Javier Perez-Garcia

All Publications

• Precision Medicine for Asthma Treatment: Unlocking the Potential of the Epigenome and Microbiome. The Journal of allergy and clinical immunology Perez-Garcia, J., Cardenas, A., Lorenzo-Diaz, F., Pino-Yanes, M. 2024

  Abstract

  Asthma is a leading worldwide biomedical concern. Patients can experience life-threatening worsening episodes (exacerbations) usually controlled by anti-inflammatory and bronchodilator drugs. However, substantial heterogeneity in treatment response exists and a subset of patients with unresolved asthma carry the major burden of this disease. The study of the epigenome and microbiome might bridge the gap between human genetics and environmental exposures to partially explain the heterogeneity in drug response. This review aims to provide a critical examination of the existing literature on the microbiome and epigenetic studies examining associations with asthma treatments and drug response, highlight convergent pathways, address current challenges, and offer future perspectives. Current epigenetic and microbiome studies have shown the bilateral relationship between asthma pharmacological interventions and the human epigenome and microbiome. These studies, focusing on corticosteroids and to a lesser extent on bronchodilators, azithromycin, immunotherapy, and mepolizumab, have improved the understanding of the molecular basis of treatment response and identified promising biomarkers for drug response prediction. Immune and inflammatory pathways (i.e., IL-2, TNF-α, NF-κB, and CEBPs) underlie microbiome-epigenetic associations with asthma treatment, representing potential therapeutic pathways to be targeted. A comprehensive evaluation of these omic biomarkers could significantly contribute to precision medicine and new therapeutic target discovery.

  View details for DOI 10.1016/j.jaci.2024.06.010

  View details for PubMedID 38906272

• Reply. The Journal of allergy and clinical immunology Perez-Garcia, J., Pino-Yanes, M., Lorenzo-Diaz, F. 2023; 152 (6): 1683-1685

  View details for DOI 10.1016/j.jaci.2023.08.023

  View details for PubMedID 37747396

• Epigenomic response to albuterol treatment in asthma-relevant airway epithelial cells. Clinical epigenetics Perez-Garcia, J., Pino-Yanes, M., Plender, E. G., Everman, J. L., Eng, C., Jackson, N. D., Moore, C. M., Beckman, K. B., Medina, V., Sharma, S., Winnica, D. E., Holguin, F., Rodríguez-Santana, J., Villar, J., Ziv, E., Seibold, M. A., Burchard, E. G. 2023; 15 (1): 156

  Abstract

  Albuterol is the first-line asthma medication used in diverse populations. Although DNA methylation (DNAm) is an epigenetic mechanism involved in asthma and bronchodilator drug response (BDR), no study has assessed whether albuterol could induce changes in the airway epithelial methylome. We aimed to characterize albuterol-induced DNAm changes in airway epithelial cells, and assess potential functional consequences and the influence of genetic variation and asthma-related clinical variables.We followed a discovery and validation study design to characterize albuterol-induced DNAm changes in paired airway epithelial cultures stimulated in vitro with albuterol. In the discovery phase, an epigenome-wide association study using paired nasal epithelial cultures from Puerto Rican children (n = 97) identified 22 CpGs genome-wide associated with repeated-use albuterol treatment (p < 9 × 10-8). Albuterol predominantly induced a hypomethylation effect on CpGs captured by the EPIC array across the genome (probability of hypomethylation: 76%, p value = 3.3 × 10-5). DNAm changes on the CpGs cg23032799 (CREB3L1), cg00483640 (MYLK4-LINC01600), and cg05673431 (KSR1) were validated in nasal epithelia from 10 independent donors (false discovery rate [FDR] < 0.05). The effect on the CpG cg23032799 (CREB3L1) was cross-tissue validated in bronchial epithelial cells at nominal level (p = 0.030). DNAm changes in these three CpGs were shown to be influenced by three independent genetic variants (FDR < 0.05). In silico analyses showed these polymorphisms regulated gene expression of nearby genes in lungs and/or fibroblasts including KSR1 and LINC01600 (6.30 × 10-14 ≤ p ≤ 6.60 × 10-5). Additionally, hypomethylation at the CpGs cg10290200 (FLNC) and cg05673431 (KSR1) was associated with increased gene expression of the genes where they are located (FDR < 0.05). Furthermore, while the epigenetic effect of albuterol was independent of the asthma status, severity, and use of medication, BDR was nominally associated with the effect on the CpG cg23032799 (CREB3L1) (p = 0.004). Gene-set enrichment analyses revealed that epigenomic modifications of albuterol could participate in asthma-relevant processes (e.g., IL-2, TNF-α, and NF-κB signaling pathways). Finally, nine differentially methylated regions were associated with albuterol treatment, including CREB3L1, MYLK4, and KSR1 (adjusted p value < 0.05).This study revealed evidence of epigenetic modifications induced by albuterol in the mucociliary airway epithelium. The epigenomic response induced by albuterol might have potential clinical implications by affecting biological pathways relevant to asthma.

