1
|
Gil MA, Cambra JM, Rodriguez-Martinez H, Cuello C, Parrilla I, Martinez EA. In-depth proteome characterization of endometrium and extraembryonic membranes during implantation in pig. J Anim Sci Biotechnol 2024; 15:43. [PMID: 38468318 DOI: 10.1186/s40104-024-01002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/24/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Proteome characterization of the porcine endometrium and extraembryonic membranes is important to understand mother-embryo cross-communication. In this study, the proteome of the endometrium and chorioallantoic membrane was characterized in pregnant sows (PS) during early gestation (d 18 and 24 of gestation) and in the endometrium of non-pregnant sows (NPS) during the same days using LC-MS/MS analysis. The UniProtKB database and ClueGO were used to obtain functional Gene Ontology annotations and biological and functional networks, respectively. RESULTS Our analysis yielded 3,254 and 3,457 proteins identified in the endometrium of PS and NPS, respectively; of these, 1,753 being common while 1,501 and 1,704 were exclusive to PS and NPS, respectively. In addition, we identified 3,968 proteins in the extraembryonic membranes of PS. Further analyses of function revealed some proteins had relevance for the immune system process and biological adhesion in endometrium while the embryonic chorion displayed abundance of proteins related to cell adhesion and cytoskeletal organization, suggesting they dominated the moment of endometrial remodeling, implantation and adhesion of the lining epithelia. Data are available via ProteomeXchange with identifier PXD042565. CONCLUSION This is the first in-depth proteomic characterization of the endometrium and extraembryonic membranes during weeks 3 to 4 of gestation; data that contribute to the molecular understanding of the dynamic environment during this critical period, associated with the majority of pregnancy losses.
Collapse
Affiliation(s)
- Maria A Gil
- Department of Medicine and Animal Surgery, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Pascual Parrilla), Murcia, Spain
| | | | - Heriberto Rodriguez-Martinez
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynaecology, Linköping University, Linköping, Sweden
| | - Cristina Cuello
- Department of Medicine and Animal Surgery, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Pascual Parrilla), Murcia, Spain
| | - Inmaculada Parrilla
- Department of Medicine and Animal Surgery, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain.
- Institute for Biomedical Research of Murcia (IMIB-Pascual Parrilla), Murcia, Spain.
| | - Emilio A Martinez
- Department of Medicine and Animal Surgery, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Pascual Parrilla), Murcia, Spain
| |
Collapse
|
2
|
Jamwal S, Jena MK, Tyagi N, Kancharla S, Kolli P, Mandadapu G, Kumar S, Mohanty AK. Proteomic Approaches to Unravel the Molecular Dynamics of Early Pregnancy in Farm Animals: An In-Depth Review. J Dev Biol 2023; 12:2. [PMID: 38248867 PMCID: PMC10801625 DOI: 10.3390/jdb12010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Infertility is a major problem in farm animals, which has a negative economic effect on farm industries. Infertility can be defined as the inability of animals to achieve a successful pregnancy. Early pregnancy is crucial to establish a successful pregnancy, and it is reported that 70-80% and 20-30% of total embryonic loss occur in cattle and pigs, respectively, during the first month of pregnancy. The advanced high-throughput proteomics techniques provide valuable tools for in-depth understanding of the implantation process in farm animals. In the present review, our goal was to compile, assess, and integrate the latest proteomic research on farm animals, specifically focused on female reproduction, which involves endometrial tissues, uterine fluids, oviductal fluids, and microRNAs. The series of studies has provided in-depth insights into the events of the implantation process by unfolding the molecular landscape of the uterine tract. The discussed data are related to pregnant vs. non-pregnant animals, pregnancy vs. oestrous cycle, different days of the early pregnancy phase, and animals with uterine infections affecting reproduction health. Some of the studies have utilized non-invasive methods and in vitro models to decipher the molecular events of embryo-maternal interaction. The proteomics data are valuable sources for discovering biomarkers for infertility in ruminants and new regulatory pathways governing embryo-uterine interaction, endometrium receptivity, and embryonic development. Here, we envisage that the identified protein signatures can serve as potential therapeutic targets and biomarkers to develop new therapeutics against pregnancy diseases.
Collapse
Affiliation(s)
- Shradha Jamwal
- Proteomics and Structural Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India; (S.J.); (N.T.); (S.K.)
| | - Manoj Kumar Jena
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Nikunj Tyagi
- Proteomics and Structural Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India; (S.J.); (N.T.); (S.K.)
| | - Sudhakar Kancharla
- Devansh Lab Werks, 234 Aquarius Drive, Homewood, AL 35209, USA; (S.K.); (G.M.)
| | - Prachetha Kolli
- Microgen Health Inc., 14225 Sullyfield Cir Suite E, Chantilly, VA 20151, USA;
| | - Gowtham Mandadapu
- Devansh Lab Werks, 234 Aquarius Drive, Homewood, AL 35209, USA; (S.K.); (G.M.)
| | - Sudarshan Kumar
- Proteomics and Structural Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India; (S.J.); (N.T.); (S.K.)
| | - Ashok Kumar Mohanty
- ICAR–Central Institute for Research on Cattle, Meerut Cantt 250001, Uttar Pradesh, India
| |
Collapse
|
3
|
Li W, Liu M, Zhou M, Zhou X, Zhang D, Duan J, Zhang A, Xu B. Downregulation of SEPTIN11 inhibits endometrial epithelial cell adhesive function in patients with elevated peripheral blood natural killer cell counts. Reprod Biomed Online 2023; 47:103203. [PMID: 37349244 DOI: 10.1016/j.rbmo.2023.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/31/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
RESEARCH QUESTION What is the underlying mechanism of IVF and embryo transfer (IVF-ET) failure in patients with elevated peripheral blood natural killer cell (pNK) counts? DESIGN Patients undergoing IVF-ET cycles for tubal obstruction or pelvic adhesion (n = 486) were assigned to three groups: high (CD56+CD16+pNK >30% [n = 49]); medium (15< CD56+CD16+pNK ≤30% [n = 211]); and normal pNK groups (5≤ CD56+CD16+pNK ≤15% [n = 226]). Their general condition, previous pregnancy history and IVF outcomes were compared. Uterine fluid and endometrial tissue from patients in the high and normal pNK groups were collected during the mid-secretory phase and studied to elucidate the molecular mechanism underlying impaired endometrial receptivity. RESULTS The highest incidence of IVF-ET cycles (P < 0.0001) and biochemical pregnancy losses (P < 0.0001), and lowest implantation and clinical pregnancy rates (both P < 0.0001), were observed in patients with pNK over 30%. No significant difference was found in the number of previous miscarriages and rate of spontaneous miscarriage in IVF outcomes. Lower Septin11 (SEPT11) expression in the uterine fluid and endometrial epithelial cells (EEC), and higher endometrial IFN-γ, was observed in patients with high pNK. Ishikawa cell and human endometrial epithelial cell (HEEC) adhesion was inhibited after SEPT11 knock-down. Elevated IFN-γ decreased the SEPT11 protein levels in Ishikawa cells and HEECs. CONCLUSIONS CD56+CD16+pNK above 30% may be a threshold for adverse IVF-ET outcomes. Low SEPT11 expression in EEC inhibits cell adhesion, which may cause impaired endometrial receptivity in patients with elevated pNK. The level of SEPT11 in mid-secretory uterine fluid could serve as a non-invasive marker to assess endometrial receptivity in these patients.
