IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions.

Cancer-related epitopes can engage the immune system against tumor cells, thus exploring epitopes derived from non-coding regions is emerging as a fascinating field in cancer immunotherapies. Here, we described a database, IEAtlas (http://bio-bigdata.hrbmu.edu.cn/IEAtlas), which aims to provide and visualize the comprehensive atlas of human leukocyte antigen (HLA)-presented immunogenic epitopes derived from non-coding regions. IEAtlas reanalyzed publicly available mass spectrometry-based HLA immunopeptidome datasets against our integrated benchmarked non-canonical open reading frame information. The current IEAtlas identified 245 870 non-canonical epitopes binding to HLA-I/II allotypes across 15 cancer types and 30 non-cancerous tissues, greatly expanding the cancer immunopeptidome. IEAtlas further evaluates the immunogenicity via several commonly used immunogenic features, including HLA binding affinity, stability and T-cell receptor recognition. In addition, IEAtlas provides the biochemical properties of epitopes as well as the clinical relevance of corresponding genes across major cancer types and normal tissues. Several flexible tools were also developed to aid retrieval and to analyze the epitopes derived from non-coding regions. Overall, IEAtlas will serve as a valuable resource for investigating the immunogenic capacity of non-canonical epitopes and the potential as therapeutic cancer vaccines.

Sensitive fluorescence ELISA for the detection of zearalenone based on self-assembly DNA nanocomposites and copper nanoclusters.

Zearalenone (ZEN), produced by Fusarium species, is a potential risk to human health. Traditional enzyme-linked immunosorbent assay (ELISA) is restricted due to low sensitivity for the detection of ZEN. Herein, enzyme nanocomposites (ALP-SA-Bio-ssDNA, ASBD) were prepared with the self-assembly strategy based on streptavidin-labeled alkaline phosphatase (SA-ALP) and dual-biotinylated ssDNA (B2-ssDNA). The enzyme nanocomposites improved the loading amount of ALP and catalyzed more ascorbic acid 2-phosphate to generate ascorbic acid (AA). Subsequently, Cu2+ could be reduced to copper nanoclusters (CuNCs) having strong fluorescence signal by AA with poly T. Benefiting from the high enzyme load of nanocomposites and the strong signal of CuNCs, the fluorescence ELISA was successfully established for the detection of ZEN. The proposed method exhibited lower limit of detection (0.26 ng mL-1) than traditional ELISA (1.55 ng mL-1). The recovery rates ranged from 92.00% to 108.38% (coefficient of variation < 9.50%) for the detection of zearalenone in corn and wheat samples. In addition, the proposed method exhibited no cross reaction with four other mycotoxins. This proposed method could be used in trace detection for food safety.

Dual-AND Logic Gate-Based Strip Assay for Amplified Detection of Four miRNAs and Diagnosis of Lung Cancer.

The detection of circulating tumor microRNAs (miRNAs) holds great promise for the noninvasive and early-stage diagnosis of cancer. However, the low abundance of lung cancer-related miRNAs and the false-positive results of single miRNA detection limited the development of strip-based point-of-care testing methods in clinic. We developed a duplex-specific nuclease (DSN)-mediated and dual-AND logic gate-based triple-line lateral flow strip detection system for the rapid and simultaneous detection of four miRNAs of lung cancer in a single strip test. This system combines DSN-mediated signal amplification with AND logic gate-based simple signal output. Meanwhile, the limit of detection of this platform was calculated to be 26.51 fM. Furthermore, this assay was used to detect lung cancer-related miRNAs from serum in a homogeneous and separation-free format, which could discriminate lung cancer patients from healthy individuals with an accuracy of 100%. Our approach provides a simple and easy-to-handle method for the diagnosis of lung cancer in clinic.

Imaging strategies for receptor tyrosine kinase dimers in living cells.

Receptor tyrosine kinases (RTKs) are the essential regulators of cell signal transduction pathways and play important roles in biological processes. RTK dimerization is generally considered the first step in receptor activation and cell communication. And the abnormal expression of RTK dimers is closely related to the occurrence and development of many diseases. Therefore, the visualization of RTK dimerization is of great significance for monitoring physiological processes. The genetic and nongenetic imaging strategies have attracted widespread attention due to their high efficiency and high sensitivity. In this review, the RTKs and their dimers as well as the advances in strategies for imaging RTK dimers are introduced. Furthermore, we analyze the limitations of existing imaging strategies and put forward suggestions for the future development of imaging probes. We expect that this review will inspire more in-depth investigation of RTK dimers, which will also broaden the application of strategies of RTK dimers in biomedical areas.

