A Comparative Evaluation of the Apically Extruded Debris from Root Canals Prepared by R-Motion NiTi File System.

Background: Apically extruded debris (AED) is an inherent concern during root canal treatment for both endodontists and general practitioners. The present study investigates the AED of the novel R-Motion single-file reciprocating system compared to standard single reciprocating and multifile rotary systems. Materials and Methods: Fifty-six moderately curved palatal roots of upper maxillary first molars were selected for the present study. The samples were then divided randomly into four groups (n = 14)- Group I: R-motion (RM), Group II: WaveOne Gold (WOG), Group III: ProTaper Next (PTN), and Group IV: HyFlex EDM (HFEDM). The researcher has modified Myers and Montgomery's method to simulate human body temperature. Vials were used to collect debris and weighted using a 0.00001 sensitive balance before and after instrumentation. The instrumentation of all experimented groups was done at 37°C, terminated at master apical file #25. An auto syringe with a side vented needle was used to deliver 8 ml of deionized water for irrigation of each sample during preparation. Vials were stored in a dry sealed desiccator which contained CaSO4 crystals, for 24 hr before weighing. The weight of the collected debris was obtained by subtracting the preinstrumentation weight from the postinstrumentation weight for each vial. The Kruskal-Wallis and Mann-Whitney U tests were performed to analyse the statistical difference in the amount of debris between the tested groups at a 0.05 significance level. Results: The RM system produced less debris extrusion than all tested groups, with a significant difference between the former and the WOG and the PTN systems. However, WOG, PTN, and HFEDM showed no statistically significant difference in the amount of AED. Conclusion: All tested groups produced apical debris in different amounts. The RM produced substantially less AED than WOG and PTN. Meanwhile, WOG, PTN, and HFEDM caused a comparable amount of AED.

Phytochemicals for the Prevention and Treatment of Renal Cell Carcinoma: Preclinical and Clinical Evidence and Molecular Mechanisms.

Renal cell carcinoma (RCC) is associated with about 90% of renal malignancies, and its incidence is increasing globally. Plant-derived compounds have gained significant attention in the scientific community for their preventative and therapeutic effects on cancer. To evaluate the anticancer potential of phytocompounds for RCC, we compiled a comprehensive and systematic review of the available literature. Our work was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. The literature search was performed using scholarly databases such as PubMed, Scopus, and ScienceDirect and keywords such as renal cell carcinoma, phytochemicals, cancer, tumor, proliferation, apoptosis, prevention, treatment, in vitro, in vivo, and clinical studies. Based on in vitro results, various phytochemicals, such as phenolics, terpenoids, alkaloids, and sulfur-containing compounds, suppressed cell viability, proliferation and growth, showed cytotoxic activity, inhibited invasion and migration, and enhanced the efficacy of chemotherapeutic drugs in RCC. In various animal tumor models, phytochemicals suppressed renal tumor growth, reduced tumor size, and hindered angiogenesis and metastasis. The relevant antineoplastic mechanisms involved upregulation of caspases, reduction in cyclin activity, induction of cell cycle arrest and apoptosis via modulation of a plethora of cell signaling pathways. Clinical studies demonstrated a reduced risk for the development of kidney cancer and enhancement of the efficacy of chemotherapeutic drugs. Both preclinical and clinical studies displayed significant promise of utilizing phytochemicals for the prevention and treatment of RCC. Further research, confirming the mechanisms and regulatory pathways, along with randomized controlled trials, are needed to establish the use of phytochemicals in clinical practice.

A Computational Text Mining-Guided Meta-Analysis Approach to Identify Potential Xerostomia Drug Targets.

