Laser Capture Microdissected Cells Research Articles

RNA-Seq analysis of laser-capture microdissected cells of the developing central starchy endosperm of maize.

Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected a high level of correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed developmental stage precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these storage programs. The mRNA-Seq data has been deposited in Gene Expression Omnibus (accession number GSE58504).

Integrative analysis of prostate cancer aggressiveness

Clinical management of prostate cancer (PC) is still highly demanding on the identification of robust biomarkers which will allow a more precise prediction of disease progression. We profiled both mRNA expression and DNA copy number alterations (CNAs) from laser capture microdissected cells from 31 PC patients and 17 patients with benign prostatic hyperplasia using Affymetrix GeneChip® technology. PC patients were subdivided into an aggressive (Gleason Score 8 or higher, and/or T3/T4 and/or N+/M+) and non-aggressive (all others) form of PC. Furthermore, we correlated the two datasets, as genes whose varied expression is due to a chromosomal alteration, may suggest a causal implication of these genes in the disease. All statistical analyses were performed in R version 2.15.0 and Bioconductor version 1.8.1., respectively. We confirmed several common altered chromosomal regions as well as recently discovered loci such as deletions on chromosomes 3p14.1-3p13 and 13q13.3-13q14.11 supporting a possible role for RYBP, RGC32, and ELF1 in tumor suppression. Integrative analysis of expression and CN data combined with data retrieved from online databases propose PTP4A3 and ELF1 as possible factors for tumor progression. Copy number data analysis revealed some significant differences between aggressive and non-aggressive tumors, while gene expression data alone could not define an aggressive group of patients. The assessment of CNA may have diagnostic and prognostic value in PC.

Reverse-phase protein microarray highlights HER2 signaling activation in immunohistochemistry/FISH/HER2-negative breast cancers

Evaluation of: Wulfkuhle JD, Berg D, Wolff C et al. Molecular analysis of HER2 signaling in human breast cancer by functional protein pathway activation mapping. Clin. Cancer Res. 18(23), 6426–6435 (2012).Exhaustive characterization and mapping of pivotal molecules and downstream effectors deregulated in breast cancer is of fundamental clinical value to define the most effective therapy. Wulfkuhle et al. applied reverse-phase protein microarray, a highly sensitive immunoassay able to perform quantitative and multiplexed analysis of total and/or modified cellular proteins, to assess protein levels and activation/phosphorylation status of the HER family (EGFR, HER2, HER3) and downstream signaling molecules in HER2+ and HER2- breast cancers. The research was performed using laser capture microdissected tumor epithelial cells from frozen samples and formalin-fixed paraffin embedded specimens, which were also analyzed by immunohistochemistry (IHC) and FISH. This study identified a subgroup of IHC/FISH/HER2- patients with HER2 activation/phosphorylation levels comparable with those obtained from IHC/FISH/HER2+ tumors. HER2 signaling activation was independent from total HER2 expression and involved HER3 and EGFR activation. These findings indicate that molecular characterization by reverse-phase protein microarray of HER2 and its partners/effectors in the signaling cascade enables the identification of a subgroup of IHC/FISH/HER2- patients showing HER2 signaling activation. These patients, currently excluded from targeted therapy administration, could potentially benefit from this and it could improve prognosis and survival.

Abstract 1157: MicroRNA-625-3p is associated with response to first-line oxaliplatin-based treatment of metastatic colorectal cancer.

Abstract The backbone of current oncologic treatment of metastatic colorectal cancer (mCRC) consists of fluoropyrimidine together with either oxaliplatin (XELOX/FOLFOX) or irinotecan (XELIRI/FOLFIRI). With an overall objective response rate of approximately 50% for either treatment combination, a major unsolved problem is that no predictors of response to these treatments currently are available. To address this issue, we profiled 742 microRNAs in laser-capture microdissected cancer cells from responding and non-responding patients receiving XELOX/FOLFOX as first-line treatment for mCRC, and identified, among others, high expression of miR-625-3p, miR-181b and miR-27b to be associated with poor clinical response. In a validation cohort of 98 mCRC patients treated first-line with XELOX, high expression of miR-625-3p was confirmed to be associated with poor response (OR 6.25, 95%CIOR [1.8; 21.0]). Independent analyses showed that miR-625-3p was not dysregulated between normal and cancer samples, nor was its expression associated with recurrence of stage II or III disease, indicating that miR-625-3p solely is a response marker. Finally, we also found that these miRNAs are up-regulated in oxaliplatin resistant HCT116/oxPt (miR-625-3p, miR-181b and miR-27b) and LoVo/oxPt (miR-181b) CRC cell lines as compared with their isogenic parental cells. Altogether, our results suggest an association between miR-625-3p and response to first-line oxaliplatin based chemotherapy of mCRC. Citation Format: Mads H. Rasmussen, Niels F. Jensen, Line S. Tarpgaard, Camilla Qvortrup, Maria U. Rømer, Jan Stenvang, Tine P. Hansen, Lise-Lotte Christensen, Jan Lindebjerg, Flemming Hansen, Benny V. Jensen, Torben F. Hansen, Anders M. Jakobsen, Per Pfeiffer, Nils Brünner, Torben F. Ørntoft, Claus L. Andersen. MicroRNA-625-3p is associated with response to first-line oxaliplatin-based treatment of metastatic colorectal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1157. doi:10.1158/1538-7445.AM2013-1157

