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Summary: Metabolites that mark aging are not fully known. We analyze 408 plasma metabolites in Long Life Family Study participants to characterize markers of age, aging, extreme longevity, and mortality. We identify 308 metabolites associated with age, 258 metabolites that change over time, 230 metabolites associated with extreme longevity, and 152 metabolites associated with mortality risk. We replicate many associations in independent studies. By summarizing the results into 19 signatures, we differentiate between metabolites that may mark aging-associated compensatory mechanisms from metabolites that mark cumulative damage of aging and from metabolites that characterize extreme longevity. We generate and validate a metabolomic clock that predicts biological age. Network analysis of the age-associated metabolites reveals a critical role of essential fatty acids to connect lipids with other metabolic processes. These results characterize many metabolites involved in aging and point to nutrition as a source of intervention for healthy aging therapeutics.

L’archeologia “civica”, rivolta ai cittadini, aperta e inclusiva, rappresenta oggi una delle più importanti opportunità per lo sviluppo della disciplina e della società. Nel presente contributo, illustreremo come l’archeologia messa a servizio della società, attraverso professionisti innovativi e multivocali, possa diventare un elemento attivo e uno strumento di interazione tra i cittadini e il paesaggio storico nel quale vivono. E come tutto questo possa generare benessere fisico e psicologico, con un forte impatto sulla salute mentale delle persone fragili e con disabilità. "Civic" archaeology, open, inclusive and targeted at citizens, represents today one of the most important opportunities for the development of both archaeology itself and society in general. In this paper, we aim to prove that through the work of innovative and multivocal professionals archaeology can indeed play a social role and become a tool of interaction between citizens and the historical landscape in which they live. This interaction has the potential to create physical and psychological well-being, with a strong impact on the mental health of vulnerable people and people with disabilities.

Abstract Head and neck cancers are a complex malignancy comprising multiple anatomical sites, with cancer of the oral cavity ranking among the deadliest and the most disfiguring cancers globally. Oral cancer (OC) constitutes a subset of head and neck cancer cases, presenting primarily as tobacco- and alcohol-associated oral squamous cell carcinoma (OSCC), with a 5-year survival rate of ~ 65%, partly due to the lack of early detection and effective treatments. OSCC arises from premalignant lesions (PMLs) in the oral cavity through a multi-step series of clinical and histopathological stages, including varying degrees of epithelial dysplasia. To gain insights into the molecular mechanisms associated with the progression of PMLs to OSCC, we profiled the whole transcriptome of 66 human PMLs comprising leukoplakia with dysplasia and hyperkeratosis non-reactive (HkNR) pathologies, alongside healthy controls and OSCC. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome toward PML evolution to OSCC. Collectively, this study reveals molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage. Graphical abstract

Quantitative trait loci (QTL) denote regions of DNA whose variation is associated with variations in quantitative traits. QTL discovery is a powerful approach to understand how changes in molecular and clinical phenotypes may be related to DNA sequence changes. However, QTL discovery analysis encompasses multiple analytical steps and the processing of multiple input files, which can be laborious, error prone, and hard to reproduce if performed manually. To facilitate and automate large-scale QTL analysis, we developed the yQTL Pipeline, where the 'y' indicates the dependent quantitative variable being modeled. Prior to the association test, the pipeline supports the calculation or the direct input of pre-defined genome-wide principal components and genetic relationship matrix when applicable. User-specified covariates can also be provided. Depending on whether familial relatedness exists among the subjects, genome-wide association tests will be performed using either a linear mixed-effect model or a linear model. The options to run an ANOVA model or testing the interaction with a covariate are also available. Using the workflow management tool Nextflow, the pipeline parallelizes the analysis steps to optimize run-time and ensure results reproducibility. In addition, a user-friendly R Shiny App is developed to facilitate result visualization. It can generate Manhattan and Miami plots of phenotype traits, genotype-phenotype boxplots, and trait-QTL connection networks. We applied the yQTL Pipeline to analyze metabolomics profiles of blood serum from the New England Centenarians Study (NECS) participants. A total of 9.1M SNPs and 1,052 metabolites across 194 participants were analyzed. Using a p-value cutoff 5e-8, we found 14,983 mQTLs associated with 312 metabolites. The built-in parallelization of our pipeline reduced the run time from ~90 min to ~26 min. Visualization using the R Shiny App revealed multiple mQTLs shared across multiple metabolites. The yQTL Pipeline is available with documentation on GitHub at https://github.com/montilab/yQTLpipeline.

LATS1/2 kinases are reported to be tumour suppressors in many cancers. Here the authors show that conditional deletion of LATS1/2 in the mature mouse luminal mammary epithelium leads to luminal-basal plasticity and development of basal-like carcinomas.

