U.S. patent application number 14/808204 was filed with the patent office on 2016-07-14 for methods for selecting competent oocytes and competent embryos with high potential for pregnancy outcome.
This patent application is currently assigned to INSERM (Institut National de la Sante et de la Recherche Medicale). The applicant listed for this patent is Said ASSOU, Samir HAMAMAH. Invention is credited to Said ASSOU, Samir HAMAMAH.
Application Number | 20160201128 14/808204 |
Document ID | / |
Family ID | 56367108 |
Filed Date | 2016-07-14 |
United States Patent
Application |
20160201128 |
Kind Code |
A1 |
HAMAMAH; Samir ; et
al. |
July 14, 2016 |
METHODS FOR SELECTING COMPETENT OOCYTES AND COMPETENT EMBRYOS WITH
HIGH POTENTIAL FOR PREGNANCY OUTCOME
Abstract
The present invention relates to a method for selecting a
competent oocyte or a competent embryo.
Inventors: |
HAMAMAH; Samir;
(Montpellier, FR) ; ASSOU; Said; (Montpellier,
FR) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
HAMAMAH; Samir
ASSOU; Said |
Montpellier
Montpellier |
|
FR
FR |
|
|
Assignee: |
INSERM (Institut National de la
Sante et de la Recherche Medicale)
Paris
FR
UNIVERSITE DE MONTPELLIER 1
Montpellier Cedex 2
FR
Centre Hospitalier Universitaire de Montpellier
Montpellier
FR
|
Family ID: |
56367108 |
Appl. No.: |
14/808204 |
Filed: |
July 24, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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13989423 |
Aug 6, 2013 |
9121066 |
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14808204 |
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Current U.S.
Class: |
506/2 ; 506/16;
536/24.5 |
Current CPC
Class: |
C12Q 1/6881 20130101;
C12N 2310/141 20130101; C12N 15/113 20130101; C12Q 2600/158
20130101; C12N 15/111 20130101; C12N 2320/10 20130101; C12Q
2600/178 20130101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. A method for selecting an oocyte that will produce, upon
fertilization, a viable embryo with a high implantation rate
leading to pregnancy, comprising a step of measuring in a cumulus
cell surrounding said oocyte the expression level of at least 5
microRNA selected from the group consisting of hsa-mir-103-1,
hsa-mir-103-2, hsa-mir-1826, hsa-let-7a-1, hsa-let-7a-2,
hsa-let-7a-3, hsa-let-7b, hsa-let-7c, hsa-let-7f, hsa-mir-1244,
hsa-mir-182, hsa-mir-21, hsa-mir-30a, hsa-mir-30d, hsa-mir-320a,
hsa-mir-508, hsa-mir-92a-1, hsa-mir-92a-2, hsa-mir-16-1,
hsa-mir-16-2, hsa-mir-1974, hsa-mir-146b, hsa-mir-886, hsa-mir-210,
hsa-mir-1979, hsa-mir-125a, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO:
8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ
ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:
17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20 and SEQ ID NO:
21.
2-10. (canceled)
11. The method according to claim 1 wherein said at least 5
microRNA are selected from the group consisting of hsa-mir-508,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-103-1, hsa-mir-103-2,
hsa-mir-1974, hsa-mir-1826, SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID
NO: 12.
12. The method according to claim 1 wherein said at least 5
microRNA are selected from the group consisting of hsa-mir-508,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-103-1, has-mir-103-2,
hsa-mir-1974, hsa-mir-1826, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO:
12, hsa-let-7b, hsa-let-7c, hsa-mir-182, hsa-mir-21, hsa-mir-30a
and hsa-mir-30d.
13. The method according to claim 1 wherein said at least 5
microRNA are selected from the group consisting of hsa-mir-182,
hsa-mir-320a, hsa-mir-210, hsa-mir-21 and has-let-7a-1.
14. The method according to claim 1 comprising a further step of
measuring in a cumulus cell surrounding said oocyte the expression
level of one or more genes selected from the group consisting of
ATF3, SIAT6, PRKACA, PLA2G5, GPC6, GOS2, RBMS1, NFIC, SLC40A1 and
WNT6.
15. A method for selecting an embryo with a high implantation rate
leading to pregnancy, comprising a step of measuring in a cumulus
cell surrounding said embryo the expression level of at least 5
microRNA selected from the group consisting of hsa-mir-103-1,
hsa-mir-103-2, hsa-mir-1826, hsa-let-7a-1, hsa-let-7a-2,
hsa-let-7a-3, hsa-let-7b, hsa-let-7c, hsa-let-7f, hsa-mir-1244,
hsa-mir-182, hsa-mir-21, hsa-mir-30a, hsa-mir-30d, hsa-mir-320a,
hsa-mir-508, hsa-mir-92a-1, hsa-mir-92a-2, hsa-mir-16-1,
hsa-mir-16-2, hsa-mir-1974, hsa-mir-146b, hsa-mir-886, hsa-mir-210,
hsa-mir-1979, hsa-mir-125a, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO:
8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ
ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:
17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20 and SEQ ID NO:
21.
16. The method according to claim 15 wherein said at least 5
microRNA are selected from the group consisting of hsa-mir-508,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-103-1, has-mir-103-2,
hsa-mir-1974, hsa-mir-1826, SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID
NO: 12.
17. The method according to claim 15 wherein said at least 5
microRNA are selected from the group consisting of hsa-mir-508,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-103-1, has-mir-103-2,
hsa-mir-1974, hsa-mir-1826, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO:
12, hsa-let-7b, hsa-let-7c, hsa-mir-182, hsa-mir-21, hsa-mir-30a
and hsa-mir-30d.
18. The method according to claim 15 wherein said at least 5
microRNA are selected from the group consisting of hsa-mir-182,
hsa-mir-320a, hsa-mir-210, hsa-mir-21 and has-let-7a-1.
19. The method according to claim 15 comprising a further step of
measuring in a cumulus cell surrounding said embryo the expression
level of one or more genes selected from the group consisting of
ATF3, SIAT6, PRKACA, PLA2G5, GPC6, GOS2, RBMS1, NFIC, SLC40A1 and
WNT6.
20. A method for selecting an oocyte that will produce, upon
fertilization, a viable embryo with a high implantation rate
leading to pregnancy or an embryo with a high implantation rate
leading to pregnancy, comprising a step of measuring in the culture
medium of cumulus cell having surrounded said oocyte or said embryo
the expression level of at least 5 microRNA selected from the group
consisting of hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826,
hsa-let-7a-1, hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c,
hsa-let-7f, hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a,
hsa-mir-30d, hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1,
hsa-mir-92a-2, hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974,
hsa-mir-146b, hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a,
SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO:
10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ
ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO:
19, SEQ ID NO: 20 and SEQ ID NO: 21.
