Descriptor-augmented machine learning for enzyme-chemical interaction predictions.

Descriptors play a pivotal role in enzyme design for the greener synthesis of biochemicals, as they could characterize enzymes and chemicals from the physicochemical and evolutionary perspective. This study examined the effects of various descriptors on the performance of Random Forest model used for enzyme-chemical relationships prediction. We curated activity data of seven specific enzyme families from the literature and developed the pipeline for evaluation the machine learning model performance using 10-fold cross-validation. The influence of protein and chemical descriptors was assessed in three scenarios, which were predicting the activity of unknown relations between known enzymes and known chemicals (new relationship evaluation), predicting the activity of novel enzymes on known chemicals (new enzyme evaluation), and predicting the activity of new chemicals on known enzymes (new chemical evaluation). The results showed that protein descriptors significantly enhanced the classification performance of model on new enzyme evaluation in three out of the seven datasets with the greatest number of enzymes, whereas chemical descriptors appear no effect. A variety of sequence-based and structure-based protein descriptors were constructed, among which the esm-2 descriptor achieved the best results. Using enzyme families as labels showed that descriptors could cluster proteins well, which could explain the contributions of descriptors to the machine learning model. As a counterpart, in the new chemical evaluation, chemical descriptors made significant improvement in four out of the seven datasets, while protein descriptors appear no effect. We attempted to evaluate the generalization ability of the model by correlating the statistics of the datasets with the performance of the models. The results showed that datasets with higher sequence similarity were more likely to get better results in the new enzyme evaluation and datasets with more enzymes were more likely beneficial from the protein descriptor strategy. This work provides guidance for the development of machine learning models for specific enzyme families.

A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis.

Elucidating the expression of microRNAs in developing single cells is critical for functional discovery. Here, we construct scCAMERA (single-cell cartography of microRNA expression based on reporter assay), utilizing promoter-driven fluorescent reporters in conjunction with imaging and lineage tracing. The cartography delineates the transcriptional activity of 54 conserved microRNAs in lineage-resolved single cells throughout C. elegans embryogenesis. The combinatorial expression of microRNAs partitions cells into fine clusters reflecting their function and anatomy. Notably, the expression of individual microRNAs exhibits high cell specificity and divergence among family members. Guided by cellular expression patterns, we identify developmental functions of specific microRNAs, including miR-1 in pharynx development and physiology, miR-232 in excretory canal morphogenesis by repressing NHR-25/NR5A, and a functional synergy between miR-232 and miR-234 in canal development, demonstrating the broad utility of scCAMERA. Furthermore, integrative analysis reveals that tissue-specific fate determinants activate microRNAs to repress protein production from leaky transcripts associated with alternative, especially neuronal, fates, thereby enhancing the fidelity of developmental fate differentiation. Collectively, our study offers rich opportunities for multidimensional expression-informed analysis of microRNA biology in metazoans.

Spatiotemporal analysis of mRNA-protein relationships enhances transcriptome-based developmental inference.

Elucidating the complex relationships between mRNA and protein expression at high spatiotemporal resolution is critical for unraveling multilevel gene regulation and enhancing mRNA-based developmental analyses. In this study, we conduct a single-cell analysis of mRNA and protein expression of transcription factors throughout C. elegans embryogenesis. Initially, cellular co-presence of mRNA and protein is low, increasing to a medium-high level (73%) upon factoring in delayed protein synthesis and long-term protein persistence. These factors substantially affect mRNA-protein concordance, leading to potential inaccuracies in mRNA-reliant gene detection and specificity characterization. Building on the learned relationship, we infer protein presence from mRNA expression and demonstrate its utility in identifying tissue-specific genes and elucidating relationships between genes and cells. This approach facilitates identifying the role of sptf-1/SP7 in neuronal lineage development. Collectively, this study provides insights into gene expression dynamics during rapid embryogenesis and approaches for improving the efficacy of transcriptome-based developmental analyses.

CircDCBLD2 alleviates liver fibrosis by regulating ferroptosis via facilitating STUB1-mediated PARK7 ubiquitination degradation.