Inference of biological network structures is often performed on high-dimensional data, yet is hindered by the limited sample size of high throughput "omics" data typically available. To overcome this challenge, often referred to as the "small n, large p problem," we exploit known organizing principles of biological networks that are sparse, modular, and likely share a large portion of their underlying architecture. We present SHINE-Structure Learning for Hierarchical Networks-a framework for defining data-driven structural constraints and incorporating a shared learning paradigm for efficiently learning multiple Markov networks from high-dimensional data at large p/n ratios not previously feasible. We evaluated SHINE on Pan-Cancer data comprising 23 tumor types, and found that learned tumor-specific networks exhibit expected graph properties of real biological networks, recapture previously validated interactions, and recapitulate findings in literature. Application of SHINE to the analysis of subtype-specific breast cancer networks identified key genes and biological processes for tumor maintenance and survival as well as potential therapeutic targets for modulating known breast cancer disease genes.

Comorbid Type 2 diabetes (T2D), a metabolic complication of obesity, associates with worse cancer outcomes for prostate, breast, head and neck, colorectal and several other solid tumors. However, the molecular mechanisms remain poorly understood. Emerging evidence shows that exosomes carry miRNAs in blood that encode the metabolic status of originating tissues and deliver their cargo to target tissues to modulate expression of critical genes. Exosomal communication potentially connects abnormal metabolism to cancer progression. Here, we hypothesized that T2D plasma exosomes induce epithelial-mesenchymal transition (EMT) and immune checkpoints in prostate cancer cells. We demonstrate that plasma exosomes from subjects with T2D induce EMT features in prostate cancer cells and upregulate the checkpoint genes CD274 and CD155. We demonstrate that specific exosomal miRNAs that are differentially abundant in plasma of T2D adults compared to nondiabetic controls (miR374a-5p, miR-93-5p and let-7b-3p) are delivered to cancer cells, thereby regulating critical target genes. We build on our previous reports showing BRD4 controls migration and dissemination of castration-resistant prostate cancer, and transcription of key EMT genes, to show that T2D exosomes require BRD4 to drive EMT and immune ligand expression. We validate our findings with gene set enrichment analysis of human prostate tumor tissue in TGCA genomic data. These results suggest novel, non-invasive approaches to evaluate and potentially block progression of prostate and other cancers in patients with comorbid T2D.

Abstract Sjögren’s syndrome (SS) is a complex autoimmune disease associated with lymphocytic infiltration and secretory dysfunction of salivary and lacrimal glands. Although the etiology of SS remains unclear, evidence suggests that epithelial damage of the glands elicits immune and fibrotic responses in SS. To define molecular changes underlying epithelial tissue damage in SS, we laser capture microdissected (LCM) labial salivary gland epithelia from 8 SS and 8 non-SS controls for analysis by RNA sequencing (RNAseq). Computational interrogation of gene expression signatures revealed that, in addition to a division of SS and non-SS samples, there was a potential intermediate state overlapping clustering of SS and non-SS samples. Differential expression analysis uncovered signaling events likely associated with distinct SS pathogenesis. Notable signals included the enrichment of IFN-γ and JAK/STAT-regulated genes, and the induction of genes encoding secreted factors, such as LTF, BMP3, and MMP7, implicated in immune responses, matrix remodeling and tissue destruction. Identification of gene expression signatures of salivary epithelia associated with mixed clinical and histopathological characteristics suggests that SS pathology may be defined by distinct molecular subtypes. We conclude that gene expression changes arising in the damaged salivary epithelia may offer novel insights into the signals contributing to SS development and progression.

Abstract Background Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data. Results To address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface. Conclusions We present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html . Video abstract

The authors evaluated the short-term neuromuscular effects on the assessment of mechanical hand—arm systems induced by vibrating tools to investigate the relationship between the force exerted and the vibration exposure. The motor task consisted of holding the instrumented handle with the dominant hand at predetermined grip force values. Five subjects took part in the tests. The tests were developed in the absence of vibration and in the presence of vibration at 5 m/s2, 7.5 m/s2 and 10 m/s2. The push and pull force values were calculated in the tests on the five subjects.

Changes of cell type composition across samples can carry biological significance and provide insight into disease and other conditions. Single cell transcriptomics has made it possible to study cell type composition at a fine resolution. Most single cell studies investigate compositional changes between samples for each cell type independently, not accounting for the fixed number of cells per sample in sequencing data. Here, we provide a metric of the distribution of cell type proportions in a sample that can be used to compare the overall distribution of cell types across multiple samples and biological conditions. This is the first method to measure overall cell type composition at the single cell level. We use the method to assess compositional changes in peripheral blood mononuclear cells (PBMCs) related to aging and extreme old age using multiple single cell datasets from individuals of four age groups across the human lifespan.

