Domain altering SNPs in the human proteome and their impact on signaling pathways

Single nucleotide polymorphisms (SNPs) constitute an important mode of genetic variations observed in the human genome. A small fraction of SNPs, about four thousand out of the ten million, has been associated with genetic disorders and complex diseases. The present study focuses on SNPs that fall on protein domains, 3D structures that facilitate connectivity of proteins in cell signaling and metabolic pathways. We scanned the human proteome using the PROSITE web tool and identified proteins with SNP containing domains. We showed that SNPs that fall on protein domains are highly statistically enriched among SNPs linked to hereditary disorders and complex diseases. Proteins whose domains are dramatically altered by the presence of an SNP are even more likely to be present among proteins linked to hereditary disorders. Proteins with domain-altering SNPs comprise highly connected nodes in cellular pathways such as the focal adhesion, the axon guidance pathway and the autoimmune disease pathways. Statistical enrichment of domain/motif signatures in interacting protein pairs indicates extensive loss of connectivity of cell signaling pathways due to domain-altering SNPs, potentially leading to hereditary disorders.     

Biochemical and molecular characterization of diseases linked to motor proteins

Recent studies have revealed that kinesin, dynein and myosin each form large superfamilies and participate in many different intracellular transport systems. Importantly, these motor proteins play significant roles in the pathogenesis of a variety of diseases. Studies using knockout mice for kinesin KIF1B have led to the identification of the cause of a human hereditary neuropathy, Charcot-Marie-Tooth disease type 2A. The function of members of the dynein superfamily whose existence has previously only been confirmed through genome databases, has been revealed by studies of immotile cilia syndrome. Unconventional myosins have been shown to function in the inner-ear cells by examination of hereditary human hearing impairment and studies using mouse models. In addition, some diseases are caused by mutations, not in the motor itself, but in the proteins associated with the motor proteins. Here, we discuss the relationship of these motor proteins and how they contribute to disease in molecular terms.     

Rational Design of ssODN to Correct Mutations by Gene Editing

Biochemistry (Moscow) - Gene editing allows to make a variety of targeted changes in genome, which can potentially be used to treat hereditary human diseases. Despite numerous studies in this area,...     

The dog genome map and its use in mammalian comparative genomics

The dog genome organization was extensively studied in the last ten years. The most important achievements are the well-developed marker genome maps, including over 3200 marker loci, and a survey of the DNA genome sequence. This knowledge, along with the most advanced map of the human genome, turned out to be very useful in comparative genomic studies. On the one hand, it has promoted the development of marker genome maps of other species of the family Canidae (red fox, arctic fox, Chinese raccoon dog) as well as studies on the evolution of their karyotype. But the most important approach is the comparative analysis of human and canine hereditary diseases. At present, causative gene mutations are known for 30 canine hereditary diseases. A majority of them have human counterparts with similar clinical and molecular features. Studies on identification of genes having a major impact on some multifactorial diseases (hip dysplasia, epilepsy) and cancers (multifocal renal cystadenocarcinoma and nodular dermatofibrosis) are advanced. Very promising are the results of gene therapy for certain canine monogenic diseases (haemophilia, hereditary retinal dystrophy, mucopolysaccharidosis), which have human equivalents. The above-mentioned examples prove a very important model role of the dog in studies of human genetic diseases. On the other hand, the identification of gene mutations responsible for hereditary diseases has a substantial impact on breeding strategy in the dog.     

OMiR: Identification of associations between OMIM diseases and microRNAs

A large number of loci for genetic diseases have been mapped on the human genome and a group of hereditary diseases among them have thus far proven unsuccessful to clone. It is conceivable that such "unclonable" diseases are not linked to abnormalities of protein coding genes (PCGs), but of non-coding RNAs (ncRNAs). We developed a novel approach termed OMiR (OMIM and miRNAs), to test whether microRNAs (miRNAs) exhibit any associations with mapped genetic diseases not yet associated with a PCG. We found that "orphan" genetic disease loci were proximal to miRNA loci more frequently than to loci for which the responsible protein coding gene is known, thus suggesting that miRNAs might be the elusive culprits. Our findings indicate that inclusion of miRNAs among the candidate genes to be considered could assist geneticists in their hunt for disease genes, particularly in the case of rare diseases.     

