Lymphoblastoid cell lines do not recapitulate physiological circulating B cell subtypes

Human lymphoblastoid cell lines (LCLs), generated through Epstein-Barr Virus (EBV) transformation of B-lymphocytes (B-cells), are a commonly used model system for identifying genetic influences on human diseases and on drug responses. We have previously used LCLs to examine the cellular effects of genetic variants that modulate the efficacy of statins, the most prescribed class of cholesterol-lowering drugs used for the prevention and treatment of cardiovascular disease. However, statin-induced gene expression differences observed in LCLs may be influenced by their transformation, and thus differ from those observed in native B-cells. To assess this possibility, we prepared LCLs and purified B-cells from the same donors, and compared mRNA profiles after 24 h incubation with simvastatin (2 µm) or sham buffer. Genes involved in cholesterol metabolism were similarly regulated between the two cell types under both the statin and sham-treated conditions, and the statin-induced changes were significantly correlated. Genes whose expression differed between the native and transformed cells were primarily implicated in cell cycle, apoptosis and alternative splicing. We found that ChIP-seq signals for MYC and EBNA2 (an EBV transcriptional co-activator) were significantly enriched in the promoters of genes up-regulated in the LCLs compared with the B-cells, and could be involved in the regulation of cell cycle and alternative splicing. Taken together, the results support the use of LCLs for the study of statin effects on cholesterol metabolism, but suggest that drug effects on cell cycle, apoptosis and alternative splicing may be affected by EBV transformation. This dataset is now uploaded to GEO at the accession number GSE51444.

BackgroundThe creation of lymphoblastoid cell lines (LCLs) through Epstein-Barr virus (EBV) transformation of B-lymphocytes can result in a valuable biomaterial for cell biology research and a renewable source of DNA. While LCLs have been used extensively in cellular and genetic studies, the process of cell transformation and expansion during culturing may introduce genomic changes that may impact their use and the interpretation of subsequent genetic findings.ResultsWe performed whole exome sequencing on a tetrad family using DNA derived from peripheral blood mononuclear cells (PBMCs) and LCLs from each individual. We generated over 4.7 GB of mappable sequence to a 125X read coverage per sample. An average of 19,354 genetic variants were identified. Comparison of the two DNA sources from each individual showed an average concordance rate of 95.69%. By lowering the variant calling parameters, the concordance rate between the paired samples increased to 99.82%. Sanger sequencing of a subset of the remaining discordant variants did confirm the presence of de novo mutations arising in LCLs.ConclusionsBy varying software stringency parameters, we identified 99% concordance between DNA sequences derived from the two different sources from the same donors. These results suggest that LCLs are an appropriate representation of the genetic material of the donor and suggest that EBV transformation can result in low-level generation of de novo mutations. Therefore, use of PBMC or early passage EBV-transformed cells is recommended. These findings have broad-reaching implications, as there are thousands of LCLs in public biorepositories and individual laboratories.

Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional genomic studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. A lingering concern, however, is that the changes associated with EBV transformation of B cells reduce the usefulness of LCLs as a surrogate model for primary tissues. To evaluate the validity of this concern, we compared global gene expression and methylation profiles between CD20+ primary B cells sampled from six individuals and six independent replicates of transformed LCLs derived from each sample. These data allowed us to obtain a detailed catalog of the genes and pathways whose regulation is affected by EBV transformation. We found that the expression levels and promoter methylation profiles of more than half of the studied genes were affected by the EBV transformation, including enrichments of genes involved in transcription regulation, cell cycle and immune response. However, we show that most of the differences in gene expression levels between LCLs and B cells are of small magnitude, and that LCLs can often recapitulate the naturally occurring gene expression variation in primary B cells. Thus, our observations suggest that inference of the genetic architecture that underlies regulatory variation in LCLs can typically be generalized to primary B cells. In contrast, inference based on functional studies in LCLs may be more limited to the cell lines.

