ORIGINAL ARTICLE Embryology
Effect of ICSI on gene expression
and development of mouse
G. Giritharan1, M.W. Li2, F. De Sebastiano1, F.J. Esteban3,
J.A. Horcajadas4, K.C.K. Lloyd2, A. Donjacour1, E. Maltepe1,
and P.F. Rinaudo1,*
1Department of Obstetric, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
2Mouse Biology Program, Center for Comparative Medicine, University of California, Davis, CA 95618, USA3Department of Experimental
Biology, Systems Biology Unit, University of Jaen, Jaen 23071, Spain4Fundacion IVI and iGenomix, Valencia 46015, Spain
*Correspondence address. Division of Reproductive Endocrinology and Infertility University of California, San Francisco, 2356 Sutter St.,
San Francisco, CA 94115, USA. Tel: +1-415-353-7475; Fax: +1-415-353-7744; E-mail: firstname.lastname@example.org
Submitted on May 9, 2010; resubmitted on August 16, 2010; accepted on September 15, 2010
background: In vitro culture (IVC) and IVF of preimplantation mouse embryos are associated with changes in gene expression. It is
however not known whether ICSI has additional effects on the transcriptome of mouse blastocysts.
methods: We compared gene expression and development of mouse blastocysts produced by ICSI and cultured in Whitten’s medium
(ICSIWM) or KSOM medium with amino acids (ICSIKSOMaa) with control blastocysts flushed out of the uterus on post coital Day 3.5 (in vivo).
In addition, we compared gene expression in embryos generated by IVF or ICSI using WM. Global pattern of gene expression was assessed
using the Affymetrix 430 2.0 chip.
results: Blastocysts from ICSI fertilization have a reduction in the number of trophoblastic and inner cell mass cells compared with
embryos generated in vivo. Approximately 1000 genes are differentially expressed between ICSI blastocyst and in vivo blastocysts; prolifer-
ation, apoptosis and morphogenetic pathways are the most common pathways altered after IVC. Unexpectedly, expression of only 41 genes
was significantly different between embryo cultured in suboptimal conditions (WM) or optimal conditions (KSOMaa).
conclusions: Our results suggest that fertilization by ICSI may play a more important role in shaping the transcriptome of the devel-
oping mouse embryo than the culture media used.
Key words: ICSI / embryos / microarray / gene expression / culture medium
It is estimated that 1% of children in the western world are born with
the help of assisted reproductive techniques (ART). Whereas these
techniques are thought to be safe, several studies report an increased
risk of unique complications associated with the use of IVF and ICSI
(Anthony, 2002; Cox et al., 2002; Hansen et al., 2002; Schieve
et al., 2002; DeBaun et al., 2003). The widespread use of ICSI, cur-
rently accounting for over 60% of the fertilization procedures in
USA (Society for Assisted Reproductive Technology, 2008 www.
sart.org) has sparked controversy because ICSI bypasses several
physiologic events which would usually occur during fertilization.
ICSI involves introduction of the sperm tail into the ooplasm and
may be associated with suboptimal sperm nuclear decondensation
(Markoulaki et al. 2007). In addition, ICSI-generated zygotes cleave
at a slower rate, have a reduced hatching rate and a reduced cell
number. ICSI zygotes also exhibit shorter calcium oscillations with
an altered pattern (Kurokawa and Fissore, 2003). Importantly,
Fernandez-Gonzalez et al. found that ICSI-generated mice using
fresh spermatozoa develop long-term consequences, such as obesity
and organomegaly, whereas ICSI-generated mice using frozen–
thawed spermatozoa had a more severe phenotype, including aber-
rant growth, abnormal behavior, early aging and increased incidence
of tumors (Fernandez-Gonzalez et al., 2008).
In our earlier studies, we showed that in vitro culture (IVC) of
zygotes to the blastocyst stage alters their global gene expression pat-
terns (Rinaudo and Schultz, 2004; Rinaudo et al., 2006). In addition,
IVF is associated with additional changes in global gene expression
and development (Giritharan et al., 2007). In order to investigate
the effect that ICSI has on mouse preimplantation embryo
& The Author 2010. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved.
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Human Reproduction, Vol.25, No.12 pp. 3012–3024, 2010
Advanced Access publication on October 1, 2010doi:10.1093/humrep/deq266
development, and expand upon our prior IVC and IVF studies, we
carried out experiments fertilizing embryos by ICSI and culturing
embryos in different conditions, both optimal and suboptimal. Specifi-
cally, morphologic and gene expression studies were performed on
blastocysts fertilized by ICSI and grown in vitro either in Whitten’s
medium (WM) (ICSIWM group) or in KSOM with amino acids
(ICSIKSOMaagroup) compared with those fertilized and grown in vivo
(in vivo group). In addition, we compared the current data from ICSI
embryos cultured in WM to our previous data from IVF embryos cul-
tured in WM. Therefore, any comparisons between the IVFWMand
ICSIWMgroups would tease out the effects of gamete manipulation
using IVF and ICSI.
Materials and Methods
Collection of mature oocytes,
preimplantation mouse embryos
and ICSI procedure
Oocytes and embryos were isolated from super-ovulated dams as pre-
viously described (Rinaudo and Schultz, 2004). Briefly, CF-1 female mice
were injected with 5 IU pregnant mare’s serum gonadotrophin and
46–48 h later with 5 IU hCG. The following morning, oocytes were
obtained from the ampullae.Spermatozoa were collected from
B6D2F1/J male mice (10–11 weeks old). After mice were sacrificed,
the two caudal epididymides were removed, punctured gently with
30-G needles under a dissecting microscope and transferred with sterile
forceps into 1 ml pre-warmed (378C) EGTA Tris-HCl buffered solution
containing 10 mM Tris–HCl, pH 8.2, 50 mM EGTA and 50 mM NaCl in
a 1.5 ml microcentrifuge tube and then incubated at 378C for 10 min.
The top 0.8 ml sperm suspension was carefully aspirated and used
immediately for ICSI. Only oocytes with first polar body were microin-
jected using a Piezo drill (PMM Controller, Prime Tech, Ibaraki, Japan),
as described (Li et al., 2009). Then fertilized oocytes were washed and cul-
tured in either WM or KSOM with amino acids to the blastocyst stage
under 5% CO2in humidified air at 378C. Late-cavitating blastocysts of
similar morphology were harvested at ?112 h post-hCG for ICSI
groups and 96 h post-hCG for control in vivo group. Each treatment was
repeated four times. Each time, sperm from one male and oocytes from
two to three females were used for fertilization of ICSI groups. For in
vivo groups, eggs were collected from two to three females after overnight
breeding as one male per female. All animal experiments were approved
by the Institutional Animal Care and Use Committee.
Differential embryo staining
A modified dual nuclear staining method described by Thouas et al. (2001)
was performed to differentially stain inner cell mass (ICM) and trophoblast
cell nuclei of fully developed blastocysts. Briefly, the blastocysts were
exposed to 1% Triton X-100 (Sigma-Aldrich, USA) in minimum essential
medium (MEM; Invitrogen Corporation, USA) for 3–5 seconds, washed
3–5 times in MEM + polyvinylpyrrolidone (PVP; Sigma-Aldrich) and
incubated in MEM + PVP containing 100 mg/ml propidium iodide
(Sigma-Aldrich) for 30 seconds. The embryos were then washed 3–5
times in MEM + PVP and fixed overnight in 100% ethanol containing
25 mg/ml of bizbenzamide (Sigma-Aldrich) at 48C. The embryos were
mounted on a clean glass slide using glycerol and kept in a dark
chamber until observed under fluorescent light using a standard Leica
microscope (Model DMRB, Leica Microsystems AG, Germany).
The embryos were observed by fluorescent microscopy, and the
numbers of ICM cell (blue) and trophectoderm (TE: red) nuclei were
counted and photographed. The staining procedure was repeated at
least three times per treatment group with different sets of blastocysts
(n ≥ 12).
