Best practices in cell culture: an overview

Rupatadine inhibits colorectal cancer cell proliferation through the PIP5K1A/Akt/CDK2 pathway

BACKGROUND

Phosphatidylinositol-4-phosphate 5-kinase type 1 alpha (PIP5K1A) acts upstream of the Akt regulatory pathway and is abnormally expressed in many types of malignancies. However, the role and mechanism of PIP5K1A in colorectal cancer (CRC) have not yet been reported. In this study, we aimed to determine the association between PIP5K1A and progression of CRC and assess the efficacy and mechanism by which rupatadine targets PIP5K1A.

METHODS

Firstly, expression and function of PIP5K1A in CRC were investigated by human colon cancer tissue chip analysis and cell proliferation assay. Next, rupatadine was screened by computational screening and cytotoxicity assay and interactions between PIP5K1A and rupatadine assessed by kinase activity detection assay and bio-layer interferometry analysis. Next, rupatadine's anti-tumor effect was evaluated by in vivo and in vitro pharmacodynamic assays. Finally, rupatadine's anti-tumor mechanism was explored by quantitative real-time reverse-transcription polymerase chain reaction, western blot, and immunofluorescence.

RESULTS

We found that PIP5K1A exerts tumor-promoting effects as a proto-oncogene in CRC and aberrant PIP5K1A expression correlates with CRC malignancy. We also found that rupatadine down-regulates cyclin-dependent kinase 2 and cyclin D1 protein expression by inhibiting the PIP5K1A/Akt/GSK-3β pathway, induces cell cycle arrest, and inhibits CRC cell proliferation in vitro and in vivo.

CONCLUSIONS

PIP5K1A is a potential drug target for treating CRC. Rupatadine, which targets PIP5K1A, could serve as a new option for treating CRC, its therapeutic mechanism being related to regulation of the Akt/GSK-3β signaling pathway.

Baicalin reduced injury of and autophagy-related gene expression in RAW264.7 cells infected with H6N6 avian influenza virus

In the present study, we investigated whether baicalin could reduce the damage caused to RAW264.7 cells following infection with H6N6 avian influenza virus. In addition, we studied the expression of autophagy-related genes. The morphological changes in cells were observed by hematoxylin and eosin (H&E) staining, and the inflammatory factors in the cell supernatant were detected by enzyme-linked immunosorbent assay (ELISA). Transmission electron microscopy (TEM) was used to detect the levels of RAW264.7 autophagosomes, and western blotting and immunofluorescence were used to detect the protein expression of autophagy marker LC3. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) was used to detect the mRNA transcription levels of autophagy key factors. The results showed that different doses of baicalin significantly reduced the H6N6 virus-induced damage of RAW264.7 cells. The contents of interleukin (IL)-1β, IL-2, IL-6, and tumor necrosis factor (TNF)-α in the cell supernatant significantly decreased. In addition, the protein expression of LC3 and Beclin-1, ATG12, ATG5 the mRNA levels were significantly decreased. This study showed that baicalin can reduce cell damage and affect the H6N6-induced autophagy level of RAW264.7 cells.

A New Cell Model Overexpressing sTGFBR3 for Studying Alzheimer's Disease In vitro

BACKGROUND

Recent studies have suggested that abnormal microglial hyperactivation has an important role in the progression of Alzheimer's disease (AD). sTGFBR3 (a shed extracellular domain of the transforming growth factor type III receptor) is a newly identified target of microglia polarization dysregulation, whose overexpression can cause abnormal accumulation of transforming growth factor β1 (TGF-β1), promoting Aβ, tau, and neuroinflammatory pathology.

OBJECTIVE

The objective of this study is to develop and validate a new cell model overexpressing sTGFBR3 for studying AD in vitro.

METHODS

BV2 cells (a microglial cell derived from C57/BL6 murine) were used as a cell model. Cells were then treated with different concentrations of lipopolysaccharide (LPS) (0, 1, or 0.3 μg/mL) for 12, 24, or 48h and then with or without sodium pervanadate (100 μM) for 30 min. Next, the effect surface optimization method was used to determine optimal experimental conditions. Finally, the optimized model was used to assess the effect of ZQX series compounds and vasicine on cell viability and protein expression. Expression of TGFBR3 and TNF-α was assessed using Western blot. MTT assay was used to assess cell viability, and enzyme- linked immunosorbent assay (ELISA) was employed to evaluate extracellular TGF-β1 and sTGFBR3.