Collapse
Affiliation(s)
- Wenzhu Li
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mengyu Liu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingjuan Zhou
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaowei Zhou
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dan Zhang
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingru Duan
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Aijun Zhang
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Bufang Xu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| |
Collapse
|
4
|
Geisert RD, Johns DN, Pfeiffer CA, Sullivan RM, Lucas CG, Simintiras CA, Redel BK, Wells KD, Spencer TE, Prather RS. Gene editing provides a tool to investigate genes involved in reproduction of pigs. Mol Reprod Dev 2023; 90:459-468. [PMID: 35736243 DOI: 10.1002/mrd.23620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/08/2022]
Abstract
CRISPR-Cas9 gene editing technology provides a method to generate loss-of-function studies to investigate, in vivo, the specific role of specific genes in regulation of reproduction. With proper design and selection of guide RNAs (gRNA) designed to specifically target genes, CRISPR-Cas9 gene editing allows investigation of factors proposed to regulate biological pathways involved with establishment and maintenance of pregnancy. The advantages and disadvantages of using the current gene editing technology in a large farm species is discussed. CRISPR-Cas9 gene editing of porcine conceptuses has generated new perspectives for the regulation of endometrial function during the establishment of pregnancy. The delicate orchestration of conceptus factors facilitates an endometrial proinflammatory response while regulating maternal immune cell migration and expansion at the implantation site is essential for establishment and maintenance of pregnancy. Recent developments and use of endometrial epithelial "organoids" to study endometrial function in vitro provides a future method to screen and target specific endometrial genes as an alternative to generating a gene edited animal model. With continuing improvements in gene editing technology, future researchers will be able to design studies to enhance our knowledge of mechanisms essential for early development and survival of the conceptus.
Collapse
Affiliation(s)
- Rodney D Geisert
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Destiny N Johns
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Caroline A Pfeiffer
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Riley M Sullivan
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Caroline G Lucas
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | | | - Bethany K Redel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Kevin D Wells
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Randall S Prather
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| |
Collapse
|
5
|
DAS MONTI, DE ANKAN, BEHERA PARTHASARATHI, ALI MOHAMMADAYUB, SUBUDHI PRASANTKUMAR, KALITA GIRIN, KAYINA ASHULIKHOZHIIO, GALI JAGANMOHANARAO. Porcine salivary proteome analysis identifies potential early pregnancy-specific protein biomarkers. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2023. [DOI: 10.56093/ijans.v93i2.119316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Early diagnosis of pregnancy is of utmost importance to optimize profit in pig husbandry. Identifying candidate protein biomarkers for early diagnosis of pregnancy in a non-invasive sample such as saliva may produce a colossallead to accomplish the purpose. Therefore, in this study, comparative salivary proteome profile of day 12 of gestation, representing elongation of blastocysts stage and non-pregnant sows was explored by label-free quantitation (LFQ) based mass spectrometry approach to identify early pregnancy biomarkers. A total of 115 proteins were identified as differentially expressed proteins (DEPs) with significant difference between non-pregnant and early pregnancy groups. Among the DEPs, majority of the proteins (82 out of 115 DEPs) were found to be down-regulated in early pregnancy group (fold change >2) compared to non-pregnant control. Functional classification and pathway analysis of the DEPs revealed involvement of most of the proteins in integrin signalling pathways, blood coagulation, carbohydrate metabolism, oxidative stress response and regulation of protein folding. Few DEPs with higher fold change during early pregnancy such as thioredoxin, heat shock 70 kDa protein 1A, alpha 1-S haptoglobin, and glutathione S-transferase pi 1 may have potential as biomarkers for early pregnancy diagnosis in pigs based on their recognized role in different pregnancy related activities. Overall, our results provide a set of salivary proteins which can be used as potential biomarkers for early pregnancy diagnosis after large scale validation.
Collapse
|
6
|
Adur MK, Seibert JT, Romoser MR, Bidne KL, Baumgard LH, Keating AF, Ross JW. Porcine endometrial heat shock proteins are differentially influenced by pregnancy status, heat stress, and altrenogest supplementation during the peri-implantation period. J Anim Sci 2022; 100:6620802. [PMID: 35772767 PMCID: PMC9246672 DOI: 10.1093/jas/skac129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/08/2022] [Indexed: 12/11/2022] Open
Abstract
Heat stress (HS) deleteriously affects multiple components of porcine reproduction and is causal to seasonal infertility. Environment-induced hyperthermia causes a HS response (HSR) typically characterized by increased abundance of intracellular heat shock proteins (HSP). Gilts exposed to HS during the peri-implantation period have compromised embryo survival, however if (or how) HS disrupts the porcine endometrium is not understood. Study objectives were to evaluate the endometrial HSP abundance in response to HS during this period and assess the effect of oral progestin (altrenogest; ALT) supplementation. Postpubertal gilts (n = 42) were artificially inseminated during behavioral estrus (n = 28) or were kept cyclic (n = 14), and randomly assigned to thermal neutral (TN; 21 ± 1 °C) or diurnal HS (35 ± 1 °C for 12 h/31.6 ± 1 °C for 12 h) conditions from day 3 to 12 postestrus (dpe). Seven of the inseminated gilts from each thermal treatment group received ALT (15 mg/d) during this period. Using quantitative PCR, transcript abundance of HSP family A (Hsp70) member 1A (HSPA1A, P = 0.001) and member 6 (HSPA6, P < 0.001), and HSP family B (small) member 8 (HSB8, P = 0.001) were increased while HSP family D (Hsp60) member 1 (HSPD1, P = 0.01) was decreased in the endometrium of pregnant gilts compared to the cyclic gilts. Protein abundance of HSPA1A decreased (P = 0.03) in pregnant gilt endometrium due to HS, while HSP family B (small) member 1 (HSPB1) increased (P = 0.01) due to HS. Oral ALT supplementation during HS reduced the transcript abundance of HSP90α family class B member 1 (HSP90AB1, P = 0.04); but HS increased HSP90AB1 (P = 0.001), HSPA1A (P = 0.02), and HSPA6 (P = 0.04) transcript abundance irrespective of ALT. ALT supplementation decreased HSP90α family class A member 1 (HSP90AA1, P = 0.001) protein abundance, irrespective of thermal environment, whereas ALT only decreased HSPA6 (P = 0.02) protein abundance in TN gilts. These results indicate a notable shift of HSP in the porcine endometrium during the peri-implantation period in response to pregnancy status and heat stress.
