Comprehensive application of AI algorithms with TCR NGS data for glioma diagnosis.

T-cell receptor (TCR) detection can examine the extent of T-cell immune responses. Therefore, the article analyzed characteristic data of glioma obtained by DNA-based TCR high-throughput sequencing, to predict the disease with fewer biomarkers and higher accuracy. We downloaded data online and obtained six TCR-related diversity indices to establish a multidimensional classification system. By comparing actual presence of the 602 correlated sequences, we obtained two-dimensional and multidimensional datasets. Multiple classification methods were utilized for both datasets with the classification accuracy of multidimensional data slightly less to two-dimensional datasets. This study reduced the TCR ß sequences through feature selection methods like RFECV (Recursive Feature Elimination with Cross-Validation). Consequently, using only the presence of these three sequences, the classification AUC value of 96.67% can be achieved. The combination of the three correlated TCR clones obtained at a source data threshold of 0.1 is: CASSLGGNTEAFF_TRBV12_TRBJ1-1, CASSYSDTGELFF_TRBV6_TRBJ2-2, and CASSLTGNTEAFF_TRBV12_TRBJ1-1. At 0.001, the combination is: CASSLGETQYF_TRBV12_TRBJ2-5, CASSLGGNQPQHF_TRBV12_TRBJ1-5, and CASSLSGNTIYF_TRBV12_TRBJ1-3. This method can serve as a potential diagnostic and therapeutic tool, facilitating diagnosis and treatment of glioma and other cancers.

Gelatin-Functionalized Carbon Nanotubes Loaded with Cisplatin for Anti-Cancer Therapy.

Cisplatin (Cp), a chemotherapeutic agent, interacts with purines on tumor DNA, causing tumor cell apoptosis. However, cisplatin has the characteristics of non-specific distribution and lack of selectivity, resulting in systemic toxicity. Moreover, it cannot maintain the drug's high concentration in the tumor-weak acid environment. These flaws of cisplatin restrict its use in clinical applications. Therefore, a pH-responsive carbon nanotube-modified nano-drug delivery system (CNTs/Gel/Cp) was constructed in this study using gelatin (Gel)-modified carbon nanotubes (CNTs/Gel) loaded with cisplatin to release drugs precisely and slowly, preventing premature inactivation and maintaining an effective concentration. When MCp:MCNTs/Gel = 1:1, the drug reaches the highest loading rate and entrapment efficiency. To achieve the sustained-release effect, CNTs/Gel/Cp can release the medicine steadily for a long time in a pH environment of 6.0. Additionally, CNTs/Gel/Cp display antitumor properties comparable to cisplatin in a manner that varies with the dosage administered. These findings indicate that CNTs/Gel/Cp have an effective, sustained release of cisplatin and a good antitumor effect, providing a theoretical and experimental basis for the clinical application of modified carbon nanotubes (CNTs) as a new drug delivery system.

Chlorogenic acid alleviates thioacetamide-induced toxicity and promotes liver development in zebrafish (Danio rerio) through the Wnt signaling pathway.

Chlorogenic acid (CGA) is a phenylpropanoid compound that is well known to improve the antioxidant capacity and other biological activities. However, the roles of CGA in the liver development of organisms are unclear. In the present study, we aimed to investigate the function of CGA in the hepatic development in thioacetamide (TAA)-induced zebrafish embryos. We found that CGA exerted certain beneficial effects on zebrafish larvae from TAA-exposed zebrafish embryos, such as increasing the liver size, body length, heart rate, acetylcholinesterase activity, and motor ability. In addition, CGA displayed an antioxidant effect on TAA-induced zebrafish embryos by enhancing the activities of superoxide dismutase (SOD), catalase (CAT), and glucose-6-phosphate dehydrogenase (G6PDH), and decreasing of the contents of malondialdehyde (MDA), reactive oxygen species (ROS), and nitric oxide (NO). The results of western blotting analysis showed that CGA inhibited cell apoptosis by increasing the levels of Bcl2 apoptosis regulator and decreasing the levels of Bcl2 associated X (Bax), apoptosis regulator and tumor protein P53. Moreover, CGA promoted cell proliferation in TAA-induced zebrafish larvae, as detected using proliferating cell nuclear antigen fluorescence immunostaining. In addition, CGA inhibited the expression of Wnt signaling pathway genes Dkk1 (encoding Dickkopf Wnt signaling pathway inhibitors), and promoted the expression of Lef1 (encoding lymphoid enhancer binding factor 1) and Wnt2bb (encoding wingless-type MMTV integration site family, member 2Bb). When the Wnt signal inhibitor IWR-1 was added, there was no significant change in liver development in the IWR-1 + TAA group compared with the IWR-1 + TAA + CGA group (p <0.05), which suggested that CGA regulates liver development via Wnt signaling pathway. Overall, our results suggested that CGA might alleviate TAA-induced toxicity in zebrafish and promote liver development through the Wnt signaling pathway, which provides a basis for the therapeutic effect of CGA on liver dysplasia.

