{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/365923"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/365923","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"Dissecting immune interactions in health and disease with multiomics and spatial technologies","abstract":"Cells are the basic building blocks of life, forming the enormous plethora of tissues and living organisms on Earth. They have a high diversity of phenotypes and functions in different environments. The high-throughput tools to profile different modalities from a single cell have grown exponentially in recent years. This now allows us to draw a complete picture of how cells function in different environments for the first time. In the work of my thesis, I use high-throughput multiomics and spatial technologies to create comprehensive cell atlases. I focus on studying the immune cell communication among themselves and with other cells in the context of disease and development. Chapter 1 starts with an outline of the background on cell biology and the impact that genomic technologies have on how we can study cellular processes. I then discuss the experimental methodology of high-throughput multiomics and spatial techniques, and computational tools for the analysis of such data. Following is the introduction to the two projects comprising the work of my thesis: (i) a multiomics study of Common Variable Immunodeficiency (CVID) and, (ii) a spatial multiomics map of the Maternal-Fetal Interface (MFI) in early pregnancy in humans. Chapter 2 outlines materials and methods used in this work, showcasing the workflow for each project. Chapter 3 details the multiomics atlas of Common Variable Immunodeficiency (CVID). This condition is characterised by defects in the function of B cells, a type of adaptive immune cells capable of producing antibodies to fight infections. I analyse gene expression and chromatin accessibility data of B cells from a pair of monozygotic CVID-discordant twins. I uncover potential defects in the epigenome of the affected twin’s B cells. Next, after in vitro stimulation of these twins’ PBMCs, I observe CVID-associated transcriptional dysregulation in immune subsets additional to those in B cells. I discover defects in the immune cell crosstalk between B cells and other immune compartments of the CVID twin. With an expanded cohort of CVID patients and healthy individuals, I go on to further validate these findings. These results show that, in addition to B-cell-intrinsic alterations, defects in cell-cell communication between B cells and other immune compartments may be compromising the correct immune response in CVID. Chapter 4 presents the work on creating a comprehensive spatial multiomics atlas of the maternal-fetal interface in early pregnancy. Firstly, I characterise the signatures and differentiation trajectories of trophoblast cells - the building blocks of placenta. I then focus on the crosstalk between invading trophoblast and maternal immune cells. I predict putative cell-cell communication events and validate in situ the selected molecules mediating these interactions. I propose a model of arterial transformation facilitated by fetal trophoblast and their communication with maternal cells. This work expands our knowledge about the cellular and molecular players in the maternal-fetal dialog in the first trimester of pregnancy, definitive of its success. Chapter 5 describes the work on modelling the dialog between decidual natural killer (dNK) cells, a type of innate immune cell most abundant in pregnant decidua, and the invading trophoblast at the maternal-fetal interface using primary trophoblast organoids (PTO). I benchmark the PTO system against the in vivo trophoblast atlas I described in chapter 4. After defining trophoblast cell states in vitro, I perform comparative analysis of PTOs stimulated with a cocktail of chemokines that in vivo are secreted by dNK cells and unstimulated PTOs as control. I propose a putative effect of the signals from dNK cells on trophoblast invasion in the first trimester of pregnancy. Lastly, Chapter 6 provides an overview of all the described work, as well as a discussion of how the novel high-throughput multiomic and spatial technologies together with in vitro models shape our current view of fundamental biology, and how they will impact future directions of research.","abstract_html":"Cells are the basic building blocks of life, forming the enormous plethora of tissues and living organisms on Earth. They have a high diversity of phenotypes and functions in different environments. The high-throughput tools to profile different modalities from a single cell have grown exponentially in recent years. This now allows us to draw a complete picture of how cells function in different environments for the first time. In the work of my thesis, I use high-throughput multiomics and spatial technologies to create comprehensive cell atlases. I focus on studying the immune cell communication among themselves and with other cells in the context of disease and development. Chapter 1 starts with an outline of the background on cell biology and the impact that genomic technologies have on how we can study cellular processes. I then discuss the experimental methodology of high-throughput multiomics and spatial