Identification of the HNSC88 Molecular Signature for Predicting Subtypes of Head and Neck Cancer

Head and neck squamous cell carcinoma (HNSC) exhibits genetic heterogeneity in etiologies, tumor sites, and biological processes, which significantly impact therapeutic strategies and prognosis. While the influence of human papillomavirus on clinical outcomes is established, the molecular subtypes determining additional treatment options for HNSC remain unclear and inconsistent. This study aims to identify distinct HNSC molecular subtypes to enhance diagnosis and prognosis accuracy. In this study, we collected three HNSC microarrays (n = 306) from the Gene Expression Omnibus (GEO), and HNSC RNA-Seq data (n = 566) from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes (DEGs) and validate our results. Two scoring methods, representative score (RS) and perturbative score (PS), were developed for DEGs to summarize their possible activation functions and influence in tumorigenesis. Based on the RS and PS scoring, we selected candidate genes to cluster TCGA samples for the identification of molecular subtypes in HNSC. We have identified 289 up-regulated DEGs and selected 88 genes (called HNSC88) using the RS and PS scoring methods. Based on HNSC88 and TCGA samples, we determined three HNSC subtypes, including one HPV-associated subtype, and two HPV-negative subtypes. One of the HPV-negative subtypes showed a relationship to smoking behavior, while the other exhibited high expression in tumor immune response. The Kaplan-Meier method was used to compare overall survival among the three subtypes. The HPV-associated subtype showed a better prognosis compared to the other two HPV-negative subtypes (log rank, p = 0.0092 and 0.0001; hazard ratio, 1.36 and 1.39). Additionally, within the HPV-negative group, the smoking-related subgroup exhibited worse prognosis compared to the subgroup with high expression in immune response (log rank, p = 0.039; hazard ratio, 1.53). The HNSC88 not only enables the identification of HPV-associated subtypes, but also proposes two potential HPV-negative subtypes with distinct prognoses and molecular signatures. This study provides valuable strategies for summarizing the roles and influences of genes in tumorigenesis for identifying molecular signatures and subtypes of HNSC.

Transcriptomic analysis of World Trade Center particulate Matter-induced pulmonary inflammation and drug treatments

Over 400,000 people are estimated to have been exposed to World Trade Center particulate matter (WTC_PM) since the attack on the Twin Towers in Lower Manhattan on September 11, 2001. Epidemiological studies have found that exposure to dust may cause respiratory ailments and cardiovascular diseases. However, limited studies have performed a systematic analysis of transcriptomic data to elucidate the biological responses to WTC_PM exposure and the therapeutic options. Here, we developed an in vivo mouse exposure model of WTC_PM and administered two drugs (i.e., rosoxacin and dexamethasone) to generate transcriptomic data from lung samples. WTC_PM exposure increased the inflammation index, and this index was significantly reduced by both drugs. We analyzed the transcriptomics derived omics data using a hierarchical systems biology model (HiSBiM) with four levels, including system, subsystem, pathway, and gene analyses. Based on the selected differentially expressed genes (DEGs) from each group, WTC_PM and the two drugs commonly affected the inflammatory responses, consistent with the inflammation index. Among these DEGs, the expression of 31 genes was affected by WTC_PM exposure and consistently reversed by the two drugs, and these genes included Psme2, Cldn18, and Prkcd, which are involved in immune- and endocrine-related subsystems and pathways such as thyroid hormone synthesis, antigen processing and presentation, and leukocyte transendothelial migration. Furthermore, the two drugs reduced the inflammatory effects of WTC_PM through distinct pathways, e.g., vascular-associated signaling by rosoxacin, whereas mTOR-dependent inflammatory signaling was found to be regulated by dexamethasone. To the best of our knowledge, this study constitutes the first investigation of transcriptomics data of WTC_PM and an exploration of potential therapies. We believe that these findings provide strategies for the development of promising optional interventions and therapies for airborne particle exposure.

[Association between muscle mass and quality of life in Shaanxi adults]

Objective: To investigate the association between muscle mass and quality of life in adults in Shaanxi adults. Methods: The data in this analysis were part of the baseline survey of the Regional Ethnic Cohort Study in Northwest China from June 2018 to May 2019 in Shaanxi Province. The participants' quality of life, including physical component summary (PCS) and mental component summary (MCS), was assessed by the 12-Item Short Form Survey, and the Body Fat Determination System measured muscle mass. A logistic regression model with adjustment for confounding factors was established to analyze the association between muscle mass and quality of life in different genders. Further, sensitivity and subgroup analyses were conducted to explore its stability. Finally, a restricted cubic spline was employed to investigate the dose-response relationship between muscle mass and quality of life in different genders. Results: A total of 20 595 participants were included, with an average age of 55.0, and 33.4% were male. After controlling for potential confounders, compared with the Q₁ group, the risk of low PCS was reduced by 20.6% (OR=0.794, 95%CI: 0.681-0.925) and the risk of low MCS was lower reduced by 20.1% (OR=0.799, 95%CI: 0.689-0.926) in female Q₅ groups. Compared with the Q₁ group, the risk of low PCS was reduced by 24.4% (OR=0.756, 95%CI: 0.644-0.888) in the male Q₂ group. However, no significant association between muscle mass and MCS in males has been found. In females, restricted cubic spline analysis showed a significant linear dose-response relationship between muscle mass and PCS and MCS. Conclusions: There is a positive association between muscle mass and quality of life in Shaanxi adults, especially females. With the increase in muscle mass, the physical and mental functions of the population continue to improve.

