Application of Next Generation Sequencing for Diagnostic Testing of Tree Fruit Viruses and Viroids

Conventional detection of viruses and virus-like diseases of plants is accomplished using a combination of molecular, serological, and biological indexing. These are the primary tools used by plant virologists to monitor and ensure trees are free of known viral pathogens. The biological indexing assay, or bioassay, is considered to be the "gold standard" as it is the only method of the three that can detect new, uncharacterized, or poorly characterized viral disease agents. Unfortunately, this method is also the most labor intensive and can take up to three years to complete. Next generation sequencing (NGS) is a technology with rapidly expanding possibilities including potential applications for the detection of plant viruses. In this study, comparisons are made between tree fruit testing by conventional and NGS methods, to demonstrate the efficacy of NGS. A comparison of 178 infected trees, many infected with several viral pathogens, demonstrated that conventional and NGS were equally capable of detecting known viruses and viroids. Comparable results were obtained for 170 of 178 of the specimens. Of the remaining eight specimens, some discrepancies were observed between viruses detected by the two methods, representing less than 5% of the specimens. NGS was further demonstrated to be equal or superior for the detection of new or poorly characterized viruses when compared with a conventional bioassay. These results validated both the effectiveness of conventional virus testing methods and the use of NGS as an additional or alternative method for plant virus detection.

Is compression bandaging accurate? The routine use of interface pressure measurements in compression bandaging of venous leg ulcers

Objective: To test the use of a low-cost, portable, battery-powered sub-bandage pressure monitor as a part of a quality control measure for graduated compression bandaging in the leg ulcer clinics.

Methods: A total of 25 healthy volunteers (mean age 40 years) providing 50 limbs were bandaged with a 4-layer compression bandaging system. Interface pressure was measured by placing pressure sensors on the skin at three points (2 cm above the medial malleolus, on the widest part of the calf and on a point midway between them) in supine and standing positions. A further 16 patients (mean age 62 years) providing 22 limb measurements also participated in this study. Bandages were reapplied in patients with the help of the pressure monitors when the target pressure was not achieved in the first attempt.

Results: The interface pressures varied with change of position and movement. With the operator blinded, the target pressure of 35–40 mmHg at the ankle was achieved in only 36% of healthy volunteers (mean±95% confidence interval, 32.3±1.6 mmHg [supine]; 38.4±2.4 mmHg [standing position]). With the help of the pressure monitors, the target pressure was achieved in 78% of the patients.

Conclusion: This result suggests that it is important to have a tool that is easy to operate, and available as a part of the quality assurance in connection with treatment and also training of care providers, nurses, etc in how to apply a compression bandage.

FOXM1 and polo-like kinase 1 are co-ordinately overexpressed in patients with gastric adenocarcinomas

BACKGROUND

Gastric cancers present late in life with advanced disease and carry a poor prognosis. Polo-like Kinase 1 (PLK1) is a mitotic kinase with regulatory functions during G2/M and mitosis in the cell cycle. In mammalian cells, there is an intricate co-regulatory relationship between PLK1 and the forkhead transcription factor FOXM1. It has been demonstrated that individually either PLK1 or FOXM1 expression predicts poorer survival. However, the co-expression of both of these markers in gastric adenocarcinomas has not been reported previously.

METHODS

We aimed to assess the expression of PLK1 and FOXM1 in Gastric adenocarcinomas in a Western Population, to examine whether there is a relationship of PLK1 to FOXM1 in cancer samples. We assess both the protein and mRNA expression in this patient population by Tissue Microarray immunohistochemistry and RT-PCR.

RESULTS

Immunohistochemistry was performed on biopsy samples from 79 patients with gastric cancer. Paired normal controls were available in 47 patients. FOXM1 expression was significantly associated with gastric adenocarcinoma (p = 0.001). PLK1 and FOXM1 co-expression was demonstrated in 6/8 (75 %) tumours when analysed by RT-PCR. FOXM1 is overexpressed in a large proportion of gastric carcinomas at the protein level and FOXM1 and PLK1 are concomitantly overexpressed at the mRNA level in this cancer type.