Epstein-Barr virus (EBV) is a member of the g-herpesvirus family estimated to infect 90% of the world’s population. Despite the high prevalence of infection, EBV-associated malignancies are largely kept in check by a strong cytotoxic T cell immune response. However, EBV causes lymphoproliferative disease in immune-deficient individuals and plays a role in the pathogenesis of African Burkitt lymphoma, Hodgkin’s disease, and nasopharyngeal carcinoma. In vitro, EBV infection of B cells results in proliferation and outgrowth of indefinitely proliferating lymphoblastoid cell lines (LCLs). Thus, LCLs represent a viable model for the pathogenesis of EBV-associated malignancies. microRNAs are small noncoding RNAs that posttranscriptionally regulate gene expression to control a variety of processes including development, cell cycle, and immunity. Their role in EBV transformation and lymphomas is currently not well understood. Results Using a miRNA microarray, we identified a number of cellular miRNAs that were over- or under-expressed comparing resting CD19+ B cells to EBV-infected, proliferating B cells and immortalized LCLs. In particular, we focused on miR-34a, whose expression was induced by EBV. This miRNA has been previously reported to be a pro-apoptotic target of p53 implicated in the response to DNA damage. Surprisingly, contrary to its regulation in other cell types, miR-34a was not found to be p53 responsive in LCLs. In order to understand the functional role of this miRNA in EBV transformation, we constructed a miRNA sponge. miR-34a knockdown in LCLs showed that these cells depend on normal miR34a expression to proliferate and to aggregate. Conclusions

Generation of human monoclonal antibodies by transformation of lymphoblastoid B cells with ras oncogene

A Lymphoma cell line from the tumor tissue was established spontaneously from a Japanese patient with Epstein-Barr virus (EBV) genome-positive Burkitt's lymphoma (BL). Additionally lymphoblastoid cell lines from peripheral blood of this patient were established either spontaneously or by in vitro infection with B95-8 EBV. Lymphoma cells showed monoclonal surface immunoglobulins (kappa and gamma) with specific chromosomal translocations, t (8; 14). In contrast, lymphoblastoid cells expressed polyclonal surface immunoglobulins without specific chromosomal abnormalities. Lymphoma cells made colonies in soft agarose approximately 10 times more than those of the lymphoblastoid cells. When each cell line was cultured at lower temperature of 33 degrees C, treated with 12-O-tetradecanoyl- phorbol-13-acetate (TPA), and superinfected with P3HR-1 EBV, all cell lines expressed 5 to 10 times higher levels of EBV early antigens (EA) and viral capsid antigen (VCA) than lymphoblastoid cell lines from healthy controls. Furthermore, lymphoblastoid cell lines obtained from peripheral blood of this patient during the period of remission also exhibited high EA and VCA inducibility and superinfectibility. These findings suggested that the lymphoid cells in this patient were genetically highly susceptible to EBV infection, and this evidence possibly linked to the lymphomagenesis of EBV genome-positive BL.

Epstein-Barr virus (EBV) transformation has been described as a routine method to establish human B lymphoblastoid cell lines. Each established lymphoblastoid cell line represents one unique genetic information carrier and can produce unlimited quantities of DNA materials available for downstream applications and research. Undoubtedly, it is of great value to human clinical and experimental genetic studies. However, the current process of EBV transformation requires much manpower in the routine renewal of medium, which is time-consuming. This situation can become a serious problem especially when establishing a human B lymphoblastoid cell bank. A modified and cost-effective protocol for EBV transformation should be considered. In the present study, process in EBV transformation was modified to fit the requirements of robot handling. 1 mL of whole blood was demonstrated to be sufficient to perform EBV transformation. Additionally, EBV transformation can performed in 96-deep-well plates that are directly and widely used with automatic work platforms. Based on these facts, a process of EBV transformation can be modified to fit the requirements of robot handling.

BackgroundA detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of a subject’s DNA. Although the mechanism of transformation and immortalization by EBV is relatively well known at the transcriptional and proteomic level, the genetic consequences of EBV transformation are less well understood. A detailed analysis of the genetic alterations introduced by EBV transformation is highly relevant, as it will inform on the usefulness and limitations of this approach.ResultsWe used whole genome sequencing to assess the genomic signature of a low-passage lymphoblastoid cell line (LCL). Specifically, we sequenced the full genome (40X) of an individual using DNA purified from fresh whole blood as well as DNA from his LCL. A total of 217.33 Gb of sequence were generated from the cell line and 238.95 Gb from the normal genomic DNA. We determined with high confidence that 99.2% of the genomes were identical, with no reproducible changes in structural variation (chromosomal rearrangements and copy number variations) or insertion/deletion polymorphisms (indels).ConclusionsOur results suggest that, at this level of resolution, the LCL is genetically indistinguishable from its genomic counterpart and therefore their use in clinical research is not likely to introduce a significant bias.

