Robust Surfactant-Assisted One-Pot Sample Preparation for Label-Free Single-Cell and Nanoscale Proteomics.

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk cells. However, such bulk measurement obscures cell-to-cell heterogeneity, precluding proteome profiling of single cells and small numbers of cells of interest. To address this issue, in the recent 5 years, there has been a surge of small sample preparation methods developed for robust and effective collection and processing of single cells and small numbers of cells for in-depth MS-based proteome profiling. Based on their broad accessibility, they can be categorized into two types: methods based on specific devices and those based on standard PCR tubes or multi-well plates. In this chapter, we describe the detailed protocol of our recently developed, easily adoptable, Surfactant-assisted One-Pot (SOP) sample preparation coupled with MS method termed SOP-MS for label-free single-cell and nanoscale proteomics. SOP-MS capitalizes on the combination of an MS-compatible surfactant, n-dodecyl-ß-D-maltoside (DDM), and standard low-bind PCR tube or multi-well plate for "all-in-one" one-pot sample preparation without sample transfer. With its robust and convenient features, SOP-MS can be readily implemented in any MS laboratory for single-cell and nanoscale proteomics. With further improvements in MS detection sensitivity and sample throughput, we believe that SOP-MS could open an avenue for single-cell proteomics with broad applicability in biological and biomedical research.

ATP7A-Regulated Enzyme Metalation and Trafficking in the Menkes Disease Puzzle.

Copper is vital for numerous cellular functions affecting all tissues and organ systems in the body. The copper pump, ATP7A is critical for whole-body, cellular, and subcellular copper homeostasis, and dysfunction due to genetic defects results in Menkes disease. ATP7A dysfunction leads to copper deficiency in nervous tissue, liver, and blood but accumulation in other tissues. Site-specific cellular deficiencies of copper lead to loss of function of copper-dependent enzymes in all tissues, and the range of Menkes disease pathologies observed can now be explained in full by lack of specific copper enzymes. New pathways involving copper activated lysosomal and steroid sulfatases link patient symptoms usually related to other inborn errors of metabolism to Menkes disease. Additionally, new roles for lysyl oxidase in activation of molecules necessary for the innate immune system, and novel adapter molecules that play roles in ERGIC trafficking of brain receptors and other proteins, are emerging. We here summarize the current knowledge of the roles of copper enzyme function in Menkes disease, with a focus on ATP7A-mediated enzyme metalation in the secretory pathway. By establishing mechanistic relationships between copper-dependent cellular processes and Menkes disease symptoms in patients will not only increase understanding of copper biology but will also allow for the identification of an expanding range of copper-dependent enzymes and pathways. This will raise awareness of rare patient symptoms, and thus aid in early diagnosis of Menkes disease patients.

Chelating principles in Menkes and Wilson diseases: Choosing the right compounds in the right combinations at the right time.

Dysregulation of copper homeostasis in humans is primarily found in two genetic diseases of copper transport, Menkes and Wilson diseases, which show symptoms of copper deficiency or overload, respectively. However, both diseases are copper storage disorders despite completely opposite clinical pictures. Clinically, Menkes disease is characterized by copper deficiency secondary to poor loading of copper-requiring enzymes although sufficient body copper. Copper accumulates in non-hepatic tissues, but is deficient in blood, liver, and brain. In contrast, Wilson disease is characterized by symptoms of copper toxicity secondary to accumulation of copper in several organs most notably brain and liver, and a saturated blood copper pool. It is a challenge to correct copper dyshomeostasis in either disease though copper depletion in Menkes disease is most challenging. Both diseases are caused by defective copper export from distinct cells, and we seek to give new angles and guidelines to improve treatment of these two complementary diseases. Therapy of Menkes disease with copper-histidine, thiocarbamate, nitrilotriacetate or lipoic acid is discussed. In Wilson disease combination of a hydrophilic chelator e.g. trientine or dimercaptosuccinate with a brain shuttle e.g. thiomolybdate or lipoate, is discussed. New chelating principles for copper removal or delivery are outlined.

Orchestration of dynamic copper navigation - new and missing pieces.

