Facile Synthesis of Aptamer-Functionalized Polydopamine-Coated Magnetic Graphene Oxide Nanocomposites for Highly Efficient Purification of His-Tagged Proteins.

Recombinant proteins hold significant importance in numerous disciplines. As the demand for expressing and purifying these proteins grows, the scientific community is in dire need of a simple yet versatile methodology that can efficiently purify these proteins. Aptamers as synthetic nucleic acid-based ligands with high affinity have shown promise in this regard, as they can capture targets through molecular recognition. In this study, novel aptamer-functionalized polydopamine-coated magnetic graphene oxide nanocomposites were facilely prepared, achieving an impressive average aptamer coverage density (45 nmol/mg). These nanocomposites exhibited a uniform structure and robust magnetic responsiveness. The findings indicated that they possess several advantages, such as rapid adsorption, substantial capacity (171.4 mg/g), and excellent reusability. Notably, due to the inherent properties of nucleic acids, the immobilized aptamer-magnetic beads can be utilized repeatedly with high purification efficiency. Finally, the nanocomposites were further employed to purify His-tagged proteins from actual samples. Remarkably, they were able to selectively and efficiently isolate His-tagged retinoid X receptor alpha protein from complex Escherichia coli lysate. The purified His-tagged retinoid X receptor alpha protein was analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This confirmed the efficacy of developed nanocomposites, reinforcing their vast potential for purification of His-tagged recombinant proteins.

Acridone-Based Host Materials for Green Phosphorescent and Thermally Activated Delayed Fluorescent OLEDs with Low-Efficiency Roll-Offs.

By linking the carbazole unit to the nitrogen atom of acridone through phenyl or pyridyl, two compounds, named 10-(4-(9H-carbazol-9-yl)phenyl)acridin-9(10H)-one (AC-Ph-Cz) and 10-(5-(9H-carbazol-9-yl)pyridin-2-yl)acridin-9(10H)-one (AC-Py-Cz) were designed and synthesized. These two materials, characterized with highly twisted and rigid structure, good thermal stability, and balanced carrier-transporting properties, were employed as host materials for green phosphorescent and thermally activated delayed fluorescent organic light-emitting diodes (OLEDs). The carbazole group, despite its small contribution to the highest occupied molecular orbitals (HOMOs) of these two materials, plays an essential role as an intramolecular host in energy delivering and improving the hole transporting ability of these two hosts. The incorporation of the electron-deficient pyridyl group as a linking group slightly improves the electron transporting capability of AC-Py-Cz. The green phosphorescent OLED (PhOLED) based on AC-Py-Cz exhibited excellent device performance with a turn-on voltage of 2.5 V, a maximum power efficiency and an external quantum efficiency (ηext ) of 89.8 lm W-1 and 25.2 %, respectively, benefitting from the better charge-balancing ability of AC-Py-Cz host due to the presence of the pyridyl bridge. More importantly, all the devices based on these two hosts showed low efficiency roll-off at high brightness due to the suppressed non-radiative transition in the emitting layer. In particular, the AC-Py-Cz-hosted green PhOLED exhibited an efficiency roll-off of 1.6 % from the maximum next at a high brightness of 1000 cd m-2 and a roll-off of 15.9 % at an extremely high brightness of 10000 cd m-2 . This study manifests that acridone-based host materials have great potential in fabricating OLEDs with low efficiency roll-off.

A 4-α-Glucanotransferase from Thermus thermophilus HB8: Secretory Expression and Characterization.

4-α-glucanotransferase (4GT, EC 2.4.1.25) catalyzes the breakdown of the α-1,4 glycosidic bonds of the starch main chain and forms new α-1,4 glycosidic bonds in the side chain, which is often used to optimize the physical and chemical properties of starch and to improve the quality of starch-based food. However, the low enzyme activity of 4GT limits its production and widespread application. Herein, the 4GT gene encoding 500 amino acids from Thermus thermophilus HB8 was cloned and expressed in Escherichia coli. The purified 4GT exhibited maximum activity at pH 7.0 and 60 °C and had a good stability at pH 6.0-8.0 and 30-60 °C. It was confirmed that 4GT possessed the catalytic function of extending the branch length of potato starch. Furthermore, the 4GT gene was successfully expressed extracellularly in Bacillus subtilis. Then, the enzyme yield of 4GT increased by 4.1 times through screening of different plasmids and hosts. Additionally, the fermentation conditions were optimized to enhance 4GT extracellular enzyme yield. Finally, a recombinant Bacillus subtilis with 299.9 U/mL enzyme yield of 4GT was obtained under the optimized fermentation process. In conclusion, this study provides a valuable reference for characterization and expression of food-grade enzymes.