Xerostomia (subjective complaint of dry mouth) is commonly associated with salivary gland hypofunction. Molecular mechanisms associated with xerostomia pathobiology are poorly understood, thus hampering drug development. Our objectives were to (i) use text-mining tools to investigate xerostomia and dry mouth concepts, (ii) identify associated molecular interactions involving genes as candidate drug targets, and (iii) determine how drugs currently used in clinical trials may impact these genes and associated pathways. PubMed and PubMed Central were used to identify search terms associated with xerostomia and/or dry mouth. Search terms were queried in pubmed2ensembl. Protein-protein interaction (PPI) networks were determined using the gene/protein network visualization program search tool for recurring instances of neighboring genes (STRING). A similar program, Cytoscape, was used to determine PPIs of overlapping gene sets. The drug-gene interaction database (DGIdb) and the clinicaltrials.gov database were used to identify potential drug targets from the xerostomia/dry mouth PPI gene set. We identified 64 search terms in common between xerostomia and dry mouth. STRING confirmed PPIs between identified genes (CL = 0.90). Cytoscape analysis determined 58 shared genes, with cytokine-cytokine receptor interaction representing the most significant pathway (p = 1.29 × 10-23) found in the Kyoto encyclopedia of genes and genomes (KEGG). Fifty-four genes in common had drug interactions, per DGIdb analysis. Eighteen drugs, targeting the xerostomia/dry mouth PPI network, have been evaluated for xerostomia, head and neck cancer oral complications, and Sjögren's Syndrome. The PPI network genes IL6R, EGFR, NFKB1, MPO, and TNFSF13B constitute a possible biomarker signature of xerostomia. Validation of the candidate biomarkers is necessary to better stratify patients at the genetic and molecular levels to facilitate drug development or to monitor response to treatment.

Development and evaluation of an online continuing education course to increase healthcare provider self-efficacy to make strong HPV vaccine recommendations to East African immigrant families.

OBJECTIVE: To develop and evaluate an online continuing education (CE) course designed to improve healthcare provider self-efficacy to make strong adolescent HPV vaccine recommendations to East African immigrant families. METHODS: Focus groups with providers and East African immigrant mothers informed course development. Providers serving East African immigrant families were recruited to view the course and complete pre-/post-test and two-month follow-up surveys. Pre-/post differences were compared with paired t-tests. RESULTS: 202 providers completed the course and pre-/post-test; 158 (78%) completed two-month follow-up. Confidence to make strong HPV vaccine recommendations to East African families increased from 68% pre-test to 98% post-test. Confidence to address common parental concerns also increased: safety, 54% pre-test, 92% post-test; fertility, 55% pre-test, 90% post-test; child too young, 68% pre-test, 92% post-test; and pork gelatin in vaccine manufacturing, 38% pre-test, 90% post-test. Two-month follow-up scores remained high (97% for overall confidence, 94%-97% for addressing parental concerns). All pre-/post-test and pre-test/two-month follow-up comparisons were statistically significant (p < 0.05). CONCLUSIONS: The online CE course focused on culturally appropriate strategies for making strong recommendations and addressing specific parental concerns was effective for increasing provider self-efficacy to recommend HPV vaccination to East African families. Similar courses could be tailored to other priority populations.

Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach

BackgroundThe COVID-19 pandemic has led to over 820,000 deaths for almost 24 million confirmed cases worldwide, as of August 27th, 2020, per WHO report. Risk factors include pre-existing conditions such as cancer, cardiovascular disease, diabetes, obesity, and cancer. There are currently no effective treatments. Our objective was to complete a meta-analysis to identify comorbidity-associated single nucleotide polymorphisms (SNPs), potentially conferring increased susceptibility to SARS-CoV-2 infection using a computational approach. ResultsSNP datasets were downloaded from publicly available GWAS catalog for 141 of 258 candidate COVID-19 comorbidities. Gene-level SNP analysis was performed to identify significant pathways by using MAGMA program. SNP annotation program was used to analyze MAGMA-identified genes. COVID-19 comorbidities from six disease categories were found to have significant associated pathways, which were validated by Q-Q plots (p<0.05). The top 250 human mRNA gene expressions for SNP-affected pathways, extracted from publicly accessible gene expression profiles, were evaluated for significant pathways. Protein-protein interactions of identified differentially expressed genes, visualized with STRING program, were significant (p<0.05). Gene interaction networks were found to be relevant to SARS and influenza pathogenesis. ConclusionPathways potentially affected by or affecting SARS-CoV-2 infection were identified in underlying medical conditions likely to confer susceptibility and/or severity to COVID-19. Our findings have implications in COVID-19 treatment development.

