201
|
Jenjaroenpun P, Wongsurawat T, Wadley TD, Wassenaar TM, Liu J, Dai Q, Wanchai V, Akel NS, Jamshidi-Parsian A, Franco AT, Boysen G, Jennings ML, Ussery DW, He C, Nookaew I. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Res 2021; 49:e7. [PMID: 32710622 DOI: 10.1101/487819] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/13/2020] [Accepted: 07/13/2020] [Indexed: 05/25/2023] Open
Abstract
Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors. The percent Error of Specific Bases (%ESB) was higher for native RNA than unmodified RNA, which enabled the detection of ribonucleotide modification sites. Based on the %ESB differences, we developed a bioinformatic tool, epitranscriptional landscape inferring from glitches of ONT signals (ELIGOS), that is based on various types of synthetic modified RNA and applied to rRNA and mRNA. ELIGOS is able to accurately predict known classes of RNA methylation sites (AUC > 0.93) in rRNAs from Escherichiacoli, yeast, and human cells, using either unmodified in vitro transcription RNA or a background error model, which mimics the systematic error of direct RNA sequencing as the reference. The well-known DRACH/RRACH motif was localized and identified, consistent with previous studies, using differential analysis of ELIGOS to study the impact of RNA m6A methyltransferase by comparing wild type and knockouts in yeast and mouse cells. Lastly, the DRACH motif could also be identified in the mRNA of three human cell lines. The mRNA modification identified by ELIGOS is at the level of individual base resolution. In summary, we have developed a bioinformatic software package to uncover native RNA modifications.
Collapse
Affiliation(s)
- Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Taylor D Wadley
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany
| | - Jun Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Visanu Wanchai
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Nisreen S Akel
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Azemat Jamshidi-Parsian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Aime T Franco
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Gunnar Boysen
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Michael L Jennings
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - David W Ussery
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| |
Collapse
|
202
|
Balzano-Nogueira L, Ramirez R, Zamkovaya T, Dailey J, Ardissone AN, Chamala S, Serrano-Quílez J, Rubio T, Haller MJ, Concannon P, Atkinson MA, Schatz DA, Triplett EW, Conesa A. Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes. Genome Biol 2021; 22:39. [PMID: 33478573 PMCID: PMC7818777 DOI: 10.1186/s13059-021-02262-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/04/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The Environmental Determinants of Diabetes in the Young (TEDDY) is a prospective birth cohort designed to study type 1 diabetes (T1D) by following children with high genetic risk. An integrative multi-omics approach was used to evaluate islet autoimmunity etiology, identify disease biomarkers, and understand progression over time. RESULTS We identify a multi-omics signature that was predictive of islet autoimmunity (IA) as early as 1 year before seroconversion. At this time, abnormalities in lipid metabolism, decreased capacity for nutrient absorption, and intracellular ROS accumulation are detected in children progressing towards IA. Additionally, extracellular matrix remodeling, inflammation, cytotoxicity, angiogenesis, and increased activity of antigen-presenting cells are observed, which may contribute to beta cell destruction. Our results indicate that altered molecular homeostasis is present in IA-developing children months before the actual detection of islet autoantibodies, which opens an interesting window of opportunity for therapeutic intervention. CONCLUSIONS The approach employed herein for assessment of the TEDDY cohort showcases the utilization of multi-omics data for the modeling of complex, multifactorial diseases, like T1D.
Collapse
Affiliation(s)
- Leandro Balzano-Nogueira
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Ricardo Ramirez
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Tatyana Zamkovaya
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Jordan Dailey
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Alexandria N Ardissone
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Srikar Chamala
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Joan Serrano-Quílez
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, 46010, Valencia, Spain
| | - Teresa Rubio
- Laboratory of Neurobiology, Prince Felipe Research Center, Valencia, Spain
| | - Michael J Haller
- Department of Pediatrics, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Patrick Concannon
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
- University of Florida Genetics Institute, Gainesville, FL, USA
| | - Mark A Atkinson
- Department of Pediatrics, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Desmond A Schatz
- Department of Pediatrics, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Eric W Triplett
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Ana Conesa
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA.
- University of Florida Genetics Institute, Gainesville, FL, USA.
| |
Collapse
|
203
|
Chappell GA, Heintz MM, Haws LC. Transcriptomic analyses of livers from mice exposed to 1,4-dioxane for up to 90 days to assess potential mode(s) of action underlying liver tumor development. Curr Res Toxicol 2021; 2:30-41. [PMID: 34345848 PMCID: PMC8320614 DOI: 10.1016/j.crtox.2021.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
1,4-Dioxane is a volatile organic compound with industrial and commercial applications as a solvent and in the manufacture of other chemicals. 1,4-Dioxane has been demonstrated to induce liver tumors in chronic rodent bioassays conducted at very high doses. The available evidence for 1,4-dioxane-induced liver tumors in rodents aligns with a threshold-dependent mode of action (MOA), with the underlying mechanism being less clear in the mouse than in rats. To gain a better understanding of the underlying molecular mechanisms related to liver tumor development in mice orally exposed to 1,4-dioxane, transcriptomics analysis was conducted on liver tissue collected from a 90-day drinking water study in female B6D2F1/Crl mice (Lafranconi et al., 2020). Using tissue samples from female mice exposed to 1,4-dioxane in the drinking water at concentrations of 0, 40, 200, 600, 2,000 or 6,000 ppm for 7, 28, and 90 days, transcriptomic analyses demonstrate minimal treatment effects on global gene expression at concentrations below 600 ppm. At higher concentrations, genes involved in phase II metabolism and mitotic cell cycle checkpoints were significantly upregulated. There was an overall lack of enrichment of genes related to DNA damage response. The increase in mitotic signaling is most prevalent in the livers of mice exposed to 1,4-dioxane at the highest concentrations for 90 days. This finding aligns with phenotypic changes reported by Lafranconi et al. (2020) after 90-days of exposure to 6,000 ppm 1,4-dioxane in the same tissues. The transcriptomics analysis further supports overarching study findings demonstrating a non-mutagenic, threshold-based, mitogenic MOA for 1,4-dioxane-induced liver tumors.
Collapse
Affiliation(s)
- G A Chappell
- ToxStrategies, Inc., Asheville, NC, United States
| | - M M Heintz
- ToxStrategies, Inc., Asheville, NC, United States
| | - L C Haws
- ToxStrategies, Inc., Austin, TX, United States
| |
Collapse
|
204
|
Gupta C, Ramegowda V, Basu S, Pereira A. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. Front Genet 2021. [PMID: 34249082 DOI: 10.1101/2020.04.29.068379] [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] [Indexed: 05/13/2023] Open
Abstract
Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.
Collapse
Affiliation(s)
- Chirag Gupta
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Venkategowda Ramegowda
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Supratim Basu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| |
Collapse
|
205
|
Zhan X, Liu Y, Yu CY, Wang TF, Zhang J, Ni D, Huang K. A pan-kidney cancer study identifies subtype specific perturbations on pathways with potential drivers in renal cell carcinoma. BMC Med Genomics 2020; 13:190. [PMID: 33371886 PMCID: PMC7771093 DOI: 10.1186/s12920-020-00827-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is a complex disease and is comprised of several histological subtypes, the most frequent of which are clear cell renal cell carcinoma (ccRCC), papillary renal cell carcinoma (PRCC) and chromophobe renal cell carcinoma (ChRCC). While lots of studies have been performed to investigate the molecular characterizations of different subtypes of RCC, our knowledge regarding the underlying mechanisms are still incomplete. As molecular alterations are eventually reflected on the pathway level to execute certain biological functions, characterizing the pathway perturbations is crucial for understanding tumorigenesis and development of RCC. METHODS In this study, we investigated the pathway perturbations of various RCC subtype against normal tissue based on differential expressed genes within a certain pathway. We explored the potential upstream regulators of subtype-specific pathways with Ingenuity Pathway Analysis (IPA). We also evaluated the relationships between subtype-specific pathways and clinical outcome with survival analysis. RESULTS In this study, we carried out a pathway-based analysis to explore the mechanisms of various RCC subtypes with TCGA RNA-seq data. Both commonly altered pathways and subtype-specific pathways were detected. To identify the distinctive characteristics of each subtype, we focused on subtype-specific perturbed pathways. Specifically, we observed that some of the altered pathways were regulated by several recurrent upstream regulators which presenting different expression patterns among distinct RCC subtypes. We also noticed that a large number of perturbed pathways were controlled by the subtype-specific upstream regulators. Moreover, we also evaluated the relationships between perturbed pathways and clinical outcome. Prognostic pathways were identified and their roles in tumor development and progression were inferred. CONCLUSIONS In summary, we evaluated the relationships among pathway perturbations, upstream regulators and clinical outcome for differential subtypes in RCC. We hypothesized that the alterations of common upstream regulators as well as subtype-specific upstream regulators work together to affect the downstream pathway perturbations and drive cancer initialization and prognosis. Our findings not only increase our understanding of the mechanisms of various RCC subtypes, but also provide targets for personalized therapeutic intervention.
Collapse
Affiliation(s)
- Xiaohui Zhan
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China.
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China.
| | - Yusong Liu
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- College of Automation, Harbin Engineering University, Harbin, 150001, Heilongjiang, China
| | - Christina Y Yu
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Tian-Fu Wang
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Dong Ni
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China.
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Regenstrief Institute, Indianapolis, 46202, USA.
| |
Collapse
|
206
|
Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions. mSystems 2020; 5:5/6/e00815-20. [PMID: 33361321 PMCID: PMC7762792 DOI: 10.1128/msystems.00815-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The results of this study highlight parallel gut microbiome traits in human and nonhuman primates, depending on subsistence strategy. Although these similarities have been reported before, the functional and ecological bases of this convergence are not fully understood. Compared with urban-industrial populations, small-scale human communities worldwide share a significant number of gut microbiome traits with nonhuman primates. This overlap is thought to be driven by analogous dietary triggers; however, the ecological and functional bases of this similarity are not fully understood. To start addressing this issue, fecal metagenomes of BaAka hunter-gatherers and traditional Bantu agriculturalists from the Central African Republic were profiled and compared with those of a sympatric western lowland gorilla group (Gorillagorilla gorilla) across two seasons of variable dietary intake. Results show that gorilla gut microbiomes shared similar functional traits with each human group, depending on seasonal dietary behavior. Specifically, parallel microbiome traits were observed between hunter-gatherers and gorillas when the latter consumed more structural polysaccharides during dry seasons, while small-scale agriculturalist and gorilla microbiomes showed significant functional overlap when gorillas consumed more seasonal ripe fruit during wet seasons. Notably, dominance of microbial transporters, transduction systems, and gut xenobiotic metabolism was observed in association with traditional agriculture and energy-dense diets in gorillas at the expense of a functional microbiome repertoire capable of metabolizing more complex polysaccharides. Differential abundance of bacterial taxa that typically distinguish traditional from industrialized human populations (e.g., Prevotella spp.) was also recapitulated in the human and gorilla groups studied, possibly reflecting the degree of polysaccharide complexity included in each group’s dietary niche. These results show conserved functional gut microbiome adaptations to analogous diets in small-scale human populations and nonhuman primates, highlighting the role of plant dietary polysaccharides and diverse environmental exposures in this convergence. IMPORTANCE The results of this study highlight parallel gut microbiome traits in human and nonhuman primates, depending on subsistence strategy. Although these similarities have been reported before, the functional and ecological bases of this convergence are not fully understood. Here, we show that this parallelism is, in part, likely modulated by the complexity of plant carbohydrates consumed and by exposures to diverse xenobiotics of natural and artificial origin. Furthermore, we discuss how divergence from these parallel microbiome traits is typically associated with adverse health outcomes in human populations living under culturally westernized subsistence patterns. This is important information as we trace the specific dietary and environmental triggers associated with the loss and gain of microbial functions as humans adapt to various dietary niches.
Collapse
|
207
|
Lataretu M, Hölzer M. RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow. Genes (Basel) 2020; 11:E1487. [PMID: 33322033 PMCID: PMC7763471 DOI: 10.3390/genes11121487] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data's computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus. We evaluated the DEG detection functionality while using qRT-PCR data serving as a reference and observed a very high correlation of the logarithmized gene expression fold changes.
Collapse
Affiliation(s)
- Marie Lataretu
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany;
| | - Martin Hölzer
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| |
Collapse
|
208
|
Bordone MC, Barbosa-Morais NL. Unraveling Targetable Systemic and Cell-Type-Specific Molecular Phenotypes of Alzheimer's and Parkinson's Brains With Digital Cytometry. Front Neurosci 2020; 14:607215. [PMID: 33362460 PMCID: PMC7756021 DOI: 10.3389/fnins.2020.607215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative disorders worldwide, with age being their major risk factor. The increasing worldwide life expectancy, together with the scarcity of available treatment choices, makes it thus pressing to find the molecular basis of AD and PD so that the causing mechanisms can be targeted. To study these mechanisms, gene expression profiles have been compared between diseased and control brain tissues. However, this approach is limited by mRNA expression profiles derived for brain tissues highly reflecting their degeneration in cellular composition but not necessarily disease-related molecular states. We therefore propose to account for cell type composition when comparing transcriptomes of healthy and diseased brain samples, so that the loss of neurons can be decoupled from pathology-associated molecular effects. This approach allowed us to identify genes and pathways putatively altered systemically and in a cell-type-dependent manner in AD and PD brains. Moreover, using chemical perturbagen data, we computationally identified candidate small molecules for specifically targeting the profiled AD/PD-associated molecular alterations. Our approach therefore not only brings new insights into the disease-specific and common molecular etiologies of AD and PD but also, in these realms, foster the discovery of more specific targets for functional and therapeutic exploration.
