAPK pathway). We report a versatile method of CD56+ CTC detection in SCLC. Numeration of CD56+ CTC at diagnosis is correlated with disease extension. Isolated CD56+ CTC are tumorigenic and show a distinct mutational profile. We report a minimal gene set as a unique signature of CD56+ CTC and identify new affected biological pathways enriched in EpCAM-independent isolated CTC in SCLC.

PMID:36869231 | DOI:10.1038/s41598-023-30536-9

Nat Commun. 2023 Mar 3;14(1):1216. doi: 10.1038/s41467-023-36627-5.

ABSTRACT

Microtubules are a ubiquitous eukaryotic cytoskeletal element typically consisting of 13 protofilaments arranged in a hollow cylinder. This arrangement is considered the canonical form and is adopted by most organisms, with rare exceptions. Here, we use in situ electron cryo-tomography and subvolume averaging to analyse the changing microtubule cytoskeleton of Plasmodium falciparum, the causative agent of malaria, throughout its life cycle. Unexpectedly, different parasite forms have distinct microtubule structures coordinated by unique organising centres. In merozoites, the most widely studied form, we observe canonical microtubules. In migrating mosquito forms, the 13 protofilament structure is further reinforced by interrupted luminal helices. Surprisingly, gametocytes contain a wide distribution of microtubule structures ranging from 13 to 18 protofilaments, doublets and triplets. Such a diversity of microtubule structures has not been observed in any other organism to date and is likely evidence of a distinct role in each life cycle form. This data provides a unique view into an unusual microtubule cytoskeleton of a relevant human pathogen.

PMID:36869034 | DOI:10.1038/s41467-023-36627-5

Antiviral Res. 2023 Mar 1:105571. doi: 10.1016/j.antiviral.2023.105571. Online ahead of print.

ABSTRACT

Development of potent and broad-spectrum antivirals against SARS-CoV-2 remains one of top priorities, especially in the case of that current vaccines cannot effectively prevent viral transmission. We previously generated a group of fusion-inhibitory lipopeptides, with one formulation being evaluated under clinical trials. In this study, we dedicated to characterize the extended N-terminal motif (residues 1161-1168) of the so-called spike (S) heptad repeat 2 (HR2) region. Alanine scanning analysis of this motif verified its critical roles in S protein-mediated cell-cell fusion. Using a panel of HR2 peptides with the N-terminal extensions, we identified a peptide termed P40, which contained four extended N-terminal residues (VDLG) and exhibited improved binding and antiviral activities, whereas the peptides with further extensions had no such effects. Then, we developed a new lipopeptide P40-LP by modifying P40 with cholesterol, which exhibited dramatically increased activities in inhibiting SARS-CoV-2 variants including divergent Omicron sublineages. Moreover, P40-LP displayed a synergistic effect with IPB24 lipopeptide that was designed containing the C-terminally extended residues, and it could effectively inhibit other human coronaviruses, including SARS-CoV, MERS-CoV, HCoV-229E, and HCoV-NL63. Taken together, our results have provided valuable insights for understanding the structure-function relationship of SARS-CoV-2 fusion protein and offered novel antiviral strategies to fight against the COVID-19 pandemic.

PMID:36868315 | DOI:10.1016/j.antiviral.2023.105571