Vers la reconstruction in silico des réseaux d'interaction des protéines : identification des interfaces DNA- et RNA-protéine, et réalisation d'une base de données d'interactions multiples des protéines

This thesis focuses on the characterization and prediction of DNA- and RNA-binding sites on protein structures, with some comparisons with protein-protein ones. We compiled and manually curated a non-redundant and representative set of 187 high resolution protein-DNA complexes, with the available 82 protein unbound conformations, that could be used as a reference benchmark. We conducted a comprehensive analysis of sequence- and structure-based properties of protein-DNA/RNA interfaces and compared them with respect to protein-protein interfaces and to non-interacting protein regions. We developed JET2DNA and JET2RNA, new methods for predicting DNA- and RNA-binding sites on protein surfaces. Combining four biologically meaningful descriptors, they outperform other machine-learning methods, in terms of predictive power and robustness to conformational changes. Our tools demonstrated to be instrumental in discovering alternative DNA/RNA-binding sites and in deciphering their properties. This could be very helpful for drug design and repurposing. To give a comprehensive view of plasticity of DNA-binding proteins and structural information on their multiple interactions, we constructed the Protein-(Protein)-DNA database (P(P)DNAdb). It comprises the 187 protein-DNA complexes in our benchmark, protein unbound forms and structures of other complexes where the proteins, or closed homologs, were in contact with other proteins. The user can access properties of the interfaces, visualize conformational changes associated to the binding of different partners and the location of the DNA-binding residues on the unbound structures and on the complexes with the other protein partners.Cette thèse porte sur la caractérisation et la prédiction des interfaces protéine-ADN et -ARN, et des comparaisons avec les interfaces protéine-protéine. Nous avons créé un ensemble non-redondant et représentatif de 187 complexes protéine-ADN à haute résolution, comprenant aussi les conformations non liées de 82 protéines. Cette base de données peut servir de référence dans le domaine. Nous avons mené une analyse exhaustive des propriétés de séquence et structurels des interfaces protéine-ADN/ARN et nous les avons comparé avec les propriétés des interfaces protéine-protéine et celles des régions protéiques non-interagissantes. Nous avons développé JET2DNA et JET2RNA, nouvelles méthodes pour la prediction des sites de liaison protéine-ADN/ARN à la surface des protéines. En combinant quatre descripteurs biologiquement pertinents, elles surpassent des méthodes par apprentissage machine. Elles permettent aussi de découvrir des sites de liaison alternatifs avec l'ADN/ARN et de déchiffrer leurs propriétés. Afin de donner un aperçu global de la plasticité des protéines interagissant avec l'ADN, nous avons construit la base de données protéine-(protéine)-ADN (P(P)DNAdb). Elle inclut les 187 complexes protéine-ADN de notre ensemble de référence, les forme libres des protéines et les structures des autres complexes où ces protéines, ou des homologues proches, sont impliqués. L'utilisateur peut accéder aux propriétés des interfaces, visualiser les changements de conformation associés à la liaison avec des partenaires différents et localiser les résidus interagissants avec l'ADN dans les autres structures de la même protéine

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

International audienceInteractions between proteins and nucleic acids are at the heart of many essential biological processes. Despite increasing structural information about how these interactions may take place, our understanding of the usage made of protein surfaces by nucleic acids is still very limited. This is in part due to the inherent complexity associated to protein surface deformability and evolution. In this work, we present a method that contributes to decipher such complexity by predicting protein-DNA interfaces and characterizing their properties. It relies on three biologically and physically meaningful descriptors, namely evolutionary conservation, physico-chemical properties and surface geometry. We carefully assessed its performance on several hundreds of protein structures and compared it to several machine-learning state-of-the-art methods. Our approach achieves a higher sensitivity compared to the other methods, with a similar precision. Importantly, we show that it is able to unravel 'hidden' binding sites by applying it to unbound protein structures and to proteins binding to DNA via multiple sites and in different conformations. It is also applicable to the detection of RNA-binding sites, without significant loss of performance. This confirms that DNA and RNA-binding sites share similar properties. Our method is implemented as a fully automated tool, [Formula: see text], freely accessible at: http://www.lcqb.upmc.fr/JET2DNA. We also provide a new dataset of 187 protein-DNA complex structures, along with a subset of 82 associated unbound structures. The set represents the largest body of high-resolution crystallographic structures of protein-DNA complexes, use biological protein assemblies as DNA-binding units, and covers all major types of protein-DNA interactions. It is available at: http://www.lcqb.upmc.fr/PDNAbenchmarks

