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Du B, Zhang Y, Zhang P, Zhang M, Yu Z, Li L, Hou L, Wang Q, Zhang X, Zhang W. Joint metabolomics and transcriptomics analysis systematically reveal the impact of MYCN in neuroblastoma. Sci Rep 2024; 14:20155. [PMID: 39215128 PMCID: PMC11364762 DOI: 10.1038/s41598-024-71211-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
The limited understanding of the molecular mechanism underlying MYCN-amplified (MNA) neuroblastoma (NB) has hindered the identification of effective therapeutic targets for MNA NB, contributing to its higher mortality rate compared to MYCN non-amplified (non-MNA) NB. Therefore, a comprehensive analysis integrating metabolomics and transcriptomics was conducted to systematically investigate the MNA NB. Metabolomics analysis utilized plasma samples from 28 MNA NB patients and 68 non-MNA NB patients, while transcriptomics analysis employed tissue samples from 15 MNA NB patients and 37 non-MNA NB patients. Notably, joint metabolomics and transcriptomics analysis was performed. A total of 46 metabolites exhibited alterations, with 21 displaying elevated levels and 25 demonstrating reduced levels in MNA NB. In addition, 884 mRNAs in MNA NB showed significant changes, among which 766 mRNAs were higher and 118 mRNAs were lower. Joint-pathway analysis revealed three aberrant pathways involving glycerolipid metabolism, purine metabolism, and lysine degradation. This study highlights the substantial differences in metabolomics and transcriptomics between MNA NB and non-MNA NB, identifying three abnormal metabolic pathways that may serve as potential targets for understanding the molecular mechanisms underlying MNA NB.
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Affiliation(s)
- Bang Du
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Yingyu Zhang
- The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, Luoyang, 471003, China
| | - Pin Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Mengxin Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Zhidan Yu
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Lifeng Li
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Ligong Hou
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Qionglin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
| | - Xianwei Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
| | - Wancun Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
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2
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Gnimpieba EZ, Hartman TW, Do T, Zylla J, Aryal S, Haas SJ, Agany DDM, Gurung BDS, Doe V, Yosufzai Z, Pan D, Campbell R, Huber VC, Sani R, Gadhamshetty V, Lushbough C. Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities. Brief Bioinform 2024; 25:bbae429. [PMID: 39266450 PMCID: PMC11392556 DOI: 10.1093/bib/bbae429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 08/04/2024] [Accepted: 08/16/2024] [Indexed: 09/14/2024] Open
Abstract
In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype-phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners-even those with minimal knowledge in computer science-to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI's Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.
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Affiliation(s)
- Etienne Z Gnimpieba
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
| | - Timothy W Hartman
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
| | - Tuyen Do
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
| | - Jessica Zylla
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
| | - Shiva Aryal
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
| | - Samuel J Haas
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
| | - Diing D M Agany
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
| | - Bichar Dip Shrestha Gurung
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
| | - Valena Doe
- Google Cloud, 1900 Reston Metro Plaza, Reston, Virginia, 20190, United States
| | - Zelaikha Yosufzai
- Health Data and AI, Deloitte Consulting LLP, 1919 N Lynn St., Suite 1500, Arlington, Virginia, 22209, United States
| | - Daniel Pan
- Health Data and AI, Deloitte Consulting LLP, 1919 N Lynn St., Suite 1500, Arlington, Virginia, 22209, United States
| | - Ross Campbell
- Health Data and AI, Deloitte Consulting LLP, 1919 N Lynn St., Suite 1500, Arlington, Virginia, 22209, United States
| | - Victor C Huber
- Basic Biomedical Sciences Division, University of South Dakota, 414 E. Clark St, Vermillion, South Dakota, 57069, United States
| | - Rajesh Sani
- South Dakota School of Mines & Technology, 501 E. Saint Joseph St., Rapid City, South Dakota, 57701, United States
| | - Venkataramana Gadhamshetty
- South Dakota School of Mines & Technology, 501 E. Saint Joseph St., Rapid City, South Dakota, 57701, United States
| | - Carol Lushbough
- Biomedical Engineering Department, University of South Dakota, 4800 N. Career Ave., Suite 221, Sioux Falls, South Dakota, 57107, United States
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Choudhury P, Dasgupta S, Bhattacharyya P, Roychowdhury S, Chaudhury K. Understanding pulmonary hypertension: the need for an integrative metabolomics and transcriptomics approach. Mol Omics 2024; 20:366-389. [PMID: 38853716 DOI: 10.1039/d3mo00266g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Pulmonary hypertension (PH), characterised by mean pulmonary arterial pressure (mPAP) >20 mm Hg at rest, is a complex pathophysiological disorder associated with multiple clinical conditions. The high prevalence of the disease along with increased mortality and morbidity makes it a global health burden. Despite major advances in understanding the disease pathophysiology, much of the underlying complex molecular mechanism remains to be elucidated. Lack of a robust diagnostic test and specific therapeutic targets also poses major challenges. This review provides a comprehensive update on the dysregulated pathways and promising candidate markers identified in PH patients using the transcriptomics and metabolomics approach. The review also highlights the need of using an integrative multi-omics approach for obtaining insight into the disease at a molecular level. The integrative multi-omics/pan-omics approach envisaged to help in bridging the gap from genotype to phenotype is outlined. Finally, the challenges commonly encountered while conducting omics-driven studies are also discussed.
