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Proteomics and their Analyses. a-b. Proteins differentially expressed during parasite infection of L-NSC (a) or S-NSC (b). ATXN2L, Ataxin 2-like; NSC2, Niemann-Pick disease, type C2; FXR1, Fragile X Mental Retardation Autosomal Homolog 1; WDFY1, WD Repeat And FYVE Domain Containing 1; UBE3A, Ubiquitin Protein Ligase E3A; USP8, Ubiquitin Specific Peptidase 8; PPP4C, Protein Phosphatase 4 Catalytic Subunit). (c) Left panel, number of differentially expressed proteins (DEPs) in S-NSC infected with T. gondii types I, II and III; right panel, GO Biological Processes significantly overrepresented (p-value < 0.01) in the set of 3,359 proteins differentially expressed in infected S-NSC compared with their respective uninfected controls (>2-fold change and false discovery rate <0.1). Nominal p-values were utilized for KEGG and GO analyses. Pathways that were robust to Benjamini Hochberg correction also are shown in Supplement B: Table S15. 

Proteomics and their Analyses. a-b. Proteins differentially expressed during parasite infection of L-NSC (a) or S-NSC (b). ATXN2L, Ataxin 2-like; NSC2, Niemann-Pick disease, type C2; FXR1, Fragile X Mental Retardation Autosomal Homolog 1; WDFY1, WD Repeat And FYVE Domain Containing 1; UBE3A, Ubiquitin Protein Ligase E3A; USP8, Ubiquitin Specific Peptidase 8; PPP4C, Protein Phosphatase 4 Catalytic Subunit). (c) Left panel, number of differentially expressed proteins (DEPs) in S-NSC infected with T. gondii types I, II and III; right panel, GO Biological Processes significantly overrepresented (p-value < 0.01) in the set of 3,359 proteins differentially expressed in infected S-NSC compared with their respective uninfected controls (>2-fold change and false discovery rate <0.1). Nominal p-values were utilized for KEGG and GO analyses. Pathways that were robust to Benjamini Hochberg correction also are shown in Supplement B: Table S15. 

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One third of humans are infected lifelong with the brain-dwelling, protozoan parasite, Toxoplasma gondii. Approximately fifteen million of these have congenital toxoplasmosis. Although neurobehavioral disease is associated with seropositivity, causality is unproven. To better understand what this parasite does to human brains, we performed a compre...

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... gene expression were also evident by miR-seq for MM6, S-NSC and S-NDC cells at 18 hours post-infection (Figs 3 and 4 and Supplement B: Tables S11 and S12). These included mirs 139, 132, 29a, 107, 218, 143, 155, 199a, 21, 16, 181b-1. L-NSC and S-NSC infections with Type I, II, III parasites were also studied using iTRAQ quantitative pro- teomics ( Fig. 5). Differential protein expression analysis of L-NSC cells identified only three primary candi- date proteins with significant fold change increases in infected cells. These proteins were Ataxin 2-like protein (ATXN2L); Fragile X-related protein 1 (FXR1); and Niemann-Pick-like protein (NPC2) (Fig. 5a, Supplement B: Table S4). An IPA ...
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... studied using iTRAQ quantitative pro- teomics ( Fig. 5). Differential protein expression analysis of L-NSC cells identified only three primary candi- date proteins with significant fold change increases in infected cells. These proteins were Ataxin 2-like protein (ATXN2L); Fragile X-related protein 1 (FXR1); and Niemann-Pick-like protein (NPC2) (Fig. 5a, Supplement B: Table S4). An IPA later showed how these three proteins were linked to transcriptomic infectomes and identified congenital toxoplasmosis susceptibility genes ( Figs 6, 7). These proteomics and transcriptomics (Figs 3-5) defined empirically, responses of human L-NSC to infection with T. ...
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... infection ( Table S15). In summary, S-NSC pro- teomics, pathway and GO enrichment analyses showed signaling pathways impacting on cell death, TOR, protein transport/localization and RNA splicing. Oxidation reduction, vesicle mediated transport, iron homeostasis and glucose metabolism were also influenced, some differentially by parasite type (Fig. 5c). Consistent with these enrichment results, prediction of alternative spliced isoforms in our transcriptomics datasets identified a number of candidate genes predicted 51 to be differentially spliced during parasite infections (Supplement B: Table S14). Each of the three ill children had new myoclonic-"infantile" spasms, or ...
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... Our transcriptomic and proteomic analyses indicated that this parasite alters neddylation (NEDD8) and ubiquitination which are key in clearing misfolded proteins, neuronal cell viability, and synaptic plasticity (Figs 3, 4, 9 and 11c). In the proteomics analyses, we also found that T. gondii modified alternative splicing (Fig. 5) and that an rMATS analysis 51 predicted transcripts that are alternatively spliced based on the S-NSC ...
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... the quantitative proteomics with L-NSC (Fig. 5a), ATXN2L, FXR1, and NPC2 were modulated. ATXN2L is a paralog of Ataxin 2, a protein that causes spinocerebellar ataxia type 2 72 . It has been shown that ATXN2L is functionally similar to Ataxin 2 with respect to RNA metabolism and also plays a role in the regulation of stress granules and processing bodies in mammalian cells 73 . ...
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... the quantitative proteomics of S-NSC (Fig. 5b) many more genes transcripts were modulated. Some of particular interest are shown in Fig. 5b as follows: WDFY1 and PPP4C, two proteins known to modulate NFκB activity, a key factor to control parasite infections, were downregulated in infected S-NSC (Fig. 5b). WDFY1 induces TLR3-and TLR4-mediated activation of NFκB and the production ...
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... the quantitative proteomics of S-NSC (Fig. 5b) many more genes transcripts were modulated. Some of particular interest are shown in Fig. 5b as follows: WDFY1 and PPP4C, two proteins known to modulate NFκB activity, a key factor to control parasite infections, were downregulated in infected S-NSC (Fig. 5b). WDFY1 induces TLR3-and TLR4-mediated activation of NFκB and the production of type I interferons and inflam- matory cytokines 76 , while PPP4C is the catalytic subunit ...
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... the quantitative proteomics of S-NSC (Fig. 5b) many more genes transcripts were modulated. Some of particular interest are shown in Fig. 5b as follows: WDFY1 and PPP4C, two proteins known to modulate NFκB activity, a key factor to control parasite infections, were downregulated in infected S-NSC (Fig. 5b). WDFY1 induces TLR3-and TLR4-mediated activation of NFκB and the production of type I interferons and inflam- matory cytokines 76 , while PPP4C is the catalytic subunit of protein phosphatase 4, a protein implicated in the activation of NFκB-mediated transcription 77 . This strongly suggests that T. gondii inhibits the human host NFkB ...
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... cell cycle are especially noteworthy in the KEGG pathways for S-NSC (Fig. 2c). Transcriptomic analysis of L-NSC reveals pathways associated with Alzheimer's, Parkinson's and Huntington diseases and disruption of oxidative phosphorylation. Also alternative splicing pathways which might cause protein misfolding and neurologic diseases are affected (Fig. 5). Transcriptomics, proteomics, and cluster deconvolution identified alterations in neddylation and ubiquitination key in clearing misfolded pro- teins, neuronal cell viability, and synaptic plasticity (Figs 3-5, 9). We are investigating whether T. gondii causes alternative splicing which can be a central cause of protein misfolding, ...

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