  View details for DOI 10.1186/s13148-023-01571-0

  View details for PubMedID 37784136

  View details for PubMedCentralID PMC10546710

• Human genetics influences microbiome composition involved in asthma exacerbations despite inhaled corticosteroid treatment. The Journal of allergy and clinical immunology Perez-Garcia, J., Espuela-Ortiz, A., Hernández-Pérez, J. M., González-Pérez, R., Poza-Guedes, P., Martin-Gonzalez, E., Eng, C., Sardón-Prado, O., Mederos-Luis, E., Corcuera-Elosegui, P., Sánchez-Machín, I., Korta-Murua, J., Villar, J., Burchard, E. G., Lorenzo-Diaz, F., Pino-Yanes, M. 2023; 152 (3): 799-806.e6

  Abstract

  The upper-airway microbiome is involved in asthma exacerbations despite inhaled corticosteroid (ICS) treatment. Although human genetics regulates microbiome composition, its influence on asthma-related airway bacteria remains unknown.We sought to identify genes and biological pathways regulating airway-microbiome traits involved in asthma exacerbations and ICS response.Saliva, nasal, and pharyngeal samples from 257 European patients with asthma were analyzed. The association of 6,296,951 genetic variants with exacerbation-related microbiome traits despite ICS treatment was tested through microbiome genome-wide association studies. Variants with 1 × 10-4 

  View details for DOI 10.1016/j.jaci.2023.05.021

  View details for PubMedID 37301411

  View details for PubMedCentralID PMC10522330

• Multi-omic approach associates blood methylome with bronchodilator drug response in pediatric asthma. The Journal of allergy and clinical immunology Perez-Garcia, J., Herrera-Luis, E., Li, A., Mak, A. C., Huntsman, S., Oh, S. S., Elhawary, J. R., Eng, C., Beckman, K. B., Hu, D., Lorenzo-Diaz, F., Lenoir, M. A., Rodriguez-Santana, J., Zaitlen, N., Villar, J., Borrell, L. N., Burchard, E. G., Pino-Yanes, M. 2023; 151 (6): 1503-1512

  Abstract

  Albuterol is the drug most widely used as asthma treatment among African Americans despite having a lower bronchodilator drug response (BDR) than other populations. Although BDR is affected by gene and environmental factors, the influence of DNA methylation is unknown.This study aimed to identify epigenetic markers in whole blood associated with BDR, study their functional consequences by multi-omic integration, and assess their clinical applicability in admixed populations with a high asthma burden.We studied 414 children and young adults (8-21 years old) with asthma in a discovery and replication design. We performed an epigenome-wide association study on 221 African Americans and replicated the results on 193 Latinos. Functional consequences were assessed by integrating epigenomics with genomics, transcriptomics, and environmental exposure data. Machine learning was used to develop a panel of epigenetic markers to classify treatment response.We identified 5 differentially methylated regions and 2 CpGs genome-wide significantly associated with BDR in African Americans located in FGL2 (cg08241295, P = 6.8 × 10-9) and DNASE2 (cg15341340, P = 7.8 × 10-8), which were regulated by genetic variation and/or associated with gene expression of nearby genes (false discovery rate < 0.05). The CpG cg15341340 was replicated in Latinos (P = 3.5 × 10-3). Moreover, a panel of 70 CpGs showed good classification for those with response and nonresponse to albuterol therapy in African American and Latino children (area under the receiver operating characteristic curve for training, 0.99; for validation, 0.70-0.71). The DNA methylation model showed similar discrimination as clinical predictors (P > .05).We report novel associations of epigenetic markers with BDR in pediatric asthma and demonstrate for the first time the applicability of pharmacoepigenetics in precision medicine of respiratory diseases.

  View details for DOI 10.1016/j.jaci.2023.01.026

  View details for PubMedID 36796456

• Alpha-1 antitrypsin deficiency and Pi*S and Pi*Z SERPINA1 variants are associated with asthma exacerbations. Pulmonology Martín-González, E., Hernández-Pérez, J. M., Pérez, J. A., Pérez-García, J., Herrera-Luis, E., González-Pérez, R., González-González, O., Mederos-Luis, E., Sánchez-Machín, I., Poza-Guedes, P., Sardón, O., Corcuera, P., Cruz, M. J., González-Barcala, F. J., Martínez-Rivera, C., Mullol, J., Muñoz, X., Olaguibel, J. M., Plaza, V., Quirce, S., Valero, A., Sastre, J., Korta-Murua, J., Del Pozo, V., Lorenzo-Díaz, F., Villar, J., Pino-Yanes, M., González-Carracedo, M. A. 2023

