Artificial intelligence in clinical research of cancers.

Several factors, including advances in computational algorithms, the availability of high-performance computing hardware, and the assembly of large community-based databases, have led to the extensive application of Artificial Intelligence (AI) in the biomedical domain for nearly 20 years. AI algorithms have attained expert-level performance in cancer research. However, only a few AI-based applications have been approved for use in the real world. Whether AI will eventually be capable of replacing medical experts has been a hot topic. In this article, we first summarize the cancer research status using AI in the past two decades, including the consensus on the procedure of AI based on an ideal paradigm and current efforts of the expertise and domain knowledge. Next, the available data of AI process in the biomedical domain are surveyed. Then, we review the methods and applications of AI in cancer clinical research categorized by the data types including radiographic imaging, cancer genome, medical records, drug information and biomedical literatures. At last, we discuss challenges in moving AI from theoretical research to real-world cancer research applications and the perspectives toward the future realization of AI participating cancer treatment.

MicroRNA-454 modulates the oxidative stress and neuronal apoptosis after cerebral ischemia/reperfusion injury via targeting NADPH oxidase 4 (NOX4).

To investigate the function of miR-454 in ischemic stroke, this study was carried out. Cerebral ischemia/reperfusion (I/R) injury animal model and a SHSY5Y cell culture model of oxygen-glucose deprivation/reoxygenation (OGD/R) were constructed. The effects of miR-454 were detected by evaluating the levels of biochemical markers, gene expression, and pathophysiological markers. The results showed that NOX4 level was elevated, while miR-454 expression was reduced in I/R brain samples and in OGD/R-treated cells. The miR-454 agomir declined NOX4 level and reactive oxygen species (ROS) production in rats suffering from I/R. Furthermore, microRNA-145 (miR-454) overexpression inhibited NOX4 level and ROS production in cells treated by OGD/R and decreased luciferase activity in cells transfected with NOX4-wild type (WT) reporter plasmid. Meanwhile, our results proved that the protected effects of miR-454 on SH-SY5Y cells treated by OGD/R were reversed by pcDNA-NOX4 transfection. MiR-454 protected animals from brain injury induced by cerebral I/R via directly regulating its target gene NOX4, illustrating a curatively potential target for treating ischemic stroke.

Circular RNA circ_0070441 regulates MPP+-triggered neurotoxic effect in SH-SY5Y cells via miR-626/IRS2 axis.

Circular RNAs (circRNAs) was suggested to play crucial regulatory roles in various human diseases, including Parkinson's disease (PD). This research aimed to investigate the function and potential mechanism of circ_0070441 in PD. MPP+ (1-methyl-4-phenylpyridinium)-treated SH-SY5Y cells was used as an in vitro cellular PD model. The expressions of circ_0070441, microRNA (miR)-626 and insulin receptor substrate 2 (IRS2) were measured by quantitative real-time polymerase chain reaction (RT-qPCR) or western blot. Cell Counting Kit-8 (CCK-8) assay, Cytotoxicity Detection Kit (Lactate Dehydrogenase), flow cytometry and Caspase-3 Assay Kit were used to detect cell viability, LDH release, cell apoptosis and caspase-3 activity, respectively. The levels of inflammation-related factors were detected by enzyme-linked immunosorbent assay (ELISA). The correlation among circ_0070441, miR-626 and IRS2 were confirmed by dual-luciferase reporter assay, RNA immunoprecipitation (RIP) assay and RNA pull-down assay. The levels of circ_0070441 and IRS2 were increased while miR-626 expression was decreased in MPP+-treated SH-SY5Y cells in dose- and time-dependent manners. Depletion of circ_0070441 alleviated MPP+-triggered neuronal damage by regulating cell apoptosis and inflammation. Circ_0070441 acted as a sponge for miR-626, and IRS2 was a target of miR-626. Besides, the neuroprotective effects of circ_0070441 knockdown or miR-626 overexpression were partly overturned by the suppression of miR-626 or IRS2 overexpression. Moreover, circ_0070441 upregulated IRS2 expression by interacting with miR-626. In summary, circ_0070441 aggravated MPP+-triggered neurotoxic effect in SH-SY5Y cells by regulating miR-626/IRS2 axis.

