A computational analysis of protein-protein interaction networks in neurodegenerative diseases

<p>Abstract</p> <p>Background</p> <p>Recent developments have meant that network theory is making an important contribution to the topological study of biological networks, such as protein-protein interaction (PPI) networks. The identification of differentially expressed genes in DNA array experiments is a source of information regarding the molecular pathways involved in disease. Thus, considering PPI analysis and gene expression studies together may provide a better understanding of multifactorial neurodegenerative diseases such as Multiple Sclerosis (MS) and Alzheimer disease (AD). The aim of this study was to assess whether the parameters of degree and betweenness, two fundamental measures in network theory, are properties that differentiate between implicated (seed-proteins) and non-implicated nodes (neighbors) in MS and AD. We used experimentally validated PPI information to obtain the neighbors for each seed group and we studied these parameters in four networks: MS-blood network; MS-brain network; AD-blood network; and AD-brain network.</p> <p>Results</p> <p>Specific features of seed-proteins were revealed, whereby they displayed a lower average degree in both diseases and tissues, and a higher betweenness in AD-brain and MS-blood networks. Additionally, the heterogeneity of the processes involved indicate that these findings are not pathway specific but rather that they are spread over different pathways.</p> <p>Conclusion</p> <p>Our findings show differential centrality properties of proteins whose gene expression is impaired in neurodegenerative diseases.</p

Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction

Background Amyloid precursor protein (APP) is widely recognized for playing a central role in Alzheimer's disease pathogenesis. Although APP is expressed in several tissues outside the human central nervous system, the functions of APP and its family members in other tissues are still poorly understood. APP is involved in several biological functions which might be potentially important for male fertility, such as cell adhesion, cell motility, signaling, and apoptosis. Furthermore, APP superfamily members are known to be associated with fertility. Knowledge on the protein networks of APP in human testis and spermatozoa will shed light on the function of APP in the male reproductive system. Results We performed a Yeast Two-Hybrid screen and a database search to study the interaction network of APP in human testis and sperm. To gain insights into the role of APP superfamily members in fertility, the study was extended to APP-like protein 2 (APLP2). We analyzed several topological properties of the APP interaction network and the biological and physiological properties of the proteins in the APP interaction network were also specified by gene ontologyand pathways analyses. We classified significant features related to the human male reproduction for the APP interacting proteins and identified modules of proteins with similar functional roles which may show cooperative behavior for male fertility. Conclusions The present work provides the first report on the APP interactome in human testis. Our approach allowed the identification of novel interactions and recognition of key APP interacting proteins for male reproduction, particularly in sperm-oocyte interaction.publishe

Redes metabólicas no envelhecimento e doenças relacionadas com o envelhecimento

Aging is a natural physiological process, but its specific causes are not entirely understood at the molecular level. During aging, the levels of the redox cofactor Nicotinamide Adenine Dinucleotide (NAD) decrease. This molecule is essential for energy production by the cell and is also a substrate to a range of enzymes that regulate gene expression and cell survival. To gain insight into the metabolic networks of age-related disorders, we took a combined bioinformatics and molecular approach. We used text-mining methods to extract protein interaction data from 1500 PubMed abstracts containing keywords related to proteostasis, aging and age-related diseases. Protein networks were obtained with Cytoscape and were submitted to parameter-based analysis. An enrichment analysis using the cytoscape plug-in ClueGo was followed. Parameter analysis revealed APP as the most central and influential protein in the network and enrichment analysis depicted a predominance of terms related to Immune system along with Cancer and Cell Cycle regulation. As a cellular model, we have used a NAD metabolism inhibitor in SH-SY5Y neuroblastoma cells to mimic the NAD decline during aging. At different time points (8h, 24h, and 48h) we measured cell viability along with the expression levels of NAMPT and NAPRT, the rate-limiting enzymes from the NAD biosynthetic nicotinamide salvage pathway and the Preiss handler pathway respectively. Our results show a 50% decrease in cell viability at 48h along with a decrease in NAPRT protein expression. No alterations in NAMPT protein levels were recorded in any measured time point. It is possible that other NAD biosynthesis pathways are activated, so further studies intended to elucidate question are required.O envelhecimento é um processo fisiológico natural, contudo as suas causas específicas não são totalmente compreendidas ao nível molecular. Durante o envelhecimento, os níveis do cofator redox Nicotinamida Adenina Dinucleotídeo (NAD+) diminuem. Esta molécula é essencial para a produção de energia por parte da célula e também é um substrato para uma variedade de enzimas que regulam a expressão genética e a sobrevivência celular. Para obter informações sobre as redes metabólicas de doenças relacionadas com o envelhecimento, adotamos uma combinação de abordagens bioinformática e molecular. Utilizamos métodos de extração de texto para extrair dados de interação proteica de 1500 resumos de artigos da PubMed contendo palavras-chave relacionadas com proteostase, envelhecimento e doenças relacionadas com o envelhecimento. As redes de proteínas foram obtidas com o Cytoscape e submetidas a uma análise baseada em parâmetros. Seguiu-se uma análise de enriquecimento usando o ClueGo um plug-in do Cytoscape. A análise de parâmetros revelou APP como a proteína mais central e influente na rede e a análise de enriquecimento retratou uma predominância de termos relacionados com o sistema imunológico, juntamente com a regulação do ciclo celular. Como modelo celular, usamos um inibidor do metabolismo do NAD+ em células de neuroblastoma SH-SY5Y para imitar o declínio do NAD+ durante o envelhecimento. Em diferentes momentos (8h, 24h, 48h e 72h), medimos a viabilidade celular juntamente com os níveis de expressão de NAMPT e NAPRT, as enzimas limitadoras de taxa das vias Salvage de Nicotinamida e Preiss-Handler, respetivamente, ambas vias de produtoras de NAD+. Os Nossos resultados mostram uma diminuição de 50% na viabilidade celular às 48h, juntamente com uma diminuição na expressão proteica de NAPRT. Não foram registadas alterações nos níveis de proteína NAMPT em nenhum momento. É possível que outras vias de biossíntese do NAD+ estejam ativas, de maneira que outros estudos com o objetivo de elucidar esta questão são necessários.Mestrado em Biomedicina Molecula