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Affiliation(s)
- Priyanka Choudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
| | - Sanjukta Dasgupta
- Department of Biotechnology, Brainware University, Barasat, West Bengal, India
| | | | | | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
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Ru M, He J, Bai Y, Zhang K, Shi Q, Gao F, Wang Y, Li B, Shen L. Integration of Proteomic and Metabolomic Data Reveals the Lipid Metabolism Disorder in the Liver of Rats Exposed to Simulated Microgravity. Biomolecules 2024; 14:682. [PMID: 38927087 PMCID: PMC11201887 DOI: 10.3390/biom14060682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Long-term exposure to microgravity is considered to cause liver lipid accumulation, thereby increasing the risk of non-alcoholic fatty liver disease (NAFLD) among astronauts. However, the reasons for this persistence of symptoms remain insufficiently investigated. In this study, we used tandem mass tag (TMT)-based quantitative proteomics techniques, as well as non-targeted metabolomics techniques based on liquid chromatography-tandem mass spectrometry (LC-MS/MS), to comprehensively analyse the relative expression levels of proteins and the abundance of metabolites associated with lipid accumulation in rat liver tissues under simulated microgravity conditions. The differential analysis revealed 63 proteins and 150 metabolites between the simulated microgravity group and the control group. By integrating differentially expressed proteins and metabolites and performing pathway enrichment analysis, we revealed the dysregulation of major metabolic pathways under simulated microgravity conditions, including the biosynthesis of unsaturated fatty acids, linoleic acid metabolism, steroid hormone biosynthesis and butanoate metabolism, indicating disrupted liver metabolism in rats due to weightlessness. Finally, we examined differentially expressed proteins associated with lipid metabolism in the liver of rats exposed to stimulated microgravity. These findings contribute to identifying the key molecules affected by microgravity and could guide the design of rational nutritional or pharmacological countermeasures for astronauts.
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Affiliation(s)
- Mengyao Ru
- School of Basic Medicine, Yan’an University, Yan’an 716000, China; (M.R.); (K.Z.)
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi’an 710032, China;
| | - Jun He
- Department of Anesthesiology, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an 710018, China;
| | - Yungang Bai
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi’an 710032, China; (Y.B.); (Y.W.)
| | - Kun Zhang
- School of Basic Medicine, Yan’an University, Yan’an 716000, China; (M.R.); (K.Z.)
