Mucus sialylation determines intestinal host-commensal homeostasis.

Intestinal mucus forms the first line of defense against bacterial invasion while providing nutrition to support microbial symbiosis. How the host controls mucus barrier integrity and commensalism is unclear. We show that terminal sialylation of glycans on intestinal mucus by ST6GALNAC1 (ST6), the dominant sialyltransferase specifically expressed in goblet cells and induced by microbial pathogen-associated molecular patterns, is essential for mucus integrity and protecting against excessive bacterial proteolytic degradation. Glycoproteomic profiling and biochemical analysis of ST6 mutations identified in patients show that decreased sialylation causes defective mucus proteins and congenital inflammatory bowel disease (IBD). Mice harboring a patient ST6 mutation have compromised mucus barriers, dysbiosis, and susceptibility to intestinal inflammation. Based on our understanding of the ST6 regulatory network, we show that treatment with sialylated mucin or a Foxo3 inhibitor can ameliorate IBD.

Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues. Proteomic, phosphoproteomic, and glycoproteomic analyses were used to characterize proteins and their modifications. In addition, whole-genome sequencing, whole-exome sequencing, methylation, RNA sequencing (RNA-seq), and microRNA sequencing (miRNA-seq) were performed on the same tissues to facilitate an integrated proteogenomic analysis and determine the impact of genomic alterations on protein expression, signaling pathways, and post-translational modifications. To ensure robust downstream analyses, tumor neoplastic cellularity was assessed via multiple orthogonal strategies using molecular features and verified via pathological estimation of tumor cellularity based on histological review. This integrated proteogenomic characterization of PDAC will serve as a valuable resource for the community, paving the way for early detection and identification of novel therapeutic targets.

EHMT2-mediated transcriptional reprogramming drives neuroendocrine transformation in non-small cell lung cancer.

The transformation of lung adenocarcinoma to small cell lung cancer (SCLC) is a recognized resistance mechanism and a hindrance to therapies using epidermal growth factor receptor tyrosine kinase inhibitors (TKIs). The paucity of pretranslational/posttranslational clinical samples limits the deeper understanding of resistance mechanisms and the exploration of effective therapeutic strategies. Here, we developed preclinical neuroendocrine (NE) transformation models. Next, we identified a transcriptional reprogramming mechanism that drives resistance to erlotinib in NE transformation cell lines and cell-derived xenograft mice. We observed the enhanced expression of genes involved in the EHMT2 and WNT/ß-catenin pathways. In addition, we demonstrated that EHMT2 increases methylation of the SFRP1 promoter region to reduce SFRP1 expression, followed by activation of the WNT/ß-catenin pathway and TKI-mediated NE transformation. Notably, the similar expression alterations of EHMT2 and SFRP1 were observed in transformed SCLC samples obtained from clinical patients. Importantly, suppression of EHMT2 with selective inhibitors restored the sensitivity of NE transformation cell lines to erlotinib and delayed resistance in cell-derived xenograft mice. We identify a transcriptional reprogramming process in NE transformation and provide a potential therapeutic target for overcoming resistance to erlotinib.

Quantitative mapping of the in vivo O-GalNAc glycoproteome in mouse tissues identifies GalNAc-T2 O-glycosites in metabolic disorder.

The family of GalNAc-Ts (GalNAcpolypeptide:N-Acetylgalactosaminyl transferases) catalyzes the first committed step in the synthesis of O-glycans, which is an abundant and biologically important protein modification. Abnormalities in the activity of individual GalNAc-Ts can result in congenital disorders of O-glycosylation (CDG) and influence a broad array of biological functions. How site-specific O-glycans regulate biology is unclear. Compiling in vivo O-glycosites would be an invaluable step in determining the function of site-specific O-glycans. We integrated chemical and enzymatic conditions that cleave O-glycosites, a higher-energy dissociation product ions-triggered electron-transfer/higher-energy collision dissociation mass spectrometry (MS) workflow and software to study nine mouse tissues and whole blood. We identified 2,154 O-glycosites from 595 glycoproteins. The O-glycosites and glycoproteins displayed consensus motifs and shared functions as classified by Gene Ontology terms. Limited overlap of O-glycosites was observed with protein O-GlcNAcylation and phosphorylation sites. Quantitative glycoproteomics and proteomics revealed a tissue-specific regulation of O-glycosites that the differential expression of Galnt isoenzymes in tissues partly contributes to. We examined the Galnt2-null mouse model, which phenocopies congenital disorder of glycosylation involving GALNT2 and revealed a network of glycoproteins that lack GalNAc-T2-specific O-glycans. The known direct and indirect functions of these glycoproteins appear consistent with the complex metabolic phenotypes observed in the Galnt2-null animals. Through this study and interrogation of databases and the literature, we have compiled an atlas of experimentally identified mouse O-glycosites consisting of 2,925 O-glycosites from 758 glycoproteins.

