A Combination of Species Identification and STR Profiling Identifies Cross-contaminated Cells from 482 Human Tumor Cell Lines

Misspellings or "miscellings"-Non-verifiable and unknown cell lines in cancer research publications

Reproducible laboratory research relies on correctly identified reagents. We have previously described gene research papers with wrongly identified nucleotide sequence(s), including papers studying miR-145. Manually verifying reagent identities in 36 recent miR-145 papers found that 56% and 17% of papers described misidentified nucleotide sequences and cell lines, respectively. We also found 5 cell line identifiers in miR-145 papers with misidentified nucleotide sequences and cell lines, and 18 cell line identifiers published elsewhere, that did not represent indexed human cell lines. These 23 identifiers were described as non-verifiable (NV), as their identities were unclear. Studying 420 papers that mentioned 8 NV identifier(s) found 235 papers (56%) that referred to 7 identifiers (BGC-803, BSG-803, BSG-823, GSE-1, HGC-7901, HGC-803, and MGC-823) as independent cell lines. We could not find any publications describing how these cell lines were established. Six cell lines were sourced from cell line repositories with externally accessible online catalogs, but these cell lines were not indexed as claimed. Some papers also stated that short tandem repeat (STR) profiles had been generated for three cell lines, yet no STR profiles could be identified. In summary, as NV cell lines represent new challenges to research integrity and reproducibility, further investigations are required to clarify their status and identities.

Current status of in vitro models for rare gynaecological cancer research

Gynaecological cancers originate within the female reproductive system and are classified according to the site in the reproductive system where they arise. However, over 50 % of these malignancies are categorized as rare, encompassing 30 distinct histological subtypes, which complicates their diagnosis and treatment. The focus of this review is to give an overview of established in vitro models for the investigation of rare gynaecological cancers, as well as an overview of available online databases that contain detailed descriptions of cell line characteristics. Cell lines represent the main models for the research of carcinogenesis, drug resistance, pharmacodynamics and novel therapy treatment options. Nowadays, classic 2D cell models are increasingly being replaced with 3D cell models, such as spheroids, organoids, and tumoroids because they provide a more accurate representation of numerous tumour characteristics, and their response to therapy differs from the response of adherent cell lines. It is crucial to use the correct cell line model, as rare tumour types can show characteristics that differ from the most common tumour types and can therefore respond unexpectedly to classic treatment. Additionally, some cell lines have been misclassified or misidentified, which could lead to false results. Even though rare gynaecological cancers are rare, this review will demonstrate that there are available options for investigation of such cancers in vitro on biologically relevant models.

Activation of the FOXM1/ASF1B/PRDX3 axis confers hyperproliferative and antioxidative stress reactivity to gastric cancer

Nucleosome assembly during DNA replication is dependent on histone chaperones. Recent studies suggest that dysregulated histone chaperones contribute to cancer progression, including gastric cancer (GC). Further studies are required to explore the prognostic and therapeutic implications of histone chaperones and their mechanisms of action in GC progression. Here we identified histone chaperone ASF1B as a potential biomarker for GC proliferation and prognosis. ASF1B was significantly upregulated in GC, which was associated with poor prognosis. In vitro and in vivo experiments demonstrated that the inhibition of ASF1B suppressed the malignant characteristics of GC, while overexpression of ASF1B had the opposite effect. Mechanistically, transcription factor FOXM1 directly bound to the ASF1B-promoter region, thereby regulating its transcription. Treatment with thiostrepton, a FOXM1 inhibitor, not only suppressed ASF1B expression, but also inhibited GC progression. Furthermore, ASF1B regulated the mitochondrial protein peroxiredoxin 3 (PRDX3) transcription in a FOXM1-dependent manner. The crucial role of ASF1B-regulated PRDX3 in GC cell proliferation and oxidative stress balance was also elucidated. In summary, our study suggests that the FOXM1-ASF1B-PRDX3 axis is a potential therapeutic target for treating GC.

Mechanism of pachymic acid in the treatment of gastric cancer based on network pharmacology and experimental verification

BACKGROUND

Pachymic acid (PA) is derived from Poria cocos. PA has a variety of pharmacological and inhibitory effects on various tumors. However, the mechanism of action of PA in gastric cancer (GC) remains unclear.

AIM

To investigate the mechanism of PA in treating GC via the combination of network pharmacology and experimental verification.

METHODS

The GeneCards and OMIM databases were used to derive the GC targets, while the Pharm Mapper database provided the PA targets. Utilizing the STRING database, a protein-protein interaction network was constructed and core targets were screened. The analyses of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis were conducted, and molecular docking and clinical correlation analyses were performed on the core targets. Ultimately, the network pharmacology findings were validated through in vitro cell assays, encompassing assessments of cell viability, apoptosis, cell cycle, cloning, and western blot analysis.

