Liver proteome alterations in psychologically distressed rats and a nootropic drug

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Liver proteome alterations in psychologically distressed rats and a nootropic drug https://t.co/psbxebYP9n @thePeerJ https://t.co/SnVEpwDrvO
Biochemistry, Biophysics and Molecular Biology

Main article text

 

Introduction

Materials & Methods

Animals and experimental design

Administration of piracetam and distress induction

Sample collection

Blood plasma biochemical parameter analysis

Liver enzyme activity assays

Liver protein extraction

GeLC-MS/MS analysis

Proteomics data analysis and biological interpretation

Statistical analysis

Results

Protein identification by GeLC-MS/MS approach

Biological interpretation of differentially accumulated proteins

Altered proteins involved in redox metabolism

Altered proteins involved in non-alcoholic fatty liver disease (NAFLD)

Altered proteins involved in ER stress

Altered proteins involved in the metabolism of xenobiotics by Cyt P450

Interaction network of differently accumulated proteins

Effect of chronic psychological distress and piracetam on animal behavior

Effect of chronic psychological distress and piracetam on plasma biomarkers

Correlational analysis among treatments, behavior, biochemical parameters, and antioxidant enzyme activity

Discussion

Redox metabolism

Non-alcoholic fatty liver disease (NAFLD)

ER stress

Metabolism of xenobiotics by Cyt P450

Effect of piracetam on animal behavior

Effect of distress and piracetam on biochemical parameters

Conclusions

Supplemental Information

Additional information on the methodology used in the GeLC-MS/MS analysis

A detailed description of the in-gel digestion, the nanoLC-MS/MS analysis, and the protein search parameters are included.

DOI: 10.7717/peerj.11483/supp-1

Experimental design

For six consecutive days, rats received piracetam (600 mg/kg), dispensed orally using a cannula, in single dose, at 7:30 am. From the first day until the fifth day, the animals were exposed to the stressor (at 8 am, after drug administration). In the sixth day, rats were sacrificed.

DOI: 10.7717/peerj.11483/supp-2

Correlation between behavior, plasma biochemical parameters, and GPX activity in rats exposed to psychological distress and piracetam

The glucose level was negatively correlated with the time the rat spent hiding (A) and positively with the head-out position (B). The direct bilirubin level was positively correlated with the time the rat spent approaching (C) and exploring (D). The total bilirubin level was negatively correlated with the time the rat spent hiding (E) and positively with the exploring time (F). The GPX activity was positively correlated to the time the rat spent hiding (G) and negatively with the exploring time (H).

DOI: 10.7717/peerj.11483/supp-3

Fold change in the abundance of redox proteins identified by GeLC-MS/MS analysis in the different conditions

S−P−: unique protein detected in S−P − condition; S+P−: unique protein detected in S+P− condition; S+P+: unique protein detected in S+P+ condition.

DOI: 10.7717/peerj.11483/supp-4

Identified proteins involved in non-alcoholic fatty liver disease (NAFLD) and Parkinson’s disease (PD) pathways according to KEGG database

The fold change was obtained from the ratio between the relative protein abundance based on the emPAI value of the indicated groups. S−P−, S+P−, S+P+, S −P+ indicate proteins that were detected only in S −P−, S+P−, S+P+, or S−P+ group respectively. n.d. indicates protein that was not detected in the experimental group. PD and both indicate proteins that are categorized only in PD pathway or in both pathways, respectively. S−P −, rats neither exposed to stress nor with piracetam treatment; S−P+, rats not exposed to stress but treated with piracetam; S+P−, rats exposed to stress without piracetam treatment; S+P+, rats exposed to stress and treated with piracetam.

DOI: 10.7717/peerj.11483/supp-5

Proteins (indicated by their protein symbol) that showed changes of 50% in protein abundance and are involved in protein processing in ER, proteosome, and metabolism of xenobiotics by Cyt P450

Most abundant indicates proteins with fold change (FD) ≥1.5. Less abundant indicates proteins with FD ≤0.66. n.d. indicates protein that was not detected in the experimental group.

