The distinct gene expression profiles of chronic lymphocytic leukemia and multiple myeloma suggest different anti-apoptotic mechanisms but predict only some differences in phenotype

The role of G protein-coupled receptors in lymphoid malignancies

B cell lymphoma consists of multiple individual diseases arising throughout the lifespan of B cell development. From pro-B cells in the bone marrow, through circulating mature memory B cells, each stage of B cell development is prone to oncogenic mutation and transformation, which can lead to a corresponding lymphoma. Therapies designed against individual types of lymphoma often target features that differ between malignant cells and the corresponding normal cells from which they arise. These genetic changes between tumor and normal cells can include oncogene activation, tumor suppressor gene repression and modified cell surface receptor expression. G protein-coupled receptors (GPCRs) are an important class of cell surface receptors that represent an ideal target for lymphoma therapeutics. GPCRs bind a wide range of ligands to relay extracellular signals through G protein-mediated signaling cascades. Each lymphoma subgroup expresses a unique pattern of GPCRs and efforts are underway to fully characterize these patterns at the genetic level. Aberrations such as overexpression, deletion and mutation of GPCRs have been characterized as having causative roles in lymphoma and such studies describing GPCRs in B cell lymphomas are summarized here.

TRIM13 (RFP2) downregulation decreases tumour cell growth in multiple myeloma through inhibition of NF Kappa B pathway and proteasome activity

Multiple myeloma (MM) is an incurable neoplasm caused by proliferation of malignant plasma cells in the bone marrow (BM). MM is characterized frequently by a complete or partial deletion of chromosome 13q14, seen in more than 50% of patients at diagnosis. Within this deleted region the tripartite motif containing 13 (TRIM13, also termed RFP2) gene product has been proposed to be a tumour suppressor gene (TSG). Here, we show that low expression levels of TRIM13 in MM are associated with chromosome 13q deletion and poor clinical outcome. We present a functional analysis of TRIM13 using a loss-of-function approach, and demonstrate that TRIM13 downregulation decreases tumour cell survival as well as cell cycle progression and proliferation of MM cells. In addition, we provide evidence for the involvement of TRIM13 downregulation in inhibiting the NF kappa B pathway and the activity of the 20S proteasome. Although this data does not support a role of TRIM13 as a TSG, it substantiates important roles of TRIM13 in MM tumour survival and proliferation, underscoring its potential role as a novel target for therapeutic intervention.

Expression of transient receptor potential vanilloid channels TRPV5 and TRPV6 in human blood lymphocytes and Jurkat leukemia T cells

Regulation of Ca(2+) entry is a key process for lymphocyte activation, cytokine synthesis and proliferation. Several members of the transient receptor potential (TRP) channel family can contribute to changes in [Ca(2+)](in); however, the properties and expression levels of these channels in human lymphocytes continue to be elusive. Here, we established and compared the expression of the most Ca(2+)-selective members of the TRPs, Ca(2+) channels transient receptor potential vanilloid 5 and 6 (TRPV5 and TRPV6), in human blood lymphocytes (HBLs) and leukemia Jurkat T cells. We found that TRPV6 and TRPV5 mRNAs are expressed in both Jurkat cells and quiescent HBLs; however, the levels of mRNAs were significantly higher in malignant cells than in quiescent lymphocytes. Western blot analysis showed TRPV5/V6 proteins in Jurkat T cells and TRPV5 protein in quiescent HBLs. However, the expression of TRPV6 protein was switched off in quiescent HBLs and turned on after mitogen stimulation of the cells with phytohemagglutinin. Inwardly directed monovalent currents that displayed characteristics of TRPV5/V6 currents were recorded in both Jurkat cells and normal HBLs. In outside-out patch-clamp studies, currents were reduced by ruthenium red, a nonspecific inhibitor of TRPV5/V6 channels. In addition, ruthenium red downregulated cell-cycle progression in both activated HBLs and Jurkat cells. Thus, we identified TRPV5 and TRPV6 calcium channels, which can be considered new candidates for Ca(2+) entry into human lymphocytes. The correlation between expression of TRPV6 channels and the proliferative status of lymphocytes suggests that TRPV6 may be involved in the physiological and/or pathological proliferation of lymphocytes.