Collapse
Affiliation(s)
- Malavika K Adur
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jacob T Seibert
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Matthew R Romoser
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Katie L Bidne
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Lance H Baumgard
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Aileen F Keating
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jason W Ross
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
7
|
Abundance of plasma proteins in response to divergent ratios of dietary ω6:ω3 fatty acids in gestating and lactating sows using a quantitative proteomics approach. J Proteomics 2022; 260:104562. [DOI: 10.1016/j.jprot.2022.104562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/07/2022] [Accepted: 03/15/2022] [Indexed: 11/23/2022]
|
8
|
Yang Q, Liu J, Wang Y, Zhao W, Wang W, Cui J, Yang J, Yue Y, Zhang S, Chu M, Lyu Q, Ma L, Tang Y, Hu Y, Miao K, Zhao H, Tian J, An L. A proteomic atlas of ligand-receptor interactions at the ovine maternal-fetal interface reveals the role of histone lactylation in uterine remodeling. J Biol Chem 2021; 298:101456. [PMID: 34861240 PMCID: PMC8733267 DOI: 10.1016/j.jbc.2021.101456] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023] Open
Abstract
Well-orchestrated maternal–fetal cross talk occurs via secreted ligands, interacting receptors, and coupled intracellular pathways between the conceptus and endometrium and is essential for successful embryo implantation. However, previous studies mostly focus on either the conceptus or the endometrium in isolation. The lack of integrated analysis impedes our understanding of early maternal–fetal cross talk. Herein, focusing on ligand–receptor complexes and coupled pathways at the maternal–fetal interface in sheep, we provide the first comprehensive proteomic map of ligand–receptor pathway cascades essential for embryo implantation. We demonstrate that these cascades are associated with cell adhesion and invasion, redox homeostasis, and the immune response. Candidate interactions and their physiological roles were further validated by functional experiments. We reveal the physical interaction of albumin and claudin 4 and their roles in facilitating embryo attachment to endometrium. We also demonstrate a novel function of enhanced conceptus glycolysis in remodeling uterine receptivity by inducing endometrial histone lactylation, a newly identified histone modification. Results from in vitro and in vivo models supported the essential role of lactate in inducing endometrial H3K18 lactylation and in regulating redox homeostasis and apoptotic balance to ensure successful implantation. By reconstructing a map of potential ligand–receptor pathway cascades at the maternal–fetal interface, our study presents new concepts for understanding molecular and cellular mechanisms that fine-tune conceptus–endometrium cross talk during implantation. This provides more direct and accurate insights for developing potential clinical intervention strategies to improve pregnancy outcomes following both natural and assisted conception.
Collapse
Affiliation(s)
- Qianying Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juan Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yue Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wei Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wenjing Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian Cui
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiajun Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuan Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Meiqiang Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingji Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lizhu Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yawen Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yupei Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Miao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haichao Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianhui Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| |
Collapse
|
9
|
Molecular Characterisation of Uterine Endometrial Proteins during Early Stages of Pregnancy in Pigs by MALDI TOF/TOF. Int J Mol Sci 2021; 22:ijms22136720. [PMID: 34201586 PMCID: PMC8267828 DOI: 10.3390/ijms22136720] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/08/2023] Open
Abstract
The molecular mechanism underlying embryonic implantation is vital to understand the correct communications between endometrium and developing conceptus during early stages of pregnancy. This study’s objective was to determine molecular changes in the uterine endometrial proteome during the preimplantation and peri-implantation between 9 days (9D), 12 days (12D), and 16 days (16D) of pregnant Polish Large White (PLW) gilts. 2DE-MALDI-TOF/TOF and ClueGOTM approaches were employed to analyse the biological networks and molecular changes in porcine endometrial proteome during maternal recognition of pregnancy. A total of sixteen differentially expressed proteins (DEPs) were identified using 2-DE gels and MALDI-TOF/TOF mass spectrometry. Comparison between 9D and 12D of pregnancy identified APOA1, CAPZB, LDHB, CCT5, ANXA4, CFB, TTR upregulated DEPs, and ANXA5, SMS downregulated DEPs. Comparison between 9D and 16D of pregnancy identified HP, APOA1, ACTB, CCT5, ANXA4, CFB upregulated DEPs and ANXA5, SMS, LDHB, ACTR3, HP, ENO3, OAT downregulated DEPs. However, a comparison between 12D and 16D of pregnancy identified HP, ACTB upregulated DEPs, and CRYM, ANXA4, ANXA5, CAPZB, LDHB, ACTR3, CCT5, ENO3, OAT, TTR down-regulated DEPs. Outcomes of this study revealed key proteins and their interactions with metabolic pathways involved in the recognition and establishment of early pregnancy in PLW gilts.