Health-related quality of life in children after surgical repair of esophageal atresia: a cross-sectional study in China.

Objective: To investigate health-related quality of life (HRQOL) in patients after surgical repair for esophageal atresia (EA) and identify its potential influencing factors. Methods: A total of 102 EA children who had previously visited our hospital participated in this cross-sectional study. Basic data and disease data of the patients were collected. The HRQOL was measured with the Pediatric Quality of Life Inventory™4.0 (PedsQL™4.0) and EA-QOL questionnaire and ranked on a reverse 0-100 scale, with a higher number indicative of a better HRQOL perception. The scores of PedsQL™4.0 in children with EA were collected and compared with that of the demographically matched healthy control group. Meanwhile, the condition-specific HRQOL of EA was analyzed by the EA-QOL questionnaire, and the potential clinical factors that influenced the HRQOL were determined by the generalized linear model. Results: The group of EA and control reached a similar score in the generic PedsQL™4.0 (EA group: 86.55 ± 9.69; control group: 89.41 ± 6.54; p = 0.670). There was no significant difference between the EA group and the control group in other domains except the school functioning. Condition-specific HRQOL in the 2-7-year-old group had the highest score in social isolation and stress domain and the lowest score in the physical health and treatment domain, with an overall quality of life score of 83.48 ± 10.22. The scores of the 8-17-year-old group were relatively high in social relationships and health and well-being and lowest in the eating domain, with an overall quality of life score of 89.43 ± 8.57. Heart malformation, complicated esophageal surgery history, respiratory symptoms,and digestive symptoms in the past 1 month were the main factors affecting the HRQOL of children aged 2-7 years. Complicated esophageal surgery history, respiratory symptoms, and digestive symptoms in the past 1 month were the main factors affecting the HRQOL of children aged 8-17 years. Conclusions: The findings suggest that patients with EA generally had a good HRQOL. However, EA children with postoperative complications and associated symptoms have lower scores in the EA-QOL questionnaire.

Identification and Validation of Autophagy-Related Genes in Necrotizing Enterocolitis.

Background: Autophagy plays an essential role in the occurrence and progression of necrotizing enterocolitis (NEC). We intend to carry out the identification and validation of the probable autophagy-related genes of NEC via bioinformatics methods and experiment trials. Methods: The autophagy-related differentially expressed genes (arDEGs) of NEC were identified by analyzing the RNA sequencing data of the experiment neonatal mouse model and dataset GSE46619. Protein-protein interactions (PPIs), Gene Ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used for the arDEGs. Then, co-expressed autophagy-related genes in two datasets were identified by Venn analysis and verified by qRT-PCR in experimental NEC. Results: Autophagy increased in experimental NEC and 47 arDEGs were identified in experimental NEC by RNA-sequencing. The PPI results proclaimed those genes interplayed with each other. The GO and KEGG enrichment results of arDEGs reported certain enriched pathways related to autophagy and macroautophagy. Furthermore, 22 arDEGs were identified in human NEC from dataset GSE46619. The GO and KEGG enrichment analysis of these genes showed similar enriched terms with the results of experimental NEC. Finally, HIF-1a, VEGFA, ITGA3, ITGA6, ITGB4, and NAMPT were identified as co-expressed autophagy-related genes by Venn analysis in human NEC from dataset GSE46619 and experimental NEC. The result of quantified real-time PCR (qRT-PCR) revealed that the expression levels of HIF-1a and ITGA3 were upregulated, while VEGFA and ITGB4 were downregulated in experimental NEC. Conclusion: We identified 47 arDEGs in experimental NEC and 22 arDEGs in human NEC via bioinformatics analysis. HIF-1a, ITGA3, VEGFA, and ITGB4 may have effects on the progression of NEC through modulating autophagy.

