Microfluidic platform for omics analysis on single cells with diverse morphology and size: A review.

BACKGROUND: Microfluidic techniques have emerged as powerful tools in single-cell research, facilitating the exploration of omics information from individual cells. Cell morphology is crucial for gene expression and physiological processes. However, there is currently a lack of integrated analysis of morphology and single-cell omics information. A critical challenge remains: what platform technologies are the best option to decode omics data of cells that are complex in morphology and size? RESULTS: This review highlights achievements in microfluidic-based single-cell omics and isolation of cells based on morphology, along with other cell sorting methods based on physical characteristics. Various microfluidic platforms for single-cell isolation are systematically presented, showcasing their diversity and adaptability. The discussion focuses on microfluidic devices tailored to the distinct single-cell isolation requirements in plants and animals, emphasizing the significance of considering cell morphology and cell size in optimizing single-cell omics strategies. Simultaneously, it explores the application of microfluidic single-cell sorting technologies to single-cell sequencing, aiming to effectively integrate information about cell shape and size. SIGNIFICANCE AND NOVELTY: The novelty lies in presenting a comprehensive overview of recent accomplishments in microfluidic-based single-cell omics, emphasizing the integration of different microfluidic platforms and their implications for cell morphology-based isolation. By underscoring the pivotal role of the specialized morphology of different cells in single-cell research, this review provides robust support for delving deeper into the exploration of single-cell omics data.

LncRNA CCAT2, involving miR-34a/TGF-ß1/Smad4 signaling, regulate hepatic stellate cells proliferation.

miR-34a targeting on Smad4 plays important role in TGF-ß1 pathway which is a dominant factor for balancing collagen production and degradation in hepatic stellate cells. TGF-ß1/Smad4 regulated collagen deposition is a hallmark of hepatic fibrosis. The potential regulation on miR-34a by LncRNAs in hepatic stellate cells (HSCs) is still reserved to be revealed. In current study, it was hypothesized that a miR-34a interactor, lncRNA CCAT2 may regulate TGF-ß1 pathway in liver fibrotic remodeling. The interaction between CCAT2 and miR-34a-5p was checked by dual luciferase assay. the effects of CCAT2 and miR-34a-5p on cell proliferation and apoptosis were verified by MTT assay, colony formation assay, and flow cytometry assay. Dual luciferase activity showed CCAT2 are targets of miR-34a-5p. Sh-CCAT2 transfection prohibit HSCs proliferation and induce HSCs apoptosis, also inhibited ECM protein synthesis in HSCs. Decreased miR-34a-5p enhanced HSCs proliferation, blocked HSCs apoptosis and promoted ECM protein production. miR-34a-5p inhibitor undo protective regulation of sh-CCAT2 in liver fibrosis. Furthermore, clinical investigation showed that CCAT2 and Smad4 expression level were significantly induced, while miR-34a-5p was significantly decreased in HBV related liver fibrosis serum. In conclusion, activated HSCs via TGF-ß1/Smad4 signaling pathway was successfully alleviated by CCAT2 inhibition through miR-34a-5p elevation.

METTL16 regulates m6A methylation on chronic hepatitis B associated gene HLA-DPB1 involved in liver fibrosis.

The role of genetic factors in the occurrence and progression of CHB (CHB) is still not fully explored. In recent years, genome-wide association studies on CHB patients have demonstrated that a large number of CHB-associated single nucleotide polymorphisms exist in the gene intron, which may regulate expression at the transcriptional level. Modification of RNA m6A methylation is one of the key mechanisms regulating gene expression. Here we show that METTL16, an m6A regulator involved in mRNA intron splicing, is differentially expressed in CHB the tissue of patients who has definite diagnosis of mild and severe fibrosis. At the same time, there are also significant differences in the expression of CHB-associated genes such as HLA-DPA1 and HLA-DPB1. The expression of HLA-DPB1 is related to METTL16. Furthermore, analyses of RNA binding of METTL16 and HLA-DPB1 show that the silencing of METTL16 in astrocytes downregulates m6A and expression of HLA-DPB1. In conclusion, METTL16 participates in the progression of CHB fibrosis by regulating the m6A level and expression of HLA-DPB1.

Explainable machine learning model for predicting spontaneous bacterial peritonitis in cirrhotic patients with ascites.