BACKGROUND: Liver fibrosis can progress to cirrhosis and hepatic carcinoma without treatment. CircDCBLD2 was found to be downregulated in liver fibrosis. However, the precise underlying mechanism requires further investigation. METHODS: qRT-PCR, Western blot, and immunohistochemistry assays were used to detect the related molecule levels. HE, Masson's trichrome, and Sirius Red staining were used to assess the pathological changes in mice's liver tissues. Flow cytometric analysis and commercial kit were used to assess the levels of lipid reactive oxygen species (ROS), malonaldehyde (MDA), glutathione (GSH), and iron. Cell viability was assessed by MTT. Immunoprecipitation was used to study the ubiquitination of PARK7. Mitophagy was determined by immunostaining and confocal imaging. RIP and Co-IP assays were used to assess the interactions of circDCBLD2/HuR, HuR/STUB1, and STUB1/PARK7. Fluorescence in situ hybridization and immunofluorescence staining were used to assess the co-localization of circDCBLD2 and HuR. RESULTS: CircDCBLD2 was downregulated, whereas PARK7 was upregulated in liver fibrosis. Ferroptosis activators increased circDCBLD2 while decreasing PARK7 in hepatic stellate cells (HSCs) and mice with liver fibrosis. CircDCBLD2 overexpression reduced cell viability and GSH, PARK7, and GPX4 expression in erastin-treated HSCs while increasing MDA and iron levels, whereas circDCBLD2 knockdown had the opposite effect. CircDCBLD2 overexpression increased STUB1-mediated PARK7 ubiquitination by promoting HuR-STUB1 binding and thus increasing STUB1 mRNA stability. PARK7 overexpression or HuR knockdown reversed the effects of circDCBLD2 overexpression on HSC activation and ferroptosis. CircDCBLD2 reduced liver fibrosis in mice by inhibiting PARK7. CONCLUSION: CircDCBLD2 overexpression increased PARK7 ubiquitination degradation by upregulating STUB1 through its interaction with HuR, inhibiting HSC activation and promoting HSC ferroptosis, ultimately enhancing liver fibrosis.

Transcriptional regulation of Glis2 in hepatic fibrosis.

The role of Gli-similar 2 (Glis2) in hepatic fibrosis (HF) is controversial. In this study, we focused on the functional and molecular mechanisms involved in the Glis2-mediated activation of hepatic stellate cells (HSCs)-a milestone event leading to HF. The expression levels of Glis2 mRNA and protein were significantly decreased in the liver tissues of patients with severe HF and in mouse fibrotic liver tissues as well as HSCs activated by TGFß1. Functional studies indicated that upregulated Glis2 significantly inhibited HSC activation and alleviated BDL-induced HF in mice. Downregulation of Glis2 was found to correlate significantly with DNA methylation of the Glis2 promoter mediated by methyltransferase 1 (DNMT1), which restricted the binding of hepatic nuclear factor 1-α (HNF1-α), a liver-specific transcription factor, to Glis2 promoters. In addition, the enrichment of DNMT1 in the Glis2 promoter region was mediated by metastasis-associated lung adenocarcinoma transcriptor-1 (MALAT1) lncRNA, leading to transcriptional silencing of Glis2 and activation of HSCs. In conclusion, our findings reveal that the upregulation of Glis2 can maintain the resting state of HSCs. The decreased expression of Glis2 under pathological conditions may lead to the occurrence and development of HF with the expression silencing of DNA methylation mediated by MALAT1 and DNMT1.

GLIS2 Prevents Hepatic Fibrosis by Competitively Binding HDAC3 to Inhibit Hepatic Stellate Cell Activation.

