Identification of synaptophysin as a hexameric channel protein of the synaptic vesicle membrane

The quaternary structure and functional properties of synaptophysin, a major integral membrane protein of small presynaptic vesicles, were investigated. Cross-linking and sedimentation studies indicate that synaptophysin is a hexameric homo-oligomer, which in electron micrographs exhibits structural features common to channel-forming proteins. On reconstitution into planar lipid bilayers, purified synaptophysin displays voltage-sensitive channel activity with an average conductance of about 150 picosiemens. Because specific channels and fusion pores have been implicated in vesicular uptake and release of secretory compounds, synaptophysin may have a role in these processes.

Actionable exomic incidental findings in 6503 participants: challenges of variant classification

Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.

How many rare diseases are there?

A lack of robust knowledge of the number of rare diseases and the number of people affected by them limits the development of approaches to ameliorate the substantial cumulative burden of rare diseases. Here, we call for coordinated efforts to more precisely define rare diseases.

Molecular characterization of synaptophysin, a major calcium-binding protein of the synaptic vesicle membrane

Synaptophysin, a mol. wt 38 000 glycopolypeptide of the synaptic vesicle membrane, was solubilized using Triton X-100 and purified by immunoaffinity or ion-exchange chromatography. From gel permeation and sucrose-density centrifugation in H2O/D2O, a Stokes radius of 7.3 nm, a partial specific volume of 0.830 and a total mol. wt of 119 000 were calculated for the native protein. Cross-linking of synaptic vesicles with glutaraldehyde, dimethylsuberimidate, or Cu2+ -o-phenantroline, resulted in the formation of a mol. wt 76 kd dimer of synaptophysin. Crosslinking of the purified protein in addition produced tri- and tetrameric adducts of the polypeptide. Native synaptophysin thus is a homooligomeric protein. Synaptophysin is N-glycosylated, since cultivation of the rat phaeochromocytoma cell line PC12 in the presence of tunicamycin reduced its mol. wt by about 6 kd. Upon transfer to nitrocellulose and incubation with 45Ca2+, synaptophysin behaved as one of the major calcium-binding proteins of the synaptic vesicle membrane. Pronase treatment of intact synaptic vesicles abolished this 45Ca2+ binding indicating that the Ca2+ binding site of synaptophysin must reside on a cytoplasmic domain of the transmembrane polypeptide. Based on these data, we propose that synaptophysin may play an important role in Ca2+-dependent neurotransmitter release.

Expression of synaptophysin during postnatal development of the mouse brain

The expression of the synaptic vesicle membrane protein, synaptophysin, was analyzed during postnatal development of the mouse cerebrum using a quantitative immunoblotting procedure. From birth to adulthood, the relative contents of synaptophysin increased 80-fold, reaching a final level of 3.5 micrograms/mg of total protein. The time course of accumulation suggests that synaptophysin expression is correlated with synaptogenesis. Thus synaptophysin may be used as a reliable marker of nerve terminal differentiation.

Synaptophysin: molecular organization and mRNA expression as determined from cloned cDNA

Synaptophysin is a major glycoprotein of Mr approximately 38,000 (in deglycosylated form: Mr approximately 34,000) characteristic of a certain class of small (30-80 nm diameter) neurosecretory vesicles, including presynaptic vesicles, but also vesicles of various neuroendocrine cells of both neuronal and epithelial phenotype. Using synaptophysin-specific antibodies we have isolated cDNA clones from rat nervous tissue libraries, which identify an approximately 2.5-kb mRNA in rat and human cells, including neuroendocrine tumours, that contains a reading frame for a polypeptide of 307 amino acids with a total mol. wt of 33 312. The deduced amino acid sequence, which was partly confirmed by comparison with sequences of two tryptic peptides obtained from purified synaptophysin, revealed four hydrophobic regions of 24 amino acids each, which are characterized, according to conformation prediction analyses, by marked alpha-helicity. The sequence shows a single potential N-glycosylation site, which is assigned to the vesicle interior, and a carboxy-terminal tail of 89 amino acids which contains glycine-rich tetrapeptide repeats, the epitope of monoclonal antibody SY38, and a number of collagenase-sensitive sites accessible on the surface of the intact vesicles. These features suggest that the polypeptide spans the vesicle membrane four times, with both N and C termini located on the outer, i.e. cytoplasmic, surface of the vesicles.

The All of Us Research Program: Data quality, utility, and diversity

The All of Us Research Program seeks to engage at least one million diverse participants to advance precision medicine and improve human health. We describe here the cloud-based Researcher Workbench that uses a data passport model to democratize access to analytical tools and participant information including survey, physical measurement, and electronic health record (EHR) data. We also present validation study findings for several common complex diseases to demonstrate use of this novel platform in 315,000 participants, 78% of whom are from groups historically underrepresented in biomedical research, including 49% self-reporting non-White races. Replication findings include medication usage pattern differences by race in depression and type 2 diabetes, validation of known cancer associations with smoking, and calculation of cardiovascular risk scores by reported race effects. The cloud-based Researcher Workbench represents an important advance in enabling secure access for a broad range of researchers to this large resource and analytical tools.

Purification and subunit structure of a putative K+-channel protein identified by its binding properties for dendrotoxin I

The binding protein for the K+-channel toxin dendrotoxin I was purified from a detergent extract of rat brain membranes. The purification procedure utilized chromatography on DEAE-Trisacryl, affinity chromatography on a dendrotoxin-I-Aca 22 column, and wheat germ agglutinin-Affigel 10 with a final 3800- to 4600-fold enrichment and a recovery of 8-16%. The high affinity (Kd, 40-100 pM) and specificity of the binding site are retained throughout the purification procedure. Analysis of the purified material on silver-stained NaDodSO4/polyacrylamide gel revealed three bands of Mr 76,000-80,000, 38,000, and 35,000. Interestingly, the binding site for 125I-labeled mast cell degranulating peptide, another putative K+-channel ligand from bee venom, which induces long-term potentiation in hippocampus, seems to reside on the same protein complex, as both binding sites copurify through the entire purification protocol.

Dendrotoxin-binding brain membrane protein displays a K+ channel activity that is stimulated by both cAMP-dependent and endogenous phosphorylations

The purified protein that binds the K+ channel ligands dendrotoxin I and mast cell degranulating peptide can be phosphorylated by cAMP-dependent protein kinase and by an endogenous protein kinase, which may be a specific K+ channel kinase. Phosphorylations take place on the toxin-binding subunit, a polypeptide of 76-80 kDa. Phosphorylation by both kinases leads to activation of the reconstituted dendrotoxin-sensitive K+ channel.

Voltage-gated K+ channels of the mammalian brain

Research on voltage-gated K+ channels of the mammalian brain has seen a flood of new data in the last 2 years. A genetic approach, based on the Shaker mutation of Drosophila, led to cDNA clones for mammalian voltage-gated K+ channels. K+ channel proteins were detected independently and purified with the help of channel specific toxins. From these studies the structure of two families of mammalian K+ channels emerged. One family is defined molecularly by the sequence homology of its members, the other by binding sites for the snake toxin dendrotoxin. The two families have several members in common. The voltage-gated K+ channels of mammalian brain are oligomers of glycosilated peptides of 65-95 kDa. The primary structure of these subunits is characterized by six to eight potential transmembrane regions, including the S4 region, the voltage-sensor of the channels. Associated with at least some K+ channels are 38- and 42-kDa peptides of unknown function. The channels give rise to non- or slow-inactivating K+ currents that are regulated through phosphorylation by both cAMP-dependent and an endogenous kinase.

Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)

Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.

Fractionation of synaptophysin-containing vesicles from rat brain and cultured PC12 pheochromocytoma cells

Synaptophysin is a transmembrane glycoprotein of neuroendocrine vesicles. Its content and distribution in subcellular fractions from cultured PC12 cells, rat brain and bovine adrenal medulla were determined by a sensitive dot immunoassay. Synaptophysin-containing fractions appeared as monodispersed populations similar to synaptic vesicles in density and size distribution. Membranes from synaptic vesicles contained approximately 100-times more synaptophysin than chromaffin granules. In conclusion, synaptophysin is located almost exclusively in vesicles of brain and PC12 cells which are distinct from dense core granules.

The receptor site for the bee venom mast cell degranulating peptide. Affinity labeling and evidence for a common molecular target for mast cell degranulating peptide and dendrotoxin I, a snake toxin active on K+ channels

The mast cell degranulating peptide (MCD) and dendrotoxin I (DTXI) are two toxins, one extracted from bee venom, the other one from snake venom, that are thought to act on voltage-sensitive K+ channels. Binding sites for the two toxins have been solubilized. The solubilized sites were stable and retained their high affinity for 125I-DTXI and 125I-MCD (Kd approximately equal to 100 pM). Interactions were found between MCD and DTXI binding sites in the solubilized state, establishing that the two different toxins act on the same protein complex. This conclusion was strengthened by the observations (i) that conditions of solubilization that eliminated 125I-MCD binding activity also eliminated 125I-DTX binding activity while both types of activities were preserved in the presence of K+ or Rb+ and (ii) that binding components for the two types of toxins had similar sedimentation coefficients and copurified in partial purifications. A component of the receptor protein for 125I-MCD has been identified; it has a Mr of 77,000 +/- 2000. This polypeptide was similar to or identical in molecular weight with that which serves as a receptor for DTXI (Mr 76,000 +/- 2000).

