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Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.

Madissoon E, Töhönen V, Vesterlund L, Katayama S, Unneberg P, Inzunza J, Hovatta O, Kere J - PLoS ONE (2014)

Bottom Line: Improvements in IVF and infertility treatment depend largely on better understanding of the molecular mechanisms for human preimplantation development.We have identified genes of possible importance for this time period by analyzing human microarray data and available data from online databases.We also describe four cancer-testis antigen families that are also highly expressed in human embryos: PRAME, SSX, GAGE and MAGEA.

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences and Nutrition; Center for Biosciences, Karolinska Institutet, Huddinge, Sweden.

ABSTRACT
Infertility is a worldwide concern that can be treated with in vitro fertilization (IVF). Improvements in IVF and infertility treatment depend largely on better understanding of the molecular mechanisms for human preimplantation development. Several large-scale studies have been conducted to identify gene expression patterns for the first five days of human development, and many functional studies utilize mouse as a model system. We have identified genes of possible importance for this time period by analyzing human microarray data and available data from online databases. We selected 70 candidate genes for human preimplantation development and investigated their expression in the early mouse development from oocyte to the 8-cell stage. Maternally loaded genes expectedly decreased in expression during development both in human and mouse. We discovered that 25 significantly upregulated genes after fertilization in human included 13 genes whose orthologs in mouse behaved differently and mimicked the expression profile of maternally expressed genes. Our findings highlight many significant differences in gene expression patterns during mouse and human preimplantation development. We also describe four cancer-testis antigen families that are also highly expressed in human embryos: PRAME, SSX, GAGE and MAGEA.

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Comparison of early upregulated genes in human and mouse.Expression values for the genes in cluster “Up” for humans (A) and their orthologs in mouse show similar (B) and different (C) expression pattern between the two organisms. The “Up-down” cluster genes in human (D) and their mouse orthologs also show similar (E) and different (F) expression pattern. Similarly expressed orthologs were upregulated (p-value <0.05) from 1-cell to 2-cell stages (cluster “Up”) in mouse and downregulated from 2-cell to 8-cell stages (cluster “Up-down”) with the exception of Trim 43a which was only up-, but not downregulated. Maternal expression pattern was observed for differently behaving orthologs (C, F), which were downregulated by the 8-cell stage with the exception of Magea2. Average log2(comparative expression) values for each stage were used for the human data obtained from Zhang et al. (2007) microarray expression dataset and average −ΔCt values were used for the mouse expression data produced in the current study. Undetected samples were attributed the −ΔCt value of −14.8.
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pone-0102949-g003: Comparison of early upregulated genes in human and mouse.Expression values for the genes in cluster “Up” for humans (A) and their orthologs in mouse show similar (B) and different (C) expression pattern between the two organisms. The “Up-down” cluster genes in human (D) and their mouse orthologs also show similar (E) and different (F) expression pattern. Similarly expressed orthologs were upregulated (p-value <0.05) from 1-cell to 2-cell stages (cluster “Up”) in mouse and downregulated from 2-cell to 8-cell stages (cluster “Up-down”) with the exception of Trim 43a which was only up-, but not downregulated. Maternal expression pattern was observed for differently behaving orthologs (C, F), which were downregulated by the 8-cell stage with the exception of Magea2. Average log2(comparative expression) values for each stage were used for the human data obtained from Zhang et al. (2007) microarray expression dataset and average −ΔCt values were used for the mouse expression data produced in the current study. Undetected samples were attributed the −ΔCt value of −14.8.

