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Aleksandra Tata

Assistant Research Professor of Cell Biology
Cell Biology

Selected Publications


Meta-Analysis of COVID-19 BAL Single-Cell RNA Sequencing Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates.

Journal Article Am J Respir Cell Mol Biol · December 2023 Single-cell RNA sequencing (scRNA-seq) of BAL cells has provided insights into coronavirus disease (COVID-19). However, reports have been limited by small patient cohorts. We performed a meta-analysis of BAL scRNA-seq data from healthy control subjects (n  ... Full text Open Access Link to item Cite

Transitional cell states sculpt tissue topology during lung regeneration.

Journal Article Cell Stem Cell · November 2, 2023 Organ regeneration requires dynamic cell interactions to reestablish cell numbers and tissue architecture. While we know the identity of progenitor cells that replace lost tissue, the transient states they give rise to and their role in repair remain elusi ... Full text Link to item Cite

Host range, transmissibility and antigenicity of a pangolin coronavirus.

Journal Article Nat Microbiol · October 2023 The pathogenic and cross-species transmission potential of SARS-CoV-2-related coronaviruses (CoVs) remain poorly characterized. Here we recovered a wild-type pangolin (Pg) CoV GD strain including derivatives encoding reporter genes using reverse genetics. ... Full text Open Access Link to item Cite

Efficient Adeno-associated Virus-mediated Transgenesis in Alveolar Stem Cells and Associated Niches.

Journal Article Am J Respir Cell Mol Biol · September 2023 Targeted delivery of transgenes to tissue-resident stem cells and related niches offers avenues for interrogating pathways and editing endogenous alleles for therapeutic interventions. Here, we survey multiple adeno-associated virus (AAV) serotypes, admini ... Full text Link to item Cite

Human lung organoids as a model for respiratory virus replication and countermeasure performance in human hosts.

Journal Article Transl Res · December 2022 Human respiratory viruses induce a wide breadth of disease phenotypes and outcomes of varying severity. Innovative models that recapitulate the human respiratory tract are needed to study such viruses, understand the virus-host interactions underlying repl ... Full text Link to item Cite

Sex differences in resilience to ferroptosis underlie sexual dimorphism in kidney injury and repair.

Journal Article Cell Rep · November 8, 2022 In both humans and mice, repair of acute kidney injury is worse in males than in females. Here, we provide evidence that this sexual dimorphism results from sex differences in ferroptosis, an iron-dependent, lipid-peroxidation-driven regulated cell death. ... Full text Open Access Link to item Cite

Multi-apical polarity of alveolar stem cells and their dynamics during lung development and regeneration.

Journal Article iScience · October 21, 2022 Epithelial cells of diverse tissues are characterized by the presence of a single apical domain. In the lung, electron microscopy studies have suggested that alveolar type-2 epithelial cells (AT2s) en face multiple alveolar sacs. However, apical and basola ... Full text Open Access Link to item Cite

Lung Regeneration: Cells, Models, and Mechanisms.

Journal Article Cold Spring Harb Perspect Biol · October 3, 2022 Lung epithelium, the lining that covers the inner surface of the respiratory tract, is directly exposed to the environment and thus susceptible to airborne toxins, irritants, and pathogen-induced damages. In adult mammalian lungs, epithelial cells are gene ... Full text Open Access Link to item Cite

Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication.

Journal Article Science signaling · October 2022 Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccin ... Full text Open Access Cite

Defined conditions for long-term expansion of murine and human alveolar epithelial stem cells in three-dimensional cultures.

Journal Article STAR Protoc · June 17, 2022 Alveolar type 2 cells (AT2s) serve as stem cells of the alveoli and restore cell numbers after injury. Here, we describe a detailed protocol for the isolation, purification, and culture of murine and human AT2s. We have developed chemically defined and str ... Full text Open Access Link to item Cite

Human distal lung maps and lineage hierarchies reveal a bipotent progenitor.

Journal Article Nature · April 2022 Featured Publication Mapping the spatial distribution and molecular identity of constituent cells is essential for understanding tissue dynamics in health and disease. We lack a comprehensive map of human distal airways, including the terminal and respiratory bronchioles (TRBs ... Full text Open Access Link to item Cite

An In Vitro Microfluidic Alveolus Model to Study Lung Biomechanics.

Journal Article Front Bioeng Biotechnol · 2022 The gas exchange units of the lung, the alveoli, are mechanically active and undergo cyclic deformation during breathing. The epithelial cells that line the alveoli contribute to lung function by reducing surface tension via surfactant secretion, which is ... Full text Open Access Link to item Cite

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair.

Journal Article Elife · July 19, 2021 Overwhelming lipid peroxidation induces ferroptotic stress and ferroptosis, a non-apoptotic form of regulated cell death that has been implicated in maladaptive renal repair in mice and humans. Using single-cell transcriptomic and mouse genetic approaches, ... Full text Open Access Link to item Cite

Epithelial cell plasticity: breaking boundaries and changing landscapes.

Journal Article EMBO Rep · July 5, 2021 Epithelial tissues respond to a wide variety of environmental and genotoxic stresses. As an adaptive mechanism, cells can deviate from their natural paths to acquire new identities, both within and across lineages. Under extreme conditions, epithelial tiss ... Full text Open Access Link to item Cite

Stem cells of submucosal glands: their function as tissue stem cells and a reserve population for airway repair

Journal Article ERS Monograph · January 1, 2021 In the human lung, SMGs are the main source of mucus, a key component of airway clearance and defence. They are tubuloacinar structures buried in the mesenchyme along the cartilaginous airways and are composed of ciliated ducts, collecting ducts, mucous tu ... Full text Cite

Identification of a Repair-Supportive Mesenchymal Cell Population during Airway Epithelial Regeneration.

Journal Article Cell Rep · December 22, 2020 Tissue regeneration requires coordinated and dynamic remodeling of stem and progenitor cells and the surrounding niche. Although the plasticity of epithelial cells has been well explored in many tissues, the dynamic changes occurring in niche cells remain ... Full text Link to item Cite

Human Lung Stem Cell-Based Alveolospheres Provide Insights into SARS-CoV-2-Mediated Interferon Responses and Pneumocyte Dysfunction.

Journal Article Cell Stem Cell · December 3, 2020 Featured Publication Coronavirus infection causes diffuse alveolar damage leading to acute respiratory distress syndrome. The absence of ex vivo models of human alveolar epithelium is hindering an understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here, we repo ... Full text Open Access Link to item Cite

Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis.

Journal Article Nat Cell Biol · August 2020 Featured Publication Stem cells undergo dynamic changes in response to injury to regenerate lost cells. However, the identity of transitional states and the mechanisms that drive their trajectories remain understudied. Using lung organoids, multiple in vivo repair models, sing ... Full text Link to item Cite

Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury.

Journal Article Cell Stem Cell · May 3, 2018 Featured Publication Cells demonstrate plasticity following injury, but the extent of this phenomenon and the cellular mechanisms involved remain underexplored. Using single-cell RNA sequencing (scRNA-seq) and lineage tracing, we uncover that myoepithelial cells (MECs) of the ... Full text Link to item Cite

Developmental History Provides a Roadmap for the Emergence of Tumor Plasticity.

Journal Article Dev Cell · March 26, 2018 We show that the loss or gain of transcription factor programs that govern embryonic cell-fate specification is associated with a form of tumor plasticity characterized by the acquisition of alternative cell fates normally characteristic of adjacent organs ... Full text Link to item Cite

Meta-Analysis of COVID-19 BAL Single-Cell RNA Sequencing Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates.

Journal Article Am J Respir Cell Mol Biol · December 2023 Single-cell RNA sequencing (scRNA-seq) of BAL cells has provided insights into coronavirus disease (COVID-19). However, reports have been limited by small patient cohorts. We performed a meta-analysis of BAL scRNA-seq data from healthy control subjects (n  ... Full text Open Access Link to item Cite

Transitional cell states sculpt tissue topology during lung regeneration.

Journal Article Cell Stem Cell · November 2, 2023 Organ regeneration requires dynamic cell interactions to reestablish cell numbers and tissue architecture. While we know the identity of progenitor cells that replace lost tissue, the transient states they give rise to and their role in repair remain elusi ... Full text Link to item Cite

Host range, transmissibility and antigenicity of a pangolin coronavirus.

Journal Article Nat Microbiol · October 2023 The pathogenic and cross-species transmission potential of SARS-CoV-2-related coronaviruses (CoVs) remain poorly characterized. Here we recovered a wild-type pangolin (Pg) CoV GD strain including derivatives encoding reporter genes using reverse genetics. ... Full text Open Access Link to item Cite

Efficient Adeno-associated Virus-mediated Transgenesis in Alveolar Stem Cells and Associated Niches.

