Developing and experimental validating a B cell exhaustion-related gene signature to assess prognosis and immunotherapeutic response in bladder cancer.

BACKGROUND: B cell exhaustion (BEX) refers to the impairment of normal B cell functions and decreased proliferation capability. However, the prognostic value of BEX-related genes in bladder cancer (BLCA) remains unclear. METHODS: BLCA cases from TCGA were used for training, while GSE5287, GSE13507, GSE31684, and GSE32894 cohorts from GEO were used for external validation. BEX-related genes were identified through literature retrieval, unsupervised clustering, and genomic difference detection. Gene pairing, LASSO, random forest, and Cox regression were employed to construct a predictive model. B cell samples from scRNAseqDB, GSE111636, and IMvigor210 were utilized to explore immunoprofiles and the predictive ability of the model in immunotherapeutic response. Additionally, 21 pairs of BLCA and paracarcinoma samples from Nanfang Hospital were used to re-confirm our findings through RT-qPCR, immunofluorescence, and flow cytometry. RESULTS: 39 BEX-related genes were identified. A 4-gene-pair signature was constructed and served as a reliable prognostic predictor across multiple datasets (pooled HR = 2.32; 95 % CI = 1.81-2.98). The signature reflected the BEX statuses of B cells (FDR < 0.05) and showed promise in evaluating immunotherapeutic sensitivity (P < 0.001). In the local cohort, CD52, TUBB6, and CAV1 were down-regulated in BLCA tissues, while TGFBI, UBE2L6, TINAGL1, and IL32 were up-regulated (all P < 0.05). Furthermore, the infiltration levels of CD19 + CD52 + and CD19 + TUBB6 + B cells in paracarcinoma samples were higher than those in BLCA samples (all P < 0.05). CONCLUSION: A BEX-related gene signature was developed to predict prognosis and immunotherapeutic sensitivity in BLCA, providing valuable guidance for personalized treatment.

Investigating the impact of regulatory B cells and regulatory B cell-related genes on bladder cancer progression and immunotherapeutic sensitivity.

BACKGROUND: Regulatory B cells (Bregs), a specialized subset of B cells that modulate immune responses and maintain immune tolerance in malignant tumors, have not been extensively investigated in the context of bladder cancer (BLCA). This study aims to elucidate the roles of Bregs and Breg-related genes in BLCA. METHODS: We assessed Breg infiltration levels in 34 pairs of BLCA and corresponding paracancerous tissues using immunohistochemical staining. We conducted transwell and wound healing assays to evaluate the impact of Bregs on the malignant phenotype of SW780 and T24 cells. Breg-related genes were identified through gene sets and transcriptional analysis. The TCGA-BLCA cohort served as the training set, while the IMvigor210 and 5 GEO cohorts were used as external validation sets. We employed LASSO regression and random forest for feature selection and developed a risk signature using Cox regression. Primary validation of the risk signature was performed through immunohistochemical staining and RT-qPCR experiments using the 34 local BLCA samples. Additionally, we employed transfection assays and flow cytometry to investigate Breg expansion ability and immunosuppressive functions. RESULTS: Breg levels in BLCA tissues were significantly elevated compared to paracancerous tissues (P < 0.05) and positively correlated with tumor malignancy (P < 0.05). Co-incubation of SW780 and T24 cells with Bregs resulted in enhanced invasion and migration abilities (all P < 0.05). We identified 27 Breg-related genes, including CD96, OAS1, and CSH1, which were integrated into the risk signature. This signature demonstrated robust prognostic classification across the 6 cohorts (pooled HR = 2.25, 95% CI = 1.52-3.33). Moreover, the signature exhibited positive associations with advanced tumor stage (P < 0.001) and Breg infiltration ratios (P < 0.05) in the local samples. Furthermore, the signature successfully predicted immunotherapeutic sensitivity in three cohorts (all P < 0.05). Knockdown of CSH1 in B cells increased Breg phenotype and enhanced suppressive ability against CD8 + T cells (all P < 0.05). CONCLUSIONS: Bregs play a pro-tumor role in the development of BLCA. The Breg-related gene signature established in this study holds great potential as a valuable tool for evaluating prognosis and predicting immunotherapeutic response in BLCA patients.

