Microarray Analysis of B-Cell Lymphoma Cell Lines with the t(14;18)

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Microarray Analysis of B-Cell Lymphoma Cell Lines with the t(14;18) Ryan S. Robetorye, Sandra D. Bohling, John W. Morgan, G. Chris Fillmore, Megan S. Lim, Kojo S.J. Elenitoba-Johnson The Journal of Molecular Diagnostics Volume 4, Issue 3, Pages 123-136 (August 2002) DOI: 10.1016/S1525-1578(10)60693-9 Copyright © 2002 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Unsupervised hierarchical clustering of gene expression data from t(14;18) and mantle-cell lymphoma cell lines using the total complement of 4364 genes. The dendrogram lists the various cell lines and also provides a measure of the relatedness of gene expression in each sample so that samples showing closely related expression profiles are juxtaposed in adjacent branches of the hierarchical dendrogram. Karpas 422, SUDHL-4, SUDHL-6, and OCI-LY1 are t(14;18)-containing B-cell lymphoma cell lines, and NCEB-1 and Granta 519 are t(11;14)-containing mantle-cell lymphoma cell lines. The t(11;14)-containing mantle-cell lymphoma cell lines are closely related and arise from the same branch of the dendrogram. The t(14;18)-containing cell lines arise from a different node and cluster separately from the t(11;14)-cell lines. The Journal of Molecular Diagnostics 2002 4, 123-136DOI: (10.1016/S1525-1578(10)60693-9) Copyright © 2002 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Hierarchical clustering of gene expression data from the four t(14;18)-positive cell lines using the list of 137 previously identified differentially expressed genes contained in Tables 2 and 4. These genes include all genes over-expressed by approximately twofold or more in at least three of the four t(14;18) cell lines and under-expressed by twofold or more in all four t(14;18) cell lines relative to tonsillar B-cells. The genes corresponding to each horizontal row of the expression matrices are listed on the right side of the figure. Genes that were validated by quantitative fluorescence PCR are denoted by asterisks. The gene expression scale is the same as for Figure 1. The Journal of Molecular Diagnostics 2002 4, 123-136DOI: (10.1016/S1525-1578(10)60693-9) Copyright © 2002 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Quantitative fluorescence RT-PCR analysis of selected differentially expressed genes identified by microarray analysis in the four t(14;18)-positive cell lines. Expression of the housekeeping gene GAPDH was used as a control for input cDNA in each RT-PCR reaction. Once the level of GAPDH expression was determined for each cDNA sample, it was used to normalize all other genes tested from the same cDNA samples as described in the Materials and Methods. RT-PCR results are depicted as amplification profiles with relative fluorescence on the y axis and cycle number on the x axis. Cell lines with the highest expression of a given gene will have a lower crossing threshold (CT), and therefore, will show an earlier onset of the exponential phase of the amplification curve for that gene. Amplification profiles are included for: (A) stearoyl-CoA desaturase, (B) v-Myb, (C) neurotrophic tyrosine kinase, receptor-related 1, (D) cyclin-dependent kinase 8, (E) human receptor-like tyrosine kinase (H-Ryk), (F) EST 1, (G) EST 2, (H) EST 3, (I) JunB, (J) JunD, (K) FosB, and (L) glyceraldehyde-3-phosphate dehydrogenase control. The Journal of Molecular Diagnostics 2002 4, 123-136DOI: (10.1016/S1525-1578(10)60693-9) Copyright © 2002 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Comparison of cDNA microarray expression data and quantitative fluorescence RT-PCR data for selected differentially expressed genes identified by microarray analysis in the four t(14;18)-positive cell lines. RT-PCR results were calculated as described in the Materials and Methods. We have consistently observed a larger dynamic range of expression for our RT-PCR data relative to the corresponding cDNA microarray expression data. Results are included for: (A) stearoyl-CoA desaturase (SCD), (B) v-Myb, (C) neurotrophic tyrosine kinase, receptor-related 1 (NTRKR1), (D) cyclin-dependent kinase 8 (CDK8), (E) human receptor-like tyrosine kinase (H-RYK), (F) EST 1, (G) EST 2, (H) EST 3, (I) JunB, (J) JunD, and (K) FosB. Note that no microarray data were available for SCD/Karpas 422 (A), SUDHL-6/CDK8 (D), and SUDHL-4/H-RYK (E). The Journal of Molecular Diagnostics 2002 4, 123-136DOI: (10.1016/S1525-1578(10)60693-9) Copyright © 2002 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions