Correlation between immunotherapy biomarker PD-L1 expression and genetic alteration in patients with non-small cell lung cancer.

Programmed death-ligand 1 (PD-L1) has been widely used in immunotherapy evaluation of patients with non-small cell lung cancer (NSCLC). However, the effect is not particularly ideal, and the association between PD-L1 and genetic alterations requires more exploration. Here, we performed targeted next-generation sequencing and PD-L1 immunohistochemistry (IHC) testing for PD-L1 expression on both tumor cells (TCs) and tumor-infiltrating immune cells (ICs) in 1549 patients. Our studies showed that surgical method of resection was positively correlated with IC+, and a low tumor mutation burden (TMB) was negatively correlated with TC+. Furthermore, we found that EGFR was mutually exclusive with both ALK and STK11. In addition, the features between PD-L1 expression status and genomic alterations were characterized. These results suggest that clinical characteristics and molecular phenotypes are associated with PD-L1 expression signatures, which may provide novel insights for improving the efficiency of immune checkpoint inhibitors (ICIs) in immunotherapy.

Genome and Transcriptome Identification of a Rice Germplasm with High Cadmium Uptake and Translocation.

The safe production of food on Cd-polluted land is an urgent problem to be solved in South China. Phytoremediation or cultivation of rice varieties with low Cd are the main strategies to solve this problem. Therefore, it is very important to clarify the regulatory mechanism of Cd accumulation in rice. Here, we identified a rice variety with an unknown genetic background, YSD, with high Cd accumulation in its roots and shoots. The Cd content in the grains and stalks were 4.1 and 2.8 times that of a commonly used japonica rice variety, ZH11, respectively. The Cd accumulation in the shoots and roots of YSD at the seedling stage was higher than that of ZH11, depending on sampling time, and the long-distance transport of Cd in the xylem sap was high. Subcellular component analysis showed that the shoots, the cell wall, organelles, and soluble fractions of YSD, showed higher Cd accumulation than ZH11, while in the roots, only the cell wall pectin showed higher Cd accumulation. Genome-wide resequencing revealed mutations in 22 genes involved in cell wall modification, synthesis, and metabolic pathways. Transcriptome analysis in Cd-treated plants showed that the expression of pectin methylesterase genes was up-regulated and the expression of pectin methylesterase inhibitor genes was down-regulated in YSD roots, but there were no significant changes in the genes related to Cd uptake, translocation, or vacuole sequestration. The yield and tiller number per plant did not differ significantly between YSD and ZH11, but the dry weight and plant height of YSD were significantly higher than that of ZH11. YSD provides an excellent germplasm for the exploration of Cd accumulation genes, and the cell wall modification genes with sequence- and expression-level variations provide potential targets for phytoremediation.

China special issue on gastrointestinal tumors-NTRK fusion in a large real-world population and clinical utility of circulating tumor DNA genotyping to guide TRK inhibitor treatment.

Neurotrophic tropomyosin receptor kinase (NTRK) gene fusions are rare oncogenic drivers and targets of TRK inhibitors in solid tumors. Little is known about NTRK fusion in Chinese patients with pan-cancer. Our study investigated the prevalence and genomic features of NTRK1/2/3 gene fusions in 67 883 Chinese patients with pan-cancer using next-generation sequencing (NGS) data and circulating tumor DNA (ctDNA) NGS to guide TRK inhibitor treatment and resistance monitoring. The prevalence of NTRK fusion (tissue NGS) in the pan-cancer population was 0.18%, with 46 unique NTRK-fusion partner pairs, of which 33 were not previously reported. NTRK2 breakpoint occurred more frequently in intron 15 than intron 12. In colorectal cancers (CRCs), compared to NTRK-negative tumors, NTRK-positive tumors displayed higher tumor mutational burden (TMB) levels (54.6 vs 17.7 mut/Mb, P < .0001). In microsatellite instability-high (MSI-H) CRC, patients with NTRK fusion had a significantly lower TMB than NTRK-negative cases (69.3 vs 79.9 mut/Mb, P = .012). The frequency of NTRK fusion in a ctDNA NGS cohort of 20 954 patients with cancer was similar to that of the tissue NGS cohort. In eight NTRK fusion ctDNA-positive patients, larotrectinib induced objective response in 75% of patients and median progression-free survival was 16.3 months. Blood samples collected from a patient with disease progression after larotrectinib treatment revealed NTRK3 G623R as the potential resistance mechanism. Our study revealed previously unreported NTRK fusion partners, associations of NTRK fusion with MSI and TMB, and the potential utility of ctDNA to screen candidates for TRK inhibitors and monitor drug resistance.