A general principle in all cells in the body is that an essential metal - here copper - is taken up at the plasma membrane, directed through cellular compartments for use in specific enzymes and pathways, stored in specific scavenging molecules if in surplus, and finally expelled from the cells. Here we attempt to provide a critical view on key concepts involved in copper transfer across membranes and through compartments in the human body. The focus of this review is on the influence of bioinorganic and thermodynamic rules on the flow in cellular copper networks. Transition of copper from one oxidation state to another will often lead to errant electrons that are highly reactive and prone to form radicals and reactive oxygen or nitrogen species (ROS and RNS). Strict control of potentially toxic oxidative species is an important part of understanding the edge of human copper metabolism. The present review critically covers translocation across simple and complex membranes as well as extracellular and intracellular copper routing. We discuss in depth four tissues with polarized cell barriers - the gut, liver, kidneys, and brain - to illustrate the similarities and differences in transcellular transfer. Copper chaperoning, buffering and binding dynamics to guide the metal to different sites are also covered, while individual molecular interaction kinetics are not detailed. Sorting and targeting mechanisms and principles crucial for correct localisation will also be touched upon.

Clinical expression of Menkes disease in females with normal karyotype.

BACKGROUND: Menkes Disease (MD) is a rare X-linked recessive fatal neurodegenerative disorder caused by mutations in the ATP7A gene, and most patients are males. Female carriers are mosaics of wild-type and mutant cells due to the random X inactivation, and they are rarely affected. In the largest cohort of MD patients reported so far which consists of 517 families we identified 9 neurologically affected carriers with normal karyotypes. METHODS: We investigated at-risk females for mutations in the ATP7A gene by sequencing or by multiplex ligation-dependent probe amplification (MLPA). We analyzed the X-inactivation pattern in affected female carriers, unaffected female carriers and non-carrier females as controls, using the human androgen-receptor gene methylation assay (HUMAR). RESULTS: The clinical symptoms of affected females are generally milder than those of affected boys with the same mutations. While a skewed inactivation of the X-chromosome which harbours the mutation was observed in 94% of 49 investigated unaffected carriers, a more varied pattern was observed in the affected carriers. Of 9 investigated affected females, preferential silencing of the normal X-chromosome was observed in 4, preferential X-inactivation of the mutant X chromosome in 2, an even X-inactivation pattern in 1, and an inconclusive pattern in 2. The X-inactivation pattern correlates with the degree of mental retardation in the affected females. Eighty-one percent of 32 investigated females in the control group had moderately skewed or an even X-inactivation pattern. CONCLUSION: The X- inactivation pattern alone cannot be used to predict the phenotypic outcome in female carriers, as even those with skewed X-inactivation of the X-chromosome harbouring the mutation might have neurological symptoms.

Exon duplications in the ATP7A gene: frequency and transcriptional behaviour.

BACKGROUND: Menkes disease (MD) is an X-linked, fatal neurodegenerative disorder of copper metabolism, caused by mutations in the ATP7A gene. Thirty-three Menkes patients in whom no mutation had been detected with standard diagnostic tools were screened for exon duplications in the ATP7A gene. METHODS: The ATP7A gene was screened for exon duplications using multiplex ligation-dependent probe amplification (MLPA). The expression level of ATP7A was investigated by real-time PCR and detailed analysis of the ATP7A mRNA was performed by RT-PCR followed by sequencing. In order to investigate whether the identified duplicated fragments originated from a single or from two different X-chromosomes, polymorphic markers located in the duplicated fragments were analyzed. RESULTS: Partial ATP7A gene duplication was identified in 20 unrelated patients including one patient with Occipital Horn Syndrome (OHS). Duplications in the ATP7A gene are estimated from our material to be the disease causing mutation in 4% of the Menkes disease patients. The duplicated regions consist of between 2 and 15 exons. In at least one of the cases, the duplication was due to an intra-chromosomal event. Characterization of the ATP7A mRNA transcripts in 11 patients revealed that the duplications were organized in tandem, in a head to tail direction. The reading frame was disrupted in all 11 cases. Small amounts of wild-type transcript were found in all patients as a result of exon-skipping events occurring in the duplicated regions. In the OHS patient with a duplication of exon 3 and 4, the duplicated out-of-frame transcript coexists with an almost equally represented wild-type transcript, presumably leading to the milder phenotype. CONCLUSIONS: In general, patients with duplication of only 2 exons exhibit a milder phenotype as compared to patients with duplication of more than 2 exons. This study provides insight into exon duplications in the ATP7A gene.