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi’an 710032, China;
| | - Qianqian Shi
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi’an 710032, China;
- School of Life Sciences, Yan’an University, Yan’an 716000, China
| | - Fang Gao
- Department of Neurobiology, The Fourth Military Medical University, Xi’an 710032, China;
| | - Yunying Wang
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi’an 710032, China; (Y.B.); (Y.W.)
| | - Baoli Li
- Yan’an Key Laboratory of Microbial Drug Innovation and Transformation, Yan’an University, Yan’an 716000, China
| | - Lan Shen
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi’an 710032, China;
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5
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Liu Z, Zhu H, Zhao J, Yu L, Que S, Xu J, Geng L, Zhou L, Valenti L, Zheng S. Multi-omics analysis reveals a crosstalk between ferroptosis and peroxisomes on steatotic graft failure after liver transplantation. MedComm (Beijing) 2024; 5:e588. [PMID: 38868330 PMCID: PMC11167151 DOI: 10.1002/mco2.588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 06/14/2024] Open
Abstract
To identify the mechanism underlying macrosteatosis (MaS)-related graft failure (GF) in liver transplantation (LT) by multi-omics network analysis. The transcriptome and metabolome were assayed in graft and recipient plasma in discovery (n = 68) and validation (n = 89) cohorts. Differentially expressed molecules were identified by MaS and GF status. Transcriptional regulatory networks were generated to explore the mechanism for MaS-related inferior post-transplant prognosis. The differentially expressed molecules associated with MaS and GF were enriched in ferroptosis and peroxisome-related pathways. Core features of MaS-related GF were presented on decreased transferrin and impaired anti-oxidative capacity dependent upon dysregulation of transcription factors hepatocyte nuclear factor 4A (HNF4A) and hypoxia-inducible factor 1A (HIF1A). Furthermore, miR-362-3p and miR-299-5p inhibited transferrin and HIF1A expression, respectively. Lower M2 macrophages but higher memory CD4 T cells were observed in MaS-related GF cases. These results were validated in clinical specimens and cellular models. Systemic analysis of multi-omics data depicted a panorama of biological pathways deregulated in MaS-related GF. Transcriptional regulatory networks centered on transferrin and anti-oxidant responses were associated with poor MaS graft quality, qualifying as potential targets to improve prognosis of patients after LT.
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Affiliation(s)
- Zhengtao Liu
- Shulan International Medical CollegeZhejiang Shuren UniversityHangzhouChina
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang ProvinceShulan International Medical CollegeZhejiang Shuren UniversityHangzhouChina
- NHC Key Laboratory of Combined Multi‐Organ TransplantationKey Laboratory of the Diagnosis and Treatment of Organ TransplantationCAMS, First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Organ TransplantationFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Shulan Hospital (Hangzhou)HangzhouChina
| | - Hai Zhu
- NHC Key Laboratory of Combined Multi‐Organ TransplantationKey Laboratory of the Diagnosis and Treatment of Organ TransplantationCAMS, First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Organ TransplantationFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Department of Hepatobiliary SurgeryFirst Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Junsheng Zhao
- Shulan International Medical CollegeZhejiang Shuren UniversityHangzhouChina
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang ProvinceShulan International Medical CollegeZhejiang Shuren UniversityHangzhouChina
| | - Lu Yu
- Shulan International Medical CollegeZhejiang Shuren UniversityHangzhouChina
- Shulan Hospital (Hangzhou)HangzhouChina
- School of MedicineZhejiang Chinese Medical UniversityHangzhouChina
| | | | - Jun Xu
- Division of Hepatobiliary and Pancreatic SurgeryDepartment of SurgeryFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Lei Geng
- Division of Hepatobiliary and Pancreatic SurgeryDepartment of SurgeryFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi‐Organ TransplantationKey Laboratory of the Diagnosis and Treatment of Organ TransplantationCAMS, First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Organ TransplantationFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Division of Hepatobiliary and Pancreatic SurgeryDepartment of SurgeryFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Luca Valenti
- Department of Pathophysiology and TransplantationUniversità degli Studi di MilanoMilanItaly
- Transfusion Medicine UnitFondazione IRCCS Ca’ Granda Ospedale Maggiore PoliclinicoMilanItaly
- Biological Resource Center UnitFondazione IRCCS Ca’ Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Shusen Zheng
- Shulan International Medical CollegeZhejiang Shuren UniversityHangzhouChina
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang ProvinceShulan International Medical CollegeZhejiang Shuren UniversityHangzhouChina
- NHC Key Laboratory of Combined Multi‐Organ TransplantationKey Laboratory of the Diagnosis and Treatment of Organ TransplantationCAMS, First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Organ TransplantationFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Shulan Hospital (Hangzhou)HangzhouChina
