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Wang Y, Thompson KN, Yan Y, Short MI, Zhang Y, Franzosa EA, Shen J, Hartmann EM, Huttenhower C. RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities. MICROBIOME 2023; 11:131. [PMID: 37312147 DOI: 10.1186/s40168-022-01449-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Characterization of microbial activity is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active ("viable") community members. Current sequence-based technologies can rarely differentiate microbial activity, due to their inability to distinguish live and dead sourced DNA. As a result, our understanding of microbial community structures and the potential mechanisms of transmission between humans and our surrounding environments remains incomplete. As a potential solution, 16S rRNA transcript-based amplicon sequencing (16S-RNA-seq) has been proposed as a reliable methodology to characterize the active components of a microbiome, but its efficacy has not been evaluated systematically. Here, we present our work to benchmark RNA-based amplicon sequencing for activity assessment in synthetic and environmentally sourced microbial communities. RESULTS In synthetic mixtures of living and heat-killed Escherichia coli and Streptococcus sanguinis, 16S-RNA-seq successfully reconstructed the active compositions of the communities. However, in the realistic environmental samples, no significant compositional differences were observed in RNA ("actively transcribed - active") vs. DNA ("whole" communities) spiked with E. coli controls, suggesting that this methodology is not appropriate for activity assessment in complex communities. The results were slightly different when validated in environmental samples of similar origins (i.e., from Boston subway systems), where samples were differentiated both by environment type as well as by library type, though compositional dissimilarities between DNA and RNA samples remained low (Bray-Curtis distance median: 0.34-0.49). To improve the interpretation of 16S-RNA-seq results, we compared our results with previous studies and found that 16S-RNA-seq suggests taxon-wise viability trends (i.e., specific taxa are universally more or less likely to be viable compared to others) in samples of similar origins. CONCLUSIONS This study provides a comprehensive evaluation of 16S-RNA-seq for viability assessment in synthetic and complex microbial communities. The results found that while 16S-RNA-seq was able to semi-quantify microbial viability in relatively simple communities, it only suggests a taxon-dependent "relative" viability in realistic communities. Video Abstract.
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Affiliation(s)
- Ya Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Kelsey N Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Meghan I Short
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA.
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Zou Z, Yu J, Huang R, Yu J. Cx43-Delivered miR-181b Negatively Regulates Sirt1/FOXO3a Signalling Pathway-Mediated Apoptosis on Intestinal Injury in Sepsis. Digestion 2023; 104:370-380. [PMID: 37231890 DOI: 10.1159/000529102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 01/09/2023] [Indexed: 05/27/2023]
Abstract
INTRODUCTION Gap junctions can transmit signals between cells, including miRNAs, leading to the amplification of adjacent cell damage. No previous study has addressed gap junctions and miRNAs in sepsis because the internal mechanism of sepsis-induced intestinal injury is complex. Therefore, we studied the relationship between connexin43 (Cx43) and miR-181b and provided a research direction for further study of sepsis. METHODS A mouse caecal ligation and puncture method was used to construct a mouse sepsis model. Firstly, damage to intestinal tissues at different time points was analysed. The levels of Cx43, miR-181b, Sirt1, and FOXO3a in intestinal tissues and the transcription and translation of the apoptosis-related genes Bim and puma, which are downstream of FOXO3a were analysed. Secondly, the effect of Cx43 levels on miR-181b and Sirt1/FOXO3a signalling pathway activity was explored by using the Cx43 inhibitor heptanol. Finally, luciferase assays were used to determine miR-181b binding to the predicted target sequence. RESULTS The results show that during sepsis, intestinal injury becomes increasingly worse with time, and the expression of Cx43 and miR-181b increase. In addition, we found that heptanol could significantly reduce intestinal injury. This finding indicates that inhibiting Cx43 regulates the transfer of miR-181b between adjacent cells, thereby reducing the activity of the Sirt1/FOXO3a signalling pathway and reducing the degree of intestinal injury during sepsis. CONCLUSIONS In sepsis, the enhancement of Cx43 gap junctions leads to an increase in miR-181b intercellular transfer, affects the downstream SIRT1/FOXO3a signalling pathway and causes cell and tissue damage.