Collapse
|
10
|
García-Vázquez FA, Moros-Nicolás C, López-Úbeda R, Rodríguez-Tobón E, Guillén-Martínez A, Ross JW, Luongo C, Matás C, Hernández-Caravaca I, Avilés M, Izquierdo-Rico MJ. Evidence of haptoglobin in the porcine female genital tract during oestrous cycle and its effect on in vitro embryo production. Sci Rep 2021; 11:12041. [PMID: 34103548 PMCID: PMC8187724 DOI: 10.1038/s41598-021-90810-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/12/2021] [Indexed: 02/05/2023] Open
Abstract
Recent evidence supports involvement of the acute phase protein haptoglobin in numerous events during mammalian reproduction. The present study represents an in-depth investigation of haptoglobin expression and secretion in the porcine oviduct and uterus, and assesses its effect on porcine in vitro embryo production. A systematic study was made of sows in different oestrous stages: late follicular, early luteal and late luteal stages. Relative haptoglobin mRNA abundance was quantified by RT-qPCR. In addition, expression of the protein was analysed by immunohistochemistry and the results were complemented by Western-blot and proteomic analyses of the oviductal and uterine fluids. In vitro porcine fertilization and embryo culture were carried out in the presence of haptoglobin. The results indicate that haptoglobin mRNA expression in the porcine oviduct and uterus is most abundant during the late luteal stage of the oestrous cycle. By means of Western blot and proteomic analyses haptoglobin presence was demonstrated in the oviduct epithelium and in the oviductal and uterine fluids in different stages of the oestrous cycle. The addition of haptoglobin during gamete co-incubation had no effect on sperm penetration, monospermy or efficiency rates; however, compared with the control group, blastocyst development was significantly improved when haptoglobin was present (haptoglobin: 64.50% vs. control: 37.83%; p < 0.05). In conclusion, the presence of haptoglobin in the oviduct and uterus of sows at different stages of the oestrous cycle suggests that it plays an important role in the reproduction process. The addition of haptoglobin during in vitro embryo production improved the blastocyst rates.
Collapse
Affiliation(s)
- Francisco A. García-Vázquez
- grid.10586.3a0000 0001 2287 8496Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, 30100 Murcia, Spain ,grid.452553.0Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Carla Moros-Nicolás
- grid.10586.3a0000 0001 2287 8496Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, 30100 Murcia, Spain ,grid.452553.0Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Rebeca López-Úbeda
- grid.10586.3a0000 0001 2287 8496Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, 30100 Murcia, Spain ,grid.452553.0Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Ernesto Rodríguez-Tobón
- grid.10586.3a0000 0001 2287 8496Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, 30100 Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Ascensión Guillén-Martínez
- grid.10586.3a0000 0001 2287 8496Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, 30100 Murcia, Spain ,grid.452553.0Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Jason W. Ross
- grid.34421.300000 0004 1936 7312Department of Animal Science, Iowa State University, Ames, IA USA
| | - Chiara Luongo
- grid.10586.3a0000 0001 2287 8496Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, 30100 Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Carmen Matás
- grid.10586.3a0000 0001 2287 8496Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, 30100 Murcia, Spain ,grid.452553.0Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Iván Hernández-Caravaca
- grid.10586.3a0000 0001 2287 8496Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, 30100 Murcia, Spain ,grid.452553.0Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Manuel Avilés
- grid.10586.3a0000 0001 2287 8496Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, 30100 Murcia, Spain ,grid.452553.0Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Mª José Izquierdo-Rico
- grid.10586.3a0000 0001 2287 8496Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, 30100 Murcia, Spain ,grid.452553.0Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain ,CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| |
Collapse
|
11
|
Yang Q, Fu W, Wang Y, Miao K, Zhao H, Wang R, Guo M, Wang Z, Tian J, An L. The proteome of IVF-induced aberrant embryo-maternal crosstalk by implantation stage in ewes. J Anim Sci Biotechnol 2020; 11:7. [PMID: 31956410 PMCID: PMC6958772 DOI: 10.1186/s40104-019-0405-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/26/2019] [Indexed: 01/17/2023] Open
Abstract
Background Implantation failure limits the success of in vitro fertilization and embryo transfer (IVF-ET). Well-organized embryo-maternal crosstalk is essential for successful implantation. Previous studies mainly focused on the aberrant development of in vitro fertilized (IVF) embryos. In contrast, the mechanism of IVF-induced aberrant embryo-maternal crosstalk is not well defined. Results In the present study, using ewes as the model, we profiled the proteome that features aberrant IVF embryo-maternal crosstalk following IVF-ET. By comparing in vivo (IVO) and IVF conceptuses, as well as matched endometrial caruncular (C) and intercaruncular (IC) areas, we filtered out 207, 295, and 403 differentially expressed proteins (DEPs) in each comparison. Proteome functional analysis showed that the IVF conceptuses were characterized by the increased abundance of energy metabolism and proliferation-related proteins, and the decreased abundance of methyl metabolism-related proteins. In addition, IVF endometrial C areas showed the decreased abundance of endometrial remodeling and redox homeostasis-related proteins; while IC areas displayed the aberrant abundance of protein homeostasis and extracellular matrix (ECM) interaction-related proteins. Based on these observations, we propose a model depicting the disrupted embryo-maternal crosstalk following IVF-ET: Aberrant energy metabolism and redox homeostasis of IVF embryos, might lead to an aberrant endometrial response to conceptus-derived pregnancy signals, thus impairing maternal receptivity. In turn, the suboptimal uterine environment might stimulate a compensation effect of the IVF conceptuses, which was revealed as enhanced energy metabolism and over-proliferation. Conclusion Systematic proteomic profiling provides insights to understand the mechanisms that underlie the aberrant IVF embryo-maternal crosstalk. This might be helpful to develop practical strategies to prevent implantation failure following IVF-ET.
Collapse
Affiliation(s)
- Qianying Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Wei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yue Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Kai Miao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Haichao Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Rui Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Min Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Zhilong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Jianhui Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Lei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
12
|
De A, Ali MA, Chutia T, Onteru SK, Behera P, Kalita G, Kumar S, Gali JM. Comparative serum proteome analysis reveals potential early pregnancy-specific protein biomarkers in pigs. Reprod Fertil Dev 2019; 31:613-631. [DOI: 10.1071/rd18227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/18/2018] [Indexed: 12/26/2022] Open
Abstract
In this study, the comparative serum proteome profile of Day 5, 12 and 16 of gestation, representing three early embryonic events, namely formation, elongation and implantation of blastocysts, and non-pregnant control were explored by a label-free quantitation-based mass spectrometric approach to identify early pregnancy biomarkers in pigs. A total of 131 proteins were identified with respect to different groups, out of which 105 were found to be differentially expressed proteins (DEPs). Among the DEPs, 54 and 66 proteins were found to be up and downregulated respectively in early pregnancy groups (fold change >2) and the maximum number of upregulated proteins was observed in the Day 12 pregnancy stage. Functional classification and pathway analysis of the DEPs revealed involvement of most of the proteins in complement and coagulation cascades, metabolic processes and immune and inflammatory responses. Proteins such as glutathione peroxidise (GPX), pregnancy zone protein (PZP), thrombospondin-1 (THBS1), α-1-antitrypsin (AAT) and mannose-binding lectin C (MBLC) were differentially expressed during early pregnancy and actively involved in different pregnancy-related activities. To the best of our knowledge, this is the first report on comparative serum protein profiling of different early pregnancy stages in pigs and our results provide a set of proteins that can be used as potential biomarkers for early pregnancy diagnosis in pigs.
