Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays

Liu, Chih Long; Prapong, Wijan; Natkunam, Yasodha; Alizadeh, Ash A.; Montgomery, Kelli; Gilks, C. Blake; Rijn, Matt van de

doi:10.1016/s0002-9440(10)64434-3

Cited by 189 publications

(152 citation statements)

References 15 publications

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“…7 Both programs are freely available on the Internet at http://rana.lbl.gov/EisenSoftware.htm. We prepared the microarray input data files and ran the Cluster program according to the method of Liu et al 9 Contour-frequency plots For each case, the five individual germinal center markers were summed yielding a combined germinal center score, and the three individual activated B-cell markers were summed yielding a combined activated B-cell score. Then, a two-dimensional grid was constructed with the activated B-cell values plotted along the X-axis and the germinal center values along the Y-axis.…”

Section: Hierarchical Cluster Analysismentioning

confidence: 99%

AIDS and non-AIDS diffuse large B-cell lymphomas express different antigen profiles

et al. 2006

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Based on gene expression profiling, diffuse large B-cell lymphomas arising in immunocompetent patients can be divided into germinal center and activated B-cell types. Since little is known about acquired immunodeficiency syndrome associated diffuse large B-cell lymphomas, we tested whether the protein expression of germinal center and activated B-cell markers differed between acquired immunodeficiency syndrome (AIDS) vs non-AIDS diffuse large B-cell lymphomas. We immunohistochemically stained tissue microarrays of 39 de novo diffuse large B-cell lymphomas: 12 AIDS associated and 27 non-AIDS, with germinal center (BCL6, CD10, CyclinH) and activated B-cell markers (MUM1, CD138, PAK1, CD44, BCL2). We scored each case for percent positive cells (0-19% ¼ 0; 20-49% ¼ 1; 50-100% ¼ 2). The activated B-cell and germinal center summation scores of each case were used as (x, y) coordinate data points to construct two-dimensional contour-frequency plots. The contour plot of non-AIDS diffuse large B-cell lymphomas showed two distinct clusters: a cluster with a high germinal center phenotype (cluster 1) and a cluster with a high activated B-cell phenotype (cluster 3). In contrast, the AIDS-related diffuse large B-cell lymphomas formed a single aggregate (cluster 2) (P ¼ 0.02, Fisher exact test). When the contour plots of the AIDS-related and the non-AIDS cases were superimposed, cluster 2 of the AIDS cases expressed an intermediate germinal center/activated B-cell phenotype compared to clusters 1 and 3 of the non-AIDS diffuse large B-cell lymphomas. Our results confirm that non-AIDS diffuse large B-cell lymphomas segregate into two groups with either germinal center or activated B-cell phenotype. We report the new finding that the AIDS status of the patient predicts the immunophenotype of the diffuse large B-cell lymphomas. We also describe a novel method for displaying immunohistochemical expression data using twodimensional contour-frequency plots. Materials and methods Lymphoma SamplesWe performed a retrospective study of 56 diffuse large B-cell lymphomas (23 AIDS-related and 33 non-AIDS) that were retrieved from the archives of

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Section: Hierarchical Cluster Analysismentioning

confidence: 99%

AIDS and non-AIDS diffuse large B-cell lymphomas express different antigen profiles

et al. 2006

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“…25 Data were clustered using Cluster and the output (clusters and dendrograms) visualized with Treeview (freeware available at http://rana.lbl.gov/) software originally designed for analyzing cDNA microarray data. 26 In brief, immunohistochemical raw scores were modified using the TMA deconvoluter by multiplying each score by the absolute value of itself and then converting the scores symmetrically about zero. This increases the magnitude of the large differences among scored samples while minimizing small differences that may not be significant due to the qualitative nature of immunohistochemical scoring.…”

Section: Unsupervised Hierarchal Cluster Analysismentioning

confidence: 99%

“…Distances were calculated using an uncentered Pearson's correlation metric, and then clustered by the average linkage method. 26 Age was scored by setting the mean to zero and then scaling the data into intervals that corresponded to our original scoring system. For age data, this produces a 5-year interval (from 30 to 66 years of age) scoring scale with a high-low cutoff of greater than 66 years and less than 30 years of age.…”

Section: Unsupervised Hierarchal Cluster Analysismentioning

confidence: 99%

“…The tissue microarray immunohistochemical scores were processed into precluster format using the TMA deconvoluter (for detail see Materials and methods). 25,26 In an unsupervised cluster analysis, 15 immunomarkers presented two broad groups of up-or downregulation in 60 leiomyomata, centered on CD24 (upregulation) and glucocorticoid receptor (downregulation) ( Figure 4a). An upregulation of the proteins from insulinsignaling pathway, sex steroid hormone cofactors, CD24 and HMGI appears to be confined to a group of about 40% patients (Figure 3a).…”