Selective enrichment of sialylated glycopeptides with mesoporous poly-melamine-formaldehyde (mPMF) material.

Analysis of glycoprotein sialylation is challenging due to the relatively low abundance of sialylated glycopeptides (SGPs) in complex biosamples and low signals of SGPs in mass spectrometry. In this study, a mesoporous poly-melamine-formaldehyde (mPMF) polymer was prepared and utilized as the high-efficiency sorbent for SGPs. The mPMF polymer featured high surface area (755.4 m2 g-1) and high density of amine and triazine functional groups. This polymer demonstrated high enrichment selectivity (resistant to 100 molar fold interference of BSA) and superior adsorption capacity (560 mg g-1) for SGPs. The high performance of mPMF toward SGPs ascribes to the unique physicochemical properties of mPMF and high density of accessible binding sites for glycopeptides. Further application of mPMF to HeLa S3 cell lysate resulted in 576 characterized glycopeptides with 218 unique glycosylation sites. This finding provides a new choice of promising extraction approach for characterization of protein glycosylation. Graphical abstract A mesoporous poly-melamine-formaldehyde (mPMF) polymer was prepared and utilized as the high-efficiency enrichment sorbent for sialylated glycopeptides (SGPs).

Antibiotic ivermectin selectively induces apoptosis in chronic myeloid leukemia through inducing mitochondrial dysfunction and oxidative stress.

Mitochondria has been a promising target in blood cancer given their unique dependencies on mitochondrial functions compared to normal hematopoietic cells. In line with this concept, we show that an anthelminthic drug ivermectin selectively kills chronic myeloid leukemia (CML) cells via inducing mitochondrial dysfunctions and oxidative stress. Ivermectin is significantly more effective in inducing caspase-dependent apoptosis in CML cell line K562 and primary CML CD34 than normal bone marrow (NBM) CD34 cells. Ivermectin also augments in vitro and in vivo efficacy of standard CML tyrosine kinase inhibitors. Mechanistically, ivermectin inhibits respiratory complex I activity and suppresses mitochondrial respiration in K562 and CML CD34 cells. Interestingly, we demonstrate that mitochondrial respiration are lower in NBM CD34 compared to malignant CD34 cells. In addition, ivermectin also induces mitochondrial dysfunctions in NBM CD34 cells in a similar manner as in CML CD34 cells whereas NBM CD34 cells are significantly less sensitive to ivermectin than CML CD34 cells. These suggest that NBM CD34 cells are more tolerable to mitochondrial dysfunctions than CML CD34 cells. Consistently, ivermectin induces higher levels of oxidative stress and damage in CML than normal counterparts. Antioxidant NAC rescues ivermectin's effects, confirming oxidative stress as the mechanism of its action in CML. Our work provides the fundamental evidence to repurpose ivermectin for CML treatment. Our work also highlights the therapeutic value of targeting mitochondria respiration in CML.

Separation behavior of basic compounds on unbonded silicon oxynitride and silica high-performance liquid chromatography stationary phases with reversed-phase eluents.

Unbonded silicon oxynitride and silica high-performance liquid chromatography stationary phases have been evaluated and compared for the separation of basic compounds of differing molecular weight, pKa , and log D using aqueous/organic mobile phases. The influences of percentage of organic modifier, buffer pH, and concentration in the mobile phase on base retention were investigated on unbonded silicon oxynitride and silica phases. The results confirmed that unbonded silicon oxynitride and silica phases demonstrated excellent separation performance for model basic compounds and both the unbonded phases examined possessed a hydrophobic/adsorption and ion-exchange character. The silicon oxynitride stationary phase exhibited high hydrophilicity compared with silica with a reversed-phase mobile phase. An ion-exclusion-type mechanism becomes predominant for the separation of three aimed bases on the silicon oxynitride column at pH 2.8. Different from silicon oxynitride stationary phase, no obvious change for the retention time of three model bases on silica stationary phase at pH 2.8 can be observed.

