Network organization of the huntingtin proteomic interactome in mammalian brain

Abstract

We used affinity-purification mass spectrometry to identify 747 candidate proteins that are complexed with Huntingtin (Htt) in distinct brain regions and ages in Huntington's disease (HD) and wild-type mouse brains. To gain a systems-level view of the Htt interactome, we applied Weighted Correlation Network Analysis to the entire proteomic data set to unveil a verifiable rank of Htt-correlated proteins and a network of Htt-interacting protein modules, with each module highlighting distinct aspects of Htt biology. Importantly, the Htt-containing module is highly enriched with proteins involved in 14-3-3 signaling, microtubule-based transport, and proteostasis. Top-ranked proteins in this module were validated as Htt interactors and genetic modifiers in an HD Drosophila model. Our study provides a compendium of spatiotemporal Htt-interacting proteins in the mammalian brain and presents an approach for analyzing proteomic interactome data sets to build in vivo protein networks in complex tissues, such as the brain.

Figure 1. Generation and characterization of a full-length Htt in vivo proteomic interactome from BACHD and wildtype mouse brains

(A) Immunoprecipitation using a human Htt-selective antibody (aa 1844–2131, clone HDB4E10) followed by Westernblot analysis using a human and mouse Htt antibody (MAB2166) confirms full-length Htt is pulled-down in both 2-month WT and 2- and 12-month BACHD soluble cortical extracts. A negative control (no Htt antibody) and 5% input loading control were also included. (B) The affinity purification followed by mass spectrometry (AP-MS) proteomic approach used to identify endogenous fl-Htt protein interactors: (1) The cortex, striatum, and cerebellum of 2- and 12-month WT and BACHD mice were homogenized, (2) The soluble lysates were subjected to anti-Htt IP using HDB4E10 and Protein G Dynabeads, (3) The immunoprecipitates were eluted with LDS loading buffer, separated on an SDS-PAGE gel, each gel was cut into 24–27 gel bands, and each gel band was subjected to in-gel trypsin digestion, (4) Approximately 750 independent LC-MS/MS analysis were performed, and (5) All mass spectra were searched using MASCOT (Matrix Science) to obtain a total of 747 high-scoring, putative Htt-interacting proteins. (C) The scheme of the spatiotemporal proteomic interactome study that includes 30 independent samples for the AP-MS experiments. (D) A schematic representation of the Htt tryptic peptides identified along the full-length Htt primary sequence (aa 1–3144). BACHD IP conditions labeled with Q and WT IP conditions labeled W. (E) Venn diagram comparison of Htt-interacting proteins identified in this study, literature-curated Htt-interacting proteins, and the published ataxia protein network. (F) Top IPA canonical signaling pathways enriched in the the Htt interactome, plotted as –log10 p-value significance. The black dotted line indicates canonical pathway genome-wide p-value significance (p < 0.05). See also Supplemental Tables S1–S3, and S5.

Figure 2. Brain regional and age-specific protein interactions revealed in Htt interactome

(A–B) Venn diagram comparison of the age (2- and 12-month) and brain region (cortex, striatum, and cerebellum) specific Htt protein interactions identified in this study. (C–D) A list of high confidence age and brain regional Htt protein interactions (protein identified in > 2 IP conditions, > 3 total peptides identified, no peptides identified in control IP). See also Supplemental Table S6.

Figure 3. Unique peptide counts as a measure of relative protein abundance reveals proteins most correlated with Htt

(A) The left panel is a Western blot analysis using anti-Htt (mAb2166) (left) of the anti-Htt immunoprecipitation (HDB4E10) of 2-month BACHD cerebellum biological duplicates (Crb2mQ1 and Crb2mQ2, red dashed box), 2-month WT cerebellum biological duplicates (Crb2mW1 and Crb2mW2, blue dashed box), and 2-month BACHD cerebellum no antibody control (Crb2mBlk). The right panel is a bar graph of unique tryptic Htt peptide counts identified across 30 experimental AP-MS conditions (right), which illustrate the reproducibility of the number of Htt peptides that is identified in duplicated sample conditions as well as the consistent variance in across sample conditions (i.e. age, brain region, genotype and with or without antibody in IP). (B) Unique peptide counts of the top ten proteins most correlated with Htt across the 30 sample conditions. (C) Htt correlation bins 1–6 (each consisting of 125 proteins, where bin 1 contains the proteins most correlated with Htt and bin 6 contains the proteins least correlated with Htt). IPA canonical pathway analysis of these bins showed their enrichment of ‘Huntington’s Disease Signaling’ (plotted as –log10 p-values values and the black dotted line indicates p < 0.05). The IPA ‘Amyloid Processing Pathway’, an Alzheimer’s disease related pathway, was used as a negative control. The number in parenthesis indicates the number of proteins identified in each category. See also Figures S1 and S2, and Supplemental Tables S7–S9.