High expression of microRNA-625-3p is associated with poor response to first-line oxaliplatin based treatment of metastatic colorectal cancer

The backbone of current cytotoxic treatment of metastatic colorectal cancer (mCRC) consists of a fluoropyrimidine together with either oxaliplatin (XELOX/FOLFOX) or irinotecan (XELIRI/FOLFIRI). With an overall objective response rate of approximately 50% for either treatment combination, a major unsolved problem is that no predictors of response to these treatments are available. To address this issue, we profiled 742 microRNAs in laser-capture microdissected cancer cells from responding and non-responding patients receiving XELOX/FOLFOX as first-line treatment for mCRC, and identified, among others, high expression of miR-625-3p, miR-181b and miR-27b to be associated with poor clinical response. In a validation cohort of 94 mCRC patients treated first-line with XELOX, high expression of miR-625-3p was confirmed to be associated with poor response (OR = 6.25, 95%CI [1.8; 21.0]). Independent analyses showed that miR-625-3p was not dysregulated between normal and cancer samples, nor was its expression associated with recurrence of stage II or III disease, indicating that miR-625-3p solely is a response marker. Finally, we also found that these miRNAs were up-regulated in oxaliplatin resistant HCT116/oxPt (miR-625-3p, miR-181b and miR-27b) and LoVo/oxPt (miR-181b) colon cancer cell lines as compared with their isogenic parental cells. Altogether, our results suggest an association between miR-625-3p and response to first-line oxaliplatin based chemotherapy of mCRC.

Olfactory receptor 51E1 protein as a potential novel tissue biomarker for small intestine neuroendocrine carcinomas

Late diagnosis hinders proper management of small intestine neuroendocrine carcinoma (SI-NEC) patients. The olfactory receptor, family 51, subfamily E, member 1 (OR51E1) has been reported as a potential novel SI-NEC marker, without protein expression recognition. Thus, we further studied whether the encoded protein may be a novel SI-NEC clinical biomarker. OR51E1 coding sequence was cloned using total RNA from SI-NEC patient specimens. Quantitative real-time PCR analysis explored OR51E1 expression in laser capture microdissected SI-NEC cells and adjacent microenvironment cells. Moreover, immunohistochemistry investigated OR51E1 protein expression on operation and biopsy material from primary SI-NECs, mesentery, and liver metastases from 70 patients. Furthermore, double immunofluorescence studies explored the potential co-localization of the vesicular monoamine transporter 1 (SLC18A1, generally referred to as VMAT1) and OR51E1 in the neoplastic cells and in the intestinal mucosa adjacent to the tumor. OR51E1 coding sequence analysis showed absence of mutation in SI-NEC patients at different stages of disease. OR51E1 expression was higher in microdissected SI-NEC cells than in the adjacent microenvironment cells. Furthermore, both membranous and cytoplasmic OR51E1 immunostaining patterns were detected in both primary SI-NECs and metastases. Briefly, 18/43 primary tumors, 7/28 mesentery metastases, and 6/18 liver metastases were 'positive' for OR51E1 in more than 50% of the tumor cells. In addition, co-localization studies showed that OR51E1 was expressed in >50% of the VMAT1 immunoreactive tumor cells and of the enterochromaffin cells in the intestinal mucosa adjacent to the tumor. OR51E1 protein is a potential novel clinical tissue biomarker for SI-NECs. Moreover, we suggest its potential therapeutic molecular target development using solid tumor radioimmunotherapy.

The Somatostatin Analogue Octreotide Inhibits Growth of Small Intestine Neuroendocrine Tumour Cells