The association of serum uric acid with all-cause and cardiovascular mortality among adults with rheumatoid arthritis: a cohort study.

OBJECTIVES: Serum uric acid (SUA) is associated with poor outcomes in patients with numerous types of disease. However, the association between SUA and the outcomes of patients with rheumatoid arthritis (RA) remains to be fully elucidated. Thus, the present study aimed to determine the associations between SUA and all-cause or cardiovascular disease (CVD)-associated mortality in adults with RA. METHODS: The data of patients with RA were collected from the National Health and Nutrition Examination Survey from 2001 to 2018. All-cause and CVD-associated mortality were identified using national death records through 31 December 2019. Weighted survival curves, Cox proportional hazards regression models, restricted cubic splines (RCS) and stratified analyses were used to assess the association between SUA levels and mortality. RESULTS: Among 2,312 patients with RA, a total of 597 all-cause deaths and 198 CVD-associated deaths were recorded during 19,133 person-years of follow-up. The results of the Kaplan-Meier curves for long-term all-cause and CVD-associated mortality demonstrated that increased levels of SUA were associated with a higher incidence of mortality. In the fully adjusted models, the highest SUA quartile exhibited hazard ratios [(HRs); 95% confidence intervals (CIs)] of 1.53 (1.10, 2.14) for all-cause mortality and 1.93 (1.14, 3.27) for CVD-associated mortality, compared with the lowest SUA quartile. The results of the RCS analysis confirmed a strong linear association between SUA levels and the HR of all-cause mortality, while a U-shaped association was observed between SUA and CVD-associated mortality. CONCLUSIONS: The results of the present study demonstrated that high SUA levels were significantly associated with increased risks of all-cause and CVD-associated mortality in patients with RA. Further studies are required to elucidate the potential impact of treatments on reducing SUA levels.

ASSOCIATION OF TESSELLATION DENSITY WITH PROGRESSION OF AXIAL LENGTH AND REFRACTION IN CHILDREN: An Artificial Intelligence-Assisted 4-Year Study.

PURPOSE: To investigate fundus tessellation density (TD) and its association with axial length (AL) elongation and spherical equivalent (SE) progression in children. METHODS: The school-based prospective cohort study enrolled 1,997 individuals aged 7 to 9 years in 11 elementary schools in Mojiang, China. Cycloplegic refraction and biometry were performed at baseline and 4-year visits. The baseline fundus photographs were taken, and TD, defined as the percentage of exposed choroidal vessel area in the photographs, was quantified using an artificial intelligence-assisted semiautomatic labeling approach. After the exclusion of 330 ineligible participants because of loss to follow-up or ineligible fundus photographs, logistic models were used to assess the association of TD with rapid AL elongation (>0.36 mm/year) and SE progression (>1.00 D/year). RESULTS: The prevalence of tessellation was 477 of 1,667 (28.6%) and mean TD was 0.008 ± 0.019. The mean AL elongation and SE progression in 4 years were 0.90 ± 0.58 mm and -1.09 ± 1.25 D. Higher TD was associated with longer baseline AL (ß, 0.030; 95% confidence interval: 0.015-0.046; P < 0.001) and more myopic baseline SE (ß, -0.017; 95% confidence interval: -0.032 to -0.002; P = 0.029). Higher TD was associated with rapid AL elongation (odds ratio, 1.128; 95% confidence interval: 1.055-1.207; P < 0.001) and SE progression (odds ratio, 1.123; 95% confidence interval: 1.020-1.237; P = 0.018). CONCLUSION: Tessellation density is a potential indicator of rapid AL elongation and refractive progression in children. TD measurement could be a routine to monitor AL elongation.

