Abstract 3737: Use of intestinal organoids as a preclinical screen for agents modulating epithelial regeneration and gastrointestinal toxicity

The mouse small intestinal in vitro organoid model was first described by Sato et al in 2009. We have further developed this model as a robust screening tool to aid the selection of lead candidates that may have efficacy preventing or treating GI toxicity, and to allow early identification of candidate toxicity. More specifically, we have been assessing the model's potential to progress the development of novel therapeutic agents to treat the GI mucositis, a common toxicity associated with cancer therapy.

The intestinal organoid culture conditions were designed to mimic the stem cell niche allowing cell differentiation and proliferation to occur. Indeed all intestinal lineages are present in the organoids and the epithelial hierarchy closely resembles that observed in vivo. Alteration of these organoid culture conditions allows identification of proliferative or cytotoxic effects, changes in differentiation and gene expression profiling of target pathways.

Sub-optimal culture conditions reduce the background level of branching within an organoid population, allowing the quantification of proliferative effects through an increase in branching above the background upon agent exposure. Examples of agents inducing branching of organoids include Wnt pathway modulators. Optimal culture conditions allow assessment of toxicity caused by agents such as chemotherapy drugs. Organoid viability can be assessed either visually or with MTS techniques. In addition, differentiation by agents such as the Notch pathway inhibitor DAPT can be assessed by histological examination of the organoids. All of these cultures can undergo gene expression profiling forming links to the observed biological observations. Proof of concept gene expression data has been generated using known GI growth factors and modulators, which have been linked to in vivo gene expression profiling to demonstrate PD linkages.

In addition, we have developed a model using APCMin+/- mice, which develop a phenotype in culture more consistent with a deregulated adenoma. Parallel assessment of agents on this model and the organoids has been useful for discriminating normal vs tumour responses, identifying agents with differential activities.

Our intestinal organoid models allow screening of multiple agents, with over 5000 screened to date including Wnt pathway regulators, cytokines, growth factor, chemotherapy drugs, steroids and lectins.

Citation Format: Sarah Hoyle, Shaun Ainsworth, Aude-Marine Bonavita, Jo Read, Alan Murdoch, Lorna Woolford, Elliott Harrison, Gino Miele, Cath Booth. Use of intestinal organoids as a preclinical screen for agents modulating epithelial regeneration and gastrointestinal toxicity. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3737. doi:10.1158/1538-7445.AM2014-3737

Rapid identification of the genus Dekkera/Brettanomyces, the Dekkera subgroup and all individual species

The genus Dekkera/Brettanomyces comprises five described species: Dekkera bruxellensis, D. anomala, Brettanomyces custersianus, B. naardenensis and B. nanus. Some of them, especially D. bruxellensis, are important spoilage organisms, particularly in the wine and beverage industries. Because of their economic importance many different methods have been developed to identify members of the genus in general and D. bruxellensis in particular. These methods vary in their rapidity, complexity and cost but, partly because of confidentiality issues, it is unclear which methods are used, or how widely, in the relevant industries. Building on previous work with the genera Saccharomyces and Zygosaccharomyces, a suite of eight PCR primer pairs has been designed either on the D1-D2 region of the 26S rRNA gene or translation elongation factor TEF1-α. These primers can specifically identify the genus as a whole, only Dekkera species, each one of the five recognised species as well as a significant subgroup of D. bruxellensis represented by NCYC 3426. Multiplexing has also been tried and it has been shown to be possible with some combinations of genus or Dekkera-level and species-specific primers. Using direct colony PCR amplification followed by gel electrophoresis, a clear positive result can be obtained in less than 3h, thus providing a quick, reliable and inexpensive way to identify target species.