Deep Sequencing of T-Cell Receptors for Monitoring Peripheral CD8+ T Cells in Chinese Advanced Non-Small-Cell Lung Cancer Patients Treated With the Anti-PD-L1 Antibody.

Background: Atezolizumab, a high-affinity engineered human anti-PD-L1 antibody, has produced a clinical benefit for patients with advanced non-small-cell lung cancer (NSCLC). However, associated with T-cell regulation, the immunomodulatory effect of PD-L1 blockade and its biomarker in peripheral immunity remains elusive. Methods: In a prospective cohort with 12 Chinese advanced NSCLC patients who received atezolizumab 1,200 mg every 3 weeks as a second-line treatment, blood samples were obtained before and 6 weeks after atezolizumab initiation, and when disease progression was confirmed. Patients were classified into a response or progression group according to response evaluation criteria in solid tumors (RECIST) 1.1. Fresh peripheral blood mononuclear cells (PBMCs) from patients were stained with antihuman CD3, CD8, and PD-1 antibodies for flow cytometry analysis. T-cell receptor (TCR)-ß chains of CD8+ T cells were analyzed by next-generation sequencing (NGS) at the deep level. Diversity, clonality, and similarity of TCR have been calculated before and after treatment in both groups. Results: Clonal expansion with high PD-1 expression was detected in all patients' peripheral CD8+ T cells before the treatment of atezolizumab. Unlike the progression group, the diversity of TCR repertoire and singletons in the TCRß pool increased over time with atezolizumab administration, and the TCR repertoire dynamically changes in the response group. The percentage of CD8+ PD-1high terminal exhausted T cells declined in the response group after the PD-L1 blockade. Two patterns of TCR changes among patients who received PD-L1-targeted immunotherapy were observed. Conclusions: Deep sequencing of the T-cell receptors confirmed the existence of CD8+ PD-1high T cells with an exhaustion phenotype in Chinese NSCLC patients. Our study demonstrated that efficient anti-PD-L1 therapy could reshape the TCR repertoire for antitumor patients. Furthermore, singleton frequency may help us select patients who are sensitive to anti-PD-L1 immunotherapy.

Protective effects and molecular mechanisms of baicalein on thioacetamide-induced toxicity in zebrafish larvae.

Baicalein is a flavonoid that is widely found in plants. Studies have shown that baicalein has anti-inflammatory, anti-cancer, and liver-protective effects. However, the effects of baicalein on TAA-induced toxicity and the underlying molecular mechanisms in zebrafish larvae are still unknown. Here, we investigated the effects of baicalein on liver development and its anti-inflammatory effects in zebrafish larvae. The results showed that baicalein has significant anti-embryonic developmental toxicity and significant antioxidant and anti-inflammatory capabilities in TAA-induced zebrafish larvae and promotes liver development and cell proliferation, reduces the expression of apoptotic proteins, and induces the expression of anti-apoptotic proteins. At the molecular level of TAA-treated zebrafish larvae, there was a decrease in the relative expression levels of mRNAs of three subfamilies, P38, ERK1, and ERK2, of the MAPK-signaling pathway and of the products of peroxisome proliferator-activated receptor (PPAR)α. Compared with TAA-treated zebrafish larvae, zebrafish larvae treated with baicalein showed an increase in the relative expression levels of P38, ERK1, and ERK2 mRNAs and the downstream products of PPARα. When MAPK signal inhibitor (SB203580) was added, it was found that liver development was inhibited and baicalin had no protective effect on TAA induced hepatotoxicity in zebrafish larvae. The results showed baicalein can protect the zebrafish larvae against toxicity induced by TAA through MAPK signal pathway. Several molecular mechanisms discovered in this study may help in the development of new drugs.