CONCLUSIONS

This study has demonstrated that FOXM1 and its target gene PLK1 are coordinately overexpressed in a proportion of gastric adenocarcinomas. This suggests that chemotherapeutic treatments that target this pathway may be of clinical utility.

All that glitters is not always gold

Biopsies from the second part of the duodenum are routinely performed in patients with unintentional weight loss. When villous atrophy and an increased intraepithelial lymphocytosis are detected, the commonest cause of it is coeliac disease. Severe villous atrophy with increased intraepithelial lymphocytosis (Marsh IIIc) is highly specific for coeliac disease. However, coeliac disease with this presentation is very rare. Milder abnormalities such as Marsh I-II (microscopic enteritis) and Marsh IIIa are not specific for coeliac disease and could occur in other conditions like those listed in the discussion. We present the case of a 74-year-old woman who, after being diagnosed with seronegative coeliac disease, failed to improve on a gluten-free diet. We discuss the differential diagnosis of coeliac disease and the possible alternative causes for villous blunting, paying particular attention to the diagnosis of small intestinal bacterial overgrowth.

Abstract P5-14-14: Trimodality therapy for inflammatory breast cancer: The fox chase experience

Objective: To evaluate the outcomes and toxicity of inflammatory breast cancer (IBC) patients (pts) treated with trimodality therapy.

Materials and Methods: A retrospective chart review of 71 non-metastatic women with IBC treated using once daily (QD) radiation fractionation between 1990 and 2011 was performed. Eighty-six% of pts underwent ER/PR receptor status testing, and 43% underwent HER-2 testing. All pts underwent a course of neoadjuvant chemotherapy. Forty-three pts had adjuvant hormonal therapy, and 7 had adjuvant trastuzumab. All pts underwent mastectomy with axillary lymph node dissection followed by chest wall irradiation to a median dose of 50 Gy (34-50), and 46 Gy to supraclavicular region in 2-Gy QD fractions. Internal mammary nodes were treated in 3 pts (4%) and a posterior axillary boost (PAB) was added in 32 (45%) cases. Scar boosts (SB) were employed in 6 patients. A univariate (UVA) analysis using Kaplan-Meier estimation method included cN, pN, pT stage, PAB, SB, dermal lymphatic invasion, lymphovascular invasion, body mass index, response to chemo (RC), close/positive surgical margins (SM), age, and triple negative (TN) receptor status. Significant predictors on UVA were included in multivariate (MVA) analysis using the Cox proportional hazard model. Primary endpoints included local-regional recurrence (LRR), distant metastasis (DM), overall survival (OS), cause specific (CSS) and disease-free survival (DFS). Acute and chronic skin reactions and lymphedema were evaluated.

Results: Median follow-up was 34 months (2-265) and the median age was 56 years (36-82). Actuarial 3 and 5 year OS was 63% and 43%, and DFS was 51% and 43%, respectively. The median time to first failure, LRR, and DM was 20 mo (1.5-147), 13.5 mo (9-18), and 21 mo (1.5-147), respectively. The first site of failure was distant for 34 (48%), and local-regional for 4 pts (6%). Twenty-five pts (35%) were without failure at the time of last follow up. UVA analysis for LRR revealed SM (p = 0.05) and RC (p = 0.002) to be significant predictors of failure, however, these were not significant on MVA. UVA for DM identified SM (p = 0.03), TN (p<0.0001), and pN (p = 0.03) to be significant predictors, with TN (p = 0.002) being the only significant variable on MVA. Significant predictors for OS on UVA were TN (p = 0.04), pN1 vs pN2 disease (p = 0.02), SM (p = 0.0008) and RC (p = 0.008). None of these remained significant on MVA. Significant predictors for CSS on UVA were TN (p = 0.008), pN (p = 0.05), SM (p = 0.0004) and RC (p = 0.002). Only SM (p = 0.01) was predictive on MVA. Significant predictors for DFS on UVA were SM (p = 0.0003), pN1 vs pN2 (p = 0.05), RC (p = 0.0006) and TN (p = 0.0001). Only RC (p = 0.005) and TN (p = 0.001) remained significant on MVA. Twelve pts developed dry, and 14 developed moist desquamation. Three pts developed CTCAE v3 G3 lymphedema, and 5 pts experienced G3 fibrosis.

