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  • Frontiers Media SA  (10)
  • 1
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    Table2.docx
    Frontiers Media SA ; 2022
    In:  Frontiers in Genetics Vol. 13 ( 2022-11-2)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 13 ( 2022-11-2)
    Abstract: Background: Although neoadjuvant chemotherapy (NAC) has become the standard treatment option for muscle invasive bladder carcinoma (MIBC), its application is still limited because of the lack of biomarkers for NAC prediction. Methods: We conducted a territory multicenter real-world study to summarize NAC practice in China and its associated clinicopathologic variables with NAC response. Then, we developed and validated a robust gene-based signature for accurate NAC prediction using weighted correlation network analysis (WGCNA), the least absolute shrinkage and selector operation (LASSO) algorithm, a multivariable binary logistic regression model, and immunohistochemistry (IHC). Results: In total, we collected 69 consecutive MIBC patients treated with NAC from four clinical centers. The application of NAC in the real world was relatively safe, with only two grade Ⅳ and seven grade Ⅲ AEs and no treatment-related deaths being reported. Among these patients, 16 patients gave up surgery after NAC, leaving 53 patients for further analysis. We divided them into pathological response and non-response groups and found that there were more patients with a higher grade and stage in the non-response group. Patients with a pathological response could benefit from a significant overall survival (OS) improvement. In addition, univariate and multivariate logistic analyses indicated that tumor grade and clinical T stage were both independent factors for predicting NAC response. Importantly, we developed and validated a five-gene-based risk score for extremely high predictive accuracy for NAC response. Conclusion: NAC was relatively safe and could significantly improve OS for MIBC patients in the real-world practice. Our five-gene-based risk score could guide personalized therapy and promote the application of NAC.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2022.1047481
    DOI: 10.3389/fgene.2022.1047481.s001
    DOI: 10.3389/fgene.2022.1047481.s002
    DOI: 10.3389/fgene.2022.1047481.s003
    DOI: 10.3389/fgene.2022.1047481.s004
    DOI: 10.3389/fgene.2022.1047481.s005
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606823-0
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  • 2
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    Table_1.xlsx
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-9-29)
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    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-9-29)
    Abstract: The flowers of tea plants ( Camellia sinensis ), as well as tea leaves, contain abundant secondary metabolites and are big potential resources for the extraction of bioactive compounds or preparation of functional foods. However, little is known about the biosynthesis and transcriptional regulation mechanisms of those metabolites in tea flowers, such as terpenoid, flavonol, catechins, caffeine, and theanine. This study finely integrated target and nontarget metabolism analyses to explore the metabolic feature of developing tea flowers. Tea flowers accumulated more abundant terpenoid compounds than young leaves. The transcriptome data of developing flowers and leaves showed that a higher expression level of later genes of terpenoid biosynthesis pathway, such as Terpene synthases gene family, in tea flowers was the candidate reason of the more abundant terpenoid compounds than in tea leaves. Differently, even though flavonol and catechin profiling between tea flowers and leaves was similar, the gene family members of flavonoid biosynthesis were selectively expressed by tea flowers and tea leaves. Transcriptome and phylogenetic analyses indicated that the regulatory mechanism of flavonol biosynthesis was perhaps different between tea flowers and leaves. However, the regulatory mechanism of catechin biosynthesis was perhaps similar between tea flowers and leaves. This study not only provides a global vision of metabolism and transcriptome in tea flowers but also uncovered the different mechanisms of biosynthesis and transcriptional regulation of those important compounds.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2022.1016692
    DOI: 10.3389/fpls.2022.1016692.s001
    DOI: 10.3389/fpls.2022.1016692.s002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 3
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    Association of serum reproductive hormones changes after neoadjuvant chemotherapy with hormone receptors expression alterations and survival outcomes in breast cancer
