Tryptophan catabolism via the kynurenine pathway regulates infection and inflammation: from mechanisms to biomarkers and therapies

BACKGROUND

L-Tryptophan (L-Trp), an essential amino acid, is the only amino acid whose level is regulated specifically by immune signals. Most proportions of Trp are catabolized via the kynurenine (Kyn) pathway (KP) which has evolved to align the food availability and environmental stimulation with the host pathophysiology and behavior. Especially, the KP plays an indispensable role in balancing the immune activation and tolerance in response to pathogens.

SCOPE OF REVIEW

In this review, we elucidate the underlying immunological regulatory network of Trp and its KP-dependent catabolites in the pathophysiological conditions by participating in multiple signaling pathways. Furthermore, the KP-based regulatory roles, biomarkers, and therapeutic strategies in pathologically immune disorders are summarized covering from acute to chronic infection and inflammation.

MAJOR CONCLUSIONS

The immunosuppressive effects dominate the functions of KP induced-Trp depletion and KP-produced metabolites during infection and inflammation. However, the extending minor branches from the KP are not confined to the immune tolerance, instead they go forward to various functions according to the specific condition. Nevertheless, persistent efforts should be made before the clinical use of KP-based strategies to monitor and cure infectious and inflammatory diseases.

Developmental adcyap1b loss leads to hemorrhage, disrupted hemostasis, and a blood coagulation cascade in zebrafish

BACKGROUND

Pituitary adenylate cyclase-activating polypeptide is a neuropeptide with diverse roles in biological processes. Its involvement in the blood coagulation cascade is unclear.

OBJECTIVES

This study unraveled adcyap1b's role in blood coagulation using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 in zebrafish. Effects were validated via adcyap1b knockdown. Gene expression changes in adcyap1b mutants were explored, linking them to clotting disorders. An analysis of proca gene splicing illuminated its role in adcyap1b-related anticoagulation deficiencies.

METHODS

Zebrafish were genetically modified using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 to induce adcyap1b knockout. Morpholino-mediated gene knockdown was employed for validation. Expression levels of coagulation factors, anticoagulant proteins, and fibrinolytic system genes were assessed in adcyap1b mutant zebrafish. Alternative splicing of proca gene was analyzed.

RESULTS

Adcyap1b mutant zebrafish exhibited severe hemorrhage, clotting disorders, and disrupted blood coagulation. Morpholino-mediated knockdown replicated observed phenotypes. Downregulation in transcripts related to coagulation factors V and IX, anticoagulation protein C, and plasminogen was observed. Abnormal alternative splicing of the proca gene was identified, providing a mechanistic explanation for anticoagulation system deficiencies.

CONCLUSION

Adcyap1b plays a crucial role in maintaining zebrafish blood coagulation and hemostasis. Its influence extends to the regulation of procoagulant and anticoagulant pathways, with abnormal alternative splicing contributing to observed deficiencies. These findings unveil a novel aspect of adcyap1b function, offering potential insights into similar processes in mammalian systems.

In silico prediction and a systematic toxicology-based in vivo investigation uncovering the mechanism of aquatic toxicity caused by beta-lactam antibiotics

Recently, beta-lactam antibiotics have gained attention as significant contributors to public health and environmental issues due to their potential toxicity. Our study employed machine learning to develop a model for assessing the aquatic toxicity of beta-lactam antibiotics on zebrafish. Notably, aztreonam (AZT), a synthetic monobactam and a subclass of beta-lactam antibiotics, demonstrated developmental effects in zebrafish embryos comparable to cephalosporins, indicating a potential for toxicity. Using a systems toxicology-based approach, we identified apoptosis and metabolic disorders as the primary pathways affected by AZT and its impurity F exposure. During the administration of monobactams, we noted that ctsbb, nos2a, and dgat2, genes associated with apoptosis and the metabolic pathway, exhibited significant differential expression. Molecular docking studies were conducted to ascertain the binding affinity between monobactam compounds and their potential targets-Ctsbb, Nos2a, and Dgat2. Furthermore, our research revealed that monobactams influence pre-mRNA alternative splicing, resulting in disruptions in the expression of genes involved in hair cells, brain, spinal cord, and fin regeneration (e.g., krt4, krt5, krt17, cyt1). Notably, we observed a correlation between the levels of rpl3 and rps7 genes, both important ribosomal proteins, and the detected alternative splicing events. Overall, this study enhances our understanding of the toxicity of beta-lactam antibiotics in zebrafish by demonstrating the developmental effects of monobactams and uncovering the underlying mechanisms at the molecular level. It also identifies potential targets for further investigation into the mechanisms of toxicity and provides valuable insights for early assessment of biological toxicity associated with antibiotic pollutants.

Metabolomic landscape of macrophage discloses an anabolic signature of dengue virus infection and antibody-dependent enhancement of viral infection

Dengue virus (DENV) infection causes dengue fever, the most prevalent arthropod-transmitted viral disease worldwide. Viruses are acellular parasites and obligately rely on host cell machinery for reproduction. Previous studies have indicated metabolomic changes in endothelial cell models and sera of animal models and patients with dengue fever. To probe the immunometabolic mechanism of DENV infection, here, we report the metabolomic landscape of a human macrophage cell model of DENV infection and its antibody-dependent enhancement. DENV infection of THP-1-derived macrophages caused 202 metabolic variants, of which amino acids occupied 23.7%, fatty acids 21.78%, carbohydrates 10.4%, organic acids 13.37%, and carnitines 10.4%. These metabolomic changes indicated an overall anabolic signature, which was characterized by the global exhaustion of amino acids, increases of cellular fatty acids, carbohydrates and pentoses, but decreases of acylcarnitine. Significant activation of metabolic pathways of glycolysis, pentose phosphate, amino acid metabolism, and tricarboxylic acid cycle collectively support the overall anabolism to meet metabolic demands of DENV replication and immune activation by viral infection. Totally 88 of 202 metabolic variants were significantly changed by DENV infection, 36 of which met the statistical standard (P<0.05, VIP>1.5) of differentially expressed metabolites, which were the predominantly decreased variants of acylcarnitine and the increased variants of fatty acids and carbohydrates. Remarkably, 11 differentially expressed metabolites were significantly distinct between DENV only infection and antibody-dependent enhancement of viral infection. Our data suggested that the anabolic activation by DENV infection integrates the viral replication and anti-viral immune activation.

Prediction of lncRNA functions using deep neural networks based on multiple networks

BACKGROUND

More and more studies show that lncRNA is widely involved in various physiological processes of the organism. However, the functions of the vast majority of them continue to be unknown. In addition, data related to lncRNAs in biological databases are constantly increasing. Therefore, it is quite urgent to develop a computing method to make the utmost of these data.

RESULTS

In this paper, we propose a new computational method based on global heterogeneous networks to predict the functions of lncRNAs, called DNGRGO. DNGRGO first calculates the similarities among proteins, miRNAs, and lncRNAs, and annotates the functions of lncRNAs according to its similar protein-coding genes, which have been labeled with gene ontology (GO). To evaluate the performance of DNGRGO, we manually annotated GO terms to lncRNAs and implemented our method on these data. Compared with the existing methods, the results of DNGRGO show superior predictive performance of maximum F-measure and coverage.

CONCLUSIONS

DNGRGO is able to annotate lncRNAs through capturing the low-dimensional features of the heterogeneous network. Moreover, the experimental results show that integrating miRNA data can help to improve the predictive performance of DNGRGO.

A deep-learning model using enhanced chest CT images to predict PD-L1 expression in non-small-cell lung cancer patients

AIM

To develop a deep-learning model using contrast-enhanced chest computed tomography (CT) images to predict programmed death-ligand 1 (PD-L1) expression in patients with non-small-cell lung cancer (NSCLC).

MATERIALS AND METHODS

Preoperative enhanced chest CT images and immunohistochemistry results for PD-L1 expression (<1% and ≥1% were defined as negative and positive, respectively) were collected retrospectively from 125 NSCLC patients to train and validate a deep-learning radiomics model (DLRM) for the prediction of PD-L1 expression in tumours. The DLRM was developed by combining the deep-learning signature (DLS) obtained from a convolutional neural network and clinicopathological factors. The indexes of the area under the curve (AUC), integrated discrimination improvement (IDI), and decision curve analysis (DCA) were used to evaluate the efficiency of the DLRM.

RESULTS

DLS and tumour stage were identified as independent predictors of PD-L1 expression by the DLRM. The AUCs of the DLRM were 0.804 (95% confidence interval: 0.697-0.911) and 0.804 (95% confidence interval: 0.679-0.929) in the training and validation cohorts, respectively. IDI analysis showed the DLRM had better diagnostic accuracy than DLS (0.0028 [p<0.05]) in the validation cohort. Additionally, DCA revealed that the DLRM had more net benefit than the DLS for clinical utility.

CONCLUSION

The proposed DLRM using enhanced chest CT images could function as a non-invasive diagnostic tool to differentiate PD-L1 expression in NSCLC patients.

