WO2023202612A1

WO2023202612A1 - The identification of endometrial immune cell densities and clustering analysis in the mid-luteal phase as predictor for pregnancy outcomes

Info

Publication number: WO2023202612A1
Application number: PCT/CN2023/089190
Authority: WO
Inventors: Chi Chiu Wang; Sze Wan HUNG; Tin Chiu LI; Tao Zhang; Pui Wah Jacqueline CHUNG; Chi Wai MAN; Xiaoyan Chen; Yiwei ZHAO
Original assignee: The Chinese University Of Hong Kong
Priority date: 2022-04-19
Filing date: 2023-04-19
Publication date: 2023-10-26

Abstract

Methods of identifying a subject as likely to have a successful implantation and good pregnancy outcomes, kits and methods of using the kits for use in methods of identifying density, spatial distribution, and an amount of endometrial cells in a sample. The methods and kits can use a multiplex immunohistochemical method to stain the endometrium samples with a panel of human antibodies against CD56 for uterine natural killer (uNK) cells, CD3 and CD8 for T cell, CD3 for pan T cells and CD68 for macrophages in order to measure the density of the various immune cells and the clustering levels between them were measured.

Description

THE IDENTIFICATION OF ENDOMETRIAL IMMUNE CELL DENSITIES AND CLUSTERING ANALYSIS IN THE MID-LUTEAL PHASE AS PREDICTOR FOR PREGNANCY OUTCOMES

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Patent Application Serial No. 63/363,226, filed April 19, 2022, which is hereby incorporated by reference in its entirety including any tables, figures, or drawings.

BACKGROUND OF THE INVENTION

In humans, most pregnancy losses occur before or during embryo implantation (Teklenburg et al. 2010) . Indeed, human embryonic aneuploidy has a great effect on reproductive failure (Franasiak et al. 2014) . Preimplantation genetic screening techniques (PGT-A) have shown that the transfer of screened euploid blastocysts can help to lead to a live birth in only just over half of all treatment cycles (Franasiak and Scott 2017) . This phenomenon indicates the importance on maternal-side endometrial assessment toward their multifactorial nature during embryonic implantation process prior to in vitro fertilization (IVF) treatment. Additionally, these endometrial characteristics, including endometrial pattern, endometrial blood flow, distinct endometrial pathology (such as altered hormonal status or inflammation) , endometrial thickness, uterine immune profile, and endometrial immune cells’ distribution relative to endometrial arterioles, have been regarded as potential prognostic factors of IVF treatment (Lédée et al. 2017; Dart et al. 1999; Liu et al. 2014; Donoghue, Paiva, Teh, Cann, Nowell, Rees, Bittinger, Obers, Bulmer, Stern, et al. 2019; Romero, Espinoza, and Mazor 2004) .

In recent years, the association on the variations in maternal endometrial characteristics, especially immune cells count and proportions, across different kinds of reproductive failure have drawn keen interest as predictor for improving pregnancy outcome after IVF. A normal immune profile of endometrium is very important for normal trophoblast invasion, placentation, immune tolerance, etc. Abnormal trophoblast invasion, placentation, and immune tolerance are associated with pregnancy complications, including but not limited to miscarriage, fetal growth restriction, preeclampsia, preterm labor, antepartum hemorrhage, intrauterine fetal death, etc. Based on a meta-analysis from 22 studies comprising of 10724 in vitro fertilization– intracytoplasmic sperm injection (IVF–ICSI) treatment cycles, it suggested that the use of endometrial thickness has a limited capacity to identify pregnancy rates after IVF–ICSI treatment (Kasius et al. 2014) . Similarly, a retrospective study indicated that endometrial CD138 count appears to be a negative prognostic indicator for patients who have experienced previous embryo transfer failure (Fan et al. 2019) . On the other hand, we found that a significant proportion of women with recurrent reproductive failure had a higher uterine natural killer (uNK) cell percentage than women without recurrent reproductive failure (Chen, Mariee, et al. 2017) . Importantly, we further observed an association between the high uNK cell density with subsequent euploid miscarriage in women with a history of recurrent miscarriage (RM) (Chen et al. 2021) . And our recent findings showed that there was significant change of four endometrial immune cell density and a significant increase in clustering between CD68⁺ and CD56⁺ cells in women with recurrent miscarriage when compared with fertile controls (Zhao et al. 2020) .

Therefore, there remains a need for identifying predictors for implantation success and pregnancy outcomes.

BRIEF SUMMARY OF THE INVENTION

The subject invention pertains to methods of identifying a subject as likely to have a successful implantation and good pregnancy outcomes, including giving birth to a live baby, by identifying density, spatial distribution, and amount of endometrial cells in a sample. The subject invention further pertains to kits and methods of using said kits for use in methods of identifying density, spatial distribution, and amount of endometrial cells in a sample. The methods and kits can use a multiplex immunohistochemical method to stain the endometrium samples with a panel of human antibodies against CD56 for uterine natural killer (uNK) cells, CD3 and CD8 for T cell, CD3 for pan T cells, and CD68 for macrophages in order to measure the density of the various immune cells and the clustering levels between each cell type. In certain embodiments, subjects who did not conceive can have a significantly higher density of uNK cells and higher clustering level between uNK cells-and-macrophages than women who did conceive.

In certain embodiments, endometrial cells properties and their clustering characteristics can be obtained about 7 to about 9 days after a luteinizing hormone (LH) surge, including, for example, in the cycle immediately preceding IVF embryo transfer.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Schematic flow diagram of subjects included.

FIGs. 2A-2H. Staining of CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells and CD68⁺ macrophages in selective LH+7 endometrium from pregnant group and non-pregnant women. Multiplex immunostaining of 4 major immune cell types on endometrial specimens obtained 7 days after the luteinizing hormone surge obtained from endometrium of pregnant group (FIG. 2A) and non-pregnant group (FIG. 2B) . After construction of a single-stained library, spectral unmixing allows imaging of single fluorophores representing (FIG. 2C) CD56⁺, (FIG. 2D) CD8⁺, (FIG. 2E) CD8⁺, (FIG. 2F) CD3⁺, (FIG. 2G) CD3⁺CD8⁺, and (FIG. 2H) a composite merged image was created incorporating all the fluorophores present in a single core after multispectral imaging. DAPI (4′, 6-diamidino-2-phenylindole) was used to stain live cell. GE, glandular epithelium; LE, luminal epithelium. Scale bar = 50 μm.

FIGs. 3A-3D. A comparison of four types of endometrial immune cell (CD56⁺ uNK cell (FIG. 3A) ; CD3⁺ CD8⁺ T cells (FIG. 3B) ; CD3⁺ T cells (FIG. 3C) ; CD68⁺ macrophages (FIG. 3D) density between non-CE infertile women which did (Pregnant, n=74) and did not (Non-pregnant, n=44) conceive after IVF-ET treatment.

FIGs. 4A-4E. A comparison of the clustering of different pairs of endometrial immune cells (CD56⁺ with CD68⁺ cell (FIG. 4A) ; CD3⁺ with CD68⁺ cells (FIG. 4B) ; CD3⁺ CD8⁺ with CD68⁺ cells (FIG. 4C) ; CD3⁺ CD8⁺ with CD56⁺ cells (FIG. 4D) ; CD3⁺ with CD56⁺ cells (FIG. 4E) between non-CE infertile women which did (Pregnant, n=74) and did not (Non-pregnant, n=44) conceive after IVF-ET treatment.

FIGs. 5A-5C. ROC analysis of CD56⁺ uNK cell density, CD56⁺ to CD68⁺ cells clustering level, and comprehensive prediction model in predicting clinical pregnancy failure in infertile women. (FIG. 5A) Prognostic value of CD56⁺ uNK cell density, (FIG. 5B) CD56⁺ to CD68⁺ cells clustering level, and (FIG. 5C) comprehensive prediction model in predicting clinical pregnancy failure in in infertile women.

FIGs. 6A-6D. Graphical representation of the AUL levels based on an L-function calculated for the endometrial immune cells clustering level.