  Abstract

  Asthma is a chronic inflammatory disease of the airways. Asthma patients may experience potentially life-threatening episodic flare-ups, known as exacerbations, which may significantly contribute to the asthma burden. The Pi*S and Pi*Z variants of the SERPINA1 gene, which usually involve alpha-1 antitrypsin (AAT) deficiency, had previously been associated with asthma. The link between AAT deficiency and asthma might be represented by the elastase/antielastase imbalance. However, their role in asthma exacerbations remains unknown. Our objective was to assess whether SERPINA1 genetic variants and reduced AAT protein levels are associated with asthma exacerbations.In the discovery analysis, SERPINA1 Pi*S and Pi*Z variants and serum AAT levels were analyzed in 369 subjects from La Palma (Canary Islands, Spain). As replication, genomic data from two studies focused on 525 Spaniards and publicly available data from UK Biobank, FinnGen, and GWAS Catalog (Open Targets Genetics) were analyzed. The associations between SERPINA1 Pi*S and Pi*Z variants and AAT deficiency with asthma exacerbations were analyzed with logistic regression models, including age, sex, and genotype principal components as covariates.In the discovery, a significant association with asthma exacerbations was found for both Pi*S (odds ratio [OR]=2.38, 95% confidence interval [CI]= 1.40-4.04, p-value=0.001) and Pi*Z (OR=3.49, 95%CI=1.55-7.85, p-value=0.003)Likewise, AAT deficiency was associated with a higher risk for asthma exacerbations (OR=5.18, 95%CI=1.58-16.92, p-value=0.007) as well as AAT protein levels (OR= 0.72, 95%CI=0.57-0.91, p-value=0.005). The Pi*Z association with exacerbations was replicated in samples from Spaniards with two generations of Canary Islander origin (OR=3.79, p-value=0.028), and a significant association with asthma hospitalizations was found in the Finnish population (OR=1.12, p-value=0.007).AAT deficiency could be a potential therapeutic target for asthma exacerbations in specific populations.

  View details for DOI 10.1016/j.pulmoe.2023.05.002

  View details for PubMedID 37236906

• The upper-airway microbiome as a biomarker of asthma exacerbations despite inhaled corticosteroid treatment. The Journal of allergy and clinical immunology Perez-Garcia, J., González-Carracedo, M., Espuela-Ortiz, A., Hernández-Pérez, J. M., González-Pérez, R., Sardón-Prado, O., Martin-Gonzalez, E., Mederos-Luis, E., Poza-Guedes, P., Corcuera-Elosegui, P., Callero, A., Sánchez-Machín, I., Korta-Murua, J., Pérez-Pérez, J. A., Villar, J., Pino-Yanes, M., Lorenzo-Diaz, F. 2023; 151 (3): 706-715

  Abstract

  The response to inhaled corticosteroids (ICS) in asthma is affected by the interplay of several factors. Among these, the role of the upper-airway microbiome has been scarcely investigated. We aimed to evaluate the association between the salivary, pharyngeal, and nasal microbiome with asthma exacerbations despite receipt of ICS.Samples from 250 asthma patients from the Genomics and Metagenomics of Asthma Severity (GEMAS) study treated with ICS were analyzed. Control/case subjects were defined by the absence/presence of asthma exacerbations in the past 6 months despite being treated with ICS. The bacterial microbiota was profiled by sequencing the V3-V4 region of the 16S rRNA gene. Differences between groups were assessed by PERMANOVA and regression models adjusted for potential confounders. A false discovery rate (FDR) of 5% was used to correct for multiple comparisons. Classification models of asthma exacerbations despite ICS treatment were built with machine learning approaches based on clinical, genetic, and microbiome data.In nasal and saliva samples, case subjects had lower bacterial diversity (Richness, Shannon, and Faith indices) than control subjects (.007 ≤ P ≤ .037). Asthma exacerbations accounted for 8% to 9% of the interindividual variation of the salivary and nasal microbiomes (.003 ≤ P ≤ .046). Three, 4, and 11 bacterial genera from the salivary, pharyngeal, and nasal microbiomes were differentially abundant between groups (4.09 × 10-12 ≤ FDR ≤ 0.047). Integrating clinical, genetic, and microbiome data showed good discrimination for the development of asthma exacerbations despite receipt of ICS (AUCtraining: 0.82 and AUCvalidation: 0.77).The diversity and composition of the upper-airway microbiome are associated with asthma exacerbations despite ICS treatment. The salivary microbiome has a potential application as a biomarker of asthma exacerbations despite receipt of ICS.

  View details for DOI 10.1016/j.jaci.2022.09.041

  View details for PubMedID 36343772

• Admixture mapping of severe asthma exacerbations in Hispanic/Latino children and youth. Thorax Herrera-Luis, E., Mak, A. C., Perez-Garcia, J., Martin-Gonzalez, E., Eng, C., Beckman, K. B., Huntsman, S., Hu, D., González-Pérez, R., Hernández-Pérez, J. M., Mederos-Luis, E., Sio, Y. Y., Poza-Guedes, P., Sardón, O., Corcuera, P., Sánchez-Machín, I., Korta-Murua, J., Martínez-Rivera, C., Mullol, J., Muñoz, X., Valero, A., Sastre, J., Garcia-Aymerich, J., Llop, S., Torrent, M., Casas, M., Rodríguez-Santana, J. R., Villar, J., Del Pozo, V., Lorenzo-Diaz, F., Williams, L. K., Melén, E., Chew, F. T., Borrell, L. N., Burchard, E. G., Pino-Yanes, M. 2023; 78 (3): 233-241