A tool for biomarker discovery in the urinary proteome: a manually curated human and animal urine protein biomarker database

Urine is an important source of biomarkers. A single proteomics assay can identify hundreds of differentially expressed proteins between disease and control samples; however, the ability to select biomarker candidates with the most promise for further validation study remains difficult. A bioinformatics tool that allows accurate and convenient comparison of all of the existing related studies can markedly aid the development of this area. In this study, we constructed the Urinary Protein Biomarker (UPB) database to collect existing studies of urinary protein biomarkers from published literature. To ensure the quality of data collection, all literature was manually curated. The website (http://122.70.220.102/biomarker) allows users to browse the database by disease categories and search by protein IDs in bulk. Researchers can easily determine whether a biomarker candidate has already been identified by another group for the same disease or for other diseases, which allows for the confidence and disease specificity of their biomarker candidate to be evaluated. Additionally, the pathophysiological processes of the diseases can be studied using our database with the hypothesis that diseases that share biomarkers may have the same pathophysiological processes. Because of the natural relationship between urinary proteins and the urinary system, this database may be especially suitable for studying the pathogenesis of urological diseases. Currently, the database contains 553 and 275 records compiled from 174 and 31 publications of human and animal studies, respectively. We found that biomarkers identified by different proteomic methods had a poor overlap with each other. The differences between sample preparation and separation methods, mass spectrometers, and data analysis algorithms may be influencing factors. Biomarkers identified from animal models also overlapped poorly with those from human samples, but the overlap rate was not lower than that of human proteomics studies. Therefore, it is not clear how well the animal models mimic human diseases.     

Understanding hereditary diseases using the dog and human as companion model systems

Animal models are requisite for genetic dissection of, and improved treatment regimens for, human hereditary diseases. While several animals have been used in academic and industrial research, the primary model for dissection of hereditary diseases has been the many strains of the laboratory mouse. However, given its greater (than the mouse) genetic similarity to the human, high number of naturally occurring hereditary diseases, unique population structure, and the availability of the complete genome sequence, the purebred dog has emerged as a powerful model for study of diseases. The major advantage the dog provides is that it is afflicted with approximately 450 hereditary diseases, about half of which have remarkable clinical similarities to corresponding diseases of the human. In addition, humankind has a strong desire to cure diseases of the dog so these two facts make the dog an ideal clinical and genetic model. This review highlights several of these shared hereditary diseases. Specifically, the canine models discussed herein have played important roles in identification of causative genes and/or have been utilized in novel therapeutic approaches of interest to the dog and human.     

Drosophila models of human neurodegenerative disease

Drosophila has provided a powerful genetic system in which to elucidate fundamental cellular pathways in the context of a developing and functioning nervous system. Recently, Drosophila has been applied toward elucidating mechanisms of human neurodegenerative disease, including Alzheimer's, Parkinson's and Huntington's diseases. Drosophila allows study of the normal function of disease proteins, as well as study of effects of familial mutations upon targeted expression of human mutant forms in the fly. These studies have revealed new insight into the normal functions of such disease proteins, as well as provided models in Drosophila that will allow genetic approaches to be applied toward elucidating ways to prevent or delay toxic effects of such disease proteins. These, and studies to come that follow from the recently completed sequence of the Drosophila genome, underscore the contributions that Drosophila as a model genetic system stands to contribute toward the understanding of human neurodegenerative disease.     

Methods of genome engineering: a new era of molecular biology

Genome sequencing now progressing much faster than our understanding of the majority of gene functions. Studies of physiological functions of various genes would not be possible without the ability to manipulate the genome. Methods of genome engineering can now be used to inactivate a gene to study consequences, introduce heterologous genes into the genome for scientific and biotechnology applications, create genes coding for fusion proteins to study gene expression, protein localization, and molecular interactions, and to develop animal models of human diseases to find appropriate treatment. Finally, genome engineering might present the possibility to cure hereditary diseases. In this review, we discuss and compare the most important methods for gene inactivation and editing, as well as methods for incorporation of heterologous genes into the genome.     

Discovering disease-genes by topological features in human protein-protein interaction network

MOTIVATION: Mining the hereditary disease-genes from human genome is one of the most important tasks in bioinformatics research. A variety of sequence features and functional similarities between known human hereditary disease-genes and those not known to be involved in disease have been systematically examined and efficient classifiers have been constructed based on the identified common patterns. The availability of human genome-wide protein-protein interactions (PPIs) provides us with new opportunity for discovering hereditary disease-genes by topological features in PPIs network. RESULTS: This analysis reveals that the hereditary disease-genes ascertained from OMIM in the literature-curated (LC) PPIs network are characterized by a larger degree, tendency to interact with other disease-genes, more common neighbors and quick communication to each other whereas those properties could not be detected from the network identified from high-throughput yeast two-hybrid mapping approach (EXP) and predicted interactions (PDT) PPIs network. KNN classifier based on those features was created and on average gained overall prediction accuracy of 0.76 in cross-validation test. Then the classifier was applied to 5262 genes on human genome and predicted 178 novel disease-genes. Some of the predictions have been validated by biological experiments.     

