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Gorla A, Witonsky J, Elhawary JR, Chen ZJ, Mefford J, Perez-Garcia J, Huntsman S, Hu D, Eng C, Woodruff PG, Sankararaman S, Ziv E, Flint J, Zaitlen N, Burchard E, Rahmani E. Epigenetic patient stratification via contrastive machine learning refines hallmark biomarkers in minoritized children with asthma. RESEARCH SQUARE 2024:rs.3.rs-5066762. [PMID: 39315258 PMCID: PMC11419268 DOI: 10.21203/rs.3.rs-5066762/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Identifying and refining clinically significant patient stratification is a critical step toward realizing the promise of precision medicine in asthma. Several peripheral blood hallmarks, including total peripheral blood eosinophil count (BEC) and immunoglobulin E (IgE) levels, are routinely used in asthma clinical practice for endotype classification and predicting response to state-of-the-art targeted biologic drugs. However, these biomarkers appear ineffective in predicting treatment outcomes in some patients, and they differ in distribution between racially and ethnically diverse populations, potentially compromising medical care and hindering health equity due to biases in drug eligibility. Here, we propose constructing an unbiased patient stratification score based on DNA methylation (DNAm) and utilizing it to refine the efficacy of hallmark biomarkers for predicting drug response. We developed Phenotype Aware Component Analysis (PACA), a novel contrastive machine-learning method for learning combinations of DNAm sites reflecting biomedically meaningful patient stratifications. Leveraging whole-blood DNAm from Latino (discovery; n=1,016) and African American (replication; n=756) pediatric asthma case-control cohorts, we applied PACA to refine the prediction of bronchodilator response (BDR) to the short-acting β2-agonist albuterol, the most used drug to treat acute bronchospasm worldwide. While BEC and IgE correlate with BDR in the general patient population, our PACA-derived DNAm score renders these biomarkers predictive of drug response only in patients with high DNAm scores. BEC correlates with BDR in patients with upper-quartile DNAm scores (OR 1.12; 95% CI [1.04, 1.22]; P=7.9 e-4) but not in patients with lower-quartile scores (OR 1.05; 95% CI [0.95, 1.17]; P=0.21); and IgE correlates with BDR in above-median (OR for response 1.42; 95% CI [1.24, 1.63]; P=3.9e-7) but not in below-median patients (OR 1.05; 95% CI [0.92, 1.2]; P=0.57). These results hold within the commonly recognized type 2 (T2)-high asthma endotype but not in T2-low patients, suggesting that our DNAm score primarily represents an unknown variation of T2 asthma. Among T2-high patients with high DNAm scores, elevated BEC or IgE also corresponds to baseline clinical presentation that is known to benefit more from biologic treatment, including higher exacerbation scores, higher allergen sensitization, lower BMI, more recent oral corticosteroids prescription, and lower lung function. Our findings suggest that BEC and IgE, the traditional asthma biomarkers of T2-high asthma, are poor biomarkers for millions worldwide. Revisiting existing drug eligibility criteria relying on these biomarkers in asthma medical care may enhance precision and equity in treatment.
