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1. Genomics of oocyte and embryo-endometrium
interaction at implantation
ANDRES SALUMETS
Competence Centre on Reproductive Medicine and Biology;
Women’s Clinic and Institute of Bio- and Translational Medicine,
University of Tartu, ESTONIA
November / 2013
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2. Andres Salumets – Short CV
• 1993 - Graduated from University of Tartu as biochemist
• 2003 - Doctoral degree from University of Helsinki
Väestöliitto Helsingin Lapsettomuusklinikka, supervised by prof. T. Tuuri and
prof. AM Suikkari
• 2010 - ... Professor of reproductive medicine at Women’s Clinic and Institute of
Bio- and Translational Medicine, University of Tartu
• 2010 - ... Head of Competence Centre on Reproductive Medicine and Biology
(CCRMB)
• 2010 - ... President of Baltic Fertility Society
• 2013 - ... Member of Executive Committee of ESHRE
• Consultant to IVF clinics in Tartu, Tallinn, Tbilisi and Delhi
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3. UNIVERSITAS TARTUENSIS and HOSPITAL
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4. Karl Ernst von Baer
(1792-1876)
1826
4

5. Humans are relatively infertile species
o The chance for pregnancy per menstrual cycle
is 1:3
o The cumulative pregnancy rate:
3 months - 60%
6 months - 75%
12 months - 85%
24 months - 95%
Infertile couples
o Average time to pregnancy 3-4 months
o Infertility exists in 10% of couples
o In vitro fertilization (IVF) is actively used in
infertility treatment
5

6. The Nobel Prize in
Physiology or
Medicine 2010
Robert G. Edwards
6

7. Major shortcomings of IVF
• IVF implantation and pregnancy results have remained almost
unchanged for 30 years. Clinical pregnancy rate of ONLY 25-30%.
• The selection of the best embryos is limited – no clear criteria to
select the best embryos for transfer. Limited use of single embryo
transfers.
• Too many multiple pregnancies, 25-30%.
• A few possibilities to help couples with recurrent IVF failure.
• Limited possibilities to analyse and modulate the endometrial
quality (receptivity).
• Poor responders and limited amount of oocytes. How to coupe
with the higher age of IVF patients?
• IVF complications, like ovarian hyperstimulation syndrome.
• Limited sources of donor oocytes and embryos.
• Too expensive.
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8. IVF is inefficient
No.
1200
1000
120,0
100,0
100,0
80,0
60,0
60,0
700
200
40
30
%
80,0
40,0
15,0
20,0
3,0
2,5
0,0
Oocytes
Zygotes
Embryos
with good
quality
Embryos Embryos
replaced implanted
Children
CA 100 IVF CYCLES
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9. Recent achievements
• Human Genome Project –
HGP, 2000 y
– 46 chromosomes, XX and XY
– ca 30 000 genes
– 10 million single nucleotide
polymorphisms (SNPs)
– CNVs – DNA copy number
variations (12% of our genome)
– Gene and chromosomal mutations
Female and male fertility and
infertility phenotypes
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10. Recent achievements – useful for IVF
High-throughput OMICs
analysing platforms for
genetics, epigenetics,
transcriptomics,
proteomics and
metabolomics
METABOLOMICS
PROTEOMICS
TRANSCIPTOMICS
Gene expression
RNA splicing
GENETICS
Genes, gene variations
DNA modifications
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11. OMICS in reproductive medicine
Polar body biopsy and genetic
analysis – oocyte chromosomal
aberrations. Preimplantation
genetic diagnosis
Gene variations related
to the ovarian reserve
and stimulation
outcome
Gene expression analysis of
sperm cells
Gene expression of cumulus cells
and proteome analysis of follicular
fluid samples
Proteome and
metabolome
analysis of
embryo’s culture
media
Biopsy and analysis of
embryo cells for
chromosomal
aberrations and gene
expression pattern
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12. Menopausal age ...
... links to DNA repair and aging pathways
• Genome-wide association study (GWAS) of women of
European ancestry, with 38,968 women in the discovery
stage, and 14,435 women in the replication stage
• Gene donors from - EGCUT (Estonian Genome Center of
University of Tartu)
• In this large 2-stage GWAS analysis we confirmed 4 previously
identified menopause loci and identified and replicated 13
novel loci associated with
p<5e-08
age age at natural menopause
OVARIAN AGING = SOMATIC AGING
Stolk et al, Nature Genetics, 2012
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13. Genes and ovarian stimulation in IVF
CUMULATED GENETIC VARIATIONS >> IMPAIRED IVF
STIMULATION OUTCOME >> EARLY MENOPAUSE
• Predicting fertility potential, infertility treatment outcome and
the duration of the reproductive period
• Fertility prediction testing (ultrasound, hormones and genetic
predisposition) – FERTILITY PRESERVATION AND OOCYTE
FREEZING
13
13