21. A method for selecting an oocyte that will produce, upon
fertilization, a viable embryo with a high implantation rate
leading to pregnancy or an embryo with a high implantation rate
leading to pregnancy, comprising a step of measuring in a bodily
fluid the expression level of at least 5 microRNA selected from the
group consisting of hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826,
hsa-let-7a-1, hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c,
hsa-let-7f, hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a,
hsa-mir-30d, hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1,
hsa-mir-92a-2, hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974,
hsa-mir-146b, hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a,
SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO:
10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ
ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO:
19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ
ID NO:24 and SEQ ID NO: 25.
22. An isolated nucleic acid molecule having the nucleotide
sequence as set forth in SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8,
SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID
NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17,
SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID
NO: 22, SEQ ID NO: 23, SEQ ID NO:24 and SEQ ID NO: 25.
23. A kit comprising means for measuring the expression level of
the microRNA of Table I.
Description
FIELD OF THE INVENTION
[0001] The present invention relates to a method for selecting a
competent oocyte or a competent embryo.
BACKGROUND OF THE INVENTION
[0002] In assisted reproductive technology (ART), pregnancy and
birth rates following in vitro fertilization (IVF) attempts remain
low. Indeed, 2 out of 3 IVF cycles fail to result in pregnancy
(SART 2004) and more than 8 out of 10 transferred embryos fail to
implant (Kovalevsky and Patrizio, 2005). In addition, more than 50%
of IVF-born babies are from multiple gestations (Reddy et al.,
2007). Preterm deliveries that result from multiple pregnancies
caused by ART are estimated to account for approximately $890
million of U.S. health care costs annually (Bromer and Seli,
2008).
[0003] The selection of embryos with higher implantation potential
has been one of the major challenges in ART. This selection is
currently based on morphological criteria such as growth rate,
early cleavage on day-1, degree of fragmentation and blastocyst
formation (Ebner et al., 2003). However, the predictive power of
this approach is still limited. With the emergence of new
technologies like `omics`, there are new biomarkers as discovery
tools that can be applied to IVF for oocyte and/or embryo selection
(Hillier, 2008).
[0004] Legal and ethical considerations make biomarkers directly
directed to oocytes or embryos difficult to implement. Thus, to
avoid any invasive method, some studies have been focused on
cumulus cells (CCs).
[0005] Indeed, transcriptomic approaches using microarray
technology, allowing the simultaneous screening of thousands of
genes, were intensively used to identify in CCs the biomarkers
related to oocyte competence, which is defined as the intrinsic
ability of oocytes to undergo meiotic maturation, fertilization and
embryonic development (McKenzie et al., 2004; van Montfoort et al.,
2008).
[0006] Using the same approach, genes expressed in CCs used as
biomarkers associated with embryo quality (McKenzie et al., 2004;
van Montfoort et al., 2008; Zhang et al., 2005) and pregnancy
outcome (Assou et al., 2008; Hamel et al., 2008; Hamel et al.,
2010; Assou et al. 2010) have also been identified.
[0007] Even if these studies target the gene expression profile of
CCs, a source of cells reflecting the biology and competence of
both oocytes and embryos, there is a need to investigate further to
develop a non-invasive method of predicting IVF outcome easier to
use and with higher reliability.
SUMMARY OF THE INVENTION
[0008] The present invention relates to a method for selecting an
oocyte that will produce, upon fertilization, a viable embryo with
a high implantation rate leading to pregnancy, comprising a step of
measuring in a cumulus cell surrounding said oocyte the expression
level of at least 5 microRNA selected from the group consisting of
hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826, hsa-let-7a-1,
hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c, hsa-let-7f,
hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a, hsa-mir-30d,
hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1, hsa-mir-92a-2,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974, hsa-mir-146b,
hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a, SEQ ID NO: 6,
SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO:
11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ
ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO:
20 and SEQ ID NO: 21.
[0009] The present invention also relates to a method for selecting
an embryo with a high implantation rate leading to pregnancy
comprising a step of measuring in a cumulus cell surrounding said
embryo the expression level of at least 5 microRNA selected from
the group consisting of hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826,
hsa-let-7a-1, hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c,
hsa-let-7f, hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a,
hsa-mir-30d, hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1,
hsa-mir-92a-2, hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974,
hsa-mir-146b, hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a,
SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO:
10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ
ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO:
19, SEQ ID NO: 20 and SEQ ID NO: 21.
[0010] The method according to the invention may comprise a further
step of measuring in a cumulus cell surrounding said oocyte or said
embryo the expression level of one or more genes selected from the
group consisting of ATF3, SIAT6, PRKACA, PLA2G5, GPC6, G0S2, RBMS1,
NFIC, SLC40A1 and WNT6.
[0011] The present invention also relates to a method for selecting
an oocyte that will produce, upon fertilization, a viable embryo
with a high implantation rate leading to pregnancy, or an embryo
with a high implantation rate leading to pregnancy, comprising a
step of measuring in a bodily fluid the expression level of at
least 5 microRNA selected from the group consisting of
hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826, hsa-let-7a-1,
hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c, hsa-let-7f,
hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a, hsa-mir-30d,
hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1, hsa-mir-92a-2,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974, hsa-mir-146b,
hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a, SEQ ID NO: 6,
SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO:
11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ
ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO:
20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO:24 and
SEQ ID NO: 25.
[0012] The present invention also relates to an isolated nucleic
acid molecule having the nucleotide sequence as set forth in SEQ ID
NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ
ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO:
15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ
ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID
NO:24 and SEQ ID NO: 25.
DETAILED DESCRIPTION OF THE INVENTION
Definitions
[0013] A used herein the tem), "competent oocyte" refers to a
female gamete or egg that when fertilized, i. e. upon
fertilization, produces a viable embryo with a high implantation
rate leading to pregnancy.
[0014] According to the invention, the oocyte may result from a
natural cycle, a modified natural cycle or a stimulated cycle for
cIVF or ICSI. The term "natural cycle" refers to the natural cycle
by which the female or woman produces an oocyte. The term "modified
natural cycle" refers to the process by which, the female or woman
produces an oocyte or two under a mild ovarian stimulation with
GnRH antagonists associated with recombinant FSH or hMG. The term
"stimulated cycle" refers to the process by which a female or a
woman produces one ore more oocytes under stimulation with GnRH
agonists or antagonists associated with recombinant FSH or hMG.
[0015] The term "cumulus cell" refers to a cell comprised in a mass
of cells that surrounds an oocyte. These cells are believed to be
involved in providing an oocyte some of its nutritional, energy and
or other requirements that are necessary to yield a viable embryo
upon fertilization.
[0016] The term "embryo" refers to a fertilized oocyte or zygote.
Said fertilization may intervene under a classical in vitro
fertilization (cIVF) or under an intracytoplasmic sperm injection
(ICSI) protocol.
[0017] The term "classical in vitro fertilization" or "cIVF" refers
to a process by which oocytes are fertilised by sperm outside of
the body, in vitro. IVF is a major treatment in infertility when in
vivo conception has failed.