Spontaneous bacterial peritonitis (SBP) is a life-threatening complication in patients with cirrhosis. We aimed to develop an explainable machine learning model to achieve the early prediction and outcome interpretation of SBP. We used CatBoost algorithm to construct MODEL-1 with 46 variables. After dimensionality reduction, we constructed MODEL-2. We calculated and compared the sensitivity and negative predictive value (NPV) of MODEL-1 and MODEL-2. Finally, we used the SHAP (SHapley Additive exPlanations) method to provide insights into the model's outcome or prediction. MODEL-2 (AUROC: 0.822; 95% confidence interval [CI] 0.783-0.856), liked MODEL-1 (AUROC: 0.822; 95% CI 0.784-0.856), could well predict the risk of SBP in cirrhotic ascites patients. The 6 most influential predictive variables were total protein, C-reactive protein, prothrombin activity, cholinesterase, lymphocyte ratio and apolipoprotein A1. For binary classifier, the sensitivity and NPV of MODEL-1 were 0.894 and 0.885, respectively, while for MODEL-2 they were 0.927 and 0.904, respectively. We applied CatBoost algorithm to establish a practical and explainable prediction model for risk of SBP in cirrhotic patients with ascites. We also identified 6 important variables closely related to the occurrence of SBP.

Identification of miR-4793-3p as a potential biomarker for bacterial infection in patients with hepatitis B virus-related liver cirrhosis: A pilot study.

Hepatitis B virus-related liver cirrhosis (HBV-LC) is susceptible to bacterial infections, which could lead to adverse prognosis in patients. MicroRNAs (miRs/miRNAs) are easily detected in peripheral blood and are involved in multiple liver diseases. The present pilot study aimed to investigate differentially expressed (DE) miRNAs in the serum of patients with HBV-LC and bacterial infection, and to identify potential biomarkers. The first batch of clinical samples was collected, including four patients with HBV-LC and infection, four patients with HBV-LC without infection, four patients with chronic hepatitis B (CHB) and four healthy controls. miRNA expression was analyzed by Affymetrix GeneChip miRNA 4.0 Array. A total of 385 DE miRNAs (upregulated, 160; downregulated, 225) were detected in patients with HBV-LC and infection compared with patients with HBV-LC without infection. miR-4793-3p was significantly upregulated in patients with HBV-LC and infection compared with its levels in the other three groups: HBV-LC without infection [log-transformed fold change (logFC)=7.96; P=0.0458), CHB (logFC=34.53; P=0.0003) and healthy controls (logFC=3.34; P=0.0219)]. Reverse transcription-quantitative PCR (RT-qPCR) was performed to validate miR-4793-3p expression in another batch of clinical samples. RT-qPCR showed that miR-4793-3p was highly expressed in patients with HBV-LC and infection compared with its levels in patients with HBV-LC without infection (P<0.05). The non-parametric random forest regression model was built to access the diagnostic value of miR-4793-3p, and the receiver operating characteristic curve demonstrated that the area under the curve was 92.2%. Target gene analysis with bioinformatics tools and Gene Expression Omnibus data (GSE46955) showed that miR-4793-3p could participate in the TGF-ß signaling pathway. Functional experiments revealed that overexpressed miR-4793-3p could impair TGF-ß function by downregulating Gremlin-1. The present pilot study suggests that miR-4793-3p could be a feasible indicator for bacterial infection in patients with HBV-LC, and it would be valuable for further research.

Telbivudine can safely reduce mother-to-child transmission in chronic hepatitis B women after 12 weeks of gestation.

BACKGROUND: To evaluate the efficacy and safety of telbivudine in chronic hepatitis B women during the second and third trimesters of pregnancy. METHODS: The week 12-34 of pregnant women were screened in this prospective non-intervention study, with HBV DNA > 106 IU/mL and alanine aminotransferase > 50 IU/L. The patients were received telbivudine treatment as a treatment group or without antiviral treatment as a control group. All infants were received recombinant hepatitis B vaccine 10 µg within 12 h of birth, at week 4 and week 24, immunoglobulin G within 12 h of birth and were detected HBV markers at the range from 7 to 12 months after delivery. RESULTS: A total of 241 patients were finally enrolled, 139 patients in telbivudine group and 102 patients in control group. HBsAg negative rate of infants was 99.3% (135/136) in telbivudine group and was 91.9% (91/99) in control group after 7 months (P = 0.005), respectively. The incidence of undetectable HBV DNA levels (47.5%) was significantly lower in telbivudine-treated mothers than that in the controls (0%), and 75.5% patients alanine aminotransferase returned to normal in telbivudine group, and 51% in control group at delivery (P < 0.001), respectively. CONCLUSIONS: Telbivudine can safely reduce mother-to-child transmission in chronic hepatitis B women after 12 weeks of gestation.

Baseline prognostic factors and statistic model to predict early virological response in lamivudine-treated patients with chronic hepatitis B.