RNA extraction and amplification
Total RNA was extracted from four independent biological replicates (10
blastocysts/replicate) using PicoPure RNA Isoloation Kit (Arcturus, USA)
according to the manufacturer’s instructions. In column DNase treatment
was performed using RNase-free DNase set (Qiagen Inc., USA) as
described in the user guide of the PicoPure RNA isolation kit to remove
the residual DNA. In each pool, five embryo equivalents of total RNA
was used for reverse transcription (RT) followed by linear amplification
of antisense cDNA strand, fragmentation and biotin labeling by using
NuGEN Ovation Biotin System (NuGEN Technologies Inc., USA).
Briefly, RNA is converted to cDNA with a unique DNA/RNA heterodu-
plex at one end. A linear isothermal DNA amplification process was con-
ducted using DNA/RNA chimeric primer, DNA polymerase and RNase H
in a homogeneous isothermal assay that provides highly efficient amplifica-
tion of DNA sequences. The amplified cDNA strands were subjected to
an enzymatic fragmentation and the fragmented product was then labeled
with biotin. RNA and cDNA mass and size distribution were determined
before and after amplification, and after fragmentation using the Agilent
Bioanalyzer (Agilent, USA). Samples with RNA integrity number (RIN)
. 8 were selected for amplification. cDNA yield before fragmentation
and labeling was 12–15 mg. Final yield of fragmented and biotinylated
cDNA was 4–4.5 mg, of which 2.2 mg were used for microarray analysis.
Fragmented and biotin labeled cDNA samples were submitted to the
Genomic Core Facility of the University of California San Francisco for
GeneChip hybridization. The samples (four biological replicates per exper-
imental group) were hybridized to mouse Affymetrix 430 2.0 GeneChips,
then washed and stained on fluidics stations and scanned at 3 mm resol-
ution according to the manufacturer’s instructions (GeneChip Analysis
Technical Manual, www.affymetrix.com).
cDNA preparation for real-time PCR analysis
RT was accomplished by utilizing the commercially available first strand
cDNA synthesis kit (iScript cDNA Synthesis Kit, Bio-Rad Laboratories,
USA). The RT reactions were performed by following the kit manufac-
turer’s protocol. For each treatment group the RT was repeated four
times with RNA from different sets of blastocyst stage embryos.
The real-time PCR was performed using TaqMan Universal PCR Master
Mix, Gene Expression Assays containing gene-specific primers and
TaqMan probe (Applied Biosystems, USA), and 0.1 embryo equivalents
of cDNA. The corresponding ABI TaqMan Assay-on-Demand probe/
primer sets used were Mm00498012_m1 (Ube2a), Mm00438084_m1
(Ccng1), Mm99999915_g1 (Gapdh) and Mm00433832_m1 (Nr3c1). The
real-time PCR was also performed using SyBr green PCR supermix
(Bio-Rad Laboratories), and primers for Bdnf, Nr3c1 and Gapdh genes
with 0.1 embryo equivalents of cDNA from each treatment group.
Primers which span at least two exons were designed using Primer3 soft-
ware. Duplicates were used for each real-time PCR reaction; a minus tem-
plate served as control. For each treatment group the real-time PCR was
repeated four times. The real-time PCR data were analyzed within the log-
linear phase of the amplification curve obtained for each probe/primer
using the comparative threshold cycle method (Bio-Rad Laboratories).
Effect of ICSI on mouse preimplantation embryo
The cell number data were analyzed by one-way analysis of variance. Cell
numbers were compared using a mean separation procedure when analy-
sis of variance showed significant F-values using Fisher’s Least Significant
Difference method. Results are reported as the mean values for each
set of data + SEM.
Microarray gene expression data analysis
Statistical analysis was carried out using the R software (http://www.
r-project.org/) and the appropriate Bioconductor packages (http://
www.bioconductor.org/) run under R. In order to remove all the possible
sources of variation of a non-biological origin between arrays, densitome-
try values between arrays were normalized using the RMA (robust multi-
array) normalization function implemented in the Bioconductor affylmGUI.
Statistically significant differences between groups were identified using the
rank product non-parametric test implemented in the Bioconductor Rank-
Prod package. Applying a Student’s t-test with such a limited number of
samples (four in each experimental group) is inappropriate as the obtained
statistical significance is not robust; in this situation the mean and the stan-
dard deviation could be easily biased by outliers. We therefore carried out
a non-parametric statistical test as a rough filter to narrow down the list of
most relevant genes (Breitling and Herzyk, 2005). This non-parametric
method is highly efficient, robust and widely used for microarray data
analysis (Cervello et al., 2010). The Rank Product method has proven
to be superior to other statistical methods for microarray data analysis
in our and other authors’ experience (Hong and Breitling, 2008). More-
over, the rank product approach includes a multiple hypothesis test for
raw P-value correction to ascertain a false positive rate similar to false dis-
covery rate correction. Data of the microarray are available at the Gene
Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo).
Genes flagged as ‘present’ or ‘marginal’ in at least one hybridization,
based on raw perfect match and mismatch as determined by ‘mas5calls’
function on the Bioconductor affymetrix package, were considered
Functional annotations were carried out using the Ingenuity Pathways
Analysis platform (http://www.ingenuity.com/).
Validation of microarray data using
Published evidence confirms that microarray data are robust and
reliable (Morey et al., 2006). In order to evaluate the reproducibility
of the data, we performed multiple quality control analysis. Initially,
we only utilized expanded blastocysts of similar morphology and we
performed the experiments using four independent biological repli-
cates. We confirmed that the quality of RNA was optimal, utilizing
only RNA samples with RIN . 8. We then performed in silico
quality control analysis of the amplified material: we found that
cRNA quality was excellent. Finally, we utilized real-time RT–PCR
to confirm the microarray results obtained in this study (Fig. 1). In par-
ticular, we chose one gene with increased expression in the ICSI group
(Ccgn1), one gene with decreased expression (Ube2a) and two genes
with no change in expression between ICSI and in vivo blastocysts
(Bdnf and Nr3c1). Results confirm similar trend between microarray
and real-time data. The only difference is represented by the statisti-
cally significant (P , 0.05) increase after RT–PCR in Nr3c1 expression
in ICSIWM blastocysts, although the increase of Nr3c1 following
microarray analysis in both media or RT–PCR in ICSIKSOMaais not
Effect of ICSI and the culture medium
on blastocyst cell number
Expanded mouse blastocysts are easily recognizable and therefore
offer an excellent end-point for morphologic assessment. In order
to investigate the effect of the method of fertilization and IVC on
cell division and cell allocation, we counted the number of ICM and
TE cell nuclei in expanded blastocysts. Only expanded blastocysts at
the same stage of development were used for analysis (Table I).
In vivo embryos had on average two additional ICM cells compared
with ICSIKSOMaa and three additional ICM cells compared with
ICSIWMembryos (P , 0.05). The ICSIWMand IVFWMembryos had
reduced number of TE cells (n ¼ 36 and 33 cells, respectively) com-
pared with the ICSIKSOMaa (n ¼ 43 cells) and the in vivo control
Figure 1 Real-time PCR verification of gene expression data.
Expression profile of brain derived neurotrophic factor (Bdnf), cyclin
G1 (Ccng1), ubiquitin-conjugating enzyme E2A (Ube2a) and the
nuclear receptor subfamily 3, group C, member 1 (Nr3c1) genes in
murine blastocysts produced by in vivo fertilization and culture
(in vivo), ICSI and IVC in KSOM with amino acids (ICSIKSOMaa) and
ICSI and IVC in WM (ICSIWM) using real-time PCR technique (A)
and microarray technique (B). Bars represent SD. Asterisk (*) indi-
cates significant difference compare with in vivo at P , 0.05. Of
note the genes tested by RT–PCR reflect the changes detected by
microarray. The only difference is represented by the statistically sig-
nificant (P , 0.05) increase after RT–PCR in Nr3c1 expression in
ICSIWMblastocysts, while the increase of Nr3c1 following microarray
analysis in both media or after RT–PCR in ICSIKSOMaais not statisti-
Giritharan et al.
embryos (n ¼ 49, P , 0.05). Of note, the development of embryos
after ICSI, was excellent. More than 70% of the injected eggs survived
and more than 90% of the surviving eggs reached the 2-cell stage in
both culture media. The blastocyst development rates for 2-cell
embryos cultured in ICSIKSOMand ICSIWM were 80.7 and 76.4%,
Effect of ICSI and in vitro embryo culture
on blastocyst global gene expression
To analyze the global pattern of gene expression we used the mouse
Affymetrix 430 2.0 microarray chip, which is believed to represent the
complete mouse genome. Out of 12 035 total non-redundant genes
with known gene symbols, 8847 (73.5%) were present in ICSIWM,
8408 (69.8%) in ICSIKSOMaaand 7758 (64.4%) in in vivo blastocysts.