Meeting Report on the 3rd Chinese American Society for Mass Spectrometry Conference-Advancing Biological and Pharmaceutical Mass Spectrometry.

Following the highly successful Chinese American Society for Mass Spectrometry (CASMS) conferences in the previous 2 years, the 3rd CASMS Conference was held virtually on August 28-31, 2023, using the Gather.Town platform to bring together scientists in the MS field. The conference offered a 4-day agenda with a scientific program consisting of two plenary lectures, and 14 parallel symposia in which a total of 70 speakers presented technological innovations and their applications in proteomics and biological MS and metabo-lipidomics and pharmaceutical MS. In addition, 16 invited speakers/panelists presented at two research-focused and three career development workshops. Moreover, 86 posters, 12 lightning talks, 3 sponsored workshops, and 11 exhibitions were presented, from which 9 poster awards and 2 lightning talk awards were selected. Furthermore, the conference featured four young investigator awardees to highlight early-career achievements in MS from our society. The conference provided a unique scientific platform for young scientists (i.e. graduate students, postdocs, and junior faculty/investigators) to present their research, meet with prominent scientists, learn about career development, and job opportunities (http://casms.org).

Global, regional and national burden of rheumatoid arthritis, and attributable risk factors from 1990 to 2019: update from the Global Burden of Disease 2019 study.

OBJECTIVES: Statistical data on the incidence, disability-adjusted life years (DALYs) and burden of rheumatoid arthritis (RA), and associated risk factors are essential for the development of effective treatment options. The Global Burden of Disease (GBD) study provides a unique opportunity to evaluate the aforementioned parameters. METHODS: The RA incidence rate, age-standardised incidence rate (ASR), DALYs and estimated annual percentage change (EAPC) between 1990 and 2019 were evaluated, using data from 204 territories and countries from the GBD 2019. Risk factors associated with DALYs in patients with RA were estimated using the comparative risk assessment framework of the GBD study. RESULTS: The results of the present study demonstrated that the incidence of RA increased from 567,462.89 to 1,074,390.80 cases, with an ASR of 13/100,000 patients between 1990 and 2019. The number of RA cases and DALYs were increased in all socio-demographic index quintiles during the study period. A significant negative association was found between EAPCs and age-standardised DALYs per 100,000 (ρ= -0.60; p<0.001). Notably, females exhibited an increased ASRs and DALYs than males, at both global and regional levels during the study period. Globally, age-standardised DALYs increased in an age-dependent manner, with the highest rate in the 60-69 years age group. Moreover, smoking was the predominant contributor to RA-associated DALYs for males worldwide, and this trend decreased from 1990 to 2019. CONCLUSIONS: The incidence rate of RA and associated DALYs are increasing worldwide, particularly among female patients. This trend is expected to increase, due an ageing population. Notably, smoking remained the predominant risk factor for RA-associated DALYs in males. Therefore, further investigations into the impact of smoking, and improvements in early diagnosis and treatment strategies for RA are required to reduce the global burden of RA.

Network pharmacology and molecular docking reveal the immunomodulatory mechanism of rhubarb peony decoction for the treatment of ulcerative colitis and irritable bowel syndrome.

Background: Ulcerative colitis (UC) and irritable bowel syndrome (IBS) share various similarities in clinical symptoms, pathogenesis, and treatment. UC concurrent IBS tends toward more severe symptoms and worse prognosis, and promising feasible therapies for the overlapping symptoms remains a challenge. Rhubarb peony decoction (RPD) is a well-known traditional Chinese medicine that has been widely applied in treating UC. RPD may exert extensive therapeutic effects on both IBS and UC. However, the common mechanism of its treatment remains unclear. We aimed to assess the potential pharmacological mechanism of RPD in the treatment of overlapping IBS and UC. Methods: The active components and targets of RPD were retrieved from ETCM, TCMSP, BATMAN-TCM, and TCM databases. The disease targets were screened by searching the DrugBank, OMIM, TTD, and PharmGKB databases. PPI network analysis was performed and visualized via the STRING platform and Cytoscape software. GO and KEGG enrichment analyses of the hub genes of RPD were predicted to elucidate the potential molecular mechanism. Subsequently, molecular docking was carried out to verify the combination of active compounds with core targets. Results: By integrating all targets of RPD and disease, a total of 31 bioactive ingredients were identified including quercetin, kaempferol, aloe-emodin, beta-sitosterol, and (+)-catechin, etc. JUN, TP53, MAPK1, RELA, MYC, and ESR1 were explored as potential therapeutic targets among 126 common drug-disease-related targets. They were enriched in the AGE-RAGE signaling pathway in diabetic complications, as well as the NF-kappa B signaling pathway and MAPK signaling pathway. Additionally, some active ingredients were identified as candidates for binding to the hub targets via molecular docking, further suggesting their anti-inflammatory and antioxidative properties. Conclusion: RPD may exert the overall treatment effect for UC and IBS overlap syndrome via the biological mechanism of "multi-ingredients, multi-targets, and multi-pathways" on inflammation, oxidative stress, immune, oncogenicity, and gut microbiota dysbiosis.