Epichloë Endophyte Enhanced Insect Resistance of Host Grass Leymus Chinensis by Affecting Volatile Organic Compound Emissions.

In plant-herbivore interactions, plant volatile organic compounds (VOCs) play an important role in anti-herbivore defense. Grasses and Epichloë endophytes often form defensive mutualistic symbioses. Most Epichloë species produce alkaloids to protect hosts from herbivores, but there is no strong evidence that endophytes can affect the insect resistance of their hosts by altering VOC emissions. In this study, a native dominant grass, sheepgrass (Leymus chinensis), and its herbivore, oriental migratory locust (Locusta migratoria), were used as experimental materials. We studied the effect of endophyte-associated VOC emissions on the insect resistance of L. chinensis. The results showed that endophyte infection enhanced insect resistance of the host, and locusts preferred the odor of endophyte-free (EF) leaves to that of endophyte-infected (EI) leaves. We determined the VOC profile of L. chinensis using gas chromatography-mass spectrometry (GC-MS), and found that endophyte infection decreased the pentadecane (an alkane) emission from uneaten plants, and increased the nonanal (an aldehyde) emission from eaten plants. The olfactory response experiment showed that locusts were attracted by high concentration of pentadecane, while repelled by high concentration of nonanal, indicating that Epichloë endophytes may increase locust resistance of L. chinensis by decreasing pentadecane while increasing nonanal emission. Our results suggest that endophytes can induce VOC-mediated defense in hosts in addition to producing alkaloids, contributing to a better understanding the endophyte-plant-herbivore interactions.

A multiple lateral flow immunoassay based on AuNP for the detection of 5 chemical contaminants in milk.

Melamine (MEL), enrofloxacin (ENR), sulfamethazine (SMZ), tetracycline (TC), and aflatoxin M1 (AFM1) are the main chemical contaminants in milk. It is necessary to detect these miscellaneous chemical contaminants in milk synchronously to ensure the safety of the milk. In this study, a multiple lateral flow immunoassay (LFIA) was developed for the detection of MEL, ENR, SMZ, TC, and AFM1 in milk. Under optimal experimental conditions, the cutoff values were 25 ng/mL for MEL, 1 ng/mL for ENR, 2.5 ng/mL for SMZ, 2.5 ng/mL for TC, and 0.25 ng/mL for AFM1 in milk samples. The limits of detection of LFIA were 0.173 ng/mL for MEL, 0.078 ng/mL for ENR, 0.059 ng/mL for SMZ, 0.082 ng/mL for TC, and 0.0064 ng/mL for AFM1. The recovery rates of LFIA in milk were 83.2-104.4% for MEL, 76.5-127.3% for ENR, 96.8-113.5% for SMZ, 107.1-166.6% for TC, and 93.5-130.3% for AFM1. The coefficients of variation were all less than 15%. As a whole, the developed multiple lateral flow immunoassay showed potential as a highly reliable and excellent tool for the rapid and sensitive screening of MEL, ENR, SMZ, TC, and AFM1 in milk.

COF-DNA Bicolor Nanoprobes for Imaging Tumor-Associated mRNAs in Living Cells.

Developing probes for the simultaneous detection of multiple tumor-associated mRNAs is beneficial for the precise diagnosis and early therapy of cancer. In this work, we prepared two COF-DNA bicolor probes at room temperature and freezing conditions and evaluated their performances in simultaneous imaging of intracellular tumor-associated mRNAs. By loading dye-labeled survivin- and TK1-mRNA recognition sequences on porphyrin COF NPs, nucleic acid-specific "off-on" nanoprobes were obtained. The nanoprobe prepared by the freezing method exhibits higher ssDNA loading density and better fluorescence quenching efficiency. Moreover, its signal-to-noise ratio is significantly higher than that prepared at room temperature, and the target recognition effect was unaffected. Significantly, the freezing-method-prepared nanoprobe has higher signal intensities in target-overexpressed cells compared to the room-temperature-prepared probe, while their signals in cells with low target expression are similar. Thus, the freezing-method-prepared nanoprobe is a promising tool for improved cancer diagnostic imaging. This work can offer new insights into the exploration of high-performance COF-based nanoprobes for multiple biomarker detection.

Design, synthesis and biological evaluation of novel procaine derivatives for intravenous anesthesia.

