Vitamin D effects on Chlamydia trachomatis infection: a case-control and experimental study.

Introduction: Vitamin D deficiency is the most common nutritional deficiency worldwide. Chronic vitamin D deficiency causes immune system dysfunction, which increases susceptibility to pathogens such as bacteria, especially intracellular parasites, and viruses. Chlamydia trachomatis (C. t) is an obligate intracellular parasitic bacterium that causes a variety of sequelae. We speculated that vitamin D might be associated with C. t infection. This study aimed to address this gap in knowledge by investigating the relationship between vitamin D and C. t infection using both in vitro and in vivo models. Methods and results: The addition of calcitriol to McCoy cell culture in vitro delayed and reduced the quantity and volume of inclusions compared to the control group. Macrophages of peritoneally lavaged mice co-cultured with McCoy decreased the infection rate and delayed the appearance of inclusions. In mice models of vitamin D deficiency, mice in the VD-group exhibited more severe genital tract inflammation and a longer duration of infection after inoculation with C. t in the genital tract. Supplementing these mice with vitamin D3 during treatment enhanced the therapeutic effect of antibiotics. We also conducted a case-control study involving 174 C. t-positive patients (95 males and 79 females) and 380 healthy volunteers (211 males and 169 females) aged 20-49 from January 2016 to March 15, 2017. Serum 25-(OH)D concentration was measured by assessing morning fasting blood samples of healthy volunteers and C. t-positive patients 1 day before antibiotic treatment and the next day after one course of treatment. The patients were followed up for 1 month and evaluated for recovery. The results showed that vitamin D deficiency was a risk factor for C. t infection and treatment failure. Conclusion: In summary, findings from experimental and clinical studies indicate a close association between vitamin D levels and C. t infection and treatment outcomes. Given the affordability and safety of vitamin D, both healthy individuals and patients should focus on vitamin D intake. Vitamin D supplementation could enhance treatment success and should be used as an adjunctive therapy alongside antibiotic therapy for C. t infections, pending confirmation in larger, prospective, randomized controlled trials.

DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock.

A wealth of experimental evidence has suggested that open chromatin regions (OCRs) are involved in many critical biological activities, such as DNA replication, enhancer activity, and gene transcription. Accurately identifying OCRs in livestock species can provide critical insights into the distribution and characteristics of OCRs for disease treatment in livestock, thereby improving animal welfare. However, most current machine-learning methods for OCR prediction were originally designed for a limited number of model organisms, such as humans and some model organisms, and thus their performance on non-model organisms, specifically livestock, is often unsatisfactory. To bridge this gap, we propose DeepOCR, a lightweight depth-separable residual network model for predicting OCRs in livestock, including chicken, cattle, and sheep. DeepOCR integrates a single convolution layer and two improved residue structure blocks to extract and learn important features from the input DNA sequences. A fully connected layer was also employed to further process the extracted features and improve the robustness of the entire network. Our benchmarking experiments demonstrated superior prediction performance of DeepOCR compared to state-of-the-art approaches on testing datasets of the three species. The source code of DeepOCR is freely available for academic purposes at https://github.com/jasonzhao371/DeepOCR/. We anticipate DeepOCR servers as a practical and reliable computational tool for OCR-related studies in livestock species.

Copper-Catalyzed Enantioselective 1,2-Allylation of Azadienes with Allylboronates.

Catalytic asymmetric 1,2-allylation of aurone-derived azadienes is very difficult to achieve due to the driving force for aromatization and the greater steric hindrance of 1,2-addition compared with 1,4-addition. By taking advantage of the ability of nitrogen ligated metal complexes, we successfully demonstrated the first example of copper-catalyzed 1,2-allylation of azadienes with allylboronates for the highly enantioselective synthesis of homoallylic amines. Meanwhile, the enantioenriched 1,4-addition products could also be obtained through a subsequent 3,3-sigmatropic rearrangement of the 1,2-addition products. Extensive DFT calculations were carried out to elucidate the origins of high regioselectivity (1,2- vs 1,4-) and enantioselectivity.

CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data.

MOTIVATION: Effective identification of cell types is of critical importance in single-cell RNA-sequencing (scRNA-seq) data analysis. To date, many supervised machine learning-based predictors have been implemented to identify cell types from scRNA-seq datasets. Despite the technical advances of these state-of-the-art tools, most existing predictors were single classifiers, of which the performances can still be significantly improved. It is therefore highly desirable to employ the ensemble learning strategy to develop more accurate computational models for robust and comprehensive identification of cell types on scRNA-seq datasets. RESULTS: We propose a two-layer stacking model, termed CTISL (Cell Type Identification by Stacking ensemble Learning), which integrates multiple classifiers to identify cell types. In the first layer, given a reference scRNA-seq dataset with known cell types, CTISL dynamically combines multiple cell-type-specific classifiers (i.e. support-vector machine and logistic regression) as the base learners to deliver the outcomes for the input of a meta-classifier in the second layer. We conducted a total of 24 benchmarking experiments on 17 human and mouse scRNA-seq datasets to evaluate and compare the prediction performance of CTISL and other state-of-the-art predictors. The experiment results demonstrate that CTISL achieves superior or competitive performance compared to these state-of-the-art approaches. We anticipate that CTISL can serve as a useful and reliable tool for cost-effective identification of cell types from scRNA-seq datasets. AVAILABILITY AND IMPLEMENTATION: The webserver and source code are freely available at http://bigdata.biocie.cn/CTISLweb/home and https://zenodo.org/records/10568906, respectively.

Copper-Catalyzed Asymmetric Allylation of N-Aryl Aldimines.

The copper-catalyzed enantioselective allylation reaction of N-aryl aldimines has been developed using a combination of Cu(OAc)2 and SPINOL-based phosphonamidite. This protocol significantly broadens the substrate scope, such that imines bearing various ortho-substituents on the N-aryl were converted smoothly into homoallylic amines in up to 99% yield and 98% ee. Taking advantage of the diversity of the N-aryl motif, three kinds of N-heterocyclic compounds were constructed, respectively, from the corresponding homoallylic amines in merely one step.

Nickel-Catalyzed Three-Component Alkylarylation of Alkenyl N-Heteroarenes.

A nickel-catalyzed three-component alkylarylation of alkenyl N-heteroarenes with α-bromocarboxylates and aryl boronic acids is reported. The protocol provides a new method to access a variety of N-heteroarene substituted diarylalkanes in moderate to good yields. It features mild reaction conditions, cheap nickel catalyst, readily available substrates, and broad substrate scope.

Efficacy and Safety of Spesolimab in Patients with Generalized Pustular Psoriasis: A Subgroup Analysis of Chinese Patients in the Effisayil 1 Trial.

INTRODUCTION: Generalized pustular psoriasis (GPP) is a rare and potentially life-threatening skin disease. The global Effisayil 1 study investigated the efficacy and safety of spesolimab, a humanized monoclonal antibody targeting the IL-36 receptor, in patients experiencing GPP flare. This analysis aimed to explore the efficacy and safety of spesolimab in the Chinese subgroup of Effisayil 1. METHODS: Effisayil 1 was a multicenter, randomized, double-blind, placebo-controlled phase II study. Eligible patients with a GPP flare were randomly assigned (2:1) to receive a single intravenous dose of spesolimab (900 mg) or placebo on day 1. On day 8, patients who had persistent symptoms that met a predefined criterion could receive open-label spesolimab. After day 8, patients with recurrent flares following clinical response could receive rescue treatment with open-label spesolimab. The primary end point was a Generalized Pustular Psoriasis Physician Global Assessment (GPPGA) pustulation sub-score of 0 at week 1. The key secondary end point was a GPPGA total score of 0 or 1 at week 1. RESULTS: Eleven Chinese patients were randomized, with five patients receiving spesolimab and six receiving placebo. At week 1, 60.0% (3/5) of patients in the spesolimab group and 16.7% (1/6) of patients in the placebo group achieved a GPPGA pustulation sub-score of 0 (risk difference 43.3%; 95% CI -22.6, 86.2); 60.0% and 16.7% of patients in the spesolimab and placebo group, respectively, achieved a GPPGA total score 0 or 1 (risk difference 43.3%; 95% CI -22.6, 86.2). Overall, four patients in each group of the spesolimab and the placebo groups reported at least one adverse event (AE) by week 1, with two and three reporting drug-related AEs, respectively. One patient reported a serious AE that was not considered to be drug related. No death occurred during the study period. CONCLUSION: In the Chinese subgroup of the Effisayil 1 study, more patients receiving spesolimab experienced lesion clearance than those on placebo at week 1, with an acceptable safety profile that was consistent with the global study population. TRIAL REGISTRATION: NCT03782792.