A cytochrome P450 system initiates 4-nitroanisole degradation in Rhodococcus sp. strain JS3073.

Nitroanisoles are used widely as synthetic intermediates and explosives. Although bacteria have been reported to degrade 4-nitroanisole (4NA) under aerobic conditions, the key enzymes and the catalytic mechanism have remained elusive. Rhodococcus sp. strain JS3073 was isolated for its ability to grow on 4NA as the sole carbon and energy source. In this study, whole cell biotransformation experiments indicated that 4NA degradation is initiated by O-demethylation to form 4-nitrophenol (PNP), which undergoes subsequent degradation by a previously established pathway involving formation of 1,2,4-benzenetriol and release of nitrite. Based on comparative transcriptomics and heterologous expression, a novel three-component cytochrome P450 system encoded by pnaABC initiates the O-demethylation of 4NA to yield formaldehyde and PNP. The pnaABC genes encode a phthalate dioxygenase type reductase (PnaA), a cytochrome P450 monooxygenase (PnaB), and an EthD family protein (PnaC) with putative function similar to ferredoxins. This unusual P450 system also has a broad substrate specificity for nitroanisole derivatives. Sequence analysis of PnaAB revealed high identity with multiple self-sufficient P450s of the CYP116B subfamily. The findings revealed the molecular basis of the catabolic pathway for 4NA initiated by an unusual O-demethylase PnaABC and extends the understanding of the diversity among P450s and their electron transport chains.

Cytokines induced memory-like NK cells engineered to express CD19 CAR exhibit enhanced responses against B cell malignancies.

CD19 chimeric antigen receptor (CAR) engineered NK cells have been used for treating patients with relapsed and/or refractory B cell malignancies and show encouraging outcomes and safety profile. However, the poor persistence of NK cells remains a major challenge for CAR NK cell therapy. Memory-like NK cells (MLNK) induced by IL-12, IL-15, and IL-18 have shown enhanced and prolonged responses to tumor re-stimulation, making them an attractive candidate for adoptive cellular immunotherapy. Here, we show efficient and stable gene delivery of CD19 CAR to memory-like NK cells using retroviral vectors with transduction efficiency comparable to those achieved with conventional NK cells. Analysis of surface molecules revealed a distinct phenotypic profile in CAR engineered memory-like NK cells (CAR MLNK), as evidenced by increased expression of CD94 and downregulation of NKp30 as well as KIR2DL1. Compared to conventional CAR NK cells, CAR MLNK cells exhibited significantly increased IFN-γ production and degranulation in response to CD19+ target cells, resulting in enhanced cytotoxic activity against CD19+ leukemia cells and lymphoma cells. Furthermore, memory properties induced by IL-12/-15/-18 improved the in vivo persistence of CAR MLNK cells and significantly suppressed tumor growth in a exnograft mouse model of lymphoma, leading to prolonged survival of CD19+ tumor-bearing mouse. Altogether, our data indicate that CD19 CAR engineered memory-like NK cells exhibited superior persistence and antitumor activity against CD19+ tumors, which might be an attractive approach for treating patient with relapse or refractory B cell malignancies.

Light-Matter Interactions in Hybrid Material Metasurfaces.

This Review focuses on the integration of plasmonic and dielectric metasurfaces with emissive or stimuli-responsive materials for manipulating light-matter interactions at the nanoscale. Metasurfaces, engineered planar structures with rationally designed building blocks, can change the local phase and intensity of electromagnetic waves at the subwavelength unit level and offers more degrees of freedom to control the flow of light. A combination of metasurfaces and nanoscale emitters facilitates access to weak and strong coupling regimes for enhanced photoluminescence, nanoscale lasing, controlled quantum emission, and formation of exciton-polaritons. In addition to emissive materials, functional materials that respond to external stimuli can be combined with metasurfaces to engineer tunable nanophotonic devices. Emerging metasurface designs including surface-functionalized, chemically tunable, and multilayer hybrid metasurfaces open prospects for diverse applications, including photocatalysis, sensing, displays, and quantum information.