A series of novel procaine derivatives for intravenous anesthesia were prepared and evaluated by physicochemical properties and pharmacodynamic experiments in vivo and in vitro. Systematic optimization of procaine led to the identification of 6f, 6g, 6h, 6o, 6p and 6q with higher TI value and moderate log D. Compared with procaine (TI = 1.65), most procaine derivatives demonstrated better security, among whichcompound 6h (TI = 2.68)was the most notable one and showed fewer adverse events in animals. The result of hNR2B-HEK293 assay indicated that compound 6h suppressed the NMDA receptor 2B subtype channel activity and it showed more than 80% inhibitory effect at the concentration of 500 µM.

The Na+-activated K+ channel Slack contributes to synaptic development and plasticity.

Human mutations of the Na+-activated K+ channel Slack (KCNT1) are associated with epilepsy and intellectual disability. Accordingly, Slack knockout mice (Slack-/-) exhibit cognitive flexibility deficits in distinct behavioral tasks. So far, however, the underlying causes as well as the role of Slack in hippocampus-dependent memory functions remain enigmatic. We now report that infant (P6-P14) Slack-/- lack both hippocampal LTD and LTP, likely due to impaired NMDA receptor (NMDAR) signaling. Postsynaptic GluN2B levels are reduced in infant Slack-/-, evidenced by lower amplitudes of NMDAR-meditated excitatory postsynaptic potentials. Low GluN2B affected NMDAR-mediated Ca2+-influx, rendering cultured hippocampal Slack-/-neurons highly insensitive to the GluN2B-specific inhibitor Ro 25-6981. Furthermore, dephosphorylation of the AMPA receptor (AMPAR) subunit GluA1 at S845, which is involved in AMPAR endocytosis during homeostatic and neuromodulator-regulated plasticity, is reduced after chemical LTD (cLTD) in infant Slack-/-. We additionally detect a lack of mGluR-induced LTD in infant Slack-/-, possibly caused by upregulation of the recycling endosome-associated small GTPase Rab4 which might accelerate AMPAR recycling from early endosomes. Interestingly, LTP and mGluR LTD, but not LTD and S845 dephosphorylation after cLTD are restored in adult Slack-/-. This together with normalized expression levels of GluN2B and Rab4 hints to developmental "restoration" of LTP expression despite Slack ablation, whereas in infant and adult brain, NMDAR-dependent LTD induction depends on this channel. Based on the present findings, NMDAR and vesicular transport might represent novel targets for the therapy of intellectual disability associated with Slack mutations. Consequently, careful modulation of hippocampal Slack activity should also improve learning abilities.

Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types.

Accumulating evidence has demonstrated that transcriptional regulation is affected by DNA methylation. Understanding the perturbation of DNA methylation-mediated regulation between transcriptional factors (TFs) and targets is crucial for human diseases. However, the global landscape of DNA methylation-mediated transcriptional dysregulation (DMTD) across cancers has not been portrayed. Here, we systematically identified DMTD by integrative analysis of transcriptome, methylome and regulatome across 22 human cancer types. Our results revealed that transcriptional regulation was affected by DNA methylation, involving hundreds of methylation-sensitive TFs (MethTFs). In addition, pan-cancer MethTFs, the regulatory activity of which is generally affected by DNA methylation across cancers, exhibit dominant functional characteristics and regulate several cancer hallmarks. Moreover, pan-cancer MethTFs were found to be affected by DNA methylation in a complex pattern. Finally, we investigated the cooperation among MethTFs and identified a network module that consisted of 43 MethTFs with prognostic potential. In summary, we systematically dissected the transcriptional dysregulation mediated by DNA methylation across cancer types, and our results provide a valuable resource for both epigenetic and transcriptional regulation communities.

Dual-target electrochemical DNA sensor for detection of Pb2+ and Hg2+ simultaneously by exonuclease I-assisted recycling signal amplification.

With the development of exonuclease, the exonuclease has been used to construct a variety of aptasensor and to realize the signal amplification. Among them, based on silver nanoparticles (Ag NPs) and exonuclease I (Exo I)-assisted cycle signal amplification strategy, we designed a novel high-sensitivity dual-target electrochemical biosensor to detect Pb2+ or Hg2+ in water. In the presence of Hg2+, the Hg2+ was fixed to the aptamer chain by thymine-Hg2+-thymine (T-Hg2+-T), resulting in the decrease of signal. When Pb2+ was present, DNA single strand S2 dissociated and was bound to Pb2+, which automatically triggered Exo I to selectively cut the single chain from the recognition site to achieve the cyclic amplification of the electrochemical signal. The interaction between aptamer and Exo I was investigated by gel electrophoresis. Under the optimum conditions in the scan range -0.20 to 0.60 V, the biosensor had high sensitivity with a linear range of 100 pg/L to 10.0 mg/L, Pb2+ or Hg2+, and the detection limits were 17.0 pg/L (R2 = 0.993) and 12.0 pg/L (R2 = 0.993), respectively. The relative standard deviation (RSD) of the sensor was 0.5-2.6%, and the recovery of spiked standard solutions was between 98.3 and 110%. The cycle amplification strategy supported by this enzyme has promising applications in detection of the two metal ions in various fields.

