Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines

Machine learning (ML) identification of covalently ligandable sites may accelerate targeted covalent inhibitor design and help expand the druggable proteome space. Here, we report the rigorous development and validation of the tree-based models and convolutional neural networks (CNNs) trained on a newly curated database (LigCys3D) of over 1000 liganded cysteines in nearly 800 proteins represented by over 10,000 three-dimensional structures in the protein data bank. The unseen tests yielded 94 and 93% area under the receiver operating characteristic curves for the tree models and CNNs, respectively. Based on the AlphaFold2 predicted structures, the ML models recapitulated the newly liganded cysteines in the PDB with over 90% recall values. To assist the community of covalent drug discoveries, we report the predicted ligandable cysteines in 392 human kinases and their locations in the sequence-aligned kinase structure, including the PH and SH2 domains. Furthermore, we disseminate a searchable online database LigCys3D (https://ligcys.computchem.org/) and a web prediction server DeepCys (https://deepcys.computchem.org/), both of which will be continuously updated and improved by including newly published experimental data. The present work represents an important step toward the ML-led integration of big genome data and structure models to annotate the human proteome space for the next-generation covalent drug discoveries.

Predictive value of crossover sign for outcome of ultrasound-guided vacuum aspiration in women with Cesarean scar pregnancy

OBJECTIVE

To examine the value of the crossover sign (COS) in predicting treatment outcome in women with a Cesarean scar pregnancy (CSP) who were treated with ultrasound-guided vacuum aspiration.

METHODS

This was a retrospective cohort study of women with CSP who underwent ultrasound-guided vacuum aspiration. Based on the relationship between the gestational sac, Cesarean scar and anterior wall of the uterus, CSPs were classified by COS type. Analysis was conducted to investigate the association between COS type (COS-1, COS-2) and treatment outcome. The incidence of treatment failure, retained pregnancy tissue, secondary therapy and bleeding ≥ 200 mL were analyzed.

RESULTS

In total, 181 eligible patients with CSP, including 90 (49.7%) women with COS-1 and 91 (50.3%) women with COS-2, were analyzed. COS-1 patients had a higher incidence of treatment failure compared with COS-2 patients (25.6% vs 8.8%; P = 0.003), as well as higher rates of retained pregnancy tissue (18.9% vs 6.6%; P = 0.013), secondary therapy (20.0% vs 6.6%; P = 0.002) and bleeding of ≥ 200 mL (13.3% vs 4.4%; P = 0.034). COS-1 and a large gestational sac (30.1-50.0 mm or >50.0 mm in diameter) were associated independently with increased risk of treatment failure (odds ratio, 4.57 (95% CI, 1.66-12.56); P = 0.003, 4.34 (95% CI, 1.35-13.94); P = 0.014 and 10.50 (95% CI, 2.54-43.46); P = 0.001, respectively).

CONCLUSIONS

Ultrasound evaluation of the relationship between the gestational sac and the endometrial line (COS classification) in women with CSP may help to predict treatment outcome among those undergoing vacuum aspiration. Among COS-1 patients, especially those with a gestational sac diameter of >30.0 mm, vacuum aspiration may be discouraged. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.

Effect of quercetin on granulosa cells development from hierarchical follicles in chicken

1. The bioflavonoid quercetin is a biologically active component, but its functional regulation of granulosa cells (GCs) during chicken follicular development is little studied. To investigate the effect of quercetin on follicular development in laying hens, an in vitro study was conducted on granulosa cells from hierarchical follicles treated with quercetin.2. The effect of quercetin on cell activity, proliferation and apoptosis of granulosa cells was detected by CCK-8, EdU and apoptosis assays. The effect on progesterone secretion from granulosa cells was investigated by enzyme-linked immunosorbent assay (ELISA). Expression of proliferating cell nuclear antigen (PCNA) mRNA and oestrogen receptors (ERs), as well as the expression of steroid acute regulatory protein (StAR), cytochrome P450 cholesterol side chain cleavage enzyme (P450scc) and 3β-hydroxysteroid dehydrogenase (3β-HSD) mRNA during progesterone synthesis, were measured by real-time quantitative polymerase chain reaction (RT-qPCR). PCNA, StAR and CYP11A1 protein expression levels were detected using Western blotting (WB).3. The results showed that treatment with quercetin in granulosa cells significantly enhanced cell vitality and proliferation, reduced apoptosis and promoted the expression of gene and protein levels of PCNA. The levels of progesterone secretion increased significantly following quercetin treatment, as did the expression levels of StAR and CYP11A1 using the Western Blot (WB) method.4. The mRNA expression levels of ERα were significantly upregulated in the 100 ng/ml and 1000 ng/ml quercetin-treated groups, while there was no significant difference in expression levels of ERβ mRNA.

Machine Learning Models to Interrogate Proteomewide Covalent Ligandabilities Directed at Cysteines

Machine learning (ML) identification of covalently ligandable sites may accelerate targeted covalent inhibitor design and help expand the druggable proteome space. Here we report the rigorous development and validation of the tree-based models and convolutional neural networks (CNNs) trained on a newly curated database (LigCys3D) of over 1,000 liganded cysteines in nearly 800 proteins represented by over 10,000 three-dimensional structures in the protein data bank. The unseen tests yielded 94% and 93% AUCs (area under the receiver operating characteristic curve) for the tree models and CNNs, respectively. Based on the AlphaFold2 predicted structures, the ML models recapitulated the newly liganded cysteines in the PDB with over 90% recall values. To assist the community of covalent drug discoveries, we report the predicted ligandable cysteines in 392 human kinases and their locations in the sequence-aligned kinase structure including the PH and SH2 domains. Furthermore, we disseminate a searchable online database LigCys3D (https://ligcys.computchem.org/) and a web prediction server DeepCys (https://deepcys.computchem.org/), both of which will be continuously updated and improved by including newly published experimental data. The present work represents a first step towards the ML-led integration of big genome data and structure models to annotate the human proteome space for the next-generation covalent drug discoveries.

Interaction of smoking and aging on emphysema and small airways disease in asymptomatic healthy men by CT-based parametric response mapping analysis

AIM

To explore whether small airway disease and emphysema were affected by the interaction between smoking and aging on chest computed tomography (CT) images of asymptomatic healthy men analysed using a quantitative imaging tool parametric response mapping (PRM).

MATERIALS AND METHODS

In this retrospective study, 95 asymptomatic healthy men underwent biphasic chest CT. The PRM classifies lung as a percentage of normal (PRMNormal%), functional small airway disease (PRMfSAD%), and emphysema (PRMEmph%). The patients were divided into groups based on their age and smoking status. Multiple linear regression analysis was applied to explore the factors influencing lung injury. Simple effects analysis was performed to explore the interaction between different age groups and smoking status.

RESULTS

The interaction between aging and smoking significantly affected PRMfSAD% and PRMEmph% (p<0.001). The age range 60-69 and smoking were associated with increased PRMfSAD% and PRMEmph% (p<0.05). Futher stratification into different age subgroups showed that smoking was associated with increased PRMfSAD% and PRMEmph% in the 50-59 year age group. Besides, smoking in the 50-59 and 60-69 years group was associated with decreased PRMNormal%, while smoking in the 60-69 years group did not significantly influence the prevalence of PRMfSAD% and PRMEmph% (p>0.05).

CONCLUSIONS

PRM reveals the interplay between smoking and aging in the development of lung injury in asymptomatic healthy men. Aging and smoking are important factors of emphysema and small airway disease in the 50-69 years group. In the 60-69 years group, aging poses a greater risk of lung injury compared to smoking.