Il paper presenta il modello dell’Area archeologica di Poggio del Molino a Populonia (Piombino, LI) attraverso l’intervento dell’Associazione culturale Past in Progress che ha, nel tempo, acquisito una grande rilevanza, soprattutto a livello internazionale: dal 2008 al 2018, i partecipanti che hanno condiviso “attivamente” l’esperienza archeologica populoniese sono stati oltre duemila. Oggi, a Poggio del Molino è in corso la realizzazione di un Parco di Archeologica Condivisa (PArCo), il primo in Italia. Caratterizzato da un grande set d’offerta didattica, contenutistica ed esperienziale, il PArCo agirà mediante la strutturazione di “esperienze” autentiche e once-in-a-lifetime per rispondere ai bisogni di turisti, volontari e visitatori extra-territoriali. Forse in un mondo in cui i viaggiatori sono “cittadini temporanei”, attrarre un turismo consapevole unito alla capacità di generare valore sono le vere frontiere naturali e contemporanee dell’archeologia pubblica. This paper outlines the management strategy implemented by the cultural association Past in Progress over the archaeological area of Poggio del Molino near Populonia (Piombino, LI). Since 2008, Past in Progress’s model has achieved particular success at the international level, with more than 2,000 participants having taken an “active” share in archaeological experiences in the territory of Populonia. More recently at Poggio del Molino, developments have been initiated to transform the area into a “Shared Archaeology Park” (Parco di Archeologia Condivisa/PArCo), the first in Italy. Characterized by a diverse set of didactic, content-based, and experiential amenities, the PArCo will serve to structure authentic and “once-in-a-lifetime” experiences, responding to the needs of tourists, volunteers, and non-local visitors. In a world in which travelers function as “temporary citizens”, generating a form of tourism which is both conscious and capable of creating real value is the real “next frontier” of public archaeology.

Summary: Proper lung function relies on the precise balance of specialized epithelial cells that coordinate to maintain homeostasis. Herein, we describe essential roles for the transcriptional regulators YAP/TAZ in maintaining lung epithelial homeostasis, reporting that conditional deletion of Yap and Wwtr1/Taz in the lung epithelium of adult mice results in severe defects, including alveolar disorganization and the development of airway mucin hypersecretion. Through in vivo lineage tracing and in vitro molecular experiments, we reveal that reduced YAP/TAZ activity promotes intrinsic goblet transdifferentiation of secretory airway epithelial cells. Global gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggest that YAP/TAZ act cooperatively with TEA domain (TEAD) transcription factors and the NuRD complex to suppress the goblet cell fate program, directly repressing the SPDEF gene. Collectively, our study identifies YAP/TAZ as critical factors in lung epithelial homeostasis and offers molecular insight into the mechanisms promoting goblet cell differentiation, which is a hallmark of many lung diseases.

Thanks to the low working temperature, less product size limitations and one order of magnitude higher deposition rates compared to the established additive manufacturing techniques, more attention has been brought to the potential of cold spraying for additive manufacturing . As a process dealing with deformation of solid particles possibly leaving non-bonded interfaces and causing work hardening, any optimization should (i) adjust spray parameters to obtain high performance as-sprayed parts and (ii) tune ductility and internal stresses by post-treatments. The present study first deals with strategies to optimize spray parameters for fabrication of high performance steel 316 L deposits. Next, the performances of deposits are further adjusted by various heat treatments. The structural strength of the freestanding samples before and after the heat treatments is evaluated under static and cyclic axial loading and supported by fatigue crack growth rate analysis. The results highlight the feasibility of obtaining high quality steel 316 L deposits using N2 as process gas, rather than the costly He that is commonly suggested. This study demonstrates the potential of cold spraying to be used for deposition of freeform structural components with a static strength comparable to that of bulk and laser-based additive manufactured materials and a fatigue strength similar to that of bulk cast material.

G Protein Suppressor 2 (GPS2) is a multifunctional protein that exerts important roles in inflammation and metabolism in adipose, liver, and immune cells. GPS2 has recently been identified as a significantly mutated gene in breast cancer and other malignancies and proposed to work as a putative tumor suppressor. However, molecular mechanisms by which GPS2 prevents cancer development and/or progression are largely unknown. Here, we have profiled the phenotypic changes induced by GPS2 depletion in MDA-MB-231 triple negative breast cancer cells and investigated the underlying molecular mechanisms. We found that GPS2-deleted MDA-MB-231 cells exhibited increased proliferative, migratory, and invasive properties in vitro, and conferred greater tumor burden in vivo in an orthotopic xenograft mouse model. Transcriptomic, proteomic and phospho-proteomic profiling of GPS2-deleted MBA-MB-231 revealed a network of altered signals that relate to cell growth and PI3K/AKT signaling. Overlay of GPS2-regulated gene expression with MDA-MB-231 cells modified to express constitutively active AKT showed significant overlap, suggesting that sustained AKT activation is associated with loss of GPS2. Accordingly, we demonstrate that the pro-oncogenic phenotypes associated with GPS2 deletion are rescued by pharmacological inhibition of AKT with MK2206. Collectively, these observations confirm a tumor suppressor role for GPS2 and reveal that loss of GPS2 promotes breast cancer cell proliferation and tumor growth through uncontrolled activation of AKT signaling. Moreover, our study points to GPS2 as a potential biomarker for a subclass of breast cancers that would be responsive to PI3K-class inhibitor drugs.

