Classical swine fever virus non-structural protein 5B hijacks host METTL14-mediated m6A modification to counteract host antiviral immune response.

Classical Swine Fever (CSF), caused by the Classical Swine Fever Virus (CSFV), inflicts significant economic losses on the global pig industry. A key factor in the challenge of eradicating this virus is its ability to evade the host's innate immune response, leading to persistent infections. In our study, we elucidate the molecular mechanism through which CSFV exploits m6A modifications to circumvent host immune surveillance, thus facilitating its proliferation. We initially discovered that m6A modifications were elevated both in vivo and in vitro upon CSFV infection, particularly noting an increase in the expression of the methyltransferase METTL14. CSFV non-structural protein 5B was found to hijack HRD1, the E3 ubiquitin ligase for METTL14, preventing METTL14 degradation. MeRIP-seq analysis further revealed that METTL14 specifically targeted and methylated TLRs, notably TLR4. METTL14-mediated regulation of TLR4 degradation, facilitated by YTHDF2, led to the accelerated mRNA decay of TLR4. Consequently, TLR4-mediated NF-κB signaling, a crucial component of the innate immune response, is suppressed by CSFV. Collectively, these data effectively highlight the viral evasion tactics, shedding light on potential antiviral strategies targeting METTL14 to curb CSFV infection.

Cellular ESCRT components are recruited to regulate the endocytic trafficking and RNA replication compartment assembly during classical swine fever virus infection.

As the important molecular machinery for membrane protein sorting in eukaryotic cells, the endosomal sorting and transport complexes (ESCRT-0/I/II/III and VPS4) usually participate in various replication stages of enveloped viruses, such as endocytosis and budding. The main subunit of ESCRT-I, Tsg101, has been previously revealed to play a role in the entry and replication of classical swine fever virus (CSFV). However, the effect of the whole ESCRT machinery during CSFV infection has not yet been well defined. Here, we systematically determine the effects of subunits of ESCRT on entry, replication, and budding of CSFV by genetic analysis. We show that EAP20 (VPS25) (ESCRT-II), CHMP4B and CHMP7 (ESCRT-III) regulate CSFV entry and assist vesicles in transporting CSFV from Clathrin, early endosomes, late endosomes to lysosomes. Importantly, we first demonstrate that HRS (ESCRT-0), VPS28 (ESCRT-I), VPS25 (ESCRT-II) and adaptor protein ALIX play important roles in the formation of virus replication complexes (VRC) together with CHMP2B/4B/7 (ESCRT-III), and VPS4A. Further analyses reveal these subunits interact with CSFV nonstructural proteins (NS) and locate in the endoplasmic reticulum, but not Golgi, suggesting the role of ESCRT in regulating VRC assembly. In addition, we demonstrate that VPS4A is close to lipid droplets (LDs), indicating the importance of lipid metabolism in the formation of VRC and nucleic acid production. Altogether, we draw a new picture of cellular ESCRT machinery in CSFV entry and VRC formation, which could provide alternative strategies for preventing and controlling the diseases caused by CSFV or other Pestivirus.

MCPIP1 restrains mucosal inflammation by orchestrating the intestinal monocyte to macrophage maturation via an ATF3-AP1S2 axis.

