The need for a worldwide consensus for cell line authentication: Experience implementing a mandatory requirement at the International Journal of Cancer

Impact of mechanical cues on key cell functions and cell-nanoparticle interactions

In recent years, it has been recognized that mechanical forces play an important regulative role in living organisms and possess a direct impact on crucial cell functions, ranging from cell growth to maintenance of tissue homeostasis. Advancements in mechanobiology have revealed the profound impact of mechanical signals on diverse cellular responses that are cell type specific. Notably, numerous studies have elucidated the pivotal role of different mechanical cues as regulatory factors influencing various cellular processes, including cell spreading, locomotion, differentiation, and proliferation. Given these insights, it is unsurprising that the responses of cells regulated by physical forces are intricately linked to the modulation of nanoparticle uptake kinetics and processing. This complex interplay underscores the significance of understanding the mechanical microenvironment in shaping cellular behaviors and, consequently, influencing how cells interact with and process nanoparticles. Nevertheless, our knowledge on how localized physical forces affect the internalization and processing of nanoparticles by cells remains rather limited. A significant gap exists in the literature concerning a systematic analysis of how mechanical cues might bias the interactions between nanoparticles and cells. Hence, our aim in this review is to provide a comprehensive and critical analysis of the existing knowledge regarding the influence of mechanical cues on the complicated dynamics of cell-nanoparticle interactions. By addressing this gap, we would like to contribute to a detailed understanding of the role that mechanical forces play in shaping the complex interplay between cells and nanoparticles.

Investigation of the mixed origins of the MGC-803 cell line reveals that it is a hybrid cell line derived from HeLa

Human cancer cell lines have an essential role in cancer research, but only authentic cell lines should be used as biological models. Authentication testing using short tandem repeat (STR) loci has shown that MGC-803 cells, which were reported to come from gastric adenocarcinoma, are similar to HeLa. In this study, we confirmed that the MGC-803 cell line contains genetic material from HeLa, including genetic sequence from human papilloma virus 18 (HPV18). Additional alleles were present on STR analysis that remained stable after extensive passaging and generation of mono-clones. This behavior is consistent with a hybrid cell line arising from cell-cell fusion. Further genetic analysis revealed that MGC-803 originated from donors with different genetic ancestries, one African (HeLa) and the other Asian. Transcriptomic analysis demonstrated that MGC-803 closely resembles HeLa and another nasopharyngeal-HeLa hybrid cell line CNE-2. Based on these findings, we conclude that MGC-803 is a hybrid cell line derived from HeLa and other cells, the latter derived from a different patient with Asian genetic ancestry.

A pair of primary colorectal cancer-derived and corresponding synchronous liver metastasis-derived organoid cell lines

Proper preclinical models for the research of colorectal cancer (CRC) and CRC liver metastases (CLM) are a clear and unmet need. Patient-derived organoids have recently emerged as a robust preclinical model, but are not available to all scientific researchers. Here, we present paired 3D organoid cell lines of CWH22 (CRC-derived) and CLM22 (CLM-derived) with sound background information and the short tandem repeats are identical to those of the normal tissue. Morphological and immunohistochemical staining, along with whole-exome sequencing (WES), confirmed that the organoids exhibited the same differentiation, molecular expression, and mutation status as the corresponding tumor tissue. Both organoids possessed mutated APC/KRAS/SMAD4/CDKN1B/KMT2C genes and wild-type TP53 and PIK3CA; stably secreted the tumor markers CEA and CA19-9, and possessed sound proliferation rates in vitro, as well as subcutaneous tumorigenicity and liver metastatic abilities in vivo. IC50 assays confirmed that both cell lines were sensitive to 5-fluorouracil, oxaliplatin, SN-38, and sotorasib. WES and karyotype analyses revealed the genomic instability status as chromosome instability. The corresponding adherent cultured CWH22-2D/CLM22-2D cells were established and compared with commonly used CRC cell lines from the ATCC. Both organoids are publicly available to all researchers and will be useful tools for specific human CRC/CLM studies both in vitro and in vivo.