Discovery of regulatory molecular events and biomarkers using 2D capillary chromatography and mass spectrometry

An important component of proteomic research is the high-throughput discovery of novel proteins and protein-protein interactions that control molecular events that contribute to critical cellular functions and human disease. The interactions of proteins are essential for cellular functions. Identifying perturbation of normal cellular protein interactions is vital for understanding the disease process and intervening to control the disease. A second area of proteomics research is the discovery of proteins that will serve as biomarkers for the early detection, diagnosis and drug treatment response for specific diseases. These studies have been referred to as clinical proteomics. To discover biomarkers, proteomics research employs the quantitative comparison of peptide and protein expression in body fluids and tissues from diseased individuals (case) versus normal individuals (control). Methods that couple 2D capillary liquid chromatography (LC) and tandem mass spectrometry (MS/MS) analysis have greatly facilitated this discovery science. Coupling 2D-LC/MS/MS analysis with automated genome-assisted spectra interpretation allows a direct, high-throughput and high-sensitivity identification of thousands of individual proteins from complex biological samples. The systematic comparison of experimental conditions and controls allows protein function or disease states to be modeled. This review discusses the different purification and quantification strategies that have been developed and used in combination with 2D-LC/MS/MS and computational analysis to examine regulatory protein networks and clinical samples.     

Discovery of regulatory molecular events and biomarkers using 2D capillary chromatography and mass spectrometry

An important component of proteomic research is the high-throughput discovery of novel proteins and protein–protein interactions that control molecular events that contribute to critical cellular functions and human disease. The interactions of proteins are essential for cellular functions. Identifying perturbation of normal cellular protein interactions is vital for understanding the disease process and intervening to control the disease. A second area of proteomics research is the discovery of proteins that will serve as biomarkers for the early detection, diagnosis and drug treatment response for specific diseases. These studies have been referred to as clinical proteomics. To discover biomarkers, proteomics research employs the quantitative comparison of peptide and protein expression in body fluids and tissues from diseased individuals (case) versus normal individuals (control). Methods that couple 2D capillary liquid chromatography (LC) and tandem mass spectrometry (MS/MS) analysis have greatly facilitated this discovery science. Coupling 2D-LC/MS/MS analysis with automated genome-assisted spectra interpretation allows a direct, high-throughput and high-sensitivity identification of thousands of individual proteins from complex biological samples. The systematic comparison of experimental conditions and controls allows protein function or disease states to be modeled. This review discusses the different purification and quantification strategies that have been developed and used in combination with 2D-LC/MS/MS and computational analysis to examine regulatory protein networks and clinical samples.     

Epigenetic silencing of genomic structural variations

A great amount of copy number variations (CNVs) are identified in the human genome. Most of them are neutral; nevertheless, the role of CNVs in the pathogenesis of hereditary diseases is still significant. Especially, this is important for neuropsychiatric disorders, such as intellectual disability and autism. When analyzing the CNV-associated diseases, the controversial question is to distinguish the pathogenic CNVs among common polymorphic variants and to predict the disease risk in other children of the family. Unfortunately, the mechanisms of phenotypic expression and incomplete penetrance of CNVs remain largely unknown. Currently, incomplete penetrance and variable expressivity of CNVs are attributed mainly to allelic interaction of different genetic variations. However, epigenetic mechanisms of gene expression regulation in the context of structural variation of the genome are poorly explored. It is possible that epigenetic modifications of the genome regions with CNVs may underlie the understanding of ways of phenotypic manifestations of structural variations in the human genome.     

Protein families and TRIBES in genome sequence space

Accurate detection of protein families allows assignment of protein function and the analysis of functional diversity in complete genomes. Recently, we presented a novel algorithm called TribeMCL for the detection of protein families that is both accurate and efficient. This method allows family analysis to be carried out on a very large scale. Using TribeMCL, we have generated a resource called TRIBES that contains protein family information, comprising annotations, protein sequence alignments and phylogenetic distributions describing 311 257 proteins from 83 completely sequenced genomes. The analysis of at least 60 934 detected protein families reveals that, with the essential families excluded, paralogy levels are similar between prokaryotes, irrespective of genome size. The number of essential families is estimated to be between 366 and 426. We also show that the currently known space of protein families is scale free and discuss the implications of this distribution. In addition, we show that smaller families are often formed by shorter proteins and discuss the reasons for this intriguing pattern. Finally, we analyse the functional diversity of protein families in entire genome sequences. The TRIBES protein family resource is accessible at http://www.ebi.ac.uk/research/cgg/tribes/.     