Sex drives intracellular conflict in yeast

Theory predicts that sex can drive the evolution of conflict within the cell. During asexual reproduction, genetic material within the cell is inherited as a single unit, selecting for cooperation both within the genome as well as between the extra-genomic elements within the cell (e.g. plasmids and endosymbionts). Under sexual reproduction, this unity is broken down as parental genomes are distributed between meiotic progeny. Genetic elements able to transmit to more than 50% of meiotic progeny have a transmission advantage over the rest of the genome and are able to spread, even where they reduce the fitness of the individual as a whole. Sexual reproduction is therefore expected to drive the evolution of selfish genetic elements (SGEs). Here, we directly test this hypothesis by studying the evolution of two independent SGEs, the 2-μm plasmid and selfish mitochondria, in populations of Saccharomyces cerevisiae. Following 22 rounds of sexual reproduction, 2-μm copy number increased by approximately 13.2 (±5.6) copies per cell, whereas in asexual populations copy number decreased by approximately 5.1 (±1.5) copies per cell. Given that the burden imposed by this parasite increases with copy number, these results support the idea that sex drives the evolution of increased SGE virulence. Moreover, we found that mitochondria that are respiratory-deficient rapidly invaded sexual but not asexual populations, demonstrating that frequent outcrossed sex can drive the de novo evolution of genetic parasites. Our study highlights the genomic perils of sex and suggests that SGEs may play a key role in driving major evolutionary transitions, such as uniparental inheritance.

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 1867: Gene expression profiles obtained from ex vivo human scalp hair to determine the effects of drug response following exposure to HDAC inhibitors

Background Plucked human scalp hair represents an ideal surrogate tissue to enable non-invasive monitoring of drug response in clinical trials. Congruence of patterns of transcriptome activity within the bulb region of plucked scalp hair show high concordance and to that of primary target tumour tissues. The ex vivo plucked scalp hair culture technique involves exposing healthy normal volunteer hair to different concentrations of a number of HDAC inhibitors and ascertain the effects that they have on gene expression. This technique is an ideal approach to identifying desirable non-invasive transcriptional biomarkers to demonstrate target engagement and define a PK/PD relationship, as well as enabling the monitoring of a well tolerated dose schedule with maximal biological effect. Materials and Methods In this study, we deployed our proprietary ex vivo culture technique to ascertain the effects that three different HDAC inhibitors had on gene expression in plucked hair. Three different concentrations of each HDAC inhibitor were incubated in culture for a period of 18 hours. RNA was extracted from the hair bulb following the culture technique and gene expression was assessed following microarray analysis. Statistically significant biomarkers (p<0.05) were identified along with genes with a greater than 2 fold change from the vehicle group. Direct comparisons in the profiles obtained following exposure to the three different HDAC inhibitors were conducted to evaluate differences in the mechanism of action of each compound. Results We were able to demonstrate from the ex vivo plucked hair study, a panel of transcriptional markers that exhibited a similar response to drug treatment following exposure to the three different HDAC inhibitors. The differentially expressed genes identified were biologically relevant as they are consistent with pathways that are known to be associated with HDAC inhibition. The results also demonstrated the potency of each of the HDAC inhibitors and provided an insight into the different mechanisms of action of each compound. The differentially expressed biomarkers identified in this study may be used in clinical settings to monitor pharmacodynamic responses in plucked scalp hair obtained from patients. Conclusions We conclude that plucked human scalp hair represents an ideal minimally invasive surrogate tissue to monitor drug response in patients receiving treatment with HDAC inhibitors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1867. doi:1538-7445.AM2012-1867

Mannose-binding lectin genotype and serum levels in patients with chronic and allergic pulmonary aspergillosis

