scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species

Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.

Tislelizumab, a novel PD-1 monoclonal antibody in urothelial cancer: A real-world study

OBJECTIVE

Tislelizumab, a monoclonal antibody against programed death protein-1 (PD-1), has shown encouraging antitumor activity in urothelial cancer. This study was designed to assess the efficacy and safety of tislelizumab in urotelial cancer in a real-world setting.

METHODS

The study was a real-world retrospective study undertaken at Liaoning Cancer Hospital & Institute, China. Eligible patients were ≥18 years. Patients received 200-mg tislelizumab monotherapy intravenously every 3 weeks until the disease progressed to intolerable toxicity. Outcomes included an objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), overall survival (OS) and safety.

RESULTS

Between March 2020 and December 2022, 33 patients were enrolled. The median follow-up was 10.17 (IQR 5.73-12.47) months. Of all 33 patients, ORR and DCR were 30.30% (95% CI 15.6%-48.7%) and 42.42% (95% CI 25.48%-60.78%), respectively. The median PFS was 5.73 (95% CI 3.27-13.00) months, with a 12-month PFS rate of 31.90% (95% CI 19.20%-53.00%). The median OS was 17.7 (95% CI 12.80-not reach) months, with a 12-month OS rate of 67.50% (95% CI 52.70%-86.40%). Eleven (33.33%) and 8 (24.24%) experienced ≥grade 3 treatment-related adverse events (TRAEs) and immune-related Aes, respectively. No treatment-related deaths occurred.

CONCLUSION

The excellent efficacy and controllable safety of tislelizumab in locally advanced or metastatic urothelial cancer suggest that it may be a promising therapeutic option for this population.

[Research progress on the structure and innervation of extraocular muscles]

In addition to the abnormalities of the extraocular muscles themselves and the nervous system innervating the extraocular muscles, the tissue pulley abnormalities around the extraocular muscles may lead to the occurrence of strabismus. In recent years, researchers have shown the intramuscular nerve distribution of the extraocular muscles using the Sihler technique. With the continuous progress of imaging technology, magnetic resonance imaging, computed tomography, anterior segment optical coherence tomography and ultrasound biomicroscopy can be used to observe the attachment sites of the extraocular muscles. This review summarizes the latest research progress on the neuroanatomy of the extraocular muscles, in order to provide reference for the clinical diagnosis and treatment of strabismus.

SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses ('pathway downstream analysis', 'upstream regulatory analysis' and 'genomic region annotation') for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, 'TF regulatory analysis' and 'Sample comparative analysis' for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.

[Hepatic cystic echinococcosis complicated with tuberculous empyema misdiagnosed as hepatic and pulmonary cystic echinococcosis: one case report]

Hepatic cystic echinococcosis is a chronic parasitic disease caused by the infection with the larvae of Echinococcus granulosus in human or animal liver tissues. As a chronic active infectious disease, tuberculous empyema mainly invades the pleural space and then causes visceral and parietal pleura thickening. It is rare to present comorbidity for hepatic cystic echinococcosis and tuberculous empyema. This case report presents a case of hepatic cystic echinococcosis complicated with tuberculous empyema misdiagnosed as hepatic and pulmonary cystic echinococcosis, aiming to improve clinicians' ability to distinguish this disorder.

Large-scale and high-resolution mass spectrometry-based proteomics profiling defines molecular subtypes of esophageal cancer for therapeutic targeting

Esophageal cancer (EC) is a type of aggressive cancer without clinically relevant molecular subtypes, hindering the development of effective strategies for treatment. To define molecular subtypes of EC, we perform mass spectrometry-based proteomic and phosphoproteomics profiling of EC tumors and adjacent non-tumor tissues, revealing a catalog of proteins and phosphosites that are dysregulated in ECs. The EC cohort is stratified into two molecular subtypes-S1 and S2-based on proteomic analysis, with the S2 subtype characterized by the upregulation of spliceosomal and ribosomal proteins, and being more aggressive. Moreover, we identify a subtype signature composed of ELOA and SCAF4, and construct a subtype diagnostic and prognostic model. Potential drugs are predicted for treating patients of S2 subtype, and three candidate drugs are validated to inhibit EC. Taken together, our proteomic analysis define molecular subtypes of EC, thus providing a potential therapeutic outlook for improving disease outcomes in patients with EC.

VARAdb: a comprehensive variation annotation database for human

With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include ‘Variation information’, ‘Regulatory information’, ‘Related genes’, ‘Chromatin accessibility’ and ‘Chromatin interaction’. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.

Integrative Epigenomic Analysis of Transcriptional Regulation of Human CircRNAs

Circular RNAs (circRNAs) are evolutionarily conserved and abundant non-coding RNAs whose functions and regulatory mechanisms remain largely unknown. Here, we identify and characterize an epigenomically distinct group of circRNAs (TAH-circRNAs), which are transcribed to a higher level than their host genes. By integrative analysis of cistromic and transcriptomic data, we find that compared with other circRNAs, TAH-circRNAs are expressed more abundantly and have more transcription factors (TFs) binding sites and lower DNA methylation levels. Concordantly, TAH-circRNAs are enriched in open and active chromatin regions. Importantly, ChIA-PET results showed that 23–52% of transcription start sites (TSSs) of TAH-circRNAs have direct interactions with cis-regulatory regions, strongly suggesting their independent transcriptional regulation from host genes. In addition, we characterize molecular features of super-enhancer-driven circRNAs in cancer biology. Together, this study comprehensively analyzes epigenomic characteristics of circRNAs and identifies a distinct group of TAH-circRNAs that are independently transcribed via enhancers and super-enhancers by TFs. These findings substantially advance our understanding of the regulatory mechanism of circRNAs and may have important implications for future investigations of this class of non-coding RNAs.

TP63, SOX2, and KLF5 Establish a Core Regulatory Circuitry That Controls Epigenetic and Transcription Patterns in Esophageal Squamous Cell Carcinoma Cell Lines

BACKGROUND & AIMS

We investigated the transcriptome of esophageal squamous cell carcinoma (ESCC) cells, activity of gene regulatory (enhancer and promoter regions), and the effects of blocking epigenetic regulatory proteins.

METHODS

We performed chromatin immunoprecipitation sequencing with antibodies against H3K4me1, H3K4me3, and H3K27ac and an assay for transposase-accessible chromatin to map the enhancer regions and accessible chromatin in 8 ESCC cell lines. We used the CRC_Mapper algorithm to identify core regulatory circuitry transcription factors in ESCC cell lines, and determined genome occupancy profiles for 3 of these factors. In ESCC cell lines, expression of transcription factors was knocked down with small hairpin RNAs, promoter and enhancer regions were disrupted by CRISPR/Cas9 genome editing, or bromodomains and extraterminal (BET) family proteins and histone deacetylases (HDACs) were inhibited with ARV-771 and romidepsin, respectively. ESCC cell lines were then analyzed by whole-transcriptome sequencing, immunoprecipitation, immunoblots, immunohistochemistry, and viability assays. Interactions between distal enhancers and promoters were identified and verified with circular chromosome conformation capture sequencing. NOD-SCID mice were given injections of modified ESCC cells, some mice where given injections of HDAC or BET inhibitors, and growth of xenograft tumors was measured.

RESULTS

We identified super-enhancer-regulated circuits and transcription factors TP63, SOX2, and KLF5 as core regulatory factors in ESCC cells. Super-enhancer regulation of ALDH3A1 mediated by core regulatory factors was required for ESCC viability. We observed direct interactions between the promoter region of TP63 and functional enhancers, mediated by the core regulatory circuitry transcription factors. Deletion of enhancer regions from ESCC cells decreased expression of the core regulatory circuitry transcription factors and reduced cell viability; these same results were observed with knockdown of each core regulatory circuitry transcription factor. Incubation of ESCC cells with BET and HDAC disrupted the core regulatory circuitry program and the epigenetic modifications observed in these cells; mice given injections of HDAC or BET inhibitors developed smaller xenograft tumors from the ESCC cell lines. Xenograft tumors grew more slowly in mice given the combination of ARV-771 and romidepsin than mice given either agent alone.

CONCLUSIONS

In epigenetic and transcriptional analyses of ESCC cell lines, we found the transcription factors TP63, SOX2, and KLF5 to be part of a core regulatory network that determines chromatin accessibility, epigenetic modifications, and gene expression patterns in these cells. A combination of epigenetic inhibitors slowed growth of xenograft tumors derived from ESCC cells in mice.