Section: Cluster Analysismentioning

confidence: 99%

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Expression profile of tuberin and some potential tumorigenic factors in 60 patients with uterine leiomyomata

et al. 2005

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Human uterine leiomyomata are the most common tumors in women of reproductive age. The pathogenesis of leiomyomata remains unknown. An animal model of Eker rats with deleted tuberous sclerosis complex gene 2 (tuberin) shows increased incidence of leiomyomata. The role of tuberin in human leiomyomata is unknown. In this study, we designed a tissue microarray with tissue cores of leiomyomata and the matched myometrium from 60 hysterectomy specimens. We examined the expression of tuberin and tuberous sclerosis complex gene 1 product hamartin, proteins of the insulin-signaling pathway, steroid receptors and some of their cofactors, and human mobility group gene A2 by immunohistochemistry. We found that nearly half of the cases displayed either reduction or loss of tuberin in leiomyomata compared with matched normal myometrium. No change of hamartin was noted. Furthermore, a significant reduction of glucocorticoid receptor was found in leiomyomata with reduced tuberin. The proteins insulin like growth factor 1, insulin-like growth factor receptor b, AKT kinase, and phosphatidylinositol 3-kinase were upregulated. Nearly half of leiomyomata show upregulation of human mobility group gene A2, along with the steroid receptor cofactors. Our findings suggest that there are two broad groups of uterine leiomyomata. One group is associated with an alteration of tuberin and glucocorticoid receptor. The other group is associated with upregulation of human mobility group gene A2 and steroid receptor cofactors.

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“…25 Unsupervised hierarchical clustering analysis, with an average linkage algorithm, was performed using Cluster software, and the clustered output was viewed using TreeView, which graphically displays relatedness in both dimensions as a dendrogram. 26 …”

Section: Interpretation and Hierarchical Cluster Analysis Of Tissue Mmentioning

confidence: 99%

Clinicopathologic implications of tissue inhibitor of metalloproteinase-1-positive diffuse large B-cell lymphoma

Choi

Lee

et al. 2006

Modern Pathology

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The tissue inhibitor of metalloproteinase-1 (TIMP-1) is a stromal factor that promotes plasmablastic differentiation, and the survival of germinal center B-cells. The expression of TIMP-1 is known to be correlated with a subset of non-Hodgkin lymphoma at the mRNA level, and Epstein-Barr virus infection in vitro. To characterize TIMP-1( þ ) diffuse large B-cell lymphoma, TIMP-1 expression was investigated in tissue microarrays from 182 cases of de novo diffuse large B-cell lymphoma and compared with prognostic factors, immunophenotypes, and Epstein-Barr virus infection status. TIMP-1 was expressed not only in tumor cells themselves, in 14 of 182 cases (8%), designated as TIMP-1( þ ) diffuse large B-cell lymphoma, but also in stromal cells like fibroblasts and endothelial cells. In univariate analysis and hierarchical clustering, our findings suggest that TIMP-1 expression may represent a distinct subgroup. In multivariate analysis, TIMP-1( þ ) diffuse large B-cell lymphoma (n ¼ 14) was associated with unfavorable outcomes compared to TIMP-1(À) diffuse large B-cell lymphoma (n ¼ 168) (odds ratio ¼ 2.5, P ¼ 0.049). Together with TIMP-1 expression, age (greater than 60 years), the presence of B-symptoms, abnormal lactate dehydrogenase level, or more advanced stage (III/IV) was correlated with a poor overall survival. However, TIMP-1 expression in diffuse large B-cell lymphoma was not correlated with other prognostic factors including: clinical stage, international prognostic index score, and nongerminal center B-cell phenotype, as well as Epstein-Barr virus infection. Our results suggest that TIMP-1 expression may be an independent negative prognostic factor in patients with diffuse large B-cell lymphoma.

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Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays

Cited by 189 publications

References 15 publications

AIDS and non-AIDS diffuse large B-cell lymphomas express different antigen profiles

AIDS and non-AIDS diffuse large B-cell lymphomas express different antigen profiles

Expression profile of tuberin and some potential tumorigenic factors in 60 patients with uterine leiomyomata

Clinicopathologic implications of tissue inhibitor of metalloproteinase-1-positive diffuse large B-cell lymphoma

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