scholarly journals Rapid and Quantitative Assessment of Cell Quality, Identity, and Functionality for Cell-Based Assays Using Real-Time Cellular Analysis

2011 ◽  
Vol 16 (3) ◽  
pp. 313-322 ◽  
Author(s):  
Jeffrey T. Irelan ◽  
Meng-Jou Wu ◽  
Jonathan Morgan ◽  
Ning Ke ◽  
Biao Xi ◽  
...  

Strict quality control of cells is required for the standardization and interpretation of results in all areas of cell-based research, especially in drug discovery. Real-time cellular analysis using electrical impedance as a readout offers a rapid and highly reproducible method for quality control as it provides a quantitative measure of overall cell morphology and growth. In a case study, the authors demonstrate that samples of a single cell line obtained from several different labs show clear differences in their impedance profiles when compared with the corresponding standard cell line. A number of kinetic parameters were derived from the impedance profiles and used to quantify the differences among these cell lines. Our findings indicate that this methodology can detect cell line differences including mix-ups or contaminations, genetic alterations, and potential epigenetic changes occurring during passaging, all of which can occur in the time scale of a screening campaign. Finally, we provide evidence that these impedance profile differences can be predictive of different outcomes in cell-based functional assays for the effects of small molecules on otherwise seemingly identical cell lines.

Cancers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3712
Author(s):  
Paola Peinado ◽  
Alvaro Andrades ◽  
Marta Cuadros ◽  
Maria Isabel Rodriguez ◽  
Isabel F. Coira ◽  
...  

Mammalian SWI/SNF (SWitch/Sucrose Non-Fermentable) complexes are ATP-dependent chromatin remodelers whose subunits have emerged among the most frequently mutated genes in cancer. Studying SWI/SNF function in cancer cell line models has unveiled vulnerabilities in SWI/SNF-mutant tumors that can lead to the discovery of new therapeutic drugs. However, choosing an appropriate cancer cell line model for SWI/SNF functional studies can be challenging because SWI/SNF subunits are frequently altered in cancer by various mechanisms, including genetic alterations and post-transcriptional mechanisms. In this work, we combined genomic, transcriptomic, and proteomic approaches to study the mutational status and the expression levels of the SWI/SNF subunits in a panel of 38 lung adenocarcinoma (LUAD) cell lines. We found that the SWI/SNF complex was mutated in more than 76% of our LUAD cell lines and there was a high variability in the expression of the different SWI/SNF subunits. These results underline the importance of the SWI/SNF complex as a tumor suppressor in LUAD and the difficulties in defining altered and unaltered cell models for the SWI/SNF complex. These findings will assist researchers in choosing the most suitable cellular models for their studies of SWI/SNF to bring all of its potential to the development of novel therapeutic applications.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4547-4547
Author(s):  
Huanling Zhu ◽  
Ting Liu ◽  
Yongqian Jia

Abstract Objective To establish an imatinib resistance cell line and to study its resistant principia. Methods K562 cells were cultured in imatinib at gradually increased concentrations to generate their resistance cell line. Clone imatinib resistance cell lines by limited dilution culture. MTT assay, real time PCR and Semi-quantity PCR, flow cytometry and HPLC were used to clarify the possible mechanisms of the resistance. Results Imatinib resistance cell line K562R was successfully induced by continuous culture in the presence of gradually increasing doses of imatinib up to 5μmol/L. K562R cells were maintained in the media containing 5μmol/L imatinib. Proliferation data showed that cell growth of K562R was not inhibited in 5 μmol/L imatinib, whereas the parental sensitive cell was significantly inhibited by up to 2μM imatinib. The IC50 of K562R was about 7.5μmol/L which was ten times higher than that of the parental cell. HPLC revealed that the intracellular imatinib concentration of K562R was strikingly lower than that of the parental cells (up to 27.8-fold). MDR1 were not detected in mRNA (by RT-PCR)and protein(by flow cytometry) levels on K562R cell, whereas hOCT1 level measured by semi-quantity PCR showed lower expression in K562R cell lines than that of parental sensitive cell, indicating that low intracellular imatinib concentration may be due to lower affluence of imatinib by low level of hOCT1. (5) Real time PCR analysis showed no BCR-ABL/G6PD gene amplification and sequence analysis of the 374bp ABL kinase domain showed no mutation in K562R cell lines. Conclusion An imatinib resistance cell line K562R has been successfully established. Low expression of hOCT1 may be a key point mediating low intracellular imaitnib accumulation in K562R cell lines.


