Diagnostic yield of next-generation sequencing in suspect primary immunodeficiencies diseases: a systematic review and meta-analysis.

To determine the diagnostic yield of Next-generation sequencing (NGS) in suspect Primary Immunodeficiencies Diseases (PIDs). This systematic review was conducted following PRISMA criteria. Searching Pubmed and Web of Science databases, the following keywords were used in the search: ("Next-generation sequencing") OR "whole exome sequencing" OR "whole genome sequencing") AND ("primary immunodeficiency disease" OR "PIDs"). We used STARD items to assess the risk of bias in the included studies. The meta-analysis included 29 studies with 5847 patients, revealing a pooled positive detection rate of 42% (95% CI 0.29-0.54, P < 0.001) for NGS in suspected PID cases. Subgroup analyses based on family history demonstrated a higher detection rate of 58% (95% CI 0.43-0.71) in patients with a family history compared to 33% (95% CI 0.21-0.46) in those without (P < 0.001). Stratification by disease types showed varied detection rates, with Severe Combined Immunodeficiency leading at 58% (P < 0.001). Among 253 PID-related genes, RAG1, ATM, BTK, and others constituted major contributors, with 34 genes not included in the 2022 IUIS gene list. The application of NGS in suspected PID patients can provide significant diagnostic results, especially in patients with a family history. Meanwhile, NGS performs excellently in accurately diagnosing disease types, and early identification of disease types can benefit patients in treatment.

Elucidating the estrogen-like effects and biocompatibility of the herbal components in the Qing' E formula.

ETHNOPHARMACOLOGICAL RELEVANCE: The Qing' E Formula (QEF) is a compound preparation that was originally recorded in the 'Prescriptions of the Bureau of Taiping People's Welfare Pharmacy' during the Song Dynasty (10th century CE). It consists of four Chinese medicinal herbs, Eucommiae Cortex (Eucommia ulmoides), Psoraleae Fructus (Psoralea corylifolium), Juglandis Semen (Juglans regia), and Garlic Rhizoma. According to traditional Chinese medicine (TCM), QEF has the ability to tonify the kidney and strengthen muscle and bone. According to the 'kidney governing bone' theory in TCM, QEF is also used to treat the symptoms of climacteric syndrome, especially osteoporosis caused by reduced production of estrogen during the perimenopausal period; however, the therapeutic roles of the individual components of the QEF and their compatibility within the formula has not been investigated. AIM OF THE STUDY: In this study, the compatibility mechanism and estrogen-like action properties of the four herbal components in the QEF was elucidated according to the organizing principle of Chinese medicine formulas using both in vitro and in vivo models. MATERIALS AND METHODS: The estrogen-like effects of QEF and its herbal components were investigated in MCF7 and HEK293 cells as well as ovariectomized (OVX) rats. The estrogen-like effects of the QEF and its components were analyzed in vitro using Cell Counting Kit-8 and Luciferase reporter gene assays. In the in vivo studies, the blood plasma levels of hormones, lipids, neurotransmitters, aromatase, superoxide dismutase (SOD), and malondialdehyde (MDA) were measured through enzyme-linked immunosorbent assays (ELISAs). The histological morphologies of the target organs after exposure to QEF were investigated by HE staining and immunohistochemical methods. The expression levels of estrogen pathway-related proteins and genes in the OVX rats were measured by Western blotting and real time quantitative PCR (RT-qPCR), respectively. RESULTS: The in vitro results showed that the QEF, Eucommia (EC) and Psoralea (PF) promoted the proliferation of MCF-7 cells and upregulated the expression of ERα, ERß and pS2 genes in the MCF-7 cells. Notably, the QEF demonstrated the most active estrogen-like effects compared to the individual ingredients. The in vivo results showed that the QEF, EC, and PF increased the uterine coefficient, upregulated the expression of both ERs (ERα and ERß) in the uterus, and increased blood serum hormone levels. QEF and its individual components ameliorated menopausal-derived lipid metabolism dysfunction, increased neurotransmitter production by stimulating the adrenal glands, enhanced the antioxidant activity in the serum by increasing the concentration of SOD, reversed ovariectomy-derived atrophy in the uterus, and reduced the weight gain associated with estrogen reduction in the OVX rats. The QEF also antagonize the loss of appetite of OVX animals caused by feeding Psoralea alone, which could explain the compatibility mechanism of Qing' E Formula with reducing toxicity and increasing efficiency. CONCLUSIONS: The estrogen-like effects of Eucommia and Psoralea were mainly mediated through activation of ERα and ERß. The phytoestrogen components regulated hormone production and the expression of related proteins and genes, which indicated that these components exhibited estrogen-like therapeutic effects. However, the QEF showed the greatest estrogen-like effects compared to the individual components. Overall, this corroborated the therapeutic prowess of the QEF and clarified the pharmacodynamic interactions between the different components extracts in the QEF.