Pair-wise comparison revealed that a significant number of genes are
differentially regulated following ICSIWM(947) or ICSIKSOMaa(1016)
compared with in vivo control embryos (Fig. 2, P , 0.05). Most of
the differentially regulated genes between the ICSI groups and in vivo
are common (ICSIKSOMaa: 78.9%—802/1016; ICSIWM: 84.6%—802/
947), with only 215 genes being uniquely different between ICSIKSOMaa
and in vivo and 145 between ICSIWMand in vivo. This finding is impor-
tant because it provides additional evidence of the robustness of the
data. Indeed, unsupervised hierarchical clustering analysis confirms
these findings (Fig. 3). The samples segregated into two major cluster-
ing branches (ICSI and in vivo). However, all the replicate samples of
the ICSI embryos cultured in WM and KSOMaa did not show a
clear separation, indicating that the ICSI procedure itself affects the
transcriptome of the blastocyst and that the culture media plays
only a minor role.
The entity of fold changes was higher than expected: 20.6% (210/
1016) of the genes were changed more than 5-folds between
ICSIKSOMaaand in vivo, and 20.4% (194/947) were different between
ICSIWMand in vivo blastocysts.
Remarkably, a reduced number of genes were differentially
expressed in ICSIKSOMaaembryos compared with ICSIWM(41 genes,
P , 0.05); in addition only three genes were changed more than
3-fold between the two groups, indicating a minor effect of culture
on gene expression following ICSI procedure.
The list of significantly different genes after each pair-wise compari-
son with the relative expression profiles is summarized in Supplemen-
tary data, Table S1.
Pathways analysis (Table II) reveals that similar classes are altered in
embryos generated by ICSI and in vivo, independently of the culture
media used. In particular there is an increase in alteration of pathways
indicatingmitochondrial dysfunction (ubiquinonebiosynthesis,
oxidative phosphorilation and mitochondrial dysfunction pathways)
and alteration of metabolic pathways (N glycan degradation,
branch chained amino acids and butanoate metabolism). Only the
hepatocytes growth factor (HGF) signaling pathway and glycolysis/
gluconeogenesis pathway are uniquely different between ICSIKSOMaa
and in vivo, while several classes are uniquely changed between ICSIWM
and in vivo [Oct4-dependent pathway; production of reactive oxygen
species (ROS) in macrophages; CDK5 signaling; TR/RXR Activation].
Functional categories analysis (Fig. 4 and Supplementary data, Table
S2) shows that cell function, development and metabolic genes are
affected by the method of fertilization and culture media used.
Whereas all conditions used affect these functions, it is clear that
the method of fertilization plays a more important role in altering
the gene expression pattern than the media used to culture embryos.
In fact, only 41 genes and two pathways (one-carbon pool by folate
and RhoA signaling pathways) were different between ICSIKSOMaaand
ICSIWM, while ?1000 genes were different between ICSI embryos
and in vivo embryos.
Effect of the method of fertilization
(IVF or ICSI) on gene expression
Comparison of ICSIWM data with our previously generated gene
expression data-IVFWM(Giritharan et al., 2007) showed differential
expression of 981 genes. Eighteen percent (177/981) of these
genes were changed more than 5-fold.
Overall multiple functional categories involved in cell function,
development and metabolism (Supplementary data, Table S2) and
pathways (Table II) are statistically different between IVFWMand
Analysis of transporter genes (Table III) and imprinted and methyl-
ation genes (Table IV) reveals that several genes are affected by the
method of fertilization.
This study, for the first time, offers a complete overview of the
changes in the global pattern of gene expression in ICSI or in vivo gen-
erated mouse embryos. This provides an overview of the transcrip-
tional consequences of fertilizing eggs by different techniques and
complements our previous work on the effect of different media
and oxygen concentration on the transcriptome of mouse blastocysts
(Rinaudo and Schultz, 2004; Rinaudo et al., 2006; Giritharan et al.,
2007). The most notable finding is that the ICSI procedure plays a
more important role in determining the blastocyst gene expression
pattern than the culture media used (WM or KSOMaa).
ICSIKSOMaa(n ¼ 31)
ICSIWM(n ¼ 12)
IVFWM(n ¼ 63)
In vivo (n ¼ 46)
Table I The method of fertilization affects the distribution of cells in ICM and TE of embryos.
Treatment # ICM cells (mean+++++SEM) # TE cells (mean+++++SEM) # Total cells (mean+++++SEM)
Numbers are expressed as means+SEM. Values with different superscripts in each column differ significantly (P , 0.05).
Effect of ICSI on mouse preimplantation embryo
Overall, there is a net reduction of ICM and TE cells in the ICSI
group compared with the in vivo control. The reduction of cells is
larger in TE cells (?26% less cells in ICSIWMand 14% in ICSIKSOMaa)
than ICM (?10% less in ICSI embryos) of ICSI embryos. Since TE cells
will give rise to the placenta, this suggests that the method of fertiliza-
tion could affect more placenta formation than the embryo itself. The
cell number data confirm findings of other investigators, who found
that, in various species, ICSI-generated zygotes cleave at a slower
rate and have reduced hatching rate and reduced cell number
(Dumoulin et al., 2000; Bedford et al., 2003; Malcuit et al., 2006).
Although it is not possible to compare the present mouse findings
with human data, it is interesting to note that lower hCG levels were
found in human IVF gestations than in in vivo conception, implying
reduced placental mass (Zegers-Hochschild et al., 1994). Assuming
that an embryo with lower cell numbers will grow less, these findings
could explain the fact that ART children have lower birthweight at
term (McDonald et al., 2009).
The gene expression results confirm the morphologic studies. The
ICSI embryos have a very distinct transcriptome compared with
embryos fertilized in vivo, as shown by the unsupervised hierarchical
clustering analysis (Fig. 3). ICSI embryos have an increased dysregula-
tion (both up- and down-regulation) in the expression of genes related
to cellular function, development and metabolism. The down-
regulation of several genes involved in cellular development and differ-
entiation (Fig. 4 and Supplementary data, Table S2) implies that an
alteration of developmental strategy could follow the preimplantation
stress and explains the reduced number of cells in ICSI embryos.
Overall, the increased number of dysregulated genes indicates that
these embryos have an increased metabolism; this would suggest
decreased fitness according to the ‘quiet embryo’ hypothesis (Leese
et al., 2008).
Pathway analysis offers additional insights (Table II): mitochondrial
dysfunction and a disproportionately higher number of metabolic path-
ways occurring in mitochondria (inositol, butanoate, urea cycle and
branched amino acid metabolism) are altered following ICSI. Individual
gene analysis confirms these findings. For example, Cox6b2 (cyto-
chrome c oxidase subunit VIb polypeptide 2) gene is increased
more than 20-fold in ICSI embryos. This gene produces an isoform
of cytochrome c oxidase, the terminal enzyme in the mitochondrial
respiratory chain, which catalyzes the electron transfer from
reduced cytochrome c to molecular oxygen (Huttemann et al.,
2003). Up-regulation of mitochondrial oxidative phosphorylation
genes indicates the increased metabolic need of the embryo.
Of note, mitochondrial dysfunction can result in reduced post-
implantation development (Thouas et al., 2006) and can have long-
lasting effects. For example, it has been hypothesized as the mechan-
ism inducing the insulin-resistant phenotype observed in offspring of
patients with type 2 diabetes (Petersen et al., 2004).
Among the signaling pathways modified after ICSI, the g amino
butyric (GABA) receptor signaling and invasiveness signaling are pro-
minent. Autocrine and paracrine GABA signaling via GABAAreceptors
slow preimplantation embryonic growth by decreasing proliferation
Figure 2 Summary of up-regulated and down-regulated genes for the following comparisons: ICSIKSOMaaversus in vivo, ICSIWMversus in vivo,
ICSIKSOMaaversus ICSIWM. Each comparison in the graph shows the number of genes statistically different when comparing the four replicates of
one group with the four replicates of the other group. The numbers below each comparison indicate how many genes are statistically up-regulated
or down-regulated (P , 0.05) more than 2-fold or 5-fold.