[0018] The term "intracytoplasmic sperm injection" or "ICSI" refers
to an in vitro fertilization procedure in which a single sperm is
injected directly into an oocyte. This procedure is most commonly
used to overcome male infertility factors, although it may also be
used where oocytes cannot easily be penetrated by sperm and
occasionally as a method of in vitro fertilization, especially that
associated with sperm donation.
[0019] The term "competent embryo" refers to an embryo with a high
implantation rate leading to pregnancy. The term "high implantation
rate" means the potential of the embryo when transferred in uterus,
to be implanted in the uterine environment and to give rise to a
viable foetus, which in turn develops into a viable offspring
absent a procedure or event that terminates said pregnancy.
[0020] Set of Predictive microRNA
[0021] The inventors have identified a set of 42 predictive
microRNA according to the invention expressed in cumulus cells and
4 predictive microRNA according to the invention expressed in
oocyte.
MicroRNA are single-stranded RNA molecules that regulate the
expression of messenger mRNA and play important roles in many
physiological processes including growth, differentiation,
apoptosis, cell cycle and development (Bushati N, et al. 2007,
microRNA functions. Annu Rev Cell Dev Biol 23:175-205). Mature
microRNA negatively regulate gene expression by targeting specific
messenger mRNA for cleavage or translation repression. Growing body
of evidence suggests that they are involved in the control of a
wide range of physiological pathway (Bartel et al., 2009). It was
discovered that some microRNAs circulate in bodily fluid. These
circulating microRNA were found to be usefulness biomarker for
diagnosis, prognosis and therapeutics, in particular in cancerology
(Kosaka N. et al., 2010). It was also been discovered than some
miRNA can be transferred from a cell to adjacent cells and induce
targeted inhibition of protein expression in the acceptor cells
(Katakowski M. et al. 2010)
[0022] Table I shows the set of predictive microRNA according to
the invention.
[0023] Some microRNA of the invention are known. They are
identified by their name. All information concerning these
microRNA, in particular their sequence, can be found on
http://www.mirbase.org.
[0024] Other microRNA are new. They are identified by their
sequence and a sequence identification number (SEQ ID NO) was
allocated to each sequences.
TABLE-US-00001 TABLE I set of predictive microRNA MicroRNA
nucleotide sequence MicroRNA name (only for new microRNA) SEQ ID
NO: 6 AGAAGGAACGUCUGGAGUUUGUGCUGGU hsa-mir-103 SEQ ID NO: 7
GUUUAUUCUAGAGAGAAUUCUUACUC SEQ ID NO: 8 AGACUUUCGGCCUAGGAUC
hsa-mir-1826 SEQ ID NO: 9 AGGUUCUGUCGUAUCAAUC hsa-mir-508
hsa-mir-16 SEQ ID NO: 10 CGAGCCGGGCCCUUCCGUC hsa-mir-182 hsa-let-7b
hsa-let-7c hsa-let-7f hsa-let-7a SEQ ID NO: 11 CGGAAAGGAGGGAAAGGGC
hsa-mir-21 SEQ ID NO: 12 CGGGCGGAGAGUAGGCAUC hsa-mir-1826
hsa-mir-92a SEQ ID NO: 13 GUGGAGCCGGGCGUGGACU SEQ ID NO: 14
CUCUUCGUCUGUCCCUAUC hsa-mir-30d hsa-mir-30a SEQ ID NO: 15
UCCAUCAAAGAUCGGCAUC SEQ ID NO: 16 UGUGGGAAGAGGGCAUCCU SEQ ID NO: 17
AGGAGCAAGAGGGCAUCCU SEQ ID NO: 18 GCGAGGCACUGUGGAGAUC SEQ ID NO: 19
AGGCAGGUGAAGGCAUCCU SEQ ID NO: 20 UGGGAUCCCGAGGCAUCCU SEQ ID NO: 21
GCAGAUCUUCCUGGGUGGUGUGGAC SEQ ID NO: 22 GGUAGUGUCGCGGGGGUGC (found
in oocyte) SEQ ID NO: 23 AAGGACUGUGAUCAUUGAA (found in oocyte) SEQ
ID NO: 24 AGCGACGUUUCAUUGAAAA (found in oocyte) SEQ ID NO: 25
GGGGGCUGUAUCAUUGACA (found in oocyte) hsa-mir-1244 hsa-mir-320a
[0025] The inventors have investigated the interaction between
these microRNA and mRNA from genes identified to be interesting
biomarkers in former studies (McKenzie et al., 2004; van Montfoort
et al., 2008; Zhang et al., 2005; Assou et al., 2008; Hamel et al.,
2008; Hamel et al., 2010; Assou et al. 2010; WO2010/118991).
[0026] MicroRNA of the present invention were found to interact
with: [0027] genes whose overexpression is predictive of an oocyte
that will produce, upon fertilization, a viable embryo with a high
implantation rate leading to pregnancy or an embryo with a high
implantation rate leading to pregnancy (group A), [0028] genes
whose overexpression is predictive of a non competent oocyte or
embryo, the embryo being unable to implant (group B), [0029] genes
whose overexpression is predictive of a non competent oocyte or
embryo due to early embryo arrest (group C), [0030] genes whose
overexpression is inversely correlated with embryo quality (group
D), [0031] genes whose overexpression is correlated with embryo
quality (group E).
[0032] Genes are known per se and are identified by their symbol.
More information about these genes as sequences or name
corresponding to the symbol can be found on Targetscan
(http://www.targetscan.org/) and MiRDB
(http://mirdb.or/cgi-bin/search.cgi).
[0033] Tables A, B, C, D and E show the microRNA contingent to
genes with which they interact.
[0034] Some microRNA, as hsa-let7a or hsa-mir-182, interact with
several genes.
[0035] Each table correspond to one group A, B, C, D and E
corresponding to specific oocyte or embryo qualities as capacity of
an embryo to implant or to develop without arrest as described
above.