Identification of single nucleotide pleomorphisms associated with periodontal disease in head and neck cancer irradiation patients by exome sequencing.

OBJECTIVE: Periodontal disease (PD) is a common oral complication in patients with head and neck cancer (HNC) undergoing radiation therapy (RT). Our objective was to identify candidate single nucleotide polymorphisms (SNPs) associated with PD in radiation-treated patients with HNC. STUDY DESIGN: DNA was extracted from the saliva of patients with HNC (n = 69) before RT. Clinical attachment loss (CAL) increment greater than 0.2 mm over 24 months after RT was used to define PD progression. After exome sequencing, SNPs associated with post-RT PD progression were identified by using logistic regression and homozygosity analyses. The web tools STRING, the Database for Annotation, Visualization and Integrated Discovery (DAVID), GeneCodis, and Ensembl Variant Effect Predictor were used for functional analysis. RESULTS: Of the 48 patients with HNC with post-RT PD progression, 24 had no tooth with 5 mm or greater pocket depth before RT, whereas of the 21 patients with HNC without progression, 11 had PD initially. A total of 330 SNPs (249 genes) with over-represented homozygous genotype (98.5% variant allele) were found to be associated with post-RT PD. Sixty of these corresponded to PD-related pathways, including previously identified genes. In patients with HNC with post-RT PD progression, SNPs were found in genes (n = 10) in contrast to those without progression (n = 7). CONCLUSIONS: The SNPs of collagen genes were identified, potentially defining susceptibility to PD in patients with HNC, and this could be further investigated to characterize PD drug targets.

Dedifferentiated endometrioid adenocarcinoma of the uterus: A case series and review of literature.

Introduction Dedifferentiated endometrioid adenocarcinoma (DEAC) was first described in 2007. However, it has only been recognised as a distinct subtype of endometrioid adenocarcinoma in the last 1-2 years. DEAC is a more aggressive histological subtype and carries a poorer prognosis. Patients with DEAC tend to present with advanced disease compared the other endometrioid adenocarcinomas. Methodology The study is a retrospective review of patients with DEAC diagnosed in two institutions in Singapore between January 2012 and October 2017. Results 7 patients were diagnosed with DEAC. The mean age was 56.4 years. All patients presented with either abnormal uterine bleeding or post menopausal bleeding. Out of the 7 patients, one was diagnosed with Stage 2 disease, 5 were diagnosed with Stage 3 disease and 1 was diagnosed with Stage 4 disease. One patient had neoadjuvant chemotherapy, followed by surgery, and completion chemotherapy post surgery. The other 6 patients (87.5%) underwent primary debulking surgery. Out of these 6 patients, 5 patients had adjuvant chemotherapy post surgery and one patient had both adjuvant chemotherapy and radiotherapy. Lymphovascular invasion was found in 71.4% of the cases. Conclusion DEAC is a more aggressive histological subtype of endometrioid adenocarcinomas. Better awareness of this condition can lead to proper diagnosis and treatment.

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis.

Characterization of the role of oral microbiome in cancer therapy-induced oral mucositis (CTOM) is critical in preventing the clinically deleterious effects on patients' health that are associated with CTOM. Funding initiatives related to the National Institutes of Health human microbiome project have resulted in groundbreaking advancements in biology and medicine during the last decade. These advancements have shown that a human being is in fact a superorganism made of human cells and associated symbiotic or commensal microbiota. In this review, we describe the state of science as it relates to fundamental knowledge on oral microbiome and its role in CTOM. We also discuss how state-of-the-art technologies and systems biology tools may be used to help tackle the difficult challenges ahead to develop effective treatments or preventive therapies for oral mucositis. We make a clear distinction between disease processes pertaining to the oral microbiome, which includes opportunistic pathogens that may be defined as pathobionts, and those infectious disease processes initiated by exogenous pathogens. We also explored the extent to which knowledge from the gastrointestinal tract in disease and intestinal mucositis could help us better understand CTOM pathobiology. Finally, we propose a model in which the oral microbiome participates in the current five-step CTOM pathobiology model. With the advent of more sophisticated metagenomics technologies and methods of analysis, much hope lies ahead to implement an effective holistic approach to treat cancer patients affected by CTOM.

