Gene expression profiling of diffuse large B-cell lymphoma supervised by CD21 expression

Effects of Different-Syllable Aggressive Calls on Food Intake and Gene Expression in Vespertilio sinensis

Social animals enjoy colony benefits but are also exposed to social stress, which affects their physiology in many ways, including alterations to their energy intake, metabolism, and even gene expression. Aggressive calls are defined as calls emitted during aggressive conflicts between individuals of the same species over resources, such as territory, food, or mates. Aggressive calls produced by animals in different aggressive states indicate different levels of competitive intentions. However, whether aggressive calls produced in different aggressive states exert different physiological effects on animals has yet to be determined. Importantly, bats live in clusters and frequently produce aggressive calls of different syllables, thus providing an ideal model for investigating this question. Here, we conducted playback experiments to investigate the effects of two types of aggressive calls representing different competitive intentions on food intake, body mass, corticosterone (CORT) concentration, and gene expression in Vespertilio sinensis. We found that the playback of both aggressive calls resulted in a significant decrease in food intake and body mass, and bats in the tonal-syllable aggressive-calls (tonal calls) playback group exhibited a more significant decrease when compared to the noisy-syllable aggressive-calls (noisy calls) playback group. Surprisingly, the weight and food intake in the white-noise group decreased the most when compared to before playback. Transcriptome results showed that, when compared to the control and white-noise groups, differentially expressed genes (DEGs) involved in energy and metabolism were detected in the noisy-calls playback group, and DEGs involved in immunity and disease were detected in the tonal-calls playback group. These results suggested that the playback of the two types of aggressive calls differentially affected body mass, food intake, and gene expression in bats. Notably, bat responses to external-noise playback (synthetic white noise) were more pronounced than the playback of the two aggressive calls, suggesting that bats have somewhat adapted to internal aggressive calls. Comparative transcriptome analysis suggested that the playback of the two syllabic aggressive calls disrupted the immune system and increased the risk of disease in bats. This study provides new insight into how animals differ in response to different social stressors and anthropogenic noise.

Novel tumor markers provide improved prediction of survival after diagnosis of human immunodeficiency virus (HIV)-related diffuse large B-cell lymphoma

Existing prognostic tools for HIV + diffuse large B-cell lymphoma (DLBCL) fail to accurately predict patient outcomes. To develop a novel prognostic algorithm incorporating molecular tumor characteristics and HIV disease factors, we included 80 patients with HIV-related DLBCL diagnosed between 1996 and 2007. Immunohistochemistry staining was used to analyze the expression of 26 tumor markers. Clinical data were collected from medical records. Logistic regression and bootstrapping were used to select and assess stability of the prognostic model, respectively. Of the tumor markers examined, expression of cMYC, Ki 67, CD44, EBV, SKP2, BCL6, p53, CD20 and IgM were associated with two-year mortality. The final prognostic model, confirmed in bootstrapped samples, included IPI, circulating CD4 cell count, history of clinical AIDS, and expression of CD44, p53, IgM and EBV. This model incorporating HIV disease history and tumor markers, achieved better prediction for two-year mortality [AUC = 0.87, 95% CI: 0.78-0.96] compared with IPI alone [AUC = 0.63 (0.51-0.75)].

The isotype of the BCR as a surrogate for the GCB and ABC molecular subtypes in diffuse large B-cell lymphoma

Gene expression profiling has identified two major molecular subtypes of diffuse large B-cell lymphoma (DLBCL) that are histologically indistinguishable but differ in cure rates. Here, we investigated whether the isotype of the B-cell receptor (BCR) expressed by the tumoral cells correlated with the molecular subtype and survival. Gene expression analysis clustered the 53 patients included in this study into three subgroups, 17 germinal center B-cell-like (GCB) cases, 26 activated B-cell-like (ABC) cases and 10 intermediate cases. The molecular subtype was correlated with the isotype, as 15/17 GCB cases expressed a secondary isotype (immunoglobulin (Ig)G or IgA), whereas 24/26 ABC cases expressed a primary isotype (IgM or IgD) (P<0.0001). There was a trend toward a worse outcome for patients with an ABC DLBCL and a shorter overall survival for patients with IgM+ tumor (P=0.21 and 0.014, respectively). Finally, fluorescence in situ hybridization (FISH) analysis revealed a striking asymmetric pattern, as the IGHM gene is conserved only on the productive IGH allele in most IgM+ tumors. Taken together, these data indicate that the isotype of the BCR is a reliable indicator for the GCB and ABC subtypes in DLBCL, and suggest that the conservation of an IgM is required for ABC DLBCL lymphomagenesis to occur.