BACKGROUND: The role of GLIS2 in fibrotic diseases is controversial. GLIS2 deficiency has been reported to contribute to renal fibrosis in mice and has also been reported to prevent high lipid-induced mice hepatic fibrosis. METHODS: Hepatic fibrosis in mice was induced by CCl4. Hematoxylin and eosin, Masson, Sirius red, and enzyme-linked immunosorbent assay were used to detect and evaluate the stage of hepatic fibrosis in humans or mice. A study model of tetracycline-responsive GLIS2 knockout hepatic stellate cells (HSCs) was constructed and named GLIS2-SG-Dox. By adding transforming growth factor ß1 to stimulate the transdifferentiation of HSCs, the activation status of HSCs was comprehensively evaluated from the aspects of cell proliferation, migration, and the amount of lipid droplets. In mechanistic studies, dual-luciferase, coimmunoprecipitation, yeast two-hybrid system, chromatin immunoprecipitation, and DNA pulldown were performed to investigate or to prove the molecular mechanism that GLIS2 was involved in regulating liver fibrosis. Throughout the study, real-time fluorescence polymerase chain reaction (quantitative reverse-transcription polymerase chain reaction) was used to detect the relative abundance of messenger RNA expression of each target gene, Western blot was used to detect the relative abundance of protein, and immunohistochemistry or immunofluorescence was used to observe the subcellular localization of the target protein. RESULTS: The expression of GLIS2 was significantly decreased in human liver fibrosis tissues and CCL4-induced mouse liver fibrosis tissues, especially in HSCs. In the GLIS2-SG-Dox cells, the peroxisome proliferator-activated receptor γ (PPAR-γ) pathway was inactive and cells underwent myofibroblastic transdifferentiation transformation. Overexpression of GLIS2 can increase the acetylation level of PPAR-γ and alleviate CCL4-induced liver fibrosis in mice. Mechanically, relatively abundant GLIS2 and histone deacetylase 3 (HDAC3) form chelates to avoid the deacetylation of PPAR-γ, so as to maintain the activation level of PPAR-γ signaling pathway in HSCs cells. In this process, HDAC3 acts as a medium for GLIS2 to influence PPAR-γ signaling. Nonetheless, when GLIS2 is absent, HDAC3 deacetylates PPAR-γ, activates HSCs, and leads to liver fibrosis. CONCLUSIONS: GLIS2 deficiency promotes myofibroblastic transdifferentiation and activation of HSCs. Mechanically, GLIS2 regulates the acetylation of PPAR-γ by competitively binding to HDAC3 in HSCs.

Circular RNA circ_GLIS2 suppresses hepatocellular carcinoma growth and metastasis.

BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) is one of the leading causes of tumour-related death. Here, we investigated the molecular mechanism of HCC by studying the function of circ_GLIS2. METHODS: Human HCC specimens and cell lines were used. Sanger sequencing, actinomycin D and RNase R treatment were performed to validate circular RNA features of circ_GLIS2. qRT-PCR, western blotting, immunostaining, and IHC were employed to examine levels of circ_GLIS2, GLIS2 mRNA, and EMT-related markers. CCK-8, colony formation, flow cytometry, wound healing assay, and transwell assays were performed to evaluate cancer cell proliferation, apoptosis, migration, and invasion. RIP and RNA pull-down assay were used to validate EIF4A3/GLIS2 mRNA interaction. MSP was performed to measure the methylation status of GLIS2 promoter. Nude mouse xenograft model was used to examine tumour growth and metastasis in vivo. RESULTS: Circ_GLIS2 and linear GLIS2 mRNA were reduced in human HCC tissues and cells. Their low levels correlated with a poor survival rate of HCC patients. Overexpression of circ_GLIS2 and GLIS2 suppressed HCC cell proliferation, migration, and invasion but promoted cell apoptosis. GLIS2 promoter region was hypermethylated in HCC cells. EIF4A3 was directly bound with GLIS2 mRNA and promoted circ_GLIS2/GLIS2 expression. Moreover, overexpression of circ_GLIS2 restrained HCC tumour growth and metastasis in vivo. CONCLUSION: Circ_GLIS2 suppresses HCC growth and metastasis by inhibiting cell proliferation, migration, and invasion, but promoting cell apoptosis. These findings provide molecular insights into the mechanism of HCC and indicate that circ_GLIS2 could serve as a diagnosis marker or therapeutic target for HCC.

CREB1 acts via the miR­922/ARID2 axis to enhance malignant behavior of liver cancer cells.