Collapse
|
13
|
Dhaenens L, Lierman S, De Clerck L, Govaert E, Deforce D, Tilleman K, De Sutter P. Endometrial stromal cell proteome mapping in repeated implantation failure and recurrent pregnancy loss cases and fertile women. Reprod Biomed Online 2018; 38:442-454. [PMID: 30612956 DOI: 10.1016/j.rbmo.2018.11.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 11/02/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022]
Abstract
RESEARCH QUESTION Are there proteomic differences between endometrial stromal cells of repeated implantation failure (RIF), recurrent pregnancy loss (RPL) and normal fertile women, and is there differential protein expression upon decidualization? DESIGN This exploratory study investigated the proteome of in-vitro cultured endometrial stromal cells of women with RIF (n = 4), women with RPL (n = 3) and normal fertile women (n = 4), comparing day 0 with 5 days of decidualization. Total proteins extracted from cell lysates were analysed by high-definition mass spectrometry. Data analysis was performed using significance analysis of microarray in R (P < 0.05; false discovery rate [FDR] 10%). RESULTS In the RIF group, ANXA6, PSMC5 and FSCN1 were up-regulated (1.9-fold, 2.5-fold and 1.9-fold, respectively), whereas PBXIP1 was down-regulated (7.7-fold) upon decidualization. In the RPL group, RPS25 and ACADVL were down-regulated (1.9-fold and 2.4-fold, respectively; FDR 10%) between the non-decidualized and the decidualized samples. In the normal fertile group VIM and RPL23A were down-regulated (1.9-fold and 2.4-fold, respectively). Comparing ratios of expression of decidualized over non-decidualized samples in the different groups revealed six differentially expressed proteins: DUX4L2, CNPY4, PDE7A, CTSK, PCBP2 and PSMD4. Comparison of RPL versus normal fertile in the decidualized condition revealed serotransferrin to be differentially expressed. The changes in expression levels for serotransferrin, ANX6, ACDVL and VIM were confirmed by western blot. CONCLUSIONS Results show a varying response of endometrial stromal cells in distinct clinical groups (RIF, RPL and normal fertile) upon in-vitro decidualization. Serotransferrin could serve as a marker for the aberrant decidualization process in RPL.
Collapse
Affiliation(s)
- Lien Dhaenens
- Department of Reproductive Medicine, Ghent Fertility and Stem Cell Team (G-Fast), Ghent University Hospital, Corneel Heymanslaan 10, Ghent 9000, Belgium.
| | - Sylvie Lierman
- Department of Reproductive Medicine, Ghent Fertility and Stem Cell Team (G-Fast), Ghent University Hospital, Corneel Heymanslaan 10, Ghent 9000, Belgium
| | - Laura De Clerck
- Department of Pharmaceutics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent 9000, Belgium
| | - Elisabeth Govaert
- Department of Pharmaceutics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent 9000, Belgium
| | - Dieter Deforce
- Department of Pharmaceutics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent 9000, Belgium
| | - Kelly Tilleman
- Department of Reproductive Medicine, Ghent Fertility and Stem Cell Team (G-Fast), Ghent University Hospital, Corneel Heymanslaan 10, Ghent 9000, Belgium
| | - Petra De Sutter
- Department of Reproductive Medicine, Ghent Fertility and Stem Cell Team (G-Fast), Ghent University Hospital, Corneel Heymanslaan 10, Ghent 9000, Belgium
| |
Collapse
|
14
|
Preliminary study on plasma proteins in pregnant and non-pregnant female dogs. Theriogenology 2017; 97:1-8. [DOI: 10.1016/j.theriogenology.2017.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 11/22/2022]
|
15
|
Soleilhavoup C, Riou C, Tsikis G, Labas V, Harichaux G, Kohnke P, Reynaud K, de Graaf SP, Gerard N, Druart X. Proteomes of the Female Genital Tract During the Oestrous Cycle. Mol Cell Proteomics 2016; 15:93-108. [PMID: 26518761 PMCID: PMC4762522 DOI: 10.1074/mcp.m115.052332] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/10/2015] [Indexed: 01/01/2023] Open
Abstract
The female genital tract includes several anatomical regions whose luminal fluids successively interact with gametes and embryos and are involved in the fertilisation and development processes. The luminal fluids from the inner cervix, the uterus and the oviduct were collected along the oestrous cycle at oestrus (Day 0 of the cycle) and during the luteal phase (Day 10) from adult cyclic ewes. The proteomes were assessed by GeLC-MS/MS and quantified by spectral counting. A set of 940 proteins were identified including 291 proteins differentially present along the cycle in one or several regions. The global analysis of the fluid proteomes revealed a general pattern of endocrine regulation of the tract, with the cervix and the oviduct showing an increased differential proteins abundance mainly at oestrus while the uterus showed an increased abundance mainly during the luteal phase. The proteins more abundant at oestrus included several families such as the heat shock proteins (HSP), the mucins, the complement cascade proteins and several redox enzymes. Other proteins known for their interaction with gametes such as oviductin (OVGP), osteopontin, HSPA8, and the spermadhesin AWN were also overexpressed at oestrus. The proteins more abundant during the luteal phase were associated with the immune system such as ceruloplasmin, lactoferrin, DMBT1, or PIGR, and also with tissue remodeling such as galectin 3 binding protein, alkaline phosphatase, CD9, or fibulin. Several proteins differentially abundant between estrus and the luteal phase, such as myosin 9 and fibronectin, were also validated by immunohistochemistry. The potential roles in sperm transit and uterine receptivity of the proteins differentially regulated along the cycle in the female genital tract are discussed.
