Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray.

BACKGROUND: The Epstein-Barr virus (EBV) is associated with lymphoid malignancies, including Burkitt's lymphoma (BL), and can transform human B cells in vitro. EBV-harboring cell lines are widely used to investigate lymphocyte transformation and oncogenesis. Qualitative EBV gene expression has been extensively described, but knowledge of quantitative transcription is lacking. We hypothesized that transcription levels of EBNA1, the gene essential for EBV persistence within an infected cell, are similar in BL cell lines. RESULTS: To compare quantitative gene transcription in the BL cell lines Namalwa, Raji, Akata, Jijoye, and P3HR1, we developed an oligonucleotide microarray chip, including 17 housekeeping genes, six latent EBV genes (EBNA1, EBNA2, EBNA3A, EBNA3C, LMP1, LMP2), and four lytic EBV genes (BZLF1, BXLF2, BKRF2, BZLF2), and used the cell line B95.8 as a reference for EBV gene transcription. Quantitative polymerase chain reaction assays were used to validate microarray results. We found that transcription levels of housekeeping genes differed considerably among BL cell lines. Using a selection of housekeeping genes with similar quantitative transcription in the tested cell lines to normalize EBV gene transcription data, we showed that transcription levels of EBNA1 were quite similar in very different BL cell lines, in contrast to transcription levels of other EBV genes. As demonstrated with Akata cells, the chip allowed us to accurately measure EBV gene transcription changes triggered by treatment interventions. CONCLUSION: Our results suggest uniform EBNA1 transcription levels in BL and that microarray profiling can reveal novel insights on quantitative EBV gene transcription and its impact on lymphocyte biology.

Human tonsillar tissue block cultures differ from autologous tonsillar cell suspension cultures in lymphocyte subset activation and cytokine gene expression.

Lymphoid tissues cultured either as tissue blocks or as cell suspensions are used to study the behaviour of immune cells within their habitat. The preservation of tissue structures in tissue blocks, which is considered to be a major advantage, has been poorly defined. We characterised the morphological evolution of tissue cultures from human palatine tonsils and compared their lymphocyte subsets and the constitutive cytokine gene expression to those in autologous tonsillar single-cell suspension cultures over time, and after adding cyclosporin A (CsA) to mimic the situation in individuals treated with immunosuppressive drugs. Density and morphology of follicles were conserved up to 4 days, during which tissue cultures exhibited similar cell viability as suspension cultures, but a significantly less frequent increase of CD95 expression in T cells, smaller variation of the proportion of CD4(+) cells and better CD21(+)/CD23(-) B-cell survival. Treatment with cyclosporin A at higher concentrations resulted in superior histologic preservation of lymphoid tissue structures and seemed to further prevent the expression of CD95 by CD3(+) cells and the activation in tissue culture of CD21(+) cells. Constitutive gene expression levels of the stromal cytokines interleukin (IL)-1beta and interleukin-6 in tissue culture were significantly higher than those in suspension cultures. These results suggest that tonsillar tissue cultures preserve their structure only for a limited time, during which they more closely reflect processes in vivo, including a state of iatrogenic immunosuppression, than do their cell suspension counterparts.

HIV-1 does not provoke alteration of cytokine gene expression in lymphoid tissue after acute infection ex vivo.

The cytokine response to invading microorganisms is critical for priming the adaptive immune response. During acute HIV infection, the response is disrupted, but the mechanism is poorly understood. We examined the cytokine response in human lymphoid tissue, acutely infected ex vivo with HIV. Lymphoid tissue was cultured either as blocks or as human lymphocyte aggregate cultures (HLAC) of tonsils and lymph nodes. This approach allowed us to examine the effects of HIV on cytokines using distinct culture techniques. In contrast to HLAC, mock-infected tissue blocks displayed a 50- to 100-fold up-regulation of mRNAs for IL-1beta, -6, and -8 in the first 6 days of culture. Parallel increases were also noted at the protein level in the supernatants. Although IL-1beta, -6, and -8 are known to synergistically enhance HIV replication, peak HIV replication (measured as p24 Ag) was similar in tissue blocks and HLAC. Surprisingly, vigorous HIV replication of CXCR4- and CCR5-tropic HIV strains did not result in characteristic mRNA profiles for IL-1beta, -2, -4, -6, -8, -10, -12, -15, IFN-gamma, TNF-alpha, TGF-beta, and beta-chemokines in tissue blocks or HLAC. The increased expression of IL-1beta, -6, and -8 in tissue blocks may approximate clinical situations with heightened immune activation; neutralization of these cytokines resulted in inhibition of HIV replication, suggesting that these cytokines may contribute to HIV replication in certain clinical settings. These results also indicate that different molecular mechanisms govern HIV replication in tissue blocks and HLAC. Prevention of effective cytokine responses may be an important mechanism that HIV uses during acute infection.

Quantitative cytokine gene expression in human tonsils at excision and during histoculture assessed by standardized and calibrated real-time PCR and novel data processing.

Real-time reverse transcription polymerase chain reaction (RT-PCR) assays were developed for the quantification of expression of the genes for human interleukin (IL)-1beta, IL-2, IL-6, IL-8, IL-10, IL-12, IL-15, interferon (IFN)-gamma, tumor necrosis factor (TNF)-alpha, transforming growth factor (TGF)-beta and for the endogenous reference hydroxymethylbilane synthase (HMBS). The assays detected as little as five plasmid copies and were 100% specific. The creation and integration of a calibration sample into the assays permitted their calibration across experiments. To handle the high number of generated data, the correlator of advanced real-time assays (CARTA) software was designed to organize samples and to automatically control and analyze TaqMan real-time RT-PCR data. The RT-PCR assays were applied to quantify levels of cytokine gene expression in human palatine tonsils at excision and during 4 days of histoculture. Similar longitudinal patterns of cytokine gene expression were observed in all donors, but the variations in spontaneous expression levels between donors were large. The expression levels in histocultures were constant over time and similar to the expression levels at excision except for IL-6 and IL-8, which markedly increased following the first 24 h of culture, possibly due to the initial stress. The standardized and calibrated RT-PCR assays quantify gene expression of human cytokines proved sensitive and specific for the investigation of cell behavior at the molecular level and the newly established CARTA software, a reliable tool for rapid data handling. Tonsil histocultures could serve as a valuable ex vivo model system for further, donor-dependent, studies on activation or repression of cytokine gene expression.

Monitoring intracellular replication of Chlamydophila (Chlamydia) pneumoniae in cell cultures and comparing clinical samples by real-time PCR.

Strains of Chlamydophila pneumoniae may be associated with respiratory disease or atherosclerosis. Two real-time quantitative PCR assays targeting the species-specific genes Cpn0278 and ArgR were developed to compare the in vitro growth of respiratory strains AR39 and K6 with that of atherosclerotic strain A03 and to quantify C. pneumoniae in clinical samples. A third real-time PCR assay was designed to assess contamination with Mycoplasma spp. The assays targeting C. pneumoniae detected DNA concentrations corresponding to 10(4) to 10(-4) inclusion-forming units (IFU)/reaction and were highly specific. AR39 exhibited the longest lag phase and period of exponential growth; K6 augmented growth rates at higher inocula; and A03 grew at highest rates. Contamination with Mycoplasma spp. of AR39 and A03 unlikely accounted for growth differences between them. Numbers of IFU in C. pneumoniae-positive respiratory secretions varied within 4 to 5 orders of magnitude. The assays described may prove valuable for pathogenicity studies.