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Affiliation(s)
- Zhaowei Zou
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jianyang Yu
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Renli Huang
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jinlong Yu
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Kawamura K, Yoshioka H, Sato C, Yajima T, Furuyama Y, Kuramochi K, Ohgane K. Fine-tuning of nitrogen-containing bisphosphonate esters that potently induce degradation of HMG-CoA reductase. Bioorg Med Chem 2023; 78:117145. [PMID: 36580745 DOI: 10.1016/j.bmc.2022.117145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
3-Hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase is the rate-limiting enzyme in the cholesterol biosynthetic pathway, and competitive inhibitors targeting the catalytic domain of this enzyme, so-called statins, are widely used for the treatment of hyperlipidemia. The membrane domain mediates the sterol-accelerated degradation, a post-translational negative feedback mechanism, and small molecules triggering such degradation have been studied as an alternative therapeutic option. Such strategies are expected to provide benefits over catalytic site inhibitors, as the inhibition leads to transcriptional and post-translational upregulation of the enzyme, necessitating a higher dose of the inhibitors and concomitantly increasing the risk of serious adverse effects, including myopathies. Through our previous study on SR12813, a synthetic small molecule that induces degradation of HMG-CoA reductase, we identified a nitrogen-containing bisphosphonate ester SRP3042 as a highly potent HMG-CoA reductase degrader. Here, we performed a systematic structure-activity relationship study to optimize its activity and physicochemical properties, specifically focusing on the reduction of lipophilicity. Mono-fluorination of tert-butyl groups on the molecules was found to increase the HMG-CoA reductase degradation activity while reducing lipophilicity, suggesting the mono-fluorination of saturated alkyl groups as a useful strategy to balance potency and lipophilicity of the lead compounds.
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Affiliation(s)
- Kota Kawamura
- Department of Applied Bioscience, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8519, Japan
| | - Hiromasa Yoshioka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1 Yayoi, Bunkyo, Tokyo 13-0032, Japan
| | - Chikako Sato
- Department of Chemistry, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
| | - Tomoko Yajima
- Department of Chemistry, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
| | - Yuuki Furuyama
- Department of Applied Bioscience, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8519, Japan
| | - Kouji Kuramochi
- Department of Applied Bioscience, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8519, Japan
| | - Kenji Ohgane
- Department of Applied Bioscience, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8519, Japan; Department of Chemistry, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan.
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Toyota Y, Yoshioka H, Sagimori I, Hashimoto Y, Ohgane K. Bisphosphonate esters interact with HMG-CoA reductase membrane domain to induce its degradation. Bioorg Med Chem 2020; 28:115576. [PMID: 32616181 DOI: 10.1016/j.bmc.2020.115576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/16/2022]
Abstract
HMG-CoA reductase (HMGCR) is a rate-limiting enzyme in the cholesterol biosynthetic pathway, and its catalytic domain is the well-known target of cholesterol-lowering drugs, statins. HMGCR is subject to layers of negative feedback loops; excess cholesterol inhibits transcription of the gene, and lanosterols and oxysterols accelerate degradation of HMGCR. A class of synthetic small molecules, bisphosphonate esters exemplified by SR12813, has been known to induce accelerated degradation of HMGCR and reduce the serum cholesterol level. Although genetic and biochemical studies revealed that the accelerated degradation requires the membrane domain of HMGCR and Insig, an oxysterol sensor on the endoplasmic reticulum membrane, the direct target of the bisphosphonate esters remains unclear. In this study, we developed a potent photoaffinity probe of the bisphosphonate esters through preliminary structure-activity relationship study and demonstrated binding of the bisphosphonate esters to the HMGCR membrane domain. These results provide an important clue to understand the elusive mechanism of the SR12813-mediated HMGCR degradation and serve as a basis to develop more potent HMGCR degraders that target the non-catalytic, membrane domain of the enzyme.
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Affiliation(s)
- Yosuke Toyota
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113 0032, Japan
| | - Hiromasa Yoshioka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113 0032, Japan
| | - Ikuya Sagimori
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113 0032, Japan
| | - Yuichi Hashimoto
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113 0032, Japan
| | - Kenji Ohgane
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113 0032, Japan.
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Sagimori I, Yoshioka H, Hashimoto Y, Ohgane K. Luciferase-based HMG-CoA reductase degradation assay for activity and selectivity profiling of oxy(lano)sterols. Bioorg Med Chem 2020; 28:115298. [PMID: 31902650 DOI: 10.1016/j.bmc.2019.115298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/21/2019] [Accepted: 12/25/2019] [Indexed: 11/18/2022]
Abstract
HMG-CoA reductase (HMGCR) is the rate-limiting enzyme in the cholesterol biosynthetic pathway, and is the target of cholesterol-lowering drugs, statins. Previous studies have demonstrated that the enzyme activity is regulated by sterol-induced degradation in addition to transcriptional regulation through sterol-regulatory-element-binding proteins (SREBPs). While 25-hydroxycholesterol induces both HMGCR degradation and SREBP inhibition in a nonselective manner, lanosterol selectively induces HMGCR degradation. Here, to clarify the structural determinants of selectivity for the two activities, we established a luciferase-based assay monitoring HMGCR degradation and used it to profile the structure-activity/selectivity relationships of oxysterols and (oxy)lanosterols. We identified several sterols that selectively induce HMGCR degradation and one sterol, 25-hydroxycholest-4-en-3-one, that selectively inhibits the SREBP pathway. These results should be helpful in designing more potent and selective HMGCR degraders.
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Affiliation(s)
- Ikuya Sagimori
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiromasa Yoshioka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yuichi Hashimoto
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kenji Ohgane
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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