Leptosphaerulina americana causing holing disease on tobacco in China

Tobacco (Nicotiana tabacum) is one of the most important industrial crops in the world. Its leaves are the main raw material for cigarettes, but they are often threatened by fungal pathogens in the production process (Wang et al. 2022). From May to June 2022, a disease of tobacco (cv K326) (15% of plants) in a 0.3-ha field in Jingxi of Guangxi Province showed symptoms of local necrosis and perforation of middle and basal leaves (Fig S1). Pieces of leaf tissue (3 × 3 mm) were excised from the edge of the necrotic lesion of each plant, treated with 75% ethanol for 10 s, soaked in 2% NaClO solution for 1-2 min, rinsed with sterile water for three times, and then plated on potato dextrose agar（PDA）medium and incubated at 28°C. Isolate TJYA13 was used for subsequent studies. After 8 days, the colony margin was yellowish brown and irregular, the center was black and plicated. The isolate TJYA13 was incubated on oatmeal agar medium at 28°C for 4 days, and many pseudothecia were observed embedded on the surface of the medium. Pseudothecium was globose or subglobose, dark brown, and size was 184.7-304.7 µm × 187.5-340.5 µm (n=20). Ascospores were usually wrapped by the saccate ascus in pseudothecium, cylindrical or ellipsoidal, with 5-6 transverse septa, and size was 12.2-18.5 µm × 35.6-51.8 µm (n=80). The morphological characteristics of ascospores were consistent with a Leptosphaerulina species (Hou et al. 2020). For accurate identification, the genomic DNA of isolate TJYA13 was extracted with Ezup Column Fungi Genomic DNA Purification Kit (Sangon, Shanghai, China). The ITS region, 28s ribosomal RNA (LSU), β-tubulin (TUB), and RNA polymerase II second largest subunit (RPB2) were amplified with primers ITS1/ITS4 (Gardes and Bruns 1993; White et al. 1990), LROR/LR7 (Rehner and Samuels 1994), Btub2Fd/Btub4Rd (Woudenberg et al. 2009), and RPB2-5F2/fRPB2-7cR (Liu et al. 1999), respectively and sequenced at Sangon Biotech (Sichuan, China). The sequences were deposited in GenBank (accession nos. OP926927, OP926933, OP939419, OP939422). The phylogenetic analysis grouped the isolate TJYA13 within the L. americana clade (Fig S2) (Hou et al. 2020). Pathogenicity of the isolate TJYA13 was verified on four healthy tobacco plants (cv K326). The mycelial plugs were inoculated on leaves sterilized with 75% ethanol, and control plants were inoculated with sterile PDA plugs. Plants were incubated at 28 ℃ and 78% humidity. After 10 days, the leaves inoculated with mycelial plugs had symptoms similar to those in the field, but there were no symptoms on the control leaves. L. americana were reisolated from the leaves inoculated with the mycelial plugs. To the best of our knowledge, this is the first report of L. americana causing holing disease on tobacco in China. This disease may reduce yields and lower quality of flue-cured tobacco leaf. Therefore, the emergence of tobacco holing disease should be noted to prevent potential damage to tobacco production in Guangxi. Reference 1. Hou L. W., et al. 2020. Stud. Mycol. 96: 309-396 2. Liu, Y. J., et al. 1999. Mol. Biol. Evol. 16:1799. 3. Rehner, S. A., and Samuels, G. J. 1994. Mycol. Res. 98:625. 4. Wang H. et al. 2022. Microorganisms. 10: 1890. 5. White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA. 6. Woudenberg, J. H. C., et al. 2009. Persoonia 22:56. The author(s) declare no conflict of interest. Funding: Funding was provided by Guangxi Zhuang Autonomous Region Tobacco Monopoly Bureau (grant no. 202,145,000,024,006). Tobacco (Nicotiana tabacum) is one of the most important industrial crops in the world. Its leaves are the main raw material for cigarettes, but they are often threatened by fungal pathogens in the production process (Wang et al. 2022). From May to June 2022, a disease of tobacco (cv K326) (15% of plants) in a 0.3-ha field in Jingxi of Guangxi Province showed symptoms of local necrosis and perforation of middle and basal leaves (Fig S1). Pieces of leaf tissue (3 × 3 mm) were excised from the edge of the necrotic lesion of each plant, treated with 75% ethanol for 10 s, soaked in 2% NaClO solution for 1-2 min, rinsed with sterile water for three times, and then plated on potato dextrose agar（PDA）medium and incubated at 28°C. Isolate TJYA13 was used for subsequent studies. After 8 days, the colony margin was yellowish brown and irregular, the center was black and plicated. The isolate TJYA13 was incubated on oatmeal agar medium at 28°C for 4 days, and many pseudothecia were observed embedded on the surface of the medium. Pseudothecium was globose or subglobose, dark brown, and size was 184.7-304.7 µm × 187.5-340.5 µm (n=20). Ascospores were usually wrapped by the saccate ascus in pseudothecium, cylindrical or ellipsoidal, with 5-6 transverse septa, and size was 12.2-18.5 µm × 35.6-51.8 µm (n=80). The morphological characteristics of ascospores were consistent with a Leptosphaerulina species (Hou et al. 2020). For accurate identification, the genomic DNA of isolate TJYA13 was extracted with Ezup Column Fungi Genomic DNA Purification Kit (Sangon, Shanghai, China). The ITS region, 28s ribosomal RNA (LSU), β-tubulin (TUB), and RNA polymerase II second largest subunit (RPB2) were amplified with primers ITS1/ITS4 (Gardes and Bruns 1993; White et al. 1990), LROR/LR7 (Rehner and Samuels 1994), Btub2Fd/Btub4Rd (Woudenberg et al. 2009), and RPB2-5F2/fRPB2-7cR (Liu et al. 1999), respectively and sequenced at Sangon Biotech (Sichuan, China). The sequences were deposited in GenBank (accession nos. OP926927, OP926933, OP939419, OP939422). The phylogenetic analysis grouped the isolate TJYA13 within the L. americana clade (Fig S2) (Hou et al. 2020). Pathogenicity of the isolate TJYA13 was verified on four healthy tobacco plants (cv K326). The mycelial plugs were inoculated on leaves sterilized with 75% ethanol, and control plants were inoculated with sterile PDA plugs. Plants were incubated at 28 ℃ and 78% humidity. After 10 days, the leaves inoculated with mycelial plugs had symptoms similar to those in the field, but there were no symptoms on the control leaves. L. americana were reisolated from the leaves inoculated with the mycelial plugs. To the best of our knowledge, this is the first report of L. americana causing holing disease on tobacco in China. This disease may reduce yields and lower quality of flue-cured tobacco leaf. Therefore, the emergence of tobacco holing disease should be noted to prevent potential damage to tobacco production in Guangxi.

[Proposal and thoughts on establishing and improving multi-level dental insurance in China]

Oral diseases are highly prevalent in China, while oral health services are generally underutilized and public health resources are wasted. Lacking oral insurance may be one of the leading causes. The basic medical insurance of China does not cover dental care in most cities, which is worthy to further discuss. To better understand the experience of dental insurance from international dental care practice, the dental coverage scope, content, co-pay ratio, and effects of oral insurance on oral health improvement from the abroad countries with typical health insurance systems were summarized by using scoping review. Then, we discussed the coverage scope for dental health of basic medical insurance and private insurance in China. We also analyzed the current issues of dental care coverage and cost-share. At last, we proposed thoughts and suggestions to establish and improve a multi-level oral health insurance system with Chinese characteristics under the basic medical insurance frame. In particular, we gave suggestions on increasing the coverage for high dental care xpenditure by ebasic medical insurance, supplying children and teenagers with preventive dental care, and encouraging private insurance companies to cover dental care expenditure.

Gut microbiota composition can reflect immune responses of latent tuberculosis infection in patients with poorly controlled diabetes

BACKGROUND

Diabetes mellitus (DM) is a major risk factor for tuberculosis (TB). Evidence has linked the DM-related dysbiosis of gut microbiota to modifiable host immunity to Mycobacterium tuberculosis infection. However, the crosslinks between gut microbiota composition and immunological effects on the development of latent TB infection (LTBI) in DM patients remain uncertain.

METHODS

We prospectively obtained stool, blood samples, and medical records from 130 patients with poorly-controlled DM (pDM), defined as ever having an HbA1c > 9.0% within previous 1 year. Among them, 43 had LTBI, as determined by QuantiFERON-TB Gold in-Tube assay. The differences in the taxonomic diversity of gut microbiota between LTBI and non-LTBI groups were investigated using 16S ribosomal RNA sequencing, and a predictive algorithm was established using a random forest model. Serum cytokine levels were measured to determine their correlations with gut microbiota.

RESULTS

Compared with non-LTBI group, the microbiota in LTBI group displayed a similar alpha-diversity but different beta-diversity, featuring decrease of Prevotella_9, Streptococcus, and Actinomyces and increase of Bacteroides, Alistipes, and Blautia at the genus level. The accuracy was 0.872 for the LTBI prediction model using the aforementioned 6 microbiome-based biomarkers. Compared with the non-LTBI group, the LTBI group had a significantly lower serum levels of IL-17F (p = 0.025) and TNF-α (p = 0.038), which were correlated with the abundance of the aforementioned 6 taxa.

CONCLUSIONS

The study results suggest that gut microbiome composition maybe associated with host immunity relevant to TB status, and gut microbial signature might be helpful for the diagnosis of LTBI.

Methotrexate inhibition of SARS-CoV-2 entry, infection and inflammation revealed by bioinformatics approach and a hamster model

Background

Drug repurposing is a fast and effective way to develop drugs for an emerging disease such as COVID-19. The main challenges of effective drug repurposing are the discoveries of the right therapeutic targets and the right drugs for combating the disease.

Methods

Here, we present a systematic repurposing approach, combining Homopharma and hierarchal systems biology networks (HiSBiN), to predict 327 therapeutic targets and 21,233 drug-target interactions of 1,592 FDA drugs for COVID-19. Among these multi-target drugs, eight candidates (along with pimozide and valsartan) were tested and methotrexate was identified to affect 14 therapeutic targets suppressing SARS-CoV-2 entry, viral replication, and COVID-19 pathologies. Through the use of in vitro (EC₅₀ = 0.4 μM) and in vivo models, we show that methotrexate is able to inhibit COVID-19 via multiple mechanisms.

Results

Our in vitro studies illustrate that methotrexate can suppress SARS-CoV-2 entry and replication by targeting furin and DHFR of the host, respectively. Additionally, methotrexate inhibits all four SARS-CoV-2 variants of concern. In a Syrian hamster model for COVID-19, methotrexate reduced virus replication, inflammation in the infected lungs. By analysis of transcriptomic analysis of collected samples from hamster lung, we uncovered that neutrophil infiltration and the pathways of innate immune response, adaptive immune response and thrombosis are modulated in the treated animals.

Conclusions

We demonstrate that this systematic repurposing approach is potentially useful to identify pharmaceutical targets, multi-target drugs and regulated pathways for a complex disease. Our findings indicate that methotrexate is established as a promising drug against SARS-CoV-2 variants and can be used to treat lung damage and inflammation in COVID-19, warranting future evaluation in clinical trials.