RESULTS

According to network pharmacology analysis, the core targets were screened, and the PI3K/AKT signaling pathway is likely to be the mechanism by which PA effectively treats GC, according to KEGG enrichment analysis. The experimental findings showed that PA could control PI3K/AKT signaling to prevent GC cell proliferation, induce apoptosis, and pause the cell cycle.

CONCLUSION

Network pharmacology demonstrated that PA could treat GC by controlling a variety of signaling pathways and acting on a variety of targets. This has also been supported by in vitro cell studies, which serve as benchmarks for further research.

Multiple approaches revealed MGc80-3 as a somatic hybrid with HeLa cells rather than a gastric cancer cell line

The short-tandem-repeats (STR) profiles of MGc80-3 and HeLa partially overlap, raising suspicion of contamination in the MGc80-3 cell line. However, there has not been any relevant study demonstrating whether MGc80-3 was fully replaced by HeLa cells, just mixed with HeLa cells (co-existing), or was a somatic hybrid with HeLa cells. In addition to STR profiling, various approaches, including single nucleotide polymorphisms genotyping, polymerase chain reaction, screening for human papillomaviruses type 18 (HPV-18) fragment, chromosome karyotyping, pathological examination of xenografts, tissue-specific-90-gene expression signature and high-throughput RNA sequencing were used to determine the nature of MGc80-3. Our study found that the abnormal STR profile, partially overlapping with that of HeLa cells (64.62% to 71.64%), could not verify MGc80-3 as a HeLa cell line. However, the STR 13.3 repeat allele in the D13S317 locus that seemed to be unique to HeLa cells was detected in MGc80-3. Almost all the MGc80-3 cells exhibited HPV-18 fragments in the genome as well as certain HeLa marker chromosomes, such as M7 and M12. The molecular assay of the 90-gene expression signature still considered MGc80-3 as a stomach cancer using an algorithmic analysis. The expression pattern of multiple genes in MGc80-3 was quite different from that in HeLa cells, which showed that certain characteristics belonged to gastric cancer cell lines. High throughput RNA sequencing showed the distinct patterns of gene expression in MGc80-3. In conclusion, MGc80-3 cell line is a somatic hybrid with HeLa cells rather than a pure gastric cancer cell line.

Heterogeneous Cellular Response of Primary and Metastatic Human Gastric Adenocarcinoma Cell Lines to Magnoflorine and Its Additive Interaction with Docetaxel

Gastric cancer is the most common cancer and remains the leading cause of cancer death worldwide. In this study, the anticancer action of magnoflorine isolated via counter-current chromatography from the methanolic extract of Berberis vulgaris root against gastric cancer in models of primary ACC-201 and AGS and metastatic MKN-74 and NCI-N87 cell lines was analyzed. Cell viability and proliferation were tested through the use of MTT and BrdU tests, respectively. Cell cycle progression and apoptosis were evaluated using flow cytometry. The interaction of magnoflorine and docetaxel has been examined through isobolographic analysis. Moreover, potential toxicity was verified in zebrafish in an in vivo model. Gastric cancer cell lines revealed different responses to magnoflorine treatment with regard to viability/proliferation, apoptosis induction and cell cycle inhibition without any undesirable changes in the development of larval zebrafish at the tested concentrations. What is more, magnoflorine in combination with docetaxel produced an additive pharmacological interaction in all studied gastric cancer cell lines, which may suggest a complementary mechanism of action of both compounds. Taken together, these findings provide a foundation for the possibility of magnoflorine as a potential therapeutic approach for gastric cancer and merits further investigation, which may pave the way for clinical uses of magnoflorine.

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.

Retraction Note: CircPSMC3 suppresses the proliferation and metastasis of gastric cancer by acting as a competitive endogenous RNA through sponging miR-296-5p

This article has been retracted. Please see the Retraction Notice for more detail: https://doi.org/10.1186/s12943-019-0958-6.

Establishment and characterization of a new Chinese hepatocellular carcinoma cell line, Hep-X1

Hepatocellular carcinoma (HCC) is a highly aggressive and heterogeneous disease. Cell lines are commonly employed as in vitro models for cell type studies. However, the success rate of HCC primary culture establishment is low. In this study, we successfully established a liver cancer cell line, Hep-X1. Primary culture and passage of surgically removed tissues were used to establish hepatoma cell lines. Morphological examination, short tandem repeat (STR) analysis, immunohistochemical staining, doubling time, karyotype analysis, plate tumor formation experiments, organoid culture, and in vivo tumor formation investigations in animals were used to identify the cell lines. A novel liver cancer cell line, Hep-X1, was established based on morphology, immunophenotype, cytogenetics, and STR analysis. The novel cell line can be a valuable model for studying primary liver cancer.

Cytotoxic Labdane Diterpenes, Norlabdane Diterpenes and Bis-Labdanic Diterpenes from the Zingiberaceae: A Systematic Review

Over the years, labdane diterpenes, norlabdane diterpenes, and bis-labdanic diterpenes with cytotoxic activities have been identified across various families in the plant kingdom including the Zingiberaceae. The present review discusses the distribution of these labdane-type diterpenes within the Zingiberaceae; their extraction, isolation, and characterization from the respective Zingiberaceae species; the structural similarities and differences within each group and between the different groups of the labdane-type diterpenes; and their cytotoxic activities against breast, cervical, liver, colorectal, pancreatic, lung and prostate cancer cell lines. The review will also provide insight into how the cytotoxic activities of the labdane-type diterpenes are influenced by their structural features.