Giritharan et al.
because of increased cellular arrest in the S phase (Andang et al.,
2008). Alteration of invasiveness signaling could indicate suboptimal
placentation. For example, Timp1, an inhibitor of cellular invasion
(Paiva et al., 2009) and Itgb5 (integrin beta 5), an integrin involved in
implantation (Massuto et al.) are up-regulated in ICSI placentas.
Alteration of multiple additional genes involved in placentation is
present. This finding provides a molecular justification of the significant
reduction in TE cells found in ICSI embryos. Prl2c2 (prolactin family 2,
subfamily c, member 2) is expressed in large trophoblastic giant cells
during the invasion (Adamson et al., 2002) and it is down-regulated
25-fold in ICSI embryos. Psg28 (pregnancy-specific glycoprotein 28)
is expressed in giant cells and spongiotrophoblast of the placenta
(Kromer et al., 1996), is implicated in immunomodulatory function
to prevent rejection of embryo/fetus (Wynne et al., 2006) and is
down-regulated more than 11-fold in ICSI blastocysts. Bex1
(brain-expressed X-linked 1) located close to Xist on the X chromo-
some, is down-regulated more than 16 times in ICSI embryos; while it
does not appear to be epigenetically regulated, it is highly expressed in
trophectodermal cells (Williams et al., 2002). Down-regulation of
these genes could be associated with reduced placental development.
Alteration of multiple cellular transporters could indicate the pla-
centa function is compromised. Among the transporter genes
(Table III), Slc7a12 (solute carrier family 7, member 12) stands out
for being down-regulated more than 18-fold in ICSI embryos; this
gene is involved in the cationic amino acid transport (Closs et al.,
2006). Dysregulation of other transporter genes has been associated
with different metabolic or storage diseases. Although so far none
of the following diseases have been linked to ART, alterations of
these genes implies metabolic stress. Slc35c1 (solute carrier family
35, member C1) encodes a GDP-fucose transporter located in the
Golgi apparatus. Mutations in this gene result in congenital disorder
of glycosylation type IIc (Lubke et al., 2001). Slc39a4 (solute carrier
family 39, member 4) encodes for a transmembrane protein required
for zinc uptake in the intestine. Mutations in this gene result in acro-
dermatitis enteropathica, a rare inherited defect in the absorption of
dietary zinc (Wang et al., 2002). Slc46a1 (solute carrier family 46
member 1) is a transmembrane proton-coupled folate transporter
that facilitates the movement of folate and heme across membranes.
Mutations in this gene cause a recessive form of folate malabsorption
(Qiu et al., 2006).
Because abnormal DNA methylation can follow culture in vitro, we
paid particular attention to imprinting and methylation genes (Doherty
et al., 2000; Rolaki et al., 2007). Several imprinted genes are different
between ICSI embryos and in vivo embryos (Table IV). Among them
Cd81 and Peg10 are changed more than 10-fold. Cd81 encodes a tet-
raspanin that functions as an organizer of multi-molecular membrane
complexes and as a result, regulates cell migration, fusion and signaling
(Hemler, 2005). Cd81 is located close to the cluster of imprinted
genes on murine chromosome 7 which is syntenic with the Beck-
with–Wiedemann syndrome associated cluster of imprinted gene
on human chromosome 11p15.5 region (Paulsen et al., 1998).
Lim et al. (2009) reported that children born after ICSI with
Figure 3 Hierarchical clustering with heat-map of ICSIKSOMaa, ICSIWMand in vivo embryos based on their gene expression profile. Unsupervised
clustering was performed to analyze similarities among replicate samples across all treatment groups tested. Colors correspond to relative RNA abun-
dance for the transcripts detected; each is represented by a horizontal bar in the heat-map. Yellow indicates high expression and blue denotes low
Effect of ICSI on mouse preimplantation embryo
Altered pathways with fold change in ICSI embryos (both ICSIWMand ICSIKSOM) compared with in vivo embryos
GABA receptor signaling0.109 Abat (4.6, 3.6), Gabra5 ( 23.1, 23.3), Gabrb2 (22.7, 22.5), Gabrg1 (22.2, 22.3), Slc6a13
Invasiveness signaling (Glioma)0.107F2r (3.6, 5.3), Itgb5 (4.2, 4.5), Rhod (5.3, 4.4), Rhoj (22.7, 22.7), Rras (3.7, 3.9), Timp1 (4.8,
Inositol metabolism 0.143 Adi1 (22.5, 22.5), Aldh16a1 (3.3, 3.7), Blvrb (9.5, 11.1), Cyba (6.5, 8.5), Dhrs1 (5.4, 4.3),
Dhrs13(3.7, 3.7),Lamb2(4.7,4.5), Ndor1(4.1,4.1),Ndufa6 (3.6,3.4),Recql4 (3.7,3.5),Retsat
(3.3, 3.5), Tm7sf2 (3.9, 3.6)
Butanoate metabolism0.133Abat (4.6, 3.6), Aldh2 (3.5, 3.5), Dcxr (14.3, 15.1), Ech1 (4.4, 5.7), Hadha (4.0, 4.1), Nlgn1
(22.6, 22.8), Oxct1 (3.9, 4.1), Sdhb (3.8, 4.0)
N-glycan degradation0.133Man1b1 (4.1, 3.4), Man1c1 (3.1, 4.2), Man2c1 (3.8, 4.2), Manea (3.2, 3.5)
Urea cycle and metabolism of amino groups 0.118 Acy3 (6.1, 4.9), Ass1 (4.1, 3.7), Oat (3.4, 4.0), Pycrl (4.0, 3.4)
Valine, leucine and isoleucine degradation0.101 Abat (4.6, 3.6), Aldh2 (3.5, 3.5), Bcat2 (4.7, 5.4), Bckdhb (4.4, 4.5), Ech1 (4.4, 5.7), Hadha (4.0,
4.1), Oxct1 (3.9, 4.1)
Glutathione metabolism0.094Gpx3 (8.0, 7.7), Gpx7 (5.3, 6.2), Gstk1 (5.8, 4.7), Gstm2 (10.6, 13.4), Mgst3 (4.3, 3.9), Oplah
Ubiquinone biosynthesis0.127 Bckdhb (4.4, 4.5), Ndufa1 (4.0, 3.9), Ndufa13 (3.8, 3.6), Ndufa3 (4.1, 4.2), Ndufa6 (3.6, 3.4),
Ndufb3 (3.8, 4.0), Ndufb7 (4.1, 4.0), Ndufs7 (4.4, 4.2), Ndufs8 (3.3, 3.3)
Oxidative phosphorylation0.105 Atp5e (3.4, 3.7), Atp5g2 (3.2, 3.9), Cox6b2 (22.9, 24.9), Cox7a1 (7.0, 5.8), Ndufa1 (4.0, 3.9),
Ndufa13 (3.8, 3.6), Ndufa3 (4.1, 4.2), Ndufa6 (3.6, 3.4), Ndufb3 (3.8, 4.0), Ndufb7 (4.1, 4.0),
Ndufs7 (4.4, 4.2), Ndufs8 (3.3, 3.3), Ppa2 (6.6, 7.7), Sdhb (3.8, 4.0), Uqcr (4.1, 4.2)
Mitochondrial dysfunction 0.092 Cox6b2 (22.9, 24.9), Cox7a1 (7.0, 5.8), Gpx7 (5.3, 6.2), Ndufa13 (3.8, 3.6), Ndufa3 (4.1, 4.2),
Ndufa6 (3.6, 3.4), Ndufb3 (3.8, 4.0), Ndufb7 (4.1, 4.0), Ndufs7 (4.4, 4.2), Ndufs8 (3.3, 3.3),
Sdhb (3.8, 4.0), Snca (22.6, 22.6)
Pathways uniquely changed between ICSIWMand in vivo embryos
Role of Oct4 in mammalian embryonic stem cell
CDK5 signaling0.034Egr1 (22.6), Ppp1r11 (3.3), Ppp1r3a (22.5)
TR/RXR activation0.033 Ppargc1a (22.2), Rxrb (3.5), Ucp2 (3.2)
Production of nitric oxide and reactive oxygen
species in macrophages
Pathways uniquely changed between ICSIKSOMand in vivo embryos
HGF signaling0.04Ccnd1 (22.2), Elf3 (3.4), Elf5 (3.7), Map3k6 (3.5)
Glycolysis/gluconeogenesis0.042Aldh3b2 (3.4), Galm (3.2), Ldha (4.0), Pfkm (3.7)
Pathways uniquely changed between ICSIKSOMand ICSIWMembryos
RhoA signaling pathways0.019Myl9 (2.05), Sept4 (2.04)
One-carbon pool by folate0.048Mthfd2 (2.33)
Pathways changed between IVFWMand ICSIWM
Invasiveness signaling (Glioma)0.125 F2r (27.87), Itgb5 (23.41), Rhod (23.28), Rhoj (2.35), Rnd2 (22.86), Rras (24.83), Timp1
Table II Overrepresented canonical pathways in comparisons among ICSIKSOM, ICSIWMand in vivo embryos (P < 0.05).