TABLE-US-00002 TABLE A microRNA interacting with genes of group A
Gene with which the microRNA interacts MicroRNA Gene Gene name
symbol Gene name ID hsa-mir-30d CAMTA1 calmodulin binding
transcription 23261 activator 1 hsa-mir-30a CAMTA1 calmodulin
binding transcription 23261 activator 1 SEQ ID NO: 15 PCK1
phosphoenolpyruvate carboxy- 5105 kinase 1 (soluble) SEQ ID NO: 16
PCK1 phosphoenolpyruvate carboxy- 5105 kinase 1 (soluble) SEQ ID
NO: 17 PCK1 phosphoenolpyruvate carboxy- 5105 kinase 1 (soluble)
SEQ ID NO: 24 SLAMF6 SLAM family member 6 114836 (found in
oocyte)
TABLE-US-00003 TABLE B microRNA interacting with genes of group B
Gene with which the microRNA interacts MicroRNA Gene Gene name
symbol Gene name ID hsa-mir-182 EGR3 early growth response 3 1960
hsa-mir-508 FOSB FBJ murine osteosarcoma viral 2354 oncogene
homolog B SEQ ID NO: 6 FOSB FBJ murine osteosarcoma viral 2354
oncogene homolog B hsa-let-7a GPC6 glypican 6 10082 hsa-mir-103
GPC6 glypican 6 10082 SEQ ID NO: 7 GPC6 'glypican 6 10082 SEQ ID
NO: 8 GPC6 glypican 6 10082 hsa-mir-1826 PDE5A phosphodiesterase
5A, cGMP- 8654 specific SEQ ID NO: 9 PDE5A phosphodiesterase 5A,
cGMP- 8654 specific hsa-mir-508 SLC40A1 solute carrier family 40
(iron- 30061 regulated transporter), member 1
TABLE-US-00004 TABLE C microRNA interacting with genes of group C
Gene with which the microRNA interacts MicroRNA Gene Gene name
symbol Gene name ID hsa-mir-16 G0S2 G0/G1switch 2 50486 SEQ ID NO:
10 GRIK5 glutamate receptor, ionotropic, 2901 kainate 5 hsa-mir-182
IGF1R insulin-like growth factor 1 3480 receptor hsa-mir-320a IGF1R
insulin-like growth factor 1 3480 receptor hsa-let-7b IGF1R
insulin-like growth factor 1 3480 receptor hsa-let-7c IGF1R
insulin-like growth factor 1 3480 receptor hsa-let-7f IGF1R
insulin-like growth factor 1 3480 receptor hsa-let-7a IGF1R
insulin-like growth factor 1 3480 receptor SEQ ID NO: 11 IGF1R
insulin-like growth factor 1 3480 receptor hsa-mir-21 NFIB nuclear
factor I/B 4781 hsa-mir-30d NFIB nuclear factor I/B 4781
hsa-mir-30a NFIB nuclear factor I/B 4781 SEQ ID NO: 12 NFIC
'nuclear factor I/C (CCAAT- 4782 binding transcription factor) SEQ
ID NO: 22 NFIC 'nuclear factor I/C (CCAAT- 4782 (found in oocyte)
binding transcription factor) hsa-mir-1826 RBMS1 RNA binding motif,
single 5937 stranded interacting protein 1
TABLE-US-00005 TABLE D MicroRNA interacting with genes of group D
Gene with which the microRNA interacts MicroRNA Gene Gene name
symbol Gene name ID SEQ ID NO: 23 FAT3 FAT tumor suppressor homolog
3 120114 (found in oocyte) (Drosophila) hsa-mir-92a SOX4 SRY (sex
determining region Y)- 6659 box 4 SEQ ID NO: 13 SOX4 'SRY (sex
determining region Y)- 6659 box 4 SEQ ID NO: 14 SOX4 'SRY (sex
determining region Y)- 6659 box 4
TABLE-US-00006 TABLE E microRNA interacting with genes of group E
Gene with which the microRNA interacts MicroRNA Gene Gene name
symbol Gene name ID SEQ ID NO: 20 EPOR erythropoietin receptor 2057
(found in oocyte) SEQ ID NO: 18 LRCH4 leucine-rich repeats and
calponin 4034 homology (CH) domain contain- ing SEQ ID NO: 19 NLRP1
NLR family, pyrin domain con- 22861 taining 1 SEQ ID NO: 20 PAX8
paired box 8 7849 SEQ ID NO: 21 SLC25A5 solute carrier family 25
(mito- 292 chondrial carrier; adenine nucle- otide translocator),
member 5 hsa-mir-1244 SLC5A12 solute carrier family 5 (sodium/
159963 glucose cotransporter), member 12 hsa-mir-320a SLCO1A2
solute carrier organic anion 6579 transporter family, member
1A2
[0036] Owing to the role of microRNA in post-transcriptional gene
regulation, the microRNA of the invention are involved in the
regulation of genes listed in tables A, B, C, D and E and
subsequently in the associated pregnancy outcome.
[0037] An object of the invention relates to a method for selecting
an oocyte that will produce, upon fertilization, a viable embryo
with a high implantation rate leading to pregnancy, comprising a
step of measuring in a cumulus cell surrounding said oocyte the
expression level of at least 5 microRNA selected from the group
consisting of hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826,
hsa-let-7a-1, hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c,
hsa-let-7f, hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a,
hsa-mir-30d, hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1,
hsa-mir-92a-2, hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974,
hsa-mir-146b, hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a,
SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO:
10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ
ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO:
19, SEQ ID NO: 20 and SEQ ID NO: 21.
[0038] The present invention also relates to a method for selecting
an embryo with a high implantation rate leading to pregnancy,
comprising a step of measuring in a cumulus cell surrounding said
embryo the expression level of at least 5 microRNA selected from
the group consisting of hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826,
hsa-let-7a-1, hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c,
hsa-let-7f, hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a,
hsa-mir-30d, hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1,
hsa-mir-92a-2, hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974,
hsa-mir-146b, hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a,
SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO:
10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ
ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO:
19, SEQ ID NO: 20 and SEQ ID NO: 21.
[0039] Typically, the expression level of 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 or
42 microRNA may be measured.
[0040] In one embodiment, the redundancy is avoided by selecting no
more than one microRNA for each gene listed in table A, B, C, D and
E.
[0041] In one embodiment, the redundancy is avoided by selecting
only one or two microRNA by group A, B, C, D or E.
[0042] In another embodiment, the methods of the present invention
comprises a step of measuring the expression level of at least 5
microRNA selected from the consisting of hsa-mir-103-1,
hsa-mir-103-2, hsa-mir-1826, hsa-let-7b, hsa-let-7c, hsa-mir-1244,
hsa-mir-182, hsa-mir-21, hsa-mir-30a, hsa-mir-30d, hsa-mir-320a,
hsa-mir-508, hsa-mir-92a-1, hsa-mir-92a-2, hsa-mir-16-1,
hsa-mir-16-2, hsa-mir-1974, hsa-mir-146b, hsa-mir-886, hsa-mir-210,
hsa-mir-1979, hsa-mir-125a, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO:
8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ
ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:
17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20 and SEQ ID NO:
21.
[0043] In another embodiment, the methods of the present invention
comprise a step of measuring the expression level of at least 5
microRNA selected from the group consisting of hsa-mir-508,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-103-1, hsa-mir-103-2,
hsa-mir-1974, hsa-mir-1826, SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID
NO: 12.
[0044] Indeed, the inventors have shown that these microRNAs
present the more significant difference in level of expression
between competent oocytes or embryos and oocytes or embryos that
are not competent.
[0045] In another embodiment, the methods of the present invention
comprise a step of measuring the expression level of at least 5
microRNA selected from the group consisting of hsa-mir-508,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-103-1, hsa-mir-103-2,
hsa-mir-1974, hsa-mir-1826, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO:
12, hsa-let-7b, hsa-let-7c, hsa-mir-182, hsa-mir-21, hsa-mir-30a
and hsa-mir-30d.
[0046] Indeed, the inventors have shown that these miRNAs interact
with genes particularly relevant in the prediction of the
competence of oocytes and embryos such as IGF1R and NFIB.