[Effects of rapid drug sensitivity testing for multidrug-resistant bacteria on the prognosis of patients with severe intra-abdominal infection]

Objective: To examine the clinical value of rapid detection of drug-resistant bacteria by immunochromatography and the effects of rapid detection on the prognosis of patients with severe intra-abdominal infection complicated by carbapenem-resistant Enterobacteriaceae (CRE) bloodstream infection. Methods: This was a retrospective cohort study. We analyzed clinical data of 73 patients with severe abdominal infections with sepsis or septic shock complicated by CRE bloodstream infection admitted to the general surgery department of Jinling Hospital between February 2022 and February 2023. Patients were divided into a colloidal gold immunochromatographic assay (GICA) group (17 patients) and conventional testing group (56 patients) based on whether a GICA for CRE had been performed on the patients' first blood culture sample during the diagnosis and treatment process. There were no statistically significant differences between the GICA and conventional testing groups in age ([55.9±17.3] vs. [47.6±16.4] years), sex ([16 men vs. one woman ] vs. [41 men vs. 15 women]), median Charlson comorbidity index (3.0[2.0,4.0] vs. 3.0[2.0, 4.8]), septic shock (10 vs. 39), or acute kidney injury (8 vs. 40) (all P>0.05). Both groups routinely underwent traditional bacterial identification and drug susceptibility testing. Additionally, patients in the GICA group were tested directly for positive blood cultures using a GICA carbapenemase test kit. The main outcomes were mortality rates on Days 28 and 90 after the first identification of CRE bloodstream infection in both groups. We also compared the microbial clearance rate, duration of hospitalization and intensive care unit stay, and time from onset of CRE bloodstream infection to initiation of targeted and appropriate antibiotics between the two groups. Results: The rate of microbial clearance of bloodstream infection was significantly greater in the GICA group than in the conventional testing group (15/17 vs. 34/56 [60.7%], χ2=4.476, P=0.034), whereas the 28-day mortality tended to be lower in the GICA than conventional testing group [5/17 vs. 44.6% [25/56], χ2=1.250, P=0.264). The 90-day mortality (8/17 vs. 53.6% [30/56], χ2=0.222, P=0.638), median duration of hospitalization (37.0 [18.0, 46.5] days vs. 45.5 [32.2, 64.8] days, Z=-1.867, P=0.062), and median duration of intensive care unit stay (18.0 [6.5, 35.0] days vs. 32.0 [5.0, 51.8] days, Z=-1.251, P=0.209). The median time between the onset of bloodstream infection and administration of antibiotics was 49.0 (38.0, 69.0) hours in the GICA group, which is significantly shorter than the 163.0 (111.8, 190.0) hours in the conventional testing group (Z=-5.731, P<0.001). The median time between the onset of bloodstream infection and administration of appropriate antibiotics was 40.0 (34.0, 80.0) hours in the GICA group, which is shorter than in the conventional testing group (68.0 [38.2, 118.8]) hours; however, this difference is not statistically significant (Z=-1.686, P=0.093). Conclusions: GICA can provide information on carbapenemase- producing pathogens faster than traditional drug sensitivity testing, enabling early administration of the optimal antibiotics. The strategy of 'carbapenemase detection first' for managing bacterial infection has the potential to improve prognosis of patients and reduce mortality rate.

[Treatment of open abdomen combined with entero-atmospheric fistula: A retrospective study]

Objective: The purpose of this study was to analyze the course and outcome of patients with combined entero-atmospheric fistulas in open abdomen treatment. Methods: In this retrospective observational study, we collected data on 214 patients with open abdomen complicated by entero-atmospheric fistulas admitted to Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School from January 2012 to January 2021. We collected their basic characteristics, aetiology, treatment plan, and prognosis, including the durations of hospitalization and open treatment, time to resumption of enteral nutrition, duration and prognosis of definitive surgery, and overall prognosis. Results: Of the 214 patients with open abdomen complicated with entero-enteral fistulas, 23 (10.7%) died (11 of multiple organ failure caused by abdominal infection, five of abdominal cavity bleeding, four of pulmonary infection, one of airway bleeding, one of necrotizing fasciitis, and one of traumatic brain injury). The remaining 191 underwent definitive surgery at our hospital. The patients who underwent definitive surgery were predominantly male (156 patients, 81.7%); their age was (46.5±2.5) years. Trauma and gastrointestinal tumors (120 cases, 62.8%) predominated among the primary causes. The reasons for abdominal opening were, in order, severe abdominal infection (137 cases, 71.7%, damage control surgery (29 cases, 15.2%), and abdominal hypertension (25 cases, 13.1%). Temporary abdominal closure measures were used to classify the participants into a skin-only suture group (104 cases) and a skin-implant group (87 cases). Compared with the skin-implant group, in the skin-suture-only group the proportion of male patients was lower (74.7% [65/87] vs. 87.5% [91/104], χ2=5.176, P=0.023), the mean age was older ([48.3±2.0] years vs. [45.0±1.9] years, t=-11.671, P<0.001), there were fewer patients with trauma (32.2% [28 /87] vs. 58.7% [61/104), χ2=13.337, P<0.001), intensive care stays were shorter ([8.9±1.0] days vs. [12.7±1.6] days, t=19.281, P<0.001), total length of stay was shorter ([29.3±2.0] days vs. [31.9±2.0] days, t=9.021,P<0.001), there was a higher percentage of colonic fistulas (18.4% [16/87] vs. 8.7% [9/104], χ2=3.948, P=0.047), but fewer multiple fistulas (11.5% [10/87] vs. 34.6% [36/104], χ2=14.440, P<0.001). As to fistula management, a higher percentage of fistula sealing methods using 3D-printed intestinal stents were implemented in the skin-only suture group (60.9% [53/87] versus 43.3% [45/104], χ2=5.907, P=0.015). Compared with the implant group, the skin-only suture group had a shorter mean time to performing provisional closure ( [9.5±0.8] days vs. [16.0±0.6] days, t=66.023, P<0.001), shorter intervals to definitive surgery ( [165.0±10.7] days vs. [198.9±8.3] days, t=26.644, P<0.001), and less use of biopatches (56.3% [49/87) vs. 71.2% [74/104], χ2=4.545, P=0.033). Conclusions: Open abdomen complicated with entero-enteral fistulas is more common in male, and is often caused by trauma and gastrointestinal tumor. Severe intra-abdominal infection is the major cause of open abdomen, and most fistulae involves the small intestine. Collection and retraction of intestinal fluid and 3D-printed entero-enteral fistula stent sealing followed by implantation and skin-only suturing is an effective means of managing entero-enteral fistulas complicating open abdominal cavity. Earlier closure of the abdominal cavity with skin-only sutures can shorten the time to definitive surgery and reduce the rate of utilization of biopatches.

[Membrane anatomy-based splenic hilar lymph node dissection for gastric cancer]

There is a consensus that selectively perform splenic lymph node dissection is necessary for high-risk patients with proximal gastric cancer to achieve radical treatment. However, there are still some outstanding issues that need to be solved during the practice of splenic lymph node dissection. These include poorly defined boundaries, technical difficulties, and blurred boundaries in No. 10 and No. 11 lymph nodes, etc. Membrane anatomy has achieved successful applications in the field of gastric and colorectal surgery in recent years. The study of membrane anatomy in the splenic hilum region is controversial due to the special location of the splenic hilum, which involves multiple organs and affiliated mesentery undergoing complex rotation, folding, and fusion during embryonic development. In this manuscript, we summarize the following points based on existing research and personal experience regarding membrane anatomy. 1. There is a membrane anatomical structure that can be used for lymph node dissection in the splenic hilum region. 2. The membrane structure in the splenic hilum region can be divided into two layers: the superficial layer is composed of the dorsal mesogastrium, and the deep layer is composed of Gerota fascia, the tail of the pancreas, and the mesentery of the transverse colon (from head to tail). 3. There is a loose space between the two layers that can be used for separation during surgery. The resection of the dorsal mesogastrium belongs to D2 dissection. The No. 10 lymph node in the deeper layer belongs to the duodenal mesentery, and the resection of the No.10 lymph node exceeds D2 dissection. The complete excision of the gastric dorsal mesentery is consistent with the D2+CME surgical mode proposed by Gong Jianping's group.

[Application value of serum protein indicators in constructing the early prediction model for the prognosis of patients with pulmonary tuberculosis]

Objective: To analyze the clinical significance of laboratory examination indicators as the key prognostic factors and to construct an early prediction model for prognosis assessment of pulmonary tuberculosis patients. Methods: The basic information, biochemical indexes and blood routine items of 163 tuberculosis patients (144 males and 19 females, aged 41-70 years, with an average age of 56 years) and 118 healthy persons who underwent physical examination (101 males and 17 females, aged 46-64 years, with an average age of 54 years) in Suzhou Fifth People's Hospital from January 2012 to December 2020 were retrospectively collected. According to the presence of Mycobacterium tuberculosis after six months of treatment, the enrolled patients were divided into a cured group (96 cases) and a treatment failure group (67 cases). To analyze the baseline levels of laboratory examination indicators between these two groups, we screened the key predictors and the binary logistic regression method in SPSS statistics software was used to construct the prediction model. Results: The baseline levels of total protein, albumin, prealbumin, glutamic-pyruvic transaminase, erythrocyte, hemoglobin and lymphocyte were significantly higher in the cured group than in the treatment failure group. After 6 months of treatment, the indexes of total protein, albumin and prealbumin increased significantly in the cured group, but remained at the low levels in the treatment failure group. Receiver operating characteristic (ROC) curve analysis showed that total protein, albumin and prealbumin as independent predictors for forecasting the prognosis of pulmonary tuberculosis patients had the highest prediction accuracy. Logistic regression analysis showed that the combination of these three key predictors could construct the best early prediction model for assessing the prognosis of pulmonary tuberculosis patients, with a prediction accuracy of 0.924 (0.886-0.961), sensitivity of 75.0%, specificity of 94%, showing an ideal prediction accuracy. Conclusions: The routine test indexes of total protein, albumin and prealbumin show good application value in the construction of early prediction model for prognosis evaluation of pulmonary tuberculosis treatment. The combined prediction model consisting of total protein, albumin and prealbumin is expected to provide a theoretical basis and reference model for precision treatment and prognosis assessment of tuberculosis patients.

ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction

With the continuous development of ribosome profiling, sequencing technology, and proteomics, evidence is mounting that noncoding RNA (ncRNA) may be a novel source of peptides or proteins. These peptides and proteins play crucial roles in inhibiting tumor progression and interfering with cancer metabolism and other essential physiological processes. Therefore, identifying ncRNAs with coding potential is vital to ncRNA functional research. However, existing studies perform well in classifying ncRNAs and mRNAs, and no research has been explicitly raised to distinguish whether ncRNA transcripts have coding potential. For this reason, we propose an attention mechanism-based bidirectional LSTM network called ABLNCPP to assess the coding possibility of ncRNA sequences. Considering the sequential information loss in previous methods, we introduce a novel nonoverlapping trinucleotide embedding (NOLTE) method for ncRNAs to obtain embeddings containing sequential features. The extensive evaluations show that ABLNCPP outperforms other state-of-the-art models. In general, ABLNCPP overcomes the bottleneck of ncRNA coding potential prediction and is expected to provide valuable contributions to cancer discovery and treatment in the future. The source code and data sets are freely available at https://github.com/YinggggJ/ABLNCPP.

[Relationship between cadmium exposure and pulmonary function level and chronic obstructive pulmonary disease]

Objective: To analyze the levels and distribution characteristics of blood cadmium and urinary cadmium in American adults, to analyze the relationship between blood cadmium and urinary cadmium and pulmonary function dose response, and to explore the effect of this index on the risk of chronic obstructive pulmonary disease. Methods: In March 2022, 3785 patients from 2007 to 2012 in NHANES database were selected as the subjects. Collect demography data such as gender and age, and test data such as lung function, blood cadmium concentration and Urine cadimium concentration. The relationship between blood and urine cadmium levels and lung function and pulmonary function and chronic obstructive pulmonary diease (COPD) was analyzed by Mann-Whitney U test or Kruskal-Wallis H test, multivariate linear regression and restricted cubic spline method. Results: The geometric mean of blood cadmium and urine cadmium in American adults was 0.37 g/L and 0.28 g/L, FEV(1) and FEV(1)/FVC among different cadmium exposure groups was statistically significant, and there was a negative linear dose-response relationship between serum Cd and urine Cd concentrations and FEV(1)/FVC levels (P(overall)<0.001, P(non-linear)=0.152; P(overall)<0.001, P(non-linear)=0.926). Compared with the lowest quartile concentration (Q1), the highest quartile blood cadmium concentration (Q4) (OR=1.934, P(trend)=0.000) and urinary cadmium concentration (OR=1.683, P(trend)=0.000) may increased the risk of chronic obstructive pulmonary disease. Conclusion: There is a negative correlation between blood cadmium, urinary cadmium levels and lung function in American adults, and cadmium may increase the risk of chronic obstructive pulmonary disease.

Evolution and development of potent monobactam sulfonate candidate IMBZ18g as a dual inhibitor against MDR Gram-negative bacteria producing ESBLs

A series of new monobactam sulfonates is continuously synthesized and evaluated for their antimicrobial efficacies against Gram-negative bacteria. Compound 33a (IMBZ18G) is highly effective in vitro and in vivo against clinically intractable multi-drug-resistant (MDR) Gram-negative strains, with a highly druglike nature. The checkerboard assay reveals its significant synergistic effect with β-lactamase inhibitor avibactam, and the MIC values against MDR enterobacteria were reduced up to 4-512 folds. X-ray co-crystal and chemoproteomic assays indicate that the anti-MDR bacteria effect of 33a results from the dual inhibition of the common PBP3 and some class A and C β-lactamases. Accordingly, preclinical studies of 33a alone and 33a‒avibactam combination as potential innovative candidates are actively going on, in the treatment of β-lactamase-producing MDR Gram-negative bacterial infections.

A Combination of In Silico ADMET Prediction, In Vivo Toxicity Evaluation, and Potential Mechanism Exploration of Brucine and Brucine N-oxide-A Comparative Study

Brucine (BRU) and brucine N-oxide (BNO) are prominent, bioactive, and toxic alkaloids in crude and processed Semen Strychni. Studies have demonstrated that BRU and BNO possess comprehensive pharmacological activities, such as anti-inflammatory and analgesic. In this context, a comparative study of BRU and BNO was performed by combination analysis of in silico ADMET prediction, in vivo toxicity evaluation, and potential action mechanism exploration. ADMET prediction showed that BRU and BNO might induce liver injury, and BRU may have a stronger hepatoxic effect. The prediction was experimentally verified using the zebrafish model. The BRU-induced hepatotoxicity of zebrafish larvae had a dose-response relationship. The mechanism of BRU-induced hepatotoxicity might relate to phosphorylation, kinase activity, and signal transduction. By comparison, signal transduction and gap junctions might involve BNO-induced hepatotoxicity. Our results provided a better understanding of BRU- and BNO-induced hepatotoxicity. We also built a foundation to elucidate the material base of the hepatotoxicity of traditional Chinese medicine Semen Strychni.

Autophagic degradation of LOX-1 is involved in the maintenance of vascular integrity injured by oxLDL and protected by Berberine

Damage to vascular endothelial cells (VECs) and vascular smooth muscle cells (VSMCs) caused by oxidized low-density lipoprotein (oxLDL) contributes to cardiovascular and cerebrovascular diseases. Protection effects of Berberine (BBR) on the cardiovascular system have been reported, however, the molecular mechanism of vascular protection is still unclear. In this study, we established two hyperlipidemia models in zebrafish and VEC-VSMC co-culture using high-cholesterol food (HCF) and oxLDL, respectively. We demonstrated that HCF doubled total cholesterol and total glyceride levels, and BBR decreased these indices in a concentration-dependent manner. Lipid staining and hematoxylin-eosin staining revealed that BBR inhibited oxLDL-induced VSMC bulge-like proliferation and migration toward VECs and prevented the HCF-induced trunk vascular obstruction in zebrafish. Immunoblot analysis, cell immunofluorescence, co-immunoprecipitation assays, and transmission electron microscopy showed that oxLDL/HCF increased lectin-like oxLDL receptor-1 (LOX-1) expression at least 5-fold and significantly inhibited autophagolysosome formation in the blood vessel cells and in zebrafish. These observations were associated with endothelial-to-mesenchymal transition (EMT) in VECs and triggered VE-cadherin ectopic expression in VSMCs, and they were responsible for aberrant VSMC migration and vascular occlusion. However, BBR, by promoting autolysosome formation and degradation of LOX-1, reversed the above events and maintained intracellular homeostasis of vessel cells and vascular integrity. In conclusion, regulation of autophagy may be an effective approach to treating oxLDL-induced cardiovascular diseases by reducing LOX-1 protein level. BBR can protect blood vessels by adjusting the oxLDL-LOX-1-EMT-autophagy axis. This study is a step toward the development of new applications of BBR.

Isatropolone/isarubrolone Cm from Streptomyces with biological activity of inducing incomplete autophagy

Isatropolones/isarubrolones are Streptomyces secondary metabolites featuring a tropolone ring in the pentacyclic scaffolds of these molecules. They are able to induce complete autophagy in human HepG2 cells. Here, methyl isatropolones (1-2) and isarubrolone (3) are identified from Streptomyces CPCC 204095. They all have a methyl tropolone ring in the pentacyclic scaffold of these molecules resolved by MS and NMR spectra. Biological activity assay indicates that isatropolone Cm (1) and isarubrolone Cm (3) induce incomplete autophagy in human HepG2 cells.