RESULTS

LPS (0.3 μg/mL) treatment for 11 h at a cell density of 60% and pervanadate concentration (100 μM) incubation for 30 min were the optimal experimental conditions for increasing membrane protein TGFBR3 overexpression, as well as extracellular sTGFBR3 and TGF-β1. Applying ZQX-5 and vasicine reversed this process by reducing extracellular TGF-β1, promoting the phosphorylation of Smad2/3, a protein downstream of TGF-β1, and inhibiting the release of the inflammatory factor TNF-α.

CONCLUSION

This new in vitro model may be a useful cell model for studying Alzheimer's disease in vitro.

Detection of viral infection in cell lines using ViralCellDetector

Cell lines are commonly used in research to study biology, including gene expression regulation, cancer progression, and drug responses. However, cross-contaminations with bacteria, mycoplasma, and viruses are common issues in cell line experiments. Detection of bacteria and mycoplasma infections in cell lines is relatively easy but identifying viral infections in cell lines is difficult. Currently, there are no established methods or tools available for detecting viral infections in cell lines. To address this challenge, we developed a tool called ViralCellDetector that detects viruses through mapping RNA-seq data to a library of virus genome. Using this tool, we observed that around 10% of experiments with the MCF7 cell line were likely infected with viruses. Furthermore, to facilitate the detection of samples with unknown sources of viral infection, we identified the differentially expressed genes involved in viral infection from two different cell lines and used these genes in a machine learning approach to classify infected samples based on the host response gene expression biomarkers. Our model reclassifies the infected and non-infected samples with an AUC of 0.91 and an accuracy of 0.93. Overall, our mapping- and marker-based approaches can detect viral infections in any cell line simply based on readily accessible RNA-seq data, allowing researchers to avoid the use of unintentionally infected cell lines in their studies.

Incubation of canine dermal fibroblasts with serum from dogs with atopic dermatitis activates extracellular matrix signalling and represses oxidative phosphorylation

The aim of this study was to investigate the effects on gene expression in canine fibroblasts after incubation with a medium enriched with atopic dermatitis canine serum (CAD) compared with healthy canine serum (CTRL) and fetal bovine serum (FBS). Differential Expression and Pathway analysis (iDEP94) in R package (v0.92) was used to identify differentially expressed genes (DEGs) with a False Discovery Rate of 0.01. DEGs from fibroblasts incubated with CAD serum were significantly upregulated and enriched in the extracellular matrix (ECM) and focal adhesion signalling but downregulated in the oxidative phosphorylation pathway. Genes involved in profibrotic processes, such as TGFB1, INHBA, ERK1/2, and the downward regulated genes (collagens and integrins), were significantly upregulated after fibroblasts were exposed to CAD serum. The observed downregulation of genes involved in oxidative phosphorylation suggests metabolic dysregulation toward a myofibroblast phenotype responsible for fibrosis. No differences were found when comparing CTRL with FBS. The DEGs identified in fibroblasts incubated with CAD serum suggest activation of signalling pathways involved in gradual differentiation through a myofibroblast precursors that represent the onset of fibrosis. Molecular and metabolic knowledge of fibroblast changes can be used to identify biomarkers of the disease and new potential pharmacological targets.

Many Common Pathogens are Present in the Operative Room Air During Surgery

BACKGROUND

The main objective of this study was to assess the sanitary measures of operating theaters using next-generation sequencing.

METHODS

Air was sampled from the operating room for the whole duration of 10 surgical days of "clean" (no infection cases) procedures (6 hip/knee arthroplasty and 4 spine cases). Controls consisted of samples at the beginning of the day (1 hour before the surgery started) and at the end of the day after terminal cleaning. One additional control sample, consisting of a culture swab that was opened and exposed to the air for 5 seconds, was collected at each time point. All samples were sent for next-generation sequencing analysis (16S rRNA sequencing) for bacterial identification.

RESULTS

Overall, 306 samples were collected (159 controls and 147 experimental). Microbial DNA was detected in only 1 control sample, while 18 (12.2%) experimental samples were positive for microbial DNA. The most common organisms retrieved were Escherichia coli (6/18, 30%), Cutibacterium acnes (3/18, 15%), and Pseudomonas aeruginosa (2/18, 11.1%). There was no difference in positive samples between arthroplasty and spine cases (P > .05).

CONCLUSION

Microbial organisms are not uncommonly present in the operating room air during hip and knee arthroplasties and spine procedures.

