Table1_Prognosis-related genes participate in immunotherapy of renal clear cell carcinoma possibly by targeting dendritic cells.XLSX

Tumor immunotherapy has become one of the most promising approaches to tumor treatment. This study aimed to screen genes involved in the response of clear cell renal cell carcinoma (ccRCC) to immunotherapy and analyze their function. Based on the Gene Expression Omnibus and The Cancer Genome Atlas datasets, we screened out nine differentially expressed genes (TYROBP, APOC1, CSTA, LY96, LAPTM5, CD300A, ALOX5, C1QA, and C1QB) associated with clinical traits and prognosis. A risk signature constructed by these nine genes could predict the survival probability for patients at 1 year, 3 years, and 5 years. The immune checkpoint blockade response rate in the high-risk group was significantly higher than in the low-risk group (49.25% vs. 24.72%, p ≤ 0.001). The nine prognosis-related genes were negatively correlated with activated dendritic cells in the low-risk group but not in the high-risk group. qRT-PCR, immunohistochemistry, and immunofluorescence showed that the nine prognosis-related genes were associated with dendritic cell activity and the PD-1 positive staining rate. In conclusion, the nine prognosis-related genes have a high prognostic value. The patients in the high-risk group were more likely to benefit from immunotherapy, and the mechanism might be related to the release of dendritic cell-mediated immunosuppression.</p

Table5_Prognosis-related genes participate in immunotherapy of renal clear cell carcinoma possibly by targeting dendritic cells.XLSX

Tumor immunotherapy has become one of the most promising approaches to tumor treatment. This study aimed to screen genes involved in the response of clear cell renal cell carcinoma (ccRCC) to immunotherapy and analyze their function. Based on the Gene Expression Omnibus and The Cancer Genome Atlas datasets, we screened out nine differentially expressed genes (TYROBP, APOC1, CSTA, LY96, LAPTM5, CD300A, ALOX5, C1QA, and C1QB) associated with clinical traits and prognosis. A risk signature constructed by these nine genes could predict the survival probability for patients at 1 year, 3 years, and 5 years. The immune checkpoint blockade response rate in the high-risk group was significantly higher than in the low-risk group (49.25% vs. 24.72%, p ≤ 0.001). The nine prognosis-related genes were negatively correlated with activated dendritic cells in the low-risk group but not in the high-risk group. qRT-PCR, immunohistochemistry, and immunofluorescence showed that the nine prognosis-related genes were associated with dendritic cell activity and the PD-1 positive staining rate. In conclusion, the nine prognosis-related genes have a high prognostic value. The patients in the high-risk group were more likely to benefit from immunotherapy, and the mechanism might be related to the release of dendritic cell-mediated immunosuppression.</p

Key Role of Persistent Free Radicals in Hydrogen Peroxide Activation by Biochar: Implications to Organic Contaminant Degradation

We investigated the activation of hydrogen peroxide (H₂O₂) by biochars (produced from pine needles, wheat, and maize straw) for 2-chlorobiphenyl (2-CB) degradation in the present study. It was found that H₂O₂ can be effectively activated by biochar, which produces hydroxyl radical (^•OH) to degrade 2-CB. Furthermore, the activation mechanism was elucidated by electron paramagnetic resonance (EPR) and salicylic acid (SA) trapping techniques. The results showed that biochar contains persistent free radicals (PFRs), typically ∼10¹⁸ unpaired spins/gram. Higher trapped [^•OH] concentrations were observed with larger decreases in PFRs concentration, when H₂O₂ was added to biochar, indicating that PFRs were the main contributor to the formation of ^•OH. This hypothesis was supported by the linear correlations between PFRs concentration and trapped [^•OH], as well as <i>k</i>_obs of 2-CB degradation. The correlation coefficients (<i>R</i>²) were 0.723 and 0.668 for PFRs concentration vs trapped [^•OH], and PFRs concentration vs <i>k</i>_obs, respectively, when all biochars pyrolyzed at different temperatures were included. For the same biochar washed by different organic solvents (methanol, hexane, dichloromethane, and toluene), the correlation coefficients markedly increased to 0.818–0.907. Single-electron transfer from PFRs to H₂O₂ was a possible mechanism for H₂O₂ activation by biochars, which was supported by free radical quenching studies. The findings of this study provide a new pathway for biochar implication and insight into the mechanism of H₂O₂ activation by carbonaceous materials (e.g., activated carbon and graphite)