Application of RapidHIT™ ID for cell authentication by fast and convenient STR profiling

BACKGROUND

As cell therapies are injected directly into the body, cell authentication is essential. Short tandem repeat (STR) profiling is used for human identification in forensics as well as for cell authentication. The standard methodology (DNA extraction, quantification, polymerase chain reaction, and capillary electrophoresis) takes at least 6 h and requires several instruments to obtain an STR profile. RapidHIT™ ID is a single automated instrument that provides an STR profile in 90 min.

OBJECTIVE

In this study, we aimed to propose a method to use RapidHIT™ ID for cell authentication.

METHODS

Four types of cells which are used for cell therapy or in the production process were used. The sensitivity of STR profiling was compared by the cell type and cell count using RapidHIT™ ID. Moreover, the effect of preservation solutions, pre-treatment with cell lysis solution, proteinase K, Flinders Technology Associates (FTA) cards, and dried or wet cotton swabs (with a single cell type or a mixture of two) were examined. The results were compared to those obtained by the standard methodology using genetic analyzer ThermoFisher SeqStudio.

RESULTS

We accomplished a high sensitivity through our proposed method that can benefit cytology laboratories. Although the pre-treatment process affected the quality of the STR profile, other variables did not significantly affect STR profiling.

CONCLUSION

As a result of the experiment, RapidHIT™ ID can be used as a faster and simpler instrument for cell authentication.

αCT1 peptide sensitizes glioma cells to temozolomide in a glioblastoma organoid platform

Glioblastoma (GBM) is the most common form of brain cancer. Even with aggressive treatment, tumor recurrence is almost universal and patient prognosis is poor because many GBM cell subpopulations, especially the mesenchymal and glioma stem cell populations, are resistant to temozolomide (TMZ), the most commonly used chemotherapeutic in GBM. For this reason, there is an urgent need for the development of new therapies that can more effectively treat GBM. Several recent studies have indicated that high expression of connexin 43 (Cx43) in GBM is associated with poor patient outcomes. It has been hypothesized that inhibition of the Cx43 hemichannels could prevent TMZ efflux and sensitize otherwise resistance cells to the treatment. In this study, we use a three-dimensional organoid model of GBM to demonstrate that combinatorial treatment with TMZ and αCT1, a Cx43 mimetic peptide, significantly improves treatment efficacy in certain populations of GBM. Confocal imaging was used to visualize changes in Cx43 expression in response to combinatorial treatment. These results indicate that Cx43 inhibition should be pursued further as an improved treatment for GBM.

Establishment and characterization of a new intrahepatic cholangiocarcinoma cell line, ICC-X3

Intrahepatic cholangiocarcinoma (ICC) is an aggressive cancer of the biliary tract that is prone to recurrence and metastasis and is characterized by poor sensitivity to chemotherapy and overall prognosis. To address this challenge, the establishment of suitable preclinical models is critical. In this study, we successfully established a new ICC cell line, named ICC-X3, from the satellite lesions of one ICC patient. The cell line was characterized with respect to phenotypic, molecular, biomarker, functional and histological properties. STR confirmed that ICC-X3 was highly consistent with primary tumor tissue. ICC-X3 cells positively expressed CK7, CK19, E-cadherin, vimentin, and Ki67. ICC-X3 was all resistant to gemcitabine, paclitaxel, 5-FU, and oxaliplatin. The cell line was able to rapidly form xenograft tumors which were highly similar to the primary tumor. The missense mutation of TP53 exon was detected in ICC-X3 cells. ICC-X3 can be used as a good experimental model to study the progression, metastasis, and drug resistance of ICC.

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.

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.

Misidentified biomedical resources: Journal guidelines are not a quick fix

Biomedical researchers routinely use a variety of biological models and resources, such as cultured cell lines, antibodies and laboratory animals. Unfortunately, these resources are not flawless: cell lines can be misidentified; for antibodies, problems with specificity, lot-to-lot consistency and sensitivity are common; and the reliability of animal models is questioned due to poor translation of animal studies to human clinical trials. In some cases, these problems can render the results of a study meaningless. As a response, some journals have implemented guidelines regarding the use and reporting of cell lines, antibodies and laboratory animals. In our study we use a portfolio of existing and newly created datasets to investigate identification and authentication information of cell lines, antibodies and organisms before and after guideline introduction, compared to journals without guidelines. We observed a general improvement of reporting quality over time, which the implementation of guidelines accelerated only in some cases. We therefore conclude that the effectiveness of journal guidelines is likely to be context dependent, affected by factors such as implementation conditions, research community support and monitoring and resource availability. Hence, journal reporting guidelines in themselves are not a quick fix to repair shortcomings in biomedical resource documentation, even though they can be part of the solution.