[Clinical characteristics of recurrent appendicitis]

Objective: To analyze clinical characteristics of recurrent appendicitis. Methods: A retrospective cohort study was carried out. Clinical data of patients who underwent appendectomy due to acute appendicitis confirmed by pathology in the Affiliated Hospital of Qingdao University from January 2011 to December 2015 were analyzed retrospectively. Exclusion criteria: (1) age of less than 18 years;(2) chronic appendicitis; (3) periappendiceal abscess; (4) appendiceal mucocele or mucinous neoplasms; (5) appendiceal neuroendocrine tumors or cancers; (6) appendicitis during pregnancy; (7) concurrent AIDS, hematological disease, autoimmune disease, inflammatory bowel disease or advanced cancer; (8) other simultaneous surgery. A total of 373 patients were enrolled the study. These patients were divided into the recurrent group (133 cases) and the first episode group (240 cases) according to the previous history of antibiotic therapy for acute appendicitis. The prevalence of recurrent appendicitis was calculated, and the clinical characteristics were analyzed, including gender, age, comorbidities and preoperative CT images. Results: Of 373 patients, 209 were male and 164 were female, with a median age of 42 (18 to 88) years. Median recurrent time of the recurrent group was 4 (1 to 60) months. Compared to the first episode group, the recurrent group had higher proportion of age <50 years [71.4% (95/133) vs. 57.5% (138/240), χ(2)=7.081, P=0.008], higher proportion of concurrent diabetes [13.5% (18/133) vs. 5.4% (13/240), χ(2)=7.399, P=0.007], shorter onset time [(41.7±13.6) hours vs. (59.4±56.2) hours, t=-3.286, P=0.001], lower proportion of abdominal tension and rebound pain [57.9% (77/133) vs. 66.7% (160/240), χ(2)=5.065, P=0.024], lower score of modified Alvarado score [(5.6±1.9) point vs. (6.1±1.9) point, t=-2.417, P=0.016], lower WBC count [(10.5±4.6) ×10(9)/L vs. (11.5±4.5)×10(9)/L, t=-1.190, P=0.047], higher percentage of lymphocyte [(19.4±14.7)% vs. (16.1±13.3)%, t=2.069, P=0.039]. In the recurrent group, ratio of length of removed appendix ≥7 cm was higher as compared with the first episode group [44.4% (59/133) vs. 32.9% (79/240), χ(2)=4.808, P=0.028], while the ratio of complicated appendicitis was significantly lower [8.3% (11/133) vs. 22.9% (55/240), χ(2)=10.823, P=0.001]. CT images were available in 129 patients, intraluminal appendicoliths was found in 19 of 50 patients (38%) in the recurrent group, while in 16 of 79 patients (20.3%) in the first episode group, and there was statistically significant difference between the two groups (χ(2)=4.880, P=0.027). Conclusions: Clinical characteristics of recurrent acute appendicitis include age less than 50 years, concurrent diabetes, short onset time, less abdominal tension or rebound pain, low modified Alvarado score, low WBC count, high percentage of lymphocyte, appendix length longer than 7 cm, non-complicated appendicitis and intraluminal appendicoliths.

SEanalysis: a web tool for super-enhancer associated regulatory analysis

Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.

[Perioperative management of pregnant women combined with congenital fibrinogen deficiency: four cases report and literature review]

Congenital fibrinogen deficiency is an autosomal recessive or dominant disorder in which quantitative (afibrinogenaemia or hypofibrinogenaemia) or qualitative (dysfibrinogenaemia) defects in the fibrinogen Aa, Bb or c protein chains that lead to reduced functional fibrinogen. We now report the perioperative management of 4 pregnant women suffering from hypofibrinogenaemia scheduled for elective caesarean section from December 2012 to October 2016 in Peking University First Hospital and review this disease with reference to classification, symptom, replacement therapy, and selection of the modes of pregnancy termination and anesthesia. The four patients were all asymptomatic, whereas there existed recurrent pregnancy loss (case 3), family history (case 2), and offspring heredity (cases 3 and 4). Routine clotting studies revealed low fibrinogen levels and prolonged thrombin time (TT) during pregnancy and on admission. However, the platelet (PLT) count, prothrombin time (PT) and activated partial thromboplastin time (APTT) were normal. All the patients were administered fibrinogen concentrate perioperatively, and underwent uncomplicated combined spinal-epidural anesthesia and uneventful surgical procedure without postpartum hemorrhage. The replacement therapy of fibrinogen or fresh frozen plasma administration was essential to avoid anesthesia and obstetric complications. Regional blockade could safely be offered in the caesarean section, providing that their coagulation defect was corrected by availability of therapeutic products and adequate response to treatment. In addition, the point-of-care rotational thrombelastometry (ROTEM) or thrombelastogram (TEG) could play an important role in an optimal perioperative management for such patients. Management plans must be tailored to each individual, taking into consideration their bleeding risk as well as potential maternal and neonatal complications.

Super-Enhancer-Driven Long Non-Coding RNA LINC01503, Regulated by TP63, Is Over-Expressed and Oncogenic in Squamous Cell Carcinoma

BACKGROUND & AIMS

Long non-coding RNAs (lncRNAs) are expressed in tissue-specific pattern, but it is not clear how these are regulated. We aimed to identify squamous cell carcinoma (SCC)-specific lncRNAs and investigate mechanisms that control their expression and function.

METHODS

We studied expression patterns and functions of 4 SCC-specific lncRNAs. We obtained 113 esophageal SCC (ESCC) and matched non-tumor esophageal tissues from a hospital in Shantou City, China, and performed quantitative reverse transcription polymerase chain reaction assays to measure expression levels of LINC01503. We collected clinical data from patients and compared expression levels with survival times. LINC01503 was knocked down using small interfering RNAs and oligonucleotides in TE7, TE5, and KYSE510 cell lines and overexpressed in KYSE30 cells. Cells were analyzed by chromatin immunoprecipitation sequencing, luciferase reporter assays, colony formation, migration and invasion, and mass spectrometry analyses. Cells were injected into nude mice and growth of xenograft tumors was measured. LINC01503 interaction with proteins was studied using fluorescence in situ hybridization, RNA pulldown, and RNA immunoprecipitation analyses.

RESULTS

We identified a lncRNA, LINC01503, which is regulated by a super enhancer and is expressed at significantly higher levels in esophageal and head and neck SCCs than in non-tumor tissues. High levels in SCCs correlated with shorter survival times of patients. The transcription factor TP63 bound to the super enhancer at the LINC01503 locus and activated its transcription. Expression of LINC01503 in ESCC cell lines increased their proliferation, colony formation, migration, and invasion. Knockdown of LINC01503 in SCC cells reduced their proliferation, colony formation, migration, and invasion, and the growth of xenograft tumors in nude mice. Expression of LINC01503 in ESCC cell lines reduced ERK2 dephosphorylation by DUSP6, leading to activation of ERK signaling via MAPK. LINC01503 disrupted the interaction between EBP1 and the p85 subunit of PI3K, increasing AKT signaling.

CONCLUSIONS

We identified an lncRNA, LINC01503, which is increased in SCC cells compared with non-tumor cells. Increased expression of LINC01503 promotes ESCC cell proliferation, migration, invasion, and growth of xenograft tumors. It might be developed as a biomarker of aggressive SCCs in patients.

