The comprehensive roles of lncRNA FAM99A/FAM99B in hepatocellular carcinoma: Expressions, regulatory mechanisms and functional pathway analysis

AIMS

The incidence and mortality of liver hepatocellular carcinoma (LIHC) were increasing year by year. The aim of this study was to investigate the comprehensive roles of lncRNA FAM99A and FAM99B in LIHC.

MAIN METHODS

According to the data of TCGA and GTEx, the expression levels of FAM99A and FAM99B in LIHC were evaluated, and the overall survival (OS), disease-free survival (DFS), immune cell infiltration and tumor stage were analyzed. The subcellular localization of FAM99A and FAM99B in various cancer cell lines was predicted by lncATLAS database. In addition, we also used ENCORI, KEGG, LinkedOmics, Metascape and other databases. It was verified by in vivo and in vitro experiments.

KEY FINDINGS

Compared with adjacent normal tissues, FAM99A and FAM99B were down-regulated in LIHC tissues, and significantly correlated with immune cell infiltration. With the progression of tumor stage and grade, the expression of FAM99A and FAM99B showed a decreasing trend, and the prognosis of patients were also poor. In addition, the biological functions, signaling pathways and protein interactions of FAM99A and FAM99B in LIHC were enriched to study the potential molecular mechanisms. The overlapping RNA binding proteins (RBP) of FAM99A and FAM99B mainly included CSTF2T, BCCIP, RBFOX2 and SF3B4. Finally, experiments showed that overexpression of FAM99A attenuated the proliferation, invasion, colony formation and tumor growth of LIHC cells.

SIGNIFICANCE

Taken together, the above studies demonstrated that FAM99A and FAM99B had an inhibitory effect on the progression of LIHC, which might be promising diagnostic biomarkers and therapeutic targets for LIHC patients.

Analysis of anti-tumor effect and mechanism of GLS1 inhibitor CB-839 in colorectal cancer using a stroma-abundant tumor model

BACKGROUND

Glutaminase 1 (GLS1), a key enzyme in glutamine metabolism in cancer cells, acts as a tumor promoter and could be a potential therapeutic target. CB-839, a GLS1-specific inhibitor, was developed recently. Herein, we aimed to elucidate the anti-tumor effects and mechanism of action of CB-839 in colorectal cancer (CRC).

METHODS

Using the UCSC Xena public database, we evaluated GLS1 expression in various cancers. Immunostaining for GLS1 was performed on 154 surgically resected human CRC specimens. Subsequently, we examined the GLS1 mRNA expression levels in eight CRC cell lines and evaluated the association between GLS1 expression and CB-839 efficacy. To create a reproducible CRC model with abundant stroma and an allogeneic immune response, we co-transplanted CT26 and stem cells into BALB/c mice and treated them with CB-839. Finally, RNA sequencing of mouse tumors was performed.

RESULTS

Database analysis showed higher GLS1 expression in CRC tissues than in normal colon tissues. Clinical samples from 114 of the 154 patients with CRC showed positive GLS1 expression. GLS1 expression in clinical CRC tissues correlated with vascular invasion. CB-839 treatment inhibited cancer cell proliferation depending on GLS1 expression in vitro and inhibited tumor growth and metastasis in the CRC mouse model. RNA sequencing revealed that CB-839 treatment inhibited stromal activation, tumor growth, migration, and angiogenesis. These findings were validated through in vitro and in vivo experiments and clinical specimen analysis.

CONCLUSIONS

GLS1 expression in CRC plays important roles in tumor progression. CB-839 has inhibitory effects on cancer proliferation and the tumor microenvironment.

Comprehensive bioinformation analysis of homeodomain-leucine zipper gene family and expression pattern of HD-Zip I under abiotic stress in Salix suchowensis

BACKGROUND

Homeodomain-leucine zipper (HD-Zip) transcription factors are plant-specific and play important roles in plant defense against environmental stresses. Identification and functional studies have been carried out in model plants such as rice, Arabidopsis thaliana, and poplar, but comprehensive analysis on the HD-Zip family of Salix suchowensis have not been reported.

RESULTS

A total of 55 HD-Zip genes were identified in the willow genome, unevenly distributed on 18 chromosomes except for chromosome 19. And segmental duplication events containing SsHD-Zip were detected on all chromosomes except chromosomes 13 and 19. The SsHD-Zip were classified into 4 subfamilies subfamilies (I-IV) according to the evolutionary analysis, and members of each subfamily shared similar domain structure and gene structure. The combination of GO annotation and promoter analysis showed that SsHD-Zip genes responded to multiple abiotic stresses. Furthermore, the results of qPCR analysis showed that the SsHD-Zip I gene exhibited different degrees of expression under salt stress, PEG treatment and heat treatment. Moreover, there was a synergistic effect between SsHD-Zip I genes under stress conditions based on coregulatory networks analysis.

CONCLUSIONS

In this study, HD-Zip transcription factors were systematically identified and analyzed at the whole genome level. These results preliminarily clarified the structural characteristics and related functions of willow HD-Zip family members, and it was found that SsHox34, SsHox36 and SsHox51 genes were significantly involved in the response to various stresses. Together, these findings laid the foundation for further research on the resistance functions of willow HD-Zip genes.

Experiential training course on spirituality for multidisciplinary palliative care teams in a hospital setting: a feasibility study

BACKGROUND

There is widespread agreement about the importance of spiritual training programs (STPs) for healthcare professionals caring for cancer patients, and that reflecting on one's spirituality is the first step. Health professionals (HPs) working in hospitals must develop this dimension to guarantee the quality of life as well as spiritual and emotional support. In this paper, we propose a possible training format for hospital professionals and assess its implementation.