Graphene oxide nanoparticles induce hepatic dysfunction through the regulation of innate immune signaling in zebrafish (Danio rerio).

Graphene oxide (GO) is an increasingly important nanomaterial that exhibits great promise in the area of bionanotechnology and nanobiomedicine. However, the toxic effects of GO on the vertebrate developmental system are still poorly understood. Here, we aimed to investigate the toxic effects and molecular mechanisms of GO exposure in larval and adult zebrafish. The results showed that the major hepatotoxic phenotype induced by GO in zebrafish embryos was a significant decrease in liver area and a dose-dependent decrease in the hepatocytes. Moreover, the number of macrophages and neutrophils in zebrafish embryos were reduced but the expressions of pro-inflammatory cytokines were increased after GO treatment. High through-put RNA-Seq identified 314 differentially expressed genes (DEGs) in GO-induced zebrafish embryos including 192 up-regulated and 122 down-regulated. KEGG and GO functional analysis revealed that steroid hormone biosynthesis, lipoprotein metabolic process, and PPAR signaling pathway were significantly enriched. Most of the lipid metabolism genes were down-regulated while majority of the immune genes were up-regulated after GO treatment. Moreover, GO induced NF-κB p65 into the nucleus and increased the protein levels of NF-κB p65, JAK2, STAT3, and Bcl2 in adult zebrafish liver. In addition, pharmacological experiments showed that inhibition of ROS and blocking the MAPK signaling could rescue the hepatotoxic phenotypes induced by GO exposure. On the contrary, pharmacological activation of PPAR-α expression have increased the hepatotoxic effects in GO-induced larval and adult zebrafish. Taken together, these informations demonstrated that GO induced hepatic dysfunction mainly through the ROS and PPAR-α mediated innate immune signaling in zebrafish.

Analysis of acoustic radiation force on a rigid sphere in a fluid-filled cylindrical cavity with an abruptly changed cross-section.

This paper studies the acoustic radiation force of a rigid sphere positioned in a fluid-filled cylindrical cavity with an abruptly changed cross-section. This cavity consists of a semi-infinite front tube and a coaxially connected semi-infinite rear tube with different cross-sectional area through a transverse planar junction. Considering a plane wave propagates along the cavity, the exact expression of the acoustic radiation force exerted on the sphere in the front tube is deduced. The effects of the distance between the sphere and the planar junction and the radius ratio of the front tube to the rear tube on acoustic radiation force are analyzed. Numerical results show that the distance influences the acoustic radiation force periodically. Both the distance and the radius ratio of the tubes affect the magnitude and the direction of acoustic radiation force. A finite element model about the calculation for the acoustic radiation force on the sphere in the fluid-filled cylindrical cavity with suddenly changed cross-section is built to validate the theoretical results. The comparison results between the theoretical computation and the finite element simulation are in good agreement with each other. This work can support future studies for the predictive control of a particle in the cavity which has an abruptly changed cross-section.

Immunotoxicity and transcriptome analysis of zebrafish embryos in response to glufosinate-ammonium exposure.