Sanghuang Tongxie Formula Ameliorates Insulin Resistance in Drosophila Through Regulating PI3K/Akt Signaling.

Insulin resistance (IR) is a pivotal pathological characteristic that affects the occurrence and development of type 2 diabetes mellitus (T2DM). Thus, the effective control of IR is of great significance for diabetes prevention and treatment. Traditional Chinese medicine (TCM) represents a valuable tool handed down to the world by the Chinese nation and has a long history of use for diabetes clinical therapy. In this study, we focused on a self-drafted TCM-patented formula, Sanghuang Tongxie Formula (SHTXF), which exhibits clinical efficacy in the treatment of diabetes. To explore the effect and molecular mechanism of SHTXF on IR in vivo, Drosophila melanogaster was used and a (Collagen) Cg > InRK1409A diabetic IR fly model was established. SHTXF water extract was found to contribute toward carbohydrate clearance from the circulating system by converting it into triglycerides (TAG), not glycogen, for nutrient storage. In addition, SHTXF activated phosphatidylinositol-3-kinase (PI3K) activity and improved protein kinase B (PKB, also termed Akt) phosphorylation. Finally, SHTXF promoted Drosophila Forkhead Box O (dFoxO) cytoplasmic localization and inhibited its transcriptional activity. Taken together, these findings not only highlight the positive role of SHTXF in ameliorating IR via the PI3K/Akt pathway but also provide potential drug targets and key insights for use in T2DM clinical treatment strategies.

MicroRNA-449 targets histone deacetylase 1 to regulate the proliferation, invasion, and apoptosis of synovial fibroblasts in rheumatoid arthritis.

BACKGROUND: Rheumatoid arthritis (RA) is a chronic joint disease. The study aimed to explore the effects of microRNA (miR)-449 and histone deacetylase 1 (HDAC1) on the proliferation, invasion, and apoptosis of synovial fibroblasts in rheumatoid arthritis. METHODS: Synovial tissue was collected from 20 patients with RA and 20 patients with osteoarthritis (OA) who underwent joint replacement surgery. RA synovial fibroblasts (RASFs) and OA synovial fibroblasts (OASFs) were isolated and cultured. Real-time quantitative PCR was used to detect the expression levels of miR-449 and HDAC1 in synovial tissues and cells. Western blot was performed to detect the cellular expression levels of HDAC1 protein, and apoptosis and invasion-related proteins. The proliferation, invasion, and apoptosis of RASFs were detected by MTT assay, Transwell assay, and flow cytometry. The dual-luciferase reporter gene was used to test the targeting relationship between inflammatory miR-449 and HDAC1. RESULTS: Compared with normal synovial tissue and OASFs, the levels of HDAC1 messenger RNA in RA synovial tissue and RASF cells were significantly increased (P<0.01), while the expression levels of miR-449 were significantly decreased (P<0.01). The dual-luciferase reporter gene experiment confirmed that miR-449 could specifically bind to the 3' untranslated region of HDAC1 to inhibit its luciferase activity (P<0.05). HDAC1 inhibition or miR-449 overexpression significantly inhibited the proliferation and invasion of RASFs (P<0.001), while inducing their apoptosis (P<0.001). HDAC1 overexpression reversed the biological effects of miR-449 on RASFs (P<0.001). CONCLUSIONS: miR-449 inhibits the proliferation and invasion of RASFs and induces their apoptosis by targeting HDAC1, thereby exerting a protective effect against RA.

Tumor necrosis factor receptor-associated factor 6 (TRAF6) inhibition modulates bone loss and matrix metalloproteinase expression levels in collagen-induced rheumatoid arthritis rat.