Assembly and Interrogation of Alzheimer’s Disease Genetic Networks Reveal Novel Regulators of Progression

Alzheimer’s disease (AD) is a complex multifactorial disorder with poorly characterized pathogenesis. Our understanding of this disease would thus benefit from an approach that addresses this complexity by elucidating the regulatory networks that are dysregulated in the neural compartment of AD patients, across distinct brain regions. Here, we use a Systems Biology (SB) approach, which has been highly successful in the dissection of cancer related phenotypes, to reverse engineer the transcriptional regulation layer of human neuronal cells and interrogate it to infer candidate Master Regulators (MRs) responsible for disease progression. Analysis of gene expression profiles from laser-captured neurons from AD and controls subjects, using the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe), yielded an interactome consisting of 488,353 transcription-factor/ target interactions. Interrogation of this interactome, using the Master Regulator INference algorithm (MARINa), identified an unbiased set of candidate MRs causally responsible for regulating the transcriptional signature of AD progression. Experimental assays in autopsyderived human brain tissue showed that three of the top candidate MRs (YY1, p300 and ZMYM3) are indeed biochemically and histopathologically dysregulated in AD brains compared to controls. Our results additionally implicate p53 and loss of acetylation homeostasis in the neurodegenerative process. This study suggests that an integrative, SB approach can be applied to AD and other neurodegenerative diseases, and provide significant novel insight on the disease progression

New methods for studying complex diseases via genetic association studies

Genome-wide association studies (GWAS) have delivered many novel insights about the etiology of many common heritable diseases. However, in most disorders studied by GWAS, the known single nucleotide polymorphisms (SNPs) associated with the disease do not account for a large portion of the genetic factors underlying the condition. This suggests that many of the undiscovered variants contributing to the risk of common diseases have weak effects or are relatively rare. This thesis introduces novel adaptations of techniques for improving detection power for both of these types of risk variants, and reports the results of analyses applying these methods to real datasets for common diseases. Chapter 2 describes a novel approach to improve the detection of weak-effect risk variants that is based on an adaptive sampling technique known as Distilled Sensing (DS). This procedure entails utilization of a portion of the total sample to exclude from consideration regions of the genome where there is no evidence of genetic association, and then testing for association with a greatly reduced number of variants in the remaining sample. Application of the method to simulated data sets and GWAS data from studies of age-related macular degeneration (AMD) demonstrated that, in many situations, DS can have superior power over traditional meta-analysis techniques to detect weak-effect loci. Chapter 3 describes an innovative pipeline to screen for rare variants in next generation sequencing (NGS) data. Since rare variants, by definition, are likely to be present in only a few individuals even in large samples, efficient methods to screen for rare causal variants are critical for advancing the utility of NGS technology. Application of our approach, which uses family-based data to identify candidate rare variants that could explain aggregation of disease in some pedigrees, resulted in the discovery of novel protein-coding variants linked to increased risk for Alzheimer's disease (AD) in African Americans. The techniques presented in this thesis address different aspects of the "missing heritability" problem and offer efficient approaches to discover novel risk variants, and thereby facilitate development of a more complete picture of genetic risk for common diseases

Linkage analyses in Caribbean Hispanic families identify novel loci associated with familial late-onset Alzheimer's disease

INTRODUCTION: We performed linkage analyses in Caribbean Hispanic families with multiple late-onset Alzheimer's disease (LOAD) cases to identify regions that may contain disease causative variants. METHODS: We selected 67 LOAD families to perform genome-wide linkage scan. Analysis of the linked regions was repeated using the entire sample of 282 families. Validated chromosomal regions were analyzed using joint linkage and association. RESULTS: We identified 26 regions linked to LOAD (HLOD ≥3.6). We validated 13 of the regions (HLOD ≥2.5) using the entire family sample. The strongest signal was at 11q12.3 (rs2232932: HLODmax = 4.7, Pjoint = 6.6 × 10(-6)), a locus located ∼2 Mb upstream of the membrane-spanning 4A gene cluster. We additionally identified a locus at 7p14.3 (rs10255835: HLODmax = 4.9, Pjoint = 1.2 × 10(-5)), a region harboring genes associated with the nervous system (GARS, GHRHR, and NEUROD6). DISCUSSION: Future sequencing efforts should focus on these regions because they may harbor familial LOAD causative mutations

drug target identification at the crossroad of neuronal apoptosis and survival

ABSTRACTIntroduction: Inappropriate activation of apoptosis may contribute to neurodegeneration, a multifaceted process that results in various chronic disorders, including Alzheimer's and Parkinson's diseases. Several in vitro and in vivo studies demonstrated that neuronal apoptosis is a multi-pathway cell-death program that requires RNA synthesis. Thus, transcriptionally activated genes whose products induce cell death can be triggered by different stimuli and antagonized by neurotrophic factors. Systems biology is now unveiling the series of intracellular signaling pathways and key drug targets at the intersection of neuronal apoptosis and survival.Areas covered: This review introduces a genomic approach that can be used to elucidate the systems biology of neuronal apoptosis and survival, and to rationally select drug targets, no longer oriented to emulate the action of growth factors at the membrane receptor level, but rather to modulate their downstream signals.Expert opinion: The advent of genomics ..