Ingenuity canonical pathways RatioGene symbol
0.044Fgf4 (22.3), Rxrb (3.5)
0.031Map3k4 (3.7), Mapk13 (3.9), Ppp1r11 (3.3), Ppp1r3a (22.5), Rnd2 (3.8)
Giritharan et al.
Beckwith–Wiedemann syndrome have an altered methylation in this
region of chromosome 11. It is, however, important to remember
that this gene is imprinted in mice but not humans and therefore con-
clusions valid in one model system may not be valid in another species.
Peg10 (Paternally expressed 10) is an imprinted gene down-regulated
more than 18-fold in ICSI embryos; it plays an important role in pla-
cental development and its deletion is associated with early embryonic
lethality (Rawn and Cross, 2008).
Interestingly, additional genes that are not imprinted but are located
on the X chromosome and therefore potentially subjected to selective
epigenetic controls were altered. Among these, Ott (ovary testis tran-
scribed) is a mouse X-linked multigene family gene specially expressed
during meiosis in testis and ovary (Kerr et al., 1996), while Slc10a3
(solute carrier family 10 member 3) belongs to the sodium/bile acid
cotransporter family and was originally cloned from placental tissue;
it maps to a GC-rich region of the X chromosome and was identified
by its proximity to a CpG island (Geyer et al., 2006).
Several genes involved in epigenetic regulation appear to be misre-
gulated. Importantly Wbp7, Smarca1 and Hdac6 are altered in ICSI
Hdac6 belongs to the histone deacetylases (HDACs) family of
enzymes that catalyze the removal of acetyl groups from lysine resi-
dues in histones and non-histone proteins, resulting in transcriptional
repression. HDACs play a role in cell growth arrest, differentiation
and death, and Hdac6 over expression has been associated with pre-
mature chromatin compaction in mouse oocytes and embryos (Verdel
et al., 2003).
Smarca1 (SWI/SNF related, matrix associated, actin-dependent
regulator of chromatin, subfamily a, member 1) encoded protein has
helicase and ATPase activity and regulates transcription by altering
chromatin structure (Magnani and Cabot, 2009).
Wbp7 (WW domain binding protein 7) is a histone methyltransfer-
ase that methylates Lysine 4 of histone H3 resulting in an epigenetic
mark favoring transcriptional activation. Mice lacking Wbp7 fail to
develop beyond E9.5 (Lubitz et al., 2007).
Urea cycle and metabolism of amino groups0.176Acy3 (23.30), Aldh18a1 (25.21), Cps1 (3.72), Oat (23.77), Pycrl (23.31), Srm (24.52)
Glutathione metabolism0.125 Ggt1 (23.80), Gpx4 (23.72), Gpx7 (24.64), Gstk1 (23.40), Gstm2 (25.77), Mgst1 (2.19),
Mgst3 (23.05), Oplah (25.19)
Phospholipid degradation 0.103 Dgka (23.23), Hmox1 (23.99), Lamb2 (23.89), Napepld (23.84), Pla1a (23.25), Pla2g10
(22.96), Plcd1 (25.23), Pld3 (23.05), Sphk2 (23.39)
Selenoamino acid metabolism0.132 Cbs (25.85), Cth (25.93), Edf1 (23.16), Ggt1 (23.80), Mars2 (23.00)
Glycerophospholipid metabolism 0.092Agpat2 (23.34), Dgka (23.23), Hmox1 (23.99), Lamb2 (23.89), Napepld (23.84), Pcyt2
(24.84), Pemt (22.59), Pla1a (23.25), Pla2g10 (22.96), Plcd1 (25.23), Pld3 (23.05),
Glutamate metabolism0.132Abat (25.49), Cad (24.01), Cps1 (3.72), Nadsyn1 (22.47), Tgm4 (23.55)
Inositol metabolism0.131 Adi1 (2.20), Aldh16a1 (23.80), Blvrb (26.23), Cyba (27.99), Dhrs1 (24.05), Dhrs13
(23.73), Hmox1 (23.99), Lamb2 (23.89), Ndor1 (23.62), Recql4 (24.66), Tm7sf2 (24.01)
Pyrimidine metabolism0.111Apobec1 (2.38), Cad (24.01), Dhodh (24.03), Mad2l2 (23.24), Nme3 (25.20), Nme4
(23.70), Nt5m (23.21), Pold1 (24.68), Pold2 (29.11), Pold4 (23.58), Poli (23.79), Polr2i
(25.06), Polr2l (25.06), Polrmt (23.35), Trub2 (23.57), Uckl1 (23.20), Upp1 (23.39)
Mitochondrial dysfunction0.115 Cox6b2 (214.50), Cox7a1 (25.05), Cox7b2 (22.33), Dhodh (24.03), Gpx4 (23.72), Gpx7
(24.64), Hsd17b10 (23.24), Ndufa3 (24.04), Ndufb3 (23.61), Ndufb7 (23.25), Ndufs2
(23.71), Ndufs7 (23.88), Ndufs8 (23.32), Park7 (23.28), Ucp2 (23.22)
Oxidative phosphorylation0.091Atp5e (23.69), Cox6b2 (214.50), Cox7a1 (25.05), Cox7b2 (22.33), Ndufa1 (23.10),
(23.32), Ppa2 (25.10), Uqcr (24.16)
Ubiquinone biosynthesis0.127Bckdhb (24.41), Edf1 (23.16), Ndufa1 (23.10), Ndufa3 (24.04), Ndufb3 (23.61), Ndufb7
(23.25), Ndufs2 (23.71), Ndufs7 (23.88), Ndufs8 (23.32)
Table II Continued
Ingenuity canonical pathwaysRatio Gene symbol
Figure 4 A total number of differentially expressed genes in cellu-
lar, developmental and metabolic functional catergories overrepre-
sented in ICSIKSOMaa, ICSIWM, and in vivo embryos (P , 0.05).
Detail information of cellular, developmental and metabolic functions
with differentially regulated genes in each comparison is listed in Sup-
plementary data, Table S2.
Effect of ICSI on mouse preimplantation embryo
The transcriptome comparison of ICSI embryos cultured in KSOMaa
or WM and the comparison of ICSIWMand IVFWMblastocysts pro-
vided some of the most unanticipated findings of the study: the
method of fertilization plays a more important role than the culture
media to determine the transcriptome of the blastocysts.
Regarding the comparison of ICSIKSOMaaand ICSIWM, it appears
that while ICSIWMembryos have a statistically reduced number of
TE cells (18% less), only 41 genes (4%—versus ?1000 genes different
between in vivo and ICSI blastocysts) were differentially expressed; in
addition the fold change differences were small and overall ,4-fold.
Interestingly, H19 is the only imprinted gene differentially expressed
being up-regulated more than 3-fold in WM. This is not surprising,
since culture in WM, as opposite to culture in KSOM, is associated
with biallelic expression of the gene (Doherty et al., 2000).