DETAILED DISCLOSURE OF THE INVENTION

Selected Definitions

As used herein, the singular forms “a” , “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Furthermore, to the extent that the terms “including” , “includes” , “having” , “has” , “with” , or variants thereof are used in either the detailed description and/or the claims, such terms are intended to be inclusive in a manner similar to the term “comprising” . The transitional terms/phrases (and any grammatical variations thereof) “comprising” , “comprises” , “comprise” , “consisting essentially of” , “consists essentially of” , “consisting” and “consists” can be used interchangeably.

The phrases “consisting essentially of” or “consists essentially of” indicate that the claim encompasses embodiments containing the specified materials or steps and those that do not materially affect the basic and novel characteristic (s) of the claim.

The term “about” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which depends in part on how the value is measured, i.e., the limitations of the measurement system. In the context of compositions containing amounts of ingredients where the term “about” is used, these compositions contain the stated amount of the ingredient with a variation (error range) of 0-10%around the value (X ± 10%) . In other contexts, the term “about” is used provides a variation (error range) of 0-10%around a given value (X ± 10%) . As is apparent, this variation represents a range that is up to 10%above or below a given value, for example, X ± 1%, X ± 2%, X ± 3%, X ± 4%, X ± 5%, X ± 6%, X ± 7%, X ± 8%, X ± 9%, or X ± 10%.

In the present disclosure, ranges are stated in shorthand to avoid having to set out at length and describe each and every value within the range. Any appropriate value within the range can be selected, where appropriate, as the upper value, lower value, or the terminus of the range. For example, a range of 0.1-1.0 represents the terminal values of 0.1 and 1.0, as well as the intermediate values of 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, and all intermediate ranges encompassed within 0.1-1.0, such as 0.2-0.5, 0.2-0.8, 0.7-1.0, etc. Values having at least two significant digits within a range are envisioned, for example, a range of 5-10 indicates all the values between 5.0 and 10.0 as well as between 5.00 and 10.00 including the terminal values. When ranges are used herein, combinations and subcombinations of ranges (e.g., subranges within the disclosed range) and specific embodiments therein are explicitly included. “Subject” refers to an animal, such as a mammal, for example a human. The methods described herein can be useful in both humans and non-human animals. In some embodiments, the subject is a mammal (such as an animal model of disease) , and in some embodiments, the subject is a human. The terms “subject” and “patient” can be used interchangeably. The animal may be for example, humans, pigs, horses, goats, cats, mice, rats, dogs, apes, fish, chimpanzees, orangutans, guinea pigs, hamsters, cows, sheep, birds, chickens, as well as any other vertebrate or invertebrate.

The terms “label, ” “detectable label, “detectable moiety, ” and like terms refer to a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include fluorescent dyes (fluorophores) , luminescent agents, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA) , biotin, enzymes acting on a substrate (e.g., horseradish peroxidase) , thiol, digoxigenin, ³²P and other isotopes, haptens, and proteins which can be made detectable, e.g., by conjugating a radiolabel to an antibody or polymer. The term includes combinations of single labeling agents, e.g., a combination of fluorophores that provides a unique detectable signature, e.g., at a particular wavelength or combination of wavelengths.

As used herein, the phrase “reproductive failure” refers to subfertility, infertility, miscarriage, implantation failure, intrauterine death, or any other pregnancy loss. As used herein, “subfertility” describes a prolonged time span of trying to become pregnant that has not reached a year. Half of women with subfertility will develop to infertility.

As used herein, a “good pregnancy outcome” is measured by successful biochemical pregnancy, clinical pregnancy, on-going pregnancy, and live birth. Biochemical pregnancy also determines a successful implantation, is assessed by a pregnancy test or hCG levels. Clinical pregnancy, on-going pregnancy, and live birth are assessed by ultrasound and a successful delivery.

As used herein, the term “implantation” refers to the stage of reproduction in which the embryo adheres to the wall of the uterus.

The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.

Any compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.

Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.

Use of Endometrial Cells to Identify Likelihood of Implantation and Pregnancy

In certain embodiments, the invention provides a method of identifying a subject as likely to have a successful implantation and good pregnancy outcomes, including giving birth to a live baby, optionally, treating the subject, the method comprising:

(a) determining a density, spatial distribution, or an amount of endometrial cells in a test sample obtained from the subject; and

(b) optionally, obtaining one or more reference values for a density, spatial distribution, or an amount of endometrial cells from a pregnant subject, and

(i) identifying the subject as likely to have a successful implantation and good pregnancy outcomes, including giving birth to a live baby, based on the density, spatial distribution, or the amount of endometrial cells in the subject with effectively equivalent or lower densities and amounts of the endometrial cells and effectively equivalent or lower clustering of two or distinct more endometrial cell types in the test sample as compared to the reference value and, optionally, administering or withholding a therapy to the subject, or

(ii) identifying the subject as not likely to have a successful implantation and good pregnancy outcomes, including giving birth to a live baby, based on the density, spatial distribution, or the amount of endometrial cells in the subject with higher densities and amount of two or more distinct endometrial cell types and higher clustering of endometrial in the test sample as compared to the reference value and, optionally, administering or withholding a therapy to the subject.

In certain embodiments, a therapy can be provided to the subject, such as, for example anti-inflammatory drugs or cell therapy. In certain embodiments, if the number of pro-inflammatory cells increased, the administration of anti-inflammatory drugs, such as, for example, prednisolone can be beneficial for embryo implantation. In certain embodiments, cell therapy, such as, for example, intrauterine transfer of peripheral blood mononuclear cells (PBMC) , regulatory T cells (Tregs) , granulocyte colony stimulating factor (G-CSF) , human chorionic gonadotropin (hCG) , or any combination thereof can adjust the endometrial immune cell profile. Immunotherapeutic approaches for treatment of implantation failure include, for example, anti-inflammatory drugs; immunosuppressants, such as, for example, cyclosporin; hCG; and endometrial scratching for use in regulating macrophages, NK cell and T cell administration, which have previously been described by Abdolmohammadi-Vahid, Samaneh et al. “Novel immunotherapeutic approaches for treatment of infertility. ” Biomedicine &pharmacotherapy = Biomedecine &pharmacotherapie vol. 84 (2016) : 1449-1459. doi: 10.1016/j. biopha. 2016.10.062 (see worldwide website: pubmed. ncbi. nlm. nih. gov/27810339/) ; Marcelo Borges Cavalcante, Ricardo Barini, Joanne Kwak-Kim, “Endometrial scratching for embryo implantation failure-uterine immune biomarkers as a selection criterion” Human Reproduction, Volume 36, Issue 5, May 2021, Pages 1446–1447, doi: 10.1093/humrep/deab061 (see worldwide website: pubmed. ncbi. nlm. nih. gov/33743537/) ; and Schumacher, A. &Zenclussen, A. C., et al. “Human Chorionic Gonadotropin-Mediated Immune Responses That Facilitate Embryo Implantation and Placentation. ” Frontiers in immunology vol. 10 (2019) p. 2896. doi: 10.3389/fimmu. 2019.02896 (see worldwide website: pubmed. ncbi. nlm. nih. gov/31921157/) , each of which is hereby incorporated by reference in its entirety. Additional therapeutics include, for example, intravenous administration of immunoglobulin (IVIG) , intralipids, and granulocyte-macrophage colony-stimulating factor (CM-CSF) .

In certain embodiments, the subject can be experiencing and/or managing reproductive failure or have experience and/or managed reproductive failure in the past. In certain embodiments, reproductive failure can be subfertility, infertility, miscarriage, implantation failure, intrauterine death, or any other pregnancy loss. Alternatively, the subject may not be experiencing and/or managing reproductive failure or have experience and/or managed reproductive failure in the past. In certain embodiments, the subject can be undergoing or have undergone natural conception and/or assisted reproductive technology. In certain embodiments, the assisted reproductive technology can be, for example, in vitro fertilization, in utero semination, or intracytoplasmic sperm injection.

