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Colloca L, Mocci E, Wang Y, Massalee R, Chen S, Clark J, Johnson K, Fidalgo GMP, Wilson GM, Goldman D, Dorsey SG. Transcriptomic Profiles Associated with Experimental Placebo Effects in Chronic Pain. Clin Pharmacol Ther 2024; 116:380-389. [PMID: 38711244 PMCID: PMC11251865 DOI: 10.1002/cpt.3286] [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: 12/21/2023] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
Gene expression networks associated with placebo effects are understudied; in this study, we identified transcriptomic profiles associated with placebo responsivity. Participants suffering from chronic pain underwent a verbal suggestion and conditioning paradigm with individually tailored thermal painful stimulations to elicit conditioned placebo effects. Participants reported pain intensity on a visual analog scale (VAS) anchored from zero = no pain to 100 = maximum imaginable pain. RNA was extracted from venous blood and RNA sequencing and validation tests were performed to identify differentially expressed genes (DEGs) associated with placebo effects, controlling for sex and level of pain. Unbiased enrichment analyses were performed to identify biological processes associated with placebo effects. Of the 10,700 protein-coding genes that passed quality control filters, 667 were found to be associated with placebo effects (FDR <0.05). Most genes (97%) upregulated were associated with larger placebo effects. The 17 top transcriptome-wide significant genes were further validated via RT-qPCR in an independent cohort of chronic pain participants. Six of them (CCDC85B, FBXL15, HAGH, PI3, SELENOM, and TNFRSF4) showed positive and significant (P < 0.05) correlation with placebo effects in the cohort. The overall DEGs were highly enriched in regulation of expression of SLITs and ROBOs (R-HSA-9010553, FDR = 1.26e-33), metabolism of RNA (R-HSA-8953854, FDR = 1.34e-30), Huntington's disease (hsa05016, FDR = 9.84e-31), and ribosome biogenesis (GO:0042254, FDR = 2.67e-15); alternations in these pathways might jeopardize the proneness to elicit placebo effects. Future studies are needed to replicate this finding and better understand the unique molecular dynamics of people who are more or less affected by pain and placebo.
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Affiliation(s)
- Luana Colloca
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
- Department of Anesthesiology, School of Medicine, University of Maryland, Baltimore, US
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, US
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, US
| | - Evelina Mocci
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, US
| | - Yang Wang
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, US
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, US
| | - Rachel Massalee
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
| | - Shuo Chen
- Maryland Psychiatry Research Center, School of Medicine, Baltimore, US
| | - Jewel Clark
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
| | - Kesha Johnson
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
| | - Gloria M. Patron Fidalgo
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, US
| | - Gerald M. Wilson
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, US
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism (NIAAA), NIH, Rockville, MD 20855, US
| | - Susan G. Dorsey
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
- Department of Anesthesiology, School of Medicine, University of Maryland, Baltimore, US
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, US
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Hannon ER, Marsit CJ, Dent AE, Embury P, Ogolla S, Midem D, Williams SM, Kazura JW. Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation. BioData Min 2024; 17:21. [PMID: 38992677 PMCID: PMC11241886 DOI: 10.1186/s13040-024-00374-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from the transcriptome versus the methylome (DNAm) influence estimates of differentially expressed genes (DEGs) and differentially methylated positions (DMPs). METHODS Transcriptome and DNAm data were obtained from PBMC RNA and DNA of Kenyan children (n = 8) before, during, and 6 weeks following uncomplicated malaria. DEGs and DMPs between time points were detected using cell-type adjusted modeling with Cibersortx or IDOL, respectively. RESULTS Most major cell types and principal components had moderate to high correlation between the two deconvolution methods (r = 0.60-0.96). Estimates of cell-type proportions and DEGs or DMPs were largely unaffected by the method, with the greatest discrepancy in the estimation of neutrophils. CONCLUSION Variation in cell-type proportions is captured similarly by both transcriptomic and methylome deconvolution methods for most major cell types.
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Affiliation(s)
- Emily R Hannon
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA.
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Arlene E Dent
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
- Division of Pediatric Infectious Diseases, Rainbow Babies and Children's Hospital, Cleveland, OH, 44106, USA
| | - Paula Embury
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
| | | | - David Midem
- Chulaimbo Sub-county Hospital, Kisumu County, Kenya
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
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Hong J, Eun JW, Baek GO, Cheong JY, Park S, Kim SS, Cho HJ, Lim SB. Multiomics profiling of buffy coat and plasma unveils etiology-specific signatures in hepatocellular carcinoma. Clin Mol Hepatol 2024; 30:360-374. [PMID: 38486508 PMCID: PMC11261225 DOI: 10.3350/cmh.2024.0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND/AIMS Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality worldwide. Despite identification of several biomarkers for HCC diagnosis, challenges such as low sensitivity and intratumoral heterogeneity have impeded early detection, highlighting the need for etiology-specific blood biomarkers. METHODS We generated whole-transcriptome sequencing (WTS) and targeted proteome data from buffy coat and plasma samples from HCC patients. By integrating etiological information on viral infection, we investigated the etiology-specific gene expression landscape at the blood level. Validation of differentially expressed genes (DEGs) was performed using publicly available RNA-seq datasets and qRT‒PCR with AUC analyses. RESULTS Differential expression analyses with multiomics data revealed distinct gene expression profiles between HBV-associated HCC and nonviral HCC, indicating the presence of etiology-specific blood biomarkers. The identified DEGs were validated across multiple independent datasets, underscoring their utility as biomarkers. Additionally, single-cell RNA-seq analysis of HCC confirmed differences in DEG expression across distinct immune cell types. CONCLUSION Our buffy coat WTS data and plasma proteome data may serve as reliable sources for identifying etiology-specific blood biomarkers of HCC and might contribute to discovery of therapeutic targets for HCC across different etiologies.
