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1.  Influence of hypoxia induced by minimally invasive prostatectomy on gene expression: implications for biomarker analysis 
Handling and processing of clinical specimens during and after surgical resection may significantly skew the molecular data obtained from analysis of those samples. Minimally invasive prostatectomy was used as a model to specifically study effects of surgical ischemia on gene expression in human clinical samples. Normal prostatic urethra cup biopsies were procured from 12 patients at three time points during laparoscopic radical prostatectomy. Homogeneous cells (stroma and epithelium) were microdissected. Transcript analysis of 3 oxygen-dependent, 3 oxygen-independent, and 3 control class genes was performed using quantitative RT-PCR. Data were analyzed by relative quantitation and two-sided t-test. Patient demographic and time covariates were fit by a linear mixed model. VEGF, an oxygen-dependent gene, showed significant expression alterations across three time points in epithelium (p=0.008), but not in stroma (p=0.66). Expression levels of VHL, STAT5B, and CYPA showed significant changes at the p<0.05 level in the stroma only. Effects of age, PSA, prostate size, Gleason score, surgery type, total surgery time, total ischemia time, and estimated blood loss on VEGF expression over time were not significant at the p<0.01 level. Therefore, surgical manipulation and tissue processing methods need to be taken into account when assessing prostatic biomarkers; however, resection does not dramatically alter mRNA profiles in prostate specimens.
PMCID: PMC2892411  PMID: 20589162
Laparoscopic surgery; prostatectomy; warm ischemia; hypoxia; tissue microdissection; gene expression analysis
2.  Split Hemianterior Tibialis Turndown Muscle Flap for Coverage of Distal Leg Wounds With Preservation of Function 
Eplasty  2014;14:e12.
Objective: A hemisplit turndown tibialis anterior muscle flap is described for coverage of distal leg wounds with preservation of active extensor function for open wounds of the distal ankle is presented. This is a new flap not previously described and is another local option for coverage of selected distal leg wounds. Methods: A description of the operative procedure and a clinical successful example is presented. Results: The split hemitibialis anterior turndown muscle flap was successful and preserved function of the muscle and tendon. Conclusions: This is another option for coverage of difficult wounds of the lower extremity without sacrifice of function of the donor muscle.
PMCID: PMC3964920  PMID: 24741383
muscle flap; tibialis anterior muscle; lower extremity wound; split muscle; tibialis anterior tendon
3.  Decrease in CD8+ lymphocyte number and altered cytokine profile in human prostate cancer 
The tumor microenvironment is comprised of multiple cell types arranged in a three-dimensional structure. Interactions amongst the various cell components play an important role in neoplasia, including the inflammatory reaction that occurs as part of the host response. In this study, the regional lymphocyte subpopulations and cytokine profiles associated with prostate cancer were examined using a quantitative imaging approach and expression microarray analysis. Lymphocytes were measured in four different epithelial phenotypes in prostate cancer specimens: carcinoma; prostatic intraepithelial neoplasia (PIN); benign prostate hyperplasia (BPH); and normal epithelium. The data indicate that CD8 positive, cytotoxic T lymphocytes are significantly decreased in regions adjacent to hyperplasia and carcinoma as compared to normal epithelium and PIN. In contrast the relative number of CD4 positive and CD20 positive lymphocytes did not change markedly. Parallel mRNA expression array analysis of the normal and tumor microenvironments identified a distinct cytokine profile in cancer, with 24 dysregulated genes in tumor epithelium and nine altered in tumor-associated stroma. Overall, these data indicate that the spatial distribution of CD8 positive, cytotoxic T lymphocytes is dysregulated in human prostate glands that contain cancer, and cytokine profiles are altered at the mRNA level.
PMCID: PMC3180108  PMID: 21969236
Prostate cancer; lymphocytes; cytokines; histomathematics; histopathology
4.  Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples 
Nature protocols  2009;4(6):902-922.
Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a valuable tool for measuring gene expression in biological samples. However, unique challenges are encountered when studies are performed on cells microdissected from tissues derived from animal models or the clinic, including specimen related issues, variability of RNA template quality and quantity, and normalization. qRT-PCR using small amounts of mRNA derived from dissected cell populations requires adaptation of standard methods to allow meaningful comparisons across sample sets. The protocol described here presents the rationale, technical steps, normalization strategy, and data analysis necessary to generate reliable gene expression measurements of transcripts from dissected samples. The entire protocol from tissue microdissection through qRT-PCR analysis requires approximately 16 hours.
doi:10.1038/nprot.2009.61
PMCID: PMC2760821  PMID: 19478806
quantitative measurements; microdissected tissues; qRT-PCR; validation; gene expression analysis; protocol; normalization strategy
5.  The Chemokine CXCL16 and Its Receptor, CXCR6, as Markers and Promoters of Inflammation-Associated Cancers 
PLoS ONE  2009;4(8):e6695.