[Regulatory effects of bio-intensity electric field on microtubule acetylation in human epidermal cell line HaCaT]

Objective: To investigate the regulatory effects of bio-intensity electric field on directional migration and microtubule acetylation in human epidermal cell line HaCaT, aiming to provide molecular theoretical basis for the clinical treatment of wound repair. Methods: The experimental research methods were used. HaCaT cells were collected and divided into simulated electric field group (n=54) placed in the electric field device without electricity for 3 h and electric field treatment group (n=52) treated with 200 mV/mm electric field for 3 h (the same treatment methods below). The cell movement direction was observed in the living cell workstation and the movement velocity, trajectory velocity, and direction of cosθ of cell movement within 3 h of treatment were calculated. HaCaT cells were divided into simulated electric field group and electric field treatment 1 h group, electric field treatment 2 h group, and electric field treatment 3 h group which were treated with 200 mV/mm electric field for corresponding time. HaCaT cells were divided into simulated electric field group and 100 mV/mm electric field group, 200 mV/mm electric field group, and 300 mV/mm electric field group treated with electric field of corresponding intensities for 3 h. The protein expression of acetylated α-tubulin was detected by Western blotting (n=3). HaCaT cells were divided into simulated electric field group and electric field treatment group, and the protein expression of acetylated α-tubulin was detected and located by immunofluorescence method (n=3). Data were statistically analyzed with Kruskal-Wallis H test,Mann-Whitney U test, Bonferroni correction, one-way analysis of variance, least significant difference test, and independent sample t test. Results: Within 3 h of treatment, compared with that in simulated electric field group, the cells in electric field treatment group had obvious tendency to move directionally, the movement velocity and trajectory velocity were increased significantly (with Z values of -8.53 and -2.05, respectively, P<0.05 or P<0.01), and the directionality was significantly enhanced (Z=-8.65, P<0.01). Compared with (0.80±0.14) in simulated electric field group, the protein expressions of acetylated α-tubulin in electric field treatment 1 h group (1.50±0.08) and electric field treatment 2 h group (1.89±0.06) were not changed obviously (P>0.05), while the protein expression of acetylated α-tubulin of cells in electric field treatment 3 h group (3.37±0.36) was increased significantly (Z=-3.06, P<0.05). After treatment for 3 h, the protein expressions of acetylated α-tubulin of cells in 100 mV/mm electric field group, 200 mV/mm electric field group, and 300 mV/mm electric field group were 1.63±0.05, 2.24±0.08, and 2.00±0.13, respectively, which were significantly more than 0.95±0.27 in simulated electric field group (P<0.01). Compared with that in 100 mV/mm electric field group, the protein expressions of acetylated α-tubulin in 200 mV/mm electric field group and 300 mV/mm electric field group were increased significantly (P<0.01); the protein expression of acetylated α-tubulin of cells in 300 mV/mm electric field group was significantly lower than that in 200 mV/mm electric field group (P<0.05). After treatment for 3 h, compared with that in simulated electric field group, the acetylated α-tubulin of cells had enhanced directional distribution and higher protein expression (t=5.78, P<0.01). Conclusions: Bio-intensity electric field can induce the directional migration of HaCaT cells and obviously up-regulate the level of α-ubulin acetylation after treatment at 200 mV/mm bio-intensity electric field for 3 h.

Systems assessment of statins hazard: Integrating in silico prediction, developmental toxicity profile and transcriptomics in zebrafish

Statins are prescribed widely as lipid-lowering agents. However, statins are associated with an increased harmful risk on public health and the ecosystem. Little is known about statins' toxicity on biological development and the underlying molecular mechanisms. We exposed zebrafish embryos to a series of statins to evaluate their development toxicity. Statins-induced embryonic developmental defects in a concentration-dependent manner. 72 h LC₅₀ values for lovastatin, simvastatin, fluvastatin, atorvastatin, rosuvastatin, and pravastatin were 0.01 μM, 0.04 μM, 1.93 μM, 37.28 μM, 79.29 μM, and 2170 μM, respectively. Moreover, the expression of genes involved in heart contraction, calcium ion binding, transcription factors, nucleus, and G protein-coupled receptor signaling pathway was altered by statins. The early growth response gene (egr4) and transcription factor genes (fosab and fosb) were screened as potential toxicity targets due to their significant upregulation based on protein-protein interaction (PPI) and drug-gene interaction network analysis. Finally, the ecotoxicity profile of statins was predicted by in silico method, and statins were high or moderate risk to aquatic organisms. We provide a systems toxicology strategy to explore the toxicity of statins and illustrate the potential mechanisms of action.

PDIA2 Bridges Endoplasmic Reticulum Stress and Metabolic Reprogramming During Malignant Transformation of Chronic Colitis

Background

Chronic inflammation contributes to approximately 20% of cancers; the underlying mechanisms are still elusive. Here, using an animal model of colitis to colon-cancerous transformation, we demonstrated that endoplasmic reticulum (ER) stress couples with metabolic reprogramming to promote a malignant transformation of chronic inflammation.

Methods

The animal model for chronic colitis to colon-cancerous transformation was established in C57BL/6N mice by azoxymethane (AOM) and dextran sodium sulfate (DSS) treatments. The differential proteins in control and AOM/DSS-treated colon mucosa were determined using proteomic analysis; the kinetics of metabolic modifications were monitored by mitochondrial oxygen flux, extracellular acidification, and targeted metabolomics; the molecule linker between ER stress and metabolic modifications were identified by coimmunoprecipitation, KEGG pathway analysis, and the subcutaneous tumor model using gene-specific knockdown colon cancer cells. Tissue array analysis were used to evaluate the differential protein in cancer and cancer-adjacent tissues.

Results

AOM/DSS treatment induced 38 tumors in 10 mice at the 14th week with the mean tumor size 9.35 ± 3.87 mm², which was significantly decreased to 5.85 ± 0.95 mm² by the ER stress inhibitor 4-phenylbutyric acid (4PBA). Seven differential proteins were determined from control (1,067 ± 48) and AOM/DSS-treated mucosa (1,077 ± 59); the level of ER protein PDIA2 (protein disulfide isomerase-associated 2) was increased over 7-fold in response to AOM/DSS treatment. PDIA2 interacted with 420 proteins that were involved in 8 signaling pathways, in particular with 53 proteins in metabolic pathways. PDIA2 translocated from ER to mitochondria and interacted with the components of complexes I and II to inhibit oxophosphorylation but increase glycolysis. Knockdown PDIA2 in colon cancer cells restored the metabolic imbalance and significantly repressed tumor growth in the xenograft animal model. 4PBA therapy inhibited the AOM/DSS-mediated overexpression of PDIA2 and metabolic modifications and suppressed colon cancer growth. In clinic, PDIA2 was overexpressed in colon cancer tissues rather than cancer-adjacent tissues and was related with the late stages and lymph node metastasis of colon cancer.

Conclusions

Persistent ER stress reprograms the metabolism to promote the malignant transformation of chronic colitis; PDIA2 serves as a molecule linker between ER stress and metabolic reprogramming. The inhibition of ER stress restores metabolic homeostasis and attenuates the cancerous transformation of chronic inflammation.

Predicting circRNA-drug sensitivity associations via graph attention auto-encoder

Background

Circular RNAs (circRNAs) play essential roles in cancer development and therapy resistance. Many studies have shown that circRNA is closely related to human health. The expression of circRNAs also affects the sensitivity of cells to drugs, thereby significantly affecting the efficacy of drugs. However, traditional biological experiments are time-consuming and expensive to validate drug-related circRNAs. Therefore, it is an important and urgent task to develop an effective computational method for predicting unknown circRNA-drug associations.

Results

In this work, we propose a computational framework (GATECDA) based on graph attention auto-encoder to predict circRNA-drug sensitivity associations. In GATECDA, we leverage multiple databases, containing the sequences of host genes of circRNAs, the structure of drugs, and circRNA-drug sensitivity associations. Based on the data, GATECDA employs Graph attention auto-encoder (GATE) to extract the low-dimensional representation of circRNA/drug, effectively retaining critical information in sparse high-dimensional features and realizing the effective fusion of nodes’ neighborhood information. Experimental results indicate that GATECDA achieves an average AUC of 89.18% under 10-fold cross-validation. Case studies further show the excellent performance of GATECDA.

Conclusions

Many experimental results and case studies show that our proposed GATECDA method can effectively predict the circRNA-drug sensitivity associations.

Isarubrolone C Promotes Autophagic Degradation of Virus Proteins via Activating ATG10S in HepG2 Cells

Isarubrolone C is a bioactive polycyclic tropoloalkaloid from Streptomyces. Our previous study showed that isarubrolone C could trigger autophagy. Here, we report isarubrolone C potential in broad-spectrum antiviral effect and its antiviral mechanism in vitro. Our results show that isarubrolone C activated autophagy and reduced levels of viral proteins in the cells harboring HCV-CORE/NS5B, HBx, ZIKV-NS5, and HIV-RT, respectively. The role of isarubrolone C in suppression of the viral proteins was via an autophagic degradation pathway rather than a proteasome pathway. Co-immunoprecipitation assays revealed that isarubrolone C promoted both autophagy flux opening and the viral proteins being enwrapped in autolysosomes. PCR assays showed that isarubrolone C elevated the transcription levels of ATG10/ATG10S and IL28A. Further, ATG10S high expression could efficiently enhance IL28A expression and the ability of isarubrolone C to degrade the viral proteins by promoting the colocalization of viral proteins with autolysosomes. Additionally, knockdown of endogenous IL28A caused both losses of the isarubrolone C antiviral effect and autolysosome formation. These results indicate that the role of isarubrolone C antiviruses is achieved by triggering the autophagic mechanism, which is mediated by endogenous ATG10S and IL28A activation. This is the first report about isarubrolone C potential of in vitro broad-spectrum antiviruses.

