Development of human central nervous system 3D in vitro models for preclinical research

Neurological disorders are a major concern in modern societies, with increasing prevalence mainly related with the higher life expectancy. Most of the current available therapeutic options can only control and ameliorate the patients’ symptoms, often be-coming refractory over time. Therapeutic breakthroughs and advances have been hampered by the lack of accurate central nervous system (CNS) models. The develop-ment of these models allows the study of the disease onset/progression mechanisms and the preclinical evaluation of novel therapeutics. This has traditionally relied on genetically engineered animal models that often diverge considerably from the human phenotype (developmentally, anatomically and physiologically) and 2D in vitro cell models, which fail to recapitulate the characteristics of the target tissue (cell-cell and cell-matrix interactions, cell polarity). The in vitro recapitulation of CNS phenotypic and functional features requires the implementation of advanced culture strategies that enable to mimic the in vivo struc-tural and molecular complexity. Models based on differentiation of human neural stem cells (hNSC) in 3D cultures have great potential as complementary tools in preclinical research, bridging the gap between human clinical studies and animal models. This thesis aimed at the development of novel human 3D in vitro CNS models by integrat-ing agitation-based culture systems and a wide array of characterization tools. Neural differentiation of hNSC as 3D neurospheres was explored in Chapter 2. Here, it was demonstrated that human midbrain-derived neural progenitor cells from fetal origin (hmNPC) can generate complex tissue-like structures containing functional dopaminergic neurons, as well as astrocytes and oligodendrocytes. Chapter 3 focused on the development of cellular characterization assays for cell aggregates based on light-sheet fluorescence imaging systems, which resulted in increased spatial resolu-tion both for fixed samples or live imaging. The applicability of the developed human 3D cell model for preclinical research was explored in Chapter 4, evaluating the poten-tial of a viral vector candidate for gene therapy. The efficacy and safety of helper-dependent CAV-2 (hd-CAV-2) for gene delivery in human neurons was evaluated, demonstrating increased neuronal tropism, efficient transgene expression and minimal toxicity. The potential of human 3D in vitro CNS models to mimic brain functions was further addressed in Chapter 5. Exploring the use of 13C-labeled substrates and Nucle-ar Magnetic Resonance (NMR) spectroscopy tools, neural metabolic signatures were evaluated showing lineage-specific metabolic specialization and establishment of neu-ron-astrocytic shuttles upon differentiation. Chapter 6 focused on transferring the knowledge and strategies described in the previous chapters for the implementation of a scalable and robust process for the 3D differentiation of hNSC derived from human induced pluripotent stem cells (hiPSC). Here, software-controlled perfusion stirred-tank bioreactors were used as technological system to sustain cell aggregation and dif-ferentiation. The work developed in this thesis provides practical and versatile new in vitro ap-proaches to model the human brain. Furthermore, the culture strategies described herein can be further extended to other sources of neural phenotypes, including pa-tient-derived hiPSC. The combination of this 3D culture strategy with the implemented characterization methods represents a powerful complementary tool applicable in the drug discovery, toxicology and disease modeling.

Exploring TM image texture and its relationships with biomass estimation in Rondônia, Brazilian Amazon

Many texture measures have been developed and used for improving land-cover classification accuracy, but rarely has research examined the role of textures in improving the performance of aboveground biomass estimations. The relationship between texture and biomass is poorly understood. This paper used Landsat Thematic Mapper (TM) data to explore relationships between TM image textures and aboveground biomass in Rondônia, Brazilian Amazon. Eight grey level co-occurrence matrix (GLCM) based texture measures (i.e., mean, variance, homogeneity, contrast, dissimilarity, entropy, second moment, and correlation), associated with seven different window sizes (5x5, 7x7, 9x9, 11x11, 15x15, 19x19, and 25x25), and five TM bands (TM 2, 3, 4, 5, and 7) were analyzed. Pearson's correlation coefficient was used to analyze texture and biomass relationships. This research indicates that most textures are weakly correlated with successional vegetation biomass, but some textures are significantly correlated with mature forest biomass. In contrast, TM spectral signatures are significantly correlated with successional vegetation biomass, but weakly correlated with mature forest biomass. Our findings imply that textures may be critical in improving mature forest biomass estimation, but relatively less important for successional vegetation biomass estimation.