Collapse
Affiliation(s)
- Marie C Bordone
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
209
|
Fan H, Lu J, Guo Y, Li D, Zhang ZM, Tsai YH, Pi WC, Ahn JH, Gong W, Xiang Y, Allison DF, Geng H, He S, Diao Y, Chen WY, Strahl BD, Cai L, Song J, Wang GG. BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis. Nat Genet 2020; 52:1384-1396. [PMID: 33139953 PMCID: PMC8330957 DOI: 10.1038/s41588-020-00729-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 09/25/2020] [Indexed: 01/09/2023]
Abstract
Trimethylated histone H3 lysine 27 (H3K27me3) regulates gene repression, cell-fate determination and differentiation. We report that a conserved bromo-adjacent homology (BAH) module of BAHCC1 (BAHCC1BAH) 'recognizes' H3K27me3 specifically and enforces silencing of H3K27me3-demarcated genes in mammalian cells. Biochemical, structural and integrated chromatin immunoprecipitation-sequencing-based analyses demonstrate that direct readout of H3K27me3 by BAHCC1 is achieved through a hydrophobic trimethyl-L-lysine-binding 'cage' formed by BAHCC1BAH, mediating colocalization of BAHCC1 and H3K27me3-marked genes. BAHCC1 is highly expressed in human acute leukemia and interacts with transcriptional corepressors. In leukemia, depletion of BAHCC1, or disruption of the BAHCC1BAH-H3K27me3 interaction, causes derepression of H3K27me3-targeted genes that are involved in tumor suppression and cell differentiation, leading to suppression of oncogenesis. In mice, introduction of a germline mutation at Bahcc1 to disrupt its H3K27me3 engagement causes partial postnatal lethality, supporting a role in development. This study identifies an H3K27me3-directed transduction pathway in mammals that relies on a conserved BAH 'reader'.
Collapse
Affiliation(s)
- Huitao Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, Riverside, CA, USA
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dongxu Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, Riverside, CA, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Wen-Chieh Pi
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Yu Xiang
- Department of Cell Biology and Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - David F Allison
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Shenghui He
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Yarui Diao
- Department of Cell Biology and Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Brian D Strahl
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, Riverside, CA, USA.
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
210
|
Castañeda-Cortés DC, Zhang J, Boan AF, Langlois VS, Fernandino JI. High temperature stress response is not sexually dimorphic at the whole-body level and is dependent on androgens to induce sex reversal. Gen Comp Endocrinol 2020; 299:113605. [PMID: 32866474 DOI: 10.1016/j.ygcen.2020.113605] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/14/2020] [Accepted: 08/24/2020] [Indexed: 12/31/2022]
Abstract
The understanding of the molecular and endocrine mechanisms behind environmentally-induced sex reversal in fish is of great importance in the context of predicting the potential effects of climate change, especially increasing temperature. Here, we demonstrate the global effects of high temperature on genome-wide transcription in medaka (Oryzias latipes) during early development. Interestingly, data analysis did not show sexual dimorphic changes, demonstrating that thermal stress is not dependent on genotypic sex. Additionally, our results revealed significant changes in several pathways under high temperature, such as stress response from brain, steroid biosynthesis, epigenetic mechanisms, and thyroid hormone biosynthesis, among others. These microarray data raised the question of what the exact molecular and hormonal mechanisms of action are for female-to-male sex reversal under high temperatures in fish. Complementary gene expression analysis revealed that androgen-related genes increase in females (XX) experiencing high water temperature. To test the involvement of androgens in thermal-induced sex reversal, an androgen antagonist was used to treat XX medaka under a high-temperature setup. Data clearly demonstrated failure of female-to-male sex reversal when androgen action is inhibited, corroborating the importance of androgens in environmentally-induced sex reversal.
Collapse
Affiliation(s)
- Diana C Castañeda-Cortés
- Laboratorio de Biología del Desarrollo - Instituto Tecnológico de Chascomús, INTECH (CONICET-UNSAM), Argentina
| | - Jing Zhang
- Department of Diagnostic Imaging, Hospital for Sick Children, Toronto, ON, Canada; Neurosciences & Mental Health, SickKids Research Institute, Toronto, ON, Canada
| | - Agustín F Boan
- Laboratorio de Biología del Desarrollo - Instituto Tecnológico de Chascomús, INTECH (CONICET-UNSAM), Argentina
| | - Valerie S Langlois
- Institut National de la Recherche Scientifique (INRS) - Centre Eau Terre Environnement, Quebec, Canada.
| | - Juan I Fernandino
- Laboratorio de Biología del Desarrollo - Instituto Tecnológico de Chascomús, INTECH (CONICET-UNSAM), Argentina.
| |
Collapse
|
211
|
Devens HR, Davidson PL, Deaker DJ, Smith KE, Wray GA, Byrne M. Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma. Mol Ecol 2020; 29:4618-4636. [PMID: 33002253 PMCID: PMC8994206 DOI: 10.1111/mec.15664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 09/01/2023]
Abstract
Ocean acidification (OA) from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but how these responses change across life history stages remains unclear. The abbreviated lecithotrophic development of the sea urchin Heliocidaris erythrogramma provides a valuable opportunity to analyse gene expression responses across a wide range of life history stages, including the benthic, post-metamorphic juvenile. We measured the transcriptional response to OA in H. erythrogramma at three stages of the life cycle (embryo, larva, and juvenile) in a controlled breeding design. The results reveal a broad range of strikingly stage-specific impacts of OA on transcription, including changes in the number and identity of affected genes; the magnitude, sign, and variance of their expression response; and the developmental trajectory of expression. The impact of OA on transcription was notably modest in relation to gene expression changes during unperturbed development and much smaller than genetic contributions from parentage. The latter result suggests that natural populations may provide an extensive genetic reservoir of resilience to OA. Taken together, these results highlight the complexity of the molecular response to OA, its substantial life history stage specificity, and the importance of contextualizing the transcriptional response to pH stress in light of normal development and standing genetic variation to better understand the capacity for marine invertebrates to adapt to OA.
Collapse
Affiliation(s)
| | | | - Dione J Deaker
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
| | - Kathryn E Smith
- The Laboratory, The Marine Biological Association, Plymouth, UK
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Maria Byrne
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
212
|
Nair SK, Eeles C, Ho C, Beri G, Yoo E, Tkachuk D, Tang A, Nijrabi P, Smirnov P, Seo H, Jennen D, Haibe-Kains B. ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. Nucleic Acids Res 2020; 48:W455-W462. [PMID: 32421831 PMCID: PMC7319553 DOI: 10.1093/nar/gkaa390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 11/12/2022] Open
Abstract
In the past few decades, major initiatives have been launched around the world to address chemical safety testing. These efforts aim to innovate and improve the efficacy of existing methods with the long-term goal of developing new risk assessment paradigms. The transcriptomic and toxicological profiling of mammalian cells has resulted in the creation of multiple toxicogenomic datasets and corresponding tools for analysis. To enable easy access and analysis of these valuable toxicogenomic data, we have developed ToxicoDB (toxicodb.ca), a free and open cloud-based platform integrating data from large in vitro toxicogenomic studies, including gene expression profiles of primary human and rat hepatocytes treated with 231 potential toxicants. To efficiently mine these complex toxicogenomic data, ToxicoDB provides users with harmonized chemical annotations, time- and dose-dependent plots of compounds across datasets, as well as the toxicity-related pathway analysis. The data in ToxicoDB have been generated using our open-source R package, ToxicoGx (github.com/bhklab/ToxicoGx). Altogether, ToxicoDB provides a streamlined process for mining highly organized, curated, and accessible toxicogenomic data that can be ultimately applied to preclinical toxicity studies and further our understanding of adverse outcomes.
Collapse
Affiliation(s)
- Sisira Kadambat Nair
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Christopher Eeles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Chantal Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Gangesh Beri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Esther Yoo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Amy Tang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Parwaiz Nijrabi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Heewon Seo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School of Oncology and Development Biology, Maastricht University, Maastricht, The Netherlands
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada.,Ontario Institute for Cancer Research, Toronto, ON M5G 1L7, Canada.,Vector Institute for Artificial Intelligence, Toronto, ON M5G 1L7, Canada
| |
Collapse
|
213
|
Wanichthanarak K, Boonchai C, Kojonna T, Chadchawan S, Sangwongchai W, Thitisaksakul M. Deciphering rice metabolic flux reprograming under salinity stress via in silico metabolic modeling. Comput Struct Biotechnol J 2020; 18:3555-3566. [PMID: 33304454 PMCID: PMC7708941 DOI: 10.1016/j.csbj.2020.11.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022] Open
Abstract
Rice is one of the most economically important commodities globally. However, rice plants are salt susceptible species in which high salinity can significantly constrain its productivity. Several physiological parameters in adaptation to salt stress have been observed, though changes in metabolic aspects remain to be elucidated. In this study, rice metabolic activities of salt-stressed flag leaf were systematically characterized. Transcriptomics and metabolomics data were combined to identify disturbed pathways, altered metabolites and metabolic hotspots within the rice metabolic network under salt stress condition. Besides, the feasible flux solutions in different context-specific metabolic networks were estimated and compared. Our findings highlighted metabolic reprogramming in primary metabolic pathways, cellular respiration, antioxidant biosynthetic pathways, and phytohormone biosynthetic pathways. Photosynthesis and hexose utilization were among the major disturbed pathways in the stressed flag leaf. Notably, the increased flux distribution of the photorespiratory pathway could contribute to cellular redox control. Predicted flux statuses in several pathways were consistent with the results from transcriptomics, end-point metabolomics, and physiological studies. Our study illustrated that the contextualized genome-scale model together with multi-omics analysis is a powerful approach to unravel the metabolic responses of rice to salinity stress.
Collapse
Key Words
- 3-PGA, 3-Phosphoglycerate
- ADH, Arogenate dehydrogenase
- ASA, Ascorbate
- CGS, Cystathionine γ-synthase
- CINV, Cytosolic invertase
- Ci, Intercellular CO2 concentration
- E, Transpiration rate
- GAPDH, Glyceraldehyde-3-phosphate dehydrogenase
- GC-TOF-MS, Gas chromatography time-of-flight mass spectrometry
- GEM, Genome-scale metabolic model
- GLYK, 3-Phosphoglycerate kinase
- GMD, Golm Metabolome Database
- GSH, Glutathione
- GSSG, Glutathione disulfide
- IAA, Indole-3-acetic acid
- IPA, Indolepyruvate
- MAPK, Mitogen-activated protein kinase
- MDH, Malate dehydrogenase
- Metabolic flux analysis
- Metabolic modeling
- Metabolomics
- Multi-omics analysis
- PFK, Phosphofructokinase
- PGK, Phosphoglycerate kinase
- PLS-DA, Partial-Least Squares Discriminant Analysis
- Pn, Net photosynthesis rate
- Rice (Oryza sativa L.)
- SOD, Superoxide dismutase
- Salinity stress
- Systems biology
- TAT, Tyrosine aminotransferase
- Transcriptomics
- gs, Stomatal conductance
- iMAT, Integrative Metabolic Analysis Tool
Collapse
Affiliation(s)
- Kwanjeera Wanichthanarak
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chuthamas Boonchai
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Future Innovation and Research in Science and Technology, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thammaporn Kojonna
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wichian Sangwongchai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Maysaya Thitisaksakul
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| |
Collapse
|
214
|
Walesky CM, Kolb KE, Winston CL, Henderson J, Kruft B, Fleming I, Ko S, Monga SP, Mueller F, Apte U, Shalek AK, Goessling W. Functional compensation precedes recovery of tissue mass following acute liver injury. Nat Commun 2020; 11:5785. [PMID: 33214549 PMCID: PMC7677389 DOI: 10.1038/s41467-020-19558-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
The liver plays a central role in metabolism, protein synthesis and detoxification. It possesses unique regenerative capacity upon injury. While many factors regulating cellular proliferation during liver repair have been identified, the mechanisms by which the injured liver maintains vital functions prior to tissue recovery are unknown. Here, we identify a new phase of functional compensation following acute liver injury that occurs prior to cellular proliferation. By coupling single-cell RNA-seq with in situ transcriptional analyses in two independent murine liver injury models, we discover adaptive reprogramming to ensure expression of both injury response and core liver function genes dependent on macrophage-derived WNT/β-catenin signaling. Interestingly, transcriptional compensation is most prominent in non-proliferating cells, clearly delineating two temporally distinct phases of liver recovery. Overall, our work describes a mechanism by which the liver maintains essential physiological functions prior to cellular reconstitution and characterizes macrophage-derived WNT signals required for this compensation. The liver possesses the ability to regenerate following sudden injury. Here, the authors use single-cell RNA-sequencing and in situ transcriptional analyses to identify a new phase of liver regeneration in mice aimed at maintaining essential functions throughout the regenerative process.
