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Dr RACHEL CLIFFORD's Outputs (24)

Interplay between genetics and epigenetics in lung fibrosis (2025)
Journal Article
Valand, A., Rajasekar, P., Wain, L. V., & Clifford, R. L. (2025). Interplay between genetics and epigenetics in lung fibrosis. International Journal of Biochemistry and Cell Biology, 180, Article 106739. https://doi.org/10.1016/j.biocel.2025.106739

Lung fibrosis, including idiopathic pulmonary fibrosis (IPF), is a complex and devastating disease characterised by the progressive scarring of lung tissue leading to compromised respiratory function. Aberrantly activated fibroblasts deposit extracel... Read More about Interplay between genetics and epigenetics in lung fibrosis.

Nepalese indoor cookstove smoke extracts alter human airway epithelial gene expression, DNA methylation and hydroxymethylation (2023)
Journal Article
Rajasekar, P., Hall, R. J., Binaya, K., Mahapatra, P. S., Puppala, S. P., Thakker, D., MacIsaac, J. L., Lin, D., Kobor, M., Bolton, C. E., Sayers, I., Hall, I. P., & Clifford, R. L. (2023). Nepalese indoor cookstove smoke extracts alter human airway epithelial gene expression, DNA methylation and hydroxymethylation. Environmental Pollution, 337, Article 122561. https://doi.org/10.1016/j.envpol.2023.122561

Household air pollution caused by inefficient cooking practices causes 4 million deaths a year worldwide. In Nepal, 86% of the rural population use solid fuels for cooking. Over 25% of premature deaths associated with air pollution are respiratory in... Read More about Nepalese indoor cookstove smoke extracts alter human airway epithelial gene expression, DNA methylation and hydroxymethylation.

Predominant DNMT and TET mediate effects of allergen on the human bronchial epithelium in a controlled air pollution exposure study (2020)
Journal Article
Li, H., Ryu, M. H., Rider, C. F., Tse, W., Clifford, R. L., Aristizabal, M. J., Wen, W., & Carlsten, C. (2021). Predominant DNMT and TET mediate effects of allergen on the human bronchial epithelium in a controlled air pollution exposure study. Journal of Allergy and Clinical Immunology, 147(5), 1671-1682. https://doi.org/10.1016/j.jaci.2020.08.044

Background

Epidemiological data show that traffic-related air pollution contributes to the increasing prevalence and severity of asthma. DNA methylation (DNAm) changes may elucidate adverse health effects of environmental exposures.

Objectives... Read More about Predominant DNMT and TET mediate effects of allergen on the human bronchial epithelium in a controlled air pollution exposure study.

TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma (2020)
Journal Article
Clifford, R. L., Yang, C. X., Fishbane, N., Patel, J., MacIsaac, J. L., McEwen, L. M., May, S. T., Castellanos-Uribe, M., Nair, P., Obeidat, M., Kobor, M. S., Knox, A. J., & Hackett, T. L. (2020). TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma. Clinical Epigenetics, 12(1), Article 145. https://doi.org/10.1186/s13148-020-00931-4

© 2020 The Author(s). Background: Mesenchymal fibroblasts are ubiquitous cells that maintain the extracellular matrix of organs. Within the lung, airway and parenchymal fibroblasts are crucial for lung development and are altered with disease, but it... Read More about TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma.

Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation (2019)
Journal Article
Clifford, R. L., Patel, J., MacIsaac, J. L., McEwen, L. M., Johnson, S. R., Shaw, D., Knox, A. J., Hackett, T.-L., & Kobor, M. S. (2019). Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation. Scientific Reports, 9(1), 1-12. https://doi.org/10.1038/s41598-019-50873-y

The airway epithelium forms the interface between the inhaled environment and the lung. The airway epithelium is dysfunctional in asthma and epigenetic mechanisms are considered a contributory factor. We hypothesised that the DNA methylation profiles... Read More about Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation.

Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD (2018)
Journal Article
Clifford, R. L., Fishbane, N., Patel, J., MacIsaac, J. L., McEwen, L. M., Fisher, A. J., Brandsma, C.-A., Nair, P., Kobor, M. S., Hackett, T.-L., & Knox, A. J. (2018). Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD. Clinical Epigenetics, 10(1), https://doi.org/10.1186/s13148-018-0464-5

Background: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease of the lungs that is currently the fourth leading cause of death worldwide. Genetic factors account for only a small amount of COPD risk, but epigenetic mechanisms, i... Read More about Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD.

Use of novel DNA methylation signatures to distinguish between human airway structural cell types (2017)
Presentation / Conference Contribution
Rajasekar, P., Clifford, R., MacIsaac, J., McEwen, L., Kobor, M., & Knox, A. Use of novel DNA methylation signatures to distinguish between human airway structural cell types. Presented at American Thoracic Society 2017 International Conference

INTRODUCTION: Chronic inflammatory and fibrotic lung diseases like asthma, COPD and pulmonary fibrosis are characterised by modified phenotype of the airway structural cells. Airway walls are comprised of a robust epithelial layer that lines the lume... Read More about Use of novel DNA methylation signatures to distinguish between human airway structural cell types.

Investigating genome wide DNA methylation in bronchial and lung fibroblasts from healthy individuals and individuals with COPD (2017)
Presentation / Conference Contribution
Clifford, R., Fishbane, N., Rajasekar, P., MacIsaac, J., McEwen, L., Fisher, A., Kobor, M., Knox, A., & Hackett, T.-L. Investigating genome wide DNA methylation in bronchial and lung fibroblasts from healthy individuals and individuals with COPD. Presented at American Thoracic Society 2017 International Conference

Rationale: Lung fibroblasts are implicated in respiratory disease pathology including chronic obstructive pulmonary disease (COPD). Phenotypic differences between fibroblasts isolated from the bronchi versus the lung parenchyma have been described bu... Read More about Investigating genome wide DNA methylation in bronchial and lung fibroblasts from healthy individuals and individuals with COPD.

The role of histone arginine methylation in gene expression of airway smooth muscle cells in asthma (2017)
Presentation / Conference Contribution
Kaczmarek, K. A., Clifford, R. L., Patel, J. K., Shaw, D., Dowden, J., & Knox, A. J. (2017, May). The role of histone arginine methylation in gene expression of airway smooth muscle cells in asthma. Poster presented at American Thoracic Society 2017 International Conference

Introduction and objectives: Asthma is estimated to affect at least 300 million people globally. About 25% of the patients do not respond to therapy; therefore we need to develop novel treatments. ASM cells have a crucial role in asthma, contributin... Read More about The role of histone arginine methylation in gene expression of airway smooth muscle cells in asthma.

P238 Investigating genome wide dna methylation in airway smooth muscle cells from asthmatic and non-asthmatic donors (2016)
Presentation / Conference Contribution
Clifford, R. L., Patel, J., Shaw, D., Knox, A., & Kobor, M. P238 Investigating genome wide dna methylation in airway smooth muscle cells from asthmatic and non-asthmatic donors

Rationale: Genetic mechanisms fail to fully explain asthma pathogenesis and environmental factors are considered to play an important role. Environmental factors may lead to permanent changes in epigenetic patterns and contribute to asthma. Epigeneti... Read More about P238 Investigating genome wide dna methylation in airway smooth muscle cells from asthmatic and non-asthmatic donors.

The role of histone arginine methylation in gene expression of airway smooth muscle cells in asthma (2016)
Journal Article
Kaczmarek, K., Clifford, R. L., Patel, J., Shaw, D., Dowden, J., & Knox, A. (2016). The role of histone arginine methylation in gene expression of airway smooth muscle cells in asthma. Thorax, 71(Suppl3), A214-A215. https://doi.org/10.1136/thoraxjnl-2016-209333.379

Introduction and objectives: Asthma is estimated to affect at least 300 million people globally. About 25% of the patients do not respond to therapy; therefore we need to develop novel treatments. ASM cells have a crucial role in asthma, contributing... Read More about The role of histone arginine methylation in gene expression of airway smooth muscle cells in asthma.