Circular RNAs in Epithelial Ovarian Cancer: From Biomarkers to Therapeutic Targets

Epithelial ovarian cancer (EOC) is the most lethal gynecological cancer, and more than 70% of patients are diagnosed at advanced stages. Despite the application of surgery and chemotherapy, the prognosis remains poor due to the high relapse rate. It is urgent to identify novel biomarkers and develop novel therapeutic strategies for EOC. Circular RNAs (circRNAs) are a class of noncoding RNAs generated from the "back-splicing" of precursor mRNA. CircRNAs exert their functions via several mechanisms, including acting as miRNA sponges, interacting with proteins, regulating transcription, and encoding functional proteins. Recent studies have identified many circRNAs that are dysregulated in EOC and may be used as diagnostic and prognostic markers. Increasing evidence has revealed that circRNAs play a critical role in ovarian cancer progression by regulating various cellular processes, including proliferation, apoptosis, metastasis, and chemosensitivity. The circRNA-based therapy may be a novel strategy that is worth exploring in the future. Here, we provide an overview of EOC and circRNA biogenesis and functions. We then discuss the dysregulations of circRNAs in EOC and the possibility of using them as diagnostic/prognostic markers. We also summarize the role of circRNAs in regulating ovarian cancer development and speculate their potential as therapeutic targets.

Established Liver Cell Lines: Are You Sure to Have the Right Ones?

In liver research, immortalized cell lines have assumed an important role in studying general physiological and pathological processes. However, misidentification and cross-contamination of cell lines is a widespread problem in biomedical sciences resulting in irreproducible results and false conclusions. Although the huge impact of working with wrong cell lines on life science research and publication has been well recognized, there are only limited efforts and strategies to prevent cell misidentification. This commentary provides a catalogue of the most important cell lines used in hepatology research, examples of misidentified cell lines, and short guidelines to be considered when working with continuous lines.

Prospecting Cellular Gold Nanoparticle Biomineralization as a Viable Alternative to Prefabricated Gold Nanoparticles

Gold nanoparticles (GNPs) have shown considerable potential in a vast number of biomedical applications. However, currently there are no clinically approved injectable GNP formulations. Conversely, gold salts have been used in the clinic for nearly a century. Further, there is evidence of GNP formation in patients treated with gold salts (i.e., chrysiasis). Recent reports evaluating this phenomenon in human cells and in murine models indicate that the use of gold ions for in situ formation of theranostic GNPs could greatly improve the delivery within dense biological tissues, increase efficiency of intracellular gold uptake, and specificity of GNP formation within cancer cells. These attributes in combination with safe clinical application of gold salts make this process a viable strategy for clinical translation. Here, the first summary of the current knowledge related to GNP biomineralization in mammalian cells is provided along with critical assessment of potential biomedical applications of this newly emergent field.

Cell line authentication: a necessity for reproducible biomedical research

Immortalized or continuous cell lines are invaluable tools in basic and preclinical research. However, the widespread use of misidentified cell lines is a serious threat to scientific reproducibility. Based on the experiences of mandatory cell line authentication at the International Journal of Cancer (IJC), we provide an overview of the issues pertinent to misidentified cell lines and discuss available solutions. We also summarize the lessons learned, revealing that at least 5% of the human cell lines used in manuscripts considered for peer review are misidentified. About 4% of the considered manuscripts are rejected for severe cell line problems, and most are subsequently published in other journals. In order to diminish such malpractice and its consequences for the scientific record, we postulate that strict multi-layered quality control is essential. Besides journals and publishers, we encourage scientists, research institutions, and funders to take action on the matter and revise their respective policies. Hence, we provide concrete recommendations on introducing regular authentication schemes and staff training, and discuss future steps for enhancing good cell culture practices.

Automatic Cancer Cell Taxonomy Using an Ensemble of Deep Neural Networks

Microscopic image-based analysis has been intensively performed for pathological studies and diagnosis of diseases. However, mis-authentication of cell lines due to misjudgments by pathologists has been recognized as a serious problem. To address this problem, we propose a deep-learning-based approach for the automatic taxonomy of cancer cell types. A total of 889 bright-field microscopic images of four cancer cell lines were acquired using a benchtop microscope. Individual cells were further segmented and augmented to increase the image dataset. Afterward, deep transfer learning was adopted to accelerate the classification of cancer types. Experiments revealed that the deep-learning-based methods outperformed traditional machine-learning-based methods. Moreover, the Wilcoxon signed-rank test showed that deep ensemble approaches outperformed individual deep-learning-based models (p < 0.001) and were in effect to achieve the classification accuracy up to 97.735%. Additional investigation with the Wilcoxon signed-rank test was conducted to consider various network design choices, such as the type of optimizer, type of learning rate scheduler, degree of fine-tuning, and use of data augmentation. Finally, it was found that the using data augmentation and updating all the weights of a network during fine-tuning improve the overall performance of individual convolutional neural network models.

