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Liu T, Li X, Pang M, Wang L, Li Y, Sun X. Machine learning-based endoplasmic reticulum-related diagnostic biomarker and immune microenvironment landscape for osteoarthritis. Aging (Albany NY) 2024; 16:4563-4578. [PMID: 38428406 PMCID: PMC10968715 DOI: 10.18632/aging.205611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/23/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Osteoarthritis (OA) is the most common degenerative joint disease worldwide. Further improving the current limited understanding of osteoarthritis has positive clinical value. METHODS OA samples were collected from GEO database and endoplasmic reticulum related genes (ERRGs) were identified. The WGCNA network was further built to identify the crucial gene module. Based on the expression profiles of characteristic ERRGs, LASSO algorithm was used to select key factors according to the minimum λ value. Random forest (RF) algorithm was used to calculate the importance of ERRGs. Subsequently, overlapping genes based on LASSO and RF algorithms were identified as ERRGs-related diagnostic biomarkers. In addition, OA specimens were also collected and performed qRT-PCR quantitative analysis of selected ERRGs. RESULTS We identified four ERRGs associated with OA risk assessment through machine learning methods, and verified the abnormal expressions of these screened markers in OA patients through in vitro experiments. The influence of selected markers on OA immune infiltration was also evaluated. CONCLUSIONS Our results provide new evidence for the role of ER stress in the OA progression, as well as new markers and potential intervention targets for OA.
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Affiliation(s)
- Tingting Liu
- Research Center for Drug Safety Evaluation of Hainan, Hainan Medical University, Haikou, Hainan 571199, China
| | - Xiaomao Li
- Jiangsu Food and Pharmaceutical Science College, Huaian, Jiangsu 223023, China
| | - Mu Pang
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine (Shenzhen Traditional Chinese Medicine Hospital), Shenzhen, Guangdong 518000, China
| | - Lifen Wang
- Research Center for Drug Safety Evaluation of Hainan, Hainan Medical University, Haikou, Hainan 571199, China
| | - Ye Li
- Chongqing Three Gorges Medical College, Chongqing 404120, China
| | - Xizhe Sun
- Research Center for Drug Safety Evaluation of Hainan, Hainan Medical University, Haikou, Hainan 571199, China
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Chu CY, Kim SY, Pryhuber GS, Mariani TJ, McGraw MD. Single-cell resolution of human airway epithelial cells exposed to bronchiolitis obliterans-associated chemicals. Am J Physiol Lung Cell Mol Physiol 2024; 326:L135-L148. [PMID: 38084407 DOI: 10.1152/ajplung.00304.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 01/24/2024] Open
Abstract
Bronchiolitis obliterans (BO) is a fibrotic lung disease characterized by progressive luminal narrowing and obliteration of the small airways. In the nontransplant population, inhalation exposure to certain chemicals is associated with BO; however, the mechanisms contributing to disease induction remain poorly understood. This study's objective was to use single-cell RNA sequencing for the identification of transcriptomic signatures common to primary human airway epithelial cells after chemical exposure to BO-associated chemicals-diacetyl or nitrogen mustard-to help explain BO induction. Primary airway epithelial cells were cultured at air-liquid interface and exposed to diacetyl, nitrogen mustard, or control vapors. Cultures were dissociated and sequenced for single-cell RNA. Differential gene expression and functional pathway analyses were compared across exposures. In total, 75,663 single cells were captured and sequenced from all exposure conditions. Unbiased clustering identified 11 discrete phenotypes, including 5 basal, 2 ciliated, and 2 secretory cell clusters. With chemical exposure, the proportion of cells assigned to keratin 5+ basal cells decreased, whereas the proportion of cells aligned to secretory cell clusters increased compared with control exposures. Functional pathway analysis identified interferon signaling and antigen processing/presentation as pathways commonly upregulated after diacetyl or nitrogen mustard exposure in a ciliated cell cluster. Conversely, the response of airway basal cells differed significantly with upregulation of the unfolded protein response in diacetyl-exposed basal cells, not seen in nitrogen mustard-exposed cultures. These new insights provide early identification of airway epithelial signatures common to BO-associated chemical exposures.NEW & NOTEWORTHY Bronchiolitis obliterans (BO) is a devastating fibrotic lung disease of the small airways, or bronchioles. This original manuscript uses single-cell RNA sequencing for identifying common signatures of chemically exposed airway epithelial cells in BO induction. Chemical exposure reduced the proportion of keratin 5+ basal cells while increasing the proportion of keratin 4+ suprabasal cells. Functional pathways contributory to these shifts differed significantly across exposures. These new results highlight similarities and differences in BO induction across exposures.