Potential Predictive Value of Intravoxel Incoherent Motion Magnetic Resonance for Xerostomia of Nasopharyngeal Carcinoma

PURPOSE/OBJECTIVE(S)

Xerostomia, caused by radiation-induced parotid damage, is the most commonly reported complications of radiotherapy (RT) to nasopharyngeal carcinoma (NPC). This study aimed to evaluate the value of IVIM MR in monitoring radiation parotid gland damage and predicting the risk of xerostomia.

MATERIALS/METHODS

A total of 54 patients were enrolled and underwent IVIM MR scans at before RT, after the fifth fraction, halfway through the course of RT, and at the end of radiotherapy. The parameters of IVIM MR include pseudo-diffusion coefficient (D*), perfusion fraction (f), and pure diffusion coefficient (D). The degree of xerostomia in NPC patients was assessed before each MR examination using the acute radiation morbidity scoring criteria proposed by the Radiation Therapy Oncology Group (RTOG). Concurrently, the time when the patient first reported suffering from xerostomia was recorded. The IVIM parameters trend throughout the RT, and the relationships between IVIM parameters and xerostomia, were analyzed.

RESULTS

All of the IVIM parameters increased from pre-RT to post-RT significantly (all p < 0.001). The increase rate of D from pre-RT to halfway through the RT was 32.61%, which was significantly higher than 15.64% from halfway to post-RT (p<0.001), indicating that cell necrosis in the first half of treatment is significantly higher than that in the second half. Both D* and F had significantly increased from pre-RT to halfway through the radiotherapy (p<0.001), with an increase rate of 19.58% and 29.38%, respectively. However, no significant increase was observed from Halfway to post-RT (p>0.05), with an increase rate of 4.10% and 8.30%, respectively. This may be due to radiation-induced vasculitic dilation that is significant in the first half of the radiotherapy but plateaus in the second half. Pre-D (OR = 23.85; 95% CI = 2.39, 237.82; p = .007) and pre-D* (OR = 0.75; 95% CI = 0.63, 0.91; p = 0.003) are independent influencing factors for xerostomia at 3 months after the completion of RT. D and F were significantly higher after the fifth fraction compared with Pre-RT (both p<0.05), respectively increased 31.25% and 25.16%. D* increase by 15% (p = 0.081). IVIM scans can assess parotid gland damage early. And the average time of parotid damage underwent IVIM scan was 5.99 ± 0.84 (day), much earlier than 11.84 ± 2.74 (day) according to RTOG.

CONCLUSION

Our study indicates that IVIM MR can dynamically monitor radiotherapy-induced parotid gland damage, and much earlier and objectively than RTOG.

Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease

Nirmatrelvir is an orally available inhibitor of SARS-CoV-2 main protease (Mpro) and the main ingredient of Paxlovid, a drug approved by the U.S. Food and Drug Administration for high-risk COVID-19 patients. Recently, a rare natural mutation, H172Y, was found to significantly reduce nirmatrelvir's inhibitory activity. As the COVID-19 cases skyrocket in China and the selective pressure of antiviral therapy builds in the US, there is an urgent need to characterize and understand how the H172Y mutation confers drug resistance. Here, we investigated the H172Y Mpro's conformational dynamics, folding stability, catalytic efficiency, and inhibitory activity using all-atom constant pH and fixed-charge molecular dynamics simulations, alchemical and empirical free energy calculations, artificial neural networks, and biochemical experiments. Our data suggest that the mutation significantly weakens the S1 pocket interactions with the N-terminus and perturbs the conformation of the oxyanion loop, leading to a decrease in the thermal stability and catalytic efficiency. Importantly, the perturbed S1 pocket dynamics weaken the nirmatrelvir binding in the P1 position, which explains the decreased inhibitory activity of nirmatrelvir. Our work demonstrates the predictive power of the combined simulation and artificial intelligence approaches, and together with biochemical experiments, they can be used to actively surveil continually emerging mutations of SARS-CoV-2 Mpro and assist the optimization of antiviral drugs. The presented approach, in general, can be applied to characterize mutation effects on any protein drug targets.

[HSDL2 overexpression promotes rectal cancer progression by regulating cancer cell cycle and promoting cell proliferation]

OBJECTIVE

To analyze the expression of hydroxysteroid dehydrogenase like 2 (HSDL2) in rectal cancer tissues and the effect of changes in HSDL2 expression level on proliferation of rectal cancer cells.

METHODS

Clinical data and tissue samples of 90 patients with rectal cancer admitted to our hospital from January 2020 to June 2022 were collected from the prospective clinical database and biological specimen database. The expression level of HSDL2 in rectal cancer and adjacent tissues was detected by immunohistochemistry, and based on the median level of HSDL2 expression, the patients were divided into high expression group (n=45) and low expression group (n=45) for analysis the correlation between HSDL2 expression level and the clinicopathological parameters. GO and KEGG enrichment analyses were performed to explore the role of HSDL2 in rectal cancer progression. The effects of changes in HSDL2 expression levels on rectal cancer cell proliferation, cell cycle and protein expressions were investigated in SW480 cells with lentivirus-mediated HSDL2 silencing or HSDL2 overexpression using CCK-8 assay, flow cytometry and Western blotting.

RESULTS

The expressions of HSDL2 and Ki67 were significantly higher in rectal cancer tissues than in the adjacent tissues (P < 0.05). Spearman correlation analysis showed that the expression of HSDL2 protein was positively correlated with Ki67, CEA and CA19-9 expressions (P < 0.01). The rectal cancer patients with high HSDL2 expressions had significantly higher likelihood of having CEA ≥5 μg/L, CA19-9 ≥37 kU/L, T3-4 stage, and N2-3 stage than those with a low HSDL2 expression (P < 0.05). GO and KEGG analysis showed that HSDL2 was mainly enriched in DNA replication and cell cycle. In SW480 cells, HSDL2 overexpression significantly promoted cell proliferation, increased cell percentage in S phase, and enhanced the expression levels of CDK6 and cyclinD1 (P < 0.05), and HSDL2 silencing produced the opposite effects (P < 0.05).

CONCLUSION

The high expression of HSDL2 in rectal cancer participates in malignant progression of the tumor by promoting the proliferation and cell cycle progress of the cancer cells.

An Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease

Nirmatrelvir is an orally available inhibitor of SARS-CoV-2 main protease (Mpro) and the main ingredient of PAXLOVID, a drug approved by FDA for high-risk COVID-19 patients. Recently, a rare natural mutation, H172Y, was found to significantly reduce nirmatrelvir's inhibitory activity. As the COVID-19 cases skyrocket in China and the selective pressure of antiviral therapy builds up in the US, there is an urgent need to characterize and understand how the H172Y mutation confers drug resistance. Here we investigated the H172Y Mpro's conformational dynamics, folding stability, catalytic efficiency, and inhibitory activity using all-atom constant pH and fixed-charge molecular dynamics simulations, alchemical and empirical free energy calculations, artificial neural networks, and biochemical experiments. Our data suggests that the mutation significantly weakens the S1 pocket interactions with the N-terminus and perturbs the conformation of the oxyanion loop, leading to a decrease in the thermal stability and catalytic efficiency. Importantly, the perturbed S1 pocket dynamics weakens the nirma-trelvir binding in the P1 position, which explains the decreased inhibitory activity of nirmatrelvir. Our work demonstrates the predictive power of the combined simulation and artificial intel-ligence approaches, and together with biochemical experiments they can be used to actively surveil continually emerging mutations of SARS-CoV-2 Mpro and assist the discovery of new antiviral drugs. The presented workflow can be applicable to characterize mutation effects on any protein drug targets.

