Translation of tissue-based artificial intelligence into clinical practice: from discovery to adoption

Digital pathology (DP), or the digitization of pathology images, has transformed oncology research and cancer diagnostics. The application of artificial intelligence (AI) and other forms of machine learning (ML) to these images allows for better interpretation of morphology, improved quantitation of biomarkers, introduction of novel concepts to discovery and diagnostics (such as spatial distribution of cellular elements), and the promise of a new paradigm of cancer biomarkers. The application of AI to tissue analysis can take several conceptual approaches, within the domains of language modelling and image analysis, such as Deep Learning Convolutional Neural Networks, Multiple Instance Learning approaches, or the modelling of risk scores and their application to ML. The use of different approaches solves different problems within pathology workflows, including assistive applications for the detection and grading of tumours, quantification of biomarkers, and the delivery of established and new image-based biomarkers for treatment prediction and prognostic purposes. All these AI formats, applied to digital tissue images, are also beginning to transform our approach to clinical trials. In parallel, the novelty of DP/AI devices and the related computational science pipeline introduces new requirements for manufacturers to build into their design, development, regulatory and post-market processes, which may need to be taken into account when using AI applied to tissues in cancer discovery. Finally, DP/AI represents challenge to the way we accredit new diagnostic tools with clinical applicability, the understanding of which will allow cancer patients to have access to a new generation of complex biomarkers.

Growth dynamics and amorphous-to-crystalline phase transformation in natural nacre

Biominerals, such as nacreous bivalve shells, are important archives of environmental information. Most marine calcifiers form their shells from amorphous calcium carbonate, hypothesised to occur via particle attachment and stepwise crystallisation of metastable precursor phases. However, the mechanism of this transformation, including the incorporation of trace elements used for environmental reconstructions, are poorly constrained. Here, using shells of the Mediterranean mussel, we explore the formation of nacre from the meso- to the atomic scale. We use a combination of strontium pulse-chase labelling experiments in aquaculture and correlated micro- to sub-nanoscale analysis to show that nacre grows in a dynamic two-step process with extensional and space-filling growth components. Furthermore, we show that nacre crystallizes via localised dissolution and reprecipitation within nanogranules. Our findings elucidate how stepwise crystallization pathways affect trace element incorporation in natural biominerals, while preserving their intricate hierarchical ultrastructure.

Polygenic risk of Social-isolation and its influence on social behavior, psychosis, depression and autism spectrum disorder

Social-isolation has been linked to a range of psychiatric issues, but the behavioral component that drives it is not well understood. Here, a GWAS is carried out to identify genetic variants which contribute to Social-isolation behaviors in up to 449,609 participants from the UK Biobank. 17 loci were identified at genome-wide significance, contributing to a 4% SNP heritability estimate. Using the Social-isolation GWAS, polygenic risk scores (PRS) were derived in ALSPAC, an independent, developmental cohort, and used to test for association with friendship quality. At age 18, friendship scores were associated with the Social-isolation PRS, demonstrating that the genetic factors are able to predict related social traits. LD score regression using the GWAS demonstrated genetic correlation with autism spectrum disorder, schizophrenia, and major depressive disorder. However, no evidence of causality was found using a conservative Mendelian randomization approach other than that of autism spectrum disorder on Social-isolation. Our results show that Social-isolation has a small heritable component which may drive those behaviors which is associated genetically with other social traits such as friendship satisfaction as well as psychiatric disorders.

BridgePRS : A powerful trans-ancestry Polygenic Risk Score method

Polygenic Risk Scores (PRS) have huge potential to contribute to biomedical research and to a future of precision medicine, but to date their calculation relies largely on Europeanancestry GWAS data. This global bias makes most PRS substantially less accurate in individuals of non-European ancestry. Here we present BridgePRS , a novel Bayesian PRS method that leverages shared genetic effects across ancestries to increase the accuracy of PRS in non-European populations. The performance of BridgePRS is evaluated in simulated data and real UK Biobank (UKB) data across 19 traits in African, South Asian and East Asian ancestry individuals, using both UKB and Biobank Japan GWAS summary statistics. BridgePRS is compared to the leading alternative, PRS-CSx , and two single-ancestry PRS methods adapted for trans-ancestry prediction. PRS trained in the UK Biobank are then validated out-of-cohort in the independent Mount Sinai (New York) Bio Me Biobank. Simulations reveal that BridgePRS performance, relative to PRS-CSx , increases as uncertainty increases: with lower heritability, higher polygenicity, greater between-population genetic diversity, and when causal variants are not present in the data. Our simulation results are consistent with real data analyses in which BridgePRS has better predictive accuracy in African ancestry samples, especially in out-of-cohort prediction (into Bio Me ), which shows a 60% boost in mean R 2 compared to PRS-CSx ( P = 2 × 10 -6 ). BridgePRS performs the full PRS analysis pipeline, is computationally efficient, and is a powerful method for deriving PRS in diverse and under-represented ancestry populations.

Abstract A23: True-T – Improved prediction by holistic artificial intelligence-based quantification of T-cell response

Introduction - Seminal work from Galon et al [PMID: 16371631], found immunohistochemical (IHC) quantification of the immune response to be prognostic in colorectal cancer (CRC). Although numerous systems for scoring T-cell subsets have been published [reviewed in PMID: 35758208] and this type of scoring is acknowledged as a bona fide diagnostic test [PMID: 32320495], it is not commonly used in general diagnostic routine. Our group reported recently that a digital pathology (DP) approach to scoring of CD3/CD4/CD8 in more than 1,500 patients was prognostic of survival in CRC Stage II & III and predictive of chemotherapy response in CRC Stage IV [PMID: 32684627]Hypothesis – An artificial intelligence (AI)-based approach to DP analysis of CD3/CD4/CD8 provides unbiased prognostic and predictive advantage in CRC.Materials & Methods - 3,123 whole slide images from 1,041 patient samples from 4 institutions in the context of the PathLAKE UK DP Consortium (Queens’s University Belfast, University of Oxford, University of Nottingham and University Hospital Coventry and Warwick). These samples represented 4 different clones [LN10 (CD3), 4B12 (CD4), 4B11 (CD8) and SP3 (CD4)] from 3 different companies, and were scanned with the Aperio AT2 scanner. Ninety-six experiments for validation and verification were carried out with open-source AI systems following protocols and pathways described before [PMID: 35626427 & PMID: 34359723].Results – We developed a combined CD3/CD4/CD8 AI scoring tool (True-T) which can quantify CD3/CD4/CD8 expressing cells with an accuracy ranging between 96.94 and 99.26; a sensitivity range of 79.27 to 85.22 and a specificity of 98.96 to 99.40. Using this novel AI method of immune cell classification, previous study findings were replicated across four UK centers using an independent cohort of CRC patients using antibody clones optimized for routine clinical diagnostics (p=0.002; HR: 2.21; 95%CI:1.24-3.94 versus p=0.006; hr: 1.84; 95% ci: 1.54-2.21 in the current and former study [PMID: 32684627] respectively). We now have integrated True-T status into a easy to use graphical user interface (GUI), which includes key determinants of CRC prognosis from within a population-representative cohort (n>600), in order to be able to model the impact of a high or low True-T score with other variables of clinical significance.Conclusion – True-T shows that a holistic AI-based quantification of T-cell response potentially improves prediction of patient prognosis over other in-silico quantitative methods in CRC and can be implemented in routine diagnostics in a seamless manner with an easy-to-use GUI.

