Molecular Biology Reports

, Volume 45, Issue 6, pp 2689–2695 | Cite as

Evaluation genotypes of cancer cell lines HCC1954 and SiHa by short tandem repeat (STR) analysis and DNA sequencing

  • Jiewen Fu
  • Jingliang Cheng
  • Xiaoyan Liu
  • Jun Li
  • Chunli Wei
  • Xiaoli Zheng
  • Tao HeEmail author
  • Junjiang FuEmail author
Original Article


Cancer cell lines are used worldwide in biomedical researches, and data interpretation solely depends on unambiguous attribution of those respective cell lines to its original sources. Approximately one-third of all cell lines have an origin other than that assumed, leading to invalid results. It is necessary to characterize the origin of cell lines. Short-tandem-repeat (STR) fingerprinting (DNA fingerprinting) is the method for characterization of genetic identity in cultured cell lines under certain experimental conditions. We showed the fingerprinting profiles in a summed and unidentified human cancer cell line comparison to HCC1954 cell line, revealing marked alterations in DNA fingerprinting profiles up to fourteen STR loci from 16 loci. Furthermore, Sanger DNA sequencing showed no c.3140A > G heterozygous mutation in the PIK3CA gene of this suspected HCC1954 cell line. In addition, we showed the fingerprinting profiles in an unidentified cancer cell line comparison to SiHa cervical cell line, revealing same DNA fingerprinting profiles. In conclusion, we have successfully authenticated and identified both suspected HCC1954 and SiHa cell lines by STR analysis and DNA sequencing. STR analysis combined DNA sequencing may be very useful to evaluate genotypes of cancer cell lines in our cancer studies, as well as in judicial authentication and forensic sciences.


Quality control Short-tandem-repeat (STR) Genotype Cancer Cell line Contamination Authentication 



The authors thank Prof. Hanchun Chen from Department of Biochemistry, Central South University in China for providing SiHa cell line and Chengdu Lilai Biotechnology Co., Ltd (Chengdu, China) for providing unauthenticated HCC1954 cell line.


This work was supported in part by the National Natural Science Foundation of China (30371493, 31701087, and 81672887), the Southwest Medical University foundation (2016-217-23), and the Joint Research Foundation of Luzhou City and Southwest Medical University (2018).

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.