Apoptotic gene expression under influence of fludarabine and cladribine in chronic lymphocytic leukemia-microarray study

BACKGROUND

A deep insight into gene expression profiling (GEP) is a key to understanding the background of disease. It can lead to identification of diagnostic and prognostic factors and then to a selection of the most appropriate therapy. The aim of this study was to evaluate differences in apoptotic gene expression in chronic lymphocytic leukemia (CLL) cells influenced by fludarabine (FA) or cladribine (2-CdA).

METHODS

GEP was performed in cells obtained from 10 untreated CLL patients and cultured in vitro with FA or 2-CdA. Ninety-three selected apoptotic genes were analyzed using 384 TaqMan® Low Density Arrays in pooled RNA.

RESULTS

Relevant results were found in a set of 27 genes, however, the most striking differences between FA and 2-CdA were observed in the following 5 genes: BAD, TNFRSF21, DAPK1, CARD 6 and CARD 9.

CONCLUSION

We have found some differences in apoptotic gene expression between FAand 2-CdA. These findings give prominence to genes qualifying for further studies currently conducted in our Department.

The role of the blood transcriptome in innate inflammation and stroke

Cerebrovascular disease is a major cause of death and disability, with a poorer outcome in patients having select risk factors including diabetes and hypertension. Risk factors and the state of cerebral ischemia-reperfusion associated with cerebrovascular occlusion are known to cause inflammatory changes. These events and the inflammatory state are reflected by transcript changes in various components of the blood and can be specifically measured. By defining these changes, new insight into cerebrovascular disease and its therapeutics is being achieved.

Relation of platelet and leukocyte inflammatory transcripts to body mass index in the Framingham heart study

BACKGROUND

Although many genetic epidemiology and biomarker studies have been conducted to examine associations of genetic variants and circulating proteins with cardiovascular disease and risk factors, there has been little study of gene expression or transcriptomics. Quantitative differences in the abundance of transcripts has been demonstrated in malignancies, but gene expression from a large community-based cohort examining risk of cardiovascular disease has never been reported.

METHODS AND RESULTS

On the basis of preliminary microarray data and previously suggested genes from the literature, we measured expression of 48 genes by high-throughput quantitative reverse-transcriptase polymerase chain reaction in 1846 participants of the Framingham Offspring cohort from RNA derived from isolated platelets and leukocytes. A multivariable stepwise regression model was used to assess clinical correlates of quantitative RNA expression. For specific inflammatory platelet-derived transcripts, including ICAM1, IFNG, IL1R1, IL6, MPO, COX2, TNF, TLR2, and TLR4, there were significant associations with higher body mass index (BMI). Compared with platelets, fewer leukocyte-derived transcripts were associated with BMI or other cardiovascular risk factors. Select transcripts were found to be highly heritable, including GPIBA and COX1. Almost uniformly, heritable transcripts were not those associated with BMI.

CONCLUSIONS

Inflammatory transcripts derived from platelets, particularly those part of the nuclear factor kappa B pathway, are associated with BMI, whereas others are heritable. This is the first study, using a large community-based cohort, to demonstrate clinical correlates of gene expression and is consistent with the hypothesis that specific peripheral-blood transcripts play a role in the pathogenesis of coronary heart disease and its risk factors.

A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia

PURPOSE

Chronic lymphocytic leukemia (CLL) is a B-cell malignancy characterized by a variable clinical course. Several parameters have prognostic capabilities but are associated with altered response to therapy in only a small subset of patients.