Evaluation of a silicon oxynitride hydrophilic interaction liquid chromatography column in saccharide and glycoside separations.

The retention characteristics of a silicon oxynitride stationary phase for carbohydrate separation were studied in hydrophilic interaction chromatography mode. Four saccharides including mono-, di-, and trisaccharides were employed to investigate the effects of water content and buffer concentration in the mobile phase on hydrophilic interaction liquid chromatography retention. For the tested saccharides, the silicon oxynitride column demonstrated excellent performance in terms of separation efficiency, hydrophilicity, and interesting separation selectivity for carbohydrates compared to the bare silica stationary phase. Finally, the silicon oxynitride hydrophilic interaction liquid chromatography column was employed in the separation of complex samples of fructooligosaccharides, saponins, and steviol glycoside from natural products. The resulting chromatograms demonstrated good separation efficiency and longer retention compared with silica, which further confirmed the advantages and potential application of silicon oxynitride stationary phase for hydrophilic interaction liquid chromatography separation.

Highly selective separation of aminoglycoside antibiotics on a zwitterionic Click TE-Cys column.

Hydrophilic interaction liquid chromatography has emerged as a valuable alternative approach to ion-pair chromatography for the separation of aminoglycoside antibiotics in recent years. However, the resolution of structurally related aminoglycosides is a great challenge owing to the limited selectivity. In this work, a cysteine-based zwitterionic stationary phase (named Click TE-Cys) was utilized and compared with five commonly used hydrophilic interaction liquid chromatography columns. Click TE-Cys displayed much better selectivity for structurally similar aminoglycosides. The retention behaviors of aminoglycosides were investigated in detail, revealing that low pH (2.7 or 3.0) and high buffer concentration (≥50 mM) were preferable for achieving good peak shape and selectivity. Effective resolution of ten aminoglycosides including spectinomycin, dihydrostreptomycin, streptomycin, gentamicin C1, gentamicin C2/C2a, gentamicin C1a, kanamycin, paromonycin, tobramycin, and neomycin was realized at optimized conditions. Additionally, spectinomycin and its related impurities were successfully resolved. The results indicated the great potential of the Click TE-Cys column in the separation of aminoglycoside mixtures and related impurities.

Mechanism of tartaric acid mediated dissipation and biotransformation of tetrabromobisphenol A and its derivatives in soil.

Biotransformation is a major dissipation process of tetrabromobisphenol A and its derivatives (TBBPAs) in soil. The biotransformation and ultimate environmental fate of TBBPAs have been widely studied, yet the effect of root exudates (especially low-molecular weight organic acids (LMWOAs)) on the fate of TBBPAs is poorly documented. Herein, the biotransformation behavior and mechanism of TBBPAs in bacteriome driven by LMWOAs were comprehensively investigated. Tartaric acid (TTA) was found to be the main component of LMWOAs in root exudates of Helianthus annus in the presence of TBBPAs, and was identified to play a key role in driving shaping bacteriome. TTA promoted shift of the dominant genus in soil bacteriome from Saccharibacteria_genera_incertae_sedis to Gemmatimonas, with a noteworthy increase of 24.90-34.65% in relative abundance of Gemmatimonas. A total of 28 conversion products were successfully identified, and ß-scission was the principal biotransformation pathway for TBBPAs. TTA facilitated the emergence of novel conversion products, including 2,4-dibromophenol, 3,5-dibromo-4-hydroxyacetophenone, para-hydroxyacetophenone, and tribromobisphenol A. These products were formed via oxidative skeletal cleavage and debromination pathways. Additionally, bisphenol A was observed during the conversion of derivatives. This study provides a comprehensive understanding about biotransformation of TBBPAs driven by TTA in soil bacteriome, offering new insights into LMWOAs-driven biotransformation mechanisms.

The bioaccumulation and biotransformation of tetrabromobisphenol A bis (allyl ether) in common carp (Cyprinus carpio).