[0047] The present invention also relates to a method for selecting
an oocyte that will produce, upon fertilization, a viable embryo
with a high implantation rate leading to pregnancy or an embryo
with a high implantation rate leading to pregnancy, comprising a
step of measuring in a bodily fluid the expression level of at
least 5 microRNA selected from the group consisting of
hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826, hsa-let-7a-1,
hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c, hsa-let-7f,
hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a, hsa-mir-30d,
hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1, hsa-mir-92a-2,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974, hsa-mir-146b,
hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a, SEQ ID NO: 6,
SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO:
11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ
ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO:
20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO:24 and
SEQ ID NO: 25.
[0048] It is well-known that microRNAs can circulate in bodily
fluid.
[0049] Thus, Zheng et al. (2011) have shown that hsa-mir-182 is
present in plasma and saliva.
[0050] Furthermore, Huang et al. (2009), Lawrie et al. (2008),
Asaga et al. (2011) and Henegan et al. (2010) have respectively
found that hsa-mir-320a, hsa-mir-210, hsa-mir-21 and hsa-let-7a-1
are circulating miRNAs.
[0051] Gunel et al. (2011) have shown that increased hsa-mir-210
levels in maternal serum can be used in noninvasive prenatal
diagnosis. The expression level of microRNA may be measured in
blood, urine, saliva or follicular liquid sample.
[0052] The blood sample to be used in the methods according to the
invention may be a whole blood sample, a serum sample, or a plasma
sample.
[0053] The bodily fluid may be taken from the oocyte donor or the
host of the embryo.
[0054] In one embodiment, the methods of the present invention
comprise a step of measuring the expression level of at least 5
microRNAs selected from the group consisting of hsa-mir-182,
hsa-mir-320a, hsa-mir-210, hsa-mir-21, hsa-let-7a-1.
[0055] The methods of the invention may further comprise a step
consisting of comparing the expression level of the microRNA in the
sample with a control, wherein detecting differential in the
expression level of the microRNA between the sample and the control
is indicative whether the oocyte produces, upon fertilization, a
viable embryo with a high implantation rate leading to pregnancy or
the embryo is with a high implantation rate leading to
pregnancy.
[0056] The control for oocyte may consist in sample comprising
cumulus cells associated with a competent oocyte or a non competent
oocyte or in sample comprising cumulus cells associated with an
embryo that gives rise to a viable foetus.
[0057] Preferably, the control consists in sample comprising
cumulus cells associated with a competent oocyte.
[0058] The control for embryo may consist in sample comprising
cumulus cells associated with an embryo that gives rise to a viable
foetus or in a sample comprising cumulus cells associated with an
embryo that does not give rise to a viable foetus.
[0059] Preferably, the control consists in sample comprising
cumulus cells associated with an embryo that gives rise to a viable
foetus.
[0060] The methods of the invention may further comprise a step of
measuring in a cumulus cell surrounding said oocyte or said embryo
the expression level of one or more genes selected from the group
consisting of ATF3, SIAT6, PRKACA, PLA2G5, GPC6, GOS2, RBMS1, NFIC,
SLC40A1 and WNT6.
[0061] Typically, the method of the invention may comprise a
further step of measuring the expression level of 1, 2, 3, 4, 5, 6,
7, 8, 9 or 10 genes selected from the group consisting of ATF3,
SIAT6, PRKACA, PLA2G5, GPC6, GOS2, RBMS1, NFIC, SLC40A1 and
WNT6.
[0062] Indeed, as described in WO2010/18991, the inventors have
identified a set of 45 genes whose measuring the level of
expression in cumulus cells is predictive of pregnancy outcome.
[0063] After complementary studies, the inventors have determined a
subset of 10 genes comprising ATF3, SIAT6, PRKACA, PLA2G5, GPC6,
GOS2, RBMS1, NFIC, SLC40A1 and WNT6. This subset appeared to be one
of the most reliable set to select an oocyte that will produce,
upon fertilization, a viable embryo with a high implantation rate
leading to pregnancy or an embryo with a high implantation rate
leading to pregnancy in regard of different clinical conditions as
shown in Table F.
TABLE-US-00007 TABLE F Clinical conditions predicted by the set of
predictive genes Gene Symbol Gene name Gene ID B: genes whose
overexpressions are predictive of embryos unable to implant PLA2G5
phospholipase A2, group V 5322 GPC6 glypican 6 10082 ATF3
activating transcription factor 3 467 SIAT6 ST3 beta-galactoside
alpha-2,3-sialyltrans- 6487 ferase 3 PRKACA protein kinase,
cAMP-dependent, catalytic, 5566 alpha SLC40A1 solute carrier family
40 (iron-regulated trans- 30061 porter), member 1 WNT6
wingless-type MMTV integration site family, 7475 member 6 C: genes
whose overexpressions are predictive of early embryo arrest NFIC
nuclear factor I/C (CCAAT-binding trans- 4782 cription factor)
RBMS1 RNA binding motif, single stranded inter- 5937 acting protein
1 G0S2 G0/G1 switch 2 50486
[0064] Preferably, genes and microRNA of the present invention
aren't measured in a redundant way that is to say that if a
microRNA is selected, the gene with which it interacts won't be
selected.
[0065] In one embodiment, to avoid any redundancy, the method of
the invention may comprise a further step of measuring the
expression level of 1 or 2 genes selected from group B and 1 or 2
genes selected from group C.
[0066] Alternatively, said one or more genes may be selected for
example from group B alone or group C alone.
Typically, 1, 2, 3, 4, 5, 6 or 7 genes may be selected from group
B. Typically, 1, 2 or 3 genes may be selected from group C.
[0067] The present invention also relates to a method for selecting
an oocyte that will produce, upon fertilization, a viable embryo
with a high implantation rate leading to pregnancy or an embryo
with a high implantation rate leading to pregnancy, comprising a
step of measuring in the culture medium of cumulus cell having
surrounded said oocyte or said embryo the expression level of at
least 5 microRNA selected from the group consisting of
hsa-mir-103-1, hsa-mir-103-2, hsa-mir-1826, hsa-let-7a-1,
hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c, hsa-let-7f,
hsa-mir-1244, hsa-mir-182, hsa-mir-21, hsa-mir-30a, hsa-mir-30d,
hsa-mir-320a, hsa-mir-508, hsa-mir-92a-1, hsa-mir-92a-2,
hsa-mir-16-1, hsa-mir-16-2, hsa-mir-1974, hsa-mir-146b,
hsa-mir-886, hsa-mir-210, hsa-mir-1979, hsa-mir-125a, SEQ ID NO: 6,
SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO:
11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ
ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO:
20 and SEQ ID NO: 21.
[0068] The methods of the invention are particularly suitable for
assessing the efficacy of an in vitro fertilization treatment.
Accordingly the invention also relates to a method for assessing
the efficacy of a controlled ovarian hyperstimulation (COS)
protocol in a female subject comprising:
[0069] i) providing from said female subject at least one oocyte
with its cumulus cells;
[0070] ii) determining by a method of the invention whether said
oocyte is an oocyte that will produce, upon fertilization, a viable
embryo with a high implantation rate leading to pregnancy e.