EXPERIMENTAL DESIGN

We used gene expression profiling methods to generate predictors of therapy response and prognosis. Genomic signatures that reflect progressive disease and responses to chemotherapy or chemoimmunotherapy were created using cancer cell lines and patient leukemia cell samples. We validated and applied these three signatures to independent clinical data from four cohorts, representing a total of 301 CLL patients.

RESULTS

A genomic signature of prognosis created from patient leukemic cell gene expression data coupled with clinical parameters significantly differentiated patients with stable disease from those with progressive disease in the training data set. The progression signature was validated in two independent data sets, showing a capacity to accurately identify patients at risk for progressive disease. In addition, genomic signatures that predict response to chlorambucil or pentostatin, cyclophosphamide, and rituximab were generated and could accurately distinguish responding and nonresponding CLL patients.

CONCLUSIONS

Thus, microarray analysis of CLL lymphocytes can be used to refine prognosis and predict response to different therapies. These results have implications for standard and investigational therapeutics in CLL patients.

Protein profiling of plasma membranes defines aberrant signaling pathways in mantle cell lymphoma

We used shotgun proteomics to identify plasma membrane and lipid raft proteins purified from B cells obtained from mantle cell lymphoma (MCL) patients in leukemic phase. Bioinformatics identified 111 transmembrane proteins, some of which were profiled in primary MCL cases, MCL-derived cell lines, and normal B cells using RT-PCR and Western blotting. Several transmembrane proteins, including CD27, CD70, and CD31 (PECAM-1), were overexpressed when compared with normal B cells. CD70 was up-regulated (>10-fold) in three of five MCL patients along with its cognate receptor CD27, which was up-regulated (4-9-fold) in five of five patients, suggesting that MCL cells may undergo autocrine stimulation via this signaling pathway. Activated calpain I and protein kinase C betaII were also detected in the plasma membranes, suggesting that these proteins are constitutively active in MCL. Protein kinase C betaII has been associated with lipid rafts, and shotgun proteomics/protein profiling revealed that key lipid raft proteins, raftlin (four of five patients) and CSK (C-terminal Src kinase)-binding protein (Cbp)/phosphoprotein associated with glycosphingolipid-enriched microdomains (PAG) (four of four patients) were down-regulated in MCL. Levels of other known lipid raft proteins, such as Lyn kinase and flotillin 1, were similar to normal B cells. However, 5-lipoxygenase (5-LO), a key enzyme in leukotriene biosynthesis, was associated with lipid rafts and was up-regulated approximately 7-fold in MCL compared with normal B cells. Significantly inhibitors of 5-LO activity (AA861) and 5-LO-activating protein (FLAP) (MK886, its activating enzyme) induced apoptosis in MCL cell lines and primary chronic lymphocytic leukemia cells, indicating an important role for the leukotriene biosynthetic pathway in MCL and other B cell malignancies. Thus, using shotgun proteomics and mRNA and protein expression profiling we identified a subset of known and unknown transmembrane proteins with aberrant expression in MCL plasma membranes. These proteins may play a role in the pathology of the disease and are potential therapeutic targets in MCL.

Inhibitor of apoptosis proteins in hematological malignancies

Apoptosis or programmed cell death is a key mechanism to control tissue homeostasis, for example, in the hematopoietic system. Thus, resistance to apoptosis can contribute to the development of leukemia or lymphoma. Inhibitors of apoptosis (IAP) proteins block cell death pathways at a central node by interfering with the activation of effector caspases. As increased expression levels of IAPs are found in hematological malignancies and have been correlated with poor prognosis, IAPs could be exploited as therapeutic targets and prognostic markers. Various strategies have been developed to target IAPs for therapeutic purposes in leukemia and lymphoma cells, including small-molecule inhibitors and antisense oligonucleotides. These agents could directly induce apoptosis in malignant cells or sensitize these cells to other cytotoxic agents. Thus, IAPs present promising targets for the development of new biomarkers and cancer therapeutics in hematological malignancies.