Myopic Vascular Changes Revealed by Optical Tomography Angiography and Their Association with Myopic Fundus Manifestations.

INTRODUCTION: We aimed to quantify and evaluate fundal vascular changes at different severities of myopia using optical tomography angiography (OCTA) and explore their association with fundus changes captured by ultra-widefield (UWF) fundus cameras. METHODS: Seventy-four participants with myopia were enrolled in the study and underwent basic ophthalmic examination, OCTA, and UWF fundus photography. Multiple parameters were obtained using OCTA (flow area, structure thickness, and vessel density) and UWF fundus cameras (tessellation and parapapillary atrophy [PPA]). RESULTS: The right eye of 30 participants with low and moderate myopia and 44 participants with high myopia (HM) were included. Patients with HM had a larger flow area of the outer retina (FA-OR) and a smaller thickness of choroid (TC). Axial length was significantly correlated with retinal and choroidal flow area and thickness in the different zones. The PPA area was positively correlated with FA-OR and negatively correlated with TC. Tessellation exhibited different levels of correlation with OCTA parameters regarding the flow area, thickness, and vessel density of the fundal layers, mainly in the inner retina. CONCLUSION: FA-OR and TC exhibited sensitive changes in patients with HM and axial elongation; therefore, they could serve as predictive OCTA biomarkers. The PPA and tessellation were connected to the vascular and structural changes revealed by OCTA.

Comparison of Clarus and Optomap Ultra-Widefield Imaging Systems before and after EVO-ICL Implantation in High Myopia.

INTRODUCTION: The aim of this study was to investigate the features of imaging differences between Clarus and Optomap ultra-widefield imaging systems after implantable collamer lens (ICL) implantation. METHODS: This was a non-randomized controlled study. Ninety-two eyes of 46 consecutive patients were enrolled. Full-scale ophthalmological examinations were conducted preoperatively. All patients underwent Clarus (CLARUS 500; Carl Zeiss, Dublin, USA) and Optomap (Daytona; Optos, UK) ultra-wide imaging sequentially under the same circumstance preoperatively and 1 month after EVO-ICL implantation. A single image was acquired from each. Dx was defined as the distance between the upper furcation of the central retinal artery and the central fovea of macula. Pixels of the optic cup and disc and Dx as well as the optic cup/disc ratio were calculated and compared on each machine before and after surgery. RESULTS: All surgeries were uneventful without complications. Safety and efficacy indices were both 100% at 1 month. Values of both optic cup and disc areas were in decrease after surgery with statistically significant differences (p < 0.001), while the cup/disc ratio remained the same (Clarus mean of differences = -0.0028, p = 0.83; Optomap mean of differences = -0.0016, p = 0.76). Dx of images captured with either machine was statistically significantly decreased (p < 0.001). Differences of both optic cup (p = 0.057) and disc (p = 0.041) areas of Clarus were more obvious than that of Optomap, while only the latter was with statistical significance. Difference of Dx of Clarus was statistically significantly larger than Optomap. CONCLUSIONS: Display ranges tend to be broadened after EVO-ICL implantation in both Clarus and Optomap ultra-widefield imaging systems, while Clarus shows a wider display range of the two, which encourages the application of Clarus when it comes to the detection of more peripheral retinal lesions.

Signal peptide of HIV-1 envelope modulates glycosylation impacting exposure of V1V2 and other epitopes.