METHODS

This is a phase 0-I study that follows the Medical Research Council (MRC) framework. The program was implemented for hospital palliative care specialists. The program included one theory lesson, three spiritual interactions, four pieces of reflective writing, and two individual follow-up sessions for each participant. The evaluation was performed quantitatively according to the MRC framework and qualitatively according to Moore's framework with data triangulation from interviews, reflective writings, and indicators.

RESULTS

The program was implemented for palliative care physicians, nurses, psychologists, and bioethicists according to the plan, and the program components were highly appreciated by the participants. The results suggest the feasibility of a training course with some corrections, regarding both the components of the training and organizational issues. The qualitative analysis confirmed a shift in the meaning of the themes we identified. The trainees went from intrapersonal spirituality to interpersonal spirituality (engagement with the other person's spirituality, acknowledging their unique spiritual and cultural worldviews, beliefs, and practices), with colleagues, patients, and people close to them. The training had an impact on Moore's Level 3b.

CONCLUSIONS

Spiritual training for hospital professionals working in palliative care is feasible. Having time dedicated to spirituality and the ongoing mentorship of spiritual care professionals were suggested as key elements. The next step is increasing awareness of spirituality from our hospital reality and creating a stable competent group (with nurses, chaplains, nuns, counselors, etc.) with the support of the management.

Comprehensive characterization and prioritization of halogenated organic compounds in fish and their implications for exposure

Fish are an important pollution indicator for biomonitoring of halogenated organic compounds (HOCs) in aquatic environments, and HOCs in fish may pose health threats to consumers. This study performed nontarget and comprehensive analyses of HOCs in fish from an e-waste recycling zone by gas chromatography-high-resolution mass spectrometry, and further prioritized their human exposure risks. A total of 1652 formulas of HOCs were found in the fish, of which 1222, 117, and 313 were organochlorines, organobromines, and organochlorine-bromines, respectively. The total concentrations of HOCs were 15.4-18.7 μg/g (wet weight), and organobromines were the predominant (14.1-16.8 μg/g). Of the HOCs, 41 % were elucidated with tentative structures and divided into 13 groups. The estimated total daily exposures of HOCs via dietary consumption of the fish for local adult residents were 3082-3744 ng/kg bw/day. The total exposures were dominated by several groups of HOCs with the following contribution order: polyhalogenated biphenyls and their derivatives > polyhalogenated diphenyl ethers > halo- (H-)alkanes/olefines > H-benzenes > H-dioxins > H-polycyclic aromatic hydrocarbons > H-phenols. The comprehensive characterization and prioritization results provide an overview of the species and distributions of HOCs in edible fish, and propose an inventory of crucial HOCs associated with high exposure risks.

Highly efficient and chemoselective blocking of free amino group by ortho-phthalaldehyde (OPA) for comprehensive analysis of protein terminome

Herein, we introduced ortho-phthalaldehyde (OPA) for blocking free amino groups and established a simple and robust method for comprehensive profiling of protein terminome based on strong cation exchange chromatography (SCX) fractionation. With the highly efficient and chemoseletive amine-group blocking, we identified 2271 canonical human protein N-termini, 1650 canonical human protein C-termini, as well as 645 protein neo-N-termini from HeLa cells.

Evolving Trends and Burden of Inflammatory Bowel Disease in Asia, 1990-2019: A Comprehensive Analysis Based on the Global Burden of Disease Study

BACKGROUND

Asia's inflammatory bowel disease (IBD) burden has rapidly increased recently, but the epidemiological trends in Asia remain unclear. We report IBD's incidence, prevalence, mortality, and Disability-Adjusted Life Years (DALY) in 52 Asian countries from 1990 to 2019.

METHODS

Data from the Global Burden of Disease 2019 were analyzed for IBD burden across 52 countries, using metrics like incidence, prevalence, mortality rates, and DALY. The epidemiological trend of IBD from 1990 to 2019 was assessed with the Joinpoint and APC methods. Decomposition and frontier analyses examined factors behind IBD case and death changes. The NORPRED forecasted Asia's morbidity and mortality trends from 2019 to 2044.

RESULTS

From 1990 to 2019, The incidence and prevalence of IBD increased in Asia, while mortality and DALY decreased. East Asia had the highest increase in disease burden. IBD incidence was highest among the 30-34 age group, with prevalence peaking in the 45-49 age group. In high-income regions, IBD peak age shifted to younger groups. Decompose analysis showed population growth as the primary factor for the increasing IBD cases in Asia. NORDPRED model predicted a continued IBD burden increase in Asia over the next 25 years.

CONCLUSIONS

Between 1990 and 2019, ASIR and ASPR of IBD in Asia increased, while ASMR and ASDR decreased. Due to population growth and aging, the IBD burden is expected to rise over the next 25 years, particularly in East Asia.

Health risk cause of water around landfill in hilly area and prevention and control countermeasures

Evaluating the health risks of the groundwater and surface water in landfill areas is of great significance to the health and safety of local residents. The current practice of health risk assessment is based only on the analysis results of groundwater and surface water samples, which reflect the current situation of water security in landfill areas. However, due to the neglect of risk causes analysis, thus a health risk assessment is insufficient to provide rigorous scientific countermeasures for risk prevention and control. The health risks caused by groundwater and surface water is mainly controlled by the water quality, which is comprehensively controlled by the conditions of its formation and evolution. When a landfill site is located in a hilly area, the environmental characteristics, causes, main controlling factors, and evolution processes of the surface water and groundwater in different parts of the catchment are significantly different. This study used a municipal solid waste landfill area in a hilly area as an example and defined the causes and main controlling factors of regional health risks caused by water based on an analysis of the characteristics of natural and anthropogenic factors affecting the groundwater and surface water. Then, prevention and control countermeasures were proposed for health risks caused by water in different parts of the landfill area. This study provides a method for the causes analysis and prevention and control countermeasures of health risks caused by water in municipal solid waste landfills in hilly areas.