    Frontiers Media SA ; 2022
    In:  Frontiers in Surgery Vol. 9 ( 2022-8-31)
    Details
    In: Frontiers in Surgery, Frontiers Media SA, Vol. 9 ( 2022-8-31)
    Abstract: This study aimed to determine the effect of neoadjuvant chemotherapy (NAC) on circulating levels of reproductive hormones and evaluate the correlation of hormone changes after NAC with hormone receptors expression alterations and relapse-free survival (RFS) outcomes in breast cancer. Methods Information from 181 breast cancer patients who received NAC was retrospectively analyzed. For hormones parameters, the median and interquartile range (IQR) were provided at baseline and the end of NAC then was compared by Wilcoxon signed-rank test. Categorical variables were represented as numbers and percentages and were compared via two-sided chi-square and Fisher's tests. The RFS outcomes were compared between patients according to hormone changes using the log-rank test. Univariate and multivariate survival analyses with hazard ratios (HR) and 95% confidence intervals (95% CI) were carried out using Cox regression. Results Sex steroids including estradiol, progesterone, testosterone, and dehydroepiandrosterone sulfate (DHEAS) levels decreased significantly after NAC among both premenopausal and postmenopausal patients (all P   & lt; 0.05). Decreased estradiol levels were associated with reduced progesterone receptor (PR) expression ( P  = 0.030). In multivariate survival analysis, the non-decreased progesterone level was strongly associated with worse RFS (non-decreased vs. decreased, HR = 7.178, 95% CI 2.340–22.019, P  = 0.001). Patients with decreased progesterone levels exhibited better 3-year RFS compared with those with non-decreased (87.6% vs. 58.3%, log-rank, P  = 0.001). Conclusion Multiple reproductive hormone levels were influenced by NAC. The change in estradiol level had a positive connection with PR expression alteration. Furthermore, an inverse association between the change in progesterone level and RFS outcomes was found. These findings may provide a theoretical basis for pre-operative endocrine therapy combined with NAC in breast cancer patients.
    Type of Medium: Online Resource
    ISSN: 2296-875X
    URL: Article
    DOI: 10.3389/fsurg.2022.947218
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2773823-1
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  • 4
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    Data_Sheet_1.DOCX
    Frontiers Media SA ; 2021
    In:  Frontiers in Nutrition Vol. 8 ( 2021-10-1)
    Details
    In: Frontiers in Nutrition, Frontiers Media SA, Vol. 8 ( 2021-10-1)
    Abstract: Chitosan oligosaccharides (COS) play a prebiotic role in many ways, whereas its function on microbiota is not fully understood. In this study, the effects of COS on metabolic syndrome were initially investigated by testing changes in the physiological indicators after adding COS to the diet of mice with high fat (group H) and low fat (group L). The results showed that COS markedly inhibited the accumulation of body weight and liver fat induced by high-fat diet, as well as restored the elevated concentration of blood glucose and fasting insulin to normal levels. Next, changes of the murine intestinal microbiota were examined. The results exhibited that COS reduced with-in-sample diversity, while the between-sample microbial diversity enhanced. Specifically, COS enriched Clostridium paraputrificum and Clostridium ramosum in the mice on a high-fat diet, while the abundance of Clostridium cocleatum was reduced. As a comparison, Parabacteroides goldsteinii and Bacteroides uniformis increased their abundance in response to COS in the low-fat diet group. Noticeably, a large amount of Akkermansia muciniphila was enriched in both high-fat or low-fat diet groups. Among the differential fecal bacteria, Clostridium ramosume was found to be positively interacted with Faecalibacterim prausnitzii and Clostridium paraputrificum ; Clostridium paraputrificum had a positive interactions with Lactococcus chungangensis and Bifidobacterium mongoliense , suggesting that COS probably ameliorate metabolic syndrome through the microbiota in view of the lipid-lowering effects of these interacted bacteria. Furthermore, the gene expression data revealed that COS improved the functions related to intestinal barrier and glucose transport, which could be the trigger and consequence of the variations in gut microbiota induced by COS. Additionally, correlation analysis found that intestinal bacteria are related to physiological parameters, which further supports the mediating role of gut microbiota in the beneficial effect of COS. In summary, our research results provide new evidence for the prebiotic effects of COS.
