{"entity": "researcher", "timestamp": "2026-07-20T13:10:52.237Z", "family": "Zhao", "given": "Cheng", "initials": "C", "orcid": "0000-0003-0518-5924", "affiliations": ["Karolinska Institutet."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4cd6a95b29e44b3fa8fed63033d26393.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4cd6a95b29e44b3fa8fed63033d26393"}}, "publications": [{"entity": "publication", "iuid": "aebab6081ba14fa69b3ca92ae5a3e10d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aebab6081ba14fa69b3ca92ae5a3e10d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aebab6081ba14fa69b3ca92ae5a3e10d"}}, "title": "The guinea pig serves as an alternative model to study human preimplantation development.", "authors": [{"family": "Canizo", "given": "Jesica Romina", "initials": "JR"}, {"family": "Zhao", "given": "Cheng", "initials": "C", "orcid": "0000-0003-0518-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cd6a95b29e44b3fa8fed63033d26393.json"}}, {"family": "Petropoulos", "given": "Sophie", "initials": "S", "orcid": "0000-0003-2293-8238", "researcher": {"href": "https://publications.scilifelab.se/researcher/0766fd90df1f4199a000eb84b06e2d31.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "volume": "27", "issue": "4", "pages": "696-710", "issn-l": null}, "abstract": "Preimplantation development is an important window of human embryogenesis. However, ethical constraints and the limitations involved in studying human embryos often necessitate the use of alternative model systems. Here we identify the guinea pig as a promising small animal model to study human preimplantation development. Using single-cell RNA-sequencing, we generated an atlas of guinea pig preimplantation development, revealing its close resemblance to early human embryogenesis in terms of the timing of compaction, early-, mid- and late-blastocyst formation, and implantation, and the spatio-temporal expression of key lineage markers. We also show conserved roles of Hippo, MEK-ERK and JAK-STAT signalling. Furthermore, multi-species analysis highlights the spatio-temporal expression of conserved and divergent genes during preimplantation development and pluripotency. The guinea pig serves as a valuable animal model for advancing preimplantation development and stem cell research, and can be leveraged to better understand the longer-term impact of early exposures on offspring outcomes.", "doi": "10.1038/s41556-025-01642-9", "pmid": "40185949", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11991919"}, {"db": "pii", "key": "10.1038/s41556-025-01642-9"}], "notes": [], "created": "2025-11-28T10:46:11.150Z", "modified": "2025-11-28T10:46:11.192Z"}, {"entity": "publication", "iuid": "9baaf85a6b744b00baac397292f47517", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9baaf85a6b744b00baac397292f47517.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9baaf85a6b744b00baac397292f47517"}}, "title": "A comprehensive human embryo reference tool using single-cell RNA-sequencing data", "authors": [{"family": "Zhao", "given": "Cheng", "initials": "C", "orcid": "0000-0003-0518-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cd6a95b29e44b3fa8fed63033d26393.json"}}, {"family": "Plaza Reyes", "given": "Alvaro", "initials": "A", "orcid": "0000-0003-1167-6316", "researcher": {"href": "https://publications.scilifelab.se/researcher/36f7ddaf16ac45bfad26c96f292f2072.json"}}, {"family": "Schell", "given": "John Paul", "initials": "JP"}, {"family": "Weltner", "given": "Jere", "initials": "J"}, {"family": "Ortega", "given": "Nicol\u00e1s M", "initials": "NM"}, {"family": "Zheng", "given": "Yi", "initials": "Y", "orcid": "0000-0002-2685-3680", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5ae32c43903498dab060a3a31695705.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Baqu\u00e9-Vidal", "given": "Laura", "initials": "L", "orcid": "0009-0008-8128-6069", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cbb3bfdf71e4002acffa6b14ef58c60.json"}}, {"family": "Sokka", "given": "Joonas", "initials": "J", "orcid": "0000-0002-0377-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/f834bc634e2049539fb66b3286020ed4.json"}}, {"family": "Trokovic", "given": "Ras", "initials": "R", "orcid": "0000-0002-3065-6663", "researcher": {"href": "https://publications.scilifelab.se/researcher/510f22386f8744e2a50d7f803b3da831.json"}}, {"family": "Cox", "given": "Brian", "initials": "B"}, {"family": "Rossant", "given": "Janet", "initials": "J", "orcid": "0000-0002-3731-5466", "researcher": {"href": "https://publications.scilifelab.se/researcher/be15218445df4636ab47e1a1dcf8d69c.json"}}, {"family": "Fu", "given": "Jianping", "initials": "J", "orcid": "0000-0001-9629-6739", "researcher": {"href": "https://publications.scilifelab.se/researcher/127bba88c5534146ae9ba1b10929bb4b.json"}}, {"family": "Petropoulos", "given": "Sophie", "initials": "S", "orcid": "0000-0003-2293-8238", "researcher": {"href": "https://publications.scilifelab.se/researcher/0766fd90df1f4199a000eb84b06e2d31.json"}}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}], "type": "journal-article", "published": "2025-01-00", "journal": {"title": "Nat