Inhibition of IRAK1 Is an Effective Therapy for Autoimmune Hypophysitis in Mice

Autoimmune hypophysitis (AH) is an autoimmune disease of the pituitary for which the pathogenesis is incompletely known. AH is often treated with corticosteroids; however, steroids may lead to considerable side effects. Using a mouse model of AH (experimental autoimmune hypophysitis, EAH), we show that interleukin-1 receptor-associated kinase 1 (IRAK1) is upregulated in the pituitaries of mice that developed EAH. We identified rosoxacin as a specific inhibitor for IRAK1 and found it could treat EAH. Rosoxacin treatment at an early stage (day 0-13) slightly reduced disease severity, whereas treatment at a later stage (day 14-27) significantly suppressed EAH. Further investigation indicated rosoxacin reduced production of autoantigen-specific antibodies. Rosoxacin downregulated production of cytokines and chemokines that may dampen T cell differentiation or recruitment to the pituitary. Finally, rosoxacin downregulated class II major histocompatibility complex expression on antigen-presenting cells that may lead to impaired activation of autoantigen-specific T cells. These data suggest that IRAK1 may play a pathogenic role in AH and that rosoxacin may be an effective drug for AH and other inflammatory diseases involving IRAK1 dysregulation.

Densest subgraph-based methods for protein-protein interaction hot spot prediction

Background

Hot spots play an important role in protein binding analysis. The residue interaction network is a key point in hot spot prediction, and several graph theory-based methods have been proposed to detect hot spots. Although the existing methods can yield some interesting residues by network analysis, low recall has limited their abilities in finding more potential hot spots.

Result

In this study, we develop three graph theory-based methods to predict hot spots from only a single residue interaction network. We detect the important residues by finding subgraphs with high densities, i.e., high average degrees. Generally, a high degree implies a high binding possibility between protein chains, and thus a subgraph with high density usually relates to binding sites that have a high rate of hot spots. By evaluating the results on 67 complexes from the SKEMPI database, our methods clearly outperform existing graph theory-based methods on recall and F-score. In particular, our main method, Min-SDS, has an average recall of over 0.665 and an f2-score of over 0.364, while the recall and f2-score of the existing methods are less than 0.400 and 0.224, respectively.

Conclusion

The Min-SDS method performs best among all tested methods on the hot spot prediction problem, and all three of our methods provide useful approaches for analyzing bionetworks. In addition, the densest subgraph-based methods predict hot spots with only one residue interaction network, which is constructed from spatial atomic coordinate data to mitigate the shortage of data from wet-lab experiments.

The Development and Evaluation of a Smartphone-Aided Diagnosis Application to Measure Tympanic Membrane Perforations

OBJECTIVES

Chronic otitis media is a long-term infection of the middle ear. It is characterized by persistent discharge from the middle ear through a perforated tympanic membrane. It is one of the most common causes of preventable hearing loss, especially in developing countries. Precise estimation of the size of tympanic membrane perforation is essential for successful clinical management. In this study, we developed a smartphone-based application to calculate the ratio of the area of tympanic membrane perforation to the area of the tympanic membrane. Twelve standardized patients and 60 medical students were involved to assess the area of tympanic membrane perforation, in particular, the percentage of perforation size.

METHODS

In total, 60 student doctors (including year 5 and year 6 medical students, intern and post-graduate year training of doctors) were recruited during their rotation at the Otolaryngology department of Taipei Medical University Shuang-Ho Hospital. Twelve standardized patients with chronic otitis media were recruited through a single otology practice. Oto-endoscopic examination was performed for all patients by using a commercially-available digital oto-endoscope, and clinical images of the tympanic membrane perforation were obtained. To demonstrate the variability of perforation size estimation by different student doctors, we calculated the percentage of perforation using the smartphone-based application for 12 tympanic membranes objectively and compared the results with those visually estimated by the 60 student doctors subjectively.

RESULTS

The variance in the visual estimation by the 60 student doctors was large. By contrast, variances in smartphone-based application calculations were smaller, indicating consistency in the results obtained from different users. The smartphone-based application accurately estimated the presence of perforation for tympanic membranes with high consistency. The differences in visual estimations can be considerably great and the variances can be large among different individuals.

CONCLUSIONS

The smartphone-based application is a dependable tool for precisely evaluating the size of tympanic membrane perforation.

Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties

Background

Human protein kinases, the key players in phosphoryl signal transduction, have been actively investigated as drug targets for complex diseases such as cancer, immune disorders, and Alzheimer’s disease, with more than 60 successful drugs developed in the past 30 years. However, many of these single-kinase inhibitors show low efficacy and drug resistance has become an issue. Owing to the occurrence of highly conserved catalytic sites and shared signaling pathways within a kinase family, multi-target kinase inhibitors have attracted attention.

Results

To design and identify such pan-kinase family inhibitors (PKFIs), we proposed PKFI sets for eight families using 200,000 experimental bioactivity data points and applied a graph convolutional network (GCN) to build classification models. Furthermore, we identified and extracted family-sensitive (only present in a family) pre-moieties (parts of complete moieties) by utilizing a visualized explanation (i.e., where the model focuses on each input) method for deep learning, gradient-weighted class activation mapping (Grad-CAM).

Conclusions

This study is the first to propose the PKFI sets, and our results point out and validate the power of GCN models in understanding the pre-moieties of PKFIs within and across different kinase families. Moreover, we highlight the discoverability of family-sensitive pre-moieties in PKFI identification and drug design.

Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations

Background

While it has been known that human protein kinases mediate most signal transductions in cells and their dysfunction can result in inflammatory diseases and cancers, it remains a challenge to find effective kinase inhibitor as drugs for these diseases. One major challenge is the compensatory upregulation of related kinases following some critical kinase inhibition. To circumvent the compensatory effect, it is desirable to have inhibitors that inhibit all the kinases belonging to the same family, instead of targeting only a few kinases. However, finding inhibitors that target a whole kinase family is laborious and time consuming in wet lab.

Results

In this paper, we present a computational approach taking advantage of interpretable deep learning models to address this challenge. Specifically, we firstly collected 9,037 inhibitor bioassay results (with 3991 active and 5046 inactive pairs) for eight kinase families (including EGFR, Jak, GSK, CLK, PIM, PKD, Akt and PKG) from the ChEMBL25 Database and the Metz Kinase Profiling Data. We generated 238 binary moiety features for each inhibitor, and used the features as input to train eight deep neural networks (DNN) models to predict whether an inhibitor is active for each kinase family. We then employed the SHapley Additive exPlanations (SHAP) to analyze the importance of each moiety feature in each classification model, identifying moieties that are in the common kinase hinge sites across the eight kinase families, as well as moieties that are specific to some kinase families. We finally validated these identified moieties using experimental crystal structures to reveal their functional importance in kinase inhibition.

Conclusion

With the SHAP methodology, we identified two common moieties for eight kinase families, 9 EGFR-specific moieties, and 6 Akt-specific moieties, that bear functional importance in kinase inhibition. Our result suggests that SHAP has the potential to help finding effective pan-kinase family inhibitors.

Trends in body mass index changes among Korean adolescents between 2005-2020, including the COVID-19 pandemic period: a national representative survey of one million adolescents

OBJECTIVE

The impact of the coronavirus disease 2019 (COVID-19) pandemic on weight gain in children and adolescents remains unknown. We aimed to identify an estimated 15-year trend in mean body mass index (BMI) changes and prevalence of obesity and overweight among Korean adolescents from 2005 to 2020, including the period of the COVID-19 pandemic.

PATIENTS AND METHODS

We analyzed data taken from a nationwide survey (Korea Youth Risk Behavior Survey), between 2005 and 2020. Representative samples of one million Korean adolescents aged 13-18 years (n=1,057,885) were examined. The 15-year trends in mean BMI and proportion of obesity or overweight, and the changes due to the COVID-19 pandemic were analyzed.

RESULTS

The data of 1,057,885 Korean adolescents were analyzed (mean age: 14.98 years; females, 48.4%). The estimated weighted mean BMI was 20.5 kg/m2 [95% confidence interval (CI), 20.4-20.5] from 2005 to 2008 and 21.5 kg/m2 (95% CI, 21.4-21.6) in 2020 (during the COVID-19 pandemic). Although the 15-year trend of mean BMI gradually increased, the change in mean BMI before and during the pandemic significantly lessened (βdiff, -0.027; 95% CI, -0.028 to -0.026). The 15-year (2005-2020) trend changes in the prevalence of obesity and overweight were similar (obesity prevalence from 2005-2008, 3.2%; 95% CI, 3.1-3.3 vs. obesity prevalence in 2020, 8.6%; 95% CI, 8.2-9.0; βdiff, -0.309; 95% CI, -0.330 to -0.288).

CONCLUSIONS

The 15-year trend of overall mean BMI and obesity and overweight prevalence demonstrated a significant increase; however, its slope decreased during the pandemic. These landmark results suggest the need for the development of precise strategies to prevent pediatric obesity and overweight during the COVID-19 pandemic.

Furin and TMPRSS2 Resistant Spike Induces Robust Humoral and Cellular Immunity Against SARS-CoV-2 Lethal Infection

An effective COVID-19 vaccine against broad SARS-CoV-2 variants is still an unmet need. In the study, the vesicular stomatitis virus (VSV)-based vector was used to express the SARS-CoV-2 Spike protein to identify better vaccine designs. The replication-competent of the recombinant VSV-spike virus with C-terminal 19 amino acid truncation (SΔ19 Rep) was generated. A single dose of SΔ19 Rep intranasal vaccination is sufficient to induce protective immunity against SARS-CoV-2 infection in hamsters. All the clones isolated from the SΔ19 Rep virus contained R682G mutation located at the Furin cleavage site. An additional S813Y mutation close to the TMPRSS2 cleavage site was identified in some clones. The enzymatic processing of S protein was blocked by these mutations. The vaccination of the R682G-S813Y virus produced a high antibody response against S protein and a robust S protein-specific CD8+ T cell response. The vaccinated animals were protected from the lethal SARS-CoV-2 (delta variant) challenge. The S antigen with resistance to enzymatic processes by Furin and TMPRSS2 will provide better immunogenicity for vaccine design.

COVID-19 susceptibility and clinical outcomes in autoimmune inflammatory rheumatic diseases (AIRDs): a systematic review and meta-analysis

OBJECTIVE

This meta-analysis aims to assess the susceptibility to and clinical outcomes of COVID-19 in autoimmune inflammatory rheumatic disease (AIRD) and following AIRD drug use.

MATERIALS AND METHODS

We included observational and case-controlled studies assessing susceptibility and clinical outcomes of COVID-19 in patients with AIRD as well as the clinical outcomes of COVID-19 with or without use of steroids and conventional synthetic disease-modifying antirheumatic drugs (csDMARDs).

RESULTS

Meta-analysis including three studies showed that patients with AIRD are not more susceptible to COVID-19 compared to patients without AIRD or the general population (OR: 1.11, 95% CI: 0.58 to 2.14). Incidence of severe outcomes of COVID-19 (OR: 1.34, 95% CI: 0.76 to 2.35) and COVID-19 related death (OR: 1.21, 95% CI: 0.68 to 2.16) also did not show significant difference. The clinical outcomes of COVID-19 among AIRD patients with and without csDMARD or steroid showed that both use of steroid (OR: 1.69, 95% CI: 0.96 to 2.98) or csDMARD (OR: 1.35, 95% CI: 0.63 to 3.08) had no effect on clinical outcomes of COVID-19.

CONCLUSIONS

AIRD does not increase susceptibility to COVID-19, not affecting the clinical outcome of COVID-19. Similarly, the use of steroids or csDMARDs for AIRD does not worsen the clinical outcome.

Discovery of moiety preference by Shapley value in protein kinase family using random forest models

Background

Human protein kinases play important roles in cancers, are highly co-regulated by kinase families rather than a single kinase, and complementarily regulate signaling pathways. Even though there are > 100,000 protein kinase inhibitors, only 67 kinase drugs are currently approved by the Food and Drug Administration (FDA).

Results

In this study, we used “merged moiety-based interpretable features (MMIFs),” which merged four moiety-based compound features, including Checkmol fingerprint, PubChem fingerprint, rings in drugs, and in-house moieties as the input features for building random forest (RF) models. By using > 200,000 bioactivity test data, we classified inhibitors as kinase family inhibitors or non-inhibitors in the machine learning. The results showed that our RF models achieved good accuracy (> 0.8) for the 10 kinase families. In addition, we found kinase common and specific moieties across families using the Shapley Additive exPlanations (SHAP) approach. We also verified our results using protein kinase complex structures containing important interactions of the hinges, DFGs, or P-loops in the ATP pocket of active sites.

Conclusions

In summary, we not only constructed highly accurate prediction models for predicting inhibitors of kinase families but also discovered common and specific inhibitor moieties between different kinase families, providing new opportunities for designing protein kinase inhibitors.

Internal limiting membrane handling in macular hole surgery: the infusion direction manipulation and infusion off techniques

OBJECTIVE

Herein, we introduce the infusion direction manipulation technique and the infusion off technique. These relatively simple methods control intra-vitreal fluid flow direction and turbulence and release negative pressure in the microforceps to facilitate handling of the internal limiting membrane. The aim of this study is to introduce an effective and uncomplicated method to handle the internal limiting membrane (ILM) during the temporal inverted ILM flap and free ILM flap techniques in macular hole surgery by controlling the direction and status of the infusion.

MATERIALS AND METHODS

The direction of the infusion flow was controlled with a free finger (usually the 4th finger) during the inverted ILM flap surgery to stabilize the flap location during the fluid-air exchange. A valved trocar was used, and the infusion was discontinued during the free ILM flap surgery. Turbulence was minimized, and negative pressure around the head-shaft junction of the microforceps was released.

RESULTS

The ILM flap remained stable in all patients who underwent macular hole surgery with our technique.

CONCLUSIONS

Infusion direction manipulation technique and infusion off technique are efficient and simple methods to handle the ILM during ILM surgery.

[Early effect of extracorporeal membrane oxygenation and factors related to early outcome in adult patients with fulminant myocarditis]

Objective: To evaluate the efficacy within the first 24 h post extracorporeal membrane pulmonary oxygenation (ECMO) and the impact of early efficacy on the prognosis of adult patients with fulminant myocarditis (FM). Methods: This retrospective case analysis study included hospitalized patients (age≥18 years) who were diagnosed with fulminant myocarditis from November 2016 to May 2021 in the First Affiliated Hospital of Zhengzhou University. Patients were divided into survival or non-survival groups according to treatment outcomes. The age, sex, treatments, drug use, ECMO use, clinical and laboratory data (before and 24 h after the use of ECMO) were analyzed. The change rate of clinical and laboratory data after 24 h use of ECMO was calculated to find differences between two groups. Multivariate logistic regression was used to analyze the related factors with in-hospital death and complication between the two groups. Results: A total of 38 FM patients treated with ECMO were included. There were 23 cases (60.5%) in the survival group, aged (39.6±13.7) years, and 17 (73.9%) cases were female. The total ECMO time was (134.4±71.3)h. There were 15 cases (39.5%) in non-survival group, aged (40.0±15.8) years, and there were 12(80.0%) female, the ECMO time was (120.1±72.4) h in this group. The proportion of tracheal intubation and continuous renal replacement therapy in the survivor group and dosage of norepinephrine within 24 h after ECMO implantation were significantly less than in non-survival group (all P<0.05). There was no significant difference in all efficacy related biochemical indexes between two groups before ECMO use. The levels of lactic acid, procalcitonin, creatinine, alanine aminotransferase, aspartate aminotransferase, creatine kinase-MB, cardiac troponin I and N-terminal B-type natriuretic peptide prosoma were significantly less in survival group than in non-survival group at 24 h after the use of ECMO (all P<0.05). Results of multivariate logistic regression analysis showed that the higher 24 h change rate of creatinine (OR=0.587, 95%CI 0.349-0.986, P=0.044) and creatine kinase-MB (OR=0.177, 95%CI 0.037-0.841, P=0.029) were positively correlated with reduced risk of in-hospital mortality. The central hemorrhage and acute kidney injury in survival group were less than in non-survivor group (P<0.05). Conclusions: After 24 h early use of ECMO in FM patients, the improvement of various efficacy related biochemical test indexes in the survival group was better than that in the non-survival group. Faster reduction of creatine kinase-MB and creatinine values within 24 h ECMO use is positively correlated with reduced risk of in-hospital mortality in adult patients with FM.

Whole-blood 3-gene Signature as a Decision Aid for Rifapentine-based TB Preventive Therapy

Background

Systemic drug reaction (SDR) is a major safety concern with weekly rifapentine plus isoniazid for 12 doses (3HP) for latent tuberculosis infection (LTBI). Identifying SDR predictors and at-risk participants before treatment can improve cost-effectiveness of the LTBI program.

Methods

We prospectively recruited 187 cases receiving 3HP (44 SDRs and 143 non-SDRs). A pilot cohort (8 SDRs and 12 non-SDRs) was selected for generating whole-blood transcriptomic data. By incorporating the hierarchical system biology model and therapy–biomarker pathway approach, candidate genes were selected and evaluated using reverse-transcription quantitative polymerase chain reaction (RT-qPCR). Then, interpretable machine learning models presenting as SHapley Additive exPlanations (SHAP) values were applied for SDR risk prediction. Finally, an independent cohort was used to evaluate the performance of these predictive models.

Results

Based on the whole-blood transcriptomic profile of the pilot cohort and the RT-qPCR results of 2 SDR and 3 non-SDR samples in the training cohort, 6 genes were selected. According to SHAP values for model construction and validation, a 3-gene model for SDR risk prediction achieved a sensitivity and specificity of 0.972 and 0.947, respectively, under a universal cutoff value for the joint of the training (28 SDRs and 104 non-SDRs) and testing (8 SDRs and 27 non-SDRs) cohorts. It also worked well across different subgroups.