A Mechanistic Understanding of Hydrogen Peroxide Decomposition by Vanadium Minerals for Diethyl Phthalate Degradation

The interaction of naturally occurring minerals with H₂O₂ affects the remediation efficiency of polluted sites in in situ chemical oxidation (ISCO) treatments. However, interactions between vanadium­(V) minerals and H₂O₂ have rarely been explored. In this study, H₂O₂ decomposition by various vanadium-containing minerals including V­(III), V­(IV), and V­(V) oxides was examined, and the mechanism of hydroxyl radical (^•OH) generation for contaminant degradation was studied. Vanadium minerals were found to catalyze H₂O₂ decomposition efficiently to produce ^•OH for diethyl phthalate (DEP) degradation in both aqueous solutions with a wide pH range and in soil slurry. Electron paramagnetic resonance (EPR), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) analyses, and free radical quenching studies suggested that ^•OH was produced via single electron transfer from V­(III)/V­(IV) to H₂O₂ followed a Fenton-like pathway on the surface of V₂O₃ and VO₂ particles, whereas the oxygen vacancy (OV) was mainly responsible for ^•OH formation on the surface of V₂O₅ particles. This study provides new insight into the mechanism of interactions between vanadium minerals and H₂O₂ during H₂O₂-based ISCO

Reductive Hexachloroethane Degradation by S₂O₈^•– with Thermal Activation of Persulfate under Anaerobic Conditions

Despite that persulfate radical (S₂O₈^•–) is an important radical species formed from the persulfate (PS) activation process, its reactivity toward contaminant degradation has rarely been explored. In this study, we found that S₂O₈^•– efficiently degrades the contaminant hexachloroethane (HCA) under anaerobic conditions, whereas HCA degradation is negligible in the presence of oxygen. We observed dechlorination products such as pentachloroethane, tetrachloroethylene, and Cl^– during HCA degradation, which suggest that HCA degradation is mainly a reductive process under anaerobic conditions. Using free radical quenching and electron paramagnetic resonance (EPR) experiments, we confirmed that S₂O₈^•– forms from the reaction between sulfate radical (SO₄^•–) and S₂O₈^2–, which are the dominant reactive species in HCA degradation. Density functional theory (DFT) calculations were used to elucidate the pathways of HCA degradation and S₂O₈^•– radical decomposition. Further investigation showed that S₂O₈^•– can efficiently degrade HCA and DDTs in soil via reduction during the thermal activation of PS under anaerobic conditions. The finding of this study provide a novel strategy for the reductive degradation of contaminant when PS-based in situ chemical oxidation used in the remediation of soil and groundwater, particularly those contaminated with highly halogenated compounds

Fate of As(III) and As(V) during Microbial Reduction of Arsenic-Bearing Ferrihydrite Facilitated by Activated Carbon

Microbial reduction of arsenic (As)-bearing Fe­(III)-(oxyhydr)­oxides is one of the major processes for the release of As in various environmental settings such as acid mine drainage, groundwater, and flooded paddy soil. Pyrogenic carbon has recently been reported to facilitate microbial extracellular reduction of Fe­(III)-(oxyhydr)­oxides. The aim of this study was to investigate the important hot topic regarding the fate and transformation of As during activated carbon (AC) facilitated microbial reduction of As-bearing ferrihydrite. Our results show that the rate and extent of Fe­(III) reduction in As-bearing ferrihydrite by <i>Shewanella oneidensis</i> MR-1 were accelerated by AC. The AC facilitated reduction caused the release of As­(III) into the solution, whereas it caused the preferential immobilization of As­(V) on the solid phase. Furthermore, AC accelerated the precipitation of vivianite and siderite in sequence during microbial reduction processes. Both of the formed vivianite and siderite had an insignificant capacity for capturing As­(III); however, As­(V) was selectively immobilized by vivianite compared to that of siderite. Taken together, our findings provide crucial insights into understanding the role of AC on the redox and immobilization of Fe and As in suboxic and anoxic environments and thus their environmental fate when pyrogenic carbons are employed for agronomic and environmental applications

Intracellular localization of SP-A2 wild-type and variants.

