Identification of a novel SNAP25 interacting protein (SIP30)

Genomic analyses in Cavalier King Charles spaniels identify loci associated with clinical signs of Chiari-like malformation and Syringomyelia

BACKGROUND

Chiari-like malformations (CM) and syringomyelia (SM) are common in Cavalier King Charles spaniels (CKCS) leading to variable manifestations of pain and scratch. Inheritance studies suggest a polygenic mode of inheritance and association studies have identified loci associated with the presence of SM on MRI. Given the poor correlation of clinical signs of CMSM with MRI findings, we hypothesized that an association study with clinical signs as the phenotype could reveal new loci of interest. The objectives of this study were to perform genome-wide association studies on CKCS using SM and clinical sign phenotypes of pain and scratch and to use whole genome sequencing (WGS) to identify variants in regions of interest. We collected DNA on 174 CKCS. Owners completed questionnaires to establish the clinical pain and scratch phenotype and magnetic resonance imaging (MRI) was used to identify CM and SM (linear T2 hyperintensity greater than 2 mm in height) in all dogs. Dogs were genotyped using the Axiom K9 HD (710,000 snps) array. GWAS analyses were performed using GEMMA and categorical and quantitative approaches were used to define clinical phenotypes. Whole genome sequencing (WGS) was performed on an Illumina HiSeq 4000 high-throughput sequencing system.

RESULTS

There were no regions associated with SM presence. The presence of signs of pain and scratch was associated with a region on Canis familiaris autosome (CFA) 26 downstream of ZWINT, previously associated with skull changes in CKCS with SM, although genome-wide significance was not reached. Loci were also associated with quantitative pain and scratch scores on CFA 13, 2 and 38. There were 66 variants that segregated with phenotype including 2 missense variants that were predicted to have moderate effects on ZWINT function.

CONCLUSIONS

The identification of a locus on CFA26 using the clinical phenotype of pain and scratch that coincided with a locus identified in a morphological study provides strong support for this as a region of interest.

The Contribution of Mosaic Chromosomal Alterations to Schizophrenia

BACKGROUND

Mosaic chromosomal alterations are implicated in neuropsychiatric disorders, but the contribution to schizophrenia (SCZ) risk for somatic copy number variations (sCNVs) emerging in early developmental stages has not been fully established.

METHODS

We analyzed blood-derived genotype arrays from 9715 patients with SCZ and 28,822 control participants of Chinese descent using a computational tool (MoChA) based on long-range chromosomal information to detect mosaic chromosomal alterations. We focused on probable early developmental sCNVs through stringent filtering. We assessed the burden of sCNVs across varying cell fraction cutoffs, as well as the frequency with which genes were involved in sCNVs. We integrated this data with the PGC (Psychiatric Genomics Consortium) dataset, which comprises 12,834 SCZ cases and 11,648 controls of European descent, and complemented it with genotyping data from postmortem brain tissue of 936 participants (449 cases and 487 controls).

RESULTS

Patients with SCZ had a significantly higher somatic losses detection rate than control participants (1.00% vs. 0.52%; odds ratio = 1.91; 95% CI, 1.47-2.49; two-sided Fisher's exact test, p = 1.49 × 10-6). Further analysis indicated that the odds ratios escalated proportionately (from 1.91 to 2.78) with the increment in cell fraction cutoffs. Recurrent sCNVs associated with SCZ (odds ratio > 8; Fisher's exact test, p < .05) were identified, including notable regions at 10q21.1 (ZWINT), 3q26.1 (SLITRK3), 1q31.1 (BRINP3) and 12q21.31-21.32 (MGAT4C and NTS) in the Chinese cohort, and some regions were validated with PGC data. Cross-tissue validation pinpointed somatic losses at loci like 1p35.3-35.2 and 19p13.3-13.2.

CONCLUSIONS

The study highlights the significant impact of mosaic chromosomal alterations on SCZ, suggesting their pivotal role in the disorder's genetic etiology.

Phylogenetic analysis of mammalian SIP30 sequences indicating accelerated adaptation of functional domain in primates

SIP30, characterized by a coiled-coil functional domain, plays a key role in regulating synaptic vesicle exocytosis and is implicated in neuropathic pain resulting from peripheral nerve injury. Because neuropathic pain is studied in primates (including human), domesticated animals, and rodents, we conducted a phylogenetic analysis of SIP30 in selected species of these three groups of mammals. SIP30 exhibits a high degree of sequence divergence in comparison to its protein binding partners SNAP25 and ZW10, which show broad sequence conservation. Notably, we observed an increased rate of change in the highly conserved coiled-coil domain in the SIP30 protein, specifically within primates. This observation suggests an accelerated adaptation of this functional domain in primate species.