Negative regulation of floral transition in Arabidopsis by HOS15-PWR-HDA9 complex

Arabidopsis HOS15/PWR/HDA9 repressor complex, which is similar to the TBL1/NcoR1/HDAC complex in animals, plays a well-known role in epigenetic regulation. PWR and HDA9 have been reported to interact with each other and modulate the flowering time by repressing AGL19 expression, whereas HOS15 and HDA9, together with the photoperiodic evening complex, regulate flowering time through repression of GI transcription. However, the role of the HOS15/PWR/HDA9 core repressor complex as a functional unit in the regulation of flowering time is yet to be explored. In this study, we reported that the loss-of-function hos15-2/pwr/hda9 triple mutant accumulates higher transcript levels of AGL19 and exhibits an early flowering phenotype similar to those of hos15, pwr, and hda9 single mutants. Interestingly, the accumulation of HOS15 in the nucleus was drastically reduced in pwr and hda9 mutants. As a result, HOS15 could not perform its role in histone deacetylation or interaction with H3 in the nucleus. Furthermore, HOS15 is also associated with the same region of the AGL19 promoter known for PWR-HDA9 binding. The acetylation level of the AGL19 promoter was increased in the hos15-2 mutant, similar to the pwr and hda9 mutants. Therefore, our findings reveal that the HOS15/PWR/HDA9 repressor complex deacetylates the promoter region of AGL19, thereby negatively regulating AGL19 transcription, which leads to early flowering in Arabidopsis.

Synergistic relationship or not? Understanding the resilience and efficiency of the tourism economy: evidence from Hainan Province, China

The COVID-19 pandemic has dealt a serious blow to the global tourism industry, causing a fracturing of and decline in tourism development efficiency and even a stagnation of tourism development in some regions. To solve the contradiction between efficiency and quality, it is necessary to ensure the endogenous power of tourism resilience while pursuing the efficiency of tourism development. This study assumes that Hainan Province follows a tourism development path led by resilience. The improved weighting method, EBM model and Haken model are used to evaluate the level of resilience, the level of efficiency and their co-evolution. The findings indicate that the core tourism cities represented by Sanya and Haikou have a high level in the individual fields of tourism development efficiency and tourism economic resilience but have limited performance in the synergistic relationship between tourism development efficiency and tourism economic resilience. In contrast, the marginal tourism cities represented by Tunchang County and Ledong County have low tourism development efficiency and resilience, but their synergistic development level is high. This result proves that co-evolution plays a dual forward and reverse driving role. Based on the identification of the order parameters, it is concluded that Hainan Province is characterized by a synergistic evolutionary synergy dominated by resilience, which is in line with the trend of social development and the sustainable development of tourism. While reasonably pursuing the tourism economy and development efficiency, we should pay attention to strengthening resilience construction based on multiple aspects, such as tourists, enterprises, organizations, governments and destinations.

The Association between Dietary Protein Diversity and Protein Patterns with Frailty in Older Chinese Adults: A Population-Based Cohort Study

OBJECTIVES

Frailty is a pervasive condition among older people worldwide. Despite the association between higher protein intake and lower frailty risk has been well documented, older individuals encounter barriers to enhancing their protein consumption due to reduced appetite and impaired digestive capacity. This study aims to delve into the potential correlation between dietary protein diversity, protein patterns, and the risk of frailty among older Chinese individuals.

DESIGN

Prospective cohort study.

SETTING

Community-based.

PARTICIPANTS

2,216 participants aged 65 and above and not frail at the baseline were recruited from the Chinese Longitudinal Healthy Longevity Survey (CLHLS) dataset spanning from 2014 to 2018.

MEASUREMENTS

Dietary protein diversity was evaluated utilizing a protein diversity score (PDS), calculated based on the results of a food frequency questionnaire. Dietary protein patterns were identified by employing principal component analysis (PCA). Frailty was ascertained using a 40-item frailty index (FI) where FI > 0.21 indicated frailty. Logistic analysis was employed to investigate the association between dietary variables and frailty.

RESULTS

541 participants were identified as frail after a 4-year follow-up. After adjusting for confounders, each 1-unit increase in PDS was linked to a 10% decrease in frailty risk. Compared to individuals with PDS ≤ 1, those with PDS scores of 2-3, 4-5, and 6 had lower risks of frailty, with OR (95% CI) of 0.78 (0.58-1.06), 0.58 (0.38-0.87), 0.42 (0.20-0.81), respectively (P trend = 0.038). Individuals who consistently maintained high PDS demonstrated a lower frailty risk in contrast to those who maintained low PDS (OR = 0.60, 95% CI, 0.41-0.87). Additionally, the "meat-fish" pattern exhibited a protective association with frailty, with OR Q4 versus Q1 (95% CI) of 0.54 (0.40-0.74), P trend < 0.001.

CONCLUSION

Maintaining a variety of dietary protein sources and following a "meat-fish" protein pattern might decrease the likelihood of frailty among the older Chinese population.

Evaluation of Tourism Development Efficiency and Spatial Spillover Effect Based on EBM Model: The Case of Hainan Island, China

Tourism development efficiency is one of the key scales to measure the development quality of tourism destination. This study improves the existing input–output index system of tourism efficiency evaluation; knowledge innovation is introduced into the input index, and environmental health pressure is introduced into the output index. Based on the case of Hainan Island, we used the EBM model compatible with radial and non-radial data to evaluate the tourism development efficiency. In order to make up the deficiency of spatial effect analysis based on the geographical distance weight matrix, the spatial spillover effect of tourism development in Hainan Island was analyzed based on a geographical distance weight matrix and an economic distance weight matrix. The findings indicate that nearly 20 years of the Hainan tourism development efficiency mean value was 0.7435, represented by Sanya, and Haikou city of Hainan’s tourism industry development level was higher. However, the spatial spillover effect of Hainan’s overall tourism development is not good. In addition to Tunchang, Ledong city suggests that an appropriate increase in tourism elements, such as investment, expands the scale of the tourism industry, and most cities follow the law of diminishing marginal utility and inappropriate scale blindly. Especially in the face of knowledge innovation becoming the main factor hindering the efficiency of tourism development, we should pay more attention to technological innovation and management reform and coordinate the relationship between tourism development and ecological environment protection.

[Recommendations of diagnosis of autoinflammatory diseases in China]

Autoinflammatory diseases (AIDs) are a group of disorders characterized by dysfunction of innate immunity which caused by gene mutations leading to coded proteins changes, finally causing uncontrolled systemic inflammation. AIDs are a group of rare rheumatic and inflammatory diseases. Here, Chinese Rheumatology Association summarized manifestations of the main AIDs, and to standardize the methods for diagnosis of AIDs.

Clinical benefits of TNF-α inhibitors in Chinese adult patients with NLRP3-associated autoinflammatory disease

BACKGROUND

Nucleotide-binding oligomerization domain-like receptor family, pyrin domain containing 3 (NLRP3)-associated autoinflammatory disease (NLRP3-AID) is a rare, heterogeneous disease entity associated with mutations in NLRP3. Biologic therapy for NLRP3-AID yields diverse results.

OBJECTIVES

We aimed to evaluate the clinical features and outcomes of Chinese adult patients with NLRP3-AID who were treated with tumour necrosis factor (TNF)-α inhibitors.