Mentions: We studied the expression patterns of the selected genes in mouse. Custom TaqMan Low Density Array Cards (TLDA) were used for detecting the expression in the following mouse preimplantation stages: MII oocytes, 1-cell, 2-cell and 8-cell embryos. Five ng of RNA per sample was used in the first experiment in three biological replicas using TaqMan custom pre-amp pool for pre-amplification of cDNA with this approach. However, many assays did not pass our quality control criteria (Figure S1A). The experiment was then repeated with 12 ng of RNA per sample and no pre-amplification step. The quality of amplification curves was improved comparing to the pre-amplified samples (Figure S1B). 69 assays were analyzed in total, 4 were used as controls, and 1 assay was rejected for technical reasons. The upregulation control Nanog was detected only in the 8-cell stage as expected and the downregulation control Nlrp5 decreased significantly from MII to 8-cell stage. Psmb6 and Hprt1 were used as endogeneous controls for normalization. Two (MII and 1-cell) or three (2-cell and 8-cell) biological replicas were used per developmental stage. Expression values were obtained using the comparative ΔCt method. A heatmap plotted for the selected genes is shown in Figure 2B. Mouse orthologs clustered remarkably different from the selected human genes (Figure 2). Human genes clustered into three groups based on the previous analysis, but mouse genes clustered as one downregulated group containing most genes, and a smaller group for genes that were significantly upregulated between 1- and 2-cell stages. Twenty-nine out of 30 orthologs for the genes in cluster “Down” were downregulated in the course of preimplantation development (p-val<0.05) similar to human, but only nine genes out of 25 in clusters “Up” or “Up-down” were upregulated by 2-cell stage in mouse. The human genes and mouse orthologs for “Up” and “Up-down” clusters are shown in Figure 3. Four and five orthologs in the human clusters “Up” and “Up-down”, respectively, were upregulated by the mouse 2-cell stage that is similar to human ZGA 4- to 8-cell stages (Figure 3B, E). However, seven and nine orthologs in the respective clusters were not upregulated by the 2-cell stage, but only downregulated by the 8-cell, except for Magea2 and 2410004A20Rik. Overall, more than half of the mouse orthologs for genes in “Up” and “Up-down” clusters shared the maternal gene expression profile being present already in the oocyte and downregulated later.


Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.

Madissoon E, Töhönen V, Vesterlund L, Katayama S, Unneberg P, Inzunza J, Hovatta O, Kere J - PLoS ONE (2014)

Comparison of early upregulated genes in human and mouse.Expression values for the genes in cluster “Up” for humans (A) and their orthologs in mouse show similar (B) and different (C) expression pattern between the two organisms. The “Up-down” cluster genes in human (D) and their mouse orthologs also show similar (E) and different (F) expression pattern. Similarly expressed orthologs were upregulated (p-value <0.05) from 1-cell to 2-cell stages (cluster “Up”) in mouse and downregulated from 2-cell to 8-cell stages (cluster “Up-down”) with the exception of Trim 43a which was only up-, but not downregulated. Maternal expression pattern was observed for differently behaving orthologs (C, F), which were downregulated by the 8-cell stage with the exception of Magea2. Average log2(comparative expression) values for each stage were used for the human data obtained from Zhang et al. (2007) microarray expression dataset and average −ΔCt values were used for the mouse expression data produced in the current study. Undetected samples were attributed the −ΔCt value of −14.8.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4121084&req=5

