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Dučić T, Sanchez-Mata A, Castillo-Sanchez J, Algarra M, Gonzalez-Munoz E. Monitoring oocyte-based human pluripotency acquisition using synchrotron-based FTIR microspectroscopy reveals specific biomolecular trajectories. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122713. [PMID: 37084681 DOI: 10.1016/j.saa.2023.122713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/09/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
The reprogramming of human somatic cells to induced pluripotent cells (iPSCs) has become a milestone and a paradigm shift in the field of regenerative medicine and human disease modeling including drug testing and genome editing. However, the molecular processes occurring during reprogramming and affecting the pluripotent state acquired remain largely unknown. Of interest, different pluripotent states have been described depending on the reprogramming factors used and the oocyte has emerged as a valuable source of information for candidate factors. The present study investigates the molecular changes occurring in somatic cells during reprogramming with either canonical (OSK) or oocyte-based (AOX15) combinations using synchrotron-radiation Fourier transform infrared (SR FTIR) spectroscopy. The data acquired by SR FTIR indicates different representation and conformation of biological relevant macromolecules (lipids, nucleic acids, carbohydrates and proteins) depending on the reprogramming combination used and at different stages during the reprogramming process. Association analysis based on cells spectra suggest that pluripotency acquisition trajectories converge at late intermediate stages while they diverge at early stages. Our results suggest that OSK and AOX15 reprogramming operates through differential mechanisms affecting nucleic acids reorganization and day 10 comes out as a candidate hinge point to further study the molecular pathways involved in the reprogramming process. This study indicates that SR FTIR approach contribute unpaired information to distinguish pluripotent states and to decipher pluripotency acquisition roadmaps and landmarks that will enable advanced biomedical applications of iPSCs.
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Affiliation(s)
- Tanja Dučić
- ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain.
| | - Alicia Sanchez-Mata
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain
| | - Jesus Castillo-Sanchez
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain
| | - Manuel Algarra
- INAMAT(2) Institute for Advanced Materials and Mathematics, Department of Sciences, Public University of Navarre, Campus de Arrosadia, 31006 Pamplona, Spain
| | - Elena Gonzalez-Munoz
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain.
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Zebrowitz E, Aslanukov A, Kajikawa T, Bedelbaeva K, Bollinger S, Zhang Y, Sarfatti D, Cheng J, Messersmith PB, Hajishengallis G, Heber-Katz E. Prolyl-hydroxylase inhibitor-induced regeneration of alveolar bone and soft tissue in a mouse model of periodontitis through metabolic reprogramming. FRONTIERS IN DENTAL MEDICINE 2022; 3:992722. [PMID: 37641630 PMCID: PMC10462383 DOI: 10.3389/fdmed.2022.992722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
Bone injuries and fractures reliably heal through a process of regeneration with restoration to original structure and function when the gap between adjacent sides of a fracture site is small. However, when there is significant volumetric loss of bone, bone regeneration usually does not occur. In the present studies, we explore a particular case of volumetric bone loss in a mouse model of human periodontal disease (PD) in which alveolar bone surrounding teeth is permanently lost and not replaced. This model employs the placement a ligature around the upper second molar for 10 days leading to inflammation and bone breakdown and faithfully replicates the bacterially-induced inflammatory etiology of human PD to induce bone degeneration. After ligature removal, mice are treated with a timed-release formulation of a small molecule inhibitor of prolylhydroxylases (PHDi; 1,4-DPCA) previously shown to induce epimorphic regeneration of soft tissue in non-regenerating mice. This PHDi induces high expression of HIF-1α and is able to shift the metabolic state from OXPHOS to aerobic glycolysis, an energetic state used by stem cells and embryonic tissue. This regenerative response was completely blocked by siHIF1a. In these studies, we show that timed-release 1,4-DPCA rapidly and completely restores PD-affected bone and soft tissue with normal anatomic fidelity and with increased stem cell markers due to site-specific stem cell migration and/or de-differentiation of local tissue, periodontal ligament (PDL) cell proliferation, and increased vascularization. In-vitro studies using gingival tissue show that 1,4-DPCA indeed induces de-differentiation and the expression of stem cell markers but does not exclude the role of migrating stem cells. Evidence of metabolic reprogramming is seen by the expression of not only HIF-1a, its gene targets, and resultant de-differentiation markers, but also the metabolic genes Glut-1, Gapdh, Pdk1, Pgk1 and Ldh-a in jaw periodontal tissue.