Octreotide is a widely used synthetic somatostatin analogue that significantly improves the management of neuroendocrine tumours (NETs). Octreotide acts through somatostatin receptors (SSTRs). However, the molecular mechanisms leading to successful disease control or symptom management, especially when SSTRs levels are low, are largely unknown. We provide novel insights into how octreotide controls NET cells. CNDT2.5 cells were treated from 1 day up to 16 months with octreotide and then were profiled using Affymetrix microarray analysis. Quantitative real-time PCR and western blot analyses were used to validate microarray profiling in silico data. WST-1 cell proliferation assay was applied to evaluate cell growth of CNDT2.5 cells in the presence or absence of 1 µM octreotide at different time points. Moreover, laser capture microdissected tumour cells and paraffin embedded tissue slides from SI-NETs at different stages of disease were used to identify transcriptional and translational expression. Microarrays analyses did not reveal relevant changes in SSTR expression levels. Unexpectedly, six novel genes were found to be upregulated by octreotide: annexin A1 (ANXA1), rho GTPase-activating protein 18 (ARHGAP18), epithelial membrane protein 1 (EMP1), growth/differentiation factor 15 (GDF15), TGF-beta type II receptor (TGFBR2) and tumour necrosis factor (ligand) superfamily member 15 (TNFSF15). Furthermore, these novel genes were expressed in tumour tissues at transcript and protein levels. We suggest that octreotide may use a potential novel framework to exert its beneficial effect as a drug and to convey its action on neuroendocrine cells. Thus, six novel genes may regulate cell growth and differentiation in normal and tumour neuroendocrine cells and have a role in a novel octreotide mechanism system.

Temporal network based analysis of cell specific vein graft transcriptome defines key pathways and hub genes in implantation injury.

Vein graft failure occurs between 1 and 6 months after implantation due to obstructive intimal hyperplasia, related in part to implantation injury. The cell-specific and temporal response of the transcriptome to vein graft implantation injury was determined by transcriptional profiling of laser capture microdissected endothelial cells (EC) and medial smooth muscle cells (SMC) from canine vein grafts, 2 hours (H) to 30 days (D) following surgery. Our results demonstrate a robust genomic response beginning at 2 H, peaking at 12–24 H, declining by 7 D, and resolving by 30 D. Gene ontology and pathway analyses of differentially expressed genes indicated that implantation injury affects inflammatory and immune responses, apoptosis, mitosis, and extracellular matrix reorganization in both cell types. Through backpropagation an integrated network was built, starting with genes differentially expressed at 30 D, followed by adding upstream interactive genes from each prior time-point. This identified significant enrichment of IL-6, IL-8, NF-κB, dendritic cell maturation, glucocorticoid receptor, and Triggering Receptor Expressed on Myeloid Cells (TREM-1) signaling, as well as PPARα activation pathways in graft EC and SMC. Interactive network-based analyses identified IL-6, IL-8, IL-1α, and Insulin Receptor (INSR) as focus hub genes within these pathways. Real-time PCR was used for the validation of two of these genes: IL-6 and IL-8, in addition to Collagen 11A1 (COL11A1), a cornerstone of the backpropagation. In conclusion, these results establish causality relationships clarifying the pathogenesis of vein graft implantation injury, and identifying novel targets for its prevention.

Alteration of the epigenome during carcinogenesis of intestinal-type gastric cancer.

34 Background: Next-generation sequencing (NGS) is opening a new era for understanding how the human genome is altered in the process of cancer development. We sought to establish an epigenome map based on the DNA methylome during gastric carcinogenesis, paving the way to a better understanding of the origins of gastric cancer using NGS-based epigenome analysis. Methods: We purified DNA in laser-capture microdissected (LCM) cells of normal mucosa, intestinal metaplasia (IM), and gastric cancer from frozen samples of one patient with intestinal type gastric tumor. Two NGS-based epigenome analyses were performed on each DNA: ‘MBD-seq’ (methylated DNA binding domain sequencing) and ‘RRBS’ (reduced representation bisulfite sequencing). Results: MBD-seq and RRBS generated ~25.7 million and ~15.1 million reads respectively, per lane on average. The sequence data matched with 79% (21,514/27,191) and 55% (14,991/27,191) of promoter sequences from UCSC genome browser, respectively. We then identified about one thousand differentially methylated promoters (DMPs), which were altered in IM and in gastric cancer or in gastric cancer compared to that of gastric mucosa. In particular, hypomethylation was detected in 30 promoters by MBD-seq and 173 by RRBS, indicating that RRBS is highly informative for identifying hypomethylated DMPs associated with gene activation during carcinogenesis. Conclusions: We identified several novel hyper- or hypomethylated biomarkers for IM or gastric cancer using NGS-based epigenome analysis. Our reference epigenome map may provide a foundation for future studies exploring the prognostic or preventive biomarker for early stage of gastric cancer.

P5-13-03: Correlation of Clinical and Molecular Findings with Pathologic Response to Preoperative Lapatinib and Trastuzumab, Separately or in Combination, Prior to Neoadjuvant Chemotherapy for HER2 Positive Breast Cancer.