[0071] Then after such a method, the embryologist may select the
oocytes that will produce, upon fertilization, a viable embryo with
a high implantation rate leading to pregnancy and in vitro
fertilized them through a classical in vitro fertilization (cIVF)
protocol or under an intracytoplasmic sperm injection (ICSI)
protocol.
[0072] A further object of the invention relates to a method for
monitoring the efficacy of a controlled ovarian hyperstimulation
(COS) protocol comprising:
[0073] i) isolating from said woman at least one oocyte with its
cumulus cells under natural, modified or stimulated cycles;
[0074] ii) determining by a method of the invention whether said
oocyte is an oocyte that will produce, upon fertilization, a viable
embryo with a high implantation rate leading to pregnancy;
[0075] iii) and monitoring the efficacy of COS treatment based on
whether it results in an oocyte that will produce, upon
fertilization, a viable embryo with a high implantation rate
leading to pregnancy.
[0076] The COS treatment may be based on at least one active
ingredient selected from the group consisting of GnRH agonists or
antagonists associated with recombinant FSH or hMG.
[0077] The present invention also relates to a method for
determining whether an embryo is an embryo with a high implantation
rate leading to pregnancy, comprising:
[0078] i) providing an oocyte with its cumulus cells
[0079] ii) in vitro fertilizing said oocyte
[0080] iii) determining whether the embryo that results from step
ii) has a high implantation rate leading to pregnancy by
determining by a method of the invention whether said oocyte of
step i), is an oocyte that will produce, upon fertilization, a
viable embryo with a high implantation rate leading to
pregnancy.
[0081] The methods of the invention are particularly suitable for
enhancing the pregnancy outcome of a female. Accordingly the
invention also relates to a method for enhancing the pregnancy
outcome of a female comprising:
[0082] i) selecting an embryo with a high implantation rate leading
to pregnancy by performing a method of the invention
[0083] iii) implanting the embryo selected at step i) in the uterus
of said female.
[0084] The method as above described will thus help embryologist to
avoid the transfer in uterus of embryos with a poor potential for
pregnancy out come.
[0085] The method as above described is also particularly suitable
for avoiding multiple pregnancies by selecting the competent embryo
able to lead to an implantation and a pregnancy.
[0086] The invention also relates to a kit for performing the
methods as above described, wherein said kit comprises means for
measuring the expression level of the microRNA of Table I that are
indicative whether the oocyte that will produce, upon
fertilization, a viable embryo with a high implantation rate
leading to pregnancy or the embryo with a high implantation rate
leading to pregnancy.
[0087] It is to note that the methods of the invention leads to an
independence from morphological considerations of the embryo. Two
embryos may have the same morphological aspects but by a method of
the invention may present a different implantation rate leading to
pregnancy.
[0088] The methods of the invention are applicable preferably to
women but may be applicable to other mammals (e.g., primates, dogs,
cats, pigs, cows . . . ).
[0089] The present invention also relates to an isolated nucleic
acid molecule having the nucleotide sequence as set forth in SEQ ID
NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ
ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO:
15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ
ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID
NO:24 and SEQ ID NO: 25.
[0090] In one embodiment, the nucleic acid molecule according to
the invention is used in diagnosis of infertility.
[0091] The present invention also relates to a method for the
diagnosis of infertility comprising the step of measuring the
expression level of at least 5 microRNA selected from the group
consisting of SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO:
9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ
ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO:
18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ
ID NO: 23, SEQ ID NO:24 and SEQ ID NO: 25.
[0092] The invention will be further illustrated by the following
figures and examples. However, these examples and figures should
not be interpreted in any way as limiting the scope of the present
invention.
[0093] FIGS. 1 to 4 are diagrams illustrating molecular pathways
and functional groupings between microRNA and biomarkers genes.
[0094] These diagrams were done by using the Ingenuity Pathways
Analysis (IPA) system (Ingenuity Systems, Redwood City, Calif.,
USA) thank to published literature related to above mentioned miRNA
and genes. Above mentioned miRNA and genes were uploaded into IPA
and overlaid onto a global molecular network developed from
information contained in the application. Networks of these miRNA
and genes were generated by IPA based on their connectivity (FIG. 1
to 4). The biological relationship between two nodes is represented
as an edge (line). All lines are supported by at least one
reference in literature, textbook, or from canonical information
stored in the Ingenuity Pathways knowledge database.
Example
[0095] Samples:
[0096] Cumulus cells and mature MII oocytes were collected from
patients consulting for conventional IVF (cIVF) or for ICSI (male
infertility). Cumulus cells were removed from a mature oocyte
(MII). CCs were partially separated mechanically from the
corresponding oocyte as previously described (Assou et al., 2008).
Unfertilized MII oocytes were collected 21 or 44 h after
insemination or after microinjection by ICSI. Cumulus cells and
oocytes were frozen at -80.degree. C. in RLT buffer (RNeasy Kit,
Qiagen, Valencia, Calif.) before miRNA extraction.
[0097] Methods for Determining the Expression Level of the
microRNA:
[0098] Determination of the expression level of the microRNA can be
performed by a variety of techniques known in the art.
[0099] Preferably, small RNA from cumulus cells and mature MII
oocyte samples was extracted after storage of samples at
-80.degree. C. in RLT RNA extraction buffer supplemented with 1
.mu.M of 2-.beta.-mercaptoethanol (M-3148, Sigma) as described in
the manufacturer's protocol (miRNeasy mini Kit, Qiagen, Valencia,
Calif.).
[0100] The 5' RNA adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3' (SEQ ID
NO: 1)) was ligated to the RNA pool with T4 RNA ligase (Ambion) in
the presence of RNase Out (Invitrogen) overnight at 25.degree. C.
The ligation reaction was stopped by the addition of 2.times.
formamide loading dye. The ligated RNA was size fractionated on a
15% TBE urea polyacrylamide gel and a 40-60 base pair fraction was
excised. RNA was eluted from the polyacrylamide gel slice in 600
.mu.L of 0.3 M NaCl overnight at 4.degree. C. The RNA was eluted
from the gel and precipitated as described above followed by
resuspension in DEPC-treated water.
[0101] The 3' RNA adapter ((SEQ ID NO: 2)
5'-pUCGUAUGCCGUCUUCUGCUUGidT-3; p, phosphate; idT, inverted
deoxythymidine) was subsequently ligated to the precipitated RNA
with T4 RNA ligase (Ambion) in the presence of RNase Out
(Invitrogen) overnight at 25.degree. C. The ligation reaction was
stopped by the addition of 10 .mu.L of 2.times. formamide loading
dye. Ligated RNA was size fractionated on a 10% TBE urea
polyacrylamide gel and the 60-100 base pair fraction was excised.
