dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.

Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.

miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up- and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.

Targeted Next-Generation Sequencing Reveals a Large Novel ß-Thalassemia Deletion that Removes the Entire HBB Gene.

ß-Thalassemia (ß-thal) is one of the most common monogenic recessive inherited diseases worldwide. The mutation spectrum of ß-thal has been increasingly broadened by various genetic testing methods. The discovery and identification of novel and rare pathogenic thalassemia variants enable better disease prevention, especially in high prevalence regions. In this study, a Chinese thalassemia family with an unclear etiology was recruited to the Thalassemia Screening Program. Blood samples collected from them were primarily screened by hematology analysis and clinical routine genetic screening. Subsequently, targeted next-generation sequencing (NGS) and Sanger sequencing were performed to find and identify a novel deletion variant. The deletion, discovered by targeted NGS, was validated through real-time quantitative polymerase chain reaction (qPCR). First, a large novel ß-thal deletion (3488 bp) related to a high Hb F level, NC_000011.9: g.5245533_5249020del (Chongqing deletion) (GRCh37/hg19), was found and identified in the proband and her mother. The deletion removed the entire ß-globin gene and led to absent ß-globin (ß0). We then validated this large novel deletion in the proband and her mother by qPCR. We first discovered and identified a large novel ß-thal deletion related to elevated Hb F level, it helps broaden the spectrum of pathogenic mutants that may cause ß-thal intermedia (ß-TI) or ß-thal major (ß-TM), paving the way for effective thalassemia screening. Next-generation sequencing has the potential of finding rare and novel thalassemia mutants.

[Chemical composition of essential oil from Thymus citriodorus and its toxic effect on liver cancer cells].

OBJECTIVE: To analyze the chemical composition of essential oil from Thymus citriodorus and its toxic effect on liver cancer cells. METHODS: The essential oil from Thymus citriodorus leaves was extracted by steam distillation, and GC-MS was used for analyzing chemical composition. 35 components were identified which accounted for 95.44% of the total peak area. The main components were borneol (28.82%), thymol (14.43%), 3, 7-dimethyl-1, 6-octadiene-3-ol (8.26%), 1-methyl-4-[alpha-hydroxy-isopropyl] cyclohexene (8.23%) and terpenes camphor (5.1%), et. al. The toxic effects on HepG2 cells and expression of NF-kappabeta65 were measured by MTT assay and confocal laser scanning microscopy, respectively. RESULTS: The IC50 of HepG2 cells inhibition was 0.34%. The mean fluorescence intensity of NF-kappabeta65 expression was as follows: control group 323.25, 2(-10) concentration group 84.18, 2(-11) concentration group 197.93 and 2(-12) concentration group 261.43. CONCLUSION: The essential oil from Thymus citriodorus leaves has strong toxic effects. The induced apoptosis mechanism may be associated with the expression of NF-kappabeta65.

Anti-adenovirus activities of shikonin, a component of Chinese herbal medicine in vitro.

Radix Lithosperm eyrthrorhizon is a common prescription compound in traditional Chinese medicine. Shikonin is a major component of Radix Lithospermi and has various biological activities. We have investigated the inhibitory effect of shikonin on the growth of adenovirus type 3 (AdV3) in vitro. The antiviral function of shikonin against AdV3 and its virus inhibition ratio were detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method (MTT). The expression of hexon protein in AdV3 was determined by immunofluorescence assay using laser scanning confocal microscopy (LSCM) and Western blot analysis. In addition, the rate of apoptosis in cells infected by AdV3 was determined by flow cytometry. Shikonin (0.0156-1 µM) inhibited growth of AdV3 in a concentration-dependent manner with a virus inhibition rate of 23.8-69.1%. Expression of hexon protein in AdV3 was higher in the virus control group than in the shikonin-treated groups as determined by immunofluorescence assay and Western blotting (p<0.05). The rate of shikonin-treated HeLa cell apoptosis had a statistically significant decrease with increasing concentration of drug (p<0.05). Our data demonstrate that shikonin possesses anti-AdV3 capabilities and that the potential antiviral mechanism might involve inhibiting the degree of apoptosis and hexon protein expression of AdV.

A retrospective study of enteral nutrition on immune and inflammatory factors after liver cancer surgery.

ABSTRACT: This retrospective study aimed to explore the effect of enteral nutrition (EN) on immune and inflammatory factors after liver cancer surgery (LCS).It was retrospectively conducted on enrolled LCS patients between January 2017 and May 2020. The medical records of 528 patient case records were collected and reviewed. After selection, a total of 80 eligible patient case records were finally included. All those patients received routine diet, and they were allocated to a treatment group (n = 40) and a control group (n = 40). In addition, patients in the treatment group also received EN. The primary outcomes were immune factors (CD4+, CD8+, CD4+/CD8+) and inflammatory factors (interleukin-1, interleukin-6, and tumor necrosis factor-α). The secondary outcomes were postoperative hospital stay (day), time to first bowel sounds (hour), time to first flatus (day), time to first defecation (day), and complications.There were not significant differences in CD4+/CD8+ (P = .34), postoperative hospital stay (P = .39), and time to first bowel sounds (P = .17) between 2 groups. However, there were significant differences in CD4+ (P < .01), CD8+ (P < .01), interleukin-1 (P < .01), interleukin-6 (P < .01), tumor necrosis factor-α (P < .01), time to first flatus (P < .01), and time to first defecation (P < .01) between 2 groups. As for complications, there were not significant differences between 2 groups (P > .05).The results of this study found that EN may benefit for patients after LCS during the recovery period. Future high quality prospective studies are needed to warrant the present conclusion.

Kinesin Family Member 11 Enhances the Self-Renewal Ability of Breast Cancer Cells by Participating in the Wnt/ß-Catenin Pathway.