Comprehensive analysis of the influence of physicochemical properties and tumor-associated environments on liposome intratumoral penetration

Poor tumor penetration is the most significant barrier to the clinical translation of nanomedicines. Despite numerous studies, little is known about how the physicochemical properties and tumor-associated environments impact liposome intratumoral penetration from a multi-factorial perspective. Thus, we developed a set of model liposomes to explore the laws of their intratumoral penetration. Our comprehensive analysis revealed that zeta potential, membrane fluidity, and size of liposomes could influence their penetration in the peripheral, intermediate, or central areas of the tumor, respectively. Moreover, protein corona and stromal cells primarily impeded liposome penetration in the tumor periphery, while the vascular vessels had a similar effect in the tumor center. Our results also revealed a non-monotonic relationship, indicating that the best condition for a single factor may not necessarily be the optimal choice when considering all the factors. The preferred size, zeta potential, and membrane fluidity for excellent tumor penetration are within the ranges of 52-72 nm, 16-24 mV, and 230-320 mp, respectively. Our study provides a comprehensive understanding of the influence of physicochemical properties and tumor-associated environments on liposome intratumoral penetration, offering explicit guidance for the precise design and rational optimization of anti-tumor liposomes.

Comprehensive mastocytosis data analysis from a single center

Mastocytosis is a very rare disorder and is divided into three prognostically distinct variants by World Health Organization: Cutaneous mastocytosis (CM), systemic mastocytosis (SM), and mast cell sarcoma or localized mast cell (MC) tumors. The wide range of complaints may cause patients to consult various clinics, with resulting mis- or underdiagnosis. Therefore, cooperation between different subspecialties is of paramount importance. In this article, we have compiled 104 adult mastocytosis cases diagnosed and followed in our Hematology and other clinics. 86 (82.7%) of 104 patients had systemic mastocytosis. Osteoporosis, disease-related complications, and secondary malignancies are important topics in this group. We know that indolent form has great survival. But smoldering or aggressive mastocytosis has a poor prognosis. CM and indolent SM have a significantly better prognosis compared to aggressive SM (p < 0.001). We found that the presence of more than 25% of mast cells in the bone marrow, the presence of concomitant marrow dysplasia, and the presence of disease-related complications affect survival (p < 0.001). In addition to the WHO classification, the IPSM scoring system is indicative of the prognosis in this rare disease.

Comprehensive analysis of fixed-time stability and energy cost for delay neural networks

This paper focuses on comprehensive analysis of fixed-time stability and energy consumed by controller in nonlinear neural networks with time-varying delays. A sufficient condition is provided to assure fixed-time stability by developing a global composite switched controller and employing inequality techniques. Then the specific expression of the upper of energy required for achieving control is deduced. Moreover, the comprehensive analysis of the energy cost and fixed-time stability is investigated utilizing a dual-objective optimization function. It illustrates that adjusting the control parameters can make the system converge to the equilibrium point under better control state. Finally, one numerical example is presented to verify the effectiveness of the provided control scheme.

Comprehensive analysis of phenolics compounds in citrus fruits peels by UPLC-PDA and UPLC-Q/TOF MS using a fused-core column

In this work, a method based on ultra-high-performance liquid chromatography with a photodiode array detector (UPLC-PDA) was developed to comprehensively analyze phenolic compounds in peels of lime (Citrus × latifolia), lemon (Citrus limon), and rangpur lime (Citrus × limonia). The reverse-phase separation was achieved with a C18 fused-core column packed with the smallest particles commercially available (1.3 um). The method was successfully coupled with high-resolution mass spectrometry (HRMS), allowing the detection of 24 phenolic compounds and five limonoids in several other citrus peels species: key lime, orange and sweet orange, tangerine, and tangerine ponkan, proving the suitability for comprehensive analysis in citrus peel matrices. Additionally, the developed method was validated according to the Food and drug administration (FDA) and National Institute of Metrology Quality and Technology (INMETRO) criteria, demonstrating specificity, linearity, accuracy, and precision according to these guidelines. System suitability parameters such as resolution, tailoring, plate count were also verified.

Comprehensive analyses of agrochemicals affecting aquatic ecosystems: A case study of Odonata communities and macrophytes in Saga Plain, northern Kyushu, Japan

The negative influence of agrochemicals (pesticides: insecticide, fungicide, and herbicide) on biodiversity is a major ecological concern. In recent decades, many insect species are reported to have rapidly declined worldwide, and pesticides, including neonicotinoids and fipronil, are suspected to be partially responsible. In Japan, application of systemic insecticides to nursery boxes in rice paddies is considered to have caused rapid declines in Sympetrum (Odonata: Libellulidae) and other dragonfly and damselfly populations since the 1990s. In addition to the direct lethal effects of pesticides, agrochemicals indirectly affect Odonata populations through reductions in macrophytes, which provide a habitat, and prey organisms. Due to technical restrictions, most previous studies first selected target chemicals and then analyzed their influence on focal organisms at various levels, from the laboratory to the field. However, in natural and agricultural environments, various chemicals co-occur and can act synergistically. Under such circumstances, targeted analyses might lead to spurious correlations between a target chemical and the abundance of organisms. To address such problems, in this study we adopted a novel technique, "Comprehensive Target Analysis with an Automated Identification and Quantification System (CTA-AIQS)" to detect wide range of agrochemicals in water environment. The relationships between a wide range of pesticides and lentic Odonata communities were surveyed in agricultural and non-agricultural areas in Saga Plain, Kyushu, Japan. We detected significant negative relationships between several insecticides, i.e., acephate, clothianidin, dinotefuran, flubendiamide, pymetrozine, and thiametoxam (marginal for benthic odonates) and the abundance of lentic Epiprocta and benthic Odonates. In contrast, the herbicides we detected were not significantly related to the abundance of aquatic macrophytes, suggesting a lower impact of herbicides on aquatic vegetation at the field level. These results highlight the need for further assessments of the influence of non-neonicotinoid insecticides on aquatic organisms.

