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Isaac S, Ellis RJ, Gusev A, Murthy VL, Udler MS, Patel CJ. Human Plasma Proteomics Links Modifiable Lifestyle Exposome to Disease Risk. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.05.07.25327178. [PMID: 40385387 PMCID: PMC12083611 DOI: 10.1101/2025.05.07.25327178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/20/2025]
Abstract
Environmental exposures influence disease risk, yet their underlying biological mechanisms remain poorly understood. We present the Human Exposomic Architecture of the Proteome (HEAP), a framework and resource integrating genetic, exposomic, and proteomic data to uncover how lifestyle influences disease through plasma proteins. Applying HEAP to 2,686 proteins in 53,014 UK Biobank participants, we identified over 11,000 exposure-protein associations across 135 lifestyle exposures. Exposures explained a substantial portion of proteomic variation, with 9% of proteins more influenced by lifestyle than genetics. Mediation analyses across 270 diseases revealed proteins linking exposures to disease risk; for instance, IGFBP1 and IGFBP2 mediated the effects of exercise and diet on type 2 diabetes. These findings were supported by concordant proteomic shifts in interventional studies of exercise and GLP1 agonists, underscoring therapeutic relevance. HEAP provides a resource for advancing disease prevention and precision medicine by revealing mechanisms through which lifestyle shapes human health.
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Affiliation(s)
- Shakson Isaac
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA. 02215
| | - Randall J. Ellis
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA. 02215
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Venkatesh L. Murthy
- Department of Internal Medicine and Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, USA
| | - Miriam S. Udler
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA. 02215
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Jinson S, Shanthikumar S, Werder RB. Evaluating the Use of iPSC-Derived Models in Understanding the Pathogenesis of Childhood Interstitial Lung Disease. Pediatr Pulmonol 2025; 60:e71143. [PMID: 40432281 PMCID: PMC12117302 DOI: 10.1002/ppul.71143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2025] [Revised: 05/13/2025] [Accepted: 05/15/2025] [Indexed: 05/29/2025]
Abstract
RATIONALE Genetic testing has significantly improved the diagnosis of childhood interstitial lung diseases (chILD), which have long challenged clinicians due to their heterogeneity and poor characterization. It is now imperative to study variants of unknown significance (VUS) to identify pathogenic mutations to optimize diagnosis and screening in patients. Furthermore, the limited treatment options for patients with chILD worsen patient outcomes. Induced pluripotent stem cell (iPSC)-derived models could be a tool to understand the effect of novel VUS and discover new therapeutic interventions. OBJECTIVE This review seeks to evaluate the fidelity of iPSC-derived models to recapitulate the pathogenic processes of chILD and test therapeutic interventions. METHODS This paper performs a systematic search over three databases to identify iPSC-derived models studying disease-causing mutations in pediatric patients with chILD and Hermansky-Pudlak Syndrome. RESULTS Of the 1452 papers initially reviewed, eight papers met the inclusion criteria using iPSC-derived models to study genetic variants. The diseases covered included common manifestations of chILDs such as surfactant protein deficiencies and hereditary pulmonary alveolar proteinosis, as well as fibrotic disorders like Hermansky-Pudlak Syndrome. These models recapitulated patient histology and key pathogenic features reported in the literature, delivering mechanistic insights into these conditions. Some papers also explored the efficacy of novel treatments, such as gene therapy. CONCLUSIONS iPSC-derived models can mimic aspects of human lung responses to provide a platform for disease modeling and therapeutic testing in chILD. There are opportunities to develop more complex multi-cellular models and for the study of a wider range of variants using these tools.
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Affiliation(s)
- Swetha Jinson
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, reNEW MelbourneMelbourneVictoriaAustralia
| | - Shivanthan Shanthikumar
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Respiratory and Sleep MedicineRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Rhiannon B. Werder
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, reNEW MelbourneMelbourneVictoriaAustralia
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Olzhabaev T, Müller L, Krause D, Schwudke D, Torda AE. Lipidome visualisation, comparison, and analysis in a vector space. PLoS Comput Biol 2025; 21:e1012892. [PMID: 40233092 PMCID: PMC12058142 DOI: 10.1371/journal.pcbi.1012892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 05/07/2025] [Accepted: 02/20/2025] [Indexed: 04/17/2025] Open
Abstract
A shallow neural network was used to embed lipid structures in a 2- or 3-dimensional space with the goal that structurally similar species have similar vectors. Tests on complete lipid databanks show that the method automatically produces distributions which follow conventional lipid classifications. The embedding is accompanied by the web-based software, Lipidome Projector. This displays user lipidomes as 2D or 3D scatterplots for quick exploratory analysis, quantitative comparison and interpretation at a structural level. Examples of published data sets were used for a qualitative comparison with literature interpretation.
