m6A-regulated tumor glycolysis: new advances in epigenetics and metabolism.

Glycolytic reprogramming is one of the most important features of cancer and plays an integral role in the progression of cancer. In cancer cells, changes in glucose metabolism meet the needs of self-proliferation, angiogenesis and lymphangiogenesis, metastasis, and also affect the immune escape, prognosis evaluation and therapeutic effect of cancer. The n6-methyladenosine (m6A) modification of RNA is widespread in eukaryotic cells. Dynamic and reversible m6A modifications are widely involved in the regulation of cancer stem cell renewal and differentiation, tumor therapy resistance, tumor microenvironment, tumor immune escape, and tumor metabolism. Lately, more and more evidences show that m6A modification can affect the glycolysis process of tumors in a variety of ways to regulate the biological behavior of tumors. In this review, we discussed the role of glycolysis in tumor genesis and development, and elaborated in detail the profound impact of m6A modification on different tumor by regulating glycolysis. We believe that m6A modified glycolysis has great significance and potential for tumor treatment.

Gold Nanotriangle-Assembled Nanoporous Structures for Electric Field-Assisted Surface-Enhanced Raman Scattering Detection of Adenosine Triphosphate.

A reliable, rapid, cost-effective, and simple method for the detection of biomolecules would greatly promote the research of analytical detection of single molecules. A nanopore-based analytical technique is promising for detecting biomolecules. Conventional electrochemical nanopores cannot distinguish biomolecules precisely because of their fast translocation speed and limited electrochemical information. Therefore, it is highly desirable to develop electrochemical surface-enhanced Raman scattering (SERS) nanopores to obtain multidimensional information. Herein, we designed and fabricated gold nanotriangle (AuNT)-assembled porous structures at the tip of a glass capillary using dithiol adenosine triphosphate (ATP) aptamers as cross-linking molecules. The AuNTs exhibited an edge length of 57.3 ± 6.2 nm and thickness of about 15 nm. The gold nanoporous structure (GPS) showed a strong ion rectification even at a high concentration of electrolyte (2 M) and a high SERS activity. Based on these designed structures, SERS and electrochemistry techniques were combined to control the rapid movement of ATP to the vicinity of the GPS by an applied potential of +1 V, where ATP was concentrated by ATP aptamers and the molecular signals were amplified by SERS. As a result, the GPS successfully detected ATP at a concentration as low as 10-7 M.

A Novel Indole Derivative with Superior Photophysical Performance for Fluorescent Probe, pH-Sensing, and Logic Gates.

An indole-related molecules have been considered as the potential fluorescent probes for biological and electrochemical sensing. However, most of the indole probes have been usually used in a single detection mode. Indolium probes that enable accurate detection in complex environments are rarely reported. Here, four novel indole derivatives including the phenyl group substituted with different functional moieties were designed on the basis of the donor-π-acceptor (D-π-A) concept. These derivatives exhibit positive solvatochromism owing to their varied molecular conformations upon contacting to various solvents and the different HOMO-LUMO gaps caused by the difference in electronic push-pull capability of the substituents. Their solid-state fluorescence emissions and multiple chromisms are observed due to the inherent twisted geometries and aggregation modes. In addition, these derivatives show dramatic color and fluorescence responses due to the protonation of the nitrogen and oxygen containing groups, and thus novel colorimetric pH sensors, fluorescent papers and logic gates have been designed.

Whole-exome sequencing analysis identifies distinct mutational profile and novel prognostic biomarkers in primary gastrointestinal diffuse large B-cell lymphoma.

BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive non-Hodgkin lymphoma, and about 10% of DLBCL cases primarily occur in the gastrointestinal tract. Previous reports have revealed that primary gastrointestinal-DLBCL (pGI-DLBCL) harbors different genetic mutations from other nodal or extranodal DLBCL. However, the exonic mutation profile of pGI-DLBCL has not been fully addressed. METHODS: We performed whole-exome sequencing of matched tumor tissues and blood samples from 53 pGI-DLBCL patients. The exonic mutation profiles were screened, and the correlations between genetic mutations and clinicopathological characteristics were analyzed. RESULTS: A total of 6,588 protein-altering events were found and the five most frequent mutated genes in our pGI-DLBCL cohort were IGLL5 (47%), TP53 (42%), BTG2 (28%), P2RY8 (26%) and PCLO (23%). Compared to the common DLBCL, significantly less or absence of MYD88 (0%), EZH2 (0%), BCL2 (2%) or CD79B (8%) mutations were identified in pGI-DLBCL. The recurrent potential driver genes were mainly enriched in pathways related to signal transduction, infectious disease and immune regulation. In addition, HBV infection had an impact on the mutational signature in pGI-DLBCL, as positive HBsAg was significantly associated with the TP53 and LRP1B mutations, two established tumor suppressor genes in many human cancers. Moreover, IGLL5 and LRP1B mutations were significantly correlated with patient overall survival and could serve as two novel prognostic biomarkers in pGI-DLBCL. CONCLUSIONS: Our study provides a comprehensive view of the exonic mutation profile of the largest pGI-DLBCL cohort to date. The results could facilitate the clinical development of novel therapeutic and prognostic biomarkers for pGI-DLBCL.

