A Novel Mitochondrial-Related Nuclear Gene Signature Predicts Overall Survival of Lung Adenocarcinoma Patients.

Background: Lung cancer is the leading cause of cancer-related death worldwide, of which lung adenocarcinoma (LUAD) is one of the main histological subtypes. Mitochondria are vital for maintaining the physiological function, and their dysfunction has been found to be correlated with tumorigenesis and disease progression. Although, some mitochondrial-related genes have been found to correlate with the clinical outcomes of multiple tumors solely. The integrated relationship between nuclear mitochondrial genes (NMGs) and the prognosis of LUAD remains unclear. Methods: The list of NMGs, gene expression data, and related clinical information of LUAD were downloaded from public databases. Bioinformatics methods were used and obtained 18 prognostic related NMGs to construct a risk signature. Results: There were 18 NMGs (NDUFS2, ATP8A2, SCO1, COX14, COA6, RRM2B, TFAM, DARS2, GARS, YARS2, EFG1, GFM1, MRPL3, MRPL44, ISCU, CABC1, HSPD1, and ETHE1) identified by LASSO regression analysis. The mRNA expression of these 18 genes was positively correlated with their relative linear copy number alteration (CNA). Meanwhile, the established risk signature could effectively distinguish high- and low-risk patients, and its predictive capacity was validated in three independent gene expression omnibus (GEO) cohorts. Notably, a significantly lower prevalence of actionable EGFR alterations was presented in patients with high-risk NMGs signature but accompanied with a more inflame immune tumor microenvironment. Additionally, multicomponent Cox regression analysis showed that the model was stable when risk score, tumor stage, and lymph node stage were considered, and the 1-, 3-, and 5-year AUC were 0.74, 0.75, and 0.70, respectively. Conclusion: Together, this study established a signature based on NMGs that is a prognostic biomarker for LUAD patients and has the potential to be widely applied in future clinical settings.

Driver gene alterations profiling of Chinese non-small cell lung cancer and the effects of co-occurring alterations on immunotherapy.

BACKGROUND: Molecular testing for alterations in oncogenic driver genes and targeted therapies have become standard procedures for non-small cell lung cancer (NSCLC) patients. However, little evidence has shed light on the pattern of co-existence of driver genes in NSCLC, and whether they may have different tumor features affecting immunotherapy is still unclarified. METHODS: Genomic alterations in 14 lung cancer-related genes were conducted in 3440 Chinese NSCLC patients using next-generation sequencing. Meanwhile, tumor mutational burden and immunotherapy dataset from the Memorial sloan kettering cancer center (MSKCC) and lung adenocarcinoma dataset from The Cancer Genome Atlas (TCGA) were utilized for analyzing the impact of the co-occurring alterations on patients' survival following immunotherapy. RESULTS: In this cohort, 90.17% of patients had at least one somatic alteration in the 14 genes, including 51% of co-occurring alterations. TP53 and epidermal growth factor receptor (EGFR) were the most prevalent genes (54.74% and 53.55%, respectively), followed by KRAS, ERBB2, ALK, PIK3CA, ROS1, RET, MET, BRAF, KIT, FGFR1, PDGFRA, and NRAS. The prevalence of TP53, EGFR, and ERBB2 in our cohort were significantly higher than that from the TCGA database, whereas KRAS, BRAF, and PDGFRA were significantly lower than the latter. Furthermore, the patients who harbored multiple alterations (8.86%, 31/350) in eight driver genes survived longer and have a higher tumor mutation burden compared to the patients with a single alteration. Similar result was found between the patients with co-occurring alteration of EGFR and other driver genes and the patients with single EGFR alteration. Meanwhile, we found a distinct immune cell infiltration feature between patients with single and multiple driver gene alterations, as well as between patients with only EGFR alteration and co-occurring groups. CONCLUSION: This study identified a unique driver gene feature and found patients harboring co-occurring alterations of EGFR and other driver genes may benefit from immunotherapy, which may provide more therapeutic selections for EGFR-mutated NSCLC patients and merit additional investigation.

Preliminary assessment of nanopore-based metagenomic sequencing for the diagnosis of prosthetic joint infection.

OBJECTIVES: Pathogen identification is crucial for the diagnosis and management of periprosthetic joint infection (PJI). Although culturing methods are the foundation of pathogen detection in PJI, false-negative results often occur. Oxford nanopore sequencing (ONS) is a promising alternative for detecting pathogens and providing information on their antimicrobial resistance (AMR) profiles, without culturing. METHODS: To evaluate the capability of metagenomic ONS (mONS) in detecting pathogens from PJI samples, both metagenomic next-generation sequencing (mNGS) and mONS were performed in 15 osteoarticular samples from nine consecutive PJI patients according to the modified Musculoskeletal Infection Society (MSIS) criteria. The sequencing data generated from both platforms were then analyzed for pathogen identification and AMR detection using an in-house-developed bioinformatics pipeline. RESULTS: Our results showed that mONS could be applied to detect the causative pathogen and characterize its AMR features in fresh PJI samples. By real-time sequencing and analysis, pathogen identification and AMR detection from the initiation of sequencing were accelerated. CONCLUSION: We showed proof of concept that mONS can function as a rapid, accurate tool in PJI diagnostic microbiology. Despite efforts to reduce host DNA, the high proportion of host DNA was still a limitation of this method that prevented full genome analysis.

Anti-influenza A virus mechanism of three representative compounds from Flos Trollii via TLRs signaling pathways.