Collapse
Affiliation(s)
- Clement Soleilhavoup
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Cindy Riou
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Guillaume Tsikis
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Valerie Labas
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France; **INRA, Plate-forme d'Analyse Intégrative des Biomolécules (PAIB), Laboratoire de Spectrométrie de Masse, F-37380 Nouzilly, France
| | - Gregoire Harichaux
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France; **INRA, Plate-forme d'Analyse Intégrative des Biomolécules (PAIB), Laboratoire de Spectrométrie de Masse, F-37380 Nouzilly, France
| | - Philippa Kohnke
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Karine Reynaud
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France; ‡‡Alfort Veterinary School, 94700 Maisons Alfort, France
| | - Simon P de Graaf
- §§Faculty of Veterinary Science, The University of Sydney NSW 2006, Australia
| | - Nadine Gerard
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - Xavier Druart
- From the ‡INRA, UMR 85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France;
| |
Collapse
|
16
|
Zhu J, Zeng X, Peng Q, Zeng S, Zhao H, Shen H, Qiao S. Maternal N-Carbamylglutamate Supplementation during Early Pregnancy Enhances Embryonic Survival and Development through Modulation of the Endometrial Proteome in Gilts. J Nutr 2015; 145:2212-20. [PMID: 26290006 DOI: 10.3945/jn.115.216333] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/22/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Early pregnancy loss is a major concern in humans and animals. N-carbamylglutamate (NCG) has been found to enhance embryonic survival during early pregnancy in rats. However, little is known about the key factors in the endometrium involved in the improvement of embryonic implantation and development induced by maternal NCG supplementation. OBJECTIVES Our objectives were to investigate whether NCG supplementation during early gestation enhanced embryonic survival and development in gilts and to uncover the related factors using the approach of endometrium proteome analysis with isobaric tags for relative and absolute quantification (iTRAQ). METHODS Uteruses and embryos/fetuses were obtained on days 14 and 28 of gestation from gilts fed a basal diet that was or was not supplemented with 0.05% NCG. The iTRAQ-based quantitative proteomics approach was performed to explore the endometrium proteome altered by NCG supplementation. RESULTS Maternal NCG supplementation significantly increased the number of total fetuses and live fetuses on day 28 of gestation by 1.32 and 1.29, respectively (P < 0.05), with a significant decrease in embryonic mortality (P < 0.05). iTRAQ results indicated that a total of 59 proteins showed at least 2-fold differences (P < 0.05), including 52 proteins that were present at higher abundance and 7 proteins present at lower abundance in NCG-supplemented gilts. The differentially expressed proteins primarily are involved in cell adhesion, energy metabolism, lipid metabolism, protein metabolism, antioxidative stress, and immune response. On day 14 of gestation, several proteins closely related to embryonic implantation and development, such as integrin-αv, integrin-β3, talin, and endothelial nitric oxide synthase, were upregulated (3.7-, 4.1-, 2.4-, and 5.4-fold increases, respectively) by NCG supplementation. CONCLUSION To our knowledge, our results provide the first evidence that altered abundance of the endometrial proteome induced by NCG supplementation is highly associated with the improvement of embryonic survival and development in gilts.
Collapse
Affiliation(s)
- Jinlong Zhu
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, and
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, and
| | - Qian Peng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, and
| | - Shenming Zeng
- Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China; and
| | - Haiyi Zhao
- Genecreate Biological Engineering Co., Ltd., National Bio-industry Base, Wuhan, China
| | - Hexiao Shen
- Genecreate Biological Engineering Co., Ltd., National Bio-industry Base, Wuhan, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, and
| |
Collapse
|
17
|
Jašarević E, Howerton CL, Howard CD, Bale TL. Alterations in the Vaginal Microbiome by Maternal Stress Are Associated With Metabolic Reprogramming of the Offspring Gut and Brain. Endocrinology 2015; 156:3265-76. [PMID: 26079804 PMCID: PMC4541625 DOI: 10.1210/en.2015-1177] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The neonate is exposed to the maternal vaginal microbiota during parturition, providing the primary source for normal gut colonization, host immune maturation, and metabolism. These early interactions between the host and microbiota occur during a critical window of neurodevelopment, suggesting early life as an important period of cross talk between the developing gut and brain. Because perturbations in the prenatal environment such as maternal stress increase neurodevelopmental disease risk, disruptions to the vaginal ecosystem could be a contributing factor in significant and long-term consequences for the offspring. Therefore, to examine the hypothesis that changes in the vaginal microbiome are associated with effects on the offspring gut microbiota and on the developing brain, we used genomic, proteomic and metabolomic technologies to examine outcomes in our mouse model of early prenatal stress. Multivariate modeling identified broad proteomic changes to the maternal vaginal environment that influence offspring microbiota composition and metabolic processes essential for normal neurodevelopment. Maternal stress altered proteins related to vaginal immunity and abundance of Lactobacillus, the prominent taxa in the maternal vagina. Loss of maternal vaginal Lactobacillus resulted in decreased transmission of this bacterium to offspring. Further, altered microbiota composition in the neonate gut corresponded with changes in metabolite profiles involved in energy balance, and with region- and sex-specific disruptions of amino acid profiles in the developing brain. Taken together, these results identify the vaginal microbiota as a novel factor by which maternal stress may contribute to reprogramming of the developing brain that may predispose individuals to neurodevelopmental disorders.