METHODS

Five patients with NLRP3-AID were diagnosed and treated with TNF-α inhibitors at Peking Union Medical College Hospital between 2017 and 2020 and were followed up for 6 to 12 months. All patients were systematically studied for treatment outcomes, including clinical manifestations and inflammatory markers.

RESULTS

All five adult NLRP3-AID patients were Chinese Han, and four patients were males. The mean age at disease onset was 4.2 ± 4.1 years, and the mean time of diagnosis delay was 19.8 ± 6 years. All patients received TNF-α inhibitors with or without methotrexate/prednisone. During follow-up, all patients achieved remarkable clinical remission of skin lesions and polyarthritis and showed improvements in acute-phase reactants, inflammatory cytokines, patient visual analogue scale, physician global assessment and 36-item Short Form (SF-36).

CONCLUSIONS

Early diagnosis and effective therapy for NLRP3-AID are essential for avoiding irreversible organ damage. TNF-α inhibitors might serve as a therapeutic alternative for patients with NLRP3-AID who have unsatisfactory responses or no access to interleukin-1 inhibitors.

A Bayesian network meta-analysis of comparison of cancer therapeutic vaccines for melanoma

Several approaches to active immunotherapy for melanoma, including peptide-based vaccines (PVs), autologous tumour cell vaccines (TCVs), allogeneic TCVs and autologous dendritic cell vaccines (DCVs), have been investigated in clinical trials. However, comprehensive evidence comparing these interventions remains unavailable. The objective of this study was to expand previous work to compare and rank the immunotherapeutic strategies for melanoma in terms of overall survival and toxic effects with a Bayesian network meta-analysis. Methodologically, we performed a network meta-analysis of head-to-head randomized controlled trials comparing and ranking cancer vaccine approaches for patients with melanoma. PubMed, MEDLINE, Embase, the Cochrane Central Register of Controlled Trials, the WHO International Clinical Trials Registry Platform and ClinicalTrials.gov were searched up to 31 July 2020. We estimated summary hazard ratios for death and risk ratios for toxicity. The effects of the underlying prognostic variable on survival benefits were examined by meta-regression. We performed subgroup analysis for the outcomes based on metastatic categories. Overall, we identified 4776 citations, of which 15 head-to-head randomized controlled trials (3162 participants) were included in the analysis. In terms of efficacy, allogeneic tumour cell vaccines plus immunotherapy adjuvants, peptide-based vaccines plus immunotherapy adjuvants and standard therapy were more effective than peptide vaccines. The proportion of women was inversely associated with mortality risk. For safety, all treatments were inferior to allogeneic tumour cell vaccines except for allogeneic tumour cell vaccines plus chemotherapy. Peptide vaccines plus immunotherapy adjuvants led to an increased risk of adverse events compared to allogeneic tumour cell vaccines plus immunotherapy adjuvants. These results suggest that allogeneic TCV and autologous DCV are better than standard therapy. PV plus immune modulators are the most effective strategy among all comparable strategies but is associated with increased toxicity. Any combination regimens for cancer therapeutic vaccines need to be balanced between risk and benefit profiles.

Treatment and outcome in deficiency of adenosine deaminase 2: a literature review

OBJECTIVES

Deficiency of adenosine deaminase 2 (DADA2) is a rare disease with varying phenotypes and disease outcomes. We aimed to summarize the treatments of DADA2 and to explore the factors associated with disease outcome.

MATERIAL AND METHODS

A systemic literature review of DADA2 was conducted. Cases were included if they had documented detailed genotypes, phenotypes, treatment protocols and outcomes. Patients were categorized into uncontrolled and controlled groups. Factors associated with disease outcome were analyzed with logistic regression models.

RESULTS

A total of 242 DADA2 patients with treatment protocols and responses were included, 17 of whom required no treatment. The general effective rate of TNFi was 78.6% (103/131). Hematological abnormalities and increased acute phase reactants are independently associated with TNFi effectiveness, OR=0.21 (95%CI 0.07-0.661, p=0.007) and 9.62 (95%CI 2.31-40.00, p=0.002), respectively. Among those 225 patients requiring active treatment, 157 (69.8%) patients were in the controlled group, and 68(30.2%) in the uncontrolled group. Neither age of disease onset nor genotype was associated with disease outcome. Increased acute phase reactants (APRs), constitutional symptoms, neurological symptoms, and treatment with TNF inhibitors (TNFi) were independently associated with disease control, while recurrent infections and severe vascular events were the main causes of mortality (10/21 and 6/21, respectively).

CONCLUSIONS

In patients requiring treatment, symptoms of systemic inflammation and vasculitis and TNFi treatment are associated with disease control; while recurrent infections and severe vascular events should be treated intensively as they are the main causes of death. Hematological abnormalities should be monitored as it would decrease TNFi effectiveness.

[Clinical and genetic studies on 76 patients with hydrocephalus caused by methylmalonic acidemia combined with homocysteinuria]

Objective: To analyze the clinical features, genetic characteristics, treatment and follow-up results of patients with hydrocephalus caused by methylmalonic acidemia combined with homocysteinuria, and to discuss the optimal strategies for assessing and treating such patients. Methods: From January 1998 to December 2020, 76 patients with hydrocephalus due to methylmalonic acidemia combined with homocysteinuria in the Department of Pediatrics in 11 hospitals including Peking University First Hospital were diagnosed by biochemical, genetic analysis and brain imaging examination. The patients were divided into operation-group and non-operation-group according to whether they underwent ventriculoperitoneal shunt. The clinical features, laboratory examinations, genotype, and follow-up data were retrospectively analyzed. Data were compared between the two groups using rank sum test, and categorical data were compared using χ² test. Results: Among the 76 patients (51 male, 25 female), 5 were detected by newborn screening, while 71 were diagnosed after clinical onset, 68 cases (96%) had early-onset, 3 cases (4%) had late-onset. The most common clinical manifestations of 74 cases with complete data were psychomotor retardation in 74 cases (100%), visual impairment in 74 cases (100%), epilepsy in 44 cases (59%), anemia in 31 cases (42%), hypotonia or hypertonia in 21 cases (28%), feeding difficulties in 19 cases (26%) and disturbance of consciousness in 17 cases (23%). Genetic analysis was performed in 76 cases, all of whom had MMACHC gene variations, including 30 homozygous variations of MMACHC c.609G>A. The most common variations were c.609G>A (94, 62.7%), followed by c.658_660del (18, 12.0%), c.567dupT (9, 6.0%) and c.217C>T (8, 5.3%). Therapy including cobalamin intramuscular injection, L-carnitine and betaine were initiated immediately after diagnosis. A ventriculoperitoneal shunt operation was performed in 41 cases (operation group), and 31 patients improved after metabolic intervention (non-operation group). There was no significant difference in the age of onset, the age of diagnosis, the blood total homocysteine, methionine, and urinary methylmalonic acid concentration between the two groups (all P>0.05). The symptoms of psychomotor development, epilepsy, and visual impairments improved gradually after a long-term follow-up in the operation group. Conclusions: Hydrocephalus is a severe complication of methylmalonic acidemia combined with homocysteinuria. The most common clinical manifestations are psychomotor retardation, visual impairment, and epilepsy. It usually occurs in early-onset patients. Early diagnosis and etiological treatment are very important. Hydrocephalus may improve after metabolic intervention in some patients. For patients with severe ventricular dilatation, prompt surgical intervention can improve the prognosis.