SIP30 involvement in vesicle exocytosis from PC12 cells

SNAP25 (synaptosome-associated protein of 25 kDa) is a core SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor) protein; and the interaction between SNAP25 and other SNARE proteins is essential for synaptic vesicle exocytosis. Identified as a SNAP25 interacting protein, SIP30 (SNAP25 interacting protein at 30 kDa) has been shown to modulate neuropathic pain behavior, and is potentially involved in the cellular process of vesicle exocytosis. Previous study demonstrated that using a vesicle secretion assay in PC12 cells, anti-SIP30 siRNA reduced vesicle exocytosis. We investigated vesicle exocytosis from PC12 cells with FM1-43 fluorescence dye, and demonstrated that anti-SIP30 siRNA reduced the pool of releasable vesicles and the rate of vesicle exocytosis, without affecting the endocytosis and recycling of the exocytosed vesicles. The results show that SIP30 is involved in vesicle exocytosis, suggesting a potential mechanism of SIP30 modulation of neuropathic pain.

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (FIS R2 = 0.942, P = 2.19 × 10-13; FROH R2 = 0.88, P = 1.81 × 10-10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.

Neuronal activity-regulated alternative mRNA splicing

Activity-regulated gene transcription underlies plasticity-dependent changes in the molecular composition and structure of neurons. Numerous genes whose expression is induced by different neuronal plasticity inducing pathways have been identified, but the alteration of gene expression levels represents only part of the complexity of the activity-regulated transcriptional program. Alternative splicing of precursor mRNA is an additional mechanism that modulates the activity-dependent transcriptional signature. Recently developed splicing sensitive transcriptome wide analyses improve our understanding of the underlying mechanisms and demonstrate to what extend the activity regulated transcriptome is alternatively spliced. So far, only for a small group of differentially spliced mRNAs of synaptic proteins, the functional implications have been studied in detail. These include examples in which differential exon usage can result in the expression of alternative proteins which interfere with or alter the function of preexisting proteins and cause a dominant negative functional block of constitutively expressed variants. Such altered proteins contribute to the structural and functional reorganization of pre- and postsynaptic terminals and to the maintenance and formation of synapses. In addition, activity-induced alternative splicing can affect the untranslated regions (UTRs) and generates mRNAs harboring different cis-regulatory elements. Such differential UTRs can influence mRNA stability, translation, and can change the targeting of mRNAs to subcellular compartments. Here, we summarize different categories of alternative splicing which are thought to contribute to synaptic remodeling, give an overview of activity-regulated alternatively spliced mRNAs of synaptic proteins that impact synaptic functions, and discuss splicing factors and epigenetic modifications as regulatory determinants.

An essential step of kinetochore formation controlled by the SNARE protein Snap29

The kinetochore is an essential structure that mediates accurate chromosome segregation in mitosis and meiosis. While many of the kinetochore components have been identified, the mechanisms of kinetochore assembly remain elusive. Here, we identify a novel role for Snap29, an unconventional SNARE, in promoting kinetochore assembly during mitosis in Drosophila and human cells. Snap29 localizes to the outer kinetochore and prevents chromosome mis‐segregation and the formation of cells with fragmented nuclei. Snap29 promotes accurate chromosome segregation by mediating the recruitment of Knl1 at the kinetochore and ensuring stable microtubule attachments. Correct Knl1 localization to kinetochore requires human or Drosophila Snap29, and is prevented by a Snap29 point mutant that blocks Snap29 release from SNARE fusion complexes. Such mutant causes ectopic Knl1 recruitment to trafficking compartments. We propose that part of the outer kinetochore is functionally similar to membrane fusion interfaces.

Moonlighting functions of the NRZ (mammalian Dsl1) complex

The yeast Dsl1 complex, which comprises Dsl1, Tip20, and Sec39/Dsl3, has been shown to participate, as a vesicle-tethering complex, in retrograde trafficking from the Golgi apparatus to the endoplasmic reticulum. Its metazoan counterpart NRZ complex, which comprises NAG, RINT1, and ZW10, is also involved in Golgi-to-ER retrograde transport, but each component of the complex has diverse cellular functions including endosome-to-Golgi transport, cytokinesis, cell cycle checkpoint, autophagy, and mRNA decay. In this review, we summarize the current knowledge of the metazoan NRZ complex and discuss the "moonlighting" functions and intercorrelation of their subunits.

