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Structure of the nuclear envelope. The nuclear envelope is composed of a double lipid bilayer punctuated with nuclear pore complexes (NPC). The INM harbors a unique set of integral proteins (green) with varying numbers of transmembrane spans. Many of these interact with the underlying nuclear lamina (red), a meshwork of intermediate filaments that provide strength and support to the membrane system. The ONM and lumen are common to the ER. Ribosomes and a shared set of integral membrane proteins (purple) are associated with the ONM and ER. The ONM also has some unique components that are believed to connect the cytoskeleton (blue filaments ) to the nuclear envelope. These proteins (known as synes/ nesprins) appear to be retained in the ONM by an interaction with INM factors (known as SUNs) that bridges the luminal space, thus linking the cytoskeleton to the nuclear lamina.
Source publication
The discovery that many inherited diseases are linked to interacting nuclear envelope proteins has raised the possibility that human genetic studies could be assisted by a fusion with proteomics. Two principles could be applied. In the first, the proteome of an organelle associated with a genetically variable disease is determined. The chromosomal...
Citations
... The nuclear envelope is linked to >30 inherited diseases and syndromes [14], each with distinct tissue-specific pathologies: for example different lamin A mutations cause muscular dystrophies, neuropathy, lipodystrophy, and multisystemic disorders. How these widely expressed nuclear envelope proteins yield tissue-specific pathologies remains unresolved, but one hypothesis is that tissue-specific nuclear envelope partners mediate the tissue-specificity of effects [15]. ...
Background:
As genome-wide approaches prove difficult with genetically heterogeneous orphan diseases, we developed a new approach to identify candidate genes. We applied this to Emery-Dreifuss muscular dystrophy (EDMD), characterised by early onset contractures, slowly progressive muscular wasting, and life-threatening heart conduction disturbances with wide intra- and inter-familial clinical variability. Roughly half of EDMD patients are linked to six genes encoding nuclear envelope proteins, but the disease mechanism remains unclear because the affected proteins function in both cell mechanics and genome regulation.
Methods:
A primer library was generated to test for mutations in 301 genes from four categories: (I) all known EDMD-linked genes; (II) genes mutated in related muscular dystrophies; (III) candidates generated by exome sequencing in five families; (IV) functional candidates - other muscle nuclear envelope proteins functioning in mechanical/genome processes affected in EDMD. This was used to sequence 56 unlinked patients with EDMD-like phenotype.
Findings:
Twenty-one patients could be clearly assigned: 18 with mutations in genes of similar muscular dystrophies; 3 with previously missed mutations in EDMD-linked genes. The other categories yielded novel candidate genes, most encoding nuclear envelope proteins with functions in gene regulation.
Interpretation:
Our multi-pronged approach identified new disease alleles and many new candidate EDMD genes. Their known functions strongly argue the EDMD pathomechanism is from altered gene regulation and mechanotransduction due to connectivity of candidates from the nuclear envelope to the plasma membrane. This approach highlights the value of testing for related diseases using primer libraries and may be applied for other genetically heterogeneous orphan diseases.
Funding:
The Wellcome Trust, Muscular Dystrophy UK, Medical Research Council, European Community's Seventh Framework Programme "Integrated European -omics research project for diagnosis and therapy in rare neuromuscular and neurodegenerative diseases (NEUROMICS)".
... 3 Proteomics may also detect specific biomarkers that represent changes in serum and cellular proteins. 72,74,75 Environmental chemicals may bind to serum proteins when reactive electrophiles bind to protein carriers in the blood and serum to form protein adducts. 76 Quantification of DNA adducts in humans is challenging, even with the use of targeted methods. ...
Biological monitoring, also termed biomonitoring, is the use of blood, urine, or other human samples to assess an individual’s state of health, responses to therapeutics, and exposure to chemicals, or other
environmental agents of concern. Biomonitoring is of considerable potential value to assess military exposures and possible contributions to health outcomes. This chapter provides a review of biomonitoring for military purposes and a perspective for research and surveillance opportunities for biomonitoring both within and outside the military. It also addresses the potential to develop partnerships to examine deployment health-related questions. Further, the chapter defines the exposome; describes several types of currently available biomonitoring; discuss toring detection methods, sample media, and “omics”
technologies available to examine biomarkers; and address the considerable range of information provided by these tools. The chapter’s last section discusses new directions in biomonitoring and big data analysis.