New and Interesting Fungi. 4

An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces ). New genera: Haudseptoria (based on Haudseptoria typhae); Hogelandia (based on Hogelandia lambearum); Neoscirrhia (based on Neoscirrhia osmundae); Nothoanungitopsis (based on Nothoanungitopsis urophyllae); Nothomicrosphaeropsis (based on Nothomicrosphaeropsis welwitschiae); Populomyces (based on Populomyces zwinianus); Pseudoacrospermum (based on Pseudoacrospermum goniomae). New species: Apiospora sasae on dead culms of Sasa veitchii (Netherlands); Apiospora stipae on dead culms of Stipa gigantea (Spain); Bagadiella eucalyptorum on leaves of Eucalyptus sp. (Australia); Calonectria singaporensis from submerged leaf litter (Singapore); Castanediella neomalaysiana on leaves of Eucalyptus sp. (Malaysia); Colletotrichum pleopeltidis on leaves of Pleopeltis sp. (South Africa); Coniochaeta deborreae from soil (Netherlands); Diaporthe durionigena on branches of Durio zibethinus (Vietnam); Floricola juncicola on dead culm of Juncus sp. (France); Haudseptoria typhae on leaf sheath of Typha sp. (Germany); Hogelandia lambearum from soil (Netherlands); Lomentospora valparaisensis from soil (Chile); Neofusicoccum mystacidii on dead stems of Mystacidium capense (South Africa); Neomycosphaerella guibourtiae on leaves of Guibourtia sp. (Angola); Niesslia neoexosporioides on dead leaves of Carex paniculata (Germany); Nothoanungitopsis urophyllae on seed capsules of Eucalyptus urophylla (South Africa); Nothomicrosphaeropsis welwitschiae on dead leaves of Welwitschia mirabilis (Namibia); Paracremonium bendijkiorum from soil (Netherlands); Paraphoma ledniceana on dead wood of Buxus sempervirens (Czech Republic); Paraphoma salicis on leaves of Salix cf. alba (Ukraine); Parasarocladium wereldwijsianum from soil (Netherlands); Peziza ligni on masonry and plastering (France); Phyllosticta phoenicis on leaves of Phoenix reclinata (South Africa); Plectosphaerella slobbergiarum from soil (Netherlands); Populomyces zwinianus from soil (Netherlands); Pseudoacrospermum goniomae on leaves of Gonioma kamassi (South Africa); Pseudopyricularia festucae on leaves of Festuca californica (USA); Sarocladium sasijaorum from soil (Netherlands); Sporothrix hypoxyli in sporocarp of Hypoxylon petriniae on Fraxinus wood (Netherlands); Superstratomyces albomucosus on Pycnanthus angolensis (Netherlands); Superstratomyces atroviridis on Pinus sylvestris (Netherlands); Superstratomyces flavomucosus on leaf of Hakea multilinearis (Australia); Superstratomyces tardicrescens from human eye specimen (USA); Taeniolella platani on twig of Platanus hispanica (Germany), and Tympanis pini on twigs of Pinus sylvestris (Spain). Citation: Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. Fungal Systematics and Evolution 7: 255-343. doi: 10.3114/fuse.2021.07.13.

HOS15-PWR chromatin remodeling complex positively regulates cold stress in Arabidopsis

Cold stress is a major environmental constraint that restrains plant growth and productivity. To cope with cold stress, plants must be able to perceive a cold signal and regulate the expression of cold-regulated (COR) genes. In our recent study, we showed that Arabidopsis HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15) acts as a substrate receptor for CULLIN4-based ubiquitin E3 ligase complex to promote cold-induced histone deacetylase 2 C (HD2C) degradation that allows the activation of COR genes. Additionally, we found that POWERDRESS (PWR), a HOS15-interacting protein, is required for the association of HOS15 with COR gene chromatin and HD2C degradation. The HOS15/PWR complex interacts with and recruits CBF transcription factors to the promoters of COR genes. Collectively, our previous findings suggest that HOS15 and PWR function as positive regulators for the expression of COR genes, and promote cold tolerance. Accordingly, we herein discuss the role of PWR in cold tolerance.

Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research

Given the scale and rapid spread of the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need for medicines that can help before vaccines are available. In this study, we present a viral-associated disease-specific chemogenomics knowledgebase (Virus-CKB) and apply our computational systems pharmacology-target mapping to rapidly predict the FDA-approved drugs which can quickly progress into clinical trials to meet the urgent demand of the COVID-19 outbreak. Virus-CKB reuses the underlying platform of our DAKB-GPCRs but adds new features like multiple-compound support, multi-cavity protein support and customizable symbol display. Our one-stop computing platform describes the chemical molecules, genes and proteins involved in viral-associated diseases regulation. To date, Virus-CKB archived 65 antiviral drugs in the market, 107 viral-related targets with 189 available 3D crystal or cryo-EM structures and 2698 chemical agents reported for these target proteins. Moreover, Virus-CKB is implemented with web applications for the prediction of the relevant protein targets and analysis and visualization of the outputs, including HTDocking, TargetHunter, BBB predictor, NGL Viewer, Spider Plot, etc. The Virus-CKB server is accessible at https://www.cbligand.org/g/virus-ckb.

Pain-CKB, A Pain-Domain-Specific Chemogenomics Knowledgebase for Target Identification and Systems Pharmacology Research

A traditional single-target analgesic, though it may be highly selective and potent, may not be sufficient to mitigate pain. An alternative strategy for alleviation of pain is to seek simultaneous modulation at multiple nodes in the network of pain-signaling pathways through a multitarget analgesic or drug combinations. Here we present a comprehensive pain-domain-specific chemogenomics knowledgebase (Pain-CKB) with integrated computing tools for target identification and systems pharmacology research. Pain-CKB is constructed on the basis of our established chemogenomics technology with new features, including multiple compound support, multicavity protein support, and customizable symbol display. The determination of bioactivity is also revised to avoid the use of complex machine learning models. Our one-stop computing platform describes the chemical molecules, genes, and proteins involved in pain regulation. To date, Pain-CKB has archived 272 analgesics in the market, 84 pain-related targets with 207 available 3D crystal or cryo-EM structures, and 234 662 chemical agents reported for these target proteins. Moreover, Pain-CKB implements user-friendly web-interfaced computing tools and applications for the prediction and analysis of the relevant protein targets and visualization of the outputs, including HTDocking, TargetHunter, BBB permeation predictor, NGL viewer, Spider Plot, etc. The Pain-CKB server is accessible at https://www.cbligand.org/g/pain-ckb.

Pain Chemogenomics Knowledgebase (Pain-CKB) for Systems Pharmacology Target Mapping and Physiologically Based Pharmacokinetic Modeling Investigation of Opioid Drug-Drug Interactions

More than 50 million adults in America suffer from chronic pain. Opioids are commonly prescribed for their effectiveness in relieving many types of pain. However, excessive prescribing of opioids can lead to abuse, addiction, and death. Non-steroidal anti-inflammatory drugs (NSAIDs), another major class of analgesic, also have many problematic side effects including headache, dizziness, vomiting, diarrhea, nausea, constipation, reduced appetite, and drowsiness. There is an urgent need for the understanding of molecular mechanisms that underlie drug abuse and addiction to aid in the design of new preventive or therapeutic agents for pain management. To facilitate pain related small-molecule signaling pathway studies and the prediction of potential therapeutic target(s) for the treatment of pain, we have constructed a comprehensive platform of a pain domain-specific chemogenomics knowledgebase (Pain-CKB) with integrated data mining computing tools. Our new computing platform describes the chemical molecules, genes, proteins, and signaling pathways involved in pain regulation. Pain-CKB is implemented with a friendly user interface for the prediction of the relevant protein targets and analysis and visualization of the outputs, including HTDocking, TargetHunter, BBB predictor, and Spider Plot. Combining these with other novel tools, we performed three case studies to systematically demonstrate how further studies can be conducted based on the data generated from Pain-CKB and its algorithms and tools. First, systems pharmacology target mapping was carried out for four FDA approved analgesics in order to identify the known target and predict off-target interactions. Subsequently, the target mapping outcomes were applied to build physiologically based pharmacokinetic (PBPK) models for acetaminophen and fentanyl to explore the drug-drug interaction (DDI) between this pair of drugs. Finally, pharmaco-analytics was conducted to explore the detailed interaction pattern of acetaminophen reactive metabolite and its hepatotoxicity target, thioredoxin reductase.