SIP30 is required for neuropathic pain-evoked aversion in rats

SIP30 (SNAP25 interacting protein of 30) is a SNAP25 interaction protein of 30 kDa that functions in neurotransmitter release. Using a chronic constriction injury (CCI) model of neuropathic pain, we profiled gene expression in the rat spinal cord and brain and identified sip30, which was upregulated after CCI. Here, we show that CCI induced a bilateral increase of SIP30 in the rostral anterior cingulate cortex (rACC), a key brain region that has been implicated in pain affect. We put rats in a chamber with one half painted white (light area) and the other half painted black (dark area), and measured neuropathic pain-evoked place escape/avoidance paradigm (PEAP) to quantify the level of negative emotion evoked by painful stimuli using a Von Frey hair. Inhibition of CCI-mediated induction of SIP30 by intra-rACC injection of shRNA targeting the rat sip30 gene reduced PEAP. Interestingly, knockdown of SIP30 did not affect CCI-induced evoked pain such as heat hyperalgesia and mechanical allodynia. Neither did it affect general learning and memory. CCI-induced upregulation of SIP30 was correlated with activation of ERK, PKA, and CREB in the rACC. Intra-rACC administration of PKA or ERK inhibitors suppressed CCI-induced SIP30 upregulation and blocked the induction of PEAP. Additionally, knockdown of SIP30 suppressed the frequency of mEPSCs and increased paired-pulse ratios in rACC slices and decreased extracellular glutamate concentrations. Together, our results highlight SIP30 as a target of PKA and ERK in the rACC to mediate neuropathic pain-evoked negative emotion via modulation of glutamate release and excitatory synaptic transmission.

Genome-wide profiling of the activity-dependent hippocampal transcriptome

Activity-dependent gene expression is central for sculpting neuronal connectivity in the brain. Despite the importance for synaptic plasticity, a comprehensive analysis of the temporal changes in the transcriptomic response to neuronal activity is lacking. In a genome wide survey we identified genes that were induced at 1, 4, 8, or 24 hours following neuronal activity in the hippocampus. According to their distinct expression kinetics we assigned these genes to five clusters, each containing approximately 200 genes. Using in situ hybridizations the regulated expression of 24 genes was validated. Apart from known activity-dependent genes our study reveals a large number of unknown induced genes with distinct expression kinetics. Among these we identified several genes with complex temporal expression patterns. Furthermore, our study provides examples for activity-induced exon switching in the coding region of genes and activity-induced alternative splicing of the 3'-UTR. One example is Zwint. In contrast to the constitutively expressed variant, the induced Zwint transcript harbors multiple regulatory elements in the 3'-UTR. Taken together, our study provides a comprehensive analysis of the transcriptomic response to neuronal activity and sheds new light on expression kinetics and alternative splicing events.

Role of SIP30 in the development and maintenance of peripheral nerve injury-induced neuropathic pain

Using the chronic constriction injury (CCI) model of neuropathic pain, we profiled gene expression in the rat spinal cord, and identified SIP30 as a gene whose expression was elevated after CCI. SIP30 was previously shown to interact with SNAP25, but whose function was otherwise unknown. We now show that in the spinal cord, SIP30 was present in the dorsal horn laminae where the peripheral nociceptive inputs first synapse, co-localizing with nociception-related neuropeptides CGRP and substance P. With the onset of neuropathic pain after CCI surgery, SIP30 mRNA and protein levels increased in the ipsilateral side of the spinal cord, suggesting a potential association between SIP30 and neuropathic pain. When CCI-upregulated SIP30 was inhibited by intrathecal antisense oligonucleotide administration, neuropathic pain was attenuated. This neuropathic pain-reducing effect was observed both during neuropathic pain onset following CCI, and after neuropathic pain was fully established, implicating SIP30 involvement in the development and maintenance phases of neuropathic pain. Using a secretion assay in PC12 cells, anti-SIP30 siRNA decreased the total pool of synaptic vesicles available for exocytosis, pointing to a potential function for SIP30. These results suggest a role of SIP30 in the development and maintenance of peripheral nerve injury-induced neuropathic pain.