OBJECTIVE: Monocyte chemotactic protein-1-induced protein 1 (MCPIP1) is highly expressed in inflamed mucosa of inflammatory bowel disease (IBD) and negatively regulates immune response, while the underlying mechanisms regulating mucosal macrophage functions remain unknown. Here, we investigated the roles of MCPIP1 in modulating the differentiation and functions of intestinal macrophages in the pathogenesis of IBD. DESIGN: ScRNA-seq was used to cluster the monocyte/macrophage lineage from macrophage-specific Mcpip1-deficient (Mcpip1 ∆Mye) mice and Mcpip1 fl/fl littermates. The differentially expressed genes were confirmed by RNA-seq, luciferase assay, CUT&Tag assay and Western blotting. Effects of MCPIP1 and the activating transcription factor 3 (ATF3)-AP1S2 axis were assessed in patients with IBD. RESULTS: Mcpip1 ∆Mye mice developed more severe dextran sulfate sodium (DSS)-induced colitis characterised by an increase in macrophage migratory capacity and M1 macrophage polarisation but a decrease in the monocyte-to-macrophage maturation in gut mucosa compared with their littermates. ScRNA-seq unravelled a proinflammatory population (Ccr2+Il-1ß+Tlr2+Cx3cr1-Cd163-Mrc1-Ly6c+) of the monocyte/macrophage lineage from lamina propria CD11b+ cells and an arrest of Mcpip1 ∆Mye monocyte-to-macrophage maturation in an Atf3-Ap1s2 axis-dependent manner. Silencing of Ap1s2 or Atf3 markedly suppressed Mcpip1 ∆Mye macrophage migration, M1-like polarisation, and production of proinflammatory cytokines and chemokines. Notably, in vivo blockage of Ap1s2 ameliorated DSS-induced colitis in Mcpip1 ΔMye mice through enhancing intestinal macrophage maturation. Furthermore, MCPIP1, ATF3 and AP1S2 were highly expressed in inflamed mucosa of active patients with IBD and blockage of ATF3 or AP1S2 significantly suppressed IBD CD14+-derived M1-like macrophage polarisation and proinflammatory cytokine production. CONCLUSIONS: Macrophage-specific Mcpip1 deficiency polarises macrophages towards M1-like phenotype, arrests macrophage maturation and exacerbates intestinal inflammation in an Atf3-Ap1s2-dependent manner, thus providing novel mechanistic insight into intestinal macrophage functions during IBD.

Outstanding Electrochemical Performance of Ni-Rich Concentration-Gradient Cathode Material LiNi0.9Co0.083Mn0.017O2 for Lithium-Ion Batteries.

The full-concentrationgradient LiNi0.9Co0.083Mn0.017O2 (CG-LNCM), consisting of core Ni-rich LiNi0.93Co0.07O2, transition zone LiNi1-x-yCoxMnyO2, and outmost shell LiNi1/3Co1/3Mn1/3O2 was prepared by a facile co-precipitation method and high-temperature calcination. CG-LNCM was then investigated with an X-ray diffractometer, ascanning electron microscope, a transmission electron microscope, and electrochemical measurements. The results demonstrate that CG-LNCM has a lower cation mixing of Li+ and Ni2+ and larger Li+ diffusion coefficients than concentration-constant LiNi0.9Co0.083Mn0.017O2 (CC-LNCM). CG-LNCM presents a higher capacity and a better rate of capability and cyclability than CC-LNCM. CG-LNCM and CC-LNCM show initial discharge capacities of 221.2 and 212.5 mAh g-1 at 0.2C (40 mA g-1) with corresponding residual discharge capacities of 177.3 and 156.1 mAh g-1 after 80 cycles, respectively. Even at high current rates of 2C and 5C, CG-LNCM exhibits high discharge capacities of 165.1 and 149.1 mAh g-1 after 100 cycles, respectively, while the residual discharge capacities of CC-LNCM are as low as 148.8 and 117.9 mAh g-1 at 2C and 5C after 100 cycles, respectively. The significantly improved electrochemical performance of CG-LNCM is attributed to its concentration-gradient microstructure and the composition distribution of concentration-gradient LiNi0.9Co0.083Mn0.017O2. The special concentration-gradient design and the facile synthesis are favorable for massive manufacturing of high-performance Ni-rich ternary cathode materials for lithium-ion batteries.

The cellular function and molecular mechanism of formaldehyde in cardiovascular disease and heart development.