Clinical presentation and mutations in Danish patients with Wilson disease.

This study describes the clinical presentation and diagnosis in all Danish patients (49, 41 unrelated) with Wilson disease (WND). On the basis of the number of diagnosed patients from 1990-2008, the prevalence was estimated to be 1:49 500. Among routinely used diagnostic tests, none were consistently indicative of WND, with the exception of the 24-h urine-Cu test, which is always outside the normal range. Mutations were identified in 100% of the screened ATP7B alleles (70 unrelated), including five novel mutations: p.1021K; p.G1158V; p.L1304F; IVS20-2A>G; Ex5_6del. In all, 70% of mutations were found in exons 8, 14, 17, 18, and 20. The most frequent mutation, p.H1069Q, comprised 18%. We propose a new and simple model that correlates genotype and age of onset. By assuming that the milder of two mutations is 'functionally dominant' and determines the age of onset, we classified 25/27 mutations as either severe (age of onset <20 years) or moderate (age of onset >20 years), and correctly predicted the age of onset in 37/39 patients. This method should be tested in other Wilson populations.

Molecular genetic mutation analysis in Menkes-disease with prenatal diagnosis.

UNLABELLED: Menkes disease (MD) is an X-linked recessive multisystemic lethal, heredodegenerative disorder. Progressive neurodegeneration and connective tissue disturbances with microscopically kinky hair are the main symptoms. Molecular genetic mutation analysis was made at a Hungarian male infant suffering from MD and prenatal diagnosis was done in this MD loaded family. METHOD: The 12th exon of ATP7A gene has been analyzed by dideoxy-finger printing (DDF), polymerase chain reaction (PCR), direct sequencing of exon 12. The specific mutation was screened from chorionic villi of the maternal aunt at the 14th gestational week. RESULTS: In the exon 12th a basic pair substitution with Arg 844 His change was detected leading to very severe fatal missense mutation.

Progressive cerebellar degenerative changes in the severe mental retardation syndrome caused by duplication of MECP2 and adjacent loci on Xq28.

Localised duplications, involving the MECP2 locus, at Xq28 have been associated with a syndrome comprising X-linked mental retardation, hypotonia and recurrent infections in males. We now present neuroradiological evidence that progressive cerebellar degenerative changes may also be a consistent feature of this syndrome, emerging in the second decade of life. We report seven affected males, from three different families who, in addition to the previously described clinical findings, have a reduction in the volume of the white matter and mild dilatation of the lateral ventricles. Three of the older patients show a consistent cerebellar degenerative phenotype. Furthermore, we describe the first female affected with the disorder. The female was mildly affected and shows X-inactivation in the ratio of 70:30, demonstrating that X-inactivation cannot be exclusively relied upon to spare the female carriers from symptoms. In conclusion, there is a radiological phenotype associated with Xq28 duplication which clearly demonstrates progressive degenerative cerebellar disease as part of the syndrome.

Molecular diagnosis of Menkes disease: genotype-phenotype correlation.

Menkes syndrome is an X-linked, fatal neurodegenerative disorder of copper metabolism, caused by mutations in the ATP7A gene, encoding a copper-transporting P1B-type ATPase. To date, a total of approximately 160 different mutations have been reported worldwide. The clinical phenotypes observed in these patients include progressive neuro-degeneration, connective-tissue abnormalities and peculiar hair. There is phenotypic variability. While the majority of the patients do not survive early childhood, milder cases leading to longer survival have been reported. In this review we focus on mutations, identified in patients with milder forms of Menkes disease, and discuss the possibility of establishing a genotype-phenotype correlation. The presence of small amounts of normal protein, or the presence of partly functional protein variants containing a less essential amino acid substitution or a truncation of the N- or C-terminus, might all result in a milder, atypical phenotype. A clear phenotype-genotype correlation is however difficult to establish, clearly illustrated by the presence of inter- and even intra-familial variability.

Mutation Detection in the Menkes Gene ATP7A Using the Protein Truncation Test.