There is little information on the role of microRNA (miR)­922 in the malignant behavior of liver cancer. The present study investigated the regulation of miR­922 expression levels by cAMP response element binding protein 1 (CREB1) in liver cancer tissue, its role in regulating malignant behavior and its potential targets in liver cancer. miR­922 expression in liver cancer cells and tissue was determined by reverse transcription­quantitative PCR. The binding of CREB1 to the promoter region of mir­922 was tested by chromatin immunoprecipitation­PCR. The predicted AT­rich interactive domain 2 (ARID2) and fidgetin, microtubule severing factor targets of miR­922 were characterized by dual luciferase reporter assay. The effects of altered ARID2 expression levels on miR­922­enhanced malignant behavior of liver cancer cells were tested. CREB1 bound to the promoter region of miR­922. Elevated miR­922 transcripts were inversely associated with ARID2 expression in liver cancer tissue and cells. miR­922 inhibited ARID2­regulated luciferase expression and was present in the miR/argonaute RISC catalytic component 2 complex. ARID2 significantly decreased malignant behavior of liver cancer MHCC97L cells. Similarly, ARID2 over­expression inhibited growth of xenograft liver cancer tumors and decreased miR­922, Bcl­2, proliferating cell nuclear antigen, cyclin D1, MMP3 and MMP9 expression and serum VEGF and TNF­α levels, but enhanced Bax expression levels in tumors. ARID2 over­expression abrogated malignant behavior promoted by miR­922 over­expression and enhanced miR­922­decreased malignant behavior of liver cancer cells. CREB induced miR­922 transcription, which targeted ARID2 to enhance malignant behavior of liver cancer cells, indicating that the CREB1/miR­922/ARID2 axis may be a potential target for liver cancer treatment.

11ß­hydroxysteroid dehydrogenase­1 is associated with the activation of hepatic stellate cells in the development of hepatic fibrosis.

Hepatic fibrosis (HF) is a common complication of numerous chronic liver diseases, but predominantly results from persistent liver inflammation or injury. If left untreated, HF can progress and develop into liver cirrhosis and even hepatocellular carcinoma. However, the underlying molecular mechanisms of HF remain unknown. The present study aimed to investigate the role of 11ß­hydroxysteroid dehydrogenase­1 (11ß­HSD1) during the development of hepatic fibrosis. An experimental rat model of liver fibrosis was induced using porcine serum. 11ß­HSD1 gene expression levels and enzyme activity during hepatic fibrogenesis were assessed. 11ß­HSD1 gene knockdown using small interfering RNA and overexpression were performed in LX2­human hepatic stellate cells (HSCs). HSCs were stimulated with transforming growth factor­ß1 (TGF­ß1). Cell cycle distribution, proliferation, collagen secretion and 11ß­HSD1 gene activity in HSCs were compared before and after stimulation. As hepatic fibrosis progressed, 11ß­HSD1 gene expression and activity increased, indicating a positive correlation with typical markers of liver fibrosis. 11ß­HSD1 inhibition markedly reduced the degree of fibrosis. The cell proliferation was increased, the number of cells in the G0/G1 phase decreased and the number of cells in the S and G2/M phases increased in the pSuper transfected group compared with the N group. In addition, the overexpression of 11ß­HSD1 enhanced the TGF­ß1­induced activation of LX2­HSCs and enzyme activity of connective tissue growth factor. 11ß­HSD1 knockdown suppressed cell proliferation by blocking the G0/G1 phase of the cell cycle, which was associated with HSC stimulation and inhibition of 11ß­HSD1 enzyme activity. In conclusion, increased 11ß­HSD1 expression in the liver may be partially responsible for hepatic fibrogenesis, which is potentially associated with HSC activation and proliferation.

HMGB1 induced inflammatory effect is blocked by CRISPLD2 via MiR155 in hepatic fibrogenesis.

A number of studies have showed that High mobility group box-1 (HMGB1), which played key role in inflammation activation by triggering the toll like receptor 4 (TLR4) signaling axis in hepatic fibrogenesis, may share similar inflammation stimulating mechanism with LPS. Herein, we introduced a recently established anti-LPS protein cysteine-rich secretory protein LCCL domain containing 2 (CRISPLD2) to investigate endogenous protection mechanism of HMGB1 induced inflammatory response. Our results shows that stromal cells and monocytes showed an evaluated pattern for CRISPLD2 expression after HMGB1 treatment, which was dependent on the integrity of TLR4 function. Pro-inflammatory Cytokines levels were significantly elevated after CRISPLD2 silencing despite the HMGB1 status. Soluble CRISPLD2 administration relieve the HMGB1 dependent pro-inflammatory cytokines release. Interestingly, we found that miRNA 155 play a key role in the process. Our data suggest that CRISPLD2 may have a unique anti-HMGB1 effect via miRNA and play an important role in immune balance.

A meta-analysis comparing the efficacy of entecavir and tenofovir for the treatment of chronic hepatitis B infection.