  Abstract

  In the USA, genetically admixed populations have the highest asthma prevalence and severe asthma exacerbations rates. This could be explained not only by environmental factors but also by genetic variants that exert ethnic-specific effects. However, no admixture mapping has been performed for severe asthma exacerbations.We sought to identify genetic variants associated with severe asthma exacerbations in Hispanic/Latino subgroups by means of admixture mapping analyses and fine mapping, and to assess their transferability to other populations and potential functional roles.We performed an admixture mapping in 1124 Puerto Rican and 625 Mexican American children with asthma. Fine-mapping of the significant peaks was performed via allelic testing of common and rare variants. We performed replication across Hispanic/Latino subgroups, and the transferability to non-Hispanic/Latino populations was assessed in 1001 African Americans, 1250 Singaporeans and 941 Europeans with asthma. The effects of the variants on gene expression and DNA methylation from whole blood were also evaluated in participants with asthma and in silico with data obtained through public databases.Genomewide significant associations of Indigenous American ancestry with severe asthma exacerbations were found at 5q32 in Mexican Americans as well as at 13q13-q13.2 and 3p13 in Puerto Ricans. The single nucleotide polymorphism (SNP) rs1144986 (C5orf46) showed consistent effects for severe asthma exacerbations across Hispanic/Latino subgroups, but it was not validated in non-Hispanics/Latinos. This SNP was associated with DPYSL3 DNA methylation and SCGB3A2 gene expression levels.Admixture mapping study of asthma exacerbations revealed a novel locus that exhibited Hispanic/Latino-specific effects and regulated DPYSL3 and SCGB3A2.

  View details for DOI 10.1136/thorax-2022-218755

  View details for PubMedID 36180068

  View details for PubMedCentralID PMC9957797

• Epigenome-Wide Association Studies of the Fractional Exhaled Nitric Oxide and Bronchodilator Drug Response in Moderate-to-Severe Pediatric Asthma. Biomedicines Martin-Almeida, M., Perez-Garcia, J., Herrera-Luis, E., Rosa-Baez, C., Gorenjak, M., Neerincx, A. H., Sardón-Prado, O., Toncheva, A. A., Harner, S., Wolff, C., Brandstetter, S., Valletta, E., Abdel-Aziz, M. I., Hashimoto, S., Berce, V., Corcuera-Elosegui, P., Korta-Murua, J., Buntrock-Döpke, H., Vijverberg, S. J., Verster, J. C., Kerssemakers, N., Hedman, A. M., Almqvist, C., Villar, J., Kraneveld, A. D., Potočnik, U., Kabesch, M., Zee, A. H., Pino-Yanes, M. 2023; 11 (3)

  Abstract

  Asthma is the most prevalent pediatric chronic disease. Bronchodilator drug response (BDR) and fractional exhaled nitric oxide (FeNO) are clinical biomarkers of asthma. Although DNA methylation (DNAm) contributes to asthma pathogenesis, the influence of DNAm on BDR and FeNO is scarcely investigated. This study aims to identify DNAm markers in whole blood associated either with BDR or FeNO in pediatric asthma. We analyzed 121 samples from children with moderate-to-severe asthma. The association of genome-wide DNAm with BDR and FeNO has been assessed using regression models, adjusting for age, sex, ancestry, and tissue heterogeneity. Cross-tissue validation was assessed in 50 nasal samples. Differentially methylated regions (DMRs) and enrichment in traits and biological pathways were assessed. A false discovery rate (FDR) < 0.1 and a genome-wide significance threshold of p < 9 × 10-8 were used to control for false-positive results. The CpG cg12835256 (PLA2G12A) was genome-wide associated with FeNO in blood samples (coefficient= -0.015, p = 2.53 × 10-9) and nominally associated in nasal samples (coefficient = -0.015, p = 0.045). Additionally, three CpGs were suggestively associated with BDR (FDR < 0.1). We identified 12 and four DMRs associated with FeNO and BDR (FDR < 0.05), respectively. An enrichment in allergic and inflammatory processes, smoking, and aging was observed. We reported novel associations of DNAm markers associated with BDR and FeNO enriched in asthma-related processes.

  View details for DOI 10.3390/biomedicines11030676

  View details for PubMedID 36979655

  View details for PubMedCentralID PMC10044864

• Novel insights into the biological pathways involved in severe asthma. Respirology (Carlton, Vic.) Perez-Garcia, J., Pino-Yanes, M. 2022; 27 (9): 680-681

  View details for DOI 10.1111/resp.14319

  View details for PubMedID 35764405

• Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response. Clinical and translational allergy Slob, E. M., Faiz, A., van Nijnatten, J., Vijverberg, S. J., Longo, C., Kutlu, M., Chew, F. T., Sio, Y. Y., Herrera-Luis, E., Espuela-Ortiz, A., Perez-Garcia, J., Pino-Yanes, M., Burchard, E. G., Potočnik, U., Gorenjak, M., Palmer, C., Maroteau, C., Turner, S., Verhamme, K., Karimi, L., Mukhopadhyay, S., Timens, W., Hiemstra, P. S., Pijnenburg, M. W., Neighbors, M., Grimbaldeston, M. A., Tew, G. W., Brandsma, C. A., Berce, V., Aliee, H., Theis, F., Sin, D. D., Li, X., van den Berge, M., Maitland-van der Zee, A. H., Koppelman, G. H. 2022; 12 (8): e12173

