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Oste DJ, Pathmendra P, Richardson RAK, Johnson G, Ao Y, Arya MD, Enochs NR, Hussein M, Kang J, Lee A, Danon JJ, Cabanac G, Labbé C, Davis AC, Stoeger T, Byrne JA. Misspellings or "miscellings"-Non-verifiable and unknown cell lines in cancer research publications. Int J Cancer 2024. [PMID: 38751110 DOI: 10.1002/ijc.34995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 06/23/2024]
Abstract
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.
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Affiliation(s)
- Danielle J Oste
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Pranujan Pathmendra
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Reese A K Richardson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Gracen Johnson
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Yida Ao
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Maya D Arya
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Naomi R Enochs
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Muhammed Hussein
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Jinghan Kang
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Aaron Lee
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan J Danon
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Guillaume Cabanac
- IRIT UMR 5505 CNRS, University of Toulouse, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
| | - Cyril Labbé
- CNRS, Grenoble INP, Laboratoire d'Informatique de Grenoble, Université Grenoble Alpes, Grenoble, France
| | - Amanda Capes Davis
- CellBank Australia, Children's Medical Research Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Stoeger
- Feinberg School of Medicine in the Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
- The Potocsnak Longevity Institute, Northwestern University, Chicago, Illinois, USA
- Simpson Querrey Lung Institute for Translational Science, Chicago, Illinois, USA
| | - Jennifer A Byrne
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- NSW Health Statewide Biobank, NSW Health Pathology, Sydney, New South Wales, Australia
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Sarntivijai S, He Y, Diehl AD. Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. BMC Bioinformatics 2019; 20:183. [PMID: 31272374 PMCID: PMC6509796 DOI: 10.1186/s12859-019-2721-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cell cultures and cell lines are widely used in life science experiments. In conjunction with the 2018 International Conference on Biomedical Ontology (ICBO-2018), the 2nd International Workshop on Cells in ExperimentaL Life Science (CELLS-2018) focused on two themes of knowledge representation, for newly-discovered cell types and for cells in disease states. This workshop included five oral presentations and a general discussion session. Two new ontologies, including the Cancer Cell Ontology (CCL) and the Ontology for Stem Cell Investigations (OSCI), were reported in the workshop. In another representation, the Cell Line Ontology (CLO) framework was applied and extended to represent cell line cells used in China and their Chinese representation. Other presentations included a report on the application of ontologies to cross-compare cell types and marker patterns used in flow cytometry studies, and a presentation on new experimental findings about novel cell types based on single cell RNA sequencing assay and their corresponding ontological representation. The general discussion session focused on the ontology design patterns in representing newly-discovered cell types and cells in disease states.
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Affiliation(s)
| | - Yongqun He
- University of Michigan Medical School, Ann Arbor, MI USA
| | - Alexander D. Diehl
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
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