Current perspective of innovative strategies for bioremediation of organic pollutants from wastewater

Organic contaminants in water are a growing environmental threat to sustainable development, with detrimental effects on the biosphere. In recent years, researchers have increasingly focused their attention on the area of bioremediation as an important tool to eliminate harmful pollutants from the environment. This review examines the application of bioremediation technologies to the removal of organic pollutants, with an emphasis on hydrocarbons and textile dyes. It applies a descriptive bibliometric analysis to study statistical practicality-vs-applicability of bioremediation of emerging organic pollutants. The paper identifies efficient pathways for bioremediation of different types of organic pollutants and outlines the potential for an eco-friendly and economical approach for the biological remediation of micropollutants by microalgae. Facts and figures on various hazardous pollutants, constraints in their current removal from water at an industrial level, and promising future solutions are carefully presented here.

Comprehensive analysis of angiogenesis subtype of squamous cell carcinoma

Background

Squamous cell carcinoma (SCC) is a disease with distinct management complexities as it displays a remarkably heterogeneous molecular subtype. However, the landscape of angiogenesis for SCC is not fully investigated.

Method and materials

The angiogenesis-related subtypes of SCC were established by using the ConsensusClusterPlus package based on angiogenesis-related genes and TCGA data. We analyzed the alteration of genes and miRNAs as well as pathways associated with angiogenesis subtypes. Next, the regulation network, the correlation with genomic characteristics, immune microenvironment, and clinical features of the angiogenesis subtypes were further investigated. Finally, the prognostic impact of the angiogenesis-related subtypes for SCC was also analyzed.

Results

A total of 1368 SCC samples were included in this study. Two angiogenesis subtypes were then identified based on the one hundred and sixty-three angiogenesis-related genes with subtype1 (angiogenesis subtype) of 951 SCC patients and subtype2 (non-angiogenesis subtype) of 417 SCC. GSEA revealed that angiogenesis and epithelial-mesenchymal transition, inflammatory response, and hypoxia were enriched in the angiogenesis subtype. Eight of the 15 immune checkpoints (ADORA2A, BTLA, CD276, CYBB, HAVCR2, SIGLEC7, SIGLEC9, and VTCN1) were significantly upregulated while C10orf54 were significantly downregulated in the angiogenesis subtype. The survival analysis revealed that the patients in the angiogenesis subtype have poorer survival outcomes than those in the non-angiogenesis subtype (P = 0.017 for disease-free interval and P = 0.00013 for overall survival).

Conclusion

Our analysis revealed a novel angiogenesis subtype classification in SCC and provides new insights into a hallmark of SCC progression.

A multiparametric approach to assessing residual pain experienced by dairy cows undergoing digestive tract surgery under multimodal analgesia

This study assessed residual pain responses of dairy cows undergoing fistulation surgery under multimodal analgesia using a multiparametric method combining behavioural and physiological indicators. A longitudinal study was conducted on five dairy cows, each acting as her own control. The surgery consisted of implanting a ruminal and a duodenal cannula in each cow. The multimodal drug protocol consisted of a combination of N-Methyl-D aspartic Acid antagonists, α2-agonists, and local anaesthetic during surgery, and non-steroidal anti-inflammatory drugs (NSAIDs) and opioid treatment postsurgery. Cow responses to surgery were monitored by direct behavioural observation, physiological assay indicators, and milk production from day (D) -6 days before surgery (D-6) to D13 postsurgery. From the data recorded, the variables that contributed most to the discrimination of days pre- and postsurgery were identified using factorial discriminant analysis. Components 1 and 2 of the factorial discriminant analysis explained 68.2% and 17.9%, respectively, of the total variance. Component 1 was mainly explained by haptoglobin (contribution to axis: 0.885), oxidative stress (ratio of oxidized gluthatione to reduced glutathione (GSH/GSSG), -0.746; vitamin E, -0.683; vitamin A, -0.597; malondialdehyde (MDA), 0.416), and behavioural indicators (general attitude, 0.594). On this axis, the higher the score, the higher were the apathy and haptoglobin and MDA concentrations, and the lower were the GSH/GSSG ratio and concentrations of vitamins A and E. This axis opposed cows on D-6 to cows on D3 and D5; cows on D1 and D13 were intermediate. Component 2 was mainly explained by the Hypothalamic-pituitary-adrenal axis (non-esterified fatty acid (NEFA), 0.686; cortisol, 0.669), milk yield (-0.725), oxidative stress (MDA, -0.584; nitric oxide (NO), 0.454), and behavioural indicators of pain (ear position, 0.467; leg postures, 0.431). On this axis, the higher the score, the higher the NEFA, cortisol, and nitric oxide concentrations; the more the ear and leg pain postures; and the lower the milk production and MDA concentrations. This axis opposed cows on D13 to cows on D1. These results suggest that cows may experience some pain only on D1, whereas on subsequent days, the inflammatory response and oxidative stress did not seem to be associated with pain. Our results should be considered for different surgeries to improve analgesia immediately after surgery, and to provide antioxidants along with NSAIDs to promote recovery.

Novel neuroprotective peptides in the venom of the solitary scoliid wasp Scolia decorata ventralis

Background

Solitary wasp venoms may be a rich source of neuroactive substances, since their venoms are used for paralyzing preys. We have been exploring bioactive constituents of solitary wasp venoms and, in this study, the component profile of the venom from a solitary scoliid wasp, Scolia decorata ventralis, was investigated through a comprehensive analysis using LC-MS. Two peptides were synthesized, and their neuroprotective properties were evaluated.

Methods

A reverse-phase HPLC connected to ESI-MS was used for LC-MS analyses. Online mass fingerprinting was performed from TIC, and data-dependent tandem mass spectrometry gave the MS/MS spectra. The sequences of two major peptide components were determined by MALDI-TOF/TOF MS analysis, confirmed by solid phase synthesis. Using the synthetic peptides, biological activities were assessed. Cell integrity tests and neuroprotection analyzes using H₂O₂ as an oxidative stress inducer were performed for both peptides.