Short-term morbidity factors associated with length of hospital stay (LOS): Development and validation of a Hip Fracture specific postoperative morbidity survey (HF-POMS).

BACKGROUND: We aimed to describe and quantify postoperative complications in the older hip fracture population, develop and validate a hip fracture postoperative morbidity survey tool (HF-POMS). METHODS: A prospective clinical observation study of patients (≥ 70 years) admitted for emergency hip fracture surgery, was conducted across three English National Health Service hospitals. Outcome data items were developed from the Postoperative Morbidity Survey (POMS), Cardiac-POMS, hip fracture postoperative literature and orthogeriatric clinical team input. Postoperative outcome data were collected on days 1, 3, 5, 8 and 15; 341 patients participated. RESULTS: A 12-domain HF-POMS tool was developed with acceptable construct validity on all HF-POMS days. Patients with high perioperative risk scores as measured by the NHFS and ASA grade were more prone to develop HF-POMS defined morbidities. High morbidity rates occurred in the following domains; renal, ambulation assistance, pain and infectious. Presence of any morbidity on postoperative days 8 and 15 was associated with subsequent length of stay of 3.08 days (95% CI 0.90-5.26, p = 0.005) and 15.81 days (95% CI 13.35-18.27, p = 0.001) respectively. Observed average length of stay was 16.9 days. HF-POMS is a reliable and valid tool for measuring early postoperative complications in hip fracture patients. Additional domains are necessary to account for all morbidity aspects in this patient population compared to the original POMS. CONCLUSION: Many patients remained in hospital for non-medical reasons. HF-POMS may be a useful tool to assist in discharge planning and randomised control trial outcome definitions.

A 1.02 µW Battery-Less, Continuous Sensing and Post-Processing SiP for Wearable Applications.

Improving system lifetime and robustness is a key to advancing self-powered platforms for real world applications. A complete self-powered, battery-less, wearable platform requires a microwatt-power system-on-chip (SoC), operating reliably within this budget, capable of surviving long periods without charging, and recovering from power loss to its previous state. To meet these requirements, we designed a wireless sensing heterogeneous system-in-package (SiP) containing an ultra-low power (ULP) SoC, a non-volatile boot memory (NVM), and a 2.4 GHz frequency shift key (FSK) radio, all integrated with custom ULP interfaces. The SoC includes a fully integrated energy harvesting platform power manager (EH-PPM) to power the SiP and other commercial sensors. The EH-PPM is designed for small loads and powers the SoC and peripherals while drawing very low operating current. The SoC also includes a digital system data-flow for sensing applications, an analog front end for ECG signal acquisition, and a cold-boot management system (CBMS) for boot and recovery from the NVM. The CBMS enables integration of the SoC with the ULP NVM to create a wearable formfactor, self-powered system capable of recovery from power loss. The SoC also includes a radio interface tightly integrated with a compression accelerator to efficiently communicate with the FSK transmitter and reduce the FSK's transmission time. This tight integration between accelerators on the SoC and peripherals is another feature that reduces the system's power consumption by reducing the code size and number of memory accesses required to perform an operation. The SoC consumes 507 nW average power while running free-fall detection, 519 nW average power while measuring ambient temperature, and 1.02 µW during continuous ECG monitoring and post-processing.

Expression of ETS1 and LEF1 in salivary glands of Sjögren syndrome patients.