Summary: Protein-protein interaction (PPI) databases are an important bioinformatics resource, yet existing literature-curated databases usually represent cell-type-agnostic interactions, which is at variance with our understanding that protein dynamics are context specific and highly dependent on their environment. Here, we provide a resource derived through data mining to infer disease- and tissue-relevant interactions by annotating existing PPI databases with cell-contextual information extracted from reporting studies. This resource is applicable to the reconstruction and analysis of disease-centric molecular interaction networks. We have made the data and method publicly available and plan to release scheduled updates in the future. We expect these resources to be of interest to a wide audience of researchers in the life sciences. The Bigger Picture: Existing literature-curated protein-protein interaction (PPI) databases usually aggregate cell-type-agnostic interactions, yet PPIs are dependent on environmental conditions. Thus, new methods and resources for inferring the context in which a PPI is reported will extend their application and use in disease-centric modeling. We expect the resource presented in this article to be of high interest to those querying known interactions of proteins of interest, reconstruction and analyses of molecular interaction networks, and multi-omics data integration approaches.

B-cell receptor (BCR) signaling pathway components represent promising treatment targets in multiple B-cell malignancies including diffuse large B-cell lymphoma (DLBCL). In in vitro and in vivo model systems, a subset of DLBCLs depend upon BCR survival signals and respond to proximal BCR/phosphoinositide 3 kinase (PI3K) blockade. However, single-agent BCR pathway inhibitors have had more limited activity in patients with DLBCL, underscoring the need for indicators of sensitivity to BCR blockade and insights into potential resistance mechanisms. Here, we report highly significant transcriptional upregulation of C-X-C chemokine receptor 4 (CXCR4) in BCR-dependent DLBCL cell lines and primary tumors following chemical spleen tyrosine kinase (SYK) inhibition, molecular SYK depletion or chemical PI3K blockade. SYK or PI3K inhibition also selectively upregulated cell surface CXCR4 protein expression in BCR-dependent DLBCLs. CXCR4 expression was directly modulated by fork-head box O1 via the PI3K/protein kinase B/forkhead box O1 signaling axis. Following chemical SYK inhibition, all BCR-dependent DLBCLs exhibited significantly increased stromal cell-derived factor-1α (SDF-1α) induced chemotaxis, consistent with the role of CXCR4 signaling in B-cell migration. Select PI3K isoform inhibitors also augmented SDF-1α induced chemotaxis. These data define CXCR4 upregulation as an indicator of sensitivity to BCR/PI3K blockade and identify CXCR4 signaling as a potential resistance mechanism in BCR-dependent DLBCLs.

A major challenge for cancer immunotherapy is sustaining T-cell activation and recruitment in immunosuppressive solid tumors. Here, we report that the levels of the Hippo pathway effector Yes-associated protein (Yap) are sharply induced upon the activation of cluster of differentiation 4 (CD4)-positive and cluster of differentiation 8 (CD8)-positive T cells and that Yap functions as an immunosuppressive factor and inhibitor of effector differentiation. Loss of Yap in T cells results in enhanced T-cell activation, differentiation, and function, which translates in vivo to an improved ability for T cells to infiltrate and repress tumors. Gene expression analyses of tumor-infiltrating T cells following Yap deletion implicates Yap as a mediator of global T-cell responses in the tumor microenvironment and as a negative regulator of T-cell tumor infiltration and patient survival in diverse human cancers. Collectively, our results indicate that Yap plays critical roles in T-cell biology and suggest that Yap inhibition improves T-cell responses in cancer.

Geometrical discontinuities in mechanical components are detrimental for the mechanical properties of the product itself. Actually, in proximity of such features, the stress increases due to the stress concentration factor, that in the case of a circular hole is equal to 3. Several solutions have been proposed to reduce the stress concentration value. In the present article, the application of a particular porous pattern that can be obtained by laser cutting with the appropriate finishing requirements is introduced in order to modify the local stress field and reduce the stress concentration value near the hole boundary.