[Treatment of psoriasis vulgaris using Bacteroides fragilis BF839: a single-arm, open preliminary clinical study].

Psoriasis is considered as an inflammatory disease driven by T cells, and its pathogenesis is closely related to the imbalance of intestinal bacteria flora. It has been reported that Bacteroides fragilis could play an anti-inflammatory role by regulating the expression of cytokines in T cells. To date, there is no report using B. fragilis to treat psoriasis. In this study, we explored the therapeutic effect of B. fragilis BF839 on psoriasis. We selected 27 psoriasis patients who were treated in the Second Affiliated Hospital of Guangzhou Medical University from April to October 2019. The patients were given B. fragilis BF839 orally for 12 weeks while maintaining the original treatment. The psoriasis area and severity index (PASI) score was evaluated before and after the treatment. The rate of drug withdrawal and reduction after 12 weeks of treatment were calculated. Our results showed that the rate of 12-week trial completion was 96.3% (26/27). We used PASIN to define the proportion of people whose PASI score decreased more than or equal to N% after treatment. At 12 weeks, PASI30, PASI50, and PASI75 were 65.4%, 42.3%, and 19.2%, respectively. The PASI score was 9.1±5.9 and 5.8±4.9 before and after 12 weeks of treatment respectively, and the difference was statistically significant (P<0.01). The effective rate of the visual analog scale (VAS) score was 42.3% at 12 weeks, and the VAS score was 2.9±2.2 and 2.3±2.1 before and after 12 weeks of treatment, respectively, which had no statistically significant difference (P>0.05). The adverse reaction rate of patients was 3.8% (1/26) within 12 weeks of treatment, including 1 case of constipation, and the rate of drug withdrawal and reduction was 60.0%. The above results suggest that B. fragilis BF839 may be functional on the treatment of psoriasis by reducing the PASI score and the drug usage rate with few side effect, which deserves further study.

Experimental and molecular docking studies of estrogen-like and anti-osteoporosis activity of compounds in Fructus Psoraleae.

ETHNOPHARMACOLOGICAL RELEVANCE: Fructus Psoraleae (FP), dry mature fruits of Cullen corylifolium (L.) Medik., has been used clinically to treat kidney yang deficiency-induced impotence, asthma and cold pain in waist and knee caused by kidney deficiency. A study of the source of the significant kidney-enhancing effect of FP revealed that it may be due to its strong estrogen-like activity. AIM OF THE STUDY: This study aimed to investigate the estrogen-like activity of the FP extract and 13 bioactive compounds in it, as well as the mechanisms underlying their estrogen-like and anti-osteoporosis activities. MATERIALS AND METHODS: The estrogen-like activities of the 75% ethanol-only FP extract, and 75% ethanol plus petroleum ether, ethyl acetate, n-butanol or water FP extracts were each measured using Cell Counting Kit-8 (CCK-8) and luciferase reporter gene assays. The compounds were identified by high-performance liquid chromatography analysis. The activation of estrogen receptor signaling by the compounds was compared with that by estradiol (E2) using the molecular docking software MOE-Dock 2008.10. The activation of the ER-Wnt-ß-catenin signaling pathway was investigated using an alkaline phosphatase (ALP) assay, qPCR analysis and Western blot analysis. RESULTS: The results revealed that the 75% ethanol plus ethyl acetate extract showed the highest estrogen-like activity among the four 75% ethanol extract fractions (further extracted with petroleum ether, ethyl acetate, n-butanol or water). Some compounds in FP showed strong estrogenic effect and anti-osteoporosis activity, and activated the Wnt-ß-catenin pathway. The isoflavone compound was the most active. CONCLUSIONS: This study demonstrated that FP has a strong estrogen-like activity and some of its component compounds have anti-osteoporosis activity by activating the ER-Wnt-ß-catenin signaling pathway. Our detections provide a new insight into the mechanisms underlying the estrogen-like and anti-osteoporosis activities of FP, as well as a better understanding of structure effects.

Establishment of an induced pluripotent stem cell line (SAHGMUi001-A) from a patient with Netherton syndrome carrying SPINK5 mutation.