As a common air pollutant, formaldehyde is widely present in nature, industrial production and consumer products. Endogenous formaldehyde is mainly produced through the oxidative deamination of methylamine catalysed by semicarbazide-sensitive amine oxidase (SSAO) and is ubiquitous in human body fluids, tissues and cells. Vascular endothelial cells and smooth muscle cells are rich in this formaldehyde-producing enzyme and are easily damaged owing to consequent cytotoxicity. Consistent with this, increasing evidence suggests that the cardiovascular system and stages of heart development are also susceptible to the harmful effects of formaldehyde. Exposure to formaldehyde from different sources can induce heart disease such as arrhythmia, myocardial infarction (MI), heart failure (HF) and atherosclerosis (AS). In particular, long-term exposure to high concentrations of formaldehyde in pregnant women is more likely to affect embryonic development and cause heart malformations than long-term exposure to low concentrations of formaldehyde. Specifically, the ability of mouse embryos to effect formaldehyde clearance is far lower than that of the rat embryos, more readily allowing its accumulation. Formaldehyde may also exert toxic effects on heart development by inducing oxidative stress and cardiomyocyte apoptosis. This review focuses on the current progress in understanding the influence and underlying mechanisms of formaldehyde on cardiovascular disease and heart development.

MicroRNA-302c-3p inhibits endothelial cell pyroptosis via directly targeting NOD-, LRR- and pyrin domain-containing protein 3 in atherosclerosis.

Inflammation and endothelial dysfunction are important participants and drivers in atherosclerosis. NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome activation and the resulting pyroptosis are involved in the initiation and vicious circle of chronic inflammation, thus playing an indispensable role in atherosclerosis. Accordingly, blocking the activation of NLRP3 inflammasome may be a promising treatment strategy to blunt the progression of atherosclerosis. In this study, it was demonstrated that miR-302c-3p exerted anti-pyroptosis effects by directly targeting NLRP3 in vivo and in vitro. In brief, the expression of miR-302c-3p was down-regulated whereas the expression of NLRP3 was up-regulated in human plaques and in vitro pyroptosis model of endothelial cells. Overexpression of miR-302c-3p suppressed endothelial cell pyroptosis by targeting specific sites of NLRP3. By comparison, down-regulation of endogenous miR-302c-3p led to the opposite results, which were reversed by silencing the expression of NLRP3. Finally, the up-regulation of miR-302c-3p inhibited the inflammation and pyroptosis of atherosclerosis mouse model. In conclusion, miR-302c-3p may be a powerful and attractive target for suppressing endothelial inflammation and pyroptosis, providing a novel strategy for preventing or alleviating the progression of atherosclerosis.

SIS3, a specific inhibitor of smad3, attenuates bleomycin-induced pulmonary fibrosis in mice.

Pulmonary fibrosis (PF) is a fatal respiratory disease with no effective medical treatments available. TGF-ß/Smads signaling has been implicated to play an essential in the pathogenesis of PF, in which Smad3 act as the integrator of pro-fibrosis signals. In this study, we determined the effect of SIS3, a specific inhibitor of Smad3, in an experimental mouse model of lung fibrosis. We observed that SIS3 treatment significantly reduced bleomycin (BLM)-induced pathological changes and collagen deposition in the lung as indicated by Masson staining, real-time PCR and hydroxyproline content assay. As expected, the levels of Smad3 phosphorylation were decreased in the lung of mice treated with SIS3. Furthermore, SIS3 treatment also suppressed BLM-induced infiltration of inflammatory cells in the lung. Taken together, our results suggest that SIS3 ameliorated BLM-induced PF in mouse lungs. Thus, targeting Smad3 with SIS3 may be an effective approach for treatment of fibrotic disorders.

Role and mechanism of miR-871-3p/Megf8 in regulating formaldehyde-induced cardiomyocyte inflammation and congenital heart disease.