Collapse
Affiliation(s)
- Chad M Walesky
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kellie E Kolb
- Institute of Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Carolyn L Winston
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jake Henderson
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Benjamin Kruft
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ira Fleming
- Institute of Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Sungjin Ko
- Department of Pathology, University of Pittsburgh, School of Medicine; and Pittsburgh Liver Research Center, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, 15261, USA
| | - Satdarshan P Monga
- Department of Pathology, University of Pittsburgh, School of Medicine; and Pittsburgh Liver Research Center, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, 15261, USA
| | - Florian Mueller
- Imaging and Modeling Unit, Institut Pasteur, UMR 3691CNRS, C3BI USR 3756 IP CNRS, Paris, France
| | - Udayan Apte
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Alex K Shalek
- Institute of Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA. .,Harvard-MIT Division of Health Sciences and Technology, Boston, MA, 02115, USA.
| | - Wolfram Goessling
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Harvard-MIT Division of Health Sciences and Technology, Boston, MA, 02115, USA. .,Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Harvard Stem Cell Institute, Cambridge, MA, 02134, USA. .,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
| |
Collapse
|
215
|
Evolution from adherent to suspension: systems biology of HEK293 cell line development. Sci Rep 2020; 10:18996. [PMID: 33149219 PMCID: PMC7642379 DOI: 10.1038/s41598-020-76137-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/22/2020] [Indexed: 01/28/2023] Open
Abstract
The need for new safe and efficacious therapies has led to an increased focus on biologics produced in mammalian cells. The human cell line HEK293 has bio-synthetic potential for human-like production attributes and is currently used for manufacturing of several therapeutic proteins and viral vectors. Despite the increased popularity of this strain we still have limited knowledge on the genetic composition of its derivatives. Here we present a genomic, transcriptomic and metabolic gene analysis of six of the most widely used HEK293 cell lines. Changes in gene copy and expression between industrial progeny cell lines and the original HEK293 were associated with cellular component organization, cell motility and cell adhesion. Changes in gene expression between adherent and suspension derivatives highlighted switching in cholesterol biosynthesis and expression of five key genes (RARG, ID1, ZIC1, LOX and DHRS3), a pattern validated in 63 human adherent or suspension cell lines of other origin.
Collapse
|
216
|
Carruthers NJ, McClellan SA, Somayajulu M, Pitchaikannu A, Bessert D, Peng X, Huitsing K, Stemmer PM, Hazlett LD. Effects of Glycyrrhizin on Multi-Drug Resistant Pseudomonas aeruginosa. Pathogens 2020; 9:pathogens9090766. [PMID: 32962036 PMCID: PMC7557769 DOI: 10.3390/pathogens9090766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
The effects of glycyrrhizin (GLY) on multi-drug resistant (MDR) systemic (MDR9) vs. ocular (B1045) Pseudomonas aeruginosa clinical isolates were determined. Proteomes of each isolate with/without GLY treatment were profiled using liquid chromatography mass spectrometry (LC-MS/MS). The effect of GLY on adherence of MDR isolates to immortalized human (HCET) and mouse (MCEC) corneal epithelial cells, and biofilm and dispersal was tested. Both isolates were treated with GLY (0.25 minimum inhibitory concentration (MIC), 10 mg/mL for MDR9 and 3.75 mg/mL for B1045) and subjected to proteomic analysis. MDR9 had a greater response to GLY (51% of identified proteins affected vs. <1% in B1045). In MDR9 vs. controls, GLY decreased the abundance of proteins for: antibiotic resistance, biofilm formation, and type III secretion. Further, antibiotic resistance and type III secretion proteins had higher control abundances in MDR9 vs. B1045. GLY (5 and 10 mg/mL) significantly reduced binding of both isolates to MCEC, and B1045 to HCET. MDR9 binding to HCET was only reduced at 10 mg/mL GLY. GLY (5 and 10 mg/mL) enhanced dispersal for both isolates, at early (6.5 h) but not later times (24–72 h). This study provides evidence that GLY has a greater effect on the proteome of MDR9 vs. B1045, yet it was equally effective at disrupting adherence and early biofilm dispersal.
Collapse
Affiliation(s)
- Nicholas J. Carruthers
- Institute of Environmental Health Sciences, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, MI 48201, USA; (N.J.C.); (P.M.S.)
| | - Sharon A. McClellan
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Mallika Somayajulu
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Ahalya Pitchaikannu
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Denise Bessert
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Xudong Peng
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao 266071, China;
| | - Kylie Huitsing
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, MI 48201, USA; (N.J.C.); (P.M.S.)
| | - Linda D. Hazlett
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
- Correspondence: ; Tel.: +1-313-577-1079; Fax: +1-313-577-3125
| |
Collapse
|
217
|
Ugalde‐Morales E, Grassmann F, Humphreys K, Li J, Eriksson M, Tobin NP, Borg Å, Vallon‐Christersson J, Hall P, Czene K. Association between breast cancer risk and disease aggressiveness: Characterizing underlying gene expression patterns. Int J Cancer 2020; 148:884-894. [PMID: 32856720 PMCID: PMC7818270 DOI: 10.1002/ijc.33270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
The association between breast cancer risk defined by the Tyrer-Cuzick score (TC) and disease prognosis is not well established. Here, we investigated the relationship between 5-year TC and disease aggressiveness and then characterized underlying molecular processes. In a case-only study (n = 2474), we studied the association of TC with molecular subtypes and tumor characteristics. In a subset of patients (n = 672), we correlated gene expression to TC and computed a low-risk TC gene expression (TC-Gx) profile, that is, a profile expected to be negatively associated with risk, which we used to test for association with disease aggressiveness. We performed enrichment analysis to pinpoint molecular processes likely to be altered in low-risk tumors. A higher TC was found to be inversely associated with more aggressive surrogate molecular subtypes and tumor characteristics (P < .05) including Ki-67 proliferation status (P < 5 × 10-07 ). Our low-risk TC-Gx, based on the weighted sum of 37 expression values of genes strongly correlated with TC, was associated with basal-like (P < 5 × 10-13 ), HER2-enriched subtype (P < 5 × 10-07 ) and worse 10-year breast cancer-specific survival (log-rank P < 5 × 10-04 ). Associations between low-risk TC-Gx and more aggressive molecular subtypes were replicated in an independent cohort from The Cancer Genome Atlas database (n = 975). Gene expression that correlated with low TC was enriched in proliferation and oncogenic signaling pathways (FDR < 0.05). Moreover, higher proliferation was a key factor explaining the association with worse survival. Women who developed breast cancer despite having a low risk were diagnosed with more aggressive tumors and had a worse prognosis, most likely driven by increased proliferation. Our findings imply the need to establish risk factors associated with more aggressive breast cancer subtypes.
Collapse
Affiliation(s)
- Emilio Ugalde‐Morales
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Felix Grassmann
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Institute of Medical SciencesUniversity of AberdeenAberdeenUK
| | - Keith Humphreys
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Swedish eScience Research Centre (SeRC)Karolinska InstitutetStockholmSweden
| | - Jingmei Li
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Department of Human GeneticsGenome Institute of SingaporeSingaporeSingapore
- Department of Surgery, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Mikael Eriksson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Nicholas P. Tobin
- Department of Oncology‐PathologyKarolinska InstitutetStockholmSweden
| | - Åke Borg
- Department of Clinical Sciences, Division of Oncology and PathologyLund UniversityLundSweden
- Department of OncologyLund University Cancer CenterLundSweden
- CREATE Health Strategic Centre for Translational Cancer ResearchLund UniversityLundSweden
- Department of Clinical Sciences, SCIBLU GenomicsLund UniversityLundSweden
| | - Johan Vallon‐Christersson
- Department of Clinical Sciences, Division of Oncology and PathologyLund UniversityLundSweden
- Department of OncologyLund University Cancer CenterLundSweden
- CREATE Health Strategic Centre for Translational Cancer ResearchLund UniversityLundSweden
| | - Per Hall
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Department of OncologySödersjukhusetStockholmSweden
| | - Kamila Czene
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| |
Collapse
|
218
|
Transcriptional responses in newly-hatched Japanese medaka (Oryzias latipes) associated with developmental malformations following diluted bitumen exposure. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100685. [DOI: 10.1016/j.cbd.2020.100685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 11/21/2022]
|
219
|
Sutherland JJ, Stevens JL, Johnson K, Elango N, Webster YW, Mills BJ, Robertson DH. A Novel Open Access Web Portal for Integrating Mechanistic and Toxicogenomic Study Results. Toxicol Sci 2020; 170:296-309. [PMID: 31020328 PMCID: PMC6657575 DOI: 10.1093/toxsci/kfz101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Applying toxicogenomics to improving the safety profile of drug candidates and crop protection molecules is most useful when it identifies relevant biological and mechanistic information that highlights risks and informs risk mitigation strategies. Pathway-based approaches, such as gene set enrichment analysis, integrate toxicogenomic data with known biological process and pathways. Network methods help define unknown biological processes and offer data reduction advantages. Integrating the 2 approaches would improve interpretation of toxicogenomic information. Barriers to the routine application of these methods in genome-wide transcriptomic studies include a need for “hands-on” computer programming experience, the selection of 1 or more analysis methods (eg pathway analysis methods), the sensitivity of results to algorithm parameters, and challenges in linking differential gene expression to variation in safety outcomes. To facilitate adoption and reproducibility of gene expression analysis in safety studies, we have developed Collaborative Toxicogeomics, an open-access integrated web portal using the Django web framework. The software, developed with the Python programming language, is modular, extensible and implements “best-practice” methods in computational biology. New study results are compared with over 4000 rodent liver experiments from Drug Matrix and open TG-GATEs. A unique feature of the software is the ability to integrate clinical chemistry and histopathology-derived outcomes with results from gene expression studies, leading to relevant mechanistic conclusions. We describe its application by analyzing the effects of several toxicants on liver gene expression and exemplify application to predicting toxicity study outcomes upon chronic treatment from expression changes in acute-duration studies.
Collapse
Affiliation(s)
- Jeffrey J Sutherland
- Indiana Biosciences Research Institute, 1345 W. 16th St. Suite 300, Indianapolis, IN 46202
| | - James L Stevens
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285.,Paradox Found LLC, 212 Wooded Lake Drive, Apex, NC 27523
| | - Kamin Johnson
- Corteva AgriscienceTM, Agriculture Division of DowDuPontTM, 9330 Zionsville Rd, Indianapolis, Indiana, 46268
| | - Navin Elango
- Corteva AgriscienceTM, Agriculture Division of DowDuPontTM, 9330 Zionsville Rd, Indianapolis, Indiana, 46268
| | - Yue W Webster
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285
| | - Bradley J Mills
- Indiana Biosciences Research Institute, 1345 W. 16th St. Suite 300, Indianapolis, IN 46202
| | - Daniel H Robertson
- Indiana Biosciences Research Institute, 1345 W. 16th St. Suite 300, Indianapolis, IN 46202
| |
Collapse
|
220
|
Thananusak R, Laoteng K, Raethong N, Zhang Y, Vongsangnak W. Metabolic Responses of Carotenoid and Cordycepin Biosynthetic Pathways in Cordyceps militaris under Light-Programming Exposure through Genome-Wide Transcriptional Analysis. BIOLOGY 2020; 9:E242. [PMID: 32825642 PMCID: PMC7576481 DOI: 10.3390/biology9090242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 11/16/2022]
Abstract
Cordyceps militaris is currently exploited for commercial production of specialty products as its biomass constituents are enriched in bioactive compounds, such as cordycepin. The rational process development is important for economically feasible production of high quality bioproducts. Light is an abiotic factor affecting the cultivation process of this entomopathogenic fungus, particularly in its carotenoid formation. To uncover the cell response to light exposure, this study aimed to systematically investigate the metabolic responses of C. militaris strain TBRC6039 using integrative genome-wide transcriptome and genome-scale metabolic network (GSMN)-driven analysis. The genome-wide transcriptome analysis showed 8747 expressed genes in the glucose and sucrose cultures grown under light-programming and dark conditions. Of them, 689 differentially expressed genes were significant in response to the light-programming exposure. Through integration with the GSMN-driven analysis using the improved network (iRT1467), the reporter metabolites, e.g., adenosine-5'-monophosphate (AMP) and 2-oxoglutarate, were identified when cultivated under the carotenoid-producing condition controlled by light-programming exposure, linking to up-regulations of the metabolic genes involved in glyoxalase system, as well as cordycepin and carotenoid biosynthesis. These results indicated that C. militaris had a metabolic control in acclimatization to light exposure through transcriptional co-regulation, which supported the cell growth and cordycepin production in addition to the accumulation of carotenoid as a photo-protective bio-pigment. This study provides a perspective in manipulating the metabolic fluxes towards the target metabolites through either genetic or physiological approaches.
Collapse
Affiliation(s)
- Roypim Thananusak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Nachon Raethong
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Yu Zhang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China;
| | - Wanwipa Vongsangnak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| |
Collapse
|
221
|
Pinheiro MJ, Bonturi N, Belouah I, Miranda EA, Lahtvee PJ. Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery. Front Bioeng Biotechnol 2020; 8:1008. [PMID: 32974324 PMCID: PMC7466555 DOI: 10.3389/fbioe.2020.01008] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/31/2020] [Indexed: 12/04/2022] Open
Abstract
The use of cell factories to convert sugars from lignocellulosic biomass into chemicals in which oleochemicals and food additives, such as carotenoids, is essential for the shift toward sustainable processes. Rhodotorula toruloides is a yeast that naturally metabolises a wide range of substrates, including lignocellulosic hydrolysates, and converts them into lipids and carotenoids. In this study, xylose, the main component of hemicellulose, was used as the sole substrate for R. toruloides, and a detailed physiology characterisation combined with absolute proteomics and genome-scale metabolic models was carried out to understand the regulation of lipid and carotenoid production. To improve these productions, oxidative stress was induced by hydrogen peroxide and light irradiation and further enhanced by adaptive laboratory evolution. Based on the online measurements of growth and CO2 excretion, three distinct growth phases were identified during batch cultivations. Majority of the intracellular flux estimations showed similar trends with the measured protein levels and demonstrated improved NADPH regeneration, phosphoketolase activity and reduced β-oxidation, correlating with increasing lipid yields. Light irradiation resulted in 70% higher carotenoid and 40% higher lipid content compared to the optimal growth conditions. The presence of hydrogen peroxide did not affect the carotenoid production but culminated in the highest lipid content of 0.65 g/gDCW. The adapted strain showed improved fitness and 2.3-fold higher carotenoid content than the parental strain. This work presents a holistic view of xylose conversion into microbial oil and carotenoids by R. toruloides, in a process toward renewable and cost-effective production of these molecules.