... In this situation traditional mutation screening, based on consecutive "searching" for a plurality of coding sequences, is too time consuming and unreasonably expensive. Furthermore, for hereditary neurodegenerations, explicit inter-and intra-familial phenotypical polymorphism is typical, it being manifested by various neurological syndromes within one nosological form among members of the same family [9][10][11][12]. ...
The aim of the study was to assess the efficacy of a diagnostic panel based on next-generation sequencing (NGS) and developed by our team, to diagnose a wide range of socially significant hereditary degenerative diseases of the brain. Materials and Methods. Using the diagnostic target NGS panel (powered by Illumina MiSeq, USA), designed to sequence the encoding area of 300 genes related to neurodegenerative diseases manifesting with movement and cognitive disorders, we performed a mutation screening of the DNA of 32 patients with an otherwise obscure diagnosis. Results. The application of the original genetic panel revealed a number of rare hereditary neurodegenerative pathologies with mutations in genes for spinocerebellar ataxias and paraplegias, parkinsonism, dystonias, and neurometabolic diseases, identified by NGS and confirmed by direct sequencing. In 11 patients, 12 mutations were found in 10 different genes, causing the development of three autosomal recessive diseases (genes DDHD1, NPC1 and RARS) and eight diseases associated with autosomal dominant inheritance (genes SPAST, SPTBN2, GRN, GCH1, LRRK2, NOTCH3 and AGER). Conclusion. Panel screening of uncertain cases of neurodegenerative diseases using this bespoke target model enabled us to reveal and subsequently confirm mutations in various genes for more than a quarter of the examined patients. © 2016, Nizhny Novgorod State Medical Academy. All rights reserved.
... Proteomics may be useful for the identification of specific biomarkers of various health anomalies and insults to the host. 21,23,24 Full proteomic analysis includes serum as well as cellular proteins from the host. ...
Military service members come in contact with a wide range of hazardous substances especially during deployment. The identification of service member's with potential exposures to infectious diseases and environmental toxic substances has been a problem for the U.S. military almost since the formation of the services and continues to be an issue today. In June and July of 2013, the Armed Forces Health Surveillance Center sponsored two meetings to address the need by the Department of Defense to perform retrospective exposure analysis that would support military force health protection efforts. The first meeting included medical professionals who were familiar with health problems that followed potential environmental or infectious disease exposures but that the military health system was unprepared to address. The second group was composed of technical experts who were asked to suggest potential material and nonmaterial solutions to address the needs of the military public health community. This supplement to Military Medicine includes the outcome of these two meetings, descriptions of some of the Department of Defense biorepositories including the large serum repository housed at Armed Forces Health Surveillance Center and discussion of additional topics related to the establishment and use of biorepositories that would support public health practice in the 21st century.
... These approaches have led to the emergence of new methods that exploit and integrate different data sources into networks in a variety of ways [4]. Inferring new knowledge from existent networks is usually based on "guilt-by-association" [5]. This extensively validated principle states that biological entities which are associated or interacting in a network are more likely to share a common function. ...
Prioritization methods have become an useful tool for mining large amounts of data to suggest promising hypotheses in early research stages. Particularly, network-based prioritization tools use a network representation for the interactions between different biological entities to identify novel indirect relationships. However, current network-based prioritization tools are strongly tailored to specific domains of interest (e.g. gene-disease prioritization) and they do not allow to consider networks with more than two types of entities (e.g. genes and diseases). Therefore, the direct application of these methods to accomplish new prioritization tasks is limited.