2019 ◽  
Author(s):  
Jacob S. Roth ◽  
Tobie D. Lee ◽  
Dorian M. Cheff ◽  
Maya L. Gosztyla ◽  
Rosita Asawa ◽  
...  

AbstractQuality control monitoring of cell lines utilized in biomedical research is of critical importance, and is critical for reproducibility of data. Two key pitfalls in tissue culture are 1) cell line authenticity, and 2) mycoplasma contamination. As a collaborative research institute, the National Center for Advancing Translational Sciences receives cell lines from a range of commercial and academic sources, that are adapted for high-throughput screening. Here, we describe the implementation of a routine NCATS-wide mycoplasma testing and short-tandem repeat (STR) testing for cell lines. Initial testing identified a >10% mycoplasma contamination rate, but the implementation of clearly defined protocols that included immediate destruction of contaminated cell lines wherever possible has led to a much-reduced mycoplasma contamination rate, and data for >2,000 cell line samples tested over 3 years, and case studies are provided. STR testing of 170 cell lines with established STR profiles revealed only 5 mis-identified cell lines received from external labs. The data collected over the three years since implementation of this systematic testing demonstrates the importance of continual vigilance for rapid identification of ‘problem’ cell lines, for ensuring reproducible data in translational science research.


2019 ◽  
Author(s):  
Graeme Benstead-Hume ◽  
Sarah K. Wooller ◽  
Samantha Dias ◽  
Lisa Woodbine ◽  
Anthony M. Carr ◽  
...  

AbstractIn this paper we explore computational approaches that enable us to identify genes that have become essential in individual cancer cell lines. Using recently published experimental cancer cell line gene essentiality data, human protein-protein interaction (PPI) network data and individual cell-line genomic alteration data we have built a range of machine learning classification models to predict cell line specific acquired essential genes. Genetic alterations found in each individual cell line were modelled by removing protein nodes to reflect loss of function mutations and changing the weights of edges in each PPI to reflect gain of function mutations and gene expression changes.We found that PPI networks can be used to successfully classify human cell line specific acquired essential genes within individual cell lines and between cell lines, even across tissue types with AUC ROC scores of between 0.75 and 0.85. Our novel perturbed PPI network models further improved prediction power compared to the base PPI model and are shown to be more sensitive to genes on which the cell becomes dependent as a result of other changes. These improvements offer opportunities for personalised therapy with each individual’s cancer cell dependencies presenting a potential tailored drug target.The overriding motivation for predicting cancer cell line specific acquired essential genes is to provide a low-cost approach to identifying personalised cancer drug targets without the cost of exhaustive loss of function screening.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4340-4340 ◽  
Author(s):  
Hans G. Drexler ◽  
Roderick A.F. MacLeod ◽  
Stefan Nagel ◽  
Willy G. Dirks ◽  
Cord C. Uphoff ◽  
...  