Abstract Background 15% of curative HER2−positive patients (pts) treated with standard trastuzumab (T)-based chemotherapy regimens recur. Our prior report (ASCO 2011 #506 using only data from paired samples N=49) identified major pathways of resistance: autophagy, stem cell, extracellular matrix, and phospho epitopes on FOXO, STAT5, EGFR. Aim: To collect proteomic and microarray data from baseline biopsies and identify molecular correlates of pathologic complete response (pCR). Methods: Randomized, open label, phase II. Eligibility: biopsy-proven HER2 positive stage II, III invasive breast cancer, healthy. After informed consent, pt randomized to T or Lapatinib (L) or both (T+L) for 2 weeks (wk) then continue same anti-HER2 agent with standard chemotherapy (FEC75 IV every 3 wk then Paclitaxel 80 mg/m2 wk x 12) then surgery. Research biopsy before and 2 wks after anti-HER2 agent analyzed by reverse phase protein microarray (RPMA) from laser capture microdissected cells, RNA expression microarray, and in-vitro stem cell studies. PCR in breast is no invasive tumor. ITT is Intent to Treat (all treated pts). Pathways identified by analytes (n=42): autophagy (Beclin 1, LC3B, ATG5), stem cell (CD44, Mushashi, E-Cadherin, Beta Catenin), extracellular matrix (Integrin, MMP). Additional informative analytes: phosphorylated HER3, IGFR1. Results: 100 pts treated: T=33, L=34, T+L=33. % pCR- ITT: ER pos/ER neg by arm: T = 40%/67%; L = 21%/50%; T+L = 58%/50%. Baseline RPMA samples N= 65 (T = 22; L= 25; T+L = 18). A) Specific analytes contributory to outcome by arm by Random Forest analysis: T: Beta Catenin Ser 33/37/Thr 41, EGFR Tyr1045. L: MMP14, E-Cadherin, LC3B, Integrin alpha5 B1, Stat 5 Tyr 694, IGFR Tyr 1131/1146, Erk Thr 202/Tyr204, NFKB Ser536, FOXO Thr24, HER3 Tyr1289. T+L: cerb2, EGFR, Met Tyr1235, CD44, E-Cadherin. B) Statistically significant endpoint ratios from network analysis that strongly correlate with pCR: T: HER3 Tyr1289/Beclin 1; PTENser380/ERK Thr202/Tyr204; GSK3B Ser21-9/Stat5 Tyr694; p70S6 Thr389/LC3B; p7026 Thr389/MMP9; FOXO Thr24-32/NFKB Ser536; Beta Catenin Ser 33–37 Thr41/LC3B. L: EGFR Tyr1045Beclin1; cerb2/Beclin1; HER3 Tyr1289/Beclin1; PI3K/FOXO Thr24,32; IRS1 Ser612/Beclin1; Mushashi/IRS1 Ser612. T+L: only 4 pts no pCR. C) Microarray analysis confirms the critical role of extracellular matrix and autophagy. Discussion: These findings support the concept that NO-pCR tumors can engage a diverse set of strategies to achieve cell survival in the face of therapy. The molecular correlates of response found in this small, underpowered study provide candidates for future patient stratification studies and generate insights for combination therapy. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-13-03.

X-linked inhibitor of apoptosis protein and active caspase-3 expression patterns in antral follicles in the sheep ovary

X-linked inhibitor of apoptosis protein (XIAP) interacts with caspases to inhibit their activity, thereby providing a potential mechanism for regulation of granulosa cell apoptosis occurring during follicular atresia. The aim of this study was to determine the presence and localization of XIAP mRNA and protein content in the sheep ovary and compare these expression patterns with active caspase-3 protein in the same antral follicles. Romney ewe estrous cycles (n=25) were synchronized with 2-3 Estrumate injections and ovarian tissue collected during the luteal and follicular phases of the cycle. The presence of XIAP mRNA was confirmed by RT-PCR using laser capture microdissected ovarian cell samples. XIAP mRNA was subsequently localized by in situ hybridization histochemistry and XIAP and active caspase-3 protein visualized by immunohistochemistry. In antral follicles extensive XIAP localization was evident in both granulosa and thecal cells. In contrast, mRNA expression was widespread in granulosa cells and only detected in thecal tissue from a small proportion of antral follicles. Active caspase-3 and XIAP comparative expression analysis showed positive XIAP mRNA expression in all late luteal phase (day 14) follicles, despite varying levels of active caspase-3 protein. A proportion of follicular phase (days 15 and 16) follicles, however, showed an inverse expression relationship at the protein and mRNA levels in both granulosa and thecal tissue, as did XIAP protein in day 14 follicles. These results suggest high XIAP may prevent activation of caspase-3, thereby regulating follicular atresia in antral follicles and could potentially be utilized as a marker of follicular health.