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Affiliation(s)
- Elan Zebrowitz
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
- Current address: New York Medical College, 40 Sunshine Cottage Rd, Valhalla New York, United States of America
| | - Azamat Aslanukov
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
| | - Tetsuhiro Kajikawa
- University of Pennsylvania School of Dental Medicine, Department of Basic and Translational Sciences, Philadelphia, Pennsylvania, United States of America
| | - Kamila Bedelbaeva
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
| | - Sam Bollinger
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
- Current address: Cancer Biology Graduate Group, Stanford, California, United States of America
| | - Yong Zhang
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
- Current address: Rockland Immunochemicals, Inc., Limerick, Pennsylvania, United States of America
| | - David Sarfatti
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
| | - Jing Cheng
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Current address: Alcon Laboratories, 11460 Johns Creek Pkwy, Duluth, Georgia, United States of America
| | - Phillip B. Messersmith
- Department of Bioengineering and Materials Science and Engineering, UC Berkeley, Berkeley California, United States of America
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - George Hajishengallis
- University of Pennsylvania School of Dental Medicine, Department of Basic and Translational Sciences, Philadelphia, Pennsylvania, United States of America
| | - Ellen Heber-Katz
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, United States of America
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Hussein AM, Balachandar N, Mathieu J, Ruohola-Baker H. Molecular Regulators of Embryonic Diapause and Cancer Diapause-like State. Cells 2022; 11:cells11192929. [PMID: 36230891 PMCID: PMC9562880 DOI: 10.3390/cells11192929] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Embryonic diapause is an enigmatic state of dormancy that interrupts the normally tight connection between developmental stages and time. This reproductive strategy and state of suspended development occurs in mice, bears, roe deer, and over 130 other mammals and favors the survival of newborns. Diapause arrests the embryo at the blastocyst stage, delaying the post-implantation development of the embryo. This months-long quiescence is reversible, in contrast to senescence that occurs in aging stem cells. Recent studies have revealed critical regulators of diapause. These findings are important since defects in the diapause state can cause a lack of regeneration and control of normal growth. Controlling this state may also have therapeutic applications since recent findings suggest that radiation and chemotherapy may lead some cancer cells to a protective diapause-like, reversible state. Interestingly, recent studies have shown the metabolic regulation of epigenetic modifications and the role of microRNAs in embryonic diapause. In this review, we discuss the molecular mechanism of diapause induction.
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Affiliation(s)
- Abdiasis M. Hussein
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Nanditaa Balachandar
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Chennai 603203, India
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Comparative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Correspondence:
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Gimeno I, García-Manrique P, Carrocera S, López-Hidalgo C, Muñoz M, Valledor L, Martín-González D, Gómez E. Non-Invasive Identification of Sex in Cultured Bovine Embryos by UHPLC-MS/MS Metabolomics. Metabolomics 2022; 18:53. [PMID: 35842860 DOI: 10.1007/s11306-022-01910-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Different gene expression between male and female bovine embryos leads to metabolic differences. OBJECTIVE We used UHPLC-MS/MS to identify sex metabolite biomarkers in embryo culture medium (CM). METHODS Embryos were produced in vitro under highly variable conditions, i.e., fertilized with 7 bulls, two breeds, and cultured with BSA or BSA + serum until Day-6. On Day-6, embryos were cultured individually for 24 h. CM of Day-7 embryos (86 female and 81 male) was collected, and Day-6 and Day-7 embryonic stages recorded. RESULTS A study by sample subsets with fixed factors (culture, bull breed, and Day-6 and Day-7 stages) tentatively identified 31 differentially accumulated metabolites through 182 subsets. Day-6 and Day-7 stage together affected 13 and 11 metabolites respectively, while 19 metabolites were affected by one or another stage and/or day. Culture supplements and individual bull changed 19 and 15 metabolites, respectively. Single bull exerted the highest influence (20 metabolites with the significantly highest p values). Lipid (93 subsets; 11 metabolites) and amino acid (55 subsets; 13 metabolites) were the most relevant classes for sex identification. CONCLUSIONS Single biomarker led to inefficient sex diagnosis, while metabolite combinations accurately identified sex. Our study is a first in non-invasive sex identification in cattle by overcoming factors that induce metabolic variation.