Tetrabromobisphenol A bis (allyl ether) (TBBPA-BAE) is an extensively used brominated flame retardant, which has raised considerable concern because of its neurotoxic and endocrine disruption effects on aquatic organisms. However, previous studies mainly focused on the parent compound before modification, tetrabromobisphenol A (TBBPA), and little information is available about the bioconcentration and biotransformation of TBBPA derivatives in fish. In this study, we investigated the tissue-specific uptake, elimination kinetic, and biotransformation of TBBPA-BAE in common carp (Cyprinus carpio). The fish were exposed to TBBPA-BAE at environmentally relevant concentrations (20 µg·L-1) for 28 days, followed by 14 days of depuration. The results showed TBBPA-BAE could rapidly accumulate in common carp. Among the seven tissues studied, the highest concentrations of TBBPA-BAE were observed in the liver (6.00 µg·g-1 wet weight [ww]) on day 24, while the longest residence time was observed in the kidney (t1/2 values of 18.7 days). Biotransformation of TBBPA-BAE was documented in the in vivo experiments, and 14 different phase I and phase II metabolites were identified in the liver. These findings suggest the biotransformation products of TBBPA-BAE should be considered for a comprehensive risk evaluation.

[Determination of nine organic amine compounds in CO2 absorption liquid by hydrophilic interaction liquid chromatography-electrostatic field orbitrap high resolution mass spectrometry].

Carbon dioxide (CO2) absorption and capture is an effective measure to achieve the "dual carbon" goal of carbon peak and carbon neutrality in China. Organic amine compounds are widely used in the industrial separation and recovery of CO2. Thus, the establishment of analytical methods for organic amine compounds is of great significance for the research and development of carbon capture and storage (CCS) technology and carbon capture, utilization and storage (CCUS) technology. In this study, a method was developed for the determination of nine organic amine compounds in CO2 absorption liquid by hydrophilic interaction liquid chromatography (HILIC)-electrostatic field orbitrap high resolution mass spectrometry. The sample was diluted with water and filtered through a 0.22 µm nylon membrane before sampling and analysis. An Accucore HILIC column (100 mm×2.1 mm, 2.6 µm) was used for separation at 30 ℃. Gradient elution was conducted using 90% acetonitrile aqueous solution containing 5 mmol/L ammonium formate and 0.1% formic acid as mobile phase A and 10% acetonitrile aqueous solution containing 5 mmol/L ammonium formate and 0.1% formic acid as mobile phase B. Determination was performed using an electrospray ion source (ESI) in the positive ion mode. The quantitative analysis was carried out by standard addition method. The chromatographic retention performance of different chromatographic columns and the influence of different mobile phases on the separation of the organic amine compounds were compared, and the method was validated. The results showed that the linear ranges of the nine organic amine compounds were 0.04-25000 ng/mL with the linear correlation coefficients (R2) greater than 0.9910. The limits of detection (LODs) of the method were in the range of 0.0004-0.0080 ng/mL, and the limits of quantification (LOQs) of the method were in the range of 0.0035-0.0400 ng/mL. The average recoveries of the method ranged from 85.30% to 104.26% with relative standard deviations (RSDs) of 0.04%-7.95% at the spiked levels of 1, 1.5 and 3 times sample concentration. The established method was applied to detect the absorption waste liquid of a cement plant, and nine organic amine compounds could be effectively detected. The stability of the actual sample was tested, and the RSDs were 0.10%-6.35% in 48 h at 4 ℃. The method is sensitive, rapid and accurate for the determination of the nine organic amine compounds in industrial waste water. It can provide reference for the detection of organic amine compounds, and provide strong technical support for the research and industrial application of CO2 capture technology.

Engineering Komagataella phaffii to biosynthesize cordycepin from methanol which drives global metabolic alterations at the transcription level.