Several studies suggest mannose-binding lectin (MBL) deficiency is associated with various manifestations of aspergillosis. MBL serum levels and function are genetically determined, but levels rise during inflammation. We address the relative frequency of deficient genotypes, the relationship between serum level and genotype and both age and disease manifestations in patients with chronic pulmonary (CPA) and allergic bronchopulmonary aspergillosis (ABPA) and severe asthma with fungal sensitization (SAFS). DNA was extracted from blood samples, and MBL2 genotyping was performed using the INNO-LiPA MBL2 kit. Serum MBL concentrations were determined using ELISA. One hundred and eight patients were evaluated, 70 (65%) with CPA, 38 (35%) with allergic disease (ABPA, SAFS or undefined) and 13 (12%) had both CPA and ABPA. The mean MBL serum level was 1849 μg L(-1) and did not differ between groups. Forty subjects (37%) had exon 1 genotypes producing nonfunctional MBL (A/B, A/C, A/D and O/O), a frequency not different from published normal controls. A/A subjects with CPA had higher levels (2981 μg L(-1)) compared with allergic A/A subjects (2202 μg L(-1)) (pc0.012). No single haplotype, genotype or allele was significantly related to any aspergillosis phenotype. Worse breathlessness was associated with higher MBL levels among A/A subjects (P = 0.009) and conversely nonfunctional genotypes. Mean MBL values were higher in those with an Medical Research Council (MRC) breathlessness score of 5 compared with those with and MRC score of 1 (P = 0.023). A/A allergic subjects (n = 27) in this study were ≈ 11 years younger than allergic A/O subjects (n = 11, P = 0.02). Subjects with worse respiratory status or more severe CPA had higher MBL serum levels (P = 0.023; P = 0.034). Bronchiectasis was not associated with MBL levels in CPA or allergic aspergillosis. MBL genotype and serum level modulate progression of aspergillosis.

Abstract C130: Plucked human scalp hairs: Potential utility as a surrogate tissue for the assessment of therapies targeting the androgen receptor

Objective: Evaluate whether plucked human scalp or eyebrow hairs obtained from male elderly healthy normal volunteers (HNVs) are suitable for assessing RNA expression patterns linked to the androgen receptor.

Procedure: For each of 12 HNV subjects plucked eyebrow and scalp hairs were obtained at 2 time points. For each time point up to three individual anagen hairs were selected for RNA extraction and representative cDNA amplification. For each sample RNA quality was assessed by agarose gel electrophoresis and cDNA quality assessed by qPCR analysis of 3 reference or “housekeeping” genes. Expression levels of a panel of 20 androgen receptor regulated genes were measured by qPCR for samples passing both RNA and cDNA quality criteria.

Results : Of the 72 scalp hairs analysed 64 (89 %) passed both RNA and cDNA quality criteria with 23 out of 24 (96%) sample collection points yielding 2 or more analysable hairs. This high success translated into available data for both time points in 11 out of 12 HNVs (92 %). In contrast, for the 72 eyebrow hairs analysed only 2 (3 %) passed RNA quality criteria with none of the collection points yielded 2 or more analysable hairs. Of the 20 test genes qPCR analysis identified a short list of 7 genes with expression levels similar to “housekeeping” genes indicating that they should be reliably detected in the majority of scalp hairs. These results are in keeping with a previous HNV study of younger male and female donors and indicate that plucked scalp hairs may be of value in the early phases of clinical development of androgen receptor based therapies.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C130.

Transcriptional regulation of plant senescence: from functional genomics to systems biology

Leaf senescence is an active process that involves the increased expression of many hundreds of genes. Many putative transcription factors show enhanced transcription during leaf senescence in Arabidopsis and functional analysis of these should help to indicate their role in controlling gene expression during leaf senescence. In this paper, we describe the analysis of knockout insertion mutants in two different senescence-enhanced genes, one encodes a heat shock transcription factor and the other a zinc finger protein. Plants mutated in these genes show accelerated leaf senescence and reduced tolerance to drought stress, indicating that expression of these genes during senescence has a protective role to maintain viability during this essential developmental process. Analysis of gene expression changes in both mutants compared to the wild-type plants indicates an increased rate of senescence but does not show clearly the pathway that is dependent on these genes for expression. The complexities of signalling networks in plant stress and the plasticity of plant responses mean that the direct consequences of mutation are very difficult to define. The usefulness of this type of approach to address the burning question of how senescence is regulated is discussed, and an alternative approach aimed at a more global analysis of gene regulation using systems biology methods is described.