GenomeConnect: matchmaking between patients, clinical laboratories, and researchers to improve genomic knowledge

As the utility of genetic and genomic testing in healthcare grows, there is need for a high-quality genomic knowledge base to improve the clinical interpretation of genomic variants. Active patient engagement can enhance communication between clinicians, patients, and researchers, contributing to knowledge building. It also encourages data sharing by patients and increases the data available for clinicians to incorporate into individualized patient care, clinical laboratories to utilize in test interpretation, and investigators to use for research. GenomeConnect is a patient portal supported by the Clinical Genome Resource (ClinGen), providing an opportunity for patients to add to the knowledge base by securely sharing their health history and genetic test results. Data can be matched with queries from clinicians, laboratory personnel, and researchers to better interpret the results of genetic testing and build a foundation to support genomic medicine. Participation is online, allowing patients to contribute regardless of location. GenomeConnect supports longitudinal, detailed clinical phenotyping and robust "matching" among research and clinical communities. Phenotype data are gathered using online health questionnaires; genotype data are obtained from genetic test reports uploaded by participants and curated by staff. GenomeConnect empowers patients to actively participate in the improvement of genomic test interpretation and clinical utility.

Inhibition of beta-bungarotoxin binding to brain membranes by mast cell degranulating peptide, toxin I, and ethylene glycol bis (beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid

The presynaptically active snake venom neurotoxin beta-bungarotoxin (beta-Butx) is known to affect neurotransmitter release by binding to a subtype of voltage-activated K+ channels. Here we show that mast cell degranulating (MCD) peptide from bee venom inhibits the binding of 125I-labeled beta-Butx to chick and rat brain membranes with apparent Ki values of 180 nM and 1100 nM, respectively. The mechanism of inhibition by MCD peptide is noncompetitive, as is inhibition of 125I-beta-Butx binding by the protease inhibitor homologue from mamba venom, toxin I. Beta-Butx and its binding antagonists thus bind to different sites of the same membrane protein. Removal of Ca2+ by ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid inhibits the binding of 125I-beta-Butx by lowering its affinity to brain membranes.

Returning a Genomic Result for an Adult-Onset Condition to the Parents of a Newborn: Insights From the BabySeq Project

The return of information from genomic sequencing in children, especially in early life, brings up complex issues around parental autonomy, the child's future autonomy, the best interest standard, and the best interests of the family. These issues are particularly important in considering the return of genomic results for adult-onset-only conditions in children. The BabySeq Project is a randomized trial used to explore the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of newborns who are healthy or sick. We discuss a case in which a variant in a gene for an actionable, adult-onset-only condition was detected, highlighting the ethical issues surrounding the return of such finding in a newborn to the newborn's parents.

Existence of different populations of the dendrotoxin I binding protein associated with neuronal K+ channels

The binding sites of dendrotoxin I, mast cell degranulating peptide, and beta-bungarotoxin are thought to be associated with neuronal K+ channels. The different binding sites seem to reside on the same molecular assembly as each toxin can allosterically inhibit the binding of the others. Affinity chromatography on a beta-BTX Aca 22 affinity column has shown that there is an heterogeneous population of dendrotoxin I binding proteins. Two subtypes were separated: DTXI binding proteins with low affinity for beta-BTX (60-70% of total) and DTXI binding proteins with high affinity for beta-BTX (30-40% of total). Binding of 125I-DTXI and 125I-MCD to the former subtype is inhibited by beta-BTX with a low affinity (IC50 = 560 nM), while inhibition at the latter subtype occurs with a high affinity (IC50 = 10-16 nM). The DTXI binding subtype with low affinity for beta-BTX contains most (85-90%) of the binding sites for 125I-MCD.