Interfacial engineering of plasmonic nanoparticle metasurfaces.

SignificanceMolecules interacting with metallic nanostructures can show tunable exciton-plasmon coupling, ranging from weak to strong. One factor that influences the interactions is the spatial organization of the molecules relative to the localized plasmon-enhanced electromagnetic fields. In this work, we show that the arrangement of aromatic dye molecules can be tuned within plasmonic hotspots by interfacial engineering of nanoparticle surfaces. By controlling the local chemical and physical interactions, we could modulate lasing thresholds. Surface-functionalized plasmonic metasurfaces open prospects for programmable light-matter interactions at the nanoscale.

Physiological Role of the Previously Unexplained Benzenetriol Dioxygenase Homolog in the Burkholderia sp. Strain SJ98 4-Nitrophenol Catabolism Pathway.

4-Nitrophenol, a priority pollutant, is degraded by Gram-positive and Gram-negative bacteria via 1,2,4-benzenetriol (BT) and hydroquinone (HQ), respectively. All enzymes involved in the two pathways have been functionally identified. So far, all Gram-negative 4-nitrophenol utilizers are from the genera Pseudomonas and Burkholderia. But it remains a mystery why pnpG, an apparently superfluous BT 1,2-dioxygenase-encoding gene, always coexists in the catabolic cluster (pnpABCDEF) encoding 4-nitrophenol degradation via HQ. Here, the physiological role of pnpG in Burkholderia sp. strain SJ98 was investigated. Deletion and complementation experiments established that pnpG is essential for strain SJ98 growing on 4-nitrocatechol rather than 4-nitrophenol. During 4-nitrophenol degradation by strain SJ98 and its two variants (pnpG deletion and complementation strains), 1,4-benzoquinone and HQ were detected, but neither 4-nitrocatechol nor BT was observed. When the above-mentioned three strains (the wild type and complementation strains with 2,2'-dipyridyl) were incubated with 4-nitrocatechol, BT was the only intermediate detected. The results established the physiological role of pnpG that encodes BT degradation in vivo. Biotransformation analyses showed that the pnpA-deleted strain was unable to degrade both 4-nitrophenol and 4-nitrocatechol. Thus, the previously characterized 4-nitrophenol monooxygenase PnpASJ98 is also essential for the conversion of 4-nitrocatechol to BT. Among 775 available complete genomes for Pseudomonas and Burkholderia, as many as 89 genomes were found to contain the putative pnpBCDEFG genes. The paucity of pnpA (3 in 775 genomes) implies that the extension of BT and HQ pathways enabling the degradation of 4-nitrophenol and 4-nitrocatechol is rarer, more recent, and likely due to the release of xenobiotic nitroaromatic compounds. IMPORTANCE An apparently superfluous gene (pnpG) encoding BT 1,2-dioxygenase is always found in the catabolic clusters involved in 4-nitrophenol degradation via HQ by Gram-negative bacteria. Our experiments reveal that pnpG is not essential for 4-nitrophenol degradation in Burkholderia sp. strain SJ98 but instead enables its degradation of 4-nitrocatechol via BT. The presence of pnpG genes broadens the range of growth substrates to include 4-nitrocatechol or BT, intermediates from the microbial degradation of many aromatic compounds in natural ecosystems. In addition, the existence of pnpCDEFG in 11.6% of the above-mentioned two genera suggests that the ability to degrade BT and HQ simultaneously is ancient. The extension of BT and HQ pathways including 4-nitrophenol degradation seems to be an adaptive evolution for responding to synthetic nitroaromatic compounds entering the environment since the industrial revolution.

A novel esterase DacApva from Comamonas sp. strain NyZ500 with deacetylation activity for acetylated polymer polyvinyl alcohol.