Clinical observations and mouse models have suggested that inflammation can be pro-tumorigenic. Since chemokines are critical in leukocyte trafficking, we hypothesized that chemokines play essential roles in inflammation-associated cancers. Screening for 37 chemokines in prostate cancer cell lines and xenografts revealed CXCL16, the ligand for the receptor CXCR6, as the most consistently expressed chemokine. Immunohistochemistry and/or immunofluorescence and confocal imaging of 121 human prostate specimens showed that CXCL16 and CXCR6 were co-expressed, both on prostate cancer cells and adjacent T cells. Expression levels of CXCL16 and CXCR6 on cancer cells correlated with poor prognostic features including high-stage and high-grade, and expression also correlated with post-inflammatory changes in the cancer stroma as revealed by loss of alpha-smooth muscle actin. Moreover, CXCL16 enhanced the growth of CXCR6-expressing cancer and primary CD4 T cells. We studied expression of CXCL16 in an additional 461 specimens covering 12 tumor types, and found that CXCL16 was expressed in multiple human cancers associated with inflammation. Our study is the first to describe the expression of CXCL16/CXCR6 on both cancer cells and adjacent T cells in humans, and to demonstrate correlations between CXCL16 and CXCR6 vs. poor both prognostic features and reactive changes in cancer stoma. Taken together, our data suggest that CXCL16 and CXCR6 may mark cancers arising in an inflammatory milieu and mediate pro-tumorigenic effects of inflammation through direct effects on cancer cell growth and by inducing the migration and proliferation of tumor-associated leukocytes.
doi:10.1371/journal.pone.0006695
PMCID: PMC2723911  PMID: 19690611
6.  Molecular Alterations in Primary Prostate Cancer After Androgen Ablation Therapy 
PURPOSE
After an initial response to androgen ablation, most prostate tumors recur, ultimately progressing to highly aggressive androgen independent (AI) cancer. The molecular mechanisms underlying progression are not well known, in part due to the rarity of AI samples from primary and metastatic sites.
EXPERIMENTAL DESIGN
We compared the gene expression profiles of ten AI primary prostate tumor biopsies with ten primary, untreated androgen-dependent (AD) tumors. Samples were laser capture microdissected, the RNA was amplified, and gene expression was assessed using Affymetrix Human Genome U133A Gene Chips. Differential expression was examined with principle component analysis (PCA) and Student t testing. Analysis of gene ontology was performed with Expression Analysis Systematic Explorer (EASE) and gene expression data were integrated with genomic alterations with DIfferential Gene locus MAPping (DIGMAP).
RESULTS
Unsupervised PCA showed that the AD and AI tumors segregated from one another. After filtering the data, 239 differentially expressed genes were identified. Two main gene ontologies were found discordant between AI and AD tumors: macromolecule biosynthesis was down-regulated and cell adhesion up-regulated in AI tumors. Other differentially expressed genes were related to IL-6 signaling, as well as angiogenesis, cell adhesion, apoptosis, oxidative stress, and hormone response. The DIGMAP analysis identified nine regions of potential chromosomal deletion in the AI tumors including 1p36, 3p21, 6p21, 8p21, 11p15, 11q12, 12q23, 16q12, and 16q21.
CONCLUSIONS
Taken together, these data identify several unique characteristics of AI prostate cancer that may hold potential for the development of targeted therapeutic intervention.
doi:10.1158/1078-0432.CCR-05-0585
PMCID: PMC1432092  PMID: 16203770
microarrays; androgen-independent prostate cancer; laser capture microdissection; RNA amplification
7.  Prostate Cancer Epigenetics: A Review on Gene Regulation 
Prostate cancer is the most common cancer in men in western countries, and its incidence is increasing steadily worldwide. Molecular changes including both genetic and epigenetic events underlying the development and progression of this disease are still not well understood. Epigenetic events are involved in gene regulation and occur through different mechanisms such as DNA methylation and histone modifications. Both DNA methylation and histone modifications affect gene regulation and play important roles either independently or by interaction in tumor initiation and progression. This review will discuss the genes associated with epigenetic alterations in prostate cancer progression: their regulation and importance as possible markers for the disease.
PMCID: PMC2759139  PMID: 19936097
epigenetics; methylation; histone modification; gene regulation; prostate cancer
8.  Tumor-associated endothelial cells display GSTP1 and RARβ2 promoter methylation in human prostate cancer 
Background
A functional blood supply is essential for tumor growth and proliferation. However, the mechanism of blood vessel recruitment to the tumor is still poorly understood. Ideally, a thorough molecular assessment of blood vessel cells would be critical in our comprehension of this process. Yet, to date, there is little known about the molecular makeup of the endothelial cells of tumor-associated blood vessels, due in part to the difficulty of isolating a pure population of endothelial cells from the heterogeneous tissue environment.
Methods
Here we describe the use of a recently developed technique, Expression Microdissection, to isolate endothelial cells from the tumor microenvironment. The methylation status of the dissected samples was evaluated for GSTP1 and RARβ2 promoters via the QMS-PCR method.
Results
Comparing GSTP1 and RARβ2 promoter methylation data, we show that 100% and 88% methylation is detected, respectively, in the tumor areas, both in epithelium and endothelium. Little to no methylation is observed in non-tumor tissue areas.
Conclusion
We applied an accurate microdissection technique to isolate endothelial cells from tissues, enabling DNA analysis such as promoter methylation status. The observations suggest that epigenetic alterations may play a role in determining the phenotype of tumor-associated vasculature.
doi:10.1186/1479-5876-4-13
PMCID: PMC1420331  PMID: 16512911

Results 1-8 (8)