Glufosinate-ammonium (Gla) is a broad-spectrum and non-selective herbicide that widely used in many countries worldwide, but the biological safety including potentially negative effects on aquatic organisms remains largely unknown. In this study, we investigated the immunotoxic effects of Gla exposure on zebrafish embryos. Firstly, Gla markedly decreased the survival rate and caused a series of morphological malformations in a dose-dependent manner. Meanwhile, the number of macrophages and neutrophils was substantially reduced upon Gla exposure. In addition, the levels of oxidative stress were changed and the antioxidant enzyme activities such as CAT and SOD were elevated with the increase of Gla concentrations. Secondly, comparative transcriptome analysis identified 1, 366 differentially expressed genes (DEGs) including 789 up-regulated and 577 down-regulated in zebrafish embryos after Gla exposure. KEGG pathway analysis revealed that metabolic pathways such as drug metabolism-cytochrome P450 was markedly regulated and proteolysis, oxidation-reduction process, and peptidase activity were significantly enriched by the GO analysis. Besides, 55 immunity-related genes were identified in the DEGs, and we found that the genes in the metabolism, redox and immunity display an unique expression profilings by clustering analysis. Finally, 8 inflammatory cytokines and chemokines were further confirmed and they were differentially regulated after Gla exposure. In summary, a global survey of zebrafish defense against glufosinate was performed, and a large number of gene expression levels regarding metabolism, redox, and immunity-related genes were acquired from RNA-Seq. This study provides valuable informations for future elucidating the molecular mechanism of herbicide induced immunotoxicity in aquatic ecosystems.

Quantitative characterization of T-cell repertoire alteration in Chinese patients with B-cell acute lymphocyte leukemia after CAR-T therapy.

Chimeric antigen receptor (CAR) T-cell therapy has displayed potent anti-leukemia activity in acute lymphocytic leukemia (ALL), acting as a new ray of hope to refractory/relapsed patients. However, the influence of CAR-T therapy on host immune system has not been well elucidated. Thus, We applied high-throughput T cell receptor ß chain sequencing to track the dynamic change of T-cell repertoire induced by CAR-T therapy in B-cell ALL patients. Six Chinese patients achieving complete remission were under observation, whose blood samples, bone marrow samples and infused CAR-T samples were collected at serial time points before and after CAR-T therapy. We observed decreased TCR diversity and increased clonality of T-cell repertoire in both peripheral blood and bone marrow after CAR-T administration. The persistent T cell clones in blood and bone marrow expanded following leukemic cell destruction and were barely detected in CAR T-cell pool. For the first time, our results demonstrated CAR-T therapy could stimulate the clonal proliferation of CAR-negative T cells in patients. Considering other groups' animal results indicating that CAR-T therapy could facilitate the proliferation of tumor antigen-specific T cells and that the emergence of these T cell clones followed the destruction of leukemic cells, they are most likely tumor antigen-specific.

Tracking pollutants in dietary fish oil: From ocean to table.

Dietary fish oil used in aquafeed transfers marine pollutants to farmed fish. However, the entire transfer route of marine pollutants in dietary fish oil from ocean to table fish has not been tracked quantitatively. To track the entire transfer route of marine pollutants from wild fish to farmed fish through dietary fish oil and evaluate the related human health risks, we obtained crude and refined fish oils originating from the same batch of wild ocean anchovy and prepared fish oil-containing purified aquafeeds to feed omnivorous lean Nile tilapia and carnivorous fatty yellow catfish for eight weeks. The potential human health risk of consumption of these fish was evaluated. Marine persistent organic pollutants (POPs) were concentrated in fish oil, but were largely removed by the refining process, particularly dioxins and polychlorinated biphenyls (PCBs). The differences in the POP concentrations between crude and refined fish oils were retained in the fillets of the farmed fish. Fillets fat content and fish growth were positively and negatively correlated to the final POPs deposition in fillets, respectively. The retention rates of marine POPs in the final fillets through fish oil-contained aquafeeds were 1.3%-5.2%, and were correlated with the POPs concentrations in feeds and fillets, feed utilization and carcass ratios. The dietary crude fish oil-contained aquafeeds are a higher hazard ratio to consumers. Prohibiting the use of crude fish oil in aquafeed and improving growth and feed efficiency in farmed fish are promising strategies to reduce health risks originating from marine POPs.

Polypeptide-functionalized NaYF4:Yb(3+),Er(3+) nanoparticles: red-emission biomarkers for high quality bioimaging using a 915 nm laser.