SIP30 is regulated by ERK in peripheral nerve injury-induced neuropathic pain

ERK plays an important role in chronic neuropathic pain. However, the underlying mechanism is largely unknown. Here we show that in chronic constriction injury-treated rat spinal cords, up-regulation of SIP30 (SNAP25-interacting protein 30), which is involved in the development and maintenance of chronic constriction injury-induced neuropathic pain, correlates with ERK activation and that the up-regulation of SIP30 is suppressed by intrathecal delivery of the MEK inhibitor U0126. In PC12 cells, up-regulation of SIP30 by nerve growth factor is also dependent on ERK activation. We found that there is an ERK-responsive region in the rat sip30 promoter. Activation of ERK promotes the recruitment of the transcription factor cyclic AMP-response element-binding protein to the sip30 gene promoter. Taken together, our results provide a potential downstream target of ERK activation-mediated neuropathic pain.

A unique residue in rab3c determines the interaction with novel binding protein Zwint-1

Exocytic events are tightly regulated cellular processes in which rab GTPases and their interacting proteins perform an important function. We set out to identify new binding partners of rab3, which mediates regulated secretion events in specialized cells. We discovered Zwint-1 as a rab3 specific binding protein that bound preferentially to rab3c. The interaction depends on a critical residue in rab3c that determines the binding efficiency of Zwint-1, which is immaterial for interaction with rabphilin3a. Rab3c and Zwint-1 are expressed highly in brain and colocalized extensively in primary hippocampal neurons. We also found that SNAP25 bound to the same region in Zwint-1 as rab3c, suggesting a new role for the kinetochore protein Zwint-1 in presynaptic events that are regulated by rab3 and SNAP25.

Reciprocal regulation of presynaptic and postsynaptic proteins in bipolar spiral ganglion neurons by neurotrophins

A unifying principle of sensory system organization is feature extraction by modality-specific neuronal maps in which arrays of neurons show systematically varied response properties and receptive fields. Only beginning to be understood, however, are the mechanisms by which these graded systems are established. In the peripheral auditory system, we have shown previously that the intrinsic firing features of spiral ganglion neurons are influenced by brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3). We now show that is but a part of a coordinated package of neurotrophin actions that also includes effects on presynaptic and postsynaptic proteins, thus encompassing the input, transmission, and output functions of the spiral ganglion neurons. Using immunocytochemical methods, we determined that proteins targeted to opposite ends of the neuron were organized and regulated in a reciprocal manner. AMPA receptor subunits GluR2 and GluR3 were enriched in base neurons compared with their apex counterparts. This distribution pattern was enhanced by exposure to BDNF but reduced by NT-3. SNAP-25 and synaptophysin were distributed and regulated in the mirror image: enriched in the apex, enhanced by NT-3 and reduced by BDNF. Moreover, we used a novel coculture to identify potential endogenous sources of neurotrophins by showing that sensory receptors from different cochlear regions were capable of altering presynaptic and postsynaptic protein levels in these neurons. From these studies, we suggest that BDNF and NT-3, which are systematically distributed in complementary gradients, are responsible for orchestrating a comprehensive set of electrophysiological specializations along the frequency contour of the cochlea.

Sensitization to the conditioned rewarding effects of morphine modulates gene expression in rat hippocampus

Opiates addiction is characterized by its long-term persistence. In order to study the enduring changes in long-term memory in hippocampus, a pivotal region for this process, we used suppression subtractive hybridization to compare hippocampal gene expression in morphine and saline-treated rats. Animals were subjected to an extended place preference paradigm consisting of four conditioning phases. Sensitization to the reinforcing effects of the drug occurred after three conditioning phases. After 25 days of treatment rats were euthanized and the complementary DNA (cDNA) from the hippocampus of morphine-dependent and saline-treated animals were then screened for differentially expressed cDNAs. The selected 177 clones were then subjected to a microarray procedure and 20 clones were found differentially regulated. The pattern of regulated genes suggests impairments in neurotransmitter release and the activation of neuroprotective pathways.

SNAREs and traffic

SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are now generally accepted to be the major players in the final stage of the docking and the subsequent fusion of diverse vesicle-mediated transport events. The SNARE-mediated process is conserved evolutionally from yeast to human, as well as mechanistically and structurally across different transport events in eukaryotic cells. In the post-genomic era, a fairly complete list of "all" SNAREs in several organisms (including human) can now be made. This review aims to summarize the key properties and the mechanism of action of SNAREs in mammalian cells.