In certain embodiments, the test sample can be from uterine tissue or a biopsy, such as, for example an endometrial biopsy. In certain embodiments, the test sample can be obtained in relation to a luteinizing hormone (LH) surge. The LH surge can signal that ovulation is about to start in the following 36 hours. It can be detected in blood or urine. The range of LH peak in blood is 6.17 to 17.2 IU/L. The LH surge can also be tested in urine with an ovulation predictor kit. When the test line is positive (as dark or darker than the control line) , LH is surging. In preferred embodiments, the sample can be obtained at least about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, or more days after the luteinizing hormone surge. In more preferred embodiments, the sample can be obtained about 1 to about 11, about 2 to about 10, about 3 to about 9, about 5 to about 9, or about 7 to about 9 days after the luteinizing hormone surge.

In certain embodiments, the endometrial cells of a subject can be obtained from the uterine tissue or endometrial biopsy, including from endometrial stromal, epithelial, endothelial, progenitor, stem, or any combination thereof (see, for example, Chen, X., et al., 2017b. and Zhao et al., 2021) . The endometrial cells can be, for example, epithelial, stromal, immune, endothelial, progenitor, stem, or any combination thereof. In preferred embodiments, the endometrial cells can be, for example, T cells, including, for example, pan T cells and/or memory T cells; macrophages; or natural killer cells, including for example, uterine natural killer cells.

In certain embodiments, the endometrial cell samples can undergo immunohistochemical staining, including, for example, a multiplex tissue staining method that can enable multispectral staining on the same specimen regardless of antibody species (see, for example, (Zhao et al. 2020) , which is hereby incorporated by reference in its entirety) . In certain embodiments, cell markers, including CD3, CD8, CD56, CD68, CD4, αβ receptor, and λδ receptor for T cells; CD80, CD86, CD163, and CD206 for macrophage; CD16 and CD49b for NK cells; and/or CD1a for DC cells. Or any combination thereof, can be used to identify the cell type. In certain embodiments, CD3 can be used to identify pan T cells and CD8 can be used to identify tissue resident memory T cells. In certain embodiments, macrophages can be defined by the presence of the marker CD68. In certain embodiments, CD56⁺ immunostaining can be used to determine the presence of uterine natural killer (uNK) cells. In certain embodiments, the density of CD56+ uNK cells can be about 9%to about 30%or about 9.15%to about 27.45%. In certain embodiments, the CD56⁺-to-CD68⁺ cells clustering level can be about 250 to about 800 or about 252.62 to about 757.86. In certain embodiments, the comprehensive prediction model, which contains the 2 significant influence variables (CD56 density and CD56-to-CD68 clustering) , can be about 0.32 to about 0.96.

In certain embodiments, a primary antibody can be used to bind to the cell markers for immunohistochemistry staining. In certain embodiments a secondary polymer or antibody can be used that binds to the primary antibody in order to label the endometrial cells. In certain embodiments, the secondary polymer or antibody can be used with any useful label, including fluorescent labels. Exemplary fluorescent labels include a quantum dot or a fluorophore. Examples of fluorescence labels for use in this method includes fluorescein, 6-FAM^TM (Applied Biosystems, Carlsbad, Calif. ) , TET^TM (Applied Biosystems, Carlsbad, Calif. ) , VIC^TM (Applied Biosystems, Carlsbad, Calif) , MAX, HEX^TM (Applied Biosystems, Carlsbad, Calif) , TYE^TM (ThermoFisher Scientific, Waltham, Mass. ) , TYE665, TYE705, TEX, JOE, Cy^TM (Amersham Biosciences, Piscataway, N. J. ) dyes (Cy2, Cy3, Cy3B, Cy3.5, Cy5, Cy5.5, Cy7) , (Molecular Probes, Inc., Eugene, Oreg. ) , Texas Red-X, (Molecular Probes, Inc., Eugene, Oreg. ) dyes (AlexaFluor 350, AlexaFluor 405, AlexaFluor 430, AlexaFluor 488, AlexaFluor 500, AlexaFluor 532, AlexaFluor 546, AlexaFluor 568, AlexaFluor 594, AlexaFluor 610, AlexaFluor 633, AlexaFluor 647, AlexaFluor 660, AlexaFluor 680, AlexaFluor 700, AlexaFluor 750) , DyLight^TM (ThermoFisher Scientific, Waltham, Mass. ) dyes (DyLight 350, DyLight 405, DyLight 488, DyLight 549, DyLight 594, DyLight 633, DyLight 649, DyLight 755) , ATTO^TM (ATTO-TEC GmbH, Siegen, Germany) dyes (ATTO 390, ATTO 425, ATTO 465, ATTO 488, ATTO 495, ATTO 520, ATTO 532, ATTO 550, ATTO 565, ATTO Rhol01, ATTO 590, ATTO 594, ATTO 610, ATTO 620, ATTO 633, ATTO 635, ATTO 637, ATTO 647, ATTO 647N, ATTO 655, ATTO 665, ATTO 680, ATTO 700, ATTO 725, ATTO 740) , (Molecular Probes, Inc., Eugene, Oreg. ) dyes (BODIPY FL, BODIPY R6G, BODIPY TMR, BODIPY 530/550, BODIPY 558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY 650/665) , HiLyte Fluor^TM (AnaSpec, Fremont, Calif. ) dyes (HiLyte Fluor 488, HiLyte Fluor 555, HiLyte Fluor 594, HiLyte Fluor 647, HiLyte Fluor 680, HiLyte Fluor 750) , AMCA, AMCA-S, Blue (Molecular Probes, Inc., Eugene, Oreg. ) , Cascade Yellow, Coumarin, Hydroxycoumarin, Rhodamine Green^TM-X (Molecular Probes, Inc., Eugene, Oreg. ) , Rhodamine Red^TM-X (Molecular Probes, Inc., Eugene, Oreg. ) , Rhodamine 6G, TMR, ABY^TM (Applied Biosystems, Carlsbad, Calif. ) , TAMRA^TM (Applied Biosystems, Carlsbad, Calif. ) , 5-TAMRA, JUN^TM (Applied Biosystems, Carlsbad, Calif. ) , ROX^TM (Applied Biosystems, Carlsbad, Calif. ) , Oregon (Life Technologies, Grand Island, N. Y. ) , Oregon Green 500, 700 (Li-Cor Biosciences, Lincoln, Nebr. ) , IRDye 800, WeIIRED D2, WeIIRED D3, WeIIRED D4, and640 (Roche Diagnostics GmbH, Mannheim, Germany) , 4-acetamido-4′-isothiocyanatostilbene-2, 2′disulfonic acid; acridine and derivatives such as acridine and acridine isothiocyanate; 4-amino-N- [3-vinylsulfonyl) phenyl] naphthalimide-3, 5 disulfonate, Lucifer Yellow VS; N- (4-anilino-1-naphthyl) maleimide; anthranilamide, Brilliant Yellow; BODIPY fluorophores (4, 4-difluoro-4-bora-3a, 4a-diaza-s-indacenes) ; coumarin and derivatives such as coumarin, 7-amino-4-methylcoumarin (AMC, Coumarin 120) , 7-amino-4-trifluoromethylcoumarin (Coumarin 151) ; cyanosine; DAPDXYL sulfonyl chloride; 4′, 6-diaminidino-2-phenylindole (DAPI) ; 5′, 5″-dibromopyrogallol-sulfonephthalein (Bromopyrogallol Red) ; 7-diethylamino-3- (4′-isothiocyanatophenyl) -4-methylcoumarin; diethylenetriamine pentaacetate; 4, 4′-diisothiocyanatodihydro-stilbene-2, 2′-disulfonic acid; 4,4′-diisothiocyanatostilbene-2, 2′-disulfonic acid; 5- [dimethylamino] naphthalene-1-sulfonyl chloride (DNS, dansyl chloride) ; 4-4′-dimethylaminophenylazo) benzoic acid (DABCYL) ; 4-dimethylaminophenylazophenyl-4′-isothiocyanate (DABITC) ; EDANS (5- [ (2-aminoethyl) amino] naphthalene-1-sulfonic acid) , eosin and derivatives such as eosin isothiocyanate; erythrosin and derivatives such as erythrosin B and erythrosin isothiocyanate; ethidium such as ethidium bromide; fluorescein and derivatives such as 5-carboxyfluorescein (FAM) , hexachlorofluorescenin, 5- (4, 6-dichlorotriazin-2-yl) aminofluorescein (DTAF) , 2′, 7′- dimethoxy-4′, 5′-dichloro-6-carboxyfluorescein (JOE) and fluorescein isothiocyanate (FITC) ; fluorescamine; green fluorescent protein and derivatives such as EBFP, EBFP2, ECFP, and YFP; IAEDANS (5- ( {2- [ (iodoacetyl) amino] ethyl} amino) naphthalene-1-sulfonic acid) , Malachite Green isothiocyanate; 4-methylumbelliferone; orthocresolphthalein; nitrotyrosine; pararosaniline; Phenol Red; B-phycoerytnin; o-phthaldialdehyde; pyrene and derivatives such as pyrene butyrate, 1-pyrenesulfonyl chloride and succinimidyl 1-pyrene butyrate; QSY 7; QSY 9; Reactive Red 4 (Brilliant Red 3B-A) ; rhodamine and derivatives such as 6-carboxy-X-rhodamine (ROX) , rhodamine isothiocyanate, lissamine rhodamine B sulfonyl chloride, rhodamine B, rhodamine 123, sulforhodamine B, sulforhodamine 101 and sulfonyl chloride derivative of sulforhodamine 101 (Texas Red) ; N, N, N′, N-tetramethyl-carboxyrhodamine (TAMRA) ; tetramethyl rhodamine; tetramethyl rhodamine isothiocyanate (TRITC) ; riboflavin; rosolic acid; and terbium chelate derivatives. In some embodiments, bright fluorophores with extinction coefficients >50,000 M^-1 cm^-1 and appropriate spectral matching with the fluorescence detection channels can be used.