Abstract The <Guide to Leukemia-Lymphoma Cell Lines> summarizes the salient characteristics of 560 cell lines: precursor B (85), mature B (155), plasma cell leukemia/myeloma (66), immature T (55), mature T (21), natural killer (10), Hodgkin lymphoma (10), anaplastic large cell lymphoma (16), myelocytic (62), monocytic (33) and erythrocytic-megakaryocytic cell lines (45). Along with other improvements, the advent of continuous human leukemia-lymphoma (LL including myeloma) cell lines as a rich resource of abundant, accessible and manipulable living cells has contributed significantly to a better understanding of the pathophysiology of hematopoietic tumors. The first LL cell lines, Burkitt lymphoma-derived lines, were established in 1963. Since then more than 1500 cell lines have been described, some 500 of them in detail. The major advantages of continuous cell lines is the unlimited supply and worldwide availability of identical cell material and the infinite viable storability in liquid nitrogen. LL cell lines are characterized generally by monoclonal origin and differentiation arrest, sustained proliferation in vitro with preservation of most cellular features, and specific genetic alterations characteristic of their tumor of origin. Recent transcriptional profiling studies have confirmed that LL cell lines stably retain the aberrant profiles typical of their tumors of origin. The most practical classification of LL cell lines assigns them to one of the physiologically occurring cell lineages, based on their immunophenotype, genotype and functional features. Truly malignant cell lines should be discerned from Epstein-Barr virus-immortalized normal cells. The efficiency of cell line establishment is rather low and the deliberate establishment of new LL cell lines remains by and large an unpredictable process. Difficulties in establishing continuous cell lines may be caused by the inappropriate selection of nutrients and growth factors. Clearly, a generally suitable microenvironment for hematopoietic cells, either malignant or normal, cannot yet be defined. The characterization and publication of new LL cell lines should provide important and informative core data, attesting to their scientific significance. Large percentages of LL cell lines are contaminated with mycoplasma (about 20%) or are cross-contaminated with other cell lines (14% in our DNA fingerprinting analysis on 622 samples covering 560 LL cell lines). Solutions to these problems are sensitive detection, effective elimination and rigorous prevention of mycoplasma infection and proper, regular authentication of cell lines. The underlying cause appears to be negligent cell culture practice. The willingness of investigators to make their LL cell lines available to others is all too often limited. There is a need in the scientific community for clean and authenticated high quality LL cell lines to which every scientist has access. These are offered by public cell line banks like the DSMZ which holds 169 LL cell lines which all have undergone a strict quality, identity and characterization program (immunoprofile, karyotype, DNA fingerprint, virus/mycoplasma check). An example of the practical utility of LL cell lines are the recent advances in studies of classical and molecular cytogenetics which in large part were made possible by cell lines. We propose a list of the most useful, robust and publicly available reference cell lines which may be used for a variety of experimental purposes. The <Guide to Leukemia-Lymphoma Cell Lines> is available on CD; inquire at <[email protected]>.


2019 ◽  
Author(s):  
Man Nie ◽  
Likun Du ◽  
Bo Zhang ◽  
Weicheng Ren ◽  
Julia Joung ◽  
...  

AbstractHistone acetyltransferases (HATs), including CREBBP and EP300, are frequently mutated in B-cell malignancies and usually play a tumor-suppressive role. In this study, we performed whole genome and transcriptome sequencing and a genome-wide CRISPR-Cas9 knockout screen to study a germinal center B-cell like diffuse large B-cell lymphoma (DLBCL) cell line (RC-K8). Using a summarizing method that is optimized to address the complexity introduced by the time-course design, we identified a distinct pattern of genetic essentialities in RC-K8, including a dependency on CREBBP and MDM2, shown already at early time points and a gradually increased dependency on oxidative phosphorylation related genes. The dependency on CREBBP is associated with the corresponding genetic alterations identified in this cell line, i.e. a balanced translocation involves EP300, which resulted in a truncated form of protein that lacks the critical bromodomain and HAT domain. We further evaluated the previously published CRISPR-Cas9 screens and identified a genetic essentiality of CREBBP or EP300 gene in a small set of cancer cell lines, including several DLBCL cell lines that are highly sensitive for EP300 knockout and with CREBBP mutations or copy number loss. The dependency of the remaining HAT function in CREBBP and/or EP300-deficient genotype was validated by testing the HAT-domain inhibitor A-485. Our study suggests that integration of the unbiased, time-course-based functional screen results with the genomic and transcriptomic data can identify druggable vulnerability in individual or subgroups of cell lines/patients, which may help to develop more effective therapeutic strategies for cancers that are genetically highly heterogeneous, like DLBCL.


