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Elucidating cell-fate decision-making of mammalian pluripotent cells through single-cell transcriptomics
Elucidating cell-fate decision-making of mammalian pluripotent cells through single-cell transcriptomics
Understanding cellular identity, heterogeneity and differentiation in mammals is crucial for solving many long-standing questions regarding regenerative medicine, developmental biology, and evolution. Recent cutting-edge molecular profiling methods have been developed to explore cell identity in different biological systems. Particularly, investigating gene expression patterns in individual cells with single-cell transcriptomics has provided significant opportunities for understanding complex tissues. By using single-cell transcriptomics, it has been possible to extract a large amount of information from cells in various tissues, such as embryonic and cancer tissues. Having access to such an extensive molecular profile from single cells paves the way to understanding factors that shape cell identity in a data-driven manner. However, to achieve this aim, the development of new and tailored computational tools are required to extract biologically meaningful information. In this dissertation, I discuss how I have explored the molecular factors that contribute to regulating cellular fate decision in different types of mammalian pluripotent cells by analysing single-cell RNA-seq (scRNA-seq) data. Specifically, I show my contributions to understanding early human and mouse development, as well as hematopoiesis in adult mice. By using state-of-the-art as well as novel computational tools and algorithms, I contributed to the first-ever single-cell characterization of a human embryo in the gastrula stage. Afterward, I demonstrate my work on elucidating stem cell state transition in early mouse development in both in vivo and in vitro models. Finally, I present my contribution to investigating the effect of the Sema4a signaling molecule on regulating hematopoietic stem cells in adult mice by computationally comparing the scRNA-seq data from wild-type and mutant mice. Overall, the studies present in the thesis demonstrate the power of single-cell transcriptomics in characterizing cellular heterogeneity and its link with cell fate decision, as well as elucidating possible mechanisms of cell differentiation in different model systems and organisms.
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Mahammadov, Elmir
2023
English
Universitätsbibliothek der Ludwig-Maximilians-Universität München
Mahammadov, Elmir (2023): Elucidating cell-fate decision-making of mammalian pluripotent cells through single-cell transcriptomics. Dissertation, LMU München: Faculty of Biology
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Abstract

Understanding cellular identity, heterogeneity and differentiation in mammals is crucial for solving many long-standing questions regarding regenerative medicine, developmental biology, and evolution. Recent cutting-edge molecular profiling methods have been developed to explore cell identity in different biological systems. Particularly, investigating gene expression patterns in individual cells with single-cell transcriptomics has provided significant opportunities for understanding complex tissues. By using single-cell transcriptomics, it has been possible to extract a large amount of information from cells in various tissues, such as embryonic and cancer tissues. Having access to such an extensive molecular profile from single cells paves the way to understanding factors that shape cell identity in a data-driven manner. However, to achieve this aim, the development of new and tailored computational tools are required to extract biologically meaningful information. In this dissertation, I discuss how I have explored the molecular factors that contribute to regulating cellular fate decision in different types of mammalian pluripotent cells by analysing single-cell RNA-seq (scRNA-seq) data. Specifically, I show my contributions to understanding early human and mouse development, as well as hematopoiesis in adult mice. By using state-of-the-art as well as novel computational tools and algorithms, I contributed to the first-ever single-cell characterization of a human embryo in the gastrula stage. Afterward, I demonstrate my work on elucidating stem cell state transition in early mouse development in both in vivo and in vitro models. Finally, I present my contribution to investigating the effect of the Sema4a signaling molecule on regulating hematopoietic stem cells in adult mice by computationally comparing the scRNA-seq data from wild-type and mutant mice. Overall, the studies present in the thesis demonstrate the power of single-cell transcriptomics in characterizing cellular heterogeneity and its link with cell fate decision, as well as elucidating possible mechanisms of cell differentiation in different model systems and organisms.