Abstract Background Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy characterized by tumor heterogeneity, locoregional metastases, and resistance to existing treatments. Although a number of genomic and molecular alterations associated with HNSCC have been identified, they have had limited impact on the clinical management of this disease. To date, few targeted therapies are available for HNSCC, and only a small fraction of patients have benefited from these treatments. A frequent feature of HNSCC is the inappropriate activation of β-catenin that has been implicated in cell survival and in the maintenance and expansion of stem cell-like populations, thought to be the underlying cause of tumor recurrence and resistance to treatment. However, the therapeutic value of targeting β-catenin activity in HNSCC has not been explored. Methods We utilized a combination of computational and experimental profiling approaches to examine the effects of blocking the interaction between β-catenin and cAMP-responsive element binding (CREB)-binding protein (CBP) using the small molecule inhibitor ICG-001. We generated and annotated in vitro treatment gene expression signatures of HNSCC cells, derived from human oral squamous cell carcinomas (OSCCs), using microarrays. We validated the anti-tumorigenic activity of ICG-001 in vivo using SCC-derived tumor xenografts in murine models, as well as embryonic zebrafish-based screens of sorted stem cell-like subpopulations. Additionally, ICG-001-inhibition signatures were overlaid with RNA-sequencing data from The Cancer Genome Atlas (TCGA) for human OSCCs to evaluate its association with tumor progression and prognosis. Results ICG-001 inhibited HNSCC cell proliferation and tumor growth in cellular and murine models, respectively, while promoting intercellular adhesion and loss of invasive phenotypes. Furthermore, ICG-001 preferentially targeted the ability of subpopulations of stem-like cells to establish metastatic tumors in zebrafish. Significantly, interrogation of the ICG-001 inhibition-associated gene expression signature in the TCGA OSCC human cohort indicated that the targeted β-catenin/CBP transcriptional activity tracked with tumor status, advanced tumor grade, and poor overall patient survival. Conclusions Collectively, our results identify β-catenin/CBP interaction as a novel target for anti-HNSCC therapy and provide evidence that derivatives of ICG-001 with enhanced inhibitory activity may serve as an effective strategy to interfere with aggressive features of HNSCC.

These days, ubiquitous computing has radically changed the way users access and interact with services and content on the Internet: novel smart mobile devices and broadband wireless communication channels allow users to seamlessly access them anytime and anywhere. Middleware infrastructures to support ubiquitous computing need to support an extremely dynamic and ever-changing scenario, where novel contents/services, devices, formats, and media channels become available. Service-oriented architectures and service composition techniques have proven to be the key in designing flexible and extensible platforms that are able to reliably support ubiquitous computing. However, current trends in service composition for ubiquitous computing tend to be either too formal and, therefore, poorly used by average final users, or too vertical and poorly flexible and extensible. This paper proposes novel service composition middleware for ubiquitous computing that relies on a translucent composition model to achieve a flexible, extensible, highly-available, but also easily understandable and usable platform. The proposed system has been widely tested, benchmarked, and deployed on a number of different and heterogeneous ubiquitous scenarios.

Impact surface treatments are well-known for their efficiency in enhancing the mechanical properties of metallic materials, especially under cyclic loadings. These processes, which encompass a wide range of surface treatments based on repetitive impacts of tools of various types, induce surface plastic deformation, compressive residual stresses, and grain refinement alter the surface roughness as a side effect. Thus, it is essential to have suitable indexes to quantify the surface features caused by the typically random nature of these treatments. Herein, we evaluated the rationality of using standard roughness parameters for describing the morphological characteristics of surfaces treated by shot peening as a representative and widely used treatment of the category. A detailed numerical model of the peening process was developed. The output data were elaborated to extract the surface roughness parameters following the standard procedures. The results revealed the validity of the surface roughness parameters to describe the topography of material treated with adequate surface coverage, also highlighting the necessity to use a set of parameters rather than the common practice of relying on single parameters. Not considering a comprehensive set of amplitude and spacing parameters can result in significant, inconsistent, and misleading results while comparing the performance of surfaces.

The clinical importance of anterior foregut endoderm (AFE) derivatives, such as thyrocytes, has led to intense research efforts for their derivation through directed differentiation of pluripotent stem cells (PSCs). Here, we identify transient overexpression of the transcription factor (TF) NKX2-1 as a powerful inductive signal for the robust derivation of thyrocyte-like cells from mouse PSC-derived AFE. This effect is highly developmental stage specific and dependent on FOXA2 expression levels and precise modulation of BMP and FGF signaling. The majority of the resulting cells express thyroid TFs (Nkx2-1, Pax8, Foxe1, Hhex) and thyroid hormone synthesis-related genes (Tg, Tpo, Nis, Iyd) at levels similar to adult mouse thyroid and give rise to functional follicle-like epithelial structures in Matrigel culture. Our findings demonstrate that NKX2-1 overexpression converts AFE to thyroid epithelium in a developmental time-sensitive manner and suggest a general methodology for manipulation of cell-fate decisions of developmental intermediates.