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Affiliation(s)
- Jiwon Hong
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, Korea
| | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Geum Ok Baek
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Seryoung Park
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, Korea
| | - Soon Sun Kim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Hyo Jung Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Su Bin Lim
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, Korea
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Popotas A, Casimir GJ, Corazza F, Lefèvre N. Sex-related immunity: could Toll-like receptors be the answer in acute inflammatory response? Front Immunol 2024; 15:1379754. [PMID: 38835761 PMCID: PMC11148260 DOI: 10.3389/fimmu.2024.1379754] [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: 01/31/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
An increasing number of studies have highlighted the existence of a sex-specific immune response, wherein men experience a worse prognosis in cases of acute inflammatory diseases. Initially, this sex-dependent inflammatory response was attributed to the influence of sex hormones. However, a growing body of evidence has shifted the focus toward the influence of chromosomes rather than sex hormones in shaping these inflammatory sex disparities. Notably, certain pattern recognition receptors, such as Toll-like receptors (TLRs), and their associated immune pathways have been implicated in driving the sex-specific immune response. These receptors are encoded by genes located on the X chromosome. TLRs are pivotal components of the innate immune system, playing crucial roles in responding to infectious diseases, including bacterial and viral pathogens, as well as trauma-related conditions. Importantly, the TLR-mediated inflammatory responses, as indicated by the production of specific proteins and cytokines, exhibit discernible sex-dependent patterns. In this review, we delve into the subject of sex bias in TLR activation and explore its clinical implications relatively to both the X chromosome and the hormonal environment. The overarching objective is to enhance our understanding of the fundamental mechanisms underlying these sex differences.
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Affiliation(s)
- Alexandros Popotas
- Laboratory of Pediatrics, Université Libre de Bruxelles, Brussels, Belgium
- Laboratory of Translational Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Georges Jacques Casimir
- Laboratory of Pediatrics, Université Libre de Bruxelles, Brussels, Belgium
- Department of Pulmonology, Allergology and Cystic Fibrosis, Queen Fabiola Childrens University Hospital (Hôpital Universitaire des Enfants Reine Fabiola) – University Hospital of Brussels (Hôpital Universitaire de Bruxelles), Brussels, Belgium
| | - Francis Corazza
- Laboratory of Translational Research, Université Libre de Bruxelles, Brussels, Belgium
- Laboratory of Immunology, Centre Hospitalier Universitaire (CHU) Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicolas Lefèvre
- Laboratory of Pediatrics, Université Libre de Bruxelles, Brussels, Belgium
- Department of Pulmonology, Allergology and Cystic Fibrosis, Queen Fabiola Childrens University Hospital (Hôpital Universitaire des Enfants Reine Fabiola) – University Hospital of Brussels (Hôpital Universitaire de Bruxelles), Brussels, Belgium
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Hannon ER, Marsit CJ, Dent AE, Embury P, Ogolla S, Midem D, Williams SM, Kazura JW. Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation. RESEARCH SQUARE 2024:rs.3.rs-3992113. [PMID: 38645047 PMCID: PMC11030537 DOI: 10.21203/rs.3.rs-3992113/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from the transcriptome versus the methylome (DNAm) influence estimates of differentially expressed genes (DEGs) and differentially methylated positions (DMPs). Methods Transcriptome and DNAm data were obtained from PBMC RNA and DNA of Kenyan children (n = 8) before, during, and 6 weeks following uncomplicated malaria. DEGs and DMPs between time points were detected using cell-type adjusted modeling with Cibersortx or IDOL, respectively. Results Most major cell types and principal components had moderate to high correlation between the two deconvolution methods (r = 0.60-0.96). Estimates of cell-type proportions and DEGs or DMPs were largely unaffected by the method, with the greatest discrepancy in the estimation of neutrophils. Conclusion Variation in cell-type proportions is captured similarly by both transcriptomic and methylome deconvolution methods for most major cell types.
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Chen Q, Guo X, Wang H, Sun S, Jiang H, Zhang P, Shang E, Zhang R, Cao Z, Niu Q, Zhang C, Liu Y, Shi L, Yu Y, Hou W, Zheng Y. Plasma-Free Blood as a Potential Alternative to Whole Blood for Transcriptomic Analysis. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:109-124. [PMID: 38884056 PMCID: PMC11169349 DOI: 10.1007/s43657-023-00121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 06/18/2024]
Abstract
RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples that are generally considered less useful byproducts during the processes of plasma and serum separation, respectively. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis. We performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns, detection of differentially expressed genes, and immunological characterizations, suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis. Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00121-1.
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Affiliation(s)
- Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Xiaorou Guo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Shanyue Sun
- Shandong Provincial Hospital, Shandong First Medical University, Jinan, 250021 China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Erfei Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Ruolan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Quanne Niu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Chao Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
- The International Human Phenome Institutes, Shanghai, 200438 China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
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Klimosch SN, Weber M, Caballé-Serrano J, Knorpp T, Munar-Frau A, Schaefer BM, Schmolz M. A Human Whole Blood Culture System Reveals Detailed Cytokine Release Profiles of Implant Materials. MEDICAL DEVICES-EVIDENCE AND RESEARCH 2024; 17:23-36. [PMID: 38196508 PMCID: PMC10775699 DOI: 10.2147/mder.s441403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Introduction Common in vitro cell culture systems for testing implant material immune compatibility either rely on immortal human leukocyte cell lines or isolated primary cells. Compared to in vivo conditions, this generates an environment of substantially reduced complexity, often lacking important immune cell types, such as neutrophil granulocytes and others. The aim of this study was to establish a reliable test system for in vitro testing of implant materials under in vivo-like conditions. Methods Test materials were incubated in closed, CO2-independent, tube-based culture vessels containing a proprietary cell culture medium and human whole blood in either a static or occasionally rotating system. Multiplex cytokine analysis was used to analyze immune cell reactions. Results To demonstrate the applicability of the test system to implant materials, three commercially available barrier membranes (polytetrafluoroethylene (PTFE), polycaprolactone (PCL) and collagen) used for dental, trauma and maxillofacial surgery, were investigated for their potential interactions with immune cells. The results showed characteristic differences between the static and rotated incubation methods and in the overall activity profiles with very low immune cell responses to PTFE, intermediate ones to collagen and strong reactions to PCL. Conclusion This in vitro human whole blood model, using a complex organotypic matrix, is an excellent, easily standardized tool for categorizing immune cell responses to implant materials. Compared to in vitro cell culture systems used for materials research, this new assay system provides a far more detailed picture of response patterns the immune system can develop when interacting with different types of materials and surfaces.