In Vitro Mimicking of Obesity-Induced Biochemical Environment to Study Obesity Impacts on Cells and Tissues

Obesity represents a heavy burden for modern healthcare. The main challenge facing obesity research progress is the unknown underlying pathways, which limits our understanding of the pathogenesis and developing therapies. Obesity induces specific biochemical environments that impact the different cells and tissues. In this piece of writing, we suggest mimicking obesity-induced in vivo biochemical environments including pH, lipids, hormones, cytokines, and glucose within an in vitro environment. The concept is to reproduce such biochemical environments and use them to treat the tissue cultures, explant cultures, and cell cultures of different biological organs. This will allow us to clarify how the obesity-induced biochemistry impacts such biological entities. It would also be important to try different environments, in terms of the compositions and concentrations of the constitutive elements, in order to establish links between the effects (impaired regeneration, cellular inflammation, etc.) and the factors constituting the environment (hormones, cytokines, etc.) as well as to reveal dose-dependent effects. We believe that such approaches will allow us to elucidate obesity mechanisms, optimize animal models, and develop therapies as well as novel tissue engineering applications.

A network pharmacology approach to evaluate the synergistic effect of dihydromyricetin and myricitrin in vine tea on the proliferation of B16F10 cells

Aim of the study

Although vine tea has demonstrated broad-spectrum anti-cancer properties, its main active compounds, dihydromyricetin (DMY) and myricitrin (MYT), exert weaker effects than the tea extracts. This study aimed to investigate the synergistic inhibitory effects of DMY and MYT on B16F10 cell proliferation and their synergistic inhibitory effects.

Methods

The effect of vine tea extracts (VTEs) and their active compounds on B16F10 cells was analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, fluorescence staining, and flow cytometry. The synergistic effects were calculated by the combination index (CI), and its mechanism was discussed by network pharmacology.

Results

Different VTEs varied in their inhibition of B16F10 cell growth, with IC₅₀ values ranging from 4.45 to 12.95 μg/mL, Among these, Guangzhou Qingyuan (Level 2), appeared to have the most potent inhibitory effect. The IC₅₀ value of mix-use of DMY and MYT was 19.94∼64.4 μM, of which DMY: MYT = 8:1 had the minimum IC₅₀ value of 19.94 μM. Combinations in the 1:1∼8:1 range had stronger effects than the isolated active compound. When they were mixed at the ratio of 1:4∼8:1, CI < 1, showing a synergistic effect. The combination of DMY and MYT also significantly inhibited the tyrosinase activity in B16F10 cells, consistent with its impact on cell proliferation. The eight potential targets were identified by network pharmacology regulating melanin metabolism, tyrosine metabolism, and melanogenesis signaling. According to the analysis of protein-protein interactions, TP53, TNF, and TYR might be critical targets for preventing and treating melanoma.

Conclusion

We found that DMY and MYT induced apoptosis of B16F10 cells, and their combined application had a significant synergistic effect. The present findings indicated that vine tea had a multi-pathway and multi-target impact on the prevention and treatment of melanoma.

Experimental Conditions That Influence the Utility of 2′7′-Dichlorodihydrofluorescein Diacetate (DCFH2-DA) as a Fluorogenic Biosensor for Mitochondrial Redox Status

Oxidative stress has been causally linked to various diseases. Electron transport chain (ETC) inhibitors such as rotenone and antimycin A are frequently used in model systems to study oxidative stress. Oxidative stress that is provoked by ETC inhibitors can be visualized using the fluorogenic probe 2′,7′-dichlorodihydrofluorescein-diacetate (DCFH₂-DA). Non-fluorescent DCFH₂-DA crosses the plasma membrane, is deacetylated to 2′,7′-dichlorodihydrofluorescein (DCFH₂) by esterases, and is oxidized to its fluorescent form 2′,7′-dichlorofluorescein (DCF) by intracellular ROS. DCF fluorescence can, therefore, be used as a semi-quantitative measure of general oxidative stress. However, the use of DCFH₂-DA is complicated by various protocol-related factors that mediate DCFH₂-to-DCF conversion independently of the degree of oxidative stress. This study therefore analyzed the influence of ancillary factors on DCF formation in the context of ETC inhibitors. It was found that ETC inhibitors trigger DCF formation in cell-free experiments when they are co-dissolved with DCFH₂-DA. Moreover, the extent of DCF formation depended on the type of culture medium that was used, the pH of the assay system, the presence of fetal calf serum, and the final DCFH₂-DA solvent concentration. Conclusively, experiments with DCFH₂-DA should not discount the influence of protocol-related factors such as medium and mitochondrial inhibitors (and possibly other compounds) on the DCFH₂-DA-DCF reaction and proper controls should always be built into the assay protocol.

Establishing Institutional Scores With the Rigor and Transparency Index: Large-scale Analysis of Scientific Reporting Quality

BACKGROUND

Improving rigor and transparency measures should lead to improvements in reproducibility across the scientific literature; however, the assessment of measures of transparency tends to be very difficult if performed manually.