  View details for DOI 10.1002/clt2.12173

  View details for PubMedID 36036237

  View details for PubMedCentralID PMC9421427

• Multi-ancestry genome-wide association study of asthma exacerbations. Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology Herrera-Luis, E., Ortega, V. E., Ampleford, E. J., Sio, Y. Y., Granell, R., de Roos, E., Terzikhan, N., Vergara, E. E., Hernandez-Pacheco, N., Perez-Garcia, J., Martin-Gonzalez, E., Lorenzo-Diaz, F., Hashimoto, S., Brinkman, P., Jorgensen, A. L., Yan, Q., Forno, E., Vijverberg, S. J., Lethem, R., Espuela-Ortiz, A., Gorenjak, M., Eng, C., González-Pérez, R., Hernández-Pérez, J. M., Poza-Guedes, P., Sardón, O., Corcuera, P., Hawkins, G. A., Marsico, A., Bahmer, T., Rabe, K. F., Hansen, G., Kopp, M. V., Rios, R., Cruz, M. J., González-Barcala, F. J., Olaguibel, J. M., Plaza, V., Quirce, S., Canino, G., Cloutier, M., Del Pozo, V., Rodriguez-Santana, J. R., Korta-Murua, J., Villar, J., Potočnik, U., Figueiredo, C., Kabesch, M., Mukhopadhyay, S., Pirmohamed, M., Hawcutt, D. B., Melén, E., Palmer, C. N., Turner, S., Maitland-van der Zee, A. H., von Mutius, E., Celedón, J. C., Brusselle, G., Chew, F. T., Bleecker, E., Meyers, D., Burchard, E. G., Pino-Yanes, M. 2022; 33 (6): e13802

  Abstract

  Asthma exacerbations are a serious public health concern due to high healthcare resource utilization, work/school productivity loss, impact on quality of life, and risk of mortality. The genetic basis of asthma exacerbations has been studied in several populations, but no prior study has performed a multi-ancestry meta-analysis of genome-wide association studies (meta-GWAS) for this trait. We aimed to identify common genetic loci associated with asthma exacerbations across diverse populations and to assess their functional role in regulating DNA methylation and gene expression.A meta-GWAS of asthma exacerbations in 4989 Europeans, 2181 Hispanics/Latinos, 1250 Singaporean Chinese, and 972 African Americans analyzed 9.6 million genetic variants. Suggestively associated variants (p ≤ 5 × 10-5 ) were assessed for replication in 36,477 European and 1078 non-European asthma patients. Functional effects on DNA methylation were assessed in 595 Hispanic/Latino and African American asthma patients and in publicly available databases. The effect on gene expression was evaluated in silico.One hundred and twenty-six independent variants were suggestively associated with asthma exacerbations in the discovery phase. Two variants independently replicated: rs12091010 located at vascular cell adhesion molecule-1/exostosin like glycosyltransferase-2 (VCAM1/EXTL2) (discovery: odds ratio (ORT allele ) = 0.82, p = 9.05 × 10-6 and replication: ORT allele  = 0.89, p = 5.35 × 10-3 ) and rs943126 from pantothenate kinase 1 (PANK1) (discovery: ORC allele  = 0.85, p = 3.10 × 10-5 and replication: ORC allele  = 0.89, p = 1.30 × 10-2 ). Both variants regulate gene expression of genes where they locate and DNA methylation levels of nearby genes in whole blood.This multi-ancestry study revealed novel suggestive regulatory loci for asthma exacerbations located in genomic regions participating in inflammation and host defense.

  View details for DOI 10.1111/pai.13802

  View details for PubMedID 35754128

  View details for PubMedCentralID PMC9671132

• Multiomics analysis identifies BIRC3 as a novel glucocorticoid response-associated gene. The Journal of allergy and clinical immunology Kan, M., Diwadkar, A. R., Shuai, H., Joo, J., Wang, A. L., Ong, M. S., Sordillo, J. E., Iribarren, C., Lu, M. X., Hernandez-Pacheco, N., Perez-Garcia, J., Gorenjak, M., Potočnik, U., Burchard, E. G., Pino-Yanes, M., Wu, A. C., Himes, B. E. 2022; 149 (6): 1981-1991

  Abstract

  Inhaled corticosteroid (ICS) response among patients with asthma is influenced by genetics, but biologically actionable insights based on associations have not been found. Various glucocorticoid response omics data sets are available to interrogate their biological effects.We sought to identify functionally relevant ICS-response genetic associations by integrating complementary multiomics data sets.Variants with P values less than 10-4 from a previous ICS-response genome-wide association study were reranked on the basis of integrative scores determined from (1) glucocorticoid receptor- and (2) RNA polymerase II-binding regions inferred from ChIP-Seq data for 3 airway cell types, (3) glucocorticoid response element motifs, (4) differentially expressed genes in response to glucocorticoid exposure according to 20 transcriptomic data sets, and (5) expression quantitative trait loci from GTEx. Candidate variants were tested for association with ICS response and asthma in 6 independent studies.Four variants had significant (q value < 0.05) multiomics integrative scores. These variants were in a locus consisting of 52 variants in high linkage disequilibrium (r2 ≥ 0.8) near glucocorticoid receptor-binding sites by the gene BIRC3. Variants were also BIRC3 expression quantitative trait loci in lung, and 2 were within/near putative glucocorticoid response element motifs. BIRC3 had increased RNA polymerase II occupancy and gene expression, with glucocorticoid exposure in 2 ChIP-Seq and 13 transcriptomic data sets. Some BIRC3 variants in the 52-variant locus were associated (P < .05) with ICS response in 3 independent studies and others with asthma in 1 study.BIRC3 should be prioritized for further functional studies of ICS response.