DOI: 10.7717/peerj.11483/supp-6

Pearson’.s correlation among treatment, biochemical parameters, antioxidant enzyme activities, and rat behaviors

Significant values are marked in bold (* p ≤ 0.05; p ≤ 0.01).

DOI: 10.7717/peerj.11483/supp-7

Raw data collected in the GeLC-MS/MS analysis from rat liver proteins for all the treatments (S−P−, S+P−, S+P+, and S−P +)

The data contain details of identified proteins: Accession number, Description, Coverage, # Peptides, # Unique Peptides, MW [kDa], calc. pI, emPAI, Score Sequest, Coverage Sequest, # Peptides Sequest, Score Mascot, Coverage Mascot, # Peptides Mascot, Score MS Amanda, Coverage MS Amanda, # Peptides MS Amanda, and identification data for each detected peptide.

DOI: 10.7717/peerj.11483/supp-8

Fold change in the abundance of liver proteins identified in the different experimental conditions

Proteins with changes in abundance of 50% were selected ( 0.66 ≤ fold change ≤1.5). The UniProtKb number accession, protein description, and fold change are showed. S−P−, S+P−, S+P+ or S−P+ in the ratio column indicates proteins only detected in a particular condition. S−P −, rats neither exposed to stress nor with piracetam treatment; S−P+, rats not exposed to stress but treated with piracetam; S+P−, rats exposed to stress without piracetam treatment; S+P+, rats exposed to stress and treated with piracetam.

DOI: 10.7717/peerj.11483/supp-9

Data collected from the KEGG pathway enrichment analysis using Metascape resource

The settings used were p-value < 0.01, minimum count of 3, enrichment factor > 1.5 and FDR > 0.05. Data show the GO pathway identifier, pathway name, log10 (p-value), log10 (q-value), gen number of upload hit list in each pathway/gene number of genome in the same pathway, list of Entrez Gene IDs of upload hits in the pathway, and the list of symbols of upload hits in the pathway.

DOI: 10.7717/peerj.11483/supp-10

Raw data from the antioxidant enzyme activity, plasma biochemical parameters, and rat behavior analyses

The individual data that were obtained in the different analyses are shown for each experimental group.

DOI: 10.7717/peerj.11483/supp-11

Data collected from the enrichment clustering analysis using the STRING protein-protein interaction database

Data collected from the enrichment clustering analysis using the STRING protein-protein interaction database. Proteins were clustered using the Markov Cluster Algorithm (MCL) with an inflation parameter of 3. Data show the cluster number and color, gene count, and protein name, identifier, and description.

DOI: 10.7717/peerj.11483/supp-12

ARRIVE guidelines 2.0 checklist

DOI: 10.7717/peerj.11483/supp-13

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Raquel González-Fernández conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Mariana Grigoruţă conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Sarahi Chávez-Martínez performed the experiments, prepared figures and/or tables, and approved the final draft.

Eliel Ruiz-May and José Valero-Galván analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

José Miguel Elizalde-Contreras performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Alejandro Martínez-Martínez conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The Institutional Committee of Ethics and Bioethics from the Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chihuahua, Mexico provided full approval for this research (No.CIBE-2017-1-34).

Data Availability

The following information was supplied regarding data availability:

The raw measurements of the proteomic analysis performed by GeLC-MS/MS and raw data obtained in the antioxidant enzyme activity, plasma biochemical parameters, and rat behavior analyses are available in the Supplementary Files.

Funding

This work was funded by the CONACYT-México grant CB-2015 (254483) to Alejandro Martínez-Martínez and SEP-PRODEP-Apoyo a Nuevos PTC (UACJ-PTC-326) to Raquel González-Fernández. Mariana Grigoruţă was supported by a doctoral fellowship from CONACYT-México (CVU 548217). The Orbitrap Fusion Tribrid Mass spectrometer was acquired by a grant to the CONACYT-México (U0004-20151, 259915). There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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