Clusters of Conserved Beta Cell Marker Genes for Assessment of Beta Cell Phenotype

Background and MethodologyThe aim of this study was to establish a gene expression blueprint of pancreatic beta cells conserved from rodents to humans and to evaluate its applicability to assess shifts in the beta cell differentiated state. Genome-wide mRNA expression profiles of isolated beta cells were compared to those of a large panel of other tissue and cell types, and transcripts with beta cell-abundant and -selective expression were identified. Iteration of this analysis in mouse, rat and human tissues generated a panel of conserved beta cell biomarkers. This panel was then used to compare isolated versus laser capture microdissected beta cells, monitor adaptations of the beta cell phenotype to fasting, and retrieve possible conserved transcriptional regulators.Principal FindingsA panel of 332 conserved beta cell biomarker genes was found to discriminate both isolated and laser capture microdissected beta cells from all other examined cell types. Of all conserved beta cell-markers, 15% were strongly beta cell-selective and functionally associated to hormone processing, 15% were shared with neuronal cells and associated to regulated synaptic vesicle transport and 30% with immune plus gut mucosal tissues reflecting active protein synthesis. Fasting specifically down-regulated the latter cluster, but preserved the neuronal and strongly beta cell-selective traits, indicating preserved differentiated state. Analysis of consensus binding site enrichment indicated major roles of CREB/ATF and various nutrient- or redox-regulated transcription factors in maintenance of differentiated beta cell phenotype.ConclusionsConserved beta cell marker genes contain major gene clusters defined by their beta cell selectivity or by their additional abundance in either neural cells or in immune plus gut mucosal cells. This panel can be used as a template to identify changes in the differentiated state of beta cells.

Nonlinear gene cluster analysis with labeling for microarray gene expression data in organ development

BackgroundThe gene networks underlying closure of the optic fissure during vertebrate eye development are not well-understood. We use a novel clustering method based on nonlinear dimension reduction with data labeling to analyze microarray data from laser capture microdissected (LCM) cells at the site and developmental stages (days 10.5 to 12.5) of optic fissure closure.ResultsOur nonlinear methods created clusters of genes that mapped onto more specific biological processes and functions related to eye development as defined by Gene Ontology at lower false discovery rates than conventional linear cluster algorithms. Our new methods build on the advantages of LCM to isolate pure phenotypic populations within complex tissues in order to identify systems biology relationships among critical gene products expressed at lower copy number.ConclusionsThe combination of LCM of embryonic organs, gene expression microarrays, and nonlinear dimension reduction with labeling is a potentially useful approach to extract subtle spatial and temporal co-variations within the gene regulatory networks that specify mammalian organogenesis and organ function. Our results motivate further analysis of nonlinear dimension reduction with labeling within other microarray data sets from LCM dissected tissues or other cell specific samples to determine the more general utility of our method for uncovering more specific biological functional relationships.

Gastric Cancer: Increased Numbers of Myeloid-Derived Suppressor Cells Are Found in Gastric Cancer Patients

Gastric cancer is one of the most common neoplasms, ranking as the second leading cause of cancer-related deaths worldwide. The predominant factor associated to gastric cancer is Helicobacter pylori infection, which leads to a chronic inflammatory response and subsequent oxyntic atrophy. Parietal cell loss result in two types of metaplasia, the intestinal metaplasia (IM) characterized by the presence of cells with goblet cell morphology and spasmolytic polypeptide-expressing metaplasia (SPEM) that shows morphological characteristics of the deep antral glands and express trefoil factor 2 (spasmolytic polypeptide). Although metaplastic lesions are considered neoplastic precursors, their direct association to cancer is still in debate. Similar to other cancers, gastric cancers are marked by global gene expression alterations. MicroRNAs (miRNAs) are small noncoding RNAs involved in the post-transcriptional regulation of gene expression and an increasing number of studies has been showing their aberrant expression in cancer. In order to identify miRNAs involved in the early stages of gastric cancer we performed a miRNA profiling on laser capture micro-dissected IM and SPEM cells from patient lesions. Using a qRT-PCR approach for quantitation of 754 human miRNAs, we identified 77 miRNAs differentially expressed in the metaplastic samples (greater than two-fold) in comparison to normal chief cells. The highest number of dysregulated miRNAs was observed in IM,which showed 45 up-regulated and 25 down-regulatedmiRNAs. In SPEM, 28 miRNAs were found up-regulated (21 of them also up-regulated in IM), whereas no down-regulation was detected. Some of the up-regulated miRNAs have already been associated to cancer in general (miR-26-a, miR-191, miR-155), as well as specifically to gastric cancer (miR-18b, miR-196b and miR-106a). However, the regulation of some of the top up-regulated miRNAs revealed here including miR-802, miR-922 and miR-622 are still poorly characterized in cancer. In a comparison with a previous mRNA profiling study performed on a similar group of samples, we observed that 108 out of the 568 mRNAs found up-regulated in IM are predicted targets of the 26 microRNAs down-regulated in IM, revealing a potential mechanism for the regulation of those genes in gastric metaplasia. Particularly interesting are 4 members of the miR-30 family, with 31 predicted mRNA targets amongst those up-regulated in IM. Although miR-30 family members have been described as down-regulated in gastric cancer, no data on their targets in this neoplasia is currently available. An extended characterization of the microRNAs identified here will provide a better understanding of their function in gastric metaplasia and progression to neoplasia, as well as might reveal useful early stage biomarkers or therapeutic targets.