OBJECTIVE AND DESIGN: We aimed to investigate the molecular mechanism underlying formaldehyde (FA)-induced congenital heart disease (CHD) using in vitro and in vivo models. MATERIALS AND SUBJECTS: Neonatal rat heart tissues and H9C2 cells were used for in vitro studies, while FA-exposed new-born rats were used for in vivo studies. TREATMENT: H9C2 cells were exposed to FA concentrations of 0, 50, 100 and 150 µM/mL for 24 h. METHODS: Whole transcriptome gene sequencing identified differentially expressed miRNAs in neonatal rat heart tissues, while Real-time quantitative PCR (RT-qPCR) assessed miR-871-3p and Megf8 expression. RNA pull-down and dual-luciferase reporter assays determined miR-871-3p and Megf8 relationships. Inflammatory cytokine expression was assessed by western blotting. A FA-induced CHD model was used to validate miR-871-3p regulatory effects in vivo. RESULTS: We identified 89 differentially expressed miRNAs, with 28 up-regulated and 61 down-regulated (fold change ≥ 2.0, P < 0.05). Inflammation (interleukin) and signalling pathways were found to control FA-induced cardiac dysplasia. miR-871-3p was upregulated in FA-exposed heart tissues, modulated inflammation, and directly targeted Megf8. In vivo experiments showed miR-871-3p knockdown inhibited FA-induced inflammation and CHD. CONCLUSION: We demonstrated miR-871-3p's role in FA-induced CHD by targeting Megf8, providing potential targets for CHD intervention and improved diagnosis and treatment strategies.

Development and validation of a novel criterion of histologic healing in ulcerative colitis defined by inflammatory cell enumeration in lamina propria mucosa: A multicenter retrospective cohort in China.

BACKGROUND: Histological healing is closely associated with improved long-term clinical outcomes and lowered relapses in patients with ulcerative colitis (UC). Here, we developed a novel diagnostic criterion for assessing histological healing in UC patients. METHODS: We conducted a retrospective cohort study in UC patients, whose treatment was iteratively optimized to achieve mucosal healing at Shanghai Tenth People's Hospital of Tongji University from January 2017 to May 2022. We identified an inflammatory cell enumeration index (ICEI) for assessing histological healing based on the proportions of eosinophils, CD177 + neutrophils, and CD40L + T cells in the colonic lamina propria under high power field (HPF), and the outcomes (risks of symptomatic relapses) of achieving histological remission vs . persistent histological inflammation using Kaplan-Meier curves. Intrareader reliability and inter-reader reliability were evaluated by each reader. The relationships to the changes in the Nancy index and the Geboes score were also assessed for responsiveness. The ICEI was further validated in a new cohort of UC patients from other nine university hospitals. RESULTS: We developed an ICEI for clinical diagnosis of histological healing, i.e., Y = 1.701X 1 + 0.758X 2 + 1.347X 3 - 7.745 (X 1 , X 2 , and X 3 represent the proportions of CD177 + neutrophils, eosinophils, and CD40L + T cells, respectively, in the colonic lamina propria under HPF). The receiver operating characteristics curve (ROC) analysis revealed that Y <-0.391 was the cutoff value for the diagnosis of histological healing and that an area under the curve (AUC) was 0.942 (95% confidence interval [CI]: 0.905-0.979) with a sensitivity of 92.5% and a specificity of 83.6% ( P  <0.001). The intraclass correlation coefficient (ICC) for the intrareader reliability was 0.855 (95% CI: 0.781-0.909), and ICEI had good inter-reader reliability of 0.832 (95% CI: 0.748-0.894). During an 18-month follow-up, patients with histological healing had a substantially better outcome compared with those with unachieved histological healing ( P  <0.001) using ICEI. During a 12-month follow-up from other nine hospitals, patients with histological healing also had a lower risk of relapse than patients with unachieved histological healing. CONCLUSIONS: ICEI can be used to predict histological healing and identify patients with a risk of relapse 12 months and 18 months after clinical therapy. Therefore, ICEI provides a promising, simplified approach to monitor histological healing and to predict the prognosis of UC. REGISTRATION: Chinese Clinical Trial Registry, No. ChiCTR2300077792.