The Histone-Modifying Complex PWR/HOS15/HD2C Epigenetically Regulates Cold Tolerance

Cold stress is a major environmental stress that severely affects plant growth and crop productivity. Arabidopsis (Arabidopsis thaliana) HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE15 (HOS15) is a substrate receptor of the CULLIN4-based CLR4 ubiquitin E3 ligase complex, which epigenetically regulates cold tolerance by degrading HISTONE DEACETYLASE2C (HD2C) to switch from repressive to permissive chromatin structure in response to cold stress. In this study, we characterized a HOS15-binding protein, POWERDRESS (PWR), and analyzed its function in the cold stress response. PWR loss-of-function plants (pwr) showed lower expression of cold-regulated (COR) genes and sensitivity to freezing. PWR interacts with HD2C through HOS15, and cold-induced HD2C degradation by HOS15 is diminished in the pwr mutant. The association of HOS15 and HD2C to promoters of cold-responsive COR genes was dependent on PWR. Consistent with these observations, the high acetylation levels of histone H3 by cold-induced and HOS15-mediated HD2C degradation were significantly reduced in pwr under cold stress. PWR also interacts with C-repeat element-binding factor transcription factors to modulate their cold-induced binding to the promoter of COR genes. Collectively, our data signify that the PWR-HOS15-HD2C histone-modifying complex regulates the expression of COR genes and the freezing tolerance of plants.

The Performance of Gene Expression Signature-Guided Drug-Disease Association in Different Categories of Drugs and Diseases

A gene expression signature (GES) is a group of genes that shows a unique expression profile as a result of perturbations by drugs, genetic modification or diseases on the transcriptional machinery. The comparisons between GES profiles have been used to investigate the relationships between drugs, their targets and diseases with quite a few successful cases reported. Especially in the study of GES-guided drugs–disease associations, researchers believe that if a GES induced by a drug is opposite to a GES induced by a disease, the drug may have potential as a treatment of that disease. In this study, we data-mined the crowd extracted expression of differential signatures (CREEDS) database to evaluate the similarity between GES profiles from drugs and their indicated diseases. Our study aims to explore the application domains of GES-guided drug–disease associations through the analysis of the similarity of GES profiles on known pairs of drug–disease associations, thereby identifying subgroups of drugs/diseases that are suitable for GES-guided drug repositioning approaches. Our results supported our hypothesis that the GES-guided drug–disease association method is better suited for some subgroups or pathways such as drugs and diseases associated with the immune system, diseases of the nervous system, non-chemotherapy drugs or the mTOR signaling pathway.

Circular RNA hsa_circ_103809 suppresses hepatocellular carcinoma proliferation and invasion by sponging miR-620

OBJECTIVE

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide, particularly in China. In recent years, numerous studies have investigated the roles of circular RNAs (circRNAs) in tumour development because circRNAs generally act as microRNA (miRNA) sponges to regulate gene expression. However, whether circRNAs are also involved in HCC progression remains largely unknown.

MATERIALS AND METHODS

In the present study, we identified a novel circRNA (hsa_circ_103809) and determined its expression in HCC tissues and cell lines by qRT-PCR assays. CCK8, colony formation, wound-healing and transwell assays were performed to assess the effects of hsa_circ_103809 and miR-620 on HCC cell proliferation, migration and invasion. Bioinformatics analysis and luciferase reporter assays were used to explore the correlation between hsa_circ_103809 and miR-620 in HCC cells.

RESULTS

The results showed that hsa_circ_103809 expression was significantly down- regulated in HCC tissues and cell lines. The ectopic expression of hsa_circ_103809 inhibited HCC cell proliferation, migration and invasion. In addition, we found that miR-620 expression was significantly up-regulated in HCC tissues and was negatively correlated with hsa_circ_103809 expression in HCC tissues. Furthermore, we found that hsa_circ_103809 could bind to miR-620 and that hsa_circ_103809 negatively regulates miR-620 expression. We also showed that hsa_circ_103809 inhibited the proliferation and invasion abilities of HCC cells by sponging miR-620.

CONCLUSIONS

Hsa_circ_103809 acts by binding to miR-620 and inhibiting the tumourigenicity of HCC. Thus, this circRNA may serve as a potential biomarker and novel therapeutic target of HCC.

[The phenotypes and genotypes in 314 patients with isolated methylmalonic acidemia]

Objectives: To summarize the clinical and genetic characteristics of the patients with isolated methylmalonic acidemia and investigate the strategies for the diagnosis, treatment and prevention. Methods: Three hundred and fourteen patients (180 males, 134 females) with isolated methylmalonic acidemia were ascertained from 26 provinces or cities across the mainland of China during January 1998 to March 2020. Genetic analysis was performed by Sanger sequencing, gene panel sequencing, whole exome sequencing, multiplex ligation-dependent probe amplification or quantitative PCR. According to the age of onset, the patients were divided to early-onset group (≤12 months of age) and the late-onset group (>12 months of age). They were treated by cobalamin, L-carnitine and (or) special diet and symptomatic treatment. Statistical analysis was done using Chi-square test. Results: Fifty-eight of 314 (18.5%) patients were detected by Newborn screening using liquid chromatography tandem mass spectrometry. Five cases (1.6%) had a postmortem diagnosis. Two hundred and fifty-one patients (79.9%) were clinically diagnosed with an age of onset ranged from 3 hours after birth to 18 years. One hundred and fifty-nine patients (71.0%) belonged to early-onset groups, 65 patients (29.0%) belonged to the late-onset group. The most common symptoms were metabolic crises, psychomotor retardation, epilepsy, anemia and multiple organ damage. Metabolic acidosis and anemia were more common in early-onset patients than that in late-onset patients (20.8%(33/159) vs. 9.2% (6/65), 34.6% (55/159) vs. 16.9% (11/165), χ(2)=4.261, 6.930, P=0.039, 0.008). Genetic tests were performed for 236 patients (75.2%), 96.2%(227/236) had molecular confirmation. One hundred and twenty-seven variants were identified in seven genes (MMUT, MMAA, MMAB, MMADHC, SUCLG1, SUCLA2, and MCEE), of which 49 were novel. The mut type, caused by the deficiency of methylmalonyl-CoA mutase, was the most common (n=211, 93%) cause of this condition. c.729_730insTT, c.1106G>A and c.914T>C were the three most frequent mutations in MMUT gene. The frequency of c.914T>C in early-onset patients was significantly higher than that in late-onset patients (8.3% (18/216) vs. 1.6% (1/64), χ(2)=3.859, P=0.037). Metabolic crisis was more frequent in mut type than the other types (72.6% (114/157) vs. 3/13, χ(2)=13.729, P=0.001),developmental delay and hypotonia were less frequent in mut type (38.2% (60/157) vs. 9/13, 25.5% (40/157) vs. 8/13, χ(2)=4.789, 7.705, P=0.030, 0.006). Of the 58 patients identified by newborn screening, 44 patients (75.9%) who were treated from asymptomatic phase developed normally whereas 14 patients (24.1%) who received treatment after developing symptoms exhibited varying degrees of psychomotor retardation. Conclusions: The characteristics of phenotypes and genotypes among Chinese patients with isolated methylmalonic acidemia were analyzed. Expanded the mutation spectrum of the associated genes. Because of the complex clinical manifestations and severe early onset of isolated methylmalonic acidemia, Newborn screening is crucial for early diagnosis and improvement of prognosis. MMUT gene is recommended for carrier screening as an effort to move the test earlier as a part of the primary prevention of birth defects.