[Aesthetic reconstruction of the scar contracture deformity in chin and neck with expanded flaps based on the "MRIS" principle]

Objective: The surgical reconstruction strategy for scar contracture deformity in chin and neck was explored, aiming to obtain better aesthetic outcome. Methods: A retrospective observational study was conducted. From December 2017 to April 2021, 34 patients with scar contracture deformity in chin and neck after burns were hospitalized in the Department of Plastic Surgery of the First Affiliated Hospital of Army Medical University (the Third Military Medical University), aged 12-54 years, including 13 males and 21 females, 4 cases with chin affected only, 7 cases with neck affected only, and 23 cases with both chin and neck affected. The scar areas were 48-252 cm2. All the patients were treated by operation with expanded flaps, following the "MRIS" principle of matching of the color and thickness of the repair flaps (match), reconstructing of the aesthetic features of subunits (reconstruction), design of incision according to the plastic principle (incision), and prevention of the surgical incision scar (scar). The rectangular or kidney shaped skin and soft tissue expander (hereinafter referred to as the expander) with rated capacity of 80-400 mL was embedded in the first stage, which was routinely expanded to 3-5 times of the rated capacity of the expander. In the second stage, scar resection and expanded flap excision were performed to repair the secondary wound, and the flap donor site was sutured directly. The expansion ratio of the expander (with average value being calculated), the type of flaps used, the reconstruction of local aesthetic morphology, the appearance of postoperative incision, the survival of flap, and the situation of donor and recipient sites observed during follow-up were recorded. Results: Among the 34 patients, the average expansion ratio of the implanted expander was 3.82 times of the rated capacity of the expander. Three cases were repaired by the expanded local pedicled flap only, 19 cases by the expanded shoulder and/or chest perforator pedicled flap only, 10 cases by the expanded local pedicled flap combined with the expanded shoulder and/or chest perforator pedicled flap, and 2 cases by the expanded local pedicled flap combined with the expanded free flap of the second intercostal perforator of internal thoracic artery. After scar resection, the shapes of lower lip and chin-lip groove were reconstructed in 10 cases, chin process reconstruction and chin lengthening were performed in 16 cases, and the cervico-mental angle and mandibular margin contour were reconstructed in 28 cases. The surgical incision was concealed, most of which were located at the natural junction or turning point of the chin and neck subunits. The vertical incision of neck was Z-shaped or fishtail-shaped. All the expanded flaps in 34 patients survived after operation, of which 8 patients had minor necrosis at the edge or tip of the expanded flaps 1-3 days after operation and healed after dressing change. During the follow-up of 3-18 months, little difference in color and thickness between the expanded flap and the skin of chin and neck was observed, and the aesthetic shape of chin and neck was significantly improved, with mild scar hyperplasia of surgical incision. Conclusions: Reconstruction of scar contracture deformity in chin and neck by using expanded flaps based on the "MRIS" principle is beneficial to improve the quality of surgery and achieve better aesthetic outcome.

In silico drug repositioning based on integrated drug targets and canonical correlation analysis

Background

Besides binding to proteins, the most recent advances in pharmacogenomics indicate drugs can regulate the expression of non-coding RNAs (ncRNAs). The polypharmacological feature in drugs enables us to find new uses for existing drugs (namely drug repositioning). However, current computational methods for drug repositioning mainly consider proteins as drug targets. Meanwhile, these methods identify only statistical relationships between drugs and diseases. They provide little information about how drug-disease associations are formed at the molecular target level.

Methods

Herein, we first comprehensively collect proteins and two categories of ncRNAs as drug targets from public databases to construct drug–target interactions. Experimentally confirmed drug-disease associations are downloaded from an established database. A canonical correlation analysis (CCA) based method is then applied to the two datasets to extract correlated sets of targets and diseases. The correlated sets are regarded as canonical components, and they are used to investigate drug’s mechanism of actions. We finally develop a strategy to predict novel drug-disease associations for drug repositioning by combining all the extracted correlated sets.

Results

We receive 400 canonical components which correlate targets with diseases in our study. We select 4 components for analysis and find some top-ranking diseases in an extracted set might be treated by drugs interfacing with the top-ranking targets in the same set. Experimental results from 10-fold cross-validations show integrating different categories of target information results in better prediction performance than only using proteins or ncRNAs as targets. When compared with 3 state-of-the-art approaches, our method receives the highest AUC value 0.8576. We use our method to predict new indications for 789 drugs and confirm 24 predictions in the top 1 predictions.

Conclusions

To the best of our knowledge, this is the first computational effort which combines both proteins and ncRNAs as drug targets for drug repositioning. Our study provides a biologically relevant interpretation regarding the forming of drug-disease associations, which is useful for guiding future biomedical tests.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01203-1.

Hazard assessment of beta-lactams: Integrating in silico and QSTR approaches with in vivo zebrafish embryo toxicity testing

Antibiotics have emerged as a well-known representative of pharmaceuticals and personal care products (PPCPs) by causing public health and environmental problems due to their potential toxicity. β-lactams are the most commonly used antibiotics in the world. This study used zebrafish embryos to evaluate the toxicity of β-lactams. The results showed that 23 β-lactam compounds induced malformation and death in a concentration-response manner. Moreover, this study established and validated quantitative structure-toxicity relationship (QSTR) models for the toxicity of β-lactams in zebrafish. These models performed well and fast in the prediction of the acute toxicity of β-lactams. Structural interpretation indicated that the β-lactam ring, the thiazolidine/dihydrothiazine rings, the side chains, and spatial configuration are the main factors responsible for the toxicity of β-lactams. The results from our previous studies and this study also revealed that the potential biological risks caused by β-lactams and their degradation products could not be ignored. This study provided important data for further environmental risk assessment of β-lactams and regulatory purposes.

[Systematic review of gut microbiota changes in patients with chronic heart failure]

Objective: To analyze the changes on gut microbiota and metabolic products in patients with chronic heart failure. Methods: By searching the Pubmed, EMBASE, Cochrane Library, and CNKI, Wanfang, and CMB databases from the day of built up to December 2019, we screened related literature exploring the intestinal flora of chronic heart failure patients, and systematic review was performed to study changes in intestinal flora composition, function, and metabolites among chronic heart failure patients. Results: A total of 10 articles were included to study the gut microbiota of patients with chronic heart failure in this analysis. The systematic review showed significant changes in β-diversity in patients with heart failure. The abundance of faecalibacterium, blautia, bacteroides, prevotella and anaerostipes was decreased, while the abundance of streptococcus, escherichia/shigella, veillonella, and enterobacte was increased. The increased microbial gene function in patients with heart failure included tryptophan metabolism, lipid metabolism, LPS synthesis,and so on, especially, bacterial genes related to trimethylamine oxide production increased significantly, while genes related to key enzymes producing the beneficial metabolite butyrate decreased significantly, and harmful metabolite trimethylamine oxide levels increased in chronic heart failure patients. Conclusion: There are significant changes in the structure, function and metabolites of intestinal flora in patients with chronic heart failure.

[Effects and molecular mechanism of histone deacetylase 6 inhibitor Tubastatin A on the prolifera- tion and movement of human skin fibroblasts]

Objective: To explore the effects and possible molecular mechanism of histone deacetylase 6 (HDAC6) inhibitor Tubastatin A on the proliferation and movement of human skin fibroblasts (HSFs). Methods: The experimental research method was used. HSFs in logarithmic growth phase were taken and divided into negative control group, 1 μmol/L Tubastatin A group, 5 μmol/L Tubastatin A group, and 10 μmol/L Tubastatin A group according to the random number table. The HSFs in negative control group were added with Dulbecco's modified eagle medium with the final volume fraction of 0.1% dimethyl sulfoxide (hereinafter referred to as the complete medium), and the other three groups were added with the complete medium with the corresponding final molarity of Tubastatin A. After 24 h of conventional culture, the cell proliferation activity was detected using cell counting kit 8 (CCK-8) method and 5-ethynyl-2'-deoxyuridine (EdU) staining; the range of motion of cells within 3 h was observed under the living cell workstation, and the curve movement velocity of the cells was calculated. The protein expressions of extracellular signal-regulated kinase 1/2 (ERK1/2) and phosphorylated ERK1/2 (p-ERK1/2) were detected by Western blotting, and the ratio of p-ERK1/2 to ERK1/2 was calculated to represent the activity of ERK1/2. The sample number in cell proliferation activity detection with CCK-8 method was 6, while the sample numbers in other experiments were 3. Data were statistically analyzed with one-way analysis of variance and least significant difference test. Results: After 24 h of culture, CCK-8 method and EdU staining showed that compared with negative control group, the cell proliferation activities in 1 μmol/L Tubastatin A group, 5 μmol/L Tubastatin A group, and 10 μmol/L Tubastatin A group were significantly decreased (P<0.01). After 24 h of culture, CCK-8 method showed that compared with 1 μmol/L Tubastatin A group, the cell proliferation activity in 10 μmol/L Tubastatin A group was significantly decreased (P<0.05); EdU staining showed that compared with 1 μmol/L Tubastatin A group, the cell proliferation activities in 5 μmol/L Tubastatin A group and 10 μmol/L Tubastatin A group were significantly decreased (P<0.05 or P<0.01). Within 3 h of observation, the ranges of cell motion in 1 μmol/L Tubastatin A group, 5 μmol/L Tubastatin A group, and 10 μmol/L Tubastatin A group were obviously reduced compared with that in negative control group. Within 3 h of observation, the curve movement velocity of cells in negative control group was (0.780±0.028) μm/min, which was obviously faster than (0.594±0.023), (0.469±0.028), and (0.391±0.021) μm/min of 1 μmol/L Tubastatin A group, 5 μmol/L Tubastatin A group, and 10 μmol/L Tubastatin A group (P<0.01); the curve movement velocity of cells in 1 μmol/L Tubastatin A group was obviously faster than those in 5 μmol/L Tubastatin A group and 10 μmol/L Tubastatin A group (P<0.01); the curve movement velocity of cells in 5 μmol/L Tubastatin A group was obviously faster than that in 10 μmol/L Tubastatin A group (P<0.05). After 24 h of culture, compared with negative control group, the activities of ERK1/2 of cells in 1 μmol/L Tubastatin A group, 5 μmol/L Tubastatin A group, and 10 μmol/L Tubastatin A group were decreased significantly (P<0.01); compared with 1 μmol/L Tubastatin A group, the activities of ERK1/2 of cells in 5 μmol/L Tubastatin A group and 10 μmol/L Tubastatin A group were decreased significantly (P<0.01); compared with 5 μmol/L Tubastatin A group, the activity of ERK1/2 of cells in 10 μmol/L Tubastatin A group was decreased significantly (P<0.05). Conclusions: HDAC6 inhibitor Tubastatin A may mediate the inhibitory effect on proliferation and movement of HSFs by inhibiting the activity of ERK1/2.