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Affiliation(s)
| | | | - Jordi Caballé-Serrano
- Department of Oral and Maxillofacial Surgery, Universitat Internacional de Catalunya, Barcelona, Spain
- Department of Periodontology, School of Dental Medicine - University of Bern, Bern, Switzerland
| | | | - Antonio Munar-Frau
- Department of Oral and Maxillofacial Surgery, Universitat Internacional de Catalunya, Barcelona, Spain
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Fiorito AM, Fakra E, Sescousse G, Ibrahim EC, Rey R. Molecular mapping of a core transcriptional signature of microglia-specific genes in schizophrenia. Transl Psychiatry 2023; 13:386. [PMID: 38092734 PMCID: PMC10719376 DOI: 10.1038/s41398-023-02677-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Besides playing a central role in neuroinflammation, microglia regulate synaptic development and is involved in plasticity. Converging lines of evidence suggest that these different processes play a critical role in schizophrenia. Furthermore, previous studies reported altered transcription of microglia genes in schizophrenia, while microglia itself seems to be involved in the etiopathology of the disease. However, the regional specificity of these brain transcriptional abnormalities remains unclear. Moreover, it is unknown whether brain and peripheral expression of microglia genes are related. Thus, we investigated the expression of a pre-registered list of 10 genes from a core signature of human microglia both at brain and peripheral levels. We included 9 independent Gene Expression Omnibus datasets (764 samples obtained from 266 individuals with schizophrenia and 237 healthy controls) from 8 different brain regions and 3 peripheral tissues. We report evidence of a widespread transcriptional alteration of microglia genes both in brain tissues (we observed a decreased expression in the cerebellum, associative striatum, hippocampus, and parietal cortex of individuals with schizophrenia compared with healthy controls) and whole blood (characterized by a mixed altered expression pattern). Our results suggest that brain underexpression of microglia genes may represent a candidate transcriptional signature for schizophrenia. Moreover, the dual brain-whole blood transcriptional alterations of microglia/macrophage genes identified support the model of schizophrenia as a whole-body disorder and lend weight to the use of blood samples as a potential source of biological peripheral biomarkers.
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Affiliation(s)
- Anna M Fiorito
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Centre Hospitalier Le Vinatier, Bron, France
| | - Eric Fakra
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Department of Psychiatry, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Guillaume Sescousse
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Centre Hospitalier Le Vinatier, Bron, France
| | - El Chérif Ibrahim
- Aix-Marseille Univ, CNRS, INT, Institut de Neurosciences de la Timone, Marseille, France
| | - Romain Rey
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France.
- Centre Hospitalier Le Vinatier, Bron, France.
- Fondation FondaMental, Créteil, France.
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Filipowicz G, Wajda A, Stypińska B, Kmiołek T, Felis-Giemza A, Stańczyk S, Czuszyńska Z, Walczyk M, Olesińska M, Paradowska-Gorycka A. Mixed Connective Tissue Disease as Different Entity: Global Methylation Aspect. Int J Mol Sci 2023; 24:15495. [PMID: 37895173 PMCID: PMC10607312 DOI: 10.3390/ijms242015495] [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: 08/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Mixed connective tissue disease (MCTD) is a very rare disorder that belongs in the rare and clinically multifactorial groups of diseases. The pathogenesis of MCTD is still unclear. The best understood epigenetic alteration is DNA methylation whose role is to regulate gene expression. In the literature, there are ever-increasing assumptions that DNA methylation can be one of the possible reasons for the development of Autoimmune Connective Tissue Diseases (ACTDs) such as systemic sclerosis (SSc) and systemic lupus erythematosus (SLE). The aim of this study was to define the global DNA methylation changes between MCTD and other ACTDs patients in whole blood samples. The study included 54 MCTD patients, 43 SSc patients, 45 SLE patients, and 43 healthy donors (HC). The global DNA methylation level was measured by ELISA. Although the global DNA methylation was not significantly different between MCTD and control, we observed that hypomethylation distinguishes the MCTD patients from the SSc and SLE patients. The present analysis revealed a statistically significant difference of global methylation between SLE and MCTD (p < 0.001), SLE and HC (p = 0.008), SSc and MCTD (p ≤ 0.001), and SSc and HC (p < 0.001), but neither between MCTD and HC (p = 0.09) nor SSc and SLE (p = 0.08). The highest % of global methylation (median, IQR) has been observed in the group of patients with SLE [0.73 (0.43, 1.22] and SSc [0,91 (0.59, 1.50)], whereas in the MCTD [0.29 (0.20, 0.54)], patients and healthy subjects [0.51 (0.24, 0.70)] were comparable. In addition, our study provided evidence of different levels of global DNA methylation between the SSc subtypes (p = 0.01). Our study showed that patients with limited SSc had a significantly higher global methylation level when compared to diffuse SSc. Our data has shown that the level of global DNA methylation may not be a good diagnostic marker to distinguish MCTD from other ACTDs. Our research provides the groundwork for a more detailed examination of the significance of global DNA methylation as a distinguishing factor in patients with MCTD compared to other ACTDs patients.
