Distinct subsets of primary effusion lymphoma can be identified based on their cellular gene expression profile and viral association - PubMed (original) (raw)
Distinct subsets of primary effusion lymphoma can be identified based on their cellular gene expression profile and viral association
Wen Fan et al. J Virol. 2005 Jan.
Abstract
Primary effusion lymphomas (PELs) are specifically associated with Kaposi's sarcoma-associated herpesvirus (KSHV) infection and most frequently occur in human immunodeficiency virus (HIV)-positive individuals as lymphomatous effusions in the serous cavities without a detectable solid tumor mass. Most PELs have concomitant Epstein-Barr virus (EBV) infection, suggesting that EBV is an important pathogenetic cofactor, although other as yet unidentified cofactors, such as cellular genetic alterations, are also likely to play a role. Lymphomatous effusions that lack KSHV also occur; these are frequently EBV associated in the setting of HIV infection. Here we used gene expression profile analysis to determine the viral impact on cellular gene expression and the pathogenesis of these lymphomatous effusions. Our results show that many genes, including cell cycle and signal transduction regulators, are differentially expressed between KSHV-positive PELs and KSHV-negative lymphomatous effusions and also between KSHV-positive, EBV-positive and KSHV-positive, EBV-negative PELs. Our results confirm that KSHV plays an important role in the pathogenesis of PELs, as its presence selects for a very distinct cellular gene expression category and a clearly different lymphoma type. Within the KSHV-positive PELs, the effect of EBV is more subtle but nevertheless clear.
Figures
FIG. 1.
Clustering of gene expression in all PELs and lymphomatous effusions. (A) Unsupervised hierarchical clustering of gene expression analysis was performed on 11,024 genes when raw expression data were greater than 150 in at least one of the 18 samples with Pearson correlation. The number above each line indicates the vertical length of each line as the correlation of relatedness. The sample dendrogram shows that all six KSHV-positive PEL cell lines (BC-1, BC-2, BC-5, PEL-5, BC-3, and BCBL) are clustered under one branch, showing the high degree of similarity in gene expression pattern. Three KSHV-negative cell lines obtained from lymphomatous effusions (BCKN-1, IBL-4, and SM-1) clustered under the other branch. This figure shows that KSHV-positive PEL are clearly different from KSHV-negative lymphomatous effusions. (B) Hierarchical clustering of statistically differentially expressed genes among KSHV-positive, EBV-positive PELs, KSHV-positive, EBV-negative PELs, and KSHV-negative, EBV-positive lymphomatous effusions is shown. Each column represents an individual sample. Those with the most similar gene expression patterns are clustered under one branch. Each row represents an individual gene. The color of each cell represents the relative gene expression level according to the color scale shown at the right side. KSHV-positive PELs have a distinct gene expression profile compared to KSHV-negative, EBV-positive lymphomatous effusions. Half of the genes are upregulated and the other half are downregulated in the PEL group compared to the KSHV-negative, EBV-positive lymphomatous effusions. Among 514 differentially expressed genes are apoptosis regulators, cell cycle regulators, transcriptional factors, and signal transduction regulators.
FIG. 2.
Hierarchical clustering of 40 statistically differentially expressed genes between KSHV-positive, EBV-positive PELs (three cell lines), KSHV-positive, EBV-negative PELs (three cell lines), and KSHV-negative, EBV-positive lymphomatous effusions (3 cell lines). Of 45 probes representing 40 different genes, SKAP55R (Src family-associated phosphoprotein 2 or SKAP55-related protein), p38δ (mitogen-activated protein kinase 13, SAPK4), GADD45β, and caspase 1 (ICE) are involved in the mitogen-activated protein kinase pathway. All these genes are upregulated in the KSHV-positive, EBV-negative PEL group. MKK4 is also a component of the JNK/p38 mitogen-activated protein kinase pathway and is upregulated in the KSHV-positive, EBV-positive PELs.
FIG. 3.
Western blot confirming the expression of p38δ/mitogen-activated protein kinase 13/SAPK4 in KSHV-positive PEL cell lines. Expression of p38δ protein in all PEL cell lines is shown in the upper row. Expression of actin protein is shown in the lower row. All KSHV-positive, EBV-negative PEL cell lines have high expression of p38δ. All KSHV-positive, EBV-positive PEL cell lines except JSC-1 have low or no expression of p38δ.
FIG. 4.
Pattern of EBV and KSHV positivity in PEL in vivo. In situ hybridization for EBER was performed in three cases of PEL without previous culture. Patient 1 showed strung positivity in all the cells, mostly nuclear but also spilling into the cytoplasm. Patient 2 showed only a small proportion of EBER-positive cells. Patient 3 was negative. Immunohistochemistry for KSHV in the specimens from the three patients showed that the vast majority of cells were positive for LANA, and a proportion also expressed viral IL-6. Magnification, 400×.
FIG. 5.
Viral status of three primary patient samples can be predicted with the 45 gene probes generated from supervised clustering. Hierarchical clustering of nine cell lines and three primary patient samples was based on 45 gene probes. The number above or below each horizontal line indicates the vertical distance of each line as the correlation of relatedness. The dendrogram shows that patient 1 was correctly clustered under one branch with the KSHV-positive, EBV-positive PELs, and patients 2 and 3 was correctly clustered under one branch with the KSHV-positive, EBV-negative PELs.
References
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