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Shi W, Cassmann TJ, Bhagwate AV, Hitosugi T, Ip WKE. Lactic acid induces transcriptional repression of macrophage inflammatory response via histone acetylation. Cell Rep 2024; 43:113746. [PMID: 38329873 PMCID: PMC10957222 DOI: 10.1016/j.celrep.2024.113746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/09/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Lactic acid has emerged as an important modulator of immune cell function. It can be produced by both gut microbiota and the host metabolism at homeostasis and during disease states. The production of lactic acid in the gut microenvironment is vital for tissue homeostasis. In the present study, we examined how lactic acid integrates cellular metabolism to shape the epigenome of macrophages during pro-inflammatory response. We found that lactic acid serves as a primary fuel source to promote histone H3K27 acetylation, which allows the expression of immunosuppressive gene program including Nr4a1. Consequently, macrophage pro-inflammatory function was transcriptionally repressed. Furthermore, the histone acetylation induced by lactic acid promotes a form of long-term immunosuppression ("trained immunosuppression"). Pre-exposure to lactic acid induces lipopolysaccharide tolerance. These findings thus indicate that lactic acid sensing and its effect on chromatin remodeling in macrophages represent a key homeostatic mechanism that can provide a tolerogenic tissue microenvironment.
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Affiliation(s)
- Weiwei Shi
- Department of Immunology, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| | - Tiffany J Cassmann
- Department of Immunology, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| | - Aditya Vijay Bhagwate
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| | - Taro Hitosugi
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| | - W K Eddie Ip
- Department of Immunology, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA; Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA.
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Brar T, Baheti S, Bhagwate AV, Kita H, Marino MJ, Lal D. Genomewide epigenetic study shows significant DNA hypermethylation in chronic rhinosinusitis versus control ethmoidal tissue. Int Forum Allergy Rhinol 2023; 13:2235-2239. [PMID: 37300454 DOI: 10.1002/alr.23205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Affiliation(s)
- Tripti Brar
- Department of Otolaryngology-Head & Neck Surgery, Mayo Clinic, Phoenix, Arizona, USA
| | - Saurabh Baheti
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Hirohito Kita
- Department of Allergy, Asthma and Clinical Immunology, Mayo Clinic, Phoenix, Arizona, USA
| | - Michael J Marino
- Department of Otolaryngology-Head & Neck Surgery, Mayo Clinic, Phoenix, Arizona, USA
| | - Devyani Lal
- Department of Otolaryngology-Head & Neck Surgery, Mayo Clinic, Phoenix, Arizona, USA
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Bhagwate AV, Liu Y, Winham SJ, McDonough SJ, Stallings-Mann ML, Heinzen EP, Davila JI, Vierkant RA, Hoskin TL, Frost M, Carter JM, Radisky DC, Cunningham JM, Degnim AC, Wang C. Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples. BMC Genomics 2019; 20:689. [PMID: 31477010 PMCID: PMC6720378 DOI: 10.1186/s12864-019-6056-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/22/2019] [Indexed: 01/20/2023] Open
Abstract
Background Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples. Results As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts. For FFPE samples, we tested two FFPE DNA extraction methods to determine impact of wet-lab procedures on variant calling: QIAGEN QIAamp DNA Mini Kit (“QA”), and QIAGEN GeneRead DNA FFPE Kit (“QGR”). We also used negative-control (NA12891) and positive control samples (Horizon Discovery Reference Standard FFPE). All DNA sample libraries were prepared for NGS according to the QIAseq Human Breast Cancer Targeted DNA Panel protocol and sequenced on the HiSeq 4000. Variant calling and filtering were performed using QIAGEN Gene Globe Data Portal. Detailed variant concordance comparisons and mutational signature analysis were performed to investigate effects of FFPE samples compared to paired fresh frozen samples, along with different DNA extraction methods. In this study, we found that five times or more variants were called with FFPE samples, compared to their paired fresh-frozen tissue samples even after applying molecular barcoding error-correction and default bioinformatics filtering recommended by the vendor. We also found that QGR as an optimized FFPE-DNA extraction approach leads to much fewer discordant variants between paired fresh frozen and FFPE samples. Approximately 92% of the uniquely called FFPE variants were of low allelic frequency range (< 5%), and collectively shared a “C > T|G > A” mutational signature known to be representative of FFPE artifacts resulting from cytosine deamination. Based on control samples and FFPE-frozen replicates, we derived an effective filtering strategy with associated empirical false-discovery estimates. Conclusions Through this study, we demonstrated feasibility of calling and filtering genetic variants from FFPE tissue samples using a combined strategy with molecular barcodes, optimized DNA extraction, and bioinformatics methods incorporating genomics context such as mutational signature and variant allelic frequency. Electronic supplementary material The online version of this article (10.1186/s12864-019-6056-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aditya Vijay Bhagwate
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Yuanhang Liu
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Stacey J Winham
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Samantha J McDonough
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | | | - Ethan P Heinzen
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Jaime I Davila
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Robert A Vierkant
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Tanya L Hoskin
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Marlene Frost
- Departments of Medical Oncology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Jodi M Carter
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Derek C Radisky
- Departments of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Julie M Cunningham
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Amy C Degnim
- Departments of Surgery, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Chen Wang
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA.
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Walker DL, Bhagwate AV, Baheti S, Smalley RL, Hilker CA, Sun Z, Cunningham JM. DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip. Epigenomics 2015; 7:1287-302. [PMID: 26192535 DOI: 10.2217/epi.15.64] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
AIMS To compare the performance of four sequence-based and one microarray methods for DNA methylation profiling. METHODS DNA from two cell lines were profiled by reduced representation bisulfite sequencing, methyl capture sequencing (SS-Meth Seq), NimbleGen SeqCapEpi CpGiant(Nimblegen MethSeq), methylated DNA immunoprecipitation (MeDIP) and the Human Methylation 450 Bead Chip (Meth450K). RESULTS & CONCLUSION Despite differences in genome-wide coverage, high correlation and concordance were observed between different methods. Significant overlap of differentially methylated regions was identified between sequenced-based platforms. MeDIP provided the best coverage for the whole genome and gene body regions, while RRBS and Nimblegen MethSeq were superior for CpGs in CpG islands and promoters. Methylation analyses can be achieved by any of the five methods but understanding their differences may better address the research question being posed.
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Affiliation(s)
- Denise L Walker
- Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA
| | | | - Saurabh Baheti
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA
| | - Regenia L Smalley
- Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA
| | | | - Zhifu Sun
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA
| | - Julie M Cunningham
- Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA.,Division of Experimental Pathology, Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN, USA
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