Influence of Hydrostatic Pressure on the Corrosion Behavior of Superhydrophobic Surfaces on Bare and Oxidized Aluminum Substrates

It is generally recognized that superhydrophobic surfaces in water may be used for corrosion resistance due to the entrapped air in the solid/liquid interface and could find potential applications in the protection of ship hull. For a superhydrophobic surface, as its immersion depth into water increases, the resultant hydrostatic pressure is also increased, and the entrapped air can be squeezed out much more easily. It is therefore predicted that high hydrostatic pressure would cause an unexpected decrease in corrosion resistance for the vessels in deep water (e.g., submarines) because of the unstable entrapped air. In this work, in order to clarify the role of hydrostatic pressure in the corrosion behavior of superhydrophobic surfaces, two typical superhydrophobic surfaces (SHSs) were prepared on bare and oxidized aluminum substrates, respectively, and then were immersed into the NaCl aqueous solutions with different depths of ∼0 cm (hydrostatic pressure ∼0 kPa), 10 cm (1 kPa), and 150 cm (15 kPa). It was found out for the SHSs on the oxidized Al, as the hydrostatic pressure increased, the corrosion behavior became severe. However, for the SHSs on the bare Al, their corrosion behavior was complex due to hydrostatic pressure. It was found that the corrosion resistance under 1 kPa was the highest. Further mechanism analysis revealed that this alleviated corrosion behavior under 1 kPa resulted from suppressing the oxygen diffusion through the liquid and reducing the subsequent corrosion rate as compared with 0 kPa, whereas the relatively low hydrostatic pressure (HP) could stabilize the entrapped air and hence enhance the corrosion resistance, compared with 15 kPa. The present study therefore provided a fundamental understanding for the applications of SHSs to prevent the corrosion, especially for various vessels in deep water.

MASAN: a novel staging system for prognosis of patients with oesophageal squamous cell carcinoma

BACKGROUND

Oesophageal squamous cell carcinoma (ESCC) is one of the most malignant cancers worldwide. Treatment of ESCC is in progress through accurate staging and risk assessment of patients. The emergence of potential molecular markers inspired us to construct novel staging systems with better accuracy by incorporating molecular markers.

METHODS

We measured H scores of 23 protein markers and analysed eight clinical factors of 77 ESCC patients in a training set, from which we identified an optimal MASAN (MYC, ANO1, SLC52A3, Age and N-stage) signature. We constructed MASAN models using Cox PH models, and created MASAN-staging systems based on k-means clustering and minimum-distance classifier. MASAN was validated in a test set (n = 77) and an independent validation set (n = 150).

RESULTS

MASAN possessed high predictive accuracies and stratified ESCC patients into three prognostic groups that were more accurate than the current pTNM-staging system for both overall survival and disease-free survival. To facilitate clinical utilisation, we also constructed MASAN-SI staging systems based on staining indices (SI) of protein markers, which possessed similar prognostic performance as MASAN.

CONCLUSION

MASAN provides a good alternative staging system for ESCC prognosis with a high precision using a simple model.

A three-lncRNA signature predicts overall survival and disease-free survival in patients with esophageal squamous cell carcinoma

BACKGROUND

Increasing evidence shows that dysregulated long non-coding RNAs (lncRNAs) can serve as potential biomarkers for cancer prognosis. However, lncRNA signatures, as potential prognostic biomarkers for esophageal squamous cell carcinoma (ESCC), have been seldom reported.

METHODS

Based on our previous transcriptome RNA sequencing analysis from 15 paired ESCC tissues and adjacent normal tissues, we selected 10 lncRNAs with high score rank and characterized the expression of those lncRNAs, by qRT-PCR, in 138 ESCC and paired adjacent normal samples. These 138 patients were divided randomly into training (n = 77) and test (n = 59) groups. A prognostic signature of lncRNAs was identified in the training group and validated in the test group and in an independent cohort (n = 119). Multivariable Cox regression analysis evaluated the independence of the signature in overall survival (OS) and disease-free survival (DFS) prediction. GO and KEGG pathway analysis, combined with cell transwell and proliferation assays, are applied to explore the function of the three lncRNAs.

RESULTS

A novel three-lncRNA signature, comprised of RP11-366H4.1.1 (ENSG00000248370), LINC00460 (ENSG00000233532) and AC093850.2 (ENSG00000230838), was identified. The signature classified patients into high-risk and low-risk groups with different overall survival (OS) and disease-free survival (DFS). For the training group, median OS: 23.1 months vs. 39.1 months, P < 0.001; median DFS: 15.2 months vs. 33.3 months, P < 0.001. For the test group, median OS: 23 months vs. 59 months, P < 0.001; median DFS: 16.4 months vs. 50.8 months, P < 0.001. For the independent cohort, median OS: 22.4 months vs. 60.4 months, P < 0.001). The signature indicates that patients in the high-risk group show poor OS and DFS, whereas patients with a low-risk group show significantly better outcome. The independence of the signature was validated by multivariable Cox regression analysis. GO and KEGG pathway analysis for 588 protein-coding genes-associated with the three lncRNAs indicated that the three lncRNAs were involved in tumorigenesis. In vitro assays further demonstrated that the three lncRNAs promoted the migration and proliferation of ESCC cells.

CONCLUSIONS

The three-lncRNA signature is a novel and potential predictor of OS and DFS for patients with ESCC.

Early Hemodynamic Response Assessment of Stereotactic Radiosurgery for a Cerebral Arteriovenous Malformation Using 4D Flow MRI

Brain AVMs treated with stereotactic radiosurgery typically demonstrate a minimum latency period of 1-3 years between treatment and nidus obliteration. Assessment of treatment response is usually limited to evaluation of AVM nidus structural changes using conventional MR imaging and MRA techniques. This report describes the use of 4D Flow MRI to also measure radiation-induced hemodynamic changes in a Spetzler-Martin grade III AVM, which were detectable as early as 6 months after treatment.

Construction and analysis of cardiac hypertrophy-associated lncRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in cardiac hypertrophy

Cardiac hypertrophy (CH) could increase cardiac after-load and lead to heart failure. Recent studies have suggested that long non-coding RNA (lncRNA) played a crucial role in the process of the cardiac hypertrophy, such as Mhrt, TERMINATOR. Some studies have further found a new interacting mechanism, competitive endogenous RNA (ceRNA), of which lncRNA could interact with micro-RNAs (miRNA) and indirectly interact with mRNAs through competing interactions. However, the mechanism of ceRNA regulated by lncRNA in the CH remained unclear. In our study, we generated a global triple network containing mRNA, miRNA and lncRNA, and extracted a CH related lncRNA-mRNA network (CHLMN) through integrating the data from starbase, miRanda database and gene expression profile. Based on the ceRNA mechanism, we analyzed the characters of CHLMN and found that 3 lncRNAs (SLC26A4-AS1, RP11-344E13.3 and MAGI1-IT1) were high related to CH. We further performed cluster module analysis and random walk with restart for the CHLMN, finally 14 lncRNAs had been discovered as the potential CH related disease genes. Our results showed that lncRNA played an important role in the CH and could shed new light to the understanding underlying mechanisms of the CH.

[Effects of recent upper respiratory-tract infections on incidence of the perioperative respiratory adverse events in children: a prospective cohort study]

OBJECTIVE

To investigate the effects of the recent upper respiratory tract infections (URI) on the incidence of perioperative respiratory adverse events in children scheduled to undergo general anesthesia and elective surgery.

METHODS

In the study, 232 children undergoing general anesthesia with laryngeal mask airway (LMA) for elective ophthalmic surgeries at Peking University First Hospital, Beijing, China, from Nov. 1, 2015 to May 10, 2016 were enrolled. On the day of the surgery, the parents of the children were preoperatively asked to fill out a questionnaire regarding the baseline characteristics and medical history of the children, including gender, age, height, weight, history of URI within the last 2 weeks before anesthesia, history of premature, long-term passive smoking exposure, habitual sleep snoring, and history of asthma. In addition, all adverse respiratory events throughout the perioperative periods (oxygen desaturation, cough, copious secretions, laryngospasm and bronchospasm) as well as peri-operative variables (number of attempts to insert the LMA successfully, anesthesia duration and so on) were recorded. Multivariate Logistic regression analysis was applied to identify independent risk factors of perioperative respiratory adverse events.

RESULTS

Among the 232 children included in the study, 28.0% (65/232) presented with a history of a recent URI within the last 2 weeks before anesthesia. The presence of the recent URI increased the incidence of oxygen desaturation (23.1% vs.12.0%, P=0.034), copious secretions (15.4% vs. 6.6%, P=0.036) and any of all the adverse respiratory events (32.3% vs. 18.6%, P=0.024). Multivariate Logistic regression analysis identified two independent risk factors of perioperative adverse respiratory events: a history of URI within the last 2 weeks before general anesthesia (OR=2.021, 95%CI: 1.023-3.994, P=0.043) and habitual sleep snoring (OR=3.660, 95%CI: 1.517-8.832, P=0.004).

