Tumor immune dysfunction and exclusion subtypes in bladder cancer and pan-cancer: a novel molecular subtyping strategy and immunotherapeutic prediction model.

BACKGROUND: Molecular subtyping is expected to enable precise treatment. However, reliable subtyping strategies for clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE), we aimed to develop a novel TIDE-based subtyping strategy to guide personalized immunotherapy in the bladder cancer (BC). METHODS: Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. Subsequently, consensus clustering was applied to classify BC patients based on TIDE marker-genes. Patients' clinicopathological, molecular features and signaling pathways of the different TIDE subtypes were well characterized. We also utilize the deconvolution algorithms to analyze the tumor microenvironment, and further explore the sensitivity and mechanisms of each subtype to immunotherapy. Furthermore, BC patient clinical information, real-world BC samples and urine samples were collected for the validation of our findings, which were used for RNA-seq analysis, H&E staining, immunohistochemistry and immunofluorescence staining, and enzyme-linked immunosorbent assay. Finally, we also explored the conservation of our novel TIDE subtypes in pan-cancers. RESULTS: We identified 69 TIDE biomarker genes and classified BC samples into three subtypes using consensus clustering. Subtype I showed the lowest TIDE status and malignancy with the best prognosis and highest sensitivity to immune checkpoint blockade (ICB) treatment, which was enriched of metabolic related signaling pathways. Subtype III represented the highest TIDE status and malignancy with the poorest prognosis and resistance to ICB treatment, resulting from its inhibitory immune microenvironment and T cell terminal exhaustion. Subtype II was in a transitional state with intermediate TIDE level, malignancy, and prognosis. We further confirmed the existence and characteristics of our novel TIDE subtypes using real-world BC samples and collected patient clinical data. This subtyping method was proved to be more efficient than previous known methods in identifying non-responders to immunotherapy. We also propose that combining our TIDE subtypes with known biomarkers can potentially improve the sensitivity and specificity of these biomarkers. Moreover, besides guiding ICB treatment, this classification approach can assist in selecting the frontline or recommended drugs. Finally, we confirmed that the TIDE subtypes are conserved across the pan-tumors. CONCLUSIONS: Our novel TIDE-based subtyping method can serve as a powerful clinical tool for BC and pan-cancer patients, and potentially guiding personalized therapy decisions for selecting potential beneficiaries and excluding resistant patients of ICB therapy.

Construction of UCNPs-aptamer-AuNPs luminescence energy transfer probe for ratio detection of Staphylococcus aureus.

A ratio luminescence probe was developed for detecting Staphylococcus aureus (S. aureus) based on luminescence energy transfer (LET) using double-wavelength emission (550 nm and 812 nm) upconversion nanoparticles (UCNPs) as donor, gold nanoparticles (AuNPs) as acceptor and the aptamer for S. aureus as the specific recognition and link unit. The LET process could cause luminescence quenching because of the spectral overlap between the acceptor and the donor at 550 nm. In the presence of S. aureus, S. aureus selectively combined with the aptamer, and the AuNPs left the surface of UCNPs, which weakened the quenching effect and restored the luminescence of UCNPs. Based on this, the ratio detection was realized by monitoring the change of the luminescence signal of the probe at 550 nm and taking the luminescence signal at 812 nm as the reference signal. Crucially, the probe has a fast reaction speed, with a reaction time of 25 min, and the detection of S. aureus is realized in the concentration range of 5.0 × 103-3.0 × 105 CFU/ml, with the detection limit of 106 CFU/ml. Therefore, the ratio probe has great potential for detecting of S. aureus in food because of its high sensitivity, fast speed and good selectivity.

Cyanine dye-assembled composite upconversion nanoparticles for the sensing and cell imaging of nitrite based on a single particle imaging method.

In this work, a single particle imaging method based on the total internal reflection (TIR) imaging platform for the sensing and cell imaging of nitrite (NO2-) in the near-infrared region using cyanine dye-assembled composite upconversion nanoparticles (UCNPs) was developed. The NaYF4:Yb,Tm@NaGdF4 UCNPs were synthesized as energy donors, and the cyanine dye IR-798 was prepared as an energy acceptor. Since the absorption spectrum of the cyanine dye IR-798 and the luminescence spectrum of upconversion nanoparticles overlapped effectively, IR-798 quenched the luminescence of the UCNPs. When NO2- was added to the cyanine dye-assembled composite upconversion nanoparticle system, NO2- destroyed the conjugate structure of IR-798, so that the luminous intensity of UCNPs could be restored. Based on the mechanism, a quantitative image analysis with high sensitivity, low sample usage, and fast response time using the TIR single particle imaging platform was developed to determine the content of nitrite in human serum samples. In addition, the UCNPs-IR-798 probe was applied to image the exogenous NO2- content in HeLa living cells based on the single particle imaging platform.