The Diagnostic Value of Combining DNA Promoter Hypermethylation With Autofluroscene Spectrum Analysis of Gastric Juice in Gastric Cancer

Gastric cancer is one of the most common neoplasms, ranking as the second leading cause of cancer-related deaths worldwide. The predominant factor associated to gastric cancer is Helicobacter pylori infection, which leads to a chronic inflammatory response and subsequent oxyntic atrophy. Parietal cell loss result in two types of metaplasia, the intestinal metaplasia (IM) characterized by the presence of cells with goblet cell morphology and spasmolytic polypeptide-expressing metaplasia (SPEM) that shows morphological characteristics of the deep antral glands and express trefoil factor 2 (spasmolytic polypeptide). Although metaplastic lesions are considered neoplastic precursors, their direct association to cancer is still in debate. Similar to other cancers, gastric cancers are marked by global gene expression alterations. MicroRNAs (miRNAs) are small noncoding RNAs involved in the post-transcriptional regulation of gene expression and an increasing number of studies has been showing their aberrant expression in cancer. In order to identify miRNAs involved in the early stages of gastric cancer we performed a miRNA profiling on laser capture micro-dissected IM and SPEM cells from patient lesions. Using a qRT-PCR approach for quantitation of 754 human miRNAs, we identified 77 miRNAs differentially expressed in the metaplastic samples (greater than two-fold) in comparison to normal chief cells. The highest number of dysregulated miRNAs was observed in IM,which showed 45 up-regulated and 25 down-regulatedmiRNAs. In SPEM, 28 miRNAs were found up-regulated (21 of them also up-regulated in IM), whereas no down-regulation was detected. Some of the up-regulated miRNAs have already been associated to cancer in general (miR-26-a, miR-191, miR-155), as well as specifically to gastric cancer (miR-18b, miR-196b and miR-106a). However, the regulation of some of the top up-regulated miRNAs revealed here including miR-802, miR-922 and miR-622 are still poorly characterized in cancer. In a comparison with a previous mRNA profiling study performed on a similar group of samples, we observed that 108 out of the 568 mRNAs found up-regulated in IM are predicted targets of the 26 microRNAs down-regulated in IM, revealing a potential mechanism for the regulation of those genes in gastric metaplasia. Particularly interesting are 4 members of the miR-30 family, with 31 predicted mRNA targets amongst those up-regulated in IM. Although miR-30 family members have been described as down-regulated in gastric cancer, no data on their targets in this neoplasia is currently available. An extended characterization of the microRNAs identified here will provide a better understanding of their function in gastric metaplasia and progression to neoplasia, as well as might reveal useful early stage biomarkers or therapeutic targets.

Global Profiling Study Reveals MicroRNA Dysregulation in Human Gastric Metaplastic Lineages

Gastric cancer is one of the most common neoplasms, ranking as the second leading cause of cancer-related deaths worldwide. The predominant factor associated to gastric cancer is Helicobacter pylori infection, which leads to a chronic inflammatory response and subsequent oxyntic atrophy. Parietal cell loss result in two types of metaplasia, the intestinal metaplasia (IM) characterized by the presence of cells with goblet cell morphology and spasmolytic polypeptide-expressing metaplasia (SPEM) that shows morphological characteristics of the deep antral glands and express trefoil factor 2 (spasmolytic polypeptide). Although metaplastic lesions are considered neoplastic precursors, their direct association to cancer is still in debate. Similar to other cancers, gastric cancers are marked by global gene expression alterations. MicroRNAs (miRNAs) are small noncoding RNAs involved in the post-transcriptional regulation of gene expression and an increasing number of studies has been showing their aberrant expression in cancer. In order to identify miRNAs involved in the early stages of gastric cancer we performed a miRNA profiling on laser capture micro-dissected IM and SPEM cells from patient lesions. Using a qRT-PCR approach for quantitation of 754 human miRNAs, we identified 77 miRNAs differentially expressed in the metaplastic samples (greater than two-fold) in comparison to normal chief cells. The highest number of dysregulated miRNAs was observed in IM,which showed 45 up-regulated and 25 down-regulatedmiRNAs. In SPEM, 28 miRNAs were found up-regulated (21 of them also up-regulated in IM), whereas no down-regulation was detected. Some of the up-regulated miRNAs have already been associated to cancer in general (miR-26-a, miR-191, miR-155), as well as specifically to gastric cancer (miR-18b, miR-196b and miR-106a). However, the regulation of some of the top up-regulated miRNAs revealed here including miR-802, miR-922 and miR-622 are still poorly characterized in cancer. In a comparison with a previous mRNA profiling study performed on a similar group of samples, we observed that 108 out of the 568 mRNAs found up-regulated in IM are predicted targets of the 26 microRNAs down-regulated in IM, revealing a potential mechanism for the regulation of those genes in gastric metaplasia. Particularly interesting are 4 members of the miR-30 family, with 31 predicted mRNA targets amongst those up-regulated in IM. Although miR-30 family members have been described as down-regulated in gastric cancer, no data on their targets in this neoplasia is currently available. An extended characterization of the microRNAs identified here will provide a better understanding of their function in gastric metaplasia and progression to neoplasia, as well as might reveal useful early stage biomarkers or therapeutic targets.