Predominantly post-transcriptional regulation of activation molecules in chronic lymphocytic leukemia: the case of transferrin receptors

Transcriptional and post-transcriptional control mechanisms have a differential impact on cellular physiology depending on activation status. Several lines of evidence suggest that chronic lymphocytic leukemia (CLL) malignant B cells resemble antigen-experienced and activated B cells. In the present study, we investigated the expression of transferrin receptor 1 (TfR1, CD71), one of the "classical" markers up-regulated upon B-cell activation, and TfR2, a novel receptor for transferrin, in peripheral blood CD19+ B cells from ten healthy individuals and 76 patients with CLL so as to gain insight into potential disease-related differences in underlying regulatory mechanisms. Marked differences in the production and expression of these receptors were detected in malignant but not in normal B cells. Specifically, TfR1 mRNA and protein levels were significantly higher in comparison to TfR2, both in normal and malignant B cells. Furthermore, discrepancies between TfR mRNA and protein expression were observed in CLL; in contrast, mRNA and protein expression levels were generally concordant in normal B cells. Exposure to actinomycin D decreased TfR1 and TfR2 mRNA levels in normal CD19+ B cells but had no effect on CLL malignant cells. The protein synthesis inhibitor cycloheximide had opposing effects in normal vs. CLL malignant B cells: thus, TfR1 and TfR2 mRNA levels were increased in normal B cells, whereas they were unaffected or even suppressed in CLL malignant B cells. These results allude to differential regulation of TfR1 and TfR2 expression in normal B cells vs. CLL. In normal B cells, transcriptional mechanisms exert a critical control over TfR1 and TfR2 expression, whereas in CLL post-transcriptional mechanisms seem to play a complementary and perhaps more important role. This type of control appears to be especially suited for modulation of genes implicated in proliferation of activated cells, like CLL malignant B cells.

Transcriptional Profiling of Hematologic Malignancies with a Low-Density DNA Microarray

Background: High-density microarrays are powerful tools for expression analysis of thousands of genes simultaneously; however, experience with low-density microarrays in gene expression studies has been limited.

Methods: We developed an optimized procedure for gene expression analysis based on a microarray containing 538 oligonucleotides and used this procedure to analyze neoplastic cell lines and whole-blood samples from healthy individuals and patients with different hematologic neoplasias. Hierarchical clustering and the Welch t-test with adjusted P values were used for data analysis.

Results: This procedure detects 0.2 fmol of mRNA and generates a linear response of 2 orders of magnitude, with CV values of <20% for hybridization and label replicates. We found statistically significant differences between Jurkat and U937 cell lines, between blood samples from 15 healthy donors and 59 chronic lymphocytic leukemia (CLL) samples, and between 6 acute myeloid leukemia patients and 4 myelodysplastic syndrome patients. A classification system constructed from the expression data predicted healthy or CLL status from a whole-blood sample with a 97% success rate.

Conclusion: Transcriptional profiling of whole-blood samples was carried out without any cellular or sample manipulation before RNA extraction. This gene expression analysis procedure uncovered statistically significant differences associated with different hematologic neoplasias and made possible the construction of a classification system that predicts the healthy or CLL status from a whole-blood sample.

Gene expression profiling data in lymphoma and leukemia: review of the literature and extrapolation of pertinent clinical applications

CONTEXT

Gene expression (GE) analyses using microarrays have become an important part of biomedical and clinical research in hematolymphoid malignancies. However, the methods are time-consuming and costly for routine clinical practice.

OBJECTIVES

To review the literature regarding GE data that may provide important information regarding pathogenesis and that may be extrapolated for use in diagnosing and prognosticating lymphomas and leukemias; to present GE findings in Hodgkin and non-Hodgkin lymphomas, acute leukemias, and chronic myeloid leukemia in detail; and to summarize the practical clinical applications in tables that are referenced throughout the text.

DATA SOURCE

PubMed was searched for pertinent literature from 1993 to 2005.