PURPOSE: Our previous studies have shown that kinesin family member 11 (KIF11) is markedly overexpressed in human breast cancer cells or tissues and positively correlated with distant metastasis and prognosis in patients with breast cancer, suggesting an important role in the regulation of cancer stem cells. Herein, we examined the role of KIF11 in breast cancer stem cells. METHODS: In the current study, we validated our previous findings through analysis of data collected in The Cancer Genome Atlas. Endogenous KIF11 was stably silenced in MCF-7 and SKBR-3 cells. Flow cytometry was used to measure the proportion of side-population (SP) cells. Mammosphere culture and tumor implantation experiments in immunodeficient mice were used to assess the self-renewal ability of breast cancer cells. Real-time polymerase chain reaction, western blot, immunofluorescence staining, luciferase reporter assays and Wnt agonist treatment were conducted to investigate the signaling pathways regulated by KIF11. RESULTS: We found that the expression level of KIF11 was positively correlated with stem cell-enrichment genes. The proportion of SP cells was significantly reduced in KIF11-silenced cells. Silencing endogenous KIF11 not only reduced the size and number of mammospheres in vitro, but also reduced the ability of breast cancer cells to form tumors in mice. Simultaneously, we found that KIF11 was involved in regulating the activation of the Wnt/ß-catenin signaling pathway. CONCLUSION: Endogenous KIF11 enhances the self-renewal of breast cancer cells by activating the Wnt/ß-catenin signaling pathway, thereby enhancing the characteristics of breast cancer stem cells.

[Apoptosis and activity changes of telomerase induced by essential oil from pine needles in HepG2 cell line].

OBJECTIVE: To study the effects of essential oil extracted from pine needles on HepG2 cell line. METHODS: HepG2 cells were treated with essential oil extracted from pine needles. Cell growth rate was determined with MTF assay, cell morphologic changes were examined under transmission electromicroscope and HE straining. Flow cytometry was used to exmine apoptotic cells. Bcl-2 gene expression was determined by flow cytometry and telomerase activity by TRAP assay. RESULTS: Essential oils from pine needles could not only repress the growth of HepG2 cells significantly, but also induce apoptosis to them. Both dose-effect and time-effect relationship could be confirmed. Typical morphology changes of apoptosis such as nuclear enrichment and karyorrhexis were observed through transmission electromicroscope and HE straining. Telomerase activity was down regulated in the essential oil extracted from pine needles induced apoptotic cells. The expression of bcl-2 gene was suppressed after the essential oil from pine needles treatement. CONCLUSION: The essential oil extracted from pine needles can inhibit cell growth of HepG2 cell line and induce apoptosis, which may associate with inhibition of telomerase activity and bcl-2 may be involved in the regulation of telomerase activity.

[Expression of bcl-2 and bax genes in the liver cancer cell line HepG2 after apoptosis induced by essential oils from Rosmarinus officinalis].

OBJECTIVE: To investigate the expression of bcl-2 and bax genes in the liver cancer cell line HepG2 after apoptosis induced by essential oils from Rosmarinus officinalis. METHODS: Essential oils from Rosmarinus officinalis were collected by steam distillation, then its chemical composition was determined by GC-MS. Expression of bcl-2 and bax genes were detected by immunohistochemical method. RESULTS: The liver cancer cell line HepG2 was treated with essential oils from Rosmarinus officinalis at various concentrations for different duration. Expression of bcl-2 gene reduced and expression of bax gene increased in a dose and time dependent manner. CONCLUSION: Essential oils from Rosmarinus officinalis can affect the pattern of bcl-2 and bax genes expressions, and this may increase the apoptosis of liver cancer cell line HepG2.

Kinesin family member 11 contributes to the progression and prognosis of human breast cancer.

The present study aimed to clarify the association between kinesin family member 11 (KIF11) and human breast cancer, and the effect of KIF11 on breast cancer cell progression. Western blot analysis, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, retroviral infection, immunohistochemistry staining, MTT assay, anchorage-independent growth ability assay and tumorigenicity assay were all used in the present study. Western blot and RT-qPCR analysis revealed that the expression of KIF11 was markedly increased in malignant cells compared with that in non-tumorous cells at the mRNA and protein level. Immunohistochemical analysis revealed that KIF11 expression was upregulated in 256/268 (95.8%) paraffin-embedded archival breast cancer biopsies. Statistical analysis demonstrated a significant association between the upregulation of KIF11 expression and the progression of breast cancer. Multivariate analysis revealed that KIF11 upregulation represents an independent prognostic indicator for the survival of patients with breast cancer. Tumorigenicity experiments were further used to evaluate the effect of KIF11 in non-obese diabetic/severe combined immunodeficient mice. Silencing endogenous KIF11 by short hairpin RNAs inhibited the proliferation of breast cancer cells in vitro and in vivo. The present results suggest that KIF11 may serve an important function in the proliferation of breast cancer and may represent a novel and useful prognostic marker for breast cancer.

Inhibitory effects of α-pinene on hepatoma carcinoma cell proliferation.

BACKGROUND: Pine needle oil from crude extract of pine needles has anti-tumor effects, but the effective component is not known. METHODS: In the present study, compounds from a steam distillation extract of pine needles were isolated and characterized. Alpha-pinene was identified as an active anti-proliferative compound on hepatoma carcinoma BEL-7402 cells using the MTT assay. RESULTS: Further experiments showed that α-pinene inhibited BEL-7402 cells by arresting cell growth in the G2/M phase of the cell cycle, downregulating Cdc25C mRNA and protein expression, and reducing cycle dependence on kinase 1(CDK1) activity. CONCLUSION: Taken together, these findings indicate that α-pinene may be useful as a potential anti-tumor drug.