Only three transporter genes are differentially regulated (Slc44a3;
Finally only two pathways were statistically different between
ICSIKSOMaaand ICSIWM(RhoA signaling and one carbon folate path-
ways). Members of the Rho family of small guanosine triphosphatases
have emerged as key regulators of the actin cytoskeleton, and further-
more, through their interaction with multiple target proteins, they
ensure coordinated control of other cellular activities such as gene tran-
scription and adhesion. Down-regulation of Mthfd2 (methylenetetrahy-
drofolate dehydrogenase—NADP+-dependent—2) is,however,
Slc10a3Sodium/bile acid cotransporter
Slc13a2Sodium-dependent dicarboxylate transporter
Slc16a6 Monocarboxylic acid transporter
Slc22a9 Organic anion transporter
Slc25a28 Mitochondrial iron transporter
Slc27a3Fatty acid transporter
Slc35c1 GDP-fucose transporter
Slc39a11Metal ion transporter
Slc3a2 Activators of dibasic and neutral amino acid transport
Slc5a12 Sodium/glucose cotransporter
Slc5a6 Sodium-dependent vitamin transporter
Neurotransmitter (GABA) transporter
Slc7a12Cationic amino acid transporter
Slc7a13 Cationic amino acid transporter
Slco6b1 Organic anion transporter
Slco6c1Organic anion transporter
Slc27a2 Fatty acid transporter
Slc27a4 Fatty acid transporter
Slc37a4 Glucose-6-phosphate transporter
Slc38a7 Sodium-coupled neutral amino acid transporter
Slc5a6Sodium-dependent vitamin transporter
Slc7a3Cationic amino acid transporter
Slco6d1 Organic anion transporter family
Table III Differentially expressed transporter genes in ICSI and IVF embryos (P < 0.05).
Gene function ICSIKSOM/
NS, not significant.
Giritharan et al.
notable as this gene is involved in folate metabolism and therefore could
result in abnormal methyl donor availability for methyltransferases.
Complementary to the findings of ICSI embryos cultured in different
media, the different gene expression pattern between IVFWMand
ICSIWMconfirms that the method of fertilization plays a fundamental
role in determining the transcriptome of the preimplantation
embryos. In fact, as many genes are different between IVFWMand
ICSIWM (984 gene) as between ICSIKSOMaa and in vivo (1016) or
ICSIWMand in vivo (947).
Pathways analysis confirms that similar pathways (Mitochondrial
function pathways and metabolic pathways) are changed between
IVFWMblastocysts and ICSIWMembryos as between ICSI embryos
(both WM and KSOMaa) and in vivo embryos.
Interestingly, among the transporters differentially expressed, a
subset is uniquely mis-expressed between IVFWMand ICSIWMblasto-
cysts (Table III). Slc27a4 is involved in translocation of long-chain fatty
acids across the plasma membrane and is required for fat absorption in
early embryogenesis (Gimeno et al., 2003). Slc37a4 (solute carrier
family 37 member 4) regulates glucose-6-phosphate transport from
the cytoplasm to the endoplasmic reticulum and is involved in ATP-
mediated calcium sequestration in the lumen of the endoplasmic reti-
culum. Mutations in this gene have been associated with various forms
of glycogen storage disease (Schaub and Heyne, 1983).
Three epigenetic genes (Wbp7, Kcnq1 and Smarca4) were differen-
tially regulated in IVFWMand ICSIWMembryos. Kcnq1 was down-
regulated in ICSI embryos while Wbp7 and Smarca4 were up-regulated
in ICSI embryos compared with IVF embryos. Smarca4 protein plays a
fundamental roles controlling gene expression during early mammalian
embryogenesis (Magnani and Cabot, 2009). Wbp7 also plays a key
role in embryo development, and regulates the apoptosis and differen-
tiation of cells into all three germ layers (Lubitz et al., 2007). Most
recent evidence revealed an association of the Kcnq1 gene with the
susceptibility to type 2 diabetes. Kcnq1 participates in the regulation
of cell volume, which is, in turn, critically important for the regulation
of metabolism by insulin. Kcnq1 counteracts the stimulation of cellular
K+ uptake by insulin and thereby influences K+-dependent insulin
signaling on glucose metabolism (Boini et al., 2009).
Importantly, this study does not address unequivocally whether the
differences in gene expression described in ICSI-produced blastocysts
are secondary to the ICSI procedure alone or the combination of ICSI
and IVC. An ideal experiment would include the transcriptome analy-
sis of blastocysts that were generated by ICSI, with the resulting two
pronuclei embryos immediately transferred to recipients to eliminate
the effects of in vivo culture. Whereas this experiment is feasible, it
is technically difficult and requires multiple manipulations. The next
best experiment is to observe the gene expression changes of
zygote generated in vivo and cultured to the blastocyst stage (IVC
embryos). We (Rinaudo and Schultz, 2004; Giritharan et al., 2007)
and others (Wang et al., 2005; Zeng and Schultz, 2005; Fernandez-
Gonzalez et al. 2009) have shown that culture conditions play an
important role in shaping gene expression in developing embryos
and blastocysts. In particular, in one study we showed that culture
media and oxygen concentration play an independent role in affecting
gene expression, with the oxygen concentration determining a syner-
gistic increase in gene misregulation. IVC of zygotes in atmospheric
oxygen (20% O2) was associated with markedly increasing misregu-
lated genes (20% O2:WM: 354 genes changed more than 2-fold com-
pared with in vivo flushed blastocysts; KSOMaa: 102 differentially
expressed gene), compared to IVC of zygotes in physiologic oxygen
concentration (5% O2: WM: 45 genes and KSOM 18 genes changed
more than 2-fold, respectively; Rinaudo et al., 2006). In a separate
study, we showed that a high number of transcripts was statistically
Asb4Ankyrin repeat and SOCS box-containing 4
H19H19 fetal liver mRNA
Igf2asInsulin-like growth factor 2, antisense
Kcnq1 Potassium voltage-gated channel, subfamily Q, member 1
Osbpl5Oxysterol binding protein-like 5
Peg10 Paternally expressed 10
Epigenetic regulating genes
Hdac6Histone deacetylase 6
Smarca1 SWI/SNF related, matrix associated, actin-dependent regulator
of chromatin, subfamily a, member 1
Wbp7WW domain binding protein 7
Mbd2 Methyl-CpG binding domain protein 2
Smarca4SWI/SNF related, matrix associated, actin-dependent regulator
of chromatin, subfamily a, member 4
Table IV Imprintedand epigenetic genes differentiallyexpressed in ICSIand IVFembryos compared within vivoembryos
with their fold changes (P < 0.05).
NS, not significant.
Effect of ICSI on mouse preimplantation embryo
different in blastocysts generated by IVF and cultured in WM 20% O2
when compared with in vivo control blastocysts, but the magnitude of
the changes in gene expression was low and only a minority of tran-
scripts (357) was changed more than 2-fold. Surprisingly, IVF
embryos were different from IVC blastocysts cultured in WM 20%
O2(3058 transcripts were statistically different but only 98 transcripts
were changed more than 2-fold; Giritharan et al., 2007). Fernandez-
Gonzalez et al. (2009) compared the gene expressions of IVC
embryos cultured in KSOM versus KSOM + fetal calf serum (FCS),
and observed that the presence of FCS during IVC affected several
genes involved in regulating epigenetic mechanisms. Their results are
particularly relevant because the same authors found that adult
animals resulting from IVC embryos cultured in KSOM + FCS dis-
played alteration of post-natal development and behavior (Fernandez-
Gonzalez et al., 2004).
The above-mentioned studies and the present findings support the
conclusion that each manipulation and culture conditions have an
independent effect on the transcriptome of the developing embryo.
Interestingly, the ICSI manipulation results in a higher number of
genes being changed compared with all the other manipulations
It is possible that the different pattern of calcium oscillation follow-
ing ICSI (Kurokawa and Fissore, 2003) triggers a different wave of gene
activation and therefore the effect of different culture media is less
prominent. Consistent with this possibility is the finding that the
S100a6 (S100 calcium binding protein A6), a calcium binding
protein, is down-regulated more than 25-folds in the ICSI groups.
S100a6 induces conformational changes and post-translational modifi-
cations of multiple cytoplasmic proteins (Santamaria-Kisiel et al.,
2006). In particular, it interacts with p53 and modulates apoptosis
(Grigorian et al., 2001).