- Division of Hepatobiliary and Pancreatic SurgeryDepartment of SurgeryFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
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Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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Wang ZX, Li PP, Jia YJ, Wen LX, Tang ZS, Wang YP, Cui F, Hu FD. Integrated metabolomic and transcriptomic analysis of triterpenoid accumulation in the roots of Codonopsis pilosula var. modesta (Nannf.) L.T.Shen at different altitudes. PHYTOCHEMICAL ANALYSIS : PCA 2024. [PMID: 38764207 DOI: 10.1002/pca.3362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/27/2024] [Accepted: 03/25/2024] [Indexed: 05/21/2024]
Abstract
INTRODUCTION Codonopsis Radix is a beneficial traditional Chinese medicine, and triterpenoid are the major bioactive constituents. Codonopsis pilosula var. modesta (Nannf.) L.T.Shen (CPM) is a precious variety of Codonopsis Radix, which is distributed at high mountain areas. The environment plays an important role in the synthesis and metabolism of active ingredients in medicinal plants, but there is no report elaborating on the effect of altitude on terpenoid metabolites accumulation in CPM. OBJECTIVES This study aims to analyse the effects of altitude on triterpenoid biosynthetic pathways and secondary metabolite accumulation in CPM. MATERIAL AND METHODS The untargeted metabolomics based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 10 triterpenoids based on ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) method were analysed at the low-altitude (1480 m) and high-altitude (2300 m) CPM fresh roots. The transcriptome based on high-throughput sequencing technology were combined to analyse the different altitude CPM triterpenoid biosynthetic pathways. RESULTS A total of 17,351 differentially expressed genes (DEGs) and 55 differentially accumulated metabolites (DAMs) were detected from the different altitude CPM, and there are significant differences in the content of the 10 triterpenoids. The results of transcriptome study showed that CPM could significantly up-regulate the gene expression levels of seven key enzymes in the triterpenoid biosynthetic pathway. CONCLUSIONS The CPM at high altitude is more likely to accumulate triterpenes than those at low altitude, which was related to the up-regulation of the gene expression levels of seven key enzymes. These results expand our understanding of how altitude affects plant metabolite biosynthesis.
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Affiliation(s)
- Zi-Xia Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Codonopsis Radix Research Institute in Gansu Province, Lanzhou, China
| | - Peng-Peng Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Codonopsis Radix Research Institute in Gansu Province, Lanzhou, China
| | - Yan-Jun Jia
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Codonopsis Radix Research Institute in Gansu Province, Lanzhou, China
| | - Long-Xia Wen
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Codonopsis Radix Research Institute in Gansu Province, Lanzhou, China
| | - Zhuo-Shi Tang
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Codonopsis Radix Research Institute in Gansu Province, Lanzhou, China
| | - Yan-Ping Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Codonopsis Radix Research Institute in Gansu Province, Lanzhou, China
| | - Fang Cui
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Codonopsis Radix Research Institute in Gansu Province, Lanzhou, China
| | - Fang-Di Hu
- School of Pharmacy, Lanzhou University, Lanzhou, China
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, China
- Codonopsis Radix Research Institute in Gansu Province, Lanzhou, China
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8
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Yan Q, Zhang G, Zhang X, Huang L. A Review of Transcriptomics and Metabolomics in Plant Quality and Environmental Response: From Bibliometric Analysis to Science Mapping and Future Trends. Metabolites 2024; 14:272. [PMID: 38786749 PMCID: PMC11123105 DOI: 10.3390/metabo14050272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Transcriptomics and metabolomics offer distinct advantages in investigating the differentially expressed genes and cellular entities that have the greatest influence on end-phenotype, making them crucial techniques for studying plant quality and environmental responses. While numerous relevant articles have been published, a comprehensive summary is currently lacking. This review aimed to understand the global and longitudinal research trends of transcriptomics and metabolomics in plant quality and environmental response (TMPQE). Utilizing bibliometric methods, we presented a comprehensive science mapping of the social structure, conceptual framework, and intellectual foundation of TMPQE. We uncovered that TMPQE research has been categorized into three distinct stages since 2020. A citation analysis of the 29 most cited articles, coupled with a content analysis of recent works (2020-2023), highlight five potential research streams in plant quality and environmental responses: (1) biosynthetic pathways, (2) abiotic stress, (3) biotic stress, (4) development and ripening, and (5) methodologies and tools. Current trends and future directions are shaped by technological advancements, species diversity, evolving research themes, and an environmental ecology focus. Overall, this review provides a novel and comprehensive perspective to understand the longitudinal trend on TMPQE.