Citation Format: Manuel Salto-Tellez, Yasmine Makhlouf, Stephanie Craig, Paul O'Reilly, Perry Maxwell, Jacqueline James. True-T – Improved prediction by holistic artificial intelligence-based quantification of T-cell response [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A23.

Prognostic value of polygenic risk scores for adults with psychosis

Polygenic risk scores (PRS) summarize genetic liability to a disease at the individual level, and the aim is to use them as biomarkers of disease and poor outcomes in real-world clinical practice. To date, few studies have assessed the prognostic value of PRS relative to standards of care. Schizophrenia (SCZ), the archetypal psychotic illness, is an ideal test case for this because the predictive power of the SCZ PRS exceeds that of most other common diseases. Here, we analyzed clinical and genetic data from two multi-ethnic cohorts totaling 8,541 adults with SCZ and related psychotic disorders, to assess whether the SCZ PRS improves the prediction of poor outcomes relative to clinical features captured in a standard psychiatric interview. For all outcomes investigated, the SCZ PRS did not improve the performance of predictive models, an observation that was generally robust to divergent case ascertainment strategies and the ancestral background of the study participants.

Repurposing FDA approved drugs as radiosensitizers for treating hypoxic prostate cancer

Background

The presence of hypoxia is a poor prognostic factor in prostate cancer and the hypoxic tumor microenvironment promotes radioresistance. There is potential for drug radiotherapy combinations to improve the therapeutic ratio. We aimed to investigate whether hypoxia-associated genes could be used to identify FDA approved drugs for repurposing for the treatment of hypoxic prostate cancer.

Methods

Hypoxia associated genes were identified and used in the connectivity mapping software QUADrATIC to identify FDA approved drugs as candidates for repurposing. Drugs identified were tested in vitro in prostate cancer cell lines (DU145, PC3, LNCAP). Cytotoxicity was investigated using the sulforhodamine B assay and radiosensitization using a clonogenic assay in normoxia and hypoxia.

Results

Menadione and gemcitabine had similar cytotoxicity in normoxia and hypoxia in all three cell lines. In DU145 cells, the radiation sensitizer enhancement ratio (SER) of menadione was 1.02 in normoxia and 1.15 in hypoxia. The SER of gemcitabine was 1.27 in normoxia and 1.09 in hypoxia. No radiosensitization was seen in PC3 cells.

Conclusion

Connectivity mapping can identify FDA approved drugs for potential repurposing that are linked to a radiobiologically relevant phenotype. Gemcitabine and menadione could be further investigated as potential radiosensitizers in prostate cancer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12894-021-00856-x.

Causal Associations Between Modifiable Risk Factors and the Alzheimer's Phenome

OBJECTIVE

The purpose of this study was to infer causal relationships between 22 previously reported risk factors for Alzheimer's disease (AD) and the "AD phenome": AD, AD age of onset (AAOS), hippocampal volume, cortical surface area and thickness, cerebrospinal fluid (CSF) levels of amyloid-β (Aβ42 ), tau, and ptau181 , and the neuropathological burden of neuritic plaques, neurofibrillary tangles (NFTs), and vascular brain injury (VBI).

METHODS

Polygenic risk scores (PRS) for the 22 risk factors were computed in 26,431 AD cases/controls and the association with AD was evaluated using logistic regression. Two-sample Mendelian randomization (MR) was used to infer the causal effect of risk factors on the AD phenome.

RESULTS

PRS for increased education and diastolic blood pressure were associated with reduced risk for AD. MR indicated that only education was causally associated with reduced risk of AD, delayed AAOS, and increased cortical surface area and thickness. Total- and LDL-cholesterol levels were causally associated with increased neuritic plaque burden, although the effects were driven by single nucleotide polymorphisms (SNPs) within the APOE locus. Diastolic blood pressure and pulse pressure are causally associated with increased risk of VBI. Furthermore, total cholesterol was associated with decreased hippocampal volume; smoking initiation with decreased cortical thickness; type 2 diabetes with an earlier AAOS; and sleep duration with increased cortical thickness.

INTERPRETATION

Our comprehensive examination of the genetic evidence for the causal relationships between previously reported risk factors in AD using PRS and MR supports a causal role for education, blood pressure, cholesterol levels, smoking, and diabetes with the AD phenome. ANN NEUROL 2021;89:54-65.

Retrospective cohort study of clinical characteristics of 2199 hospitalised patients with COVID-19 in New York City

OBJECTIVE

The COVID-19 pandemic is a global public health crisis, with over 33 million cases and 999 000 deaths worldwide. Data are needed regarding the clinical course of hospitalised patients, particularly in the USA. We aimed to compare clinical characteristic of patients with COVID-19 who had in-hospital mortality with those who were discharged alive.

DESIGN

Demographic, clinical and outcomes data for patients admitted to five Mount Sinai Health System hospitals with confirmed COVID-19 between 27 February and 2 April 2020 were identified through institutional electronic health records. We performed a retrospective comparative analysis of patients who had in-hospital mortality or were discharged alive.

SETTING

All patients were admitted to the Mount Sinai Health System, a large quaternary care urban hospital system.

PARTICIPANTS

Participants over the age of 18 years were included.

PRIMARY OUTCOMES

We investigated in-hospital mortality during the study period.

RESULTS

A total of 2199 patients with COVID-19 were hospitalised during the study period. As of 2 April, 1121 (51%) patients remained hospitalised, and 1078 (49%) completed their hospital course. Of the latter, the overall mortality was 29%, and 36% required intensive care. The median age was 65 years overall and 75 years in those who died. Pre-existing conditions were present in 65% of those who died and 46% of those discharged. In those who died, the admission median lymphocyte percentage was 11.7%, D-dimer was 2.4 μg/mL, C reactive protein was 162 mg/L and procalcitonin was 0.44 ng/mL. In those discharged, the admission median lymphocyte percentage was 16.6%, D-dimer was 0.93 μg/mL, C reactive protein was 79 mg/L and procalcitonin was 0.09 ng/mL.

CONCLUSIONS

In our cohort of hospitalised patients, requirement of intensive care and mortality were high. Patients who died typically had more pre-existing conditions and greater perturbations in inflammatory markers as compared with those who were discharged.

RALB GTPase: a critical regulator of DR5 expression and TRAIL sensitivity in KRAS mutant colorectal cancer

RAS mutant (MT) metastatic colorectal cancer (mCRC) is resistant to MEK1/2 inhibition and remains a difficult-to-treat group. Therefore, there is an unmet need for novel treatment options for RASMT mCRC. RALA and RALB GTPases function downstream of RAS and have been found to be key regulators of several cell functions implicated in KRAS-driven tumorigenesis. However, their role as regulators of the apoptotic machinery remains to be elucidated. Here, we found that inhibition of RALB expression, but not RALA, resulted in Caspase-8-dependent cell death in KRASMT CRC cells, which was not further increased following MEK1/2 inhibition. Proteomic analysis and mechanistic studies revealed that RALB depletion induced a marked upregulation of the pro-apoptotic cell surface TRAIL Death Receptor 5 (DR5) (also known as TRAIL-R2), primarily through modulating DR5 protein lysosomal degradation. Moreover, DR5 knockdown or knockout attenuated siRALB-induced apoptosis, confirming the role of the extrinsic apoptotic pathway as a regulator of siRALB-induced cell death. Importantly, TRAIL treatment resulted in the association of RALB with the death-inducing signalling complex (DISC) and targeting RALB using pharmacologic inhibition or RNAi approaches triggered a potent increase in TRAIL-induced cell death in KRASMT CRC cells. Significantly, high RALB mRNA levels were found in the poor prognostic Colorectal Cancer Intrinsic Subtypes (CRIS)-B CRC subgroup. Collectively, this study provides to our knowledge the first evidence for a role for RALB in apoptotic priming and suggests that RALB inhibition may be a promising strategy to improve response to TRAIL treatment in poor prognostic RASMT CRIS-B CRC.