Electrochemiluminescence biosensor for determination of lead(II) ions using signal amplification by Au@SiO2 and tripropylamine-endonuclease assisted cycling process.

MXene@Au as the base and Au@SiO2 as signal amplification factor were used for constructing an ultrasensitive "on-off" electrochemiluminescence (ECL) biosensor for the detection of Pb2+ in water. The use of MXene@Au composite provided a good interface environment for the loading of tris(2,2-bipyridyl)ruthenium(II) (Ru(bpy)32+) on the electrode. Based on resonance energy transfer, the Au (core) SiO2 (shell) (Au@SiO2) nanoparticles stimulate electron transport and promote tripropylamine (TPrA) oxidation. The luminescence effect of Au@SiO2 was five times that of AuNPs and SiO2 nanomaterials alone, and the ECL intensity was greatly improved. In addition, Pb2+ activated the aptamer to exert its endonuclease activity, which realized the signal cycle amplification in the process of Pb2+ detection. When Pb2+ was added, the ECL signal weakened, and the Pb2+ concentration was detected according to the decreased ECL intensity. Under optimized experimental conditions, this aptamer sensor for Pb2+ has a wide detection range (0.1 to 1 × 106 ng L-1) and a low detection limit (0.059 ng L-1). The relative standard deviation (RSD) of the sensor is 0.39-0.99%, and the recovery of spiked standard is between 90.00 and 125.70%. The sensor shows good selectivity and high sensitivity in actual water sample analysis. This signal amplification strategy possibly provides a new method for the detection of other heavy metal ions and small molecules.

MIR22HG acts as a tumor suppressor via TGFß/SMAD signaling and facilitates immunotherapy in colorectal cancer.

BACKGROUND: Long noncoding RNAs (lncRNAs) are emerging as critical regulatory elements and play fundamental roles in the biology of various cancers. However, we are still lack of knowledge about their expression patterns and functions in human colorectal cancer (CRC). METHODS: Differentially expressed lncRNAs in CRC were identified by bioinformatics screen and the level of MIR22HG in CRC and control tissues were determined by qRT-PCR. Cell viability and migration capacities were examined by MTT and transwell assay. Mouse model was used to examine the function and rational immunotherapy of MIR22HG in vivo. RESULTS: We systematically investigated the expression pattern of lncRNAs and revealed MIR22HG acts as a tumor suppressor in CRC. The expression of MIR22HG was significantly decreased in CRC, which was mainly driven by copy number deletion. Reduced expression of MIR22HG was significantly associated with poor overall survival. Silencing of MIR22HG promoted cell survival, proliferation and tumor metastasis in vitro and in vivo. Mechanistically, MIR22HG exerts its tumor suppressive activity by competitively interacting with SMAD2 and modulating the activity of TGFß pathway. Decreased MIR22HG promoted the epithelial-mesenchymal transition in CRC. Importantly, we found that MIR22HG expression is significantly correlated with CD8A and overexpression of MIR22HG triggers T cell infiltration, enhancing the clinical benefits of immunotherapy. CONCLUSION: MIR22HG acts as a tumor suppressor in CRC. Our data provide mechanistic insights into the regulation of MIR22HG in TGFß pathway and facilitates immunotherapy in cancer.

The role of international partnerships in improving urethral reconstruction in low- and middle-income countries.

PURPOSE: To explore the impact of education and training in international surgical partnerships on outcomes of urethral stricture disease in low- and middle-income countries. To encourage data collection and outcomes assessments to promote evidence-based and safe surgical care. METHODS: Qualitative data were collected through observation of a reconstructive surgical workshop held by IVUmed at a host site in Dakar, Senegal. Quantitative data were collected through a retrospective review of 11 years of hospital data to assess surgical outcomes of urethral stricture disease before and after IVUmed started reconstructive workshops at the site. RESULTS: In the 11-year study period, 569 patients underwent 774 surgical procedures for urethral strictures. The numbers and types of urethroplasty techniques increased after IVUmed started its workshops. The average number of urethroplasties increased from 10 to 18.75/year. There was a statistically significant improvement in the mean success rate of urethroplasties from 12.7% before to 29% after the workshops. Anastomotic urethroplasty success rates doubled from 16.7 to 35.1%, but this was not statistically significant (p = 0.07). The improved success rate was sustained in cases performed without an IVUmed provider. CONCLUSIONS: Urethral stricture disease treatment in low- and middle-income countries is fraught with challenges due to complex presentations and limited subspecialty training. Improper preoperative management, lack of specialty instruments, and suboptimal wound care all contribute to poor outcomes. International surgical groups like IVUmed who employ the "teach-the-teacher" model enhance local practitioner expertise and independence leading to long-term improvements in patient outcomes. Tailoring practice guidelines to the local resource framework and encouraging data collection and outcomes assessment are vital components of providing responsible care and should be encouraged.