OBJECTIVE: Primary Sjögren's syndrome (pSS) is a systemic autoimmune disease affecting exocrine glands, thereby causing dry mouth and eyes (sicca). Our objective was to determine the expression of pSS pathogenic biomarker MMP9 and its putative transcription factors ETS1 and LEF1, in labial salivary glands of pSS patients. METHODS: Sicca patients were assigned to three groups based on focus score (FS): non-pSS sicca (i.e., GR1 [FS = 0] and GR2 [0 < FS < 1]) and pSS (i.e., GR3 [FS ≥ 1]). We determined the mRNA and protein expression of MMP9, ETS1, and LEF1 in salivary gland biopsies. Also, ETS1-CD4 and LEF1-CD4 co-expression analyses were performed. RESULTS: The mRNA expression of MMP9, ETS1, and LEF1 was upregulated in GR3 compared to GR1 (p < 0.01). Most GR3 salivary gland areas had moderate to high MMP9, ETS1, and LEF1 protein expression compared to GR1 and GR2. Further, ETS1-CD4 and LEF1-CD4 dual staining demonstrated that both salivary gland epithelial cells and lymphocytic infiltrates had increased levels of ETS1 and LEF1. Moreover, there was a strong correlation between ETS1(+)-CD4(-) and LEF1(+)-CD4(-) cells. CONCLUSION: These results suggest, for the first time, a concerted increase in ETS1 and LEF1 expression in salivary gland epithelial cells of pSS patients that is reflective of the etiopathogenesis of pSS.

Text mining-based in silico drug discovery in oral mucositis caused by high-dose cancer therapy.

INTRODUCTION: Oral mucositis (OM) is a major dose-limiting side effect of chemotherapy and radiation used in cancer treatment. Due to the complex nature of OM, currently available drug-based treatments are of limited efficacy. OBJECTIVES: Our objectives were (i) to determine genes and molecular pathways associated with OM and wound healing using computational tools and publicly available data and (ii) to identify drugs formulated for topical use targeting the relevant OM molecular pathways. METHODS: OM and wound healing-associated genes were determined by text mining, and the intersection of the two gene sets was selected for gene ontology analysis using the GeneCodis program. Protein interaction network analysis was performed using STRING-db. Enriched gene sets belonging to the identified pathways were queried against the Drug-Gene Interaction database to find drug candidates for topical use in OM. RESULTS: Our analysis identified 447 genes common to both the "OM" and "wound healing" text mining concepts. Gene enrichment analysis yielded 20 genes representing six pathways and targetable by a total of 32 drugs which could possibly be formulated for topical application. A manual search on ClinicalTrials.gov confirmed no relevant pathway/drug candidate had been overlooked. Twenty-five of the 32 drugs can directly affect the PTGS2 (COX-2) pathway, the pathway that has been targeted in previous clinical trials with limited success. CONCLUSIONS: Drug discovery using in silico text mining and pathway analysis tools can facilitate the identification of existing drugs that have the potential of topical administration to improve OM treatment.

Biosemantics guided gene expression profiling of Sjögren's syndrome: a comparative analysis with systemic lupus erythematosus and rheumatoid arthritis.

BACKGROUND: Sjögren's syndrome (SS) shares many clinical and pathological similarities with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). These autoimmune diseases mostly affect women. In this study, concept profile analysis (CPA) and gene expression meta-analysis were used to identify genes potentially involved in SS pathogenesis. METHODS: Human genes associated with SS, SLE, and RA were identified using the CPA tool, Anni 2.1. The differential mRNA expression of genes common to SS and SLE (SS-SLE) was determined in female peripheral blood mononuclear cells (PBMCs) using NCBI-GEO2R. Differentially expressed (DE) SS-SLE PBMC genes in common with the SS-SLE CPA-identified genes were analyzed for differential expression in salivary glands or synovial biopsies, and for genes common to SS and RA and SLE and RA, analyzing differential expression in salivary glands in SS, synovial fibroblasts in RA, and synovial fluid in SLE. Among common genes, DE genes found in salivary gland mRNA expression in patients with SS were used for gene enrichment and SS molecular network construction. Secondary analysis was performed to identify DE genes unique to the disease site tissues, by excluding PBMC and CPA common DE genes to complement the SS network. RESULTS: We identified 22 DE genes in salivary gland datasets in SS that have not previously been clearly associated with SS pathogenesis. Among these, higher levels of checkpoint kinase 1 (CHEK1), V-Ets avian erythroblastosis virus E26 oncogene homolog 1 (ETS1), and lymphoid enhancer binding factor 1 (LEF1) were significantly correlated with higher matrix metalloproteinase 9 (MMP9) levels. Higher MMP9 levels have been implicated in degradation of salivary gland structural integrity, leading to hypo-salivation in patients with SS. Salivary gland mRNA expression of MMP9 and the expression of cytokine CXCL10 were higher in patients with SS. CXCL10 has been shown to increase MMP9 expression and therefore may also play an important role in SS pathogenesis. CONCLUSION: Using CPA and gene expression analysis, we identified factors targeting MMP9 expression and/or function, namely CHEK1, CXCL10, ETS1, LEF1, and tissue inhibitor of metalloproteinase 1; altered mRNA expression of these could increase expression/activity of MMP9 in a concerted manner, thereby potentially impacting SS pathogenesis.