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Affiliation(s)
- Gabriela Filipowicz
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Barbara Stypińska
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Tomasz Kmiołek
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Anna Felis-Giemza
- Biologic Therapy Center, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland (S.S.)
| | - Sandra Stańczyk
- Biologic Therapy Center, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland (S.S.)
| | - Zenobia Czuszyńska
- Department of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdansk, Smulochowskiego 17, 80-214 Gdansk, Poland
| | - Marcela Walczyk
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland
| | - Marzena Olesińska
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
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Lee J, Kim H, Kim M, Yoon S, Lee S. Role of lymphoid lineage cells aberrantly expressing alarmins S100A8/A9 in determining the severity of COVID-19. Genes Genomics 2023; 45:337-346. [PMID: 36107397 PMCID: PMC9476394 DOI: 10.1007/s13258-022-01285-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/08/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Alarmins S100A8 and S100A9 are recognized as hallmarks of severe COVID-19 and are primarily produced in myeloid cells, such as monocytes and neutrophils. As single-cell RNA-sequencing (scRNA-seq) data from patients with COVID-19 revealed the expression of S100A8/A9 in lymphoid cells in patients with severe COVID-19. OBJECTIVE We investigated the characteristics of lymphoid cells expressing S100A8/A9 in COVID-19 patients. METHODS Publicly available scRNA-seq data from patients with mild (N = 12) or severe (N = 7) COVID-19 were reanalyzed. The data were further divided into the following two groups based on the time of sample collection (from infection-onset): within 6 days (early phase) and after 6 days (late phase). Differential expression and gene set enrichment analyses were performed between S100A8/A9High and S100A8/A9Low lymphoid cells. Finally, cell-cell interaction analysis was performed to investigate the role of lymphoid cells expressing high levels of S100A8/A9 in COVID-19. RESULTS S100A8/A9 overexpression was observed in lymphoid cells, including B cells, T cells, and NK cells, in patients with severe COVID-19 (compared to patients with mild COVID-19). Cells exhibiting strong interferon/cytokine responses were found to be associated with the severity of COVID-19. Furthermore, differences in S100A8/A9-TLR4/RAGE interactions were confirmed between patients with severe and mild disease. CONCLUSIONS Lymphoid cells overexpressing S100A8/A9 contribute to the dysregulation of the innate immune response in patients with severe COVID-19, specifically during the early phase of infection. This study fosters a better understanding of the hyper-induction of pro-inflammatory cytokine expression and the generation of a cytokine storm in response to COVID-19 infection.
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Affiliation(s)
- Joongho Lee
- Department of Computer Science and Engineering, Graduate School, Dankook University, Yongin-si, Republic of Korea
| | - Hanbyeol Kim
- Department of Computer Science and Engineering, Graduate School, Dankook University, Yongin-si, Republic of Korea
| | - Minsoo Kim
- Department of Computer Science and Engineering, Graduate School, Dankook University, Yongin-si, Republic of Korea
| | - Seokhyun Yoon
- Department of Computer Science and Engineering, Graduate School, Dankook University, Yongin-si, Republic of Korea. .,Department of Electronics and Electrical Engineering, College of Engineering, Dankook University, Yongin-si, Republic of Korea.
| | - Sanghun Lee
- Department of Bioconvergence Engineering, Graduate School, Dankook University, Yongin-si, Republic of Korea.
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11
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Justin Margret J, Jain SK. Overview of gene expression techniques with an emphasis on vitamin D related studies. Curr Med Res Opin 2023; 39:205-217. [PMID: 36537177 DOI: 10.1080/03007995.2022.2159148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Each cell controls when and how its genes must be expressed for proper function. Every function in a cell is driven by signaling molecules through various regulatory cascades. Different cells in a multicellular organism may express very different sets of genes, even though they contain the same DNA. The set of genes expressed in a cell determines the set of proteins and functional RNAs it contains, giving it its unique properties. Malfunction in gene expression harms the cell and can lead to the development of various disease conditions. The use of rapid high-throughput gene expression profiling unravels the complexity of human disease at various levels. Peripheral blood mononuclear cells (PBMC) have been used frequently to understand gene expression homeostasis in various disease conditions. However, more studies are required to validate whether PBMC gene expression patterns accurately reflect the expression of other cells or tissues. Vitamin D, which is responsible for a multitude of health consequences, is also an immune modulatory hormone with major biological activities in the innate and adaptive immune systems. Vitamin D exerts its diverse biological effects in target tissues by regulating gene expression and its deficiency, is recognized as a public health problem worldwide. Understanding the genetic factors that affect vitamin D has the potential benefit that it will make it easier to identify individuals who require supplementation. Different technological advances in gene expression can be used to identify and assess the severity of disease and aid in the development of novel therapeutic interventions. This review focuses on different gene expression approaches and various clinical studies of vitamin D to investigate the role of gene expression in identifying the molecular signature of the disease.
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Affiliation(s)
- Jeffrey Justin Margret
- Department of Pediatrics, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
| | - Sushil K Jain
- Department of Pediatrics, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
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12
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Whole blood transcriptome profiling identifies gene expression subnetworks and a key gene characteristic of the rare type of osteomyelitis. Biochem Biophys Rep 2022; 32:101328. [PMID: 36065290 PMCID: PMC9440381 DOI: 10.1016/j.bbrep.2022.101328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022] Open
Abstract
Chronic non-bacterial osteomyelitis (CNO) is a rare and severe inflammatory bone disorder that can occur in the jaw. It is often associated with systemic conditions including autoimmune deficiency. Medical management of patients and establishment of a correct diagnosis are difficult as the etiology of the disease remains unknown. Therefore, little is known about the disease characteristics at the gene expression level. Here, we explored aspects of CNO based on whole blood RNA sequencing (>6 Gb per sample) of 11 patients and 9 healthy controls in Japan and on a recently developed method that is applicable to small datasets, can estimate a directed gene network, and extract a subnetwork of genes underlying patient characteristics. We identified nine subnetworks, comprising 26 differentially regulated edges and 36 genes, with the gene encoding glycophorin C (GYPC) presenting the highest discrimination ability. The expression of the gene was mostly lower in patients with CNO than in the healthy controls, suggesting an abnormal status of red cells in patients with CNO. This study enhances our understanding of CNO at the transcriptome level and further provides a framework for whole blood RNA sequencing and analysis of data obtained for a better diagnosis of the disease. We explored new aspects of chronic non-bacterial osteomyelitis (CNO) via whole-blood RNA-seq and gene network analysis. Nine subnetworks of genes were identified. A GYPC-encoding gene had the highest discrimination ability in these subnetworks. The expression level of the gene suggested an abnormal status of red cells in the patients.