HIV-1 envelope (Env) is a trimer of gp120-gp41 heterodimers, synthesized from a precursor gp160 that contains an ER-targeting signal peptide (SP) at its amino-terminus. Each trimer is swathed by ~90 N-linked glycans, comprising complex-type and oligomannose-type glycans, which play an important role in determining virus sensitivity to neutralizing antibodies. We previously examined the effects of single point SP mutations on Env properties and functions. Here, we aimed to understand the impact of the SP diversity on glycosylation of virus-derived Env and virus neutralization by swapping SPs. Analyses of site-specific glycans revealed that SP swapping altered Env glycan content and occupancy on multiple N-linked glycosites, including conserved N156 and N160 glycans in the V1V2 region at the Env trimer apex and N88 at the trimer base. Virus neutralization was also affected, especially by antibodies against V1V2, V3, and gp41. Likewise, SP swaps affected the recognition of soluble and cell-associated Env by antibodies targeting distinct V1V2 configurations, V3 crown, and gp41 epitopes. These data highlight the contribution of SP sequence diversity in shaping the Env glycan content and its impact on the configuration and accessibility of V1V2 and other Env epitopes.

Measurement of Time-Dependent Drive Flux on the Capsule for Indirectly Driven Inertial Confinement Fusion Experiments.

A new method for measuring the time-dependent drive flux at the hohlraum center is proposed as a better alternative to conventional wall-based techniques. The drive flux here is obtained by simultaneous measurement of the reemitted flux and shock velocity from a three-layered "cakelike" sample. With these two independent observables, the influence induced by the uncertainty of the material parameters of the sample can be effectively decreased. The influence from the closure of the laser entrance hole, which was the main challenge in conventional wall-based techniques, was avoided through localized reemitted flux measurement, facilitating drive flux measurement throughout the entire time history. These studies pave a new way for probing the time-dependent drive flux, for both cylindrical hohlraums and novel hohlraums with six laser entrance holes.

Analysis of risk factors for the development of type 2 diabetes mellitus complicated with Hashimoto's thyroiditis.

AIMS: The purpose of this study is to elucidate the correlation between thyroid hormone, glycosylated hemoglobin (HbA1c), vitamin D and type 2 diabetes mellitus (T2DM) with Hashimoto's thyroiditis (HT), and to seek the independent predictors affecting disease development. METHODS: The study included 44 T2DM with HT, 94 T2DM, and 112 healthy subjects. We investigated some laboratory factors like thyroid hormone and compared the levels. Independent predictors determination by logistic univariate regression analysis were analyzed. The diagnostic value of thyroid-stimulating hormone (TSH) and threshold concentration were determined by ROC curve. RESULTS: In T2DM with HT group, levels of PTH, HbA1c were lower and levels of TSH were significantly higher, when compared with T2DM group. But there was no significant difference in vitamin D between these two groups. In both logistic univariate regression analysis and multiple logistic regression analysis, TSH, HbA1c were independent predictors for T2DM with HT. Based on the ROC curve, the best cut-off value of the TSH was 4 mIU/L (sensitivity 72.7%, specificity 94.6%, AUC = 0.832) for predicting T2DM with HT in T2DM patients. CONCLUSIONS: TSH has increased risk for T2DM evolving into T2DM complicated with HT, so it is important to monitor the concentrations of TSH in patients with T2DM. Although vitamin D was not the independent predictor in T2DM with HT development, effect of vitamin D deficiency on the progress of diabetes and its complications should be taken into consideration.

Axial length shortening after orthokeratology and its relationship with myopic control.