Suppression subtractive hybridization and microarray identification of estrogen-regulated hypothalamic genes

The gonadal steroid estrogen is a pleiotropic hormone that has multiple effects on numerous cellular functions. One of estrogen's major targets is the brain, where the steroid not only affects growth, differentiation, and survival of neurons, but also regulates cell excitability. Because estrogen modulates multiple, overlapping signaling pathways, it has been difficult to scrutinize the transcriptional activity of the steroid. Therefore, we still lack a global picture of how different genes interact and are regulated by estrogen. Herein we report the use of suppression subtractive hybridization followed by custom microarray analysis of thousands of genes that are differentially expressed during the negative feedback phase of the female reproductive cycle. We have found a number of key transcripts that are regulated by estrogen and contribute to the alteration in synaptic transmission and hence excitability of hypothalamic neurons (e.g., GABA neurons). These include gec-1, GABA(B)R2, PI3 kinase subunit p55gamma, and a number of proteins containing pleckstrin homology domains that are critical for plasma membrane targeting. Studies are underway to refine our analysis to individual nuclei and individual cells. However, what has emerged from this highly sensitive microarray analysis is that estrogen affects neuronal plasticity in hypothalamic neurons not only by transcription of new membrane proteins (e.g., receptors and channels), but also by altering expression of downstream signaling molecules and proteins involved in neurosecretory pathways.

Implication of ZW10 in membrane trafficking between the endoplasmic reticulum and Golgi

ZW10, a dynamitin-interacting protein associated with kinetochores, is known to participate directly in turning off of the spindle checkpoint. In the present study, we show that ZW10 is located in the endoplasmic reticulum as well as in the cytosol during interphase, and forms a subcomplex with RINT-1 (Rad50-interacting protein) and p31 in a large complex comprising syntaxin 18, an endoplasmic reticulum-localized t-SNARE implicated in membrane trafficking. Like conventional syntaxin-binding proteins, ZW10, RINT-1 and p31 dissociated from syntaxin 18 upon Mg(2+)-ATP treatment in the presence of NSF and alpha-SNAP, whereas the subcomplex was not disassembled. Overexpression, microinjection and knockdown experiments revealed that ZW10 is involved in membrane trafficking between the endoplasmic reticulum and Golgi. The present results disclose an unexpected role for a spindle checkpoint protein, ZW10, during interphase.

Proteomics Analysis of Rat Brain Postsynaptic Density

The postsynaptic density contains multiple protein complexes that together relay the presynaptic neurotransmitter input to the activation of the postsynaptic neuron. In the present study we took two independent proteome approaches for the characterization of the protein complement of the postsynaptic density, namely 1) two-dimensional gel electrophoresis separation of proteins in conjunction with mass spectrometry to identify the tryptic peptides of the protein spots and 2) isolation of the trypsin-digested sample that was labeled with isotope-coded affinity tag, followed by liquid chromatography-tandem mass spectrometry for the partial separation and identification of the peptides, respectively. Functional grouping of the identified proteins indicates that the postsynaptic density is a structurally and functionally complex organelle that may be involved in a broad range of synaptic activities. These proteins include the receptors and ion channels for glutamate neurotransmission, proteins for maintenance and modulation of synaptic architecture, sorting and trafficking of membrane proteins, generation of anaerobic energy, scaffolding and signaling, local protein synthesis, and correct protein folding and breakdown of synaptic proteins. Together, these results imply that the postsynaptic density may have the ability to function (semi-) autonomously and may direct various cellular functions in order to integrate synaptic physiology.

What is the role of SNARE proteins in membrane fusion?

Soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE) proteins have been at the fore-front of research on biological membrane fusion for some time. The subcellular localization of SNAREs and their ability to form the so-called SNARE complex may be integral to determining the specificity of intracellular fusion (the SNARE hypothesis) and/or serving as the minimal fusion machinery. Both the SNARE hypothesis and the idea of the minimal fusion machinery have been challenged by a number of experimental observations in various model systems, suggesting that SNAREs may have other functions. Considering recent advances in the SNARE literature, it appears that SNAREs may actually function as part of a complex fusion "machine." Their role in the machinery could be any one or a combination of roles, including establishing tight membrane contact, formation of a scaffolding on which to build the machine, binding of lipid surfaces, and many others. It is also possible that complexations other than the classic SNARE complex participate in membrane fusion.