The reliability of immunohistochemistry as a prescreening method for the diagnosis of hereditary nonpolyposis colorectal cancer (HNPCC) - Results of an international collaborative study

Hereditary nonpolyposis colorectal cancer syndrome (HNPCC) is an autosomal dominant condition accounting for 2–5% of all colorectal carcinomas as well as a small subset of endometrial, upper urinary tract and other gastrointestinal cancers. An assay to detect the underlying defect in HNPCC, inactivation of a DNA mismatch repair enzyme, would be useful in identifying HNPCC probands. Monoclonal antibodies against hMLH1 and hMSH2, two DNA mismatch repair proteins which account for most HNPCC cancers, are commercially available. This study sought to investigate the potential utility of these antibodies in determining the expression status of these proteins in paraffin-embedded formalin-fixed tissue and to identify key technical protocol components associated with successful staining. A set of 20 colorectal carcinoma cases of known hMLH1 and hMSH2 mutation and expression status underwent immunoperoxidase staining at multiple institutions, each of which used their own technical protocol. Staining for hMSH2 was successful in most laboratories while staining for hMLH1 proved problematic in multiple labs. However, a significant minority of laboratories demonstrated excellent results including high discriminatory power with both monoclonal antibodies. These laboratories appropriately identified hMLH1 or hMSH2 inactivation with high sensitivity and specificity. The key protocol point associated with successful staining was an antigen retrieval step involving heat treatment and either EDTA or citrate buffer. This study demonstrates the potential utility of immunohistochemistry in detecting HNPCC probands and identifies key technical components for successful staining.

Implicaciones del uso de fuentes exógenas de fitasa sobre los rendimientos productivos y valor nutricional de las dietas en aves. Repercusiones medioambientales

En los últimos años, y debido a un aumento de las producciones intensivas de cerdos y aves en el marco de la UE, se han desarrollado muchos estudios intentando minimizar el impacto contaminante del exceso de nitrógeno y fósforo que las deyecciones de estos animales producen en el medio ambiente. La disminución del contenido de N procedente de las deyecciones se ha abordado con diferentes estrategias nutricionales (formulación con aminoácidos disponibles, mejora de la utilización de la proteína con diferentes enzimas, etc.). El fósforo es un mineral imprescindible para el crecimiento de los animales, debido a su influencia en el ciclo energético, en la formación de huesos y como regulador de la ingesta. El fósforo presente en los vegetales (base de la alimentación de las aves) se encuentra básicamente formando el ácido fítico, muy poco asimilable por los animales. Por tal motivo, se suplementan las dietas con fósforo inorgánico, a menudo en exceso, que en parte revierte al medio ambiente, dando lugar a problemas medioambientales en áreas de gran concentración de producciones intensivas de animales. En la ultima década se ha estudiado el efecto que la incorporación de la enzima fitasa produce en el aumento de la biodisponibilidad del fósforo fítico (Kornegay et al., 1996), con lo que se reduce la cantidad de fósforo inorgánico añadido a las dietas y, por tanto, la disminución del fósforo excretado. Se ha descrito que la incorporación de este enzima produce ademas mejoras de la disponibilidad de otros minerales (calcio, zinc, cobre, hierro, etc.) (Broz et al., 1994; Schoner et al., 1991; Roberson and Edwards, 1994; Yi et al., 1997; Sebastian et al., 1996), pero dependientes del nivel de calcio y de vitamina D3 (Qian et al., 1996; Qian et al., 1997; Edwards, 1993; Lei et al., 1994), y de la fuente de fibra (Ravindran et al. 1995). También se han descrito mejoras en la digestibilidad de la proteína y los aminoácidos (Yi et al., 1996a; Mroz et al., 1994) , aunque en este campo existe cierta controversia, ya que la respuesta depende de la cantidad y procedencia del ácido fitico de la dieta (O’Dell and Boland, 1976). Sin embargo, casi todos los ensayos se han realizado con dietas a base de maíz-soja, en tanto que a nivel de la UE cada vez más se utilizan otro tipo de ingredientes para las raciones (trigo, cebada, girasol, guisantes, subproductos, etc.). Algunos de estos ingredientes se caracterizan por tener una actividad fitasa endógena nada despreciable (Eeckout and De Paepe, 1994) que, en general, no se ha tenido en cuenta, pero que puede verse afectada en los procesos de granulación. Por otro lado, los efectos beneficiosos de la adición de fitasa a las dietas parecen ser, en ocasiones, más importantes en los aumentos de consumo y mejores índices de conversión que en los derivados de la propia liberación del fósforo, es decir, en los llamados “side effects”, (básicamente, mejora de parámetros productivos, del valor de energía de las dietas, de la utilización de diversos minerales, y de la proteína), aunque existe una gran controversia en algunos de estos efectos. Existen muy pocos estudios sobre el papel de la fibra y otros hidratos de carbono en la actuación de estos enzima (interacción positiva o negativa).

Essential Bacillus subtilis genes.

To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximately 4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden-Meyerhof-Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life.

