BiP-Day 2014, disponibile l’abstract book

In vista dell’evento questo venerdì, abbiamo deciso di rendere disponibile in formato digitale l’abstract book del BiP-Day 2014. Nello specifico abbiamo rilasciato due versioni dello stesso:

– una versione PDF per lettura su schermo (formato A4);
– una versione, sempre in PDF, predisposta con “impaginazione per stampa libretto” su supporto cartaceo (formato libretto, fronte-retro, lato corto(.

Buon download!

An experimental solution for accurate screening and interpretation of structural genetic variants

P. Cazzati, Rita De Molfetta, R. Greco, L. Loberafo, F. Nigro, P. Noviello, N. Tempesta, M. Carella, Stefano Castellana, T. Mazza, O. Palumbo, P. Palumbo

Motivations

The progressive cost reduction of the DNA investigation technologies facilitates the acquisition and the employment of genomic data for clinical purposes. Genetic information can drive both clinicians and researchers towards a more personalized medicine. In order to support genome-based diagnosis, Exprivia, as industrial partner for the PON02_00619_3461281 Project in collaboration with Casa Sollievo della Sofferenza as scientific partner, proposed to establish a network between clinical facilities and molecular genetics laboratories.

Methods

The following prototypes software packages have been developed:

  • A portal to support the collaboration between physician and laboratories through clinical-genomic data exchange, by collecting clinical data (focused on Human Phenotype Ontology); the opportunity to launch and follow the experimental procedure from the committed laboratory; the acquisition of the corresponding medical report.
  • A knowledge base to store the detected genetic alterations and find out possible correlations among phenotypic abnormalities and other clinical data in order to support epidemiologic studies.
  • A bioinformatic pipeline for the interpretation of experimental outcomes based on centralized public and local genetic data resources and for the evaluation of clinical role of the genetic alterations and relative pathogenicity.

Results

We have tested the prototypes software packages for the interpretation of Copy Number Variants (CNVs) coming from array Comparative Genomic Hybridization experiments (‘aCGH’).

The pipeline reduces the time of analysis and facilitates the data interpretation. The portal simplifies the data entry process, thanks to the integration of standardized description of the individual phenotype, and supports the diagnosis evaluation.

Conclusions

This work has led to the development of software modules that manage different data typologies, according to a standard procedure that integrates clinical and genomic information, and correlates them with phenotypic description. From the clinical side, this resource allows the collection of patients anamnesis, its follow-up and the possibility to contribute to epidemiological studies. From the laboratory side, the portal allows to detect novel CNVs, on the basis that shared CNVs from patient with different phenotypes are probably functionally neutral while shared CNVs from patient with similar phenotypes can putatively be considered as “pathogenic” and concur to define new syndromes.

Phylogenetic diversity as an approach to look at change in hierarchical structured data as biological communities

A. Sandionigi , Saverio Vicario, E. M. Prosdocimi, A. Galimberti, A. Ferri, A. Bruno, Bachir Balech, V. Mezzasalma, M. Casiraghi

Motivations

Biological diversity was early identified in ecological studies as an important emergent property of natural systems, linked to the ability to persist through time. Unfortunately the difficulties in identifying common metrics for diversity contributed to produce a vast literature with unclear conclusion. Within an information theoretical framework it is possible to define diversity as the exponential of Shannon entropy and thereby obtain a self consistent measure of overall within and between group diversity. This framework was recently enlarged to take into account that biological entities (lineage, guild, species, or group of individuals) are differently diverse by using tree shaped similarity structure, allowing to define phylogenetic diversity within the frame of information theory (Chao A, Chiu CH, Jost 2010; Marcon and Herault 2014: Sandionigi A et al 2014).

Methods

21 pairs of larva bees and its parassite were sampled across 7 beehives in northern Italy. The microbiomes were extracted from each biological sample and V3 SSU region was amplified and sequenced with 454 FLX technologies. The reads were de-noised using ACACIA and the chimera detector of USEARCH. We compared the phylogenetic diversity approach as implemented in our tool PhyLOH with the distance approach (Jaccard, Chord, wUnifrac, Unifrac) implemented in QIIME taking in account or not phylogenetic information and abundance.