Evaluation of the delivery fee exemption policy in ghana: population estimates of changes in delivery service utilization in two regions

SUMMARY OBJECTIVES

To determine changes in the proportion of deliveries at health facilities and the proportion attended by health professionals after delivery fee exemption implementation.

DESIGN

Pre and post intervention implementation cluster-sampled household survey.

SETTING

Central and Volta regions of Ghana.

PARTICIPANTS

Women who had delivered in these regions during the fee exemption policy and an equivalent period of time prior to it.

MAIN OUTCOME MEASURES

Place of delivery and person attending.

RESULTS

After fee exemption implementation the likelihood of delivering in a health facility increased significantly in Central (OR 1.83, p<0.001) and Volta (OR 1.34, p<0.05) regions when accounting for the mothers' education and poverty levels and the clustered data. Results from Central Region showed increases in facility deliveries mainly occurred in health centres (from 13.7% to 22.3% of deliveries), and were attended by midwives (from 49.0% to 59.7%). There was evidence that after implementation some inequalities in the uptake of facility deliveries decreased. The greatest increase in the proportion of deliveries taking place in facilities occurred among women with the lowest levels of education (Central Region) and wealth (Volta Region). These changes reduced the differentials observed.

CONCLUSIONS

After the implementation of fee exemption the proportion of deliveries in health facilities increased in both regions. Although changes cannot be directly attributed to delivery fee exemption, results demonstrating that the greatest increases in facility-based deliveries occurred among the poorest and least educated women are consistent with the expectation that the policy would particularly benefit women with the greatest financial barrier to health care and at the greatest risk of maternal mortality.

Automated osteoporosis risk assessment by dentists: a new pathway to diagnosis

General dental practitioners use a vast amount of panoramic radiography in their routine clinical work, but valuable information about patients' osteoporotic status is not collected. There are many reasons for this, but one of the prime reasons must be the disruption involved in clinical routine with lengthy manual radiographic assessment. We have developed computer software, based on active shape modeling that will automatically detect the mandibular cortex on panoramic radiographs, and then measure its width. Automatic or semi-automatic measurement of the cortical width will indicate the osteoporotic risk of the patient. The aim of our work was to assess the computer search technique's ability to measure the mandibular cortical width and to assess its potential for detection of osteoporosis of the hip, spine and femoral neck. Mandibular cortical width was measured using the manually initialized (semi-automatic) method and, when assessed for diagnosing osteoporosis at one of the three measurement sites, gave an area under the ROC curve (A(z))=0.816 (95% CI=0.784 to 0.845) and for the automatically initialized searches, A(z)=0.759 (95% CI=0.724 to 0.791). The difference between areas=0.057 (95% Confidence interval=0.025 to 0.089), p<0.0001. For diagnosing osteoporosis at the femoral neck, mandibular cortical width derived from the manually initialized fit gave an area under the ROC curve (A(z))=0.835 (95% CI=0.805 to 0.863) and for the automatically initialized searches A(z)=0.805 (95% CI=0.773 to 0.835). The difference in A(z) values between active shape modeling search methods=0.030 (95% CI=-0.010 to 0.070), and this was not significant, p=0.138. We concluded that measurement of mandibular cortical width using active shape modeling is capable of diagnosing skeletal osteoporosis with good diagnostic ability and repeatability.