Probing Multidimensional Structural Information of Single Molecules Transporting through a Sub-10 nm Conical Plasmonic Nanopore by SERS.

Probing the orientation and oxygenation state of single molecules (SMs) is of great importance for understanding the advanced structure of individual molecules. Here, we manipulate molecules transporting through the hot spot of a sub-10 nm conical gold nanopore and acquire the multidimensional structural information of the SMs by surface enhanced Raman scattering (SERS) detection. The sub-10 nm size and conical shape of the plasmonic nanopore guarantee its high detection sensitivity. SERS spectra show a high correlation with the orientations of small-sized single rhodamine 6G (R6G) during transport. Meanwhile, SERS spectra of a single hemoglobin (Hb) reveal both the vertical/parallel orientations of the porphyrin ring and oxygenated/deoxygenated states of Hb. The present study provides a new strategy for bridging the primary sequence and the advanced structure of SMs.

[Changes of histology and ultrastructure of otopoint "Stomach" area in rabbits with chronic gastritis].

OBJECTIVE: To observe the histological and ultrastructural changes of the otopoint "Stomach" (MA-IC) area in chronic gastritis rabbits so as to provide a foundation for auricular acupoint diagnosis and treatment. METHODS: A total of 20 New Zealand rabbits (half male and half female) were randomly and equally divided into control and model groups. The chronic gastritis model was established by gavage of 5% sodium salicylate each day for 5 weeks, while the rabbits of the control group received gavage of clear water at the same volume. Morphological changes of the tissues of gastric mucosa, otopoint "Stomach" and auricular control point were observed under light microscope after staining with hematoxylin-eosin (H.E.), and given scores (0-3 points) according to the levels of inflammatory cells. The ultrastructural changes of the otopoint "Stomach" tissue were observed under transmission electronic microscope (TEM). RESULTS: H.E. staining revealed smoothness of the gastric smooth muscle with no or a few of inflammatory cells in the control group, and appearance of gastric mucosal hemorrhage and erosion, slightly disordered epithelial glands and infiltration of a large number of lymphocytes in the mucosal layer with some clustered lymphocyte aggregation foci in the model group. The pathological score of gastric mucous in the model group was significantly higher than that in the control group (P<0.01). Under light microscope, no obvious changes were observed in the skin of the otopoint "Stomach" of the control group and the control point of the model group, whereas hyperplasia and abscission in the epidermic cuticle and spinous layer and basal layer, dermal tissue and inflammatory cell infiltration were observed in the otopoint "Stomach" of the model group. Results of TEM observation showed no significant changes in the ultrastructure of the otopoint "Stomach" in the control group, and swollen and vacuolated epidermal keratinocyte mitochondria, reduced keratin filament aggregation, widened local cell space, unclear desmosome structure, activation of the dermal fibroblasts, and an increase of the myelinated nerve mitochondria in the "Stomach" region in the model group. CONCLUSION: The otopoint "Stomach" tissue has structural damage and hyperplasia in chronic gastritis rabbits, suggesting a special correlation between the otopoint "Stomach" and gastric tissue, hence, providing a morphological basis for otopoint diagnosis and treatment.

Origin and Composition of Nanoparticles Induced in a Complex Plastic-Brittle Transition Process of Xiaomei Shear Zone, Hainan Island, China.