The advent of high-throughput sequencing technologies has led to the need for flexible and user-friendly data preprocessing platforms. The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It combines the Nextflow scripting language and Anaconda package manager to generate modular computational workflows. We have used Pipeliner to create several pipelines for sequencing data processing including bulk RNA-sequencing (RNA-seq), single-cell RNA-seq, as well as digital gene expression data. This report highlights the design methodology behind Pipeliner that enables the development of highly flexible and reproducible pipelines that are easy to extend and maintain on multiple computing environments. We also provide a quick start user guide demonstrating how to setup and execute available pipelines with toy datasets.

The need to reduce per sample cost of RNA-seq profiling for scalable data generation has led to the emergence of highly multiplexed RNA-seq. These technologies utilize barcoding of cDNA sequences in order to combine multiple samples into a single sequencing lane to be separated during data processing. In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq, microarrays, as well as another low-cost highly multiplexed technique known as 3′ digital gene expression (3′DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3′DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures.

The identification of genetic alteration combinations as drivers of a given phenotypic outcome, such as drug sensitivity, gene or protein expression, and pathway activity, is a challenging task that is essential to gaining new biological insights and to discovering therapeutic targets. Existing methods designed to predict complementary drivers of such outcomes lack analytical flexibility, including the support for joint analyses of multiple genomic alteration types, such as somatic mutations and copy number alterations, multiple scoring functions, and rigorous significance and reproducibility testing procedures. To address these limitations, we developed Candidate Driver Analysis or CaDrA, an integrative framework that implements a step-wise heuristic search approach to identify functionally relevant subsets of genomic features that, together, are maximally associated with a specific outcome of interest. We show CaDrA’s overall high sensitivity and specificity for typically sized multi-omic datasets using simulated data, and demonstrate CaDrA’s ability to identify known mutations linked with sensitivity of cancer cells to drug treatment using data from the Cancer Cell Line Encyclopedia (CCLE). We further apply CaDrA to identify novel regulators of oncogenic activity mediated by Hippo signaling pathway effectors YAP and TAZ in primary breast cancer tumors using data from The Cancer Genome Atlas (TCGA), which we functionally validate in vitro. Finally, we use pan-cancer TCGA protein expression data to show the high reproducibility of CaDrA’s search procedure. Collectively, this work demonstrates the utility of our framework for supporting the fast querying of large, publicly available multi-omics datasets, including but not limited to TCGA and CCLE, for potential drivers of a given target profile of interest.

For decades, the aryl hydrocarbon receptor (AHR) was studied for its role in environmental chemical toxicity i.e., as a quirk of nature and a mediator of unintended consequences of human pollution. During that period, it was not certain that the AHR had a “normal” physiological function. However, the ongoing accumulation of data from an ever-expanding variety of studies on cancer, cancer immunity, autoimmunity, organ development, and other areas bears witness to a staggering array of AHR-controlled normal and pathological activities. The objective of this review is to discuss how the AHR has gone from a likely contributor to genotoxic environmental carcinogen-induced cancer to a master regulator of malignant cell progression and cancer aggression. Particular focus is placed on the association between AHR activity and poor cancer outcomes, feedback loops that control chronic AHR activity in cancer, and the role of chronically active AHR in driving cancer cell invasion, migration, cancer stem cell characteristics, and survival.

Sarcoidosis is a common disease that involve almost constantly the lung. Usually the onset is insidious, and symptoms are slowly ingravescent. Very rarely, as in the case here reported, sarcoidosis can cause an acute respiratory failure with acute respiratory distress syndrome (ARDS). A 20-year-old girl from Pakistan presented for acute fatigue, fever, and cough with a chest X-ray displayed the micronodular interstitial disease. Despite of anti-tuberculosis therapy, ARDS developed in a few days requiring continuous positive airway pressure treatment. Examinations on transbronchial specimens obtained by bronchoscopy permitted to reach the diagnosis of sarcoidosis and steroid therapy improved rapidly clinical conditions. This is the first case report reported in Europe that confirms the rare onset of sarcoidosis as ARDS. Steroid therapy allows to cure rapidly this severe complication.

