scholarly journals Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression

Blood ◽  
2012 ◽  
Vol 120 (13) ◽  
pp. 2639-2649 ◽  
Author(s):  
Han-Yu Chuang ◽  
Laura Rassenti ◽  
Michelle Salcedo ◽  
Kate Licon ◽  
Alexander Kohlmann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Lymphocytic Leukemia ◽  
Disease Progression ◽  
Expression Profiles ◽  
Treatment Strategies ◽  
Gene Expression Profiles ◽  
Lymphocytic Leukemia ◽  
Cancer Evolution ◽  
Sample Collection ◽  
Over Time

Abstract The clinical course of patients with chronic lymphocytic leukemia (CLL) is heterogeneous. Several prognostic factors have been identified that can stratify patients into groups that differ in their relative tendency for disease progression and/or survival. Here, we pursued a subnetwork-based analysis of gene expression profiles to discriminate between groups of patients with disparate risks for CLL progression. From an initial cohort of 130 patients, we identified 38 prognostic subnetworks that could predict the relative risk for disease progression requiring therapy from the time of sample collection, more accurately than established markers. The prognostic power of these subnetworks then was validated on 2 other cohorts of patients. We noted reduced divergence in gene expression between leukemia cells of CLL patients classified at diagnosis with aggressive versus indolent disease over time. The predictive subnetworks vary in levels of expression over time but exhibit increased similarity at later time points before therapy, suggesting that degenerate pathways apparently converge into common pathways that are associated with disease progression. As such, these results have implications for understanding cancer evolution and for the development of novel treatment strategies for patients with CLL.

Functional Somatic and Germline Variants in the NF-κB Pathway in Chronic Lymphocytic Leukemia

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 560-560 ◽  
Author(s):  
Ma. Reina Improgo ◽  
Adam Kiezun ◽  
Yaoyu Wang ◽  
Lillian Werner ◽  
Petar Stojanov ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Chronic Lymphocytic Leukemia ◽  
Transcriptional Activity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Lymphocytic Leukemia ◽  
Wild Type ◽  
Rt Pcr ◽  
Germline Variants

Abstract Abstract 560 Nuclear factor kappa B (NF-κB) encompasses a family of transcription factors involved in oncogenic processes including cellular proliferation and apoptotic inhibition. Constitutive activation of NF-κB has been observed in hematologic malignancies and is thought to confer resistance to chemotherapeutic agents. Here, we examine the role of the NF-κB pathway in chronic lymphocytic leukemia (CLL). Whole-exome sequencing was performed using tumor and matched germline DNA from 167 CLL patients. We identified 51 patients (30%) carrying 53 non-silent somatic variants in genes of the canonical NF-κB pathway, which consists of 272 genes as defined by the Ingenuity Pathway Analysis tool. Of the 99 patients whose germline sequences have been analyzed to date, 27 patients (27%) carry 34 non-silent germline variants in NF-κB pathway genes. A total of 67 patients (40%) have at least one non-silent somatic or germline variant. Variants in the NFKB1 gene, itself, were also observed: a somatic variant, H66R, found in two patients, and two germline variants, Y89F and R849W, each found in one patient. To evaluate the functional consequences of the NFKB1 variants, we performed site-directed mutagenesis to generate full-length NFKB1 cDNAs encoding these variants. We subsequently measured transcriptional activity of wild-type and mutant NFKB1 via luciferase assays in HEK293T cells using reporter cassettes containing the NFKB1 response element. Transcriptional activity of the three NFKB1 variants was found to be at least 2-fold higher than that of wild-type NFKB1 (p<0.0001). We further hypothesized that this increased transcriptional activity would lead to increased expression of NFKB1 downstream target genes. Analysis of gene expression profiles from Affymetrix HG-U133 Plus 2.0 Arrays of 65 CLL patient samples showed that the NFKB1 downstream targets CCL3, CCL4, and CD69 are upregulated in NFKB1 variants. To validate these results, we performed quantitative RT-PCR in patients with (n=3) or without (n=9) NFKB1 variants and confirmed upregulation of CCL3 (p=0.0286), CCL4 (p=0.0384), and CD69 (p=0.0263). Direct transfection of HEK293T cells with NFKB1 variants also resulted in a 3.3-fold upregulation of CCL3 (p=0.05). To test the hypothesis that deregulation of the NF-κB pathway is a key mechanism in CLL, we compared gene expression profiles of NF-κB pathway genes between CLL patient samples (n=146) and normal B cells (n=16) and found overall upregulation of the NF-κB pathway in CLL (Kolmogorov-Smirnov test, p=2.2e-16). K-means clustering and principal component analysis (PCA) further revealed that CLL patients can be divided into two subgroups exhibiting differential magnitude of NF-κB pathway upregulation. Studies in progress aim to identify the clinical significance of these subgroups. Finally, we assessed the effect of inhibiting the NF-κB pathway using the cell permeant NF-κB inhibitor, SN50. We performed Annexin V/PI staining 24 hours post-treatment in CLL cells with (n=9) or without (n=3) NF-κB pathway variants. SN50 increased cell death 1.8-fold in all cells tested (p<0.0001). Quantitative RT-PCR also showed a 59% decrease in expression of CCL3 one hour post-treatment, confirming inhibition of the NF-κB pathway. In conclusion, our findings demonstrate that a high proportion of CLL patients harbor somatic and germline variants in NF-κB pathway genes, some of which appear to be functional. Furthermore, the NF-κB pathway is upregulated in CLL and pharmacological inhibition of the pathway leads to increased cancer cell death. Functional characterization of NF-κB pathway variants offers mechanistic insight into the disease, providing novel targets for therapy. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia

2014 ◽  
Author(s):  
Simone Ecker ◽  
Vera Pancaldi ◽  
Daniel Rico ◽  
Alfonso Valencia
Keyword(s):  
Gene Expression ◽  
Chronic Lymphocytic Leukemia ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cellular Communication ◽  
Lymphocytic Leukemia ◽  
Resistance To Therapy ◽  
Expression Variability ◽  
Disease Subtype ◽  
Aggressive Subtype

Background: Chronic Lymphocytic Leukemia (CLL) presents two subtypes which have drastically different clinical outcomes. So far, these two subtypes are not associated to clear differences in gene expression profiles. Interestingly, recent results have highlighted important roles for heterogeneity, both at the genetic and at the epigenetic level in CLL progression. Results: We propose to use gene expression variability across patients to investigate differences between the two CLL subtypes. We find that the most aggressive type of this disease shows higher variability of gene expression across patients and we elaborate on this observation to produce a method that classifies patients into clinical subtypes. Finally, we find that, overall, genes that show higher variability in the aggressive subtype are related to cell cycle, development and inter-cellular communication, probably related to faster progression of this disease subtype. Conclusions: There are strong relations between disease subtype and gene expression variability linking significantly increased expression variability to phenotypes such as aggressiveness and resistance to therapy in CLL.

scholarly journals Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells✪

2001 ◽  
Vol 194 (11) ◽  
pp. 1625-1638 ◽  
Author(s):  
Ulf Klein ◽  
Yuhai Tu ◽  
Gustavo A. Stolovitzky ◽  
Michela Mattioli ◽  
Giorgio Cattoretti ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cells ◽  
Chronic Lymphocytic Leukemia ◽  
B Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Variable Region ◽  
Memory B Cells ◽  
Lymphocytic Leukemia ◽  
Cell Subpopulations

B cell–derived chronic lymphocytic leukemia (B-CLL) represents a common malignancy whose cell derivation and pathogenesis are unknown. Recent studies have shown that &gt;50% of CLLs display hypermutated immunoglobulin variable region (IgV) sequences and a more favorable prognosis, suggesting that they may represent a distinct subset of CLLs which have transited through germinal centers (GCs), the physiologic site of IgV hypermutation. To further investigate the phenotype of CLLs, their cellular derivation and their relationship to normal B cells, we have analyzed their gene expression profiles using oligonucleotide-based DNA chip microarrays representative of ∼12,000 genes. The results show that CLLs display a common and characteristic gene expression profile that is largely independent of their IgV genotype. Nevertheless, a restricted number of genes (&lt;30) have been identified whose differential expression can distinguish IgV mutated versus unmutated cases and identify them in independent panels of cases. Comparison of CLL profiles with those of purified normal B cell subpopulations indicates that the common CLL profile is more related to memory B cells than to those derived from naive B cells, CD5+ B cells, and GC centroblasts and centrocytes. Finally, this analysis has identified a subset of genes specifically expressed by CLL cells of potential pathogenetic and clinical relevance.

