Browsing by Author "Iqbal, Fatima"

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    Aorta-specific DNA methylation patterns in cell-free DNA from patients with bicuspid aortic valve-associated aortopathy
    (2021-07-28) Maredia, Ashna; Guzzardi, David; Aleinati, Mohammad; Iqbal, Fatima; Khaira, Arshroop; Madhu, Aiswarya; Wang, Xuemei; Barker, Alex J.; McCarthy, Patrick M.; Fedak, Paul W. M.; Greenway, Steven C.
    Abstract Background The dilation of the aorta that occurs as a consequence of a congenitally bicuspid aortic valve (BAV) is associated with a risk of dissection, aneurysm or rupture. With progressive aortopathy, surgery is often recommended, but current patient selection strategies have limitations. A blood-based assay to identify those who would most benefit from prophylactic surgery would be an important medical advance. In a proof-of-concept study, we sought to identify aorta-specific differentially methylated regions (DMRs) detectable in plasma cell-free DNA (cfDNA) obtained from patients undergoing surgery for BAV-associated aortopathy. Methods We used bioinformatics and publicly available human methylomes to identify aorta-specific DMRs. We used data from 4D-flow cardiac magnetic resonance imaging to identify regions of elevated aortic wall shear stress (WSS) in patients with BAV-associated aortopathy undergoing surgery and correlated WSS regions with aortic tissue cell death assessed using TUNEL staining. Cell-free DNA was isolated from patient plasma, and levels of candidate DMRs were correlated with aortic diameter and aortic wall cell death. Results Aortic wall cell death was not associated with maximal aortic diameter but was significantly associated with elevated WSS. We identified 24 candidate aorta-specific DMRs and selected 4 for further study. A DMR on chromosome 11 was specific for the aorta and correlated significantly with aortic wall cell death. Plasma levels of total and aorta-specific cfDNA did not correlate with aortic diameter. Conclusions In a cohort of patients undergoing surgery for BAV-associated aortopathy, elevated WSS created by abnormal flow hemodynamics was associated with increased aortic wall cell death which supports the use of aorta-specific cfDNA as a potential tool to identify aortopathy and stratify patient risk.
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    Investigating Pulmonary Vascular Disease in Patients with Long COVID using Methylation Patterns in Cell-free DNA
    (2024-06-26) Iqbal, Fatima; Greenway, Steven; Weatherald, Jason; Halloran, Kieran; Fine, Nowell; Gordon, Paul
    Introduction: Coronavirus-19 disease (COVID-19) continues to influence the health and quality of life of Canadians to this day, even after recovering from the initial infection itself. Long COVID is a heterogenous and multi-organ disease that captures a range of symptoms that are prevalent months after infection, including persistent breathlessness (dyspnea for >12 weeks post-infection). Hypoxia and inflammation are important potential mechanisms for long COVID that cause endothelial damage and changes to the pulmonary vasculature which may contribute to unexplained dyspnea. Tissue-specific damage can be characterized using fragments of DNA released into the circulation known as cell-free DNA (cfDNA). Importantly, these fragments retain epigenetic information that can be leveraged to determine the tissue of origin as well as disease-specific methylation changes. Objective: To develop a cfDNA methylation assay to characterize cell-specific damage in PVD groups and delimitate the role of PVD in long COVID. Specific Aims: Aim 1: Identify and validate DMRs for pulmonary cell types. Aim 2: Use Nanopore sequencing to find tissue and disease-specific DMRs. Aim 3: Associate levels of DMRs in patients with PVD and long COVID with clinical presentations. Key Results and Significance: We have validated the specificity of endothelial cell and pulmonary tissue DMRs against a tissue panel to quantify cell-specific injury in patient cfDNA. We have also performed Nanopore sequencing of cfDNA from patients with long COVID, Pulmonary Arterial Hypertension (PAH), and Chronic Thromboembolic Pulmonary Hypertension (CTEPH). We have used this data to demonstrate disease-specific methylation patterning. Our work has also highlighted some gaps to address in order to use the advantages of a PCR-free, Bisulfite-conversion-free and absolute quantification of cfDNA methylation via Nanopore sequencing.