The efficacy of entecavir and tenofovir in patients with chronic hepatitis B virus (HBV) is inconsistent. To address this issue, we conducted a meta-analysis based on a current review of the literature addressing the efficacy and safety of entecavir and tenofovir. Electronic databases were searched through June 2014 for relevant clinical trials. We included 2 randomized controlled trials, 2 prospective cohort studies, and 7 case-control studies that included 1,656 patients. In the entecavir group, 842 of 992 were nucleos(t)ide-naïve chronic HBV patients, and in the tenofovir group 481 of 664 were nucleos(t)ide-naïve. The virological response to tenofovir was superior to entecavir (RR: 0.82; 95%CI: 0.72-0.93), especially in nucleos(t)ide-naïve chronic HBV patients at 48 weeks (RR: 0.78; 95%CI: 0.65-0.92). Additionally, there was no difference between entecavir and tenofovir for virological response at 24 weeks (RR: 0.87, 95%CI: 0.71-1.05). The alanine aminotransferase normalization rate, serological response, and adverse event rate were also not significantly different between entecavir and tenofovir at 24 or 48 weeks after treatment. These results suggest that tenofovir is a better choice to treat chronic HBV patients than entecavir as it is better able to suppress HBV viral load and has a similar safety profile.

[Analysis of the prophylactic effect of nucleosides against reactivation of HBV in HBsAg-positive patients with non-hepatic tumors after chemotherapy].

OBJECTIVE: To investigate the efficacy of nucleosides as a prophylactic agent against reactivation of hepatitis B virus (HBV) in HBsAg-positive patients with non-hepatic tumors after chemotherapy. METHODS: Fifty-eight patients with non-hepatic tumors were divided into prevention group and control group. The patients of prevention group received nucleosides as a prophylactic agent before chemotherapy and were compared with the control ones about the clinical manifestation of HBV reactivation. Then, the patients of the control group were divided into three groups according to antiviral drugs, use or not and time of the use. The patients having HBV reactivation but never received nucleosides were included in the group A, the patients receiving nucleosides after having HBV reactivation were divided into the group B, and the patients receiving nucleosides before HBV reactivation were divided into the group C. The progression, prognosis and curative effect among the three groups were compared. RESULTS: The rate of HBV reactivation, incidence of severe hepatitis, mortality rate of the control group (61.1%, 27.8%, 16.7%) were significantly higher than those of the prevention group (13.6%, 0, 0), and liver dysfunction was more serious than that in the prevention group. In the control group, all the 5 patients of group A died of liver failure. Of the 13 patients in the group B, 4 cases suffered from severe hepatitis and 1 of them died of the disease. Of the 18 patients in the group C, 4 cases suffered from HBV reactivation, but the clinical manifestation was milder than that of the group B. CONCLUSION: Nucleosides can be used as a prophylactic measure to prevent HBV reactivation. If chemotherapy had begun, the use of nucleosides may reduce the risk of HBV reactivation. Even if patients had suffered from HBV reactivation, the use of nucleosides may still help the recovery of liver function and improve prognosis.

[Analysis of antibiotics treatment in 86 cases of liver transplant recipients].

OBJECTIVE: To analyze the characteristic of bacterial infections, and the relationship between antibiotics treatment and bacterial infections after liver transplantation, and to prevent antibiotic-resistant bacterial infections. METHODS: 86 liver transplant recipients were retrospected. Different indexes including limited daily dose, the frequency of medication, drug use index were used to evaluate the rationality of the use of antibiotics, three-dimensional test was used to explore extended-spectrum beta-lactamase and AmpC enzyme of Gram-negative bacteria. RESULTS: The major pathogens of infection after liver transplantation were Enterococcus faecalis, Enterobacter cloacae, fungi and E. coli. Pre-operative antibiotic utilization rate was 83.7%, it was mainly a single use of antibiotics; After- operative antibiotic usage was 100.0%, it was mainly joint use of two or three antibiotics; The top 3 antibiotics used were cephalosporins, the combined enzyme inhibitors and penicillin. Antibiotics with drug utilization index (DUI) more than 1.1 included ampicillin and Lalin proxy. 43.3% and 31.8% of Gram -Negative bacteria produced ESBLs and AmpC, respectively, while 21.3% Gram -Negative bacteria produced two enzymes. CONCLUSION: There is high incidence of bacterial infections after liver transplantation. The use of antibiotics is high dose, high-frequency and reasonable; High resistance of bacterial infections was prone to develop and the prevention of the high resistance of bacterial infections is very important.