Conclusions: We found that TN predicted for a higher rate of DM and worse DFS. Improved CR predicted for better DFS. Age < 45, SM, pN2 disease and poor RC were not predictive of LRR. Use of SB did not improve LRR, although this cohort was small. Overall, our results show encouraging 3 and 5 year OS rates and acceptable toxicity for IBC pts treated with trimodality therapy.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-14-14.

Clinical and histological resolution of collagenous sprue following gluten-free diet and discontinuation of non-steroidal anti-inflammatory drugs (NSAIDs)

Collagenous sprue is a rare small bowel enteropathy that has overlapping clinical features with coeliac disease; it is commonly associated with arthritic autoimmune conditions, which often require non-steroidal anti-inflammatory drugs (NSAIDs). In the limited published literature available, there are putative suggestions of a link between NSAID use and collagen deposition in intestinal subepithelia in such patients. The authors present a case of a 43-year-old woman with long-standing NSAID use for autoimmune polyarthropathy and positive coeliac antibodies. However, distal duodenal biopsies revealed a thickened band of subepithelial collagen with villous atrophic appearances consistent with collagenous sprue. The patient was treated with a gluten-free diet and her NSAIDs were discontinued. After 6 months, her gastrointestinal symptoms had resolved with complete histological resolution of the collagenous subepithelial bands and villous atrophy on duodenal biopsy.

Classification of canine nonangiogenic, nonlymphogenic, gastrointestinal sarcomas based on microscopic, immunohistochemical, and molecular characteristics

Canine nonangiogenic, nonlymphogenic, gastrointestinal sarcomas have been previously diagnosed as gastrointestinal stromal tumors (GIST), leiomyosarcomas, or nonspecified spindle cell sarcomas, but diagnostic criteria for each entity are poorly defined. We propose a classification for canine nonangiogenic, nonlymphogenic, gastrointestinal sarcomas based on microscopic, immunohistochemical, and molecular characteristics. Applying the classification to 40 canine nonangiogenic, nonlymphogenic, gastrointestinal sarcomas documented its diagnostic and prognostic value. Eighteen (45%) sarcomas were classified as GIST based on positive KIT immunoreactivity. All GISTs were positive for vimentin, 14 (78%) were positive for S-100, and 6 (33%) were positive for smooth muscle actin (SMA). In contrast to their human counterparts, canine GISTs occurred mainly in the small intestine (67%) but commonly metastasized (5/18) to liver, lymph nodes, and omentum. Six GISTs had an activated KIT mutation in exon 11 of c-Kit, but no mutations were detected in exons 8, 9, 13, and 17. Twelve (30%) sarcomas were classified as leiomyosarcomas based on positive labeling for SMA and negative labeling for KIT. Four of these neoplasms were well differentiated leiomyosarcomas characterized by weak to no labeling for vimentin, and 8 were poorly differentiated leiomyosarcomas characterized by strong labeling for vimentin. None of the leiomyosarcomas metastasized, but poorly differentiated leiomyosarcomas had a higher risk of local invasion. Ten (25%) sarcomas were classified as non-GIST/nonleiomyosarcomas that were negative for KIT and SMA but positive for vimentin and either S-100 and/or PGP 9.5. These neoplasms most likely represent sarcomas of neurogenic differentiation resembling Schwann cells or perineurial or endoneurial fibroblasts, respectively.

The FOXM1-PLK1 axis is commonly upregulated in oesophageal adenocarcinoma

BACKGROUND

The transcription factor FOXM1 is an important regulator of the cell cycle through controlling periodic gene expression during the G2 and M phases. One key target for FOXM1 is the gene encoding the protein kinase PLK1 and PLK1 itself acts in a positive feedback loop to phosphorylate and activate FOXM1. Both FOXM1 and PLK1 have been shown to be overexpressed in a variety of different tumour types.

METHODS

We have used a combination of RT-PCR, western blotting, tissue microarrays and metadata analysis of microarray data to study whether the FOXM1-PLK1 regulatory axis is upregulated and operational in oesophageal adenocarcinoma.

