Maria Giovanna Valente

RFID as a new ICT tool to monitor specimen life cycle and quality control in a biobank

Background Biospecimen quality is crucial for clinical and translational research and its loss is one of the main obstacles to experimental activities. Beside the quality of samples, preanalytical variations render the results derived from specimens of different biobanks or even within the same biobank incomparable. Specimens collected along the years should be managed with a heterogeneous life cycle. Hence, we propose to collect detailed data concerning the whole life cycle of stored samples employing radio-frequency identification (RFID) technology. Methods We describe the processing chain of blood biosamples that is operative at the biobank of IRCSS San Raffaele, Rome, Italy (BioBIM). We focus on the problem of tracing the stages following automated preanalytical processing: we collected the time stamps of all events that could affect the biological quality of the specimens by means of RFID tags and readers. Results We developed a pilot study on a fragment of the life cycle, namely the storage between the end of the preanalytics and the beginning of the analytics, which is usually not traced by automated tools because it typically includes manual handling. By adopting RFID devices we identified the possible critical time delays. At 1, 3 and 6 months RFID-tagged specimens cryopreserved at -80°C were successfully read. Conclusions We were able to record detailed information about the storage phases and a fully documented specimen life cycle. This will allow us to promote and tune up the best practices in biobanking because i) it will be possible to classify sample features with a sharper resolution, which allows future utilization of stored material; ii) cost-effective policies can be adopted in processing, storing and selecting specimens; iii) after using each aliquot, we can study the life cycle of the specimen with a possible feedback on the procedures.

Venous thromboembolism risk prediction in ambulatory cancer patients: Clinical significance of neutrophil/lymphocyte ratio and platelet/lymphocyte ratio

Neutrophil/lymphocyte (NLR) and platelet/lymphocyte (PLR) ratios might represent a yet unrecognized risk factor for venous thromboembolism (VTE) in cancer out‐patients receiving chemotherapy. Accordingly, this study was aimed at analyzing the significance of these novel markers in the risk prediction of a first VTE episode in a population representative of a general practice cohort. To this purpose, a mono‐institutional cohort study was conducted to retrospectively analyze NLR and PLR in 810 consecutive cancer out‐patients with primary or relapsing solid cancer at the start of a new chemotherapy regimen. Over a median follow‐up of 9.2 months, VTE occurred in 6.7% of patients. Incidental VTE was diagnosed at time of restaging in 47% of cases. Median pre‐chemotherapy NLR (p = 0.015) and PLR (p = 0.040) were significantly higher in patients with intermediate risk class who developed symptomatic VTE with a twofold increased VTE risk for both inflammation‐based markers (NLR: p = 0.022; PLR: p = 0.037) and a worst 1‐year VTE‐free survival for patients with high NLR or PLR. However, only PLR (HR = 2.4, p = 0.027) confirmed to be an independent predictor of future VTE in patients in the intermediate risk class in multivariate analysis, together with ECOG performance status (HR = 3.4, p = 0.0002) and bevacizumab use (HR = 4.7, p = 0.012). We may, thus, conclude that PLR, but to a lesser extent NLR, could represent useful clinical predictors of VTE, especially in selected categories of patients such as those in the intermediate risk class in whom the assessment of PLR could allow a better risk stratification of VTE without additional costs to the national health systems.

SPRECware: software tools for Standard PREanalytical Code (SPREC) labeling – effective exchange and search of stored biospecimens

Biobanks provide stored material to basic, translational, and epidemiological research and this material should be transferred without institute-dependent intrinsic bias. The ISBER Biospecimen Science Working Group has released a “Standard PREanalytical Code” (SPREC), which is a proposal for a standard coding of the preanalytical options that have been adopted in order to track and make explicit the preanalytical variations in the collection, preparation, and storage of specimens. In this paper we address 2 issues arising in any biobank or biolaboratory aiming at adopting SPREC: (i) reducing the burden required to adopt this standard coding, and (ii) maximize the immediate benefits of this adoption by providing a free, dedicated software tool. We propose SPRECware, a vision encompassing tools and solutions for the best exploitation of SPREC based on information technology (www.sprecware.org). As a first step, we make available SPRECbase, a software tool useful for generating, storing, managing, and exchanging SPREC-related information associated to specimens. Adopting SPREC is useful both for internal purposes (such as finding the samples having some given preanalytical features), and for exchanging the preanalytical information associated to biological samples between Laboratory Information Systems. In case of a common adoption of this coding, it would be easy to find out whether and where, among the participating Biological Resource Centers, the specimens for a given study are available in order to carry out a planned experiment.