    Type of Medium: Online Resource
    ISSN: 2296-861X
    URL: Article
    URL: Article
    DOI: 10.3389/fnut.2021.743492
    DOI: 10.3389/fnut.2021.743492.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2776676-7
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  • 5
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    KLSD: a kinase database focused on ligand similarity and diversity
    Frontiers Media SA ; 2024
    In:  Frontiers in Pharmacology Vol. 15 ( 2024-6-18)
    Details
    In: Frontiers in Pharmacology, Frontiers Media SA, Vol. 15 ( 2024-6-18)
    Abstract: Due to the similarity and diversity among kinases, small molecule kinase inhibitors (SMKIs) often display multi-target effects or selectivity, which have a strong correlation with the efficacy and safety of these inhibitors. However, due to the limited number of well-known popular databases and their restricted data mining capabilities, along with the significant scarcity of databases focusing on the pharmacological similarity and diversity of SMIKIs, researchers find it challenging to quickly access relevant information. The KLIFS database is representative of specialized application databases in the field, focusing on kinase structure and co-crystallised kinase-ligand interactions, whereas the KLSD database in this paper emphasizes the analysis of SMKIs among all reported kinase targets. To solve the current problem of the lack of professional application databases in kinase research and to provide centralized, standardized, reliable and efficient data resources for kinase researchers, this paper proposes a research program based on the ChEMBL database. It focuses on kinase ligands activities comparisons. This scheme extracts kinase data and standardizes and normalizes them, then performs kinase target difference analysis to achieve kinase activity threshold judgement. It then constructs a specialized and personalized kinase database platform, adopts the front-end and back-end separation technology of SpringBoot architecture, constructs an extensible WEB application, handles the storage, retrieval and analysis of the data, ultimately realizing data visualization and interaction. This study aims to develop a kinase database platform to collect, organize, and provide standardized data related to kinases. By offering essential resources and tools, it supports kinase research and drug development, thereby advancing scientific research and innovation in kinase-related fields. It is freely accessible at: http://ai.njucm.edu.cn:8080 .
    Type of Medium: Online Resource
    ISSN: 1663-9812
    URL: Article
    DOI: 10.3389/fphar.2024.1400136
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2024
    detail.hit.zdb_id: 2587355-6
    SSG: 15,3
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  • 6
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    Table_9.XLSX
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-4-29)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-4-29)
    Abstract: Upland cotton ( Gossypium hirsutum ) has long been an important fiber crop, but the narrow genetic diversity of modern G. hirsutum limits the potential for simultaneous improvement of yield and fiber quality. It is an effective approach to broaden the genetic base of G. hirsutum through introgression of novel alleles from G. barbadense with excellent fiber quality. In the present study, an interspecific chromosome segment substitution lines (CSSLs) population was established using G. barbadense cultivar Pima S-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. A total of 105 quantitative trait loci (QTL), including 85 QTL for fiber quality and 20 QTL for lint percentage (LP), were identified based on phenotypic data collected from four environments. Among these QTL, 25 stable QTL were detected in two or more environments, including four for LP, eleven for fiber length (FL), three for fiber strength (FS), six for fiber micronaire (FM), and one for fiber elongation (FE). Eleven QTL clusters were observed on nine chromosomes, of which seven QTL clusters harbored stable QTL. Moreover, eleven major QTL for fiber quality were verified through analysis of introgressed segments of the eight superior lines with the best comprehensive phenotypes. A total of 586 putative candidate genes were identified for 25 stable QTL associated with lint percentage and fiber quality through transcriptome analysis. Furthermore, three candidate genes for FL, GH_A08G1681 ( GhSCPL40 ), GH_A12G2328 ( GhPBL19 ), and GH_D02G0370 ( GhHSP22.7 ), and one candidate gene for FM, GH_D05G1346 ( GhAPG ), were identified through RNA-Seq and qRT-PCR analysis. These results lay the foundation for understanding the molecular regulatory mechanism of fiber development and provide valuable information for marker-assisted selection (MAS) in cotton breeding.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