Role and relevance of fish cell lines in advanced in vitro research

Introduction

Cell line derived from fish has been established as a promising tool for studying many key issues of aquaculture covering fish growth, disease, reproduction, genetics, and biotechnology. In addition, fish cell lines are very useful in vitro models for toxicological, pathological, and immunological studies. The easier maintenance of fish cell lines in flexible temperature regimes and hypoxic conditions make them preferable in vitro tools over mammalian cell lines. Great excitement has been observed in establishing and characterizing new fish cell lines representing diverse fish species and tissue types. The well-characterized and authenticated cell lines are of utmost essential as these represent cellular functions very similar to in vivo state of an organism otherwise it would affect the reproducibility of scientific research.

Conclusion

The fish cell lines have exhibited encouraging results in several key aspects of in vitro research in aquaculture including virology, nutrition and metabolism, production of vaccines, and transgenic fish production. The review paper reports the cell lines developed from fish, their characterization, and biobanking along with their potential applications and challenges in in vitro research.

The Extensive and Expensive Impacts of HEp-2 [HeLa], Intestine 407 [HeLa], and Other False Cell Lines in Journal Publications

Cell lines are essential models for biomedical research. However, they have a common and important problem that needs to be addressed. Cell lines can be misidentified, meaning that they no longer correspond to the donor from whom the cells were first obtained. This problem may arise due to cross-contamination: the accidental introduction of cells from another culture. The contaminant, which is often a rapidly dividing cell line, will overgrow and replace the original culture. The end result is a false cell line, also known as a misidentified or imposter cell line. False cell lines may come from an entirely different species, tissue, or cell type than the original donor. If undetected, false cell lines produce unreliable and irreproducible results that pollute the biomedical literature and threaten the development of reliable drug discovery and meaningful patient treatments.The goal of this study was to ascertain how widespread this problem is and how it affects the literature, as well as to estimate how much funding has been used to produce pools of scientific literature of questionable value. We focus on HEp-2 [HeLa] and Intestine 407 [HeLa], two false cell lines that are widely used in the scientific literature but were shown to be cross-contaminated in 1967. These two cell lines have been used in 8497 and 1397 published articles and extensively described as laryngeal cancer and normal intestine, respectively, rather than their true identity: the cervical cancer cell line HeLa. Discussed are tools, approaches, and resources that can address this issue-both retrospectively and prospectively.

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.

Traceability Methods for Cell Line Authentication and Mycoplasma Detection

Many laboratories struggle with mycoplasma contamination and cell line misidentification when growing cells in culture. These well-documented issues affect the scientific research community and have detrimental downstream effects. Research published with suspect cultures can produce misleading results. There is increasing pressure to verify the integrity of experimental and established cell lines before publishing. Therefore, laboratories need to define how and when to perform these critical tests, analyze the results, and determine action plans if disparities exist. Our laboratory is committed to producing cell lines of the highest quality for use in experiments; thus, we created a surveillance strategy for these potential problems. We developed processes for both testing and tracing cell line authentication and mycoplasma detection data. Using these methods, we can protect the integrity of our patient and commercial cell lines, maintaining reliable cultures for our research.

Endometriotic cell culture contamination and authenticity: a source of bias in in vitro research?

STUDY QUESTION

Are the primary cell cultures and cell lines used in endometriosis research of sufficient quality?

SUMMARY ANSWER

Primary cells used in endometriosis research lack purity and phenotypic characterisation, and cell lines are not genotypically authenticated.

WHAT IS KNOWN ALREADY

The poor reproducibility of in vitro research and the lack of authenticity of the cell lines used represent reasons of concern in the field of reproductive biology and endometriosis research.

STUDY DESIGN, SIZE, DURATION

In the present study, past in vitro research in the field of endometriosis was systematically reviewed to determine whether the appropriate quality controls were considered. In addition, we explored the performance of Paired Box 2 (Pax2) as an endometrium specific marker in endometrial and endometriotic primary cell cultures; we also characterised the most diffused endometriosis cell lines with respect to important markers including the short tandem repeat (STR) profile.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Literature review part: almost 300 published protocols describing the isolation and creation of primary cell cultures from endometriosis were reviewed. Wet-lab part: primary cells isolated from 13 endometriosis patients were analysed by immunohistochemistry, immunofluorescence and FACS for the expression of Pax2. Cell lines Z11 and Z12, the most diffused endometriosis cell lines, were characterised with respect to the expression of Pax2, steroid hormone receptors and STR profile.

MAIN RESULTS AND THE ROLE OF CHANCE

From the literature review work, we underscored the lack of sufficient cell purity and phenotypic characterisation of primary cell cultures, which present high risk of contaminations from surrounding non-endometriotic tissues. Past work based on the use of cell lines was reviewed as well, and it emerged that cell line authentication was never performed.

In an effort to address these weaknesses for future research, we present data on the performance of Pax2, a suitable marker to exclude ovarian (and other non-endometrial) cell contaminations from primary cell cultures; STR profiles of cell lines Z11 and Z12 were analysed and indicated that the cells were authentic. These profiles are now available for authentication purposes to researchers wishing to perform experiments with these cells.

A quality control pipeline to assure sufficient quality of in vitro research in the field of reproductive biology and endometriosis is proposed. We encourage scientists, research institutes, journal reviewers, editors and funding bodies to raise awareness of the problem and adopt appropriate policies to solve it in the future.

LARGE-SCALE DATA

STR profiles of cell lines Z11 and Z12 are deposited at the Cellosaurus database—web.expasy.org.

LIMITATIONS, REASONS FOR CAUTION

There may be additional markers suitable to assess cell quality.

WIDER IMPLICATIONS OF THE FINDINGS

Future in vitro research in endometriosis and the reliability of outcomes can be improved by using the recommendations presented in this study.

STUDY FUNDING/COMPETING INTEREST(S)

The study was partly financed by the ‘Stichting Fertility Foundation’ (The Netherlands). The authors declare no existing conflict of interest.

TRIAL REGISTRATION NUMBER

Non-applicable.

Gynaecological cancers and their cell lines

Cell lines are widely used for various research purposes including cancer and drug research. Recently, there have been studies that pointed to discrepancies in the literature and usage of cell lines. That is why we have prepared a comprehensive overview of the most common gynaecological cancer cell lines, their literature, a list of currently available cell lines, and new findings compared with the original studies. A literature review was conducted via MEDLINE, PubMed and ScienceDirect for reviews in the last 5 years to identify research and other studies related to gynaecological cancer cell lines. We present an overview of the current literature with reference to the original studies and pointed to certain inconsistencies in the literature. The adherence to culturing rulesets and the international guidelines helps in minimizing replication failure between institutions. Evidence from the latest research suggests that despite certain drawbacks, variations of cancer cell lines can also be useful in regard to a more diverse genomic landscape.

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.

CCLA: an accurate method and web server for cancer cell line authentication using gene expression profiles

Cancer cell lines (CCLs) as important model systems play critical roles in cancer research. The misidentification and contamination of CCLs are serious problems, leading to unreliable results and waste of resources. Current methods for CCL authentication are mainly based on the CCL-specific genetic polymorphism, whereas no method is available for CCL authentication using gene expression profiles. Here, we developed a novel method and homonymic web server (CCLA, Cancer Cell Line Authentication, http://bioinfo.life.hust.edu.cn/web/CCLA/) to authenticate 1291 human CCLs of 28 tissues using gene expression profiles. CCLA showed an excellent speed advantage and high accuracy for CCL authentication, a top 1 accuracy of 96.58 or 92.15% (top 3 accuracy of 100 or 95.11%) for microarray or RNA-Seq validation data (719 samples, 461 CCLs), respectively. To the best of our knowledge, CCLA is the first approach to authenticate CCLs using gene expression data. Users can freely and conveniently authenticate CCLs using gene expression profiles or NCBI GEO accession on CCLA website.