As a water-soluble polymer, the widely used polyvinyl alcohol (PVA) is produced from hydrolysis of polyvinyl acetate. Microbial PVA carbon backbone cleavage via a two-step reaction of dehydrogenation and hydrolysis has been well studied. Content of acetyl group is a pivotal factor affecting performance of PVA derivatives in industrial application, and deacetylation is a non-negligible part in PVA degradation. However, the genetic and biochemical studies of its deacetylation remain largely elusive. Here, Comamonas sp. strain NyZ500 was isolated for its capability of growing on acetylated PVA from activated sludge. A spontaneous PVA-utilization deficient mutant strain NyZ501 was obtained when strain NyZ500 was cultured in rich media. Comparative analysis between the genomes of these two strains revealed a fragment (containing a putative hydrolase gene dacApva ) deletion in NyZ501 and dacApva-complemented strain NyZ501 restored the ability to grow on PVA. DacApva, which shares 21% identity with xylan esterase AxeA1 from Prevotella ruminicola 23, is a unique deacetylase catalyzing the conversion of acetylated PVA and its derivatives to deacetylated counterparts. This indicates that strain NyZ500 utilizes acetylated PVA via acetate as a carbon source to grow. DacApva also possessed the deacetylation ability for acetylated xylan and the antibiotic intermediate 7-aminocephalosporanic acid (7ACA) but the enzymes for the above two compounds had no activities against PVA derivatives. This study enhanced our understanding of the diversity of microbial degradation of PVA and DacApva characterized here is also a potential biocatalyst for the eco-friendly biotransformation of PVA derivatives and other acetylated compounds.IMPORTANCE: Water-soluble PVA, which possesses a very robust ability to accumulate in the environment, has a very grave environmental impact due to its widespread use in industrial and household applications. On the other hand, chemical transformation of PVA derivatives is currently being carried out at high energy consumption and high pollution conditions using hazardous chemicals (such as NaOH, methanol) under high temperatures. The DacApva reported here performs PVA deacetylation under mild conditions, then it has a great potential to be developed into an eco-friendly biocatalyst for biotransformation of PVA derivatives. DacApva also has deacetylation activity for compounds other than PVA derivatives, which facilitates its development into a broad-spectrum deacetylation biocatalyst for production of certain desired compounds.

Plasmonic Photoelectrocatalysis in Copper-Platinum Core-Shell Nanoparticle Lattices.

This paper reports that strongly coupled bimetallic core-shell nanoparticle arrays show photoelectrocatalytic activity for hydrogen evolution reactions (HER). We fabricated large-area Cu-Pt nanoparticle lattices by combining top-down lithography and solution-based chemistry. These coupled lattices support two different types of plasmon modes, localized surface plasmons from individual particles and surface lattice resonances (SLRs) from the 2D lattice, that increased HER catalytic activity under white-light illumination up to 60%. Comparing photoelectrocatalytic performances of the two plasmon modes at different wavelength ranges, we found that SLRs had two-fold activity enhancement over that from localized surface plasmons.

Soft skin layers for reconfigurable and programmable nanowrinkles.

Wrinkling skin layers on pre-strained polymer sheets has drawn significant interest as a method to create reconfigurable surface patterns. Compared to widely studied metal or silica films, softer polymer skins are more tolerant to crack formation when the surface topography is tuned under applied strain. This Mini-review discusses recent progress in mechano-responsive wrinkles based on polymer skin materials. Control over the skin thickness with nanometer accuracy allows for tuning of the wrinkle wavelength and orientation over length scales from nanometer to micrometer regimes. Furthermore, soft skin layers enable texturing of two-dimensional electronic materials with programmable feature sizes and structural hierarchy because of the conformal adhesion to the substrates. Soft skin systems open prospects to tailor a range of surface properties via external stimuli important for applications such as smart windows, microfluidics, and nanoelectronics.

Ultranarrow plasmon resonances from annealed nanoparticle lattices.

This paper reports how the spectral linewidths of plasmon resonances can be narrowed down to a few nanometers by optimizing the morphology, surface roughness, and crystallinity of metal nanoparticles (NPs) in two-dimensional (2D) lattices. We developed thermal annealing procedures to achieve ultranarrow surface lattice resonances (SLRs) with full-width at half-maxima linewidths as narrow as 4 nm from arrays of Au, Ag, Al, and Cu NPs. Besides annealing, we developed a chemical vapor deposition process to use Cu NPs as catalytic substrates for graphene growth. Graphene-encapsulated Cu NPs showed the narrowest SLR linewidths (2 nm) and were stable for months. These ultranarrow SLR nanocavity modes supported even narrower lasing emission spectra and high nonlinearity in the input-output light-light curves.