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Affiliation(s)
| | | | | | - Linfang Huang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, HaiDian District, Beijing 100193, China; (Q.Y.); (G.Z.); (X.Z.)
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9
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Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024; 100:fiae058. [PMID: 38653719 PMCID: PMC11067971 DOI: 10.1093/femsec/fiae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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10
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Marie L, Breitler JC, Bamogo PKA, Bordeaux M, Lacombe S, Rios M, Lebrun M, Boulanger R, Lefort E, Nakamura S, Motoyoshi Y, Mieulet D, Campa C, Legendre L, Bertrand B. Combined sensory, volatilome and transcriptome analyses identify a limonene terpene synthase as a major contributor to the characteristic aroma of a Coffea arabica L. specialty coffee. BMC PLANT BIOLOGY 2024; 24:238. [PMID: 38566027 PMCID: PMC10988958 DOI: 10.1186/s12870-024-04890-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND The fruity aromatic bouquet of coffee has attracted recent interest to differentiate high value market produce as specialty coffee. Although the volatile compounds present in green and roasted coffee beans have been extensively described, no study has yet linked varietal molecular differences to the greater abundance of specific substances and support the aroma specificity of specialty coffees. RESULTS This study compared four Arabica genotypes including one, Geisha Especial, suggested to generate specialty coffee. Formal sensory evaluations of coffee beverages stressed the importance of coffee genotype in aroma perception and that Geisha Especial-made coffee stood out by having fine fruity, and floral, aromas and a more balanced acidity. Comparative SPME-GC-MS analyses of green and roasted bean volatile compounds indicated that those of Geisha Especial differed by having greater amounts of limonene and 3-methylbutanoic acid in agreement with the coffee cup aroma perception. A search for gene ontology differences of ripening beans transcriptomes of the four varieties revealed that they differed by metabolic processes linked to terpene biosynthesis due to the greater gene expression of prenyl-pyrophosphate biosynthetic genes and terpene synthases. Only one terpene synthase (CaTPS10-like) had an expression pattern that paralleled limonene loss during the final stage of berry ripening and limonene content in the studied four varieties beans. Its functional expression in tobacco leaves confirmed its functioning as a limonene synthase. CONCLUSIONS Taken together, these data indicate that coffee variety genotypic specificities may influence ripe berry chemotype and final coffee aroma unicity. For the specialty coffee variety Geisha Especial, greater expression of terpene biosynthetic genes including CaTPS10-like, a limonene synthase, resulted in the greater abundance of limonene in green beans, roasted beans and a unique citrus note of the coffee drink.
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Affiliation(s)
- Lison Marie
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France.
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France.
| | - Jean-Christophe Breitler
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
| | - Pingdwende Kader Aziz Bamogo
- PHIM (Plant Health Institute of Montpellier), University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, Montpellier, F-34398, France
| | | | - Séverine Lacombe
- PHIM (Plant Health Institute of Montpellier), University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Maëlle Rios
- PHIM (Plant Health Institute of Montpellier), University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Marc Lebrun
- CIRAD, UMR QualiSud, Montpellier, F-34398, France
- QualiSud, University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, University of La Réunion, University of Avignon, Montpellier, F-34398, France
| | - Renaud Boulanger
- CIRAD, UMR QualiSud, Montpellier, F-34398, France
- QualiSud, University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, University of La Réunion, University of Avignon, Montpellier, F-34398, France
| | - Eveline Lefort
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
| | - Sunao Nakamura
- Research Institute, Suntory Global Innovation Center Limited, 8-1-1, Seika-dai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Yudai Motoyoshi
- Research Institute, Suntory Global Innovation Center Limited, 8-1-1, Seika-dai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Delphine Mieulet
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
| | - Claudine Campa
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
| | - Laurent Legendre
- INRAE, UR 1115 Plantes et Systèmes de Culture Horticoles, Site Agroparc, Avignon, 84914, France
| | - Benoît Bertrand
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
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11
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Hou C, Song X, Xiong Z, Wang G, Xia Y, Ai L. Investigating the Role of β-Disodium Glycerophosphate and Urea in Promoting Growth of Streptococcus thermophilus from Omics-Integrated Genome-Scale Models. Foods 2024; 13:1006. [PMID: 38611312 PMCID: PMC11011449 DOI: 10.3390/foods13071006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
This study investigates the impact of urea and β-GP on the growth of Streptococcus thermophilus S-3, a bacterium commonly used in industrial fermentation processes. Through a series of growth experiments, transcriptome, metabolome, and omics-based analyses, the research demonstrates that both urea and β-GP can enhance the biomass of S. thermophilus, with urea showing a more significant effect. The optimal urea concentration for growth was determined to be 3 g/L in M17 medium. The study also highlights the metabolic pathways influenced by urea and β-GP, particularly the galactose metabolism pathway, which is crucial for cell growth when lactose is the substrate. The integration of omics data into the genome-scale metabolic model of S. thermophilus, iCH502, allowed for a more accurate prediction of metabolic fluxes and growth rates. The study concludes that urea can serve as a viable substitute for β-GP in the cultivation of S. thermophilus, offering potential cost and efficiency benefits in industrial fermentation processes. The findings are supported by validation experiments with 11 additional strains of S. thermophilus, which showed increased biomass in UM17 medium.
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Affiliation(s)
| | | | | | | | | | - Lianzhong Ai
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; (C.H.); (X.S.); (Z.X.); (G.W.); (Y.X.)
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12
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Zhou Y, Li F, Fu K, Zhang Y, Zheng N, Tang H, Xu Z, Luo L, Han J, Yang L, Zhou B. Bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate Enhances foxo1-Mediated Lipophagy to Remodel Lipid Metabolism in Zebrafish Liver. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4581-4593. [PMID: 38422554 DOI: 10.1021/acs.est.4c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
An emerging environmental contaminant, bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate (TBPH), can bioaccumulate in the liver and affect hepatic lipid metabolism. However, the in-depth mechanism has yet to be comprehensively explored. In this study, we utilized transgenic zebrafish Tg (Apo14: GFP) to image the interference of TBPH on zebrafish liver development and lipid metabolism at the early development stage. Using integrated lipidomic and transcriptomic analyses to profile the lipid remodeling effect, we uncovered the potential effects of TBPH on lipophagy-related signaling pathways in zebrafish larvae. Decreased lipid contents accompanied by enhanced lipophagy were confirmed by the measurements of Oil Red O staining and transmission electron microscopy in liver tissues. Particularly, the regulatory role of the foxo1 factor was validated via its transcriptional inhibitor. Double immunofluorescence staining integrated with biochemical analysis indicated that the enhanced lipophagy and mitochondrial fatty acid oxidation induced by TBPH were reversed by the foxo1 inhibitor. To summarize, our study reveals, for the first time, the essential role of foxo1-mediated lipophagy in TBPH-induced lipid metabolic disorders and hepatoxicity, providing new insights for metabolic disease studies and ecological health risk assessment of TBPH.