CONCLUSION

A history of a recent URI within 2 weeks before general anesthesia was associated with a higher incidence of oxygen desaturation, copious secretions and the overall respiratory adverse events. For the children with recent URI, we recommend the general anesthesia and elective surgery should be postponed for at least 2 weeks after the URI.

Blood service in the Tibetan regions of Garzê and Aba, China: a longitudinal survey

BACKGROUND

Garzê and Aba form the second largest Tibetan-inhabited area of China. Blood services have never been reported for this region before.

OBJECTIVE

To assess the current situation and analyse whether a safe and adequate blood supply has been developed in both Garzê and Aba.

METHODS

We conducted a longitudinal survey covering the period 2011-2016. The subjects of interest were recruited from non-remunerated voluntary donation, blood testing, clinical transfusion practices and infrastructure of local blood service systems.

RESULTS

The donation rate and blood collection volume were below the average levels of both the Sichuan Province and mainland China. Component therapy was widely used, but inappropriate usage of whole blood existed. A lack of national specific standards for people on the plateaus led to local blood transfusions being conducted without full clinical assessment. Endemic and frequently occurring disease, such as hydatid disease and gastrointestinal disease, were inevitable risks for blood utilisation and safety. The potential influence of religious belief and traditions, like 'male-leaving marriages', of Tibetans on donor recruitment and blood safety requires further research.

CONCLUSIONS

A relatively safe and complete blood service system has been developed in this region. However, there is still an urgent need for comprehensive and effective support from the government in terms of policies and finance. As an epidemic area of hydatid disease and sexually transmitted disease, this region needs to emphasise public health measures, such as blood safety and inappropriate usage of blood products.

Natural ageing responses of duplex structured Mg-Li based alloys

Natural ageing responses of duplex structured Mg-6%Li and Mg-6%Li-6%Zn-1.2%Y alloys have been investigated. Microstructural analyses revealed that the precipitation and coarsening process of α-Mg particles could occur in β-Li phases of both two alloys during ageing process. Since a certain amount of Mg atoms in β-Li phases were consumed for the precipitation of abundant tiny MgLiZn particles, the size of α-Mg precipitates in Mg-6%Li-6%Zn-1.2%Y alloy was relatively smaller than that in Mg-6%Li alloy. Micro hardness measurements demonstrated that with the ageing time increasing, the α-Mg phases in Mg-6%Li alloy could have a constant hardness value of 41 HV, but the contained β-Li phases exhibited a slight age-softening response. Compared with the Mg-6%Li alloy, the age-softening response of β-Li phases in Mg-6%Li-6%Zn-1.2%Y alloy was much more profound. Meanwhile, a normal age-hardening response of α-Mg phases was maintained. Tensile results indicated that obvious ageing-softening phenomenon in terms of macro tensile strength occurred in both two alloys. Failure analysis demonstrated that for the Mg-6%Li alloy, cracks were preferentially initiated at α-Mg/β-Li interfaces. For the Mg-6%Li-6%Zn-1.2%Y alloy, cracks occurred at both α-Mg/β-Li interfaces and slip bands in α-Mg and β-Li phases.

Protein-coding genes combined with long non-coding RNAs predict prognosis in esophageal squamous cell carcinoma patients as a novel clinical multi-dimensional signature

Esophageal carcinoma is one of the most malignant gastrointestinal cancers worldwide, and has a high mortality rate. Both protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs) have been shown to play an important role in the development of malignant tumors. However, the clinical significance of PCGs combined lncRNAs is yet to be investigated in esophageal squamous cell carcinoma (ESCC). Using probe re-annotation, univariable Cox regression and the random survival forest algorithm to identify PCG-lncRNA combinations predictive of the overall survival, we found a signature comprised of three PCGs (ANGPTL7, OBP2A, SLC27A5) and two lncRNAs (RP11-702B10.1, RP11-523H24.3) to have the highest accurate prediction, with an area under ROC curve (AUC) of 0.85 in the training group and 0.63 in the test group, and it was significantly associated with the survival of ESCC patients in the training group (median survival: 32.2 months > 60 months, P < 0.001). The application of the signature to the test group showed similar prognostic values (median survival: 39.3 months vs. >60 months, P = 0.03). The chi-square test and multivariable Cox regression analysis showed that the three-PCG, two-lncRNA signature was an independent prognostic factor for patients with ESCC. Stratified analysis suggested that the PCG-lncRNA signature combined with the TNM stage could more accurately categorize ESCC patients. Our study suggests that the three-PCG, two-lncRNA signature has clinical significance for the prognosis of patients with ESCC. This signature can serve as a potential auxiliary biomarker of the TNM stage to subdivide ESCC patients more precisely.

Abdominal wall endometriosis occurring after cesarean section: an underestimated complication

The aim of the study was to review patients characteristics, describe the exact anatomic locations and size of the endometriosis in the abdominal wall, and discuss the factors that may contribute to mesh use during abdominal wall endometriosis (AWE) resection.

MATERIALS AND METHODS

Patients diagnosed with AWE in their surgical scars from January 2008 to December 2014 were documented. Descriptive data was collected and analyzed.

RESULTS

A total of 95 patients with an age ranging from 26 to 48 years, with a mean age of 33.5 ?5.0 years at the time of excision were analyzed. The mean diameter of the mass was 3.25 cm in the present series with an average of 4.97 cm in the mesh group by ultrasound. A total of 18 patients had mesh therapy for fascia defect compared with 77 non-mesh therapy patients. The size of the lesions, the mean duration of symptoms for painful mass, and level of the serum CA125 were statistically different between mesh group and non-mesh group (p < 0.05). Cases of endometriosis lesions limited to the adipose layer had significant lower chance of using mesh (p < 0.05). However, adipose layer endometriosis lesions that had penetrated through the fascia layer and invaded into rectus abdominis muscle layer with/without peritoneum layer had significant higher chance of using mesh (p < 0.05).

CONCLUSIONS

The more common position for scar endometriosis may be in the adipose layer at the corner of the surgical scar. Mesh therapy should be considered before surgery when the diameter of the abdominal wall mass detected by ultrasound is more than five em and/or when the lesions invade into rectus abdominis muscle with/without peritoneum tissues from adipose and fascia layers.

Prevalence of hepatitis A viral RNA and antibodies among Chinese blood donors

Like other developing countries, China was reported to have a relatively high seroprevalence of anti-hepatitis A antibodies (anti-HAV). However, no studies have evaluated the prevalence of anti-HAV and HAV RNA among voluntary blood donors with or without elevated serum alanine transaminase (ALT) levels. Anti-HAV antibodies were detected using an enzyme-linked immunosorbent assay, and reverse transcription quantitative polymerase chain reaction was carried out for detection of HAV RNA. In the current study, we analyzed a total of 450 serum samples with elevated ALT levels (≥40 U/L) and 278 serum samples with non-elevated ALT levels. Seroprevalence rates of anti-HAV were 51.6% in donors with elevated ALT and 41.4% in donors with non-elevated ALT; however, none of the samples was positive for HAV RNA. The results of our study showed lower seroprevalence rates of anti-HAV in blood donors (irrespective of ALT levels) than those in published data on Chinese populations. Although donors with elevated ALT had statistically higher prevalence rates of anti- HAV than did those with non-elevated ALT, none of the serum samples had detectable levels of the active virus. In conclusion, our results demonstrate that the transmission of hepatitis A by blood transfusion will occur rarely.

Application of indirect linkage analysis and direct genotyping to hemophilia A carrier detection in Sichuan, China

Hemophilia A (HA) is an inherited X-linked bleeding disorder caused by mutations in the factor VIII gene. Prenatal detection in female carriers from families with HA is important to reduce the number of HA patients. The purpose of this study was to detect carriers in families with HA from Sichuan, China, using linkage analysis and a direct genotyping method. A total of 18 HA families were studied. Using a combination of intron 22 inversion, intron 1 inversion, the BclI polymorphic site in intron 18, the HindIII polymorphic site in intron 19, and dinucleotide CA-repeat markers in introns 1, 13, 22, and 24, we were able to detect HA in 88.9% (16/18) of the families studied. HA was detected in the remaining two families by direct genotyping. This study gave the participants a good understanding of their genetic condition and gave us a preliminary understanding of the prevalence of each mutation in Sichuan HA patients.