Cordycepin has the potential to be an alternative to the disputed herbicide glyphosate. However, current laborious and time-consuming production strategies at low yields based on Cordyceps militaris lead to extremely high cost and restrict its application in the field of agriculture. In this study, Komagataella phaffii (syn. Pichia pastoris) was engineered to biosynthesize cordycepin from methanol, which could be converted from CO2. Combined with fermentation optimization, cordycepin content in broth reached as high as 2.68 ± 0.04 g/L within 168 h, around 15.95 mg/(L·h) in productivity. Additionally, a deaminated product of cordycepin was identified at neutral or weakly alkaline starting pH during fermentation. Transcriptome analysis found the yeast producing cordycepin was experiencing severe inhibition in methanol assimilation and peroxisome biogenesis, responsible for delayed growth and decreased carbon flux to pentose phosphate pathway (PPP) which led to lack of precursor supply. Amino acid interconversion and disruption in RNA metabolism were also due to accumulation of cordycepin. The study provided a unique platform for the manufacture of cordycepin based on the emerging non-conventional yeast and gave practical strategies for further optimization of the microbial cell factory.

Construction and Validation of Convenient Clinicopathologic Signatures for Predicting the Prognosis of Stage I-III Gastric Cancer.

Background: Patients with stage I-III gastric cancer (GC) undergoing R0 radical resection display extremely different prognoses. How to discriminate high-risk patients with poor survival conveniently is a clinical conundrum to be solved urgently. Methods: Patients with stage I-III GC from 2010 to 2016 were included in our study. The associations of clinicopathological features with disease-free survival (DFS) and overall survival (OS) were examined via Cox proportional hazard model. Nomograms were developed which systematically integrated prognosis-related features. Kaplan-Meier survival analysis was performed to compare DFS and OS among groups. The results were then externally validated by The Sixth Affiliated Hospital, Sun Yat-sen University. Results: A total of 585 and 410 patients were included in the discovery cohort and the validation cohort, respectively. T stage, N stage, lymphatic/vascular/nerve infiltration, preoperative CEA, and CA19-9 were independent prognostic factors (P < 0.05). Two prognostic signatures with a concordance index (C-index) of 0.7502 for DFS and 0.7341 for OS were developed based on the nomograms. The 3-year and 5-year calibration curves showed a perfect correlation between predicted and observed outcomes. Patients were divided into three risk groups (low, intermediate, high), and distinct differences were noticed (p < 0.001). Similar results were achieved in the validation cohort. Notably, a free website was constructed based on our signatures to predict the recurrence risk and survival time of patients with stage I-III GC. Conclusions: The signatures demonstrate the powerful ability to conveniently identify distinct subpopulations, which may provide significant suggestions for individual follow-up and adjuvant therapy.

Blocking IbmiR319a Impacts Plant Architecture and Reduces Drought Tolerance in Sweet Potato.

MicroRNA319 (miR319) plays a key role in plant growth, development, and multiple resistance by repressing the expression of targeted TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) genes. Two members, IbmiR319a and IbmiR319c, were discovered in the miR319 gene family in sweet potato (Ipomoea batatas [L.] Lam). Here, we focused on the biological function and potential molecular mechanism of the response of IbmiR319a to drought stress in sweet potato. Blocking IbmiR319a in transgenic sweet potato (MIM319) resulted in a slim and tender phenotype and greater sensitivity to drought stress. Microscopic observations revealed that blocking IbmiR319a decreased the cell width and increased the stomatal distribution in the adaxial leaf epidermis, and also increased the intercellular space in the leaf and petiole. We also found that the lignin content was reduced, which led to increased brittleness in MIM319. Quantitative real-time PCR showed that the expression levels of key genes in the lignin biosynthesis pathway were much lower in the MIM319 lines than in the wild type. Ectopic expression of IbmiR319a-targeted genes IbTCP11 and IbTCP17 in Arabidopsis resulted in similar phenotypes to MIM319. We also showed that the expression of IbTCP11 and IbTCP17 was largely induced by drought stress. Transcriptome analysis indicated that cell growth-related pathways, such as plant hormonal signaling, were significantly downregulated with the blocking of IbmiR319a. Taken together, our findings suggest that IbmiR319a affects plant architecture by targeting IbTCP11/17 to control the response to drought stress in sweet potato.

Zirconia layer coated mesoporous silica microspheres as HILIC SPE materials for selective glycopeptide enrichment.