Is SOD2 Ala16Val Polymorphism Associated with Migraine with Aura Phenotype

Several studies suggest a role of oxidative stress in the physiopathology of migraine, particularly in the form with aura. In a case-control study, we investigated the association between migraine and superoxide dismutase 1 (SOD1) and superoxide dismutase 2 (SOD2) genes in a cohort of 490 consecutive unrelated Caucasian migraineurs (migraine with aura [MwA], n=107; migraine without aura [MwoA], n=246; chronic migraine [CM], n=137) and 246 healthy controls recruited at our Headache and Pain Unit and stored in the Interinstitutional Multidisciplinary BioBank (BioBIM). Migraine phenotype was carefully detailed using face-to-face interviews. We examined polymorphisms of SOD1 gene (A/C substitution-rs2234694) and SOD2 gene (C/T transition-rs4880-Ala16Val). The rs4880 TT (Val/Val) genotype was associated (p=0.042) with the presence of unilateral cranial autonomic symptoms (UAs) in MwA patients. We also found a mild correlation between SOD2 rs4880 genotype and the type of acute migraine treatment (p=0.048) in MwA patients. Our findings suggest that SOD2 is a disease-modifier gene influencing oxidative mechanisms in MwA. These observations lead to the hypothesis that SOD2 polymorphism may cause a defective control of the oxidative phenomena linked to cortical spreading depression, the neurophysiological hallmark of migraine aura, causing an overstimulation of trigeminal neurons and UAs triggering.

Impact of statins on the coagulation status of type 2 diabetes patients evaluated by a novel thrombin-generation assay

PurposeDyslipidemia is common in type 2 diabetes (T2D) and contributes to cardiovascular disease (CVD) by exacerbating atherosclerosis and hypercoagulability. Statins can stabilize atherosclerotic plaque and reduce prothrombotic status. In the present study we aimed to evaluate the coagulation activity and the effect of statins on procoagulant state of T2D patients using a novel activated protein C (APC)-dependent thrombin-generation assay.MethodsProcoagulant status (by HemosIL ThromboPath (ThP) assay) and in vivo platelet activation (by plasma soluble (s)CD40L levels) were analyzed in a retrospective, cross-sectional study of 198 patients with long-standing T2D and 198 controls.ResultsProcoagulant status of T2D patients was enhanced when compared to control subjects (p < 0.0001). Similarly, sCD40L levels were increased in T2D (p < 0.0001). When testing ThP as the dependent variable in a multivariate regression model, sCD40L (p < 0.0001) and statin treatment (p = 0.019) were independent predictors of the procoagulant state of T2D patients. Subgroup analysis showed a significant improvement of coagulability in T2D patients on statins (p = 0.012).ConclusionsThe use of a standardized, easy-to-run, and commercially available APC-dependent thrombin-generation assay detected the presence of a procoagulant status in a large series of patients with long-standing T2D and demonstrated a significant impact of statins in the coagulation status of patients with T2D.

A reliable and reproducible technique for DNA fingerprinting in biorepositories: a pilot study from BioBIM

Standard operating procedures (SOPs) optimization for nucleic acid extraction from stored samples is of crucial importance in a biological repository, considering the large number of collected samples and their future downstream molecular and biological applications. However, the validity of molecular studies using stored specimens depends not only on the integrity of the biological samples, but also on the procedures that ensure the traceability of the same sample, certifying its uniqueness, and ensuring the identification of potential sample contaminations. With this aim, we have developed a rapid, reliable, low-cost, and simple DNA fingerprinting tool for a routine use in quality control of biorepositories samples. The method consists of a double ALU insertion/deletion genotyping panel suitable for uniqueness, identification of sample contaminations, and gender validation. Preliminary data suggest that this easy-to-use DNA fingerprinting protocol could routinely provide assurances of DNA identity and quality in a biorepository setting.