14. Oocytes in ovaries ... IVF and
fertility & menopause
Oocyte stem
cells in ovaries –
renewal of
oocytes?
Genetic variations leading
to more oocytes in IVF.
Genetic testing of IVF
patients and personalised
stimulation protocols
Genetic variations DISCOVERED
leading to earlier menopause
and accelerated follicular death
(earlier age-related infertility)
GENE TESTING
and IMPROVED IVF OUTCOME
Better drugs for IVF
hormonal stimulation
(more oocytes from
poor responders)
Drugs postponing
the menopause and
prolonging the
reproductive
lifespan
Oocyte freezing and
biobanking
14

15. Chromosomal aberrations
Stage of conception
and pregnancy
0
(weeks)
6-8
20
40
Sperm cells - 1-2%
Oocytes - ca 20% (POSITIVE RELATIONSHIP WITH WOMAN’S AGE!)
Preimplantation stage embryos - 20-50%
Spontaneous abortions (6-20) - 35%
DOWN SYNDROME
TRISOMY 21
Stillbirths (20-40) - 4%
Live births - 0,3%
Woman’s age ↑
More chromosomal aberrations in
oocytes ↑
Fewer embryo implantations and
pregnancies ↓
More spontaneous abortions ↑
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16. Genomic analysis in IVF
• Polar body and embryo diagnostics
FISH – limited number of chromosomes
• Array and sequencing based technologies
- Analysis of all chromosomes and gene
transcripts from single cell!
• 90% of the embryos
are chromosomally
abnormal (polar body
vs embryo diagnostics)
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17. EMBRYO SELECTION and -OMICS
Genomics
Chromosomes
SNPs and mutations
Transcriptomics
Single mRNAs
mRNA arrays
Proteomics
Immuno-techniques
Microscopics
Oocytes
Embryos
Mass spectrometry, MS
Metabolomics
HPLC
MS and spectroscopy
17

18. Ultra-sensitive sensors for embryo selection
SENSOR OVERVIEW
Sensor
overview
HLA-G and HCG
HLA-G
“sandwich”
TIRF measurement
Image
18

19. The window of implantation (WOI)
ES
MS
LS
WOI
 20.-24. cycle
day
 6-8 days after
ovulation
 48 hours
PINOPODES
ES, no
TR 1 pinopodes
Altmäe et al, Reprod Sci, 2011
MS, fully developed
pinopodes
LS, no pinopodes
Inf, few pinopodes
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20. Fertile women vs women with unexplained infertility
Abnormalities in gene expression pathways
GENE EXPRESSION
HISTOLOGY
Altmäe et al., MHR, 2010
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21. ENDOMETRIAL RECEPTIVITY MARKERS
 We identified a number of genes in the embryo-endometrial
interactions that are known to be involved in the implantation
process, like LEP, LEPR, VCAN, TGFB1, laminins, collagens and fibulins
 In addition, several new molecules involved in the interactions were
identified, like APP, BMP2, DSC2, PDGFRA, ADAMST1 and others
21
Altmäe et al., 2012, Mol Endocrinology

22. Individualised day for embryo transfer
DAYS
D1
D2
D3
D4
D5
Women 1
Women 2
Women 3
Endometrial biopsy and gene
expression analysis
Women 1
Women 2
Women 3
Array analysis
Selection of the BEST day for (frozen) embryo transfer!
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23. FUTURE VIEW WITHOUT LIMITATIONS
In vitro produced oocyte!
Granulosa
cells
Genetic analysis of oocytes,
polar bodies and granulosa
cells
Oocytes
Sertoli
cells
Oocyte freezing
and banking
IVF
DIFFERENTIATION OF:
• Embryonal stem cells
• Induced pluripotent stem
cells, iPS cells
Endometrial cell transplantation
and improved implantation
Spermatogonia
and sperm cells
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In vitro produced sperms!

24. Thank you for the attention
Andres.Salumets@ccrmb.ee