Carcinoma associated fibroblasts (CAFs) form the main constituents of tumor stroma and play an important role in tumor growth and invasion. The presence of CAFs is a strong predictor of poor prognosis of head and neck squamous cell carcinoma. Despite significant progress in determining the role of CAFs in tumor progression, the mechanisms contributing to their activation remain poorly characterized, in part due to fibroblast heterogeneity and the scarcity of reliable fibroblast surface markers. To search for such markers in oral squamous cell carcinoma (OSCC), we applied a novel approach that uses RNA-sequencing data derived from the cancer genome atlas (TCGA). Specifically, our strategy allowed for an unbiased identification of genes whose expression was closely associated with a set of bona fide stroma-specific transcripts, namely the interstitial collagens COL1A1, COL1A2, and COL3A1. Among the top hits were genes involved in cellular matrix remodeling and tumor invasion and migration, including platelet-derived growth factor receptor beta (PDGFRβ), which was found to be the highest-ranking receptor protein genome-wide. Similar analyses performed on ten additional TCGA cancer datasets revealed that other tumor types shared CAF markers with OSCC, including PDGFRβ, which was found to significantly correlate with the reference collagen expression in ten of the 11 cancer types tested. Subsequent immunostaining of OSCC specimens demonstrated that PDGFRβ was abundantly expressed in stromal fibroblasts of all tested cases (12/12), while it was absent in tumor cells, with greater specificity than other known markers such as alpha smooth muscle actin or podoplanin (3/11). Overall, this study identified PDGFRβ as a novel marker of stromal activation in OSCC, and further characterized a list of promising candidate CAF markers that may be relevant to other carcinomas. Our novel approach provides for a fast and accurate method to identify CAF markers without the need for large-scale immunostaining experiments.

We have postulated that the aryl hydrocarbon receptor (AHR) drives the later, more lethal stages of some cancers when chronically activated by endogenous ligands. However, other studies have suggested that, under some circumstances, the AHR can oppose tumor aggression. Resolving this apparent contradiction is critical to the design of AHR-targeted cancer therapeutics. Molecular (siRNA, shRNA, AHR repressor, CRISPR-Cas9) and pharmacological (AHR inhibitors) approaches were used to confirm the hypothesis that AHR inhibition reduces human cancer cell invasion (irregular colony growth in 3D Matrigel cultures and Boyden chambers), migration (scratch wound assay) and metastasis (human cancer cell xenografts in zebrafish). Furthermore, these assays were used for a head-to-head comparison between AHR antagonists and agonists. AHR inhibition or knockdown/knockout consistently reduced human ER−/PR−/Her2− and inflammatory breast cancer cell invasion, migration, and metastasis. This was associated with a decrease in invasion-associated genes (e.g., Fibronectin, VCAM1, Thrombospondin, MMP1) and an increase in CDH1/E-cadherin, previously associated with decreased tumor aggression. Paradoxically, AHR agonists (2,3,7,8-tetrachlorodibenzo-p-dioxin and/or 3,3′-diindolylmethane) similarly inhibited irregular colony formation in Matrigel and blocked metastasis in vivo but accelerated migration. These data demonstrate the complexity of modulating AHR activity in cancer while suggesting that AHR inhibitors, and, under some circumstances, AHR agonists, may be useful as cancer therapeutics.

BACKGROUND:Despite an overall decrease in incidence of and mortality from cancer, about 40% of Americans will be diagnosed with the disease in their lifetime, and around 20% will die of it. Current approaches to test carcinogenic chemicals adopt the 2-year rodent bioassay, which is costly and time-consuming. As a result, fewer than 2% of the chemicals on the market have actually been tested. However, evidence accumulated to date suggests that gene expression profiles from model organisms exposed to chemical compounds reflect underlying mechanisms of action, and that these toxicogenomic models could be used in the prediction of chemical carcinogenicity. RESULTS:In this study, we used a rat-based microarray dataset from the NTP DrugMatrix Database to test the ability of toxicogenomics to model carcinogenicity. We analyzed 1,221 gene-expression profiles obtained from rats treated with 127 well-characterized compounds, including genotoxic and non-genotoxic carcinogens. We built a classifier that predicts a chemical's carcinogenic potential with an AUC of 0.78, and validated it on an independent dataset from the Japanese Toxicogenomics Project consisting of 2,065 profiles from 72 compounds. Finally, we identified differentially expressed genes associated with chemical carcinogenesis, and developed novel data-driven approaches for the molecular characterization of the response to chemical stressors. CONCLUSION:Here, we validate a toxicogenomic approach to predict carcinogenicity and provide strong evidence that, with a larger set of compounds, we should be able to improve the sensitivity and specificity of the predictions. We found that the prediction of carcinogenicity is tissue-dependent and that the results also confirm and expand upon previous studies implicating DNA damage, the peroxisome proliferator-activated receptor, the aryl hydrocarbon receptor, and regenerative pathology in the response to carcinogen exposure.