Results

Online mass fingerprinting revealed that the venom contains 123 components, and the MS/MS analysis resulted in 33 full sequences of peptide components. The two main peptides, α-scoliidine (DYVTVKGFSPLR) and β-scoliidine (DYVTVKGFSPLRKA), present homology with the bradykinin C-terminal. Despite this, both peptides did not behave as substrates or inhibitors of ACE, indicating that they do not interact with this metallopeptidase. In further studies, β-scoliidine, but not α -scoliidine, showed protective effects against oxidative stress-induced neurotoxicity in PC12 cells through integrity and metabolism cell assays. Interestingly, β-scoliidine has the extension of the KA dipeptide at the C-terminal in comparison with α-scoliidine.

Conclusion

Comprehensive LC-MS and MS/MS analyses from the Scolia decorata ventralis venom displayed the component profile of this venom. β-scoliidine showed an effective cytoprotective effect, probably due to the observed increase in the number of cells. This is the first report of solitary wasp venom peptides showing neuroprotective activity.

Comprehensive analysis of DNA damage repair in squamous cell carcinoma subtypes

AIMS

Defective components resulting from DNA damage and repair mechanisms have been found to be underlying causes that affect the development and progression of different types of cancers, including squamous cell carcinoma (SCC). A more detailed classification of SCC is necessary for better application of DNA damage repair therapies.

MATERIALS AND METHODS

We aimed to characterize the molecular profile of SCC by developing a classification system based on DNA damage repair gene expression profiles. An integrative analysis was performed using a metadata set of 1374 SCC human samples from the UCSC Genome Browser. We then analyzed genomic alterations and mutations, and genes-TF-microRNA regulatory relationships and conducted enrichment, survival, and immune infiltration analyses.

KEY FINDINGS

This study was conducted on a total of 1374 SCC patients and 402 DNA damage repair genes. Two subtypes were established using consensus clustering, with 1143 patients being of the Non DDR subtype and 231 patients being of the DDR subtype. MATH, mutation burden, and heterogeneity were significantly higher in Non-DDR subtype than in DDR subtype. Next, a total of 1081 differentially expressed genes and 21 microRNAs were identified between the two subtypes and a genes-TF-microRNA regulatory network was constructed. In addition, stromal score, immune score and ESTIMATE score were significantly lower for the Non-DDR subtype, while tumor purity was significantly lower for the DDR subtype. In addition, five pathways associated with DNA damage repair were all enriched in the DDR subtype.

SIGNIFICANCE

Our study established two subtypes of SCC based on DNA damage repair, which may help to predict prognosis and determine the most suitable treatment for SCC patients.

MAGEA10 expression is a predictive marker of early hepatic recurrence after curative gastrectomy for gastric and gastroesophageal junction cancer

BACKGROUND

Resection for hepatic recurrence after gastrectomy in patients with gastric cancer may be curative; however, the prediction of hepatic recurrence remains intractable. Therefore, we aimed to explore predictive markers for hepatic recurrence in gastric and gastroesophageal junction cancer based on genetic information.

METHODS

This study recruited 154 patients who underwent curative gastrectomy for pathological stage II or III primary gastric and gastroesophageal junction adenocarcinoma. Genes associated with hepatic recurrence were comprehensively analyzed using whole-exome sequencing and gene expression profiling (GEP), followed by immunohistochemistry analysis for MAGEA10. The cumulative incidences of hepatic recurrence, relapse-free survival, and overall survival were evaluated.

RESULTS

A total of 12 patients with early hepatic recurrences were found within 2 years of surgery. Although there were no distinct gene mutations in recurrent patients, upregulation of MAGEA10 was identified in patients with early hepatic recurrence using GEP analysis. Immunostaining for MAGEA10 stained the cell nuclei in 29 (18.8%) of 154 samples. Furthermore, protein expression of MAGEA10 on immunohistochemistry was significantly related to a high MAGEA10 mRNA expression, high cumulative incidences of hepatic recurrence, and poor relapse-free survival. Overall survival did not differ significantly between positive and negative immunohistochemical staining for MAGEA10. The sensitivity and specificity of MAGEA10 staining for early hepatic recurrence were 58.3% and 84.5%, respectively.

CONCLUSIONS

MAGEA10 represents a promising predictive marker for early hepatic recurrence after curative gastrectomy for gastric and gastroesophageal junction cancer.

Comprehensive analysis and comparison of proteins in salivary exosomes of climacteric and adolescent females

Currently, it is difficult to extract exosomes with stable physicochemical properties from saliva. Furthermore, due to inadequate availability of basic data, the application of salivary exosomes as a diagnostic material is limited. In this study, we aimed to investigate an easier method for extraction of exosomes from whole saliva and compared proteins in salivary exosomes derived from subjects of two age groups. Salivary exosomes were extracted from nine females (56.7 ± 1.17 years old; climacteric or 19.9 ± 0.20 years old; adolescent) using commercial reagents and kits and detected using western blotting with anti-exosome marker antibodies. Exosome particle size and exosome-containing proteins were identified using NanoSight^® and liquid chromatography with tandem mass spectrometry, respectively. In addition, an efficient method of exosome extraction from saliva using a reagent and without the use of an ultracentrifuge was shown. Our results showed a higher total protein content and larger particle size in climacteric exosomes than in adolescent exosomes. However, adolescent exosomes showed a larger variety of proteins (780 proteins) than the climacteric exosomes (573 proteins). Altogether, 893 proteins were identified in the salivary exosomes. Although viral process-, ribosome- and structural molecule-related proteins were higher in the adolescent exosomes, the levels of major salivary proteins such as immunoglobulins and amylase, were higher in the climacteric exosomes than in the adolescent exosomes. The data presented, which show the fundamental protein composition of salivary exosomes and the changes that occur with age, are beneficial in both diagnostic and biotechnological applications.