Characterization of dicarboxylic acids, oxoacids, and α-dicarbonyls in PM2.5 within the urban boundary layer in southern China: Sources and formation pathways

Low-molecular-weight dicarboxylic acids, which are important components of secondary organic aerosols, have been extensively studied in recent years. Many studies have focused on ground-level observations and literature reports on the vertical distribution of the organic aerosols within the urban boundary layer are limited. In this study, the vertical profiles of dicarboxylic acids and related organic compounds (DCRCs) in PM_2.5 were investigated at altitudinal levels (ground level and 488 m above the ground level) at the Canton Tower in Guangzhou, southern China, to elucidate their primary sources and secondary formation processes. The concentrations of DCRCs at ground level were generally higher than those at 488 m. Oxalic acid (C₂) was the most abundant species, followed by succinic acid (C₄) and malonic acid (C₃) at both heights. The higher ratio of DCRCs-bound carbon to organic carbon (i.e., DCRCs-C/OC) at 488 m (4.8 ± 1.2%) relative to that at ground level (2.7 ± 0.5%) indicated a higher degree of aerosol aging at 488 m. The abundance of C₂ was increased and the conversion of C₄ to C₃ was enhanced due to the photochemical oxidation of its homologues during long-range transport periods. The increase in C₂ was associated with in-cloud processes during pollution periods. Principal component analysis showed that DCRCs were mainly derived from atmospheric secondary processing and biomass burning was also an important source of long-chain carboxylic acids during autumn in Guangzhou. Our results illustrate that secondary processing and biomass burning play prominent roles in controlling the abundance of DCRCs. Furthermore, DCRCs are affected by air masses from regional areas, oxidation of their precursors via vertical transport and in-cloud processes.

MSCFS: inferring circRNA functional similarity based on multiple data sources

Background

More and more evidence shows that circRNA plays an important role in various biological processes and human health. Therefore, inferring the circRNA’s potential functions and obtaining circRNA functional similarity has become more and more significant. However, there is no effective approach to explore the functional similarity of circRNAs.

Methods

In this paper, we propose a new approach, called MSCFS, to calculate the functional similarity of circRNA by integrating multiple data sources. We combine circRNA-disease association, circRNA-gene-Gene Ontology association, and circRNA sequence information to explore the functional similarity of circRNA. Firstly, we employ different learning representation methods from three data sources to establish three circRNA functional similarity networks. Then we integrate the three networks to obtain the final circRNA functional similarity.

Results

We utilize circRNA–miRNA association similarity and circRNA co-expression similarity to evaluate the performance of MSCFS. The results show a positive correlation with miRNA association (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R=0.213$$\end{document}R=0.213) and circRNA co-expression similarity (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R=0.8991$$\end{document}R=0.8991). Finally, we construct a circRNA functional similarity network and perform case analysis. The result shows our method can be applied to infer new potential functions of circRNA and other associations.

Conclusions

MSCFS combines multiple data sources related to circRNA functions. Correlation analysis and case analyses prove that MSCFS is a useful method to explore circRNA functional similarity.

LDAH2V: Exploring Meta-Paths Across Multiple Networks for lncRNA-Disease Association Prediction

Accumulating evidence has demonstrated dysfunctions of long non-coding RNAs (lncRNAs) are involved in various complex human diseases. However, even today, the relationships between lncRNAs and diseases remain unknown in most cases. Developing effective computational approaches to identify potential lncRNA-disease associations has become a hot topic. Existing network-based approaches are usually focused on the intrinsic features of lncRNAs and diseases but ignore the heterogeneous information of biological networks. Considering the limitations in previous methods, we propose LDAH2V, an efficient computational framework for predicting potential lncRNA-disease associations. LDAH2V uses the HIN2Vec to calculate the meta-path and feature vector for each lncRNA-disease pair in the heterogeneous information network (HIN), which consists of lncRNA similarity network, disease similarity network, miRNA similarity network, and the associations between them. Then, a Gradient Boosting Tree (GBT) classifier to predict lncRNA-disease associations is built with the feature vectors. The results show that LDAH2V performs significantly better than the four existing state-of-the-art methods and gains an AUC of 0.97 in the 10-fold cross-validation test. Furthermore, case studies of colon cancer and ovarian cancer-related lncRNAs have been confirmed in related databases and medical literature.

[Surveillance and genetic characteristics of imported cases of measles virus of D8 genotype in Hebei province]

Objective: To understand the epidemiological and genotypic characteristics of imported cases of measles virus of D8 genotype in Hebei province. Methods: Epidemiological investigation of measles cases in surveillance was carried out. The throat swabs of the measles cases in acute phase were collected for real time RT-PCR identification, measles virus culture and genotype identification. Results: A total of 36 imported measles cases of genotype D8 were detected. The cases were mainly distributed in 8 counties of Handan city. Number of confirmed measles cases in Cheng'an county was the highest, accounting for 58.33% (21/36) of all the reported cases. All patients had fever and rash, and 55.55% (20/36) of the cases were under 2 years old and 86.11% (31/36) of the cases had no immunization history. The children with pneumonia accounted for 44.12% (15/34) of the total children with D8 genotype measles virus infection. The nucleotide and amino acid homologies between the imported measles virus genotype D8 and the WHO reference strain of D8 genotype (D8-Manchester.UNK/30.94) were 98.4%-98.6% and 97.3%, respectively. Compared with the strains of H1 genotype in China, the nucleotide and amino acid homologies were 92.8%-93.1% and 93.3%, respectively. Conclusions: The imported cases of measles virus of D8 genotype might have caused local transmission in Hebei province. Molecular epidemiological surveillance for measles virus needs to be further strengthened. It is necessary to detect and control the epidemic early and improve the coverage rate and timely rate of measles vaccination. It is also important to prevent cross infection in hospitals.

In vivo and in silico evaluations of survival and cardiac developmental toxicity of quinolone antibiotics in zebrafish embryos (Danio rerio)

Quinolones are ranked as the second most commonly used class of antibiotics in China, despite their adverse clinical and environmental effects. However, information on their cardiac developmental toxicity to zebrafish is limited. This study investigates the relationships between different quinolone structures and toxicity in zebrafish embryos using in vivo and in silico methods. All of the experimentally tested quinolones show cardiac developmental toxicity potential and present mortality and teratogenic effects in a dose-dependent manner. Theoretically, the acute toxicity values predicted using quantitative structure-toxicity relationship (QSTR) modeling based on previously reported LC₅₀ values are in good agreement with the in vivo results. Further investigation demonstrates that the hormetic concentration response of some quinolones may be related to methylation on the piperazine ring at the C-7 position. The amino group at the C-5 position, the methylated or ethylated piperazine group at the C-7 position, halogens at the C-8 position and a cyclopropyl ring at N1 position may be responsible for cardiac developmental toxicity. In terms of survival (key ecological endpoint), the naridine ring is more toxic than the quinoline ring. This combined approach can predict the acute and cardiac developmental toxicity of other quinolones and impurities.