AB1277 AUTOANTIBODIES IN NLRP3-ASSOCIATED AUTOINFLAMMATORY DISEASE: A CASE REPORT AND LITERATURE REVIEW

Background:

We present the first report of high-titer autoantibodies inNLRP3-associated autoinflammatory disease(NLRP3-AID).Because systemic autoinflammatory disease(SAID) is characterised by the lack of autoreactive T-cells or autoantibodies,we made a systemic review on the theme of autoantibody in SAID to clarify this phenomenon.

Objectives:

We present the first report of high-titer autoantibodiesNLRP3-AID, and discuss autoantibody in classical SAID.

Methods:

We collected the clinical data of the patient withNLRP3-AID who had high-titer autoantibodies,and made a systemic review about autoantibody in SAID.

Results:

A 38-year-old Chinese Han patient was definitely diagnosed asNLRP3-AID because of cold-triggered urticaria-like rash and fever,arthralgia,binaural sensorineural deafness,chronic meningitis,high inflammatory marker and de novoNLRP3T348M variant. Figure 1 shows pedigree of the patient.Meanwhile,she had positive antinuclear antibody(ANA) with a nucleolar pattern of 1:160, positive anti-β2GPI antibody 54-68 AU/ml (normal range < 20 AU/ml) and positive lupus anticoagulant 1.24-1.29 (normal range ≤ 1.2). Literature review found that 13 articles reported autoantibodies in Familial Mediterranean fever (FMF), and there was no autoantibody reported in hyperimmunoglobulinemia D syndrome (HIDS),TNF receptor–associated periodic syndrome(TRAPS) andNLRP3-AID. The prevalence of ANA,anti-dsDNA,RF and anti-CCP in patients with FMF was similar to healthy controls.

Fig. 1.

Pedigree of the patient. The black arrow indicates the proband. The asterisks indicate the individuals who had clinical manifestations and carry the NLRP3 T348M variant.

Conclusion:

Patients withNLRP3-AID can have high-titer ANA and APLs by accident. If patients with high-titer autoantibodies have characteristic manifestations of SAIDs instead of typical features of autoimmune diseases, we should make the final diagnosis through detailed investigation and genetic testing.

References:

[1]Ben-Chetrit E, Gattorno M, Gul A, et al. Consensus proposal for taxonomy and definition of the autoinflammatory diseases (AIDs): a Delphi study. Annals of the rheumatic diseases 2018; 77(11): 1558-65.

[2]Kuemmerle-Deschner JB, Ozen S, Tyrrell PN, et al. Diagnostic criteria for cryopyrin-associated periodic syndrome (CAPS). Annals of the rheumatic diseases 2017; 76(6): 942-7.

Disclosure of Interests:

None declared

Venturiales

Members of Venturiales (Dothideomycetes) are widely distributed, and comprise saprobes, as well as plant, human and animal pathogens. In spite of their economic importance, the general lack of cultures and DNA data has resulted in taxa being poorly resolved. In the present study five loci, ITS, LSU rDNA, tef1, tub2 and rpb2 are used for analysing 115 venturialean taxa representing 30 genera in three families in the current classification of Venturiales. Based on the multigene phylogenetic analysis, morphological and ecological characteristics, one new family, Cylindrosympodiaceae, and eight new genera are described, namely Bellamyces, Fagicola, Fraxinicola, Fuscohilum,Neofusicladium, Parafusicladium, Pinaceicola and Sterila. In addition, 12 species are described as new to science, and 41 new combinations are proposed. The taxonomic status of 153 species have been re-evaluated with 20 species excluded from Venturiales. Based on this revision of Venturiales, morphological characteristics such as conidial arrangement (solitary or in chains) or conidiogenesis (blastic-solitary, sympodial or annellidic), proved to be significant at generic level. Venturia as currently defined represents a generic complex. Furthermore, plant pathogens appear more terminal in phylogenetic analyses within Venturiaceae and Sympoventuriaceae, suggesting that the ancestral state of Venturiales is most likely saprobic.

Insight into Ginkgo biloba L. Extract on the Improved Spatial Learning and Memory by Chemogenomics Knowledgebase, Molecular Docking, Molecular Dynamics Simulation, and Bioassay Validations

Epilepsy is a common cause of serious cognitive disorders and is known to have impact on patients' memory and executive functions. Therefore, the development of antiepileptic drugs for the improvement of spatial learning and memory in patients with epileptic cognitive dysfunction is important. In the present work, we systematically predicted and analyzed the potential effects of Ginkgo terpene trilactones (GTTL) on cognition and pathologic changes utilizing in silico and in vivo approaches. Based on our established chemogenomics knowledgebase, we first conducted the network systems pharmacology analysis to predict that ginkgolide A/B/C may target 5-HT 1A, 5-HT 1B, and 5-HT 2B. The detailed interactions were then further validated by molecular docking and molecular dynamics (MD) simulations. In addition, status epilepticus (SE) was induced by lithium-pilocarpine injection in adult Wistar male rats, and the results of enzyme-linked immunosorbent assay (ELISA) demonstrated that administration with GTTL can increase the expression of brain-derived neurotrophic factor (BDNF) when compared to the model group. Interestingly, recent studies suggest that the occurrence of a reciprocal involvement of 5-HT receptor activation along with the hippocampal BDNF-increased expression can significantly ameliorate neurologic changes and reverse behavioral deficits in status epilepticus rats while improving cognitive function and alleviating neuronal injury. Therefore, we evaluated the effects of GTTL (bilobalide, ginkgolide A, ginkgolide B, and ginkgolide C) on synergistic antiepileptic effect. Our experimental data showed that the spatial learning and memory abilities (e.g., electroencephalography analysis and Morris water maze test for behavioral assessment) of rats administrated with GTTL were significantly improved under the middle dose (80 mg/kg, GTTL) and high dose (160 mg/kg, GTTL). Moreover, the number of neurons in the hippocampus of the GTTL group increased when compared to the model group. Our studies showed that GTTL not only protected rat cerebral hippocampal neurons against epilepsy but also improved the learning and memory ability. Therefore, GTTL may be a potential drug candidate for the prevention and/or treatment of epilepsy.

Bibliometrics Analysis of Forensic Toxicology Literature of Mainland Chinese Scholars in SCIE Journals

Abstract

Objective To conduct bibliometrics analysis of forensic toxicology literature of mainland Chinese scholars published in SCIE journals between 1998 and 2018. Methods Gephi 0.9.2 software was used for bibliometrics analysis. The status of forensic toxicology research in mainland China was network visualized through data analysis of institutional cooperation, author collaboration, fund support, keywords co-occurrence as well as literature interpretation. Results The total number of papers published in SCIE journals in the past twenty years by mainland Chinese scholars was 242, and increased year by year. Thematic studies, such as analysis and evaluation of toxins in hair, identification of new psychoactive substances, optical enantiomer analysis of amphetamines, analysis of toxic animal and plant components, etc, reached the international advanced level. Conclusion The forensic toxicology discipline in our country has developed rapidly in recent years. The opening and development of forensic science in colleges and universities, the constant emerging of new research teams, especially the funding of major special projects of National Natural Science Foundation of China and the Ministry of Science and Technology, have promoted high level research output and academic status of Chinese forensic toxicology on the international stage.