Figure 4. Weighted Gene Correlation Network Analysis (WGCNA) of Htt interactome

(A) Cluster dendrogram generated by hierarchical clustering of proteins on the basis of topological overlap. Modules of correlated proteins were assigned colors and names (Cyan, Red, Blue, Yellow, Green, Navy, Brown, and Pink respectively) and are indicated by the horizontal bar beneath the dengrogram, where all unassigned proteins were placed in the Grey module (labeled Color Modules). The number in the color modules represents the number of proteins assigned to each module. Pairwise correlations were calculated for each protein to the Htt protein, and the p-value significance is colored below in the horizontal bar where a significant (p < 0.05, red) or non-significant correlation (p > 0.05, blue) with Htt protein levels is indicated. (B) Barplot depicting the –log10 p-values of the pairwise correlations between each module’s eigenprotein (see text) and Htt. Dotted black line: significance level at p < 0.05. (C) IPA canonical pathway analysis of each module to show their enrichment of ‘Huntington’s Disease Signaling’ (plotted as –log10 p-values values and the black dotted line indicates p < 0.05). See also Supplemental Tables S10 and S11.

Figure 5. Enrichment of Htt interactome modules and meta-networks in specific sample conditions

(A–F) The heat map correlation profiles (rows) across samples (columns) for proteins in the following color modules are shown: A) Red B) Blue C) Pink D) Yellow E) Green F) Cyan where green indicates areas of low correlation profiles and red indicates areas of high correlation profiles. The 30 sample conditions are indicated by brain regions, genotype (BACHD vs WT), and age (2m, 12m) or control IP lacking Htt antibody (Blank or Blk). The two duplicated conditions (two separate columns) are labeled only once. (G) Module eigenprotein meta-network reveals the cortical-enriched sub-network and the cerebellum-enriched sub-network.

Figure 6. Functional annotation of top Htt-correlated modules

(A–F) The Visant plots, IPA, and GO terms most enriched terms or signaling pathways in the top Htt-correlated modules are shown for: A) Red B) Blue C) Pink D) Yellow E) Green and F) Cyan Modules. Key characteristic describing each module is summarized in the parenthesis. Visant plots are shown representing the top 150 protein connections in each color module. The enlarged labeled nodes represent the top 15 proteins with the largest module connectivity values (kwithin) for each module, and the nodes in the middle of each Visant plot are the “hub genes” for each module. See also Supplemental Tables S10, S13, and S14

Figure 7. Validation of Red Module proteins in Htt interactome uncovers Htt-interacting proteins in WT and BACHD mice and novel genetic modifiers of disease in a fly model of HD

(A) Co-immunoprecipitation of top MM.Red proteins from 2-month WT and BACHD mouse brains. Htt was immunoprecipitated with anti-Htt (clone HDB4E10) and probed with mouse monoclonal antibody MAB2166. The 10% input for each protein (left panels) and resulting immunoprecipitations are shown (right panels). A no Htt antibody negative control was performed in parallel to confirm specific protein interaction. F8a1 (Hap40) served as the positive control for Htt protein interaction. (B) Reciprocal co-immunoprecipitation of Htt and Vps35 in 2-month WT and BACHD mouse brains. Anti-alpha tubulin was used as a loading control. (C) Table summarizing the effects caused by modulating the levels of the indicated Red Module proteins on NT-Htt[128Q]-induced motor performance in a HD Drosophila model. (D–G) Charts represent motor performance as a function of age. Each chart includes controls (elav-GAL4) and animals expressing NT-Htt[128Q] either alone or together with a loss of function allele targeting the Drosophila homolog of the indicated gene (red continuous lines). Control flies show robust motor performance for the duration of the experiment (black dashed line). Animals expressing NT-Htt[128Q] in the nervous system using elav-GAL4 show a progressive decline in their motor performance (blue discontinuous lines). D and G show the suppressor effect of decreasing the levels of the Drosophila homologs of Vps35 and Hsp90ab1. E and F show the enhancer effect of decreasing the levels of the Drosophila homologs of Ywhae and Tcp1/Cct1. Error bars represent standard error of the mean (SEM). Two experimental replicates are shown for the NT-Htt128Q and the NT-Htt128Q/modifier animals except for G. See also Figure S4.