Revealing the Genetic Diversity of Chinese Chlamydia trachomatis Strains Directly From Clinical Samples Through Selective Whole Genome Amplification.

BACKGROUND: Chlamydia trachomatis is the causative agent of the most prevalent bacterial sexually transmitted infections globally. Whole genome sequencing is essential for molecular Chlamydia surveillance; however, its application is hampered by the pathogen's low abundance in clinical specimens and the expensive labor-intensive nature of existing enrichment methodologies for Chlamydia. METHODS: We developed a targeted whole genome amplification tool termed SWITCH by integrating phi29 DNA polymerase-mediated amplification with meticulously designed primer sets to enrich the C trachomatis genome, followed by whole genome sequencing. This method underwent evaluation through testing synthetic and clinical specimens. RESULTS: SWITCH demonstrated robust ability to achieve up to 98.3% genomic coverage of C trachomatis from as few as 26.4 genomic copies present in synthetic specimens, and it exhibited excellent performance across diverse C trachomatis serovars. Utilizing SWITCH, we directly generated 21 Chlamydia genomes from 26 clinical samples, enabling us to gain insights into the genetic relationships and phylogeny of current Chlamydia strains circulating in the country. Remarkably, this study marked the first instance of generating Chinese Chlamydia genomes directly from clinical samples. CONCLUSIONS: SWITCH represents a practical cost-efficient approach to enrich the Chlamydia genome directly from clinical specimens, offering an efficient avenue for molecular surveillance of Chlamydia.

A novel prognostic model predicts overall survival in patients with nasopharyngeal carcinoma based on clinical features and blood biomarkers.

This study aims to develop and validate a novel prognostic model to estimate overall survival (OS) in nasopharyngeal carcinoma (NPC) patients based on clinical features and blood biomarkers. We assessed the model's incremental value to the TNM staging system, clinical treatment, and Epstein-Barr virus (EBV) DNA copy number for individual OS estimation. We retrospectively analyzed 519 consecutive patients with NPC. A prognostic model was generated using the Lasso regression model in the training cohort. Then we compared the predictive accuracy of the novel prognostic model with TNM staging, clinical treatment, and EBV DNA copy number using concordance index (C-index), time-dependent ROC (tdROC), and decision curve analysis (DCA). Subsequently, we built a nomogram for OS incorporating the prognostic model, TNM staging, and clinical treatment. Finally, we stratified patients into high-risk and low-risk groups according to the model risk score, and we analyzed the survival time of these two groups using Kaplan-Meier survival plots. All results were validated in the independent validation cohort. Using the Lasso regression, we established a prognostic model consisting of 13 variables with respect to patient prognosis. The C-index, tdROC, and DCA showed that the prognostic model had good predictive accuracy and discriminatory power in the training cohort than did TNM staging, clinical treatment, and EBV DNA copy number. Nomogram consisting of the prognostic model, TNM staging, clinical treatment, and EBV DNA copy number showed some superior net benefit. Based on the model risk score, we split the patients into two subgroups: low-risk (risk score ≤ -1.423) and high-risk (risk score > -1.423). There were significant differences in OS between the two subgroups of patients. Similar results were observed in the validation cohort. The proposed novel prognostic model based on clinical features and serological markers may represent a promising tool for estimating OS in NPC patients.

Upregulation of circ-0000745 in acute lymphoblastic leukemia enhanced cell proliferation by activating ERK pathway.

Acute lymphoblastic leukemia (ALL) is a common hematologic malignancy. Circular RNAs (circRNAs) have been reported as an important factor in regulating cellular process expressed in all hematopoietic compartment. But the molecular mechanism of circRNAs in ALL remain unclear. In this study, we observed circ-0000745 upregulated in leukemia cells (Kasumi-1 and KG-1). Upregulated the expression of circ-0000745 significantly enhanced the proliferation of Kasumi-1 and KG-1 cells, and reduced the ratio of apoptosis cells. Knock down the endogenous expression of circ-0000745 suppressed the cell proliferation and increased the ratio of apoptosis cells. Furthermore, western blot assay showed that overexpression of circ-0000745 increased the activity of ERK1/2. Altogether, these results revealed that upregulated circ-0000745 in leukemia cells could promoter cell viability by increasing the activation of ERK pathway. This study supported the important of circRNAs in the process of acute lymphoblastic leukemia, and provided a new biomarker on ALL diagnosis and therapy.