Characterization of protein glycosylation requires highly specific methods for the enrichment of glycopeptides because of their sub-stoichiometric glycosylation-site occupancy. The hydrophilic affinity based strategy has attracted more attention, owing to its broad glycan specificity, good reproducibility, and compatibility with mass spectrometric (MS) analysis. Several polar matrices have emerged for hydrophilic interaction chromatography (HILIC) approaches, including sepharose, cellulose, ZIC-HILIC and titania. Here, we present the solid-phase extraction (SPE) utility of zirconia coated mesoporous silica (ZrO(2)/MPS) microspheres for glycopeptide isolation prior to MS analysis. The high specificity of this SPE approach was demonstrated by the enrichment of glycopeptides from the digests of model glycoproteins in HILIC mode. ZrO(2)/MPS microspheres show superior selectivity and glycosylation heterogeneity coverage for glycopeptide enrichment to conventional sepharose. Furthermore, digested mixtures of the phosphoprotein α-casein and IgG were also treated with ZrO(2)/MPS HILIC SPE materials, which exhibited that glycopeptides could be effectively enriched with interference from phosphorylated peptides.

Photochemical reaction of tricresyl phosphate (TCP) in aqueous solution: Influencing factors and photolysis products.

Organophosphate triesters (OPEs) have caused great concern as a class of emerging environmental contaminants due to their widespread use and their toxicity to organisms. However, the phototransformation behavior of OPE is still not fully understood, which is important for understanding their environmental fate. In the present study, the photodegradation of tricresyl phosphate (TCP), one of the most widely detected OPEs in aqueous environments, was investigated including the direct photolysis and in the presence of several natural water factors, NO2-, Fe3+ and humic acid. The degradation process followed the pseudo-first-order kinetics, with rate constant increasing slightly with increasing initial TCP concentration. The presence of NO2- and Fe3+ was observed to promote the photochemical loss of TCP, while humic acid played a negative role on TCP transformation. Electron spin resonance (EPR) analysis showed that carbon-centered radical was produced in the photolysis process of TCP, and hydroxyl radical contributed to the promotion of rate constant for Fe3+ and NO2-. Four photolysis products were tentatively identified by HPLC-LTQ-Orbitrap MS analysis, and the possible degradation pathways of TCP were proposed. These findings provide a meaningful reference for the fate and transformation of OPEs in natural water.

Psychological resilience and positive coping styles among Chinese undergraduate students: a cross-sectional study.

BACKGROUND: Psychological resilience and coping strategies have been found to be related to various psychological and mental health problems. Evaluations of the relationship between resilience and coping style among university students are important for developing effective health promotion strategies focused on resilience intervention to benefit students' health and well-being. The relationship between psychological resilience and coping styles has usually been examined among adults and patients. Very few studies have investigated the relationship between resilience and coping style in university students. The present study aimed to investigate the associations between psychological resilience, students' characteristics (gender, major and grade) and coping styles among undergraduate students. METHODS: A cross-sectional survey was conducted among undergraduate students in Shandong Province, China. Undergraduate students were randomly selected from 6 universities in 3 cities of the province using a stratified random sampling method. The questionnaire included questions on the participants' demographic information, including gender, grade and major, measures of psychological resilience and coping style. Coping style was measured by the Simplified Coping Style Questionnaire (SCSQ). The Asian Resilience Scale (ARS) was applied to evaluate undergraduates' psychological resilience. Multivariable regression analysis was used to examine the relationships between resilience, students' characteristics and positive coping styles. RESULTS: A sample of 1743 undergraduates was analysed. The mean psychological resilience score was 70.41. The mean score for positive coping style was 24.72. Multiple regression analysis showed that three factors of psychological resilience, mood control, self-plasticity and coping flexibility, were all significant factors for positive coping styles (regression coefficient = 0.34, 0.35, 0.14, p < 0.01 for the three factors, respectively). Medical students and females had higher scores for positive coping styles than non-medical students and males (p < 0.01). CONCLUSIONS: The research revealed that females and medical students are more likely than males and non-medical students to adopt positive coping styles. Higher psychological resilience is associated with a better positive coping style. The findings suggest that psychological education and health promotion programmes that target strengthening psychological resilience among undergraduate students may help foster positive coping styles to benefit their mental health and psychological well-being.

[Application of immune cell infiltration in the diagnosis and prognosis of non-small cell lung cancer].