Dithranol: An Insight into its Novel Delivery Cargos for Psoriasis Management

OBJECTIVE

Dithranol (DTH) is a well-known moiety that has long been used promisingly to impede and treat skin disorders, particularly psoriasis. Nowadays, a rekindled interest in the use of DTH for this disorder has been observed. Side effects associated with conventional topical formulations of this moiety have aroused the interest of the scientific community in investigating novel cargos of DTH for psoriasis management.

RESULTS

Previous research has evidenced the anti-inflammatory and anti-proliferating potential of DTH. Numerous studies have indicated that DTH inhibits polymorphonuclear (PMN) leucocyte, modulates epidermal cell receptors and promotes anti-psoriatic action. However, some deterrent factors like poor solubility, stability, toxicity, staining and skin irritation hamper its use as a potential therapeutic agent. With the adoption of novel drug delivery technologies, the above mentioned inherent limitations of DTH have been compensated to reestablish this drug moiety.

CONCLUSION

This article reviews novel drug delivery aspects, safety concerns, clinical evidence, current status, and future opportunities of DTH in the management of psoriasis. Further, it will update researchers on this promising drug moiety, which is free from systemic adverse responses in comparison to other therapeutic molecules like steroids, for psoriasis treatment.

Aptamer Cocktail to Detect Multiple Species of Mycoplasma in Cell Culture

Mycoplasma contamination of cell line cultures is a common, yet often undetected problem in research laboratories. Many of the existing techniques to detect mycoplasma contamination of cultured cells are time-consuming, expensive, and have significant drawbacks. Here, we describe a mycoplasma detection system that is useful for detecting multiple species of mycoplasma in infected cell lines. The system contains three dye-labeled detection aptamers that can specifically bind to mycoplasma-infected cells and a dye-labeled control aptamer that minimally binds to cells. With this system, mycoplasma-contaminated cells can be detected within 30 min by using a flow cytometer, fluorescence microscope, or microplate reader. Further, this system may be used to detect mycoplasma-contaminated culture medium. This study presents an novel mycoplasma detection model that is simple, rapid, inexpensive, and sensitive.

Establishment of a novel human cell line retaining the characteristics of the original pancreatic adenocarcinoma, and evaluation of MEK as a therapeutic target

Pancreatic cancer is a lethal solid malignancy with limited therapeutic options. The development of novel therapeutic drugs requires adequate new cell line models. A new pancreatic cancer cell line, designated PDXPC1, was established from one pancreatic ductal adenocarcinoma (PDAC) patient-derived xenograft. The PDXPC1 cells were stably cultured for >2 years and had a stable short tandem repeat profile. The PDXPC1 cell line retained the key mutations of the primary tumor, along with the epithelial origin and other important protein expression. The PDXPC1 cells induced rapid in vivo tumor growth, both subcutaneously and orthotopically, in a mouse model with an elevated CA199 level. The PDXPC1 cells showed weak growth, invasion and migration potency compared to another pancreatic cancer cell line, but were relatively resistant to multiple anti-cancer drugs. Interestingly, the MEK inhibitor trametinib significantly inhibited the proliferation of PDXPC1 cells, and not that of Panc-1 cells, by inactivating MEK/ERK/MYC signaling and activating the apoptotic pathway via Bcl-2 degradation. In conclusion, the PDXPC1 cell line, capturing the major characteristics of the primary tumor, may be a suitable tool for studying the underlying mechanisms of chemo-resistance in PDAC and developing new targeted therapeutic options.

Endometrial cancer and its cell lines

Endometrial cancer is one of the most common gynaecological malignancies worldwide. One type of research in this field is the growing of cell lines (CLs) and cultures, which can be used to explore the biological mechanisms of cancer. The purpose of this review is to offer an overview of the current literature and highlight the importance of correct CL studies. We carried out a literature analysis of more than 60 articles from the Pubmed, Medline databases that were almost exclusively published in indexed journals in the last 10 years as well as the primary originating scientific studies of specific CLs. We then summarized the newest findings and recommendations. Cell lines are becoming widely used as in vitro tumour models. Recent work has shown inconsistencies in nomenclature and culturing of CLs. Their genomic evolution leads to a high degree of variation across CL strains therefore it is of the utmost importance to recognize the variability within laboratory cancer models. Laboratories must adapt, incorporate additional characterisation techniques and view this situation as an opportunity to improve the reproducibility of pre-clinical cancer research. The authors offer a comprehensive literature review about endometrial cancer CLs, a review of the current literature and advice on culturing CLs.

