Time course analysis of gene expression identifies multiple genes with differential expression in patients with in-stent restenosis

Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models

Molecularly targeted therapeutics hold promise of revolutionizing treatments of advanced malignancies. However, a large number of patients do not respond to these treatments. Here, we take a systems biology approach to understand the molecular mechanisms that prevent breast cancer (BC) cells from responding to lapatinib, a dual kinase inhibitor that targets human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR). To this end, we analysed temporal gene expression profiles of four BC cell lines, two of which respond and the remaining two do not respond to lapatinib. For this analysis, we developed a Gaussian process based algorithm which can accurately find differentially expressed genes by analysing time course gene expression profiles at a fraction of the computational cost of other state-of-the-art algorithms. Our analysis identified 519 potential genes which are characteristic of lapatinib non-responsiveness in the tested cell lines. Data from the Genomics of Drug Sensitivity in Cancer (GDSC) database suggested that the basal expressions 120 of the above genes correlate with the response of BC cells to HER2 and/or EGFR targeted therapies. We selected 27 genes from the larger panel of 519 genes for experimental verification and 16 of these were successfully validated. Further bioinformatics analysis identified vitamin D receptor (VDR) as a potential target of interest for lapatinib non-responsive BC cells. Experimentally, calcitriol, a commonly used reagent for VDR targeted therapy, in combination with lapatinib additively inhibited proliferation in two HER2 positive cell lines, lapatinib insensitive MDA-MB-453 and lapatinib resistant HCC 1954-L cells.

Detecting cognizable trends of gene expression in a time series RNA-sequencing experiment: a bootstrap approach

Study of temporal trajectory of gene expression is important. RNA sequencing is popular in genome-scale studies of transcription. Because of high expenses involved, many time-course RNA sequencing studies are challenged by inadequacy of sample sizes. This poses difficulties in conducting formal statistical tests of significance of null hypotheses. We propose a bootstrap algorithm to identify 'cognizable' 'time-trends' of gene expression. Properties of the proposed algorithm are derived using a simulation study. The proposed algorithm captured known 'time-trends' in the simulated data with a high probability of success, even when sample sizes were small (n < 10). The proposed statistical method is efficient and robust to capture 'cognizable' 'time-trends' in RNA sequencing data.

Systemic inflammation as a predictor of clinical outcomes after lower extremity angioplasty/stenting

OBJECTIVE

The activation state of the systemic inflammatory milieu has been proposed as a critical regulator of vascular repair after injury. We evaluated the early inflammatory response after endovascular intervention for symptomatic peripheral arterial disease to determine its association with clinical success or failure.

METHODS

Blood samples were obtained from 14 patients undergoing lower extremity angioplasty/stenting and analyzed using high-throughput gene arrays, multiplex serum protein analyses, and flow cytometry.

RESULTS

Time-dependent plasma protein and monocyte phenotype analyses demonstrated endovascular revascularization had a modest influence on the overall activation state of the systemic inflammatory system, with baseline variability exceeding the perturbations induced by the intervention. In contrast, specific time-dependent changes in the monocyte genome are evident in the initial 28 days, predominately in those genes associated with leukocyte extravasation. Investigating the relationship between inflammation and the 1-year success or failure of the intervention showed no single plasma protein was correlated with outcome, but a more comprehensive cluster analysis revealed a clear pattern of protein expression that was closely related to the clinical phenotype. Corresponding examination of the monocyte genome identified a gene subset at 1 day postprocedure that was predictive of clinical outcome, with most of these genes active in cell-cycle signaling.

CONCLUSIONS

Although the global influence of angioplasty/stenting on systemic inflammation was modest, circulating cytokine and monocyte genome analyses support a pattern of early inflammation that is associated with ultimate intervention success vs failure. Molecular profiles incorporating genes involved in monocyte cell-cycle progression and homing, or proinflammatory cytokines, or both, offer the most promise for the development of class prediction tools for clinical application.

Mmp-9 expression after metallic stent placement in patients with colorectal cancer: association with in-stent restenosis

PURPOSE

To verify the expression of matrix metalloproteinase (MMP)-9 in stent-induced hyperplastic tissue from patients with colorectal cancer who received colorectal stents as a bridge to surgery.

MATERIALS AND METHODS

This prospective study was institutional review board-approved, and informed consent was obtained from all patients. Eleven patients (nine men, two women; mean age, 67 years; age range, 53-82 years) with malignant colorectal obstructions who received a colorectal stent between May and December 2010 were included. Tissue specimens were analyzed for MMP-9 and MMP-2 expression. After resection, the tissue was segmented into three parts: tumor tissue, stent-induced tissue hyperplasia, and normal colon tissue. MMP-9 and MMP-2 expression were determined by using zymography, Western blot analysis, and real-time reverse-transcription (qRT) polymerase chain reaction (PCR). Significance of differences between groups was evaluated with Friedman analysis of variance test. Signed-rank test was used to determine differences between malignant tumor tissue and stent-induced hyperplastic tissue groups.

RESULTS

Stent placement was technically successful in all 11 patients. Stent-induced hyperplastic tissues were found in all patients. Zymography (P = .003) and Western blot analysis (P = .008) showed that expression of MMP-9 was higher in malignant tumor tissue and stent-induced hyperplastic tissue groups compared with normal colorectal tissue group, demonstrating significant differences between groups but no significant differences between malignant tumor and stent-induced hyperplastic tissues. As for results of qRT PCR analysis, the stent-induced hyperplastic tissue group showed increases in messenger RNA expression level of MMP-9 compared with the malignant tumor tissue group (50.42-fold ± 66.30 higher).

CONCLUSION

High expression of MMP-9 is closely associated with stent-induced colorectal tissue hyperplasia in patients with colorectal cancer.