OBJECTIVE

This study addresses the enhancement of the Rigor and Transparency Index (RTI, version 2.0), which attempts to automatically assess the rigor and transparency of journals, institutions, and countries using manuscripts scored on criteria found in reproducibility guidelines (eg, Materials Design, Analysis, and Reporting checklist criteria).

METHODS

The RTI tracks 27 entity types using natural language processing techniques such as Bidirectional Long Short-term Memory Conditional Random Field-based models and regular expressions; this allowed us to assess over 2 million papers accessed through PubMed Central.

RESULTS

Between 1997 and 2020 (where data were readily available in our data set), rigor and transparency measures showed general improvement (RTI 2.29 to 4.13), suggesting that authors are taking the need for improved reporting seriously. The top-scoring journals in 2020 were the Journal of Neurochemistry (6.23), British Journal of Pharmacology (6.07), and Nature Neuroscience (5.93). We extracted the institution and country of origin from the author affiliations to expand our analysis beyond journals. Among institutions publishing >1000 papers in 2020 (in the PubMed Central open access set), Capital Medical University (4.75), Yonsei University (4.58), and University of Copenhagen (4.53) were the top performers in terms of RTI. In country-level performance, we found that Ethiopia and Norway consistently topped the RTI charts of countries with 100 or more papers per year. In addition, we tested our assumption that the RTI may serve as a reliable proxy for scientific replicability (ie, a high RTI represents papers containing sufficient information for replication efforts). Using work by the Reproducibility Project: Cancer Biology, we determined that replication papers (RTI 7.61, SD 0.78) scored significantly higher (P<.001) than the original papers (RTI 3.39, SD 1.12), which according to the project required additional information from authors to begin replication efforts.

CONCLUSIONS

These results align with our view that RTI may serve as a reliable proxy for scientific replicability. Unfortunately, RTI measures for journals, institutions, and countries fall short of the replicated paper average. If we consider the RTI of these replication studies as a target for future manuscripts, more work will be needed to ensure that the average manuscript contains sufficient information for replication attempts.

[Identification of microRNAs targeting vitamin D receptor and their effect on parathyroid hormone secretion in secondary hyperparathyroidism]

OBJECTIVE

To identify the miRNAs targeting vitamin D receptor (VDR) gene and their effect on parathyroid hormone (PTH) secretion in secondary hyperparathyroidism.

METHODS

Primary parathyroid cells with secondary hyperparathyroidism were isolated by collagenase digestion and cultured. The miRNAs targeting VDR were screened by bioinformatics methods and full transcriptome sequencing, and dual-luciferase reporter assay was used to verify the targeting relationship between VDR and the screened miRNA. The effects of overexpression or inhibition of the candidate miRNA on VDR mRNA and protein expressions and PTH secretion were evaluated using qRT-PCR and Western blotting. The expression levels of the candidate miRNAs and VDR mRNA in clinical specimens of parathyroid tissues were verified by qRT-PCR, and the expression of VDR protein was detected by immunohistochemistry.

RESULTS

We successfully isolated primary parathyroid cells. Dual-luciferase reporter assay verified the targeting relationship of hsa-miR-149-5p, hsa-miR-221-5p, hsa-miR-222-3p, hsa-miR-29a-5p, hsa-miR-301a-5p, hsa-miR-873-5p, hsa-miR-93-3p with VDR, and among them, the overexpression of hsa-miR-149-5p and hsa-miR-301a-5p significantly increased PTH secretion in the parathyroid cells. In patients with secondary hyperparathyroidism, hsa-miR-149-5p was highly expressed in the parathyroid tissues (P=0.046), where the expressions of VDR mRNA (P=0.0267) and protein were both decreased.

CONCLUSION

The two miRNAs, hsa-miR-149-5p and hsa-miR-301a-5p, may promote the secretion of PTH in patients with secondary hyperparathyroidism by down-regulating the expression of VDR gene.

Toward Best Practices for Controlling Mammalian Cell Culture Environments

The characterization, control, and reporting of environmental conditions in mammalian cell cultures is fundamental to ensure physiological relevance and reproducibility in basic and preclinical biomedical research. The potential issue of environment instability in routine cell cultures in affecting biomedical experiments was identified many decades ago. Despite existing evidence showing variable environmental conditions can affect a suite of cellular responses and key experimental readouts, the underreporting of critical parameters affecting cell culture environments in published experiments remains a serious problem. Here, we outline the main sources of potential problems, improved guidelines for reporting, and deliver recommendations to facilitate improved culture-system based research. Addressing the lack of attention paid to culture environments is critical to improve the reproducibility and translation of preclinical research, but constitutes only an initial step towards enhancing the relevance of in vitro cell cultures towards in vivo physiology.