PURPOSE: To determine the pattern of axial variation in subjects with initial shortened axial length during the entire period of orthokeratology and to discuss the possibility of shortened AL after one month of orthokeratology becoming a predictor of myopia control. METHOD: This study retrospectively included 106 children with myopia aged 8 to 14 wearing OK lenses. Fifty-four eyes with shortened axial length (AL) at the first-month visit were enrolled in the axial length shortening (ALS) group, and fifty-two eyes without shortened AL were enrolled in the no axial length shortening (NALS) group. Axial length and refractive error at baseline and within the entire period of orthokeratology (20 months), including fitting, washout period and re-wear, were measured. Eighty-five children who started wearing single vision spectacle were also included as a control group. RESULTS: In the ALS group, AL became longer after shortening and slowly exceeded baseline; afterward, AL experienced a rebound during the washout period and shortened again if OK lenses were re-worn. After washout period, significant difference in AL (ALS:0.28 ± 0.19 mm, NALS: 0.52 ± 0.17 mm) and spherical equivalent (ALS:-0.43 ± 0.44D, NALS:-0.91 ± 0.40D) between the two groups were found(P<0.05). The changes in AL and SE were both significantly correlated with the changes in AL at the first-month visit (P<0.05). CONCLUSION: After AL is shortened in the initial stage of orthokeratology, it will experience a rapid rebound during the washout period, and the shortening can reappear when re-wearing OK lenses. Hence, the evaluation of orthokeratology will be more objective and accurate after the wash-out period. In addition, the existence and degree of axial shortening can be used as a predictor of long-term myopia development.

Immediate effect in retina and choroid after 650 nm low-level red light therapy in children.

INTRODUCTION: To investigate the changes in the retina and choroid of children after 650 nm low-level red light therapy (LLRLT). METHODS: In this prospective study, 25 subjects in the Shanghai Eye and ENT Hospital of Fudan University were included from August 2021 to September 2021. One eye was randomly selected to receive LLRLT for 3 minutes. Swept-source optical coherence tomography (OCT) and OCT angiography (OCTA) were used to measure retinal fovea perfusion density (RFPD), retinal fovea thickness (RFT), choroidal fovea blood flow (CFBF), and choroidal fovea thickness (CFT) before LLRLT, 5 minutes and 1 hour after LLRLT. Baseline characteristics between LLRLT and non-LLRLT eyes were compared. Changes in the retinal and choroidal parameters were analyzed by ANCOVA models. SAS software was used for data analysis. The difference was considered statistically significant if p < 0.05. RESULTS: There was no difference in baseline characteristics between LLRLT eyes and non-LLRLT eyes. The RFPD in LLRLT eyes significantly increased 5 minutes after LLRLT and the increment was 1.70±0.83 % (p = 0.0389). The RFPD significantly decreased from 5 minutes to 1 hour after LLRLT with a mean of -2.62±0.86 % decrement (p = 0.0031). The RFPD levels returned to baseline at 1 hour after LLRLT (p = 0.8646). However, compared with insignificant RFPD changes in non-LLRLT eyes, there was no significant difference in RFPD changes at any sampling point. No significant changes in RFT, CFBF, and CFT were found in LLRLT eyes at each sampling point. CONCLUSION: Although LLRLT has no effect on the choroid, it may cause a short-term transient increase in RFPD. It will provide theoretical support for the role of LLRLT in myopia control.

Correction of Bcl-x splicing improves responses to imatinib in chronic myeloid leukaemia cells and mouse models.

Imatinib mesylate (IM) resistance has become a major clinical problem for chronic myeloid leukaemia (CML). It is known that Bcl-x splicing is deregulated and is involved in multiple malignant cancer initiation and chemotherapy resistance, including CML. The aim of the present study was to correct the abnormal splicing of Bcl-x in CML and investigate the subsequent malignant phenotype changes, especially response to IM. The aberrant Bcl-x splicing in CML cells was effectively restored using vivo-Morpholino Antisense Oligomer (vMO). CCK-8 cell viability assay and flow cytometry showed that restoring of Bcl-x splicing increases IM-induced growth inhibition and apoptosis of K562 cells. Moreover, a more significant similar phenomenon was observed in imatinib-resistant CML cell lines K562/G01. Finally, establishment of CML xenograft model had also proved that correcting Bcl-x splicing in vivo can also enhance the anti-tumor effect of IM. Our findings suggest that vMO co-operating with IM can effectively increase the sensitivity of CML cells to IM both in vitro and in vivo, and Bcl-x splicing could become good candidates for chemotherapy-sensitized target in IM-resistant CML.

Mass Spectrometric Mapping of Glycoproteins Modified by Tn-Antigen Using Solid-Phase Capture and Enzymatic Release.