S133 Investigating genome wide dna methylation in airway and parenchymal fibroblasts from healthy individuals and individuals with copd (2016)
Presentation / Conference Contribution
Clifford, R. L., Fishbane, N., Rajasekar, P., Fisher, A., Kobor, M., Knox, A., & Hackett, T. S133 Investigating genome wide dna methylation in airway and parenchymal fibroblasts from healthy individuals and individuals with copd

Rationale: Lung fibroblasts are implicated in respiratory disease pathology including chronic obstructive pulmonary disease (COPD). Phenotypic differences between fibroblasts isolated from the airway versus the parenchyma have been described but no s... Read More about S133 Investigating genome wide dna methylation in airway and parenchymal fibroblasts from healthy individuals and individuals with copd.

Amplification of TGFβ Induced ITGB6 Gene Transcription May Promote Pulmonary Fibrosis (2016)
Journal Article
Porte, J., Tatler, A. L., Jenkins, G., Goodwin, A. T., Clifford, R., Gbolahan, O., Saini, G., John, A. E., Violette, S. M., Weinreb, P. H., Parfrey, H., Wolters, P. J., Gauldie, J., & Kolb, M. (2016). Amplification of TGFβ Induced ITGB6 Gene Transcription May Promote Pulmonary Fibrosis. PLoS ONE, 11(8), 1-19. https://doi.org/10.1371/journal.pone.0158047

© 2016 Tatler et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are cre... Read More about Amplification of TGFβ Induced ITGB6 Gene Transcription May Promote Pulmonary Fibrosis.

Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation (2016)
Journal Article
Clifford, R. L., Jones, M. J., MacIsaac, J. L., McEwen, L. M., Goodman, S. J., Mostafavi, S., Kobor, M. S., & Carlsten, C. (2017). Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation. Journal of Allergy and Clinical Immunology, 139(1), https://doi.org/10.1016/j.jaci.2016.03.046

Background

Allergic disease affects 30% to 40% of the world's population, and its development is determined by the interplay between environmental and inherited factors. Air pollution, primarily consisting of diesel exhaust emissions, has increase... Read More about Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation.

CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: Regulation by BET (2015)
Journal Article
Clifford, R. L., Patel, J. K., John, A. E., Tatler, A. L., Mazengarb, L., Brightling, C. E., & Knox, A. J. (2015). CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: Regulation by BET. AJP - Lung Cellular and Molecular Physiology, 308(9), L962-L972. https://doi.org/10.1152/ajplung.00021.2015

© 2015 The American Physiological Society. Asthma is characterized by airway inflammation and remodeling and CXCL8 is a CXC chemokine that drives steroid-resistant neutrophilic airway inflammation. We have shown that airway smooth muscle (ASM) cells... Read More about CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: Regulation by BET.

Epigenetics and miRNA emerge as key regulators of smooth muscle cell phenotype and function (2012)
Journal Article
Clifford, R. L., Singer, C. A., & John, A. E. (2013). Epigenetics and miRNA emerge as key regulators of smooth muscle cell phenotype and function. Pulmonary Pharmacology and Therapeutics, 26(1), 75-85. https://doi.org/10.1016/j.pupt.2012.07.002

Regulation of phenotypic plasticity in smooth muscle requires an understanding of the mechanisms regulating phenotype-specific genes and the processes dysregulated during pathogenesis. Decades of study in airway smooth muscle has provided extensive k... Read More about Epigenetics and miRNA emerge as key regulators of smooth muscle cell phenotype and function.

Abnormal Histone Methylation Is Responsible for Increased Vascular Endothelial Growth Factor 165a Secretion from Airway Smooth Muscle Cells in Asthma (2012)
Journal Article
Clifford, R. L., John, A. E., Brightling, C. E., & Knox, A. J. (2012). Abnormal Histone Methylation Is Responsible for Increased Vascular Endothelial Growth Factor 165a Secretion from Airway Smooth Muscle Cells in Asthma. Journal of Immunology, 189(2), 819-831. https://doi.org/10.4049/jimmunol.1103641

Vascular endothelial growth factor (VEGF), a key angiogenic molecule, is aberrantly expressed in several diseases including asthma where it contributes to bronchial vascular remodeling and chronic inflammation. Asthmatic human airway smooth muscle ce... Read More about Abnormal Histone Methylation Is Responsible for Increased Vascular Endothelial Growth Factor 165a Secretion from Airway Smooth Muscle Cells in Asthma.