A hybrid boronate affinity probe for the selective detection of cis-diol containing compounds in tea beverages.

UiO-66-NH2 nanocomposite was post-modified with 4-mercaptophenylboronic acid (MPBA) by the method of in situ hybridization reaction. The hybrid boronate affinity material UiO-NH2 @P (TEPIC-co-MPBA) was characterized by scanning electron microscopy, X-ray diffraction and Fourier-transform infrared spectroscopy. The material was applied as fluorescent probe for the detection of cis-diol containing compounds based on the boronate affinity mechanism, and exhibited high specific selectively. The proposed method exhibited good linearity for the detection of catechol in the range of 0.50 to 8.00 µg ml-1 . The detection limit was 0.13 µg ml-1 . The tactic was successfully applied to analyze the total polyphenols in tea beverages for catechol, and relative recovery was in 98.86-106.00%. Therefore, this work provided a promising strategy for the recognition of cis-diol containing compounds.

OsWUS promotes tiller bud growth by establishing weak apical dominance in rice.

Two branching strategies are exhibited in crops: enhanced apical dominance, as in maize; or weak apical dominance, as in rice. However, the underlying mechanism of weak apical dominance remains elusive. OsWUS, an ortholog of Arabidopsis WUSCHEL (WUS) in rice, is required for tiller development. In this study, we identified and functionally characterized a low-tillering mutant decreased culm number 1 (dc1) that resulted from loss-of-function of OsWUS. The dc1 tiller buds are viable but repressed by the main culm apex, leading to stronger apical dominance than that of the wild-type (WT). Auxin response is enhanced in the dc1 mutant, and knocking out the auxin action-associated gene ABERRANT SPIKELET AND PANICLE 1 (ASP1) de-repressed growth of the tiller buds in the dc1 mutant, suggesting that OsWUS and ASP1 are both involved in outgrowth of the rice tiller bud. Decapitation triggers higher contents of cytokinins in the shoot base of the dc1 mutant compared with those in the WT, and exogenous application of cytokinin is not sufficient for sustained growth of the dc1 tiller bud. Transcriptome analysis indicated that expression levels of transcription factors putatively bound by ORYZA SATIVA HOMEOBOX 1 (OSH1) are changed in response to decapitation and display a greater fold change in the dc1 mutant than that in the WT. Collectively, these findings reveal an important role of OsWUS in tiller bud growth by influencing apical dominance, and provide the basis for an improved understanding of tiller bud development in rice.

IL-36γ-armed oncolytic virus exerts superior efficacy through induction of potent adaptive antitumor immunity.

In this study, we aimed to apply the cytokine IL-36γ to cancer immunotherapy by constructing new oncolytic vaccinia viruses (OV) expressing interleukin-36γ (IL-36γ-OVs), leveraging unique synergism between OV and IL-36γ's ability to promote antitumor adaptive immunity and modulate tumor microenvironment (TME). IL-36γ-OV had dramatic therapeutic efficacies in multiple murine tumor models, frequently leading to complete cancer eradication in large fractions of mice. Mechanistically, IL-36-γ-armed OV induced infiltration of lymphocytes and dendritic cells, decreased myeloid-derived suppressor cells and M2-like tumor-associated macrophages, and T cell differentiation into effector cells. Further study showed that IL-36γ-OV increased the number of tumor antigen-specific CD4+ and CD8+ T cells and the therapeutic efficacy depended on both CD8+ and CD4+ T cells. These results demonstrate that these IL36γ-armed OVs exert potent therapeutic efficacy mainly though antitumor immunity and they may hold great potential to advance treatment in human cancer patients.

Sensitive detection of sulfide ions in red region based on luminescence resonance energy transfer between upconversion nanoparticles and dye-670.

Many sulfides are toxic substances that easily harm the respiratory tract, therefore affecting respiratory function or damaging other organs of the body, leading to its failure. Therefore, there is a pressing need to develop methods for sensitive detection of sulfur ions (S2- ). Based on luminescence resonance energy transfer (LRET) theory, we report the construction of a near-infrared (NIR) excitation luminescence probe using NaGdF4 :Yb3+ ,Er3+ @NaYF4 upconversion nanoparticles (UCNPs) as the donor and dye-670 as the receptor for detection of S2- . When UCNPs and dye-670 molecules were combined using ligand exchange and electrostatic attraction, LRET occurred and UCNP luminescence was quenched. When S2- was added to the system, sulfide ions were able to destroy the double bond of the dye, inhibiting LRET and restoring UCNP luminescence. Under optimum condition, the linear range of S2- detection was 0.65-18.2 µM, and the detection limit was 34.2 nM. This method was applied for determination of S2- in water with satisfactory results.

