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1. Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218

   https://doi.org/10.1038/s41398-020-00966-4  

   Jurkiewicz, Magdalena ; Moser, Dirk ; Koller, Antonius ; Yu, Lei ; Chen, Emily I. ; Bennett, David A. ; Canli, Turhan ( August 2020 , Translational Psychiatry)

   Recent genome-wide studies have begun to identify gene variants, expression profiles, and regulators associated with neuroticism, anxiety disorders, and depression. We conducted a set of experimental cell culture studies of gene regulation by micro RNAs (miRNAs), based on genome-wide transcriptome, proteome, and miRNA expression data from twentypostmortemsamples of lateral amygdala from donors with known neuroticism scores. Using Ingenuity Pathway Analysis and TargetScan, we identified a list of mRNA–protein–miRNA sets whose expression patterns were consistent with miRNA-based translational repression, as a function of trait anxiety. Here, we focused on one gene from that list, which is of particular translational significancemore »in Psychiatry: synaptic vesicle glycoprotein 2A (SV2A) is the binding site of the anticonvulsant drug levetiracetam ((S)-α-Ethyl-2-oxo-1-pyrrolidineacetamide), which has shown promise in anxiety disorder treatments. We confirmed thatSV2Ais associated with neuroticism or anxiety using an original GWAS of a community cohort (N = 1,706), and cross-referencing a published GWAS of multiple cohorts (Ns ranging from 340,569 to 390,278).Postmortemamygdala expression profiling implicated three putative regulatory miRNAs to targetSV2A: miR-133a, miR-138, and miR-218. Moving from association to experimental causal testing in cell culture, we used a luciferase assay to demonstrate that miR-133a and miR-218, but not miR-138, significantly decreased relative luciferase activity from theSV2Adual-luciferase construct. In human neuroblastoma cells, transfection with miR-133a and miR-218 reduced both endogenousSV2AmRNA and protein levels, confirming miRNA targeting of theSV2Agene. This study illustrates the utility of combiningpostmortemgene expression data with GWAS to guide experimental cell culture assays examining gene regulatory mechanisms that may contribute to complex human traits. Identifying specific molecular mechanisms of gene regulation may be useful for future clinical applications in anxiety disorders or other forms of psychopathology.

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2. Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes

   https://doi.org/10.1038/s41467-019-12372-6  

   Guo, Syuan-Ming ; Veneziano, Remi ; Gordonov, Simon ; Li, Li ; Danielson, Eric ; Perez de Arce, Karen ; Park, Demian ; Kulesa, Anthony B. ; Wamhoff, Eike-Christian ; Blainey, Paul C. ; et al ( September 2019 , Nature Communications)

   Synapses contain hundreds of distinct proteins whose heterogeneous expression levels are determinants of synaptic plasticity and signal transmission relevant to a range of diseases. Here, we use diffusible nucleic acid imaging probes to profile neuronal synapses using multiplexed confocal and super-resolution microscopy. Confocal imaging is performed using high-affinity locked nucleic acid imaging probes that stably yet reversibly bind to oligonucleotides conjugated to antibodies and peptides. Super-resolution PAINT imaging of the same targets is performed using low-affinity DNA imaging probes to resolve nanometer-scale synaptic protein organization across nine distinct protein targets. Our approach enables the quantitative analysis of thousands ofmore »synapses in neuronal culture to identify putative synaptic sub-types and co-localization patterns from one dozen proteins. Application to characterize synaptic reorganization following neuronal activity blockade reveals coordinated upregulation of the post-synaptic proteins PSD-95, SHANK3 and Homer-1b/c, as well as increased correlation between synaptic markers in the active and synaptic vesicle zones.

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3. Oligodendrocytes express synaptic proteins that modulate myelin sheath formation

   https://doi.org/10.1038/s41467-019-12059-y  

   Hughes, Alexandria N. ; Appel, Bruce ( September 2019 , Nature Communications)

   Vesicular release from neurons promotes myelin sheath growth on axons. Oligodendrocytes express proteins that allow dendrites to respond to vesicular release at synapses, suggesting that axon-myelin contacts use similar communication mechanisms as synapses to form myelin sheaths. To test this, we used fusion proteins to track synaptic vesicle localization and membrane fusion in zebrafish during developmental myelination and investigated expression and localization of PSD95, a dendritic post-synaptic protein, within oligodendrocytes. Synaptic vesicles accumulate and exocytose at ensheathment sites with variable patterning and most sheaths localize PSD95 with patterning similar to exocytosis site location. Disruption of candidate PDZ-binding transsynaptic adhesionmore »proteins in oligodendrocytes cause variable effects on sheath length and number. One candidate, Cadm1b, localizes to myelin sheaths where both PDZ binding and extracellular adhesion to axons mediate sheath growth. Our work raises the possibility that axon-glial communication contributes to myelin plasticity, providing new targets for mechanistic unraveling of developmental myelination.