Lamivudine is a potent nucleoside analogue used in treating chronic hepatitis B (CHB). However, resistance to the drug remains a problem. We analyzed all lamivudine recipients in this trial to determine the baseline characteristics and a model to predict early virological response reflecting the long-term effect of lamivudine. In this prospective trial, 230 patients who had not treated with nucleotide analogue with chronic HBV infection were assigned to receive 100 mg of lamivudine once daily for 24 weeks at least. All patients were followed up every 2 week. Cox proportional hazard regression model analyses were employed to evaluate baseline variables and to develop a statistical model. Female (P = 0.042), baseline higher serum aspartate aminotransferase (AST) (P = 0.002), and lower level of HBV-DNA (P = 0.016) were identified to be associated with higher possibility of early virological response. A model was established based on these variables to calculate the risk scores (R) for CHB patients. R > -0.45 suggested early virological response to lamivudine. The model was validated among an independent set of 40 patients. The gender as well as baseline AST and HBV-DNA levels can predict early virological response. The model provides a better tool for response prediction based on the three prognostic factors.

Baseline prognostic factors and statistic model to predict early virological response in telbivudine-treated patients with chronic hepatitis B.

BACKGROUND: Hepatitis B virus (HBV) infection is still a worldwide disease, which may cause liver cirrhosis or even hepatocellular carcinoma. Telbivudine is a potent nucleoside analogue used in the treatment of chronic hepatitis B (CHB); however, drug resistance has remained a challenge. As early virological response can predict long-term efficacy of nucleotide analogue treatment, numerous studies have been conducted in this area. OBJECTIVES: The aim of this study was to establish baseline prognostic factors and a statistical model to predict early virological response in telbivudine-treated CHB patients. PATIENTS AND METHODS: One hundred and eight CHB patients without any experience of nucleotide analogue therapy were assigned to receive telbivudine (600 mg, once daily) for at least 24 weeks, and then were followed up every two weeks. Cox proportional hazard regression model analyses were employed to evaluate baseline variables, and further developing a statistical model to predict early virological response. RESULTS: Negative family history of HBV infection (P = 0.000235), baseline higher serum TBIL (P = 0.038714) and AST (P = 0.020684) concentrations, and lower level of HBV-DNA (P = 0.0034784) were identified to be associated with higher possibility of early virological response. A model was established based on these variables to calculate the risk scores (R) for CHB patients. R > -0.38 suggested early virological response to telbivudine. The model was validated among an independent set of 20 patients. CONCLUSIONS: Family history as well as baseline bilirubin, AST and HBV DNA levels can predict early virological response. The model provides a better tool for response prediction based on the four prognostic factors.

[The impact of early rapid virological response on the outcomes of hepatitis B associated acute on chronic liver failure during antiviral treatment].

OBJECTIVE: To investigate the impact of early rapid virological response on the outcomes of hepatitis B associated acute on chronic liver failure during antiviral treatment. METHODS: 106 acute on chronic liver failure patients in our hospital from January 2008 to July 2010 were enrolled in present study retrospectively. Besides internal medicine therapy, all patients received lamivudine (100 mg/d) or entecavir (0.5 mg/d) treatment. The profile of liver biochemistry, prothrombin time activity and viral load were detected at baseline and week 4, respectively. The patients were divided into HBV DNA negative group and HBV DNA positive group according to the viral load at week 4. The clinical features and treatment outcomes were compared between groups. Frequency variables were compared by x2 test or Fisher's exact test. Continuous variables were compared using independent samples T-test. The factors that impact on the treatment outcomes were determined using stepwise multivariate logistic regression analysis. RESULTS: At the week 4, the TBil and PTA in HBV DNA positive group [(261.6+/-205.6)mumol/L and 44.7%+/-19.7%, respectively] were significantly different from those in HBV DNA negative group [(160.1+/-173.4) mumol/L and 56.8%+/-23.1%, respectively] ( t = 2.190 and -2.077, respectively, P less than 0.05). The non-effective rate of HBVDNA positive group (50%, 9/18) was significantly higher than that of HBV DNA negative group (14.8%, 13/88) (x2 = 9.235, P less than 0.01). By using stepwise multivariate logistic regression analysis, the disease stage and HBV DNA undetectable at week 4 were the independent factor. The OR values of disease stage and HBV DNA undetectable were 6.559 and 0.209, respectively, and 95% CI was 2.316~18.576 and 0.058~0.747, respectively. CONCLUSION: The rapid suppression of viral load by nucleotide analogue may improve the efficacy of hepatitis B associated acute on chronic liver failure treatment. The early rapid virological response within first 4 weeks may contribute to the prediction of the treatment outcomes.