Methylation- and homologous recombination deficiency-related mutant genes predict the prognosis of lung adenocarcinoma.

BACKGROUND: Lung adenocarcinoma (LUAD) is a lung cancer subtype with poor prognosis. We investigated the prognostic value of methylation- and homologous recombination deficiency (HRD)-associated gene signatures in LUAD. METHODS: Data on RNA sequencing, somatic mutations, and methylation were obtained from TCGA database. HRD scores were used to stratify patients with LUAD into high and low HRD groups and identify differentially mutated and expressed genes (DMEGs). Pearson correlation analysis between DMEGs and methylation yielded methylation-associated DMEGs. Cox regression analysis was used to construct a prognostic model, and the distribution of clinical features in the high- and low-risk groups was compared. RESULTS: Patients with different HRD scores showed different DNA mutation patterns. There were 272 differentially mutated genes and 6294 differentially expressed genes. Fifty-seven DMEGs were obtained; the top 10 upregulated genes were COL11A1, EXO1, ASPM, COL12A1, COL2A1, COL3A1, COL5A2, DIAPH3, CAD, and SLC25A13, while the top 10 downregulated genes were C7, ERN2, DLC1, SCN7A, SMARCA2, CARD11, LAMA2, ITIH5, FRY, and EPHB6. Forty-two DMEGs were negatively correlated with 259 methylation sites. Gene ontology and pathway enrichment analysis of the DMEGs revealed enrichment of loci involved in extracellular matrix-related remodeling and signaling. Six out of the 42 methylation-associated DMEGs were significantly associated with LUAD prognosis and included in the prognostic model. The model effectively stratified high- and low-risk patients, with the high-risk group having more patients with advanced stage disease. CONCLUSION: We developed a novel prognostic model for LUAD based on methylation and HRD. Methylation-associated DMEGs may function as biomarkers and therapeutic targets for LUAD. Further studies are needed to elucidate their roles in LUAD carcinogenesis.

Live HeLa cells preconcentrate and differentiate inorganic arsenic species.

Live HeLa cells immobilized on Sephadex G-50 beads were used as a medium for the preconcentration and speciation of inorganic arsenic. The sorption of arsenic species by live HeLa cells involves both surface uptake and bioaccumulation within the cells. At pH 3.0, the cells accumulate arsenate with high specificity over arsenite: 83.0 +/- 1.3% of the arsenate was sorbed while the retention of arsenite was negligible at 2.1 +/- 0.6%. The speciation of inorganic arsenic could thus be performed by direct determination of arsenate followed by quantifying total inorganic arsenic after conversion of arsenite to arsenate. We formed a disposable live cell preconcentration microcolumn with the live HeLa cells immobilized on Sephadex G-50 beads. After the sample was passed through the column for sorption to occur, the cells and any retained arsenate were stripped with 2 M HNO(3). The arsenic in the 30 microL eluate was directly measured by graphite furnace atomic absorption spectrometry. A new microcolumn was used for each sample. With a sample volume of 450 muL, a S/N = 3 limit of detection (LOD) of 0.05 microg/L and a linear range of 0.15-2.5 microg/L were attained; the relative standard deviation (RSD) was 1.7% at 1.25 microg/L. The procedure was validated by arsenic speciation in certified reference river water.

Cell-sorption of paramagnetic metal ions on a cell-immobilized micro-column in the presence of an external magnetic field.

The cell-sorption of paramagnetic ions of Mn2+ and Cr3+ onto a Chlorella vulgaris (C. vulgaris) cell-immobilized micro-column was significantly improved in the presence of an external magnetic field generated in a finite solenoid, by placing the micro-column in the center of the solenoid in a sequential injection system. Magnetic field creates an opposite drift velocity on the hydrated paramagnetic ions against the flow of the sample zone, retards the moving velocity of the metal ions and provides extra contacting time with the cells on the micro-column and offers more chances for the paramagnetic ions to interact with the various functional groups or binding sites on the cell surface, which significantly facilitates cell-sorption of the paramagnetic ions. The sorption efficiencies of Mn2+ and Cr3+ at the 20 microg L(-1) level were improved from 45 to 80% and 60 to 90%, respectively, in a magnetic field of 240 mT. The system was applied for the separation/preconcentration of ultra-trace level of manganese. The presence of an external magnetic field significantly alleviated the interfering effects from coexisting metal ions. Within a liner range of 0.025-0.5 microg L(-1) and a sampling volume of 500 microL, an enrichment factor of 21.2, a limit of detection of 0.008 microg L(-1), along with a sampling frequency of 20 h(-1) was attained, achieving a precision of 2.1% R.S.D. (0.2 microg L(-1)). Manganese contents in a certified reference material of riverine water and a snow water were analyzed.

Hyphenation of flow injection/sequential injection with chemical hydride/vapor generation atomic fluorescence spectrometry.

The dominant role played by flow injection/sequential injection (FI/SI, including lab-on-valve, LOV) in automatic on-line sample pretreatments coupling to various detection techniques is amply demonstrated by the large number of publications it has given rise to. Among these, its hyphenation with hydride/vapor generation atomic fluorescence spectrometry (HG/VG-AFS) has become one of the most attractive sub-branches during the last years, attributed not only to the high sensitivity of this technique, but also to the superb separation capability of hydride/vapor forming elements from complex sample matrices. In addition, it also provides potentials for the speciation of the elements of interest. It is worth mentioning that quite a few novel developments of sample pretreatment have emerged recently, which attracted extensive attentions from the related fields of research. The aim of this mini-review is thus to illustrate the state-of-the-art progress of implementing flow injection/sequential injection and miniaturized lab-on-valve systems for on-line hydride/vapor generation separation and preconcentration of vapor forming elements followed with detection by atomic fluorescence spectrometry, within the period from 2004 up to now. Future perspectives in this field are also discussed.