Hospitalised COVID-19 patients of the Mount Sinai Health System: a retrospective observational study using the electronic medical records

OBJECTIVE

To assess association of clinical features on COVID-19 patient outcomes.

DESIGN

Retrospective observational study using electronic medical record data.

SETTING

Five member hospitals from the Mount Sinai Health System in New York City (NYC).

PARTICIPANTS

28 336 patients tested for SARS-CoV-2 from 24 February 2020 to 15 April 2020, including 6158 laboratory-confirmed COVID-19 cases.

MAIN OUTCOMES AND MEASURES

Positive test rates and in-hospital mortality were assessed for different racial groups. Among positive cases admitted to the hospital (N=3273), we estimated HR for both discharge and death across various explanatory variables, including patient demographics, hospital site and unit, smoking status, vital signs, lab results and comorbidities.

RESULTS

Hispanics (29%) and African Americans (25%) had disproportionately high positive case rates relative to their representation in the overall NYC population (p<0.05); however, no differences in mortality rates were observed in hospitalised patients based on race. Outcomes differed significantly between hospitals (Gray's T=248.9; p<0.05), reflecting differences in average baseline age and underlying comorbidities. Significant risk factors for mortality included age (HR 1.05, 95% CI 1.04 to 1.06; p=1.15e-32), oxygen saturation (HR 0.985, 95% CI 0.982 to 0.988; p=1.57e-17), care in intensive care unit areas (HR 1.58, 95% CI 1.29 to 1.92; p=7.81e-6) and elevated creatinine (HR 1.75, 95% CI 1.47 to 2.10; p=7.48e-10), white cell count (HR 1.02, 95% CI 1.01 to 1.04; p=8.4e-3) and body mass index (BMI) (HR 1.02, 95% CI 1.00 to 1.03; p=1.09e-2). Deceased patients were more likely to have elevated markers of inflammation.

CONCLUSIONS

While race was associated with higher risk of infection, we did not find racial disparities in inpatient mortality suggesting that outcomes in a single tertiary care health system are comparable across races. In addition, we identified key clinical features associated with reduced mortality and discharge. These findings could help to identify which COVID-19 patients are at greatest risk of a severe infection response and predict survival.

Cannabis use, depression and self-harm: phenotypic and genetic relationships

BACKGROUND AND AIMS

The use of cannabis has previously been linked to both depression and self-harm; however, the role of genetics in this relationship is unclear. This study aimed to estimate the phenotypic and genetic associations between cannabis use and depression and self-harm.

DESIGN

Cross-sectional data collected through UK Biobank were used to test the phenotypic association between cannabis use, depression and self-harm. UK Biobank genetic data were then combined with consortia genome-wide association study summary statistics to further test the genetic relationships between these traits using LD score regression, polygenic risk scoring and Mendelian randomization methods.

SETTING

United Kingdom, with additional international consortia data.

PARTICIPANTS

A total of 126 291 British adults aged between 40 and 70 years, recruited into UK Biobank.

MEASUREMENTS

Phenotypic outcomes were life-time history of cannabis use (including initial and continued cannabis use), depression (including single-episode and recurrent depression) and self-harm. Genome-wide genetic data were used and assessment centre, batch and the first six principal components were included as key covariates when handling genetic data.

FINDINGS

In UK Biobank, cannabis use is associated with an increased likelihood of depression [odds ratio (OR) = 1.64, 95% confidence interval (CI) = 1.59-1.70] and self-harm (OR = 2.85, 95% CI = 2.69-3.01). The strength of this phenotypic association is stronger when more severe trait definitions of cannabis use and depression are considered. Using consortia genome-wide summary statistics, significant genetic correlations are seen between cannabis use and depression [rg = 0.289, standard error (SE) = 0.036]. Polygenic risk scores for cannabis use and depression explain a small but significant proportion of variance in cannabis use, depression and self-harm within a UK Biobank target sample. However, two-sample Mendelian randomization analyses were not significant.

CONCLUSIONS

Cannabis use appeared to be both phenotypically and genetically associated with depression and self-harm. Limitations in statistical power mean that conclusions could not be made on the direction of causality between these traits.

The psychological impact of Stevens-Johnson syndrome and toxic epidermal necrolysis on patients' lives: a Critically Appraised Topic

CLINICAL SCENARIO

A 65-year-old man presented with a 12-h history of deteriorating rash. Two weeks previously he had completed a course of neoadjuvant chemotherapy for ductal carcinoma of the breast. On examination there were bullae, widespread atypical targetoid lesions and 15% epidermal detachment. There was no mucosal involvement on presentation, but subsequently it did evolve. Skin biopsy showed subepidermal blistering with epidermal necrosis. This confirmed our clinical diagnosis of overlap Stevens-Johnson syndrome (SJS)/toxic epidermal necrolysis (TEN). On transfer to intensive care he was anxious and fearful.

MANAGEMENT QUESTION

What are the psychological impacts of SJS/TEN on this man's life?

BACKGROUND

SJS and TEN have devastating outcomes for those affected.

OBJECTIVES

To conduct a Critically Appraised Topic to (i) analyse existing research related to the psychological impact of SJS and TEN and (ii) apply the results to the clinical scenario.

METHODS

Seven electronic databases were searched for publications focusing on the psychological impact of SJS/TEN on adults over 18 years of age.

RESULTS

Six studies met the inclusion criteria. Healthcare practitioners' (HCPs') lack of information around the disorder was highlighted. Patients experienced undue stress and fear. Some patients had symptoms aligned to post-traumatic stress disorder (PTSD), anxiety and depression.

DISCUSSION AND RECOMMENDATION

The evidence suggests that SJS and TEN impact psychologically on patients' lives. Education of HCPs, to address their lack of awareness and information on SJS/TEN, should facilitate their capacity to provide information and support to patients, thereby reducing patient anxiety. On discharge, a follow-up appointment with relevant HCPs to reduce the possibility of PTSD occurring should be considered.

Defining the molecular evolution of extrauterine high grade serous carcinoma

OBJECTIVE

High grade serous carcinoma (HGSC) is the most common and most aggressive, subtype of epithelial ovarian cancer. It presents as advanced stage disease with poor prognosis. Recent pathological evidence strongly suggests HGSC arises from the fallopian tube via the precursor lesion; serous tubal intraepithelial carcinoma (STIC). However, further definition of the molecular evolution of HGSC has major implications for both clinical management and research. This study aims to more clearly define the molecular pathogenesis of HGSC.

METHODS

Six cases of HGSC were identified at the Northern Ireland Gynaecological Cancer Centre (NIGCC) that each contained ovarian HGSC (HGSC), omental HGSC (OMT), STIC, normal fallopian tube epithelium (FTE) and normal ovarian surface epithelium (OSE). The relevant formalin-fixed paraffin embedded (FFPE) tissue samples were retrieved from the pathology archive via the Northern Ireland Biobank following attaining ethical approval (NIB11:005). Full microarray-based gene expression profiling was performed on the cohort. The resulting data was analysed bioinformatically and the results were validated in a HGSC-specific in-vitro model.