Micro and nano structures of quartz schist, plagioclase granite, and granitic gneiss in the Xiaomei Shear Zone located in southeastern Hainan Island, China are observed using Scanning Electron Microscope (SEM). Ultramicroscopic analyses indicate that three types of nanoparticles were found in the samples, including spherical nanoparticles, agglomerated nanoparticles and nanofibers. These nanoparticles are mainly developed in the fracture zones. The more fractures there are, the more nanoparticles are developed. Energy dispersive spectrometer (EDS) and X-ray diffraction (XRD) are used to ascertain the composition of the nanoparticles. The results suggest that the nanoparticles are mainly composed of silicate, dolomite and calcite, rich in O, Si, Al, Ca. Based on our results, we suggest that nanoparticle formation is a complex, plastic-brittle transition process. Thermal decomposition driven by steady shearing possibly forms well-organized nanoparticles, while fast-moving dislocations by shock-like stress release possibly forms radial nanofibers.

Fibroblast CEBPD/SDF4 axis in response to chemotherapy-induced angiogenesis through CXCR4.

Cancer-associated fibroblasts (CAFs) play an essential role in supporting cancer progression. However, the details and consequent effects in response to the communication between CAFs and angiogenesis remain largely uninvestigated, especially in anticancer drug treatments. We found that cisplatin and 5-fluorouracil could induce fibroblast differentiation toward myofibroblasts via CCAAT/enhancer-binding protein delta (CEBPD) and consequently promote proliferation, migration, and in vitro tube formation of vascular endothelial cells and angiogenesis in vivo. Stromal-cell-derived factor 4 (SDF4) is responsive to anticancer drugs via CEBPD activation in CAFs and contributes to create a permissive environment for tumor cell angiogenesis and promotion of distant metastasis. Importantly, we demonstrated that SDF4 interacts with CXCR4 to trigger VEGFD expression through the activation of the ERK1/2 and p38 pathways in endothelial cells. Taken together, our novel findings support that SDF4 can be a therapeutic target in inhibition of angiogenesis for chemotherapy drug-administrated cancer patients.

Prediction of Prognosis for cHCC-CC Patients After Surgery: Comparison of Tumor Marker Score Based on AFP, CEA, CA19-9, and Other Clinical Stages.

BACKGROUND: The effectiveness of clinical stage as a prognostic factor in combined hepatocellular carcinoma and cholangiocarcinoma (cHCC-CC) patients is controversial. PATIENTS AND METHODS: Medical records of all pathologically confirmed cHCC-CC patients from 2000 to 2017 at West China Hospital were retrieved. Tumor marker score (TMS) was determined from optimal AFP, CEA, and CA19-9 cutoff values. Interaction and subgroup analysis were conducted according to potential confounders. Prognostic value of TMS and other prognostic models were evaluated by Kaplan-Meier (K-M) analysis, c-index, and time-dependent receiver operating curves (td-ROC). RESULTS: Optimal cutoff values for preoperative AFP, CEA, and CA19-9 were 10.76 ng/mL, 5.24 ng/mL, and 31.54 U/mL, respectively. Among 128 patients, 24, 58, and 46 were classified into TMS 0, TMS 1, and TMS ≥ 2, respectively. TMS could stratify our series into groups of statistically different prognosis. Subgroup analysis according to potential confounders and test for interactions showed that TMS 1 and TMS ≥ 2 were stable risk factors relative to TMS 0. Univariate (HR: TMS1 = 2.30, p = 0.014; TMS ≥ 2 = 5.1, p < 0.001) and multivariate Cox regression analyses (HR: TMS1 = 1.72, p = 0.124; TMS ≥ 2 = 4.15, p < 0.001) identified TMS as an independent prognostic risk factor. TMS had good discrimination (c-index 0.666, 95% CI 0.619-0.714), and calibration plots revealed favorable consistency. Area under the curve (AUC) value of td-ROC for TMS and integrated AUC was higher than for other clinical stages at any month within 5 years postoperation. CONCLUSION: TMS exhibited optimal prognostic value over other widely used clinical stages for cHCC-CC after surgery and may guide clinicians in prognostic prediction.

Three-Dimensional Metamaterial for Plasmon-Enhanced Raman Scattering at any Excitation Wavelengths from the Visible to Near-Infrared Range.

Plasmonic materials with highly confined electromagnetic fields at resonance wavelengths have been widely used to enhance Raman scattering signals. To achieve the maximum enhancement, the resonance peaks of the plasmonic materials should overlap with the excitation and emission wavelengths of target molecules, which is difficult for most of the plasmonic materials possessing a few narrow resonance peaks. Here, we report an ultrabroadband plasmonic metamaterial absorber (BPMA) that can absorb 99% of the incident light energy and excite plasmon resonance from the ultraviolet to near-infrared range (250-1900 nm), which allows us to observe efficient plasmon-enhanced Raman scattering (PERS) with any excitation sources. As demonstrated by the investigation on a self-assembled monolayer of the nonresonant molecule 4-mercaptobenzonitrile, the BPMA exhibits high PERS performance with a detection limit of down to 10-12 M under any excitation sources of three different lasers and excellent uniformity (∼5.51%) and reproducibility (∼5.50%), which corroborates the potential for high-throughput production with low cost and at a large scale. This work offers a novel platform for anti-interference PERS analysis in dynamic and complex environments.