Collapse
Affiliation(s)
- Eldin Jašarević
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6046
| | - Christopher L Howerton
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6046
| | - Christopher D Howard
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6046
| | - Tracy L Bale
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6046
| |
Collapse
|
18
|
Jalali BM, Bogacki M, Dietrich M, Likszo P, Wasielak M. Proteomic analysis of porcine endometrial tissue during peri-implantation period reveals altered protein abundance. J Proteomics 2015; 125:76-88. [PMID: 25976747 DOI: 10.1016/j.jprot.2015.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/27/2015] [Accepted: 05/06/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED In mammals, successful pregnancy depends upon the readiness of uterus for implantation, followed by correct communication between the endometrium and the developing conceptus. The objective of this study was to elucidate changes in protein abundance associated with progression of estrous cycle and pregnancy from Day 9 to Day 12. We analyzed porcine endometrial tissue lysates by 2D-DIGE. Abundance of several proteins was altered depending upon the pregnancy status of animals. MALDI-TOF/TOF was used to identify a number of these proteins. Endometrial proteins that increased from Day 9 to Day 12 of cycle included annexin A4, beta-actin, apolipoprotein, ceruloplasmin and afamin. Changes in protein abundances associated with conceptus secreted factors, including haptoglobin, prolyl-4-hydroxylase, aldose-reductase and transthyretin, were also observed. Functional analysis revealed that endometrial proteins with altered abundance on Day 12 irrespective of the reproductive status were related to growth and remodeling, acute phase response and free radical scavenging, whereas transport and small molecule biochemistry were the functions activated in the pregnant endometrium as compared to the cyclic endometrium. These data provide information on dynamic physiological processes associated with uterine endometrial function of the cyclic and pregnant endometrium during period of maternal recognition of pregnancy in pigs and may potentially demonstrate a protein profile associated with successful pregnancy. BIOLOGICAL SIGNIFICANCE In pigs, the fertility rates are generally very high but the early embryonic loss that occurs during the second and third weeks of gestation critically affects the potential litter size. Temporal changes that take place in the uterine environment during the period of early pregnancy in pigs and a cross-talk between the uterus and the embryo play an important role in embryonic survival and successful pregnancy. A better understanding of the molecular changes associated with these processes will pave way for understanding of endometrial functions and help towards increasing embryo survival. In this study, we present a 2D-DIGE based analysis of changes in porcine endometrial proteome that are associated with progression of cycle and progression of pregnancy. The network analysis of the results clearly revealed the pathways that are involved in rendering the endometrium receptive to the presence of embryo and also the changes that are result of molecular communication between the endometrium and the conceptuses. This comprehensive identification of proteomic changes in the porcine endometrium could be a foundation for targeted studies of proteins and pathways potentially involved in abnormal endometrial receptivity, placentation and embryo loss.
Collapse
Affiliation(s)
- Beenu Moza Jalali
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland.
| | - Marek Bogacki
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Mariola Dietrich
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Pawel Likszo
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Marta Wasielak
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| |
Collapse
|
19
|
Mitra A, Boroujeni MB. Application of gel-based proteomic technique in female reproductive investigations. J Hum Reprod Sci 2015; 8:18-24. [PMID: 25838744 PMCID: PMC4381377 DOI: 10.4103/0974-1208.153121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/15/2015] [Accepted: 02/27/2015] [Indexed: 01/06/2023] Open
Abstract
Recently, gel-based proteomics has been increasingly applied to investigate proteins involved in female reproductive tract in healthy and disease states. Gel-based proteomics coupled by mass spectrometry (MS) facilitate the identification of new proteins playing roles in cellular and molecular interactions underlying female reproductive biology and it is a useful method to identify novel biomarkers of diseases by studying thousands of proteins simultaneously involved in female reproductive tract in healthy state compared to disease state. This review will discuss the best studies areas contributed to female reproductive biology in which gel-based proteomics coupled by MS has been applied to generate proteome of female reproductive tract in a healthy state.
Collapse
Affiliation(s)
- Arianmanesh Mitra
- Department of Anatomical Sciences, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mandana Beigi Boroujeni
- Department of Anatomical Sciences, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| |
Collapse
|
20
|
Inyawilert W, Fu TY, Lin CT, Tang PC. Let-7-mediated suppression of mucin 1 expression in the mouse uterus during embryo implantation. J Reprod Dev 2015; 61:138-44. [PMID: 25739861 PMCID: PMC4410312 DOI: 10.1262/jrd.2014-106] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mucin 1 (Muc1) is an integral transmembrane mucin glycoprotein expressed on the apical surface of most epithelia. It is considered to be a barrier to the regulation of embryo implantation by inhibiting attachment of the embryo to the endometrium. Therefore, loss of Muc1 on the surface of uterine epithelial cells is necessary for embryo implantation. Studies have demonstrated that microRNAs (miRNAs) play a key role in enhancing embryo implantation in mammals. In this study, we investigated the regulatory role of two miRNAs (let-7a and let-7b) on the expression of Muc1 in mouse uteri during implantation. Western blotting indicated that Muc1 expression was highest on day1 of pregnancy and constantly decreased thereafter until day 4. In contrast to Muc1 expression, increased expression of let-7a and let-7b was evident on day 4 of pregnancy as measured by real-time reverse transcription-polymerase chain reaction
(real-time RT-PCR). We demonstrated direct binding of let-7a and let-7b to the 3’untranslated region of muc1. Furthermore, Muc1 expression was suppressed after transfection of mouse uterine epithelial cells isolated from day 1 of pregnancy with let-7a and let-7b. In summary, the present study provides evidence that Muc1 is a direct target of let-7a and let-7b. Additionally, the current study suggests that miRNAs are novel targets which can be used to facilitate a successful pregnancy and repair implantation failure.
Collapse
Affiliation(s)
- Wilasinee Inyawilert
- Department of Animal Science, National Chung Hsing University, Taichung 40227, Taiwan
| | | | | | | |
Collapse
|
21
|
Gu T, Zhu MJ, Schroyen M, Qu L, Nettleton D, Kuhar D, Lunney JK, Ross JW, Zhao SH, Tuggle CK. Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation. BMC Genomics 2014; 15:156. [PMID: 24564230 PMCID: PMC3940021 DOI: 10.1186/1471-2164-15-156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 02/17/2014] [Indexed: 12/03/2022] Open
Abstract
Background Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large percentage of the developing conceptuses are lost. However, the gene expression and regulatory networks in the endometrium contributing to the establishment of the maternal: placental interface remain poorly understood. Results We characterized the endometrial gene expression profile during the peri-implantation stage of development by comparing two breeds that demonstrate very different reproductive efficiencies. We employed the porcine Affymetrix GeneChip® to assay the transcriptomic profiles of genes expressed in the uterine endometrium obtained from Meishan and Yorkshire gilts (n = 4 for each breed) on day 12 of gestation (M12 and Y12, respectively). Total of 17,076 probesets were identified as "present" in at least two arrays. A mixed model-based statistical analysis predicted a total of 2,656 (q < 0.1) transcripts as differentially expressed between Meishan and Yorkshire pigs. Eighteen differentially expressed transcripts of interest were validated by quantitative real-time PCR. Gene ontology (GO) annotation revealed that the known functions of the differentially expressed genes were involved in a series of important biological processes relevant to early pregnancy establishment in the pig. Conclusions The results identified endometrial gene expression profiles of two breeds differing in litter size and identified candidate genes that are related to known physiological pathways related to reproductive prolificacy. These findings provide a deeper understanding of molecular pathways differing between two breeds at the critical peri-implantation stage of pregnancy, which can be utilized to better understand the events contributing to pregnancy establishment in the pig.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Shu-hong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, P, R, China.