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Affiliation(s)
- Timur Olzhabaev
- Centre for Bioinformatics, University of Hamburg, Hamburg, Germany
- Bioanalytical Chemistry, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Lukas Müller
- Centre for Bioinformatics, University of Hamburg, Hamburg, Germany
- Bioanalytical Chemistry, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Daniel Krause
- Bioanalytical Chemistry, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Dominik Schwudke
- Bioanalytical Chemistry, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Thematic Translational Unit Tuberculosis, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
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Louvrier C, Desroziers T, Soreze Y, Delgado Rodriguez M, Thomas L, Nau V, Dastot-Le Moal F, Bernstein JA, Cole FS, Damme M, Fischer A, Griese M, Hinds D, Keehan L, Milla C, Mohammad H, Rips J, Wambach JA, Wegner DJ, Amselem S, Legendre M, Giurgea I, Karabina SA, Breuer O, Coulomb l'Herminé A, Nathan N. Bi-allelic LAMP3 variants in childhood interstitial lung disease: a surfactant-related disease. EBioMedicine 2025; 113:105626. [PMID: 40023045 PMCID: PMC11914748 DOI: 10.1016/j.ebiom.2025.105626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 02/10/2025] [Accepted: 02/14/2025] [Indexed: 03/04/2025] Open
Abstract
BACKGROUND LAMP3 encodes a lysosomal membrane protein associated with lamellar bodies and has recently been proposed as a candidate gene for childhood interstitial lung diseases (chILD). Here, we identified two LAMP3 variants in a proband with chILD and performed functional validation of these variants as well as the previously reported variants to demonstrate the role of LAMP3 in pathology. METHODS LAMP3 variants were identified by exome sequencing. Ex vivo studies included mRNA analysis from nasal brushing and lung tissue and immunohistochemistry from lung biopsy. In vitro functional analyses in the A549 cell line included immunofluorescence staining and expression analysis of LAMP3. Interactions between LAMP3 and the surfactant protein (SP)-B and SP-C were evaluated by co-immunoprecipitation. FINDINGS Two heterozygous LAMP3 variants (Y302Qfs∗2 and T268M) were identified in a 15 year old boy with chILD. LAMP3 mRNA revealed that the frameshift variant resulted in nonsense-mediated mRNA decay. Reduced LAMP3 expression was confirmed in the patient's lung tissue. Functional studies of the T268M and the previously reported G288R variant revealed reduced levels of the mutant proteins. In addition, impaired N-glycosylation and protein instability were demonstrated with the T268M variant. Finally, we provided evidence for an interaction between LAMP3 and SP-B and SP-C, revealing a direct link between LAMP3 and surfactant metabolism. INTERPRETATION LAMP3 bi-allelic variants leading to LAMP3 dysfunction emerges as a cause of chILD associated with a heterogeneous phenotype that remains to be further defined. The close links between LAMP3 and surfactant metabolism could explain the pathophysiology of this genetic disease. FUNDING No specific funding.
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Affiliation(s)
- Camille Louvrier
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France; Assistance Publique Hôpitaux de Paris, Medical Genetics Department, Armand Trousseau Hospital, Paris, France.