  View details for DOI 10.1016/j.jaci.2021.11.025

  View details for PubMedID 34971648

  View details for PubMedCentralID PMC9177524

• Epigenome-wide association study of lung function in Latino children and youth with asthma. Clinical epigenetics Herrera-Luis, E., Li, A., Mak, A. C., Perez-Garcia, J., Elhawary, J. R., Oh, S. S., Hu, D., Eng, C., Keys, K. L., Huntsman, S., Beckman, K. B., Borrell, L. N., Rodriguez-Santana, J., Burchard, E. G., Pino-Yanes, M. 2022; 14 (1): 9

  Abstract

  DNA methylation studies have associated methylation levels at different CpG sites or genomic regions with lung function. Moreover, genetic ancestry has been associated with lung function in Latinos. However, no epigenome-wide association study (EWAS) of lung function has been performed in this population. Here, we aimed to identify DNA methylation patterns associated with lung function in pediatric asthma among Latinos.We conducted an EWAS in whole blood from 250 Puerto Rican and 148 Mexican American children and young adults with asthma. A total of five CpGs exceeded the genome-wide significance threshold of p = 1.17 × 10-7 in the combined analyses from Puerto Ricans and Mexican Americans: cg06035600 (MAP3K6, p = 6.13 × 10-8) showed significant association with pre-bronchodilator Tiffeneau-Pinelli index, the probes cg00914963 (TBC1D16, p = 1.04 × 10-7), cg16405908 (MRGPRE, p = 2.05 × 10-8), and cg07428101 (MUC2, p = 5.02 × 10-9) were associated with post-bronchodilator forced vital capacity (FVC), and cg20515679 (KCNJ6) with post-bronchodilator Tiffeneau-Pinelli index (p = 1.13 × 10-8). However, these markers did not show significant associations in publicly available data from Europeans (p > 0.05). A methylation quantitative trait loci analysis revealed that methylation levels at these CpG sites were regulated by genetic variation in Latinos and the Biobank-based Integrative Omics Studies (BIOS) consortium. Additionally, two differentially methylated regions in REXOC and AURKC were associated with pre-bronchodilator Tiffeneau-Pinelli index (adjusted p < 0.05) in Puerto Ricans and Mexican Americans. Moreover, we replicated some of the previous differentially methylated signals associated with lung function in non-Latino populations.We replicated previous associations of epigenetic markers with lung function in whole blood and identified novel population-specific associations shared among Latino subgroups.

  View details for DOI 10.1186/s13148-022-01227-5

  View details for PubMedID 35033200

  View details for PubMedCentralID PMC8760660

• Genome-wide association studies of exacerbations in children using long-acting beta2-agonists. Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology Slob, E. M., Richards, L. B., Vijverberg, S. J., Longo, C., Koppelman, G. H., Pijnenburg, M. W., Bel, E. H., Neerincx, A. H., Herrera Luis, E., Perez-Garcia, J., Tim Chew, F., Yie Sio, Y., Andiappan, A. K., Turner, S. W., Mukhopadhyay, S., Palmer, C. N., Hawcutt, D., Jorgensen, A. L., Burchard, E. G., Hernandez-Pacheco, N., Pino-Yanes, M., Maitland-van der Zee, A. H. 2021; 32 (6): 1197-1207

  Abstract

  Some children with asthma experience exacerbations despite long-acting beta2-agonist (LABA) treatment. While this variability is partly caused by genetic variation, no genome-wide study until now has investigated which genetic factors associated with risk of exacerbations despite LABA use in children with asthma. We aimed to assess whether genetic variation was associated with exacerbations in children treated with LABA from a global consortium.A meta-analysis of genome-wide association studies (meta-GWAS) was performed in 1,425 children and young adults with asthma (age 6-21 years) with reported regular use of LABA from six studies within the PiCA consortium using a random effects model. The primary outcome of each study was defined as any exacerbation within the past 6 or 12 months, including at least one of the following: 1) hospital admissions for asthma, 2) a course of oral corticosteroids or 3) emergency room visits because of asthma.Genome-wide association results for a total of 82 996 common single nucleotide polymorphisms (SNPs, MAF ≥1%) with high imputation quality were meta-analysed. Eight independent variants were suggestively (P-value threshold ≤5 × 10-6 ) associated with exacerbations despite LABA use.No strong effects of single nucleotide polymorphisms (SNPs) on exacerbations during LABA use were identified. We identified two loci (TBX3 and EPHA7) that were previously implicated in the response to short-acting beta2-agonists (SABA). These loci merit further investigation in response to LABA and SABA use.

