Yan Zhang’s research while affiliated with Aerospace Information Research Institute, Chinese Academy of Sciences and other places

Background Cystic fibrosis (CF) is a common monogenic multisystem disease caused primarily by variants in the CFTR gene. Emerging evidence suggests that some variants, which are described as missense, synonymous or nonsense variants in the literature or databases, may be deleterious by affecting the pre-mRNA splicing process. Methods We analyzed 27 exonic variants in the CFTR gene utilizing bioinformatics tools and identified candidate variants that could lead to splicing changes through minigene assays. Ultimately, we selected eight candidate variants to assess their effects on pre-mRNA splicing. The numbering of DNA variants is based on the complementary DNA (cDNA)sequence of CFTR (Ref Seq NM_000492.4). Results This study assessed the impact of CFTR variants on exon splicing by combining predictive bioinformatics tools with minigene assays. Among the eight candidate single nucleotide alterations, five variants (c.488A>T,c.1117G>T, c.1209G>T, c.3239A>G and c.3367G>C) were identified as causing exon skipping. Conclusion Our study employed a minigene system, which offers great flexibility for assessing aberrant splicing patterns when patient mRNA samples are not accessible, to investigate the effects of exonic variants on pre-mRNA splicing. Our experimental outcomes highlight the importance of analyzing exonic variations at the mRNA level.

Sepsis-induced skeletal muscle atrophy is common in septic patients with the increases risk of mortality and is associated with myocellular mitochondrial dysfunction. Nevertheless, the specific mechanism of sepsis muscle atrophy remains unclear. Here we conducted a clinical retrospective analysis and observed the elevation of skeletal muscle index (ΔSMI) was an independent risk factor for 60-day mortality in septic patients. Moreover, in mouse model of sepsis, the skeletal muscle atrophy was also observed, which was associated with the upregulation of S100a8/a9-mediated mitochondrial dysfunction. Inhibition of S100a8/a9 significantly improved mitochondrial function and alleviated muscle atrophy. Conversely, administration of recombinant S100a8/a9 protein exacerbated mitochondrial energy exhaustion and myocyte atrophy. Mechanistically, S100a8/a9 binding to RAGE induced Drp1 phosphorylation and mitochondrial fragmentation, resulting in muscle atrophy. Additionally, RAGE ablation or administration of Drp1 inhibitor significantly reduced Drp1-mediated mitochondrial fission, improved mitochondrial morphology and function. Our findings indicated the pivotal role of S100a8/a9 in driving the mitochondrial fragmentation in septic muscle atrophy. Targeting S100a8/a9-RAGE-initiated mitochondrial fission might offer a promising therapeutic intervention against septic muscle atrophy.

The application and drug development of plant-derived natural products are often limited by their low abundance in medicinal plants and the lack of structural complexity and diversity. Herein, we design a concise enzyme cascade to efficiently produce natural and unnatural protoberberine alkaloids from cost-effective, readily available substrates. Through enzyme discovery and engineering, along with systematic optimization of the berberine bridge enzyme to address remaining manufacturing challenges in protoberberine alkaloid biosynthesis, the high production of drug Rotundine is achieved at an impressive gram-scale titer, demonstrating its industrial potential. More importantly, this cascade also enables the efficient biosynthesis of various unnatural halogenated protoberberine alkaloids. Thus, this work not only unlocks the potential of enzyme cascades in overcoming longstanding challenges in the efficient biosynthesis of plant-derived alkaloids, but also opens avenues to introduce structural complexity and diversity into alkaloids through synthetic biology, offering significant potential for drug development.

Background Malignant melanoma (MM) is a highly aggressive cancer. Different subtypes have different sensitivities to immunotherapy and lack peripheral blood markers. Few studies have examined the role of inflammatory markers in predicting the overall survival (OS) in stage IV acral melanoma (AM) and cutaneous melanoma (CM) patients receiving immunotherapy. Purpose This study aimed to investigate the value of inflammatory markers in efficacy and prognosis for stage IV melanoma patients who underwent immunotherapy. Patients and Methods This multicenter study reviewed the clinicopathological characteristics and inflammatory markers of 94 stage IV AM and CM patients receiving PD-1 inhibitors therapy. Pearson’s chi-squared test or Fisher’s exact test was used to compare baseline characteristics. The optimal cut-off values for these markers were stratified using time-dependent receiver operating characteristic curves (t-ROC). Kaplan-Meier (KM) curves and Log rank test were used to explore the relationship between inflammatory markers and survival outcomes. Cox regression analysis was performed to screen for independent prognostic factors and a nomogram was constructed. The model ability was tested by the C-index, t-ROC, calibration curves, and decision curve analysis curves. Results High NLR level was significantly correlated with lymph node metastasis and 3 or above metastatic sites (P=0.009, P=0.012). High PNI level favored a better ECOG PS (P=0.023). According to the KM curves, patients with baseline NLR>2.37, PNI<=42.65, and RLR>11.08 had worse OS (P<0.001, P<0.001, P<0.001). Cox regression analysis based on P<0.05 showed that M1c/M1d (P<0.001), NLR (P=0.003), and PNI (P<0.001) were significantly correlated with OS, and were visualized in a nomogram. C-index, t-ROC, area under the curve (AUC), and calibration curves revealed promising discrimination and accuracy of the nomogram. Decision curve analysis curves showed good clinical utility. Conclusion We established a prognostic predictive model based on distant metastatic sites, NLR, and PNI, and verified its superior performance and potential for clinical application.