Implication for future health
The most important clinical question relates to the long-term signifi-
cance of the observed gene changes. These changes could be self-
limited and isolated, like T-wave changes found on a healthy person
EKG following intense physical exercise. In fact, while one rodent
study found differences in selected gene expression in blastocysts gen-
erated by ICSI with mature spermatozoa or round spermatid injection
(ROSI; Hayashi et al., 2003), other studies did not find any obvious
long-term health consequences in ROSI mice (Tamashiro et al.
1999; Meng et al., 2002). On the other hand, it is possible that
some of the differentially regulated genes might alter the development
of additional genes, and as a result, potentially affect cellular and tissue
development, as asserted by the developmental origin of health and
disease hypothesis (Barker, 1998). Indeed, a cohort of ART pubertal
children has been found to have slightly worse metabolic parameters
than spontaneously conceived children of infertile couples (Ceelen
et al., 2008). We believe that our database provides fundamental
resources for understanding how the method of fertilization and
culture conditions affect mouse preimplantation embryo develop-
ment. Therefore the provided gene list could be useful to uncover
the cellular mechanisms that can
Overall, it appears that ICSI, IVF and in vivo produced mouse blas-
tocysts have a very different transcriptome.
lead to long-term health
Supplementary data are available at http://humrep.oxfordjournals.
G.G.: Conception and design, collection and assembly of data and
manuscript writing. M.W.L.: Collection of data. F.S.: Collection of
data. F.J.E.: Data analysis and interpretation. J.A.H., A.D., E.M.: Data
analysis and interpretation. K.C.K.L.: Collection of data. P.R.: Con-
ception and design, manuscript writing and final approval of
This research was supported by NICHD/NIH through cooperative
agreement 1U54HD055764 as part of the Specialized Cooperative
Centers Program in Reproduction and Infertility Research.
Adamson SL, Lu Y, Whiteley KJ, Holmyard D, Hemberger M, Pfarrer C,
Cross JC. Interactions between trophoblast cells and the maternal
and fetal circulation in the mouse placenta. Dev Biol 2002;250:358–73.
Andang M, Hjerling-Leffler J, Moliner A, Lundgren TK, Castelo-Branco G,
Nanou E, Pozas E, Bryja V, Halliez S, Nishimaru H et al. Histone
proliferation. Nature 2008;451:460–464.
Anthony SBS, Dorrepaal C, Lindner K, Braat D, Ouden A Congenital
malformations in 4224 children conceived after IVF. Hum Reprod
Barker DJ. Mothers, Babies and Health in Later Life, 2nd edn. Glasgow:
Churchill Livingstone, 1998.
Bedford SJ, Kurokawa M, Hinrichs K, Fissore RA. Intracellular calcium
oscillations and activation in horse oocytes injected with stallion
sperm extracts or spermatozoa. Reproduction 2003;126:489–499.
Boini KM, Graf D, Hennige AM, Koka S, Kempe DS, Wang K,
Ackermann TF, Foller M, Vallon V, Pfeifer K et al. Enhanced insulin
sensitivity of gene-targeted mice lacking functional KCNQ1. Am J
Physiol Regul Integr Comp Physiol 2009;296:R1695–R1701.
Breitling R, Herzyk P. Rank-based methods as a non-parametric alternative
of the T-statistic for the analysis of biological microarray data. J Bioinform
Comput Biol 2005;3:1171–1189.
Ceelen M, van Weissenbruch MM, Vermeiden JP, van Leeuwen FE,
Delemarre-van de Waal HA. Cardiometabolic differences in children
born after in vitro fertilization: follow-up study. J Clin Endocrinol Metab
Cervello I, Gil-Sanchis C, Mas A, Delgado-Rosas F, Martinez-Conejero JA,
Galan A, Martinez-Romero A, Martinez S, Navarro I, Ferro J et al.
Human endometrialside population
phenotypic and functional features of somatic stem cells. PLoS One
Closs EI, Boissel JP, Habermeier A, Rotmann A. Structure and function of
cationic amino acid transporters (CATs). J Membr Biol 2006;213:67–77.
Cox GF, Burger J, Lip V, Mau UA, Sperling K, Wu BL, Horsthemke B.
Intracytoplasmic sperm injection may increase the risk of imprinting
defects. Am J Hum Genet 2002;71:162–164.
regulationof stem cell
Giritharan et al.
DeBaun MR, Niemitz EL, Feinberg AP. Association of in vitro fertilization
with Beckwith-Wiedemann syndrome and epigenetic alterations of LIT1
and H19. Am J Hum Genet 2003;72:156–160.
Doherty AS, Mann MR, Tremblay KD, Bartolomei MS, Schultz RM.
Differential effects of culture on imprinted H19 expression in the
preimplantation mouse embryo. Biol Reprod 2000;62:1526–1535.
Dumoulin JC, Coonen E, Bras M, van Wissen LC, Ignoul-Vanvuchelen R,
Bergers-Jansen JM, Derhaag JG, Geraedts JP, Evers JL. Comparison of
in-vitro development of embryos originating from either conventional
in-vitro fertilization or intracytoplasmic sperm injection. Hum Reprod
Fernandez-Gonzalez R, Moreira P, Bilbao A, Jimenez A, Perez-Crespo M,
Ramirez MA, Rodriguez De Fonseca F, Pintado B, Gutierrez-Adan A.
Long-term effect of in vitro culture of mouse embryos with serum on
mRNA expression of imprinting genes, development, and behavior.
Proc Natl Acad Sci USA 2004;101:5880–5885.
Fernandez-Gonzalez R, Moreira PN, Perez-Crespo M, Sanchez-Martin M,
Ramirez MA, Pericuesta E, Bilbao A, Bermejo-Alvarez P, de Dios
Hourcade J, de Fonseca FR et al. Long-term effects of mouse
intracytoplasmic sperm injection with DNA-fragmented sperm on
health and behavior of adult offspring. Biol Reprod 2008;78:761–772.
Fernandez-Gonzalez R, de Dios Hourcade J, Lopez-Vidriero I, Benguria A,
De Fonseca FR, Gutierrez-Adan A. Analysis of gene transcription
alterationsat the blastocyst
consequences of in vitro culture in mice. Reproduction 2009;137:
Geyer J, Wilke T, Petzinger E. The solute carrier family SLC10: more than
a family of bile acid transporters regarding function and phylogenetic
Gimeno RE, Hirsch DJ, Punreddy S, Sun Y, Ortegon AM, Wu H, Daniels T,
Stricker-Krongrad A, Lodish HF, Stahl A. Targeted deletion of fatty acid
transport protein-4 results in early embryonic lethality. J Biol Chem 2003;
Giritharan G, Talbi S, Donjacour A, Di Sebastiano F, Dobson AT,
Rinaudo PF. Effect of in vitro fertilization on gene expression and
development of mouse preimplantation embryos. Reproduction 2007;
Grigorian M, Andresen S, Tulchinsky E, Kriajevska M, Carlberg C, Kruse C,
Cohn M, Ambartsumian N, Christensen A, Selivanova G et al. Tumor
suppressor p53 protein is a new target for the metastasis-associated
Mts1/S100A4 protein: functional consequences of their interaction.
J Biol Chem 2001;276:22699–22708.
Hansen M, Kurinczuk JJ, Bower C, Webb S. The risk of major birth defects
after intracytoplasmic sperm injection and in vitro fertilization. N Engl J
Hayashi S, Yang J, Christenson L, Yanagimachi R, Hecht NB. Mouse
preimplantation embryos developed from oocytes injected with round
spermatids or spermatozoa have similar but distinct patterns of early
messenger RNA expression. Biol Reprod 2003;69:1170–1176.
Hemler ME. Tetraspanin functions and associated microdomains. Nat Rev
Hong F, Breitling RA. comparison of meta-analysis methods for detecting
differentially expressed genes in microarray experiments. Bioinformatics
Huttemann M, Jaradat S, Grossman LI. Cytochrome c oxidase of mammals
contains a testes-specific isoform of subunit VIb—the counterpart to
testes-specific cytochrome c? Mol Reprod Dev 2003;66:8–16.
Kerr SM, Taggart MH, Lee M, Cooke HJ. Ott, a mouse X-linked multigene
family expressed specifically during meiosis. Hum Mol Genet 1996;
Kromer B, Finkenzeller D, Wessels J, Dveksler G, Thompson J,
Zimmermann W. Coordinate expression of splice variants of the
murine pregnancy-specific glycoprotein (PSG) gene family during
placental development. Eur J Biochem/FEBS 1996;242:280–287.