Inflammasome-Associated Gastric Tumorigenesis Is Independent of the NLRP3 Pattern Recognition Receptor

Inflammasomes are important multiprotein regulatory complexes of innate immunity and have recently emerged as playing divergent roles in numerous inflammation-associated cancers. Among these include gastric cancer (GC), the third leading cause of cancer-associated death worldwide, and we have previously discovered a pro-tumorigenic role for the key inflammasome adaptor apoptosis-associated speck-like protein containing a CARD (ASC) in the spontaneous genetic gp130^F/F mouse model for GC. However, the identity of the specific pattern recognition receptors (PRRs) that activate tumor-promoting inflammasomes during GC is unknown. Here, we investigated the role of the best-characterized inflammasome-associated PRR, nucleotide-binding domain, and leucine-rich repeat containing receptor, pyrin domain-containing (NLRP) 3, in GC. In gastric tumors of gp130^F/F mice, although NLRP3 expression was elevated at the mRNA (qPCR) and protein (immunohistochemistry) levels, genetic ablation of NLRP3 in gp130^F/F:Nlrp3^-/- mice did not alleviate the development of gastric tumors. Similarly, cellular processes associated with tumorigenesis in the gastric mucosa, namely, proliferation, apoptosis, and inflammation, were comparable between gp130^F/F and gp130^F/F:Nlrp3^-/- mice. Furthermore, inflammasome activation levels, determined by immunoblotting and immunohistochemistry for cleaved Caspase-1, which along with ASC is another integral component of inflammasome complexes, were unchanged in gp130^F/F and gp130^F/F:Nlrp3^-/- gastric tumors. We also observed variable NLRP3 expression levels (mRNA and protein) among independent GC patient cohorts, and NLRP3 was not prognostic for survival outcomes. Taken together, these data suggest that NLRP3 does not play a major role in promoting inflammasome-driven gastric tumorigenesis, and thus pave the way for further investigations to uncover the key inflammasome-associated PRR implicated in GC.

Development and Evaluation of a TaqMan Real-Time PCR Assay for the Rapid Detection of Cross-Contamination of RD (Human) and L20B (Mouse) Cell Lines Used in Poliovirus Surveillance

BACKGROUND

The cross-contamination of cell lines in culture is a persistent problem. Genetically modified L20B (Mouse) and RD (Human Rhabdomyosarcoma) cell lines are commonly used in poliovirus research, surveillance, and diagnostics. Cross-contamination between these cell lines leads to unreproducible results and unreliable surveillance data, negatively affecting public health. The gold standard method for cell authentication is Short Tandem Repeats analysis, which is time-consuming and expensive. The disadvantage of STR is limited detection of interspecies contamination.

METHODS

This assay targets the mitochondrial cytochrome c oxidase subunit I (MTCO1) gene, a highly conserved and emergent DNA barcode region for detection of cross-contamination in RD and L20B cell lines. The MagNA Pure Compact instrument and ABI 7500 Fast Dx Real-time PCR systems were used for DNA extraction and to perform real-time PCR respectively.

RESULTS

The newly developed assay is very sensitive with a limit of detection of 100 RD cells/1 million L20B/mL. The amplification efficiency and R2-value were 102.26% and 0.9969 respectively. We evaluated specificity of the assay with five human and four mouse cell lines, as well as monkey and rat cell lines. The assay showed no cross-reactivity with genomic DNA from human, mouse, rat, or monkey cell lines. The analytical sensitivity was also evaluated by spiking varying amounts of RD cells (0.001% - 10%) into L20B cells. There was no difference in CT values when running single-plex or duplex PCR reactions with similar experimental conditions.

CONCLUSIONS

We have developed and validated a TaqMan real-time PCR assay, a sensitive method for the detection of cross-contamination of RD and L20B cell lines.

When AIE meets enzymes

Applications of AIEgens in biosensing, disease diagnosis, and drug release.

Pancreatic Tumor Microenvironment Factor Promotes Cancer Stemness via SPP1-CD44 Axis

BACKGROUND & AIMS

Tumor-microenvironment factors and cancer stem cells (CSCs) play a critical role in the aggressiveness of pancreatic cancer (PC). However, the degree to which tumor-microenvironment factors promote stemness remains unexplored. Here, we examined whether cancer-associated fibroblasts (CAFs) promote CSC features in PC.

METHODS

PC cells were treated long-term (30, 60, and 90 days) with conditioned media (CM)-derived from normal human fibroblasts (NFs) and CAFs. The stemness features of tumorsphere formation and stemness populations, along with CSCs markers, were analyzed using 2-dimensional and 3-dimensional sodium alginate bead-based co-culture models. Immunohistochemistry and immunofluorescence staining were performed for CSCs and fibroblast markers in autochthonous KrasG12D/+; Trp53R172H/+; Pdx1-Cre mice and human pancreatic tumors. Polymerase chain reaction array and gene knockdown were performed to identify the mechanism of stemness enrichment.