A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium

Genome-wide association studies (GWAS) have been successful in identifying common genetic variation involved in susceptibility to etiologically complex disease. We conducted a GWAS to identify common genetic variation involved in susceptibility to upper aero-digestive tract (UADT) cancers. Genome-wide genotyping was carried out using the Illumina HumanHap300 beadchips in 2,091 UADT cancer cases and 3,513 controls from two large European multi-centre UADT cancer studies, as well as 4,821 generic controls. The 19 top-ranked variants were investigated further in an additional 6,514 UADT cancer cases and 7,892 controls of European descent from an additional 13 UADT cancer studies participating in the INHANCE consortium. Five common variants presented evidence for significant association in the combined analysis (p≤5×10−7). Two novel variants were identified, a 4q21 variant (rs1494961, p = 1×10−8) located near DNA repair related genes HEL308 and FAM175A (or Abraxas) and a 12q24 variant (rs4767364, p = 2×10−8) located in an extended linkage disequilibrium region that contains multiple genes including the aldehyde dehydrogenase 2 (ALDH2) gene. Three remaining variants are located in the ADH gene cluster and were identified previously in a candidate gene study involving some of these samples. The association between these three variants and UADT cancers was independently replicated in 5,092 UADT cancer cases and 6,794 controls non-overlapping samples presented here (rs1573496-ADH7, p = 5×10−8; rs1229984-ADH1B, p = 7×10−9; and rs698-ADH1C, p = 0.02). These results implicate two variants at 4q21 and 12q24 and further highlight three ADH variants in UADT cancer susceptibility.

Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.

The European Prospective Investigation into Cancer and nutrition (EPIC) is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS) and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88%) performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies.

Genome-wide association study identifies variants associated with progression of liver fibrosis from HCV infection.

Polymorphisms in IL28B were shown to affect clearance of hepatitis C virus (HCV) infection in genome-wide association (GWA) studies. Only a fraction of patients with chronic HCV infection develop liver fibrosis, a process that might also be affected by genetic factors. We performed a 2-stage GWA study of liver fibrosis progression related to HCV infection. We studied well-characterized HCV-infected patients of European descent who underwent liver biopsies before treatment. We defined various liver fibrosis phenotypes on the basis of METAVIR scores, with and without taking the duration of HCV infection into account. Our GWA analyses were conducted on a filtered primary cohort of 1161 patients using 780,650 single nucleotide polymorphisms (SNPs). We genotyped 96 SNPs with P values <5 × 10(-5) from an independent replication cohort of 962 patients. We then assessed the most interesting replicated SNPs using DNA samples collected from 219 patients who participated in separate GWA studies of HCV clearance. In the combined cohort of 2342 HCV-infected patients, the SNPs rs16851720 (in the total sample) and rs4374383 (in patients who received blood transfusions) were associated with fibrosis progression (P(combined) = 8.9 × 10(-9) and 1.1 × 10(-9), respectively). The SNP rs16851720 is located within RNF7, which encodes an antioxidant that protects against apoptosis. The SNP rs4374383, together with another replicated SNP, rs9380516 (P(combined) = 5.4 × 10(-7)), were linked to the functionally related genes MERTK and TULP1, which encode factors involved in phagocytosis of apoptotic cells by macrophages. Our GWA study identified several susceptibility loci for HCV-induced liver fibrosis; these were linked to genes that regulate apoptosis. Apoptotic control might therefore be involved in liver fibrosis.

Toxicity screenings of nanomaterials: challenges due to interference with assay processes and components of classic in vitro tests.

Given the multiplicity of nanoparticles (NPs), there is a requirement to develop screening strategies to evaluate their toxicity. Within the EU-funded FP7 NanoTEST project, a panel of medically relevant NPs has been used to develop alternative testing strategies of NPs used in medical diagnostics. As conventional toxicity tests cannot necessarily be directly applied to NPs in the same manner as for soluble chemicals and drugs, we determined the extent of interference of NPs with each assay process and components. In this study, we fully characterized the panel of NP suspensions used in this project (poly(lactic-co-glycolic acid)-polyethylene oxide [PLGA-PEO], TiO2, SiO2, and uncoated and oleic-acid coated Fe3O4) and showed that many NP characteristics (composition, size, coatings, and agglomeration) interfere with a range of in vitro cytotoxicity assays (WST-1, MTT, lactate dehydrogenase, neutral red, propidium iodide, (3)H-thymidine incorporation, and cell counting), pro-inflammatory response evaluation (ELISA for GM-CSF, IL-6, and IL-8), and oxidative stress detection (monoBromoBimane, dichlorofluorescein, and NO assays). Interferences were assay specific as well as NP specific. We propose how to integrate and avoid interference with testing systems as a first step of a screening strategy for biomedical NPs.

Towards an alternative testing strategy for nanomaterials used in nanomedicine: Lessons from NanoTEST.