Abstract 4413: A 5-gene model predicts clinical outcome in ER+/PR+, early stage breast cancers treated with adjuvant tamoxifen

Abstract Purpose: Patients with primary breast carcinomas expressing of both estrogen (ERα) and progesterone receptors (PR) are more likely to respond to Tamoxifen therapy than those with ERα and PR negative cancers, especially in women with early stage lesions. However, a significant number of these patients exhibiting clinicopathologic features suggesting good response and prognosis will relapse within 10 years. Additional markers are needed to identify patients at risk for breast cancer recurrence after administrative hormone therapy. Procedures: Ten candidate genes associated with estrogen signaling were selected from a group of 200 genes identified from microarray studies of laser capture microdissected breast carcinoma cells of ER positive breast cancers and combined with those for conventional biomarkers (ESR1, PGR, ERBB2). Carcinoma cell content and pathology of each biopsy was confirmed. Expression of this 13-gene subset was analyzed by RT-qPCR in de-identified frozen tissue specimens from early stage, ER+/PR+ breast cancers treated with adjuvant Tamoxifen. A multivariate model was created by Cox regression using a training set of tissue sections from 36 biopsy specimens, and then applied to an independent validation set of sections from 24 specimens. Results: A 5-gene model was derived from the training set that exhibited significant correlations with both relapse-free and overall survival. Applying this model to Kaplan-Meier regression, patients were separated into low risk (100% relapse-free at 150 months) and high risk (60% relapse-free at 150 months) groups (P = 0.03). When this model was applied to the validation set, similar risk stratification was achieved for both relapse-free and overall survival (P = 0.01 and 0.04, respectively). No significant difference in clinical features (e.g., tumor grade, tumor size and nodal status) was observed between the high and low risk groups. Conclusions: We developed a 5-gene model composed of PgR, BCL2, ERBB4 JM-a, RERG and CD34 that identified a subset of early stage, ER+/PR+ breast cancers patients treated with Tamoxifen that exhibited high recurrence rates, although their clinicopathologic features suggested good prognosis and response. Furthermore, absence of association of the 5-gene model with tumor grade suggests the gene expression profile provides clinically relevant predictive information independent of proliferation. Supported in part by grants from the Phi Beta Psi Sorority Charity Trust and a CTSP award from the Commonwealth of Kentucky. DAK was a recipient of a Graduate Fellowship from the Integrated Programs in Biomedical Sciences, University of Louisville, and the Spatola Graduate Fellowship from IMD3. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4413. doi:10.1158/1538-7445.AM2011-4413

Abstract 2406: Molecular characterization of ciclooxigenase-2 in canine proliferative inflammatory atrophy of the prostate

Abstract Due to the importance and incidence of prostatic carcinoma in man, some animals are being used as a model in the investigation of the pathogenesis and development of this lesion. Similarly to men, the dog presents a spontaneous development of prostate cancer, which is locally invasive and can develop bone metastasis. Proliferative inflammatory atrophy (PIA) is considered a pre-neoplastic lesion in men. Overexpression of COX-2 has been associated with PIA, PIN and prostatic carcinoma playing a role in angiogenesis, apoptosis inhibition, increasing of invasive capacity, metastasis and inflammation in different prostatic affections. The aim of this study was to assess the protein and gene expression of COX-2 in laser capture microdissected stroma and epithelial cells of PIA foci in canine prostate by immunohistochemistry (IHC) and qRT-PCR. For IHC, 38 PIA lesions arranged in a tissue microarray were evaluated. Frozen fragments from 17 PIA and 3 normal prostatic tissues were used for COX2 gene expression. Our results showed increased COX2 gene expression in stromal cells compared to epithelial cells. High level of COX-2 protein expression was observed in 87% of PIA lesions, despite epithelial or stromal compartment. The In the present study, the stroma presented an important role, since the COX-2 gene expression in canine PIA lesions was increased in this cell compartment. To the best of our knowledge, this is the first report of COX2 gene expression in canine PIA. Since high levels of COX-2 have been associated to the risk of developing of prostate cancer in man, dog can be used as a natural model for this disease. The stroma can act as paracrine way in the epithelial cells, stimulating epithelial proliferation, reducing the apoptosis of this compartment and promoting angiogenesis in the microenvironment, factor that contribute to prostatic carcinogenesis and that the protein expression is increased in this lesion. Sponcer: Fapesp (Fundação de Apoio a Pesqusia do Estado de São Paulo) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2406. doi:10.1158/1538-7445.AM2011-2406