In certain embodiments, imaging mass cytometry, multiplexed ion beam imaging, and fluorescence-based multiplexed immunohistochemistry/immunofluorescence (IHC/IF) can be used are all alternatives to the multiplex tissue staining method as described above.

In certain embodiments, the labelled endometrial cells can be counted using a standardized cell counting protocol, including the protocol as described by (Lash et al. 2016) , which is hereby incorporated by reference in its entirety. In certain embodiments, the number of endometrial cells, including, for example, CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells, CD68⁺ macrophages and other cells in the endometrial stroma (CD56^-/CD8^-/CD3^-/CD68^-and DAPI (4′, 6-diamidino-2-phenylindole) stained) can be counted automatically using, for example, Tissue Finder Software 14.0; or, the cells can be counted manually. In certain embodiments, all stromal cells can be counted, including the cells surrounding the blood vessels. The number of endometrial cells, including, for example, CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells and CD68⁺ macrophages, can be calculated as a percentage from all stromal cells.

In certain embodiments, the spatial distribution of the endometrial cells can be determined using an established methodology, as described by (Zhao et al. 2020) , which is hereby incorporated by reference in its entirety. In certain embodiments, the relative spatial distribution of each individual endometrial immune cell can be determined. The spatial distribution can be based on the X and Y position of each single cell in a tissue microarray image to be considered as a bivariate point pattern (see, of example, (Carstens et al. 2017) , which is hereby incorporated by reference in its entirety) . In certain embodiments, this bivariate point pattern can then be characterized by bivariate K-and L-functions, generalized from Ripley’s K-and L-functions (Ripley 1976) . Alternatively, Moran’s I spatial statistic can be used to measure the correlation that occurs among samples that are geographically close, and Semivariogram Analysis can be used to measure the spatial dependence between two observations as a function of the distance between them (see worldwide website: wiki. landscapetoolbox. org/doku. php/spatial_analysis_methods: home) . In certain embodiments, the toolbox ‘spatstat’ in R can be used for the estimation of the L-function (see, for example, (Baddeley, Rubak, and Turner 2015) , which is hereby incorporated by reference in its entirety. Alternatives to spatstat include, for example, splancs; (B.SRowlingson and P. JDiggle 1993) (Bivand 2001) spatial ( (Ripley 2001) (Venables and Ripley 1999) ) , ptproc (Peng 2003) and SSLib (Harte 2003) ) . For each of the tissue microarray images, the L-function can be estimated for a range of r from 0 to 20 μm to represent the enhanced probability for cell–cell contact (see, for example, (Carstens et al. 2017) ; “enhanced probability” is a maximized probability that there will be cell-cell contact. The level of clustering (physical distance) of different pairs of immune cells can be represented by the area under the curve of their L-function (AUL) and a low cell-cell clustering level will correspond to a low AUL value, whereas a high cell-cell clustering level can correspond to a high AUL value. Referring to FIG. 6D, the black line represents LabI =r, blue area represents High AUL, while pink area represent low AUL. Red line represents expected normal distribution. Low cell-cell clustering level is further defined in FIG. 6A. An AUL reference value of 0.5 suggests no discrimination, between about 0.5 to about 0.7 is considered poor, between about 0.7 to about 0.8 is considered acceptable, between about 0.8 to about 0.9 is considered excellent, and above about 0.9 is considered outstanding. High cell-cell clustering level is further defined in FIG. 6B. In certain embodiments, the density of the endometrial cells, including, for example, CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells, and/or CD68⁺ macrophages cells, in subjects not likely to have a successful implantation and good pregnancy outcomes, including giving birth to a live baby, can be significantly higher than those of the pregnant reference subjects. In certain embodiments, clustering of two of more distinct endometrial cell types, including, for example, CD56⁺ uNK cells with CD68⁺macrophages in subjects not likely to have a successful implantation and good pregnancy outcomes, including giving birth to a live baby, can be significantly higher than those of the pregnant reference subjects.

In any aspects or embodiments disclosed herein, subjects having elevated levels of the aforementioned variables show an increase of at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%of the variables relative to levels in a reference sample. Further, in any aspects or embodiments disclosed herein, subjects having lower levels of the aforementioned variables show a decrease of at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%of the variables relative to levels in a reference sample. In any aspects or embodiments disclosed herein, subjects having effectively equivalent levels of the aforementioned variables show levels within about 1%, 2%, 3%, 4%, or 5%of the variables relative to levels in a reference sample.

A further embodiment of the invention provides a kit comprising reagents to carry out the methods of the current invention. In one embodiment, the kit comprises:

(a) instructions for obtaining endometrial cells from uterine tissue or an endometrial biopsy from a subject;

(b) compounds for labelling the endometrial cells; and instructions for labelling the endometrial cells;

(c) instructions for counting the labelled endometrial cells; and

(d) instructions for determining the spatial distribution of each immunostained endometrial cell.

In certain embodiment, the kit provides components for labelling by immunostaining the endometrial cells using, for example one or more primary antibodies, one or more polymers and/or antibodies that bind to the primary antibody, one or more fluorophores and instructions for immunostaining the endometrial cells. In certain embodiments, each of the one or more primary antibodies can bind to CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells, or CD68⁺macrophages.

In certain embodiments, the kit can be used to identify a subject as likely to have a successful implantation and good pregnancy outcomes, including giving birth to a live baby, in which after determining a density, spatial distribution, or an amount of endometrial cells in a test sample obtained from the subject according to the instructions of the kit, one or more reference values for a density, spatial distribution, or an amount of endometrial cells from a pregnant subject can also be determined using the kit. In certain embodiments, the subject can be identified as likely to have a successful implantation and good pregnancy outcomes, including giving birth to a live baby, based on the density, spatial distribution, and/or the amount of endometrial cells in the subject with effectively equivalent or lower densities and amounts of the endometrial cells and effectively equivalent or lower clustering of two or distinct more endometrial cell types in the test sample as compared to the reference value, or the subject can be identified the subject as not likely to have a successful implantation or good pregnancy outcomes, including giving birth to a live baby, based on the density, spatial distribution, and/or the amount of endometrial cells in the subject with higher densities and amount of two or more distinct endometrial cell types and higher clustering of endometrial in the test sample as compared to the reference value.