RESULTS

The carcinogenesis of HGSC was investigated and showed the molecular profile of HGSC to be more closely related to normal FTE than OSE. STIC lesions also clustered closely with HGSC, indicating a common molecular origin.

CONCLUSION

This study provides strong evidence suggesting that extrauterine HGSC arises from the fimbria of the distal fallopian tube. Furthermore, several potential pathways were identified which could be targeted by novel therapies for HGSC. These findings have significant translational relevance for both primary prevention and clinical management of the disease.

Translational AI and Deep Learning in Diagnostic Pathology

There has been an exponential growth in the application of AI in health and in pathology. This is resulting in the innovation of deep learning technologies that are specifically aimed at cellular imaging and practical applications that could transform diagnostic pathology. This paper reviews the different approaches to deep learning in pathology, the public grand challenges that have driven this innovation and a range of emerging applications in pathology. The translation of AI into clinical practice will require applications to be embedded seamlessly within digital pathology workflows, driving an integrated approach to diagnostics and providing pathologists with new tools that accelerate workflow and improve diagnostic consistency and reduce errors. The clearance of digital pathology for primary diagnosis in the US by some manufacturers provides the platform on which to deliver practical AI. AI and computational pathology will continue to mature as researchers, clinicians, industry, regulatory organizations and patient advocacy groups work together to innovate and deliver new technologies to health care providers: technologies which are better, faster, cheaper, more precise, and safe.

GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI

Early childhood growth patterns are associated with adult health, yet the genetic factors and the developmental stages involved are not fully understood. Here, we combine genome-wide association studies with modeling of longitudinal growth traits to study the genetics of infant and child growth, followed by functional, pathway, genetic correlation, risk score, and colocalization analyses to determine how developmental timings, molecular pathways, and genetic determinants of these traits overlap with those of adult health. We found a robust overlap between the genetics of child and adult body mass index (BMI), with variants associated with adult BMI acting as early as 4 to 6 years old. However, we demonstrated a completely distinct genetic makeup for peak BMI during infancy, influenced by variation at the LEPR/LEPROT locus. These findings suggest that different genetic factors control infant and child BMI. In light of the obesity epidemic, these findings are important to inform the timing and targets of prevention strategies.

Abstract 704: RALB GTPase: A critical regulator of DR5 cell surface expression and TRAIL sensitivity in RAS mutant colorectal cancer

RAS mutant (MT) metastatic colorectal cancer (mCRC) remains a difficult-to-treat group. RALA and RALB GTPases function downstream of RAS and have been found to be key regulators of several cell functions and implicated in KRAS-driven tumourigenesis. However, their role as regulators of the apoptotic machinery remains to be elucidated. Here, we found that inhibition of RALB expression, but not RALA, resulted in caspase 8-dependent cell death in KRASMT cells, that was not further increased following MEK1/2 inhibition. Proteomics analysis and mechanistic studies revealed that RALB inhibition induces marked upregulation of the pro-apoptotic cell-surface TRAIL Death Receptor 5 (DR5) receptor in KRASMT CRC. Moreover, DR5 knockout also attenuated siRALB-induced apoptosis, confirming the role of the extrinsic apoptotic pathway as regulator of siRALB-induced cell death. Importantly, TRAIL treatment resulted in acute association of RALB with the death-inducing signalling complex (DISC) and targeting RALB using pharmacologic inhibition or RNAi approaches, resulted in a potent increase in TRAIL-induced cell death in RASMT CRC. Significantly, high RALB mRNA levels were found in the poor prognostic CRIS-B CRC subgroup. Collectively, this study provides the first evidence for a role of RALB in apoptotic priming and that RALB inhibition may be a promising strategy to improve response to TRAIL treatment in poor prognostic RASMT CRC.

Citation Format: Hajrah Khawaja, Jamie Z. Roberts, Arman Javadi, Paul O'Reilly, Darragh McArt, Wendy L. Allen, Markus Morrison, Richard Kennedy, Nicolas Vitale, Patrick G. Johnston, Tim Harrison, Daniel B. Longley, Emma Evergren, Sandra Van Schaeybroeck. RALB GTPase: A critical regulator of DR5 cell surface expression and TRAIL sensitivity in RAS mutant colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 704.

Abstract LB-042: Cancer cell intrinsic gene expression signatures minimize the confounding effects of intratumoral heterogeneity in colorectal cancer patient classification

The application of transcriptional gene signatures to stratify tumors into prognostic and predictive subtypes has evolved rapidly since the original landmark studies demonstrated the clinical utility of this approach in breast cancer. While the number of published signatures continues to increase, the likelihood of individual signatures achieving clinical utility has remained very low, with some estimates putting this figure below 1%. Transcriptional intratumoral heterogeneity (ITH), resulting from variation in stromal components at different regions of a tumor, has been shown to undermine molecular stratification of colorectal cancer (CRC) patients into prognostic and predictive subgroups. The degree of gene expression changes associated with variation in tumor microenvironment (TME) content may even mask the relatively more subtle changes associated with genetic variability and heterogeneity within the tumor epithelium. This variation in TME content, and subsequent ITH, at different regions of the tumor has long been recognised; however, in the era of precision medicine, the implications of such microenvironmental alterations in confounding patient classification are of increased importance.

To examine this issue, a panel of clinically relevant prognostic and predictive transcriptional gene signatures were selected in order to assess the potential for discordant classification of patient samples based on the tumoral region profiled. Using these clinically relevant CRC gene expression signatures, we assessed the susceptibility of each signature to the confounding effects of ITH using gene expression microarray data obtained from multiple tumor regions of a cohort of 24 patients, including central tumor, the tumor invasive front and lymph node metastasis.

Consensus annotated gene lists for each of the gene signatures were used, followed by in silico analysis within our multiregional clinical dataset. Sample clustering alongside correlative assessment revealed variation in the ability of each signature to cluster samples according to patient-of-origin rather than region-of-origin within the multiregion dataset. Signatures focused on cancer-cell intrinsic gene expression were found to produce more clinically useful, patient-centred classifiers, as exemplified by the recently developed CRC intrinsic signature (CRIS), which robustly clustered samples by patient rather than sample region. These findings highlight the potential of cancer-cell intrinsic signatures to reliably stratify CRC patients by minimising the confounding effects of ITH.

In conclusion, our data support the clinical evaluation of signatures based on intrinsic gene expression, such as CRIS, which are unaffected by the confounding variable of transcriptional ITH and therefore have the potential to be used clinically to inform precision medicine decisions, ultimately leading to improved patient outcomes.