2015 ◽  
Vol 68 (9) ◽  
pp. 746-751 ◽  
Author(s):  
Tahrim Hasan ◽  
Beverley Carter ◽  
Nash Denic ◽  
Luis Gai ◽  
Jennifer Power ◽  
...  

Quality control (QC) for immunohistochemistry (IHC) analysis routinely incorporates archived specimens for on-slide control material. We have assessed the utility of cell-line-derived xenograft (CDX) tumours for QC in breast estrogen receptor (ER) and progesterone receptor (PR) biomarker testing. Immunoblot and IHC analyses were used to select cell lines with different steady-state levels of ER and PR expression. CDX tumours all demonstrated consistent and comparable expression of ER and PR with corresponding cell lines from which they were derived. Three pathologists experienced in breast biomarker reporting scored tumours from different locations on mammary fat pads to determine reproducibility. Tumours from different locations were consistently scored as identical, and the CDX tumours representing different levels of biomarker expression were similar to patient-derived controls. Pathologists could not consistently distinguish CDX tumours from patient-derived controls, suggesting that within the appropriate quality management setting, CDX tumours may serve as control material for reporting purposes.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4423-4423
Author(s):  
David A. Estes ◽  
Rahul Poria ◽  
Debbie M. Lovato ◽  
Hadya M. Khawaja ◽  
Claudia L. Quan ◽  
...  

Abstract Acquisition of drug resistance in tumor cells in children with T-cell acute lymphoblastic leukemia (T-ALL) during chemotherapy results in relapse and poor outcome. T-ALL cell lines that have acquired resistance to chemotherapeutics are therefore critical tools for the study of acquired resistance, yet there is a paucity of cell lines available for study. In this study, we hypothesize that drug resistant T-ALL cells can be produced by prolonged exposure to chemotherapeutics and that microarray analysis can be employed to identify the gene products responsible for acquired drug resistance. By incrementally increasing the drug concentration in growth media, we have produced T-ALL cell lines (Jurkat and Sup T1) that grow well in the presence of therapeutic concentrations of L-asparaginase (ASNase) and daunorubicin (DNR). The genetic profiles of the drug-resistant cell lines were compared to their parental progenitors using the Affymetrix HG-U133Plus2 GeneChip platform, capable of hybridizing ~54,000 genes and ESTs/chip. Signal intensity was normalized using the robust multi-array average (RMA) technique in GeneSpring 7.2. The Sup T1 and Jurkat ASNase-resistant cell lines increased their IC50s 26-fold (0.044 IU/mL to 1.14 IU/mL) and 320-fold (0.003 IU/mL to 0.96 IU/mL), respectively. The IC50 of the Jurkat DNR resistant cell line increased 77-fold (30 nM to 2300 nM), and 4.0-fold, (0.46 nM to 1.85 nM), respectively. Notably, DNR resistant Jurkat cells were also resistant to therapeutic concentrations of vincristine and prednisolone, but not ASNase. In contrast, the ASNase resistant cell lines remained sensitive to DNR, vincristine, and prednisolone. Microarray data comparing DNR-resistant and parental cell lines showed 288 genes upregulated >1.5-fold in the resistant line. Two sets of genes were the most upregulated in the drug resistant cells in comparison to parental cells. ABCB1 (ABC transporter P-glycoprotein) was upregulated ~940-fold and genes coding for 6 different killer-cell immunoglobulin-like receptors (KIRs) were upregulated >6-fold. In the case of the ASNase-resistant cell lines, 96 genes were found to be upregulated >1.5-fold in both Jurkat and Sup T1 lines. The most highly upregulated gene in both cell lines was argininosuccinate synthase (ASS), 32-fold upregulated in Jurkat and 6.5-fold in Sup T1. All expression results were confirmed by qRT-PCR. These genes have previously been implicated in the acquisition of drug resistance: ASS is critical for responding to asparagine depletion caused by ASNase. ABCB1 acts as a molecular pump capable of lowering intracellular concentrations of substrate chemotherapeutics such as DNR, vincristine, and prednisolone, consistent with our observation of multi-drug resistance in that cell line. To our knowledge, this is the first description of DNR and ASNase resistant Jurkat and Sup T1 T-ALL cell lines. In addition, our results suggest that microarray technology is a valid method for elucidating the genetic nature of drug resistance in T-ALL cell lines, making it a productive approach to identify mechanisms of chemotherapy resistance. Finally, these cell lines will serve as useful tools for studying mechanisms of chemotherapeutic resistance in T-ALL.