In spite of recent advances in describing the health outcomes of exposure to nanoparticles (NPs), it still remains unclear how exactly NPs interact with their cellular targets. Size, surface, mass, geometry, and composition may all play a beneficial role as well as causing toxicity. Concerns of scientists, politicians and the public about potential health hazards associated with NPs need to be answered. With the variety of exposure routes available, there is potential for NPs to reach every organ in the body but we know little about the impact this might have. The main objective of the FP7 NanoTEST project ( www.nanotest-fp7.eu ) was a better understanding of mechanisms of interactions of NPs employed in nanomedicine with cells, tissues and organs and to address critical issues relating to toxicity testing especially with respect to alternatives to tests on animals. Here we describe an approach towards alternative testing strategies for hazard and risk assessment of nanomaterials, highlighting the adaptation of standard methods demanded by the special physicochemical features of nanomaterials and bioavailability studies. The work has assessed a broad range of toxicity tests, cell models and NP types and concentrations taking into account the inherent impact of NP properties and the effects of changes in experimental conditions using well-characterized NPs. The results of the studies have been used to generate recommendations for a suitable and robust testing strategy which can be applied to new medical NPs as they are developed.

Prescription médicamenteuse inappropriée: les nouveaux critères STOPP/START [Prescribing inappropriate medication: the new STOPP/START criteria].

Prescribing inappropriate medication (PIM) is a common public health problem. Mainly due to associated adverse drugs events (ADE), it results in major morbidity and mortality, as well as increased healthcare utilization. For a long time, the systematic review of medications prescribed appeared as a solution for limiting PIM and the ADE associated with such prescriptions. With this aim and since 2008, the list of STOPP-START criteria has appeared as attractive in its design, as well as logical and easy to use. The initial version has just been updated and improved. After having detailed all improvements provided to the 2008 version, we present the result of its adaptation into French language by a group of French-speaking expert from Belgium, Canada, France, and Switzerland.

Les critères STOPP/START.v2 : adaptation en langue française. [STOPP/START.v2 criteria: Adaptation into French language]

Objectif STOPP/START est un outil de détection de la prescription médicamenteuse potentiellement inappropriée chez la personne de 65 ans ou plus. La version initiale de 2008 vient d'être mise à jour et améliorée par ses auteurs. Nous en présentons l'adaptation et la validation en langue française. Méthodes L'adaptation en français de l'outil STOPP/START.v2 a été réalisée par deux experts, confirmée par la méthode de traduction-inverse, et finalisée d'après les commentaires de neufs évaluateurs francophones, gériatres, pharmaciens cliniciens, et médecin généraliste de quatre pays (France, Belgique, Suisse, Canada). La validation a été complétée par une analyse de concordance inter-juge (CCI) des critères STOPP/START.v2 appliqués à dix vignettes cliniques standardisées. Résultats Les 115 critères de STOPP/START.v2 en français sont, par rapport à la version originale anglaise, identiques par leur classification mais adaptés en termes de présentation (critères START.v2 commençant par la condition clinique, et accompagnés par une justification du caractère inapproprié de l'omission) voire de formulation de certains critères. Cette adaptation en français est validée par (i) la traduction-inverse montrant le respect du sens clinique de la version originale, (ii) l'identification semblable des critères lorsque appliqués à dix vignettes cliniques par les neuf évaluateurs, et (iii) le haut niveau de concordance de ces neuf évaluations tant pour STOPP.v2 (CCI 0,849) que pour START.v2 (CCI 0,921). Conclusion L'adaptation en langue française des critères STOPP/START.v2 fournit aux cliniciens un outil de détection de la prescription médicamenteuse potentiellement inappropriée chez les personnes de 65 ans et plus qui est logique, fiable et facile à utiliser. Objective STOPP/START is a screening tool to detect potentially inappropriate prescribing in persons aged 65 or older. Its Irish authors recently updated and improved the initially published version of 2008. We present the adaptation and validation into French language of this updated tool. Methods STOPP/START.v2 was adapted into French by two experts, then confirmed by a translation-back translation method and finalised according to the comments of nine French-speaking assessors - geriatricians, pharmacologists and a general physician - from four countries (France, Belgium, Switzerland, and Canada). The validation was completed by an inter-rater reliability (IRR) analysis of the STOPP/START.v2 criteria applied to 10 standardized clinical vignettes. Results In comparison to the original English version, the 115 STOPP/START.v2 criteria in French language classify in identical manner, but the presentation has been adjusted (START.v2 first specifies the clinical condition followed by an explanation of the inappropriateness of the prescription or omission). This adaptation into French language was validated by means of (i) the translation/back-translation, which showed that the French version complied with the clinical meaning of the original criteria; (ii) the similar screening results when applied by the nine specialists to the 10 cases; and (iii) the high level of inter-rater reliability of these 9 evaluations, for both STOPP (IRR 0.849) and START.v2 (IRR 0.921). Conclusion The adaptation into French of the STOPP/START.v2 criteria provides clinicians with a screening tool to detect potentially inappropriate prescribing in patients aged 65 and older that is more logical, more reliable and easier to use.