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Comprehensive and quantitative proteomic analyses of zebrafish plasma reveals conserved protein profiles between genders and between zebrafish and human.

Li C, Tan XF, Lim TK, Lin Q, Gong Z - Sci Rep (2016)

Bottom Line: The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar.Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements.Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, Singapore 117543.

ABSTRACT
Omic approaches have been increasingly used in the zebrafish model for holistic understanding of molecular events and mechanisms of tissue functions. However, plasma is rarely used for omic profiling because of the technical challenges in collecting sufficient blood. In this study, we employed two mass spectrometric (MS) approaches for a comprehensive characterization of zebrafish plasma proteome, i.e. conventional shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) for an overview study and quantitative SWATH (Sequential Window Acquisition of all THeoretical fragment-ion spectra) for comparison between genders. 959 proteins were identified in the shotgun profiling with estimated concentrations spanning almost five orders of magnitudes. Other than the presence of a few highly abundant female egg yolk precursor proteins (vitellogenins), the proteomic profiles of male and female plasmas were very similar in both number and abundance and there were basically no other highly gender-biased proteins. The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar. Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements. Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

No MeSH data available.


Tissue expression of plasma proteins.(A) Distribution of plasma proteins based on tissues of expression. (B) Comparison of tissue expression of plasma proteins between females and males. Only those proteins expressed in a single tissue are used for comparison.
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f3: Tissue expression of plasma proteins.(A) Distribution of plasma proteins based on tissues of expression. (B) Comparison of tissue expression of plasma proteins between females and males. Only those proteins expressed in a single tissue are used for comparison.

Mentions: To determine which organs are major contributors to plasma proteins, the 910 Gene IDs were input to DAVID database for information on tissue expression. Information on tissue expression was retrieved for 452 genes (Supplementary Table S3). Most of the proteins were found to be expressed in whole body or in multiple organs (Fig. 3A). 135 genes had reported expression in only one individual organ, including liver (37), kidney (31), olfactory epithelium (21), eye (11), ovary (9) and brain (8) (blue bars in Fig. 3A). If the abundance of proteins is taken into account, the liver is the single predominant site of production for plasma proteins, with 37 proteins accounting for about 30% of total plasma protein content in both genders (Supplementary Table S3). These 37 proteins included high abundance proteins such as Vtgs and some complement components. There were also other abundant proteins that were expressed in both the liver and other organs, such as apolipoproteins. In fact, according to our in-house zebrafish liver transcriptome generated by RNA sequencing, mRNAs for at least 323 plasma proteins detected in the present study are also expressed in the liver, among which Vtg mRNAs take up as much as 78% of female liver transcriptome6. The extremely high expression of Vtgs in the liver leads to the high abundance of total Vtgs (>40%) in the plasma of female. Since the expression level of liver secreted proteins is generally in agreement with corresponding plasma protein concentrations34, alteration of liver functions could result in prominent changes in plasma proteome. Unlike those from liver, proteins from other organs are present at low concentrations (Supplementary Table S3). For example, 31 proteins from kidney only make up about 1–2% of total mass, while 21 proteins from olfactory epithelium only make up 0.1%.


Comprehensive and quantitative proteomic analyses of zebrafish plasma reveals conserved protein profiles between genders and between zebrafish and human.

Li C, Tan XF, Lim TK, Lin Q, Gong Z - Sci Rep (2016)

Tissue expression of plasma proteins.(A) Distribution of plasma proteins based on tissues of expression. (B) Comparison of tissue expression of plasma proteins between females and males. Only those proteins expressed in a single tissue are used for comparison.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829857&req=5

f3: Tissue expression of plasma proteins.(A) Distribution of plasma proteins based on tissues of expression. (B) Comparison of tissue expression of plasma proteins between females and males. Only those proteins expressed in a single tissue are used for comparison.
Mentions: To determine which organs are major contributors to plasma proteins, the 910 Gene IDs were input to DAVID database for information on tissue expression. Information on tissue expression was retrieved for 452 genes (Supplementary Table S3). Most of the proteins were found to be expressed in whole body or in multiple organs (Fig. 3A). 135 genes had reported expression in only one individual organ, including liver (37), kidney (31), olfactory epithelium (21), eye (11), ovary (9) and brain (8) (blue bars in Fig. 3A). If the abundance of proteins is taken into account, the liver is the single predominant site of production for plasma proteins, with 37 proteins accounting for about 30% of total plasma protein content in both genders (Supplementary Table S3). These 37 proteins included high abundance proteins such as Vtgs and some complement components. There were also other abundant proteins that were expressed in both the liver and other organs, such as apolipoproteins. In fact, according to our in-house zebrafish liver transcriptome generated by RNA sequencing, mRNAs for at least 323 plasma proteins detected in the present study are also expressed in the liver, among which Vtg mRNAs take up as much as 78% of female liver transcriptome6. The extremely high expression of Vtgs in the liver leads to the high abundance of total Vtgs (>40%) in the plasma of female. Since the expression level of liver secreted proteins is generally in agreement with corresponding plasma protein concentrations34, alteration of liver functions could result in prominent changes in plasma proteome. Unlike those from liver, proteins from other organs are present at low concentrations (Supplementary Table S3). For example, 31 proteins from kidney only make up about 1–2% of total mass, while 21 proteins from olfactory epithelium only make up 0.1%.

Bottom Line: The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar.Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements.Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, Singapore 117543.

ABSTRACT
Omic approaches have been increasingly used in the zebrafish model for holistic understanding of molecular events and mechanisms of tissue functions. However, plasma is rarely used for omic profiling because of the technical challenges in collecting sufficient blood. In this study, we employed two mass spectrometric (MS) approaches for a comprehensive characterization of zebrafish plasma proteome, i.e. conventional shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) for an overview study and quantitative SWATH (Sequential Window Acquisition of all THeoretical fragment-ion spectra) for comparison between genders. 959 proteins were identified in the shotgun profiling with estimated concentrations spanning almost five orders of magnitudes. Other than the presence of a few highly abundant female egg yolk precursor proteins (vitellogenins), the proteomic profiles of male and female plasmas were very similar in both number and abundance and there were basically no other highly gender-biased proteins. The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar. Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements. Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

No MeSH data available.