We prepared poly-L-aspartic acid (PASP) functionalized NaYF4:Yb(3+),Er(3+) upconversion nanoparticles (UCNP-PASP). These nanoparticles can give red upconversion emission under excitation at 915 nm, whose wavelength of emission and excitation is located in the optical window of biological tissue. Dynamic laser scatting and zeta potentials of UCNP-PASP were used to study their stabilities in different aqueous solution. To understand the mechanism of the red emission of UCNP-PASP, photoluminescence spectra of samples were recorded before and after modification with PASP, poly acrylic acid (PAA), and poly(ether imide) (PEI) ligands under excitation at 915 and 980 nm, respectively. The cytotoxicity of the UCNP-PASP was also examined on a A549 cell and KB cell by 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide (MTT) assay. Moreover, the PASP-functionalized UCNP was employed as a potential biomarker for in vitro and in vivo experiments of upconversion luminescence imaging.

Enhanced dual contrast agent, Co(2+)-doped NaYF4:Yb(3+),Tm(3+) nanorods, for near infrared-to-near infrared upconversion luminescence and magnetic resonance imaging.

Dual-modality imaging with magnetic resonance (MR) and upconversion luminescence (UCL) is a promising technique for molecular imaging in biomedical research. Multifunctional lanthanide-based nanoparticles have been widely investigated as agents for contrast enhanced MR and fluorescence imaging. However, the use of rare earth fluoride nanoparticles for dual-modality imaging of T2-weighted MR and UCL is rarely reported. We find that NaYF4:Yb(3+),Tm(3+),Co(2+) (MUC) nanorods can be applied as a high-performance dual contrast agent for both T2-weighted MR and UCL dual-modality imaging. After modification with 6-O-carboxymethyl chitosan (OCC), MUC nanorods can be endocytosed by cells without showing signs of cytotoxicity. High-quality UCL images of living cells incubated with MUC-OCC nanorods were acquired on a near-infrared (NIR) confocal microscopy under the excitation at 980 nm. Moreover, MUC-OCC nanorods display high transverse (r2) relaxivities in vitro. The application of low-dose MUC-OCC nanorods for NIR-to-NIR UCL and MR dual-modality in vivo imaging was also carried out successfully. In addition, the toxicity of MUC-OCC nanorods was evaluated by MTT assay, serological tests and histological analysis of visceral organs.

[Determination of organochlorine pesticides in soils using gas chromatography-tandem mass spectrometry].

A method was developed for the determination of organochlorine pesticides (OCPs) in soils using accelerated solvent extraction (ASE, Florisil cleanup in the extraction cell) and gel permeation chromatography (GPC) on-line concentration prior to the determination by ga chromatography-triple quadrupole tandem mass spectrometry (GC-MS/MS). And then 20 agricultural soil samples in Shanghai suburbs were determined. Multiple reaction monitoring (MRM) was applied to qualify and quantify the target compounds. In the different linear ranges (included in 0.001 - 0.2 mg/L) of each pesticide, the correlation coefficients were higher than 0.995. The average recoveries in spiked soils were 65.9% - 140.0% with the relative standard deviations of 1.5% - 20.3% (n = 5). The limits of detection (LOD) (S/N = 3) for these pesticides were from 0.1 to 3.0 microg/kg and the limits of quantification (LOQ) (S/N = 10)were from 0.3 to 8.0 microg/kg. Among these soils, hexachlorocyclohexane (HCHs) and hexachlorobenzene (HCB) were detected little with a content ranges of 1.82 - 3.70 and 0.94 -9.8 microg/kg, respectively. DDTs (including 2-(2-chlorophenyl)-2-(4-chloropenyl) -1,1,1-trichloroethane (p, p'-DDT), 2,2-bis (4-chlorophenyl)-1,1-dichloro-ethylene (p,p'-DDE), 2,2-bis (4-chlorophenyl)-1,1-dichloroethane (p,p'-DDD)) were found widely with a range of 1.08 - 308.76 microg/kg and mean value of 53.28 microg/kg. The content ratio of DDT/( DDE + DDD) were less than 1.0 in 85% soil samples, indicating that DDT might come from the early days.