Single-cell transcriptome analysis indicates fatty acid metabolism-mediated metastasis and immunosuppression in male breast cancer.

Male breast cancer (MBC) is a rare but aggressive malignancy with cellular and immunological characteristics that remain unclear. Here, we perform transcriptomic analysis for 111,038 single cells from tumor tissues of six MBC and thirteen female breast cancer (FBC) patients. We find that that MBC has significantly lower infiltration of T cells relative to FBC. Metastasis-related programs are more active in cancer cells from MBC. The activated fatty acid metabolism involved with FASN is related to cancer cell metastasis and low immune infiltration of MBC. T cells in MBC show activation of p38 MAPK and lipid oxidation pathways, indicating a dysfunctional state. In contrast, T cells in FBC exhibit higher expression of cytotoxic markers and immune activation pathways mediated by immune-modulatory cytokines. Moreover, we identify the inhibitory interactions between cancer cells and T cells in MBC. Our study provides important information for understanding the tumor immunology and metabolism of MBC.

Synthesis of Cyclopenta[b]indoles via Sc(III)-Catalyzed Annulation of Vinyl Diazoacetates with Indole-Derived Unsaturated Imines.

A Lewis acid Sc(OTf)3-catalyzed annulation reaction of vinyl diazoacetates with in situ formed α,ß-unsaturated imines for the preparation of indole-fused tricyclic rings has been reported. This strategy involves a sequential addition/rebound addition process of vinyl diazoacetates and an in situ dedinitrogenation. This annulation protocol features low-cost catalysts, mild reaction conditions, and facilely prepared substrates.

Cyclization of Vinyl Diazo Compounds with Benzofuran-Derived Azadienes Enabled by NaBArF4.

An unprecedented cycloaddition of vinyl diazo compounds with benzofuran-derived azadienes catalyzed by rarely independently used NaBArF4 has been established. Benzofuran-fused hydropyridines were constructed with excellent yields and high diastereoselectivity via a Na+-catalyzed inverse-electron-demand aza-Diels-Alder reaction. Notably, this transformation also features good compatibility with a one-pot protocol to deliver the spiro[benzofuran-cyclopentene] skeleton, as well as perfect atom economy and simple reaction conditions.

Efficacy and Safety of AbobotulinumtoxinA for the Treatment of Glabellar Lines in Chinese Patients: A Pivotal, Phase 3, Randomized, Double-Blind and Open-Label Phase Study.