Multi-Parameter Phenotypic Analysis of Members of Chronic Lymphocytic Leukemia Clones Identifies Distinct Proliferative and Resting/Re-Entry Compartments with Discrete Gene Expression Profiles.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 668-668 ◽  
Author(s):  
Carlo Calissano ◽  
Rajendra N Damle ◽  
Xiao J. Yan ◽  
Wentian Li ◽  
Sonia Marsilio ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Lymphocytic Leukemia ◽  
Cell Signaling ◽  
Expression Profiles ◽  
Cell Movement ◽  
Gene Expression Profiles ◽  
Lymphocytic Leukemia ◽  
Phenotypic Analysis ◽  
Ki 67 ◽  
And Migration

Abstract Abstract 668 Background. In vivo studies of deuterium (2H) incorporation into newly-synthesized DNA of chronic lymphocytic leukemia (B-CLL) B cells indicate that the disease is dynamic, with ongoing birth and death of individual members of a leukemic clone. Therefore, a detailed phenotypic analysis might define the “life cycle” of subpopulations of leukemic cells within a B-CLL clone, thereby identifying recently-born members and members born earlier. Such an extended phenotype could enable structural and genetic characterization of the intra-clonal heterogeneity that birth and death create, and thereby help understand the biology of B-CLL cells and define novel cell surface markers or marker combinations as therapeutic targets. Methods. Our previous studies indicated that B-CLL clones could be subdivided into three populations based on relative densities of expression of CXCR4 and CD5. The CXCR4dimCD5bright subpopulation is enriched in cells with 2H-labeled, newly-synthesized DNA and contains significantly more Ki-67+ and MCM6+ cells than CXCR4intCD5int cells within the same clone. These latter cells in turn are enriched for the same parameters compared to the CXCR4brightCD5dim fraction. We have now identified other markers associated with the CXCR4dimCD5bright subpopulation (“proliferative compartment”) and the CXCR4brightCD5dim (“resting/re-entry compartment”) in B-CLL. PBMC from 20 B-CLL cases were subjected to multi-parameter immunofluorescent, flow cytometric analyses to define the expression of CD11a, CD20, CD23, CD27, CD38, CD47, CD49d, CD52, or Fcƒ×RII on the CD19+CXCR4dimCD5bright and CD19+CXCR4brightCD5dim B-CLL cell subpopulations. Companion studies were performed on Ki-67+ and Ki-67- subpopulations. Finally, gene expression profiling was performed on CXCR4dimCD5bright, CXCR4intCD5int, and CXCR4brightCD5dim subsets of 12 B-CLL cases using the Illumina HumanWG-6 platform. Results. Compared to CXCR4brightCD5dim cells within a clone, the CXCR4dimCD5bright compartment contained significantly more cells expressing CD23, CD52 (both p<0.0001), CD11a (p<0.001), CD20, CD38 (both p<0.01) and CD49d (p<0.05). In addition, this same fraction expressed significantly higher densities of Fcƒ×RIIb (p<0.0001), CD23, CD52 (both p<0.01), and CD11a (p<0.05). Gene expression profiles comparing the two subsets revealed over 1,309 significant differences. Functional activities associated with these genes differed dramatically between the two compartments. Of the top 25 over-expressed genes in the CXCR4dimCD5bright proliferative compartment, 11 related to proliferation (e.g., NAPSA, MARCKS, CCND2), 10 were involved in cell signaling and activation (e.g., GPR183, ADAP1), and 4 related to cell movement and migration (e.g., CXCR3). In the CXCR4brightCD5dim resting/re-entry compartment, 12 of the 25 most overexpressed genes were involved in apoptosis and cell death (e.g., RXR2, HRK), 7 in cell signaling (e.g., ADARB1, RAB37) and 5 in cell movement and migration (e.g., MDK, IRS2). Conclusions. These studies defined a reciprocal, extended surface membrane phenotype that distinguishes cells of the proliferative and the resting/re-entry compartments in B-CLL. This phenotype is based both on the percent of expressing cells and on the density of expression of well-defined surface molecules. In addition, gene expression analyses identified genes differentially expressed between the two compartments. These data support the notion that cells in these two compartments are a phenotypic continuum, with the former having divided recently and trafficking from the location where division occurred and the latter having divided earlier, being less robust, and attempting to traffic back to a lymphoid microenvironment to obtain survival signals. We suggest that targeting these two populations with appropriate monoclonal antibodies, many of which are currently in clinical trials in B-CLL and other B-cell lymphoproliferative disorders, may have a beneficial effect. Although this approach may not immediately diminish the bulk of the leukemic mass, it would preferentially eliminate the small fraction of cells that sustains a B-CLL clone and the fraction of cells that maintain a B-CLL clone after receiving survival signals, thereby permitting the remaining cells to die spontaneously. Disclosures: Allen: Antisoma: Research Funding.