techniques, and computational tools for the analysis of such data. Following is the introduction to the two projects comprising the work of my thesis: (i) a multiomics study of Common Variable Immunodeficiency (CVID) and, (ii) a spatial multiomics map of the Maternal-Fetal Interface (MFI) in early pregnancy in humans. Chapter 2 outlines materials and methods used in this work, showcasing the workflow for each project. Chapter 3 details the multiomics atlas of Common Variable Immunodeficiency (CVID). This condition is characterised by defects in the function of B cells, a type of adaptive immune cells capable of producing antibodies to fight infections. I analyse gene expression and chromatin accessibility data of B cells from a pair of monozygotic CVID-discordant twins. I uncover potential defects in the epigenome of the affected twin’s B cells. Next, after in vitro stimulation of these twins’ PBMCs, I observe CVID-associated transcriptional dysregulation in immune subsets additional to those in B cells. I discover defects in the immune cell crosstalk between B cells and other immune compartments of the CVID twin. With an expanded cohort of CVID patients and healthy individuals, I go on to further validate these findings. These results show that, in addition to B-cell-intrinsic alterations, defects in cell-cell communication between B cells and other immune compartments may be compromising the correct immune response in CVID. Chapter 4 presents the work on creating a comprehensive spatial multiomics atlas of the maternal-fetal interface in early pregnancy. Firstly, I characterise the signatures and differentiation trajectories of trophoblast cells - the building blocks of placenta. I then focus on the crosstalk between invading trophoblast and maternal immune cells. I predict putative cell-cell communication events and validate in situ the selected molecules mediating these interactions. I propose a model of arterial transformation facilitated by fetal trophoblast and their communication with maternal cells. This work expands our knowledge about the cellular and molecular players in the maternal-fetal dialog in the first trimester of pregnancy, definitive of its success. Chapter 5 describes the work on modelling the dialog between decidual natural killer (dNK) cells, a type of innate immune cell most abundant in pregnant decidua, and the invading trophoblast at the maternal-fetal interface using primary trophoblast organoids (PTO). I benchmark the PTO system against the in vivo trophoblast atlas I described in chapter 4. After defining trophoblast cell states in vitro, I perform comparative analysis of PTOs stimulated with a cocktail of chemokines that in vivo are secreted by dNK cells and unstimulated PTOs as control. I propose a putative effect of the signals from dNK cells on trophoblast invasion in the first trimester of pregnancy. Lastly, Chapter 6 provides an overview of all the described work, as well as a discussion of how the novel high-throughput multiomic and spatial technologies together with in vitro models shape our current view of fundamental biology, and how they will impact future directions of research.","abstract_has_math":false,"creators":["Arutyunyan, Anna"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Vento-Tormo, Roser"],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-09-01","date_published":"2023-09-01","updated_at":"2026-07-24T01:33:18Z","subjects":["Cell-cell communication","CVID","Maternal-fetal interface","Single-cell genomics"],"languages":["eng"],"rights":[],"rights_urls":["https://www.repository.cam.ac.uk/bitstreams/1a2f169f-d642-4cff-8bce-a85981250c3e/download","https://www.rioxx.net/licenses/all-rights-reserved/"],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.106984","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Vento-Tormo, Roser"]},{"key":"dc:contributor.sponsor","label":"Sponsor","values":["Wellcome Trust 4-Year PhD Studentship"]},{"key":"dc:creator","label":"Author","values":["Arutyunyan, Anna"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2023-09-01"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/365923"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Cell-cell communication","CVID","Maternal-fetal interface","Single-cell genomics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["https://www.repository.cam.ac.uk/bitstreams/1a2f169f-d642-4cff-8bce-a85981250c3e/download","https://www.rioxx.net/licenses/all-rights-reserved/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.17863/CAM.106984"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://www.repository.cam.ac.uk/bitstreams/061771b9-3ef9-4882-8b15-6fea9c7c9af7/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Cells are the basic building blocks of life, forming the enormous plethora of tissues and living organisms on Earth. 