This work presents ProphNet, a generic network-based prioritization tool that allows to integrate an arbitrary number of interrelated biological entities to accomplish any prioritization task. We tested the performance of ProphNet in comparison with leading network-based prioritization methods, namely rcNet and DomainRBF, for gene-disease and domain-disease prioritization, respectively. The results obtained by ProphNet show a significant improvement in terms of sensitivity and specificity for both tasks. We also applied ProphNet to disease-gene prioritization on Alzheimer, Diabetes Mellitus Type 2 and Breast Cancer to validate the results and identify putative candidate genes involved in these diseases.
ProphNet works on top of any heterogeneous network by integrating information of different types of biological entities to rank entities of a specific type according to their degree of relationship with a query set of entities of another type. Our method works by propagating information across data networks and measuring the correlation between the propagated values for a query and a target sets of entities. ProphNet is available at: http://genome2.ugr.es/prophnet. A Matlab implementation of the algorithm is also available at the website.
... We found that their expression is increased and their localization altered in wz mouse muscle. emerin is essential for tethering inner and outer nuclear membrane [77]. The widening and extension of the nuclear envelope and lamina in wz muscles detected by eM are in accordance with the alterations in lamins, emerin and lap2 protein levels and distributions. ...
Marinesco-Sjögren syndrome (MSS) features cerebellar ataxia, mental retardation, cataracts, and progressive vacuolar myopathy with peculiar myonuclear alterations. Most MSS patients carry homozygous or compound heterozygous SIL1 mutations. SIL1 is a nucleotide exchange factor for the endoplasmic reticulum resident chaperone BiP which controls a plethora of essential processes in the endoplasmic reticulum. In this study we made use of the spontaneous Sil1 mouse mutant woozy to explore pathomechanisms leading to Sil1 deficiency-related skeletal muscle pathology. We found severe, progressive myopathy characterized by alterations of the sarcoplasmic reticulum, accumulation of autophagic vacuoles, mitochondrial changes, and prominent myonuclear pathology including nuclear envelope and nuclear lamina alterations. These abnormalities were remarkably similar to the myopathy in human patients with MSS. In particular, the presence of perinuclear membranous structures which have been reported as an ultrastructural hallmark of MSS-related myopathy could be confirmed in woozy muscles. We found that these structures are derived from the nuclear envelope and nuclear lamina and associate with proliferations of the sarcoplasmic reticulum. In line with impaired function of BiP secondary to loss of its nucleotide exchange factor Sil1, we observed activation of the unfolded protein response and the endoplasmic-reticulum-associated protein degradation-pathway. Despite initiation of the autophagy-lysosomal system, autophagic clearance was found ineffective which is in agreement with the formation of autophagic vacuoles. This report identifies woozy muscle as a faithful phenocopy of the MSS myopathy. Moreover, we provide a link between two well-established disease mechanisms in skeletal muscle, dysfunction of chaperones and nuclear envelope pathology.
... A potential resolution can be found in the "guilt by association" hypothesis that disease-causing mutations in relatively ubiquitous NE proteins might disrupt binding to as yet unidentified tissue-specific partner proteins to generate pathology in that particular tissue. 31 This idea is supported by observations that many disease-linked NE proteins appear to function in complexes and that few have specific enzymatic functions themselves that could result in pathologies. Apart from the structural functions of the lamins and NETs of the SUN and nesprin families, the proteins thus far mutated in NE diseases have few inherent functions. ...
Nuclear envelope links to inherited disease gave the conundrum of how mutations in near-ubiquitous proteins can yield many distinct pathologies, each focused in different tissues. One conundrum-resolving hypothesis is that tissue-specific partner proteins mediate these pathologies. Such partner proteins may have now been identified with recent proteome studies determining nuclear envelope composition in different tissues. These studies revealed that the majority of the total nuclear envelope proteins are tissue restricted in their expression. Moreover, functions have been found for a number these tissue-restricted nuclear envelope proteins that fit with mechanisms proposed to explain how the nuclear envelope could mediate disease, including defects in mechanical stability, cell cycle regulation, signaling, genome organization, gene expression, nucleocytoplasmic transport, and differentiation. The wide range of functions to which these proteins contribute is consistent with not only their involvement in tissue-specific nuclear envelope disease pathologies, but also tissue evolution.