SERS Detection of Nucleobases in Single Silver Plasmonic Nanopores.

Conventional ion current-based nanopore techniques that identify single molecules are hampered by limitations of providing only the ionic current information. Here, we introduce a silver nanotriangle-based nanopore (diameter < 50 nm) system for detecting molecule translocation using surface-enhanced Raman scattering. Rhodamine 6G is used as a model molecule to study the effect of an electric field (-1 V) on the mass transport. The four DNA bases also show significantly different SERS signals when they are transported into the plasmonic nanopore. The observations suggest that in the electric field, analyte molecules are driven into the nanopipette through the hot spot of the silver nanopore. The plasmonic nanopore shows great potential as a highly sensitive SERS platform for detecting molecule transport and paves the way for single molecule probing.

Recognition of plastic nanoparticles using a single gold nanopore fabricated at the tip of a glass nanopipette.

A single gold nanopore with high surface enhanced Raman spectroscopy (SERS) activity is fabricated on the tip of a glass nanopipette. Polystyrene (PS) nanospheres can be recognized from the SERS spectrum while passing through the single nanopore.

Surface-Enhanced Raman Scattering Probing the Translocation of DNA and Amino Acid through Plasmonic Nanopores.

DNA and amino acids are important biomolecules in living organisms. Probing such biomolecules with structural characters can provide valuable information for life study. Here, gold plasmonic nanopores (GPNs) with high SERS activity (a local enhancement factor higher than 109) are synthesized at the tip of a glass nanopipette. An electric field drives individual molecules to translocate through the GPNs, which enables in situ collection of the surface-enhanced Raman scattering (SERS). Nonresonant biomolecules, including nucleobases, amino acids, and oligonucleotides (DNA), with single nucleobase differences can be distinguished. The intensity of SERS is tunable by modulating the affinity between DNA and the GPNs. The present study shows the feasibility of applying a plasmonic nanopore to DNA and protein detection, which may also provide an easy way for tracking single molecule translocation by developing a well-defined single plasmonic nanopore.

Local environment in biopsy better predict the pathological response to neoadjuvant chemoradiotherapy in rectal cancer.

Neoadjuvant chemoradiotherapy (nCRT) followed by surgery is the standard treatment for locally advanced rectal cancer. Here, we analyzed the impact of local and systemic environments on the tumor response to preoperative chemoradiotherapy in rectal cancer. We recruited 141 patients with rectal cancer treated with nCRT. We evaluated the local tumor environment, including tumor-infiltrating lymphocytes (TILs), intratumor budding (ITB), and the systemic inflammatory environment, including the neutrophil-to-lymphocyte ratio (NLR) and C-reactive protein (CRP) level. Our finding revealed that tumor regression was significantly associated with the density of CD8+ TILs in the intraepithelial, the presence of ITB, the combination of NLR and CRP (NLR-CRP) value, and the combination of CD8+ intraepithelial TIL (iTIL) density and ITB presence. Moreover, multivariate analysis showed that only the combination of CD8+ iTILs and ITB was an independent predictive factor for the pathological response to nCRT in rectal cancer. Our finding demonstrate that the local tumor environment was a better predictor of the tumor response than the systemic environment and thus provided new insight into screening for patients who are more likely to benefit from cancer treatment.

Using an interpolation-based method (IDVequ) to predict the combined toxicities of hormetic ionic liquids.