Collapse
Affiliation(s)
- Marina Julio Pinheiro
- Institute of Technology, University of Tartu, Tartu, Estonia
- Department of Materials and Bioprocess Engineering, School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | | | - Isma Belouah
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Everson Alves Miranda
- Department of Materials and Bioprocess Engineering, School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | | |
Collapse
|
222
|
Landberg J, Wright NR, Wulff T, Herrgård MJ, Nielsen AT. CRISPR interference of nucleotide biosynthesis improves production of a single-domain antibody in Escherichia coli. Biotechnol Bioeng 2020; 117:3835-3848. [PMID: 32808670 PMCID: PMC7818426 DOI: 10.1002/bit.27536] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/23/2022]
Abstract
Growth decoupling can be used to optimize the production of biochemicals and proteins in cell factories. Inhibition of excess biomass formation allows for carbon to be utilized efficiently for product formation instead of growth, resulting in increased product yields and titers. Here, we used CRISPR interference to increase the production of a single‐domain antibody (sdAb) by inhibiting growth during production. First, we screened 21 sgRNA targets in the purine and pyrimidine biosynthesis pathways and found that the repression of 11 pathway genes led to the increased green fluorescent protein production and decreased growth. The sgRNA targets pyrF, pyrG, and cmk were selected and further used to improve the production of two versions of an expression‐optimized sdAb. Proteomics analysis of the sdAb‐producing pyrF, pyrG, and cmk growth decoupling strains showed significantly decreased RpoS levels and an increase of ribosome‐associated proteins, indicating that the growth decoupling strains do not enter stationary phase and maintain their capacity for protein synthesis upon growth inhibition. Finally, sdAb production was scaled up to shake‐flask fermentation where the product yield was improved 2.6‐fold compared to the control strain with no sgRNA target sequence. An sdAb content of 14.6% was reached in the best‐performing pyrG growth decoupling strain.
Collapse
Affiliation(s)
- Jenny Landberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Naia Risager Wright
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
223
|
Xie D, Wang TT, Huang SJ, Deng JJ, Ren YJ, Yang Y, Wu JQ, Zhang L, Fei K, Sun XW, She YL, Chen C. Radiomics nomogram for prediction disease-free survival and adjuvant chemotherapy benefits in patients with resected stage I lung adenocarcinoma. Transl Lung Cancer Res 2020; 9:1112-1123. [PMID: 32953490 PMCID: PMC7481634 DOI: 10.21037/tlcr-19-577] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Robust imaging biomarkers are needed for risk stratification in stage I lung adenocarcinoma patients in order to select optimal treatment regimen. We aimed to construct and validate a radiomics nomogram for predicting the disease-free survival (DFS) of patients with resected stage I lung adenocarcinoma, and further identifying candidates benefit from adjuvant chemotherapy (ACT). Methods Using radiomics approach, we analyzed 554 patients' computed tomography (CT) images from three multicenter cohorts. Prognostic radiomics features were extracted from computed tomography (CT) images and selected using least absolute shrinkage and selection operator (LASSO) Cox regression model to build a radiomics signature for DFS stratification. The biological basis of radiomics was explored in the Radiogenomics dataset (n=79) by gene set enrichment analysis (GSEA). Then a nomogram that integrated the signature with these significant clinicopathologic factors in the multivariate analysis were constructed in the training cohort (n=238), and its prognostic accuracy was evaluated in the validation cohort (n=237). Finally, the predictive value of nomogram for ACT benefits was assessed. Results The radiomics signature with higher score was significantly associated with worse DFS in both the training and validation cohorts (P<0.001). The GSEA presented that the signature was highly correlated to characteristic metabolic process and immune system during cancer progression. Multivariable analysis revealed that age (P=0.031), pathologic TNM stage (P=0.043), histologic subtype (P=0.010) and the signature (P<0.001) were independently associated with patients' DFS. The integrated radiomics nomogram showed good discrimination performance, as well as good calibration and clinical utility, for DFS prediction in the validation cohort. We further found that the patients with high points (point ≥8.788) defined by the radiomics nomogram obtained a significant favorable response to ACT (P=0.04) while patients with low points (point <8.788) showed no survival difference (P=0.7). Conclusions The radiomics nomogram could be used for prognostic prediction and ACT benefits identification for patient with resected stage I lung adenocarcinoma.
Collapse
Affiliation(s)
- Dong Xie
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ting-Ting Wang
- Department of Radiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shu-Jung Huang
- Research Institute of Oncology and Hematology, CancerCare Manitoba & University of Manitoba, Winnipeg, MB, Canada
| | - Jia-Jun Deng
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi-Jiu Ren
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yang Yang
- Department of Radiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun-Qi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lei Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ke Fei
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi-Wen Sun
- Department of Radiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yun-Lang She
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
224
|
Zhou JG, Yang J, Jin SH, Xiao S, Shi L, Zhang TY, Ma H, Gaipl US. Development and Validation of a Gene Signature for Prediction of Relapse in Stage I Testicular Germ Cell Tumors. Front Oncol 2020; 10:1147. [PMID: 32850325 PMCID: PMC7412879 DOI: 10.3389/fonc.2020.01147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/08/2020] [Indexed: 01/18/2023] Open
Abstract
Background: Testicular germ cell tumors (TGCTs) are commonly diagnosed tumors in young men. However, a satisfactory approach to predict relapse of stage I TGCTs is still lacking. Therefore, this study aimed to develop a robust risk score model for stage I TGCTs. Method: RNA-sequence data of stage I TGCTs and normal testis samples were downloaded and analyzed to identify different expression genes. Gene-based prognostic model was constructed in The Cancer Genome Atlas (TCGA) using least absolute shrinkage and selection operator (LASSO) regression analysis and validated in GSE99420 dataset. Potential biological functions of the genes in prognostic model were determined via Gene Set Enrichment Analysis (GSEA) between high-risk and low-risk patients. Results: A total of 9,391 differentially expressed genes and 84 prognosis-related genes were identified. An eight-gene-based risk score model was constructed to divide patients into high or low risk of relapse. The low-risk patients had a significantly better relapse-free survival (RFS) than high-risk patients in both training and validation cohorts (HR = 0.129, 95% CI = 0.059-0.284, P < 0.001; HR = 0.277, 95% CI = 0.116-0.661, P = 0.004, respectively). The area under the receiver operating characteristic curve (AUC) values at 5 years was 0.805 and 0.724 in the training and validation cohorts, respectively. Functional enrichment analyses showed that DNA replication, ribosome, cell cycle, and TGF-beta signaling pathway may contribute to the relapse process. Conclusion: In summary, our analysis provided a novel eight-gene signature that could predict RFS in stage I TGCT patients.
Collapse
Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Jie Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Su-Han Jin
- Department of Orthodontics, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Siyu Xiao
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lei Shi
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Ting-You Zhang
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hu Ma
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Udo S. Gaipl
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| |
Collapse
|
225
|
Kim HN, Ponte F, Nookaew I, Ucer Ozgurel S, Marques-Carvalho A, Iyer S, Warren A, Aykin-Burns N, Krager K, Sardao VA, Han L, de Cabo R, Zhao H, Jilka RL, Manolagas SC, Almeida M. Estrogens decrease osteoclast number by attenuating mitochondria oxidative phosphorylation and ATP production in early osteoclast precursors. Sci Rep 2020; 10:11933. [PMID: 32686739 PMCID: PMC7371870 DOI: 10.1038/s41598-020-68890-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023] Open
Abstract
Loss of estrogens at menopause is a major cause of osteoporosis and increased fracture risk. Estrogens protect against bone loss by decreasing osteoclast number through direct actions on cells of the myeloid lineage. Here, we investigated the molecular mechanism of this effect. We report that 17β-estradiol (E2) decreased osteoclast number by promoting the apoptosis of early osteoclast progenitors, but not mature osteoclasts. This effect was abrogated in cells lacking Bak/Bax-two pro-apoptotic members of the Bcl-2 family of proteins required for mitochondrial apoptotic death. FasL has been previously implicated in the pro-apoptotic actions of E2. However, we show herein that FasL-deficient mice lose bone mass following ovariectomy indistinguishably from FasL-intact controls, indicating that FasL is not a major contributor to the anti-osteoclastogenic actions of estrogens. Instead, using microarray analysis we have elucidated that ERα-mediated estrogen signaling in osteoclast progenitors decreases "oxidative phosphorylation" and the expression of mitochondria complex I genes. Additionally, E2 decreased the activity of complex I and oxygen consumption rate. Similar to E2, the complex I inhibitor Rotenone decreased osteoclastogenesis by promoting osteoclast progenitor apoptosis via Bak/Bax. These findings demonstrate that estrogens decrease osteoclast number by attenuating respiration, and thereby, promoting mitochondrial apoptotic death of early osteoclast progenitors.
Collapse
Affiliation(s)
- Ha-Neui Kim
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA
| | - Filipa Ponte
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Serra Ucer Ozgurel
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA
| | - Adriana Marques-Carvalho
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, UC-Biotech, Biocant Park, Cantanhede, Portugal
| | - Srividhya Iyer
- Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Aaron Warren
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA
| | - Nukhet Aykin-Burns
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Kimberly Krager
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Vilma A Sardao
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, UC-Biotech, Biocant Park, Cantanhede, Portugal
| | - Li Han
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, NIA, NIH, Baltimore, MD, USA
| | - Haibo Zhao
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA
| | - Robert L Jilka
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA
| | - Stavros C Manolagas
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA.,Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, USA.,Central Arkansas Veterans Healthcare System, Little Rock, AR, 72205, USA
| | - Maria Almeida
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, 4301 W. Markham St. #587, Little Rock, 72205-7199, USA. .,Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, USA. .,Central Arkansas Veterans Healthcare System, Little Rock, AR, 72205, USA.
| |
Collapse
|
226
|
Furuya S, Cichocki JA, Konganti K, Dreval K, Uehara T, Katou Y, Fukushima H, Kono H, Pogribny IP, Argemi J, Bataller R, Rusyn I. Histopathological and Molecular Signatures of a Mouse Model of Acute-on-Chronic Alcoholic Liver Injury Demonstrate Concordance With Human Alcoholic Hepatitis. Toxicol Sci 2020; 170:427-437. [PMID: 30517762 DOI: 10.1093/toxsci/kfy292] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human alcoholic hepatitis (AH) carries a high mortality rate. AH is an acute-on-chronic form of liver injury characterized by hepatic steatosis, ballooned hepatocytes, neutrophil infiltration, and pericellular fibrosis. We aimed to study the pathogenesis of AH in an animal model which combines chronic hepatic fibrosis with intragastric alcohol administration. Adult male C57BL6/J mice were treated with CCl4 (0.2 ml/kg, 2×weekly by intraperitoneal injections for 6 weeks) to induce chronic liver fibrosis. Then, ethyl alcohol (up to 25 g/kg/day for 3 weeks) was administered continuously to mice via a gastric feeding tube, with or without one-half dose of CCl4. Liver and serum markers and liver transcriptome were evaluated to characterize acute-on-chronic-alcoholic liver disease in our model. CCl4 or alcohol treatment alone induced liver fibrosis or steatohepatitis, respectively, findings that were consistent with expected pathology. Combined treatment resulted in a marked exacerbation of liver injury, as evident by the development of inflammation, steatosis, and pericellular fibrosis, pathological features of human AH. E. coli and Candida were also detected in livers of mice cotreated with CCl4 and alcohol, indicating pathogen translocation from gut to liver, similar to human AH. Importantly, liver transcriptomic changes specific to combined treatment group demonstrated close concordance with pathways perturbed in patients with severe AH. Overall, mice treated with CCl4 and alcohol displayed key molecular and pathological characteristics of human AH-pericellular fibrosis, increased hepatic bacterial load, and dysregulation of the same molecular pathways. This model may be useful for developing therapeutics for AH.