RESULTS

Long-term treatment of PC cells with CAF-CM enriched stemness, as indicated by significantly higher CD44+, ALDH+, and AF+ populations in PC cells. Increased tumorsphere formation and elevated CSC, self-renewal, and drug-resistance markers in CAF-CM-treated PC cells were observed. In addition, CAFs co-cultured with PC cells in the 3-dimensional model showed a substantial increase in stemness features. CD44 and α-smooth muscle actin were positively correlated and their expressions progressively increased from the early to late stages of KrasG12D/+; Trp53R172H/+; Pdx1-Cre mouse and human pancreatic tumors. Osteopontin/secreted phosphoprotein 1 was identified as the top differentially overexpressed gene in CAF-CM-treated PC cells and knockdown of osteopontin/secreted phosphoprotein 1 significantly reduced stemness characteristics in CAF-CM-treated PC cells.

CONCLUSIONS

Our data uncovered novel insight into the interplay between CAF and enrichment of stemness population through the osteopontin/secreted phosphoprotein 1-CD44 axis in PC.

Cell Coding Arrays Based on Fluorescent Glycan Nanoparticles for Cell Line Identification and Cell Contamination Evaluation

Cell lines are applied on a large scale in the field of biomedicine, but they are susceptible to issues such as misidentification and cross-contamination. This situation is becoming worse over time due to the rapid growth of the biomedical field, and thus there is an urgent need for a more effective strategy to address the problem. As described herein, a cell coding method is established based on two types of uniform and stable glycan nanoparticles that are synthesized using the graft-copolymerization-induced self-assembly (GISA) method, which further exhibit distinct fluorescent properties due to elaborate modification with fluorescent labeling molecules. The different affinity between each nanoparticle and various cell lines results in clearly distinguishable differences in their endocytosis degrees, thus resulting in distinct characteristic fluorescence intensities. Through flow cytometry measurements, the specific signals of each cell sample can be recorded and turned into a map divided into different regions by statistical processing. Using this sensing array strategy, we have successfully identified six human cell lines, including one normal type and five tumor types. Moreover, cell contamination evaluation of different cell lines with HeLa cells as the contaminant in a semiquantitative analysis has also been successfully achieved. Notably, the whole process of nanoparticle fabrication and fluorescent testing is facile and the results are highly reliable.

A silver lining in cell line authentication: Short tandem repeat analysis of 1373 cases in China from 2010 to 2019

Continuous cell lines are practical models that are widely used in the study of disease mechanisms and particularly cancers. However, the issue of cell line cross-contamination has existed since the 1960s, despite repeated advocation for cell line authentication by many experts. Furthermore, cell line abuse has been underestimated and underreported. The China Center for Type Culture Collection (CCTCC) received 1373 cell samples for authentication from 2010 to 2019, and has found that the quality of cell lines has improved during this time, offering a positive outlook for the future.

Orexins/Hypocretins and Cancer: A Neuropeptide as Emerging Target

Over 20 years ago, orexin neuropeptides (Orexin-A/hypocretin-1 and Orexin-B/hypocretins-2) produced from the same precursor in hypothalamus were identified. These two neurotransmitters and their receptors (OX1R and OX1R), present in the central and peripheral nervous system, play a major role in wakefulness but also in drug addiction, food consumption, homeostasis, hormone secretion, reproductive function, lipolysis and blood pressure regulation. With respect to these biological functions, orexins were involved in various pathologies encompassing narcolepsy, neurodegenerative diseases, chronic inflammations, metabolic syndrome and cancers. The expression of OX1R in various cancers including colon, pancreas and prostate cancers associated with its ability to induce a proapoptotic activity in tumor cells, suggested that the orexins/OX1R system could have a promising therapeutic role. The present review summarizes the relationship between cancers and orexins/OX1R system as an emerging target.

Establishment and characterization of a new human colon cancer cell line, PUMC-CRC1

Colorectal cancer (CRC) is one of the most common and fatal gastrointestinal cancers worldwide. Considering their diversity, the establishment of new continuous CRC cell lines with clear genetic backgrounds will provide useful tools for exploring molecular mechanisms, screening and evaluating antitumor drugs in CRC studies. Our de novo CRC cell line, PUMC-CRC1 (Peking Union Medical College Colorectal Cancer 1) was derived from a 47-year-old Chinese female patient diagnosed with moderately to poorly differentiated colon adenocarcinoma. Multiple experiments were used for full characterization. The new cell line was epithelial-like and was passaged for more than 40 times, with a population doubling time of 44 h in vitro, detected by cell counts. The cells exhibited complicated chromosomal abnormalities. The tumor formation rate in SCID mice was 100%. The xenograft tumor was adenocarcinoma with poor to moderate differentiation by Haematoxylin and Eosin staining (H&E) sections. Immunohistochemistry (IHC) analysis and next-generation sequencing (NGS) revealed microsatellite stable (MSS), APC (p.T1493fs) inactivation, KRAS (p.G12V) activation, and SMAD4 (p.V506A) mutation. Quality control of the cell line proved mycoplasma negative and identical STR profile with that of the original tissue, and no interspecific or intraspecific cross contamination was detected. In conclusion, PUMC-CRC1 was a newly established and well characterized human colon cancer cell line, which might be a good model for both in vitro and in vivo studies of the mechanism of colon cancer progression and the treatment strategies for MSS CRC.