The primary structure of bdellin B-3 from the leech Hirudo medicinalis. Bdellin B-3 is a compact proteinase inhibitor of a "non-classical" Kazal type. It is present in the leech in a high molecular mass form

A proteinase inhibitor was isolated from extracts of the leech Hirudo medicinalis by gel filtration and anion exchange chromatography. This inhibitor is similar to the bdellins in that it blocks the activity of trypsin, plasmin and sperm acrosin but has a molecular mass, as estimated by SDS polyacrylamide electrophoresis, of about 20 kDa, whereas the bdellins have molecular masses in the range 5-6 kDa. It is therefore designated as high-molecular mass bdellin B-3 (HMB). The amino-acid sequence of the inhibitor was elucidated as far as position 56. This revealed that the molecule consists of a bdellin B-3 moiety, corresponding to the N-terminal 46 residues, which is then extended at the C-terminus by a polypeptide chain of the composition Asx15, Glx25, Gly6, Val, His26-27 and Lys4. It has been formerly concluded from a partial amino-acid sequence that bdellin B-3 is a Kazal-type inhibitor. However, the complete sequence of bdellin B-3, represented by the N-terminal 46 residues of HMB, discloses that bdellin B-3 is a non-classical Kazal-type inhibitor when the number of amino-acid residues between half-cystines are considered. Presuming that formation of disulfide bridges principally follows the same pattern as in classical Kazal-type inhibitors the bdellin B-3 molecule was modeled based on the known three-dimensional structure of the third ovomucoid domains. This showed that a compact arrangement of the peptide chain of bdellin B-3 is conceivable.(ABSTRACT TRUNCATED AT 250 WORDS)

The Medical Genome Initiative: moving whole-genome sequencing for rare disease diagnosis to the clinic

Clinical whole-genome sequencing (WGS) offers clear diagnostic benefits for patients with rare disease. However, there are barriers to its widespread adoption, including a lack of standards for clinical practice. The Medical Genome Initiative consortium was formed to provide practical guidance and support the development of standards for the use of clinical WGS.

Immunological evidence for a relationship between the dendrotoxin-binding protein and the mammalian homologue of the Drosophila Shaker K+ channel

Polyclonal antibodies were raised against two synthetic peptides from different parts of the predicted amino acid sequence of the mouse homologue (MBK1) of the Drosophila Shaker K+ channel. The antibodies recognized the toxin-binding subunit of the dendrotoxin-binding proteins from rat and bovine brain. The results suggest that the dendrotoxin-binding protein is related to the expression products of the mammalian homologue of the Shaker gene.

Beta-bungarotoxin-induced cell-death of neurons in chick retina

The cytotoxicity of beta-bungarotoxin (beta-BTX), a snake venom neurotoxin with phospholipase A2 activity, for chick neurons was investigated using organ and monolayer cultures of retina. Beta-BTX led to a marked reduction in the total activities of choline acetyltransferase and glutamate decarboxylase of retina cultures at concentrations as low as 100 pM. The total activity of lactate dehydrogenase was, however, much less affected by beta-BTX. Also, the total activity of tyrosine hydroxylase of organ-cultured retina decreased only at 30-50 fold higher concentrations of the toxin. The total activity of the glial marker glutamine synthetase was not changed by beta-BTX. In contrast to this selectivity for neurons displayed by beta-BTX, non-neurotoxic phospholipases A2 from bee venom and porcine pancreas led to a simultaneous loss of both neuronal and glial marker enzymes. Light and electron microscopy of organ-cultured retina showed that only cells in the ganglion cell layer and the inner third of the amacrine cell layer degenerated after incubation with beta-BTX. In the toxin-sensitive cells, the Golgi apparatus and the endoplasmatic reticulum appeared the first subcellular structures to be affected. It is concluded that beta-BTX preferentially recognizes and/or destroys cholinergic and GABAergic cells in the amacrine and ganglion cell layers of the developing chick retina. This toxin may thus be a useful probe to investigate cell surface properties of cholinergic and GABAergic neurons in the chick central nervous system.

Identification by cross-linking of a beta-bungarotoxin binding polypeptide in chick brain membranes

beta-Bungarotoxin (beta-BTX) is a snake venom neurotoxin which inhibits neurotransmitter release from different types of nerve terminals. To identify presynaptic membrane components potentially important in neurosecretion, 125I-labeled beta-BTX (mol. wt. 21 000) was cross-linked to a high-affinity binding site in synaptic membrane fractions of chick brain using the photoactivable cross-linker N-succinimidyl-6(4'-azido-2'-nitrophenylamino)-hexanoate. Electrophoretic analysis of the cross-linked membrane proteins under both reducing and non-reducing conditions revealed a single [125I]beta-BTX-polypeptide adduct of apparent mol. wt. 116 000 (+/- 2000). The labeling of this band was prevented under conditions previously shown to inhibit the binding of [125I]beta-BTX to its high-affinity binding site. It is concluded that the cross-linking procedure identified a polypeptide of the presynaptic binding site for beta-BTX, and that this polypeptide has a mol. wt. of 95 000.