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Kirksey MA, Lessard SG, Khan M, Birch GA, Oliver D, Singh P, Rotundo V, Sideris A, Gonzalez Della Valle A, Parks ML, Sculco PK, Otero M. Association of circulating gene expression signatures with stiffness following total knee arthroplasty for osteoarthritis: a pilot study. Sci Rep 2022; 12:12651. [PMID: 35879399 PMCID: PMC9314445 DOI: 10.1038/s41598-022-16868-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Abstract
A subset of patients undergoing total knee arthroplasty (TKA) for knee osteoarthritis develop debilitating knee stiffness (reduced range of motion) for poorly understood reasons. Dysregulated inflammatory and immune responses to surgery correlate with reduced surgical outcomes, but the dysregulated gene signatures in patients with stiffness after TKA are poorly defined. As a consequence, we are limited in our ability to identify patients at risk of developing poor surgical outcomes and develop preventative approaches. In this pilot study we aimed to identify perioperative blood gene signatures in patients undergoing TKA for knee osteoarthritis and its association with early surgical outcomes, specifically knee range of motion. To do this, we integrated clinical outcomes collected at 6 weeks after surgery with transcriptomics analyses in blood samples collected immediately before surgery and at 24 h after surgery. We found that patients with stiffness at 6 weeks after surgery have a more variable and attenuated circulating gene expression response immediately after surgery. Our results suggest that patients with stiffness following TKA may have distinct gene expression signatures detectable in peripheral blood in the immediate postoperative period.
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Affiliation(s)
- Meghan A Kirksey
- Hospital for Special Surgery, New York, NY, 10021, USA.,Department of Anesthesiology, Critical Care, and Pain Management, Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10021, USA
| | - Samantha G Lessard
- Hospital for Special Surgery, New York, NY, 10021, USA.,HSS Research Institute, Hospital for Special Surgery, New York, NY, 10021, USA.,Orthopedic Soft Tissue Research Program, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Marjan Khan
- Hospital for Special Surgery, New York, NY, 10021, USA.,HSS Research Institute, Hospital for Special Surgery, New York, NY, 10021, USA.,Orthopedic Soft Tissue Research Program, Hospital for Special Surgery, New York, NY, 10021, USA
| | - George A Birch
- Hospital for Special Surgery, New York, NY, 10021, USA.,Department of Anesthesiology, Critical Care, and Pain Management, Hospital for Special Surgery, New York, NY, 10021, USA
| | - David Oliver
- Hospital for Special Surgery, New York, NY, 10021, USA.,HSS Research Institute, Hospital for Special Surgery, New York, NY, 10021, USA.,The David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Purva Singh
- Hospital for Special Surgery, New York, NY, 10021, USA.,HSS Research Institute, Hospital for Special Surgery, New York, NY, 10021, USA.,Orthopedic Soft Tissue Research Program, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Valeria Rotundo
- Hospital for Special Surgery, New York, NY, 10021, USA.,Department of Anesthesiology, Critical Care, and Pain Management, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Alexandra Sideris
- Hospital for Special Surgery, New York, NY, 10021, USA.,Department of Anesthesiology, Critical Care, and Pain Management, Hospital for Special Surgery, New York, NY, 10021, USA
| | | | - Alejandro Gonzalez Della Valle
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10021, USA.,The Stavros Niarchos Foundation Complex Joint Reconstruction Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Michael L Parks
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10021, USA.,The Stavros Niarchos Foundation Complex Joint Reconstruction Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Peter K Sculco
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10021, USA.,The Stavros Niarchos Foundation Complex Joint Reconstruction Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Miguel Otero
- Hospital for Special Surgery, New York, NY, 10021, USA. .,Weill Cornell Medical College, New York, NY, 10021, USA. .,HSS Research Institute, Hospital for Special Surgery, New York, NY, 10021, USA. .,Orthopedic Soft Tissue Research Program, Hospital for Special Surgery, New York, NY, 10021, USA. .,The David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
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14
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Blood transcriptome profiling identifies 2 candidate endotypes of atopic dermatitis. J Allergy Clin Immunol 2022; 150:385-395. [PMID: 35182548 DOI: 10.1016/j.jaci.2022.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/15/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Few studies have analyzed the blood transcriptome in atopic dermatitis (AD). OBJECTIVE We explored blood transcriptomic features of moderate to severe AD. METHODS Blood messenger RNA sequencing on 60 adults from the TREATgermany registry including 49 patients before and after dupilumab treatment, as well as from an independent cohort of 31 patients and 43 controls was performed. Patient clustering, differential expression, correlation and coexpression network analysis, and unsupervised learning were conducted. RESULTS AD patients showed pronounced inflammatory expression signatures with increased myeloid and IL-5-related patterns, and clearly segregated into 2 distinct clusters, with striking differences in particular for transcripts involved in eosinophil signaling. The eosinophil-high endotype showed a more pronounced global dysregulation, a positive correlation between disease activity and signatures related to IL-5 signaling, and strong correlations with several target proteins of antibodies or small molecules under development for AD. In contrast, the eosinophil-low endotype showed little transcriptomic dysregulation and no association between disease activity and gene expression. Clinical improvement with receipt of dupilumab was accompanied by a decrease of innate immune responses and an increase of lymphocyte signatures including B-cell activation and natural killer cell composition and/or function. The proportion of super responders was higher in the eosinophil-low endotype (32% vs 11%). Continued downregulation of IL18RAP, IFNG, and granzyme A in the eosinophil-high endotype suggests a residual disturbance of natural killer cell function despite clinical improvement. CONCLUSION AD can be stratified into eosinophilic and noneosinophilic endotypes; such stratification may be useful when assessing stratified trial designs and treatment strategies.