MATERIALS AND METHODS

Study subjects

Women undergoing embryo transfer during IVF treatment at the Prince of Wales Hospital, The Chinese University of Hong Kong, from September 2017 to December 2019 were recruited for this study. The inclusion criteria were: (a) Non-smoking women between the ages of 20 and 40, (b) normal menstrual cycle (25-35 days) , (c) a single high-quality blastocysts, which was defined as a grade ≥ 4BB (Alpha Scientists in Reproductive and Embryology 2011) , in a natural cycle preceding frozen-thawed embryo transfer with the use of nondonor oocytes. The exclusion criteria included: (a) the presence of hydrosalpinx; (b) structural uterine abnormalities, examined by 3-dimensional (3-D) ultrasonography, such as fibroid, endometrial polyp or intra uterine adhesions; (c) parental chromosomal abnormalities; (d) day-2 (D2) follicle-stimulating hormone (FSH) >10 IU/L or mid-luteal progesterone <30nmol/L; (e) significant medical conditions such as systemic lupus erythematosus which are known to affect the immune system; (f) abnormal thyroid function; and (g) intake of any antibiotics, estrogen or progestogen hormonal therapy, steroid treatment or intrauterine contraceptive device within three months of recruitment.

Ethical approval was obtained from our institutional review board at the Joint Chinese University of Hong Kong-New Territories East Cluster Clinical Research Ethics Committee (CREC Ref: 2015.386; 2014.575) for this study. All patients provided informed consent prior to participation of this study.

Endometrial biopsy

All participants in this study performed daily urine dipstick test from day 9 of the menstrual cycle onwards to detect the luteinizing hormone (LH) surge and endometrial biopsies were precisely obtained on day LH+7 in the non-conception cycles, which is equivalent to day 5–6 after ovulation. Women who did not have a clearly identifiable LH surge were excluded from the study. A Pipelle sampler (Prodimed, Neuilly-en-Thelle, France) or Pipet Curet (Cooper Surgical, Trumbull, CT) was used to obtain endometrial specimens. The specimens were then immediately placed into 10%neutral buffered formalin for overnight fixation at room temperature and then embedded into paraffin wax.

In order to avoid the changes in immune cell density which are related to an underline infective process (such as chronic endometritis (CE) ) , an additional CD138⁺ cell staining was performed by an experienced pathologist who was blinded to the clinical details of the specimen according to our published protocol (Liu et al. 2018) . The presence of CE was defined as CD138⁺ cell count more than 5.15 cells/10 mm², which was based on reference range derived from a normal fertile control population (Liu et al. 2018) .

Multiplex immunohistochemical staining of endometrial immune cells

In this study, the marker CD3 and CD8 were used to identify pan T cells and tissue resident memory T cells, respectively. Macrophages were then defined by the presence of the marker CD68. CD56⁺ immunostaining was used to determine uNK cells. To obtain the optimal result, we undergone stringent testing on the antibodies to ensure they are compatible with paraffin-embedded sections and the multispectral staining. The details on the antibodies for this study can be found in Table 1.

Instead of the traditional immunohistochemical staining of endometrial immune cells, we employed the multiplex tissue staining method (Opal 7-color Manual IHC KT, Akoya Biosciences) . The advantage of this system can enable multispectral staining on the same specimen regardless of antibody species. The tissue process and detailed staining of the immune cells were carried out as described in our previous publication (Zhao et al. 2020) .

Table 1. Protocol for multiplex immunofluorescent staining of CD3⁺, CD8⁺, CD68⁺ and CD56⁺ cells

Note: RT, room temperature; Ms, mouse; Rb, rabbit.

Cell counting methodology

Prior to performing the image-processing, a spectral library was established with the Nuance Image Analysis software (PerkinElmer, Waltham, MA, USA) using multispectral images obtained from single stained slides for each marker and matched-fluorophore to capture all the lights emitted by spectral peaks of all fluorophores (FIGs. 2A-2H) . The cell counting method was referenced from a standardized protocol (Lash et al. 2016) . In brief, the number of CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells, CD68⁺ macrophages and other cells in the endometrial stroma (CD56^-/CD8^-/CD3^-/CD68^-and DAPI stained) were counted automatically usingTissue Finder Software 14.0. For cell counting, 10×20 fields (with at least 8000 stromal cells) were captured using theWorkstation. All stromal cells were counted, including the cells surrounding the blood vessels. The number of CD56⁺ uNK cells, CD8⁺CD3⁺T cells, CD3⁺ T cells and CD68⁺ macrophages were calculated as a percentage from all stromal cells for each image, and the final cell count was reported from an average of at least 4 fields.

Quantification of endometrial immune cells spatial distribution

The spatial distribution was determined using our previous methodology (Zhao et al. 2020) . In brief, under each 200 times microscope vision, the relative spatial distribution of each individual endometrial immune cell was determined. This is based on the X and Y position of each single cell to be considered as a bivariate point pattern (Carstens et al. 2017) . This bivariate point pattern can then be characterized by bivariate K-and L-functions, generalized from Ripley’s K-and L-functions (Ripley 1976) . We used the toolbox ‘spatstat’ in R for the estimation of the L-function (Baddeley, Rubak, and Turner 2015) . For each of the tissue microarray images, the L-function was estimated for a range of r from 0 to 20 μm to represent the enhanced probability for cell–cell contact (Carstens et al. 2017) . The level of clustering (physical distance) of different pairs of immune cells is represented by the area under the curve of their L-function (AUL) and a low cell-cell clustering level will correspond to a low AUL value (FIG. 6A) , whereas a high cell-cell clustering level will correspond to a high AUL value (FIG. 6B) .

IVF procedure

Ovarian stimulation was initiated by human menopausal gonadotropins (Pergonal, Serono) or recombinant follicle-stimulating hormone (Gonad-F, Serono) . The ovulation trigger used was 10,000 U human chorionic gonadotropin (hCG) (Profasi, Serono) administered intramuscularly when three or more leading follicles reached 16 mm or more in diameter on transvaginal ultrasound. Transvaginal oocyte retrieval was performed 36 h after hCG trigger. Luteal support was commenced in the evening of oocyte retrieval in the form of vaginal progesterone, either with 90 mg daily dose Crinone (Merck) or Endometrin (Ferring) 100 mg total dissolved solids. No immunomodulators were given other than progesterone for luteal phase support. Frozen-thawed ET was monitored for endometrial thickness, ovarian activity, and hormonal levels, as described previously (Law et al. 2019) . In this study, used fertilized oocytes culture system (Yeung et al. 2019) and embryo cryopreservation (Zhang et al. 2020) are followed as previously described by our group. Blastocysts were thawed and transferred 5 days after the estimated day of ovulation.

Confirmation of pregnancy

Women who underwent blastocyst transfer in our center are routinely asked to have a blood sample 9 days afterwards for serum β-hCG measurement to verify if pregnancy had occurred and have a transvaginal ultrasonography 23 days after ET to confirm viability and location of the pregnancy. For the purpose of this study, women who have demonstrable fetal heart beats at gestational age of at least 20 weeks formed the pregnant group, and women who had negative serum β-hCG (< 5 mIU/L) 9 days after blastocyst transfer formed the non-pregnant group.

Statistical analysis

Statistical analysis was performed using SPSS version 25.0 (IBM, Chicago, IL, USA) . The normality of distributions was evaluated with the Shapiro-Wilk test. For continuous variables, data were presented as mean ± SD for normally distributed data, or as median with range for variables that were not normally distributed data. Results were analyzed using independent t-test within-group variability in normally distributed data, Wilcoxon; ranking test for unrelated data, and Mann -Whitney-test for variability between groups if not normally distributed. Logistic regression analysis was used to estimate the independent prognostic factors for pregnancy success. The receiver operating characteristic curve (ROC) and the area under the curve (AUC) was used to estimate the prognostic significance of the immune cells in predicting the pregnancy outcome. The validity of markers was measured by the area under the ROC curve. P < 0.05 was considered statistically significant.