Evolutionary analysis of stakeholder behavior in green retrofitting of traditional residential buildings based on dissemination and game models.

To achieve carbon peaking and carbon neutrality goals in China, green retrofitting of traditional residential buildings is the one of the important ways. Therefore, the dynamics process of the change of the resident group intention to retrofit and its impact on the behavior of the tripartite game between the government, investment retrofitting enterprises and residents needs to be analyzed. Firstly, a dissemination model of green retrofitting intentions among resident groups is constructed, and it is coupled with the tripartite game model. Then, through numerical simulation, the dissemination laws of intention for green retrofitting among resident groups and its influence on the evolution process of the tripartite game are analyzed. The results show that: (1) The rate at which the triad of government, investment retrofitting enterprises and residents reaches steady state is influenced by the impact of changes in the level of social climate on the rate of conversion of potential and participating residents to immune residents. When the rate of enterprises investment and residents participation increases, the rate of government choice of incentive strategies decreases; (2) greater government regulation and subsidies will increase the intention of residents and retrofitting enterprises to participate. The ideal steady state without government incentives can be achieved when the group size of participating residents is increased by improving the level of government publicity and education and the technology level of the enterprises; (3) the intention of enterprises to invest is closely related to the cognitive benefits and the level of risk perception of residents. The conclusions of the study can be used as a reference for the government to make green retrofitting policies for traditional residential buildings.

Evolutionary analysis of resident groups' intention to participate in green retrofit PPP projects of traditional apartment complexes.

Green retrofit PPP projects of traditional apartment complexes play an important role in promoting the green and low-carbon transformation of the construction industry and achieving China's "double carbon" goals. The integrated retrofit of apartment complexes presupposes that the resident groups agree to the retrofit. Therefore, it is necessary to study the evolutionary mechanism of residents' intention to green retrofit and the transformation process of their behavior, and to explore how to enhance residents' intention to participate. First, the dissemination model of residents' intention to green retrofit is constructed. Then, the strategic interaction among government, social capitals and residents under the PPP model is introduced into the dissemination model to define the state transformation probability of resident groups. Finally, the evolution laws of residents' intention to green retrofit are analyzed. The results show that: (1) the behavior of government regulation and social capitals' effort to retrofit can motivate the number of the resident agreeing to green retrofit to meet the proportional limit, (2) the faster the government chooses the strategy of regulation and the social capitals choose the strategy of effort to retrofit, the faster the number of residents agreeing to green retrofit reaches a steady state, (3) when the level of government publicity and education is too low, the cost of government regulation or the subsidy given to residents is too high, the green retrofit of traditional apartment complexes cannot be achieved. The research conclusions can provide a reference for the government to formulate green retrofit policies.

Porcine Mx proteins inhibit pseudorabies virus replication through interfering with early gene synthesis.

Pseudorabies virus (PRV) is an enveloped, linear double-stranded DNA herpesvirus that resulted in huge financial losses to the swine industry. In addition to vaccination, the development of antiviral molecules is also a beneficial supplement to the control of Pseudorabies (PR). Although our previous studies have shown that porcine Mx protein (poMx1/2) significantly inhibited the proliferation of RNA virus, it was unknown whether poMx1/2 could inhibit porcine DNA virus, such as PRV. In this study, it was investigated the inhibitory effect of porcine Mx1/2 protein on PRV multiplication. The results showed that both poMx1 and poMx2 had anti-PRV activities, which required GTPase ability and stable oligomerization. Interestingly, the two GTPase deficient mutants (G52Q and T148A) of poMx2 also had the antiviral ability against PRV, which was consistent with previous reports, indicating that these mutants recognized and blocked the viral targets. Mechanistically, the antiviral restriction of poMx1/2 came from their inhibition of the early gene synthesis of PRV. Our results for the first time shed light on the antiviral activities of two poMx proteins against DNA virus. The data from this study provide further insights to develop new strategies for preventing and controlling the diseases caused by PRV.