BACKGROUND: Various botulinumtoxinA formulations are approved for glabellar lines treatment worldwide, including abobotulinumtoxinA (Dysport®). OBJECTIVES: Assess abobotulinumtoxinA superiority versus placebo and non-inferiority versus active comparator (onabotulinumtoxinA; Botox®), for the treatment of Chinese patients with moderate/severe glabellar lines. METHODS: Phase 3, randomized study (NCT02450526) comprising a double-blind (cycle 1) phase and an open-label (cycles 2-5) phase. Patients received abobotulinumtoxinA 50 units or matching placebo (5:1), active comparator (onabotulinumtoxinA 20 units) or matching placebo (5:1). In cycles 2-5, eligible patients were retreated with abobotulinumtoxinA only. Responders had glabellar lines of none/mild severity. PRIMARY ENDPOINT: responder rates at cycle 1, day 29 at maximum frown with abobotulinumtoxinA versus placebo (for superiority; by investigator's live assessment [ILA] and subject's self-assessment [SSA]), and versus active comparator (for non-inferiority; by ILA). Treatment-emergent adverse events were recorded. RESULTS: Overall, 520 patients were randomized. Superiority and non-inferiority, respectively, were demonstrated for abobotulinumtoxinA versus placebo (ILA, SSA; both p < 0.0001) and abobotulinumtoxinA versus active comparator. AbobotulinumtoxinA efficacy was maintained over open-label cycles; median time to onset of efficacy was 2.0 days. After 6 months, 17% of patients treated with abobotulinumtoxinA remained responders. AbobotulinumtoxinA was well-tolerated. Safety results were in line with the known profile of abobotulinumtoxinA; adverse events rate decreased with repeated treatment. CONCLUSIONS: After a single injection, abobotulinumtoxinA demonstrated superiority versus placebo and non-inferiority versus onabotulinumtoxinA for the treatment of moderate-to-severe glabellar lines in Chinese patients. Multiple injections of abobotulinumtoxinA demonstrated efficacy and safety in the treatment of glabellar lines in Chinese patients. LEVEL OF EVIDENCE I: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Botulinum toxin injections can be used to smooth frown lines that appear between the eyebrows (known as glabellar lines) in patients who have moderate or severe frown lines. This study looked at how injections of a botulinum toxin (abobotulinumtoxinA [aboBoNT-A]) could help with smoothing frown lines in patients from China compared with an injection of another botulinum toxin called onabotulinumtoxinA (onaBoNT-A) or placebo (saltwater, no treatment). The study included 520 patients from China, 18­65 years old, who had moderate or severe frown lines. All patients received a first injection of either aboBoNT-A, onaBoNT-A, or saltwater, and were studied for 12 weeks. After the first injection, patients could receive up to four more injections of aboBoNT-A, given at 12-week intervals, if their frown lines became moderate or severe again. Most patients (92%) had not previously received any botulinum toxin injections. The results showed that single and repeat injections of aboBoNT-A helped to smooth moderate and severe frown lines. The researchers found that after a single injection, aboBoNT-A was superior to no treatment and was similar to onaBoNT-A. Patients recorded a response to aboBoNT-A after 2 days and the response lasted for 6 months in 17% of patients. The effect on frown lines was maintained after repeat injections and aboBoNT-A was well tolerated by patients. These results suggest that aboBoNT-A is a suitable treatment for smoothing frown lines in patients from China with moderate to severe frown lines.

MSINGB: A Novel Computational Method Based on NGBoost for Identifying Microsatellite Instability Status from Tumor Mutation Annotation Data.

Microsatellite instability (MSI), a vital mutator phenotype caused by DNA mismatch repair deficiency, is frequently observed in several tumors. MSI is recognized as a critical molecular biomarker for diagnosis, prognosis, and therapeutic selection in several cancers. Identifying MSI status for current gold standard methods based on experimental analysis is laborious, time-consuming, and costly. Although several computational methods based on machine learning have been proposed to identify MSI status, we need to further understand which machine learning model would favor identification for MSI and which feature subset is strongly related to MSI. On this basis, more effective machine learning-based methods can be developed to improve the performance of MSI status identification. In this work, we present MSINGB, an NGBoost-based method for identifying MSI status from tumor somatic mutation annotation data. MSINGB first evaluates the prediction performance of 11 popular machine learning algorithms and 9 deep learning models to identify MSI. Among 20 models, NGBoost, a novel natural gradient boosting method, achieves the overall best performance. MSINGB then introduces two feature selection strategies to find the compact feature subset, which is strongly related to MSI, and employs the SHAP approach to interpreting how selected features impact the model prediction. MSINGB achieves a better prediction performance on both the tenfold cross-validation test and independent test compared with state-of-the-art methods.