Histone Deacetylase HDA9 With ABI4 Contributes to Abscisic Acid Homeostasis in Drought Stress Response

Drought stress, a major environmental factor, significantly affects plant growth and reproduction. Plants have evolved complex molecular mechanisms to tolerate drought stress. In this study, we investigated the function of the Arabidopsis thaliana RPD3-type HISTONE DEACETYLASE 9 (HDA9) in response to drought stress. The loss-of-function mutants hda9-1 and hda9-2 were insensitive to abscisic acid (ABA) and sensitive to drought stress. The ABA content in the hda9-1 mutant was reduced in wild type (WT) plant. Most histone deacetylases in animals and plants form complexes with other chromatin-remodeling components, such as transcription factors. In this study, we found that HDA9 interacts with the ABA INSENSITIVE 4 (ABI4) transcription factor using a yeast two-hybrid assay and coimmunoprecipitation. The expression of CYP707A1 and CYP707A2, which encode (+)-ABA 8'-hydroxylases, key enzymes in ABA catabolic pathways, was highly induced in hda9-1, hda9-2, abi4, and hda9-1 abi4 mutants upon drought stress. Chromatin immunoprecipitation and quantitative PCR showed that the HDA9 and ABI4 complex repressed the expression of CYP707A1 and CYP707A2 by directly binding to their promoters in response to drought stress. Taken together, these data suggest that HDA9 and ABI4 form a repressive complex to regulate the expression of CYP707A1 and CYP707A2 in response to drought stress in Arabidopsis.

[A report of clinical characteristics of 2 Chinese pedigrees with haploinsufficiency of A20 and literature review]

Objective: To summarize the clinical characteristics of patients with haploinsufficiency of A20 (HA20). Methods: The clinical manifestations, laboratory examinations, treatment, outcome and genetic analysis of 4 cases with HA20 hospitalized in Peking Union Medical College Hospital were analysed.Further literature review was done after searching articles in PubMed and Wangfang databases with the key words "HA20" "A20 haploinsufficiency" "TNFAIP3" up to the date of September 2019. Results: The 4 patients were a father and a daughter, as well as a mother and a daughter. Their phenotypes were quite variable, but all of them have been suffering from recurrent oral ulcer since childhood. Elevation of C-reactive protein (13-33 mg/L) and erythrocyte sedimentation rate (21-60 mm/1h) were found in these 4 patients, and there was positive antinuclear antibody in proband 1.The father in pedigree 1 and the 2 patients in pedigrees 2 have been diagnosed with Behçet disease and the proband 1 with undifferentiated connective tissue disease. The 2 patients in pedigree 1 have developed Hashimoto's thyroiditis. After gene sequencing analysis, it was found that all the 4 patients have heterozygous nonsense mutations in TNFAIP3 gene, that is, c.811C>T, p.R271X in pedigree 1 and c.133C>T, p.R45X in pedigree 2.The diagnosis of HA20 was eventually established when sequencing results and their clinical manifestations were both compatible with this disease.A total of 21 articles were retrieved, all in English, with a total of 91 cases from 39 families (including the 4 cases reported in this paper). HA20 was reported more often in female (57, 64.8%). Most patients develop symptoms from childhood, but as many as 53.4% (47 cases) are not correctly diagnosed until adulthood. Oral ulcers, genital ulcers, periodic fever, gastrointestinal symptoms, rashes, and arthritis are the primary manifestations.Hashimoto's thyroiditis is the most common autoimmune diseases that HA20 patients coexist with. Laboratory tests were characterized by significantly elevated inflammatory markers and low to moderate titers of autoantibodies in some patients.Most HA20 patients were reported to have nonsense mutations or shift mutations of TNFAIP3 gene, which leads to truncation of A20 protein, and only a small number of patients have missense mutation. In terms of treatment, anti-TNF treatment and anti-interleukin 1 is believed to be an effective and the most optimal therapy. The treatment effect is variable and requires long term observations. Conclusions: The clinical phenotypes of HA20 are complex. For patients with both autoinflammatory and autoimmune characteristics, family history should be inquired in detail and gene sequencing should be performed if necessary.

Rheostatic Control of ABA Signaling through HOS15-Mediated OST1 Degradation

Dehydrating stresses trigger the accumulation of abscisic acid (ABA), a key plant stress-signaling hormone that activates Snf1-Related Kinases (SnRK2s) to mount adaptive responses. However, the regulatory circuits that terminate the SnRK2s signal relay after acclimation or post-stress conditions remain to be defined. Here, we show that the desensitization of the ABA signal is achieved by the regulation of OST1 (SnRK2.6) protein stability via the E3-ubiquitin ligase HOS15. Upon ABA signal, HOS15-induced degradation of OST1 is inhibited and stabilized OST1 promotes the stress response. When the ABA signal terminates, protein phosphatases ABI1/2 promote rapid degradation of OST1 via HOS15. Notably, we found that even in the presence of ABA, OST1 levels are also depleted within hours of ABA signal onset. The unexpected dynamics of OST1 abundance are then resolved by systematic mathematical modeling, demonstrating a desensitizing feedback loop by which OST1-induced upregulation of ABI1/2 leads to the degradation of OST1. This model illustrates the complex rheostat dynamics underlying the ABA-induced stress response and desensitization.

AvrRpm1 Functions as an ADP-Ribosyl Transferase to Modify NOI Domain-Containing Proteins, Including Arabidopsis and Soybean RPM1-Interacting Protein4

The Pseudomonas syringae effector protein AvrRpm1 activates the Arabidopsis (Arabidopsis thaliana) intracellular innate immune receptor protein RESISTANCE TO PSEUDOMONAS MACULICOLA1 (RPM1) via modification of a second Arabidopsis protein, RPM1-INTERACTING PROTEIN4 (AtRIN4). Prior work has shown that AvrRpm1 induces phosphorylation of AtRIN4, but homology modeling indicated that AvrRpm1 may be an ADP-ribosyl transferase. Here, we show that AvrRpm1 induces ADP-ribosylation of RIN4 proteins from both Arabidopsis and soybean (Glycine max) within two highly conserved nitrate-induced (NOI) domains. It also ADP ribosylates at least 10 additional Arabidopsis NOI domain-containing proteins. The ADP-ribosylation activity of AvrRpm1 is required for subsequent phosphorylation on Thr-166 of AtRIN4, an event that is necessary and sufficient for RPM1 activation. We also show that the C-terminal NOI domain of AtRIN4 interacts with the exocyst subunits EXO70B1, EXO70E1, EXO70E2, and EXO70F1. Mutation of either EXO70B1 or EXO70E2 inhibited secretion of callose induced by the bacterial flagellin-derived peptide flg22. Substitution of RIN4 Thr-166 with Asp enhanced the association of AtRIN4 with EXO70E2, which we posit inhibits its callose deposition function. Collectively, these data indicate that AvrRpm1 ADP-ribosyl transferase activity contributes to virulence by promoting phosphorylation of RIN4 Thr-166, which inhibits the secretion of defense compounds by promoting the inhibitory association of RIN4 with EXO70 proteins.plantcell;31/11/2664/FX1F1fx1.