Chemically-blocked antibody microarray for multiplexed high-throughput profiling of specific protein glycosylation in complex samples

In this study, we describe an effective protocol for use in a multiplexed high-throughput antibody microarray with glycan binding protein detection that allows for the glycosylation profiling of specific proteins. Glycosylation of proteins is the most prevalent post-translational modification found on proteins, and leads diversified modifications of the physical, chemical, and biological properties of proteins. Because the glycosylation machinery is particularly susceptible to disease progression and malignant transformation, aberrant glycosylation has been recognized as early detection biomarkers for cancer and other diseases. However, current methods to study protein glycosylation typically are too complicated or expensive for use in most normal laboratory or clinical settings and a more practical method to study protein glycosylation is needed. The new protocol described in this study makes use of a chemically blocked antibody microarray with glycan-binding protein (GBP) detection and significantly reduces the time, cost, and lab equipment requirements needed to study protein glycosylation. In this method, multiple immobilized glycoprotein-specific antibodies are printed directly onto the microarray slides and the N-glycans on the antibodies are blocked. The blocked, immobilized glycoprotein-specific antibodies are able to capture and isolate glycoproteins from a complex sample that is applied directly onto the microarray slides. Glycan detection then can be performed by the application of biotinylated lectins and other GBPs to the microarray slide, while binding levels can be determined using Dylight 549-Streptavidin. Through the use of an antibody panel and probing with multiple biotinylated lectins, this method allows for an effective glycosylation profile of the different proteins found in a given human or animal sample to be developed.     

The role of mitochondria in inherited neurodegenerative diseases

In the past decade, the genetic causes underlying familial forms of many neurodegenerative disorders, such as Huntington's disease, Parkinson's disease, Alzheimer's disease, amyotrophic lateral sclerosis, Friedreich ataxia, hereditary spastic paraplegia, dominant optic atrophy, Charcot-Marie-Tooth type 2A, neuropathy ataxia and retinitis pigmentosa, and Leber's hereditary optic atrophy have been elucidated. However, the common pathogenic mechanisms of neuronal death are still largely unknown. Recently, mitochondrial dysfunction has emerged as a potential 'lowest common denominator' linking these disorders. In this review, we discuss the body of evidence supporting the role of mitochondria in the pathogenesis of hereditary neurodegenerative diseases. We summarize the principal features of genetic diseases caused by abnormalities of mitochondrial proteins encoded by the mitochondrial or the nuclear genomes. We then address genetic diseases where mutant proteins are localized in multiple cell compartments, including mitochondria and where mitochondrial defects are likely to be directly caused by the mutant proteins. Finally, we describe examples of neurodegenerative disorders where mitochondrial dysfunction may be 'secondary' and probably concomitant with degenerative events in other cell organelles, but may still play an important role in the neuronal decay. Understanding the contribution of mitochondrial dysfunction to neurodegeneration and its pathophysiological basis will significantly impact our ability to develop more effective therapies for neurodegenerative diseases.     

Somatic genome variations in health and disease

It is hard to imagine that all the cells of the human organism (about 10(14)) share identical genome. Moreover, the number of mitoses (about 10(16)) required for the organism's development and maturation during ontogeny suggests that at least a proportion of them could be abnormal leading, thereby, to large-scale genomic alterations in somatic cells. Experimental data do demonstrate such genomic variations to exist and to be involved in human development and interindividual genetic variability in health and disease. However, since current genomic technologies are mainly based on methods, which analyze genomes from a large pool of cells, intercellular or somatic genome variations are significantly less appreciated in modern bioscience. Here, a review of somatic genome variations occurring at all levels of genome organization (i.e. DNA sequence, subchromosomal and chromosomal) in health and disease is presented. Looking through the available literature, it was possible to show that the somatic cell genome is extremely variable. Additionally, being mainly associated with chromosome or genome instability (most commonly manifesting as aneuploidy), somatic genome variations are involved in pathogenesis of numerous human diseases. The latter mainly concerns diseases of the brain (i.e. autism, schizophrenia, Alzheimer's disease) and immune system (autoimmune diseases), chromosomal and some monogenic syndromes, cancers, infertility and prenatal mortality. Taking into account data on somatic genome variations and chromosome instability, it becomes possible to show that related processes can underlie non-malignant pathology such as (neuro)degeneration or other local tissue dysfunctions. Together, we suggest that detection and characterization of somatic genome behavior and variations can provide new opportunities for human genome research and genetics.