Of yeast and men: Dissecting the interaction between fungi and immune response

Il lavoro riportato in questa tesi si pone l’obiettivo di comprendere i meccanismi che governano l’interazione tra le cellule del sistema immunitario e i microrganismi, attraverso un approccio di Systems Biology. Questo lavoro combina infatti il tradizionale lavoro di laboratorio e l’analisi a livello trascrizionale, con metodi computazionali e bioinformatici, allo scopo di comprendere la risposta delle cellule dendritiche ai funghi, in particolare al lievito non patogeno Saccharomyces cerevisiae. Questo lavoro ha due obiettivi principali: in primo luogo, lo sviluppo di un approccio analitico in grado di facilitare l’interpretazione dei dati ottenuti da sistemi ad alte prestazioni (come i microarray o la proteomica) e aumentare la possibilità di confronto tra diversi esperimenti. Accanto ad esso è stato sviluppato un modello per rappresentare le reti di segnalazione indotte dalla risposta immunitaria, dal riconoscimento recettoriale all’attivazione cellulare. In secondo luogo, attraverso l'integrazione dei diversi risultati, è stata indagata la la capacità delle cellule dendritiche di discriminare tra microrganismi patogeni e non patogeni. Combinando l'analisi trascrizionale con esperimenti volti a comprendere il ruolo dei diversi recettori nel riconoscimento ai funghi, e la risposta immunitaria indotta dalle cellule dendritiche, abbiamo identificato meccanismi di risposta diversi a C. albicans e S. cerevisiae. Abbiamo inoltre osservato come l'interazione tra spore e lieviti sia cruciale per il commensalismo di S. cerevisiae. L'integrazione di un approccio di System Biology a dati funzionali offre nuovi strumenti per comprendere i meccanismi di virulenza associati ai funghi: non solo il dimorfismo ma anche l’utilizzo di diversi recettori sulla superficie delle cellule dendritiche possono mediare la presentazione dell'antigene, condizionare la tipologia della risposta adattative e, in ultima analisi, favorire il commensalismo o l’infezione.The research presented here aimed at using a Systems Biology approach to understand the mechanism governing a fruitful interaction between microbes and the human system. Systems Biology requires the acquisition of information on the different levels of regulation of a biological system and its integration in the development of models, that could predict the outcome of stimuli and changes in variables controlling the dynamic nature of the system. This work combined traditional wet-lab work and genome wide analyses of transcription and gene regulation, with computational and bioinformatic methods to dissect the response of dendritic cells to fungi, in particular to the harmless Saccharomyces cerevisiae. This work had two main goals: first, the implementation of an analytical approach that would facilitate the interpretation of the ‘-omics’ results and increase the comparability between different data sets, lessening the problems associated with the use of different types of data and array platforms; and the development of new pathway structure to allow temporal dissection of the immune response associated to the pattern recognition receptor sensing; secondly, by integration of different results, to investigate the immune response that discriminates between friends or foes. Combining transcriptional analysis with receptor-specific blocking and cytokine production assays, we determined that DCs respond differently to C. albicans and S. cerevisiae and in the latter case, the interplay between spores and yeasts is crucial for the commensalism of S. cerevisiae. The integration of a System Biology approach to functional data offers new interpretive clues to the mechanisms of fungal virulence: rather than dimorphism per se, the engagement of different recognition receptors on DCs might select the mode of fungal internalization and antigen presentation, condition the nature of the T-helper response and, ultimately, favor saprophytism or infection

Extension of Chronological Lifespan by Hexokinase Mutation in Kluyveromyces lactis Involves Increased Level of the Mitochondrial Chaperonin Hsp60

Oxidative damage, mitochondrial dysfunction, genomic instability, and telomere shortening represent all molecular processes proposed as causal factors in aging. Lifespan can be increased by metabolism through an influence on such processes. Glucose reduction extends chronological lifespan (CLS) of Saccharomyces cerevisiae through metabolic adaptation to respiration. To answer the question if the reduced CLS could be ascribed to glucose per se or to glucose repression of respiratory enzymes, we used the Kluyveromyces lactis yeast, where glucose repression does not affect the respiratory function. We identified the unique hexokinase, encoded by RAG5 gene, as an important player in influencing yeast lifespan by modulating mitochondrial functionality and the level of the mitochondrial chaperonin Hsp60. In this context, this hexokinase might have a regulatory role in the influence of CLS, shedding new light on the complex regulation played by hexokinases

Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments

Widespread use of microarrays has generated large amounts of data, the interrogation of the public microarray repositories, identifying similarities between microarray experiments is now one of the major challenges. Approaches using defined group of genes, such as pathways and cellular networks (pathway analysis), have been proposed to improve the interpretation of microarray experiments. We propose a novel method to compare microarray experiments at the pathway level, this method consists of two steps: first, generate pathway signatures, a set of descriptors recapitulating the biologically meaningful pathways related to some clinical/biological variable of interest, second, use these signatures to interrogate microarray databases. We demonstrate that our approach provides more reliable results than with gene-based approaches. While gene-based approaches tend to suffer from bias generated by the analytical procedures employed, our pathway based method successfully groups together similar samples, independently of the experimental design. The results presented are potentially of great interest to improve the ability to query and compare experiments in public repositories of microarray data. As a matter of fact, this method can be used to retrieve data from public microarray databases and perform comparisons at the pathway level

Age and Gender Affect the Composition of Fungal Population of the Human Gastrointestinal Tract

The fungal component of the human gut microbiota has been neglected for long time due to the low relative abundance of fungi with respect to bacteria, and only recently few reports have explored its composition and dynamics in health or disease. The application of metagenomics methods to the full understanding of fungal communities is currently limited by the under representation of fungal DNA with respect to the bacterial one, as well as by the limited ability to discriminate passengers from colonizers. Here we investigated the gut mycobiota of a cohort of healthy subjects in order to reduce the gap of knowledge concerning fungal intestinal communities in the healthy status further screening for phenotypical traits that could reflect fungi adaptation to the host. We studied the fecal fungal populations of 111 healthy subjects by means of cultivation on fungal selective media and by amplicon-based ITS1 metagenomics analysis on a subset of 57 individuals. We then characterized the isolated fungi for their tolerance to gastrointestinal tract-like challenges and their susceptibility to antifungals. A total of 34 different fungal species were isolated showing several phenotypic characteristics associated with intestinal environment such as tolerance to body temperature (37°C), to acidic and oxidative stress and to bile salts exposure. We found a high frequency of azoles resistance in fungal isolates, with potential and significant clinical impact. Analyses of fungal communities revealed that the human gut mycobiota differs in function of individuals’ life stage in a gender-related fashion. The combination of metagenomics and fungal cultivation allowed an in-depth understanding of the fungal intestinal community structure associated to the healthy status and the commensalism-related traits of isolated fungi. We further discussed comparatively the results of sequencing and cultivation to critically evaluate the application of metagenomics-based approaches to fungal gut populations

Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut

The quest to discover the variety of ecological niches inhabited by Saccharomyces cerevisiae has led to research in areas as diverse as wineries, oak trees, and insect guts. The discovery of fungal communities in the human gastrointestinal tract suggested the host's gut as a potential reservoir for yeast adaptation. Here we report the existence of yeast populations associated with the human gut (HG) that differ from those isolated from other human body sites. Phylogenetic analysis on 12 microsatellite loci and 1,715 combined CDSs from whole‐genome sequencing revealed three subclusters of HG strains with further evidence of clonal colonization within the host's gut. The presence of such subclusters was supported by other genomic features, such as copy number variation, absence/introgressions of CDSs and relative polymorphism frequency. Functional analysis of CDSs specific of the different subclusters suggested possible alterations in cell wall composition and sporulation features. The phenotypic analysis combined with immunological profiling of these strains further showed that sporulation was related with strain‐specific genomic characteristics in the immune recognition pattern. We conclude that both genetic and environmental factors involved in cell wall remodeling and sporulation are the main drivers of adaptation in S. cerevisiae populations in the human gut

Long-term supplementation with anthocyanin-rich or -poor Rubus idaeus berries does not influence microvascular architecture nor cognitive outcome in the APP/PS-1 mouse model of Alzheimer’s disease