Building Gene Networks by Analyzing Gene Expression Profiles

2019 ◽  
pp. 27-44
Author(s):  
Crescenzio Gallo
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Networks ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Expression Data ◽  
Gene Expressions ◽  
Over Time

The possible applications of modeling and simulation in the field of bioinformatics are very extensive, ranging from understanding basic metabolic paths to exploring genetic variability. Experimental results carried out with DNA microarrays allow researchers to measure expression levels for thousands of genes simultaneously, across different conditions and over time. A key step in the analysis of gene expression data is the detection of groups of genes that manifest similar expression patterns. In this chapter, the authors examine various methods for analyzing gene expression data, addressing the important topics of (1) selecting the most differentially expressed genes, (2) grouping them by means of their relationships, and (3) classifying samples based on gene expressions.

scholarly journals A Study of Gene Expression Changes in Human Spinal and Oculomotor Neurons; Identifying Potential Links to Sporadic ALS

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 448
Author(s):  
Aayan N. Patel ◽  
Dennis Mathew
Keyword(s):  
Gene Expression ◽  
Disease Progression ◽  
Motor Neurons ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Tissue Samples ◽  
Disease Symptoms ◽  
Sporadic Als ◽  
Oculomotor Neurons ◽  
Als Patients

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that causes compromised function of motor neurons and neuronal death. However, oculomotor neurons are largely spared from disease symptoms. The underlying causes for sporadic ALS as well as for the resistance of oculomotor neurons to disease symptoms remain poorly understood. In this bioinformatic-analysis, we compared the gene expression profiles of spinal and oculomotor tissue samples from control individuals and sporadic ALS patients. We show that the genes GAD2 and GABRE (involved in GABA signaling), and CALB1 (involved in intracellular Ca2+ ion buffering) are downregulated in the spinal tissues of ALS patients, but their endogenous levels are higher in oculomotor tissues relative to the spinal tissues. Our results suggest that the downregulation of these genes and processes in spinal tissues are related to sporadic ALS disease progression and their upregulation in oculomotor neurons confer upon them resistance to ALS symptoms. These results build upon prevailing models of excitotoxicity that are relevant to sporadic ALS disease progression and point out unique opportunities for better understanding the progression of neurodegenerative properties associated with sporadic ALS.

scholarly journals CD49d promotes disease progression in chronic lymphocytic leukemia: new insights from CD49d bimodal expression

Blood ◽  
2020 ◽  
Vol 135 (15) ◽  
pp. 1244-1254 ◽  
Author(s):  
Erika Tissino ◽  
Federico Pozzo ◽  
Dania Benedetti ◽  
Chiara Caldana ◽  
Tamara Bittolo ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Disease Progression ◽  
Prognostic Biomarker ◽  
Lymphocytic Leukemia ◽  
Prognostic Impact ◽  
Clinical Behavior ◽  
Cutoff Value ◽  
Sequential Samples ◽  
Homogeneous Pattern ◽  
Over Time

Abstract CD49d is a remarkable prognostic biomarker of chronic lymphocytic leukemia (CLL). The cutoff value for the extensively validated 30% of positive CLL cells is able to separate CLL patients into 2 subgroups with different prognoses, but it does not consider the pattern of CD49d expression. In the present study, we analyzed a cohort of 1630 CLL samples and identified the presence of ∼20% of CLL cases (n = 313) characterized by a bimodal expression of CD49d, that is, concomitant presence of a CD49d+ subpopulation and a CD49d− subpopulation. At variance with the highly stable CD49d expression observed in CLL patients with a homogeneous pattern of CD49d expression, CD49d bimodal CLL showed a higher level of variability in sequential samples, and an increase in the CD49d+ subpopulation over time after therapy. The CD49d+ subpopulation from CD49d bimodal CLL displayed higher levels of proliferation compared with the CD49d− cells; and was more highly represented in the bone marrow compared with peripheral blood (PB), and in PB CLL subsets expressing the CXCR4dim/CD5bright phenotype, known to be enriched in proliferative cells. From a clinical standpoint, CLL patients with CD49d bimodal expression, regardless of whether the CD49d+ subpopulation exceeded the 30% cutoff or not, experienced clinical behavior similar to CD49d+ CLL, both in chemoimmunotherapy (n = 1522) and in ibrutinib (n = 158) settings. Altogether, these results suggest that CD49d can drive disease progression in CLL, and that the pattern of CD49d expression should also be considered to improve the prognostic impact of this biomarker in CLL.

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