Plasma-only circulating tumor DNA analysis detects minimal residual disease and predicts early relapse in hepatocellular carcinoma patients undergoing curative resection.

Background: Minimal residual disease (MRD) is considered an essential factor leading to relapse within 2 years (early relapse) after radical surgery, which is challenging to be detected by conventional imaging. Circulating tumor DNA (ctDNA) provides a novel approach for detecting MRD and predicting clinical outcomes. Here, we tried to construct a fixed panel for plasma-only ctDNA NGS to enable tumor-uninformed MRD detection in hepatocellular carcinoma (HCC). Methods: Here, we performed the followings: (i) profiling genomic alteration spectrum of ctDNA from the Chinese HCC cohort consisting of 493 individuals by NGS; (ii) screening of MRD monitoring genes; and (iii) performance evaluation of MRD monitoring genes in predicting early relapse in the ZJZS2020 cohort comprising 20 HCC patients who underwent curative resection. Results: A total of 493 plasma samples from the Chinese HCC cohort were detected using a 381/733-gene NGS panel to characterize the mutational spectrum of ctDNA. Most patients (94.1%, 464/493) had at least one mutation in ctDNA. The variants fell most frequently in TP53 (45.1%), LRP1B (20.2%), TERT (20.2%), FAT1 (16.2%), and CTNNB1 (13.4%). By customized filtering strategy, 13 MRD monitoring genes were identified, and any plasma sample with one or more MRD monitoring gene mutations was considered MRD-positive. In the ZJZS2020 cohort, MRD positivity presented a sensitivity of 75% (6/8) and a specificity of 100% (6/6) in identifying early postoperative relapse. The Kaplan-Meier analysis revealed a significantly short relapse-free survival (RFS; median RFS, 4.2 months vs. NR, P=0.002) in the MRD-positive patients versus those with MRD negativity. Cox regression analyses revealed MRD positivity as an independent predictor of poor RFS (HR 13.00, 95% CI 2.60-69.00, P=0.002). Conclusions: We successfully developed a 13-gene panel for plasma-only MRD detection, which was effective and convenient for predicting the risk of early postoperative relapse in HCC.

Molecular Landscape of ERBB2 Alterations in 14,956 Solid Tumors.

ERBB2 abnormalities frequently occur and serve as rationale therapeutic targets in cancer. In this study, clinical and next-generation sequencing data from 14,956 patients across more than 20 tumor types were collected. A total of 406 (2.7%) patients were identified with ERBB2 amplifications, and 303 (2.0%) patients with pathogenic somatic ERBB2 mutations. ERBB2 amplifications fell most frequently in breast (15.9%) and stomach (8.3%) cancers. Somatic ERBB2 SNVs/indels occurred most common in bladder/urinary tract (7.3%) and intestine (6.1%) cancers. The top mutated ERBB2 SNVs/indels were p.Y772_A775dup (25.5%) and p.S310F/Y (19.9%). Significantly higher rates of ERBB2 SNV/indels were found in women compared to men (2.8% vs. 1.5%, p < 0.0001). CDK12 was the most common co-amplification gene with ERBB2 in cancers with a high frequency of ERBB2 amplifications. Patients with ERBB2 amplifications or mutations had higher TMB compared with patients with non-ERBB2 alterations. The study provided the landscape of ERBB2 alterations across a variety of solid tumors that may benefit from anti-HER2 agents.