BACKGROUND: Rheumatoid arthritis (RA) is a main characterized by persistent synovitis, systemic inflammation, and autoantibodies. Tumor necrosis factor receptor-associated factor 6 (TRAF6) is an E3 ubiquitin ligase and is a crucial cytoplasm signal adaptor that can regulate critical biological processes. This research aims to explore the function of TRAF6 on bone loss and matrix metalloproteinase (MMP) expression in collagen-induced RA rats. METHODS: The RA model in rats (Sprague Dawley rat, 5-6 weeks old, weight 246.88±8.31 g) was set up via using collagen-induced RA. The shRNA-TRAF6 knockdown efficiency was tested using real-time reverse transcription-polymerase chain reaction (qRT-PCR) and western blot, respectively. The rats were divided into four groups: the control group, RA group, RA + shRNA-NC group, and RA + TRAF6-shRNA group. The tartrate-resistant acidic phosphatase (TRAP), hematoxylin and eosin (H&E), and Saffron O staining were employed to test the bone injury. The mRNA and protein expressive of Osteoclast-associated receptor (OSCAR), TRAP, Osterix (Osx), Collagen type I alpha 1 (COL1A1), Distal-less homeobox2 (Dlx2), tissue inhibitor of metalloproteinase (TIMP), matrix metalloproteinase-1(MMP-1), Cyclooxygenase 2 (COX2) and qRT-PCR performed MMP-13 and western blot, respectively. RESULTS: The mRNA and protein expression levels of TRAF6 were down-regulated in the RA + TRAF6- shRNA group. After the levels of TRAF6 were inhibited, the levels of bone volume/total volume (BV/TV), trabecular bone thickness (Tb.Th), and trabecular bone number (Tb.N) were increased, while the levels of trabecular bone space (Tb.Sp), Osteocalcin and ALP were deceased. The mRNA and protein expression levels of OSCAR, TRAP, MMP-1, COX2, and MMP-13 were reduced obviously in the RA + TRAF6- shRNA group compared with the RA + shRNA-NC group, while the levels of TIMP-1, OSX, CoL1A1, and DLx2 were enhanced obviously. CONCLUSIONS: Inhibition of TRAF6 reduces bone loss and MMP expression levels in collagen-induced RA rat, and supplies an alternative treatment method in RA.

Effects of UCH-L1 on alpha-synuclein over-expression mouse model of Parkinson's disease.

The rare inherited form of Parkinson's disease (PD), PARK5, is caused by a missense mutation in ubiquitin carboxy-terminal hydrolase-L1 (UCH-L1) gene, resulting in Ile93Met substitution in its gene product (UCH-L1(Ile93Met)). PARK5 is inherited in an autosomal-dominant mode, but whether the Ile93Met mutation gives rise to a gain-of-toxic-function or loss-of-function of UCH-L1 protein remains controversial. Here, we investigated the selective vulnerabilities of dopaminergic (DA) neurons in UCH-L1-transgenic (Tg) and spontaneous UCH-L1-null gracile axonal dystrophy mice to an important PD-causing insult, abnormal accumulation of alpha-synuclein (alphaSyn). Immunohistochemistry of midbrain sections of a patient with sporadic PD showed alphaSyn- and UCH-L1-double-positive Lewy bodies in nigral DA neurons, suggesting physical and/or functional interaction between the two proteins in human PD brain. Recombinant adeno-associated viral vector-mediated over-expression of alphaSyn for 4 weeks significantly enhanced the loss of nigral DA cell bodies in UCH-L1(Ile93Met)-Tg mice, but had weak effects in age-matched UCH-L1(wild-type)-Tg mice and non-Tg littermates. In contrast, the extent of alphaSyn-induced DA cell loss in gracile axonal dystrophy mice was not significantly different from wild-type littermates at 13-weeks post-injection. Our results support the hypothesis that PARK5 is caused by a gain-of-toxic-function of UCH-L1(Ile93Met) mutant, and suggest that regulation of UCH-L1 in nigral DA cells could be a future target for treatment of PD.

SIRT1 promotes tumor-like invasion of fibroblast-like synoviocytes in rheumatoid arthritis via targeting TIMP1.