Collapse
Affiliation(s)
| | | | - Kranti Konganti
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas 77843
| | - Kostiantyn Dreval
- Program in Cancer Genetics, Epigenetics and Genomics, Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico 87102
| | - Takeki Uehara
- Laboratory of Veterinary Pathology, Osaka Prefecture University, Osaka, Japan
| | - Yuuki Katou
- Laboratory of Veterinary Pathology, Osaka Prefecture University, Osaka, Japan
| | | | - Hiroshi Kono
- First Department of Surgery, University of Yamanashi, Yamanashi, Japan
| | - Igor P Pogribny
- National Center for Toxicological Research, U.S. FDA, Jefferson, Arkansas 72079
| | - Josepmaria Argemi
- Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Ramon Bataller
- Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences
| |
Collapse
|
227
|
Hodge K, Makjaroen J, Robinson J, Khoomrung S, Pisitkun T. Deep Proteomic Deconvolution of Interferons and HBV Transfection Effects on a Hepatoblastoma Cell Line. ACS OMEGA 2020; 5:16796-16810. [PMID: 32685848 PMCID: PMC7364717 DOI: 10.1021/acsomega.0c01865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/15/2020] [Indexed: 05/13/2023]
Abstract
Interferons are commonly utilized in the treatment of chronic hepatitis B virus (HBV) infection but are not effective for all patients. A deep understanding of the limitations of interferon treatment requires delineation of its activity at multiple "omic" levels. While myriad studies have characterized the transcriptomic effects of interferon treatment, surprisingly, few have examined interferon-induced effects at the proteomic level. To remedy this paucity, we stimulated HepG2 cells with both IFN-α and IFN-λ and performed proteomic analysis versus unstimulated cells. Alongside, we examined the effects of HBV transfection in the same cell line, reasoning that parallel IFN and HBV analysis might allow determination of cases where HBV transfection counters the effects of interferons. More than 6000 proteins were identified, with multiple replicates allowing for differential expression analysis at high confidence. Drawing on a compendium of transcriptomic data, as well as proteomic half-life data, we suggest means by which transcriptomic results diverge from our proteomic results. We also invoke a recent multiomic study of HBV-related hepatocarcinoma (HCC), showing that despite HBV's role in initiating HCC, the regulated proteomic landscapes of HBV transfection and HCC do not strongly align. Special focus is applied to the proteasome, with numerous components divergently altered under IFN and HBV-transfection conditions. We also examine alterations of other protein groups relevant to HLA complex peptide display, unveiling intriguing alterations in a number of ubiquitin ligases. Finally, we invoke genome-scale metabolic modeling to predict relevant alterations to the metabolic landscape under experimental conditions. Our data should be useful as a resource for interferon and HBV researchers.
Collapse
Affiliation(s)
- Kenneth Hodge
- The
Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Jiradej Makjaroen
- The
Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Jonathan Robinson
- Department
of Biology and Biological Engineering, National Bioinformatics Infrastructure
Sweden, Science for Life Laboratory, Chalmers
University of Technology, Kemivägen 10, Gothenburg 412 96, Sweden
- Wallenberg
Center for Protein Research, Chalmers University
of Technology, Kemivägen
10, Gothenburg 412 96, Sweden
| | - Sakda Khoomrung
- Metabolomics
and Systems Biology, Department of Biochemistry, and Siriraj Metabolomics
and Phenomics Center Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Center
for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Trairak Pisitkun
- The
Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
- . Phone: +6692-537-0549
| |
Collapse
|
228
|
Kulterer OC, Niederstaetter L, Herz CT, Haug AR, Bileck A, Pils D, Kautzky-Willer A, Gerner C, Kiefer FW. The Presence of Active Brown Adipose Tissue Determines Cold-Induced Energy Expenditure and Oxylipin Profiles in Humans. J Clin Endocrinol Metab 2020; 105:5825408. [PMID: 32343312 DOI: 10.1210/clinem/dgaa183] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/09/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Accumulating evidence links brown adipose tissue (BAT) to increased cold-induced energy expenditure (CIEE) and regulation of lipid metabolism in humans. BAT has also been proposed as a novel source for biologically active lipid mediators including polyunsaturated fatty acids (PUFAs) and oxylipins. However, little is known about cold-mediated differences in energy expenditure and various lipid species between individuals with detectable BAT positive (BATpos) and those without BAT negative (BATneg). METHODS Here we investigated a unique cohort of matched BATpos and BATneg individuals identified by 18F-fluorodeoxyglucose positron emission tomography combined with computed tomography ([18F]-FDG PET/CT). BAT function, CIEE, and circulating oxylipins, were analyzed before and after short-term cold exposure using [18F]-FDG PET/CT, indirect calorimetry, and high-resolution mass spectrometry, respectively. RESULTS We found that active BAT is the major determinant of CIEE since only BATpos individuals experienced significantly increased energy expenditure in response to cold. A single bout of moderate cold exposure resulted in the dissipation of an additional 20 kcal excess energy in BATpos but not in BATneg individuals. The presence of BAT was associated with a unique systemic PUFA and oxylipin profile characterized by increased levels of anti-inflammatory omega-3 fatty acids as well as cytochrome P450 products but decreased concentrations of some proinflammatory hydroxyeicosatetraenoic acids when compared with BATneg individuals. Notably, cold exposure raised circulating levels of various lipids, including the recently identified BAT-derived circulating factors (BATokines) DiHOME and 12-HEPE, only in BATpos individuals. CONCLUSIONS In summary, our data emphasize that BAT in humans is a major contributor toward cold-mediated energy dissipation and a critical organ in the regulation of the systemic lipid pool.
Collapse
Affiliation(s)
- Oana C Kulterer
- Clinical Division of Endocrinology and Metabolism, Department of Medicine III, Medical University of Vienna, Vienna, Austria
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Austria
| | - Laura Niederstaetter
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Carsten T Herz
- Clinical Division of Endocrinology and Metabolism, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Alexander R Haug
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Austria
- Christian-Doppler Laboratory for Applied Metabolomics, Division of Nuclear Medicine, Medical University of Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Dietmar Pils
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Alexandra Kautzky-Willer
- Clinical Division of Endocrinology and Metabolism, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Florian W Kiefer
- Clinical Division of Endocrinology and Metabolism, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
229
|
Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study. Sci Rep 2020; 10:9624. [PMID: 32541680 PMCID: PMC7295773 DOI: 10.1038/s41598-020-66598-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/22/2020] [Indexed: 02/07/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) drastically affects the population of Middle East countries with an ever-increasing number of overweight and obese individuals. The precise links between T2DM and gut microbiome composition remain elusive in these populations. Here, we performed 16 S rRNA and ITS2- gene based microbial profiling of 50 stool samples from Emirati adults with or without T2DM. The four major enterotypes initially described in westernized cohorts were retrieved in this Emirati population. T2DM and non-T2DM healthy controls had different microbiome compositions, with an enrichment in Prevotella enterotype in non-T2DM controls whereas T2DM individuals had a higher proportion of the dysbiotic Bacteroides 2 enterotype. No significant differences in microbial diversity were observed in T2DM individuals after controlling for cofounding factors, contrasting with reports from westernized cohorts. Interestingly, fungal diversity was significantly decreased in Bacteroides 2 enterotype. Functional profiling from 16 S rRNA gene data showed marked differences between T2DM and non-T2DM controls, with an enrichment in amino acid degradation and LPS-related modules in T2DM individuals, whereas non-T2DM controls had increased abundance of carbohydrate degradation modules in concordance with enterotype composition. These differences provide an insight into gut microbiome composition in Emirati population and its potential role in the development of diabetes mellitus.
Collapse
|
230
|
Tomić TT, Olausson J, Rehammar A, Deland L, Muth A, Ejeskär K, Nilsson S, Kristiansson E, Wassén ON, Abel F. MYO5B mutations in pheochromocytoma/paraganglioma promote cancer progression. PLoS Genet 2020; 16:e1008803. [PMID: 32511227 PMCID: PMC7329139 DOI: 10.1371/journal.pgen.1008803] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 07/01/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022] Open
Abstract
Identification of additional cancer-associated genes and secondary mutations driving the metastatic progression in pheochromocytoma and paraganglioma (PPGL) is important for subtyping, and may provide optimization of therapeutic regimens. We recently reported novel recurrent nonsynonymous mutations in the MYO5B gene in metastatic PPGL. Here, we explored the functional impact of these MYO5B mutations, and analyzed MYO5B expression in primary PPGL tumor cases in relation to mutation status. Immunohistochemistry and mRNA expression analysis in 30 PPGL tumors revealed an increased MYO5B expression in metastatic compared to non-metastatic cases. In addition, subcellular localization of MYO5B protein was altered from cytoplasmic to membranous in some metastatic tumors, and the strongest and most abnormal expression pattern was observed in a paraganglioma harboring a somatic MYO5B:p.G1611S mutation. In addition to five previously discovered MYO5B mutations, the present study of 30 PPGL (8 previous and 22 new samples) also revealed two, and hence recurrent, mutations in the gene paralog MYO5A. The three MYO5B missense mutations with the highest prediction scores (p.L587P, p.G1611S and p.R1641C) were selected and functionally validated using site directed mutagenesis and stable transfection into human neuroblastoma cells (SK-N-AS) and embryonic kidney cells (HEK293). In vitro analysis showed a significant increased proliferation rate in all three MYO5B mutated clones. The two somatically derived mutations, p.L587P and p.G1611S, were also found to increase the migration rate. Expression analysis of MYO5B mutants compared to wild type clones, demonstrated a significant enrichment of genes involved in migration, proliferation, cell adhesion, glucose metabolism, and cellular homeostasis. Our study validates the functional role of novel MYO5B mutations in proliferation and migration, and suggest the MYO5-pathway to be involved in the malignant progression in some PPGL tumors. Up to 25% of pheochromocytoma/paraganglioma (PPGL) cases develop metastatic disease with poor outcome and few treatment options. The disease mechanism is not fully understood, and to date there are no reliable markers to predict malignancy. We have recently discovered novel missense mutations in the non-conventional myosin 5 gene (MYO5B), an endosomal transport protein, which we now show enhances progression and migration in PPGLs. MYO5B mutations were preferentially found in patients with metastatic disease and SDH deficiency (germline SDHB-mutations). Abolished SDH activity result in a metabolic switch to aerobic glycolysis requiring increased glucose consumption. Since the MYO5B mutations were found to drive progression through downstream up-regulation of glucose metabolism genes, e.g. glucagon, we hypothesize that these mutations may fuel the pseudohypoxic state by altering glucose uptake in cancer cells. Our result is the first to link the myosin 5 genes to PPGL tumorigenesis. Further, it shows that the tumor progression route in PPGL is complex, with contribution from several genetic factors. An increasing number of studies show dysregulation and importance of the MYO5-proteins in cancer, but little is still known about the precise role and mechanism of mutations, hence more research in this area is needed.
Collapse
Affiliation(s)
- Tajana Tešan Tomić
- Department of Pathology and Genetics, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Josefin Olausson
- Department of Pathology and Genetics, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Anna Rehammar
- Department of Mathematical Sciences, Chalmers University of Technology and Biostatistics, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lily Deland
- Department of Pathology and Genetics, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Andreas Muth
- Department of Surgery, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Surgery, Section of endocrine and sarcoma surgery, Gothenborg, Sweden
| | - Katarina Ejeskär
- School of Health and Education, University of Skövde, Skövde, Sweden
| | - Staffan Nilsson
- Department of Pathology and Genetics, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology and Biostatistics, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and Biostatistics, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ola Nilsson Wassén
- Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Frida Abel
- Department of Pathology and Genetics, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
231
|
Hasle N, Cooke A, Srivatsan S, Huang H, Stephany JJ, Krieger Z, Jackson D, Tang W, Pendyala S, Monnat RJ, Trapnell C, Hatch EM, Fowler DM. High-throughput, microscope-based sorting to dissect cellular heterogeneity. Mol Syst Biol 2020; 16:e9442. [PMID: 32500953 PMCID: PMC7273721 DOI: 10.15252/msb.20209442] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Microscopy is a powerful tool for characterizing complex cellular phenotypes, but linking these phenotypes to genotype or RNA expression at scale remains challenging. Here, we present Visual Cell Sorting, a method that physically separates hundreds of thousands of live cells based on their visual phenotype. Automated imaging and phenotypic analysis directs selective illumination of Dendra2, a photoconvertible fluorescent protein expressed in live cells; these photoactivated cells are then isolated using fluorescence-activated cell sorting. First, we use Visual Cell Sorting to assess hundreds of nuclear localization sequence variants in a pooled format, identifying variants that improve nuclear localization and enabling annotation of nuclear localization sequences in thousands of human proteins. Second, we recover cells that retain normal nuclear morphologies after paclitaxel treatment, and then derive their single-cell transcriptomes to identify pathways associated with paclitaxel resistance in cancers. Unlike alternative methods, Visual Cell Sorting depends on inexpensive reagents and commercially available hardware. As such, it can be readily deployed to uncover the relationships between visual cellular phenotypes and internal states, including genotypes and gene expression programs.
Collapse
Affiliation(s)
- Nicholas Hasle
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Sanjay Srivatsan
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Heather Huang
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Jason J Stephany
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Zachary Krieger
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Dana Jackson
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Weiliang Tang
- Department of PathologyUniversity of WashingtonSeattleWAUSA
| | - Sriram Pendyala
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Raymond J Monnat
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of PathologyUniversity of WashingtonSeattleWAUSA
| | - Cole Trapnell
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Emily M Hatch
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Douglas M Fowler
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of BioengineeringUniversity of WashingtonSeattleWAUSA
| |
Collapse
|
232
|
Suppli MP, Bagger JI, Lund A, Demant M, van Hall G, Strandberg C, Kønig MJ, Rigbolt K, Langhoff JL, Wewer Albrechtsen NJ, Holst JJ, Vilsbøll T, Knop FK. Glucagon Resistance at the Level of Amino Acid Turnover in Obese Subjects With Hepatic Steatosis. Diabetes 2020; 69:1090-1099. [PMID: 31974144 DOI: 10.2337/db19-0715] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022]
Abstract
Glucagon secretion is regulated by circulating glucose, but it has turned out that amino acids also play an important role and that hepatic amino acid metabolism and glucagon are linked in a mutual feedback cycle, the liver-α-cell axis. On the basis of this knowledge, we hypothesized that hepatic steatosis might impair glucagon's action on hepatic amino acid metabolism and lead to hyperaminoacidemia and hyperglucagonemia. We subjected 15 healthy lean and 15 obese steatotic male participants to a pancreatic clamp with somatostatin and evaluated hepatic glucose and amino acid metabolism when glucagon was at basal levels and at high physiological levels. The degree of steatosis was evaluated from liver biopsy specimens. Total RNA sequencing of liver biopsy specimens from the obese steatotic individuals revealed perturbations in the expression of genes predominantly involved in amino acid metabolism. This group was characterized by fasting hyperglucagonemia, hyperaminoacidemia, and no lowering of amino acid levels in response to high levels of glucagon. Endogenous glucose production was similar between lean and obese individuals. Our results suggest that hepatic steatosis causes resistance to the effect of glucagon on amino acid metabolism. This results in increased amino acid concentrations and increased glucagon secretion, providing a likely explanation for fatty liver-associated hyperglucagonemia.