Environment impact and probabilistic health risks of PAHs in dusts surrounding an iron and steel enterprise.

Dust can be regarded as environmental medium that indicates the level and spatial distribution of polycyclic aromatic hydrocarbons (PAHs) coming from different pollution sources. In this study, samples including road dust, roof dust, and bare soil near an iron and steel enterprise (ISE) in Laiwu city of North China were collected. To assess the environment impact, atmosphere particulates and one flue dust from a coking plant were simultaneously sampled. Sixteen USEPA PAHs were detected quantitatively by Gas Chromatography Mass Spectrometry (GC-MS). A laser particle size analyzer was used to obtain the grain size of the dust particle samples. The results showed that PAH concentrations displayed great variability in the dust samples. The ∑16PAHs concentration was found to be between 0.460 and 46.970 µg/g (avg ± sd 10.892 ± 1.185 µg/g) in road dust, between 0.670 and 17.140 µg/g (avg ± sd 6.751 ± 0.692 µg/g) in roof dust, and 13.990 ± 1.203 µg/g in bare soil. In the environment atmosphere sites, the ∑16 PAHs value in PM2.5 constituted a very large proportion of PM10, indicating that PAHs in finer particle sizes should be given greater emphasis. The ∑16PAHs concentration was relatively high in the area close to the ISE because of the great impact of the ISE industrial activities. PAH concentration curves were similar, and the most abundant individual PAHs in the atmosphere sites were BbF, BkF, and Flu, and BbF, BkF, and Chry in dusts. Toxicity analysis revealed that PAHs with four rings, including carcinogenic PAHs, were the dominant pollutants in the studied area. The toxic equivalency value (TEQBaP), the carcinogenic health risk assessment value recommended by the US EPA, was calculated for seven carcinogenic PAHs, revealing that they account for more than 93.0% of the total TEQBap of the 16 PAHs and indicating the major toxic equivalent concentration contributor. Incremental lifetime cancer risk (ILCR) estimation results showed that PAHs tended to bring about great health risks through skin contact, followed by ingestion and inhalation. By comparison, road dust exhibited greater carcinogenic risks than roof dust, and bare soil may undergo heavier pollution. Therefore, the results of this study would be helpful in the effort to understand the PAHs pollution from the steel industry, which will provide some guidance for the probabilistic assessment of local health risks.

Distribution Pattern, Emission Characteristics and Environmental Impact of Polycyclic Aromatic Hydrocarbons (PAHs) in Download Ash and Dust from Iron and Steel Enterprise.

Download ash and emission dust samples were collected from sintering, coking, ironmaking and steelmaking processes of iron and steel enterprises in Laiwu. Sixteen kinds of polycyclic aromatic hydrocarbons (PAHs) in the United States Environmental Protection Agency (USEPA) priority controlled lists were quantitatively analyzed using Gas Chromatography-Mass Spectrometer (GC-MS). Laser particle size analyzer was used to obtain the distribution pattern of download ash. It was found that the diameter distribution pattern from four production processes was quite different. The proportion of fine particulate (0-2.5 µm) was the highest (72.62%) in the steelmaking refining process, and was 28.962% in the ironmaking process. Moreover, the particle size in download ash from steelmaking refining is all less than 10 µm and that from the ironmaking process was 52.92%. The medium-sized particles (10-100 µm) were dominant in sinter and coking download ashes. The total PAHs (∑16PAHs) mass concentration ranged from 0.49 ± 0.06 to 69.63 ± 5.57 µg·g-1 in download ash samples, and varied from 2.815 ± 0.253 to 19.429 ± 2.545 µg·m-3 in emission dust samples. The ∑16PAHs values were both largest in download ash and dust emission from the coking process (69.63 ± 5.57 µg·g-1 and 19.429 ± 2.545 µg·m-3, respectively). The most abundant individual PAHs were benzo[b]fluoranthene, benzo[k]fluoranthene, phenanthrene, benzo[a]anthracene in ash samples, and benzo[a]anthracene, benzo[k]fluoranthene, benzo[b]fluoranthene and indeno[1,2,3-cd]pyrene in emission dust samples. Dominant compounds were high-molecular weight (four- to six-ring) PAHs in both ash and dust samples. The concentration order of individual compounds in PM10 and PM2.5 in ambient air around the steel plant was completely consistent with each other, and the concentration of ∑16PAHs was the highest in the steel plant and lowest in Daqin village because of upwind of the steel plant. The concentrations of benzo[b]fluoranthene and fluoranthene in ambient air were comparatively high, and were in accordance with the higher concentration of the two monomers in the download ash samples, which suggested that the effect of the emission flue gas from the steel plant on ambient air was necessary to concern.