ETHNOPHARMACOLOGICAL RELEVANCE: Flos Trollii is the dried flowers of Trollius chinensis. It has been used as a traditional herbal medicine for the treatment of upper respiratory tract infection, tonsillitis and pharyngitis in China for a long history. Veratric acid, vitexin, and trolline are the representative compounds of phenolic acids, flavonoids and alkaloids in this herbal medicine. All of these three compounds show antiviral activity which is related to the efficacy of Flos Trollii. AIM OF THE STUDY: To investigate the anti-influenza A virus mechanism of the three representative compounds from the perspective of regulating TLRs signaling pathways, so as to understand the relevant efficacy of Flos Trollii. MATERIALS AND METHODS: Influenza A virus A/FM/1/47 (H1N1) and mouse peritoneal macrophages (RAW264.7) were used in the whole process of investigation. MTT assay was conducted to select the appropriate experimental concentrations of the three compounds on RAW264.7 cells. Western blot, RT-PCR, and ELISA assays were performed to determine the protein and mRNA expression of key factors and related inflammatory factors of TLRs signaling pathways. Griess method was employed to detect the production of NO. RESULTS: The three representative compounds reduced the inflammatory factors including NO, IL-6, and TNF-α and enhanced the production of IFN-ß through dynamically regulating the TLRs 3, 4 and 7 pathways. Veratric acid significantly down-regulated the protein expression of TLR3 and IRF3 as well as the mRNA expression of TBK1 and TRIF. Vitexin significantly down-regulated the protein expression of TBK1 and IRF3 as well as the mRNA expression of TLR3, TBK1, TRIF and IRF3 while up-regulated the protein expression of TLR4 and IKKα. Trolline significantly down-regulated the protein expression of TLR7 whereas significantly up-regulated the protein expression of TLR4, IKKα and TAK1. CONCLUSIONS: The three representative compounds from Flos Trollii play their parts in anti-H1N1 viral effect through partially down-regulating TLRs 3 and 7 pathways and up-regulating TLR4 pathway. They counteract the inflammatory injury caused by excessive production of NO, IL-1, IL-6, and TNF-α induced by virus infection and enhance the production of IFN-ß so as to eliminate the virus.

Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing.

OBJECTIVES: Identification of the underlying pathogens of infective endocarditis (IE) is critical for precision therapy. METHODS: We evaluated a metagenomic method with next-generation sequencing (NGS) for the direct detection of pathogens from the resected valves of 44 IE patients and seven rejected IE patients according to the modified Duke criteria. RESULTS: NGS displayed sensitivity, specificity, positive predictive values and negative predictive values of 97.6%, 85.7%, 97.6%, and 85.7% compared with 46.2%, 100%, 100%, and 12.5% for blood culture and 17.1%, 100%, 100%, and 17.1% for valve culture and 51.4%, 100%, 100%, and 26.1% for valve Gram staining, respectively. CONCLUSIONS: NGS technique had superior sensitivity and shorter turnaround time compared with culture-based methods for identifying causative pathogens of IE. The NGS technology should be considered an essential supplement to culture-based methods, particularly for unculturable or difficult-to-culture microorganisms.

Investigation of the effective components of the flowers of Trollius chinensis from the perspectives of intestinal bacterial transformation and intestinal absorption.

CONTEXT: The flowers of Trollius chinensis Bunge (Ranunculaceae), used for respiratory tract infections, mainly contain flavonoids, phenolic acids, and alkaloids; however, the effective components are debatable because of their unclear in vivo activities. OBJECTIVE: This study investigates the effective components from the perspectives of biotransformation and absorption. MATERIALS AND METHODS: Both single person derived- and multiple people-derived intestinal florae were used to investigate the biotransformation of aqueous extract of the flowers of T. chinensis (AEOF) at the concentrations of 15.0, 30.0, and 60.0 mg/mL, respectively, for 72 h. Both human colon adenocarcinoma cell line (Caco-2) monolayers and everted gut sacs were employed to evaluate the intestinal absorption of the intestinal bacterial transformed AEOF at the concentrations of 10, 20, and 30 mg/mL, respectively, for 180 min. RESULTS: 2″-O-ß-l-Galactopyranosylorientin, orientin, vitexin, quercetin, veratric acid, proglobeflowery acid, and trolline in AEOF were not transformed by intestinal bacteria, while isoquercetin and trollioside were completely transformed. The Papp values of 2″-O-ß-l-galactopyranosylorientin, orientin, and vitexin calculated based on the experimental data of intestinal absorption were at the levels of 10-5, whereas those of veratric acid, proglobeflowery acid, and trolline were at 10-4. The mass ratio of flavonoids to phenolic acids to alkaloids changed from 16:10:7 to 9:12:8 before and after absorption. DISCUSSION AND CONCLUSION: The dominant position of flavonoids was replaced by phenolic acids after absorption. In addition to flavonoids which are usually considered as the dominant effective ones, phenolic acids and alkaloids should be also very important for the efficacy of these flowers.

Transformation of trollioside and isoquercetin by human intestinal flora in vitro.

The present study was designed to determine the intestinal bacterial metabolites of trollioside and isoquercetin and their antibacterial activities. A systematic in vitro biotransformation investigation on trollioside and isoquercetin, including metabolite identification, metabolic pathway deduction, and time course, was accomplished using a human intestinal bacterial model. The metabolites were analyzed and identified by HPLC and HPLC-MS. The antibacterial activities of trollioside, isoquercetin, and their metabolites were evaluated using the broth microdilution method with berberine as a positive control, and their potency was measured as minimal inhibitory concentration (MIC). Our results indicated that trollioside and isoquercetin were metabolized by human intestinal flora through O-deglycosylation, yielding aglycones proglobeflowery acid and quercetin, respectively The antibacterial activities of both metabolites were more potent than that of their parent compounds. In conclusion, trollioside and isoquercetin are totally and rapidly transformed by human intestinal bacteria in vitro and the transformation favors the improvement of the antibacterial activities of the parent compounds.