DOI: 10.5061/dryad.stqjq2cc8
title: Synaptometry by time-of-flight (SynTOF) mass spectrometry data from NHP

description: Western and Mediterranean diets differentially affect cerebral cortical
 gene expression, brain structure, and socioemotional behavior in
 middle-aged, female nonhuman primates (Macaca fascicularis). Here we
 quantified the impact of these diets on the presynaptic proteome of
 approximately 3.6 million synapses isolated from the lateral temporal
 cortex with synaptometry time of flight (SynTOF) mass spectrometry, a
 powerful technology for quantifying the molecular diversity of single
 presynapses. Associations between the presynaptic proteome, adjacent
 cortex transcriptome, and multi-system phenotypes were assessed using a
 machine learning approach. Subjects were socially housed macaques (Macaca
 fascicularis) randomized to eat Mediterranean (n=17) or Western (n=19)
 diets for 31 months prior to brain retrieval. Six presynaptic
 proteins (DAT, Aβ42, calreticulin, LC3B, K48-Ubiquitin, SLC6A8) were
 elevated in the presynaptic proteome by the Mediterranean compared to the
 Western diet (p&lt;0.05). Transcriptomic data from adjacent cortex
 predicted all the SynTOF markers. The SPATA22 transcript was positively
 correlated with three SynTOF markers (LRRK2, TMEM230 and Aβ40) (all
 p&lt;0.05), while TFAP2C was positively correlated with SynTOF markers
 pTau, CD47, PARKIN and GAD65 (p&lt;0.05). The multi-system
 phenotypes significantly predicted 26 SynTOF markers. The strongest
 relationships were between synaptosome GFAP and MRI-determined changes in
 white matter (p&lt;0.001). Numerous SynTOF markers were inversely
 correlated with hepatosteatosis (e.g., Aβ42, Aβ40, DAT and K48-Ubiquitin
 adjusted p’s&lt;0.05), suggesting relationships between liver health
 and the presynapse proteome. SynTOF markers were also associated with
 behavioral and physiological measures of social environmental stress.
 Together these observations demonstrate that diet composition drives
 temporal presynaptic protein composition, that transcriptional profiles
 strongly predict the presynaptic proteomic profile, and that presynaptic
 proteins were closely associated with peripheral metabolism, stress
 responsivity, neuroanatomy, and socioemotional behavior. These data
 demonstrate brain phenotypes and brain-body interactions which can be
 influenced by diet composition, with potential implications for
 nutritional approaches to brain and body health.
description: <strong><em>Synaptometry</em></strong> <strong><em>by time-of-flight (SynTOF) mass spectrometry.</em></strong> Following our established and published protocol for a SynTOF panel<sup>1,2</sup>, synaptosome samples were prepared, barcoded, and stained. Mass Synaptometry data were acquired, debarcoded, and sequentially gated for % negative and positive events. positive events were selected by CD56 and SNAP25, and nonpresynaptic events selected by CD11b, gephyrin, PSD95, and MBP. Nonpresynaptic events were removed from downstream analyses. Synaptosome processing and analysis pipelines were previously described by us at <sup>2,3,4</sup>. [1] Gajera CR, Fernandez R, Postupna N, et al. Mass synaptometry: High-dimensional multi parametric assay for single synapses. J Neurosci Methods 2019;312:73-83. [2] Gajera CR, Fernandez R, Montine KS, et al. Mass-tag barcoding for multiplexed analysis of human synaptosomes and other anuclear events. Cytometry A 2021;99:939-945 [3] Berson E, Gajera CR, Phongpreecha T, et al. Cross-species comparative analysis of single presynapses. Sci Rep 2023;13:13849. [4] Gajera CR, Fernandez R, Postupna N, et al. Mass Synaptometry: Applying Mass Cytometry to Single Synapse Analysis. Methods Mol Biol 2022;2417:69-88.
description: # SynTOF NHP
 [https://doi.org/10.5061/dryad.stqjq2cc8](https://doi.org/10.5061/dryad.stqjq2cc8) ## Description of the data and file structure Single-cell presynapse from NHP. ### Files and variables #### File: single\_event\_data.zip **Description:** Single-presynapse data from NHP. This folder contains data files representing single events measured from individual specimens. Each file is formatted as a table with: * The first column corresponds to the event number * Other columns represent markers used in the study. Code to read and process these data files is provided (see below). #### File: Metadata.csv **Description:** Metadata information linking specimen to their diet group and batch group. This file provides metadata linking each specimen to its corresponding diet and batch groups. The columns in the file are as follows: 1. *File Name:* Matches the names of the files in the *single_**event*_*data* folder. 2. *Cohort ("BC009"=Cohort1, "BC010"=Cohort2):* Specifies the batch group of the specimen. 3. *Diet:* Indicates the diet group of the specimen. ## Code/software Code to read and process the data is available at [https://github.com/elo-nsrb/Brain-study-NHP-2024](https://github.com/elo-nsrb/Brain-study-NHP-2024).