Accuracy in osteoporosis diagnosis of a combination of mandibular cortical width measurement on dental panoramic radiographs and a clinical risk index (OSIRIS): the OSTEODENT project

Clinical questionnaires and dental radiographic findings have both been suggested as methods of identifying women at risk of having osteoporosis and who might benefit from bone densitometry. The aim of this study was to measure the diagnostic accuracy of a combination of mandibular cortical width (MCW) measured from dental panoramic radiographs (DPRs) and the osteoporosis index of risk (OSIRIS) in the diagnosis of osteoporosis. 653 women (age range 45-70 years, mean age 54.95 years) in four European centres underwent standardised dual X-ray energy absorptiometry (DXA) to provide reference data on osteoporosis status. Each subject was interviewed to derive OSIRIS scores and underwent DPR examination. MCW was measured directly by five observers. Receiver Operating Characteristic (ROC) curve analysis was used to calculate sensitivities and specificities of the clinical and radiographic tests for the diagnosis of osteoporosis. 512 (78.4%) of the study population were classified as having normal BMD and 141 (21.6%) as having osteoporosis. Using ROC analysis, OSIRIS gave a ROC curve area (A(z)) of 0.838, with a sensitivity of 70.9% and a specificity of 79.5% at a diagnostic threshold of <or=+1. MCW on DPRs gave Az values for the five observers ranging from 0.71 to 0.78, providing sensitivities between 41.0% and 59.6% and specificities of between 81.8% and 90.3% at a diagnostic threshold of a 3 mm MCW and sensitivities between 94.2% and 99.3% and specificities of between 9.8% and 23.7% at a diagnostic threshold of a 4.5 mm MCW. Inter-observer repeatability was less than 2.15 mm for 95% of subjects. Combining clinical and radiographic tests had the effect of improving specificity at the expense of a fall in sensitivity. Diagnostic thresholds for MCW and OSIRIS can be chosen to provide the sensitivity and specificity combination that best suits locally determined needs. However, the addition of OSIRIS as a stepwise 'follow-up' test to radiographic assessment of MCW should only be performed if the aim is to have a test for which the highest achievable specificity is desired.

Comparative gene expression in brain regions of human alcoholics

The mesocorticolimbic system is the reward centre of the brain and the major target for drugs of abuse including alcohol. Neuroadaptive changes in this region are thought to underlie the process of tolerance and dependence. Recently, several research groups have searched for alcohol-responsive genes using high-throughput microarrays and well-characterized human post-mortem material. Comparison of data from these studies of cortical regions highlights the differences in experimental approach and selection of cases. However, alcohol-responsive gene sets associated with transcription, oxidative stress and energy production were common to these studies. In marked contrast, alcohol-responsive genes in the nucleus accumbens and the ventral tegmental area are primarily associated with changes in neurotransmission and signal transduction. These data support the concept that, within cortical regions, changes in gene expression are associated with alcoholism-related pathology. In the dopaminergic tract of the mesocorticolimbic system, alcohol-responsive gene sets suggest long-term neuroplastic changes in synaptic transmission.

Comparison of resection and radiofrequency ablation for treatment of solitary colorectal liver metastases

BACKGROUND

Liver resection is the treatment of choice for patients with solitary colorectal liver metastases. In recent years, however, radiofrequency ablation has been used increasingly in the treatment of colorectal liver metastases. In the absence of randomized clinical trials, this study aimed to compare outcome in patients with solitary colorectal liver metastases treated by surgery or by radiofrequency ablation.

METHODS

Solitary colorectal liver metastases were treated by radiofrequency destruction in 25 patients. The indications were extrahepatic disease in seven, vessel contiguity in nine and co-morbidity in nine patients. Outcome was compared with that of 20 patients who were treated by liver resection for solitary metastases and had no evidence of extrahepatic disease. Most patients in both groups also received systemic chemotherapy.

RESULTS

Median survival after liver resection was 41 (range 0-97) months with a 3-year survival rate of 55.4 per cent. There was one postoperative death and morbidity was minimal. Median survival after radiofrequency ablation was 37 (range 9-67) months with a 3-year survival rate of 52.6 per cent.

CONCLUSION

Survival after resection and radiofrequency ablation of solitary colorectal liver metastases was comparable. The latter is less invasive and requires either an overnight stay or day-case facilities only.