CONCLUSIONS

Gene expression profiling of lymphomas and leukemias aids in the diagnosis and prognostication of these diseases. The extrapolation of these findings to more timely, efficient, and cost-effective methods, such as flow cytometry and immunohistochemistry, results in better diagnostic tools to manage the diseases. Flow cytometric and immunohistochemical applications of the information gained from GE profiling assist in the management of chronic lymphocytic leukemia, other low-grade B-cell non-Hodgkin lymphomas and leukemias, diffuse large B-cell lymphoma, nodular lymphocyte-predominant Hodgkin lymphoma, and classic Hodgkin lymphoma. For practical clinical use, GE profiling of precursor B acute lymphoblastic leukemia, precursor T acute lymphoblastic leukemia, and acute myeloid leukemia has supported most of the information that has been obtained by cytogenetic and molecular studies (except for the identification of FLT3 mutations for molecular analysis), but extrapolation of the analyses leaves much to be gained based on the GE profiling data.

The Mark Coventry Award: white blood cell gene expression: a new approach toward the study and diagnosis of infection

We introduce a new genomic approach toward the study and diagnosis of infection. Our purpose is to show that synovial fluid white blood cells express a gene expression "signature" that differentiates septic from aseptic inflammation. Synovial fluid was aspirated from patients with acute Staphylococcus aureus infections or acute gout of the knee. Differential cell counts included predominantly neutrophils in all aspirates. Ribonucleic acid was isolated from the synovial-fluid white blood cells and was analyzed on the Affymetrix U133A GeneChip. The neutrophils from a patient whose knee is infected with Staphylococcus aureus can be distinguished from the neutrophils found in gout by nature of their differential gene expression. There are 1615 genes that have an expression level that is significantly different between the groups. The 124 most significant differences are in genes from immune pathways including the interleukin pathway, the tumor necrosis factor pathway, and the antibacterial response. The neutrophils at a site of infection (Staphylococcus aureus) express different genes than the neutrophils at a site of aseptic inflammation (gout). To our knowledge, this is the first in vivo demonstration of this principle. The differences in neutrophil gene expression may be used to develop simple laboratory tests that distinguish the causes of inflammation in a total joint arthroplasty.

LEVEL OF EVIDENCE

Diagnostic study, Level II-1. See the Guidelines for Authors for a complete description of levels of evidence.

Functional gene expression analysis of clonal plasma cells identifies a unique molecular profile for light chain amyloidosis

Immunoglobulin light chain amyloidosis (AL) is characterized by a clonal expansion of plasma cells within the bone marrow. Gene expression analysis was used to identify a unique molecular profile for AL using enriched plasma cells (CD138+) from the bone marrow of 24 patients with AL and 28 patients with multiple myeloma (MM) and 6 healthy controls. Class prediction analysis (PAM) revealed a subset of 12 genes, which included TNFRSF7 (CD27), SDF-1, and PSMA2, that distinguished between these 2 groups with an estimated and observed accuracy of classification of 92%. This model was validated with an independent dataset of 11 patients with AL and 12 patients with MM with 87% accuracy. Differential expression for the most discriminant genes in the 12-gene subset was validated using quantitative real-time polymerase chain reaction and protein expression analysis, which upheld the observations from the micro-array expression data. Functional analyses using a novel network mapping software revealed a number of potentially significant pathways that were dysregulated in patients with AL, with those regulating proliferation, apoptosis, cell signaling, chemotaxis, and migration being substantially represented. This study provides new insight into the molecular profile of clonal plasma cells and its functional relevance in the pathogenesis of light chain amyloidosis.