pone-0102949-g003: Comparison of early upregulated genes in human and mouse.Expression values for the genes in cluster “Up” for humans (A) and their orthologs in mouse show similar (B) and different (C) expression pattern between the two organisms. The “Up-down” cluster genes in human (D) and their mouse orthologs also show similar (E) and different (F) expression pattern. Similarly expressed orthologs were upregulated (p-value <0.05) from 1-cell to 2-cell stages (cluster “Up”) in mouse and downregulated from 2-cell to 8-cell stages (cluster “Up-down”) with the exception of Trim 43a which was only up-, but not downregulated. Maternal expression pattern was observed for differently behaving orthologs (C, F), which were downregulated by the 8-cell stage with the exception of Magea2. Average log2(comparative expression) values for each stage were used for the human data obtained from Zhang et al. (2007) microarray expression dataset and average −ΔCt values were used for the mouse expression data produced in the current study. Undetected samples were attributed the −ΔCt value of −14.8.
Mentions: We studied the expression patterns of the selected genes in mouse. Custom TaqMan Low Density Array Cards (TLDA) were used for detecting the expression in the following mouse preimplantation stages: MII oocytes, 1-cell, 2-cell and 8-cell embryos. Five ng of RNA per sample was used in the first experiment in three biological replicas using TaqMan custom pre-amp pool for pre-amplification of cDNA with this approach. However, many assays did not pass our quality control criteria (Figure S1A). The experiment was then repeated with 12 ng of RNA per sample and no pre-amplification step. The quality of amplification curves was improved comparing to the pre-amplified samples (Figure S1B). 69 assays were analyzed in total, 4 were used as controls, and 1 assay was rejected for technical reasons. The upregulation control Nanog was detected only in the 8-cell stage as expected and the downregulation control Nlrp5 decreased significantly from MII to 8-cell stage. Psmb6 and Hprt1 were used as endogeneous controls for normalization. Two (MII and 1-cell) or three (2-cell and 8-cell) biological replicas were used per developmental stage. Expression values were obtained using the comparative ΔCt method. A heatmap plotted for the selected genes is shown in Figure 2B. Mouse orthologs clustered remarkably different from the selected human genes (Figure 2). Human genes clustered into three groups based on the previous analysis, but mouse genes clustered as one downregulated group containing most genes, and a smaller group for genes that were significantly upregulated between 1- and 2-cell stages. Twenty-nine out of 30 orthologs for the genes in cluster “Down” were downregulated in the course of preimplantation development (p-val<0.05) similar to human, but only nine genes out of 25 in clusters “Up” or “Up-down” were upregulated by 2-cell stage in mouse. The human genes and mouse orthologs for “Up” and “Up-down” clusters are shown in Figure 3. Four and five orthologs in the human clusters “Up” and “Up-down”, respectively, were upregulated by the mouse 2-cell stage that is similar to human ZGA 4- to 8-cell stages (Figure 3B, E). However, seven and nine orthologs in the respective clusters were not upregulated by the 2-cell stage, but only downregulated by the 8-cell, except for Magea2 and 2410004A20Rik. Overall, more than half of the mouse orthologs for genes in “Up” and “Up-down” clusters shared the maternal gene expression profile being present already in the oocyte and downregulated later.

Bottom Line: Improvements in IVF and infertility treatment depend largely on better understanding of the molecular mechanisms for human preimplantation development.We have identified genes of possible importance for this time period by analyzing human microarray data and available data from online databases.We also describe four cancer-testis antigen families that are also highly expressed in human embryos: PRAME, SSX, GAGE and MAGEA.

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences and Nutrition; Center for Biosciences, Karolinska Institutet, Huddinge, Sweden.

ABSTRACT
Infertility is a worldwide concern that can be treated with in vitro fertilization (IVF). Improvements in IVF and infertility treatment depend largely on better understanding of the molecular mechanisms for human preimplantation development. Several large-scale studies have been conducted to identify gene expression patterns for the first five days of human development, and many functional studies utilize mouse as a model system. We have identified genes of possible importance for this time period by analyzing human microarray data and available data from online databases. We selected 70 candidate genes for human preimplantation development and investigated their expression in the early mouse development from oocyte to the 8-cell stage. Maternally loaded genes expectedly decreased in expression during development both in human and mouse. We discovered that 25 significantly upregulated genes after fertilization in human included 13 genes whose orthologs in mouse behaved differently and mimicked the expression profile of maternally expressed genes. Our findings highlight many significant differences in gene expression patterns during mouse and human preimplantation development. We also describe four cancer-testis antigen families that are also highly expressed in human embryos: PRAME, SSX, GAGE and MAGEA.

Show MeSH
Related in: MedlinePlus