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Affiliation(s)
- Isabel Gimeno
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Pablo García-Manrique
- Molecular Mass Spectrometry Unit, Scientific and Technical Services, University of Oviedo, Catedrático Rodrigo Uria s/n, 33006, Oviedo, Spain
| | - Susana Carrocera
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Cristina López-Hidalgo
- Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Catedrático Rodrigo Uria s/n, 33006, Oviedo, Spain
| | - Marta Muñoz
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Luis Valledor
- Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Catedrático Rodrigo Uria s/n, 33006, Oviedo, Spain
| | - David Martín-González
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Enrique Gómez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394, Gijón, Spain.
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Detraux D, Renard P. Succinate as a New Actor in Pluripotency and Early Development? Metabolites 2022; 12:metabo12070651. [PMID: 35888775 PMCID: PMC9325148 DOI: 10.3390/metabo12070651] [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: 05/30/2022] [Revised: 07/01/2022] [Accepted: 07/13/2022] [Indexed: 02/07/2023] Open
Abstract
Pluripotent cells have been stabilized from pre- and post-implantation blastocysts, representing respectively naïve and primed stages of embryonic stem cells (ESCs) with distinct epigenetic, metabolic and transcriptomic features. Beside these two well characterized pluripotent stages, several intermediate states have been reported, as well as a small subpopulation of cells that have reacquired features of the 2C-embryo (2C-like cells) in naïve mouse ESC culture. Altogether, these represent a continuum of distinct pluripotency stages, characterized by metabolic transitions, for which we propose a new role for a long-known metabolite: succinate. Mostly seen as the metabolite of the TCA, succinate is also at the crossroad of several mitochondrial biochemical pathways. Its role also extends far beyond the mitochondrion, as it can be secreted, modify proteins by lysine succinylation and inhibit the activity of alpha-ketoglutarate-dependent dioxygenases, such as prolyl hydroxylase (PHDs) or histone and DNA demethylases. When released in the extracellular compartment, succinate can trigger several key transduction pathways after binding to SUCNR1, a G-Protein Coupled Receptor. In this review, we highlight the different intra- and extracellular roles that succinate might play in the fields of early pluripotency and embryo development.