The RNA was eluted from the polyacrylamide gel and precipitated
from the gel as described above and resuspended in 5.0 .mu.L of
DEPC water. The RNA was converted to single-stranded cDNA using
Superscript II reverse transcriptase (Invitrogen) and Illumina's
small RNA RT-Primer (5'-CAAGCAGAAGACGGCATACGA-3' (SEQ ID NO: 3))
following the manufacturer's instructions. The resulting cDNA was
PCR-amplified with Hotstart Phusion DNA Polymerase (NEB) in 15
cycles using Illumina's small RNA primer set (5'-CAAGCAGAAGACG
GCATACGA-3' (SEQ ID NO: 4); 5'-AATGATACGGCGACCACCGA-3' (SEQ ID NO:
5)).
[0102] PCR products were purified on a 12% TBE urea polyacrylamide
gel and eluted into elution buffer (5:1, LoTE: 7.5 M ammonium
acetate) overnight at 4.degree. C. The resulting gel slurry was
passed through a Spin-X filter (Corning) and precipitated by the
addition of 1100 .mu.L of ethanol, 133 .mu.L of 7.5 M ammonium
acetate and 3 .mu.L of mussel glycogen (20 mg/mL; Invitrogen).
After washing with 75% ethanol, the pellet was allowed to air dry
at 25.degree. C. and dissolved in EB buffer (Qiagen) by incubation
at 4.degree. C. for 10 min. The purified PCR products were
quantified on the Agilent DNA 1000 chip and diluted to 10 nM for
sequencing on the Illumina 1G.
[0103] Small RNA Annotation
[0104] We trimmed all reads at 30 nt to reduce the number of unique
sequences. We counted the occurrences of each unique sequence read
and used only the unique sequences for further analysis. All
sequence tags are mapped onto the human reference genome using the
SOAP program following the mirTools web server procedure (Zhu E L,
Zhao F Q, et al., NAR 2010). Subsequently, these unique sequence
tags are also aligned against miRBase (Griffiths-Jones, S et al.
NAR 2008), Rfam (Griffiths-Jones, S et al, NAR 2005), repeat
database produced by RepeatMasker (Tarailo-Graovac, M. and Chen, N.
(2009) Curr. Protoc. Bioinform., Chapter 4, Unit 4. 108.) and the
coding genes of the reference genome. In this way, the unique
sequence tags can be classified into the following categories:
known microRNA, degradation fragments of non-coding RNA, genomic
repeats and mRNA. In case of conflict, a hierarchy is conducted to
assign the tag into a unique category, which starts with non-coding
RNA, then known microRNA and followed by repeat associated RNA and
mRNA. Sequences that are assigned to none of these annotations but
can be mapped to the reference genome are classified as
`unclassified`.
[0105] A microRNA target prediction were done using known microRNA
and TargetScan data (release 4.0) which provides predicted targets
for known microRNAs (http://www.targetscan.org/).
[0106] Differential Expression Detection
[0107] To compare differentially expressed microRNA between
multiple samples, read count of each identified microRNA is
normalized to the total number of microRNA read counts that are
matched to the reference genome in each sample. The statistical
significance (P-value) is inferred based on a Bayesian method
(Audic, S. and Claverie, J. M. (1997) Genome Res.,), which was
developed for analyzing digital gene expression profiles and could
account for the sampling variability of tags with low counts. In
default, a specific microRNA will be deemed to be significantly
differentially expressed when the P-value given by this method is
0.01 and there is at least a 2-fold change in normalized sequence
counts.
[0108] Novel microRNA Prediction
[0109] Sequences that do not fall into above annotation categories
but matched on the reference genome are used to detect candidate
novel microRNA genes. In default, 100 nucleotides of genomic
sequence flanking each side of these sequences are extracted and
their RNA secondary structures are predicted using RNAfold
(Hofacker, I. L. NAR 2003). Novel microRNAs are identified by
folding the flanking genomic sequence using the miRDeep
program.
[0110] Methods for Determining the Expression Level of the
Genes:
[0111] Determination of the expression level of genes as ATF3,
SIAT6, PRKACA, PLA2G5, GPC6, G0S2, RBMS1, NFIC, SLC40A1 or WNT6 can
be performed by a variety of techniques. Generally, the expression
level as determined is a relative expression level.
[0112] Some of these methods are well described in
WO2010/118991.
[0113] Results
[0114] Analysis of level of expression of microRNA in CCs has
permitted to identify candidate microRNA biomarkers.
[0115] Known microRNA
[0116] Known microRNA from CCs group are listed in Table G.
TABLE-US-00008 TABLE G Set of known predicitve microRNA: microRNAs
Length startend location e_value hsa-mir-1974 26 1 . . . 26 45 . .
. 70 2.00E-10 hsa-let-7b 18 1 . . . 18 6 . . . 23 7.00E-06
hsa-mir-1244 22 1 . . . 22 57 . . . 78 4.00E-08 hsa-mir-30d 24 1 .
. . 24 6 . . . 29 3.00E-09 hsa-mir-182 19 1 . . . 19 28 . . . 46
2.00E-06 hsa-mir-146b 24 1 . . . 24 9 . . . 32 3.00E-09 hsa-let-7c
19 1 . . . 19 11 . . . 29 2.00E-06 hsa-mir-92a-2 22 1 . . . 22 48 .
. . 69 4.00E-08 hsa-mir-92a-1 22 1 . . . 22 48 . . . 69 4.00E-08
hsa-mir-886 25 1 . . . 25 15 . . . 39 7.00E-10 hsa-mir-508 22 1 . .
. 22 61 . . . 82 4.00E-08 hsa-mir-320a 18 1 . . . 18 52 . . . 69
7.00E-06 hsa-mir-30a 24 1 . . . 24 6 . . . 29 3.00E-09 hsa-mir-210
19 1 . . . 19 66 . . . 84 2.00E-06 hsa-mir-21 22 1 . . . 22 9 . . .
30 4.00E-08 hsa-mir-1979 24 1 . . . 24 6 . . . 29 3.00E-09
hsa-mir-1826 24 1 . . . 24 1 . . . 24 3.00E-09 hsa-mir-16-2 19 1 .
. . 19 10 . . . 28 2.00E-06 hsa-mir-16-1 19 1 . . . 19 14 . . . 32
2.00E-06 hsa-mir-125a 24 1 . . . 24 15 . . . 38 3.00E-09
hsa-mir-103-2 22 1 . . . 22 48 . . . 69 4.00E-08 hsa-mir-103-1 22 1
. . . 22 48 . . . 69 4.00E-08 hsa-let-7a-3 20 1 . . . 20 4 . . . 23
5.00E-07 hsa-let-7a-2 20 1 . . . 20 5 . . . 24 5.00E-07
hsa-let-7a-1 20 1 . . . 20 6 . . . 25 5.00E-07 hsa-let-7f 22 1 . .
. 22 7 . . . 28 4.00E-07
[0117] The interaction between these microRNA and mRNA from gene
identified to be potential biomarkers by the inventors
(WO2010/118991, Assou et al., 2008; Assou et al. 2010) was studied
by using TargetScan.