  View details for DOI 10.1111/pai.13494

  View details for PubMedID 33706416

  View details for PubMedCentralID PMC8328929

• A System Pharmacology Multi-Omics Approach toward Uncontrolled Pediatric Asthma. Journal of personalized medicine Abdel-Aziz, M. I., Neerincx, A. H., Vijverberg, S. J., Hashimoto, S., Brinkman, P., Gorenjak, M., Toncheva, A. A., Harner, S., Brandstetter, S., Wolff, C., Perez-Garcia, J., Hedman, A. M., Almqvist, C., Corcuera-Elosegui, P., Korta-Murua, J., Sardón-Prado, O., Pino-Yanes, M., Potočnik, U., Kabesch, M., Kraneveld, A. D., Maitland-van der Zee, A. H. 2021; 11 (6)

  Abstract

  There is a clinical need to identify children with poor asthma control as early as possible, to optimize treatment and/or to find therapeutic alternatives. Here, we present the "Systems Pharmacology Approach to Uncontrolled Pediatric Asthma" (SysPharmPediA) study, which aims to establish a pediatric cohort of moderate-to-severe uncontrolled and controlled patients with asthma, to investigate pathophysiological mechanisms underlying uncontrolled moderate-to-severe asthma in children on maintenance treatment, using a multi-omics systems medicine approach. In this multicenter observational case-control study, moderate-to-severe asthmatic children (age; 6-17 years) were included from four European countries (Netherlands, Germany, Spain, and Slovenia). Subjects were classified based on asthma control and number of exacerbations. Demographics, current and past patient/family history, and clinical characteristics were collected. In addition, systems-wide omics layers, including epi(genomics), transcriptomics, microbiome, proteomics, and metabolomics were evaluated from multiple samples. In all, 145 children were included in this cohort, 91 with uncontrolled (median age = 12 years, 43% females) and 54 with controlled asthma (median age = 11.7 years, 37% females). The two groups did not show statistically significant differences in age, sex, and body mass index z-score distribution. Comprehensive information and diverse noninvasive biosampling procedures for various omics analyses will provide the opportunity to delineate underlying pathophysiological mechanisms of moderate-to-severe uncontrolled pediatric asthma. This eventually might reveal novel biomarkers, which could potentially be used for noninvasive personalized diagnostics and/or treatment.

  View details for DOI 10.3390/jpm11060484

  View details for PubMedID 34071272

  View details for PubMedCentralID PMC8227234

• Genome-wide association study of asthma exacerbations despite inhaled corticosteroid use. The European respiratory journal Hernandez-Pacheco, N., Vijverberg, S. J., Herrera-Luis, E., Li, J., Sio, Y. Y., Granell, R., Corrales, A., Maroteau, C., Lethem, R., Perez-Garcia, J., Farzan, N., Repnik, K., Gorenjak, M., Soares, P., Karimi, L., Schieck, M., Pérez-Méndez, L., Berce, V., Tavendale, R., Eng, C., Sardon, O., Kull, I., Mukhopadhyay, S., Pirmohamed, M., Verhamme, K. M., Burchard, E. G., Kabesch, M., Hawcutt, D. B., Melén, E., Potočnik, U., Chew, F. T., Tantisira, K. G., Turner, S., Palmer, C. N., Flores, C., Pino-Yanes, M., Maitland-van der Zee, A. H. 2021; 57 (5)

  Abstract

  Substantial variability in response to asthma treatment with inhaled corticosteroids (ICS) has been described among individuals and populations, suggesting the contribution of genetic factors. Nonetheless, only a few genes have been identified to date. We aimed to identify genetic variants associated with asthma exacerbations despite ICS use in European children and young adults and to validate the findings in non-Europeans. Moreover, we explored whether a gene-set enrichment analysis could suggest potential novel asthma therapies.A genome-wide association study (GWAS) of asthma exacerbations was tested in 2681 children of European descent treated with ICS from eight studies. Suggestive association signals were followed up for replication in 538 European asthma patients. Further evaluation was performed in 1773 non-Europeans. Variants revealed by published GWAS were assessed for replication. Additionally, gene-set enrichment analysis focused on drugs was performed.10 independent variants were associated with asthma exacerbations despite ICS treatment in the discovery phase (p≤5×10-6). Of those, one variant at the CACNA2D3-WNT5A locus was nominally replicated in Europeans (rs67026078; p=0.010), but this was not validated in non-European populations. Five other genes associated with ICS response in previous studies were replicated. Additionally, an enrichment of associations in genes regulated by trichostatin A treatment was found.The intergenic region of CACNA2D3 and WNT5A was revealed as a novel locus for asthma exacerbations despite ICS treatment in European populations. Genes associated were related to trichostatin A, suggesting that this drug could regulate the molecular mechanisms involved in treatment response.