Collapse
Affiliation(s)
- Malte P Suppli
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Jonatan I Bagger
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Asger Lund
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Mia Demant
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Gerrit van Hall
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical Metabolomics Core Facility, Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Strandberg
- Department of Radiology, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Merete J Kønig
- Department of Radiology, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | | | - Jill L Langhoff
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Nicolai J Wewer Albrechtsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jens J Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tina Vilsbøll
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Filip K Knop
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| |
Collapse
|
233
|
Titz B, Szostak J, Sewer A, Phillips B, Nury C, Schneider T, Dijon S, Lavrynenko O, Elamin A, Guedj E, Tsin Wong E, Lebrun S, Vuillaume G, Kondylis A, Gubian S, Cano S, Leroy P, Keppler B, Ivanov NV, Vanscheeuwijck P, Martin F, Peitsch MC, Hoeng J. Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke. Comput Struct Biotechnol J 2020; 18:1056-1073. [PMID: 32419906 PMCID: PMC7218232 DOI: 10.1016/j.csbj.2020.04.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/19/2020] [Indexed: 12/15/2022] Open
Abstract
Multi-omics systems toxicology study, comprising five omics data modalities. Multi-Omics Factor Analysis and multi-modality functional network interpretation. Cigarettes smoke (CS) induced complex immunoregulatory interactions across molecular layers. Aerosols from two heat-not-burn tobacco products had less impact on lungs than CS.
Cigarette smoke (CS) causes adverse health effects and, for smoker who do not quit, modified risk tobacco products (MRTPs) can be an alternative to reduce the risk of developing smoking-related diseases. Standard toxicological endpoints can lack sensitivity, with systems toxicology approaches yielding broader insights into toxicological mechanisms. In a 6-month systems toxicology study on ApoE−/− mice, we conducted an integrative multi-omics analysis to assess the effects of aerosols from the Carbon Heated Tobacco Product (CHTP) 1.2 and Tobacco Heating System (THS) 2.2—a potential and a candidate MRTP based on the heat-not-burn (HnB) principle—compared with CS at matched nicotine concentrations. Molecular exposure effects in the lungs were measured by mRNA/microRNA transcriptomics, proteomics, metabolomics, and lipidomics. Integrative data analysis included Multi-Omics Factor Analysis and multi-modality functional network interpretation. Across all five data modalities, CS exposure was associated with an increased inflammatory and oxidative stress response, and lipid/surfactant alterations. Upon HnB aerosol exposure these effects were much more limited or absent, with reversal of CS-induced effects upon cessation and switching to CHTP 1.2. Functional network analysis revealed CS-induced complex immunoregulatory interactions across the investigated molecular layers (e.g., itaconate, quinolinate, and miR-146) and highlighted the engagement of the heme–Hmox–bilirubin oxidative stress axis by CS. This work exemplifies how multi-omics approaches can be leveraged within systems toxicology studies and the generated multi-omics data set can facilitate the development of analysis methods and can yield further insights into the effects of toxicological exposures on the lung of mice.
Collapse
Key Words
- CHTP, Carbon Heated Tobacco Product
- COPD, chronic obstructive pulmonary disease
- CS, cigarette smoke
- Cigarette smoking
- Inhalation toxicology
- LC, liquid chromatography
- MOFA, Multi-Omics Factor Analysis
- MS, mass spectrometry
- Modified risk tobacco product (MRTP)
- Multi-omics
- PCSF, prize-collecting Steiner forest
- ROS, reactive oxygen species
- Systems toxicology
- THS, Tobacco Heating System
- cMRTP, candidate modified risk tobacco product
- sGCCA, sparse generalized canonical correlation analysis
Collapse
Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Justyna Szostak
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Alain Sewer
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Thomas Schneider
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Sophie Dijon
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Oksana Lavrynenko
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Ee Tsin Wong
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Stefan Lebrun
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Grégory Vuillaume
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Athanasios Kondylis
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Sylvain Gubian
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Stephane Cano
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Patrice Leroy
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | | | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | | | - Florian Martin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| |
Collapse
|
234
|
Chappell GA, Thompson CM, Wolf JC, Cullen JM, Klaunig JE, Haws LC. Assessment of the Mode of Action Underlying the Effects of GenX in Mouse Liver and Implications for Assessing Human Health Risks. Toxicol Pathol 2020; 48:494-508. [PMID: 32138627 PMCID: PMC7153225 DOI: 10.1177/0192623320905803] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
GenX is an alternative to environmentally persistent long-chain perfluoroalkyl and polyfluoroalkyl substances. Mice exposed to GenX exhibit liver hypertrophy, elevated peroxisomal enzyme activity, and other apical endpoints consistent with peroxisome proliferators. To investigate the potential role of peroxisome proliferator-activated receptor alpha (PPARα) activation in mice, and other molecular signals potentially related to observed liver changes, RNA sequencing was conducted on paraffin-embedded liver sections from a 90-day subchronic toxicity study of GenX conducted in mice. Differentially expressed genes were identified for each treatment group, and gene set enrichment analysis was conducted using gene sets that represent biological processes and known canonical pathways. Peroxisome signaling and fatty acid metabolism were among the most significantly enriched gene sets in both sexes at 0.5 and 5 mg/kg GenX; no pathways were enriched at 0.1 mg/kg. Gene sets specific to the PPARα subtype were significantly enriched. These findings were phenotypically anchored to histopathological changes in the same tissue blocks: hypertrophy, mitoses, and apoptosis. In vitro PPARα transactivation assays indicated that GenX activates mouse PPARα. These results indicate that the liver changes observed in GenX-treated mice occur via a mode of action (MOA) involving PPARα, an important finding for human health risk assessment as this MOA has limited relevance to humans.
Collapse
Affiliation(s)
| | | | | | - John M. Cullen
- North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - James E. Klaunig
- Indiana University, School of Public Health, Bloomington, IN, USA
| | | |
Collapse
|
235
|
Li X, Chen J, Andersen JM, Chu J, Jensen PR. Cofactor Engineering Redirects Secondary Metabolism and Enhances Erythromycin Production in Saccharopolyspora erythraea. ACS Synth Biol 2020; 9:655-670. [PMID: 32078772 DOI: 10.1021/acssynbio.9b00528] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Saccharopolyspora erythraea is used for industrial erythromycin production. To explore the physiological role of intracellular energy state in metabolic regulation by S. erythraea, we initially overexpressed the F1 part of the endogenous F1F0-ATPase in the high yielding erythromycin producing strain E3. The F1-ATPase expression resulted in lower [ATP]/[ADP] ratios, which was accompanied by a strong increase in the production of a reddish pigment and a decreased erythromycin production. Subsequent transcriptional analysis revealed that the lower intracellular [ATP]/[ADP] ratios exerted a pleotropic regulation on the metabolism of S. erythraea. The lower [ATP]/[ADP] ratios induced physiological changes to restore the energy balance, mainly via pathways that tend to produce ATP or regenerate NADH. The F1-ATPase overexpression strain exhibited a state of redox stress, which was correlated to an alteration of electron transport at the branch of the terminal oxidases, and S. erythraea channeled the enhanced glycolytic flux toward a reddish pigment in order to reduce NADH formation. The production of erythromycin was decreased, which is in accordance with the net ATP requirement and the excess NADH formed through this pathway. Partial growth inhibition by apramycin increased the intracellular [ATP]/[ADP] ratios and demonstrated a positive correlation between [ATP]/[ADP] ratios and erythromycin synthesis. Finally, overexpression of the entire F1F0-ATPase complex resulted in 28% enhanced erythromycin production and markedly reduced pigment synthesis in E3. The work illustrates a feasible strategy to optimize the distribution of fluxes in secondary metabolism.
Collapse
Affiliation(s)
- Xiaobo Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Jun Chen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Joakim M. Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
| | - Peter R. Jensen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| |
Collapse
|
236
|
Doron G, Klontzas ME, Mantalaris A, Guldberg RE, Temenoff JS. Multiomics characterization of mesenchymal stromal cells cultured in monolayer and as aggregates. Biotechnol Bioeng 2020; 117:1761-1778. [DOI: 10.1002/bit.27317] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Gilad Doron
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Institute of Technology and Emory UniversityAtlanta Georgia
| | - Michail E. Klontzas
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Institute of Technology and Emory UniversityAtlanta Georgia
- Emory University School of MedicineWinship Cancer InstituteAtlanta Georgia
| | - Athanasios Mantalaris
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Institute of Technology and Emory UniversityAtlanta Georgia
| | - Robert E. Guldberg
- Parker H. Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta Georgia
- George W. Woodruff School of Mechanical EngineeringGeorgia Institute of TechnologyAtlanta Georgia
- Knight Campus for Accelerating Scientific ImpactUniversity of OregonEugene Oregon
| | - Johnna S. Temenoff
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Institute of Technology and Emory UniversityAtlanta Georgia
- Parker H. Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta Georgia
| |
Collapse
|
237
|
Lo Sasso G, Phillips BW, Sewer A, Battey JND, Kondylis A, Talikka M, Titz B, Guedj E, Peric D, Bornand D, Dulize R, Merg C, Corciulo M, Ouadi S, Yanuar R, Tung CK, Ivanov NV, Peitsch MC, Hoeng J. The reduction of DSS-induced colitis severity in mice exposed to cigarette smoke is linked to immune modulation and microbial shifts. Sci Rep 2020; 10:3829. [PMID: 32123204 PMCID: PMC7052152 DOI: 10.1038/s41598-020-60175-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/24/2020] [Indexed: 12/15/2022] Open
Abstract
Exposure to cigarette smoke (CS) causes detrimental health effects, increasing the risk of cardiovascular, pulmonary diseases and carcinogenesis in exposed individuals. The impact of CS on Inflammatory Bowel Disease (IBD) has been established by a number of epidemiological and clinical studies. In fact, CS is associated with a higher risk of developing Crohn's disease (CD) while inversely correlates with the development, disease risks, and relapse rate of ulcerative colitis (UC). To investigate the effect of CS exposure on experimental colitis, we performed a comprehensive and integrated comparative analysis of colon transcriptome and microbiome in mice exposed to dextran sodium sulfate (DSS) and CS. Colon transcriptome analysis revealed that CS downregulated specific pathways in a concentration-dependent manner, affecting both the inflammatory state and composition of the gut microbiome. Metagenomics analysis demonstrated that CS can modulate DSS-induced dysbiosis of specific bacterial genera, contributing to resolve the inflammation or accelerate recovery. The risks of smoking far outweigh any possible benefit, thus smoking cessation must always be encouraged because of its significant health benefits. However, the inverse association between active smoking and the development of UC cannot be ignored and the present study lays the foundation for investigating potential molecular mechanisms responsible for the attenuation of colitis by certain compounds of tobacco when decoupled from combustion.
Collapse
Affiliation(s)
- Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Blaine W Phillips
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Alain Sewer
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - James N D Battey
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Athanasios Kondylis
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Marja Talikka
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Dariusz Peric
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - David Bornand
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Remi Dulize
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Celine Merg
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Maica Corciulo
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Sonia Ouadi
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Rendy Yanuar
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Ching Keong Tung
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| |
Collapse
|
238
|
Hess JL, Tylee DS, Barve R, de Jong S, Ophoff RA, Kumarasinghe N, Tooney P, Schall U, Gardiner E, Beveridge NJ, Scott RJ, Yasawardene S, Perera A, Mendis J, Carr V, Kelly B, Cairns M, Tsuang MT, Glatt SJ. Transcriptomic abnormalities in peripheral blood in bipolar disorder, and discrimination of the major psychoses. Schizophr Res 2020; 217:124-135. [PMID: 31391148 PMCID: PMC6997041 DOI: 10.1016/j.schres.2019.07.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
We performed a transcriptome-wide meta-analysis and gene co-expression network analysis to identify genes and gene networks dysregulated in the peripheral blood of bipolar disorder (BD) cases relative to unaffected comparison subjects, and determined the specificity of the transcriptomic signatures of BD and schizophrenia (SZ). Nineteen genes and 4 gene modules were significantly differentially expressed in BD cases. Thirteen gene modules were shown to be differentially expressed in a combined case-group of BD and SZ subjects called "major psychosis", including genes biologically linked to apoptosis, reactive oxygen, chromatin remodeling, and immune signaling. No modules were differentially expressed between BD and SZ cases. Machine-learning classifiers trained to separate diagnostic classes based solely on gene expression profiles could distinguish BD cases from unaffected comparison subjects with an area under the curve (AUC) of 0.724, as well as BD cases from SZ cases with AUC = 0.677 in withheld test samples. We introduced a novel and straightforward method called "polytranscript risk scoring" that could distinguish BD cases from unaffected subjects (AUC = 0.672) and SZ cases (AUC = 0.607) significantly better than expected by chance. Taken together, our results highlighted gene expression alterations common to BD and SZ that involve biological processes of inflammation, oxidative stress, apoptosis, and chromatin regulation, and highlight disorder-specific changes in gene expression that discriminate the major psychoses.