Rationalized Development of a Campus-Wide Cell Line Dataset for Implementation in the Biobank LIMS System at Bioresource Center Ghent

The Bioresource center Ghent is the central hospital-integrated biobank of Ghent University Hospital. Our mission is to facilitate translational biomedical research by collecting, storing and providing high quality biospecimens to researchers. Several of our biobank partners store large amounts of cell lines. As cell lines are highly important both in basic research and preclinical screening phases, good annotation, authentication, and quality of these cell lines is pivotal in translational biomedical science. A Biobank Information Management System (BIMS) was implemented as sample and data management system for human bodily material. The samples are annotated by the use of defined datasets, based on the BRISQ (Biospecimen Reporting for Improved Study Quality) and Minimum Information About Biobank data Sharing (MIABIS) guidelines completed with SPREC (Standard PREanalytical Coding) information. However, the defined dataset for human bodily material is not ideal to capture the specific cell line data. Therefore, we set out to develop a rationalized cell line dataset. Through comparison of different datasets of online cell banks (human, animal, and stem cell), we established an extended cell line dataset of 156 data fields that was further analyzed until a smaller dataset—the survey dataset of 54 data fields—was obtained. The survey dataset was spread throughout our campus to all cell line users to rationalize the fields of the dataset and their potential use. Analysis of the survey data revealed only small differences in preferences in data fields between human, animal, and stem cell lines. Hence, one essential dataset for human, animal and stem cell lines was compiled consisting of 33 data fields. The essential dataset was prepared for implementation in our BIMS system. Good Clinical Data Management Practices formed the basis of our decisions in the implementation phase. Known standards, reference lists and ontologies (such as ICD-10-CM, animal taxonomy, cell line ontology…) were considered. The semantics of the data fields were clearly defined, enhancing the data quality of the stored cell lines. Therefore, we created an essential cell line dataset with defined data fields, useable for multiple cell line users.

An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines

Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancestral origin of cancer cell lines is rarely acknowledged and often unknown. Using genome-wide genotyping data from 1,393 cancer cell lines from the Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), we estimated the genetic ancestral origin for each cell line. Our data indicate that cancer cell line collections are not representative of the diverse ancestry and admixture characterizing human populations. We discuss the implications of genetic ancestry and diversity of cellular models for cancer research and present an interactive tool, Estimated Cell Line Ancestry (ECLA), where ancestry can be visualized with reference populations of the 1000 Genomes Project. Cancer researchers can use this resource to identify cell line models for their studies by taking ancestral origins into consideration.

Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines

The use of misidentified and contaminated cell lines continues to be a problem in biomedical research. Research Resource Identifiers (RRIDs) should reduce the prevalence of misidentified and contaminated cell lines in the literature by alerting researchers to cell lines that are on the list of problematic cell lines, which is maintained by the International Cell Line Authentication Committee (ICLAC) and the Cellosaurus database. To test this assertion, we text-mined the methods sections of about two million papers in PubMed Central, identifying 305,161 unique cell-line names in 150,459 articles. We estimate that 8.6% of these cell lines were on the list of problematic cell lines, whereas only 3.3% of the cell lines in the 634 papers that included RRIDs were on the problematic list. This suggests that the use of RRIDs is associated with a lower reported use of problematic cell lines.