RESULTS

FOXM1 and PLK1 are expressed in oesophageal adenocarcinoma-derived cell lines and demonstrate cross-regulatory interactions. Importantly, we also demonstrate the concomitant overexpression of FOXM1 and PLK1 in a large proportion of oesophageal adenocarcinoma samples. This co-association was extended to the additional FOXM1 target genes CCNB1, AURKB and CKS1. In a cohort of patients who subsequently underwent surgery, the expression of several FOXM1 target genes was prognostic for overall survival.

CONCLUSIONS

FOXM1 and its target gene PLK1 are commonly overexpressed in oesophageal adenocarcinomas and this association can be extended to other FOXM1 target genes, providing potentially important biomarkers for predicting post-surgery disease survival.

Assessment of Histopathological Response in Gastric and Gastro-Oesophageal Junction Adenocarcinoma following Neoadjuvant Chemotherapy: Which Scoring System to Use?

Background. The standard of care for patients with operable gastric and gastro-oesophageal junction (GOJ) tumours involves neoadjuvant chemotherapy. This improves survival and reduces risk of tumour recurrence following surgery. The various grading criteria published to assess histological response to neoadjuvant treatments have never been compared in terms of their reproducibility and ability to predict survival. Methods. A study was carried out of 66 patients with gastric and GOJ (types II and III) adenocarcinoma treated with neoadjuvant chemotherapy according to the MAGIC protocol. Histology slides were reviewed independently by two histopathologists using three published grading systems (Mandard, Japanese, and Becker). Histological, demographic, and survival data were collected. The kappa statistic was used to assess interobserver reproducibility. Results. Three (5%) patients had a complete pathological response. There was reasonable interobserver agreement for the grading systems: κ-scores = 0.44 (Mandard), 0.28 (Japanese), and 0.51 (Becker). Only Mandard and Becker scores provided prognostic information: 5-year overall survival rates of 100% for complete or near complete responders versus 35% for nonresponders () for both. Positive lymph nodes () and resection margins () were associated with poor survival. Conclusion. Becker’s score is most reproducible for the evaluation of histological response. Furthermore, lymph node and resection margins status provides prognostic information.

Examination of weight control practices in a non-clinical sample of college women

The current study examined healthy weight control practices among a sample of college women enrolled at an urban university (N=715; age=19.87±1.16; 77.2% Caucasian; 13.4% African American, 7.2% Asian, 2.2% other races). Participants completed measures as part of an on-line study about health habits, behaviors, and attitudes. Items from the Three Factor Eating Questionnaire were selected and evaluated with exploratory factor analysis to create a healthy weight control practices scale. Results revealed that college women, regardless of weight status, used a comparable number (four of eight) of practices. Examination of racial differences between Caucasian and African American women revealed that normal weight African American women used significantly fewer strategies than Caucasian women. Of note, greater use of healthy weight control practices was associated with higher cognitive restraint, drive for thinness, minutes of physical activity, and more frequent use of compensatory strategies. Higher scores on measures of binge and disinhibited eating, body dissatisfaction, negative affect, and depressive symptoms were associated with greater use of healthy weight control practices by underweight/normal weight but not by overweight/obese college women. Results suggest that among a sample of college females, a combination of healthy and potentially unhealthy weight control practices occurs. Implications of the findings suggest the need for effective weight management and eating disorder prevention programs for this critical developmental life stage. Such programs should be designed to help students learn how to appropriately use healthy weight control practices, as motivations for use may vary by weight status.