Determination of the quality of lipoproteins by Raman spectroscopy in obese and healthy subjects

Lipoproteins (LPs) are multimolecular complexes of lipids and proteins responsible for transporting fatty acids, cholesterol, and micronutrients (carotenoids) through the body. The quantification of triglycerides and cholesterol carried by lipoproteins is a leading clinical parameter to assess the increased risk of cardiovascular events. However, in recent times, the study of the overall "quality" of lipoproteins, defined by their biochemical composition and oxidation state, has emerged as necessary to improve the definition of the cardiovascular risk. In this work, we present Raman spectroscopy (RS) as an effective method to immediately detect the functional groups relative to the principal biochemical components and the level of unsaturated lipids present in LPs. Furthermore, we show how RS can reveal the differences in the biochemical composition and oxidation state of LPs extracted from a cohort of obese patients (Ob) and a control group of healthy subjects (HC). In particular, RS revealed how low-density lipoproteins (LDLs) from obese patients are enriched in triglycerides and more oxidized than those from the control group, while high-density lipoproteins (HDLs) from Ob patients were depleted in cholesterol and phospholipids. RS analysis also allowed the study of the relationship between the levels of carotenoids present in the different classes of LPs highlighting how this parameter depends on the disease severity. Overall, these results demonstrated that RS is a viable approach for quickly and effectively gaining information on LPs' biochemical composition and oxidation state, providing an immediate measure of their quality. Besides, RS further proved the role of LPs in obesity and metabolic dysfunctions

Trauma na gestante: análise da mortalidade materna e fetal

Foram analisadas retrospectivamente 26 pacientes gestantes traumatizadas, num período de nove anos. A média de idade foi 23,7 anos (16-42). A idade gestacional variou de dez a quarenta semanas (média 21,5 semanas); a maioria (46,1%) no segundo trimestre. O mecanismo predominante (65,3%) foi o trauma abdominal fechado por acidente automobilístico (atropelamento ou colisão). Na admissão, oito (30,7%) pacientes apresentavam alterações hemodinâmicas. Seis doentes (23,0%) apresentavam sangramento vaginal e, destas, quatro estavam hemodinamicamente normais. Analisamos a mortalidade materna, a mortalidade fetal e suas causas. Comparamos também a mediana dos valores do RTS e TRISS entre os grupos, sobrevida materno-fetal, sobrevida materna e óbito materno-fetal. Todas as gestantes admitidas com sangramento vaginal apresentaram óbito fetal. A mortalidade materna foi de 11,5%, por choque hemorrágico. A mortalidade fetal foi de 30,7%, sendo que 37,5% destes óbitos foram provocados pela morte materna. A principal causa de mortalidade fetal foi o descolamento de placenta (50,0%). Os índices de trauma, RTS e TRISS, foram significativamente menor (p=0,0025 e p<0,0001) no grupo óbito materno-fetal, porém esses índices não apresentaram valor prognóstico na mortalidade fetal

Morphological and immunophenotypical changes of human bone marrow adipocytes in marrow metastasis and myelofibrosis