Conclusions

The prediction model for 3HP-related SDRs serves as a guide for establishing a safe and personalized regimen to foster the implementation of an LTBI program. Additionally, it provides a potential translational value for future studies on drug-related hypersensitivity.

Repurposing existing drugs: identification of SARS-CoV-2 3C-like protease inhibitors

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for coronavirus disease 2019 (COVID-19). Since its emergence, the COVID-19 pandemic has not only distressed medical services but also caused economic upheavals, marking urgent the need for effective therapeutics. The experience of combating SARS-CoV and MERS-CoV has shown that inhibiting the 3-chymotrypsin-like protease (3CLpro) blocks the replication of the virus. Given the well-studied properties of FDA-approved drugs, identification of SARS-CoV-2 3CLpro inhibitors in an FDA-approved drug library would be of great therapeutic value. Here, we screened a library consisting of 774 FDA-approved drugs for potent SARS-CoV-2 3CLpro inhibitors, using an intramolecularly quenched fluorescence (IQF) peptide substrate. Ethacrynic acid, naproxen, allopurinol, butenafine hydrochloride, raloxifene hydrochloride, tranylcypromine hydrochloride, and saquinavir mesylate have been found to block the proteolytic activity of SARS-CoV-2 3CLpro. The inhibitory activity of these repurposing drugs against SARS-CoV-2 3CLpro highlights their therapeutic potential for treating COVID-19 and other Betacoronavirus infections.

Efficacy and safety of epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) monotherapy for advanced EGFR-mutated non-small cell lung cancer: systematic review and meta-analysis

OBJECTIVE

It is controversial whether there is efficacy or safety benefit of epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) in advanced EGFR-mutated non-small cell lung cancer (NSCLC) compared to standard chemotherapy. We aim to assess the efficacy and safety of EGFR-TKIs compared to other chemotherapeutics in EGFR-mutated NSCLC.

MATERIALS AND METHODS

Up to April 27th, 2020, PubMed, Embase, Medline, Scopus, Cochrane library, and ClinicalTrials.gov were searched for articles or trials meeting the inclusion criteria. After filtering, 230 eligible studies were initially identified. Data extraction followed PRISMA and included outcomes were progression-free survival (PFS), overall survival (OS), and severe adverse events (SAEs). Direct and indirect meta-analyses were generated in the context of log-linear mixed-effects models, with fixed effects for each relative comparison and random effects for each study.

RESULTS

The results showed that EGFR-TKI therapy had improved PFS with a hazard ratio (HR) of 0.40 (95% CI: 0.36-0.44, p<0.001) compared to standard chemotherapy. Nevertheless, the EGFR-TKIs showed no benefit on OS (HR: 0.96, 95% CI: 0.83-1.10, p=0.556). In the analysis of adverse events, EGFR-TKIs had fewer SAEs than standard chemotherapy (HR: 0.29, 95% CI: 0.26-0.33, p<0.001).

CONCLUSIONS

Our systemic review indicates that EGFR-TKI therapy has improved PFS, and reduced SAEs compared to standard chemotherapy in advanced EGFR-mutated NSCLC.

Validation of a Personalized Hearing Screening Mobile Health Application for Persons with Moderate Hearing Impairment

Hearing impairment is a frequent human sensory impairment. It was estimated that over 50% of those aged >75 years experience hearing impairment in the United States. Several hearing impairment–related factors are detectable through screening; thus, further deterioration can be avoided. Early identification of hearing impairment is the key to effective management. However, hearing screening resources are scarce or inaccessible, underlining the importance of developing user-friendly mobile health care systems for universal hearing screening. Mobile health (mHealth) applications (apps) act as platforms for personalized hearing screening to evaluate an individual’s risk of developing hearing impairment. We aimed to evaluate and compare the accuracy of smartphone-based air conduction and bone conduction audiometry self-tests with that of standard air conduction and bone conduction pure-tone audiometry tests. Moreover, we evaluated the use of smartphone-based air conduction and bone conduction audiometry self-tests in conductive hearing loss diagnosis. We recruited 103 patients (206 ears) from an otology clinic. All patients were aged ≥20 years. Patients who were diagnosed with active otorrhea was excluded. Moderate hearing impairment was defined as hearing loss with mean hearing thresholds >40 dB. All patients underwent four hearing tests performed by a board-certified audiologist: a smartphone-based air conduction audiometry self-test, smartphone-based bone conduction audiometry self-test, standard air-conduction pure-tone audiometry, and standard bone conduction pure-tone audiometry. We compared and analyzed the results of the smartphone-based air conduction and bone conduction audiometry self-tests with those of the standard air conduction and bone conduction pure-tone audiometry tests. The sensitivity of the smartphone-based air conduction audiometry self-test was 0.80 (95% confidence interval CI = 0.71–0.88) and its specificity was 0.84 (95% CI = 0.76–0.90), respectively. The sensitivity of the smartphone-based bone conduction audiometry self-test was 0.64 (95% CI = 0.53–0.75) and its specificity was 0.71 (95% CI = 0.62–0.78). Among all the ears, 24 were diagnosed with conductive hearing loss. The smartphone-based audiometry self-tests correctly diagnosed conductive hearing loss in 17 of those ears. The personalized smartphone-based audiometry self-tests correctly diagnosed hearing loss with high sensitivity and high specificity, and they can be a reliable screening test to rule out moderate hearing impairment among the population. It provided patients with moderate hearing impairment with personalized strategies for symptomatic control and facilitated individual case management for medical practitioners.

A novel EGFR inhibitor suppresses survivin expression and tumor growth in human gefitinib-resistant EGFR-wild type and -T790M non-small cell lung cancer

Tyrosine kinase inhibitors of epidermal growth factor receptor (EGFR-TKIs) are currently used therapy for non-small cell lung cancer (NSCLC) patients; however, drug resistance during cancer treatment is a critical problem. Survivin is an anti-apoptosis protein, which promotes cell proliferation and tumor growth that highly expressed in various human cancers. Here, we show a novel synthetic compound derived from gefitinib, do-decyl-4-(4-(3-(4-(3-chloro-4-fluorophenylamino)-7-methoxyquinazolin-6-yloxy)propyl) piper-azin-1-yl)-4-oxobutanoate, which is named as SP101 that inhibits survivin expression and tumor growth in both the EGFR-wild type and -T790M of NSCLC. SP101 blocked EGFR kinase activity and induced apoptosis in the A549 (EGFR-wild type) and H1975 (EGFR-T790M) lung cancer cells. SP101 reduced survivin proteins and increased active caspase 3 for inducing apoptosis. Ectopic expression of survivin by a survivin-expressed vector attenuated the SP101-induced cell death in lung cancer cells. Moreover, SP101 inhibited the gefitinib-resistant tumor growth in the xenograft human H1975 lung tumors of nude mice. SP101 substantially reduced survivin proteins but conversely elicited active caspase 3 proteins in tumor tissues. Besides, SP101 exerted anticancer abilities in the gefitinib resistant cancer cells separated from pleural effusion of a clinical lung cancer patient. Consistently, SP101 decreased the survivin proteins and the patient-derived xenografted lung tumor growth in nude mice. Anti-tumor ability of SP101 was also confirmed in the murine lung cancer model harboring EGFR T790M-L858R. Together, SP101 is a new EGFR inhibitor with inhibiting survivin that can be developed for treating EGFR wild-type and EGFR-mutational gefitinib-resistance in human lung cancers.

Can Face- and Smartphone-Touching Behaviors Be Altered with Personal Hygiene Reminders during the COVID-19 Pandemic Period? An Observational Study

As part of the new measures to prevent the spread of the 2019 coronavirus disease (COVID-19), medical students were advised to wear a mask in class and avoid touching their faces. Few studies have analyzed the influence of health education on the frequency of face- and smartphone-touching behaviors during the COVID-19 pandemic. This research compared the frequency of in-class face- and smartphone-touching behaviors of medical students before and after the delivery of personal hygiene education during the COVID-19 pandemic. A behavioral observational study was conducted involving medical students at Taipei Medical University. Eighty medical students were recruited during a lecture on otorhinolaryngology. All medical students were required to wear a mask. Their face- and smartphone-touching behavior was observed by viewing the 4 k resolution video tape recorded in class. The recording lasted for 2 h, comprising 1 h prior to the health educational reminder and 1 h afterwards. The frequencies of hand-to-face contact and hand-to-smartphone contact were analyzed before and after the delivery of health education emphasizing personal hygiene. Comprehensive health education and reminders effectively reduce the rate of face- and smartphone-touching behaviors.