Suppression of tissue inhibitor of matrix metalloproteinase (TIMP) is associated with the tumor-like invasion of fibroblast-like synoviocytes (FLSs) that occurs during rheumatoid arthritis-related cartilage destruction. Silent information regulator 2 homolog1 (SIRT1), a histone deacetylase, is widely involved in transcriptional regulation, genomic stability, metabolism and DNA repair. Recent studies suggest that SIRT1 may also impact inflammatory response and the proliferation of FLSs in rheumatoid arthritis (RA). However, it is unknown whether SIRT1 has a role in the tumor-like invasion of FLSs in rheumatoid arthritis. Herein we report that SIRT1 contributes to FLS invasion and cartilage destruction via a TIMP1-dependent mechanism. Elevated SIRT1 in RA synovia suppresses TIMP1 expression via deacetylation of TIMP1-associated histones, thereby disrupting the binding of the transcription factor specificity protein 1 (Sp1) to the TIMP1 promoter. In rats with collagen-induced arthritis, depletion of SIRT1 remarkably promoted TIMP1 expression in synovial tissues and ameliorated cartilage destruction. These results describe a new role for SIRT1 and demonstrate its potential value as a therapeutic target for rheumatoid arthritis.

[Expression and purification ficolin 3 and its role for RAW264.7 macrophage activation in vitro].

OBJECTIVE: To establish a prokaryotic expression plasmid of ficolin-3, express and purify the fusion protein His-ficolin 3 in E.coli, and explore the role of ficolin-3 in the activation of RAW264.7 macrophages. METHODS: Using the cDNA from human peripheral blood mononuclear cells as template, human ficolin-3 cDNA was amplified by PCR and inserted into vector pET22b. The recombinant plasmid pET22b-ficolin 3 was identified by digestion of XhoI and SalI and confirmed by DNA sequencing. Thereafter, the protein His-ficolin 3 was induced and purified in E.coli BL21. His-fincolin 3 at different concentrations was added into RAW264.7 cells. With the protein His as control, the effects of His-fincolin 3 on the phagocytosis of RAW264.7 cells to chicken red blood cells (CRBCs) and on the production of IL-6, IL-12 and TNF-α were tested by flow cytometry and ELISA, respectively. RESULTS: Enzyme digestion and sequencing confirmed that recombinant plasmid pET22b-ficolin 3 was established as expected. SDS-PAGE showed the expression of soluble His-ficolin 3 of Mr 33 000. The purity of the products was over 90%. Western blotting further identified His-ficolin 3. Compared with His protein, His-ficolin 3 improved the phagocytosis of RAW264.7 cells in a dose-dependent manner, and it raised the secretion of IL-6, IL-12 and TNF-α in RAW264.7 cells. CONCLUSION: The plasmid pETb-ficolin 3 was cloned successfully and the purity of the protein His-ficolin 3 was over 90%. His-ficolin 3 could induce the activation of RAW264.7 cells obviously.

Recombinant human granulocyte colony-stimulating factor protects against MPTP-induced dopaminergic cell death in mice by altering Bcl-2/Bax expression levels.

Granulocyte colony-stimulating factor (G-CSF) has been used for the treatment of neutropenia in hematologic disorders. The neuroprotective effects of G-CSF were reported in neurological disease models. In the present study, we examined whether G-CSF can protect dopaminergic neurons against MPTP-induced cell death in a mouse model of Parkinson's disease. Mice of one group were injected intraperitoneally with MPTP for five consecutive days, those of another group with MPTP and intraperitoneal G-CSF at 2 days and 1 day before the first MPTP injection, and 30 min before each MPTP injection, while control mice received saline injections. Immunohistochemistry, western blotting analysis, and HPLC were performed to evaluate damage of substantia nigra dopaminergic neurons and expression of Bcl-2 and Bax protein. MPTP induced dopaminergic cell death in the substantia nigra. G-CSF significantly prevented MPTP-induced loss of tyrosine hydroxylase-positive neurons (p < 0.05), increased Bcl-2 protein and decreased Bax protein expression. Our findings indicate that G-CSF provides neuroprotection against MPTP-induced cell death and this effect is mediated by increasing Bcl-2 expression levels and decreasing Bax expression levels in C57BL/6 mice.