Immune cell infiltration is of great significance for the diagnosis and prognosis of cancer. In this study, we collected gene expression data of non-small cell lung cancer (NSCLC) and normal tissues included in TCGA database, obtained the proportion of 22 immune cells by CIBERSORT tool, and then evaluated the infiltration of immune cells. Subsequently, based on the proportion of 22 immune cells, a classification model of NSCLC tissues and normal tissues was constructed using machine learning methods. The AUC, sensitivity and specificity of classification model built by random forest algorithm reached 0.987, 0.98 and 0.84, respectively. In addition, the AUC, sensitivity and specificity of classification model of lung adenocarcinoma and lung squamous carcinoma tissues constructed by random forest method 0.827, 0.75 and 0.77, respectively. Finally, we constructed a prognosis model of NSCLC by combining the immunocyte score composed of 8 strongly correlated features of 22 immunocyte features screened by LASSO regression with clinical features. After evaluation and verification, C-index reached 0.71 and the calibration curves of three years and five years were well fitted in the prognosis model, which could accurately predict the degree of prognostic risk. This study aims to provide a new strategy for the diagnosis and prognosis of NSCLC based on the classification model and prognosis model established by immune cell infiltration.

INeo-Epp: A Novel T-Cell HLA Class-I Immunogenicity or Neoantigenic Epitope Prediction Method Based on Sequence-Related Amino Acid Features.

In silico T-cell epitope prediction plays an important role in immunization experimental design and vaccine preparation. Currently, most epitope prediction research focuses on peptide processing and presentation, e.g., proteasomal cleavage, transporter associated with antigen processing (TAP), and major histocompatibility complex (MHC) combination. To date, however, the mechanism for the immunogenicity of epitopes remains unclear. It is generally agreed upon that T-cell immunogenicity may be influenced by the foreignness, accessibility, molecular weight, molecular structure, molecular conformation, chemical properties, and physical properties of target peptides to different degrees. In this work, we tried to combine these factors. Firstly, we collected significant experimental HLA-I T-cell immunogenic peptide data, as well as the potential immunogenic amino acid properties. Several characteristics were extracted, including the amino acid physicochemical property of the epitope sequence, peptide entropy, eluted ligand likelihood percentile rank (EL rank(%)) score, and frequency score for an immunogenic peptide. Subsequently, a random forest classifier for T-cell immunogenic HLA-I presenting antigen epitopes and neoantigens was constructed. The classification results for the antigen epitopes outperformed the previous research (the optimal AUC = 0.81, external validation data set AUC = 0.77). As mutational epitopes generated by the coding region contain only the alterations of one or two amino acids, we assume that these characteristics might also be applied to the classification of the endogenic mutational neoepitopes also called "neoantigens." Based on mutation information and sequence-related amino acid characteristics, a prediction model of a neoantigen was established as well (the optimal AUC = 0.78). Further, an easy-to-use web-based tool "INeo-Epp" was developed for the prediction of human immunogenic antigen epitopes and neoantigen epitopes.

dbPepNeo: a manually curated database for human tumor neoantigen peptides.

Neoantigens can function as actual antigens to facilitate tumor rejection, which play a crucial role in cancer immunology and immunotherapy. Emerging evidence revealed that neoantigens can be used to develop personalized, cancer-specific vaccines. To date, large numbers of immunogenomic peptides have been computationally predicted to be potential neoantigens. However, experimental validation remains the gold standard for potential clinical application. Experimentally validated neoantigens are rare and mostly appear scattered among scientific papers and various databases. Here, we constructed dbPepNeo, a specific database for human leukocyte antigen class I (HLA-I) binding neoantigen peptides based on mass spectrometry (MS) validation or immunoassay in human tumors. According to the verification methods of these neoantigens, the collection of peptides was classified as 295 high confidence, 247 medium confidence and 407 794 low confidence neoantigens, respectively. This can serve as a valuable resource to aid further screening for effective neoantigens, optimize a neoantigen prediction pipeline and study T-cell receptor (TCR) recognition. Three applications of dbPepNeo are shown. In summary, this work resulted in a platform to promote the screening and confirmation of potential neoantigens in cancer immunotherapy. Database URL: www.biostatistics.online/dbPepNeo/.