Search for massive supersymmetric particles decaying to many jets using the ATLAS detector in pp collisions at s√=8TeV

Results of a search for decays of massive particles to fully hadronic final states are presented. This search uses 20.3 fb−1 of data collected by the ATLAS detector in s√=8TeV proton--proton collisions at the LHC. Signatures based on high jet multiplicities without requirements on the missing transverse momentum are used to search for R-parity-violating supersymmetric gluino pair production with subsequent decays to quarks. The analysis is performed using a requirement on the number of jets, in combination with separate requirements on the number of b-tagged jets, as well as a topological observable formed from the scalar sum of the mass values of large-radius jets in the event. Results are interpreted in the context of all possible branching ratios of direct gluino decays to various quark flavors. No significant deviation is observed from the expected Standard Model backgrounds estimated using jet-counting as well as data-driven templates of the total-jet-mass spectra. Gluino pair decays to ten or more quarks via intermediate neutralinos are excluded for a gluino with mass mg~<1TeV for a neutralino mass mχ~01=500GeV. Direct gluino decays to six quarks are excluded for mg~<917GeV for light-flavor final states, and results for various flavor hypotheses are presented.

Observation and measurements of the production of prompt and non-prompt J/ψ mesons in association with a Z boson in pp collisions at s√ = 8 TeV with the ATLAS detector

The production of a Z boson in association with a J/ψ meson in proton--proton collisions probes the production mechanisms of quarkonium and heavy flavour in association with vector bosons, and allows studies of multiple parton scattering. Using 20.3fb−1 of data collected with the ATLAS experiment at the LHC, in pp collisions at s√=8 TeV, the first measurement of associated Z+J/ψ production is presented for both prompt and non-prompt J/ψ production, with both signatures having a significance in excess of 5σ. The inclusive production cross-sections for Z boson production (in μ+μ− or e+e− decay modes) in association with prompt and non-prompt J/ψ(→μ+μ−) are measured relative to the inclusive production rate of Z bosons in the same fiducial volume to be (88±16±6)×10−8 and (157±22±10)×10−8 respectively. Normalised differential production cross-sections are also determined as a function of the J/ψ transverse momentum. The fraction of signal events arising from single and double parton scattering is estimated, and a lower limit of 5.3 (3.7)mb at 68 (95) confidence level is placed on the effective cross-section regulating double parton interactions.

HOXA9 as a key regulator in glioma initiation, aggressiveness and response to therapy

Tese de Doutoramento em Ciências da Saúde

Lipids under stress - a lipidomic approach for the study of mood disorders

The emerging field of lipidomics has identified lipids as key players in disease physiology. Their physicochemical diversity allows precise control of cell structure and signaling events through modulation of membrane prop- erties and trafficking of proteins. As such, lipids are important regulators of brain function and have been implicated in neurodegenerative and mood disorders. Importantly, environmental chronic stress has been associated with anxiety and depression and its exposure in rodents has been extensively used as a model to study these diseases. With the accessibility to modern mass- spectrometry lipidomic platforms, it is now possible to snapshot the extensively interconnected lipid network. Here, we review the fundamentals of lipid biology and outline a framework for the interpretation of lipidomic studies as a new approach to study brain pathophysiology. Thus, lipid profiling provides an exciting avenue for the identification of disease signatures with important implications for diagnosis and treatment of mood disorders.

