Pathogenic germline variants in BRCA1 and TP53 increase lung cancer risk in Chinese.

BACKGROUD: Multiple studies have identified pathogenic germline variants in cancer susceptibility genes (CSGs) in Chinese lung cancer patients; however, accurate assessment of these variants' contributions to cancer predisposition is always hampered by the absence of data on the prevalence of these variants in the general population. It is necessary to conduct a large-scale case-control study to identify CSGs that significantly increase the risk of lung cancer. MATERIALS AND METHODS: We performed targeted sequencing of a CSGs panel in 1117 lung cancer patients and 16,327 controls from the general Chinese population. RESULTS: In comparison to controls, lung cancer patients had a considerably higher prevalence of pathogenic and likely pathogenic (P/LP) variations. Among lung cancer patients, 72% of P/LP variants carriers did not have a family cancer history, who would be ignored if germline testing was only provided for patients meeting family history-based criteria. Furthermore, compared to individuals with late-onset lung cancer, patients with early-onset lung cancer had a considerably higher prevalence of P/LP variations. With odds ratios (ORs) ranging from 4-fold (BRCA1: OR, 4.193; 95%CI, 1.382-10.768) to 29-fold (TP53: OR, 29.281; 95%CI, 1.523-1705.506), P/LP variants in the BRCA1 and TP53 genes were discovered to be strongly related to increased lung cancer risk. Additionally, with ORs ranging from 7.322-fold to infinity, we discovered 23 variations previously categorized as non-P/LP variants were highly enriched in lung cancer patients. CONCLUSION: Our findings indicated that P/LP variants in BRCA1 and TP53 conferred increased risk of lung cancer in Chinese.

A MALDI-TOF mass spectrometry-based method for detection of copy number variations in BRCA1 and BRCA2 genes.

Background: Identifying germline mutations in BRCA1 and BRCA2 genes (BRCAs) would benefit the carriers in multiple aspects. In addition to single-nucleotide variations and small indels, copy number variations (CNVs) is also an indispensable component of identifiable mutations in BRCAs. A sensitive, rapid and throughput-flexible method to detect CNVs would be preferred to meet the rising clinical requirements for BRCAs testing. Methods: We developed a MALDI-TOF-MS-based method (MS assay) which included three steps: first, multiplex end-point PCR followed by a single base extension reaction; second, automated analyte transfer and data acquisition; third, data analysis. We applied MS assay to detect CNVs in BRCAs in 293 Chinese patients with ovarian or pancreatic cancer. All the samples were examined by targeted next-generation sequencing (TS) simultaneously. Samples were further cross-validated by multiplex ligation-dependent probe amplification (MLPA) if the results from MS assay and TS were inconsistent. Long range PCR was then applied to identify the exact breakpoints in BRCAs. Results: MS assay introduced highly multiplexed panels to detect CNVs of BRCAs semi-quantitatively. Simplified on-board data analysis was available for MS assay and no complex bioinformatics was needed. The turnaround time of MS assay was less than 8 hours with a hands-on time of only 40 min. Compared to TS, MS assay exhibited higher sensitivity (100% vs. 75%) and was more flexible in throughput, with the reagent cost per sample remaining constant no matter how many samples were examined per assay. A total of eight CNVs in BRCAs were detected from the 293 samples, and the molecular breakpoints were successfully identified in five samples through long-range PCR followed by Sanger sequencing. Conclusion: Our results suggested that MS assay might be an effective method in primary screening for CNVs in genes such as BRCAs, especially when short turnaround time and/or high sensitivity is a top priority.

Constructing a Ring-like Self-Aggregation SERS Sensor with the Coffee Ring Effect for Ultrasensitive Detection and Photocatalytic Degradation of the Herbicides Paraquat and Diquat.

A strategy for building ring-like deposit surface-enhanced Raman scattering (SERS) sensors with the coffee ring effect through the functional modification of the silica nanoparticle surface encapsulated by free-tagged Ag nanoparticles is addressed along with their applications in the SERS-based detection and degradation of target species, including paraquat, diquat, and their free radicals. The nanogap formed by two interparticles with SERS hotspots provides a gigantic amplification signal for the Raman scattering intensity of the analyte molecule located approximately at the hotspots. The enhanced Raman spectrum signals of these target analytes were achieved through the hotspot region of the surface plasmon resonance (SPR) located on the embankment formed by self-aggregation of SiO2@Ag nanoparticles due to the coffee ring effect. Meanwhile, the intrinsic properties of Ag nanoparticles embedded onto the silica surface were applied to photocatalytically degrade the target analytes by harvesting energy from sunlight. The SERS sensor detected the analytes down to 10-9 M in the aqueous solution.