Identification of long non-coding RNA in formaldehyde-induced cardiac dysplasia in rats.

Formaldehyde exposure during pregnancy can cause fetal congenital heart disease (CHD). However, the regulatory mechanism remains unclear. Studies on the biology of long non-coding RNAs (lncRNAs) show that lncRNAs can influence cardiac development and disease. However, expression patterns and regulatory mechanisms of action of lncRNAs in formaldehyde-induced CHD remain unclear. We used high-throughput sequencing strategies as a means of identifying lncRNA expression profiles in heart tissues of normal and formaldehyde-exposed newborn rats. Overall, 763 differentially expressed lncRNAs were identified, including 325 and 438 that were respectively up-regulated and down-regulated. GO and KEGG analyses indicated that the Ras and hedgehog signaling pathways may be important regulatory pathways in CHD caused by exposure to formaldehyde. A lncRNA-miRNA-mRNA co-expression network was constructed and a key miRNA, rno-miR-665, was identified. Furthermore, qRT-PCR analysis verified that the novel lncRNAs: MSTRG.27313.2, MSTRG.30629.2, MSTRG.36520.33, MSTRG.91234.1, and MSTRG.91233.9, were upregulated in the formaldehyde-exposed group. These differentially expressed lncRNAs identified during formaldehyde-induced CHD in newborn rats help explain CHD pathogenesis and provide an effective reference for diagnosing and treating CHD.

Dysregulation of CD177+ neutrophils on intraepithelial lymphocytes exacerbates gut inflammation via decreasing microbiota-derived DMF.

Neutrophils synergize with intestinal resident intraepithelial lymphocytes (IELs) to serve as the first-line defense and maintain intestinal homeostasis. However, the underlying mechanisms whereby neutrophils regulate IELs to inhibit intestinal inflammation are still not completely understood. Here, we found that depletion of neutrophils (especially CD177+ subset) caused expansion of colitogenic TCRγδ+CD8αα+ IELs, increased intestinal inflammation, and dysbiosis after dextran sulfate sodium exposure or Citrobacter rodentium infection in mice. scRNA-seq analysis revealed a pyroptosis-related gene signature and hyperresponsiveness to microbiota in TCRγδ+CD8αα+ IELs from colitic Cd177-/- mice. Microbiota-derived fumarate and its derivative dimethyl fumarate (DMF), as well as fumarate-producing microbiotas, decreased in the feces of colitic Cd177-/- mice. Elimination of dysbiosis by antibiotics treatment or co-housing procedure and DMF supplementation restrained TCRγδ+CD8αα+ IEL activation. Consistently, DMF significantly alleviated intestinal mucosal inflammation in mice through restricting gasdermin D (GSDMD)-induced pyroptosis of TCRγδ+CD8αα+ IELs. Therefore, our data reveal that neutrophils inhibit intestinal inflammation by promoting microbiota-derived DMF to regulate TCRγδ+CD8αα+ IEL activation in a GSDMD-mediated pyroptosis-dependent manner, and that DMF may serve as a therapeutic target for the management of intestinal inflammation.

Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.