Unsuitability of lymphoblastoid cell lines as surrogate of cryopreserved isolated lymphocytes for the analysis of DNA double-strand break repair activity

Previous results indicated that lymphoblastoid cell lines (LCL) with a BRCA1 mutation are hypersensitive to the chromosome-damaging effects of gamma irradiation or hydrogen peroxide as revealed by the micronucleus test. We now investigated six LCL (three with and three without a BRCA1 mutation) in more detail, to see whether LCL represent a useful model for the investigation of mechanisms responsible for the known mutagen sensitivity of lymphocytes from women carrying a BRCA1 mutation. Our results show that there is no systematic difference in radiation sensitivity between LCL with and without a BRCA1 mutation. Spontaneous and gamma radiation-induced micronucleus frequencies were in same range. Furthermore, cytotoxic effects (reduced cell proliferation, reduced viability) induced by gamma radiation were not different. The only difference found was an induction of micronuclei by 10 microM hydrogen peroxide in BRCA1 cell lines while a concentration of 20 microM hydrogen peroxide was necessary to induce micronuclei in control cells. Comet assay experiments did not reveal differences with regard to the induction and removal of primary DNA damage. Furthermore, expression of BRCA1 mRNA after gamma irradiation showed considerable variability and there was no clear difference between cell lines with and without BRCA mutation. These results indicate that LCL with a BRCA1 mutation do not generally show the same mutagen sensitivity as lymphocytes with the same BRCA1 mutation. Therefore, the use of LCL to study the mechanisms underlying mutagen sensitivity due to a heterozygous BRCA1 mutation seems to be limited.

Previous studies have demonstrated that approximately one-third of human lymphoblastoid cell lines (LCLs) are deficient in removing O6-methylguanine residues because of the lack of O6-alkylguanine-DNA alkyltransferase (O6-AGT) activity. Such LCLs have been designated Mex-, while the proficient LCLs are Mex+. Our determinations of O6-AGT activity as a function of cellular protein concentration on 37 previously-established LCLs disclosed that the expression of the enzyme was high in 14 (Mex+) and barely detectable in 16 (Mex-). The other seven LCLs showed intermediate activity of the enzyme. By contrast, all of the 28 LCLs that we newly established contained high enzyme activity, implying that they consisted of mainly Mex+ cells. Since the conventional O6-AGT assay on Mex+ cell populations was not capable of detecting the co-existence of Mex- cells as a minor component, we attempted to determine the proportion of Mex- phenotype in newly-immortalized lymphoblastoid cell clones which had been established directly on semisolid agar. All of the 15 independent clones derived from a single blood sample also showed high O6-AGT activity, rendering it unlikely that Epstein-Barr virus transformation per se was responsible for the generation of Mex- LCLs. These results collectively indicate that Mex+ cells predominate in LCLs shortly after establishment and also suggest that the possible growth advantage for Mex- cells should play an important role in the subsequent development of Mex- LCLs during the long-term culture in vitro.

Stathmin is an important microtubule (MT)-destabilizing protein, and its activity is differently attenuated by phosphorylation at one or more of its four phosphorylatable serine residues (Ser-16, Ser-25, Ser-38, and Ser-63). This phosphorylation of stathmin plays important roles in mitotic spindle formation. We observed increasing levels of phosphorylated stathmin in Epstein-Barr virus (EBV)-harboring lymphoblastoid cell lines (LCLs) and nasopharyngeal carcinoma (NPC) cell lines during the EBV lytic cycle. These suggest that EBV lytic products may be involved in the regulation of stathmin phosphorylation. BGLF4 is an EBV-encoded kinase and has similar kinase activity to cdc2, an important kinase that phosphorylates serine residues 25 and 38 of stathmin during mitosis. Using an siRNA approach, we demonstrated that BGLF4 contributes to the phosphorylation of stathmin in EBV-harboring NPC. Moreover, we confirmed that BGLF4 interacts with and phosphorylates stathmin using an in vitro kinase assay and an in vivo two-dimensional electrophoresis assay. Interestingly, unlike cdc2, BGLF4 was shown to phosphorylate non-proline directed serine residues of stathmin (Ser-16) and it mediated phosphorylation of stathmin predominantly at serines 16, 25, and 38, indicating that BGLF4 can down-regulate the activity of stathmin. Finally, we demonstrated that the pattern of MT organization was changed in BGLF4-expressing cells, possibly through phosphorylation of stathmin. In conclusion, we have shown that a viral Ser/Thr kinase can directly modulate the activity of stathmin and this contributes to alteration of cellular MT dynamics and then may modulate the associated cellular processes.