Journal Article Am J Respir Cell Mol Biol · September 2023 Targeted delivery of transgenes to tissue-resident stem cells and related niches offers avenues for interrogating pathways and editing endogenous alleles for therapeutic interventions. Here, we survey multiple adeno-associated virus (AAV) serotypes, admini ... Full text Link to item Cite

Human lung organoids as a model for respiratory virus replication and countermeasure performance in human hosts.

Journal Article Transl Res · December 2022 Human respiratory viruses induce a wide breadth of disease phenotypes and outcomes of varying severity. Innovative models that recapitulate the human respiratory tract are needed to study such viruses, understand the virus-host interactions underlying repl ... Full text Link to item Cite

Sex differences in resilience to ferroptosis underlie sexual dimorphism in kidney injury and repair.

Journal Article Cell Rep · November 8, 2022 In both humans and mice, repair of acute kidney injury is worse in males than in females. Here, we provide evidence that this sexual dimorphism results from sex differences in ferroptosis, an iron-dependent, lipid-peroxidation-driven regulated cell death. ... Full text Open Access Link to item Cite

Multi-apical polarity of alveolar stem cells and their dynamics during lung development and regeneration.

Journal Article iScience · October 21, 2022 Epithelial cells of diverse tissues are characterized by the presence of a single apical domain. In the lung, electron microscopy studies have suggested that alveolar type-2 epithelial cells (AT2s) en face multiple alveolar sacs. However, apical and basola ... Full text Open Access Link to item Cite

Lung Regeneration: Cells, Models, and Mechanisms.

Journal Article Cold Spring Harb Perspect Biol · October 3, 2022 Lung epithelium, the lining that covers the inner surface of the respiratory tract, is directly exposed to the environment and thus susceptible to airborne toxins, irritants, and pathogen-induced damages. In adult mammalian lungs, epithelial cells are gene ... Full text Open Access Link to item Cite

Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication.

Journal Article Science signaling · October 2022 Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccin ... Full text Open Access Cite

Defined conditions for long-term expansion of murine and human alveolar epithelial stem cells in three-dimensional cultures.

Journal Article STAR Protoc · June 17, 2022 Alveolar type 2 cells (AT2s) serve as stem cells of the alveoli and restore cell numbers after injury. Here, we describe a detailed protocol for the isolation, purification, and culture of murine and human AT2s. We have developed chemically defined and str ... Full text Open Access Link to item Cite

Human distal lung maps and lineage hierarchies reveal a bipotent progenitor.

Journal Article Nature · April 2022 Featured Publication Mapping the spatial distribution and molecular identity of constituent cells is essential for understanding tissue dynamics in health and disease. We lack a comprehensive map of human distal airways, including the terminal and respiratory bronchioles (TRBs ... Full text Open Access Link to item Cite

An In Vitro Microfluidic Alveolus Model to Study Lung Biomechanics.

Journal Article Front Bioeng Biotechnol · 2022 The gas exchange units of the lung, the alveoli, are mechanically active and undergo cyclic deformation during breathing. The epithelial cells that line the alveoli contribute to lung function by reducing surface tension via surfactant secretion, which is ... Full text Open Access Link to item Cite

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair.

Journal Article Elife · July 19, 2021 Overwhelming lipid peroxidation induces ferroptotic stress and ferroptosis, a non-apoptotic form of regulated cell death that has been implicated in maladaptive renal repair in mice and humans. Using single-cell transcriptomic and mouse genetic approaches, ... Full text Open Access Link to item Cite

Epithelial cell plasticity: breaking boundaries and changing landscapes.

Journal Article EMBO Rep · July 5, 2021 Epithelial tissues respond to a wide variety of environmental and genotoxic stresses. As an adaptive mechanism, cells can deviate from their natural paths to acquire new identities, both within and across lineages. Under extreme conditions, epithelial tiss ... Full text Open Access Link to item Cite

Stem cells of submucosal glands: their function as tissue stem cells and a reserve population for airway repair

Journal Article ERS Monograph · January 1, 2021 In the human lung, SMGs are the main source of mucus, a key component of airway clearance and defence. They are tubuloacinar structures buried in the mesenchyme along the cartilaginous airways and are composed of ciliated ducts, collecting ducts, mucous tu ... Full text Cite

Identification of a Repair-Supportive Mesenchymal Cell Population during Airway Epithelial Regeneration.