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15
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Piotrowski ER, Tift MS, Crocker DE, Pearson AB, Vázquez-Medina JP, Keith AD, Khudyakov JI. Ontogeny of Carbon Monoxide-Related Gene Expression in a Deep-Diving Marine Mammal. Front Physiol 2021; 12:762102. [PMID: 34744798 PMCID: PMC8567018 DOI: 10.3389/fphys.2021.762102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Marine mammals such as northern elephant seals (NES) routinely experience hypoxemia and ischemia-reperfusion events to many tissues during deep dives with no apparent adverse effects. Adaptations to diving include increased antioxidants and elevated oxygen storage capacity associated with high hemoprotein content in blood and muscle. The natural turnover of heme by heme oxygenase enzymes (encoded by HMOX1 and HMOX2) produces endogenous carbon monoxide (CO), which is present at high levels in NES blood and has been shown to have cytoprotective effects in laboratory systems exposed to hypoxia. To understand how pathways associated with endogenous CO production and signaling change across ontogeny in diving mammals, we measured muscle CO and baseline expression of 17 CO-related genes in skeletal muscle and whole blood of three age classes of NES. Muscle CO levels approached those of animals exposed to high exogenous CO, increased with age, and were significantly correlated with gene expression levels. Muscle expression of genes associated with CO production and antioxidant defenses (HMOX1, BVR, GPX3, PRDX1) increased with age and was highest in adult females, while that of genes associated with protection from lipid peroxidation (GPX4, PRDX6, PRDX1, SIRT1) was highest in adult males. In contrast, muscle expression of mitochondrial biogenesis regulators (PGC1A, ESRRA, ESRRG) was highest in pups, while genes associated with inflammation (HMOX2, NRF2, IL1B) did not vary with age or sex. Blood expression of genes involved in regulation of inflammation (IL1B, NRF2, BVR, IL10) was highest in pups, while HMOX1, HMOX2 and pro-inflammatory markers (TLR4, CCL4, PRDX1, TNFA) did not vary with age. We propose that ontogenetic upregulation of baseline HMOX1 expression in skeletal muscle of NES may, in part, underlie increases in CO levels and expression of genes encoding antioxidant enzymes. HMOX2, in turn, may play a role in regulating inflammation related to ischemia and reperfusion in muscle and circulating immune cells. Our data suggest putative ontogenetic mechanisms that may enable phocid pups to transition to a deep-diving lifestyle, including high baseline expression of genes associated with mitochondrial biogenesis and immune system activation during postnatal development and increased expression of genes associated with protection from lipid peroxidation in adulthood.
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Affiliation(s)
| | - Michael S. Tift
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Daniel E. Crocker
- Biology Department, Sonoma State University, Rohnert Park, CA, United States
| | - Anna B. Pearson
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States
| | - José P. Vázquez-Medina
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Anna D. Keith
- Department of Biological Sciences, University of the Pacific, Stockton, CA, United States
| | - Jane I. Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, United States
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16
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Gamaleldin MA, Imbaby SAE. The role of tumor necrosis factor receptor superfamily member 4 (TNFRSF4) gene expression in diagnosis and prognosis of acute myeloid leukemia. Mol Biol Rep 2021; 48:6831-6843. [PMID: 34453673 DOI: 10.1007/s11033-021-06682-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Acute myeloid leukemia (AML) is still challenging in predicting the prognosis due to its high heterogeneity. Molecular aberrations and abnormalities play a significant prognostic role in AML patients. Our aim of the study was to investigate the prognostic role of TNFRSF4 gene expression in AML patients and its potential effect on treatment protocols. METHODS Bone marrow mononuclear cells were analyzed for TNFRSF4 expression by real-time quantitative PCR as well as of FLT3/ITD and NPM1 mutations in 80 newly diagnosed AML patients and 80 control subjects. RESULTS TNFRSF4 was significantly overexpressed in the AML patients (p < 0.001). TNFRSF4 expression was associated with unfavorable clinical outcomes including treatment response, relapse free survival, and overall survival. On multivariate testing, TNFRSF4 high expression proved to be an independent prognostic marker for clinical remission and relapse free survival but not overall survival. CONCLUSION TNFRSF4 expression was revealed as an unfavorable prognostic marker and might be a target for immunotherapy in the future.
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Affiliation(s)
- Marwa Ahmed Gamaleldin
- Clinical Pathology Department, Faculty of Medicine, University of Alexandria, Alexandria, Egypt.
| | - Salma Alaa Eldin Imbaby
- Clinical Pathology Department, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
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17
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Rhein C, Zoicas I, Marx LM, Zeitler S, Hepp T, von Zimmermann C, Mühle C, Richter-Schmidinger T, Lenz B, Erim Y, Reichel M, Gulbins E, Kornhuber J. mRNA Expression of SMPD1 Encoding Acid Sphingomyelinase Decreases upon Antidepressant Treatment. Int J Mol Sci 2021; 22:ijms22115700. [PMID: 34071826 PMCID: PMC8198802 DOI: 10.3390/ijms22115700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/14/2021] [Accepted: 05/23/2021] [Indexed: 12/24/2022] Open
Abstract
Major depressive disorder (MDD) is a severe psychiatric condition with key symptoms of low mood and lack of motivation, joy, and pleasure. Recently, the acid sphingomyelinase (ASM)/ceramide system has been implicated in the pathogenesis of MDD. ASM is a lysosomal glycoprotein that catalyzes the hydrolysis of sphingomyelin, an abundant component of membranes, into the bioactive sphingolipid ceramide, which impacts signaling pathways. ASM activity is inhibited by several common antidepressant drugs. Human and murine studies have confirmed that increased ASM activity and ceramide levels are correlated with MDD. To define a molecular marker for treatment monitoring, we investigated the mRNA expression of SMPD1, which encodes ASM, in primary cell culture models, a mouse study, and a human study with untreated MDD patients before and after antidepressive treatment. Our cell culture study showed that a common antidepressant inhibited ASM activity at the enzymatic level and also at the transcriptional level. In a genetically modified mouse line with depressive-like behavior, Smpd1 mRNA expression in dorsal hippocampal tissue was significantly decreased after treatment with a common antidepressant. The large human study showed that SMPD1 mRNA expression in untreated MDD patients decreased significantly after antidepressive treatment. This translational study shows that SMPD1 mRNA expression could serve as a molecular marker for treatment and adherence monitoring of MDD.