Collapse
Affiliation(s)
- Jonathan L Hess
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Daniel S Tylee
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Rahul Barve
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Simone de Jong
- MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA; Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nishantha Kumarasinghe
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia.; Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka; Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Paul Tooney
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Hunter Medical Research Institute, Newcastle, Australia
| | - Ulrich Schall
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia.; Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Erin Gardiner
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Natalie Jane Beveridge
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia.; Hunter Medical Research Institute, Newcastle, Australia; Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Rodney J Scott
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Hunter Medical Research Institute, Newcastle, Australia
| | - Surangi Yasawardene
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Antionette Perera
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Jayan Mendis
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Vaughan Carr
- School of Psychiatry, University of New South Wales, Kensington, New South Wales, Australia
| | - Brian Kelly
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia.; Hunter Medical Research Institute, Newcastle, Australia; Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Murray Cairns
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia; Hunter Medical Research Institute, Newcastle, Australia; Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Ming T Tsuang
- Center for Behavioral Genomics, Department of Psychiatry, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA; Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, USA
| | - Stephen J Glatt
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA.
| |
Collapse
|
239
|
Chen X, Ji B, Hao X, Li X, Eisele F, Nyström T, Petranovic D. FMN reduces Amyloid-β toxicity in yeast by regulating redox status and cellular metabolism. Nat Commun 2020; 11:867. [PMID: 32054832 PMCID: PMC7018843 DOI: 10.1038/s41467-020-14525-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 01/07/2020] [Indexed: 01/09/2023] Open
Abstract
Alzheimer's disease (AD) is defined by progressive neurodegeneration, with oligomerization and aggregation of amyloid-β peptides (Aβ) playing a pivotal role in its pathogenesis. In recent years, the yeast Saccharomyces cerevisiae has been successfully used to clarify the roles of different human proteins involved in neurodegeneration. Here, we report a genome-wide synthetic genetic interaction array to identify toxicity modifiers of Aβ42, using yeast as the model organism. We find that FMN1, the gene encoding riboflavin kinase, and its metabolic product flavin mononucleotide (FMN) reduce Aβ42 toxicity. Classic experimental analyses combined with RNAseq show the effects of FMN supplementation to include reducing misfolded protein load, altering cellular metabolism, increasing NADH/(NADH + NAD+) and NADPH/(NADPH + NADP+) ratios and increasing resistance to oxidative stress. Additionally, FMN supplementation modifies Htt103QP toxicity and α-synuclein toxicity in the humanized yeast. Our findings offer insights for reducing cytotoxicity of Aβ42, and potentially other misfolded proteins, via FMN-dependent cellular pathways.
Collapse
Affiliation(s)
- Xin Chen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Boyang Ji
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, SE40530, Gothenburg, Sweden
| | - Xiaowei Li
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Frederik Eisele
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, SE40530, Gothenburg, Sweden
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, SE40530, Gothenburg, Sweden
| | - Dina Petranovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
| |
Collapse
|
240
|
Sarathy C, Kutmon M, Lenz M, Adriaens ME, Evelo CT, Arts IC. EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models. Metabolites 2020; 10:metabo10020066. [PMID: 32059585 PMCID: PMC7074156 DOI: 10.3390/metabo10020066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022] Open
Abstract
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1260) and large (human, Recon 2.2) genome-scale metabolic models. EFMviz is open-source and integrated into COBRA Toolbox. The analysis workflows used for the two use cases are detailed in the two tutorials provided with EFMviz along with the data used in this study.
Collapse
Affiliation(s)
- Chaitra Sarathy
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands
- Correspondence:
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands
- Department of Bioinformatics—BiGCaT, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Michael Lenz
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Preventive Cardiology and Preventive Medicine—Center for Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Michiel E. Adriaens
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Chris T. Evelo
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands
- Department of Bioinformatics—BiGCaT, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ilja C.W. Arts
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands
- Department of Epidemiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6229 ER Maastricht, The Netherlands
| |
Collapse
|
241
|
Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis. Cells 2020; 9:cells9020401. [PMID: 32050592 PMCID: PMC7072658 DOI: 10.3390/cells9020401] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/24/2020] [Accepted: 02/05/2020] [Indexed: 12/26/2022] Open
Abstract
Beyond comparative genomics, we identified 85 sugar transporter genes in Cordyceps militaris, clustering into nine subfamilies as sequence- and phylogenetic-based functional classification, presuming the versatile capability of the fungal growths on a range of sugars. Further analysis of the global gene expression patterns of C. militaris showed 123 genes were significantly expressed across the sucrose, glucose, and xylose cultures. The sugar transporters specific for pentose were then identified by gene-set enrichment analysis. Of them, the putative pentose transporter, CCM_06358 gene, was highest expressed in the xylose culture, and its functional role in xylose transport was discovered by the analysis of conserved structural motifs. In addition, a battery of molecular modeling methods, including homology modeling, transport pathway analysis, residue interaction network combined with molecular mechanics Poisson–Boltzmann surface area simulation (MM-PBSA), was implemented for probing the structure and function of the selected pentose transporter (CCM_06358) as a representative of sugar transportome in C. militaris. Considering the network bottlenecks and structural organizations, we further identified key amino acids (Phe38 and Trp441) and their interactions with other residues, contributing the xylose transport function, as verified by binding free energy calculation. The strategy used herein generated remarkably valuable biological information, which is applicable for the study of sugar transportome and the structure engineering of targeted transporter proteins that might link to the production of bioactive compounds derived from xylose metabolism, such as cordycepin.
Collapse
|
242
|
Ægidius HM, Veidal SS, Feigh M, Hallenborg P, Puglia M, Pers TH, Vrang N, Jelsing J, Kornum BR, Blagoev B, Rigbolt KTG. Multi-omics characterization of a diet-induced obese model of non-alcoholic steatohepatitis. Sci Rep 2020; 10:1148. [PMID: 31980690 PMCID: PMC6981216 DOI: 10.1038/s41598-020-58059-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
To improve the understanding of the complex biological processes underlying the development of non-alcoholic steatohepatitis (NASH), a multi-omics approach combining bulk RNA-sequencing based transcriptomics, quantitative proteomics and single-cell RNA-sequencing was used to characterize tissue biopsies from histologically validated diet-induced obese (DIO) NASH mice compared to chow-fed controls. Bulk RNA-sequencing and proteomics showed a clear distinction between phenotypes and a good correspondence between mRNA and protein level regulations, apart from specific regulatory events discovered by each technology. Transcriptomics-based gene set enrichment analysis revealed changes associated with key clinical manifestations of NASH, including impaired lipid metabolism, increased extracellular matrix formation/remodeling and pro-inflammatory responses, whereas proteomics-based gene set enrichment analysis pinpointed metabolic pathway perturbations. Integration with single-cell RNA-sequencing data identified key regulated cell types involved in development of NASH demonstrating the cellular heterogeneity and complexity of NASH pathogenesis.
Collapse
Affiliation(s)
| | | | | | - Philip Hallenborg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Michele Puglia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Niels Vrang
- Gubra, Hørsholm Kongevej 11B, Hørsholm, Denmark
| | | | - Birgitte R Kornum
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | |
Collapse
|
243
|
Szostak J, Wong ET, Titz B, Lee T, Wong SK, Low T, Lee KM, Zhang J, Kumar A, Schlage WK, Guedj E, Phillips B, Leroy P, Buettner A, Xiang Y, Martin F, Sewer A, Kuczaj A, Ivanov NV, Luettich K, Vanscheeuwijck P, Peitsch MC, Hoeng J. A 6-month systems toxicology inhalation study in ApoE -/- mice demonstrates reduced cardiovascular effects of E-vapor aerosols compared with cigarette smoke. Am J Physiol Heart Circ Physiol 2020; 318:H604-H631. [PMID: 31975625 DOI: 10.1152/ajpheart.00613.2019] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Smoking cigarettes is harmful to the cardiovascular system. Considerable attention has been paid to the reduced harm potential of alternative nicotine-containing inhalable products such as e-cigarettes. We investigated the effects of E-vapor aerosols or cigarette smoke (CS) on atherosclerosis progression, cardiovascular function, and molecular changes in the heart and aorta of female apolipoprotein E-deficient (ApoE-/-) mice. The mice were exposed to aerosols from three different E-vapor formulations: 1) carrier (propylene glycol and vegetable glycerol), 2) base (carrier and nicotine), or 3) test (base and flavor) or to CS from 3R4F reference cigarettes for up to 6 mo. Concentrations of CS and base or test aerosols were matched at 35 µg nicotine/L. Exposure to CS, compared with sham-exposed fresh air controls, accelerated atherosclerotic plaque formation, whereas no such effect was seen for any of the three E-vapor aerosols. Molecular changes indicated disease mechanisms related to oxidative stress and inflammation in general, plus changes in calcium regulation, and altered cytoskeletal organization and microtubule dynamics in the left ventricle. While ejection fraction, fractional shortening, cardiac output, and isovolumic contraction time remained unchanged following E-vapor aerosols exposure, the nicotine-containing base and test aerosols caused an increase in isovolumic relaxation time similar to CS. A nicotine-related increase in pulse wave velocity and arterial stiffness was also observed, but it was significantly lower for base and test aerosols than for CS. These results demonstrate that in comparison with CS, E-vapor aerosols induce substantially lower biological responses associated with smoking-related cardiovascular diseases.NEW & NOTEWORTHY Analysis of key urinary oxidative stress markers and proinflammatory cytokines showed an absence of oxidative stress and inflammation in the animals exposed to E-vapor aerosols. Conversely, animals exposed to conventional cigarette smoke had high urinary levels of these markers. When compared with conventional cigarette smoke, E-vapor aerosols induced smaller atherosclerotic plaque surface area and volume. Systolic and diastolic cardiac function, as well as endothelial function, were further significantly less affected by electronic cigarette aerosols than conventional cigarette smoke. Molecular analysis demonstrated that E-vapor aerosols induce significantly smaller transcriptomic dysregulation in the heart and aorta compared with conventional cigarette smoke.
Collapse
Affiliation(s)
- Justyna Szostak
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Ee Tsin Wong
- Philip Morris International Research and development, Philip Morris International Research Laboratories, Singapore
| | - Bjoern Titz
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Tom Lee
- Philip Morris International Research and development, Philip Morris International Research Laboratories, Singapore
| | - Sin Kei Wong
- Philip Morris International Research and development, Philip Morris International Research Laboratories, Singapore
| | - Tiffany Low
- Philip Morris International Research and development, Philip Morris International Research Laboratories, Singapore
| | | | | | | | | | - Emmanuel Guedj
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Blaine Phillips
- Philip Morris International Research and development, Philip Morris International Research Laboratories, Singapore
| | - Patrice Leroy
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | | | - Yang Xiang
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Florian Martin
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Alain Sewer
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Arkadiusz Kuczaj
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Karsta Luettich
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Patrick Vanscheeuwijck
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris International Research and Development, Philip Morris Products, Neuchâtel, Switzerland
| |
Collapse
|
244
|
Hakkaart X, Liu Y, Hulst M, El Masoudi A, Peuscher E, Pronk J, van Gulik W, Daran-Lapujade P. Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO 2 levels. Biotechnol Bioeng 2020; 117:721-735. [PMID: 31654410 PMCID: PMC7028085 DOI: 10.1002/bit.27210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/12/2019] [Accepted: 10/22/2019] [Indexed: 12/21/2022]
Abstract
Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic‐acid yield and recovery include slow growth, low pH, and high CO2. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and combined impacts of low pH (3.0) and high CO2 (50%) on slow‐growing chemostat and retentostat cultures of the reference strain S. cerevisiae CEN.PK113‐7D. Combined exposure to low pH and high CO2 led to increased maintenance‐energy requirements and death rates in aerobic, glucose‐limited cultures. Further experiments showed that these effects were predominantly caused by low pH. Growth under ammonium‐limited, energy‐excess conditions did not aggravate or ameliorate these adverse impacts. Despite the absence of a synergistic effect of low pH and high CO2 on physiology, high CO2 strongly affected genome‐wide transcriptional responses to low pH. Interference of high CO2 with low‐pH signaling is consistent with low‐pH and high‐CO2 signals being relayed via common (MAPK) signaling pathways, notably the cell wall integrity, high‐osmolarity glycerol, and calcineurin pathways. This study highlights the need to further increase robustness of cell factories to low pH for carboxylic‐acid production, even in organisms that are already applied at industrial scale.