[0118] TargetScan predicts biological targets of miRNAs by
searching for the presence of conserved 8mer and 7mer sites that
match the seed region of each miRNA (Lewis et al., 2005). As an
option, nonconserved sites are also predicted. Also identified are
sites with mismatches in the seed region that are compensated by
conserved 3' pairing (Friedman et al., 2009). In mammals,
predictions are ranked based on the predicted efficacy of targeting
as calculated using the context scores of the sites (Grimson et
al., 2007). TargetScanHuman considers matches to annotated human
UTRs and their orthologs, as defined by UCSC whole-genome
alignments. Conserved targeting has also been detected within open
reading frames (ORFs).
Other database as MiRDB (http://mirdb.org/cgi-bin/search.cgi) and
Ingenuity (IPA) have also been used. Some of these interactions are
illustrated in FIGS. 1 to 4.
[0119] New microRNA Biomarkers
[0120] The inventors have identified novel microRNA among the
unclassified sequences in their libraries. After annotation, 5,165
of the microRNA sequences in the CCs library remained unclassified
because they derived from unannotated regions of the human genome.
Novel microRNA were identified. These microRNA regulate the
expression of 7 gene biomarkers such as: (PCK1 (3 microRNA:SEQ ID
NO: 15; SEQ ID NO: 16; SEQ ID NO: 17); GPC6 (2 microRNA:SEQ ID NO:
7, SEQ ID NO: 8); SOX4 (2 microRNA:SEQ ID NO: 13, SEQ ID NO: 14);
SLC25A5 (1 microRNA:SEQ ID NO: 21); NFIC (1 microRNA:SEQ ID NO: 12;
SEQ ID NO: 22); IGF1R (1 microRNA:SEQ ID NO:11); GIRK5 (1
microRNA:SEQ ID NO: 10)).
[0121] Interactions microARN and Genes Identified to be Interesting
Biomarkers
[0122] The inventors have investigated the interaction between
these microRNA and mRNA from genes identified to be interesting
biomarkers in former studies (McKenzie et al., 2004; van Montfoort
et al., 2008; Zhang et al., 2005; Assou et al., 2008; Hamel et al.,
2008; Hamel et al., 2010; Assou et al. 2010; WO2010/118991).
[0123] MiRNA are known to be post-transcriptional regulators that
bind to complementary sequences on target messenger RNA transcripts
(mRNAs), usually resulting in translational repression or target
degradation and gene silencing (Bartel et DP (2009)).
[0124] Thus, without being bound by theory, the under-expression of
most microRNA that interact with a gene whose overexpression is
predictive of a competent oocyte or a competent embryo is
predictive of an oocyte that will produce, upon fertilization, a
viable embryo with a high implantation rate leading to pregnancy or
of an embryo with a high implantation rate leading to
pregnancy.
[0125] In the same way, the under-expression of most microRNA that
interact with a gene whose overexpression is predictive of an
oocyte or an embryo that is not competent is predictive of an
oocyte or an embryo that is not competent.
[0126] For example, SEQ ID NO: 23, hsa-mir-92a, SEQ ID NO: 13 and
SEQ ID NO: 14 interact with genes of group D. Thus, their
under-expression can be predictive of a bad quality embryo.
[0127] Conversely, the overexpression of most microRNA that
interact with a gene whose under-expression is predictive of a
competent oocyte or a competent embryo is predictive of an oocyte
that will produce, upon fertilization, a viable embryo with a high
implantation rate leading to pregnancy or of an embryo with a high
implantation rate leading to pregnancy.
[0128] By extension, the overexpression of most miRNA that interact
with a gene whose overexpression is predictive of embryo unable to
implant, early embryo arrest or a bad quality embryo is predictive
of an oocyte that will produce, upon fertilization, a viable embryo
with a high implantation rate leading to pregnancy or of an embryo
with a high implantation rate leading to pregnancy.
[0129] For example, overexpression of a miRNA interacting with
genes of groups B, C and D can be predictive of an oocyte that will
produce, upon fertilization, a viable embryo with a high
implantation rate leading to pregnancy or of an embryo with a high
implantation rate leading to pregnancy when it is
under-expressed.
CONCLUSION
[0130] CC gene and microRNA expression analysis begins to be a
valuable tool for improving embryo selection, either for fresh
embryo replacement or for freezing. According to our preliminary
data, there is no relationship between the gene expression profile
of CCs and the embryo morphological aspects. It is time to
reconsider the notion that embryos presenting a low grade according
morphological aspects are able to achieve pregnancy. Indeed, during
the last decade, the availability of technical platforms, small RNA
library sequencing and whole genome microarrays has rapidly
generated data on the molecular mechanisms of the CC-oocyte
complex. Today, these technologies provide potential predictive
biomarkers as non-invasive tools for clinical applications.
Finally, this concept reveals the potential of CCs microRNA to
serve as molecular biomarkers for embryo selection.
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Sequence CWU 1
1
25126RNAArtificial SequenceSynthetic oligonucleotide adapter
sequence 1guucagaguu cuacaguccg acgauc 26222RNAArtificial
SequenceSynthetic oligonucleotide adaptersequence 2ucguaugccg
ucuucugcuu gu 22321DNAArtificial SequenceSynthetic oligonucleotide
primer 3caagcagaag acggcatacg a 21421DNAArtificial
SequenceSynthetic oligonucleotide primer 4caagcagaag acggcatacg a
21520DNAArtificial SequenceSynthetic oligonucleotide primer
5aatgatacgg cgaccaccga 20628RNAHomo sapiens 6agaaggaacg ucuggaguuu
gugcuggu 28726RNAHomo sapiens 7guuuauucua gagagaauuc uuacuc
26819RNAHomo sapiens 8agacuuucgg ccuaggauc 19919RNAHomo sapiens
9agguucuguc guaucaauc 191019RNAHomo sapiens 10cgagccgggc ccuuccguc
191119RNAHomo sapiens 11cggaaaggag ggaaagggc 191219RNAHomo sapiens
12cgggcggaga guaggcauc 191319RNAHomo sapiens 13guggagccgg gcguggacu
191419RNAHomo sapiens 14cucuucgucu gucccuauc 191519RNAHomo sapiens
15uccaucaaag aucggcauc 191619RNAHomo sapiens 16ugugggaaga gggcauccu
191719RNAHomo sapiens 17aggagcaaga gggcauccu 191819RNAHomo sapiens
18gcgaggcacu guggagauc 191919RNAHomo sapiens 19aggcagguga aggcauccu
192019RNAHomo sapiens 20ugggaucccg aggcauccu 192125RNAHomo sapiens
21gcagaucuuc cuggguggug uggac 252219RNAHomo sapiens 22gguagugucg
cgggggugc 192319RNAHomo sapiens 23aaggacugug aucauugaa
192419RNAHomo sapiens 24agcgacguuu cauugaaaa 192519RNAHomo sapiens
25gggggcugua ucauugaca 19
* * * * *
References