  1. 1.
    Yu M, Selvaraj SK, Liang-Chu MM, Aghajani S, Busse M, Yuan J, Lee G, Peale F, Klijn C, Bourgon R et al (2015) A resource for cell line authentication, annotation and quality control. Nature 520:307–311. CrossRefPubMedGoogle Scholar
  2. 2.
    Kofanova OA, Mathieson W, Thomas GA, Betsou F (2014) DNA fingerprinting: a quality control case study for human biospecimen authentication. Biopreserv Biobank 12:151–153. CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Boonstra JJ, van Marion R, Beer DG, Lin L, Chaves P, Ribeiro C, Pereira AD, Roque L, Darnton SJ, Altorki NK et al (2010) Verification and unmasking of widely used human esophageal adenocarcinoma cell lines. J Natl Cancer Inst 102:271–274. CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Geraghty RJ, Capes-Davis A, Davis JM, Downward J, Freshney RI, Knezevic I, Lovell-Badge R, Masters JR, Meredith J, Stacey GN et al (2014) Guidelines for the use of cell lines in biomedical research. Br J Cancer 111:1021–1046. CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Nojadeh JN, Behrouz Sharif S, Sakhinia E (2018) Microsatellite instability in colorectal cancer. EXCLI J 17:159–168. CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Zou X, Li Y, Wei Z, Wang T, Hu Y, Zhu Y, Li J, Tang R (2018) Population data and forensic efficiency of 21 autosomal STR loci included in AGCU EX22 amplification system in the Wanzhou Han population. Int J Legal Med 132:153–155. CrossRefPubMedGoogle Scholar
  7. 7.
    Li Y, Shang Q, Li P, Cao J, Zhu L, Jager MJ, Fan X, Ge S, Jia R (2018) Characterization of a conjunctival melanoma cell line CM-AS16, newly-established from a metastatic Han Chinese patient. Experim Eye Res 173:51–63. CrossRefGoogle Scholar
  8. 8.
    Korch C, Hall EM, Dirks WG, Ewing M, Faries M, Varella-Garcia M, Robinson S, Storts D, Turner JA, Wang Y et al (2018) Authentication of M14 melanoma cell line proves misidentification of MDA-MB-435 breast cancer cell line. Int J Cancer 142:561–572. CrossRefPubMedGoogle Scholar
  9. 9.
    Nims RW, Sykes G, Cottrill K, Ikonomi P, Elmore E (2010) Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification. In Vitro Cell Dev Biol Animal 46:811–819. CrossRefGoogle Scholar
  10. 10.
    Kerrigan L, Nims RW (2011) Authentication of human cell-based products: the role of a new consensus standard. Regen Med 6:255–260. CrossRefPubMedGoogle Scholar
  11. 11.
    Li J, Khan MA, Wei C, Cheng J, Chen H, Yang L, Ijaz I, Fu J (2017) Thymoquinone inhibits the migration and invasive characteristics of cervical cancer cells SiHa and CaSki in vitro by targeting epithelial to mesenchymal transition associated transcription factors Twist1 and Zeb1. Molecules. CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Fu J, Qin L, He T, Qin J, Hong J, Wong J, Liao L, Xu J (2011) The TWIST/Mi2/NuRD protein complex and its essential role in cancer metastasis. Cell Res 21:275–289. CrossRefPubMedGoogle Scholar
  13. 13.
    Fu J, Li L, Lu G (2002) Relationship between microdeletion on Y chromosome and patients with idiopathic azoospermia and severe oligozoospermia in the Chinese. Chin Med J 115:72–75PubMedGoogle Scholar
  14. 14.
    Fu J, Ma L, Cheng J, Yang L, Wei C, Fu S, Lv H, Chen R, Fu J (2018) A novel, homozygous nonsense variant of the CDHR1 gene in a Chinese family causes autosomal recessive retinal dystrophy by NGS-based genetic diagnosis. J Cell Mol Med 22:5662–5669. CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Cheng J, Fu S, Wei C, Tania M, Khan MA, Imani S, Zhou B, Chen H, Xiao X, Wu J et al (2017) Evaluation of PIK3CA mutations as a biomarker in Chinese breast carcinomas from Western China. Cancer Biomark 19:85–92. CrossRefPubMedGoogle Scholar
  16. 16.
    Zhao Q, Kirkness EF, Caballero OL, Galante PA, Parmigiani RB, Edsall L, Kuan S, Ye Z, Levy S, Vasconcelos AT et al (2010) Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. Genome Biol 11:R114. CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Mei ZQ, Zhang XQ, Khan MA, Imani S, Liu XY, Zou H, Wei CL, Fu JJ (2017) Genetic analysis of penthorum chinense pursh by improved RAPD and ISSR in China. Electron J Biotechnol 30:6–11. CrossRefGoogle Scholar
  18. 18.
    von der Heyde S, Bender C, Henjes F, Sonntag J, Korf U, Beissbarth T (2014) Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines. BMC Syst Biol 8:75. CrossRefPubMedGoogle Scholar
  19. 19.
    Fu J, Yang L, Khan MA, Mei Z (2013) Genetic characterization and authentication of Lonicera japonica Thunb. by using improved RAPD analysis. Mol Biol Rep 40:5993–5999. CrossRefPubMedGoogle Scholar
  20. 20.
    Mei Z, Zhang X, Liu X, Imani S, Fu J (2017) Genetic analysis of Canarium album in different areas of China by improved RAPD and ISSR. C R Biol 340:558–564. CrossRefPubMedGoogle Scholar
  21. 21.
    Alonso A, Barrio PA, Muller P, Kocher S, Berger B, Martin P, Bodner M, Willuweit S, Parson W, Roewer L et al (2018) Current state-of-art of STR sequencing in forensic genetics. Electrophoresis. CrossRefPubMedGoogle Scholar
  22. 22.
    Butler JM, Hill CR (2012) Biology and genetics of new autosomal STR loci useful for forensic DNA analysis. Forensic Sci Rev 24:15–26PubMedGoogle Scholar
  23. 23.
    Fang Y, Guo Y, Xie T, Jin X, Lan Q, Zhou Y, Zhu B (2018) Forensic molecular genetic diversity analysis of Chinese Hui ethnic group based on a novel STR panel. Int J Legal Med. CrossRefPubMedGoogle Scholar
  24. 24.
    Christgen M, Lehmann U (2007) MDA-MB-435: the questionable use of a melanoma cell line as a model for human breast cancer is ongoing. Cancer Biol Ther 6:1355–1357CrossRefGoogle Scholar
  25. 25.
    Chambers AF (2009) MDA-MB-435 and M14 cell lines: identical but not M14 melanoma? Cancer Res 69:5292–5293. CrossRefPubMedGoogle Scholar
  26. 26.
    Capes-Davis A, Alston-Roberts C, Kerrigan L, Reid YA, Barrett T, Burnett EC, Cooper JR, Freshney RI, Healy L, Kohara A et al (2013) Beware imposters: MA-1, a novel MALT lymphoma cell line, is misidentified and corresponds to Pfeiffer, a diffuse large B-cell lymphoma cell line. Genes Chromosom Cancer 52:986–988. CrossRefPubMedGoogle Scholar
  27. 27.
    Kuo SH, Tsai HJ, Weng WH, Li CC, Yeh KH, Chen LT, Cheng AL (2014) Beware imposters: MA-1, a novel MALT lymphoma cell line, is misidentified and corresponds to Pfeiffer, a diffuse large B-cell lymphoma cell line-A reply: despite the same 8-code STR, MA-1 and Pfeiffer are cytogenetically diverse. Genes Chromosom Cancer 53:211–213. CrossRefPubMedGoogle Scholar
  28. 28.
    Tudrej P, Olbryt M, Zembala-Nozynska E, Kujawa KA, Cortez AJ, Fiszer-Kierzkowska A, Piglowski W, Nikiel B, Glowala-Kosinska M, Bartkowska-Chrobok A et al (2018) Establishment and characterization of the novel high-grade serous ovarian cancer cell line OVPA8. Int J Mol Sci. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
  2. 2.Judicial Authentication CenterSouthwest Medical UniversityLuzhouChina

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