Primary effect of chemotherapy on the transcription profile of AIDS-related Kaposi's sarcoma

Gene Expression: the Key to Understanding HIV-1 Infection?

Gene expression profiling of the host response to HIV infection has promised to fill the gaps in our knowledge and provide new insights toward vaccine and cure. However, despite 20 years of research, the biggest questions remained unanswered. A literature review identified 62 studies examining gene expression dysregulation in samples from individuals living with HIV. Changes in gene expression were dependent on cell/tissue type, stage of infection, viremia, and treatment status. Some cell types, notably CD4⁺ T cells, exhibit upregulation of cell cycle, interferon-related, and apoptosis genes consistent with depletion. Others, including CD8⁺ T cells and natural killer cells, exhibit perturbed function in the absence of direct infection with HIV. Dysregulation is greatest during acute infection. Differences in study design and data reporting limit comparability of existing research and do not as yet provide a coherent overview of gene expression in HIV. This review outlines the extraordinarily complex host response to HIV and offers recommendations to realize the full potential of HIV host transcriptomics.

Athymic nude mice as an experimental model for cancer treatment

Athymic nude mice, a murine strain bearing spontaneous deletion in the Foxn1 gene that causes deteriorated or absent thymus (which results in inhibited immune system with reduction of number of T cells), represent a widely used model in cancer research having long lasting history as a tool for preclinical testing of drugs. The review describes three models of athymic mice that utilize cancer cell lines to induce tumors. In addition, various methods that can be applied in order to evaluate activity of anticancer agents in these models are shown and discussed. Although each model has certain disadvantages, they are still considered as inevitable instruments in many fields of cancer research, particularly in finding new drugs that would more effectively combat the cancer disease or enhance the use of current chemotherapy. Finally, the review summarizes strengths and weaknesses as well as future perspectives of the athymic nude mice model in cancer research.

Expression of Kaposi's sarcoma-associated herpesvirus-encoded K10/10.1 protein in tissues and its interaction with poly(A)-binding protein

The K10/10.1 protein is encoded by a cluster of interferon regulatory factor (IRF) homologues in the Kaposi's sarcoma-associated herpesvirus (KSHV, human herpesvirus 8, HHV-8) genome. In the present study, we showed that an anti-K10 antibody reacted with a 110-kDa protein encoded by the K10/10.1 gene of KSHV in KSHV-infected primary effusion lymphoma (PEL) cell lines. Expression of K10/10.1 protein was induced by phorbol ester in KSHV-infected cells. A reporter gene assay demonstrated that K10/10.1 protein did not influence promoter activity of human interferon genes, regardless of its homology to human IRFs. Poly(A)-binding protein (PABP) was identified as a partner of K10/10.1 protein. Immunoprecipitation revealed that K10/10.1 protein interacted with PABP specifically in PEL cell lines. IFA revealed co-localization of K10/10.1 protein and PABP in the nucleus of KSHV-infected cells. These data suggest that K10/10.1 protein may affect the translational status or stability of mRNA in host cells.

Cancer target discovery using SAGE

Cancer is a genetic disease. Genetic events including mutations, chromosomal gains, losses and rearrangements, along with epigenetic alterations, lead to significant transcriptional changes in cancer cells. Changes in the expression of many genes associated with the onset and progression of cancer likely contribute to the cancerous phenotype. SAGE (Serial Analysis of Gene Expression) is an expression profiling method that allows for global, unbiased and quantitative characterisation of transcriptomes. The expression of thousands of genes can be analysed simultaneously without prior knowledge of their sequence, thus leading to the discovery of novel transcripts. In addition to characterising normal and malignant gene expression patterns, SAGE can be used to identify downstream targets of tumour suppressors and oncogenes and further annotate genomes. Comprehensive analyses of expression profiles using SAGE will yield many new diagnostic and prognostic markers as well as therapeutic targets in cancer.

Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping

The identity and developmental potential of a human cell is specified by its epigenome that is largely defined by patterns of chromatin modifications including histone acetylation. Here we report high-resolution genome-wide mapping of diacetylation of histone H3 at Lys 9 and Lys 14 in resting and activated human T cells by genome-wide mapping technique (GMAT). Our data show that high levels of the H3 acetylation are detected in gene-rich regions. The chromatin accessibility and gene expression of a genetic domain is correlated with hyperacetylation of promoters and other regulatory elements but not with generally elevated acetylation of the entire domain. Islands of acetylation are identified in the intergenic and transcribed regions. The locations of the 46,813 acetylation islands identified in this study are significantly correlated with conserved noncoding sequences (CNSs) and many of them are colocalized with known regulatory elements in T cells. TCR signaling induces 4045 new acetylation loci that may mediate the global chromatin remodeling and gene activation. We propose that the acetylation islands are epigenetic marks that allow prediction of functional regulatory elements.

Serial analysis of gene expression (SAGE): advances, analysis and applications to pigment cell research

As cells progress from normal to diseased states, they may undergo a series of gene expression changes. Advances in molecular biology allow us to examine a host of these changes at once, in a high throughput fashion. Serial analysis of gene expression (SAGE) allows for the expression profiling of the complete transcriptome of a given cell, and has the potential for identifying novel genes as well as those in low abundance. In this review, we will outline the technique, how one analyzes the massive amounts of data generated, and describe pigment cell libraries currently in the making.

Gene expression profile of AIDS-related Kaposi's sarcoma

BACKGROUND

Kaposi's Sarcoma (KS) is a proliferation of aberrant vascular structures lined by spindle cells, and is caused by a gammaherpes virus (HHV8/KSHV). Its course is aggravated by co-infection with HIV-1, where the timing of infection with HIV-1 and HHV8 is important for the clinical outcome.

METHODS

In order to better understand the pathogenesis of KS, we have analysed tissue from two AIDS-KS lesions, and from normal skin by serial analysis of gene expression (SAGE). Semi-quantitative RT-PCR was then used to validate the results.

RESULTS

The expression profile of AIDS-related KS (AIDS-KS) reflects an active process in the skin. Transcripts of HHV8 were found to be very low, and HIV-1 mRNA was not detected by SAGE, although it could be found using RT-PCR. Comparing the expression profile of AIDS-KS tissue with publicly available SAGE libraries suggested that AIDS-KS mRNA levels are most similar to those in an artificially mixed library of endothelial cells and leukocytes, in line with the description of KS lesions as containing spindle cells with endothelial characteristics, and an inflammatory infiltrate. At least 64 transcripts were found to be significantly elevated, and 28 were statistically downregulated in AIDS-KS compared to normal skin. Five of the upregulated mRNAs, including Tie 1 and sialoadhesin/CD169, were confirmed by semi-quantitative PCR to be elevated in additional AIDS-KS biopsies. Antibodies to sialoadhesin/CD169, a known marker of activated macrophages, were shown to specifically label tumour macrophages.

CONCLUSION

The expression profile of AIDS-KS showed 64 genes to be significantly upregulated, and 28 genes downregulated, compared with normal skin. One of the genes with increased expression was sialoadhesin (CD169). Antibodies to sialoadhesin/CD169 specifically labelled tumour-associated macrophages, suggesting that macrophages present in AIDS-KS lesions belong to a subset of human CD169+ macrophages.