In the field of computational toxicology, predicting toxicological interaction or hormesis effect of a mixture from individuals is still a challenge. The two most frequently used model concentration addition (CA) and independent action (IA) also cannot solve these challenges perfectly. In this paper, we used IDVequ (an interpolation method based on the Delaunay triangulation and Voronoi tessellation as well as the training set of direct equipartition ray design (EquRay) mixtures) to predict the toxicities of binary mixtures composed of hormetic ionic liquids (ILs). One of the purposes is to verify the predictive ability of IDVequ. The other one is to improve the risk assessment of ILs mixtures especial hormetic ILs, because the toxicity reports of ILs mixtures are rarely reported in particular the toxicity of the hormetic ILs mixtures. Hence, we determined time-dependent toxicities of four ILs and their binary mixtures (designed by EquRay) to Vibrio qinghaiensis sp.-Q67 at first. Then, mixture toxicities were predicted and compared using the IDVequ and CA. The results show that, the accuracy of IDVequ is higher than the accuracy of CA. And, more important, to some mixtures out of the CA application, IDVequ also can predict the mixture effects accurately. It showed that IDVequ can be applied to predict the toxicity of any binary mixture regardless of the type of concentration-response curve of the components. These toxicity data provided useful information for researching the prediction of hormesis or toxicological interaction of the mixture and toxicities of ILs mixtures.

A single nanoparticle-based real-time monitoring of biocatalytic progress and detection of hydrogen peroxide.

This paper reported a new method to observe the catalytic progress of the natural horseradish peroxidase (HRP) in-situ on single gold nanoparticles (GNPs) by the combination of dark field imaging and plasmonic resonance scattering spectra. The produced single HRP-GNP exhibited localized catalytic property toward H2O2-Diaminobenzidine (DAB), which could be used to detect the concentration of H2O2 in micro/nanospace. The linear range for H2O2 sensing was from 0.01 µM to 5 µM with a detection limit of 10 nM. The new design strategy could be applied for a broader bioanalysis situation by substituting the HRP with other specified biocatalyst.

Structural Change of a Single Ag Nanoparticle Observed by Dark-field Microspectroscopy.

Silver nanoparticles (AgNPs) have been widely used as photocatalysts and nanosensors. Observation of the spectroscopy of a single AgNP greatly helps us understand the catalytic characteristics and morphology change of the AgNP during reactions. In the present study, AgNPs physically adsorbed on indium tin oxide (ITO) conductive glass were electrochemically reduced and oxidized, and the plasmonic resonance Rayleigh scattering (PRRS) spectrum of an individual AgNP was observed under a dark-field microscopy (DFM) equipped with a spectrometer. The electrochemical oxidization of the AgNP under constant potential caused a redshift of the PRRS peak for 30±5 nm. However, electrochemical reduction of the AgNP could not make the PRRS peak completely shift back to the initial position. In situ AFM and SEM characterization confirmed that very small Ag fragments (<10 nm) formed around the AgNP core during electrochemical oxidization. Results showed that dark-field microspectroscopy could be used as a sensitive tool for estimating the morphology/structural changes of nanoparticles that can hardly be observed through the cyclic voltammograms of multiple AgNPs.

Insight into the Unique Fluorescence Quenching Property of Metal-Organic Frameworks upon DNA Binding.

Metal-organic frameworks (MOFs) have been successfully used as efficient quenchers for fluorescent DNA detection. However, the surface charge property of MOFs can inevitably affect their fluorescence quenching behavior. Herein, nanoscale MOFs (NMOFs), including MOF nanosheets and nanoparticles, have been employed to investigate the relationship between the fluorescence quenching and surface properties of NMOFs. We find that the positively and negatively charged NMOFs exhibited totally opposite fluorescence quenching properties toward negatively charged FAM-labeled double-stranded DNA (dsDNA). On the contrast, they show negligible influence on the sensing of positively charged TAMRA-labeled dsDNA. This study provides a new insight of the fluorescence quenching property of NMOFs and offers a new concept for construction of ratiometric fluorescence DNA biosensors.

Copper-Nitrogen-Doped Graphene Hybrid as an Electrochemical Sensing Platform for Distinguishing DNA Bases.

An electrochemical sensor using ultralight and porous copper-nitrogen-doped graphene (CuNRGO) nanocomposite as the electrocatalyst has been constructed to simultaneously determine DNA bases such as guanine (G) and cytosine (C), adenine (A), and thymine (T). The nanocomposite is synthesized by thermally annealing an ice-templated structure of graphene oxide (GO) and Cu(phen)2. Because of the unique structure and the presence of Cu2+-N active sites, the CuNRGO exhibits outstanding electrocatalytic activity toward the oxidation of free DNA bases. After optimizing the experimental conditions, the CuNRGO-based electrochemical sensor shows good linear responses for the G, A, T, and C bases in the concentration ranges of 0.132-6.62 µM, 0.37-5.18 µM, 198.2-5551 µM, and 270.0-1575 µM, respectively. The results demonstrate that CuNRGO is a promising electrocatalyst for electrochemical sensing devices.