Sophie Petropoulos

Karolinska Institutet | KI · Department of Clinical Science, Intervention and Technology - CLINTEC

The ability to study human post-implantation development remains limited due to ethical and technical challenges associated with intrauterine development after implantation1. Embryo-like models with spatially organized morphogenesis of all defining embryonic and extra-embryonic tissues of the post-implantation human conceptus (i.e., embryonic disk,...

Single-cell genomics allow the characterization and quantification of molecular heterogeneity from a wide variety of tissues. Here, we describe the manual dissociation and collection of single cells, a method adapted for the characterization of precious small tissues like preimplantation embryos. We also describe the acquisition of mouse embryos by...

Study question How does the small non-coding RNA (sncRNA) expression profile of the human embryo change from day three (E3) to seven (E7) of preimplantation development? Summary answer From E3 to E7, micro-RNA expression becomes more dynamic, targeting genes important for lineage segregation. What is known already The drivers of lineage specifica...

Our ability to study early human post-implantation development remains highly limited due to the ethical and technical challenges associated with intrauterine development of the human embryo after implantation. Despite the great progress made on human gastruloids, axioloids and in vitro cultured blastoids, such elegant models do not constitute an i...

Studying various animal models is important for comparative biology and to better understand evolutionary development. Furthermore, when aiming to translate findings to human development, it is crucial to select an appropriate animal model that closely resembles the specific aspect of development under study. The guinea pig is highlighted as a usef...

The development of single-cell multiomics has provided the ability to systematically investigate cellular diversity and heterogeneity in different biological systems via comprehensive delineations of individual cellular states. Single-cell RNA sequencing in particular has served as a powerful tool to the study of the molecular circuitries underlyin...

Fluorescence in situ hybridization (FISH) provides a valuable tool for studying the spatial localization of and expression level of genes and cell function in diverse biological contexts. In this chapter, we describe a protocol for the simultaneous detection of RNA (including single-molecule (sm)RNA) and DNA in mammalian embryos using FISH. RNA FIS...

Non-healing skin wound is a problematic complication associated with diabetes. Therapeutic gases delivered by biomaterials have demonstrated powerful wound healing capabilities, but the mechanisms by which they promote skin regeneration remain unclear. Here, we demonstrated the benefit of a carbon monoxide-releasing hyaluronan hydrogel (CO@HAG) in...

Characterizing T cell populations and understanding their developmental relationships may help design more effective cancer immunotherapies. We coupled single-cell transcriptomics and T cell receptor (TCR) αβ profiling of intratumoral and peripheral T cells in ovarian cancer patients to identify transcriptional programs and infer their relationship...

In brief Human embryogenesis still remains largely unexplored. This review helps identify some of our current gaps in knowledge pertaining to preimplantation development, which may have implications for understanding fundamental aspects of human development, assisted reproductive technologies, and stem cell biology. Abstract Preimplantation develo...

Different formative pluripotent stem cells harboring similar functional properties have been recently established to be lineage neutral and germline competent yet have distinct molecular identities. Here, we show that WNT/β-catenin signaling activation sustains transient mouse epiblast-like cells as epiblast-like stem cells (EpiLSCs). EpiLSCs displ...

Ovaries are central to development, fertility, and reproduction of women. A particularly interesting feature of ovaries is their accelerated aging compared to other tissues, leading to loss of function far before other organs senesce. The limited pool of ovarian follicles is generated before birth and once exhausted, menopause will inevitably comme...

The preconceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of assisted reproductive technologies (ART; ∼25%), additives and adjuvants, such as glucocorticoids, are used to improve the success r...

The pre-conceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of Assisted Reproductive Technologies (ART; ~25%), additives and adjuvants, such as glucocorticoids, are utilized to improve the succ...

Study question Is the guinea pig a good model for human preimplantation embryo development? Summary answer Preimplantation guinea pig embryos better recapitulate the human embryo compared to the mouse, offering a promising new model to study preimplantation, naive pluripotency and infertility. What is known already Mouse embryos have historically...

Background: Immune checkpoint blockade (ICB) of PD-1 and/or CTLA-4 can induce long-lasting clinical responses in several neoplasias. However, despite the successful response in some cancer, it is still ineffective for other malignant lesions such as ovarian cancer. Studies on T cell dynamics demonstrated that antitumor immune response from ICB is m...