  View details for DOI 10.1183/13993003.03388-2020

  View details for PubMedID 33303529

  View details for PubMedCentralID PMC8122045

• The Genomics and Metagenomics of Asthma Severity (GEMAS) Study: Rationale and Design. Journal of personalized medicine Perez-Garcia, J., Hernández-Pérez, J. M., González-Pérez, R., Sardón, O., Martin-Gonzalez, E., Espuela-Ortiz, A., Mederos-Luis, E., Callero, A., Herrera-Luis, E., Corcuera, P., Sánchez-Machín, I., Poza-Guedes, P., González García, L. M., Ramírez-Martín, P., Pérez-Negrín, L., Izaguirre-Flores, H., Barrios-Recio, J., Pérez-Rodríguez, E., Alcoba-Florez, J., Cañas, J. A., Rodrigo Muñoz, J. M., Del Pozo, V., Korta-Murua, J., Pérez Méndez, L. I., Hernandez-Ferrer, M., Villar, J., Lorenzo-Diaz, F., Pino-Yanes, M. 2020; 10 (3)

  Abstract

  Asthma exacerbations are a major contributor to the global disease burden, but no significant predictive biomarkers are known. The Genomics and Metagenomics of Asthma Severity (GEMAS) study aims to assess the role of genomics and the microbiome in severe asthma exacerbations. Here, we present the design of GEMAS and the characteristics of patients recruited from March 2018 to March 2020. Different biological samples and demographic and clinical variables were collected from asthma patients recruited by allergy and pulmonary medicine units in several hospitals from Spain. Cases and controls were defined by the presence/absence of severe asthma exacerbations in the past year (oral corticosteroid use, emergency room visits, and/or asthma-related hospitalizations). A total of 137 cases and 120 controls were recruited. After stratifying by recruitment location (i.e., Canary Islands and Basque Country), cases and controls did not differ for most demographic and clinical variables (p > 0.05). However, cases showed a higher proportion of characteristics inherent to asthma exacerbations (impaired lung function, severe disease, uncontrolled asthma, gastroesophageal reflux, and use of asthma medications) compared to controls (p < 0.05). Similar results were found after stratification by recruitment unit. Thereby, asthma patients enrolled in GEMAS are balanced for potential confounders and have clinical characteristics that support the phenotype definition. GEMAS will improve the knowledge of potential biomarkers of asthma exacerbations.

  View details for DOI 10.3390/jpm10030123

  View details for PubMedID 32933076

  View details for PubMedCentralID PMC7563269

• Precision Medicine in Childhood Asthma: Omic Studies of Treatment Response. International journal of molecular sciences Perez-Garcia, J., Herrera-Luis, E., Lorenzo-Diaz, F., González, M., Sardón, O., Villar, J., Pino-Yanes, M. 2020; 21 (8)

  Abstract

  Asthma is a heterogeneous and multifactorial respiratory disease with an important impact on childhood. Difficult-to-treat asthma is not uncommon among children, and it causes a high burden to the patient, caregivers, and society. This review aims to summarize the recent findings on pediatric asthma treatment response revealed by different omic approaches conducted in 2018-2019. A total of 13 studies were performed during this period to assess the role of genomics, epigenomics, transcriptomics, metabolomics, and the microbiome in the response to short-acting beta agonists, inhaled corticosteroids, and leukotriene receptor antagonists. These studies have identified novel associations of genetic markers, epigenetic modifications, metabolites, bacteria, and molecular mechanisms involved in asthma treatment response. This knowledge will allow us establishing molecular biomarkers that could be integrated with clinical information to improve the management of children with asthma.

  View details for DOI 10.3390/ijms21082908

  View details for PubMedID 32326339

  View details for PubMedCentralID PMC7215369

• Pharmacogenetics of Pediatric Asthma: Current Perspectives. Pharmacogenomics and personalized medicine Perez-Garcia, J., Espuela-Ortiz, A., Lorenzo-Diaz, F., Pino-Yanes, M. 2020; 13: 89-103

  Abstract

  Asthma is a chronic respiratory disease that affects 339 million people worldwide and has a considerable impact on the pediatric population. Asthma symptoms can be controlled by pharmacological treatment. However, some patients do not respond to therapy and continue suffering from symptoms, which impair the quality of life of patients and limit their daily activity. Genetic variation has been shown to have a role in treatment response. The aim of this review is to update the main findings described in pharmacogenetic studies of pediatric asthma published from January 1, 2018 to December 31, 2019. During this period, the response to short-acting beta-agonists and inhaled corticosteroids in childhood asthma has been evaluated by eleven candidate-gene studies, one meta-analysis of a candidate gene, and six pharmacogenomic studies. The findings have allowed validating the association of genes previously related to asthma treatment response (ADRB2, GSDMB, FCER2, VEGFA, SPAT2SL, ASB3, and COL2A1), and identifying novel associations (PRKG1, DNAH5, IL1RL1, CRISPLD2, MMP9, APOBEC3B-APOBEC3C, EDDM3B, and BBS9). However, some results are not consistent across studies, highlighting the need to conduct larger studies in diverse populations with more homogeneous definitions of treatment response. Once stronger evidence was established, genetic variants will have the potential to be applied in clinical practice as biomarkers of treatment response enhancing asthma management and improving the quality of life of asthma patients.

  View details for DOI 10.2147/PGPM.S201276

  View details for PubMedID 32256100

  View details for PubMedCentralID PMC7090194