Factoriality and the pin-reutenauer procedure

We consider implicit signatures over finite semigroups determined by sets of pseudonatural numbers. We prove that, under relatively simple hypotheses on a pseudovariety V of semigroups, the finitely generated free algebra for the largest such signature is closed under taking factors within the free pro-V semigroup on the same set of generators. Furthermore, we show that the natural analogue of the Pin-Reutenauer descriptive procedure for the closure of a rational language in the free group with respect to the profinite topology holds for the pseudovariety of all finite semigroups. As an application, we establish that a pseudovariety enjoys this property if and only if it is full.

Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.

Metabolic traits are molecular phenotypes that can drive clinical phenotypes and may predict disease progression. Here, we report results from a metabolome- and genome-wide association study on (1)H-NMR urine metabolic profiles. The study was conducted within an untargeted approach, employing a novel method for compound identification. From our discovery cohort of 835 Caucasian individuals who participated in the CoLaus study, we identified 139 suggestively significant (P<5×10(-8)) and independent associations between single nucleotide polymorphisms (SNP) and metabolome features. Fifty-six of these associations replicated in the TasteSensomics cohort, comprising 601 individuals from São Paulo of vastly diverse ethnic background. They correspond to eleven gene-metabolite associations, six of which had been previously identified in the urine metabolome and three in the serum metabolome. Our key novel findings are the associations of two SNPs with NMR spectral signatures pointing to fucose (rs492602, P = 6.9×10(-44)) and lysine (rs8101881, P = 1.2×10(-33)), respectively. Fine-mapping of the first locus pinpointed the FUT2 gene, which encodes a fucosyltransferase enzyme and has previously been associated with Crohn's disease. This implicates fucose as a potential prognostic disease marker, for which there is already published evidence from a mouse model. The second SNP lies within the SLC7A9 gene, rare mutations of which have been linked to severe kidney damage. The replication of previous associations and our new discoveries demonstrate the potential of untargeted metabolomics GWAS to robustly identify molecular disease markers.