2020 ◽  
Vol 25 (5) ◽  
pp. 491-497 ◽  
Author(s):  
Jacob S. Roth ◽  
Tobie D. Lee ◽  
Dorian M. Cheff ◽  
Maya L. Gosztyla ◽  
Rosita R. Asawa ◽  
...  

Quality control monitoring of cell lines utilized in biomedical research is of utmost importance and is critical for the reproducibility of data. Two key pitfalls in tissue culture are 1) cell line authenticity and 2) Mycoplasma contamination. As a collaborative research institute, the National Center for Advancing Translational Sciences (NCATS) receives cell lines from a range of commercial and academic sources, which are adapted for high-throughput screening. Here, we describe the implementation of routine NCATS-wide Mycoplasma testing and short tandem repeat (STR) testing for cell lines. Initial testing identified a >10% Mycoplasma contamination rate. While the implementation of systematic testing has not fully suppressed Mycoplasma contamination rates, clearly defined protocols that include the immediate destruction of contaminated cell lines wherever possible has enabled rapid intervention and removal of compromised cell lines. Data for >2000 cell line samples tested over 3 years, and case studies are provided. STR testing of 186 cell lines with established STR profiles revealed only five misidentified cell lines, all of which were received from external labs. The data collected over the 3 years since implementation of this systematic testing demonstrate the importance of continual vigilance for rapid identification of “problem” cell lines, for ensuring reproducible data in translational science research.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2472-2472 ◽  
Author(s):  
Marleen Bakkus ◽  
Sylvie Dujardin ◽  
Ivan Van Riet ◽  
Marc De Waele

Abstract MicroRNAs (miRNAs) are small RNA molecules that negatively regulate gene expression at the post transcriptional level. Over the past few years, these miRNAs have been shown to be widely involved in diverse biological processes, like apoptosis, cell metabolism and cancer. The aim of this study was to compare the miRNA expression in multiple myeloma plasma cells to that in their normal counterparts. A subset of ten miRNAs was chosen based upon evidence in the literature for their role in tumorigenesis with special emphasis on B cell malignancies. The expression of mature miRNAs was examined with quantitative real-time reverse transcription based polymerase chain reaction (TaqMan®MicroRNA assay) in 7 human multiple myeloma (MM) cell lines, in purified bone marrow derived plasma cells from 4 MM patients, one MGUS patient and 3 healthy adults. The plasma cells from patients and controls were positively selected using CD138-coated microbeads. Our results showed that miR-15a and miR-21 were equally expressed in cell lines, patients and healthy controls. Therefore, these 2 miRNAs were used for normalization. All data were compared with the data derived from normal plasma cells. Higher expression was seen for let-7a, miR-16 and 2 members of the miR-17 cluster (miR-17-5p and miR-19b) both in MM patients and cell lines. Expression of miR-16 was much higher in the MM plasma cells than in the MGUS plasma cells (only one sample). The miR-181a showed a heterogeneous expression in cell lines but was normally expressed in patients. The miR-372 expression was below the level of accurate quantification in all samples. There was a dramatic difference between the stroma dependent (MM5.1) and the stroma independent cell line (MM5.2) in miR-155 expression. The miR-143 was less abundant in all cell lines and in one MM sample that contained more than 90% plasma cells. Interestingly, the MM5.2 cell line, which is stroma independent, reflecting a more aggressive MM stage, showed also a much lower expression for miR-143 than the stroma dependent counterpart (MM5.1). In summary, the results of this study show that there is a difference in miRNA expression between MM plasma cells and their healthy counterparts and also between more and less aggressive MM plasma cells, suggesting that miRNAs could play a role in disease onset and progression.


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