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Affiliation(s)
- Chin-Yi Chu
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - So-Young Kim
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
| | - Matthew D McGraw
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
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Trempus CS, Papas BN, Sifre MI, Bortner CD, Scappini E, Tucker CJ, Xu X, Johnson KL, Deterding LJ, Williams JG, Johnson DJ, Li JL, Sutton D, Ganta C, Mahapatra D, Arif M, Basu A, Pommerolle L, Cinar R, Perl AK, Garantziotis S. Functional Pdgfra fibroblast heterogeneity in normal and fibrotic mouse lung. JCI Insight 2023; 8:e164380. [PMID: 37824216 PMCID: PMC10721331 DOI: 10.1172/jci.insight.164380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/06/2023] [Indexed: 10/14/2023] Open
Abstract
Aberrant fibroblast function plays a key role in the pathogenesis of idiopathic pulmonary fibrosis, a devastating disease of unrelenting extracellular matrix deposition in response to lung injury. Platelet-derived growth factor α-positive (Pdgfra+) lipofibroblasts (LipoFBs) are essential for lung injury response and maintenance of a functional alveolar stem cell niche. Little is known about the effects of lung injury on LipoFB function. Here, we used single-cell RNA-Seq (scRNA-Seq) technology and PdgfraGFP lineage tracing to generate a transcriptomic profile of Pdgfra+ fibroblasts in normal and injured mouse lungs 14 days after bleomycin exposure, generating 11 unique transcriptomic clusters that segregated according to treatment. While normal and injured LipoFBs shared a common gene signature, injured LipoFBs acquired fibrogenic pathway activity with an attenuation of lipogenic pathways. In a 3D organoid model, injured Pdgfra+ fibroblast-supported organoids were morphologically distinct from those cultured with normal fibroblasts, and scRNA-Seq analysis suggested distinct transcriptomic changes in alveolar epithelia supported by injured Pdgfra+ fibroblasts. In summary, while LipoFBs in injured lung have not migrated from their niche and retain their lipogenic identity, they acquire a potentially reversible fibrogenic profile, which may alter the kinetics of epithelial regeneration and potentially contribute to dysregulated repair, leading to fibrosis.