Citation Format: Philip D. Dunne, Paul O'Reilly, Aideen Roddy, Matthew Alderdice, Susan Richman, Tim Maughan, Simon McDade, Patrick Johnston, Daniel Longley, Elaine Kay, Darragh McArt, Mark Lawler. Cancer cell intrinsic gene expression signatures minimize the confounding effects of intratumoral heterogeneity in colorectal cancer patient classification [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-042. doi:10.1158/1538-7445.AM2017-LB-042

Seroepidemiological and phylogenetic characterization of neurotropic enteroviruses in Ireland, 2005-2014

Enteroviruses (EVs) are associated with a broad spectrum of clinical presentation, including aseptic meningitis (AM), encephalitis, hand, foot and mouth disease, acute flaccid paralysis, and acute flaccid myelitis. Epidemics occur sporadically and are associated with increased cases of AM in children. The present study describes the seroepidemiological analysis of circulating EVs in Ireland from 2005 to 2014 and phylogenetic characterization of echovirus 30 (E-30), enterovirus A71 (EV-A71), and enterovirus D68 (EV-D68). EV VP1 genotyping was applied to viral isolates and clinical samples, including cerebrospinal fluid (CSF), and those isolates that remained untypeable by neutralising anti-sera. An increase in AM cases from 2010 to 2014 was associated with an E-30 genogroup variant VII and sequences clustered phylogenetically with those detected in AM outbreaks in France and Italy. EV-D68 viral RNA was not detected in CSF samples and no neurological involvement was reported. Three EV-A71 positive CSF samples were identified in patients presenting with AM. A phylogenetic analysis of respiratory-associated EV-D68 and EV-A71 cases in circulation was performed to determine baseline epidemiological data. EV-D68 segregated with clades B and B(1) and EV-A71 clustered as subgenogroup C2. The EV VP1 genotyping method was more sensitive than neutralising anti-sera methods by virus culture and importantly demonstrated concordance between EV genotypes in faecal and CSF samples which should facilitate EV screening by less invasive sampling approaches in AM presentations.

Rotavirus Gastroenteritis is Associated with Increased Morbidity and Mortality in Children with Inherited Metabolic Disorders

Rotavirus is the leading cause of infantile diarrhoea worldwide in children <5 years1. Although mortality rates are low in Ireland, certain populations are more susceptible to the associated morbidity and mortality of infection. A retrospective chart review of 14 patients with confirmed IMDs who were admitted to Temple Street Children's Hospital between 2010 to 2015 with rotavirus infection were compared with 14 randomly selected age matched controls. The median length of stay was 7 days (SD25.3) in IMD patients versus 1.5 days (SD 2.1) in the controls. IV fluids were required on average for 4.5 days (range 0-17) in IMD patients versus 0.63 days (range 0-3) in controls. This report highlights the increased morbidity of rotavirus infection in patients with IMD compared to healthy children. This vulnerable population are likely to benefit from the recent introduction of the rotavirus oral vaccination in October 2016.

An Examination of Polygenic Score Risk Prediction in Individuals With First-Episode Psychosis

BACKGROUND

Polygenic risk scores (PRSs) have successfully summarized genome-wide effects of genetic variants in schizophrenia with significant predictive power. In a clinical sample of first-episode psychosis (FEP) patients, we estimated the ability of PRSs to discriminate case-control status and to predict the development of schizophrenia as opposed to other psychoses.

METHODS

The sample (445 case and 265 control subjects) was genotyped on the Illumina HumanCore Exome BeadChip with an additional 828 control subjects of African ancestry genotyped on the Illumina Multi-Ethnic Genotyping Array. To calculate PRSs, we used the results from the latest Psychiatric Genomics Consortium schizophrenia meta-analysis. We examined the association of PRSs with case-control status and with schizophrenia versus other psychoses in European and African ancestry FEP patients and in a second sample of 248 case subjects with chronic psychosis.

RESULTS

PRS had good discriminative ability of case-control status in FEP European ancestry individuals (9.4% of the variance explained, p < 10^-6), but lower in individuals of African ancestry (R² = 1.1%, p = .004). Furthermore, PRS distinguished European ancestry case subjects who went on to acquire a schizophrenia diagnosis from those who developed other psychotic disorders (R² = 9.2%, p = .002).

CONCLUSIONS

PRS was a powerful predictor of case-control status in a European sample of patients with FEP, even though a large proportion did not have an established diagnosis of schizophrenia at the time of assessment. PRS was significantly different between those case subjects who developed schizophrenia from those who did not, although the discriminative accuracy may not yet be sufficient for clinical utility in FEP.

A Prospective Analysis of the Relationship between Chronic Diseases and Adiposity in older adults: Findings from the Lifeways Cross-Generation Cohort Study of a Thousand Families 2001-2014

This study assesses the relationship between body mass index (BMI) and adult chronic diseases (diabetes mellitus type 2 [DM2], cardiovascular diseases [CVD] and cancers), in grandparents in the Lifeways Cross-Generation Cohort Study. BMI was either measured or reported, at baseline or 10-year follow-up, in 1,244 grandparents. Cumulative morbidity data were recorded at baseline, 3 and 10-year follow-up through questionnaires, General Practice note search, or both. Just over 42% of grandparents were overweight and 32.1% obese. In the multivariate analysis BMI showed a strong linear association with both DM2 (ptrend <0.001) and CVD (ptrend <0.001). There were no significant associations with cancers, but case numbers were small. Results were similar for waist circumference. This prospective study presents novel Irish data and confirms other recent Irish cross-sectional reports on adiposity and adult chronic disease, highlighting the need for effective health promotion interventions in older adults.

Theoretical modeling of the effect of polymer chain immobilization rates on holographic recording in photopolymers

This paper introduces an improved mathematical model for holographic grating formation in an acrylamide-based photopolymer, which consists of partial differential equations derived from physical laws. The model is based on the two-way diffusion theory of [Appl. Opt.43, 2900 (2004)10.1364/AO.43.002900APOPAI1559-128X], which assumes short polymer chains are free to diffuse, and generalizes a similar model presented in [J. Opt. Soc. Am. B27, 197 (2010)10.1364/JOSAB.27.000197JOBPDE0740-3224] by introducing an immobilization rate governed by chain growth and cross-linking. Numerical simulations were carried out in order to investigate the behavior of the photopolymer system for short and long exposures, with particular emphasis on the effect of recording parameters (such as illumination frequency and intensity), as well as material permeability, on refractive index modulation, refractive index profile, and grating distortion. The model reproduces many well-known experimental observations, such as the decrease of refractive index modulation at high spatial frequencies and appearance of higher harmonics in the refractive index profile when the diffusion rate is much slower than the polymerization rate. These properties are supported by a theoretical investigation which uses perturbation techniques to approximate the solution over various time scales.

The Bhutani Nomogram Reduces Incidence of Severe Hyperbilirubinaemia in Term and Near Term Infants

Very high bilirubin levels can have devastating neurodevelopmental effects on infants including hearing loss and cerebral palsy. A previous study in our institution determined the rate of, and factors associated with, bilirubin values above exchange transfusion level. Since this study the Bhutani nomogram was introduced to help identify infants at risk of severe hyperbilirubinaemia. In our study we looked at the initial serum bilirubin taken in infants 36 weeks and 2.5 kgs. Our results show that since this nomogram was introduced there has been a significant reduction in the number of infants reaching exchange transfusion levels. We also showed that the Bhutani nomogram could successfully be used in a population of unknown direct Coombs status.