| | - Tifenn Desroziers
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France
| | - Yohan Soreze
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France; Assistance Publique Hôpitaux de Paris, Intensive Care Unit, Armand Trousseau Hospital, Paris, France
| | - Martha Delgado Rodriguez
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France
| | - Lucie Thomas
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France
| | - Valérie Nau
- Assistance Publique Hôpitaux de Paris, Medical Genetics Department, Armand Trousseau Hospital, Paris, France
| | - Florence Dastot-Le Moal
- Assistance Publique Hôpitaux de Paris, Medical Genetics Department, Armand Trousseau Hospital, Paris, France
| | - Jonathan A Bernstein
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - F Sessions Cole
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Markus Damme
- Christian-Albrechts-University Kiel, Biochemical Institute, Kiel, Germany
| | - Anthony Fischer
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Matthias Griese
- Department of Pediatric Pneumology, Dr von Hauner Children's Hospital, Ludwig-Maximilians-University, German Center for Lung Research, Munich, Germany
| | - Daniel Hinds
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Laura Keehan
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Carlos Milla
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Hadhud Mohammad
- Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Jonathan Rips
- Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Jennifer A Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Daniel J Wegner
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Serge Amselem
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France; Assistance Publique Hôpitaux de Paris, Medical Genetics Department, Armand Trousseau Hospital, Paris, France
| | - Marie Legendre
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France; Assistance Publique Hôpitaux de Paris, Medical Genetics Department, Armand Trousseau Hospital, Paris, France
| | - Irina Giurgea
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France; Assistance Publique Hôpitaux de Paris, Medical Genetics Department, Armand Trousseau Hospital, Paris, France
| | - Sonia Athina Karabina
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France
| | - Oded Breuer
- Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Aurore Coulomb l'Herminé
- Assistance Publique Hôpitaux de Paris, Pathology Department, Sorbonne University, Armand Trousseau Hospital, Paris, France
| | - Nadia Nathan
- Sorbonne University, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France; Assistance Publique Hôpitaux de Paris, Pediatric Pulmonology Department, Reference Centre for Rare Lung Diseases (RespiRare), Armand Trousseau Hospital, Paris, France
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Kim SK, Sung E, Lim K. Recent advances and applications of human lung alveolar organoids. Mol Cells 2024; 47:100140. [PMID: 39490990 PMCID: PMC11629183 DOI: 10.1016/j.mocell.2024.100140] [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: 09/24/2024] [Revised: 10/21/2024] [Accepted: 10/22/2024] [Indexed: 11/05/2024] Open
Abstract
The human lung alveolus is a well-structured and coordinated pulmonary unit, allowing them to perform diverse functions. While there has been significant progress in understanding the molecular and cellular mechanisms behind human alveolar development and pulmonary diseases, the underlying mechanisms of alveolar differentiation and disease development are still unclear, mainly due to the limited availability of human tissues and a lack of proper in vitro lung model systems mimicking human lung physiology. In this review, we summarize recent advances in creating human lung organoid models that mimic alveolar epithelial cell types. Moreover, we discuss how lung alveolar organoid systems are being applied to recent cutting-edge research on lung development, regeneration, and diseases.
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Affiliation(s)
- Sun Kyung Kim
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Eunho Sung
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Kyungtae Lim
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea.
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Ekpruke CD, Alford R, Rousselle D, Babayev M, Sharma S, Commodore S, Buechlein A, Rusch DB, Silveyra P. Transcriptomics analysis of allergen-induced inflammatory gene expression in the Four-Core Genotype mouse model. Physiol Genomics 2024; 56:235-245. [PMID: 38047309 PMCID: PMC11281817 DOI: 10.1152/physiolgenomics.00112.2023] [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: 09/26/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023] Open
Abstract
Sex differences in allergic inflammation have been reported, but the mechanisms underlying these differences remain unknown. Contributions of both sex hormones and sex-related genes to these mechanisms have been previously suggested in clinical and animal studies. Here, Four-Core Genotypes (FCG) mouse model was used to study the inflammatory response to house dust mite (HDM) challenge and identify differentially expressed genes (DEGs) and regulatory pathways in lung tissue. Briefly, adult mice (8-10 wk old) of the FCG (XXM, XXF, XYM, XYF) were challenged intranasally with 25 μg of HDM or vehicle (PBS-control group) 5 days/wk for 5 wk (n = 3/10 group). At 72 h after the last exposure, we analyzed the eosinophils and neutrophils in the bronchoalveolar lavage (BAL) of FCG mice. We extracted lung tissue and determined DEGs using Templated Oligo-Sequencing (TempO-Seq). DEG analysis was performed using the DESeq2 package and gene enrichment analysis was done using Ingenuity Pathway Analysis. A total of 2,863 DEGs were identified in the FCG. Results revealed increased eosinophilia and neutrophilia in the HDM-treated group with the most significantly expressed genes in XYF phenotype and a predominant effect of female hormones vs. chromosomes. Regardless of the sex hormones, mice with female chromosomes had more downregulated genes in the HDM group but this was reversed in the control group. Interestingly, genes associated with inflammatory responses were overrepresented in the XXM and XYF genotypes treated with HDM. Sex hormones and chromosomes contribute to inflammatory responses to HDM challenge, with female hormones exerting a predominant effect mediated by inflammatory DEGs.NEW & NOTEWORTHY Gene expression profiling helps to provide deep insight into the global view of disease-related mechanisms and responses to therapy. Using the Four-Core Genotype mouse model, our findings revealed the influence of sex hormones and sex chromosomes in the gene expression of lungs exposed to an aeroallergen (House Dust Mite) and identified sex-specific pathways to better understand sex disparities associated with allergic airway inflammation.