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Affiliation(s)
| | | | | | | | | | | | - Xin Xu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Katina L. Johnson
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Leesa J. Deterding
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Jason G. Williams
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | | | | | - Deloris Sutton
- Comparative & Molecular Pathogenesis Branch, National Institute of Environmental Health Sciences, Division of Translational Toxicology, Research Triangle Park, North Carolina, USA
| | - Charan Ganta
- Comparative & Molecular Pathogenesis Branch, National Institute of Environmental Health Sciences, Division of Translational Toxicology, Research Triangle Park, North Carolina, USA
- Inotiv, Research Triangle Park, North Carolina, USA
| | | | - Muhammad Arif
- Section on Fibrotic Disorders, and
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, Maryland, USA
| | | | | | | | - Anne K. Perl
- Division of Pulmonary Biology, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
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Sakamoto N, Okuno D, Tokito T, Yura H, Kido T, Ishimoto H, Tanaka Y, Mukae H. HSP47: A Therapeutic Target in Pulmonary Fibrosis. Biomedicines 2023; 11:2387. [PMID: 37760828 PMCID: PMC10525413 DOI: 10.3390/biomedicines11092387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/19/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease characterized by a progressive decline in lung function and poor prognosis. The deposition of the extracellular matrix (ECM) by myofibroblasts contributes to the stiffening of lung tissue and impaired oxygen exchange in IPF. Type I collagen is the major ECM component and predominant collagen protein deposited in chronic fibrosis, suggesting that type I collagen could be a target of drugs for fibrosis treatment. Heat shock protein 47 (HSP47), encoded by the serpin peptidase inhibitor clade H, member 1 gene, is a stress-inducible collagen-binding protein. It is an endoplasmic reticulum-resident molecular chaperone essential for the correct folding of procollagen. HSP47 expression is increased in cellular and animal models of pulmonary fibrosis and correlates with pathological manifestations in human interstitial lung diseases. Various factors affect HSP47 expression directly or indirectly in pulmonary fibrosis models. Overall, understanding the relationship between HSP47 expression and pulmonary fibrosis may contribute to the development of novel therapeutic strategies.
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Affiliation(s)
- Noriho Sakamoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Daisuke Okuno
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Takatomo Tokito
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Hirokazu Yura
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Takashi Kido
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Hiroshi Ishimoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, Nagasaki 852-8588, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
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Yang L, Xia H, Gilbertsen A, Smith K, Racila E, Bitterman PB, Henke CA. IL-8 concurrently promotes idiopathic pulmonary fibrosis mesenchymal progenitor cell senescence and PD-L1 expression enabling escape from immune cell surveillance. Am J Physiol Lung Cell Mol Physiol 2023; 324:L849-L862. [PMID: 37121574 PMCID: PMC10228676 DOI: 10.1152/ajplung.00028.2023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease. We discovered fibrogenic mesenchymal progenitor cells (MPCs) in the lungs of IPF patients that display cell-autonomous fibrogenicity and drive fibrotic progression. In a study of the IPF MPC nuclear proteome, we identified DNA damage as one of the most altered functions in IPF MPCs. In prior work we found that IL-8 drives IPF MPC self-renewal. IL-8 can promote replicative stress and DNA damage and induce senescence through the CXCR2 receptor. We hypothesized that IL-8 promotes DNA damage-mediated senescence in IPF MPCs. We show that IL-8 induces DNA damage and promotes IPF MPC senescence. We discovered that IL-8 concurrently promotes senescence and upregulation of the programmed death ligand 1 (PD-L1) in a CXCR2-dependent manner. Disruption of programmed cell death protein-1 (PD-1)-PD-L1 interaction promotes natural killer (NK) cell killing of IPF MPCs in vitro and arrests IPF MPC-mediated experimental lung fibrosis in vivo. Immunohistochemical (IHC) analysis of IPF lung tissue identified PD-L1-expressing IPF MPCs codistributing with NK cells and β-galactosidase-positive cells. Our data indicate that IL-8 simultaneously promotes IPF MPC DNA damage-induced senescence and high PD-L1 expression, enabling IPF MPCs to elude immune cell-targeted removal. Disruption of PD-1-PD-L1 interaction may limit IPF MPC-mediated fibrotic progression.NEW & NOTEWORTHY Here we show that IL-8 concurrently promotes senescence and upregulation of PD-L1 in IPF MPCs. IHC analysis identifies the presence of senescent IPF MPCs intermingled with NK cells in the fibroblastic focus, suggesting that senescent MPCs elude immune cell surveillance. We demonstrate that disruption of PD-1/PD-L1 interaction promotes NK cell killing of IPF MPCs and arrests IPF MPC-mediated experimental lung fibrosis. Disruption of PD-1/PD-L1 interaction may be one means to limit fibrotic progression.