Mental health service users' experiences of mental health care: an integrative literature review

A number of studies have highlighted issues around the relationship between service users and providers. The recovery model is predominant in mental health as is the recognition of the importance of person-centred practice. The authors completed an in-depth search of the literature to answer the question: What are service users' experiences of the mental health service? Three key themes emerged: acknowledging a mental health problem and seeking help; building relationships through participation in care; and working towards continuity of care. The review adds to the current body of knowledge by providing greater detail into the importance of relationships between service users and providers and how these may impact on the delivery of care in the mental health service. The overarching theme that emerged was the importance of the relationship between the service user and provider as a basis for interaction and support. This review has specific implications for mental health nursing. Despite the recognition made in policy documents for change, issues with stigma, poor attitudes and communication persist. There is a need for a fundamental shift in the provider-service user relationship to facilitate true service-user engagement in their care. The aim of this integrative literature review was to identify mental health service users' experiences of services. The rationale for this review was based on the growing emphasis and requirements for health services to deliver care and support, which recognizes the preferences of individuals. Contemporary models of mental health care strive to promote inclusion and empowerment. This review seeks to add to our current understanding of how service users experience care and support in order to determine to what extent the principles of contemporary models of mental health care are embedded in practice. A robust search of Web of Science, the Cochrane Database, Science Direct, EBSCO host (Academic Search Complete, MEDLINE, CINAHL Plus Full-Text), PsycINFO, PsycARTICLES, Social Sciences Full Text and the United Kingdom and Ireland Reference Centre for data published between 1 January 2008 and 31 December 2012 was completed. The initial search retrieved 272 609 papers. The authors used a staged approach and the application of predetermined inclusion/exclusion criteria, thus the numbers of papers for inclusion were reduced to 34. Data extraction, quality assessment and thematic analysis were completed for the included studies. Satisfaction with the mental health service was moderately good. However, accessing services could be difficult because of a lack of knowledge and the stigma surrounding mental health. Large surveys document moderate satisfaction ratings; however, feelings of fear regarding how services function and the lack of treatment choice remain. The main finding from this review is while people may express satisfaction with mental health services, there are still issues around three main themes: acknowledging a mental health problem and seeking help; building relationship through participation and care; and working towards continuity of care. Elements of the recovery model appear to be lacking in relation to user involvement, empowerment and decision making. There is a need for a fundamental shift in the context of the provider-service user relationship to fully facilitate service users' engagement in their care.

Enediynyl peptides and iso-coumarinyl methyl sulfones as inhibitors of proprotein convertases PCSK8/SKI-1/S1P and PCSK4/PC4: Design, synthesis and biological evaluations

The proprotein convertases PCSK8 and PCSK4 are, respectively, the 8th and 4th members of Ca(+2)-dependent serine endoprotease of Proprotein Convertase Subtilisin Kexin (PCSK) super family structurally related to the bacterial subtilisin and yeast kexin. The membrane bound PCSK8 (also called SKI-1 or S1P) is implicated in sterol regulation and lipid synthesis via its role in the maturation of human (h) SREBP-2. It also plays role in cartilage formation, bone mineralization, as well as viral pathogenesis. On the other hand, PCSK4 has been linked to mammalian fertilization and placenta growth. Owing to these findings, interest has grown to develop specific inhibitors against these enzymes for potential biochemical and therapeutic applications. In this study we developed two types of small molecule inhibitors of PCSK8 and PCSK4 and demonstrated their anti-proteolytic activities in vitro cell-free and in vitro cell culture systems. These are isocoumarinyl methyl sulfone derivatives and enediyne amino acid containing peptides. Our in vitro data suggested that one of the 7 sulfone derivatives (methyl phenyl sulfone) inhibited PCSK8 with inhibition constant Ki ∼255μM. It also blocked PCSK8-mediated processing of hSREBP-2 in HepG2 cell in a concentration-dependent manner. However all 7 iso-coumarinyl methyl sulfones inhibited htrypsin with IC50 ranging from 2 to 165μM. In contrast, all our designed enediynyl peptides inhibited PCSK8 and PCSK4 activity with Ki and IC50 in low μM or high nM ranges. All compounds exhibited competitive inhibition as indicated by their enzyme kinetic plots and observed dependence of IC50 value on substrate concentration. Our study confirmed that incorporation at the substrate cleavage site of 'Enediyne amino acid' generates potent inhibitors of PCSK8 and PCSK4. This represents a novel approach for future development of inhibitors of PCSK or other enzymes.

LDL-R promoting activity of peptides derived from human PCSK9 catalytic domain (153-421): design, synthesis and biochemical evaluation

BACKGROUND

High level of Low Density Lipoprotein-Cholesterol (LDL-C) in circulation in the blood is associated with an elevated risk of cardiovascular disease (CVD) and stroke. Currently the statin drugs which inhibit the enzyme HMG-CoA reductase responsible for cholesterol synthesis in the liver are very effective in lowering LDL-cholesterol. However these drugs are often associated with serious side effects particularly for ∼10-12% of cases. Therefore there is a need to develop non-statin based cholesterol reducing agents. Recently it was revealed that the secreted Proprotein Convertase Subtilisin Kexin 9 (PCSK9) binds with LDL-receptor (LDL-R) causing its degradation in the lysosome with the result of LDL-C accumulating in the blood. Thus PCSK9 has become an alternative target for development of non-statin cholesterol reducing agents. It is established that the catalytic domain of PCSK9 (aa153-421) and the EGF-A domain of LDL-R (aa314-355) are involved in the above bind leading to the reduction of LDL-R level and accumulation of LDL-C.

OBJECTIVE

The major goal of this study is to identify peptide/s from the catalytic domain of hPCSK9 that can block the binding of hPCSK9 and LDL-R and therefore can reduce LDL-R degradation leading to the clearance of LDL-C from the plasma.

RESULTS

Using 51 synthetic linear peptides (P1-P51) of 15aa long with 10 amino acids overlapping sequences spanning the entire catalytic segment of hPCSK9 (aa153-421), we identified two domains of hPCSK9 namely (aa323-358) and (aa365-384) that exhibited strong binding affinity towards synthetic EGF-A peptide. The results were based on mass spectrometry, fluorescence spectroscopy and native gel electrophoresis. Thus peptides containing the above segments in part (P35-P39 and P42-P47) exhibited LDL-R promoting activity when added exogenously to culture medium of growing human hepatic cells like HepG2 and HuH7. The effects were particularly significant with peptides P36, P37, P46 and P47. Interestingly, the first two peptides are present within the disulphide loop Cys(323)-Cys(358) and contain the key gain of function mutation D(374)/Y site while the last two peptides contain another disulphide bridge loop Cys(375)-Cys(378) and the second most potent gain of function mutation R(357)/H. Further studies revealed that S-S bridged cyclic loop peptide hPCSK9(365-384) exhibited the highest (∼3.5-fold) LDL-R promoting activity in both HepG2 and HuH7 when applied at 5 μM concentration level. This effect is completely abrogated when one of the Cys residues is substituted by Ala thereby preventing any S-S bond formation. This suggested its critical role in the bioactivity. It is proposed that LDL-R promoting activity of this and other selected PCSK9 catalytic peptides such as P36, P37, P46 and P47 are most likely mediated via intervention of PCSK9:LDL-R complex formation. Our findings may find useful application in future development of small molecule PCSK9 inhibitors for intervention of hypercholesterolemia and associated cardiovascular disease.

Co-acting gene networks predict TRAIL responsiveness of tumour cells with high accuracy

Background

Identification of differentially expressed genes from transcriptomic studies is one of the most common mechanisms to identify tumor biomarkers. This approach however is not well suited to identify interaction between genes whose protein products potentially influence each other, which limits its power to identify molecular wiring of tumour cells dictating response to a drug. Due to the fact that signal transduction pathways are not linear and highly interlinked, the biological response they drive may be better described by the relative amount of their components and their functional relationships than by their individual, absolute expression.