Collapse
Affiliation(s)
- Xavier Hakkaart
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Yaya Liu
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Mandy Hulst
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Anissa El Masoudi
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Eveline Peuscher
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Jack Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| |
Collapse
|
245
|
Chen D, Zhao X, Sui Z, Niu H, Chen L, Hu C, Xuan Q, Hou X, Zhang R, Zhou L, Li Y, Yuan H, Zhang Y, Wu J, Zhang L, Wu R, Piao HL, Xu G, Jia W. A multi-omics investigation of the molecular characteristics and classification of six metabolic syndrome relevant diseases. Am J Cancer Res 2020; 10:2029-2046. [PMID: 32089734 PMCID: PMC7019171 DOI: 10.7150/thno.41106] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 11/24/2019] [Indexed: 12/12/2022] Open
Abstract
Metabolic syndrome (MTS) is a cluster of concurrent metabolic abnormal conditions. MTS and its component metabolic diseases are heterogeneous and closely related, making their relationships complicated, thus hindering precision treatment. Methods: We collected seven groups of samples (group a: healthy individuals; group b: obesity; group c: MTS; group d: hyperglycemia, group e: hypertension, group f: hyperlipidemia; group g: type II diabetes, n=7 for each group). We examined the molecular characteristics of each sample by metabolomic, proteomic and peptidomic profiling analysis. The differential molecules (including metabolites, proteins and peptides) between each disease group and the healthy group were recognized by statistical analyses. Furthermore, a two-step clustering workflow which combines multi-omics and clinical information was used to redefine molecularly and clinically differential groups. Meanwhile, molecular, clinical, network and pathway based analyses were used to identify the group-specific biological features. Results: Both shared and disease-specific molecular profiles among the six types of diseases were identified. Meanwhile, the patients were stratified into three distinct groups which were different from original disease definitions but presented significant differences in glucose and lipid metabolism (Group 1: relatively favorable metabolic conditions; Group 2: severe dyslipidemia; Group 3: dysregulated insulin and glucose). Group specific biological signatures were also systematically described. The dyslipidemia group showed higher levels in multiple lipid metabolites like phosphatidylserine and phosphatidylcholine, and showed significant up-regulations in lipid and amino acid metabolism pathways. The glucose dysregulated group showed higher levels in many polypeptides from proteins contributing to immune response. The another group, with better glucose/lipid metabolism ability, showed higher levels in lipid regulating enzymes like the lecithin cholesterol acyltransferase and proteins involved in complement and coagulation cascades. Conclusions: This multi-omics based study provides a general view of the complex relationships and an alternative classification for various metabolic diseases where the cross-talk or compensatory mechanism between the immune and metabolism systems plays a critical role.
Collapse
|
246
|
Szostak J, Titz B, Schlage WK, Guedj E, Sewer A, Phillips B, Leroy P, Buettner A, Neau L, Trivedi K, Martin F, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J. Structural, functional, and molecular impact on the cardiovascular system in ApoE -/- mice exposed to aerosol from candidate modified risk tobacco products, Carbon Heated Tobacco Product 1.2 and Tobacco Heating System 2.2, compared with cigarette smoke. Chem Biol Interact 2020; 315:108887. [PMID: 31705857 DOI: 10.1016/j.cbi.2019.108887] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/14/2019] [Accepted: 10/28/2019] [Indexed: 12/26/2022]
Abstract
AIM To investigate the molecular, structural, and functional impact of aerosols from candidate modified risk tobacco products (cMRTP), the Carbon Heated Tobacco Product (CHTP) 1.2 and Tobacco Heating System (THS) 2.2, compared with that of mainstream cigarette smoke (CS) on the cardiovascular system of ApoE-/- mice. METHODS Female ApoE-/- mice were exposed to aerosols from THS 2.2 and CHTP 1.2 or to CS from the 3R4F reference cigarette for up to 6 months at matching nicotine concentrations. A Cessation and a Switching group (3 months exposure to 3R4F CS followed by filtered air or CHTP 1.2 for 3 months) were included. Cardiovascular effects were investigated by echocardiographic, histopathological, immunohistochemical, and transcriptomics analyses. RESULTS Continuous exposure to cMRTP aerosols did not affect atherosclerosis progression, heart function, left ventricular (LV) structure, or the cardiovascular transcriptome. Exposure to 3R4F CS triggered atherosclerosis progression, reduced systolic ejection fraction and fractional shortening, caused heart LV hypertrophy, and initiated significant dysregulation in the transcriptomes of the heart ventricle and thoracic aorta. Importantly, the structural, functional, and molecular changes caused by 3R4F CS were improved in the smoking cessation and switching groups. CONCLUSION Exposure to cMRTP aerosols lacked most of the CS exposure-related functional, structural, and molecular effects. Smoking cessation or switching to CHTP 1.2 aerosol caused similar recovery from the 3R4F CS effects in the ApoE-/- model, with no further acceleration of plaque progression beyond the aging-related rate.
Collapse
Affiliation(s)
- Justyna Szostak
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Walter K Schlage
- Biology Consultant, Max-Baermann-Str. 21, 51429, Bergisch Gladbach, Germany.
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Alain Sewer
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Blaine Phillips
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore.
| | - Patrice Leroy
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | | | - Laurent Neau
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Keyur Trivedi
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Florian Martin
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Patrick Vanscheeuwijck
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| |
Collapse
|
247
|
Comprehensive expression-based isoform biomarkers predictive of drug responses based on isoform co-expression networks and clinical data. Genomics 2020; 112:647-658. [DOI: 10.1016/j.ygeno.2019.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/21/2019] [Accepted: 04/23/2019] [Indexed: 11/19/2022]
|
248
|
Bongaarts A, van Scheppingen J, Korotkov A, Mijnsbergen C, Anink JJ, Jansen FE, Spliet WGM, den Dunnen WFA, Gruber VE, Scholl T, Samueli S, Hainfellner JA, Feucht M, Kotulska K, Jozwiak S, Grajkowska W, Buccoliero AM, Caporalini C, Giordano F, Genitori L, Coras R, Blümcke I, Krsek P, Zamecnik J, Meijer L, Scicluna BP, Schouten-van Meeteren AYN, Mühlebner A, Mills JD, Aronica E. The coding and non-coding transcriptional landscape of subependymal giant cell astrocytomas. Brain 2020; 143:131-149. [PMID: 31834371 PMCID: PMC6935755 DOI: 10.1093/brain/awz370] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is an autosomal dominantly inherited neurocutaneous disorder caused by inactivating mutations in TSC1 or TSC2, key regulators of the mechanistic target of rapamycin complex 1 (mTORC1) pathway. In the CNS, TSC is characterized by cortical tubers, subependymal nodules and subependymal giant cell astrocytomas (SEGAs). SEGAs may lead to impaired circulation of CSF resulting in hydrocephalus and raised intracranial pressure in patients with TSC. Currently, surgical resection and mTORC1 inhibitors are the recommended treatment options for patients with SEGA. In the present study, high-throughput RNA-sequencing (SEGAs n = 19, periventricular control n = 8) was used in combination with computational approaches to unravel the complexity of SEGA development. We identified 9400 mRNAs and 94 microRNAs differentially expressed in SEGAs compared to control tissue. The SEGA transcriptome profile was enriched for the mitogen-activated protein kinase (MAPK) pathway, a major regulator of cell proliferation and survival. Analysis at the protein level confirmed that extracellular signal-regulated kinase (ERK) is activated in SEGAs. Subsequently, the inhibition of ERK independently of mTORC1 blockade decreased efficiently the proliferation of primary patient-derived SEGA cultures. Furthermore, we found that LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4 and LAMTOR5 were overexpressed at both gene and protein levels in SEGA compared to control tissue. Taken together LAMTOR1-5 can form a complex, known as the 'Ragulator' complex, which is known to activate both mTORC1 and MAPK/ERK pathways. Overall, this study shows that the MAPK/ERK pathway could be used as a target for treatment independent of, or in combination with mTORC1 inhibitors for TSC patients. Moreover, our study provides initial evidence of a possible link between the constitutive activated mTORC1 pathway and a secondary driver pathway of tumour growth.
Collapse
Affiliation(s)
- Anika Bongaarts
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Anatoly Korotkov
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Caroline Mijnsbergen
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jasper J Anink
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Floor E Jansen
- Department of Pediatric Neurology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wim G M Spliet
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilfred F A den Dunnen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Victoria E Gruber
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Theresa Scholl
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Sharon Samueli
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | | | - Martha Feucht
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw, Poland
| | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw, Poland
- Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Wieslawa Grajkowska
- Department of Pathology, Children's Memorial Health Institute, Warsaw, Poland
| | | | | | - Flavio Giordano
- Department of Neurosurgery, Anna Meyer Children's Hospital, Florence, Italy
| | - Lorenzo Genitori
- Department of Neurosurgery, Anna Meyer Children's Hospital, Florence, Italy
| | - Roland Coras
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Pavel Krsek
- Department of Paediatric Neurology, Charles University, 2nd Faculty of Medicine, Motol University Hospital, Prague, Czech Republic
| | - Josef Zamecnik
- Department of Pathology and Molecular Medicine, Charles University, 2nd Faculty of Medicine, Motol University Hospital, Prague, Czech Republic
| | - Lisethe Meijer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine and Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Antoinette Y N Schouten-van Meeteren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Angelika Mühlebner
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - James D Mills
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), The Netherlands
| |
Collapse
|
249
|
Rajkumar AP, Bidkhori G, Shoaie S, Clarke E, Morrin H, Hye A, Williams G, Ballard C, Francis P, Aarsland D. Postmortem Cortical Transcriptomics of Lewy Body Dementia Reveal Mitochondrial Dysfunction and Lack of Neuroinflammation. Am J Geriatr Psychiatry 2020; 28:75-86. [PMID: 31327631 DOI: 10.1016/j.jagp.2019.06.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 01/13/2023]
Abstract
OBJECTIVE Prevalence of Lewy body dementias (LBD) is second only to Alzheimer's disease (AD) among people with neurodegenerative dementia. LBD cause earlier mortality, more intense neuropsychiatric symptoms, more caregivers' burden, and higher costs than AD. The molecular mechanisms underlying LBD are largely unknown. As advancing molecular level mechanistic understanding is essential for identifying reliable peripheral biomarkers and novel therapeutic targets for LBD, the authors aimed to identify differentially expressed genes (DEG), and dysfunctional molecular networks in postmortem LBD brains. METHODS The authors investigated the transcriptomics of postmortem anterior cingulate and dorsolateral prefrontal cortices of people with pathology-verified LBD using next-generation RNA-sequencing. The authors verified the identified DEG using high-throughput quantitative polymerase chain reactions. Functional implications of identified DEG and the consequent metabolic reprogramming were evaluated by Ingenuity pathway analyses, genome-scale metabolic modeling, reporter metabolite analyses, and in silico gene silencing. RESULTS The authors identified and verified 12 novel DEGs (MPO, SELE, CTSG, ALPI, ABCA13, GALNT6, SST, RBM3, CSF3, SLC4A1, OXTR, and RAB44) in LBD brains with genome-wide statistical significance. The authors documented statistically significant down-regulation of several cytokine genes. Identified dysfunctional molecular networks highlighted the contributions of mitochondrial dysfunction, oxidative stress, and immunosenescence toward neurodegeneration in LBD. CONCLUSION Our findings support that chronic microglial activation and neuroinflammation, well-documented in AD, are notably absent in LBD. The lack of neuroinflammation in LBD brains was corroborated by statistically significant down-regulation of several inflammatory markers. Identified DEGs, especially down-regulated inflammatory markers, may aid distinguishing LBD from AD, and their biomarker potential warrant further investigation.
Collapse
Affiliation(s)
- Anto P Rajkumar
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; Mental Health of Older Adults and Dementia Clinical Academic Group, South London and Maudsley NHS foundation Trust, London, UK.
| | - Gholamreza Bidkhori
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Emily Clarke
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | | | - Abdul Hye
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS foundation trust, London, UK
| | - Gareth Williams
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Clive Ballard
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; The Medical School, Exeter University, Exeter, UK
| | - Paul Francis
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Dag Aarsland
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; Mental Health of Older Adults and Dementia Clinical Academic Group, South London and Maudsley NHS foundation Trust, London, UK
| |
Collapse
|
250
|
Bergman A, Vitay D, Hellgren J, Chen Y, Nielsen J, Siewers V. Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome. FEMS Yeast Res 2019; 19:5423327. [PMID: 30924859 PMCID: PMC6755256 DOI: 10.1093/femsyr/foz027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/27/2019] [Indexed: 12/16/2022] Open
Abstract
Microbial conversion of biomass to fatty acids (FA) and products derived thereof is an attractive alternative to the traditional oleochemical production route from animal and plant lipids. This study examined if NADPH-costly FA biosynthesis could be enhanced by overexpressing the transcription factor Stb5 in Saccharomyces cerevisiae. Stb5 activates expression of multiple genes encoding enzymes within the pentose phosphate pathway (PPP) and other NADPH-producing reactions. Overexpression of STB5 led to a decreased growth rate and an increased free fatty acid (FFA) production during growth on glucose. The improved FFA synthetic ability in the glucose phase was shown to be independent of flux through the oxidative PPP. RNAseq analysis revealed that STB5 overexpression had wide-ranging effects on the transcriptome in the batch phase, and appeared to cause a counterintuitive phenotype with reduced flux through the oxidative PPP. During glucose limitation, when an increased NADPH supply is likely less harmful, an overall induction of the proposed target genes of Stb5 (eg. GND1/2, TAL1, ALD6, YEF1) was observed. Taken together, the strategy of utilizing STB5 overexpression to increase NADPH supply for reductive biosynthesis is suggested to have potential in strains engineered to have strong ability to consume excess NADPH, alleviating a potential redox imbalance.
Collapse
Affiliation(s)
- Alexandra Bergman
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden
| | - Dóra Vitay
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden
| | - John Hellgren
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden
| | - Yun Chen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, DK2800 Kgs. Lyngby, Denmark
| | - Verena Siewers
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE41296 Gothenburg, Sweden
| |
Collapse
|