Identification of a robust functional subpathway signature for pancreatic ductal adenocarcinoma by comprehensive and integrated analyses

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy and its mortality continues to rise globally. Because of its high heterogeneity and complex molecular landscapes, published gene signatures have demonstrated low specificity and robustness. Functional signatures containing a group of genes involved in similar biological functions may display a more robust performance.

METHODS

The present study was designed to excavate potential functional signatures for PDAC by analyzing maximal number of datasets extracted from available databases with a recently developed method of FAIME (Functional Analysis of Individual Microarray Expression) in a comprehensive and integrated way.

RESULTS

Eleven PDAC datasets were extracted from GEO, ICGC and TCGA databases. By systemically analyzing these datasets, we identified a robust functional signature of subpathway (path:00982_1), which belongs to the drug metabolism-cytochrome P450 pathway. The signature has displayed a more powerful and robust capacity in predicting prognosis, drug response and chemotherapeutic efficacy for PDAC, particularly for the classical subtype, in comparison with published gene signatures and clinically used TNM staging system. This signature was verified by meta-analyses and validated in available cell line and clinical datasets with chemotherapeutic efficacy.

CONCLUSION

The present study has identified a novel functional PDAC signature, which has the potential to improve the current systems for predicting the prognosis and monitoring drug response, and to serve a linkage to therapeutic options for combating PDAC. However, the involvement of path:00982_1 subpathway in the metabolism of anti-PDAC chemotherapeutic drugs, particularly its biological interpretation, requires a further investigation. Video Abstract.

Comprehensive Analysis of Protein Glycation Reveals Its Potential Impacts on Protein Degradation and Gene Expression in Human Cells

Glycation as a type of non-enzymatic protein modification is related to aging and chronic diseases, especially diabetes. Global analysis of protein glycation will aid in a better understanding of its formation mechanism and biological significance. In this work, we comprehensively investigated protein glycation in human cells (HEK293T, Jurkat, and MCF7 cells). The current results indicated that this non-enzymatic modification was not random, and protein at the extracellular regions and the nucleus were more frequently glycated. Systematic and site-specific analysis of glycated proteins allowed us to study the effect of the primary sequences and secondary structures of proteins on glycation. Furthermore, nearly every enzyme in the glycolytic pathway was found to be glycated and a possible mechanism was proposed. Many glycation sites were also previously reported as acetylation and ubiquitination sites, which strongly suggested that this non-enzymatic modification may disturb protein degradation and gene expression. The current results will facilitate further studies of protein glycation in biomedical and clinical research.

Mutations of key driver genes in colorectal cancer progression and metastasis

The association between mutations of key driver genes and colorectal cancer (CRC) metastasis has been investigated by many studies. However, the results of these studies have been contradictory. Here, we perform a comprehensive analysis to screen key driver genes from the TCGA database and validate the roles of these mutations in CRC metastasis. Using bioinformatics analysis, we identified six key driver genes, namely APC, KRAS, BRAF, PIK3CA, SMAD4 and p53. Through a systematic search, 120 articles published by November 30, 2017, were included, which all showed roles for these gene mutations in CRC metastasis. A meta-analysis showed that KRAS mutations (combined OR 1.18, 95% CI 1.05-1.33) and p53 mutations (combined OR 1.49, 95% CI 1.23-1.80) were associated with CRC metastasis, including lymphatic and distant metastases. Moreover, CRC patients with a KRAS mutation (combined OR 1.29, 95% CI 1.13-1.47), p53 mutation (combined OR 1.35, 95% CI 1.06-1.72) or SMAD4 mutation (combined OR 2.04, 95% CI 1.41-2.95) were at a higher risk of distant metastasis. Subgroup analysis stratified by ethnic populations indicated that the BRAF mutation was related to CRC metastasis (combined OR 1.42, 95% CI 1.18-1.71) and distant metastasis (combined OR 1.51, 95% CI 1.20-1.91) in an Asian population. No significant association was found between mutations of APC or PIK3CA and CRC metastasis. In conclusion, mutations of KRAS, p53, SMAD4 and BRAF play significant roles in CRC metastasis and may be both potential biomarkers of CRC metastasis as well as therapeutic targets.

Target screening analysis of 970 semi-volatile organic compounds adsorbed on atmospheric particulate matter in Hanoi, Vietnam

Vietnam's rapid economic development has resulted in dramatic increases in construction and the number of transportation vehicles. There is now growing public concern regarding increasing air pollution, especially in big cities; however, little information is available on air quality, particularly regarding semi-volatile organic compounds (SVOCs) adsorbed on atmospheric particulate matter. Here, we determined the frequency and concentrations of 970 SVOCs in 48 air particle samples collected by means of high-volume air sampling in Hanoi, Vietnam, by using a target screening method and a gas chromatography-mass spectrometry database. A total of 118 compounds (12.2% of the target compounds) were detected at least once in the samples, and the number of chemicals detected in each sample ranged from 85 to 103 (median, 92). For samples collected near a heavily trafficked road, the concentrations of target compounds in the samples were higher in samples collected during the day than in those collected at night, whereas the opposite was true for samples collected in a highly populated residential area with industrial activities related to the production of fresh noodles. Sixteen PAHs were detected at high concentrations in nearly 100% of the samples. Eighteen pesticides were detected, with permethrin being detected the most frequently (>70% samples), which can be explained by the use of permethrin-based Permecide 50 EC for dengue fever control during the sampling period. Endocrine-disrupting chemicals (i.e., bisphenol A, 4-nitrophenol) and pharmaceuticals and personal care products (diethyltoluamide, caffeine) were detected in over 90% of the samples. Seven sterols, five phthalate compounds and five organophosphorus flame retardants were detected in the samples. This is the first comprehensive survey of SVOCs adsorbed on atmospheric particulate matter in Vietnam, and as such, this study provides important new information about the frequency and concentrations of atmospheric SVOC contamination. The variety of chemicals detected in this study implies an abundance of pollution sources; further investigations to determine these pollution sources and the risks posed by the detected SVOCs to human health are warranted.