Cohn process influences the functional anticoagulant activity of human protein C

Cohn fraction IV (CFIV) is a byproduct of a plasma fractionation process known as the Cohn process. It is an inexpensive source of protein C, retaining about 90% of protein C (PC) in human plasma. We investigated whether PC is affected during the Cohn process and evaluated correlations among coagulant activity, amidolytic activity and PC antigen during the Cohn process. CFIV was redissolved with citrate-buffered saline for 5 h at 4°C, and then centrifuged at 3500 g for 40 min at 4°C. Functional anticoagulant activity was measured with a one-stage coagulation method based on activated partial thromboplastin time. The functional amidolytic activity of PC was determined using chromogenic substrate assay, and measurement of PC antigen was performed by ELISA. In CFIV, anticoagulant activity declined significantly, with a loss of >80%, while amidolytic activity was not significantly altered, compared to PC antigen. Prior to the Cohn process, high-rank correlations were observed in cryosupernatant, with rs = 0.921 for anticoagulant and amidolytic activities (P = 0.009), 0.896 for anticoagulant activity and antigen (P = 0.014) and 0.832 for amidolytic activity and antigen (P = 0.031). After the Cohn process in CFIV, there was also a high correlation between amidolytic activity and antigen (rs = 0.782, P = 0.038). There were no significant correlations between anticoagulant activity and antigen (rs = 0.223, P = 0.653), or anticoagulant and amidolytic activity (rs = 0.236, P = 0.675). We conclude that the Cohn process significantly influences the anticoagulant activity of PC. Compared to the antigen, PC lost greater than 80% of its anticoagulant activity, but retained its amidolytic activity, during the Cohn process.

Expression and fast preparation of biologically active recombinant human coagulation factor VII in CHO-K1 cells

Human coagulation factor VII (FVII) plays an important role in the blood coagulation process and exists in micro amounts in human plasma; therefore, any attempt at the large-scale production of FVII in significant quantities is challenging. The purpose of this study was to express and obtain biologically active recombinant FVII (rFVII) from Chinese hamster ovary K1 (CHO-K1) cells. The full-length FVII cDNA was isolated from a HepG2 cell line and then subcloned in pcDNA3.1 to construct an expression vector, pcDNA-FVII. CHO-K1 cells were transfected with 1 µg pcDNA-FVII. The cell line that stably expressed secretory FVII was screened using 900 µg/mL G418. The FVII copy number in CHO-K1 cells was detected by quantitative polymerase chain reaction (qPCR). The rFVII was purified in ligand affinity chromatography medium. The purified protein was detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis. The biological activity of the purified FVII protein was determined by a prothrombin time assay. Three cell lines that permanently expressed rFVII were screened. The qPCR results demonstrated that each CHO-K1 cell harbored two FVII DNA copies. The SDS-PAGE and Western blot analysis showed that the purified protein was about 50 kDa. The purity of the target protein was 95%. The prothrombin time assay indicated that the FVII-specific activity of rFVII was 2573 ± 75 IU/mg. This method enabled the fast preparation of high-purity rFVII from CHO-K1 cells, and the purified protein had good biological activity.

Comprehensive bioinformation analysis of the mRNA profile of fascin knockdown in esophageal squamous cell carcinoma

BACKGROUND

Fascin, an actin-bundling protein forming actin bundles including filopodia and stress fibers, is overexpressed in multiple human epithelial cancers including esophageal squamous cell carcinoma (ESCC). Previously we conducted a microarray experiment to analyze fascin knockdown by RNAi in ESCC.

METHOD

In this study, the differentially expressed genes from mRNA expression profilomg of fascin knockdown were analyzed by multiple bioinformatics methods for a comprehensive understanding of the role of fascin.

RESULTS

Gene Ontology enrichment found terms associated with cytoskeleton organization, including cell adhesion, actin filament binding and actin cytoskeleton, which might be related to fascin function. Except GO categories, the differentially expressed genes were annotated by 45 functional categories from the Functional Annotation Chart of DAVID. Subpathway analysis showed thirty-nine pathways were disturbed by the differentially expressed genes, providing more detailed information than traditional pathway enrichment analysis. Two subpathways derivated from regulation of the actin cytoskeleton were shown. Promoter analysis results indicated distinguishing sequence patterns and transcription factors in response to the co-expression of downregulated or upregulated differentially expressed genes. MNB1A, c-ETS, GATA2 and Prrx2 potentially regulate the transcription of the downregulated gene set, while Arnt-Ahr, ZNF42, Ubx and TCF11-MafG might co-regulate the upregulated genes.

CONCLUSIONS

This multiple bioinformatic analysis helps provide a comprehensive understanding of the roles of fascin after its knockdown in ESCC.

Construction of tissue-engineered composite intervertebral disc and preliminary morphological and biochemical evaluation

The aim of this study was to construct tissue-engineered composite intervertebral disc (IVD) consisting of demineralized bone matrix gelatin (DBMG) and collagen II/hyaluronate/chondroitin-6-sulfate (CII/HyA-CS) scaffolds seeded with anulus fibrosus (AF) and nucleus pulposus (NP) cells, respectively. The cell-scaffold hybrids were implanted in the subcutaneous space of the dorsum of athymic mice and harvested at 4, 8, and 12 weeks. At each time point, the gross and histological morphology and biochemical properties were evaluated. Our results are as following: the gross morphology and histology of the composite resembled those of native IVD. Morphological studies revealed progressive tissue formation and junction integration between AF and NP regions. Biochemical composition detection indicated that the content of DNA, proteoglycan and hydroxyproline increased with time, and were similar to native tissue at 12 weeks. All these results demonstrated the feasibility of creating a tissue-engineered composite IVD with similar morphological and biochemical properties to the native tissue.

Differentiation of colonic polyps by confocal laser endomicroscopy

BACKGROUND AND STUDY AIM

The real-time identification and removal of adenomas is a cost-effective strategy to improve the prognosis of colorectal cancer. Confocal laser endomicroscopy (CLE) could provide real-time histological-level observation. We aimed to evaluate the efficacy of CLE diagnosis using a simple classification system that differentiates adenomas from non-neoplastic polyps with intravenous fluorescein staining alone.

PATIENTS AND METHODS

An endoscope integrated confocal laser microscopy system was used in this study. CLE images of 35 colonic polyps, including 15 hyperplastic polyps and 20 adenomas confirmed by histology, were first evaluated to develop criteria for diagnosis of neoplastic and non-neoplastic polyps. The diagnostic criteria included goblet cell depletion, villous architecture, and microvascular alterations. We then performed a prospective study of colonic polyps found during CLE and classified them according to the established criteria. A total of 115 patients with 115 colonic polyps were included. The real-time CLE diagnosis was compared with that from histology. The stored CLE images were evaluated later by a blinded observer.

RESULTS

The sensitivity, specificity, positive predictive value, and negative predictive value of real-time CLE in identifying colonic adenomas were 93.9 % (95 % confidence interval [CI] 85.4 - 97.6), 95.9 % (95 % CI 86.2 - 98.9), 96.9 % (95 % CI 89 - 99), and 92.2 % (95 % CI 81 - 97), respectively, compared with histological results. Interobserver agreement between real-time and post-CLE still-image evaluation was excellent (kappa = 0.929). Goblet cell depletion alone had a sensitivity of 84.9 % (95 % CI 73 - 92) and a specificity of 87.8 % (95 % CI 75 - 95), as well as excellent interobserver agreement (kappa = 0.824).

CONCLUSIONS

Endoscope integrated CLE with fluorescein staining may reliably assist in the real-time identification of colonic adenomas. Among three diagnostic categories, goblet cell depletion can be used to distinguish adenomas and hyperplastic polyps.

Identification of pathways involved in paclitaxel activity in cervical cancer

Paclitaxel is one of the key chemotherapeutic drugs widely used to treat various types of cancer. Many cervical cancer patients exhibit selectivity in response to thereapy, however, which is considered to be correlated with drug-gene-pathways. The aim of this study was to identify pathways involved in paclitaxel activity in cervical cancer. Gene expression data was obtained from the NCBI Gene Expression Omnibus and the associations between paclitaxel and genes from DrugBank, MATADOR, TTD, CTD and SuperTarget databases. Differentially expressed genes in cervical cancer were identified using the significance analysis of microarrays (SAM) statistical technique. Pathway analysis was performed according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database using the software package SubpathwayMiner to predict target genes of paclitaxel in cervical cancer and regulated pathways. We found that paclitaxel, which exhibits anticancer activity in cervical cancer, may interact with these differentially expressed genes and their corresponding signaling pathways. Our study presents the first in-depth, large-scale analysis of pathways involved in paclitaxel activity in cervical cancer. Interestingly, these pathways have not been reported to be involved in other tumors. Thus our findings may contribute to the understanding of the mechanisms underlying paclitaxel resistance in cervical cancer.

MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features

Synergistic regulations among multiple microRNAs (miRNAs) are important to understand the mechanisms of complex post-transcriptional regulations in humans. Complex diseases are affected by several miRNAs rather than a single miRNA. So, it is a challenge to identify miRNA synergism and thereby further determine miRNA functions at a system-wide level and investigate disease miRNA features in the miRNA–miRNA synergistic network from a new view. Here, we constructed a miRNA–miRNA functional synergistic network (MFSN) via co-regulating functional modules that have three features: common targets of corresponding miRNA pairs, enriched in the same gene ontology category and close proximity in the protein interaction network. Predicted miRNA synergism is validated by significantly high co-expression of functional modules and significantly negative regulation to functional modules. We found that the MFSN exhibits a scale free, small world and modular architecture. Furthermore, the topological features of disease miRNAs in the MFSN are distinct from non-disease miRNAs. They have more synergism, indicating their higher complexity of functions and are the global central cores of the MFSN. In addition, miRNAs associated with the same disease are close to each other. The structure of the MFSN and the features of disease miRNAs are validated to be robust using different miRNA target data sets.

Confocal laser endomicroscopy for superficial esophageal squamous cell carcinoma

BACKGROUND AND STUDY AIMS

Confocal laser endomicroscopy (CLE) allows subsurface imaging of gastrointestinal mucosa in vivo. The goal of the present study was to compare the endomicroscopic characteristics of cells and intrapapillary capillary loops (IPCLs) in normal and superficial esophageal squamous cell carcinoma (SESC).

PATIENTS AND METHODS

We recruited consecutive patients with SESC diagnosed by conventional endoscopy and confirmed by histopathology between July 2006 and May 2008. The confocal endoscopic images of these patients were collected and compared with the corresponding histology. The characteristic patterns of cells and IPCLs was then analyzed from these images of malignant and normal mucosa. The quality of images and interobserver variations of two endoscopists were also evaluated.

RESULTS

Overall, 64 samples from 57 subjects (27 SESCs, 30 controls) were examined by CLE. The confocal images corresponded to the hematoxylin and eosin staining from the same sites. The confocal images showed that there was a significantly higher proportion of squamous epithelial cells with irregular arrangement (79.4 % vs. 10.0 %, P < 0.001), increased diameter of IPCLs (26.0 microm vs. 19.2 microm, P < 0.001), and irregular shape IPCLs (82.4 % vs. 36.7 %, P = 0.0002) in the SESC group compared with the controls. Massive IPCLs with tortuous vessels (44.1 % vs. 0 %, P < 0.0001), and long branching IPCLs (23.5 % vs. 3.3 %, P = 0.0204) were frequently observed in the SESC group. In this study, about 35.5 % of images were graded as good quality, and the interobserver agreement for the prediction of cancerous mucosa was graded as substantial.

CONCLUSIONS

CLE can be used to distinguish cancerous from normal epithelium, which gives it potential value for early detection of esophageal carcinoma. The difficulty in obtaining good images in the esophagus by CLE is a latent problem.

Cytotoxicity induced by grape seed proanthocyanidins: role of nitric oxide

Grape seed proanthocyanidin extract (GPSE) at high doses has been shown to exhibit cytotoxicity that is associated with increased apoptotic cell death. Nitric oxide (NO), being a regulator of apoptosis, can be increased in production by the administration of GSPE. In a chick cardiomyocyte study, we demonstrated that high-dose (500 microg/ml) GSPE produces a significantly high level of NO that contributes to increased apoptotic cell death detected by propidium iodide and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) staining. It is also associated with the depletion of intracellular glutathione (GSH), probably due to increased consumption by NO with the formation of S-nitrosoglutathione. Co-treatment with L-NAME, a NO synthase inhibitor, results in reduction of NO and apoptotic cell death. The decline in reduced GSH/oxidized GSH (GSSG) ratio is also reversed. N-Acetylcysteine, a thiol compound that reacts directly with NO, can reduce the increased NO generation and reverse the decreased GSH/GSSG ratio, thereby attenuating the cytotoxicity induced by high-dose GSPE. Taken together, these results suggest that endogenous NO synthase (NOS) activation and excessive NO production play a key role in the pathogenesis of high-dose GSPE-induced cytotoxicity.

Hydrocarbon charging histories of the Ordovician reservoir in the Tahe oil field, Tarim Basin, China

The Ordovician reservoir of the Tahe oil field went through many tectonic reconstructions, and was characterized by multiple hydrocarbon chargings. The aim of this study was to unravel the complex charging histories. Systematic analysis of fluid inclusions was employed to complete the investigation. Fluorescence observation of oil inclusions under UV light, and microthermometry of both oil and aqueous inclusions in 105 core samples taken from the Ordovician reservoir indicated that the Ordovician reservoir underwent four oil chargings and a gas charging. The hydrocarbon chargings occurred at the late Hercynian, the Indo-Sinian and Yanshan, the early Himalaya, the middle Himalaya, and the late Himalaya, respectively. The critical hydrocarbon charging time was at the late Hercynian.

A novel locus (DSAP2) for disseminated superficial actinic porokeratosis maps to chromosome 15q25.1-26.1

BACKGROUND

Disseminated superficial actinic porokeratosis (DSAP) is a chronic cutaneous disorder characterized by multiple superficial keratotic lesions surrounded by a slightly raised keratotic border. It develops in teenagers in sun-exposed areas of skin and usually follows an autosomal dominant inheritance pattern. The first locus for DSAP was localized to chromosome 12q23.2-24.1, but no gene responsible for porokeratosis has been identified to date.

OBJECTIVES

To determine whether DSAP is a genetically heterogeneous disorder and to identify the disease gene locus in a three-generation Chinese family with DSAP.

METHODS

Genetic linkage analysis was carried out in this family using 15 microsatellite markers between D12S1671 and D12S369 on chromosome 12q, followed by a genome-wide scan with 382 microsatellite markers from the autosomes.

RESULTS

Genetic linkage analysis with chromosome 12q markers suggested that the locus in this family is not linked to chromosome 12q. A genome-wide scan and fine mapping finally localized the locus for DSAP in this family to a 6.4-cM region between markers D15S1023 and D15S1030 at chromosome 15q25.1-26.1. This DSAP locus was named DSAP2.

CONCLUSIONS

The previous results and this study have shown that DSAP is a genetically heterogeneous disorder; a novel locus for DSAP, termed DSAP2, was mapped to a 6.4-cM region between markers D15S1023 and D15S1030.

Expression of the amino-terminal domain of platelet glycoprotein Ib alpha: exploitation of a calmodulin tag for determination of its functional activity

Platelet glycoprotein (GP) Ibalpha is a component of the GPIb-IX receptor complex, which is involved in multiple physiological and pathological processes, including platelet adhesion at sites of vascular injury, thrombin binding, Bernard-Soulier syndrome, platelet-type von Willebrand disease, and immune-mediated thrombocytopenias. The amino-terminal domain of approximately 300 residues of GPIbalpha mediates both normal biological function (by providing the sites for direct ligand interaction) and aberrant function (through amino acid substitutions). To investigate the molecular interactions mediated by this region of GPIbalpha, we have developed a recombinant baculovirus to facilitate its expression as a calmodulin fusion protein from insect cells. By employing the calmodulin tag, the fusion protein could be obtained at >90% purity after a single isolation step at yields of 8 mg/L of insect cell medium (purified fusion protein). The recombinant GPIbalpha fragment was shown to be posttranslationally sulfated and glycosylated, although its glycosylation differed from that of the equivalent GPIbalpha fragment isolated from human platelets. The differential glycosylation, however, did not affect the function of the recombinant GPIbalpha fragment in either von Willebrand factor (vWf) or thrombin binding as these were both found to be identical to those of the same-length GPIbalpha fragment derived from human platelets. The calmodulin tag was also exploited in the development of assays to measure directly vWf and thrombin binding, since it did not interfere with either, demonstrating the feasibility for the use of this soluble receptor fusion protein in detailed biophysical assays to investigate the molecular mode of binding of platelet glycoprotein Ibalpha to these ligands.