Marine Anthraquinones: Pharmacological and Toxicological Issues

The marine ecosystem, populated by a myriad of animals, plants, and microorganisms, is an inexhaustible reservoir of pharmacologically active molecules. Among the multiple secondary metabolites produced by marine sources, there are anthraquinones and their derivatives. Besides being mainly known to be produced by terrestrial species, even marine organisms and the uncountable kingdom of marine microorganisms biosynthesize anthraquinones. Anthraquinones possess many different biological activities, including a remarkable antitumor activity. However, due to their peculiar chemical structures, anthraquinones are often associated with toxicological issues, even relevant, such as genotoxicity and mutagenicity. The aim of this review is to critically describe the anticancer potential of anthraquinones derived from marine sources and their genotoxic and mutagenic potential. Marine-derived anthraquinones show a promising anticancer potential, although clinical studies are missing. Additionally, an in-depth investigation of their toxicological profile is needed before advocating anthraquinones as a therapeutic armamentarium in the oncological area.

Role of the long non-coding RNA LINC00052 in tumors

Long intergenic non-protein coding RNA 52 (LINC00052) is a non-coding RNA with >200 nucleotides in length, which exerts important effects on several physiological and pathological processes of the human body. Recent studies have demonstrated that LINC00052 plays key roles in the tumorigenesis, progression and metastasis of multiple types of human cancer, including hepatocellular carcinoma, breast cancer, colorectal cancer, cervical carcinoma and gastric cancer. However, the associations between LINC00052 and these tumors remain unclear. The present review summarizes the biological functions of LINC00052 during the pathogenic process of certain tumors, and discusses its potential therapeutic targets.

P2Y receptors for extracellular nucleotides: Contributions to cancer progression and therapeutic implications

Purinergic receptors for extracellular nucleotides and nucleosides contribute to a vast array of cellular and tissue functions, including cell proliferation, intracellular and transmembrane ion flux, immunomodulation and thrombosis. In mammals, the purinergic receptor system is composed of G protein-coupled P1 receptors A₁, A_2A, A_2B and A₃ for extracellular adenosine, P2X1-7 receptors that are ATP-gated ion channels and G protein-coupled P2Y_{1,2,4,6,11,12,13 and 14} receptors for extracellular ATP, ADP, UTP, UDP and/or UDP-glucose. Recent studies have implicated specific P2Y receptor subtypes in numerous oncogenic processes, including cancer tumorigenesis, metastasis and chemotherapeutic drug resistance, where G protein-mediated signaling cascades modulate intracellular ion concentrations and activate downstream protein kinases, Src family kinases as well as numerous mitogen-activated protein kinases. We are honored to contribute to this special issue dedicated to the founder of the field of purinergic signaling, Dr. Geoffrey Burnstock, by reviewing the diverse roles of P2Y receptors in the initiation, progression and metastasis of specific cancers with an emphasis on pharmacological and genetic strategies employed to delineate cell-specific and P2Y receptor subtype-specific responses that have been investigated using in vitro and in vivo cancer models. We further highlight bioinformatic and empirical evidence on P2Y receptor expression in human clinical specimens and cover clinical perspectives where P2Y receptor-targeting interventions may have therapeutic relevance to cancer treatment.

Towards image-based cancer cell lines authentication using deep neural networks

Although short tandem repeat (STR) analysis is available as a reliable method for the determination of the genetic origin of cell lines, the occurrence of misauthenticated cell lines remains an important issue. Reasons include the cost, effort and time associated with STR analysis. Moreover, there are currently no methods for the discrimination between isogenic cell lines (cell lines of the same genetic origin, e.g. different cell lines derived from the same organism, clonal sublines, sublines adapted to grow under certain conditions). Hence, additional complementary, ideally low-cost and low-effort methods are required that enable (1) the monitoring of cell line identity as part of the daily laboratory routine and 2) the authentication of isogenic cell lines. In this research, we automate the process of cell line identification by image-based analysis using deep convolutional neural networks. Two different convolutional neural networks models (MobileNet and InceptionResNet V2) were trained to automatically identify four parental cancer cell line (COLO 704, EFO-21, EFO-27 and UKF-NB-3) and their sublines adapted to the anti-cancer drugs cisplatin (COLO-704rCDDP1000, EFO-21rCDDP2000, EFO-27rCDDP2000) or oxaliplatin (UKF-NB-3rOXALI2000), hence resulting in an eight-class problem. Our best performing model, InceptionResNet V2, achieved an average of 0.91 F1-score on tenfold cross validation with an average area under the curve (AUC) of 0.95, for the 8-class problem. Our best model also achieved an average F1-score of 0.94 and 0.96 on the authentication through a classification process of the four parental cell lines and the respective drug-adapted cells, respectively, on a four-class problem separately. These findings provide the basis for further development of the application of deep learning for the automation of cell line authentication into a readily available easy-to-use methodology that enables routine monitoring of the identity of cell lines including isogenic cell lines. It should be noted that, this is just a proof of principal that, images can also be used as a method for authentication of cancer cell lines and not a replacement for the STR method.