Genome-wide analysis of poplar SAUR gene family and expression profiles under cold, polyethylene glycol and indole-3-acetic acid treatments

Small auxin-up RNA (SAUR) proteins play an important role in the regulation of plant growth and development. Here, we identified 105 SAUR genes and comprehensively analyzed them in Populus trichocarpa. Based on the phylogenetic relationships, the PtSAURs were classified into ten subfamilies. Of the 105 PtSAURs, 100 were randomly distributed along the nineteen chromosomes, while the remaining genes were located along unassigned scafoolds. These genes mainly evolved through segmental duplications. In total, 94 PtSAURs contained no introns, and each group had a similar conserved motif structure. A promoter analysis revealed various cis-elements related to growth, development and stress responses, and a synteny analysis established orthologous relationships among SAURs in Arabidopsis, rice, grape and poplar. The qRT-PCR and tissue expression analyses indicated that PtSAURs show different expression levels in various tissues in response to different treatments. PtSAUR53 was located on the nuclear and plasma membrane by conducting subcellular localization analysis. This study provides a comprehensive overview of poplar SAUR proteins and a foundation for further investigations for functional analysis of SAURs in poplar growth and development. At the same time, it will be valuable to further study the poplar SAUR genes to reveal their biological effects.

Chemometric and high-resolution mass spectrometry tools for the characterization and comparison of raw and treated wastewater samples of a pilot plant on the SIPIBEL site

Due to its key role in the contamination of natural resources, the assessment of raw and treated wastewater effluents is a current major concern and urges comprehensive analytical methods capable of selectively capturing the chemodiversity of these samples. In this context, the overall objective of this work can be summarized as (i) the assessment of the performance of secondary and tertiary (advanced oxidation) wastewater treatments through multivariate analysis followed by (ii) the comprehensive characterization of wastewater samples based on their spectral fingerprints and a combination of suspect and non-target screening approaches. Several compounds, belonging to different sources of contamination were annotated and/or partially identified: pharmaceuticals, metabolites and transformation compounds, human activity markers, surfactants, and polyethoxy compounds. These results highlight the contribution of filtering and screening tools such as monoisotopic exact mass, mass defect, MS/MS data-dependent acquisitions, isotopic pattern and retention time to the selection, and the identification of environmental contaminants and their metabolites/degradation products. This paper completes the target study conducted in the SIPIBEL site and offers an alternative for the assessment of treatment processes by broadening the spectrum to a larger number of compounds and the correlations between them.

Development of a comprehensive screening method for more than 300 organic chemicals in water samples using a combination of solid-phase extraction and liquid chromatography-time-of-flight-mass spectrometry

A comprehensive screening method for 311 organic compounds with a wide range of physicochemical properties (log Pow -2.2-8.53) in water samples was developed by combining solid-phase extraction with liquid chromatography-high-resolution time-of-flight mass spectrometry. Method optimization using 128 pesticides revealed that tandem extraction with styrene-divinylbenzene polymer and activated carbon solid-phase extraction cartridges at pH 7.0 was optimal. The developed screening method was able to extract 190 model compounds with average recovery of 80.8% and average relative standard deviations (RSD) of 13.5% from spiked reagent water at 0.20 μg L^-1, and 87.1% recovery and 10.8% RSD at 0.05 μg L^-1. Spike-recovery testing (0.20 μg L^-1) using real sewage treatment plant effluents resulted in an average recovery and average RSD of 190 model compounds of 77.4 and 13.1%, respectively. The method was applied to the influent and effluent of five sewage treatment plants in Kitakyushu, Japan, with 29 out of 311 analytes being observed at least once. The results showed that this method can screen for a large number of chemicals with a wide range of physicochemical properties quickly and at low operational cost, something that is difficult to achieve using conventional analytical methods. This method will find utility in target screening of hazardous chemicals with a high risk in environmental waters, and for confirming the safety of water after environmental incidents.

Heavy metals in the riverbed surface sediment of the Yellow River, China

One hundred and eleven riverbed surface sediment (RSS) samples were collected to determine the heavy metal concentration throughout the Inner Mongolia reach of the Yellow River (IMYR), which has been subjected to rapid economic and industrial development over the past several decades. Comprehensive analysis of heavy metal contamination, including the enrichment factor, geo-accumulation index, contamination factor, pollution load index, risk index, principal component analysis (PCA), hierarchical cluster analysis (HCA), and Pearson correlation analysis, was performed. The results demonstrated that a low ecological risk with a moderate level of heavy metal contamination was present in the IMYR due to the risk index (RI) being less than 150 and the pollution load index (PLI) being above 1, and the averaged concentrations of Co, Cr, Cu, Mn, Ni, Ti, V, and Zn in the RSS, with standard deviations, were 144 ± 69, 77.91 ± 39.28, 22.95 ± 7.67, 596 ± 151, 28.50 ± 8.01, 3793 ± 487, 69.11 ± 18.44, and 50.19 ± 19.26 mg kg^-1, respectively. PCA, HCA, and Pearson correlation analysis revealed that most of the RSS was heavily contaminated with Zn, Ni, and Cu, due to the influence of anthropogenic activities; moderately contaminated with Ti, Mn, V and Cr because of the dual influence of anthropogenic activities and nature; and slightly to not contaminated with Co because it occurs mainly in the bordering desert areas. Graphic abstract ᅟ.