GWAS of Chronic Spontaneous Urticaria Reveals Genetic Overlap with Autoimmune Diseases, Not Atopic Diseases.

Although chronic spontaneous urticaria (CSU) is a common disease, GWASs of CSU are lacking. We aimed to identify susceptibility SNPs by performing a GWAS in Chinese Han adults with CSU. The discovery cohort included 430 CSU cases and 482 healthy controls. The GWAS findings were validated in 800 CSU cases and 900 healthy controls. Genetic, functional enrichment, and bioinformatic analyses of genome-wide significant SNPs were performed to assess the association between CSU and autoimmunity or atopy. Five genome-wide significant SNPs were identified: rs434124/LILRA3, rs61986182/IGHG1/2, rs73075571/TDGF1, rs9378141/HLA-G, and rs3789612/PTPN22. The first four SNPs were in linkage disequilibrium with autoimmune-related diseases‒associated SNPs and were cis-expression quantitative trait loci in immune cells. The five SNPs-annotated genes were significantly enriched in immune processes. Higher polygenic risk scores and allele frequencies of rs3789612∗T, rs9378141∗C, and rs73075571∗G were significantly associated with autoimmune-related CSU phenotypes, including positive antithyroglobulin IgG, positive anti-FcεRIα IgG, total IgE <40 IU/ml, and positive antithyroid peroxidase IgG but not with atopic or allergic sensitized CSU phenotypes. This GWAS of CSU identifies five risk loci and reveals that CSU shares genetic overlap with autoimmune diseases and that genetic factors predisposing to CSU mainly manifest through associations with autoimmune traits.

Single-cell RNA sequencing unveils the communications between malignant T and myeloid cells contributing to tumor growth and immunosuppression in cutaneous T-cell lymphoma.

Cutaneous T cell lymphoma (CTCL) is characterized by the accumulation of malignant T cells in the skin. However, advanced CTCL pathophysiology remains elusive and therapeutic options are limited due to the high intratumoral heterogeneity and complicated tumor microenvironment (TME). By comparing the single-cell RNA-seq (scRNA-seq) data from advanced CTCL patients and healthy controls (HCs), we showed that CTCL had a higher enrichment of T/NK and myeloid cells. Subpopulations of T cells (CXCR3+, GNLY+, CREM+, and MKI67+ T cells), with high proliferation, stemness, and copy number variation (CNV) levels, contribute to the malignancy of CTCL. Besides, CCL13+ monocytes/macrophages and LAMP3+ cDC cells were enriched and mediated the immunosuppression via inhibitory interactions with malignant T cells, such as CD47-SIRPA, MIF-CD74, and CCR1-CCL18. Notably, elevated expressions of S100A9 and its receptor TLR4, as well as the activation of downstream toll-like receptor and NF-κB pathway were observed in both malignant cells and myeloid cells in CTCL. Cell co-culture experiments further confirmed that the interaction between malignant CTCL cells and macrophages contributed to tumor growth via S100A9 upregulation and NF-kb activation. Our results showed that blocking the S100A9-TLR4 interaction using tasquinimod could inactivate the NF-κB pathway and inhibit the growth of CTCL tumor cells, and trigger cell apoptosis. Collectively, our study revealed a landscape of immunosuppressive TME mediated by interactions between malignant T cells and myeloid cells, and provided novel targets and potential treatment strategies for advanced CTCL patients.

Natural Coevolution of Tumor and Immunoenvironment in Glioblastoma.