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Affiliation(s)
- Carolyn Damilola Ekpruke
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, Indiana, United States
| | - Rachel Alford
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, Indiana, United States
| | - Dustin Rousselle
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, Indiana, United States
| | - Maksat Babayev
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, Indiana, United States
| | - Shikha Sharma
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, Indiana, United States
| | - Sarah Commodore
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, Indiana, United States
| | - Aaron Buechlein
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, United States
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, United States
| | - Patricia Silveyra
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, Indiana, United States
- School of Medicine, Indiana University, Indianapolis, Indiana, United States
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Liu Y, Liu S, Yan L, Zhang Q, Liu W, Huang X, Liu S. Contribution of m5C RNA Modification-Related Genes to Prognosis and Immunotherapy Prediction in Patients with Ovarian Cancer. Mediators Inflamm 2023; 2023:1400267. [PMID: 38022687 PMCID: PMC10661868 DOI: 10.1155/2023/1400267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/03/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Background 5-Methylcytosine (m5C) RNA modification is closely implicated in the occurrence of a variety of cancers. Here, we established a novel prognostic signature for ovarian cancer (OC) patients based on m5C RNA modification-related genes and explored the correlation between these genes with the tumor immune microenvironment. Methods Methylated-RNA immunoprecipitation sequencing helped us to identify candidate genes related to m5C RNA modification at first. Based on TCGA database, we screened the differentially expressed candidate genes related to the prognosis and constructed a prognostic model using LASSO Cox regression analyses. Notably, the accuracy of the model was evaluated by Kaplan-Meier analysis and receiver operator characteristic curves. Independent prognostic risk factors were investigated by Cox proportional hazard model. Furthermore, we also analyzed the biological functions and pathways involved in the signature. Finally, the immune response of the model was visualized in great detail. Results Totally, 2,493 candidate genes proved to be involved in m5C modification of RNA for OC. We developed a signature with prognostic value consisting of six m5C RNA modification-related genes. Specially, samples have been split into two cohorts with low- and high-risk scores according to the model, in which the low-risk OC patients exhibited dramatically better overall survival time than those with high-risk scores. Besides, not only was this model a prognostic factor independent of other clinical characteristics but it predicted the intensity of the immune response in OC. Significantly, the accuracy and availability of the signature were verified by ICGC database. Conclusions Our study bridged the gap between m5C RNA modification and the prognosis of OC and was expected to provide an effective breakthrough for immunotherapy in OC patients.
