Bridging Cancer Biology with the Clinic: Relative Expression of a <i>GRHL2</i>-Mediated Gene-Set Pair Predicts Breast Cancer Metastasis

Identification and characterization of crucial gene target(s) that will allow focused therapeutics development remains a challenge. We have interrogated the putative therapeutic targets associated with the transcription factor Grainy head-like 2 (GRHL2), a critical epithelial regulatory factor. We demonstrate the possibility to define the molecular functions of critical genes in terms of their personalized expression profiles, allowing appropriate functional conclusions to be derived. A novel methodology, relative expression analysis with gene-set pairs (RXA-GSP), is designed to explore the potential clinical utility of cancer-biology discovery. Observing that Grhl2-overexpression leads to increased metastatic potential in vitro, we established a model assuming Grhl2-induced or -inhibited genes confer poor or favorable prognosis respectively for cancer metastasis. Training on public gene expression profiles of 995 breast cancer patients, this method prioritized one gene-set pair (GRHL2, CDH2, FN1, CITED2, MKI67 versus CTNNB1 and CTNNA3) from all 2717 possible gene-set pairs (GSPs). The identified GSP significantly dichotomized 295 independent patients for metastasis-free survival (log-rank tested p = 0.002; severe empirical p = 0.035). It also showed evidence of clinical prognostication in another independent 388 patients collected from three studies (log-rank tested p = 3.3e–6). This GSP is independent of most traditional prognostic indicators, and is only significantly associated with the histological grade of breast cancer (p = 0.0017), a GRHL2-associated clinical character (p = 6.8e–6, Spearman correlation), suggesting that this GSP is reflective of GRHL2-mediated events. Furthermore, a literature review indicates the therapeutic potential of the identified genes. This research demonstrates a novel strategy to integrate both biological experiments and clinical gene expression profiles for extracting and elucidating the genomic impact of a novel factor, GRHL2, and its associated gene-sets on the breast cancer prognosis. Importantly, the RXA-GSP method helps to individualize breast cancer treatment. It also has the potential to contribute considerably to basic biological investigation, clinical tools, and potential therapeutic targets.</p

Bridging Cancer Biology with the Clinic: Relative Expression of a <em>GRHL2</em>-Mediated Gene-Set Pair Predicts Breast Cancer Metastasis

<div><p>Identification and characterization of crucial gene target(s) that will allow focused therapeutics development remains a challenge. We have interrogated the putative therapeutic targets associated with the transcription factor Grainy head-like 2 (<i>GRHL2</i>), a critical epithelial regulatory factor. We demonstrate the possibility to define the molecular functions of critical genes in terms of their personalized expression profiles, allowing appropriate functional conclusions to be derived. A novel methodology, relative expression analysis with gene-set pairs (RXA-GSP), is designed to explore the potential clinical utility of cancer-biology discovery. Observing that <i>Grhl2</i>-overexpression leads to increased metastatic potential <i>in vitro</i>, we established a model assuming <i>Grhl2</i>-induced or -inhibited genes confer poor or favorable prognosis respectively for cancer metastasis. Training on public gene expression profiles of 995 breast cancer patients, this method prioritized one gene-set pair (<i>GRHL2, CDH2, FN1, CITED2, MKI67 versus CTNNB1</i> and <i>CTNNA3</i>) from all 2717 possible gene-set pairs (GSPs). The identified GSP significantly dichotomized 295 independent patients for metastasis-free survival (log-rank tested p = 0.002; severe empirical p = 0.035). It also showed evidence of clinical prognostication in another independent 388 patients collected from three studies (log-rank tested p = 3.3e–6). This GSP is independent of most traditional prognostic indicators, and is only significantly associated with the histological grade of breast cancer (p = 0.0017), a <i>GRHL2</i>-associated clinical character (p = 6.8e–6, Spearman correlation), suggesting that this GSP is reflective of <i>GRHL2</i>-mediated events. Furthermore, a literature review indicates the therapeutic potential of the identified genes. This research demonstrates a novel strategy to integrate both biological experiments and clinical gene expression profiles for extracting and elucidating the genomic impact of a novel factor, <i>GRHL2</i>, and its associated gene-sets on the breast cancer prognosis. Importantly, the RXA-GSP method helps to individualize breast cancer treatment. It also has the potential to contribute considerably to basic biological investigation, clinical tools, and potential therapeutic targets.</p> </div

A gene-set pair shows significant prognosis for breast cancer distant metastasis-free survival (DMFS).

<p>The positive individualized prognostic index, i.e. relatively higher expression of the poor-prognosis gene-set (<i>GRHL2, CDH2, FN1, CITED2, MKI67</i>) compared to the good-prognosis gene-set (<i>CTNNB1, CTNNA3</i>), significantly predicts unfavorable DMFS in the training datasets (<b>Panels A</b> 1–3). Importantly, the identified GSP shows significant prognosis in two independent validation datasets (<b>Panel B</b>), theoretically (<b>Panels B</b> 1–2) and empirically (<b>Panels B</b> 3).</p

High level expression of <i>GRHL2</i> contributes to increased metastatic potential.

<p><b>A</b>) Temporal comparison of wound repair in MCF7 and MDCK cells in which <i>Grhl2</i> expression is baseline (Control) or enforced (<i>Grhl2</i>+). <b>B</b>) Boyden chamber migration and invasion assays on control and <i>Grhl2</i> overexpressed (<i>Grhl2</i>+) stable clones for MDCK cells. Fraction of seeded cells that migrated to the bottom chamber at 48 hours is dramatically higher in <i>Grhl2</i>+ clones than in the controls. Data represent mean±SD from triplicates. <b>C</b>) Continuous expression measurement of <i>GRHL2</i> is significantly correlated with the histological tumor grade and the measurement of tumor size in mm (p = 6.8e–6 and 0.041, respectively, Spearman measurement). <b>D</b>) <i>GRHL2</i> expression is significantly higher in patients with grade III breast tumors when compared with grade I or II tumors (two-sided t-test with unequal-variance). <b>E</b>) <i>GRHL2</i> expression reaches significance in patients with large tumors at diagnosis (>2 cm) when compared to smaller tumors (two-sided t-test with unequal-variance).</p