Menkes disease (MD) is a rare recessively inherited lethal disorder of copper metabolism. The gene ATP7A defective in MD consists of 23 exons and the coding region encompasses 4500 bp. About 300 distinct mutations, representing all types, have been identified in ATP7A. However all mutations identified so far in the exon 2 to exon 7, corresponding to 1869 bp of the coding sequence, result in truncated protein products. No missense mutations have been identified in this region. As about 30% of the total number of mutations identified are located in exon 2 to exon 7, we have designed a protein truncation test (PTT) for rapid detecting of mutations in this part of the gene. In order to determine the applicability of the test, we analysed RNA obtained from eleven MD patients with known mutations in this region. As a truncated product could be identified in all the included samples, PTT proves to be a useful technique for rapid detection of mutations in the N-terminal part of the ATP7A gene. Furthermore as MD is a X-linked disease, normally only affecting boys, the risk of false negative results, due to nonsense mediated RNA decay, leading to allelic exclusion, can be left out of account.

Evidence that translation reinitiation leads to a partially functional Menkes protein containing two copper-binding sites.

Menkes disease (MD) is an X-linked recessive disorder of copper metabolism. It is caused by mutations in the ATP7A gene encoding a copper-translocating P-type ATPase, which contains six N-terminal copper-binding sites (CBS1-CBS6). Most patients die in early childhood. We investigated the functional effect of a large frameshift deletion in ATP7A (including exons 3 and 4) identified in a patient with MD with unexpectedly mild symptoms and long survival. The mutated transcript, ATP7A(Delta ex3+ex4), contains a premature termination codon after 46 codons. Although such transcripts are generally degraded by nonsense-mediated mRNA decay (NMD), it was established by real-time PCR quantification that the ATP7A(Delta ex3+ex4) transcript was protected from degradation. A combination of in vitro translation, recombinant expression, and immunocytochemical analysis provided evidence that the ATP7A(Delta ex3+ex4) transcript was protected from degradation because of reinitiation of protein translation. Our findings suggest that reinitiation takes place at two downstream internal codons. The putative N-terminally truncated proteins contain only CBS5 and CBS6. Cellular localization and copper-dependent trafficking of the major part of endogenous and recombinant ATP7A(Delta ex3+ex4) proteins were similar to the wild-type ATP7A protein. Furthermore, the ATP7A(Delta ex3+ex4) cDNA was able to rescue a yeast strain lacking the homologous gene, CCC2. In summary, we propose that reinitiation of the NMD-resistant ATP7A(Delta ex3+ex4) transcript leads to the synthesis of N-terminally truncated and at-least-partially functional Menkes proteins missing CBS1-CBS4. This finding--that a mutation that would have been assumed to be null is not--highlights the need to examine the biochemical phenotype of patients to deduce the efficacy of copper therapy.

Homozygosity for a gross partial gene deletion of the C-terminal end of ATP7B in a Wilson patient with hepatic and no neurological manifestations.

We identified a partial gene deletion of ATP7B in a patient with Wilson disease with hepatic onset. The deletion covered exon 20 including major parts of the flanking introns. The breakpoints were identified and the size of the deletion determined to be 2144 bp. The deletion is predicted to lead to a mutated protein product containing 45 aberrant amino acids after transmembrane domain 7, and lacking the transmembrane domain 8 as well as the entire C-terminal cytoplasmic tail. This is the first time a partial gene deletion has been demonstrated in ATP7B. The patient presented at age 10 with hepatic manifestations, including severe jaundice, hepato-splenomegaly, ascites, and spider naevi. The liver biopsy showed fibrosis and early signs of cirrhosis. There was a Kayser-Fleischer ring but no neurological manifestations. All symptoms disappeared with penicillamine therapy. This suggests that the C-terminal cytoplasmatic tail of ATP7B, is not essential for its neurological function. Large deletions in ATP7B may be an overlooked cause of Wilson disease. Patients that are homozygotes for deletions may be valuable for the understanding of the function of various regions of the ATP7B protein.

Identification and analysis of 21 novel disease-causing amino acid substitutions in the conserved part of ATP7A.