[Determination of five hormone drug residues in fish tissue by high performance liquid chromatography with gel permeation chromatographic clean-up].

A method was developed for the determination of five hormone residues in fish tissue by high performance liquid chromatography (HPLC) with gel permeation chromatographic (GPC) clean-up. The sample was extracted with ethyl acetate-methanol (8:2, v/v). The extract was cleaned-up on a Pharmadex LH-20 gel permeation column (450 mm x 15 mm) and eluted with methanol-ethyl acetate-acetic acid (800:200:2, v/v/v). The analysis was performed on an Agilent TC-C18 column (250 mm x 4. 6 mm, 5 microm) using acetonitrile-water (45:55, v/v) as the mobile phase at a flow rate of 1.2 mL/min and the detection wavelengths were set at 222 nm and 245 nm. All of the 5 hormone residues had good linear relationships (r > 0.999) in the range of 0.05-2.5 mg/L. The limits of detection (LOD) were from 10 to 24 microg/kg. The average recoveries for all the five hormone residues were from 60.1% to 89.0%, with relative standard deviations (RSDs) from 2.0% to 7.4%. The method is simple, rapid, and can be applied for the analysis of the five hormone residues in fish tissue.

The Arabidopsis nitrate transporter NRT1.8 functions in nitrate removal from the xylem sap and mediates cadmium tolerance.

Long-distance transport of nitrate requires xylem loading and unloading, a successive process that determines nitrate distribution and subsequent assimilation efficiency. Here, we report the functional characterization of NRT1.8, a member of the nitrate transporter (NRT1) family in Arabidopsis thaliana. NRT1.8 is upregulated by nitrate. Histochemical analysis using promoter-beta-glucuronidase fusions, as well as in situ hybridization, showed that NRT1.8 is expressed predominantly in xylem parenchyma cells within the vasculature. Transient expression of the NRT1.8:enhanced green fluorescent protein fusion in onion epidermal cells and Arabidopsis protoplasts indicated that NRT1.8 is plasma membrane localized. Electrophysiological and nitrate uptake analyses using Xenopus laevis oocytes showed that NRT1.8 mediates low-affinity nitrate uptake. Functional disruption of NRT1.8 significantly increased the nitrate concentration in xylem sap. These data together suggest that NRT1.8 functions to remove nitrate from xylem vessels. Interestingly, NRT1.8 was the only nitrate assimilatory pathway gene that was strongly upregulated by cadmium (Cd(2+)) stress in roots, and the nrt1.8-1 mutant showed a nitrate-dependent Cd(2+)-sensitive phenotype. Further analyses showed that Cd(2+) stress increases the proportion of nitrate allocated to wild-type roots compared with the nrt1.8-1 mutant. These data suggest that NRT1.8-regulated nitrate distribution plays an important role in Cd(2+) tolerance.