Convergent alteration of lung tissue microbiota and tumor cells in lung cancer.

Microbiota-host interaction plays an important role in cancer predisposing, initiation, progression, and response to therapy. Here, we explored the composition of lung tissue microbiota in 143 Chinese patients through conducting 16S rRNA gene sequencing, while TP53 mutation in tumor cells was assessed simultaneously. We found PAH-degrading microbes were more abundant in lung tumor microbiota from smokers. Furthermore, TP53 mutation was more prevalent in smokers, and TP53-mutated tumor harbored more Massilia, as well as Acidovorax that was also capable of degrading PAH. Further analysis showed DNA recombination and repair pathway was enriched in microbiota of smokers, which was convergent to the alteration occurred in tumor cells. Meanwhile, the microbiota of TP53-mutated tumor also exhibited dysregulation of p53 signaling pathway. Our results provided insights into the association of lung commensal microbes with tobacco exposure and host gene mutation, suggesting microbiota and tumor cells might undergo convergent alteration and mutually benefit each other.

A Novel Aerobic Degradation Pathway for Thiobencarb Is Initiated by the TmoAB Two-Component Flavin Mononucleotide-Dependent Monooxygenase System in Acidovorax sp. Strain T1.

Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. strain T1. Thiobencarb was oxidized and cleaved at the C-S bond, generating diethylcarbamothioic S-acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in the strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28 to 32% identity with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum, alkanesulfonate monooxygenase from Pseudomonas savastanoi, and dibenzothiophene monooxygenase from Rhodococcus sp. TmoB shared 25 to 37% identity with reported flavin reductases and oxidized NADH but not NADPH. TmoAB is a flavin mononucleotide (FMN)-dependent monooxygenase and catalyzed the C-S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC, was located 7,129 bp downstream of tmoAB, and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD+ as a cofactor. A gene cluster responsible for the complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis.IMPORTANCE Microbial degradation is the main factor in thiobencarb dissipation in soil. In previous studies, thiobencarb was degraded initially via N-deethylation, sulfoxidation, hydroxylation, and dechlorination. However, enzymes and genes involved in the microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in Acidovorax sp. strain T1 and identified a novel two-component FMN-dependent monooxygenase system, TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C-S bond, producing diethylcarbamothioic S-acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical, and genetic foundation of thiobencarb degradation in this microorganism.

Sphingobium phenoxybenzoativorans sp. nov., a 2-phenoxybenzoic-acid-degrading bacterium.

A Gram-stain-negative, aerobic, yellow-pigmented, rod-shaped bacterium, designated strain SC_3T, was isolated from pesticide-contaminated soil sediment. The strain was able to mineralize 2-phenoxybenzoic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SC_3T formed a monophyletic lineage in the genus Sphingobium, and showed highest similarity to the type strains of Sphingobium abikonense (97.0 %), followed by Sphingobium lactosutens (96.8 %) and Sphingobium cloacae (96.7 %). The DNA-DNA relatedness between strain SC_3T and its closest phylogenetic neighbours was lower than 70 %. The major fatty acids (>5 % of the total) were summed feature 8 (comprising C18:1ω7c/C18:1ω6c), summed feature 3 (comprising C16:1ω7c/C16:1ω6c), C14:0 2-OH, C16:0 and C17:1ω6c. The predominant quinone was ubiquinone Q-10, and the major polyamine was spermidine. The polar lipid profile contained diphosphatidylglycerol (DPG), sphingoglycolipid (SGL), phosphatidylethanolamine (PDME), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), an unknown aminolipid (AL), two unknown lipids (L1, L2) and several unknown phospholipids (PL1-6). The genomic DNA G+C content of strain SC_3T was 62.9 mol%. On the basis of phenotypic, chemotaxonomic, phylogenetic and genotypic data, strain SC_3T represents a novel species of the genus Sphingobium, for which the name Sphingobium phenoxybenzoativorans sp. nov. is proposed. The type strain is SC_3T ( = CCTCC AB 2014349T = KACC 42448T).