Results

We tested phyloH to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloH, was able to discriminate varroa microbiome from that of parasitized honeybees.

Conclusions

The phylogenetic diversity approach seems more sensitive than distance method and allow a more fine grain data exploration by inspecting the branch contribution to beta diversity. The method need to be enlarged to take in account phylogenetic uncertainty.


A bioinformatics approach for the prioritization of disease candidate human mtDNA mutations

Mariangela Santorsola, Claudia Calabrese, M. A. Diroma, G. Girolimetti, R. Clima, G. Gasparre, Marcella Attimonelli

Motivations

Assigning a pathogenic role to mitochondrial mutations and unveiling the potential involvement of the mitochondrial genome in diseases are challenging tasks in the field of human mitochondrial medicine. With this aim in mind, we designed a prioritization process in order to recognize rare disease-causing mutations for further investigations.

Methods

The prioritization process here implemented is based on the application of MToolBox software to mtDNA sequences. The workflow relies on an exhaustive functional annotation of mtDNA variants such as nucleotide variability, observed in the genomes of healthy subjects stored in HmtDB ; annotations from Mitomap; estimation of a disease score based on predictions of pathogenicity for non-synonymous changes.

Results

The disease score was estimated as the weighted mean of the probabilities that an amino acid substitution may be deleterious provided by several pathogenicity predictors. Disease score and nucleotide variability cutoff points were then established in order to discriminate events contributing to a defective phenotype. The prioritization criteria took into account the non-synonymous mutations recognized by rCRS, RSRS and Macro-Haplogroup Consensus Sequences at same time, non-haplogroup defining, featuring nucleotide variability lower than the variability cutoff and disease score higher than disease score cutoff.

Conclusions

The protocol was tested on mtDNA samples of colorectal adenocarcinoma from High Throughput and ovarian cancer from Sanger sequencing, enabling in the latter case the inference of also somatic non-synonymous mutations on the strength of prioritization criteria.


Docking-based virtual screening of chemical libraries for the identification of new apoptosis-inducer drugs

G Punzi, A Onofrio, S Todisco, MA DiNoia, G Parisi, G Redavid, MT Ricatti, Anna De Grassi, Ciro Leonardo Pierri

Motivations

Most of current cancer chemotherapeutics cause cell death via apoptosis. A recently proposed new powerful chemotherapy target is the mitochondrial ADP/ATP carrier (AAC). AAC plays a key role in the cell viability because it translocates the synthesized ATP from the mitochondrial matrix to the cytosol. Furthermore, AAC is a key component of the mitochondrial permeability transition pore that regulates mitochondrial apoptosis. Carboxyatractyloside (CATR) and Bongkrekic acid (BKA) are powerful and highly specific AAC inhibitors, and they can induce mitochondrial dysfunction at molecular level and poisoning at physiological level. For identifying other specific AAC inhibitors we performed docking-based virtual screening of an in-house developed chemical library.

Methods

In our analyses we used the crystallized AAC-CATR complex and the Autodock suite for screening a chemical library consisting of 10,000 bioactive compounds (that include also CATR and BKA as reference inhibitors) to identify a set of molecules with a high binding affinity for mitochondrial AAC. Autodock analyses are based on a Free Energy scoring function, already validated on various sets of protein–ligand complex structures, which evaluates the fitness between the AAC and the screened ligands. In vitro assays were performed for validating in silico predictions.

Results

From the virtual screening we identified 15 ligands predicted to have similar physical-chemical properties (in terms of binding energy) to those shown by CATR and BKA. The 15 candidates were used in in vitro transport assays and it was found that 4 of them were good AAC inhibitors. The inhibition constants of the known AAC inhibitors, i.e. CATR and BKA, were found to be 7nM and 1,8 mM respectively, whereas the inhibiton constants of the 4 newly identified inhibitors range between 0.2 and 2 mM.

Conclusions

Our analyses and simulations suggest that: 1) our computational strategy successfully identifies molecules with high affinity for AAC 2) in vitro assays show that those molecules are active as AAC inhibitors in the submicromolar range, and thus they can be used as scaffolds for drawing new potential drugs to be emplyed as apoptosis inducers.