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Affiliation(s)
- Aditya Gorla
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Jonathan Witonsky
- Division of Allergy, Immunology, and Bone Marrow Transplant, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer R Elhawary
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Zeyuan Johnson Chen
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Joel Mefford
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, University of La Laguna, La Laguna, Spain
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Prescott G Woodruff
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sriram Sankararaman
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan Flint
- Department of Psychiatry and Behavioral Sciences, Brain Research Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Noah Zaitlen
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Esteban Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Elior Rahmani
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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Shigemasa R, Masuko H, Oshima H, Hyodo K, Kitazawa H, Kanazawa J, Yatagai Y, Iijima H, Naito T, Saito T, Konno S, Hirota T, Tamari M, Sakamoto T, Hizawa N. The primary ciliary dyskinesia-related genetic risk score is associated with susceptibility to adult-onset asthma. PLoS One 2024; 19:e0300000. [PMID: 38457400 PMCID: PMC10923447 DOI: 10.1371/journal.pone.0300000] [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: 07/25/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Disturbance of mucociliary clearance is an important factor in the pathogenesis of asthma. We hypothesized that common variants in genes responsible for ciliary function may contribute to the development of asthma with certain phenotypes. METHODS Three independent adult Japanese populations (including a total of 1,158 patients with asthma and 2,203 non-asthmatic healthy participants) were studied. First, based on the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/), we selected 12 common single-nucleotide polymorphisms (SNPs) with molecular consequences (missense, nonsense, and 3'-untranslated region mutation) in 5 primary ciliary dyskinesia (PCD)-related genes and calculated a PCD-genetic risk score (GRS) as a cumulative effect of these PCD-related genes. Second, we performed a two-step cluster analysis using 3 variables, including PCD-GRS, forced expiratory volume in 1 second (%predicted FEV1), and age of asthma onset. RESULTS Compared to adult asthma clusters with an average PCD-GRS, clusters with high and low PCD-GRS had similar overall characteristics: adult-onset, female predominance, preserved lung function, and fewer features of type 2 immunity as determined by IgE reactivity and blood eosinophil counts. The allele frequency of rs1530496, a SNP representing an expression quantitative trait locus (eQTL) of DNAH5 in the lung, showed the largest statistically significant difference between the PCD-GRS-High and PCD-GRS-Low asthma clusters (p = 1.4 x 10-15). CONCLUSION Genes associated with PCD, particularly the common SNPs associated with abnormal expression of DNAH5, may have a certain influence on the development of adult-onset asthma, perhaps through impaired mucociliary clearance.
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Affiliation(s)
- Rie Shigemasa
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hironori Masuko
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hisayuki Oshima
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kentaro Hyodo
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Haruna Kitazawa
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Jun Kanazawa
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yohei Yatagai
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | | | | | - Takefumi Saito
- National Hospital Organization Ibaraki Higashi National Hospital, Tokai, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Tomomitsu Hirota
- Research Center for Medical Science, The Jikei University School of Medicine, Tokyo, Japan
| | - Mayumi Tamari
- Research Center for Medical Science, The Jikei University School of Medicine, Tokyo, Japan
| | - Tohru Sakamoto
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nobuyuki Hizawa
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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Hizawa N. The understanding of asthma pathogenesis in the era of precision medicine. Allergol Int 2023; 72:3-10. [PMID: 36195530 DOI: 10.1016/j.alit.2022.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023] Open
Abstract
Asthma is a syndrome with extremely diverse clinical phenotypes in which the onset, severity, and response to treatment are defined by the complex interplay of many genetic and environmental factors. Environmental factors epigenetically affect gene expression, and the disease is driven by a multidimensional dynamic network involving RNA and protein molecules derived from gene expression, as well as various metabolic products. In other words, specific pathophysiological mechanisms or endotypes are dynamic networks that arise in response to individual genotypes and the various environmental factors to which individuals have been exposed since before birth, such as diet, infection, air pollution, smoking, antibiotic use, and the bacterial flora of the intestinal tract, skin, and lungs. A key feature of asthma genome scans is their potential to reveal the molecular pathways that lead to pathogenesis. Endotypes that drive the disease have a significant impact on the phenotypes of asthma patients, including their drug responsiveness. Understanding endotypes will lead to not only the implementation of therapies that are tailored to the specific molecular network(s) underlying the patient's condition, but also to the development of therapeutic strategies that target individual endotypes, as well as to precision health, which will enable the prediction of disease onset with high accuracy from an early stage and the implementation of preventive strategies based on endotypes. Understanding of endotypes will pave the way for the practice of precision medicine in asthma care, moving away from 'one-size-fits-all' medicine and population-based prevention approaches that do not take individuals' susceptibility into account.
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Affiliation(s)
- Nobuyuki Hizawa
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
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