<p>CHO-K1 Cells were transiently transfected with SP-A2 wild-type, G231V, F198S, Q223K plasmids, 48 h after transfection, the cells were fixed by 4% PFA, the localization of SP-A2 was examined by indirect immunofluorescence assay, and images were collected by confocal microscopy as described in Materials and Methods. Wild-type and Q223K distributed evenly in cellular which colocalized in part with calreticulin (ER marker) (<b>H,T</b>). Most of G231V, F198S mutants colocalized with calreticulin (<b>L,P</b>). Scale bar 10 µm.</p

Expression of SP-A2 wild-type and mutant protein and mRNA in CHO-K1 cells.

<p>(<b>A</b>) SP-A2 schematic. SP-A2 is tagged with V5 epitope at amino acid position 21 follow the signal sequence, four functional domains are indicated, and various mutations are also listed. <b>CRD</b>, carbohydrate recognition domain. (<b>B</b>) CHO-K1 cells were transiently transfected with vector (pcDNA3.0), V5-tagged SP-A2 wild-type, G231V, F198S and Q223K variants full-length cDNA plasmids. Forty-eight hours after transfection, equal amounts of total protein from cell lysate or media were subjected to SDS-PAGE and followed by immunoblot analysis using a monoclonal antibody that recognizes the V5 epitope. (<b>C</b>) Stably expressing vector, V5-tagged SP-A2 wild-type, G231V, F198S and Q223K variants in CHO-K1 cells. 5×10⁵ cells/well were seeded and cultured in 6-well plate for 48 h, cell lysate and medium were collected and analyzed by SDS-PAGE and western blotting. (<b>D</b>) CHO-K1 cells were transiently transfected with plasmids pcDNA3.0, V5-tagged SP-A2 wild-type, G231V, F198S and Q223K variants. Forty-eight hours later, total RNA was extracted and RT-PCR was performed using primers specific to SP-A2 and GAPDH gene.</p

Analysis of glycosylation modifications of human SP-A2 in cell lysate and medium.

<p>CHO-K1 Cells were transiently expressed SP-A2 wild-type, G231V, F198S or d (100–133) plasmids for 48 h and the cell lysate (<b>A and C</b>) or medium (<b>B</b>) were treated without or with (+) PNGase F, Endo H, Neuraminidase, O-glycosidase as described in Materials and methods. Digestion products were subjected to SDS-PAGE, transferred to NC membranes, immunoblotted with anti-V5 antibody. <b>a</b>.Mature and sialylated SP-A2 protein. <b>b.</b> Desialylated SP-A2. <b>c.</b> Immature N-glycosylated SP-A2, but not sialylated. <b>d.</b> Deglycosylated SP-A2. Presence and linkage patterns of terminally linked sialic acids on mature secreted SP-A2 from medium were further analyzed by immuoprecipitation and Western blotting, followed by detection with digoxigenin-labeled lectins and anti-digoxigenin-alkaline phosphatase system (<b>D and E</b>). To assess lectin binding efficiency and specificity both positive control glycoproteins (fetuin for <i>α</i>(2,3)-linkage and transferrin for <i>α</i>(2,6)-linkage) and negative control (N-Glycosidase F treated transferrin) were included.</p

SP-A2 G231V, F198S proteins partially degraded through proteasome pathway but not lysosome or autophagy pathway.

<p>(<b>A–D</b>) CHO-K1 Cells were transiently expressed SP-A2 wild-type, G231V, F198S, Q223K plasmids, 24 h later change medium and treated the cell with ALLN (<b>A</b>), MG-132 (<b>B</b>), 3-MA (<b>C</b>), leupeptin (<b>D</b>) for 24 h, then cell lysate and medium were collected, analyzed by SDS-PAGE and western blotting. (<b>E</b>) SP-A2 Neck region (100–133) mutant expression is increased by inhibition of proteasome pathway but not lysosome or autophagy pathway. The amount of each SP-A variant was normalized to its expression in the absence of inhibitors. Data are shown as the mean±S.D. for at least three independent transfection experiments.</p