Coevolution of restriction factors and retroviruses

Les virus exploitent la machinerie cellulaire de l'hôte pour se répliquer. Ils doivent s'adapter pour infecter la cellule hôte de manière optimale tout en échappant à la vigilance du système de défense de l'hôte. Ainsi l'hôte et les virus se livrent à de constantes batailles évolutives. Mon travail de thèse a porté sur l'étude des signatures évolutives de facteurs de l'hôte agissant comme des 'facteurs de restriction' en bloquant la réplication rétrovirale chez les primates. Plus spécifiquement, mon travail a visé à utiliser des données évolutives pour renseigner les analyses fonctionnelles et la biologie. Nous avons étudié le facteur anti-VIH-1 nommé TRIM5a (i) chez les prosimiens pour mieux comprendre son rôle dans le contrôle d'un lentivirus endogène, (ii) dans son activité contre d'autres anciennes infections représentées par des rétrovirus endogènes humains et (iii) en tant que protéine capable de générer des mutants de la capside. Premièrement nous nous sommes intéressés à TRIM5a chez deux espèces de lémuriens dont Microcebus murinus qui porte le lentivirus endogène PSIV dans son génome depuis plusieurs millions d'années,. Nous avons observé que TRIM5a chez M. murinus a un spectre d'activité antivirale réduit à l'opposé de TRIM5a chez le Lemur catta - non porteur du PSIV endogène - qui bloque une large variété de rétrovirus dont le PSIV. De ce fait TRIM5a aurait pu contribuer à protéger certaines espèces de lémuriens vis-à-vis d'anciennes infections par le PSIV. A l'inverse du PSIV, des virus dérivés des rétrovirus endogènes humains HERV-K and HERV-H se sont révélés largement résistants à l'inhibition par TRIM5a. Ces données illustrent une absence de protection par TRIM5a face à d'autres anciennes infections rétrovirales. Puis, pour évaluer l'impact de la protéine TRIM5a humaine sur le VIH-1, nous avons testé l'effet de mutations des résidues sous sélection positive dans la capside du VIH-1 sur l'inhibition par TRIM5a. Nos résultats montrent que TRIM5a ne jouerait pas un rôle significatif dans l'évolution de la capside du VIH-1. Enfin notre travail a porté sur le facteur anti-VIH-1 SAMHD1 récemment découvert, que nous avons séquencé chez 25 espèces de primates. L'analyse évolutive des sites sous sélection positive et des expériences fonctionnelles ont permis d'identifier le domaine de SAMHD1 interagissant avec la protéine lentivirale Vpx. De même que d'autres protéines virales contrecarrent les facteurs de restriction en les menant à la dégradation, nous avons observé que Vpx induit la dégradation de SAMHD1 de manière spécifique à l'espèce. Ces découvertes contribuent à comprendre comment les facteurs de restriction et les virus co-évoluent pour se neutraliser l'un l'autre. - Viruses hijack the host cellular machinery to replicate. They adapt to infect optimally host cells while escaping host defense systems. Viruses and the host coevolve in an evolutionary struggle. My thesis work has been devoted to study the evolutionary signatures of host factors acting as restriction factors that block retroviral replication in primates. Specifically, my work aimed at using evolutionary data to inform functional analyses and biology. We studied the anti-HIV-1 factor TRIM5a (i) in prosimians to better understand its possible role in the control of an endogenous lentivirus, (ii) in its activity against other ancient infections - as represented by HERVs, and (iii) as a protein capable of generating escape mutants in the viral capsid. First, my work focused on two lemur species, one of which was the gray mouse lemur that carries the endogenous lentivirus PSIV integrated in its genome for several million years. TRIM5a from gray mouse lemur exhibited a limited antiviral spectrum as opposed to TRIM5a from ring-tailed lemur - not a host of PSIV - that is able to block diverse retroviruses notably PSIV. These results support the possible contribution of TRIM5a in protecting lemur species from ancient infection by PSIV. In contrast, chimeric viruses derived from two human endogenous retroviruses were broadly resistant to TRIM5a-mediated restriction, suggesting TRIM5a lack of activity against other types of ancient infections. To evaluate the recent impact of human TRIM5a on HIV-1 evolution, we tested whether variants at positively selected sites in the HIV-1 capsid affected the ability of human TRIM5a alleles to restrict HIV-1. Our results indicate that TRIM5a does not play a significant role in the evolution of HIV1 capsid. At last, our work concentrated on the newly discovered anti-HIV-1 restriction factor SAMHD1. We determined its coding sequence in a panel of 25 species of primates. Evolutionary analyses of positively selected sites in SAMHD1 domains and functional assays identified the domain of SAMHD1 interacting with the lentiviral protein Vpx. Similar to other viral countermeasures targeting cellular restriction factors, Vpx was responsible of the degradation of SAMHD1 orthologs in a species-specific manner. These findings contributed to understanding how restriction factors and viruses evolve to counteract each other.

A novel gene expression signature in peripheral blood mononuclear cells for early detection of colorectal cancer.

BACKGROUND: Early detection and treatment of colorectal adenomatous polyps (AP) and colorectal cancer (CRC) is associated with decreased mortality for CRC. However, accurate, non-invasive and compliant tests to screen for AP and early stages of CRC are not yet available. A blood-based screening test is highly attractive due to limited invasiveness and high acceptance rate among patients. AIM: To demonstrate whether gene expression signatures in the peripheral blood mononuclear cells (PBMC) were able to detect the presence of AP and early stages CRC. METHODS: A total of 85 PBMC samples derived from colonoscopy-verified subjects without lesion (controls) (n = 41), with AP (n = 21) or with CRC (n = 23) were used as training sets. A 42-gene panel for CRC and AP discrimination, including genes identified by Digital Gene Expression-tag profiling of PBMC, and genes previously characterised and reported in the literature, was validated on the training set by qPCR. Logistic regression analysis followed by bootstrap validation determined CRC- and AP-specific classifiers, which discriminate patients with CRC and AP from controls. RESULTS: The CRC and AP classifiers were able to detect CRC with a sensitivity of 78% and AP with a sensitivity of 46% respectively. Both classifiers had a specificity of 92% with very low false-positive detection when applied on subjects with inflammatory bowel disease (n = 23) or tumours other than CRC (n = 14). CONCLUSION: This pilot study demonstrates the potential of developing a minimally invasive, accurate test to screen patients at average risk for colorectal cancer, based on gene expression analysis of peripheral blood mononuclear cells obtained from a simple blood sample.

