Date added: 17/12/2014 2014 Year in Review

 

2014 Year in Review

 

2014 has been a year of Scientific Reproducibility initiatives. In this our final mailing for the year, we'll revisit 14 reproducibility initiatives related to cultured cells that we've covered in 2014. And, to finish on a lighter note, we'll also give you an oddly memorable cell line contamination quote from 2014.

 

Contamination of cell lines due to the presence of additional cell populations - either microbial or from other, unrelated cell lines – was first described in the 1960s. It remains a serious problem today, with 10-30% of cell lines believed to be affected worldwide. Awareness of the problem and Good Cell Culture Practice are essential to improve the quality of results obtained with cultured cells.

 

Researcher Studies

 

1. Selection of Breast Cancer Cell Lines

 
An article titled, "Preclinical Models to Study Breast Cancer," was published on 4 June 2014 in Clinical Cancer Drugs. Here, researchers provide practical examples to illustrate the challenges and the solutions to developing breast cancer projects. To read the article, click here.


2. Review of Ovarian Cancer Cell Lines

 
An article titled, "Reliable in vitro studies require appropriate ovarian cancer cell lines," was published in the Journal of Ovarian Research on 7 June 2014. Here, researchers review 153 normal and/or ovarian cancer cell lines commercially available from five cell repositories. To read the article, click here.


3. Colorectal Cancer Cell Lines: Representative Models

 
An article titled, "Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer," was published in Cancer Research on 15 June 2014. Here, researchers conclude that their results establish that human colorectal cancer lines are representative of the main subtypes of primary tumors at the genomic level, further validating their utility as tools to investigate colorectal cancer biology and drug responses. To read the article, click here.


4. Mycoplasma Contamination in RNA-Seq Data


An article titled, "Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive," was released from the bioRχiv preprint server on 11 July 2014. Here, researchers show that 11% of sequence data from 9,395 rodent and primate samples from 884 series (or projects) in the NCBI Sequence Read Archive are contaminated by mycoplasmal DNA sequences. To read the article, click here.


5. Methylation Profiling of Breast Cancer Cell Lines


An article titled, "Do Breast Cancer Cell Lines Provide a Relevant Model of the Patient Tumor Methylome?" was published in PLOS One on 26 August 2014. Here, researchers report on the first systematic, genome-wide comparison of DNA methylation profiles of cancer cell lines and primary tumors. To read the article, click here.


6. Characterization of Ovarian Cancer Cell Lines


An article titled, "Ovarian Cancer Cell Line Panel (OCCP): Clinical Importance of In Vitro Morphological Subtypes," was published in the journal PLOS One on 17 September 2014. Here, researchers characterize 39 ovarian cancer cell lines under uniform conditions for growth characteristics, mRNA/microRNA expression, exon sequencing, drug response for clinically-relevant therapeutics and collated all available information on the original clinical features and site of origin. To read the article, click here.


Research Institution Initiatives


7. MD Anderson Cancer Centre: Cell Line Authentication Policy


To prevent the necessity for retraction of papers in which cell lines are found not to be of the reported lineage, the MD Anderson Cancer Center - The University of Texas (MDA; Houston, TX, US) implemented a cell line authentication policy in 2010 that requires all researchers to validate their cell lines at least once per year. Assistant Professor Karina Eterovic, Director of the MDA Characterized Cell Line Core (CCLC) facility, told me in August 2014 that the policy was well accepted by the MDA community and since its implementation the number of misidentified cell lines at MDA has decreased from 12% to less than 3%. To read the MDA policy, click here.


8. CRUK CI: Mycoplasma Testing Policy


To reduce the incidence of mycoplasma contamination, the Cancer Research UK Cambridge Institute (CRUK CI; Cambridge, UK) has implemented a very strict cell culture quarantine and mycoplasma testing policy and a rapid decontamination procedure. In September 2014, Mr Bob Geraghty, who heads up the CRUK CI Biorepository and Cell Services Core, told me that the early detection and elimination of mycoplasma infection in research cell cultures is vital both to the integrity of scientific data and to prevent the spread of infection to other cell lines. In 2007/8, 336 cell lines were tested for mycoplasma at the CRUK CI and that number has increased each year since, with 1,373 cell lines tested in 2012/13.