The recruitment of Fas-associated death domain/caspase-8 in Ras-induced apoptosis

Oncogenic Ras induces cells to undergo apoptosis after inhibition of protein kinase C (PKC) activity. The integration of differential signaling pathways is required for full execution of apoptosis. In this study, we used Jurkat as well as Fas/FADD-defective cell lines expressing v-ras to determine the upstream elements required for activation of the caspase cascade in PKC/Ras-mediated apoptosis. During this Ras-induced apoptotic process, caspase-8 was activated, possibly through its binding to Fas-associated death domain (FADD), in Jurkat/ras and Jurkat/Fas(m)/ras cells but not in Jurkat/FADD(m)/ras cells. c-Jun NH(2)-terminal kinase (JNK) was activated in all three cell lines expressing ras in response to apoptotic stimulation. Suppression of JNK by dn-JNK1 blocked the interaction of FADD and caspase-8 and partially protected Jurkat/ras and Jurkat/Fas(m)/ras cells from apoptosis. However, dn-JNK1 had no effect on PKC/Ras-induced apoptosis in Jurkat/FADD(m)/ras cells. The results indicate that FADD/caspase-8 signaling is involved in PKC/Ras-mediated apoptosis, and JNK may be an upstream effector of caspase activation.

Increased oxidative and nitrative stress in human stomach associated with cagA+ Helicobacter pylori infection and inflammation

In order to study the role of Helicobacter pylori infection in gastric carcinogenesis, we have measured oxidized (carbonyls) and nitrated (nitrotyrosine-containing) proteins as markers for oxidative and nitrative stress in 216 human gastric biopsies using dot and western immunoblots and correlated the results with H. pylori, cagA status, expression of interleukin-8 and inducible nitric oxide synthase (iNOS) mRNAs, and gastric pathology. Higher levels of both oxidized and nitrated proteins were found in patients with either chronic gastritis or duodenal ulcer than in those with normal mucosa. The levels of modified proteins were significantly higher in inflamed samples infected with H. pylori, especially cagA+ strains, and in those with expression of interleukin-8 and iNOS mRNAs than in those negative for these parameters. These results indicate that infection with cagA+ H. pylori induces significant oxidative and nitrative stress in stomach mucosa, contributing to the pathogenesis of H. pylori-associated gastroduodenal diseases.

Platelet glycoprotein Ib alpha binds to thrombin anion-binding exosite II inducing allosteric changes in the activity of thrombin

The glycoprotein (GP) Ib-IX complex is a platelet surface receptor that binds thrombin as one of its ligands, although the biological significance of thrombin interaction remains unclear. In this study we have used several approaches to investigate the GPIb alpha-thrombin interaction in more detail and to study its effect on the thrombin-induced elaboration of fibrin. We found that both glycocalicin and the amino-terminal fragment of GPIb alpha reduced the release of fibrinopeptide A from fibrinogen by about 50% by a noncompetitive allosteric mechanism. Similarly, GPIb alpha caused in thrombin an allosteric reduction in the rate of turnover of the small peptide substrate d-Phe-Pro-Arg-pNA. The K(d) for the glycocalicin-thrombin interaction was 1 microm at physiological ionic strength but was highly salt-dependent, decreasing to 0.19 microm at 100 mm NaCl (Gamma(salt) = -4.2). The salt dependence was characteristic of other thrombin ligands that bind to exosite II of this enzyme, and we confirmed this as the GPIb alpha-binding site on thrombin by using thrombin mutants and by competition binding studies. R68E or R70E mutations in exosite I of thrombin had little effect on its interaction with GPIb alpha. Both the allosteric inhibition of fibrinogen turnover caused by GPIb alpha binding to these mutants, and the K(d) values for their interactions with GPIb alpha were similar to those of wild-type thrombin. In contrast, R89E and K248E mutations in exosite II of thrombin markedly increased the K(d) values for the interactions of these thrombin mutants with GPIb alpha by 10- and 25-fold, respectively. Finally, we demonstrated that low molecular weight heparin (which binds to thrombin exosite II) but not hirugen (residues 54-65 of hirudin, which binds to exosite I of thrombin) inhibited thrombin binding to GPIb alpha. These data demonstrate that GPIb alpha binds to thrombin exosite II and in so doing causes a conformational change in the active site of thrombin by an allosteric mechanism that alters the accessibility of both its natural substrate, fibrinogen, and the small peptidyl substrate d-Phe-Pro-Arg-pNA.

Nitrated and oxidized plasma proteins in smokers and lung cancer patients

Cigarette smoking is a cause of lung cancer and other respiratory diseases. Oxidants either present in cigarette smoke and/or formed in the lung of smokers may trigger oxidative and nitrative damage to DNA and cellular components, contributing to carcinogenesis. We have used immunodot and Western blot analyses to measure nitrated (nitrotyrosine-containing) and oxidized (carbonyl-containing) proteins in plasma samples collected from 52 lung cancer patients and 43 control subjects (heavy and light smokers, nonsmokers with or without exposure to environmental tobacco smoke). The levels of nitrated proteins were significantly higher in lung cancer patients than in controls (P = 0.003). On the other hand, the levels of oxidized proteins were significantly higher in smokers than in nonsmokers (P < 0.001). Western-blot analyses showed the presence of two to five nitrated proteins and one oxidized protein. Using immunoprecipitation and Western-blot analyses with eight different antibodies against human plasma proteins, we identified fibrinogen, transferrin, plasminogen, and ceruloplasmin as nitrated proteins and fibrinogen as the only oxidized protein present in human plasma of lung cancer patients and smokers. Our results indicate that cigarette smoking increases oxidative stress and that during lung cancer development, formation of reactive nitrogen species results in nitration and oxidation of plasma proteins.

[Potential anxiolytic role of c-fos antisense oligonucleotide in social-defeated rats]

OBJECTIVES

This study was to explore the therapeutic potential of c-fos antisense phosphorothioate oligonucleotide and the possible molecular mechanism.

METHODS

On the basis of the sequence of c-fos mRNA, two 15-mer phosphorothioated oligodeoxynucleotide(ODN) were synthesized. Antisense ODN was corresponded to the initiation codon of c-fos mRNA. The complementary sense and vehicle(saline) served as controls. Anxiety was induced in rats by a social-defeated paradigm and then rats were given a 5-minute exposure to the plus maze and open field test. Rats were injected c-fos antisense, sense ODNs and vehicles into the lateral ventricle through stainless-steel guide cannulate implanted unilaterally from the beginning of the experiment. The expression of the protein product of the immediate early gene c-fos was analyzed with immunochemistry in different brain regions, such as the amygdala and paraventricularis hypothalami nucleus. Computer assisted image analysis was performed to quantify the results of immuno-cytochemistry.

RESULTS

Socially defeated c-fos antisense-treated rats displayed obviously reduced anxiety-related behavior, as they spent significantly more time in the open arms of the plus maze compared to sense ODN- and vehicle-treated rats. The behavioral effects were similar to those of established anti-anxiety drugs(diazepam). Antisense oligodeoxynucleotide significantly decreased Fos positive nucleus in paraventricularis hypothalami nucleus. The inhibitory efficiency was 57.03%.

CONCLUSION

Our data provide further evidence that c-fos is involved in acute stress elicited anxiety related behavior.

Platelet glycoprotein ibalpha is a counterreceptor for the leukocyte integrin Mac-1 (CD11b/CD18)

The firm adhesion and transplatelet migration of leukocytes on vascular thrombus are both dependent on the interaction of the leukocyte integrin, Mac-1, and a heretofore unknown platelet counterreceptor. Here, we identify the platelet counterreceptor as glycoprotein (GP) Ibalpha, a component of the GP Ib-IX-V complex, the platelet von Willebrand factor (vWf) receptor. THP-1 monocytic cells and transfected cells that express Mac-1 adhered to GP Ibalpha-coated wells. Inhibition studies with monoclonal antibodies or receptor ligands showed that the interaction involves the Mac-1 I domain (homologous to the vWf A1 domain), and the GP Ibalpha leucine-rich repeat and COOH-terminal flanking regions. The specificity of the interaction was confirmed by the finding that neutrophils from wild-type mice, but not from Mac-1-deficient mice, bound to purified GP Ibalpha and to adherent platelets, the latter adhesion being inhibited by pretreatment of the platelets with mocarhagin, a protease that specifically cleaves GP Ibalpha. Finally, immobilized GP Ibalpha supported the rolling and firm adhesion of THP-1 cells under conditions of flow. These observations provide a molecular target for disrupting leukocyte-platelet complexes that promote vascular inflammation in thrombosis, atherosclerosis, and angioplasty-related restenosis.