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    URL: Article
    URL: Article
    URL: Article
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    URL: Article
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    DOI: 10.3389/fpls.2022.882051
    DOI: 10.3389/fpls.2022.882051.s001
    DOI: 10.3389/fpls.2022.882051.s002
    DOI: 10.3389/fpls.2022.882051.s003
    DOI: 10.3389/fpls.2022.882051.s004
    DOI: 10.3389/fpls.2022.882051.s005
    DOI: 10.3389/fpls.2022.882051.s006
    DOI: 10.3389/fpls.2022.882051.s007
    DOI: 10.3389/fpls.2022.882051.s008
    DOI: 10.3389/fpls.2022.882051.s009
    DOI: 10.3389/fpls.2022.882051.s010
    DOI: 10.3389/fpls.2022.882051.s011
    DOI: 10.3389/fpls.2022.882051.s012
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2687947-5
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  • 7
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    Table_1.DOCX
    Frontiers Media SA ; 2023
    In:  Frontiers in Neurology Vol. 14 ( 2023-9-29)
    Details
    In: Frontiers in Neurology, Frontiers Media SA, Vol. 14 ( 2023-9-29)
    Abstract: Aquaporin-4 (AQP4) antibody-seropositive optic neuritis (AQP4-ON) is one of the most common types of optic neuritis in China. However, the association between AQP4-ON and vision-related quality of life (QoL) and depression remains poorly understood. Methods In this cross-sectional study, 57 patients with optic neuritis were evaluated for their vision-related QoL using a Chinese version of the 25-item National Eye Institute Visual Function Questionnaire (VFQ-25) and assessed for depressive symptoms using a Chinese version of the Beck Depression Inventory-II (BDI-II). Data regarding participants’ age, sex, visual acuity, and the number of recurrence events were gathered. Linear regression analysis was employed to investigate the relationships between AQP4-ON and vision-related QoL, as well as depression. Results Of the 57 included patients, 28 were AQP4-ON, and 29 were idiopathic optic neuritis (ION). AQP4-ON demonstrated a significant correlation with a decreased VFQ-25 composite score (Mean difference, −11.65 [95% CI, −21.61 to −1.69]; p  = 0.023) and an increased BDI-II score (Mean difference, 6.48 [95% CI, 0.25 to 12.71]; p  = 0.042) when compared to ION. The BDI-II score was correlated with the VFQ-25 composite score (Spearman ρ = −0.469; p   & lt; 0.001) but not with the visual acuity in the worse-seeing eye (Spearman ρ = 0.024; p  = 0.860) or in the better-seeing eye (Spearman ρ = −0.039; p  = 0.775), bilateral severe visual impairment (Spearman ρ = 0.039; p  = 0.772) or the number of recurrence events (Spearman ρ = 0.184; p  = 0.171). Conclusion AQP4-positive optic neuritis is associated with a decline in vision-related quality of life as well as an increased likelihood of experiencing depression. It is crucial for clinicians to assess both vision-related QoL and depression in patients with AQP4-positive optic neuritis to provide patient-centered care.
    Type of Medium: Online Resource
    ISSN: 1664-2295
    URL: Article
    URL: Article
    DOI: 10.3389/fneur.2023.1265170
    DOI: 10.3389/fneur.2023.1265170.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2564214-5
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  • 8
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    DataSheet_1.zip
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-10-27)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-10-27)
    Abstract: Limonium Sinense (Girard) Kuntze is a traditional Chinese medicinal herb, showing blood replenishment, anti-tumour, anti-hepatitis, and immunomodulation activities amongst others. However, the mechanism of its pharmacological activities remains largely unknown. Here, we investigated the effects of bioactive ingredients from Limonium Sinense using an integrated approach. Water extracts from Limonium Sinense (LSW) showed a strong growth inhibitory effect on multiple cells in both 2D and 3D cultures. Global transcriptomic profiling and further connectivity map (CMap) analysis identified several similarly acting therapeutic candidates, including Tubulin inhibitors and hypoxia-inducible factor (HIF) modulators. The effect of LSW on the cell cycle was verified with flow cytometry showing a G2/M phase arrest. Integrated analysis suggested a role for gallic acid in mediating HIF activation. Taken together, this study provides novel insights into the bioactive ingredients in Limonium Sinense , highlighting the rich natural resource and therapeutic values of herbal plants.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2022.994036