Transcriptional profiling of CD4 T cells identifies distinct subgroups of HIV-1 elite controllers.

Human immunodeficiency virus type 1 (HIV-1) elite controllers maintain undetectable levels of viral replication in the absence of antiretroviral therapy (ART), but their underlying immunological and virological characteristics may vary. Here, we used a whole-genome transcriptional profiling approach to characterize gene expression signatures of CD4 T cells from an unselected cohort of elite controllers. The transcriptional profiles for the majority of elite controllers were similar to those of ART-treated patients but different from those of HIV-1-negative persons. Yet, a smaller proportion of elite controllers showed an alternative gene expression pattern that was indistinguishable from that of HIV-1-negative persons but different from that of highly active antiretroviral therapy (HAART)-treated individuals. Elite controllers with the latter gene expression signature had significantly higher CD4 T cell counts and lower levels of HIV-1-specific CD8(+) T cell responses but did not significantly differ from other elite controllers in terms of HLA class I alleles, HIV-1 viral loads determined by ultrasensitive single-copy PCR assays, or chemokine receptor polymorphisms. Thus, these data identify a specific subgroup of elite controllers whose immunological and gene expression characteristics approximate those of HIV-1-negative persons.

COLOX: a new blood-based test for colorectal cancer screening

INTRODUCTION/OBJECTIVES: Detection rates for adenoma and early colorectal cancer (CRC) are insufficient due to low compliance towards invasive screening procedures, like colonoscopy.Available non-invasive screening tests have unfortunately low sensitivity and specificity performances.Therefore, there is a large unmet need calling for a cost-effective, reliable and non-invasive test to screen for early neoplastic and pre-neoplastic lesions AIMS & Methods: The objective is to develop a screening test able to detect early CRCs and adenomas.This test is based on a nucleic acids multi-gene assay performed on peripheral blood mononuclear cells (PBMCs).A colonoscopy-controlled feasibility study was conducted on 179 subjects.The first 92 subjects was used as training set to generate a statistical significant signature.Colonoscopy revealed 21 subjects with CRC,30 with adenoma bigger than 1 cm and 41 with no neoplastic or inflammatory lesions.The second group of 48 subjects (controls, CRC and polyps) was used as a test set and will be kept blinded for the entire data analysis.To determine the organ and disease specificity 38 subjects were used:24 with inflammatory bowel disease (IBD),14 with other cancers than CRC (OC).Blood samples were taken from each patient the day of the colonoscopy and PBMCs were purified. Total RNA was extracted following standard procedures.Multiplex RT-qPCR was applied on 92 different candidate biomarkers.Different univariate and multivariate statistical methods were applied on these candidates and among them 60 biomarkers with significant p-values (<0.01) were selected.These biomarkers are involved in several different biological functions as cellular movement,cell signaling and interaction,tissue and cellular development,cancer and cell growth and proliferation.Two distinct biomarker signatures are used to separate patients without lesion from those with cancer or with adenoma, named COLOX CRC and COLOX POL respectively.COLOX performances were validated using random resampling method, bootstrap. RESULTS: COLOX CRC and POL tests successfully separate patients without lesions from those with CRC (Se 67%,Sp 93%,AUC 0.87) and from those with adenoma bigger than 1cm (Se 63%,Sp 83%,AUC 0.77),respectively. 6/24 patients in the IBD group and 1/14 patients in the OC group have a positive COLOX CRC CONCLUSION: The two COLOX tests demonstrated a high sensitivity and specificity to detect the presence of CRCs and adenomas bigger than 1 cm.A prospective, multicenter, pivotal study is underway in order to confirm these promising results in a larger cohort.