Tn-antigen (Tn), a single N-acetylgalactosamine (GalNAc) monosaccharide attached to protein Ser/Thr residues, is found on most cancer yet rarely detected in adult normal tissues as reported in previous studies, featuring it as one of the most distinctive signatures of cancer. Although it is important in cancer, Tn modified glycoproteins are not entirely clear owing to the lack of a suitable method. Knowing the Tn-glycosylated proteins and glycosylation sites are essential to the prevention, diagnosis, and therapy of cancer associated with the expression of Tn. Here, we introduce a method named EXoO-Tn for large-scale mapping of Tn-glycosylated proteins and glycosylation sites. EXoO-Tn utilizes solid-phase immobilization of proteolytic peptides of proteins, which modifies Tn by glycosyltransferase C1GalT1 with isotopically labeled UDP-Gal(13C6), to tag and convert Tn to Gal(13C6)-Tn, which gives rise to a unique glycan mass. The exquisite Gal(13C6) modified Tn are then recognized by a human-gut-bacterial enzyme, OpeRATOR, and released at the N-termini of the Gal(13C6)-Tn-occupied Ser/Thr residues from immobilized peptides to yield site-containing glycopeptides. The effectiveness of EXoO-Tn was benchmarked by analyzing Jurkat cells, where 947 Tn-glycosylation sites from 480 glycoproteins were mapped. The EXoO-Tn was further applied to the analysis of pancreatic cancer sera, where Tn-glycoproteins were identified. Given the significance of Tn in cancer, EXoO-Tn is anticipated to have broad translational and clinical utilities.

Theoretical development and experimental validation on the measurement of temperature by extended X-ray absorption fine structure.

A systematic investigation on the theoretical framework of the ultra-fast measurement of temperature by extended X-ray absorption fine structure (EXAFS) applied in laser-driven-compression experiments has been carried out and a new temperature measurement scheme based on the EXAFS cumulant expansion analysis and anharmonic correlated Debye model has been advanced. By considering the anharmonic effect of thermal vibration and avoiding the employment of the empirical model as well as parameters which have large inherent uncertainties in the temperature determination, this new scheme is theoretically more accurate than traditional ones. Then the performance of the new measurement scheme and traditional methods were validated on a synchrotron radiation platform by temperature-dependent EXAFS (TDEXAFS) experiments on Au, Fe, V and Ti; the results showed that the new scheme could provide the most accurate measured temperatures with much lower uncertainties. This accurate scheme gives a firmer physical ground to the EXAFS temperature measurement technique and can expect to be applied in laser-driven compression experiments and promote the development of matter state research at extreme conditions.

Alterations of HIV-1 envelope phenotype and antibody-mediated neutralization by signal peptide mutations.

HIV-1 envelope glycoprotein (Env) mediates virus attachment and entry into the host cells. Like other membrane-bound and secreted proteins, HIV-1 Env contains at its N terminus a signal peptide (SP) that directs the nascent Env to the endoplasmic reticulum (ER) where Env synthesis and post-translational modifications take place. SP is cleaved during Env biosynthesis but potentially influences the phenotypic traits of the Env protein. The Env SP sequences of HIV-1 isolates display high sequence variability, and the significance of such variability is unclear. We postulate that changes in the Env SP influence Env transport through the ER-Golgi secretory pathway and Env folding and/or glycosylation that impact on Env incorporation into virions, receptor binding and antibody recognition. We first evaluated the consequences of mutating the charged residues in the Env SP in the context of infectious molecular clone HIV-1 REJO.c/2864. Results show that three different mutations affecting histidine at position 12 affected Env incorporation into virions that correlated with reduction of virus infectivity and DC-SIGN-mediated virus capture and transmission. Mutations at positions 8, 12, and 15 also rendered the virus more resistant to neutralization by monoclonal antibodies against the Env V1V2 region. These mutations affected the oligosaccharide composition of N-glycans as shown by changes in Env reactivity with specific lectins and by mass spectrometry. Increased neutralization resistance and N-glycan composition changes were also observed when analogous mutations were introduced to another HIV-1 strain, JRFL. To the best of our knowledge, this is the first study showing that certain residues in the HIV-1 Env SP can affect virus neutralization sensitivity by modulating oligosaccharide moieties on the Env N-glycans. The HIV-1 Env SP sequences thus may be under selective pressure to balance virus infectiousness with virus resistance to the host antibody responses. (289 words).