[CART therapy followed by allo-HSCT for patients with B-cell acute lymphoblastic leukemia relapsing after the first hematopoietic stem cell transplantation]

目的

观察嵌合抗原受体T细胞（CART）序贯二次异基因造血干细胞移植（allo-HSCT）治疗移植后复发急性B淋巴细胞白血病（B-ALL）的疗效。

方法

回顾性分析2015年10月至2020年6月在河北燕达陆道培医院接受二次allo-HSCT的41例B-ALL患者的临床资料，入选患者均为移植后骨髓形态学或髓外复发且二次移植前接受CART治疗。

结果

全部41例患者中男21例、女20例，二次移植时中位年龄为16（3～46）岁。移植后骨髓复发31例（75.6％）、髓外复发5例（12.2％）、骨髓和髓外复发5例（12.2％）。复发后接受CD19-CART治疗35例（85.4％）、CD22-CART治疗2例（4.9％）、CD19-CART联合CD22-CART治疗4例（9.8％）。二次移植后预期3年总生存（OS）率为48.9％（95％ CI 23.0％～70.6％）、无白血病生存（LFS）率为41.8％（95％ CI 17.3％～64.9％），累积复发率（RI）为8.8％（95％ CI 2.9％～26.4％），非复发相关死亡率（NRM）为51.1％（95％ CI 31.2％～83.6％）。首次移植后复发时间≤6个月组（10例）二次移植后1年OS率低于复发时间>6个月组（31例）［45.0％（95％ CI 12.7％～73.5％）对75.0％（95％ CI 51.4％～88.8％），P＝0.017］。

结论

CART序贯二次allo-HSCT可使部分造血干细胞移植后复发B-ALL患者获得长生存，但NRM较高，移植方案有待进一步改进。

[Comparison of the clinical outcomes of haploidentical and matched-sibling donor stem cell transplantation for T cell acute lymphoblastic leukemia in complete remission]

目的

比较亲缘单倍型造血干细胞移植（HIDT）和同胞相合造血干细胞移植（MSDT）治疗完全缓解期（CR）急性T淋巴细胞白血病（T-ALL）的疗效。

方法

回顾性分析2012年5月至2017年5月间在河北燕达陆道培医院接受HIDT（81例）和MSDT（17例）的CR期T-ALL患者的临床特点和预后。

结果

HIDT组、MSDT组移植后100 d Ⅱ～Ⅳ度急性GVHD发生率分别为51.9％（95％CI42.0％～64.0％）、29.4％（95％CI 14.1％～61.4％）（P＝0.072），Ⅲ/Ⅳ度急性GVHD发生率分别为9.8％（95％CI 5.1％～19.1％）、11.8％（95％CI 3.2％～43.3％）（P＝1.000），巨细胞病毒（CMV）血症发生率分别为53.1％（95％CI 43.3％～65.2％）、29.4％（95％CI 14.1％～61.4％）（P＝0.115），EB病毒（EBV）血症发生率分别为35.8％（95％CI 26.8％～47.9％）、11.8％（95％CI 3.2％～43.3％）（P＝0.048）。HIDT、MSDT两组移植后5年总生存（OS）率分别为60.5％（95％CI 5.4％～49.0％）、68.8％（95％CI 11.8％～40.0％）（P＝0.315），无白血病生存（LFS）率分别为58.0％（95％CI 5.5％～46.5％）、68.8％（95％CI11.8％～40.0％）（P＝0.258），累积复发率分别为16.1％（95％ CI 9.8％～26.4％）、11.8％（95％ CI3.2％～43.3％）（P＝0.643），非复发死亡率（NRM）分别为25.9％（95％CI 17.9％～37.5％）、19.4％（95％CI6.9％～54.4％）（P＝0.386）。

结论

对于CR期T-ALL患者，当缺乏合适供者时，HIDT可作为替代选择。

Investigation of combining-efficiency loss induced by a diffractive optical element in a single-aperture coherent beam combining system

Filled-aperture geometries can be obtained using a diffractive optical element (DOE) in the coherent beam combining (CBC) architecture. Minimizing the beam deviation is crucial to maintain single-aperture output and reduce the combining-efficiency losses. In this study, we developed a theoretical model for investigating the combining-efficiency losses with beam deviation in a DOE-based CBC architecture. The beam deviations induced by the DOE-mount-tilt error, emitter-incident angular error, and DOE-groove-tilt error are discussed theoretically in detail and verified experimentally. The combining-efficiency losses caused by the three error sources are calculated. Meanwhile, the combining-efficiency losses affected by the beam size and the DOE period are analyzed. For an 11-channel CBC architecture with a DOE period of 50 µm and a beam size of 30 mm, the maximum combining-efficiency losses caused by the three error sources were 3.2%, 1.87%, and 36.41%, respectively, whereas those in case of a DOE period of 20 µm and a beam size of 10 mm were 14.34%, 8.58%, and 25.29%, respectively. We found that the combining-efficiency loss is most sensitive to the DOE-groove-tilt error.

[Investigation and clinical analysis of a family with germline CEBPA mutations in acute myeloid leukemia]

目的

探讨伴CEBPA基因突变的家族性急性髓系白血病（AML）的临床特征、病因及转归，提高对家族性白血病的认识。

方法

调查一个伴CEBPA基因突变AML家系患者的发病年龄、临床特征、转归及预后并绘制家系谱。对先证者采集骨髓及口腔黏膜细胞，与先证者有血缘关系的亲属，采集外周血，通过基因测序技术检测基因突变。

结果

该家系共有10人诊断为AML，其中男4例，女6例，中位年龄9（3～48）岁。10例患者中，6例死亡，其中4例未进行治疗，1例患者化疗后生存3年复发死亡，1例采取中药及支持治疗生存2年后死亡。4例患者生存，1例接受化疗患者生存达15年，3例患者接受化疗联合造血干细胞移植，至随访截止，生存时间分别为6、9、28个月。对先证者及8名与先证者有血缘关系的亲属进行基因测序，发现5例存在胚系CEBPA TAD p.G36Afs*124突变，其中4例确诊为AML，1例随访至今未发病。

结论

伴CEBPA基因突变的家族性AML多在儿童及青壮年期发病，具有完全或接近完全的外显率，通过积极治疗，大多预后良好。

In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces

BACKGROUND

Drug repositioning refers to the identification of new indications for existing drugs. Drug-based inference methods for drug repositioning apply some unique features of drugs for new indication prediction. Complementary information is provided by these different features. It is therefore necessary to integrate these features for more accurate in silico drug repositioning.

RESULTS

In this study, we collect 3 different types of drug features (i.e., chemical, genomic and pharmacological spaces) from public databases. Similarities between drugs are separately calculated based on each of the features. We further develop a fusion method to combine the 3 similarity measurements. We test the inference abilities of the 4 similarity datasets in drug repositioning under the guilt-by-association principle. Leave-one-out cross-validations show the integrated similarity measurement IntegratedSim receives the best prediction performance, with the highest AUC value of 0.8451 and the highest AUPR value of 0.2201. Case studies demonstrate IntegratedSim produces the largest numbers of confirmed predictions in most cases. Moreover, we compare our integration method with 3 other similarity-fusion methods using the datasets in our study. Cross-validation results suggest our method improves the prediction accuracy in terms of AUC and AUPR values.

CONCLUSIONS

Our study suggests that the 3 drug features used in our manuscript are valuable information for drug repositioning. The comparative results indicate that integration of the 3 drug features would improve drug-disease association prediction. Our study provides a strategy for the fusion of different drug features for in silico drug repositioning.

Relationships between resilience and quality of life in parents of children with cancer

CLINICALTRIALS.GOV ID

NCT03631485.

[Analysis of the effect of transgluteal percutaneous drainage in the treatment of deep pelvic abscess]

Objective: To investigate the safety and feasibility of transgluteal percutaneous drainage using double catheterization cannula in the treatment of deep pelvic abscess. Methods: A retrospective analysis of the clinical data of patients who underwent transgluteal percutaneous drainage using double catheterization cannula with deep pelvic abscesses admitted to the Jinling Hospital from May 2017 to September 2020 was conducted. Seven patients were enrolled, including 5 males and 2 females, who aged 26-74 (median 53.0) years old, and all of them had digestive fistula. One male patient was punctured again due to the tube falling off, and a total of 7 patients underwent 8 times of transgluteal percutaneous drainage, all under the guidance of CT. The puncture and drainage steps of the double catheterization cannula group are as follows: (1) Locate the puncture point under CT in the lateral position; (2) Place the trocar into the abscess cavity; (3) Confirm that the trocar is located in the abscess cavity under CT; (4) Pull out the inner core and insert into the double catheterization cannula through the operating hole; (5) Confirmthat the double catheterization cannula is located in the abscess cavity under CT; (6) The double catheterization cannula is properly fixed to prevent it from falling off. The white blood cells, C-reactive protein (CRP), procalcitonin, and interleukin-6 (IL-6) of all patients before the drainage and 1 days, 3 days, and 5 days after the drainage were collected, as well as the bacterial culture results of the drainage fluid. The changes of various infection biomarkers before and after the drainage were compared. Results: All 7 patients were cured. No complications such as hemorrhage and severe pain were observed. The average time with drainage tube was 60.8 (18-126) days. Five patients finally underwent gastrointestinal reconstruction surgery due to gastrointestinal fistula. The median serum interleukin-6 of patients before drainage, 1 day, 3 days and 5 days after drainage were 181.6 (113.0, 405.4) μg/L, 122.2 (55.8, 226.0) μg/L, 59.2 (29.0,203.5) μg/L and 64.1 (30.0,88.4) μg/L, respectively.The level of serum interleukin-6 at 3 days and 5 days after drainage was significantly lower than before drainage (F=3.586, P=0.026). Although the white blood cell count, C-reactive protein, and procalcitonin decreased gradually after drainage compared with before drainage, the difference was not statistically significant (all P>0.05). Conclusion: Transgluteal percutaneous drainage with double catheterization cannula is simple and effective, and can be used for the treatment of deep pelvic abscess.

DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features

Background

Circular RNAs (circRNAs) are special noncoding RNA molecules with closed loop structures. Compared with the traditional linear RNA, circRNA is more stable and not easily degraded. Many studies have shown that circRNAs are involved in the regulation of various diseases and cancers. Determining the functions of circRNAs in mammalian cells is of great significance for revealing their mechanism of action in physiological and pathological processes, diagnosis and treatment of diseases. However, determining the functions of circRNAs on a large scale is a challenging task because of the high experimental costs.

Results

In this paper, we present a hierarchical deep learning model, DeepciRGO, which can effectively predict gene ontology functions of circRNAs. We build a heterogeneous network containing circRNA co-expressions, protein–protein interactions and protein–circRNA interactions. The topology features of proteins and circRNAs are calculated using a novel representation learning approach HIN2Vec across the heterogeneous network. Then, a deep multi-label hierarchical classification model is trained with the topology features to predict the biological process function in the gene ontology for each circRNA. In particular, we manually curated a benchmark dataset containing 185 GO annotations for 62 circRNAs, namely, circRNA2GO-62. The DeepciRGO achieves promising performance on the circRNA2GO-62 dataset with a maximum F-measure of 0.412, a recall score of 0.400, and an accuracy of 0.425, which are significantly better than other state-of-the-art RNA function prediction methods. In addition, we demonstrate the considerable potential of integrating multiple interactions and association networks.

Conclusions

DeepciRGO will be a useful tool for accurately annotating circRNAs. The experimental results show that integrating multi-source data can help to improve the predictive performance of DeepciRGO. Moreover, The model also can combine RNA structure and sequence information to further optimize predictive performance.

CXCL-10/CXCR3 in macrophages regulates tissue repair by controlling the expression of Arg1, VEGFa and TNFα

Macrophages have been reported to participate in inflammation, tissue homeostasis and tissue repair. The detailed mechanism of macrophage-mediated tissue repair is not clear. CXCL-10, secreted by monocytes, endothelial cells and fibroblasts, mediates immune response and angiogenesis by binding to CXCR3. In this study, the expression of CXCL-10 and CXCR3 in porcine lung injury induced by porcine reproductive and respiratory syndrome virus (PRRSV) infection was firstly examined. The results showed that the expression of both CXCL-10 and CXCR3 increased in the infected pig lungs. In addition, the increased expression of CXCL-10 and CXCR3 in macrophage treated by poly (I:C) was also observed, suggesting the autocrine system existed in macrophages. Furthermore, CXCL-10 treatment induced upregulation of Arg1 and VEGFa, and downregulation of TNFα in macrophage, and CXCR3 antagonist AMG487 treatment presented the contrary effects on the expression of Arg1, VEGFa, and TNFα. CXCL- 10-stimulated effects were dependent on PI3K/Akt signaling pathway. Wound-healing assay showed that CXCL-10 treatment macrophage conditioned medium promoted the healing process of endothelial cells. Our results suggested that CXCL-10/CXCR3 in macrophage may mediate tissue repair by regulating the macrophage expression of Arg1, VEGFa and TNFα. Modulation of CXCL-10/CXCR3 axis in macrophage may be a potential therapeutic strategy for tissue injury and repair.

[Prognostic analysis of allogeneic hematopoietic stem cell transplantation for Philadelphia chromosome-positive acute lymphoblastic leukemia in complete remission in the era of tyrosine kinase inhibitors]

目的

探讨在酪氨酸激酶抑制剂（TKI）时代Ph染色体阳性急性淋巴细胞白血病（Ph⁺ALL）在完全缓解（CR）状态下行异基因造血干细胞移植（allo-HSCT）的预后和影响因素。

方法

回顾性分析2012年5月至2017年5月河北燕达陆道培医院收治的116例在CR状态下行allo-HSCT的Ph⁺ALL患者的预后及其影响因素。

结果

116例患者中男72例，女44例。中位年龄20（4～64）岁。同胞全相合移植21例，亲缘单倍型移植77例，非血缘移植18例。5年总生存（OS）率为73.2％（95％CI 63.8％～80.5％），其中诊断至移植间隔时间<180 d的亚组5年OS率为87.5％。5年无病生存（DFS）率为61.4％（95％CI 51.8％～69.7％）。5年细胞形态及分子学水平复发累积发生率为18.5％（95％CI 12.6％～27.3％）。5年移植相关死亡率（TRM）为19.9％（95％CI 13.8％～28.7％）。多因素分析显示，15～39岁（HR＝2.730，P＝0.044）、诊断至移植间隔时间≥180 d（HR＝4.534，P＝0.010）、发生Ⅲ～Ⅳ度急性移植物抗宿主病（aGVHD）（HR＝7.558，P＝0.000）是影响患者OS的不利因素；发生局限型慢性移植物抗宿主病（cGVHD）是影响患者OS的有利因素（HR＝0.300，P＝0.034）。而性别、起病时WBC（<30×10⁹/L，≥30×10⁹/L）、BCR-ABL融合基因类型、体细胞突变类型、移植前状态（CR₁，>CR₁）、移植前微小残留病（MRD）水平（MRD阴性，MRD阳性）、预处理方案（全身照射方案，白消安为基础方案）、预处理方案强度、移植类型、GVHD预防方案（环孢素A，他克莫司）、抗胸腺细胞免疫球蛋白的种类、巨细胞病毒和EB病毒血症的有无对OS的影响无统计学意义。

结论

TKI时代Ph⁺ALL在CR状态下行allo-HSCT时，影响生存的因素有年龄、诊断至移植间隔时间和发生重度aGVHD。

[Application of membrane anatomy in key technologies during gastric cancer surgery: guidance and compromise]

Different from classical surgical anatomy which only pays attention to the morphology and structure of human organs, modern membrane anatomy focuses on not only the relationship between morphology and structure, but also the biological behavior characteristics of tumors. Membrane antomy is a theoretical system with interpretation on both the structural and disease function, so it has been accepted by more and more gastrointestinal surgeons. However, the theoretical system of gastric membrane anatomy is not mature yet. The stomach and its mesentery have undergone complex rotation and fusion in the process of embryonic development, so that surgeons have different understandings of the gastric membrane anatomy. Therefore, it is easy to cause various confusion and misunderstanding, resulting in deviations between the theory of membrane anatomy and the practice of surgery. In the present study, the mesentery of the stomach is divided into different regions, and the embryonic development process is traced back. The application and compromise encountered in the radical gastrectomy of gastric cancer will be expounded according to the membrane anatomy theory combined with the author's experience of operation.

Human iPS Cells Loaded with MnO2-Based Nanoprobes for Photodynamic and Simultaneous Enhanced Immunotherapy Against Cancer

HIGHLIGHTS

MnO₂@Ce6 nanoprobes-loaded-iPS cells (iPS-MnO₂@Ce6) were developed for enhanced photodynamic and immunotherapy against cancer. Under the guidance of multi-mode real-time imaging, iPS-MnO₂@Ce6 achieved an enhanced photodynamic therapeutic effect and stimulated a strong anti-tumor immune response in the tumor-bearing mouse.

ABSTRACT

How to trigger strong anti-tumor immune responses has become a focus for tumor therapy. Here, we report the human-induced pluripotent stem cells (iPSs) to deliver MnO₂@Ce6 nanoprobes into tumors for simultaneous photodynamic therapy (PDT) and enhanced immunotherapy. Ce6 photosensitizer was attached on manganese dioxide (MnO₂) nanoparticles, and resultant MnO₂@Ce6 nanoprobes were delivered into mitomycin-treated iPSs to form iPS-MnO₂@Ce6 nanoprobes. The iPS-MnO₂@Ce6 actively targeted in vivo tumors, the acidic microenvironment triggered interaction between MnO₂ and H₂O₂, released large quantities of oxygen, alleviated hypoxia in tumor. Upon PDT, singlet oxygen formed, broken iPSs released tumor-shared antigens, which evoked an intensive innate and adaptive immune response against the tumor, improving dendritic cells matured, effector T cells, and natural killer cells were activated. Meanwhile, regulatory T cells were reduced, and then the immune response induced by iPS-MnO₂@Ce6 was markedly stronger than the immune reaction induced by MnO₂@Ce6 (P < 0.05). The iPS-MnO₂@Ce6 markedly inhibited tumor growth and metastasis and reduced mortality in mice models with tumor. Human iPSs loaded with MnO₂-based nanoprobes are a promising strategy for simultaneous PDT and enhanced immunotherapy against tumor and own clinical translational prospect. [Image: see text]

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s40820-020-00452-y) contains supplementary material, which is available to authorized users.