Microbial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for detecting precancerous adenomas. We performed cross-cohort analyses on whole metagenome sequencing data of 750 samples via xMarkerFinder to identify adenoma-associated microbial multimodal signatures. Our data revealed that fungal species outperformed species from other kingdoms with an area under the ROC curve (AUC) of 0.71 in distinguishing adenomas from controls. The microbial SNVs, including dark SNVs with synonymous mutations, displayed the strongest diagnostic capability with an AUC value of 0.89, sensitivity of 0.79, specificity of 0.85, and Matthews correlation coefficient (MCC) of 0.74. SNV biomarkers also exhibited outstanding performances in three independent validation cohorts (AUCs = 0.83, 0.82, 0.76; sensitivity = 1.0, 0.72, 0.93; specificity = 0.67, 0.81, 0.67, MCCs = 0.69, 0.83, 0.72) with high disease specificity for adenoma. In further support of the above results, functional analyses revealed more frequent inter-kingdom associations between bacteria and fungi, and abnormalities in quorum sensing, purine and butanoate metabolism in adenoma, which were validated in a newly recruited cohort via qRT-PCR. Therefore, these data extend our understanding of adenoma-associated multimodal alterations in the gut microbiome and provide a rationale of microbial SNVs for the early detection of CRC.

Roles of long non-coding RNAs in angiogenesis-related diseases: Focusing on non-neoplastic aspects.

Angiogenesis is a key process in organ and tissue morphogenesis, as well as growth during human development, and is coordinated by pro- and anti-angiogenic factors. When this balance is affected, the related physiological and pathological changes lead to disease. Long non-coding RNAs (lncRNAs) are an important class of non-coding RNAs that do not encode proteins, but play a dynamic role in regulating gene expression. LncRNAs have been reported to be extensively involved in angiogenesis, particularly tumor angiogenesis. The non-tumor aspects have received relatively little attention and summary, but there is a broad space for research and exploration on lncRNA-targeted angiogenesis in this area. In this review, we focus on lncRNAs in angiogenesis-related diseases other than tumors, such as atherosclerosis, myocardial infarction, stroke, diabetic complications, hypertension, osteoporosis, dermatosis, as well as, endocrine, neurological, and other systemic disorders. Moreover, multiple cell types have been implicated in lncRNA-targeted angiogenesis, but only endothelial cells have attracted widespread attention. Thus, we explore the roles of other cells. Finally, we summarize the potential research directions in the area of lncRNAs and angiogenesis that can be undertaken by combining cutting-edge technology and interdisciplinary research, which will provide new insights into the involvement of lncRNAs in angiogenesis-related diseases.

Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence.

Dysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising noninvasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a multidimensional analysis on the microbial metagenomes of CD. We collected fecal metagenomic datasets generated from eight cohorts that altogether include 870 CD patients and 548 healthy controls. Microbial alterations in CD patients were assessed at multidimensional levels including species, gene, and SNV level, and then diagnostic models were constructed using artificial intelligence algorithm. A total of 227 species, 1047 microbial genes, and 21,877 microbial SNVs were identified that differed between CD and controls. The species, gene, and SNV models achieved an average AUC of 0.97, 0.95, and 0.77, respectively. Notably, the gene model exhibited superior diagnostic capability, achieving an average AUC of 0.89 and 0.91 for internal and external validations, respectively. Moreover, the gene model was specific for CD against other microbiome-related diseases. Furthermore, we found that phosphotransferase system (PTS) contributed substantially to the diagnostic capability of the gene model. The outstanding performance of PTS was mainly explained by genes celB and manY, which demonstrated high predictabilities for CD with metagenomic datasets and was validated in an independent cohort by qRT-PCR analysis. Our global metagenomic analysis unravels the multidimensional alterations of the microbial communities in CD and identifies microbial genes as robust diagnostic biomarkers across geographically and culturally distinct cohorts.

Identification and experimental validation of autophagy-related genes in abdominal aortic aneurysm.