Authentication, characterization and contamination detection of cell lines, xenografts and organoids by barcode deep NGS sequencing

Misidentification and contamination of biobank samples (e.g. cell lines) have plagued biomedical research. Short tandem repeat (STR) and single-nucleotide polymorphism assays are widely used to authenticate biosamples and detect contamination, but with insufficient sensitivity at 5–10% and 3–5%, respectively. Here, we describe a deep NGS-based method with significantly higher sensitivity (≤1%). It can be used to authenticate human and mouse cell lines, xenografts and organoids. It can also reliably identify and quantify contamination of human cell line samples, contaminated with only small amount of other cell samples; detect and quantify species-specific components in human–mouse mixed samples (e.g. xenografts) with 0.1% sensitivity; detect mycoplasma contamination; and infer population structure and gender of human samples. By adopting DNA barcoding technology, we are able to profile 100–200 samples in a single run at per-sample cost comparable to conventional STR assays, providing a truly high-throughput and low-cost assay for building and maintaining high-quality biobanks.

Multifunctional Supramolecular Assemblies with Aggregation-Induced Emission (AIE) for Cell Line Identification, Cell Contamination Evaluation, and Cancer Cell Discrimination

It is undoubted the important role of cells in biology and medicine, but worldwide misidentified and cross-contaminated cell lines have caused much trouble in related fields. Herein, three kinds of supramolecular AIE (aggregation-induced emission) nanoassemblies were constructed by the host-guest interaction between tetraphenylethene (TPE) derivatives and cucurbit[8]uril (CB[8]). Based on the recognized mechanism of AIE, the TPE derivatives could achieve stronger fluorescence emission and higher fluorescence quantum yield after assembling with CB[8]. Moreover, the constructed supramolecular AIE complexes obtained well-confirmed nanostructures and exhibited different sizes and shapes. Correspondingly, they generated characteristic biological properties and fluorescence enhancement of cells. Inspired by the concept of Big Data Analysis, these fluorescence signals were further transformed into a unique fingerprint of cells via linear discriminant analysis. Immediately, we realized the veracious identification between a normal cell line, two cancer cell lines, and two metastasized cancer cell lines in a qualitative analysis. More importantly, it was well used to monitor the evaluation of cross-contaminated cells and the discrimination of cancer cells. As a proper bioapplication of ideal supramolecular nanomaterials, this system was easy to learn and apply, and the whole procedure was kept to 20 min, without cell disruption, centrifugation, or washing steps.

Functional and transcriptomic characterization of cisplatin-resistant AGS and MKN-28 gastric cancer cell lines

Gastric cancer (GC) is a significant cancer-related cause of death worldwide. The most used chemotherapeutic regimen in GC is based on platinum drugs such as cisplatin (CDDP). However, CDDP resistance reduces advanced GC survival. In vitro drug-resistant cell model would help in the understanding of molecular mechanisms underlying this drug-resistance phenomenon. The aim of this study was to characterize new models of CDDP-resistant GC cell lines (AGS R-CDDP and MKN-28 R-CDDP) obtained through a stepwise increasing drug doses method, in order to understand the molecular mechanisms underlying chemoresistance as well as identify new therapeutic targets for the treatment of GC. Cell viability assays, cell death assays and the expression of resistance molecular markers confirmed that AGS R-CDDP and MKN-28 R-CDDP are reliable CDDP-resistant models. RNA-seq and bioinformatics analyses identified a total of 189 DEGs, including 178 up-regulated genes and 11 down-regulated genes, associated mainly to molecular functions involved in CDDP-resistance. DEGs were enriched in 23 metabolic pathways, among which the most enriched was the inflammation mediated by chemokine and cytokine signaling pathway. Finally, the higher mRNA expression of SERPINA1, BTC and CCL5, three up-regulated DEGs associated to CDDP resistance found by RNA-seq analysis was confirmed. In summary, this study showed that AGS R-CDDP and MKN-28 R-CDDP are reliable models of CDDP resistance because resemble many of resistant phenotype in GC, being also useful to assess potential therapeutic targets for the treatment of gastric cancers resistant to CDDP. In addition, we identified several DEGs associated with molecular functions such as binding, catalytic activity, transcription regulator activity and transporter activity, as well as signaling pathways associated with inflammation process, which could be involved in the development of CDDP resistance in GC. Further studies are necessary to clarify the role of inflammatory processes in GC resistant to CDDP and these models could be useful for these purposes.

Rapid detection of low-level HeLa cell contamination in cell culture using nested PCR

HeLa cells are a commonly used cell line in many biological research areas. They are not picky for culture medium and proliferate rapidly. HeLa cells are a notorious source of cell cross‐contamination and have been found to be able to contaminate a wide range of cell lines in cell culture. In this study, we reported a simple and efficient method for detecting the presence of HeLa cell contamination in cell culture. HPV‐18 was used as a biomarker. The cell culture supernatant was used directly as the template for nested PCR without extracting nucleic acid. By PCR amplification of the cell culture supernatant with the designed primers, we were able to detect the presence of HeLa cells in the culture. The sensitivity of this method can reach 1%, which is 10‐fold higher than Short tandem repeat sequence (STR) profiling. This simple, rapid, and “noninvasive” quality checking method should find applications in routine cell culture practice.

Major changes of cell function and toxicant sensitivity in cultured cells undergoing mild, quasi-natural genetic drift

Genomic drift affects the functional properties of cell lines, and the reproducibility of data from in vitro studies. While chromosomal aberrations and mutations in single pivotal genes are well explored, little is known about effects of minor, possibly pleiotropic, genome changes. We addressed this question for the human dopaminergic neuronal precursor cell line LUHMES by comparing two subpopulations (SP) maintained either at the American-Type-Culture-Collection (ATCC) or by the original provider (UKN). Drastic differences in susceptibility towards the specific dopaminergic toxicant 1-methyl-4-phenylpyridinium (MPP+) were observed. Whole-genome sequencing was performed to identify underlying genetic differences. While both SP had normal chromosome structures, they displayed about 70 differences on the level of amino acid changing events. Some of these differences were confirmed biochemically, but none offered a direct explanation for the altered toxicant sensitivity pattern. As second approach, markers known to be relevant for the intended use of the cells were specifically tested. The “ATCC” cells rapidly down-regulated the dopamine-transporter and tyrosine-hydroxylase after differentiation, while “UKN” cells maintained functional levels. As the respective genes were not altered themselves, we conclude that polygenic complex upstream changes can have drastic effects on biochemical features and toxicological responses of relatively similar SP of cells.

Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations

Meta-analysis of datasets available in public repositories are used to gather and summarise experiments performed across laboratories, as well as to explore consistency of scientific findings. As data quality and biological equivalency across samples may obscure such analyses and consequently their conclusions, we investigated the comparability of 85 public RNA-seq cell line datasets. Thousands of pairwise comparisons of single nucleotide variants in 139 samples revealed variable genetic heterogeneity of the eight cell line populations analysed as well as variable data quality. The H9 and HCT116 cell lines were found to be remarkably stable across laboratories (with median concordances of 99.2% and 98.5%, respectively), in contrast to the highly variable HeLa cells (89.3%). We show that the genetic heterogeneity encountered greatly affects gene expression between same-cell comparisons, highlighting the importance of interrogating the biological equivalency of samples when comparing experimental datasets. Both the number of differentially expressed genes and the expression levels negatively correlate with the genetic heterogeneity. Finally, we demonstrate how comparing genetically heterogeneous datasets affect gene expression analyses and that high dissimilarity between same-cell datasets alters the expression of more than 300 cancer-related genes, which are often the focus of studies using cell lines.

Systematic Review: Characteristics and Preclinical Uses of Bladder Cancer Cell Lines

BACKGROUND

Bladder cancer (BC) cell lines are indispensable in basic and preclinical research. Currently, an up-to-date and comprehensive overview of available BC cell lines is not available.

OBJECTIVE

To provide an overview and resources on the origin, pathological and molecular characteristics of commonly used human, murine and canine BC cell lines.

METHODS

A PubMed search was performed for relevant articles published between 1980 and 2017 according to the following MeSH terms: cell line; cell line, tumor; urinary bladder neoplasms; carcinoma, transitional cell. The Cellosaurus database was searched, using the term "bladder" and/or "urothelial carcinoma". We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

RESULTS

We provide information on 157 human, murine and canine BC cell lines. 103 human BC cell lines have molecular data available, of which 69 have been profiled by at least one "omic" technology. We outline how these cell lines are currently being used for in vitro and in vivo experimental models. These results allow direct comparison of BC cell lines to patient samples, providing information needed to make informed decisions on the most genomically appropriate cell line to answer research questions. Furthermore, we show that cross-contamination remains an issue and describe guidelines for prevention.

CONCLUSIONS

In the BC field, multiple human, murine and canine BC cell lines have been developed and many have become indispensable for in vitro and in vivo research. High-throughput -omic technologies have dramatically increased the amount of molecular data on these cell lines. We synthesized a comprehensive overview of these data as a resource for the BC scientific community.