The secret lives of cancer cell lines

The extent of genetic and epigenetic diversity between and within patient tumors is being mapped in ever more detail. It is clear that cancer is an evolutionary process in which tumor cell intrinsic and extrinsic forces shape clonal selection. The pre-clinical oncology pipeline uses model systems of human cancer - including mouse models, cell lines, patient-derived organoids and patient-derived xenografts - to study tumor biology and assess the efficacy of putative therapeutic agents. Model systems cannot completely replicate the environment of human tumors and, even within the same cancer model, data are often irreproducible between laboratories. One hypothesis is that ongoing evolutionary processes remain relevant in laboratory models, leading to divergence over time. In a recent edition of Nature, Ben-David and colleagues showed that different stocks of widely used cancer cell lines - a staple of cancer research over many decades - are highly heterogeneous in terms of their genetics, transcriptomics and responses to therapies. The authors find compelling evidence of positive selection based on ongoing mutational processes and chromosomal instability. Thus, the origin, culture conditions and cumulative number of population doublings of cell lines likely influence experimental outcomes. Here, we summarize the key findings of this important study and discuss the practical implications of this work for researchers using cell lines in the laboratory.

A comprehensive analysis of e-CAS cell line reveals they are mouse macrophages

The 3Rs principles (Replacement, Reduction and Refinement) are focused on finding alternatives to the use of animals in research. In this regard, cell lines are popular and useful tools for the replacement of primary cells in in vitro studies. However, around 15–30% of cell lines used in research have been misidentified or cross-contaminated generating concerns about the results obtained from experiments that use them. Here we described how old aliquots of an equine macrophage cell line (e-CAS) stored at the Animal Health Trust did not contain equine cells but macrophages of murine origin (m-CAS).

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.

Building capacity to encourage research reproducibility and #MakeResearchTrue

Background

Research into study replication and reporting has led to wide concern about a reproducibility crisis. Reproducibility is coming to the attention of major grant funders, including the National Institutes of Health, which launched new grant application instructions regarding rigor and reproducibility in 2015.

Study Purpose

In this case study, the authors present one library’s work to help increase awareness of reproducibility and to build capacity for our institution to improve reproducibility of ongoing and future research.

Case Presentation

Library faculty partnered with campus research leaders to create a daylong conference on research reproducibility, followed by a post-conference day with workshops and an additional seminar. Attendees came from nearly all schools and colleges on campus, as well as from other institutions, nationally and internationally. Feedback on the conference was positive, leading to efforts to sustain the momentum achieved at the conference. New networking and educational opportunities are in development.

Discussion

Libraries are uniquely positioned to lead educational and capacity-building efforts on campus around research reproducibility. Costs are high and partnerships are required, but such efforts can lead to positive change institution-wide.

Authentication of M14 melanoma cell line proves misidentification of MDA-MB-435 breast cancer cell line

A variety of analytical approaches have indicated that melanoma cell line UCLA‐SO‐M14 (M14) and breast carcinoma cell line MDA‐MB‐435 originate from a common donor. This indicates that at some point in the past, one of these cell lines became misidentified, meaning that it ceased to correspond to the reported donor and instead became falsely identified (through cross‐contamination or other means) as a cell line from a different donor. Initial studies concluded that MDA‐MB‐435 was the misidentified cell line and M14 was the authentic cell line, although contradictory evidence has been published, resulting in further confusion. To address this question, we obtained early samples of the melanoma cell line (M14), a lymphoblastoid cell line from the same donor (ML14), and donor serum preserved at the originator's institution. M14 samples were cryopreserved in December 1975, before MDA‐MB‐435 cells were established in culture. Through a series of molecular characterizations, including short tandem repeat (STR) profiling and cytogenetic analysis, we demonstrated that later samples of M14 and MDA‐MB‐435 correspond to samples of M14 frozen in 1975, to the lymphoblastoid cell line ML14, and to the melanoma donor's STR profile, sex and blood type. This work demonstrates conclusively that M14 is the authentic cell line and MDA‐MB‐435 is misidentified. With clear provenance information and authentication testing of early samples, it is possible to resolve debates regarding the origins of problematic cell lines that are widely used in cancer research.

What's new?

A variety of analytical approaches have indicated that melanoma cell line M14 and breast carcinoma cell line MDA‐MB‐435 originate from a common donor, but there is ongoing debate regarding which is the misidentified cell line. Here, authentication testing of M14 from 1975 (prior to the establishment of MDA‐MB‐435), with comparison to donor serum and lymphoblastoid cell line ML14, shows that M14 is the authentic cell line and MDA‐MB‐435 is a misidentified derivative. With clear provenance information and authentication testing of early samples, debates regarding the origins of problematic cell lines that are widely used in cancer research can be resolved.