Analysis of PSA recurrence-free survival.

a<p>Log rank test (univariate analysis) or Wald test (multivariate analysis).</p>b<p>Analyzed as a continuous variable.</p>c<p>Stratification based on limited representation of Gleason 6 and 4+4 cases.</p>d<p>Stratifies pathologic stage based on organ confinement.</p

A proliferation signature cluster in prostate cancer.

<p>(<b>A</b>) Unsupervised cluster analysis of prostate cancers (data set from ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020293#pone.0020293-Lapointe1" target="_blank">[19]</a>) reveals molecular subtypes of prostate cancer (1, 2 and 3, labeled), and gene-expression features reflecting underlying biological processes. <i>Left</i>, thumbnail heatmap of the cluster analysis. <i>Right</i>, enlarged view of the “proliferation cluster”, with selected genes shown (<i>MKI67</i>, <i>TOP2A</i> and <i>E2F1</i> in red text, marked by arrow). Red and green expression levels reflect high and low values, respectively (see key). Red filled circles (<i>below</i>) identify lymph node metastases. (<b>B</b>) Overlap matrix of proliferation cluster genes (N = 94) with canonical pathway (CP) gene sets identifies top gene set matches (all significant, <i>P</i><0.001) all relating to cell-cycle/proliferation. Solid blue fill indicates overlapping membership between proliferation cluster and queried gene sets.</p

Immunostaining of Ki-67, TOP2A and E2F1 are prognostic.

<p>(<b>A</b>) Immunostaining of proliferation markers Ki-67, TOP2A and E2F1; representative positive and negative cases shown. (<b>B</b>) Pairwise comparison of immunostain scores across cases. Pearson correlation (R) values shown. (<b>C</b>) Kaplan-Meier analysis of Ki-67 (<5% <i>vs.</i> ≥5% tumor nuclei), TOP2A (<5% <i>vs.</i> ≥5% tumor nuclei) and E2F1 (<50% <i>vs.</i> ≥50% tumor nuclei) immunostaining. <i>P</i>-values (log-rank test) shown. (<b>D</b>) Kaplan-Meier analysis of combined marker staining (see keys). <i>P</i>-values (log-rank test) shown.</p

Receiver-operating characteristic (ROC) curve analysis.

a<p>Evaluated at 8 years follow-up (the median follow-up time).</p>b<p>Analyzed as a continuous variable.</p>c<p>Stratification based on limited representation of Gleason 6 and 4+4 cases.</p>d<p>Stratifies pathologic stage based on organ confinement.</p

Clinicopathological characteristics of tissue microarray cases.

a<p>Determined from pathology report (not tissue microarray core).</p

Incorporation of proliferation index improves prognostic value.

<p>(<b>A</b>) Kaplan-Meier analysis comparing multivariate models based on clinicopathologic data (<i>left</i>) and clinicopathologic data plus the tri-marker proliferation index (<i>right</i>). Cases are grouped by tertile. Log-rank test <i>P</i>-values are indicated. (<b>B</b>) ROC curve analysis comparing multivariate models based on clinicopathologic data (<i>left</i>) and clinicopathologic data plus the tri-marker proliferation index (<i>right</i>). Analysis done at 8 years follow-up (the median follow-up time for the cohort). Areas under the curve (AUC) are indicated.</p

Image_3_Tissue-Specific Expression of the Low-Affinity IgG Receptor, FcγRIIb, on Human Mast Cells.PDF

<p>Immediate hypersensitivity reactions are induced by the interaction of allergens with specific IgE antibodies bound via FcεRI to mast cells and basophils. While these specific IgE antibodies are needed to trigger such reactions, not all individuals harboring IgE exhibit symptoms of allergy. The lack of responsiveness seen in some subjects correlates with the presence of IgG antibodies of the same specificity. In cell culture studies and in vivo animal models of food allergy and anaphylaxis such IgG antibodies have been shown to exert suppression via FcγRIIb. However, the reported absence of this inhibitory receptor on primary mast cells derived from human skin has raised questions about the role of IgG-mediated inhibition of immediate hypersensitivity in human subjects. Here, we tested the hypothesis that mast cell FcγRIIb expression might be tissue specific. Utilizing a combination of flow cytometry, quantitative PCR, and immunofluorescence staining of mast cells derived from the tissues of humanized mice, human skin, or in fixed paraffin-embedded sections of human tissues, we confirm that FcγRIIb is absent from dermal mast cells but is expressed by mast cells throughout the gastrointestinal tract. IgE-induced systemic anaphylaxis in humanized mice is strongly inhibited by antigen-specific IgG. These findings support the concept that IgG, signaling via FcγRIIb, plays a physiological role in suppressing hypersensitivity reactions.</p

Image_2_Tissue-Specific Expression of the Low-Affinity IgG Receptor, FcγRIIb, on Human Mast Cells.PDF

<p>Immediate hypersensitivity reactions are induced by the interaction of allergens with specific IgE antibodies bound via FcεRI to mast cells and basophils. While these specific IgE antibodies are needed to trigger such reactions, not all individuals harboring IgE exhibit symptoms of allergy. The lack of responsiveness seen in some subjects correlates with the presence of IgG antibodies of the same specificity. In cell culture studies and in vivo animal models of food allergy and anaphylaxis such IgG antibodies have been shown to exert suppression via FcγRIIb. However, the reported absence of this inhibitory receptor on primary mast cells derived from human skin has raised questions about the role of IgG-mediated inhibition of immediate hypersensitivity in human subjects. Here, we tested the hypothesis that mast cell FcγRIIb expression might be tissue specific. Utilizing a combination of flow cytometry, quantitative PCR, and immunofluorescence staining of mast cells derived from the tissues of humanized mice, human skin, or in fixed paraffin-embedded sections of human tissues, we confirm that FcγRIIb is absent from dermal mast cells but is expressed by mast cells throughout the gastrointestinal tract. IgE-induced systemic anaphylaxis in humanized mice is strongly inhibited by antigen-specific IgG. These findings support the concept that IgG, signaling via FcγRIIb, plays a physiological role in suppressing hypersensitivity reactions.</p

Histological Architecture of CSR Gene Expression in Breast Cancer

<p>Representative ISH of <i>LOXL2</i> and <i>SDFR1</i> and IHC of PLOD2, PLAUR, and ESDN are shown (magnification, 200×). Panels for <i>LOXL2</i>, PLAUR, PLOD2, and ESDN represent cores of normal and invasive ductal breast carcinoma from different patients on the same tissue microarray. Panels for <i>SDFR1</i> demonstrate staining in adjacent normal and carcinoma cells on the same tissue section. Arrows highlight spindle-shaped stromal cells that stain positive for <i>SDFR1</i> and PLOD2. No signal was detected for the sense probe for ISH or for control IHC without the primary antibody.</p

Prognostic Value of Fibroblast CSR in Epithelial Tumors

<p>Kaplan–Meier survival curves of tumors stratified into two classes using the fibroblast CSR are shown for stage I and IIA breast cancer (van 't Veer et al. 2002) (A), stage I and II lung adenocarcinoma (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020007#pbio-0020007-Bhattacharjee1" target="_blank">Bhattacharjee et al. 2001</a>) (B), lung adenocarcinoma of all stages (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020007#pbio-0020007-Garber1" target="_blank">Garber et al. 2001</a>) (C), and stage III gastric carcinoma (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020007#pbio-0020007-Leung1" target="_blank">Leung et al. 2002</a>) (D).</p