Design, assessment, and in vivo evaluation of a computational model illustrating the role of CAV1 in CD4+ T-lymphocytes

Caveolin-1 (CAV1) is a vital scaffold protein heterogeneously expressed in both healthy and malignant tissue. We focus on the role of CAV1 when overexpressed in T-cell leukemia. Previously, we have shown that CAV1 is involved in cell-to-cell communication, cellular proliferation, and immune synapse formation; however, the molecular mechanisms have not been elucidated. We hypothesize that the role of CAV1 in immune synapse formation contributes to immune regulation during leukemic progression, thereby warranting studies of the role of CAV1 in CD4+ T-cells in relation to antigen-presenting cells. To address this need, we developed a computational model of a CD4+ immune effector T-cell to mimic cellular dynamics and molecular signaling under healthy and immunocompromised conditions (i.e., leukemic conditions). Using the Cell Collective computational modeling software, the CD4+ T-cell model was constructed and simulated under CAV1+/+, CAV1+/−, and CAV1−/− conditions to produce a hypothetical immune response. This model allowed us to predict and examine the heterogeneous effects and mechanisms of CAV1 in silico. Experimental results indicate a signature of molecules involved in cellular proliferation, cell survival, and cytoskeletal rearrangement that were highly affected by CAV1 knock out. With this comprehensive model of a CD4+ T-cell, we then validated in vivo protein expression levels. Based on this study, we modeled a CD4+ T-cell, manipulated gene expression in immunocompromised versus competent settings, validated these manipulations in an in vivo murine model, and corroborated acute T-cell leukemia gene expression profiles in human beings. Moreover, we can model an immunocompetent versus an immunocompromised microenvironment to better understand how signaling is regulated in patients with leukemia

Conserved Molecular Underpinnings and Characterization of a Role for Caveolin-1 in the Tumor Microenvironment of Mature T-Cell Lymphomas

Neoplasms of extra-thymic T-cell origin represent a rare and difficult population characterized by poor clinical outcome, aggressive presentation, and poorly defined molecular characteristics. Much work has been done to gain greater insights into distinguishing features among malignant subtypes, but there also exists a need to identify unifying characteristics to assist in rapid diagnosis and subsequent potential treatment. Herein, we investigated gene expression data of five different mature T-cell lymphoma subtypes (n = 187) and found 21 genes to be up- and down-regulated across all malignancies in comparison to healthy CD4+ and CD8+ T-cell controls (n = 52). From these results, we sought to characterize a role for caveolin-1 (CAV1), a gene with previous description in the progression of both solid and hematological tumors. Caveolin-1 was upregulated, albeit with a heterogeneous nature, across all mature T-cell lymphoma subtypes, a finding confirmed using immunohistochemical staining on an independent sampling of mature T-cell lymphoma biopsies (n = 65 cases). Further, stratifying malignant samples in accordance with high and low CAV1 expression revealed that higher expression of CAV1 in mature T-cell lymphomas is analogous with an enhanced inflammatory and invasive gene expression profile. Taken together, these results demonstrate a role for CAV1 in the tumor microenvironment of mature T-cell malignancies and point toward potential prognostic implications

Correction: Conserved Molecular Underpinnings and Characterization of a Role for Caveolin-1 in the Tumor Microenvironment of Mature T-Cell Lymphomas.

[This corrects the article DOI: 10.1371/journal.pone.0142682.]

Publically available, chip-matched GEO DataSets of mature T-cell lymphomas and healthy CD4⁺ and CD8⁺ T cells utilized for gene expression profiling.

<p>AITL, angioimmunoblastic T-cell lymphoma; ALCL, anaplastic large cell lymphoma; ATLL, adult T-cell leukemia/lymphoma; HSTL, hepatosplenic T-cell lymphoma; PTCL-NOS, peripheral T-cell lymphoma, not otherwise specified; PMID, PubMed identifier</p><p>Publically available, chip-matched GEO DataSets of mature T-cell lymphomas and healthy CD4⁺ and CD8⁺ T cells utilized for gene expression profiling.</p

Immunohistochemical staining of mature T-cell lymphoma biopsies.

<p>Representative positive and negative lymphoid-staining samples for BCL10, CAV1, GILZ, and CD90 are presented. All images were taken at 60x magnification. No healthy lymph nodes were negative for BCL10 lymphoid staining. Yellow arrowheads in ALCL positive sample point toward punctate CAV1 staining in hallmark horse-shoe nuclei tumor cells.</p

Summary of diagnoses, patient characteristics, and staining properties of T-cell lymphoma histological samples from the Ly6161 tissue microarray from U.S. Biomax, Inc.

<p>¹ Age reported in years</p><p>² Percentages reflect staining observed in lymphoid cells</p><p>Summary of diagnoses, patient characteristics, and staining properties of T-cell lymphoma histological samples from the Ly6161 tissue microarray from U.S. Biomax, Inc.</p

Long non-Coding RNA 273 is computationally predicted to interact with members of a CAV1-interaction network.

<p>(A) Boxplot of normalized AFFX-HUMRGE/M10098_5_at (<i>LINC00273</i>) probe signal for <i>CAV1</i>-Low and <i>CAV1</i>-High expression groups. Continuous line represents median value, discontinuous line represents mean value. (B) CAV1-interacting proteins upregulated in the <i>CAV1</i>-High expression group. Interaction network viewed in String evidence view, connection lines are defined by in-Fig box. (C) CAV1-interacting proteins upregulated in the <i>CAV1</i>-Low expression group. Interaction network viewed in String evidence view, connection lines are defined by in-Fig box.</p

Computational predictions for RNA-protein interactions between <i>LINC00273</i> and CAV1-interacting proteins.

<p>* Proteins in the <i>CAV1</i>-Low interaction network</p><p>¹ Interactions scored positive at values ≥50</p><p>² Interactions scored positive at values ≥0.5</p><p>³ Interactions scored positive at values ≥0.5</p><p>Computational predictions for RNA-protein interactions between <i>LINC00273</i> and CAV1-interacting proteins.</p

PANTHER enrichment analysis of genes upregulated in the <i>CAV1</i>-High tumor microenvironment.

<p>¹ p-values calculated using the Bonferroni correction</p><p>PANTHER enrichment analysis of genes upregulated in the <i>CAV1</i>-High tumor microenvironment.</p