Factors Associated with Sedentary Behavior in Patients with Intermittent Claudication.

OBJECTIVES: Time spent in sedentary behavior has been associated with cardio-metabolic risk factors in the general population and in patients with symptomatic peripheral artery disease (PAD). Given the association of sedentary behavior and poor health outcomes, it is important to identify factors associated with sedentary behavior in these patients. The aim of this study was to identify factors associated with the sedentary time in patients with symptomatic PAD. METHODS: The sample included 297 patients with symptomatic PAD. Sedentary behavior was assessed using a step activity monitor and the patients were divided into tertiles. Demographic data, body mass index, comorbid conditions, and measures of severity of PAD (ankle brachial index, ischemic window, claudication measurements, peak oxygen uptake and walking economy) were obtained. RESULTS: Patients in the highest tertile (i.e. more sedentary) had a higher body mass index and a higher prevalence of diabetes mellitus, metabolic syndrome, and obesity than patients in the lowest tertile, whereas their peak walking time, peak oxygen uptake, and walking economy were lower (p < .05 for all). Using multiple regression procedures, the factors associated with the sedentary time were male sex (b = .217, R2 = .180, p = .001), body mass index (b = .154, R2 = .059, p = .013), peak walking time (b = -.360, R2 = .066, p ≤ .001), and walking economy (b = -.187, R2 = .142, p = .004). CONCLUSION: In patients with symptomatic PAD, greater time spent in sedentary behavior was found in men, and in patients with higher body mass index, lower peak walking time, and lower walking economy.

[Characteristics and management of ST-elevation myocardial infarction in France: Regional variations in 2010]. / Prise en charge du syndrome coronaire aigu avec sus-décalage de ST en France : variations régionales en 2010.

Data on regional variations in the characteristics, management and early outcome of patients admitted with ST-elevation myocardial infarction (STEMI) in France are limited. We used data from the FAST-MI 2010 registry to determine whether regional specificities existed, dividing the French territory into 6 larger geographical regions. Variations in the patients' characteristics were found, partly related to regional variations in demography. Acute reperfusion strategy showed more use of primary percutaneous coronary intervention in the greater Paris area, compared to other regions, which would be expected owing to geography and local availability of catheterization laboratories. Overall, however, in-hospital management showed more similarities than differences across regions. Complications, and in particular in-hospital mortality, did not differ significantly among regions.

A multi-criteria analysis approach for ranking and selection of microorganisms for the production of oils for biodiesel production.

Oleaginous microorganisms have potential to be used to produce oils as alternative feedstock for biodiesel production. Microalgae (Chlorella protothecoides and Chlorella zofingiensis), yeasts (Cryptococcus albidus and Rhodotorula mucilaginosa), and fungi (Aspergillus oryzae and Mucor plumbeus) were investigated for their ability to produce oil from glucose, xylose and glycerol. Multi-criteria analysis (MCA) using analytic hierarchy process (AHP) and preference ranking organization method for the enrichment of evaluations (PROMETHEE) with graphical analysis for interactive aid (GAIA), was used to rank and select the preferred microorganisms for oil production for biodiesel application. This was based on a number of criteria viz., oil concentration, content, production rate and yield, substrate consumption rate, fatty acids composition, biomass harvesting and nutrient costs. PROMETHEE selected A. oryzae, M. plumbeus and R. mucilaginosa as the most prospective species for oil production. However, further analysis by GAIA Webs identified A. oryzae and M. plumbeus as the best performing microorganisms.