Disruption of microvascular architecture is a common pathogenic mechanism in the progression of Alzheimer's disease (AD). Given the anti-angiogenic activity of berry (poly)phenols, we investigated whether long-term feeding of Rubus idaeus (raspberries) could ameliorate cerebral microvascular pathology and improve cognition in the APP/PS-1 mouse model of AD. Male C57Bl/6J mice (50 wild type, 50 APP/PS-1) aged 4-months were fed for 24-weeks, with a normal diet enriched with either 100 mg/day glucose (control diet) or supplemented with glucose and freeze-dried anthocyanin-rich (red) or -poor (yellow) raspberries (100 mg/day) and assessed/sampled post intervention. Cerebral microvascular architecture of wild-type mice was characterised by regularly spaced capillaries with uniform diameters, unlike APP/PS-1 transgenic mice which showed dysregulated microvascular architecture. Long-term feeding of raspberries demonstrated limited modulation of microbiota and no substantive effect on microvascular architecture or cognition in either mice model although changes were evident in endogenous cerebral and plasmatic metabolite

Telaprevir twice daily is noninferior to telaprevir every 8 hours for patients with chronic hepatitis C.

Background & Aims We performed an open-label, multicenter, phase 3 study of the safety and efficacy of twice-daily telaprevir in treatment-naive patients with chronic hepatitis C virus (HCV) genotype 1 infection, including those with cirrhosis. Methods Patients were randomly assigned to groups treated with telaprevir 1125 mg twice daily or 750 mg every 8 hours plus peginterferon alfa-2a and ribavirin for 12 weeks; patients were then treated with peginterferon alfa-2a and ribavirin alone for 12 weeks if their level of HCV RNA at week 4 was <25 IU/mL or for 36 weeks if their level was higher. The primary objective was to demonstrate noninferiority of telaprevir twice daily versus every 8 hours in producing a sustained virological response 12 weeks after the end of therapy (SVR12) (based on a -11% lower limit of the 95% lower confidence interval for the difference between groups). Results At baseline, of 740 patients, 85% had levels of HCV RNA ≥800,000 IU/mL, 28% had fibrosis (F3-F4), 14% had cirrhosis (F4), 57% were infected with HCV genotype 1a, and 71% had the non-CC IL28B genotype. Of patients who were treated with telaprevir twice daily, 74.3% achieved SVR12 compared with 72.8% of patients who were treated with telaprevir every 8 hours (difference in response, 1.5%; 95% confidence interval, -4.9% to 12.0%), so telaprevir twice daily is noninferior to telaprevir every 8 hours. All subgroups of patients who were treated with telaprevir twice daily versus those who were treated every 8 hours had similar rates of SVR12. The most frequent adverse events (AEs) in the telaprevir phase were fatigue (47%), pruritus (43%), anemia (42%), nausea (37%), rash (35%), and headache (26%); serious AEs were reported in 9% of patients. Rates of AEs and serious AEs were similar or slightly higher among patients treated with telaprevir every 8 hours. Conclusions Based on a phase 3 trial, telaprevir twice daily is noninferior to every 8 hours in producing SVR12, with similar levels of safety and tolerability. These results support use of telaprevir twice daily in patients with chronic HCV genotype 1 infection, including those with cirrhosis. ClinicalTrials.gov, Number: NCT0124176

Long-term supplementation with anthocyanin-rich or -poor Rubus idaeus berries does not influence microvascular architecture nor cognitive outcome in the APP/PS-1 mouse model of Alzheimer's disease

Disruption of microvascular architecture is a common pathogenic mechanism in the progression of Alzheimer's disease (AD). Given the anti-angiogenic activity of berry (poly)phenols, we investigated whether long-term feeding of Rubus idaeus (raspberries) could ameliorate cerebral microvascular pathology and improve cognition in the APP/PS-1 mouse model of AD. Male C57Bl/6J mice (50 wild type, 50 APP/PS-1) aged 4-months were fed for 24-weeks, with a normal diet enriched with either 100 mg/day glucose (control diet) or supplemented with glucose and freeze-dried anthocyanin-rich (red) or -poor (yellow) raspberries (100 mg/day) and assessed/sampled post intervention. Cerebral microvascular architecture of wild-type mice was characterised by regularly spaced capillaries with uniform diameters, unlike APP/PS-1 transgenic mice which showed dysregulated microvascular architecture. Long-term feeding of raspberries demonstrated limited modulation of microbiota and no substantive effect on microvascular architecture or cognition in either mice model although changes were evident in endogenous cerebral and plasmatic metabolite

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions