1
|
Madaj ZB, Dahabieh MS, Kamalumpundi V, Muhire B, Pettinga J, Siwicki RA, Ellis AE, Isaguirre C, Escobar Galvis ML, DeCamp L, Jones RG, Givan SA, Adams M, Sheldon RD. Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-'omics analysis of the liver metabolic response to viral infection. RNA Biol 2023; 20:186-197. [PMID: 37095747 PMCID: PMC10132226 DOI: 10.1080/15476286.2023.2204586] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Here, we provide an in-depth analysis of the usefulness of single-sample metabolite/RNA extraction for multi-'omics readout. Using pulverized frozen livers of mice injected with lymphocytic choriomeningitis virus (LCMV) or vehicle (Veh), we isolated RNA prior (RNA) or following metabolite extraction (MetRNA). RNA sequencing (RNAseq) data were evaluated for differential expression analysis and dispersion, and differential metabolite abundance was determined. Both RNA and MetRNA clustered together by principal component analysis, indicating that inter-individual differences were the largest source of variance. Over 85% of LCMV versus Veh differentially expressed genes were shared between extraction methods, with the remaining 15% evenly and randomly divided between groups. Differentially expressed genes unique to the extraction method were attributed to randomness around the 0.05 FDR cut-off and stochastic changes in variance and mean expression. In addition, analysis using the mean absolute difference showed no difference in the dispersion of transcripts between extraction methods. Altogether, our data show that prior metabolite extraction preserves RNAseq data quality, which enables us to confidently perform integrated pathway enrichment analysis on metabolomics and RNAseq data from a single sample. This analysis revealed pyrimidine metabolism as the most LCMV-impacted pathway. Combined analysis of genes and metabolites in the pathway exposed a pattern in the degradation of pyrimidine nucleotides leading to uracil generation. In support of this, uracil was among the most differentially abundant metabolites in serum upon LCMV infection. Our data suggest that hepatic uracil export is a novel phenotypic feature of acute infection and highlight the usefulness of our integrated single-sample multi-'omics approach.
Collapse
Affiliation(s)
- Zachary B Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Michael S Dahabieh
- Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Vijayvardhan Kamalumpundi
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Brejnev Muhire
- Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - J Pettinga
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Rebecca A Siwicki
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Genomics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Abigail E Ellis
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Christine Isaguirre
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Lisa DeCamp
- Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Russell G Jones
- Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Scott A Givan
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Marie Adams
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Genomics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| |
Collapse
|
2
|
Bambouskova M, Potuckova L, Paulenda T, Kerndl M, Mogilenko DA, Lizotte K, Swain A, Hayes S, Sheldon RD, Kim H, Kapadnis U, Ellis AE, Isaguirre C, Burdess S, Laha A, Amarasinghe GK, Chubukov V, Roddy TP, Diamond MS, Jones RJ, Simons DM, Artyomov MN. -Itaconate confers tolerance to late NLRP3 inflammasome activation. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.15.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Abstract
Itaconate is a unique regulatory metabolite that is induced upon toll-like receptor (TLR) stimulation in myeloid cells. Here, we demonstrate major inflammatory tolerance and cell death phenotypes associated with itaconate production in activated macrophages. We show that endogenous itaconate is a key regulator of the signal 2 of NLRP3 inflammasome activation after long LPS priming which establishes tolerance to late NLRP3 inflammasome activation. We show that itaconate acts synergistically with iNOS and the ability of various TLR ligands to establish NLRP3 inflammasome tolerance depends on the pattern of co-expression of IRG1 and iNOS. Mechanistically, itaconate accumulation upon prolonged inflammatory stimulation prevents full caspase-1 activation and processing of gasdermin D, which we demonstrate to be post-translationally modified by endogenous itaconate. Altogether, our data demonstrate that metabolic rewiring in inflammatory macrophages establishes tolerance to NLRP3 inflammasome activation which, if uncontrolled, can result in pyroptotic cell death and tissue damage.
Collapse
|
3
|
Bambouskova M, Potuckova L, Paulenda T, Kerndl M, Mogilenko DA, Lizotte K, Swain A, Hayes S, Sheldon RD, Kim H, Kapadnis U, Ellis AE, Isaguirre C, Burdess S, Laha A, Amarasinghe GK, Chubukov V, Roddy TP, Diamond MS, Jones RG, Simons DM, Artyomov MN. Itaconate confers tolerance to late NLRP3 inflammasome activation. Cell Rep 2021; 34:108756. [PMID: 33691097 PMCID: PMC8039864 DOI: 10.1016/j.celrep.2021.108756] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [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: 09/10/2020] [Revised: 12/09/2020] [Accepted: 01/26/2021] [Indexed: 12/21/2022] Open
Abstract
Itaconate is a unique regulatory metabolite that is induced upon Toll-like receptor (TLR) stimulation in myeloid cells. Here, we demonstrate major inflammatory tolerance and cell death phenotypes associated with itaconate production in activated macrophages. We show that endogenous itaconate is a key regulator of the signal 2 of NLR family pyrin domain containing 3 (NLRP3) inflammasome activation after long lipopolysaccharide (LPS) priming, which establishes tolerance to late NLRP3 inflammasome activation. We show that itaconate acts synergistically with inducible nitric oxide synthase (iNOS) and that the ability of various TLR ligands to establish NLRP3 inflammasome tolerance depends on the pattern of co-expression of IRG1 and iNOS. Mechanistically, itaconate accumulation upon prolonged inflammatory stimulation prevents full caspase-1 activation and processing of gasdermin D, which we demonstrate to be post-translationally modified by endogenous itaconate. Altogether, our data demonstrate that metabolic rewiring in inflammatory macrophages establishes tolerance to NLRP3 inflammasome activation that, if uncontrolled, can result in pyroptotic cell death and tissue damage. Bambouskova et al. determine the in vitro phenotype of Irg1−/− macrophages and define itaconate as a key regulator of tolerance to late NLRP3 inflammasome activation.
Collapse
Affiliation(s)
- Monika Bambouskova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lucie Potuckova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tomas Paulenda
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martina Kerndl
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Institute for Vascular Biology, Centre for Physiology and Pharmacology, Medical University Vienna, 1090 Vienna, Austria; Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, 1090 Vienna, Austria
| | - Denis A Mogilenko
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kate Lizotte
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sebastian Hayes
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Ryan D Sheldon
- Van Andel Research Institute, Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Grand Rapids, MI 49503, USA
| | - Hyeryun Kim
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Unnati Kapadnis
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Abigail E Ellis
- Van Andel Research Institute, Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Grand Rapids, MI 49503, USA
| | - Christine Isaguirre
- Van Andel Research Institute, Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Grand Rapids, MI 49503, USA
| | - Samantha Burdess
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anwesha Laha
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Victor Chubukov
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Thomas P Roddy
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Russell G Jones
- Van Andel Research Institute, Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Grand Rapids, MI 49503, USA
| | - Donald M Simons
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
4
|
Zhong Y, Liu Z, Isaguirre C, Liu Y, Liao W. Fungal fermentation on anaerobic digestate for lipid-based biofuel production. Biotechnol Biofuels 2016; 9:253. [PMID: 27895707 PMCID: PMC5117520 DOI: 10.1186/s13068-016-0654-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/22/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Anaerobic digestate is the effluent from anaerobic digestion of organic wastes. It contains a significant amount of nutrients and lignocellulosic materials, even though anaerobic digestion consumed a large portion of organic matters in the wastes. Utilizing the nutrients and lignocellulosic materials in the digestate is critical to significantly improve efficiency of anaerobic digestion technology and generate value-added chemical and fuel products from the organic wastes. Therefore, this study focused on developing an integrated process that uses biogas energy to power fungal fermentation and converts remaining carbon sources, nutrients, and water in the digestate into biofuel precursor-lipid. RESULTS The process contains two unit operations of anaerobic digestion and digestate utilization. The digestate utilization includes alkali treatment of the mixture feed of solid and liquid digestates, enzymatic hydrolysis for mono-sugar release, overliming detoxification, and fungal fermentation for lipid accumulation. The experimental results conclude that 5 h and 30 °C were the preferred conditions for the overliming detoxification regarding lipid accumulation of the following fungal cultivation. The repeated-batch fungal fermentation enhanced lipid accumulation, which led to a final lipid concentration of 3.16 g/L on the digestate with 10% dry matter. The mass and energy balance analysis further indicates that the digestate had enough water for the process uses and the biogas energy was able to balance the needs of individual unit operations. CONCLUSIONS A fresh-water-free and energy-positive process of lipid production from anaerobic digestate was achieved by integrating anaerobic digestion and fungal fermentation. The integration addresses the issues that both biofuel industry and waste management encounter-high water and energy demand of biofuel precursor production and few digestate utilization approaches of organic waste treatment.