Novel possibility for cutaneous melanoma treatment by means of rosmarinic acid action on purinergic signaling

Cancer cases have increased significantly in Brazil and worldwide, with cutaneous melanoma (CM) being responsible for nearly 57,000 deaths in the world. Thus, this review article aims at exploring and proposed hypotheses with respect to the possibility that RA can be a promising and alternative compound to be used as an adjuvant in melanoma treatment, acting on purinergic signaling. The scarcity of articles evidencing the action of this compound in this signaling pathway requires further studies. Considering diverse evidence found in the literature, we hypothesize that RA can be an effective candidate for the treatment of CM acting as a modulating molecule of purinergic cellular pathway through P2X7 blocking, mitigating the Warburg effect, and as antagonic molecule of the P2Y12 receptor, reducing the formation of adhesive molecules that prevent adherence in tumor cells. In this way, our proposals for CM treatment based on targeting purinergic signaling permeate the integral practice, going from intracell to extracell. Undoubtedly, much is still to be discovered and elucidated about this promising compound, this paper being an interesting work baseline to support more research studies.

EFNA3 Is a Prognostic Biomarker Correlated With Immune Cell Infiltration and Immune Checkpoints in Gastric Cancer

Background: Ephrin A3 (EFNA3), like most genes in the ephrin family, plays a central role in embryonic development and can be dysregulated in a variety of tumors. However, the relationship between EFNA3 and gastric cancer (GC) prognosis and tumor-infiltrating lymphocytes remains unclear.

Methods: Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) were used to analyze the expression of EFNA3. Kaplan-Meier plots and GEPIA2 were used to evaluate the relationship between EFNA3 expression and GC prognosis. Univariable survival and multivariate Cox analyses were used to compare various clinical characteristics with survival. LinkedOmics database was used for gene set enrichment analysis (GSEA). TIMER database and CIBERSORT algorithm were used to examine the relationship between EFNA3 expression and immune infiltration in GC and to explore cumulative survival in GC. The relationship between EFNA3 and immune checkpoints was examined using cBioPortal genomics analysis. Finally, EFNA3 expression in GC cells and tissues was assayed using quantitative real-time polymerase chain reaction.

Results: EFNA3 expression differs in a variety of cancers, and EFNA3 expression was higher in GC tissue than normal gastric tissue. GC patients with high expression of EFNA3 had worse overall survival, disease-free survival, and first progression. Multivariate analysis identified EFNA3 as an independent prognostic factor for GC. GSEA identified ribosome, cell cycle, ribosome biogenesis in eukaryotes, and aminoacyl-tRNA biosynthesis pathways as differentially enriched in patients with high EFNA3 expression. B cells, CD8⁺ T cells, CD4⁺ T cells, macrophages, neutrophils, and dendritic cells were significantly negatively correlated with a variety of immune markers. EFNA3 participates in changes in GC immune checkpoint markers in a collinear manner. EFNA3 expression in HGC-27, AGS, MKN45, and NCI-N87 was cell lines higher than that in GES-1, and patients with high expression of EFNA3 had a worse prognosis.

Conclusion: EFNA3 can be used as a prognostic and immune infiltration and checkpoint marker in GC patients.

Culture of Adherent Cancer Cell Lines

Adherent cell lines grow attached to the surface of a cell culture vessel. Due to the adherent nature of the cells, enzymes, such as trypsin, are required to lift the cells from the cell culture vessel for harvesting or subculturing. Many cancer cell lines are adherent, rendering adherent cell culture a critical experimental method in the fields of cell biology, biochemistry, and cancer research. In this chapter, we outline the protocols for culturing and maintaining adherent cells. We detail the procedures for preparing cell culture medium, thawing and reviving frozen adherent cells, subculturing adherent cells, freezing cells, and counting cells. Most notably, we outline the best techniques and practices for optimal growth of healthy adherent cells while diminishing the risk of contamination.

Treating Cells as Reagents to Design Reproducible Assays

The reproducibility of high-throughput cell-based assays is dependent on having a consistent source of cells for each experiment. Developing an understanding of the nature of cells growing in vitro and factors that influence their responsiveness to test compounds will contribute to the development of reproducible cell-based assays. Using good cell culture practices and establishing standard operating procedures (SOPs) for handling cultures can eliminate several potential contributors to variability in the responsiveness and performance of cells. The SOPs for handling each cell type must have clear and detailed instructions that can be understood and followed among different laboratories. The SOPs should include documenting the source of cells and authenticating their identity, both of which have become required to achieve peer acceptance of experimental data. Variability caused by biological issues such as phenotypic drift can be reduced by using standardized subculture procedures or using cryopreserved cells to set up experiments. Variability caused by inconsistent dispensing of cells per well and edge effects can be identified by measuring how many cells are present and whether they are alive or dead. Multiplex methods for real-time measurement of viable or dead cell number in each sample can be used for normalizing data and determining if proliferation or cytotoxicity has occurred during the experiment. Following good cell culture practices will go a long way toward executing reproducible cell-based assays. Resources will be included describing good cell culture practices, cell line authentication, and multiplex determination of cell number as an internal control.