A single-particle enumeration method for the detection of Fe2+ based on a near-infrared core-shell upconversion nanoparticle and IR-808 dye composite nanoprobe.

Ferrous ion (Fe2+) is an important component of hemoglobin and plays a role in transporting O2 to human tissues. If iron deficiency is present, iron deficiency anemia may occur, so it is critical to develop sensitive and accurate methods to detect Fe2+. Herein, a novel luminescence energy transfer (ET) system has been designed for the sensitive detection of Fe2+ by a single-particle enumeration (SPE) method in the near-infrared (NIR) region through combining NIR-to-NIR ß-NaGdF4:Yb,Tm@NaYF4 upconversion nanoparticles (UCNPs) and IR-808 dye. IR-808 dye can quench the luminescence of the UCNPs because of the efficient overlap between the absorption spectrum of IR-808 and the emission spectrum of the UCNPs. When Fe2+ and H2O2 are added to the system, the Fenton reaction produces hydroxyl radicals (˙OH). The generated ˙OH reacts with IR-808 and the structure of IR-808 is destroyed. As a result, the ET process is suppressed, causing recovery of the luminescence of the UCNPs, which is reflected as an increase in the number of luminescent particles. Accurate quantification of Fe2+ is achieved by statistically counting the target concentration-dependent luminescent particles. Under the optimal conditions, the linear detection range of Fe2+ is 5-10 000 nM, which is much wider than the ensemble luminescence spectra measurements in bulk solution. Moreover, this strategy can be applied to detection in serum samples with satisfactory results.

Turn-on detection of glutathione S-transferase based on luminescence resonance energy transfer between near-infrared to near-infrared core-shell upconversion nanoparticles and organic dye.

Glutathione S-transferase (GST) is a detoxification enzyme of the liver and kidney. Based on the toxicological effect of GST, it is of great significance to develop a rapid and sensitive detection method for GST. In this work, a new luminescence resonance energy transfer (LRET) system has been designed to detect glutathione S-transferase in the near-infrared (NIR) region by utilizing NaGdF4:Yb3+,Tm3+@NaYF4 upconversion nanoparticles (UCNPs) as the donor and NIR dye-806@Glutathione (IR806@GSH) as the acceptor. NaGdF4:Yb3+,Tm3+@NaYF4 UCNPs were synthesized by a coprecipitation method and surface modification of NOBF4. The donor (positively charged) interacted with the acceptor (negatively charged) via electrostatic interactions to bring them into close proximity; then, LRET occurred and the luminescence was quenched. In the presence of GST, GST can specifically interact with the GSH of IR806@GSH molecule, making IR806@GSH far away from the donor surface, inhibiting the LRET, and restoring the luminescence of the UCNPs. There was a good linear relationship between the luminescence recovery intensity of UCNPs and GST concentration, ranging from 0.11 to 14.19 nM, and the detection of limit was 0.06 nM. The method has been used in the detection of GST in human serum samples and is expected to have potential applications in the biological field. Graphical abstract A luminescence resonance energy transfer system was developed for determination of glutathione S-transferase in the near-infrared region by utilizing NaGdF4:Yb3+,Tm3+@NaYF4 upconversion nanoparticles as the donor and NIR dye-806@Glutathione as the acceptor.

Gut microbiota dysbiosis signature is associated with the colorectal carcinogenesis sequence and improves the diagnosis of colorectal lesions.

BACKGROUND AND AIM: The gut microbiota is associated with colorectal lesions in cases of precancer and colorectal cancer (CRC). However, there are apparent differences in studies on the gut microbiota in the pathogenic sequence from precancer to cancer. Here, we characterize the gut microbiota signatures of colorectal precancer and cancer and test their utility in detecting colorectal lesions in two independent Chinese cohorts. METHODS: Stool samples collected from patients with precancer and CRC were subjected to 16S ribosomal RNA gene sequencing and metagenomic shotgun sequencing analyses, which revealed the microbial signatures of the two disease stages. RESULTS: In comparison with healthy controls, lower microbial richness and diversity were observed in precancer and intensive interbacterial associations were found in CRC. We identified 41 bacteria that showed gradual increases while 12 bacteria showed gradual decreases at the genus level gradually during the development of CRC. Novel CRC-associated pathogenetic species were identified. Species units that contributed to altered microbial functions were identified in CRC patients and healthy controls. The microbial panel showed a comparable ability to fecal immunochemical test (FIT) in detecting CRC. However, the combination of microbes and FIT significantly improved the detection ability and sensitivity of colon lesions based on 18 genera. Microbial network analysis revealed a significant positive correlation among beneficial microbes and a negative correlation in detrimental phenotypes. CONCLUSIONS: Microbial dysbiosis was revealed in colorectal lesions. The combination of microbial markers and FIT improved the CRC detection ability, which might assist in the early diagnosis of CRC.