All patents, patent applications, provisional applications, and publications referred to or cited herein are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification.

Following are examples that illustrate procedures for practicing the invention. These examples should not be construed as limiting. All percentages are by weight and all solvent mixture proportions are by volume unless otherwise noted.

EXAMPLES

EXAMPLE 1-DEMOGRAPHICS

All participants underwent endometrial scratch around the time of implantation (LH+7) and had IHC staining for CD138. From 128 women consented to participate in this study, 10 patients were excluded due to confirmation of chronic endometritis (CD138⁺ cell count more than 5.15 cells/10 mm²) frozen-thawed single-embryo transfer (FIG. 1) . A total of 118 subjects were included in the analysis with a mean age 35.92 (±3.12) years and mean 22.15 (±2.50) BMI kg/m2. After stratification on pregnancy outcome, there were 74 women in pregnant group and 44 in non-pregnant group. The demographics of the two groups of women were compared in Table 2. There was no significant difference among the demographics and clinicopathological characteristics related to fertility between pregnant group and non-pregnant group.

Table 2. Demographics of women included in the study (n = 118) .

Note: Data are presented as mean ± standard deviation (SD) for parametric data and median (range) for nonparametric data. P value are calculated by the t test (normally distribute variables) or Wilcoxon rank sum test (non-normally distribute variables) . P value <0.05 was considered statistically significant.

EXAMPLE 2-COMPARISON OF CD56+ uNK CELL, CD8+CD3+ T CELL, CD3+ T CELL AND CD68+ MACROPHAGE DENSITIES BETWEEN PREGNANT AND NON-PREGNANT WOMEN

By using multiplex immunohistochemical staining, the detection of CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells and CD68⁺ macrophages which present throughout the stroma in selective LH+7 endometrium from women in pregnant group (FIGs. 2A-2C) and women in non-pregnant group (FIGs. 2D-2F) were observed. Toward analyzing the four immune cells density, the median density of CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells and CD68⁺ macrophages from 74 pregnant controls were 7.66% (range 1.13-21.56%) , 2.53% (range 0.39-7.53%) , 2.99% (range 1.24-6.78%) and 2.88% (range 0.52-10.96%) , respectively (FIGs. 3A-3D) . While for the 44 non-pregnant women, the median density of CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells and CD68⁺ macrophages were 8.94% (range 1.37-27.20%) , 3.07% (range 0.94-10.39%) , 2.74% (range 0.56-6.79%) and 3.38% (range 0.54-7.95%) , respectively (FIGs. 3A-3D) . The density of CD56⁺ uNK cell in non-pregnant women was significantly higher (p = 0.024) than in pregnant controls (FIG. 3A) . On the contrary, the CD8⁺CD3⁺ T cell, CD3⁺ T cell and CD68⁺ macrophage densities between pregnant and non-pregnant women have no significant difference (FIGs. 3B-3D) .

EXAMPLE 3-COMPARISON OF THE CLUSTERING LEVELS OF DIFFERENT PAIRS OF ENDOMETRIAL IMMUNE CELLS BETWEEN PREGNANT AND NON-PREGNANT WOMEN

The level of clustering between any of the 2 endometrial immune cell types (except CD8⁺CD3⁺ T cells which were found to co-localized with CD3⁺ T cells) was represented by the area under the L-function and analyzed using R program. There was a significant increase (p = 0.048) in clustering level between CD56⁺ uNK cells and CD68⁺ macrophages in non-pregnant women when compared with pregnant controls (FIG. 4A) . On the other hand, the clustering of other pairing of immune cells did not show any significant difference between pregnant and non-pregnant women (FIGs. 4B-4E) .

EXAMPLE 4-LOGISTIC REGRESSION ANALYSIS FOR SIGNIFICANT PREDICTORS FOR PREGNANCY SUCCESS

Logistic regression analysis showed CD56⁺ uNK cells density and clustering level between CD56⁺ uNK cells and CD68⁺ macrophages to be significant predictors to pregnancy with a confidence interval (1.023-1.345 and 1.000-1.023, respectively) , and OR (1.173 and 1.012, respectively) . The other variables did not affect the prediction (Table 3) .

Table 3. Logistic regression analysis for significant predictors of pregnancy success among the studied groups.

EXAMPLE 5-PROGNOSTIC SIGNIFICANCE OF CD56⁺ uNK CELLS AND CD56-CD68 CLUSTERING LEVEL AS A PREDICTIVE MODEL FOR PREGNANCY OUTCOME AFTER IVF IN NON-CE PATIENTS

Several ROC curves were drawn for the 118 patients to compare the method of single diagnosis and comprehensive prediction model that predicted pregnancy outcomes based on a published protocol (Pencina et al. 2008) . Based on the logistic regression, the variables of CD56⁺ uNK cells density and CD56-CD68 clustering level were used for the single and comprehensive model evaluation. The areas under the curves (AUC) for CD56⁺ uNK cells density, CD56⁺-to-CD68⁺ cells clustering level, and comprehensive prediction model were 0.629 (95%CI, 0.525–0.733) , 0.609 (95%CI, 0.506-0.712) and 0.656 (95%CI, 0.553–0.760) , respectively (FIGs. 5A-5C and Table 4) . The AUC showed that the comprehensive prediction model provided the highest prediction to pregnancy than those with single model. The cut-off ranges for CD56⁺ uNK cells density, CD56⁺-to-CD68⁺ cells clustering level, and comprehensive prediction model were 9.15～27.45%, 252.62～757.86 and 0.32～0.96 respectively, shown in Table 4.

Table 4. Validity of single diagnosis and comprehensive prediction model on success of pregnancy.

Note: AUC: Area under curve; +PV: Positive predictive value; -PV: Negative predictive value. *: Significant (P < 0.05) ; **: Highly Significant (P < 0.01) .

Comprehensive predictive equation contains the 2 significant influence variables (CD56 density and CD56-to-CD68 clustering) .

EXAMPLE 6-PREDICTIVE MODEL FOR PREGNANCY OUTCOME AFTER IVF IN NON-CE PATIENTS

We employed multiplex staining technique to simultaneously measure the four immune cells density in peri-implantation endometrium on day 7 after LH surge in non-CE infertile women with different pregnancy outcomes. Our result showed that only the density of CD56⁺uNK cells in non-pregnant women were significantly higher than those of the pregnant control subjects. In addition, we found that CD56⁺ uNK cells have higher clustering level with CD68⁺macrophages in non-pregnant women than in pregnant controls. These two indicators synergistically distinguish more patients with pregnancy success than individuals immune cell profiling. Therefore, the combination of two indicators may help to predict clinical pregnancy outcomes after IVF-ET treatment in the non-CE population with increased accuracy.

Many previous studies have shown that CE was associated with recurrent implantation failure or recurrent miscarriage (Liu et al. 2018; Kitaya et al. 2017; McQueen et al. 2015; Johnston-MacAnanny et al. 2010) . Similarly, our team also found there was a significant association between high uNK cell density and CE (Chen et al. 2020) . At the same time, the use of antibiotic therapy was shown to improve pregnancy outcomes in patients suffering from recurrent reproductive failure (Cicinelli et al. 2018; Kitaya et al. 2017; Vitagliano et al. 2018) . However, most previous studies mainly performed on patients with recurrent reproductive failure without identification on the presence CE, with relatively fewer studies focusing on infertile patients who had failed embryo transfer less than three times (Kasius et al. 2011; Fan et al. 2019) . To avoid the altered immune cell density with this underline infective process, a stricter criterion on the exclusion of CE would be necessary.