Empirical assessment of biases in cerebrospinal fluid biomarkers of Alzheimer's disease: an umbrella review and re-analysis of data from meta-analyses

OBJECTIVE

Alzheimer's disease (AD) is a leading cause of years lived with disability in older age, and several cerebrospinal fluid (CSF) markers have been proposed in individual meta-analyses to be associated with AD but field-wide evaluation and scrutiny of the literature is not available.

MATERIALS AND METHODS

We performed an umbrella review for the reported associations between CSF biomarkers and AD. Data from available meta-analyses were reanalyzed using both random and fixed effects models. We also estimated between-study heterogeneity, small-study effects, excess significance, and prediction interval.

RESULTS

A total of 38 meta-analyses on CSF markers from 11 eligible articles were identified and reanalyzed. In 14 (36%) of the meta-analyses, the summary estimate and the results of the largest study showed non-concordant results in terms of statistical significance. Large heterogeneity (I2≥75%) was observed in 73% and small-study effects under Egger's test were shown in 28% of CSF biomarkers.

CONCLUSIONS

Our results suggest that there is an excess of statistically significant results and significant biases in the literature of CSF biomarkers for AD. Therefore, the results of CSF biomarkers should be interpreted with caution.

Ugonin J Acts as a SARS-CoV-2 3C-like Protease Inhibitor and Exhibits Anti-inflammatory Properties

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes severe “flu-like” symptoms that can progress to acute respiratory distress syndrome (ARDS), pneumonia, renal failure, and death. From the therapeutic perspective, 3-chymotrypsin-like protein (3CLpro) is a plausible target for direct-acting antiviral agents because of its indispensable role in viral replication. The flavonoid ugonin J (UJ) has been reported to have antioxidative and anti-inflammatory activities. However, the potential of UJ as an antiviral agent remains unexplored. In this study, we investigated the therapeutic activity of UJ against SARS-CoV-2 infection. Importantly, UJ has a distinct inhibitory activity against SARS-CoV-2 3CLpro, compared to luteolin, kaempferol, and isokaempferide. Specifically, UJ blocks the active site of SARS-CoV-2 3CLpro by forming hydrogen bonding and van der Waals interactions with H163, M165 and E166, G143 and C145, Q189, and P168 in subsites S1, S1′, S2, and S4, respectively. In addition, UJ forms strong, stable interactions with core pharmacophore anchors of SARS-CoV-2 3CLpro in a computational model. UJ shows consistent anti-inflammatory activity in inflamed human alveolar basal epithelial A549 cells. Furthermore, UJ has a 50% cytotoxic concentration (CC₅₀) and a 50% effective concentration (EC₅₀₎ values of about 783 and 2.38 µM, respectively, with a selectivity index (SI) value of 329, in SARS-CoV-2-infected Vero E6 cells. Taken together, UJ is a direct-acting antiviral that obstructs the activity of a fundamental protease of SARS-CoV-2, offering the therapeutic potential for SARS-CoV-2 infection.

[Association of maternal anxiety with congenital heart disease in offspring based on case-control study]

Objective: To explore the association of maternal anxiety with congenital heart disease (CHD) in offspring. Methods: A case-control study design was used in this study. The data were collected in Shaanxi province from January 2014 to December 2016. Neonatal information is provided through specialized hospitals or institutions. Logistic regression model with adjustment for confounding factors was established to analyze the association between maternal perinatal anxiety and CHD in offspring. Meanwhile, subgroup analysis was carried out to explore its stability. Results: Our study included 2 429 subjects, consisting of 773 cases and 1 656 controls. Women with anxiety during pregnancy accounted for 10.3% in the case group, while 7.8% in the control group. After adjusting for confounding factors, the level of maternal anxiety during pregnancy was positively correlated with CHD in the offspring (OR=1.04, 95%CI: 1.01-1.07). The risk of CHD in the offspring of mothers with anxiety during pregnancy was 1.43 times higher than that in those whose mothers had no anxiety (OR=1.43, 95%CI: 1.00-2.05). Conclusion: Maternal anxiety during pregnancy is probably a risk factor for congenital heart disease in offspring.

Body mass index and mortality in patients with cardiovascular disease: an umbrella review of meta-analyses

OBJECTIVE

Although many previous meta-analyses of epidemiological studies have demonstrated a relationship between body mass index (BMI) and mortality, inconsistent findings among cardiovascular disease patients have been observed. Thus, we performed an umbrella review to understand the strength of evidence and validity of claimed associations between BMI and mortality in patients with cardiovascular diseases.

MATERIALS AND METHODS

We comprehensively re-analyzed the data of meta-analyses of observational studies and randomized controlled trials on associations between BMI and mortality among patients with cardiovascular diseases. We also assessed the strength of evidence of the re-analyzed outcomes, which were determined from the criteria including statistical significance of the p-value of random-effects, as well as fixed-effects meta-analyses, small-study effects, between-study heterogeneity, and a 95% prediction interval.

RESULTS

We ran comprehensive re-analysis of the data from the 21 selected studies, which contained a total of 108 meta-analyses; 23 were graded as convincing evidence and 12 were suggestive, 42 were weak, and 23 were non-significant.

CONCLUSIONS

Underweight increased mortality in acute coronary syndrome (ACS), heart failure, and after therapeutic intervention for patients with cardiovascular diseases. Overweight, on the other hand decreased mortality in patient's ACS, atrial fibrillation, and heart failure with convincing evidence.

[Consistency of peripheral whole blood and venous serum procalcitonin in children: a multicenter parallel controlled study]

Objective: To explore the consistency of peripheral whole blood and venous serum procalcitonin (PCT) levels, and the value of peripheral whole blood PCT in evaluating pediatric bacterial infection. Methods: This multicenter cross-sectional parallel control study was conducted in 11 children's hospital. All the 1 898 patients older than 28 days admitted to these hospitals from March 2018 to February 2019 had their peripheral whole blood and venous serum PCT detected simultaneously with unified equipment, reagent and method. According to the venous serum PCT level, the patients were stratified to subgroups. Analysis of variance and chi-square test were used to compare the demographic characteristics among groups. And the correlation between the peripheral blood and venous serum PCT level was investigated by quantitative Pearson correlation analysis.The PCT resultes were also converted into ranked data to further test the consistency between the two sampling methods by Spearman's rank correlation test. Furthermore, the ranked data were converted into binary data to evaluate the consistency and investigate the best cut-off of peripheral blood PCT level in predicting bacterial infection. Results: A total of 1 898 valid samples were included (1 098 males, 800 females),age 27.4(12.2,56.7) months. There was a good correlation between PCT values of peripheral whole blood and venous serum (r=0.97, P<0.01). The linear regression equation was PCT_{venous serum}=0.135+0.929×PCT_{peripheral whole blood}. However, when stratified to 5 levels, PCT results showed diverse and unsatisfied consistency between the two sampling methods (r=0.51-0.92, all P<0.01). But after PCT was converted to ordinal categorical variables, the stratified analysis showed that the coincidence rate of the measured values by the two sampling methods in each boundary area was 84.9%-97.1%. The dichotomous variables also showed a good consistency (coincidence rate 96.8%-99.3%, Youden index 0.82-0.89). According to the severity of disease, the serum PCT value was classified into 4 intervals（<0.5、0.5-<2.0、2.0-<10.0、≥10.0 μg/L）, and the peripheral blood PCT value also showed a good predictive value (AUC value was 0.991 2-0.997 9). The optimal cut points of peripheral whole blood PCT value 0.5、1.0、2.0、10.0 μg/L corresponding to venous serum PCT values were 0.395, 0.595, 1.175 and 3.545 μg/L, respectively. Conclusions: There is a good correlation between peripheral whole blood PCT value and the venous serum PCT value, which means that the peripheral whole blood PCT could facilitate the identification of infection and clinical severity. Besides, the sampling of peripheral whole blood is simple and easy to repeat.

Pharmacophore anchor models of ATAT1 to discover potential inhibitors and lead optimization

Post-translation modification of microtubules is associated with many diseases like cancer. Alpha Tubulin Acetyltransferase 1 (ATAT1) is a major enzyme that acetylates 'Lys-40' in alpha-tubulin on the luminal side of microtubules and is a drug target that lacks inhibitors. Here, we developed pharmacophore anchor models of ATAT1 which were constructed statistically using thousands of docked compounds, for drug design and investigating binding mechanisms. Our models infer the compound moiety preferences with the physico-chemical properties for the ATAT1 binding site. The results from the pharmacophore anchor models show the three main sub-pockets, including S1 acetyl site, S2 adenine site, and S3 diphosphate site with anchors, where conserved moieties interact with respective sub-pocket residues in each site and help in guiding inhibitor discovery. We validated these key anchors by analyzing 162 homologous protein sequences (>99 species) and over 10 structures with various bound ligands and mutations. Our results were consistent with previous works also providing new interesting insights. Our models applied in virtual screening predicted several ATAT1 potential inhibitors. We believe that our model is useful for future inhibitor discovery and for guiding lead optimization.