The first lineage choice in human embryo development separates trophectoderm from the inner cell mass. Naïve human embryonic stem cells are derived from the inner cell mass and offer possibilities to explore how lineage integrity is maintained. Here, we discover that polycomb repressive complex 2 (PRC2) maintains naïve pluripotency and restricts di...

While critical for neurotransmitter synthesis, 14-3-3 proteins are often assumed to have redundant functions due to their ubiquitous expression, but despite this assumption, various 14-3-3 isoforms have been implicated in regulating metabolism. We previously reported contributions of 14-3-3ζ in β-cell function, but these studies were performed in t...

While critical for neurotransmitter synthesis in the brain, members of the 14-3-3 protein family are often assumed to have redundant, over-lapping roles due to their high sequence homology and ubiquitous expression. Despite this assumption, various mammalian 14-3-3 isoforms have now been implicated in regulating cellular and organismal metabolism;...

Two recent papers in Nature show that human blastocyst-like structures (or blastoids) can be generated from human pluripotent stem cells (Yu et al 2021) or through reprogramming of fibroblasts (Liu et al 2021), respectively. Both papers perform extensive single cell transcriptional analysis and compare blastoid cells with the cells in preimplantati...

Totipotency is the ability of a single cell to give rise to all of the differentiated cell types that build the conceptus, yet how to capture this property in vitro remains incompletely understood. Defining totipotency relies on a variety of assays of variable stringency. Here, we describe criteria to define totipotency. We explain how distinct cri...

The human ovary orchestrates sex hormone production and undergoes monthly structural changes to release mature oocytes. The outer lining of the ovary (cortex) has a key role in defining fertility in women as it harbors the ovarian reserve. It has been suggested that oogonial stem cells exist in the ovarian cortex and that these can be captured by D...

Totipotency is the ability of a single cell to give rise to all the differentiated cells that build the conceptus, yet how to capture this property in vitro remains incompletely understood. Defining totipotency relies upon a variety of assays of variable stringency. Here we describe criteria to define totipotency. We illustrate how distinct criteri...

The human ovary orchestrates sex hormone production and undergoes monthly structural changes to release mature oocytes. The outer lining of the ovary (cortex) has a key role in defining fertility in women as it harbors the ovarian reserve. It has been postulated that putative oogonial stem cells exist in the ovarian cortex and that these can be cap...

The human ovary orchestrates sex hormone production and undergoes monthly structural changes to release mature oocytes. The outer lining of the ovary (cortex) has a key role in defining fertility in women as it harbors the ovarian reserve. It has been postulated that putative oogonial stem cells exist in the ovarian cortex and that these can be cap...

Background The idea that changes to the host immune system are critical for cancer progression was proposed a century ago and recently regained experimental support. Results Herein, the hypothesis that hepatocellular carcinoma (HCC) leaves a molecular signature in the host peripheral immune system was tested by profiling DNA methylation in periphe...

DNA methylation is an important enzymatic covalent modification of DNA that plays an important role in genome regulation. DNA methylation patterns are fashioned during development and could be altered in response to experience and exposure. Aberrations in DNA methylation patterns are noted in cancer and other diseases. It is therefore extremely imp...

In this chapter, commonly used methods to assess the genome-wide DNA methylation status are reviewed and compared. The methods described in this chapter include enrichment-based method, Methylated DNA Immunoprecipitation (MeDIP), paired with microarray technology and next generation sequencing, and sodium bisulfate-based techniques including Infini...

Epithelial cells connect via cell-cell junctions to form sheets of cells with separate cellular compartments. These cellular connections are essential for the generation of cellular forms and shapes consistent with organ function. Tissue modulation is dependent on the fine-tuning of mechanical forces that are transmitted in part through the actin c...

Table S2. List of Differentially Expressed Genes between Each Cell Type, Related to Figure 7

Table S4. Details of Antibodies Used for Flow Cytometry and Immunofluorescence Microscopy, Related to Figure 3

Table S5. Information about the Setup of the Flow Cytometers, Related to Figure 3

Imaging was performed at the Live Cell Imaging Facility/Nikon Center of Excellence, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden, supported by grants from the Knut and Alice Wallenberg Foundation, the Swedish Research Council, the Centre for Innovative Medicine, and the Jonasson donation to the School of Technolo...