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Affiliation(s)
- Cosima Rhein
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
- Department of Psychosomatic Medicine and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), D-91054 Erlangen, Germany; (T.H.); (Y.E.)
- Correspondence: ; Tel.: +49-9131-85-44542
| | - Iulia Zoicas
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
| | - Lena M. Marx
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
| | - Stefanie Zeitler
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
| | - Tobias Hepp
- Department of Psychosomatic Medicine and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), D-91054 Erlangen, Germany; (T.H.); (Y.E.)
- Institute of Medical Informatics, Biometry and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), D-91054 Erlangen, Germany
| | - Claudia von Zimmermann
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
| | - Christiane Mühle
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
| | - Tanja Richter-Schmidinger
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
| | - Bernd Lenz
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health (CIMH), Medical Faculty Mannheim, Heidelberg University, D-68159 Mannheim, Germany
| | - Yesim Erim
- Department of Psychosomatic Medicine and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), D-91054 Erlangen, Germany; (T.H.); (Y.E.)
| | - Martin Reichel
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
| | - Erich Gulbins
- Department of Molecular Biology, University Hospital, University of Duisburg-Essen, D-45147 Essen, Germany;
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 6, D-91054 Erlangen, Germany; (I.Z.); (L.M.M.); (S.Z.); (C.v.Z.); (C.M.); (T.R.-S.); (B.L.); (M.R.); (J.K.)
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18
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Sheikhpour M, Maleki M, Ebrahimi Vargoorani M, Amiri V. A review of epigenetic changes in asthma: methylation and acetylation. Clin Epigenetics 2021; 13:65. [PMID: 33781317 PMCID: PMC8008616 DOI: 10.1186/s13148-021-01049-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/04/2021] [Indexed: 12/30/2022] Open
Abstract
Several studies show that childhood and adulthood asthma and its symptoms can be modulated through epigenetic modifications. Epigenetic changes are inheritable modifications that can modify the gene expression without changing the DNA sequence. The most common epigenetic alternations consist of DNA methylation and histone modifications. How these changes lead to asthmatic phenotype or promote the asthma features, in particular by immune pathways regulation, is an understudied topic. Since external effects, like exposure to tobacco smoke, air pollution, and drugs, influence both asthma development and the epigenome, elucidating the role of epigenetic changes in asthma is of great importance. This review presents available evidence on the epigenetic process that drives asthma genes and pathways, with a particular focus on DNA methylation, histone methylation, and acetylation. We gathered and assessed studies conducted in this field over the past two decades. Our study examined asthma in different aspects and also shed light on the limitations and the important factors involved in the outcomes of the studies. To date, most of the studies in this area have been carried out on DNA methylation. Therefore, the need for diagnostic and therapeutic applications through this molecular process calls for more research on the histone modifications in this disease.
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Affiliation(s)
- Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Mobina Maleki
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Ebrahimi Vargoorani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, College of Basic Sciences, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Vahid Amiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
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Iweala OI, Choudhary SK, Addison CT, Commins SP. T and B Lymphocyte Transcriptional States Differentiate between Sensitized and Unsensitized Individuals in Alpha-Gal Syndrome. Int J Mol Sci 2021; 22:ijms22063185. [PMID: 33804792 PMCID: PMC8003943 DOI: 10.3390/ijms22063185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
The mechanisms of pathogenesis driving alpha-gal syndrome (AGS) are not fully understood. Differences in immune gene expression between AGS individuals and non-allergic controls may illuminate molecular pathways and targets critical for AGS development. We performed immune expression profiling with RNA from the peripheral blood mononuclear cells (PBMCs) of seven controls, 15 AGS participants, and two participants sensitized but not allergic to alpha-gal using the NanoString nCounter PanCancer immune profiling panel, which includes 770 genes from 14 different cell types. The top differentially expressed genes (DEG) between AGS subjects and controls included transcription factors regulating immune gene expression, such as the NFκB pathway (NFKBIA, NFKB2, REL), antigen presentation molecules, type 2/allergic immune responses, itch, and allergic dermatitis. The differential expression of genes linked to T and B cell function was also identified, including transcription factor BCL-6, markers of antigen experience (CD44) and memory (CD27), chemokine receptors (CXCR3, CXCR6), and regulators of B-cell proliferation, cell cycle entry and immunoglobulin production (CD70). The PBMCs from AGS subjects also had increased TNF and IFN-gamma mRNA expression compared to controls. AGS is associated with a distinct gene expression profile in circulating PBMCs. DEGs related to antigen presentation, antigen-experienced T-cells, and type 2 immune responses may promote the development of alpha-gal specific IgE and the maintenance of AGS.
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Affiliation(s)
- Onyinye I. Iweala
- Department of Pediatrics, University of North Carolina Food Allergy Initiative, Division of Allergy, Immunology and Rheumatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.K.C.); (C.T.A.); (S.P.C.)
- Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
| | - Shailesh K. Choudhary
- Department of Pediatrics, University of North Carolina Food Allergy Initiative, Division of Allergy, Immunology and Rheumatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.K.C.); (C.T.A.); (S.P.C.)
- Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Claire T. Addison
- Department of Pediatrics, University of North Carolina Food Allergy Initiative, Division of Allergy, Immunology and Rheumatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.K.C.); (C.T.A.); (S.P.C.)
- Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Scott P. Commins
- Department of Pediatrics, University of North Carolina Food Allergy Initiative, Division of Allergy, Immunology and Rheumatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.K.C.); (C.T.A.); (S.P.C.)
- Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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20
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Ranaivomanana P, Rabodoarivelo MS, Ndiaye MDB, Rakotosamimanana N, Rasolofo V. Different PPD-stimulated cytokine responses from patients infected with genetically distinct Mycobacterium tuberculosis complex lineages. Int J Infect Dis 2021; 104:725-731. [PMID: 33556615 DOI: 10.1016/j.ijid.2021.01.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/08/2021] [Accepted: 01/30/2021] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES The genetic diversity of Mycobacterium tuberculosis complex (MTBC) influences the immune response of the host, which may affect the immunodiagnostic tests and biomarker assessment studies used for tuberculosis (TB). This study aimed to determine whether the mycobacterial-antigen-stimulated cytokine responses vary with the genotype of the MTBC infecting the patient. METHODS Eighty-one patients with confirmed active pulmonary TB were recruited, and MTBC clinical strains were isolated from their sputum for bacterial lineage single-nucleotide polymorphism typing. Whole blood was drawn from the patients to measure the purified protein derivative (PPD)-stimulated cytokine responses (GM-CSF, IFN-γ, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, TNF-α, IFN-α, IL-12, eotaxin, IL-13, IL-15, IL-17, MIP1-α, MIP1-β, MCP1, IL1RA, IP10, IL2R, MIG) with the Luminex multiplex immunoassay. RESULTS Of the 24 cytokines studied, three were produced differentially in whole blood dependent on the infecting lineage of MTBC. Decreased production of IL-17 was observed in patients infected with modern lineages compared with patients infected with ancestral lineages (P < 0.01), and production of IFN-γ and IL-2 was significantly decreased in patients infected with lineage 4 strains compared with patients infected with lineage 3 strains (P < 0.05). CONCLUSION MTBC strains belonging to lineage 4 induced a decreased whole-blood PPD-stimulated pro-inflammatory cytokine response.
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Affiliation(s)
- Paulo Ranaivomanana
- Mycobacteria Unit, Institut Pasteur de Madagascar, B.P. Ambatofotsikely, Antananarivo, Madagascar
| | | | | | - Niaina Rakotosamimanana
- Mycobacteria Unit, Institut Pasteur de Madagascar, B.P. Ambatofotsikely, Antananarivo, Madagascar.
| | - Voahangy Rasolofo
- Mycobacteria Unit, Institut Pasteur de Madagascar, B.P. Ambatofotsikely, Antananarivo, Madagascar
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21
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Abstract
Progress in genomic analytical technologies has improved our possibilities to obtain information regarding DNA, RNA, and their dynamic changes that occur over time or in response to specific challenges. This information describes the blueprint for cells, tissues, and organisms and has fundamental importance for all living organisms. This review focuses on the technological challenges to analyze the transcriptome and what is the impact of transcriptomics on precision medicine. The transcriptome is a term that covers all RNA present in cells and a substantial part of it will never be translated into protein but is nevertheless functional in determining cell phenotype. Recent developments in transcriptomics have challenged the fundamentals of the central dogma of biology by providing evidence of pervasive transcription of the genome. Such massive transcriptional activity is challenging the definition of a gene and especially the term "pseudogene" that has now been demonstrated in many examples to be both transcribed and translated. We also review the common sources of biomaterials for transcriptomics and justify the suitability of whole blood RNA as the current optimal analyte for clinical transcriptomics. At the end of the review, a brief overview of the clinical implications of transcriptomics in clinical trial design and clinical diagnosis is given. Finally, we introduce the transcriptome as a target for modern drug development as a tool for extending our capacity for precision medicine in multiple diseases.
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Affiliation(s)
| | - Abigail L Pfaff
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch 6150, Australia
- Perron Institute for Neurological and Translational Science, Nedlands 6009, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool L69 3BX, UK
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch 6150, Australia
- Perron Institute for Neurological and Translational Science, Nedlands 6009, Australia
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22
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Boulet LP, Côté A, Abd-Elaziz K, Gauvreau G, Diamant Z. Allergen bronchoprovocation test: an important research tool supporting precision medicine. Curr Opin Pulm Med 2021; 27:15-22. [PMID: 33065599 DOI: 10.1097/mcp.0000000000000742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Allergen bronchoprovocation test (ABT) has been used to study asthma pathophysiology and as a disease-modelling tool to assess the properties and efficacy of new asthma drugs. In view of the complexity and heterogeneity of asthma, which has driven the definition of several phenotypes and endotypes, we aim to discuss the role of ABT in the era of precision medicine and provide guidance for clinicians how to interpret and use available data to understand the implications for the benefits of asthma treatment. RECENT FINDINGS In this review, we summarize background knowledge and applications of ABT and provide an update with recent publications on this topic. In the past years, several studies have been published on ABT in combination with non-invasive and invasive airway samplings and innovative detection techniques allowing to study several inflammatory mechanisms linked to Th2-pathway and allergen-induced pathophysiology throughout the airways. SUMMARY ABT is a valuable research tool, which has strongly contributed to precision medicine by helping to define allergen-triggered key inflammatory pathways and airway pathophysiology, and thus helped to shape our understanding of allergen-driven asthma phenotypes and endotypes. In addition, ABT has been instrumental to assess the interactions and effects of new-targeted asthma treatments along these pathways.
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Affiliation(s)
- Louis-Philippe Boulet
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec Heart and Lung Institute, Université Laval, Québec, Canada
| | - Andréanne Côté
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec Heart and Lung Institute, Université Laval, Québec, Canada
| | | | - Gail Gauvreau
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Zuzana Diamant
- Department of Respiratory Medicine and Allergology, Institute for Clinical Science, Skane University Hospital, Lund University, Lund, Sweden
- Department of Respiratory Medicine, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
- Department Clinical Pharmacy and Pharmacology, University Groningen, University Medicine Ctr Groningen, Groningen, The Netherlands
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