| | | |
Collapse
|
22
|
Wang Y, Wang C, Hou Z, Miao K, Zhao H, Wang R, Guo M, Wu Z, Tian J, An L. Comparative analysis of proteomic profiles between endometrial caruncular and intercaruncular areas in ewes during the peri-implantation period. J Anim Sci Biotechnol 2013; 4:39. [PMID: 24093944 PMCID: PMC3892124 DOI: 10.1186/2049-1891-4-39] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/23/2013] [Indexed: 01/24/2023] Open
Abstract
The endometrium of sheep consists of plenty of raised aglandular areas called caruncular (C), and intensely glandular intercaruncular areas (IC). In order to better understand the endometrium involved mechanisms of implantation, we used LC-MS/MS technique to profile the proteome of ovine endometrial C areas and IC areas separately during the peri-implantation period, and then compared the proteomic profiles between these two areas. We successfully detected 1740 and 1813 proteins in C areas and IC areas respectively. By comparing the proteome of these two areas, we found 170 differentially expressed proteins (DEPs) (P < 0.05), functional bioinformatics analysis showed these DEPs were mainly involved in growth and remodeling of endometrial tissue, cell adhesion and protein transport, and so on. Our study, for the first time, provided a proteomic reference for elucidating the differences between C and IC areas, as an integrated function unit respectively, during the peri-implantation period. The results could help us to better understand the implantation in the ewes. In addition, we established a relatively detailed protein database of ovine endometrium, which provide a unique reference for further studies.
Collapse
Affiliation(s)
- Yang Wang
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National engineering laboratory for animal breeding, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| | - Chao Wang
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National engineering laboratory for animal breeding, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Kai Miao
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National engineering laboratory for animal breeding, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| | - Haichao Zhao
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National engineering laboratory for animal breeding, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| | - Rui Wang
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National engineering laboratory for animal breeding, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| | - Min Guo
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National engineering laboratory for animal breeding, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| | - Zhonghong Wu
- State Key Laboratory of Animal Nutrition, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| | - Jianhui Tian
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National engineering laboratory for animal breeding, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| | - Lei An
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National engineering laboratory for animal breeding, College of Animal Sciences and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian, Beijing 100193, China
| |
Collapse
|
23
|
Stojanova D, Ceci M, Malerba D, Dzeroski S. Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction. BMC Bioinformatics 2013; 14:285. [PMID: 24070402 PMCID: PMC3850549 DOI: 10.1186/1471-2105-14-285] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 09/18/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ontologies and catalogs of gene functions, such as the Gene Ontology (GO) and MIPS-FUN, assume that functional classes are organized hierarchically, that is, general functions include more specific ones. This has recently motivated the development of several machine learning algorithms for gene function prediction that leverages on this hierarchical organization where instances may belong to multiple classes. In addition, it is possible to exploit relationships among examples, since it is plausible that related genes tend to share functional annotations. Although these relationships have been identified and extensively studied in the area of protein-protein interaction (PPI) networks, they have not received much attention in hierarchical and multi-class gene function prediction. Relations between genes introduce autocorrelation in functional annotations and violate the assumption that instances are independently and identically distributed (i.i.d.), which underlines most machine learning algorithms. Although the explicit consideration of these relations brings additional complexity to the learning process, we expect substantial benefits in predictive accuracy of learned classifiers. RESULTS This article demonstrates the benefits (in terms of predictive accuracy) of considering autocorrelation in multi-class gene function prediction. We develop a tree-based algorithm for considering network autocorrelation in the setting of Hierarchical Multi-label Classification (HMC). We empirically evaluate the proposed algorithm, called NHMC (Network Hierarchical Multi-label Classification), on 12 yeast datasets using each of the MIPS-FUN and GO annotation schemes and exploiting 2 different PPI networks. The results clearly show that taking autocorrelation into account improves the predictive performance of the learned models for predicting gene function. CONCLUSIONS Our newly developed method for HMC takes into account network information in the learning phase: When used for gene function prediction in the context of PPI networks, the explicit consideration of network autocorrelation increases the predictive performance of the learned models. Overall, we found that this holds for different gene features/ descriptions, functional annotation schemes, and PPI networks: Best results are achieved when the PPI network is dense and contains a large proportion of function-relevant interactions.
Collapse
Affiliation(s)
- Daniela Stojanova
- Department of Knowledge Technologies, JoŽef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia.
| | | | | | | |
Collapse
|
24
|
The Akt/mTor signaling cascade is modified during placentation in the porcine uterine tissue. Reprod Biol 2013; 13:184-94. [PMID: 24011189 DOI: 10.1016/j.repbio.2013.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/14/2022]
Abstract
Recently we showed that essential components for the initiation of protein synthesis, namely the eukaryotic initiation factor 4E (eIF4E, mRNA-cap-binding protein) and its repressors 4E-BP1 as well as 4E-BP2, are proteolytically processed in the porcine endometrium during implantation. Here, the situation during placentation was compared with ovariectomized (OVX) animals and animals on pregnancy day 1 (PD1). Furthermore, the research was extended to factors which phosphorylate eIF4E and 4E-BPs and regulate their activities. These are the protein kinase B/mammalian target of rapamycin kinase (Akt/mTor) with the regulators Raptor and Rictor as well as the mitogen activated protein kinases (MAPKs): extra cellular-signal regulated kinase 1 and 2 (ERK1 and ERK2). Striking differences in the placentation site (PS) and the areas aside from PS (peri-PS) were observed. EIF4E and 4E-BP2 truncation as well as 4E-BP1 degradation took place in the endometrium of the peri-PS on PD24. Accompanied by a fragmentation of Akt/mTor, no expression of Rictor was observed, whereas the abundance of Raptor was not altered. On the contrary, MAPKs expression and phosphorylation remained almost stable in the peri-PS. In conclusion, the results indicated that on PD24 the translational regulation was shifted to 4E-BP2 control. Furthermore, the Akt/mTor signaling cascade seemed to be down regulated which suggest reduced phosphorylation of 4E-BP2. Whereas Akt was proteolyzed, the observed mTor fragments represented most likely splicing variants. The results indicate that translational control of gene expression is an important feature in the porcine endometrium during early pregnancy.
Collapse
|
25
|
Novel differential transcript expression identified by LongSAGE in the mouse endometrium during the implantation window. Mol Biol Rep 2012; 40:651-63. [DOI: 10.1007/s11033-012-2104-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/03/2012] [Indexed: 12/31/2022]
|