Effect of selenium status on the response of unfit horses to exercise

Exercise is known to increase reactive oxygen species and alter glutathione peroxidase activity (GPx), a selenoenzyme responsible for neutralising hydrogen peroxide. This study evaluated the effect of selenium (Se) status on the response of unfit horses to mild exercise. 25 mature horses received one of four dietary treatments for 29 weeks: low Se (LS, n=6), adequate Se (AS, sodium selenite, n=6), high organic Se (SP; Sel-Plex®, n=7) or high inorganic Se (SS, sodium selenite, n=6). Total dietary Se concentration for LS, AS, SP and SS was 0.06, 0.12, 0.3 and 0.3 mg/kg respectively. Blood samples were collected before and at 0, 4 and 24 h after a 36 min exercise test covering 4.41 km. Blood samples were evaluated for blood GPx, pro-inflammatory cytokine expression, serum malondialdehyde (MDA), creatine kinase (CK), aspartate aminotransferase (AST) and blood pro-inflammatory cytokine expression. Data were analysed as ANOVA with repeated measures. Prior to the exercise test blood Se was higher (P<0.01) for SP and SS than AS and LS. An effect of treatment and treatment×time (P<0.05) existed for GPx. Post-exercise GPx decreased in LS and did not recover by 24 h while remaining unchanged in AS. GPx increased in SP and decreased in SS post-exercise, but both returned to pre-values at 24 h. Serum MDA was elevated at 24 h (P<0.05), but unaffected by treatment. Serum CK and AST were unaffected by Se status (P≯0.05). Pro-inflammatory cytokine expression was unaffected by Se status, although tumour necrosis factor alpha decreased immediately after exercise followed by an increase post-exercise while granzyme B was elevated immediately post-exercise (time, P<0.05). Overall Se status had minimal effects on exercise response in unfit horses. The differences in post-exercise GPx response may warrant further investigation.

Google governance: increasing the effectiveness of critical care physicians through the use of an online usergroup

AIMS

The aim of this study was to describe the use of an online user group to enhance communication and productivity by critical care specialists.

METHODS

In this article, we provide a description of the first 6 months of use of an online user group by senior retrieval physicians.

RESULTS

Initially developed as a communication and online discussion tool, our online user group evolved to include a number of other utilities that support clinical governance. These included a repository for useful files, educational presentations, online rostering and "portfolio pages", updating aspects of an individual specialist's non-clinical activity. Its applications continue to evolve in number and utility. Participating physicians perceive an increase in organisational efficiency.

CONCLUSIONS

An online user group such as Google Groups may provide powerful support to an organisation's clinical governance. We recommend this tool to other services with limited administrative personnel.

Low mood and challenging behaviour in people with severe and profound intellectual disabilities

BACKGROUND

We investigated the relationship between low mood and challenging behaviour in people in the severe and profound range of intellectual disability, while controlling for the presence of potentially confounding variables such as diagnosis of autism, physical and sensory problems and ill health.

METHODS

The key workers of 52 people with severe and profound intellectual disability completed measures of depression, communication, challenging behaviour and provided information on relevant demographic and health variables.

RESULTS

Using the Mood, Interest and Pleasure Questionnaire for classification of mood, a significant difference was found between a 'low mood' and 'normothymic' group in the reported occurrence of challenging behaviour. This difference remained even when confounding variables such as the presence of autism, health and sensory difficulties were controlled. The frequency and severity of challenging behaviour was predicted by measures indicating the presence of low mood.

CONCLUSION

People with severe and profound show clear and measurable signs of low mood, and in this relatively small sample of institutionalised individuals, low mood was associated with challenging behaviour.

Lymphedema secondary to breast cancer: how choice of measure influences diagnosis, prevalence, and identifiable risk factors

Research on secondary lymphedema primarily uses indirect methods for diagnosis. This paper compares prevalence and cumulative burden following breast cancer surgery, as well as personal, treatment, and behavioral characteristics associated with lymphedema, using different assessment techniques. Lymphedema status was assessed at three-monthly intervals between six- and 18-months post-surgery in a population-based sample of Australian women with recently diagnosed, unilateral, invasive breast cancer, using three methods: bioimpedance spectroscopy (BIS), difference between sum of arm circumferences (SOAC) and self-report. Depending on the method, point prevalence ranged between 8 to 28%, with 1 in 5 to 2 in 5 women experiencing lymphedema at some point in time. Of those with lymphedema defined by BIS, almost 40%-60% went undetected, and 40%-12% were misclassified as having lymphedema, based on self-report and SOAC, respectively. The choice of measure also had significant implications for identified risk factors. Over 10 characteristics were associated with lymphedema, however only one, experiencing other upper-body symptoms at baseline, influenced odds of lymphedema across all three methods. These findings highlight that secondary lymphedema poses a significant public health problem. Utilizing the most accurate and reliable method for assessment is crucial to advance our understanding of preventive and treatment strategies.