Results

Gene expression microarray data for 109 tumor cell lines with known sensitivity to the death ligand cytokine tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) was used to identify genes with potential functional relationships determining responsiveness to TRAIL-induced apoptosis. The machine learning technique Random Forest in the statistical environment “R” with backward elimination was used to identify the key predictors of TRAIL sensitivity and differentially expressed genes were identified using the software GeneSpring. Gene co-regulation and statistical interaction was assessed with q-order partial correlation analysis and non-rejection rate. Biological (functional) interactions amongst the co-acting genes were studied with Ingenuity network analysis. Prediction accuracy was assessed by calculating the area under the receiver operator curve using an independent dataset. We show that the gene panel identified could predict TRAIL-sensitivity with a very high degree of sensitivity and specificity (AUC = 0 · 84). The genes in the panel are co-regulated and at least 40% of them functionally interact in signal transduction pathways that regulate cell death and cell survival, cellular differentiation and morphogenesis. Importantly, only 12% of the TRAIL-predictor genes were differentially expressed highlighting the importance of functional interactions in predicting the biological response.

Conclusions

The advantage of co-acting gene clusters is that this analysis does not depend on differential expression and is able to incorporate direct- and indirect gene interactions as well as tissue- and cell-specific characteristics. This approach (1) identified a descriptor of TRAIL sensitivity which performs significantly better as a predictor of TRAIL sensitivity than any previously reported gene signatures, (2) identified potential novel regulators of TRAIL-responsiveness and (3) provided a systematic view highlighting fundamental differences between the molecular wiring of sensitive and resistant cell types.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1144) contains supplementary material, which is available to authorized users.

The South Asian genome

The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.

Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression

MOTIVATION

A typical genome-wide association study searches for associations between single nucleotide polymorphisms (SNPs) and a univariate phenotype. However, there is a growing interest to investigate associations between genomics data and multivariate phenotypes, for example, in gene expression or metabolomics studies. A common approach is to perform a univariate test between each genotype-phenotype pair, and then to apply a stringent significance cutoff to account for the large number of tests performed. However, this approach has limited ability to uncover dependencies involving multiple variables. Another trend in the current genetics is the investigation of the impact of rare variants on the phenotype, where the standard methods often fail owing to lack of power when the minor allele is present in only a limited number of individuals.

RESULTS

We propose a new statistical approach based on Bayesian reduced rank regression to assess the impact of multiple SNPs on a high-dimensional phenotype. Because of the method's ability to combine information over multiple SNPs and phenotypes, it is particularly suitable for detecting associations involving rare variants. We demonstrate the potential of our method and compare it with alternatives using the Northern Finland Birth Cohort with 4702 individuals, for whom genome-wide SNP data along with lipoprotein profiles comprising 74 traits are available. We discovered two genes (XRCC4 and MTHFD2L) without previously reported associations, which replicated in a combined analysis of two additional cohorts: 2390 individuals from the Cardiovascular Risk in Young Finns study and 3659 individuals from the FINRISK study.

AVAILABILITY AND IMPLEMENTATION

R-code freely available for download at http://users.ics.aalto.fi/pemartti/gene_metabolome/.

Distinct roles for Ste20-like kinase SLK in muscle function and regeneration

BACKGROUND

Cell growth and terminal differentiation are controlled by complex signaling systems that regulate the tissue-specific expression of genes controlling cell fate and morphogenesis. We have previously reported that the Ste20-like kinase SLK is expressed in muscle tissue and is required for cell motility. However, the specific function of SLK in muscle tissue is still poorly understood.

METHODS

To gain further insights into the role of SLK in differentiated muscles, we expressed a kinase-inactive SLK from the human skeletal muscle actin promoter. Transgenic muscles were surveyed for potential defects. Standard histological procedures and cardiotoxin-induced regeneration assays we used to investigate the role of SLK in myogenesis and muscle repair.

RESULTS

High levels of kinase-inactive SLK in muscle tissue produced an overall decrease in SLK activity in muscle tissue, resulting in altered muscle organization, reduced litter sizes, and reduced breeding capacity. The transgenic mice did not show any differences in fiber-type distribution but displayed enhanced regeneration capacity in vivo and more robust differentiation in vitro.

CONCLUSIONS

Our results show that SLK activity is required for optimal muscle development in the embryo and muscle physiology in the adult. However, reduced kinase activity during muscle repair enhances regeneration and differentiation. Together, these results suggest complex and distinct roles for SLK in muscle development and function.

SLK-mediated phosphorylation of paxillin is required for focal adhesion turnover and cell migration

Focal adhesion turnover is a complex process required for cell migration. We have previously shown that the Ste20-like kinase (SLK) is required for cell migration and efficient focal adhesion (FA) turnover in a FA kinase (FAK)-dependent manner. However, the role of SLK in this process remains unclear. Using a candidate substrate approach, we show that SLK phosphorylates the adhesion adapter protein paxillin on serine 250. Serine 250 phosphorylation is required for paxillin redistribution and cell motility. Mutation of paxillin serine 250 prevents its phosphorylation by SLK in vitro and results in impaired migration in vivo as evidenced by an accumulation of phospho-FAK-Tyr397 and altered FA turnover rates. Together, our data suggest that SLK phosphorylation of paxillin on serine 250 is required for FAK-dependent FA dynamics.

Deaths associated with human adenovirus-14p1 infections, Europe, 2009-2010

Human adenovirus (HAdV) serotype 14 is rarely identified. However, an emerging variant, termed HAdV-14p1, recently has been described in the United States in association with outbreaks of acute respiratory disease with high rates of illness and death. We retrospectively analyzed specimens confirmed positive for HAdV by immunofluorescence, virus culture, or real-time PCR during July 1, 2009-July 31, 2010, and describe 9 cases of HAdV-14p1 infection with characteristic mutations in the fiber and E1A genes that are phylogenetically indistinguishable from the viruses previously detected in the United States. Three patients died; 2 were immunocompromised, and 1 was an immunocompetent adult. We propose that surveillance should be increased for HAdV-14p1 and recommend that this virus be considered in the differential diagnosis of sudden-onset acute respiratory disease, particularly fatal infections, for which an etiology is not clear.

The Ldb1 and Ldb2 transcriptional cofactors interact with the Ste20-like kinase SLK and regulate cell migration

Cell migration involves a multitude of signals that converge on cytoskeletal reorganization, essential for development, immune responses, and tissue repair. Here, we show that the microtubule-associated Ste20 kinase SLK, required for cell migration, interacts with the LIM domain binding transcriptional cofactor proteins Ldb1/CLIM2 and Ldb2/CLIM1/NLI. We demonstrate that Ldb1 and 2 bind directly to the SLK carboxy-terminal AT1-46 homology domain in vitro and in vivo. We find that Ldb1 and -2 colocalize with SLK in migrating cells and that both knockdown and overexpression of either factor results in increased motility. Supporting this, knockdown of Ldb1 increases focal adhesion turnover and enhances migration in fibroblasts. We propose that Ldb1/2 function to maintain SLK in an inactive state before its activation. These findings highlight a novel function for Ldb1 and -2 and expand their role to include the control of cell migration.