Necessity of conserved asparagine residues in the leucine-rich repeats of platelet glycoprotein Ib alpha for the proper conformation and function of the ligand-binding region

The polypeptides of the platelet von Willebrand factor (vWf) receptor, the GP Ib-IX-V complex, each contain tandem repeats of a sequence that assigns them to the leucine-rich repeat protein family. Here, we studied the role of conserved Asn residues in the leucine-rich repeats of GP Ib alpha, the ligand-binding subunit of the complex. We replaced the Asn residue in the sixth position of the first or sixth leucine-rich repeat (of seven) either with a bulky, charged Lys residue or with a Ser residue (sometimes found in the same position of other leucine-rich repeats) and studied the effect of the mutations on complex expression, modulator-dependent vWf binding, and interactions with immobilized vWf under fluid shear stress. As predicted, the Lys substitutions yielded more severe phenotypes, producing proteins that either were rapidly degraded within the cell (mutant N158K) or failed to bind vWf in the presence of ristocetin or roll on immobilized vWf under fluid shear stress (mutant N41K). The binding of function-blocking GP Ib alpha antibodies to the N41K mutant was either significantly reduced (AK2 and SZ2) or abolished (AN51 and CLB-MB45). Ser mutations were tolerated much better, although both mutants demonstrated subtle defects in vWf binding. These results suggest a vital role for the conserved asparagine residues in the leucine-rich repeats of GP Ib alpha for the structure and functions of this polypeptide. The finding that mutations in the first leucine-rich repeat had a much more profound effect on vWf binding indicates that the more N-terminal repeats may be directly involved in this interaction.

Preconditioning in cardiomyocytes protects by attenuating oxidant stress at reperfusion

Cardiomyocyte death after ischemia/reperfusion correlates with oxidant stress, and antioxidants confer protection in that model. Preconditioning (PC) with hypoxia or adenosine also confers protection, leading us to hypothesize that PC protects by attenuating oxidant generation during subsequent ischemia/reperfusion. Chick cardiomyocytes were preconditioned with 10 minutes of hypoxia or adenosine (100 micromol/L), followed by 1 hour of simulated ischemia and 3 hours of reperfusion. Adenosine PC decreased cell death from 50+/-3% to 18+/-4% and enhanced the return of contractions during reperfusion, as observed previously with hypoxic PC. A transient burst of dichlorofluorescein (sensitive to H2O2 oxidation that was significantly attenuated by PC initiated by hypoxia or adenosine was seen at reperfusion. The protein kinase C (PKC) inhibitor Go-6976 and the mitochondrial ATP-sensitive K(+) (K(ATP)) channel inhibitor 5-hydroxydecanoate each abolished protection and abrogated the PC-induced attenuation of reperfusion oxidant stress. By contrast, when given only at reperfusion, the K(+) channel opener pinacidil or the antioxidants 2-mercaptopropionylglycine and 1,10-phenanthroline decreased oxidant stress at reperfusion and improved survival and return of contractions. Thus, PC protection is associated with an attenuation of the oxidant burst at reperfusion, regardless of the method by which PC is triggered. Loss of PC protection associated with PKC inhibition or K(ATP) channel inhibitors is associated with a restoration of that oxidant stress. These results suggest a mechanism for PC protection and reveal a functional link between PKC activation and K(ATP) channel activation in that pathway.

Interaction of von Willebrand factor domain A1 with platelet glycoprotein Ibalpha-(1-289). Slow intrinsic binding kinetics mediate rapid platelet adhesion

We investigated the crucial hemostatic interaction between von Willebrand factor (VWF) and platelet glycoprotein (GP) Ibalpha. Recombinant VWF A1 domain (residues Glu(497)-Pro(705) of VWF) bound stoichiometrically to a GPIbalpha-calmodulin fusion protein (residues His(1)-Val(289) of GPIbalpha; GPIbalpha-CaM) immobilized on W-7-agarose with a K(d) of 3.3 microM. The variant VWF A1(R545A) bound to GPIbalpha-CaM 20-fold more tightly, mainly because the association rate constant k(on) increased from 1,100 to 8,800 M(-1) s(-1). The GPIbalpha mutations G233V and M239V cause platelet-type pseudo-von Willebrand disease, and VWF A1 bound to GPIbalpha(G233V)-CaM and GPIbalpha(M239V)-CaM with a K(d) of 1.0 and 0.63 microM, respectively. The increased affinity of VWF A1 for GPIbalpha(M239V)-CaM was explained by an increase in k(on) to 4,500 M(-1) s(-1). GPIbalpha-CaM bound with similar affinity to recombinant VWF A1, to multimeric plasma VWF, and to a fragment of dispase-digested plasma VWF (residues Leu(480)/Val(481)-Gly(718)). VWF A1 and A1(R545A) bound to platelets with affinities and rate constants similar to those for binding to GPIbalpha-CaM, and botrocetin had the expected positively cooperative effect on the binding of VWF A1 to GPIbalpha-CaM. Therefore, allosteric regulation by botrocetin of VWF A1 binding to GPIbalpha, and the increased binding affinity caused by mutations in VWF or GPIbalpha, are reproduced by isolated structural domains. The substantial increase in k(on) caused by mutations in either A1 or GPIbalpha suggests that productive interaction requires rate-limiting conformational changes in both binding sites. The exceptionally slow k(on) and k(off) provide important new constraints on models for rapid platelet tethering at high wall shear rates.

Threonine-145/methionine-145 variants of baculovirus produced recombinant ligand binding domain of GPIbalpha express HPA-2 epitopes and show equal binding of von Willebrand factor

Glycoprotein (GP) Ibalpha is the functionally dominant subunit of the platelet GPIb-IX-V receptor complex, with the von Willebrand factor (vWF) binding site residing on the amino-terminus. A threonine for methionine-145 replacement of GPIbalpha is associated with the human platelet antigen (HPA)-2 system. To study the structural and functional consequences of this mutation, both forms of GPIbalpha were expressed as calmodulin fusion proteins in insect cells. Both recombinant proteins were recognized by their respective alloantibodies, independent of glycosylation or intactness of disulfide bonds, and gave similar results to platelet-derived GPIbalpha in antibody detection assays. Resonant mirror studies showed that vWF binding was not affected by the HPA-2 mutation; however, vWF binding was partially inhibited by IgG HPA-2 antibodies. Our data are compatible with an involvement of the leucine-rich repeat domain of GPIbalpha in vWF binding and indicate that recombinant GPIbalpha may be used to detect HPA-2 antibodies. (Blood. 2000;95:205-211)

Coexpression of interleukin-8 and inducible nitric oxide synthase in gastric mucosa infected with cagA+ Helicobacter pylori

The cagA-positive Helicobacter pylori strains are thought to be able to induce interleukin-8 expression and to be associated with gastroduodenal diseases. Inducible nitric oxide synthase (iNOS) may be involved in inflammatory pathogenesis. Our aim was to investigate the interrelationships between cagA and the expression of interleukin-8 and iNOS messenger RNAs, and with the type and degree of inflammation in gastric mucosa. In biopsies from 108 Chinese patients, the cagA, 16S rRNA, interleukin-8, and iNOS mRNAs were analyzed using reverse-transcription polymerase chain reaction. Specimens infected with cagA-positive strains had significantly more severe infiltration by mononuclear and polymorphonuclear leukocytes and more frequently expressed interleukin-8 and iNOS mRNAs than those infected with cagA-negative strains. iNOS and interleukin-8 mRNAs were significantly more frequently expressed together in the specimens with moderate or severe inflammation than in those with normal mucosa or mild inflammation. Our data suggest that interleukin-8 and excess nitric oxide play important roles in the pathogenesis of H. pylori-associated gastroduodenal diseases.