AIM: Autophagy plays essential roles in abdominal aortic aneurysm (AAA) development and progression. The objective of this study was to verify the autophagy-related genes (ARGs) underlying AAA empirically and using bioinformatics analysis. METHODS: Two gene expression profile datasets GSE98278 and GSE57691 were downloaded from the Gene Expression Omnibus (GEO) database, and principal component analysis was performed. Following, the R software (version 4.0.0) was employed to analyze potentially differentially expressed genes related with AAA and autophagy. Subsequently, the candidate genes were screened using protein-protein interaction (PPI), gene ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Finally, quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the RNA expression levels of the top five selected abnormal ARGs in clinical samples obtained from the normal and AAA patients. RESULTS: According to the information contained (97 AAA patients and 10 healthy controls) in the two datasets, a total of 44 differentially expressed autophagy-related genes (6 up-regulated genes and 38 down-regulated genes) were screened. GO enrichment analysis of differentially expressed autophagy-related genes (DEARGs) demonstrated that some enrichment items were associated with inflammation, and PPI analysis indicated interaction between these genes. RT-qPCR results presented that the expression levels of IL6, PPARG, SOD1, and MAP1LC3B were in accordance with the bioinformatics prediction results acquired from the mRNA chip. CONCLUSION: Bioinformatics analysis identified 44 potential autophagy-related differentially expressed genes in AAA. Further verification by RT- qPCR presented that IL6, PPARG, SOD1, and MAP1LC3B may affect the development of AAA by regulating autophagy. These findings might help explain the pathogenesis of AAA and be helpful in its diagnosis and treatment.

Comprehensive evaluation of circRNAs in cirrhotic cardiomyopathy before and after liver transplantation.

Cirrhotic cardiomyopathy (CCM) is a common complication of liver cirrhosis. Many patients with cirrhotic livers do not die from liver failure but from abnormal hemodynamics secondary to liver cirrhosis. Liver transplantation is one of the most effective treatments for liver diseases. Recent studies have found that liver transplantation can reverse CCM and improve cardiac function; however, its role and remedial mechanism remain unclear. Circular RNAs (circRNAs) have become an important marker for diagnosing diseases. The differential expression of circRNAs is associated with heart diseases. In this study, we used gene sequencing to detect the circRNA expression profile of patients with CCM before and after liver transplantation and predicted the differential circRNA target genes. The results showed that a total of 1495 circRNAs were dysregulated after liver transplantation, 1319 genes were downregulated, and 176 were upregulated (P < 0.05, log2 (fold change) > 2.0). The qRT-PCR results showed that circ-ASAP1, circ-N4BP2L2, circ-EXOC6B were significantly downregulated (P < 0.05), which were consistent with the RNA sequencing data, and circ-ASAP1 had the most significant difference. Bioinformatics analysis suggested that mTOR and MAPK signaling pathways might be involved in the pathogenesis of CCM. By constructing a circRNA-miRNA-mRNA interaction network, hsa-miR-197-3p, hsa-miR-483-3p, and hsa-miR-885-3p, particularly key miRNA (hsa-miR-483-3p), were found to be the major potential genes involved in CCM regulation. In summary, this study suggested that circRNAs play a crucial regulatory role in the occurrence of CCM before and after liver transplantation, and their potential biological function might be the key to diagnosis and treatment.

Integrative multi-omics deciphers the spatial characteristics of host-gut microbiota interactions in Crohn's disease.

Dysregulated host-microbial interactions play critical roles in initiation and perpetuation of gut inflammation in Crohn's disease (CD). However, the spatial distribution and interaction network across the intestine and its accessory tissues are still elusive. Here, we profile the host proteins and tissue microbes in 540 samples from the intestinal mucosa, submucosa-muscularis-serosa, mesenteric adipose tissues, mesentery, and mesenteric lymph nodes of 30 CD patients and spatially decipher the host-microbial interactions. We observe aberrant antimicrobial immunity and metabolic processes across multi-tissues during CD and determine bacterial transmission along with altered microbial communities and ecological patterns. Moreover, we identify several candidate interaction pairs between host proteins and microbes associated with perpetuation of gut inflammation and bacterial transmigration across multi-tissues in CD. Signature alterations in host proteins (e.g., SAA2 and GOLM1) and microbes (e.g., Alistipes and Streptococcus) are further imprinted in serum and fecal samples as potential diagnostic biomarkers, thus providing a rationale for precision diagnosis.