An integrated systematic approach for investigating microcurrent electrical nerve stimulation (MENS) efficacy in STZ-induced diabetes mellitus

Diabetes mellitus (DM) is a major metabolic disorder and an increasing health problem worldwide. Effective non-invasive therapies for DM are still lacking. Here, we have developed Microcurrent electrical nerve stimulation (MENS), a non-invasive therapy, and tested on 46 mice clustered into five groups, such as control, STZ-induced DM, and MENS treatment groups. Experimental results show that MENS treatment is able to improve seven biochemical indexes (e.g., hemoglobin A1c and glucose level). To investigate the mechanisms of MENS treatment on STZ-induced DM, we selected six representative samples to perform microarray experiments for several groups and developed an integrated Hierarchical System Biology Model (HiSBiM) to analyze these omics data. The results indicate that MENS can affect fatty acid metabolism pathways, peroxisome proliferator-activated receptor (PPAR) signaling pathway and cell cycle. Additionally, the DM biochemical indexes and omics data profiles of MENS treatment were found to be consistent. We then compared the therapeutic effects of MENS with anti-diabetic compounds (e.g., quercetin, metformin, and rosiglitazone), using the HiSBiM four-level biological functions and processes of multiple omics data. The results show MENS and these anti-diabetic compounds have similar effect pathways highly correlated to the diabetes processes, such as the PPAR signaling pathway, bile secretion, and insulin signaling pathways. We believe that MENS is an effective and non-invasive therapy for DM and our HiSBiM is an useful method for investigating multiple omics data.

CoMI: consensus mutual information for tissue-specific gene signatures

Background

The gene signatures have been considered as a promising early diagnosis and prognostic analysis to identify disease subtypes and to determine subsequent treatments. Tissue-specific gene signatures of a specific disease are an emergency requirement for precision medicine to improve the accuracy and reduce the side effects. Currently, many approaches have been proposed for identifying gene signatures for diagnosis and prognostic. However, they often lack of tissue-specific gene signatures.

Results

Here, we propose a new method, consensus mutual information (CoMI) for analyzing omics data and discovering gene signatures. CoMI can identify differentially expressed genes in multiple cancer omics data for reflecting both cancer-related and tissue-specific signatures, such as Cell growth and death in multiple cancers, Xenobiotics biodegradation and metabolism in LIHC, and Nervous system in GBM. Our method identified 50-gene signatures effectively distinguishing the GBM patients into high- and low-risk groups (log-rank p = 0.006) for diagnosis and prognosis.

Conclusions

Our results demonstrate that CoMI can identify significant and consistent gene signatures with tissue-specific properties and can predict clinical outcomes for interested diseases. We believe that CoMI is useful for analyzing omics data and discovering gene signatures of diseases.

Uncovering Flexible Active Site Conformations of SARS-CoV-2 3CL Proteases through Protease Pharmacophore Clusters and COVID-19 Drug Repurposing

The infectious SARS-CoV-2 causes COVID-19, which is now a global pandemic. Aiming for effective treatments, we focused on the key drug target, the viral 3C-like (3CL) protease. We modeled a big dataset with 42 SARS-CoV-2 3CL protease-ligand complex structures from ∼98.7% similar SARS-CoV 3CL protease with abundant complex structures. The diverse flexible active site conformations identified in the dataset were clustered into six protease pharmacophore clusters (PPCs). For the PPCs with distinct flexible protease active sites and diverse interaction environments, we identified pharmacophore anchor hotspots. A total of 11 "PPC consensus anchors" (a distinct set observed in each PPC) were observed, of which three "PPC core anchors" EHV2, HV1, and V3 are strongly conserved across PPCs. The six PPC cavities were then applied in virtual screening of 2122 FDA drugs for repurposing, using core anchor-derived "PPC scoring S" to yield seven drug candidates. Experimental testing by SARS-CoV-2 3CL protease inhibition assay and antiviral cytopathic effect assays discovered active hits, Boceprevir and Telaprevir (HCV drugs) and Nelfinavir (HIV drug). Specifically, Boceprevir showed strong protease inhibition with micromolar IC₅₀ of 1.42 μM and an antiviral activity with EC₅₀ of 49.89 μM, whereas Telaprevir showed moderate protease inhibition only with an IC₅₀ of 11.47 μM. Nelfinavir solely showed antiviral activity with a micromolar EC₅₀ value of 3.28 μM. Analysis of binding mechanisms of protease inhibitors revealed the role of PPC core anchors. Our PPCs revealed the flexible protease active site conformations, which successfully enabled drug repurposing.

The inhibitory effects of PGG and EGCG against the SARS-CoV-2 3C-like protease

The coronavirus disease (COVID-19) pandemic, resulting from human-to-human transmission of a novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), has led to a global health crisis. Given that the 3 chymotrypsin-like protease (3CLpro) of SARS-CoV-2 plays an indispensable role in viral polyprotein processing, its successful inhibition halts viral replication and thus constrains virus spread. Therefore, developing an effective SARS-CoV-2 3CLpro inhibitor to treat COVID-19 is imperative. A fluorescence resonance energy transfer (FRET)-based method was used to assess the proteolytic activity of SARS-CoV-2 3CLpro using intramolecularly quenched fluorogenic peptide substrates corresponding to the cleavage sequence of SARS-CoV-2 3CLpro. Molecular modeling with GEMDOCK was used to simulate the molecular interactions between drugs and the binding pocket of SARS-CoV-2 3CLpro. This study revealed that the V_max of SARS-CoV-2 3CLpro was about 2-fold higher than that of SARS-CoV 3CLpro. Interestingly, the proteolytic activity of SARS-CoV-2 3CLpro is slightly more efficient than that of SARS-CoV 3CLpro. Meanwhile, natural compounds PGG and EGCG showed remarkable inhibitory activity against SARS-CoV-2 3CLpro than against SARS-CoV 3CLpro. In molecular docking, PGG and EGCG strongly interacted with the substrate binding pocket of SARS-CoV-2 3CLpro, forming hydrogen bonds with multiple residues, including the catalytic residues C145 and H41. The activities of PGG and EGCG against SARS-CoV-2 3CLpro demonstrate their inhibition of viral protease activity and highlight their therapeutic potentials for treating SARS-CoV-2 infection.

[Research progress of curcumin in the prevention and treatment of periodontitis]

Curcumin is a plant-derived polyphenol extracted from the rhizome of turmeric. As curcumin has such favorable properties as anti-inflammation, anti-oxidation, anti-angiogenesis, immune regulation, anti-bacterial and pro-apoptosis and showed few side effects, the application of curcumin in prevention and treatment of periodontal diseases is promising. This article reviewed the research progress of curcumin in the prevention and treatment of periodontitis.

[Clinical characteristics and survival analysis of 15 cases of HIV-negative plasmablastic lymphoma]

目的

分析HIV阴性的浆母细胞淋巴瘤（PBL）患者的临床病理特征及转归。

方法

回顾性分析海军军医大学附属长海医院2013年1月至2019年8月诊断及治疗的15例HIV阴性PBL患者的临床病理资料及随访结果。

结果

15例HIV阴性PBL患者中男8例，女7例，中位年龄59（17~69）岁，均无明确的免疫抑制状态。所有患者均出现结外受累，Ann Arbor-Cotswolds分期Ⅰ、Ⅱ、Ⅲ、Ⅳ期分别为1例（6.7%）、2例（13.3%）、3例（20.0%）、9例（60.0%）。病理形态表现为类似免疫母细胞的大肿瘤细胞弥漫性增生，免疫组化示肿瘤细胞主要表达浆细胞标志CD38、CD138、Mum-1，B细胞标志CD20、CD10、PAX-5、BCL-6少见，Ki-67中位数为80%（70%~90%）。3例患者行EBER原位杂交检测，1例阳性。15例患者均接受化疗，80%（12/15）联合硼替佐米作为一线治疗。最佳疗效6例完全缓解（其中2例分别于治疗后4.9和26.1个月疾病进展），2例部分缓解（分别于治疗后3.0和6.8个月疾病进展），4例疾病进展，3例无法评估。中位随访时间30.3（4.8~61.1）个月，11例患者中位无进展生存（PFS）期6.8（95%CI 2.5~11.1）个月，预计3年PFS率为21.2%（95%CI 1.4%~56.8%）。所有患者中位总生存（OS）期为17.9（95%CI 5.6~30.2）个月，预计3年OS率为38.5%（95%CI 12.0%~65.0%）。