Translocation t(X;11)(q13;q23) in B-cell chronic lymphocytic leukemia disrupts two novel genes

Deletion of chromosome region 11q22-q23 defines a subgroup of patients with B-cell chronic lymphocytic leukemia (B-CLL) characterized by poor survival. Although the tumor-suppressor gene ATM in the consensus deletion region was found to be biallelically inactivated in about one third of B-CLL cases, in the majority of those who have this deletion, inactivation of the remaining ATM allele was not observed. To identify a second disease-associated gene, we investigated two B-CLL cases with translocation breakpoints in the critical 11q23 deletion region. In one case, a t(X;11)(q13;q23) was cloned and two novel genes were isolated. The breakpoint on 11q23 affected the ARHGAP20 gene, which encodes a protein predicted to be involved in the regulation of Rho family GTPases. The breakpoint on Xq13 occurred in BRWD3, which codes for a putative novel transcription factor. The rearrangement of ARHGAP20 and BRWD3 did not result in fusion transcripts, but it disrupted both genes. Mutation analysis of 28 B-CLL samples with monoallelic deletions and two B-CLL samples with 11q23 translocations detected no deleterious mutation in the remaining copy of ARHGAP20. Quantitative expression analysis in 22 B-CLLs revealed significant up-regulation of ARHGAP20 in CLL B cells, whereas BRWD3 was slightly down-regulated. Thus, deregulation of ARHGAP20 by altered gene expression or by gene disruption (but not point mutation) might be a general molecular mechanism of B-CLL leukemogenesis.

Expression of PAX5 in CD20-positive multiple myeloma assessed by immunohistochemistry and oligonucleotide microarray

Silencing of PAX5 gene by upregulation of B-lymphocyte-induced maturation protein-1 (PRDM1) is essential for terminal differentiation of B cells to plasma cells. To investigate PAX5 gene expression and its protein product, B-cell-specific activator protein (BSAP), in a subgroup of multiple myeloma characterized by CD20 expression, we studied PAX5/BSAP by immunohistochemistry in 25 cases of myeloma, all expressing moderate to strong CD20 by flow cytometric analysis, and correlated the results with PAX5 and PRDM1 mRNA levels analyzed by the Affymetrix HuGeneFL GeneChip microarray in 17 cases. Using paraffin-embedded bone marrow biopsy sections, we found PAX5/BSAP was expressed in 72% (18/25) of cases overall with an intensity ranging from weak (10, 56%) to strong (8, 44%). PAX5/BSAP was negative in 10 randomly selected CD20-negative myelomas included as negative controls. PAX5 mRNA levels correlated inversely with that of PRDM1 in both CD20-positive and CD20-negative myelomas and failed to predict the expression levels of PAX5/BSAP, suggesting that detected PAX5/BSAP likely represents remnant of earlier stage of development. We conclude that CD20-positive myelomas expressing PAX5/BSAP can present as a diagnostic pitfall mimicking B-cell neoplasms with plasmacytoid differentiation.

Advances in the understanding of biology and prognosis in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) has a heterogeneous clinical course and outcome. Recent advances in the diagnosis and molecular characterization of CLL permit improved prediction of disease prognosis, which could result in better management. We review the biology and diagnosis of CLL and the role of analysis of immunoglobulin heavy-chain variable region mutation status, molecular cytogenetics (interphase fluorescence in situ hybridization), and the expression of CD38 and ZAP-70 in the evaluation and management of patients with CLL.

Alemtuzumab (CAMPATH 1H) does not kill chronic lymphocytic leukemia cells in serum free medium

The mechanism of action of alemtuzumab (CAMPATH 1H) in chronic lymphocytic leukemia (CLL) is uncertain. We tested the hypothesis that alemtuzumab alone can induce apoptosis in cultured CLL cells. Purified peripheral blood B-lymphocytes from CLL patients were treated in serum free medium (AIM-V). There was minimal spontaneous apoptosis in untreated cells. Alemtuzumab ligation did not alter the membrane distribution of CD52 in single cells but many cells formed transient, small, tightly adherent clusters. Alemtuzumab alone did not induce apoptosis. In contrast, alemtuzumab plus complement was rapidly cytotoxic. We conclude that alemtuzumab does not cause apoptosis in purified CLL B cells cultured in serum free medium.