Netherton syndrome (NS) is a rare, autosomal recessive hereditary skin disease caused by mutations in SPINK5 gene, characterized with severe skin barrier damage. A human induced pluripotent stem cell (iPSC) line has been established with electroporation method from urine-derived cells of a NS patient carrying a compound heterozygous mutation c.2260A > T (p.K754X) and c.2423C > T(p.T808I) in SPINK5 gene. This iPSC line may serve as a valuable model for the research of pathogenesis of NS, and the mechanisms and therapeutics for skin barrier damage.

Next-Generation Glycan Microarray Enabled by DNA-Coded Glycan Library and Next-Generation Sequencing Technology.

Interactions of glycans with proteins, cells, and microorganisms play important roles in cell-cell adhesion and host-pathogen interaction. Glycan microarray technology, in which multiple glycan structures are immobilized on a single glass slide and interrogated with glycan-binding proteins (GBPs), has become an indispensable tool in the study of protein-glycan interactions. Despite its great success, the current format of the glycan microarray requires expensive, specialized instrumentation and labor-intensive assay and image processing procedures, which limit automation and possibilities for high-throughput analyses. Furthermore, the current microarray is not suitable for assaying interaction with intact cells due to their large size compared to the two-dimensional microarray surface. To address these limitations, we developed the next-generation glycan microarray (NGGM) based on artificial DNA coding of glycan structures. In this novel approach, a glycan library is presented as a mixture of glycans and glycoconjugates, each of which is coded with a unique oligonucleotide sequence (code). The glycan mixture is interrogated by GBPs followed by the separation of unbound coded glycans. The DNA sequences that identify individual bound glycans are quantitatively sequenced (decoded) by powerful next-generation sequencing (NGS) technology, and copied numbers of the DNA codes represent relative binding specificities of corresponding glycan structures to GBPs. We demonstrate that NGGM generates glycan-GBP binding data that are consistent with that generated in a slide-based glycan microarray. More importantly, the solution phase binding assay is directly applicable to identifying glycan binding to intact cells, which is often challenging using glass slide-based glycan microarrays.

Development of a Time-Resolved Fluorescence Resonance Energy Transfer Ultrahigh-Throughput Screening Assay for Targeting the NSD3 and MYC Interaction.

Epigenetic modulators play critical roles in reprogramming of cellular functions, emerging as a new class of promising therapeutic targets. Nuclear receptor binding SET domain protein 3 (NSD3) is a member of the lysine methyltransferase family. Interestingly, the short isoform of NSD3 without the methyltransferase fragment, NSD3S, exhibits oncogenic activity in a wide range of cancers. We recently showed that NSD3S interacts with MYC, a central regulator of tumorigenesis, suggesting a mechanism by which NSD3S regulates cell proliferation through engaging MYC. Thus, small molecule inhibitors of the NSD3S/MYC interaction will be valuable tools for understanding the function of NSD3 in tumorigenesis for potential cancer therapeutic discovery. Here we report the development of a cell lysate-based time-resolved fluorescence resonance energy transfer (TR-FRET) assay in an ultrahigh-throughput screening (uHTS) format to monitor the interaction of NSD3S with MYC. In our TR-FRET assay, anti-Flag-terbium and anti-glutathione S-transferase (GST)-d2, a paired fluorophores, were used to indirectly label Flag-tagged NSD3 and GST-MYC in HEK293T cell lysates. This TR-FRET assay is robust in a 1,536-well uHTS format, with signal-to-background >8 and a Z' factor >0.7. A pilot screening with the Spectrum library of 2,000 compounds identified several positive hits. One positive compound was confirmed to disrupt the NSD3/MYC interaction in an orthogonal protein-protein interaction assay. Thus, our optimized uHTS assay could be applied to future scaling up of a screening campaign to identify small molecule inhibitors targeting the NSD3/MYC interaction.

Aurora kinase A interacts with H-Ras and potentiates Ras-MAPK signaling.

In cancer, upregulated Ras promotes cellular transformation and proliferation in part through activation of oncogenic Ras-MAPK signaling. While directly inhibiting Ras has proven challenging, new insights into Ras regulation through protein-protein interactions may offer unique opportunities for therapeutic intervention. Here we report the identification and validation of Aurora kinase A (Aurora A) as a novel Ras binding protein. We demonstrate that the kinase domain of Aurora A mediates the interaction with the N-terminal domain of H-Ras. Further more, the interaction of Aurora A and H-Ras exists in a protein complex with Raf-1. We show that binding of H-Ras to Raf-1 and subsequent MAPK signaling is enhanced by Aurora A, and requires active H-Ras. Thus, the functional linkage between Aurora A and the H-Ras/Raf-1 protein complex may provide a mechanism for Aurora A's oncogenic activity through direct activation of the Ras/MAPK pathway.