Expansió accelerada de l’univers i teories de gravetat modificada a grans escales

Estudi realitzat a partir d’una estada al Physics Department de la New York University, United States, Estats Units, entre 2006 i 2008. Una de les observacions de més impacte en la cosmologia moderna ha estat la determinació empírica que l’Univers es troba actualment en una fase d’Expansió Accelerada (EA). Aquest fenòmen implica que o bé l’Univers està dominat per un nou sector de matèria/energia, o bé la Relativitat General deixa de tenir validesa a escales cosmològiques. La primera possibilitat comprèn els models d’Energia Fosca (EF), i el seu principal problema és que l’EF ha de tenir propietats tan especials que es fan difícils de justificar teòricament. La segona possibilitat requereix la construcció de teories consistents de Gravetat Modificada a Grans Distàncies (GMGD), que són una generalització dels models de gravetat massiva. L’interès fenomenològic per aquestes teories també va resorgir amb l’aparició dels primers exemples de models de GMGD, com ara el model de Dvali, Gabadadze i Porrati (DGP), que consisteix en un tipus de brana en una dimensió extra. Malauradament, però, aquest model no permet explicar de forma consistent l’EA de l’Univers. Un dels objectius d’aquest projecte ha estat establir la viabilitat interna i fenomenològica dels models de GMGD. Des del punt de vista fenomenològic, ens hem centrat en la questió més important a la pràctica: trobar signatures observacionals que permetin distingir els models de GMGD dels d’EF. A nivell més teòric, també hem investigat el significat de les inestabilitats del model DGP.L’altre gran objectiu que ens vam proposar va ser la construcció de noves teories de GMGD. En la segona part d’aquest projecte, hem elaborat i mostrat la consistència del model “DGP en Cascada”, que generalitza el model DGP a més dimensions extra, i representa el segon model consistent i invariant-Lorentz a l’espai pla conegut. L’existència d’altres models de GMGD més enllà de DGP és de gran interès atès que podria permetre obtenir l’EA de l’Univers de forma purament geomètrica.

Fine structural variations of alphabetaTCRs selected by vaccination with natural versus altered self-antigen in melanoma patients.

Immunotherapy of cancer is often performed with altered "analog" peptide Ags optimized for HLA class I binding, resulting in enhanced immunogenicity, but the induced T cell responses require further evaluation. Recently, we demonstrated fine specificity differences and enhanced recognition of naturally presented Ag by T cells after vaccination with natural Melan-A/MART-1 peptide, as compared with analog peptide. In this study, we compared the TCR primary structures of 1489 HLA-A*0201/Melan-A(26-35)-specific CD8 T cells derived from both cohorts of patients. Although a strong preference for TRAV12-2 segment usage was present in nearly all patients, usage of particular TRAJ gene segments and CDR3alpha composition differed slightly after vaccination with natural vs analog peptide. Moreover, TCR beta-chain repertoires were broader after natural than analog peptide vaccination. In all patients, we observed a marked conservation of the CDR3beta amino acid composition with recurrent sequences centered on a glycyl-leucyl/valyl/alanyl-glycyl motif. In contrast to viral-specific TCR repertoires, such "public" motifs were primarily expressed by nondominant T cell clonotypes, which contrasted with "private" CDR3beta signatures frequently found in T cell clonotypes that dominated repertoires of individual patients. Interestingly, no differences in functional avidity were observed between public and private T cell clonotypes. Collectively, our data indicate that T cell repertoires generated against natural or analog Melan-A peptide exhibited slightly distinct but otherwise overlapping and structurally conserved TCR features, suggesting that the differences in binding affinity/avidity of TCRs toward pMHC observed in the two cohorts of patients are caused by subtle structural TCR variations.

Evolutionary genomics and HIV restriction factors.

PURPOSE OF REVIEW: To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. RECENT FINDINGS: Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. SUMMARY: Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.