Journal Article Cell Rep · December 22, 2020 Tissue regeneration requires coordinated and dynamic remodeling of stem and progenitor cells and the surrounding niche. Although the plasticity of epithelial cells has been well explored in many tissues, the dynamic changes occurring in niche cells remain ... Full text Link to item Cite

Human Lung Stem Cell-Based Alveolospheres Provide Insights into SARS-CoV-2-Mediated Interferon Responses and Pneumocyte Dysfunction.

Journal Article Cell Stem Cell · December 3, 2020 Featured Publication Coronavirus infection causes diffuse alveolar damage leading to acute respiratory distress syndrome. The absence of ex vivo models of human alveolar epithelium is hindering an understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here, we repo ... Full text Open Access Link to item Cite

Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis.

Journal Article Nat Cell Biol · August 2020 Featured Publication Stem cells undergo dynamic changes in response to injury to regenerate lost cells. However, the identity of transitional states and the mechanisms that drive their trajectories remain understudied. Using lung organoids, multiple in vivo repair models, sing ... Full text Link to item Cite

Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury.

Journal Article Cell Stem Cell · May 3, 2018 Featured Publication Cells demonstrate plasticity following injury, but the extent of this phenomenon and the cellular mechanisms involved remain underexplored. Using single-cell RNA sequencing (scRNA-seq) and lineage tracing, we uncover that myoepithelial cells (MECs) of the ... Full text Link to item Cite

Developmental History Provides a Roadmap for the Emergence of Tumor Plasticity.

Journal Article Dev Cell · March 26, 2018 We show that the loss or gain of transcription factor programs that govern embryonic cell-fate specification is associated with a form of tumor plasticity characterized by the acquisition of alternative cell fates normally characteristic of adjacent organs ... Full text Link to item Cite

Blood-Brain Barrier Permeability Is Regulated by Lipid Transport-Dependent Suppression of Caveolae-Mediated Transcytosis.

Journal Article Neuron · May 3, 2017 The blood-brain barrier (BBB) provides a constant homeostatic brain environment that is essential for proper neural function. An unusually low rate of vesicular transport (transcytosis) has been identified as one of the two unique properties of CNS endothe ... Full text Link to item Cite

Temporal modulation of collective cell behavior controls vascular network topology.

Journal Article Elife · February 24, 2016 Vascular network density determines the amount of oxygen and nutrients delivered to host tissues, but how the vast diversity of densities is generated is unknown. Reiterations of endothelial-tip-cell selection, sprout extension and anastomosis are the basi ... Full text Link to item Cite

Neuropilin-1 functions as a VEGFR2 co-receptor to guide developmental angiogenesis independent of ligand binding.

Journal Article Elife · September 22, 2014 During development, tissue repair, and tumor growth, most blood vessel networks are generated through angiogenesis. Vascular endothelial growth factor (VEGF) is a key regulator of this process and currently both VEGF and its receptors, VEGFR1, VEGFR2, and ... Full text Link to item Cite

An image-based RNAi screen identifies SH3BP1 as a key effector of Semaphorin 3E-PlexinD1 signaling.

Journal Article J Cell Biol · May 26, 2014 Extracellular signals have to be precisely interpreted intracellularly and translated into diverse cellular behaviors often mediated by cytoskeletal changes. Semaphorins are one of the largest families of guidance cues and play a critical role in many syst ... Full text Link to item Cite

The Wnt/JNK signaling target gene alcam is required for embryonic kidney development.

Journal Article Development · May 2014 Proper development of nephrons is essential for kidney function. β-Catenin-independent Wnt signaling through Fzd8, Inversin, Daam1, RhoA and Myosin is required for nephric tubule morphogenesis. Here, we provide a novel mechanism through which non-canonical ... Full text Link to item Cite

WT1 and Sox11 regulate synergistically the promoter of the Wnt4 gene that encodes a critical signal for nephrogenesis.

Journal Article Exp Cell Res · June 10, 2012 Wnt4, a member of the Wnt superfamily of signaling molecules, is critical for mammalian kidney development, since nephrogenesis fails in its absence, while Wnt4 signaling induces mesenchyme-to-epithelium transition and associated tubulogenesis in the unind ... Full text Link to item Cite