Collapse
Affiliation(s)
- Yuan Zhong
- Department of Biosystems and Agricultural Engineering, Anaerobic Digestion Research and Education Center (ADREC), Michigan State University, 524 South Shaw Lane, Room 202, East Lansing, MI 48824 USA
| | - Zhiguo Liu
- Department of Biosystems and Agricultural Engineering, Anaerobic Digestion Research and Education Center (ADREC), Michigan State University, 524 South Shaw Lane, Room 202, East Lansing, MI 48824 USA
| | - Christine Isaguirre
- Department of Biosystems and Agricultural Engineering, Anaerobic Digestion Research and Education Center (ADREC), Michigan State University, 524 South Shaw Lane, Room 202, East Lansing, MI 48824 USA
| | - Yan Liu
- Department of Biosystems and Agricultural Engineering, Anaerobic Digestion Research and Education Center (ADREC), Michigan State University, 524 South Shaw Lane, Room 202, East Lansing, MI 48824 USA
| | - Wei Liao
- Department of Biosystems and Agricultural Engineering, Anaerobic Digestion Research and Education Center (ADREC), Michigan State University, 524 South Shaw Lane, Room 202, East Lansing, MI 48824 USA
| |
Collapse
|
5
|
Ruan Z, Hollinshead W, Isaguirre C, Tang YJ, Liao W, Liu Y. Effects of inhibitory compounds in lignocellulosic hydrolysates on Mortierella isabellina growth and carbon utilization. Bioresour Technol 2015; 183:18-24. [PMID: 25710679 DOI: 10.1016/j.biortech.2015.02.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 05/05/2023]
Abstract
Oleaginous fungus Mortierella isabellina showed excellent lipid conversion on non-detoxified lignocellulosic hydrolysate. This study investigated the effects of inhibitory compounds (furfural, hydroxymethylfurfural, and ferulic and coumaric acids) in lignocellulosic hydrolysate on M. isabellina growth and lipid production. M. isabellina can tolerate furfural (∼1 g/L), hydroxymethylfurfural (∼2.5 g/L), ferulic (∼0.5 g/L) and coumaric acid (∼0.5 g/L) with normal growth rates. Synergistic effect of these inhibitors (2 g/L furfural, 0.4 g/L hydroxymethylfurfural, 0.02 g/L ferulic acid and 0.02 g/L coumaric acid) moderately reduces total fungal growth (by 28%), while the presence of these inhibitors has minor impact on cell lipid contents and lipid profiles. In the presence of inhibitory compounds, (13)C-tracing has revealed that M. isabellina can simultaneously utilize glucose and acetate, and acetate is mainly assimilated for synthesis of lipid and TCA cycle amino acids. The results also demonstrate that glucose has strong catabolite repression for xylose utilization for biomass and lipid production in the presence of inhibitors.
Collapse
Affiliation(s)
- Zhenhua Ruan
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48823, USA
| | - Whitney Hollinshead
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, USA
| | - Christine Isaguirre
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48823, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, USA
| | - Wei Liao
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48823, USA
| | - Yan Liu
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48823, USA.
| |
Collapse
|