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Affiliation(s)
- Yibin Liu
- Department of Gynecology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei 050011, China
| | - Shouze Liu
- Department of Gynecology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei 050011, China
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
| | - Lu Yan
- Department of Gynecology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei 050011, China
| | - Qianqian Zhang
- Department of Gynecology and Obstetrics, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Wenhua Liu
- Department of Pain, Cangzhou Hospital of Integrated TCM-WM Hebei, Cangzhou, Hebei 061001, China
| | - Xianghua Huang
- Department of Gynecology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei 050011, China
| | - Shikai Liu
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
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Xu W, Ma X, Wang Q, Ye J, Wang N, Ye Z, Chen T. GCN5L1 regulates pulmonary surfactant production by modulating lamellar body biogenesis and trafficking in mouse alveolar epithelial cells. Cell Mol Biol Lett 2023; 28:90. [PMID: 37936104 PMCID: PMC10631113 DOI: 10.1186/s11658-023-00506-0] [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: 06/05/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND The pulmonary surfactant that lines the air-liquid surface within alveoli is a protein-lipid mixture essential for gas exchange. Surfactant lipids and proteins are synthesized and stored in the lamellar body (LB) before being secreted from alveolar type II (AT2) cells. The molecular and cellular mechanisms that regulate these processes are incompletely understood. We previously identified an essential role of general control of amino acid synthesis 5 like 1 (GCN5L1) and the biogenesis of lysosome-related organelle complex 1 subunit 1 (BLOS1) in surfactant system development in zebrafish. Here, we explored the role of GCN5L1 in pulmonary surfactant regulation. METHOD GCN5L1 knockout cell lines were generated with the CRISPR/Cas9 system. Cell viability was analyzed by MTT assay. Released surfactant proteins were measured by ELISA. Released surfactant lipids were measured based on coupled enzymatic reactions. Gene overexpression was mediated through lentivirus. The RNA levels were detected through RNA-sequencing (RNA-seq) and quantitative reverse transcription (qRT)- polymerase chain reaction (PCR). The protein levels were detected through western blotting. The cellular localization was analyzed by immunofluorescence. Morphology of the lamellar body was analyzed through transmission electron microscopy (TEM), Lysotracker staining, and BODIPY phosphatidylcholine labeling. RESULTS Knocking out GCN5L1 in MLE-12 significantly decreased the release of surfactant proteins and lipids. We detected the downregulation of some surfactant-related genes and misregulation of the ROS-Erk-Foxo1-Cebpα axis in mutant cells. Modulating the activity of the axis or reconstructing the mitochondrial expression of GCN5L1 could partially restore the expression of these surfactant-related genes. We further showed that MLE-12 cells contained many LB-like organelles that were lipid enriched and positive for multiple LB markers. These organelles were smaller in size and accumulated in the absence of GCN5L1, indicating both biogenesis and trafficking defects. Accumulated endogenous surfactant protein (SP)-B or exogenously expressed SP-B/SP-C in adenosine triphosphate-binding cassette transporterA3 (ABCA3)-positive organelles was detected in mutant cells. GCN5L1 localized to the mitochondria and LBs. Reconstruction of mitochondrial GCN5L1 expression rescued the organelle morphology but failed to restore the trafficking defect and surfactant release, indicating specific roles associated with different subcellular localizations. CONCLUSIONS In summary, our study identified GCN5L1 as a new regulator of pulmonary surfactant that plays a role in the biogenesis and positioning/trafficking of surfactant-containing LBs.
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Affiliation(s)
- Wenqin Xu
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, China
- Clinical Research Center for Critical Respiratory Medicine of Anhui Province, Wannan Medical College, Wuhu, China
| | - Xiaocui Ma
- Henan Clinical Research Center of Childhood Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Qing Wang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, China
- Clinical Research Center for Critical Respiratory Medicine of Anhui Province, Wannan Medical College, Wuhu, China
| | - Jingjing Ye
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, China
- Clinical Research Center for Critical Respiratory Medicine of Anhui Province, Wannan Medical College, Wuhu, China
| | - Nengqian Wang
- Department of Pediatrics, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Zhenzhen Ye
- Department of Pediatrics, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Tianbing Chen
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China.
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wannan Medical College, Wuhu, China.
- Clinical Research Center for Critical Respiratory Medicine of Anhui Province, Wannan Medical College, Wuhu, China.
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Shadrina MI, Slominsky PA. Genetic Architecture of Parkinson's Disease. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:417-433. [PMID: 37076287 DOI: 10.1134/s0006297923030100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 03/28/2023]
Abstract
Year 2022 marks 25 years since the first mutation in familial autosomal dominant Parkinson's disease was identified. Over the years, our understanding of the role of genetic factors in the pathogenesis of familial and idiopathic forms of Parkinson's disease has expanded significantly - a number of genes for the familial form of the disease have been identified, and DNA markers for an increased risk of developing its sporadic form have been found. But, despite all the success achieved, we are far from an accurate assessment of the contribution of genetic and, even more so, epigenetic factors to the disease development. The review summarizes the information accumulated to date on the genetic architecture of Parkinson's disease and formulates issues that need to be addressed, which are primarily related to the assessment of epigenetic factors in the disease pathogenesis.
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Affiliation(s)
- Maria I Shadrina
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia.
| | - Petr A Slominsky
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
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