Data from comprehensive analysis of nuclear localization signals

This article describes data related to a research article titled "Comprehensive analysis of the dynamic structure of nuclear localization signals" by Yamagishi et al. [1]. In this article, we provide the data covering wider range of the mammalian NLSs in UniProt (Universal Protein Resource) [2] regardless of their conformations. To be more specific as follows: We have extracted all NLSs which are clearly indicated as "NLS" with evidence type (a code from the Evidence Codes Ontology) [3] in UniProt. A total of 1364 NLSs in 1186 proteins were extracted from UniProt. The number of NLSs found in each protein (UniProt ID), the sequence length of NLSs and their distribution are shown.

Groundwater screening for 940 organic micro-pollutants in Hanoi and Ho Chi Minh City, Vietnam

Groundwater is the main source of drinking water for more than half of the residents of Hanoi (HN). It also provides about one third of the total water demand for residents of Ho Chi Minh City (HCM). However, due to rapid urbanization and frequent discharges of untreated urban wastewater to surface water, freshwater is widely contaminated by man-made chemicals, which may result in groundwater pollution. As part of an ongoing campaign to collect baseline information on the occurrence of organic micro-pollutants (OMPs) in the aquatic environment in Vietnam, 43 water samples were collected from 26 groundwater wells in HN (22) and HCM (4) in September 2013 and August 2014. Samples were analyzed by gas chromatography-mass spectrometry (GC-MS) and the resulting chromatograms were screened for 940 OMPs by an automated identification and quantification system (AIQS) within a GC-MS database. A total of 74 compounds were detected, with between 4 and 43 (median 18) compounds found at each site. Overall, contamination levels were low, with over 89 % of the detected concentrations that were less than 0.5 μg L(-1). Results suggest that most of the sampled aquifers have been impacted by non-point source pollution. Most of the contaminants detected are either currently not regulated in drinking water or are present at low levels. A health risk assessment for detected contaminants implied that there were no risks to humans. Since this study was based on a limited number of samples, especially in HCM, further, more detailed studies on the occurrence of OMPs in groundwater in HCM and a full risk assessment of detected contaminants should be prioritized.

Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry

Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics has been a subject of dramatic developments over the past decade. This review focuses on state of the art in LC-MS-based lipidomics, covering all the steps of global lipidomic profiling. On the basis of review of 185 original papers and application notes, we can conclude that typical LC-MS-based lipidomics methods involve: (1) extraction using chloroform/MeOH or MTBE/MeOH protocols, both with addition of internal standards covering each lipid class; (2) separation of lipids using short microbore columns with sub-2-μm or 2.6-2.8-μm (fused-core) particle size with C18 or C8 sorbent with analysis time <30 min; (3) electrospray ionization in positive- and negative-ion modes with full spectra acquisition using high-resolution MS with capability to MS/MS. Phospholipids (phosphatidylcholines, phosphatidylethanolamines, phosphatidylinositols, phosphatidylserines, phosphatidylglycerols) followed by sphingomyelins, di- and tri-acylglycerols, and ceramides were the most frequently targeted lipid species.

Screening and analysis of 940 organic micro-pollutants in river sediments in Vietnam using an automated identification and quantification database system for GC-MS

In order to obtain a detailed picture of pollution by organic micro-pollutants in Vietnamese rivers, 940 semi-volatile organic compounds in river sediments collected from four major cities were examined by a comprehensive gas chromatography-mass spectrometry-database. The number of detected chemicals at each site ranged from 49 to 158 (median 96 out of 940) with 185 analytes detected at least once in the survey. The substances detected with high frequency (over 80%) and high concentrations were n-alkanes, phthalates, sterols and PAHs. For most substances, sediments from metropolitan areas (Hanoi and Ho Chi Minh City) were more heavily contaminated than those in rural and suburban areas. Sterols were observed in nearly 100% of sediments at extremely high concentrations, suggesting that the studied rivers were contaminated by sewage. Pyrethroids (permethrin-1 and -2) were the most dominant insecticides found in inner canals of Hanoi and Ho Chi Minh City. Deltamethrin was only detected at a site in Hanoi at an elevated concentration. This reflects that pyrethroids are used for the protection of private and public health rather than for agriculture. p,p'-DDE and p,p'-DDD were the dominant members of the DDT family of chemicals detected, indicating no recent inputs of DDTs in the study areas. PCBs residues were lower than those in other Asian countries, which suggest historically much lower use of PCBs in Vietnam. PAHs pollution in urban areas is caused by the runoff of petroleum products and vehicle exhaust gases, whereas in rural and suburban areas, the combustion of fossil fuels and biomass is major sources of PAHs. Overall, the study confirmed that rivers in Vietnam were heavily polluted mainly by domestic wastewater.

Target and screening analysis of 940 micro-pollutants in sediments in Tokyo Bay, Japan

Urban societies are using an increasingly diverse array of chemicals, many of which ultimately end up accumulating in urban harbors, where they can act as contaminants alone or as part of a mixture. In attempt to grasp a more complete picture of anthropogenic chemicals in an urban harbor, we analyzed 940 organic chemicals in sediments in Tokyo Bay, one of the most densely populated and modernized areas in the world. For the chemical analysis, we used targeted analytical methods using a GC-MS-MS and a GC-MS-SIM, and a screening analysis using an automated identification and quantification system with a GC-MS database. We detected 195 organic chemicals in the sediments; the sum of concentrations of compounds detected varied from 6095 to 39140μgkg(-1)dry wt. Since their concentrations increased with proximity to the innermost part of the bay, their sources seem to be mainly sewage treatment plants (STPs) and rivers flowing to this area. Additional confirmation comes from the nature of the identified pollutants, which are characteristic of chemicals used in households as well as fecal matter, business activities and urban run-off. From these results, it was confirmed that sediments in Tokyo Bay are still polluted with a wide range of chemicals, particularly domestic chemicals, despite nearly 100% of wastewater from household and business activities being treated by STPs.