The bone marrow adipose tissue constitutes more than two-thirds of the bone marrow volume in adult life and is known to have unique metabolic and functional properties. In neoplastic disorders, bone marrow adipocytes (BMAds) contribute to create a favorable microenvironment to survival and proliferation of cancer cells. Many studies explored the molecular crosstalk between BMAds and neoplastic cells, predominantly in ex-vivo experimental systems or in animal models. However, little is known on the features of BMAds in the human neoplastic marrow. The aim of our study was to analyze the in situ changes in morphology and immunophenotype of BMAds in two different types of neoplastic marrow conditions. We selected a series of archival iliac crest and vertebral bone biopsies from patients with bone marrow metastasis (MET), patients with myeloproliferative neoplasia with grade-3 myelofibrosis (MPN-MF) and age-matched controls (CTR). We observed a significant reduction in the number of BMAds in MET and MPN-MF compared to CTR. Accordingly, in the same groups, we also detected a significant reduction in the mean cell diameter and area. Immunolocalization of different adipocyte markers showed that, compared to CTR, in both MET and MPN-MF the percentages of adiponectin- and phosphorylated hormone sensitive lipase-positive BMAds were significantly reduced and increased respectively. No statistically significant difference was found between MET and MPN-MF. Interestingly, in one MET sample, “remodeled” BMAds containing a large lipid vacuole and multiple, smaller and polarized lipid droplets were identified. In conclusion, our data show that in different types of marrow cancers, BMAds undergo significant quantitative and qualitative changes, which need to be further investigated in future studies

"Delirium Day": A nationwide point prevalence study of delirium in older hospitalized patients using an easy standardized diagnostic tool

Background: To date, delirium prevalence in adult acute hospital populations has been estimated generally from pooled findings of single-center studies and/or among specific patient populations. Furthermore, the number of participants in these studies has not exceeded a few hundred. To overcome these limitations, we have determined, in a multicenter study, the prevalence of delirium over a single day among a large population of patients admitted to acute and rehabilitation hospital wards in Italy. Methods: This is a point prevalence study (called "Delirium Day") including 1867 older patients (aged 65 years or more) across 108 acute and 12 rehabilitation wards in Italian hospitals. Delirium was assessed on the same day in all patients using the 4AT, a validated and briefly administered tool which does not require training. We also collected data regarding motoric subtypes of delirium, functional and nutritional status, dementia, comorbidity, medications, feeding tubes, peripheral venous and urinary catheters, and physical restraints. Results: The mean sample age was 82.0 ± 7.5 years (58 % female). Overall, 429 patients (22.9 %) had delirium. Hypoactive was the commonest subtype (132/344 patients, 38.5 %), followed by mixed, hyperactive, and nonmotoric delirium. The prevalence was highest in Neurology (28.5 %) and Geriatrics (24.7 %), lowest in Rehabilitation (14.0 %), and intermediate in Orthopedic (20.6 %) and Internal Medicine wards (21.4 %). In a multivariable logistic regression, age (odds ratio [OR] 1.03, 95 % confidence interval [CI] 1.01-1.05), Activities of Daily Living dependence (OR 1.19, 95 % CI 1.12-1.27), dementia (OR 3.25, 95 % CI 2.41-4.38), malnutrition (OR 2.01, 95 % CI 1.29-3.14), and use of antipsychotics (OR 2.03, 95 % CI 1.45-2.82), feeding tubes (OR 2.51, 95 % CI 1.11-5.66), peripheral venous catheters (OR 1.41, 95 % CI 1.06-1.87), urinary catheters (OR 1.73, 95 % CI 1.30-2.29), and physical restraints (OR 1.84, 95 % CI 1.40-2.40) were associated with delirium. Admission to Neurology wards was also associated with delirium (OR 2.00, 95 % CI 1.29-3.14), while admission to other settings was not. Conclusions: Delirium occurred in more than one out of five patients in acute and rehabilitation hospital wards. Prevalence was highest in Neurology and lowest in Rehabilitation divisions. The "Delirium Day" project might become a useful method to assess delirium across hospital settings and a benchmarking platform for future surveys