Mitochondrial integrated stress response controls lung epithelial cell fate

Hypercapnia alters stromal-derived Wnt production limiting β-catenin signaling and proliferation in alveolar type 2 cells

(2023) Laura A. Dada et al.   JCI Insight

Mitochondrial redox adaptations enable alternative aspartate synthesis in SDH-deficient cells

(2023) Madeleine L Hart et al.   eLife

Lung Injury Induces Alveolar Type 2 Cell Hypertrophy and Polyploidy with Implications for Repair and Regeneration

(2022) Anthea Weng et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Three-axis classification of mouse lung mesenchymal cells reveals two populations of myofibroblasts

(2022) Odemaris Narvaez del Pilar et al.   DEVELOPMENT

Compartmentalized metabolism supports midgestation mammalian development

(2022) Ashley Solmonson et al.   NATURE

Mitochondrial electron transport chain is necessary for NLRP3 inflammasome activation

(2022) Leah K. Billingham et al.   NATURE IMMUNOLOGY

Reduced expression of mitochondrial complex I subunit Ndufs2 does not impact healthspan in mice

(2022) Gregory S. McElroy et al.   Scientific Reports

FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction

(2022) Marijana Croon et al.   Science Advances

OMA1-mediated integrated stress response protects against ferroptosis in mitochondrial cardiomyopathy

(2022) Sofia Ahola et al.   Cell Metabolism

Asparagine couples mitochondrial respiration to ATF4 activity and tumor growth

(2021) Abigail S. Krall et al.   Cell Metabolism

Single cell transcriptomic analysis of murine lung development on hyperoxia-induced damage

(2021) Maria Hurskainen et al.   Nature Communications

eIF2B conformation and assembly state regulates the integrated stress response

(2021) Michael Schoof et al.   eLife

Resetting proteostasis with ISRIB promotes epithelial differentiation to attenuate pulmonary fibrosis

(2021) Satoshi Watanabe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

(2021) Zhiqiang Pang et al.   NUCLEIC ACIDS RESEARCH

A single-cell atlas of mouse lung development

(2021) Nicholas M. Negretti et al.   DEVELOPMENT

A census of the lung: CellCards from LungMAP

(2021) Xin Sun et al.   DEVELOPMENTAL CELL

Human alveolar type 2 epithelium transdifferentiates into metaplastic KRT5+ basal cells

(2021) Jaymin J. Kathiriya et al.   NATURE CELL BIOLOGY

Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism

(2021) Dylan Gerard Ryan et al.   eLife

Ineffectual AEC2-to-AEC1 Differentiation in IPF: Persistence of KRT8hi Transitional State

(2020) Peng Jiang et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Mitochondrial stress is relayed to the cytosol by an OMA1–DELE1–HRI pathway

(2020) Xiaoyan Guo et al.   NATURE

A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol

(2020) Evelyn Fessler et al.   NATURE

The Cellular and Physiological Basis for Lung Repair and Regeneration: Past, Present, and Future

(2020) Maria C. Basil et al.   Cell Stem Cell

Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell

(2020) Eran Mick et al.   eLife

NAD+ Regeneration Rescues Lifespan, but Not Ataxia, in a Mouse Model of Brain Mitochondrial Complex I Dysfunction

(2020) Gregory S. McElroy et al.   Cell Metabolism

Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration

(2020) Jinwook Choi et al.   Cell Stem Cell

Mitochondrial ubiquinol oxidation is necessary for tumour growth

(2020) Inmaculada Martínez-Reyes et al.   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

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

(2020) Yoshihiko Kobayashi et al.   NATURE CELL BIOLOGY

Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis

(2020) Maximilian Strunz et al.   Nature Communications

Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

(2020) Taylor S. Adams et al.   Science Advances

Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

(2020) Arun C. Habermann et al.   Science Advances

dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit

(2020) Daniel G Bunis et al.   BIOINFORMATICS

Lung transplantation for patients with severe COVID-19

(2020) Ankit Bharat et al.   Science Translational Medicine

eIF2B activator prevents neurological defects caused by a chronic integrated stress response

(2019) Yao Liang Wong et al.   eLife

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

BBKNN: fast batch alignment of single cell transcriptomes

(2019) Krzysztof Polański et al.   BIOINFORMATICS

Fibroblast Growth Factor 21 Drives Dynamics of Local and Systemic Stress Responses in Mitochondrial Myopathy with mtDNA Deletions

(2019) Saara Forsström et al.   Cell Metabolism

Extraction and Quantitation of Nicotinamide Adenine Dinucleotide Redox Cofactors

(2018) Wenyun Lu et al.   ANTIOXIDANTS & REDOX SIGNALING

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data

(2018) Jasmine Chong et al.   BIOINFORMATICS

Aspartate is a limiting metabolite for cancer cell proliferation under hypoxia and in tumours

(2018) Javier Garcia-Bermudez et al.   NATURE CELL BIOLOGY

Aspartate is an endogenous metabolic limitation for tumour growth

(2018) Lucas B. Sullivan et al.   NATURE CELL BIOLOGY

Pulmonary alveolar type I cell population consists of two distinct subtypes that differ in cell fate

(2018) Yanjie Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells

(2018) Ahmad N. Nabhan et al.   SCIENCE

Human lung development: recent progress and new challenges

(2018) Marko Z. Nikolić et al.   DEVELOPMENT

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor

(2018) William J. Zacharias et al.   NATURE

Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals

(2017) Pedro M. Quirós et al.   JOURNAL OF CELL BIOLOGY

The Transcription Factor ATF5 Mediates a Mammalian Mitochondrial UPR

(2016) Christopher J. Fiorese et al.   CURRENT BIOLOGY

Oxygen Sensing by Arterial Chemoreceptors Depends on Mitochondrial Complex I Signaling

(2015) M. Carmen Fernández-Agüera et al.   Cell Metabolism

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Lung development: orchestrating the generation and regeneration of a complex organ

(2014) M. Herriges et al.   DEVELOPMENT

Alveolar progenitor and stem cells in lung development, renewal and cancer

(2014) Tushar J. Desai et al.   NATURE

Type 2 alveolar cells are stem cells in adult lung

(2013) Christina E. Barkauskas et al.   JOURNAL OF CLINICAL INVESTIGATION

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Differential Impairment of Catecholaminergic Cell Maturation and Survival by Genetic Mitochondrial Complex II Dysfunction

(2012) B. Diaz-Castro et al.   MOLECULAR AND CELLULAR BIOLOGY

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Unfolding communities in large complex networks: Combining defensive and offensive label propagation for core extraction

(2011) Lovro Šubelj et al.   PHYSICAL REVIEW E