E2F2 inhibition induces autophagy via the PI3K/Akt/mTOR pathway in gastric cancer

Background: E2F2 is a member of the E2F transcription factor family and has important but not fully understood biological functions in cancers. The biological role of E2F2 in gastric cancer (GC) also remains unclear.

Methods: We examined the expression levels of E2F2 in GC using publicly available datasets such as TIMER, Oncomine, GEPIA, UALCAN, etc., and in our patient cohort, using quantitative real-time PCR, western blotting, and immunohistochemistry. We further investigated the effects of E2F2 on phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) signaling, autophagy, and the migration and invasion of GC cells by the wound healing assay, Transwell assay and transmission electron microscopy.

Results: E2F2 was highly expressed in both GC tissues and cells compared with normal gastric tissues/cells. High E2F2 expression was associated with poor overall survival (OS). In addition, the expression of E2F2 in GC was strongly correlated with a variety of immune markers. E2F2 overexpression promoted the migration and invasiveness of GC cells in vitro through inhibition of PI3K/Akt/mTOR-mediated autophagy.

Conclusion: High E2F2 expression was associated with the characteristics of invasive tumors and poor prognosis. E2F2 also had potential modulatory effects on tumor immunity. We discovered a novel function of E2F2 in the regulation of PI3K/Akt/mTOR-mediated autophagy and the downstream processes of cell migration and invasion.

5-Fluorouracil enhances the chemosensitivity of gastric cancer to TRAIL via inhibition of the MAPK pathway

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has the ability to selectively trigger cancer cell apoptosis and can be used as a target for tumor therapy. However, gastric cancer cells are usually insensitive to TRAIL so reducing this drug resistance may improve the treatment of gastric cancer. In this study, we used Cell Counting Kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) experiments to determine the effects of 5-fluorouracil (5-FU) and TRAIL on the proliferation of gastric cancer cells. An Annexin V/propidium iodide (PI) staining experiment was used to detect apoptosis, and Western blotting was used to analyze the expression levels of apoptosis-related proteins and mitogen-activated protein kinase (MAPK) pathway proteins. The antitumor effects of 5-FU and TRAIL were verified in vivo using a nude mouse tumorigenesis experiment, and a TUNEL assay was performed to evaluate apoptosis in tumor tissue from the nude mice. We found the combination of 5-FU and TRAIL had a greater inhibitory effect on the proliferation of gastric cancer cells than 5-FU or TRAIL alone both in vivo and in vitro. 5-FU enhanced TRAIL-induced gastric cancer cell apoptosis by inactivating the MAPK pathway. Overall, our analysis firstly provided new insights into the role of 5-FU in increasing sensitivity to TRAIL. 5-FU can be used as a sensitizer for TRAIL, and its administration is a potential strategy for the treatment of gastric cancer.

Expression profile analysis of a new testis-specifically expressed gene C17ORF64 and its association with cell apoptosis in MCF-7 cells

With the increasing incidence of male infertility, identification and investigation the functions of new genes related to spermatogenesis are effective avenues to elucidate the decline of testicular function. In this study, a new gene, C17ORF64 (chromosome 17 open reading frame 64), was identified from mouse testes and its potential function was studied.RT-PCR and qRT-PCR assay showed that C17ORF64 mRNA was expressed exclusively in mouse testes and up-regulated from the 3-week old to 6-month old testes during postpartum development, which is consistent with C17ORF64 protein expression profile by western blotting analysis. Immunohistochemical analysis revealed that C17ORF64 protein was mainly localized in the cytoplasm of spermatogonia and spermatocytes, which is verified by GFP- labeled C17ORF64 gene expressed in GC-1 cells. C17ORF64 overexpression not only promoted cell apoptosis in MCF-7 cells, but also significantly decreased cell viability via MTT assay. Flow cytometric assay showed that C17ORF64 overexpression could inhibit cell cycle progression by arresting G1/S transition. Western blot and qRT-PCR analysis revealed that C17ORF64 overexpression inhibited the expression of anti-apoptotic protein bcl-2 and increased the expressions of pro-apoptotic protein caspase-3, caspase-8, caspase-9, Bax, P21 and P53. Taken together, our results confirmed C17ORF64 testis-specific expression pattern and, for the first time, demonstrated that C17ORF64 could inhibit cell viability and accelerate apoptosis in MCF-7 cells through caspase-3 regulatory pathways.