Isocitrate dehydrogenase (IDH) wild-type glioblastoma (GBM) has a dismal prognosis. A better understanding of tumor evolution holds the key to developing more effective treatment. Here we study GBM's natural evolutionary trajectory by using rare multifocal samples. We sequenced 61,062 single cells from eight multifocal IDH wild-type primary GBMs and defined a natural evolution signature (NES) of the tumor. We show that the NES significantly associates with the activation of transcription factors that regulate brain development, including MYBL2 and FOSL2. Hypoxia is involved in inducing NES transition potentially via activation of the HIF1A-FOSL2 axis. High-NES tumor cells could recruit and polarize bone marrow-derived macrophages through activation of the FOSL2-ANXA1-FPR1/3 axis. These polarized macrophages can efficiently suppress T-cell activity and accelerate NES transition in tumor cells. Moreover, the polarized macrophages could upregulate CCL2 to induce tumor cell migration. SIGNIFICANCE: GBM progression could be induced by hypoxia via the HIF1A-FOSL2 axis. Tumor-derived ANXA1 is associated with recruitment and polarization of bone marrow-derived macrophages to suppress the immunoenvironment. The polarized macrophages promote tumor cell NES transition and migration. This article is highlighted in the In This Issue feature, p. 2711.

14-day famciclovir treatment significantly reduces the incidence of postherpetic neuralgia in elderly patients with herpes zoster.

WHAT IS KNOWN AND OBJECTIVE: Pain is the main symptom of herpes zoster (HZ), whilst postherpetic neuralgia (PHN) is a long-term unbearable pain, which seriously affects the quality of life of patients and is also the most intractable problem for clinicians. Early antiviral treatment is considered as a key measure to reduce acute pain and PHN. Nevertheless, most patients still have long-term pain after 7 days of antiviral treatment, and some patients will develop PHN. This study aimed to investigate whether prolonged duration of antiviral therapy could reduce HZ acute pain and the occurrence of PHN. METHODS: The outpatient data of HZ patients over 50 years old who visited the Dermatology Department from January 2016 to May 2018 were retrospectively analysed. According to the different courses of treatment of famciclovir (FCV), the patients were divided into 7-day FCV group and 14-day FCV group. The numerical rating scale (NRS) score at the first visit and on the 7th, 14th and 21st days after the start of treatment, the adverse drug reactions and the incidence of PHN were compared between the two groups. RESULTS: A total of 219 patients were involved in the analysis. For acute pain control, the 14-day FCV group was better than the 7-day FCV group. For patients with mild initial pain, there was no significant difference in NRS between the two treatments. For patients with moderate-to-severe initial pain, the NRS in the 14-day FCV group was significantly lower than that of the 7-day FCV group on the 14th and 21st days after starting treatment. PHN occurred in patients with moderate-to-severe initial pain, and the incidence was significantly lower in the 14-day FCV group than in the 7-day FCV group. There was no significant difference in the number of adverse reactions between the two groups. WHAT IS NEW AND CONCLUSION: Compared with the traditional 7-day antiviral therapy, the 14-day course of FCV can reduce the acute pain and the incidence of PHN in elderly patients with HZ, especially in patients with moderate to severe initial pain. Prolonging the course of medication did not increase the side effects.

Clinical guideline for the diagnosis and treatment of cutaneous warts (2022).

AIM: Cutaneous warts caused by human papillomavirus are benign proliferative lesions that occur at any ages in human lives. Updated, comprehensive and systematic evidence-based guidelines to guide clinical practice are urgently needed. METHODS: We collaborated with multidisciplinary experts to formulate this guideline based on evidences of already published literature, focusing on 13 clinical questions elected by a panel of experts. We adopted Grading of Recommendations Assessment, Development and Evaluation (GRADE) system to form classification of recommendations as well as the improved Delphi method to retain respective recommendations with a consensus degree of over 80%. RESULTS: Our guideline covered aspects of the diagnosis and treatment of cutaneous warts such as diagnostic gold standard, transmission routes, laboratory tests, treatment principle, clinical cure criterion, definitions, and treatments of common warts, flat warts, plantar warts, condyloma acuminatum, and epidermodysplasia verruciformis. Recommendations about special population such as children and pregnant women are also listed. In total, 49 recommendations have been obtained. CONCLUSIONS: It is a comprehensive and systematic evidence-based guideline and we hope this guideline could systematically and effectively guide the clinical practice of cutaneous warts and improve the overall levels of medical services.