ATP7A encodes a copper-translocating ATPase that belongs to the large family of P-type ATPases. Eight conserved regions define the core of the P-type ATPase superfamily. We report here the identification of 21 novel missense mutations in the conserved part of ATP7A that encodes the residues p.V842-p.S1404. Using the coordinates of X-ray crystal structures of the sarcoplasmic reticulum Ca(2+)-ATPase, as determined in the presence and absence of Ca(2+), we created structural homology models of ATP7A. By mapping the substituted residues onto the models, we found that these residues are more clustered three-dimensionally than expected from the primary sequence. The location of the substituted residues in conserved regions supports the functional similarities between the two types of P-type ATPases. An immunofluorescence analysis of Menkes fibroblasts suggested that the localization of a large number of the mutated ATP7A protein variants was correct. In the absence of copper, they were located in perinuclear regions of the cells, just like the wild type. However, two of the mutated ATP7A variants showed only partly correct localization, and in five cultures no ATP7A protein could be detected. These findings suggest that although a disease-causing mutation may indicate a functional significance of the affected residue, this is not always the case.

Variable clinical expression of an identical mutation in the ATP7A gene for Menkes disease/occipital horn syndrome in three affected males in a single family.

Two maternal half-brothers presented with huge cephalic hematoma, fatal in one. Skin morphology disclosed lack of elastic fibres. Their maternal uncle is moderately mentally handicapped and has extensive connective tissue disorders. In all these patients, an identical missense mutation in the ATP7A gene was found and confirmed Menkes' disease.

X-linked Menkes disease: first documented report of germ-line mosaicism.

This work investigated a three-generation Menkes disease family, where germ-line mosaicism was suspected in the maternal grandmother of the index patient. She had given birth to 2 boys who died of suspected Menkes disease on the basis of clinical and photographic evidence. Biochemical analysis of the index patient confirmed the diagnosis of Menkes disease, and DNA analysis established a partial gene deletion (EX11_EX23del), involving exons 11-23 and the 3'-untranslated region (UTR) of ATP7A. A junction fragment was detectable by Southern blot analysis, which enabled carrier analysis. The mother was demonstrated to be a carrier, whereas analysis of lymphoblasts and skin fibroblasts from the maternal grandmother gave no indication of a partial gene deletion. No materials were available from the possibly affected maternal uncles. Further genetic analyses, including biochemical testing of the grandmother and haplotype analysis using four intragenic markers on DNA from selected members of the family, corroborated this finding. The combined results from DNA analyses showed that the grandmother had transmitted three different ATP7A haplotypes to her offspring: (1) the at-risk allele (CA(B))-1 and the deletion; (2) the at-risk allele (CA(B))-1 without deletion; and (3) the second allele (CAB)-2 without deletion. In conclusion, our study demonstrated segregation of Menkes disease within the family investigated that can best be explained by extensive germ-line mosaicism in the maternal grandmother. The finding of germ-line mosaicism has obvious implications for genetic counseling of Menkes disease families.

Screening of 383 unrelated patients affected with Menkes disease and finding of 57 gross deletions in ATP7A.

Menkes disease (MD) is an X-linked multisystemic lethal disorder of copper metabolism dominated by neurodegenerative symptoms and connective tissue disturbances. MD results from mutations in the ATP7A gene, which encodes a membrane-bound copper transporting P-type ATPase located in the trans-Golgi network. In this study we describe screening of 383 unrelated patients affected with Menkes disease for gross deletions in ATP7A gene and finding of 57 patients. The present data suggests that gross deletion of ATP7A is the disease-causing mutation in 14.9% of the Menkes disease patients. Except for a few cases, gross gene deletions result in the classical form of Menkes disease with death in early childhood.

[Mitochondrial diseases. Clinical features, investigation and genetics]. / Mitokondriesygdomme. Klinik, udredning og genetik.

The aim of this article is to give an overview of mitochondrial disorders. Mitochondria are responsible for the generation of energy in the cells. The term, mitochondrial disorders, usually refers to disorders of the respiratory chain. These disorders can be caused by mutations in the DNA of the mitochondria or in the nuclear DNA. A characteristic feature is that all tissues can be affected, and a defect is expressed differently in different tissues. Highly differentiated energy-demanding tissues, such as neurons and muscle cells, are often affected. Mitochondrial disorders are difficult to diagnose. The investigations comprise metabolic screening, respiratory chain enzyme analysis in muscle tissue, muscle histology, and mutation analysis. The focus of this article is on diagnostic evaluation of childhood disorders, because investigation and diagnosis are particularly difficult in children.