Human pluripotent stem cells (PSCs) exist in naive and primed states and provide important models to investigate the earliest stages of human development. Naive cells can be obtained through primed-to-naive resetting, but there are no reliable methods to prospectively isolate unmodified naive cells during this process. Here we report comprehensive...

Background/aims: Viral infection during pregnancy is known to affect the fetal brain. The toll-like receptor (TLR)-3 is a pattern recognition receptor activated by viruses known to elicit adverse fetal neurological outcomes. The P-glycoprotein (P-gp) efflux transporter protects the developing fetus by limiting the transfer of substrates across bot...

Excel file of differentially expressed genes from SCDE analysis between lineages within each developmental time point.DOI: http://dx.doi.org/10.7554/eLife.22906.008

Excel file of differentially expressed genes from SCDE analysis between ?Cdx2-low? and ?Cdx2-high? cell populations (based on PCA groupings) at the early 32 cell stage.Top 50 ?Cdx2-low? genes and top 50 ?Cdx2-high? genes used as ICM- and TE-specific gene signature, respectively.DOI: http://dx.doi.org/10.7554/eLife.22906.006

Excel file of differentially expressed genes from SCDE analysis between developmental time points within each lineage.DOI: http://dx.doi.org/10.7554/eLife.22906.009

(Cell 165, 1012–1026; May 5, 2016) Several errors occurred during the preparation of the above article analyzing the transcriptomes of single cells from human embryos at embryonic days (E) 3–7 and describing the segregation of prelineage (prelin) cells into trophectoderm (TE), primitive endoderm (PE), and epiblast (EPI) and X chromosome dynamics. W...

Scientific Reports 6 : Article number: 28995 10.1038/srep28995 ; published online: 14 July 2016 ; updated: 02 September 2016 The original version of this Article contained a typographical error in the spelling of the author Sophie Petropoulos, which was incorrectly given as Sophie Petropoulous.

Leucine twenty homeobox gene (LEUTX) is a PAIRED (PRD)-like homeobox gene that is expressed nearly exclusively in human preimplantation embryos. We previously identified a novel transcription start site for the predicted human LEUTX gene based on the transcriptional analysis of human preimplantation embryos. The novel variant encodes a protein with...

PAIRED (PRD)-like homeobox genes belong to a class of predicted transcription factor genes. Several of these PRD-like homeobox genes have been predicted in silico from genomic sequence but until recently had no evidence of transcript expression. We found recently that nine PRD-like homeobox genes, ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB, NOBOX, TPRX1...

Pluripotency, differentiation and X chromosome inactivation (XCI) are key aspects of embryonic development. However, the underlying relationship and mechanisms among these processes remain unclear. Here we systematically dissected these features along developmental progression using mouse embryonic stem cells (mESCs) and single-cell RNA sequencing...

Familial dysautonomia (FD) is an autosomal recessive congenital neuropathy, primarily presented in Ashkenazi Jews. The most common mutation in FD patients results from a single base pair substitution of an intronic splice site in the IKBKAP gene which disrupts normal mRNA splicing and leads to tissue-specific reduction of IKBKAP protein (IKAP). To...

List of 300 maintained lineage-specific genes (100 genes from each of the lineages, EPI, PE, and TE) and their mean expression levels per lineage and embryonic day. These genes were top-ranked with respect to tending to maintain their lineage specificity from E5 to E7 and were used for GO analysis (Figure 2) and for developmental progression analys...

Table S1. Differential Gene Expression Analysis of Preimplantation Lineage Differences, Related to Figure 2 Differential expression test-statistica per lineage and embryonic day, for all RefSeq genes with respect to contrasting lineages.

Table S4. Differential Gene Expression and Gene Ontology Analysis of TE Subpopulation Differences, Related to Figure 3 Differential expression test-statistica per sub-population and embryonic day (E6 and E7), for all RefSeq genes, with respect to contrasting TE sub-populations. Rightmost columns contain Gene Ontology gene set enrichment analysis r...

Correlations were calculated amongst the top 300 maintained lineage genes (100 from each lineage).

Gene set enrichment analysis of Gene Ontology terms with respect to 300 maintained lineage genes (Table S2).

Table S5. Differential Gene Expression Analysis of Embryonic Day Differences, Related to Figure 4 Differential expression test-statistica per embryonic day and lineage, for all RefSeq genes, with respect to contrasting embryonic days.