A novel method of amplification of FFPET-derived RNA enables accurate disease classification with microarrays

A new method for amplification and labeling of RNA is assessed that permits gene expression microarray analysis of formalin-fixed paraffin-embedded tissue (FFPET) samples. Valid biological data were obtained using gene expression microarrays of diffuse large B-cell lymphoma (DLBCL) FFPET samples. We examined 59 matched DLBCL patient samples, FFPET, and fresh/frozen. The samples contained both prognostic subgroups of DLBCL: germinal center B-cell (GCB) and activated B-cell (ABC). Fresh/frozen (FF) samples were amplified by both the traditional Eberwine oligo-dT method and a new method described herein. The matching FFPET samples were also amplified using the new method. Here we detail the comparison of results from all three datasets of matched samples. An established classification model built from previous data accurately classified these new samples. This new method provides a useful technology advance for microarray analysis of FFPET archival samples.

Clinical significance of co-expression of CD21 and LFA-1 in B-cell lymphoma

We previously reported that the prognosis of CD21-positive diffuse large B-cell lymphoma (DLBCL) is significantly favorable to that of CD21-negative DLBCL (Otsuka et al. in Br J Haematol 127:416-424, 2004). In this study, we attempted to clarify the biological significance of CD21 expression in B-cell lymphoma (BCL) by performing in vitro experiments using CD21 transfection into a CD21-negative lymphoma cell line and analyzing clinical data from lymphoma samples. Established clones of CD21 transfectants showed homotypic aggregation in suspension culture. Analysis of integrin expression revealed that LFA-1 appeared to be expressed on CD21 transfectants, and the cell aggregation was abrogated by anti-LFA-1 antibody. The CD21 transfectants could adhere to plastic plates coated with ICAM-1. Moreover, flow cytometry and/or immunohistochemical analyses of clinical BCL samples (n = 29) revealed positive for CD21 in all cases; LFA-1 was also expressed without exception. All BCL cells isolated from cavity fluids (n = 10) failed to express both CD21 and LFA-1. These data suggest that CD21 is tightly related to LFA-1 expression in BCL and the absence of CD21/LFA-1 expression is associated with pleural/peritoneal fluid involvement by BCL, a potential indicator of disease progression of BCL.

The use of gene array technology and proteomics in the search of new targets of diseases for therapeutics

The advent of functional genomics has been greatly broadening our view and accelerating our way in numerous medical research fields. The complete genomic data acquired from the human genome project and the desperate clinical need of comprehensive analytical tools to study complex diseases, has allowed rapid evolution of genomic and proteomic technologies, speeding the rate and number of discoveries in new biomarkers. By jointly using genomics, proteomics and bioinformatics there is a great potential to make considerable contribution to biomarker identification and to revolutionize both the development of new therapies and drug development process.

Gene expression profiling of peripheral T-cell lymphoma including gammadelta T-cell lymphoma

The gene expression profile of peripheral gammadelta T-cell lymphoma (gammadeltaTCL) has not been investigated. Using oligonucleotide microarrays, we analyzed total RNA from 7 patients with gammadeltaTCL (4 hepatosplenic, 1 cutaneous, 1 intestinal, and 1 thyroidal) and 27 patients with alphabetaTCL (11 peripheral TCL-unspecified, 15 angioimmunoblastic TCL, and 1 hepatosplenic). Unsupervised microarray analyses classified all hepatosplenic gammadeltaTCLs into a single cluster, whereas other gammadeltaTCLs were scattered within the alphabetaTCL distribution. We identified a T-cell receptor signature gene set, which accurately classified gammadeltaTCL and alphabetaTCL. A classifier based on gene expression under supervised analysis correctly identified gammadeltaTCL. One case of hepatosplenic alphabetaTCL was placed in the gammadeltaTCL grouping. gammadeltaTCL signature genes included genes encoding killer cell immunoglobulin-like receptors and killer cell lectin-like receptors. Our results indicate that hepatosplenic gammadeltaTCL is a distinct form of peripheral TCL and suggest that nonhepatosplenic gammadeltaTCLs are heterogeneous in gene expression.