The Ste20-like kinase SLK is required for ErbB2-driven breast cancer cell motility

The Ste20-like kinase, SLK, is involved in the control of cell motility through its effects on actin reorganization and focal adhesion turnover. Here we investigated the role of SLK in chemotaxis downstream of the tyrosine kinase receptor, HER2/ErbB2/Neu, which is frequently overexpressed in human breast cancers. Our results show that SLK is required for the efficient cell migration of human and mouse mammary epithelial cell lines in the presence of the Neu activator, heregulin, as a chemoattractant. SLK activity is stimulated by heregulin treatment or by overexpression of activated Neu. Phosphorylation of tyrosine 1201 or tyrosines 1226/7 on Neu is a key event for SLK activation and cell migration, and cancer cell invasion mediated by these tyrosines is inhibited by kinase-inactive SLK. Signaling pathway inhibitors show that Neu-mediated SLK activation is dependent on MEK, PI3K, PLCgamma and Shc signaling. Furthermore, heregulin-stimulated SLK activity requires signals from the focal adhesion proteins, FAK and src. Finally, phospho-FAK analysis shows that SLK is required for Neu-dependent focal adhesion turnover. Together, these studies define an interaction between Neu and SLK signaling in the regulation of cancer cell motility.

Clarithromycin with low dose dexamethasone and thalidomide is effective therapy in relapsed/refractory myeloma

A combination of clarithromycin, low dose of thalidomide and low dose dexamethasone was used in a phase II study to treat patients with relapsed and refractory myeloma. Thirty patients received clarithromycin 250 mg twice daily and thalidomide 50 mg at night on an ongoing basis with 4-d pulses of 10 mg dexamethasone given monthly. Eight patients had permitted escalation of thalidomide dosage up to 200 mg daily. The combination was well tolerated and could be given to elderly, infirm and severely cytopenic patients. Response rates were high, with 89% achieving at least 50% reduction in paraprotein and a 96% overall response rate. Although clarithromycin has only minimal anti-myeloma properties when used as a single agent, its combination with thalidomide and dexamethasone appears very effective, allowing these to be used in lower and more tolerable doses with good clinical effects.

A comparative study of the effect of hydrogen peroxide versus normal saline on the strength of the bone-cement interface

Hydrogen peroxide has been used for decades as an effervescent haemostatic agent in arthroplasty. Recently it has been shown to adversely affect the material properties of PMMA. We aim to assess whether any such deleterious effects are demonstrated in an experimental model which mimics the clinical use of hydrogen peroxide. Matched pairs of cancellous bone samples were treated with a swab soaked in either saline or a 3% solution of hydrogen peroxide, prior to manufacture of cement-bone constructs using Palacos or Simplex cement. Thirty pairs were then compared by subjecting them to a torsional shear force until failure and a further thirty pairs were tested to failure in tension. There was no significant difference between the mean torques to failure for the Palacos-peroxide group versus the Palacos-saline group, or the Simplex-peroxide versus the Simplex-saline group (p=0.31 and 0.71 respectively). Similarly there was no significant difference between the mean tension loads to failure for the Palacos-peroxide group versus the Palacos-saline group, and the Simplex-peroxide versus the Simplex-saline group (p=0.79 and 0.23 respectively). We conclude that the use of hydrogen peroxide as an effervescent haemostatic agent has no detrimental effect on the mechanical integrity of the bone-cement interface when compared to normal saline.

Comparison of the efficacies of disinfectants to control microbial contamination in dental unit water systems in general dental practices across the European Union

Water delivered by dental unit water systems (DUWS) in general dental practices can harbor high numbers of bacteria, including opportunistic pathogens. Biofilms on tubing within DUWS provide a reservoir for microorganisms and should be controlled. This study compared disinfection products for their ability to meet the American Dental Association's guideline of <200 CFU x ml(-1) for DUWS water. Alpron, BioBlue, Dentosept, Oxygenal, Sanosil, Sterilex Ultra, and Ster4Spray were tested in DUWS (n = 134) in Denmark, Germany, Greece, Ireland, The Netherlands, Spain, and the United Kingdom. Weekly water samples were tested for total viable counts (TVCs) on yeast extract agar, and, where possible, the effects of products on established biofilm (TVCs) were measured. A 4- to 5-week baseline measurement period was followed by 6 to 8 weeks of disinfection (intermittent or continuous product application). DUWS water TVCs before disinfection ranged from 0 to 5.41 log CFU x ml(-1). Disinfectants achieved reductions in the median water TVC ranging from 0.69 (Ster4Spray) to 3.11 (Dentosept) log CFU x ml(-1), although occasional high values (up to 4.88 log CFU x ml(-1)) occurred with all products. Before treatment, 64% of all baseline samples exceeded American Dental Association guidelines, compared to only 17% following commencement of treatment; where tested, biofilm TVCs were reduced to below detectable levels. The antimicrobial efficacies of products varied (e.g., 91% of water samples from DUWS treated with Dentosept or Oxygenal met American Dental Association guidelines, compared to 60% of those treated with Ster4Spray). Overall, the continuously applied products performed better than those applied intermittently. The most effective products were Dentosept and Oxygenal, although Dentosept gave the most consistent and sustained antimicrobial effect over time.

Microbial contamination of dental unit water systems

INTRODUCTION

Dental unit water systems (DUWS) may serve as a reservoir for biofilms that contribute to high numbers of bacteria in the water used during dental treatment. These microbes are predominantly harmless but potentially pathogenic organisms can also be present in the biofilm. This may pose a potential health risk for patients and dental personnel.

AIM

to determine the microbial levels of DUWS in dental practices.

MATERIALS AND METHOD

A cross-sectional study of water and tubing samples from 30 general dental practices (15 health board and 15 private surgeries) was undertaken as part of a pan-European investigation of the microbial qualitative and quantitative aspects of DUWS.

RESULTS

Microbial loads ranged from 100 to 104 cfu ml-1 and exceeded the European guidelines for drinking water in many cases. The available evidence suggested the presence of isolates most likely belonging to families of aquatic and soil bacteria. It was not possible to draw distinct conclusions correlating microbial loads with dental unit parameters, including age of the unit, water source and chemistry and presence or absence of anti-retraction devices. Opportunistic or true pathogens were not detected. Yeasts were observed in samples from three units although further analysis confirmed that these were not Candida albicans. A decontamination strategy applied to one of the units eliminated the yeasts completely.

CONCLUSIONS

Dental practitioners must be knowledgeable regarding microbial contamination and biofilm formation in dental unit waterlines. There is a need for development of European evidence-based guidelines and reliable control regimes for microbial contamination of DUWS.

The fatigue strength of compact bone in torsion

We have conducted a series of fatigue tests on samples of bovine compact bone loaded in cyclic torsion. The fatigue strength (i.e. the range of stress needed to cause failure in a given number of cycles) was found to be lower than the fatigue strength of the same material in compression by more than a factor of two. We also tested intact chicken metatarsals and found a similar reduction in strength compared to compression testing of chicken tibiae. These results were predicted using a theoretical model in which fatigue failure was assumed to be dependent on the growth of microcracks, oriented approximately parallel to the bone's longitudinal axis but having misorientation angles of up to 30 degrees. An effective stress range was derived which is a function of the normal and shear stresses, and thus of the Mode I and Mode II stress intensities experienced by the crack. These results may have important consequences for the understanding of fatigue in bone in vivo; relatively small amounts of longitudinal shear stress, which are often ignored in analysis, may contribute significantly to fatigue failures. This may shed light on the phenomenon of stress fractures and on the need for repair and adaptation in living bone.