Soft Skin Layers Enable Area-Specific, Multiscale Graphene Wrinkles with Switchable Orientations.

This paper reports a method to realize crack-free graphene wrinkles with variable spatial wavelengths and switchable orientations. Graphene supported on a thin fluoropolymer and prestrained elastomer substrate can exhibit conformal wrinkling after strain relief. The wrinkle orientation could be switched beyond the intrinsic fracture limit of graphene for hundreds of cycles of stretching and releasing without forming cracks. Mechanical modeling revealed that the fluoropolymer layer mediated the structural evolution of the graphene wrinkles without crack formation or delamination. Patterned fluoropolymer layers with different thicknesses produced wrinkles with controlled wavelengths and orientations while maintaining the mechanical integrity of graphene under high tensile strain.

Graphene Wrinkles Enable Spatially Defined Chemistry.

This paper reports a scalable approach to achieve spatially selective graphene functionalization using multiscale wrinkles. Graphene wrinkles were formed by relieving the strain in thermoplastic polystyrene substrates conformally coated with fluoropolymer and graphene skin layers. Chemical reactivity of a fluorination process could be tuned by changing the local curvature of the graphene nanostructures. Patterned areas of graphene nanowrinkles and crumples followed by a single-process plasma reaction resulted in substrates with regions having different fluorination levels. Notably, conductivity of the functionalized graphene nanostructures could be locally tuned as a function of feature size without affecting the mechanical properties.

Lattice-Resonance Metalenses for Fully Reconfigurable Imaging.

This paper describes a reconfigurable metalens system that can image at visible wavelengths based on arrays of coupled plasmonic nanoparticles. These lenses manipulated the wavefront and focused light by exciting surface lattice resonances that were tuned by patterned polymer blocks on single-particle sites. Predictive design of the dielectric nanoblocks was performed using an evolutionary algorithm to create a range of three-dimensional focusing responses. For scalability, we demonstrated a simple technique for erasing and writing the polymer nanostructures on the metal nanoparticle arrays in a single step using solvent-assisted nanoscale embossing. This reconfigurable materials platform enables tunable focusing with diffraction-limited resolution and offers prospects for highly adaptive, compact imaging.

Strain in a single wrinkle on an MoS2 flake for in-plane realignment of band structure for enhanced photo-response.

Since 2D transition metal dichalcogenides (TMDs) exhibit strain-tunable bandgaps, locally confining strain can allow lateral manipulation of their band structure, in-plane carrier transport and optical transitions. Herein, we show that a single wrinkle (width = 10 nm-10 µm) on an MoS2 flake can induce confined uniaxial strain to reduce the local bandgap (40-60 meV per % deformation), producing a microscopic exciton funnel with an enhancement in photocurrent over flat MoS2 devices. This study also shows that wrinkles can spatially reconfigure the distribution of dopants and enhance the light absorption in the MoS2 layer via Fabry-Perot interference in its nanocavity. In the field-effect transistor studies on the MoS2 flat-wrinkle-flat device-structure, a higher carrier mobility and an improvement in the on/off ratio were exhibited in the devices with a single wrinkle. This phenomenon is attributed to the built-in potential induced by the bandgap reduction at the wrinkle site and the change in doping of the suspended wrinkle. The wrinkle-induced tunability of the local bandgap and manipulation of the spatial transport barriers, and the enhanced light absorption can enable development of next-generation electronic and optoelectronic devices guided by in-plane deformation of 2D nanomaterials.

Adhesion Energy of MoS2 Thin Films on Silicon-Based Substrates Determined via the Attributes of a Single MoS2 Wrinkle.