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4. Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses

   https://doi.org/10.1038/s41598-020-77993-0  

   Du, Zhiqiang ; Regan, Jeniece ; Bartom, Elizabeth ; Wu, Wei-Sheng ; Zhang, Li ; Goncharoff, Dustin Kenneth ; Li, Liming ( December 2020 , Scientific Reports)

   Transcriptional regulators are prevalent among identified prions inSaccharomyces cerevisiae, however, it is unclear how prions affect genome-wide transcription.We show here that the prion ([SWI⁺]) and mutant (swi1∆)forms of Swi1, a subunit of the SWI/SNF chromatin-remodeling complex, confer dramatically distinct transcriptomic profiles. In [SWI⁺] cells, genes encoding for 34 transcription factors (TFs) and 24 Swi1-interacting proteins can undergo transcriptional modifications. Several TFs show enhanced aggregation in [SWI⁺] cells. Further analyses suggest that such alterations are key factors in specifying the transcriptomic signatures of [SWI⁺] cells. Interestingly,swi1∆and [SWI⁺] impose distinct and oftentimes opposite effects on cellular functions. Translation-associated activities, in particular, aremore »significantly reduced inswi1∆cells. Although bothswi1∆and [SWI⁺] cells are similarly sensitive to thermal, osmotic and drought stresses, harmful, neutral or beneficial effects were observed for a panel of tested chemical stressors. Further analyses suggest that the environmental stress response (ESR) is mechanistically different betweenswi1∆and [SWI⁺] cells—stress-inducible ESR (iESR) are repressed by [SWI⁺] but unchanged byswi1∆while stress-repressible ESR (rESR) are induced by [SWI⁺] but repressed byswi1∆. Our work thus demonstrates primarily gain-of-function outcomes through transcriptomic modifications by [SWI⁺] and highlights a prion-mediated regulation of transcription and phenotypes in yeast.

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5. VER/VEGF receptors regulate AMPA receptor surface levels and glutamatergic behavior

   https://doi.org/10.1371/journal.pgen.1009375  

   Luth, Eric S. ; Hodul, Molly ; Rennich, Bethany J. ; Riccio, Carmino ; Hofer, Julia ; Markoja, Kaitlin ; Juo, Peter ( February 2021 , PLOS Genetics)

   Hart, Anne C. (Ed.)

   Several intracellular trafficking pathways contribute to the regulation of AMPA receptor (AMPAR) levels at synapses and the control of synaptic strength. While much has been learned about these intracellular trafficking pathways, a major challenge is to understand how extracellular factors, such as growth factors, neuropeptides and hormones, impinge on specific AMPAR trafficking pathways to alter synaptic function and behavior. Here, we identify the secreted ligand PVF-1 and its cognate VEGF receptor homologs, VER-1 and VER-4, as regulators of glutamate signaling in C . elegans . Loss of function mutations in ver-1 , ver-4 , or pvf-1 , result in decreasedmore »cell surface levels of the AMPAR GLR-1 and defects in glutamatergic behavior. Rescue experiments indicate that PVF-1 is expressed and released from muscle, whereas the VERs function in GLR-1-expressing neurons to regulate surface levels of GLR-1 and glutamatergic behavior. Additionally, ver-4 is unable to rescue glutamatergic behavior in the absence of pvf-1 , suggesting that VER function requires endogenous PVF-1. Inducible expression of a pvf-1 rescuing transgene suggests that PVF-1 can function in the mature nervous system to regulate GLR-1 signaling. Genetic double mutant analysis suggests that the VERs act together with the VPS-35/retromer recycling complex to promote cell surface levels of GLR-1. Our data support a genetic model whereby PVF-1/VER signaling acts with retromer to promote recycling and cell surface levels of GLR-1 to control behavior.« less