Abstract 509: The CTGF antibody FG-3019 blocks CTGF-stimulated migration in ovarian cancer cells

Abstract Ovarian tumors generally arise from the surface epithelium of the ovary, and require interactions with host stroma to promote tumor cell proliferation and expansion. The signaling mechanisms between tumor-associated stroma and adjacent ovarian epithelial tumor cells remain unclear. We have previously analyzed gene expression profiles of laser-capture microdissected stromal cells from normal ovary and ovarian tumors and have demonstrated that normal ovarian stroma undergoes significant gene expression changes in response to the epithelial tumor microenvironment. Connective Tissue Growth Factor (CTGF), a TGF-β-regulated gene, was identified as specifically up-regulated in tumor-associated versus normal stroma. CTGF is a component of the tumor microenvironment with a demonstrated role in tumor progression and metastasis. FG-3019, a fully human monoclonal antibody against CTGF, is currently under clinical investigation in pancreatic cancer. The aim of this current study was to further elucidate the role of CTGF in ovarian cancer and examine its potential as a therapeutic target. We demonstrate that normal ovarian fibroblasts and ovarian cancer-associated fibroblasts treated with TGF-β secreted high levels of CTGF, whereas ovarian cancer epithelial cells secreted significantly lower levels. We next assessed the paracrine effect of CTGF on three different ovarian cancer cell lines, A224, OVCAR3, and SKOV3. Expression of endogenous CTGF is low in these cells which is consistent with the level found in primary ovarian tumor cells. Addition of recombinant CTGF for 6-hr stimulated migration of A224 (443 ± 20.5 vs. 85 ± 24.4 cells), OVCAR3 (104 ± 11.7 vs. 68 ± 30.1 cells) and SKOV3 (334 ± 45.6 vs. 82 ± 16.6 cells) in a transwell migration assay. Addition of the CTGF-blocking antibody FG-3019 significantly inhibited transwell migration in the presence of recombinant CTGF in all three cell lines (from 443 ± 20.5 to 197 ± 65.4 cells in A224, 334 ± 45.6 to 119 ± 29.0 cells in SKOV3 and 104 ± 11.7 to 36 ± 2.5 cells in OVCAR3). However, recombinant CTGF did not promote proliferation of these cell lines. We demonstrate that CTGF may contribute to ovarian tumor biology and that its function can be blocked by FG-3019, thus determining CTGF as a potential therapeutic target in ovarian tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 509. doi:10.1158/1538-7445.AM2011-509

LINE-1 Hypomethylation During Primary Colon Cancer Progression

BackgroundMethylation levels of genomic repeats such as long interspersed nucleotide elements (LINE-1) are representative of global methylation status and play an important role in maintenance of genomic stability. The objective of the study was to assess LINE-1 methylation status in colorectal cancer (CRC) in relation to adenomatous and malignant progression, tissue heterogeneity, and TNM-stage.Methodology/Principal FindingsDNA was collected by laser-capture microdissection (LCM) from normal, adenoma, and cancer tissue from 25 patients with TisN0M0 and from 92 primary CRC patients of various TNM-stages. The paraffin-embedded tissue sections were treated by in-situ DNA sodium bisulfite modification (SBM). LINE-1 hypomethylation index (LHI) was measured by absolute quantitative analysis of methylated alleles (AQAMA) realtime PCR; a greater index indicated enhanced hypomethylation. LHI in normal, cancer mesenchymal, adenoma, and CRC tissue was 0.38 (SD 0.07), 0.37 (SD 0.09), 0.49 (SD 0.10) and 0.53 (SD 0.08), respectively. LHI was significantly greater in adenoma tissue compared to its contiguous normal epithelium (P = 0.0003) and cancer mesenchymal tissue (P<0.0001). LHI did not differ significantly between adenoma and early cancer tissue of Tis stage (P = 0.20). LHI elevated with higher T-stage (P<0.04), was significantly greater in node-positive than node-negative CRC patients (P = 0.03), and was significantly greater in stage IV than all other disease stages (P<0.05).Conclusion/SignificanceBy using in-situ SBM and LCM cell selection we demonstrated early onset of LINE-1 demethylation during adenomatous change of colorectal epithelial cells and demonstrated that LINE-1 demethylation progression is linear in relation to TNM-stage progression.