In Vitro Differentiation of Tumor-Associated Macrophages from Monocyte Precursors with Modified Melanoma-Conditioned Medium

Tumor-associated macrophages (TAMs) are one of most important components of the tumor microenvironment. Although many assays have been developed to differentiate monocytes into macrophages (Mϕ) for studying the biology of TAMs in vitro, little is known whether the macrophages induced by these approaches can recapitulate the biology of TAMs present in the tumor microenvironment. We have developed a novel assay to differentiate human monocytes into TAMs using modified melanoma-conditioned medium, which is derived from the concentrated tumor cell culture medium. Characterization of these modified melanoma-conditioned medium-induced macrophages (MCMI-Mϕ) by multiple flow cytometry, Luminex, microarray, and immunohistochemistry analyses indicates that MCMI-Mϕ are phenotypically and functionally highly similar to the TAMs present in the tumor microenvironment.

Microfluidic and Microscale Assays to Examine Regenerative Strategies in the Neuro Retina

Bioengineering systems have transformed scientific knowledge of cellular behaviors in the nervous system (NS) and pioneered innovative, regenerative therapies to treat adult neural disorders. Microscale systems with characteristic lengths of single to hundreds of microns have examined the development and specialized behaviors of numerous neuromuscular and neurosensory components of the NS. The visual system is comprised of the eye sensory organ and its connecting pathways to the visual cortex. Significant vision loss arises from dysfunction in the retina, the photosensitive tissue at the eye posterior that achieves phototransduction of light to form images in the brain. Retinal regenerative medicine has embraced microfluidic technologies to manipulate stem-like cells for transplantation therapies, where de/differentiated cells are introduced within adult tissue to replace dysfunctional or damaged neurons. Microfluidic systems coupled with stem cell biology and biomaterials have produced exciting advances to restore vision. The current article reviews contemporary microfluidic technologies and microfluidics-enhanced bioassays, developed to interrogate cellular responses to adult retinal cues. The focus is on applications of microfluidics and microscale assays within mammalian sensory retina, or neuro retina, comprised of five types of retinal neurons (photoreceptors, horizontal, bipolar, amacrine, retinal ganglion) and one neuroglia (Müller), but excludes the non-sensory, retinal pigmented epithelium.

Expression and function of transmembrane 4 superfamily proteins in digestive system cancers

Background

Although the medical level is constantly improving, cancer is still a major disease that threatens human health, and very effective treatments have not been found. In recent years, studies have found that four-transmembrane superfamily proteins are involved in multiple stages of tumorigenesis and development, but their expression and function in tumors have not been systematically studied.

Methods

We used the Oncomine database to analyze the mRNA expression levels of TSPAN family in various cancers. Then differentially expressed genes were screened out and verified by liver cancer, colorectal cancer, and gastric cancer cells by q-PCR and Western blot analysis. CCK8 and EDU analysis are used to detect cell proliferation, Cell wound scrape assay and Cell invasion assay are used to analyze cell invasion and metastasis. Nude tumor formation test used to verify the tumor suppressive effect of TSPAN7 in vivo.

Results

Differential analysis of 33 TSPAN proteins revealed that a total of 11 proteins showed differential expression in 10% of independent analyses, namely TSPAN1, TSPAN3, TSPAN5, TSPAN6, TSPAN7, TSPAN8, TSPAN13, TSPAN25, TSPAN26, TSPAN29, TSPAN30. TSPAN7 is the only four-transmembrane protein with reduced expression in three types of digestive tract tumors, so we chose TSPAN7 to be selected for cellular and molecular level verification. We found that compared with normal cells, the expression of TSPAN7 in liver cancer cells was significantly reduced, while the expression of gastric and colon cancer was not significantly different from that of normal cells. In addition, we also found that the high expression of Tspan7 not only inhibited the proliferation of HCC-LM3 cells, but also inhibited its invasion and metastasis.

Conclusions

Our study evaluated the expression and function of the TSPANs family in digestive cancers and explored TSPAN7 in hepatoma cells in detail. We found some members of the TSPAN family show significant expression differences between cancer and normal tissues, of which TSPAN7 may be a potential biomarker for liver cancer.

Anti-caries effect of resin infiltrant modified by quaternary ammonium monomers

OBJECTIVES

Resin infiltrant is used in early enamel caries. However, commercial resin infiltrant lacks persistent antibacterial activity. Dimethylaminododecyl methacrylate (DMADDM) was added to resin infiltrant to give it sustainable antibacterial properties and inhibit demineralization.