Funding Agency Initiatives


9. PCF: Cell Line Authentication Initiative


In 2014, the Prostate Cancer Foundation (PCF; Santa Monica, CA, USA) implemented its Cell Line Authentication Initiative (CLAI), which aims to improve the reproducibility of prostate cancer research. Under the initiative, prostate cancer researchers currently funded by the PCF will be required to report results on cell line authentication and mycoplasma testing in their annual progress report. To read the CLAI Mission Statement, click here.


Research Journal Initiatives


10. GIT Laboratory Journal: Cell Line Quality Series

 
Members and colleagues of the International Cell Line Authentication Committee (ICLAC) published a series of three articles in GIT Laboratory Journal Europe in 2014.


The first article, titled "Quality Matters: Cell Lines and their Use in Research," was published on 21 February 2014. Here, the authors discuss what continuous cell lines are used for and their common problems. To read the article, click here.


The second article, titled "ICLAC: Obtaining Cell Lines from Reliable Sources," was published on 17 April 2014. Here, the authors discuss the advantages of obtaining cell lines from a cell repository, the authentication testing that repositories perform, and the reference datasets from those repositories that labs can now access. To read the article, click here.


The third article, titled "ICLAC: Cell Banking," was published on 5 June 2014. Here, the authors explain how cell repositories or culture collections handle and ship their own cell lines to achieve good cell culture quality. To read the article, click here.

 

Research Community Initiatives

 

11. ICLAC: Naming a Cell Line


ICLAC released a document titled, "Naming a Cell Line," from its website on 9 May 2014 to help address what it considered "an increasing number of cell lines with identical names but coming from different donors." Here, ICLAC set out essential requirements for cell line names and recommend a naming format. To read the document, click here.


12. ICLAC: Checklist for Manuscripts and Grant Applications


ICLAC released a document titled, "Cell Line Checklist for Manuscripts and Grant Applications," from its website on 9 May 2014. The checklist has been written as a resource for scientists who write or review manuscripts and grant applications that use cell lines. The use of the checklist will help the author or reviewer to look for obvious cell line quality concerns. The checklist may also be used to communicate any quality concerns to be addressed prior to publication or funding. To read the document, click here.


13. Guidelines for the Use of Cell Lines in Biomedical Research


An ad hoc committee of international experts in cell biology and cell culture published an update of the 1999 United Kingdom Coordinating Committee on Cancer Research Guidelines for the Use of Cell Lines in Cancer Research in the British Journal of Cancer on 12 August 2014. The article titled, "Guidelines for the use of cell lines in biomedical research," highlights problems that continue to affect cell culture and recommends how they may be identified, avoided or, where possible, eliminated. To read the 2014 Guidelines, click here.


14. Consensus on Reporting Principles

 

In June 2014, the National Institute of Health (NIH; Bethesda, MA, US), the Nature Publishing Group (NPG) and the journal Science, held a joint workshop with the editors of more than 30 science journals on the issue of reproducibility and rigor of research findings. Director of the NIH, Dr Francis Collins, has said that: "The workshop focused on the common opportunities in the scientific publishing arena to enhance rigor and further support research that is reproducible, robust, and transparent." To facilitate these goals, the journal editors at that workshop came to consensus on a set of principles and guidelines in reporting preclinical research. The common set, titled "Proposed Principles and Guidelines for Reporting Preclinical Research," was posted on the NIH website in November 2014, along with information on endorsing journals. The Principles and Guidelines state that the source, authentication and Mycoplasma contamination status of cell lines should be reported. To read the Principles and Guidelines, click here.


Best Quote of 2014

 

"If we get it wrong again, that's really our fault, and somebody should throw something at us if we do, because there's really no excuse for that."


- Professor Robert Clarke, Georgetown University (Washington D.C., US), on National Public Radio (NPR), "Mistaken Identities Plague Lab Work With Human Cells", 9 December 2014. To read the article or listen to the radio report, click here.

 
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