Understanding the energetics of adhesion between two-dimensional nanomaterials and their supporting substrates is crucial for the design and fabrication of corrersponding structures with controlled interfacial effects that influence phononics, charge-carrier distribution, and electronic response. Here, we show a mechanical energy model that equates the adhesion energy of MoS2 on rigid and flat substrates (SiO2 and Si3N4) to the attributes of a single wrinkle in a MoS2 flake. The amplitude of the observed wrinkles was normalized for thickness (A/t) to select the wrinkles valid for the model. The adhesion energy values of 0.170 ± 0.033 J m-2 for MoS2 on SiO2 and 0.252 ± 0.041 J m-2 for MoS2 on Si3N4 were determined. This mechanical energy model is consistent with the model based on the local equilibrium at the contact point in the Young's equation. We also propose a method to measure the plane-strain in wrinkled MoS2. The geometrical properties (symmetry and normalized dimensions) of wrinkles and substrate effects are also discussed.

Increased Hierarchical Wrinklons on Stiff Metal Thin Film on a Liquid Meniscus.

Wrinklons-the hierarchical merging of wrinkles-are observed on several surfaces including thin films, curtains, graphene sheets, and skin. Wrinklons are a consequence of the interplay between bending, stretching, and gravitational energies and generally exhibit 1 to 2 hierarchical transitions (λn+1 = 2λn). Here we show that parallel and self-similar wrinklons on ultrathin cobalt/chromium film atop a contracting silicone oil meniscus can produce up to 5 hierarchical wrinklon transitions near the fluid-solid boundary. Further, these wrinklons do not follow the standard von-Kármán wrinklon scaling near the edge, attributed to the added surface energy (L/λ ∝ (A/t)(0.31)). A model developed via scale analysis shows (a) the relationship between wavelength and length of the wrinkles and (b) a linear relation between the amplitude and the length of wrinkles at all observed hierarchic levels (L ∝ A), fitted well with previous literature results. This work provides a mechanism for thin-film metal wrinkling on liquids and shows that surface stretching effects can allow increased hierarchical levels in wrinklons.

Confined, Oriented, and Electrically Anisotropic Graphene Wrinkles on Bacteria.

Curvature-induced dipole moment and orbital rehybridization in graphene wrinkles modify its electrical properties and induces transport anisotropy. Current wrinkling processes are based on contraction of the entire substrate and do not produce confined or directed wrinkles. Here we show that selective desiccation of a bacterium under impermeable and flexible graphene via a flap-valve operation produces axially aligned graphene wrinkles of wavelength 32.4-34.3 nm, consistent with modified Föppl-von Kármán mechanics (confinement ∼0.7 × 4 µm(2)). Further, an electrophoretically oriented bacterial device with confined wrinkles aligned with van der Pauw electrodes was fabricated and exhibited an anisotropic transport barrier (ΔE = 1.69 meV). Theoretical models were developed to describe the wrinkle formation mechanism. The results obtained show bio-induced production of confined, well-oriented, and electrically anisotropic graphene wrinkles, which can be applied in electronics, bioelectromechanics, and strain patterning.

Roseomonas eburnea sp. nov., isolated from activated sludge.

A Gram-stain-negative, aerobic, short rod-shaped, non-endospore-forming, ivory-pigmented and non-motile bacterium, designated strain BUT-5T, was isolated from activated sludge of an herbicides-manufacturing wastewater treatment facility in Jiangsu Province, China. The major fatty acids (>5 % of total fatty acids) were C16 : 0, C18 : 1 2-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant respiratory quinone was ubiquinone Q-10. The polar lipids profile of strain BUT-5T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unknown aminolipids. The DNA G+C content was 67.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-5T showed the highest sequence similarities to Roseomonas soli 5N26T (97.5 % 16S rRNA gene sequence similarity), followed by Roseomonas lacus TH-G33T (97.3 %) and Roseomonas terrae DS-48T (97.1 %). Strain BUT-5T showed low DNA-DNA relatedness with Roseomonas soli KACC 16376T (41 %), Roseomonas lacus KACC 11678T (46 %) and Roseomonas terrae KACC 12677T (42 %), respectively. On the basis of phenotypic and genotypic properties, as well as chemotaxonomic data, strain BUT-5T represents a novel species of the genus Roseomonas, for which the name Roseomonas eburnea sp. nov. is proposed. The type strain is BUT-5T ( = CCTCC AB2013276T = KACC 17166T).