Overexpression of periostin in stroma positively associated with aggressive prostate cancer.

BACKGROUND: Periostin is an important extracellular matrix protein involved in cell development and adhesion. Previously, we identified periostin to be up-regulated in aggressive prostate cancer (CaP) using quantitative glycoproteomics and mass spectrometry. The expression of periostin was further evaluated in primary radical prostatectomy (RP) prostate tumors and adjacent non-tumorous prostate tissues using immunohistochemistry (IHC). Our IHC results revealed a low background periostin levels in the adjacent non-tumorous prostate tissues, but overexpressed periostin levels in the peritumoral stroma of primary CaP tumors. METHODS: In this study, periostin expression in CaP was further examined on multiple tissue microarrays (TMAs), which were conducted in four laboratories. To achieve consistent staining, all TMAs were stained with same protocol and scored by same image computation tool to determine the total periostin staining intensities. The TMAs were further scored by pathologists to characterize the stromal staining and epithelial staining. RESULTS: The periostin staining was observed mainly in peritumoral stromal cells and in some cases in tumor epithelial cells though the stronger staining was found in peritumoral stromal cells. Both periostin stromal staining and epithelial staining can differentiate BPH from CaP including low grade CaP (Gleason score ≤6), with significant p-value of 2.2e-16 and 0.001, respectively. Periostin epithelial staining differentiated PIN from low grade CaP (Gleason score ≤6) (p=0.001), while periostin stromal staining differentiated low grade Cap (Gleason score ≤6) from high grade Cap (Gleason score ≤6) (p=1.7e-05). In addition, a positive correlation between total periostin staining and Gleason score was observed (r=0.87, p=0.002). CONCLUSIONS: The results showed that periostin staining was positively correlated with increasing Gleason score and the aggressiveness of prostate disease.

The identification of trans-associations between prostate cancer GWAS SNPs and RNA expression differences in tumor-adjacent stroma.

Here we tested the hypothesis that SNPs associated with prostate cancer risk, might differentially affect RNA expression in prostate cancer stroma. The most significant 35 SNP loci were selected from Genome Wide Association (GWA) studies of ~40,000 patients. We also selected 4030 transcripts previously associated with prostate cancer diagnosis and prognosis. eQTL analysis was carried out by a modified BAYES method to analyze the associations between the risk variants and expressed transcripts jointly in a single model. We observed 47 significant associations between eight risk variants and the expression patterns of 46 genes. This is the first study to identify associations between multiple SNPs and multiple in trans gene expression differences in cancer stroma. Potentially, a combination of SNPs and associated expression differences in prostate stroma may increase the power of risk assessment for individuals, and for cancer progression.

A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors.

HER2-positive breast cancer accounts for 25% of all cases and has a poor prognosis. Although progress has been made in understanding signal transduction, little is known of how HER2 achieves gene regulation. We performed whole genome expression analysis on a HER2⁺ and HER2⁻ breast cancer cell lines and compared these results to expression in 812 primary tumors stratified by their HER2 expression level. Chip-on-chip with anti-RNA polymerase II was compared among breast cancer cell lines to identify genes that are potentially activated by HER2. The expression levels of these HER2-dependent POL II binding genes were determined for the 812 HER2+/- breast cancer tissues. Genes differentially expressed between HER2+/- cell lines were generally regulated in the same direction as in breast cancer tissues. We identified genes that had POLII binding in HER2⁺ cell lines, but without significant gene expression. Of 737 such genes "poised" for expression in cell lines, 113 genes were significantly differentially expressed in breast tumors in a HER2-dependent manner. Pathway analysis of these 113 genes revealed that a large group of genes were associated with stem cell and progenitor cell control as indicated by networks centered on NANOG, SOX2, OCT3/4. HER2 directs POL II binding to a large number of genes in breast cancer cells. A "poised" class of genes in HER2⁺ cell lines with POLII binding and low RNA expression but is differentially expressed in primary tumors, strongly suggests a role of the microenvironment and further suggests a role for stem cells proliferation in HER2-regulated breast cancer tissue.