结论

HIV阴性PBL侵袭性强，结外受累常见，多数患者诊断时分期较晚。通过以硼替佐米为基础的强化疗方案序贯自体造血干细胞移植可望获得长期生存。

Zika Virus NS3 Protease Pharmacophore Anchor Model and Drug Discovery

Zika virus (ZIKV) of the flaviviridae family, is the cause of emerging infections characterized by fever, Guillain-Barré syndrome (GBS) in adults and microcephaly in newborns. There exists an urgent unmet clinical need for anti-ZIKV drugs for the treatment of infected individuals. In the current work, we aimed at the promising virus drug target, ZIKV NS3 protease and constructed a Pharmacophore Anchor (PA) model for the active site. The PA model reveals a total of 12 anchors (E, H, V) mapped across the active site subpockets. We further identified five of these anchors to be critical core anchors (CEH1, CH3, CH7, CV1, CV3) conserved across flaviviral proteases. The ZIKV protease PA model was then applied in anchor-enhanced virtual screening yielding 14 potential antiviral candidates, which were tested by in vitro assays. We discovered FDA drugs Asunaprevir and Simeprevir to have potent anti-ZIKV activities with EC₅₀ values 4.7 µM and 0.4 µM, inhibiting the viral protease with IC₅₀ values 6.0 µM and 2.6 µM respectively. Additionally, the PA model anchors aided in the exploration of inhibitor binding mechanisms. In conclusion, our PA model serves as a promising guide map for ZIKV protease targeted drug discovery and the identified ‘previr’ FDA drugs are promising for anti-ZIKV treatments.

[Inhibitors of RAS Might Be a Good Choice for the Therapy of COVID-19 Pneumonia]

The novel coronavirus 2019 (COVID-19) infected patients by binding human ACE2, leading to severe pneumonia and highly mortality rate in patients. At present, there is no definite and effective treatment for COVID-19. ACE2 plays an important role in the RAS, and the imbalance between ACE/Ang II/AT1R pathway and ACE2/Ang (1-7)/Mas receptor pathway in the RAS system will lead to multi-system inflammation. Increased ACE and Ang II are poor prognostic factors for severe pneumonia. Animal studies have shown that RAS inhibitors could effectively relieve symptoms of acute severe pneumonia and respiratory failure. The binding of COVID-19 and ACE2 resulted in the exhaustion of ACE2, and then ACE2/Ang (1-7)/Mas receptor pathway was inhibited. The balance of the RAS system was broken, and this would lead to the exacerbation of acute severe pneumonia. Therefore, we speculate that ACEI and AT1R inhibitors could be used in patients with COVID-19 pneumonia under the condition of controlling blood pressure, and might reduce the pulmonary inflammatory response and mortality.

[Inhibitors of RAS Might Be a Good Choice for the Therapy of COVID-19 Pneumonia]

The novel coronavirus 2019 (COVID-19) infected patients by binding human ACE2, leading to severe pneumonia and highly mortality rate in patients. At present, there is no definite and effective treatment for COVID-19. ACE2 plays an important role in the RAS, and the imbalance between ACE/Ang II/AT1R pathway and ACE2/Ang (1-7)/Mas receptor pathway in the RAS system will lead to multi-system inflammation. Increased ACE and Ang II are poor prognostic factors for severe pneumonia. Animal studies have shown that RAS inhibitors could effectively relieve symptoms of acute severe pneumonia and respiratory failure. The binding of COVID-19 and ACE2 resulted in the exhaustion of ACE2, and then ACE2/Ang (1-7)/Mas receptor pathway was inhibited. The balance of the RAS system was broken, and this would lead to the exacerbation of acute severe pneumonia. Therefore, we speculate that ACEI and AT1R inhibitors could be used in patients with COVID-19 pneumonia under the condition of controlling blood pressure, and might reduce the pulmonary inflammatory response and mortality.

[Effect of consolidation before allogeneic hematopoietic stem cell transplantation for non-favorable acute myeloid leukemia patients with first complete remisson and negative minimal residual disease]

目的

探讨异基因造血干细胞移植（allo-HSCT）前巩固化疗对第1次形态学完全缓解且微小残留病阴性（CR₁/MRD⁻）中/高危急性髓系白血病（AML）患者预后的影响。

方法

对2010年1月至2019年3月在CR₁/MRD⁻状态下接受allo-HSCT的155例中/高危AML（不含急性早幼粒细胞白血病）患者进行回顾性分析。

结果

全部155例患者中，102例获得CR₁/MRD⁻后接受移植前巩固化疗（巩固组），53例获得CR₁/MRD⁻后直接行allo-HSCT（非巩固组），两组中位年龄分别为39（18~56）岁、38（19~67）岁。巩固组、非巩固组移植后5年总生存率分别为（59.3±7.5）%、（62.2±6.9）%（P=0.919），无复发生存率分别为（53.0±8.9）%、（61.6±7.0）%（P=0.936），累积复发率分别为（21.9±5.4）%、（18.3±6.0）%（P=0.942），非复发死亡率分别为（22.4±4.3）%、（28.4±6.5）%（P=0.464）。多因素分析显示，移植前是否接受巩固化疗及其疗程（<2个/≥2个）对预后无显著影响。

结论

中/高危AML患者可在获得CR₁/MRD⁻后直接进行allo-HSCT。

[Prognostic value of donor chimerism at +90 days after allogeneic hematopoietic stem cell transplantation in young patients with intermediate-risk acute myeloid leukemia]

Objective: To investigate the relationship between donor chimerism and relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Methods: The clinical data of 105 patients with acute myeloid leukemia (AML) who underwent allo-HSCT and recurrence-free survival>90 days from January 2010 to January 2019 were retrospectively analyzed. The bone marrow samples were collected at 15, 30, 60, 90, 180, 270, 360 days after transplantation. Donor chimerism was detected by single nucleotide polymorphism (SNP) -PCR. Results: Of the 105 patients, 43 cases were male and 62 cases were female, with a median age of 38 (16-60) years. Till April 2019, the median follow-up was 843 (94-3 261) days. Ninety days after transplantation, 18 cases relapsed, 33 cases died, and 72 cases survived. The 3-year overall survival (OS) rate was (66.8±5.1) %, and the recurrence-free survival (RFS) rate was (65.1±5.0) %. Pre-transplant disease status, pre-transplant minimal residual disease (MRD) , and 90 day post-transplantation chimerism were independent risk factors related to RFS. The risk of recurrence was significantly increased in patients with a donor chimerism rate ≤97.24% at 90 days after transplantation[HR=6.921 (95%CI 2.669-17.950) , P<0.001], which was considered as a sign of early relapse. Conclusion: SNP-PCR is an applicable method for detecting donor chimerism in patients after allo-HSCT. Chimerism rate equal or less than 97.24% at 90 days after transplantation predicts a higher risk of relapse.

Omics-based Investigation of Diet-induced Obesity Synergized with HBx, Src, and p53 Mutation Accelerating Hepatocarcinogenesis in Zebrafish Model

The primary type of liver cancer, hepatocellular carcinoma (HCC), has been associated with nonalcoholic steatohepatitis, diabetes, and obesity. Previous studies have identified some genetic risk factors, such as hepatitis B virus X antigens, overexpression of SRC oncogene, and mutation of the p53 tumor suppressor gene; however, the synergism between diet and genetic risk factors is still unclear. To investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis, we used zebrafish with four genetic backgrounds and overfeeding or high-fat-diet-induced obesity with an omics-based expression of genes and histopathological changes. The results show that overfeeding and high-fat diet can induce obesity and nonalcoholic steatohepatitis in wild-type fish. In HBx, Src (p53-) triple transgenic zebrafish, diet-induced obesity accelerated HCC formation at five months of age and increased the cancer incidence threefold. We developed a global omics data analysis method to investigate genes, pathways, and biological systems based on microarray and next-generation sequencing (NGS, RNA-seq) omics data of zebrafish with four diet and genetic risk factors. The results show that two Kyoto Encyclopedia of Genes and Genomes (KEGG) systems, metabolism and genetic information processing, as well as the pathways of fatty acid metabolism, steroid biosynthesis, and ribosome biogenesis, are activated during hepatocarcinogenesis. This study provides a systematic view of the synergism between genetic and diet factors in the dynamic liver cancer formation process, and indicate that overfeeding or a high-fat diet and the risk genes have a synergistic effect in causing liver cancer by affecting fatty acid metabolism and ribosome biogenesis.