Devolution has definitely become a ‘flagship’ in the Italian political debate. It has affected any aspect of public policy over the last 17 years and the cultural sector has not been spared. Its key aim is to decentralise legal and administration powers in a way that could reduce the burden of State offices work and set up a more efficient and effective administration able to meet citizens’ needs. After a long tradition of centralized policies and administration, long, costly and often in efficient procedures required a profound change. The reforms were so ledby the ideal to implement public policies closest to citizens’ needs, to provide direct responses and increase their participation to local governments’ actions (democratization and participative policy), to deliver more effective services (better performance) and distribute more equally the burden of administrative work of State offices (decentralisation of day-to-day administration). La Devolution e la politica culturale italiana La Devolution riveste un punto centrale nel dibattito politico italiano: ha riguardato ogni aspetto della politica pubblica negli ultimi 17 anni, e il settore culturale non ne è stato risparmiato. L'obbiettivo principale è quello di decentralizzare i poteri giuridici e amministrativi in modo da ridurre il peso del lavoro degli uffici pubblici statali, e di organizzare un'amministrazione più efficiente ed efficace in grado di soddisfare le necessità dei cittadini. Dopo una lunga tradizione basata su politica e amministrazione centralizzate, procedure lunghe, costose e spesso inefficienti richiedevano un profondo cambiamento. Le riforme sono state quindi indirizzate all'implemento di politiche pubbliche più vicine ai cittadini, a incrementare la loro partecipazione nelle azioni di governo locali (politica di democratizzazione e partecipativa), a fornire servizi più efficienti (migliori prestazioni) e a distribuire più equamente il carico amministrativo degli uffici statali (decentralizzazione dell'amministrazione quotidiana).

Ogni frammento è testimone di un passato che in esso è racchiuso. Spesso però il suo essere degradato ne compromette la leggibilità. L’esigenza di ‘capire’ al fine distudiare ed intervenire in modo corretto sull’opera ha bisogno del duplice supporto storico e scientifico. Per questo motivo la tecnologia può aiutarci in primis ad indagare la consistenza materica del reperto e successivamente a trovare soluzioni adeguate per la sua valorizzazione. Le nuove tecniche di documentazione, le analisi di laboratorio, i sistemi per la fruizione del patrimonio forniscono sempre più una serie di dati utili al processo di rifunzionalizzazione dell’opera. L’utilizzo della tecnologia ha permesso di introdurre modalità di analisi sempre più precise e dettagliate sia nei procedimenti che nei risultati. E' interessante quindi valutare come essa sia stata in grado modifi care gli sviluppi e studiare il suo impatto economico all’interno del processo di valorizzazione del bene. Technological development of cultural heritage Technology can help us fi rstly to investigate the material consistency of the fi ndings and then to fi nd appropriate solutions for its development. The new technical documentation, laboratory testing, systems for the use of more heritage providing a range of useful data to the process of reutilization of the work.

Diffuse large B cell lymphoma (DLBCL) is a clinically and genetically heterogeneous disease. A small subset of DLBCLs has translocations involving the MYC locus and an additional group has a molecular signature resembling Burkitt lymphoma (mBL). Presently, identification of such cases by morphology is unreliable and relies on cytogenetic or complex molecular methods such as gene transcriptional profiling. Herein, we describe an immunohistochemical (IHC) method for identifying DLBCLs with increased MYC protein expression. We tested 77 cases of DLBCL and identified 15 cases with high MYC protein expression (nuclear staining in >50% of tumor cells). All MYC translocation positive cases had increased MYC protein expression by this IHC assay. In addition, gene set enrichment analysis (GSEA) of the DLBCL transcriptional profiles revealed that tumors with increased MYC protein expression (regardless of underlying MYC translocation status) had coordinate upregulation of MYC target genes, providing molecular confirmation of the IHC results. We then generated a molecular classifier derived from the MYC IHC results in our cases and employed it to successfully classify mBLs from two previously reported independent case series, providing additional confirmation that the MYC IHC results identify clinically important subsets of DLBCLs. Lastly, we found that DLBCLs with high MYC protein expression had inferior overall survival when treated with R-CHOP. In conclusion, the IHC method described herein can be used to readily identify the biologically and clinically distinct cases of MYC-driven DLBCL, which represent a clinically significant subset of DLBCL cases due to their inferior overall survival.

IRIS is an advanced integral pressurized water reactor, developed by an international consortium led by Westinghouse. The licensing process requires the execution of integral and separate effect tests on a properly scaled reactor simulator for reactor concept, safety system verification, and code assessment. Within the framework of an Italian R&D program on Nuclear Fission, managed by ENEA and supported by the Ministry of Economic Development, the SPES3 facility is under design and will be built and operated at SIET laboratories. SPES3 simulates the primary, secondary, and containment systems of IRIS with 1 : 100 volume scale, full elevation, and prototypical thermal-hydraulic conditions. The simulation of the facility with the RELAP5 code and the execution of the tests will provide a reliable tool for data extrapolation and safety analyses of the final IRIS design. This paper summarises the main design steps of the SPES3 integral test facility, underlying choices and phases that lead to the final design.