Around the implantation period, there is a major change in the proportion and number of endometrial immune cells. The uNK cell is one of the most widely studied immune cells for women with reproductive failure. With the density of uNK cells vary greatly in the stroma throughout the whole menstrual cycle, they are the most abundant immune cells in the endometrium and decidua during the late secretory phase and at the window of implantation till early pregnancy (Givan et al. 1997; Bulmer and Lash 2005; Flynn et al. 2000; Moffett-King 2002; Manaster et al. 2008) . The finding in this study regrading uNK cell density is consistent with several previous observations in women with recurrent miscarriage (Tang, Alfirevic, and Quenby 2011; Tuckerman et al. 2007; Chen, Mariee, et al. 2017; Chen et al. 2021; Zhao et al. 2020) , recurrent implantation failure (Tang, Alfirevic, and Quenby 2011; Chen, Mariee, et al. 2017; Tuckerman et al. 2010; Ledee-Bataille et al. 2005) and infertile women (Kofod et al. 2017; Marron, Walsh, and Harrity 2019) when compared to fertile subjects. On the contrary, a few studies including that of Fukui et al., which analyzed uNK cells by flow cytometry in patients undergoing IVF, showed no significant difference in uNK cells density between non-pregnant group and those with successful pregnancy (Fukui et al. 1999) . Similarly, Donoghue et al. also found no difference in uNK cell numbers between women with RIF and those with successful embryo implantation (Donoghue, Paiva, Teh, Cann, Nowell, Rees, Bittinger, Obers, Bulmer, and Stern 2019) . On the other hand, the exact functional properties of uNK cells remains to be elucidated. It has been suggested that they may be a significant source of cytokines to alter the local immune responses. For example, the uNK cells were found to produce IFN-γ and IL-10 following activation with IL-12 and IL-15, which are important during embryo implantation (Eriksson et al. 2004) . In addition, the role of uNK cells in spiral artery remodeling has been reported (Smith et al. 2009; Harris 2010; Robson et al. 2012; Liu et al. 2019) . The presence of uNK cells is often detected aggregated around the spiral arteries and arterioles in both the secretory phase and early pregnancy. Based on their distribution during pregnancy, this may reflect the function of uNK cells in mediating vascular changes for implantation and maintenance of pregnancy (Smith et al. 2009; Chen, Man, et al. 2017) and the direction to initiate decidualization or menstruation (Kimber 2005) . As uNK cells and macrophages are both involved during spiral artery remodeling, they may help to remodel the spiral artery by producing cytokines, growth factors and other factors. In addition, macrophages helped to clear the apoptotic cells and cell debris during spiral artery remodeling (Faas and de Vos 2017) .

Macrophages have also been reported to downregulate the cytotoxicity of uNK cells through the secretion of IL-10 and TGF-β (Yang et al. 2017) . In this study, in accordance with the required cell-cell contact necessary for endometrial immune cells’ biological function, there was significantly increase in clustering of CD56⁺ uNK cells/CD68⁺ macrophages and CD3⁺ T cell/CD68⁺ macrophages in non-pregnant women when compared to pregnant women. This suggested that CD68⁺ macrophages within the direct vicinity of CD56⁺ cells and CD3⁺ T cells to have important biological function. Such that, the measurement of endometrial immune cell-cell contact may improve the comprehension of dysfunctional endometrium in reproductive failure. Based on our results, we suggest that patients with high uNK cell counts be treated appropriately. Non-CE infertile women with high uNK cell counts may not need an antibiotic therapy. Whilst we have observed significant changes in immune cell density and clustering among infertile women, the clinical significance of the observation has yet to be studied the functional changes.

The vast majority of previous studies mainly focused on single endometrial immune cell density to assess endometrial function. However, our study suggests that multiple evaluations can further improve the clinical usefulness of such measurements. Additionally, this study utilized specimens that were precisely timed on day LH+7. With the rapid changes in endometrial morphology and function during the time of implantation, it is very important that the biopsies collected were precisely timed to ensure synchronization. The novelty of the present study lies on the spatial relationship between these endometrial immune cells. This may provide important clues to the role played by immune cell-to-cell interaction during normal and pathological pregnancy. Importantly, our study introduced a novel perspective to aid in the prediction of clinical pregnancy after the frozen-thawed embryo transfer, which may also throw light upon the measurement of endometrial receptivity.

It should be understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and the scope of the appended claims. In addition, any elements or limitations of any invention or embodiment thereof disclosed herein can be combined with any and/or all other elements or limitations (individually or in any combination) or any other invention or embodiment thereof disclosed herein, and all such combinations are contemplated with the scope of the invention without limitation thereto.

EMBODIMENTS

Embodiment 1. A method of identifying a subject as likely to have a successful implantation and give birth to a live baby and treating the subject, the method comprising:

(a) determining a density, spatial distribution, or an amount of endometrial cells in a test sample obtained from the subject about 7 to about 9 days after a luteinizing hormone surge; and

(b) obtaining one or more reference values for a density, spatial distribution, or an amount of endometrial cells from a pregnant subject, and

(i) identifying the subject as likely to have a successful implantation and give birth to a live baby based on the density, spatial distribution, or the amount of endometrial cells about 7 to about 9 days after the luteinizing hormone surge in the subject with effectively equivalent or lower densities and amounts of the endometrial cells and effectively equivalent or lower clustering of two or distinct more endometrial cell types in the test sample as compared to the reference value and administering or withholding a therapy to the subject, or

(ii) identifying the subject as not likely to have a successful implantation and give birth to a live baby based on the density, spatial distribution, or the amount of endometrial cells about 7 to about 9 days after the luteinizing hormone surge in the subject with higher densities and amount of two or more distinct endometrial cell types and higher clustering of endometrial in the test sample as compared to the reference value and administering or withholding a therapy to the subject.

Embodiment 2. The method of embodiment 1, wherein the test sample is from uterine tissue or an endometrial biopsy.

Embodiment 3. The method of embodiment 1, wherein the endometrial cells are epithelial, stromal, immune, endothelial, progenitor, stem, or any combination thereof.

Embodiment 4. The method of embodiment 1, wherein the spatial distribution is the level of physical distance and clustering between individual endometrial cells.

Embodiment 5. The method of embodiment 1, wherein the endometrial cell types are CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells, CD68⁺ macrophages, or any combination thereof.

Embodiment 6. The method of embodiment 1, wherein the one or more reference values are obtained about 7 days after a luteinizing hormone surge.

Embodiment 7. The method of embodiment 1, wherein the subject is managing reproductive failure.

Embodiment 8. The method of embodiment 7, wherein the reproductive failure is subfertility, infertility, miscarriage, implantation failure, or intrauterine death.

Embodiment 9. The method of embodiment 1, wherein the subject is undergoing natural conception or assisted reproductive technology.

Embodiment 10. The method of embodiment 9, wherein the assisted reproductive technology is in vitro fertilization, in utero semination, or intracytoplasmic sperm injection.

Embodiment 11. The method of embodiment 1, wherein the therapy is administration of an anti-inflammatory drug, immunosuppressive drug, intravenous immunoglobulin (IVIG) , intralipids, granulocyte-macrophage colony stimulating factor (CM-CSF) , or cell therapy, endometrial scratching, or any combination thereof.

Embodiment 12. The method of embodiment 11, wherein cell therapy comprises intrauterine transfer of peripheral blood mononuclear cells (PBMC) , regulatory T cells (Tregs) , granulocyte colony stimulating factor (G-CSF) , human chorionic gonadotropin (hCG) , or any combination thereof.

Embodiment 13. The method of embodiment 11, wherein the anti-inflammatory drug is prednisolone, and the immunosuppressive drug is cyclosporin.

Embodiment 14. A kit comprising, in one or more containers:

(b) one or more primary antibodies, one or more polymers, and fluorophore; and instructions for immunostaining the endometrial cells;

(c) instructions for counting the immunostained endometrial cells; and

(d) instructions for determining the spatial distribution of individual immunostained endometrial cells.

Embodiment 15. The kit of embodiment 14, wherein the endometrial cells are epithelial, stromal, immune, endothelial, progenitor, stem, or any combination thereof.