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Gimeno I, García-Manrique P, Carrocera S, López-Hidalgo C, Valledor L, Martín-González D, Gómez E. The Metabolic Signature of In Vitro Produced Bovine Embryos Helps Predict Pregnancy and Birth after Embryo Transfer. Metabolites 2021; 11:484. [PMID: 34436426 PMCID: PMC8399324 DOI: 10.3390/metabo11080484] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022] Open
Abstract
In vitro produced (IVP) embryos show large metabolic variability induced by breed, culture conditions, embryonic stage and sex and gamete donors. We hypothesized that the birth potential could be accurately predicted by UHPLC-MS/MS in culture medium (CM) with the discrimination of factors inducing metabolic variation. Day-6 embryos were developed in single CM (modified synthetic oviduct fluid) for 24 h and transferred to recipients as fresh (28 ETs) or frozen/thawed (58 ETs) Day-7 blastocysts. Variability was induced with seven bulls, slaughterhouse oocyte donors, culture conditions (serum + Bovine Serum Albumin [BSA] or BSA alone) prior to single culture embryonic stage records (Day-6: morula, early blastocyst, blastocyst; Day-7: expanding blastocyst; fully expanded blastocysts) and cryopreservation. Retained metabolite signals (6111) were analyzed as a function of pregnancy at Day-40, Day-62 and birth in a combinatorial block study with all fixed factors. We identified 34 accumulated metabolites through 511 blocks, 198 for birth, 166 for Day-62 and 147 for Day-40. The relative abundance of metabolites was higher within blocks from non-pregnant (460) than from pregnant (51) embryos. Taxonomy classified lipids (12 fatty acids and derivatives; 224 blocks), amino acids (12) and derivatives (3) (186 blocks), benzenoids (4; 58 blocks), tri-carboxylic acids (2; 41 blocks) and 5-Hydroxy-l-tryptophan (2 blocks). Some metabolites were effective as single biomarkers in 95 blocks (Receiver Operating Characteristic - Area Under the Curve [ROC-AUC]: 0.700-1.000). In contrast, more accurate predictions within the largest data sets were obtained with combinations of 2, 3 and 4 single metabolites in 206 blocks (ROC-AUC = 0.800-1.000). Pregnancy-prone embryos consumed more amino acids and citric acid, and depleted less lipids and cis-aconitic acid. Big metabolic differences between embryos support efficient pregnancy and birth prediction when analyzed in discriminant conditions.
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Affiliation(s)
- Isabel Gimeno
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394 Gijón, Spain; (I.G.); (S.C.); (D.M.-G.)
| | - Pablo García-Manrique
- Molecular Mass Spectrometry Unit, Scientific and Technical Services, University of Oviedo, Catedrático Rodrigo Uria s/n, 33006 Oviedo, Spain;
| | - Susana Carrocera
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394 Gijón, Spain; (I.G.); (S.C.); (D.M.-G.)
| | - Cristina López-Hidalgo
- Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Catedrático Rodrigo Uria s/n, 33006 Oviedo, Spain; (C.L.-H.); (L.V.)
| | - Luis Valledor
- Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Catedrático Rodrigo Uria s/n, 33006 Oviedo, Spain; (C.L.-H.); (L.V.)
| | - David Martín-González
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394 Gijón, Spain; (I.G.); (S.C.); (D.M.-G.)
| | - Enrique Gómez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Camino de Rioseco 1225, 33394 Gijón, Spain; (I.G.); (S.C.); (D.M.-G.)
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Kim HK, Ha TW, Lee MR. Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming. Int J Mol Sci 2021; 22:ijms22115988. [PMID: 34206025 PMCID: PMC8198005 DOI: 10.3390/ijms22115988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg in a highly organized programmatic fashion. Since the recent formation of the Human Cell Atlas consortium, establishing the Human Cell Atlas at the single-cell level has been an ongoing activity with the goal of understanding the mechanisms underlying diseases and vital cellular activities at the level of the single cell. In particular, transcriptome analysis of embryonic stem cells at the single-cell level is of great importance, as these cells are responsible for determining cell fate. Here, we review single-cell analysis techniques that have been actively used in recent years, introduce the single-cell analysis studies currently in progress in pluripotent stem cells and reprogramming, and forecast future studies.
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Comparative Metabolomic Profiling of Rat Embryonic and Induced Pluripotent Stem Cells. Stem Cell Rev Rep 2020; 16:1256-1265. [DOI: 10.1007/s12015-020-10052-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
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An introduction to the special issue on: "Naïve pluripotency in non-rodent species: From embryos to pluripotent stem cell lines". Exp Cell Res 2020; 395:112147. [PMID: 32540402 DOI: 10.1016/j.yexcr.2020.112147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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