... The nuclear proteomes have been studied in a variety of human organs and cells (Albrethsen et al., 2009;Andersen et al., 2002;Dreger et al., 2001;Henrich et al., 2007;Schenk et al., 2012;Tchapyjnikov et al., 2010;Torrente et al., 2011;Wilkie and Schirmer, 2006). Most of the studies used crude nuclear pellets without further purification or fractionation. ...
The dynamic regulation of transcriptional events is fundamental to many aspects of neuronal cell functions. However, proteomics methods have not been routinely used in global neuroproteomics analyses of transcriptional regulators because they are much less abundant than the "house-keeping" proteins in cells and tissues. Recent improvements in both biochemical preparations of nuclear proteins and detection sensitivities of proteomics technologies have made the global analysis of nuclear transcriptional regulators possible. We report here an optimized neuroproteomic method for the analysis of transcriptional regulators in the nuclear extracts of SHSY-5Y neuroblastoma cells by combining an improved nuclear protein extraction procedure with multidimensional peptide separation approaches. We found that rigorous removal of cytoplasmic proteins and solubilization of DNA-associated proteins improved the number of nuclear proteins identified. Furthermore, we discovered that multidimensional peptide separations by either strong cation exchange (SCX) chromatography or electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) analysis detected more than 1,800 nuclear proteins through the application of our technique, which constitute one of the largest datasets of nuclear proteins reported for a neuronal cell. Thus, in-depth analyses of transcriptional regulators for studying neurological diseases are increasingly feasible.
... The reports to date of direct patho-physiology implications for altered NE protein function indicate that this is an area ripe for discovery. For example, several recent reviews have documented the clear evidence for devastating human inherited diseases linked to genes encoding lamins and lamin-associated INM proteins899091. Proteomic characterization of the NE proteome across multiple different cell types [12,92,93], paired with continued studies of INM protein targeting and INM protein functions will be needed to contribute to a deeper understanding of the tissue-specific nature of INM disease alleles899091. Expanded analysis of the INM trafficking mechanisms and INM protein function in model systems [94] will allow a further convergence of temporal and spatial requirements for NE-associated proteins from the single cell level to the context of multicellular organism development, cell differentiation, and tissue morphogenesis. ...
... For example, several recent reviews have documented the clear evidence for devastating human inherited diseases linked to genes encoding lamins and lamin-associated INM proteins899091. Proteomic characterization of the NE proteome across multiple different cell types [12,92,93], paired with continued studies of INM protein targeting and INM protein functions will be needed to contribute to a deeper understanding of the tissue-specific nature of INM disease alleles899091. Expanded analysis of the INM trafficking mechanisms and INM protein function in model systems [94] will allow a further convergence of temporal and spatial requirements for NE-associated proteins from the single cell level to the context of multicellular organism development, cell differentiation, and tissue morphogenesis. ...
The nuclear envelope (NE) in eukaryotic cells serves as the physical barrier between the nucleus and cytoplasm. Until recently, mechanisms for establishing the composition of the inner nuclear membrane (INM) remained uncharted. Current findings uncover multiple pathways for trafficking of integral and peripheral INM proteins. A major route for INM protein transport occurs through the nuclear pore complexes (NPCs) with additional requirements for nuclear localization sequences, transport receptors, and Ran-GTP. Studies also reveal a putative NPC-independent vesicular pathway for NE trafficking. INM perturbations lead to changes in nuclear physiology highlighting the potential human disease impacts of continued NE discoveries.
... Hence, the formation of structures in the nucleus is influenced by many molecules, and provides an elegant mechanism not only to concentrate factors when they are needed, but also to segregate factors away from sites where they are debilitating [154]. The movement of molecules is not restricted within the nucleus, and the latest reports suggest that several nuclear proteins have regulatory functions in the whole cell [20,257]. The nuclear envelope should not be considered as an insuperable frontier that is simply keeping everything together. ...