Kurokawa M, Fissore RA. ICSI-generated mouse zygotes exhibit altered
calcium oscillations, inositol 1,4,5-trisphosphate receptor-1 down-
regulation, and embryo development. Mol Hum Reprod 2003;
Leese HJ, Baumann CG, Brison DR, McEvoy TG, Sturmey RG. Metabolism
of the viable mammalian embryo: quietness revisited. Mol Hum Reprod
Li MW, Willis BJ, Griffey SM, Spearow JL, Lloyd KC. Assessment of three
generations of mice derived by ICSI using freeze-dried sperm. Zygote
Lim D, Bowdin SC, Tee L, Kirby GA, Blair E, Fryer A, Lam W, Oley C,
Cole T, Brueton LA et al. Clinical and molecular genetic features
reproductive technologies. Hum Reprod 2009;24:741–747.
Lubitz S, Glaser S, Schaft J, Stewart AF, Anastassiadis K. Increased
apoptosis and skewed differentiation in mouse embryonic stem cells
lacking the histone methyltransferase Mll2. Mol Biol Cell 2007;
Lubke T, Marquardt T, Etzioni A, Hartmann E, von Figura K, Korner C.
Complementation cloning identifies CDG-IIc, a new type of congenital
disorders of glycosylation, as a GDP-fucose transporter deficiency.
Nat Genet 2001;28:73–76.
Magnani L, Cabot RA. Manipulation of SMARCA2 and SMARCA4
transcript levels in porcine embryos differentially alters development
and expressionof SMARCA1,
Malcuit C, Maserati M, Takahashi Y, Page R, Fissore RA. Intracytoplasmic
sperm injection in the bovine induces abnormal [Ca2+]i responses and
oocyte activation. Reprod Fertil Dev 2006;18:39–51.
Markoulaki S, Kurokawa M, Yoon SY, Matson S, Ducibella T, Fissore R.
Comparison of Ca2 + and CaMKII responses in IVF and ICSI in the
mouse. Mol Hum Reprod 2007;13:265–272.
Massuto DA, Kneese EC, Johnson GA, Burghardt RC, Hooper RN,
Ing NH, Jaeger LA. Transforming growth factor beta (TGFB) signaling
is activated during porcine implantation: proposed role for latency-
associated peptide interactions with integrins at the conceptus-
maternal interface. Reproduction 2010;139:465–478.
McDonald SD, Han Z, Mulla S, Murphy KE, Beyene J, Ohlsson A. Preterm
birth and low birth weight among in vitro fertilization singletons: a
systematic review and meta-analyses. Eur J Obstet Gynecol Reprod Biol
Meng X, Akutsu H, Schoene K, Reifsteck C, Fox EP, Olson S, Sariola H,
Yanagimachi R, Baetscher M. Transgene insertion induced dominant
male sterility and rescue of male fertility using round spermatid
injection. Biol Reprod 2002;66:726–734.
Morey JS, Ryan JC, Van Dolah FM. Microarray validation: factors influencing
correlation between oligonucleotide microarrays and real-time PCR. Biol
Proced Online 2006;8:175–193.
Paiva P, Salamonsen LA, Manuelpillai U, Dimitriadis E. Interleukin 11
inhibits human trophoblast invasion indicating a likely role in the
decidual restraint of trophoblast invasion during placentation. Biol
Paulsen M, Davies KR, Bowden LM, Villar AJ, Franck O, Fuermann M,
Dean WL, Moore TF, Rodrigues N, Davies KE et al. Syntenic
organization of the mouse distal chromosome 7 imprinting cluster and
the Beckwith–Wiedemann syndrome region in chromosome 11p15.5.
Hum Mol Genet 1998;7:1149–1159.
SOX2, NANOG,and EIF1.
Effect of ICSI on mouse preimplantation embryo
Petersen KF, Dufour S, Befroy D, Garcia R, Shulman GI. Impaired Download full-text
mitochondrial activity in the insulin-resistant offspring of patients with
type 2 diabetes. N Engl J Med 2004;350:664–671.
Qiu A, Jansen M, Sakaris A, Min SH, Chattopadhyay S, Tsai E, Sandoval C,
Zhao R, Akabas MH, Goldman ID. Identification of an intestinal folate
malabsorption. Cell 2006;127:917–928.
Rawn SM, Cross JC. The evolution, regulation, and function of
placenta-specific genes. Annu Rev Cell Dev Biol 2008;24:159–181.
Rinaudo P, Schultz RM. Effects of embryo culture on global pattern of gene
expression in preimplantation mouse embryos. Reproduction 2004;
Rinaudo PF, Giritharan G, Talbi S, Dobson AT, Schultz RM. Effects of
oxygen tension on gene expression in preimplantation mouse
embryos. Fertil Steril 2006;86(Suppl 4):1252–1265, 1265. e1–36.
Rolaki A, Coukos G, Loutradis D, DeLisser HM, Coutifaris C,
Makrigiannakis A. Luteogenic hormones act through a vascular
endothelial growth factor-dependent mechanism to up-regulate alpha
5 beta 1 and alpha v beta 3 integrins, promoting the migration and
survival of human luteinized granulosa cells. Am J Pathol 2007;
Santamaria-Kisiel L, Rintala-Dempsey AC, Shaw GS. Calcium-dependent
and -independent interactions of the S100 protein family. Biochem J
Schaub J, Heyne K. Glycogen storage disease type Ib. Eur J Pediatr 1983;
Schieve LA, Meikle SF, Ferre C, Peterson HB, Jeng G, Wilcox LS. Low and
very low birth weight in infants conceived with use of assisted
reproductive technology. N Engl J Med 2002;346:731–737.
Society for Assisted Reproductive Technology. Centers for Disease
Control and Prevention, American Society for Reproductive Medicine,
2007. Assisted Reproductive Technology Success Rates: National
Summary and Fertility Clinic Reports, Atlanta, GA: U.S. Department
of Health and Human Services, Centers for Disease Control and
basis for hereditaryfolate
Tamashiro KL, Kimura Y, Blanchard RJ, Blanchard DC, Yanagimachi R.
Bypassing spermiogenesis for several generations does not have
detrimental consequences on the fertility and neurobehavior of
offspring: a study using the mouse. J Assist Reprod Genet 1999;
Thouas GA, Korfiatis NA, French AJ, Jones GM, Trounson AO. Simplified
technique for differential staining of inner cell mass and trophectoderm
cells of mouse and bovine blastocysts. Reprod Biomed Online 2001;
Thouas GA, Trounson AO, Jones GM. Developmental effects of
sublethal mitochondrial injury in mouse oocytes. Biol Reprod 2006;
Verdel A, Seigneurin-Berny D, Faure AK, Eddahbi M, Khochbin S,
Nonchev S. HDAC6-induced premature chromatin compaction in
mouse oocytes and fertilised eggs. Zygote 2003;11:323–328.
Wang K, Zhou B, Kuo YM, Zemansky J, Gitschier JA. novel member of a
zinc transporter family is defective in acrodermatitis enteropathica. Am J
Hum Genet 2002;71:66–73.
Wang S, Cowan CA, Chipperfield H, Powers RD. Gene expression in the
preimplantation embryo: in-vitro developmental changes. Reprod Biomed
Williams JW, Hawes SM, Patel B, Latham KE. Trophectoderm-specific
expression of the X-linked Bex1/Rex3 gene in preimplantation stage
mouse embryos. Mol Reprod Dev 2002;61:281–287.
Wynne F, Ball M, McLellan AS, Dockery P, Zimmermann W, Moore T.
Mouse pregnancy-specific glycoproteins: tissue-specific expression and
evidence of association with maternal vasculature. Reproduction 2006;
Zegers-Hochschild F, Altieri E, Fabres C, Fernandez E, Mackenna A,
Orihuela P. Predictive value of human chorionic gonadotrophin in the
outcome of early pregnancy after in-vitro fertilization and spontaneous
conception. Hum Reprod 1994;9:1550–1555.
Zeng F, Schultz RM. RNA transcript profiling during zygotic gene
activation in the preimplantation mouse embryo. Dev Biol 2005;283:
Giritharan et al.