Deoxyribonucleic acid profiling analysis of 40 human thyroid cancer cell lines reveals cross-contamination resulting in cell line redundancy and misidentification

Schweppe, Rebecca E.; Klopper, Joshua P.; Korch, Christopher; Pugazhenthi, Umarani; Benezra, Miriam; Knauf, Jeffrey A.; Fagin, James A.; Marlow, Laura A.; Copland, John A.; Smallridge, Robert C.; Haugen, Bryan R.

doi:10.1210/jc.2008-1102

Cited by 565Thyroid Cancer Diagnosis and TreatmentIdentification and Quantification in FoodCervical Cancer and HPV Research

Deoxyribonucleic acid profiling analysis of 40 human thyroid cancer cell lines reveals cross-contamination resulting in cell line redundancy and misidentification

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Schweppe, Rebecca E., Klopper, Joshua P., Korch, Christopher, Pugazhenthi, Umarani, Benezra, Miriam, Knauf, Jeffrey A., Fagin, James A., Marlow, Laura A. +3 more·2008·The Journal of Clinical Endocrinology & Metabolism

DOI 10.1210/jc.2008-1102PMC PMC2582569

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Abstract

CONTEXT: Cell lines derived from human cancers provide critical tools to study disease mechanisms and develop novel therapies. Recent reports indicate that up to 36% of cell lines are cross- contaminated. OBJECTIVE: We evaluated 40 reported thyroid cancer-derived cell lines using short tandem repeat and single nucleotide polymorphism array analysis. RESULTS: Only 23 of 40 cell lines tested have unique genetic profiles. The following groups of cell lines are likely derivatives of the same cell line: BHP5-16, BHP17-10, BHP14-9, and NPA87; BHP2-7, BHP10-3, BHP7-13, and TPC1; KAT5, KAT10, KAT4, KAT7, KAT50, KAK1, ARO81-1, and MRO87-1; and K1 and K2. The unique cell lines include BCPAP, KTC1, TT2609-C02, FTC133, ML1, WRO82-1, 8505C, SW1736, Cal-62, T235, T238, Uhth-104, ACT-1, HTh74, KAT18, TTA1, FRO81-2, HTh7, C643, BHT101, and KTC-2. The misidentified cell lines included the DRO90-1, which matched the melanoma-derived cell line, A-375. The ARO81-1 and its derivatives matched the HT-29 colon cancer cell line, and the NPA87 and its derivatives matched the M14/MDA-MB-435S melanoma cell line. TTF-1 and Pax-8 mRNA levels were determined in the unique cell lines. CONCLUSIONS: Many of these human cell lines have been widely used in the thyroid cancer field for the past 20 yr and are not only redundant, but not of thyroid origin. These results emphasize the importance of cell line integrity, and provide the short tandem repeat profiles for a panel of thyroid cancer cell lines that can be used as a reference for comparison of cell lines from other laboratories.

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Schweppe and colleagues showed that nearly 50% of thyroid cell lines were misidentified.
“Similarly, Schweppe and colleagues showed that nearly 50% of thyroid cell lines were misidentified [13].”
From Genetic Insights into the Economic Toll of Cell Line Misidentification: A Comprehensive Review (2026) · cites this paper as [13]
The Abstract and Discussion (pages unavailable) report substantial problems among the 40 presumptive thyroid cancer cell lines, including redundancy and misidentification. The Discussion identifies 12 redundant lines unlikely to be of thyroid origin, six redundant lines likely of thyroid origin, and one additional line unlikely to be of thyroid origin. Thus nearly half had an identity or redundancy problem, but the paper does not say that nearly half were misidentified in the narrower sense of being nonthyroid lines. (LLM, conf=0.84)
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Cell lines were authenticated by STR DNA profiling and matched with their respective STR profiles in published studies and/or ECACC and DSMZ databases at all loci tested in common.
“Cell lines were authenticated by short tandem repeat (STR) DNA profiling, and matched with their respective STR profiles as shown in previously published studies, and/or in the European Collection for Cell Cultures (ECACC) and the German Collection of Microorganisms and Cell Cultures (DSMZ) databases at all loci tested in common [48].”
From Restoration of p53 using the novel MDM2-p53 antagonist APG115 suppresses dedifferentiated papillary thyroid cancer cells (2017) · cites this paper as [48]