Methods", "issn": "1548-7091", "issn-l": "1548-7091", "volume": "22", "issue": "1", "pages": "193-206"}, "abstract": "Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of embryo models hinges on their molecular, cellular and structural fidelities to their in vivo counterparts. To authenticate human embryo models, single-cell RNA sequencing has been utilized for unbiased transcriptional profiling. However, an organized and integrated human single-cell RNA-sequencing dataset, serving as a universal reference for benchmarking human embryo models, remains unavailable. Here we developed such a reference through the integration of six published human datasets covering development from the zygote to the gastrula. Lineage annotations are contrasted and validated with available human and nonhuman primate datasets. Using stabilized Uniform Manifold Approximation and Projection, we constructed an early embryogenesis prediction tool, where query datasets can be projected on the reference and annotated with predicted cell identities. Using this reference tool, we examined published human embryo models, highlighting the risk of misannotation when relevant references are not utilized for benchmarking and authentication.", "doi": "10.1038/s41592-024-02493-2", "pmid": "39543283", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11725501"}, {"db": "pii", "key": "10.1038/s41592-024-02493-2"}], "notes": [], "created": "2024-11-14T12:28:22.114Z", "modified": "2025-12-04T19:32:09.248Z"}, {"entity": "publication", "iuid": "f0f43f9275cf45ba9bedab180ad79085", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0f43f9275cf45ba9bedab180ad79085.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0f43f9275cf45ba9bedab180ad79085"}}, "title": "Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.", "authors": [{"family": "Zhao", "given": "Cheng", "initials": "C", "orcid": "0000-0003-0518-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cd6a95b29e44b3fa8fed63033d26393.json"}}, {"family": "Biondic", "given": "Savana", "initials": "S"}, {"family": "Vandal", "given": "Katherine", "initials": "K"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M"}, {"family": "Sommer", "given": "Theresa Maria", "initials": "TM"}, {"family": "Canizo", "given": "Jesica", "initials": "J"}, {"family": "Clark", "given": "Stephen", "initials": "S"}, {"family": "Raymond", "given": "Pascal", "initials": "P"}, {"family": "Zenklusen", "given": "Daniel R", "initials": "DR", "orcid": "0000-0002-0067-0093", "researcher": {"href": "https://publications.scilifelab.se/researcher/570efd02034b4c8c809c51476378da15.json"}}, {"family": "Rivron", "given": "Nicolas", "initials": "N"}, {"family": "Reik", "given": "Wolf", "initials": "W"}, {"family": "Petropoulos", "given": "Sophie", "initials": "S", "orcid": "0000-0003-2293-8238", "researcher": {"href": "https://publications.scilifelab.se/researcher/0766fd90df1f4199a000eb84b06e2d31.json"}}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Genome Res.", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "32", "issue": "9", "pages": "1627-1641"}, "abstract": "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; \u223c25%), additives and adjuvants, such as glucocorticoids, are used to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and the ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study, we present a comprehensive single-cell transcriptome, methylome, and small RNA atlas in the day 7 human embryo. We show that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the TE lineage, and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sublineages, supported by the presence of extravillous trophoblast markers in the polar sublineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation-DNA methylation and microRNAs (miRNAs)-likely underlies the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.", "doi": "10.1101/gr.276665.122", "pmid": "35948369", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9528977"}, {"db": "pii", "key": "gr.276665.122"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2022-08-12T08:24:11.793Z", "modified": "2024-01-16T13:48:35.397Z"}]}