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Following is the introduction to the two projects comprising the work of my thesis: (i) a multiomics study of Common Variable Immunodeficiency (CVID) and, (ii) a spatial multiomics map of the Maternal-Fetal Interface (MFI) in early pregnancy in humans. Chapter 2 outlines materials and methods used in this work, showcasing the workflow for each project. Chapter 3 details the multiomics atlas of Common Variable Immunodeficiency (CVID). This condition is characterised by defects in the function of B cells, a type of adaptive immune cells capable of producing antibodies to fight infections. I analyse gene expression and chromatin accessibility data of B cells from a pair of monozygotic CVID-discordant twins. I uncover potential defects in the epigenome of the affected twin’s B cells. Next, after in vitro stimulation of these twins’ PBMCs, I observe CVID-associated transcriptional dysregulation in immune subsets additional to those in B cells. I discover defects in the immune cell crosstalk between B cells and other immune compartments of the CVID twin. With an expanded cohort of CVID patients and healthy individuals, I go on to further validate these findings. These results show that, in addition to B-cell-intrinsic alterations, defects in cell-cell communication between B cells and other immune compartments may be compromising the correct immune response in CVID. Chapter 4 presents the work on creating a comprehensive spatial multiomics atlas of the maternal-fetal interface in early pregnancy. Firstly, I characterise the signatures and differentiation trajectories of trophoblast cells - the building blocks of placenta. I then focus on the crosstalk between invading trophoblast and maternal immune cells. I predict putative cell-cell communication events and validate in situ the selected molecules mediating these interactions. I propose a model of arterial transformation facilitated by fetal trophoblast and their communication with maternal cells. This work expands our knowledge about the cellular and molecular players in the maternal-fetal dialog in the first trimester of pregnancy, definitive of its success. Chapter 5 describes the work on modelling the dialog between decidual natural killer (dNK) cells, a type of innate immune cell most abundant in pregnant decidua, and the invading trophoblast at the maternal-fetal interface using primary trophoblast organoids (PTO). I benchmark the PTO system against the in vivo trophoblast atlas I described in chapter 4. After defining trophoblast cell states in vitro, I perform comparative analysis of PTOs stimulated with a cocktail of chemokines that in vivo are secreted by dNK cells and unstimulated PTOs as control. I propose a putative effect of the signals from dNK cells on trophoblast invasion in the first trimester of pregnancy. 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Following is the introduction to the two projects comprising the work of my thesis: (i) a multiomics study of Common Variable Immunodeficiency (CVID) and, (ii) a spatial multiomics map of the Maternal-Fetal Interface (MFI) in early pregnancy in humans. Chapter 2 outlines materials and methods used in this work, showcasing the workflow for each project. Chapter 3 details the multiomics atlas of Common Variable Immunodeficiency (CVID). This condition is characterised by defects in the function of B cells, a type of adaptive immune cells capable of producing antibodies to fight infections. I analyse gene expression and chromatin accessibility data of B cells from a pair of monozygotic CVID-discordant twins. I uncover potential defects in the epigenome of the affected twin’s B cells. Next, after in vitro stimulation of these twins’ PBMCs, I observe CVID-associated transcriptional dysregulation in immune subsets additional to those in B cells. I discover defects in the immune cell crosstalk between B cells and other immune compartments of the CVID twin. With an expanded cohort of CVID patients and healthy individuals, I go on to further validate these findings. These results show that, in addition to B-cell-intrinsic alterations, defects in cell-cell communication between B cells and other immune compartments may be compromising the correct immune response in CVID. Chapter 4 presents the work on creating a comprehensive spatial multiomics atlas of the maternal-fetal interface in early pregnancy. Firstly, I characterise the signatures and differentiation trajectories of trophoblast cells - the building blocks of placenta. I then focus on the crosstalk between invading trophoblast and maternal immune cells. I predict putative cell-cell communication events and validate in situ the selected molecules mediating these interactions. I propose a model of arterial transformation facilitated by fetal trophoblast and their communication with maternal cells. This work expands our knowledge about the cellular and molecular players in the maternal-fetal dialog in the first trimester of pregnancy, definitive of its success. Chapter 5 describes the work on modelling the dialog between decidual natural killer (dNK) cells, a type of innate immune cell most abundant in pregnant decidua, and the invading trophoblast at the maternal-fetal interface using primary trophoblast organoids (PTO). I benchmark the PTO system against the in vivo trophoblast atlas I described in chapter 4. After defining trophoblast cell states in vitro, I perform comparative analysis of PTOs stimulated with a cocktail of chemokines that in vivo are secreted by dNK cells and unstimulated PTOs as control. I propose a putative effect of the signals from dNK cells on trophoblast invasion in the first trimester of pregnancy. 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