An AT-rich region in the APC gene may cause misinterpretation of familial adenomatous polyposis molecular screening†

Familial adenomatous polyposis (FAP) is an autosomal‐dominant condition mainly due to a mutation of the adenomatous polyposis coli (APC) gene. The present study reports evidence of a technical issue occurring during the mutational analysis of APC exon 4. Genetic conventional direct sequence analysis of a repetitive AT‐rich region in the splice acceptor site of APC intron 3 could be misinterpreted as a pathogenetic frameshift result. However, this potential bias may be bypassed adopting a method for random mutagenesis of DNA based on the use of a triphosphate nucleoside analogues mixture. Using this method as a second‐level analysis, we also demonstrated the nonpathogenic nature of the variant in the poly A trait in APC exon 4 region (c.423‐4delA) that do not result in aberrant splicing of APC exons 3–4; conversely, we did not find a previously reported T deletion/insertion polymorphism. Hum Mutat 33:895–898, 2012.

Shorter telomere length in schizophrenia: Evidence from a real-world population and meta-analysis of most recent literature

Schizophrenia is a severe, chronic mental disorder. Schizophrenia is visualized as an accelerated cellular aging syndrome characterized by early onset of cardiovascular disease causing premature mortality. In human aging involves alterations in telomere length (TL). To investigate the presence of TL shortening in schizophrenia and psychiatric syndromes associated, this condition was studied in leukocytes (LTL) of a sample of patients suffering from schizophrenia and other psychotic disorders, and compared with a group of non-psychiatric controls. We explored the relationship between LTL and age, gender, and smoking habit with the aim to control whether these potential confounding factors may influence the rate of telomeres shortening. We also performed a new comprehensive meta-analysis including studies on LTL in schizophrenia patients compared to healthy subjects published in the last two years and the results of the present study. Our results suggest that a diagnosis of schizophrenia, more than gender, age, cigarette smoking or alcohol drinking, is the most important condition responsible of the LTL shortening. A strong LTL shortening was observed in patients affected by schizophrenia, Schizoaffective disorder, and Psychosis not otherwise specified when they were younger than 50 years, while in the group of older subjects no major differences were observed. Additional evidence supporting the causal link of schizophrenia with accelerated telomeres shortening came from the analysis of the updated meta-analysis. The availability of a personalized profile of mechanistic pathways, risk factors, and clinical features may pose the basis for a rehabilitative treatment addressing individual needs of the psychiatric patients.

Progesterone receptor gene (PROGINS) polymorphism correlates with late onset of migraine.

Progesterone influences central neuronal excitability, a key event in migraine pathophysiology. Progesterone receptor gene (PGR) rs1042838 (G/T - Val660Leu) variant is indicative of PROGINS haplotype and associated to a reduced PGR activity. With the aim of investigating whether any type of association existed between this genetic variant and migraine pathophysiology, genotyping was performed in 380 consecutive migraine patients and 185 age-, sex-, and race-ethnicity-matched healthy controls from Interinstitutional Multidisciplinary BioBank (BioBIM) of IRCCS San Raffaele Pisana, Rome, Italy. rs1042838 genotypes did not correlate with demographics or clinical migraine features. However, TT (Leu) genotype was significantly associated with a later age of migraine onset: Patients affected by migraine with aura showed a linear relationship between copy number of the T allele carried by the individual and the age of migraine onset. Our data suggest that the PROGINS PGR polymorphism does not directly predispose to migraine but significantly delays migraine onset probably via a reduction in brain neuronal excitability.

Prognostic Significance of Neutrophil–to–lymphocyte Ratio in the Framework of the 8th TNM Edition for Breast Cancer

Background/Aim: To investigate whether neutrophil–to–lymphocyte ratio (NLR) might represent an additional biological criterion able to identify patients with worse prognosis within the 8th edition TNM prognostic staging system for breast cancer (BC). Patients and Methods. Pre-treatment NLR was retrospectively analyzed in 475 BC women prospectively followed for a mean time of 3.8 years. The optimal NLR cutoff, identified by ROC analysis, was set at 2. Results: Elevated pre-treatment NLR was associated with worse disease-free survival (DFS) (HR=2.28) and overall survival (OS) (HR=3.39). The prognostic value of NLR was mostly evident in stage I BC (HR for DFS=2.89; HR for OS=1.30), in whom NLR significantly stratified patients who developed distant metastasis (HR= 4.62), but not local recurrence. Conclusion: NLR might provide important information in risk stratification, especially in stage I BC patients in whom the presence of a high NLR might raise the question as to whether they should be more aggressively managed.