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Affiliation(s)
- Libang Yang
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
| | - Hong Xia
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
| | - Adam Gilbertsen
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
| | - Karen Smith
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
| | - Emil Racila
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, United States
| | - Peter B Bitterman
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
| | - Craig A Henke
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
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Guang Z, Min Z, Jun-Tan L, Tian-Xu D, Xiang G. Single-cell protein activity analysis reveals a novel subpopulation of chondrocytes and the corresponding key master regulator proteins associated with anti-senescence and OA progression. Front Immunol 2023; 14:1077003. [PMID: 37033917 PMCID: PMC10077735 DOI: 10.3389/fimmu.2023.1077003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Background Osteoarthritis (OA) is a prevalent senescence-related disease with substantial joint pain, loss of joint function, and cartilage degeneration. Because of the paucity of single-cell studies of OA and the gene dropout problem of single-cell RNA sequencing, it is difficult to acquire an in-depth understanding of the molecular characteristics of various chondrocyte clusters. Methods Here, we aimed to provide new insights into chondrocyte senescence and a rationale for the development of effective intervention strategies for OA by using published single-cell RNA-sequencing data sets and the metaVIPER algorithm (Virtual Inference of Protein activity by Enriched Regulon). This algorithm was employed to present a proteome catalog of 62,449 chondrocytes from the cartilage of healthy individuals and OA patients at single-cell resolution. Furthermore, histopathologic analysis was carried out in cartilage samples from clinical patients and experimental mouse models of OA to validate above results. Results We identified 16 protein-activity-based chondrocyte clusters as well as the underlying master regulators in each cluster. By assessing the enrichment score of each cluster in bulk RNA-sequencing data, followed by gene-set variation analysis, we preliminarily identified a novel subpopulation of chondrocytes (cluster 3). This clinically relevant cluster was predicted to be the main chondrocyte cluster responsible for maintaining cellular homeostasis and anti-senescence. Specifically, we uncovered a set of the key leading-edge proteins of cluster 3 by validating the robustness of the above results using another human chondrocyte single-cell RNA-sequencing data set, consisting of 24,675 chondrocytes. Furthermore, cartilage samples from clinical patients and experimental mouse models of OA were used to evaluate the expression patterns of these leading-edge proteins, and the results indicated that NDRG2, TSPYL2, JMJD6 and HMGB2 are closely associated with OA pathogenesis and might play critical roles in modulating cellular homeostasis and anti-senescence in chondrocytes. Conclusion Our study revealed a novel subpopulation of chondrocytes that are critical for anti-progression of OA and the corresponding master regulator proteins, which might serve as therapeutic targets in OA.
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Affiliation(s)
- Zhao Guang
- Department of Orthopedics, The Fourth Hospital of China Medical University, Shenyang, China
| | - Zhang Min
- Department of Obstetrics, The Fourth Hospital of China Medical University, Shenyang, China
| | - Li Jun-Tan
- Department of Sport Medicine and Joint Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Dou Tian-Xu
- Department of Sport Medicine and Joint Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Gao Xiang
- Department of Orthopedics, The Fourth Hospital of China Medical University, Shenyang, China
- *Correspondence: Gao Xiang,
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Endoplasmic Reticulum Stress in Chronic Obstructive Pulmonary Disease: Mechanisms and Future Perspectives. Biomolecules 2022; 12:biom12111637. [DOI: 10.3390/biom12111637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
The endoplasmic reticulum (ER) is an integral organelle for maintaining protein homeostasis. Multiple factors can disrupt protein folding in the lumen of the ER, triggering ER stress and activating the unfolded protein response (UPR), which interrelates with various damage mechanisms, such as inflammation, apoptosis, and autophagy. Numerous studies have linked ER stress and UPR to the progression of chronic obstructive pulmonary disease (COPD). This review focuses on the mechanisms of other cellular processes triggered by UPR and summarizes drug intervention strategies targeting the UPR pathway in COPD to explore new therapeutic approaches and preventive measures for COPD.
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