Embodiment 16. The kit of embodiment 14, wherein the one or more primary antibody binds to CD3, CD8, CD68, CD56, CD4, αβ receptor, λδ receptor, CD80, CD86, CD163, CD206, CD16 CD49b, CD1a, or any combination thereof.

Embodiment 17. The kit of embodiment 14, wherein the endometrial cells comprise a T cell, natural killer cell, macrophage, or combination thereof.

Embodiment 18. The kit of embodiment 14, wherein the endometrial cells are obtained about 7 days after a luteinizing hormone surge in the subject.

Embodiment 19. A method of using a kit to determine a density, spatial distribution, and an amount of endometrial cells in a sample obtained from a subject, the method comprising:

(i) obtaining endometrial cells from uterine tissue or an endometrial biopsy from the subject;

(ii) obtaining a kit according to embodiment 14;

(iii) using components of the kit for immunostaining the endometrial cells;

(iv) counting the immunostained endometrial cell; and

(v) determining the spatial distribution of individual immunostained endometrial cells.

Embodiment 20. The method of embodiment 19, further comprising:

(vi) obtaining one or more reference values for a density, spatial distribution, or an amount of endometrial cells from a pregnant subject, and

(i) identifying the subject as likely to have a successful implantation and give birth to a live baby based on the density, spatial distribution, or the amount of endometrial cells in the subject with effectively equivalent or lower densities and amounts of the endometrial cells and effectively equivalent or lower clustering of the two of more distinct endometrial cell types in the test sample as compared to the reference value, or

(ii) identifying the subject as not likely to have a successful implantation and give birth to a live baby based on the density, spatial distribution, or the amount of endometrial cells in the subject with higher densities and amount of the endometrial cells and higher clustering of two or more distinct endometrial cell types in the test sample as compared to the reference value.

Embodiment 21. The method of embodiment 19, wherein the endometrial cells comprise a T cell, natural killer cells, macrophage, or combination thereof.

Embodiment 22. The method of embodiment 19, wherein the endometrial cells are epithelial, stromal, immune, endothelial, progenitor, stem, or any combination thereof.

Embodiment 23. The method of embodiment 19, wherein the one or more primary antibody binds to CD3, CD8, CD68, CD56, CD4, αβ receptor, λδ receptor, CD80, CD86, CD163, CD206, CD16 CD49b, CD1a, or any combination thereof.

Embodiment 24. The method of embodiment 19, wherein the endometrial cells are obtained about 7 days after a luteinizing hormone surge.

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Claims

A method of identifying a subject as likely to have a successful implantation and give birth to a live baby and treating the subject, the method comprising:

(a) determining a density, spatial distribution, or an amount of endometrial cells in a test sample obtained from the subject about 7 to about 9 days after a luteinizing hormone surge; and

(b) obtaining one or more reference values for a density, spatial distribution, or an amount of endometrial cells from a pregnant subject, and

(i) identifying the subject as likely to have a successful implantation and give birth to a live baby based on the density, spatial distribution, or the amount of endometrial cells about 7 to about 9 days after the luteinizing hormone surge in the subject with effectively equivalent or lower densities and amounts of the endometrial cells and effectively equivalent or lower clustering of two or distinct more endometrial cell types in the test sample as compared to the reference value and administering or withholding a therapy to the subject, or

(ii) identifying the subject as not likely to have a successful implantation and give birth to a live baby based on the density, spatial distribution, or the amount of endometrial cells about 7 to about 9 days after the luteinizing hormone surge in the subject with higher densities and amount of two or more distinct endometrial cell types and higher clustering of endometrial in the test sample as compared to the reference value and administering or withholding a therapy to the subject.
The method of claim 1, wherein the test sample is from uterine tissue or an endometrial biopsy.
The method of claim 1, wherein the endometrial cells are epithelial, stromal, immune, endothelial, progenitor, stem, or any combination thereof.
The method of claim 1, wherein the spatial distribution is the level of physical distance and clustering between individual endometrial cells.
The method of claim 1, wherein the endometrial cell types are CD56⁺ uNK cells, CD8⁺CD3⁺ T cells, CD3⁺ T cells, CD68⁺ macrophages, or any combination thereof.
The method of claim 1, wherein the one or more reference values are obtained about 7 days after a luteinizing hormone surge.
The method of claim 1, wherein the subject is managing reproductive failure.
The method of claim 7, wherein the reproductive failure is subfertility, infertility, miscarriage, implantation failure, or intrauterine death.
The method of claim 1, wherein the subject is undergoing natural conception or assisted reproductive technology.
The method of claim 9, wherein the assisted reproductive technology is in vitro fertilization, in utero semination, or intracytoplasmic sperm injection.
The method of claim 1, wherein the therapy is administration of an anti-inflammatory drug, immunosuppressive drug, intravenous immunoglobulin (IVIG) , intralipids, granulocyte-macrophage colony stimulating factor (CM-CSF) , or cell therapy, endometrial scratching, or any combination thereof.
The method of claim 11, wherein cell therapy comprises intrauterine transfer of peripheral blood mononuclear cells (PBMC) , regulatory T cells (Tregs) , granulocyte colony stimulating factor (G-CSF) , human chorionic gonadotropin (hCG) , or any combination thereof.
The method of claim 11, wherein the anti-inflammatory drug is prednisolone, and the immunosuppressive drug is cyclosporin.
A kit comprising, in one or more containers:

(a) instructions for obtaining endometrial cells from uterine tissue or an endometrial biopsy from a subject;

(b) one or more primary antibodies, one or more polymers, and fluorophore; and instructions for immunostaining the endometrial cells;

(c) instructions for counting the immunostained endometrial cells; and

(d) instructions for determining the spatial distribution of individual immunostained endometrial cells.
The kit of claim 14, wherein the endometrial cells are epithelial, stromal, immune, endothelial, progenitor, stem, or any combination thereof.
The kit of claim 14, wherein the one or more primary antibody binds to CD3, CD8, CD68, CD56, CD4, αβ receptor, λδ receptor, CD80, CD86, CD163, CD206, CD16 CD49b, CD1a, or any combination thereof.
The kit of claim 14, wherein the endometrial cells comprise a T cell, natural killer cell, macrophage, or combination thereof.
The kit of claim 14, wherein the endometrial cells are obtained about 7 days after a luteinizing hormone surge in the subject.
A method of using a kit to determine a density, spatial distribution, and an amount of endometrial cells in a sample obtained from a subject, the method comprising:

(i) obtaining endometrial cells from uterine tissue or an endometrial biopsy from the subject;

(ii) obtaining a kit according to claim 14;

(iii) using components of the kit for immunostaining the endometrial cells;

(iv) counting the immunostained endometrial cell; and

(v) determining the spatial distribution of individual immunostained endometrial cells.
The method of claim 19, further comprising:

(vi) obtaining one or more reference values for a density, spatial distribution, or an amount of endometrial cells from a pregnant subject, and

(i) identifying the subject as likely to have a successful implantation and give birth to a live baby based on the density, spatial distribution, or the amount of endometrial cells in the subject with effectively equivalent or lower densities and amounts of the endometrial cells and effectively equivalent or lower clustering of the two of more distinct endometrial cell types in the test sample as compared to the reference value, or

(ii) identifying the subject as not likely to have a successful implantation and give birth to a live baby based on the density, spatial distribution, or the amount of endometrial cells in the subject with higher densities and amount of the endometrial cells and higher clustering of two or more distinct endometrial cell types in the test sample as compared to the reference value.
The method of claim 19, wherein the endometrial cells comprise a T cell, natural killer cells, macrophage, or combination thereof.
The method of claim 19, wherein the endometrial cells are epithelial, stromal, immune, endothelial, progenitor, stem, or any combination thereof.
The method of claim 19, wherein the one or more primary antibody binds to CD3, CD8, CD68, CD56, CD4, αβ receptor, λδ receptor, CD80, CD86, CD163, CD206, CD16 CD49b, CD1a, or any combination thereof.
The method of claim 19, wherein the endometrial cells are obtained about 7 days after a luteinizing hormone surge.