METHODS

After the application of resin infiltrant to bovine enamel, cytotoxicity, surface roughness, and aesthetics were assessed. A multi-species biofilm was incubated on the enamel disk before and one month after microbial-aging. After a 48-h anaerobic incubation, biomass accumulation, metabolic activity, and lactic acid were analyzed using a crystal violet assay, an MTT (3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, and a lactic acid assay. Biofilm structure and composition were determined by live/dead staining, exopolysaccharide (EPS) staining, scanning electron microscopy (SEM), and quantitative polymerase chain reaction (qPCR). The depth and content of demineralization were tested by transverse microradiography (TMR).

RESULTS

Incorporating DMADDM did not increase the cytotoxicity or change the physical properties when the mass fraction of the DMADDM was 2.5-10 %. The modification decreased the amount of bacterial biofilm, metabolic activity, lactic acid production, EPS, and the proportion of Streptococcus mutans in the biofilms. It also provided anti-demineralization effects. The surface roughness and antibacterial ability were not changed after one month of microbial-aging.

CONCLUSION

The incorporation of DMADDM improved the antibacterial and anti-demineralization effects of the material. It demonstrated a sustained antibacterial effect.

CLINICAL SIGNIFICANCE

The antibacterial modification might be a potential choice for future clinical applications to inhibit early enamel caries.

HuH-7 reference genome profile: complex karyotype composed of massive loss of heterozygosity

Human cell lines represent a valuable resource as in vitro experimental models. A hepatoma cell line, HuH-7 (JCRB0403), has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. However, an accurate genome profile, which can be served as a reliable reference, has not been available. In this study, we performed M-FISH, SNP microarray and amplicon sequencing to characterize the cell line. Single cell analysis of metaphases revealed a high level of heterogeneity with a mode of 60 chromosomes. Cytogenetic results demonstrated chromosome abnormalities involving every chromosome in addition to a massive loss of heterozygosity, which accounts for 55.3% of the genome, consistent with the homozygous variants seen in the sequence analysis. We provide empirical data that the HuH-7 cell line is composed of highly heterogeneous cell populations, suggesting that besides cell line authentication, the quality of cell lines needs to be taken into consideration in the future use of tumor cell lines.

Screening for 15 pathogenic viruses in human cell lines registered at the JCRB Cell Bank: characterization of in vitro human cells by viral infection

Human cell lines have been used in a variety of research fields as an in vitro model. These cells are all derived from human tissue samples, thus there is a possibility of virus infection. Virus tests are routinely performed in clinical practice, but are limited in cell lines. In this study, we investigated 15 kinds of viruses in 844 human cell lines registered at the Japanese Collection of Research Bioresources (JCRB) Cell Bank. Our real-time PCR analysis revealed that six viruses, EBV, HTLV-1, HBV, B19V, HHV-6 and HHV-7, were detected in 43 cell lines. Of them, 20 cell lines were transformed by intentional infection in vitro with EBV or HTLV-1. Viruses in the other 23 cell lines and one EBV transformed cell line are derived from an in vivo infection, including five de novo identifications of EBV, B19V or HHV-7 carriers. Among them, 17 cell lines were established from patients diagnosed with virus-associated diseases. However, the other seven cell lines originated from in vivo cells unrelated to disease or cellular tropism. Our approach to screen for a set of 15 viruses in each cell line has worked efficiently to identify these rare cases. Virus tests in cell lines contribute not only to safety assessments but also to investigation of in vivo viral infection which can be a characteristic feature of cell lines.

Best practices for authenticating cell lines

Experiments using cell cultures are only valid to the extent that the cell culture is a true model system for the biological system being investigated. To assure that a cell line is and remains an appropriate biological model, its identity, purity, ploidy, and phenotype must be maintained. These characteristics comprise and determine the authenticity of a cell line. Routine monitoring of the cell line through microscopic examination of morphology can help to determine authenticity, as can the determination of phenotypic status. Assays designed to confirm cell identity and ploidy and freedom from cross-contaminating cell types may need to be performed at certain times, as such information may not be obtained through morphologic and phenotypic examinations alone. The best practices associated with establishing cell line authenticity are described in this article.

Best practices for the use and evaluation of animal serum as a component of cell culture medium

Animal serum is a common additive for cell culture medium and is often required at 5 to 10% (v/v) for the attachment and growth of primary and continuous anchorage-dependent (monolayer) cultures. The use of animal serum in cell culture medium confers several advantages and also some risks. This article discusses the use of animal serum as a component of cell culture medium. The best practices associated with the sourcing, storage, thawing, testing, and mitigation of risk associated with the use of animal sera are among the topics described in this article.