Green Synthesis of Gold Nanoparticles Using Carrageenan Oligosaccharide and Their In Vitro Antitumor Activity.

Gold nanoparticles (AuNPs) have been widely used in catalysis, photothermal therapy, and targeted drug delivery. Carrageenan oligosaccharide (CAO) derived from marine red algae was used as a reducing and capping agent to obtain AuNPs by an eco-friendly, efficient, and simple synthetic route for the first time. The synthetic conditions of AuNPs were optimized by response surface methodology (RSM), and the CAO-AuNPs obtained were demonstrated to be ellipsoidal, stable and crystalline by means of transmission electron microscopy (TEM), scanning electron microscopy (SEM) and X-ray diffraction (XRD). The CAO-AuNPs showed localized surface plasmon resonance (LSPR) oscillation at about 530 nm with a mean diameter of 35 ± 8 nm. The zeta potential of CAO-AuNPs was around -20 mV, which was related to the negatively charged CAO around AuNPs. The CAO-AuNPs exhibited significant cytotoxic activities to HCT-116 and MDA-MB-231 cells, which could be a promising nanomaterial for drug delivery.

Oleanolic acid attenuates TGF-ß1-induced epithelial-mesenchymal transition in NRK-52E cells.

BACKGROUND: Epithelial-to-mesenchymal transition (EMT) plays an important role in the progression of renal interstitial fibrosis, which finally leads to renal failure. Oleanolic acid (OA), an activator of NF-E2-related factor 2 (Nrf2), is reported to attenuate renal fibrosis in mice with unilateral ureteral obstruction. However, the role of OA in the regulation of EMT and the underlying mechanisms remain to be investigated. This study aimed to evaluate the effects of OA on EMT of renal proximal tubular epithelial cell line (NRK-52E) induced by TGF-ß1, and to elucidate its underlying mechanism. METHODS: Cells were incubated with TGF-ß1 in the presence or absence of OA. The epithelial marker E-cadherin, the mesenchymal markers, α-smooth muscle actin (α-SMA), fibronectin, Nrf2, klotho, the signal transducer (p-Smad2/3), EMT initiator (Snail), and ILK were assayed by western blotting. RESULTS: Our results showed that the NRK-52E cells incubated with TGF-ß1 induced EMT with transition to the spindle-like morphology, down-regulated the expression of E-cadherin but up-regulated the expression of α-SMA and fibronectin. However, the treatment with OA reversed all EMT markers in a dose-dependent manner. OA also restored the expression of Nrf2 and klotho, decreased the phosphorylation of Smad2/3, ILK, and Snail in cells which was initiated by TGF-ß1. CONCLUSION: OA can attenuate TGF-ß1 mediate EMT in renal tubular epithelial cells and may be a promising therapeutic agent in the treatment of renal fibrosis.

Gene polymorphism of rs556621 but Not rs11984041 is associated with the risk of large artery atherosclerotic stroke in a Xinjiang Uyghur population.

BACKGROUND: Stroke is one of the main causes of death and adult chronic disability. Recently, 2 independent genome-wide association studies reported that the genetic variants (rs556621 and rs11984041) are significantly associated with large artery atherosclerosis (LAA). METHODS: To determine whether these 2 variants are associated with the pathogenesis of LAA in stroke patients from the Xinjiang Uyghur autonomous region of China, both variants were evaluated in a series of 733 LAA stroke patients (434 Han and 299 Uyghur) and 725 age-, gender-, smoking-, alcohol habits- and ethnicity-matched controls (401 Han and 324 Uyghur). RESULTS: For rs556621, significant differences in genotypic and allelic distributions were observed between Uyghur patients and controls (P = .045 for genotypic distribution, P = .042 for allelic distribution) but not in the Chinese Han cohort (P > .05). No significant differences were found in genotypic and allele distributions between patients and controls for rs11984041 in either the Chinese Han or Uyghur cohort (P > .05). CONCLUSIONS: The variant rs556621 but not rs11984041 may increase susceptibility of LAA stroke in the Xinjiang Uyghur population.