BackgroundSemi-immunity against the malaria parasite is defined by a protection against clinical episodes of malaria and is partially mediated by a repertoire of inhibitory antibodies directed against the blood stage of Plasmodium falciparum, in particular against surface proteins of merozoites, the invasive form of the parasite. Such antibodies may be used for preventive or therapeutic treatment of P.falciparum malaria. Here, the isolation and characterization of novel human monoclonal antibodies (humAbs) for such applications is described.MethodsB lymphocytes had been selected by flow cytometry for specificity against merozoite surface proteins, including the merozoite surface protein 10 (MSP10). After Epstein-Barr virus (EBV) transformation and identification of promising resulting lymphoblastoid cell lines (LCLs), human immunoglobulin heavy and light chain variable regions (Vh or Vl regions) were secured, cloned into plant expression vectors and transiently produced in Nicotiana benthamiana in the context of human full-size IgG1:κ. The specificity and the affinity of the generated antibodies were assessed by ELISA, dotblot and surface plasmon resonance (SPR) spectroscopy. The growth inhibitory activity was evaluated based on growth inhibition assays (GIAs) using the parasite strain 3D7A.ResultsSupernatants from two LCLs, 5E8 and 5F6, showed reactivity against the second (5E8) or first (5F6) epidermal growth factor (EGF)-like domain of MSP10. The isolated V regions were recombinantly expressed in their natural pairing as well as in combination with each other. The resulting recombinant humAbs showed affinities of 9.27 × 10−7 M [humAb10.1 (H5F6:κ5E8)], 5.46 × 10−9 M [humAb10.2 (H5F6:κ5F6)] and 4.34 × 10−9 M [humAb10.3 (H5E8:κ5E8)]. In GIAs, these antibodies exhibited EC50 values of 4.1 mg/ml [95% confidence interval (CI) 2.6–6.6 mg/ml], 6.9 mg/ml (CI 5.5–8.6 mg/ml) and 9.5 mg/ml (CI 5.5–16.4 mg/ml), respectively.ConclusionThis report describes a platform for the isolation of human antibodies from semi-immune blood donors by EBV transformation and their subsequent characterization after transient expression in plants. To our knowledge, the presented antibodies are the first humAbs directed against P. falciparum MSP10 to be described. They recognize the EGF-like folds of MSP10 and bind these with high affinity. Moreover, these antibodies inhibit P. falciparum 3D7A growth in vitro.

Lymphoblastoid cell lines (LCLs) have been by far the most prevalent cell type used to study the genetics underlying normal and disease-relevant human phenotypic variation, across personal to epidemiological scales. In contrast, only few studies have explored the use of LCLs in functional genomics and mechanistic studies. Two major reasons are technical, as (1) interrogating the sub-cellular spatial information of LCLs is challenged by their non-adherent nature, and (2) LCLs are refractory to gene transfection. Methodological details relating to techniques that overcome these limitations are scarce, largely inadequate (without additional knowledge and expertise), and optimisation has never been described. Here we compare, optimise, and convey such methods in-depth. We provide a robust method to adhere LCLs to coverslips, which maintained cellular integrity, morphology, and permitted visualisation of sub-cellular structures and protein localisation. Next, we developed the use of lentiviral-based gene delivery to LCLs. Through empirical and combinatorial testing of multiple transduction conditions, we improved transduction efficiency from 3% up to 48%. Furthermore, we established strategies to purify transduced cells, to achieve sustainable cultures containing >85% transduced cells. Collectively, our methodologies provide a vital resource that enables the use of LCLs in functional cell and molecular biology experiments. Potential applications include the characterisation of genetic variants of unknown significance, the interrogation of cellular disease pathways and mechanisms, and high-throughput discovery of genetic modifiers of disease states among others.

In order to understand mechanistic relationships between signaling pathways regulating mitogen-activated protein kinase (MAPK) phosphorylation and Epstein-Barr virus (EBV) reactivation, we compared MAPK phosphorylation, and EBV reactivation and latency in Burkitt's lymphoma cell lines (BLCLs) versus B lymphoblastoid cell lines (LCLs). EBV was reactivated in the BLCLs Akata and Raji, and in a LCL OB-R33 cells after cross-linking surface immunoglobulin (sIg) with anti-Ig. After stimulation with anti-Ig, MAPK phosphorylation was strongly induced in all BLCLs and in a few LCLs, but not in other LCLs. MAPK was constitutively phosphorylated in most LCLs but not in BLCLs. Expression of EBNA2 and LMP1, and LMP2A was analyzed with both immunoblotting and RT-PCR. EBNA2 and LMP1 were expressed in most LCLs and in some BLCLs. LMP2A was expressed in all BLCLs and LCLs except Namalwa cells. To test the hypothesis that LMPI induces constitutive MAPK phosphorylation, the LMP1 expression vector was transfected into Akata cells. MAPK phosphorylation was not induced in such transfected cells. Our results indicate that BLCLs and LCLs respectively have distinct MAPK phosphorylation patterns, and that induction of MAPK phosphorylation correlates with EBV reactivation in a few cell lines but not in most of the tested cell lines.