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Mutational Profile of Advanced Primary and Metastatic Radioactive Iodine-Refractory Thyroid Cancers Reveals Distinct Pathogenetic Roles for BRAF, PIK3CA , and AKT1
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Assembly and Initial Characterization of a Panel of 85 Genomically Validated Cell Lines from Diverse Head and Neck Tumor Sites
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Reproducibility: changing the policies and culture of cell line authentication
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Resveratrol Induces Differentiation Markers Expression in Anaplastic Thyroid Carcinoma via Activation of Notch1 Signaling and Suppresses Cell Growth
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Genetic Profiling Reveals Cross-Contamination and Misidentification of 6 Adenoid Cystic Carcinoma Cell Lines: ACC2, ACC3, ACCM, ACCNS, ACCS and CAC2
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Expression of hypoxia-inducible factor 1α in thyroid carcinomas
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miR-451a is underexpressed and targets AKT/mTOR pathway in papillary thyroid carcinoma
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Redifferentiation of radioiodine-refractory thyroid cancers
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Downregulation of Rap1GAP through Epigenetic Silencing and Loss of Heterozygosity Promotes Invasion and Progression of Thyroid Tumors
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Chrysin activates Notch1 signaling and suppresses tumor growth of anaplastic thyroid carcinoma in vitro and in vivo
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Targeting BRAFV600E with PLX4720 Displays Potent Antimigratory and Anti-invasive Activity in Preclinical Models of Human Thyroid Cancer
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Genetic Alterations in the Phosphoinositide 3-Kinase/Akt Signaling Pathway Confer Sensitivity of Thyroid Cancer Cells to Therapeutic Targeting of Akt and Mammalian Target of Rapamycin
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SRGAP1 Is a Candidate Gene for Papillary Thyroid Carcinoma Susceptibility
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Thyroid cancer stem cells
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The Sonic Hedgehog Signaling Pathway Maintains the Cancer Stem Cell Self-Renewal of Anaplastic Thyroid Cancer by Inducing Snail Expression
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Authors: Schweppe, R. E., Klopper, J. P., Korch, C., Pugazhenthi, U., Benezra, M., Knauf, J. A., Fagin, J. A., Marlow, L. A., Copland, J. A., Smallridge, R. C., & Haugen, B. R.
Affiliations: University of Colorado Cancer Center (US)
Memorial Sloan Kettering Cancer Center (US)
Mayo Clinic in Florida (US)
ORCID: Schweppe, Rebecca E.
Klopper, Joshua P.
Korch, Christopher
Pugazhenthi, Umarani
Benezra, Miriam
Knauf, Jeffrey A.
Fagin, James A.
Marlow, Laura A.
Copland, John A.
Haugen, Bryan R.
Venue: The Journal of Clinical Endocrinology & Metabolism
Publisher: The Endocrine Society
Published: 2008-11-01
Volume: 93
Issue: 11
Pages: 4331-4341
ISSN: 0021-972X (ISSN-L)
1945-7197
DOI: 10.1210/jc.2008-1102
PMC: PMC2582569
OpenAlex: W2027855079
Cited by: 563
References: 86
Citations by year: 2026: 3 · 2025: 7 · 2024: 11 · 2023: 28 · 2022: 9 · 2021: 21 · 2020: 22 · 2019: 27 · 2018: 33 · 2017: 33 · 2016: 38 · 2015: 40 · 2014: 29 · 2013: 47 · 2012: 54
FWCI: 38.71
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: The Journal of Clinical Endocrinology & Metabolism (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Florida Department of Health
Memorial Sloan-Kettering Cancer Center
National Institutes of Health (CA-04-6934, P 30CA046934)
University of Colorado Denver
Cancer Center, University of Colorado (P30 CA046934, CA046934)
National Cancer Institute (CA 046934, CA 50706, CA-72597, CA100560, R01CA100560, R01CA050706, R01CA072597, P30CA15083, P30CA015083, P30CA046934)
Topics: Health Sciences › Medicine › Endocrinology, Diabetes and Metabolism › Thyroid Cancer Diagnosis and Treatment
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Identification and Quantification in Food
Health Sciences › Medicine › Epidemiology › Cervical Cancer and HPV Research
Keywords: thyroid cancer cell lines, cell line contamination, cell line misidentification, short tandem repeat profiling, DNA fingerprinting, TTF-1, PAX8
MeSH terms: Colonic Neoplasms, DNA, Neoplasm, Female, Humans, Male, Melanoma, Mutation, Neoplasm Proteins, RNA, Messenger, Thyroid Neoplasms, Reproducibility of Results, Adenocarcinoma, Follicular, Cell Culture Techniques, Polymorphism, Single Nucleotide, Gene Expression Profiling, Cell Line, Tumor

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Deoxyribonucleic acid profiling analysis of 40 human thyroid cancer cell lines reveals cross-contamination resulting in cell line redundancy and misidentification

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