    DOI: 10.3389/fpls.2022.994036.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2687947-5
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  • 9
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    Table_1.docx
    Frontiers Media SA ; 2021
    In:  Frontiers in Oncology Vol. 11 ( 2021-6-21)
    Details
    In: Frontiers in Oncology, Frontiers Media SA, Vol. 11 ( 2021-6-21)
    Abstract: The aim of this study was to assess the prognostic influence of Ki67 index changes in patients with primary triple-negative breast cancer (TNBC) treated with neoadjuvant chemotherapy (NAC), and to evaluate whether the combination of Ki67 index changes and residual disease (RD) tumor-infiltrating lymphocytes (TILs) provides additional prognostic information for this group. Materials and Methods Data from 109 patients with primary TNBC and RD after NAC were analyzed retrospectively. Ki67 changes and RD TIL levels were investigated for associations with recurrence-free survival (RFS) and overall survival (OS) using Kaplan–Meier and Cox analyses. Results Ki67 index decreased after NAC in 53 patients (48.6%) and high RD TIL levels (≥30%) were observed in 54 patients (49.5%). In multivariate Cox analyses, no Ki67 decrease status and low RD TIL levels were significantly associated with reduced RFS (hazard ratio (HR): 2.038, 95% confidence interval (CI): 1.135–3.658, P = 0.017; HR: 2.493, 95% CI: 1.335–4.653, P = 0.004), and OS (HR: 2.187, 95% CI: 1.173–4.077, P = 0.014; HR: 2.499, 95% CI: 1.285–4.858, P = 0.007), respectively. Notably, low RD TIL levels were significantly associated with reduced RFS (HR: 3.567, 95% CI: 1.475–8.624, P = 0.005) and reduced OS (HR: 3.873, 95% CI: 1.512–9.918, P = 0.005) in only the no Ki67 decrease group. The differences in 3-year RFS and OS between patients with no Ki67 decrease and low or high RD TIL levels were 24.4% vs 79.1% (P = 0.0001) and 33.1% vs 87.5% (P = 0.0001), respectively. Conclusion Ki67 index changes and RD TIL levels were associated with the prognosis of patients with primary TNBC with RD after NAC. RD TIL levels had greater prognostic significance in the no Ki67 decrease group.
    Type of Medium: Online Resource
    ISSN: 2234-943X
    URL: Article
    URL: Article
    DOI: 10.3389/fonc.2021.668610
    DOI: 10.3389/fonc.2021.668610.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2649216-7
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  • 10
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    Integrating RNA-Seq With GWAS Reveals a Novel SNP in Immune-Related HLA-DQB1 Gene Associated With Occupational Pulmonary Fibrosis Risk: A Multi-Stage Study
    Frontiers Media SA ; 2022
    In:  Frontiers in Immunology Vol. 12 ( 2022-1-17)
    Details
    In: Frontiers in Immunology, Frontiers Media SA, Vol. 12 ( 2022-1-17)
    Abstract: To evaluate the association between single-nucleotide polymorphisms (SNPs) in RNA-seq identified mRNAs and silicosis susceptibility. Methods A comprehensive RNA-seq was performed to screen for differently expressed mRNAs in the peripheral blood lymphocytes of eight subjects exposed to silica dust (four silicosis cases and four healthy controls). Following this, the SNPs located on the shortlisted mRNAs, which may affect silicosis susceptibility, were screened through silicosis-related genome-wide association studies (GWAS) (155 silicosis cases and 141 healthy controls), whereas functional expression quantitative trait locus (eQTL)-SNPs were identified using the GTEx database. Finally, the association between functional eQTL-SNPs and silicosis susceptibility (194 silicosis cases and 235 healthy controls) was validated. Results A total of 70 differentially expressed mRNAs (fold change & gt; 2 or fold change & lt; 0.5, P & lt; 0.05) was obtained using RNA-seq. Furthermore, 476 SNPs located on the shortlisted mRNAs, which may affect silicosis susceptibility ( P & lt; 0.05) were obtained using GWAS, whereas subsequent six functional eQTL-SNPs were identified. The mutant A allele of rs9273410 in HLA-DQB1 indicated a potential increase in silicosis susceptibility in the validation stage (additive model: odds ratio (OR)= 1.31, 95% confidence interval (CI) = 0.99–1.74, P = 0.061), whereas the combination of GWAS and the validation results indicated that the mutant A allele of rs9273410 was associated with increased silicosis susceptibility (additive model: OR = 1.35, 95% CI =1.09–1.68, P = 0.006). Conclusion The mutant A allele of rs9273410 was associated with increased silicosis susceptibility by modulating the expression of HLA-DQB1 .
    Type of Medium: Online Resource
    ISSN: 1664-3224
    URL: Article
    DOI: 10.3389/fimmu.2021.796932
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606827-8
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