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Affiliation(s)
- Yuxi Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fan Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiyu Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yindan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Zheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijia Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Zhixiang Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Lijun Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Jian Han
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Lihua Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Bingsheng Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Zhao B, Suo L, Wu Y, Chen T, Tulafu H, Lu Q, Liu W, Sammad A, Wu C, Fu X. Stress adaptation in Tibetan cashmere goats is governed by inherent metabolic differences and manifested through variable cashmere phenotypes. Genomics 2024; 116:110801. [PMID: 38286347 DOI: 10.1016/j.ygeno.2024.110801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/17/2023] [Accepted: 01/25/2024] [Indexed: 01/31/2024]
Abstract
Tibetan cashmere goats are not only served as a valuable model for studying adaptation to hypoxia and high-altitude conditions but also playing a pivotal role in bolstering local economies through the provision of premium quality cashmere yarn. In this study, we performed an integration and network analysis of metabolomic, transcriptomic and proteomic to elucidate the role of differentially expressed genes, important metabolites, and relevant cellular and metabolic pathways between the fine (average 12.04 ± 0.03 μm of mean fiber diameter) and coarse cashmere (average 14.88 ± 0.05 μm of mean fber diameter) producing by Tibetan cashmere goats. We identified a distinction of 56 and 71 differential metabolites (DMs) between the F and C cashmere groups under positive and negative ion modes, respectively. The KEGG pathway enrichment analysis of these DMs highlighted numerous pathways predominantly involved in amino acid and protein metabolism, as indicated by the finding that the most impactful pathway was the mammalian target of rapamycin (mTOR) signalling pathway. In the F group, we identified a distinctive metabolic profile where amino acid metabolites including serine, histidine, asparagine, glutamic acid, arginine, valine, aspartic acid, tyrosine, and methionine were upregulated, while lysine, isoleucine, glutamine, tryptophan, and threonine were downregulated. The regulatory network and gene co-expression network revealed crucial genes, metabolites, and metabolic pathways. The integrative omics analysis revealed a high enrichment of several pathways, notably encompassing protein digestion and absorption, sphingolipid signalling, and the synaptic vesicle cycle. Within the sphere of our integrative analysis, DNMT3B was identified as a paramount gene, intricately associated with significant proteins such as HMCN1, CPB2, GNG12, and LRP1. Our present study delineated the molecular underpinnings governing the variations in cashmere characteristics by conducting comprehensive analyses across metabolomic, transcriptomic, and proteomic dimensions. This research provided newly insights into the mechanisms regulating cashmere traits and facilitated the advancement of selective breeding programs aimed at cultivating high-quality superfine Tibetan cashmere goats.
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Affiliation(s)
- Bingru Zhao
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi Xinjiang 830011, China
| | - Langda Suo
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850009, China
| | - Yujiang Wu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850009, China
| | - Tong Chen
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi Xinjiang 830011, China
| | - Hanikezi Tulafu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi Xinjiang 830011, China
| | - Qingwei Lu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi Xinjiang 830011, China; College of Animal Science, Xinjiang Agricultural University, Urumqi Xinjiang 830052, China
| | - Wenna Liu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi Xinjiang 830011, China; College of Animal Science, Xinjiang Agricultural University, Urumqi Xinjiang 830052, China
| | - Abdul Sammad
- College of Animal Sciences and Technology, China Agricultural University, Beijing 100193, China
| | - Cuiling Wu
- Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang/ International Center for the Collaborative Management of Cross-border Pest in Central Asia College of Life Sciences, School of Life Sciences, Xinjiang Normal University, Urumqi Xinjiang 830017, China.
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi Xinjiang 830011, China.
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14
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Coussement L, Van Criekinge W, De Meyer T. Quantitative transcriptomic and epigenomic data analysis: a primer. BIOINFORMATICS ADVANCES 2024; 4:vbae019. [PMID: 38586118 PMCID: PMC10997052 DOI: 10.1093/bioadv/vbae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 04/09/2024]
Abstract
The advent of microarray and second generation sequencing technology has revolutionized the field of molecular biology, allowing researchers to quantitatively assess transcriptomic and epigenomic features in a comprehensive and cost-efficient manner. Moreover, technical advancements have pushed the resolution of these sequencing techniques to the single cell level. As a result, the bottleneck of molecular biology research has shifted from the bench to the subsequent omics data analysis. Even though most methodologies share the same general strategy, state-of-the-art literature typically focuses on data type specific approaches and already assumes expert knowledge. Here, however, we aim at providing conceptual insight in the principles of genome-wide quantitative transcriptomic and epigenomic (including open chromatin assay) data analysis by describing a generic workflow. By starting from a general framework and its assumptions, the need for alternative or additional data-analytical solutions when working with specific data types becomes clear, and are hence introduced. Thus, we aim to enable readers with basic omics expertise to deepen their conceptual and statistical understanding of general strategies and pitfalls in omics data analysis and to facilitate subsequent progression to more specialized literature.
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Affiliation(s)
- Louis Coussement
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, 9000, Belgium
| | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, 9000, Belgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, 9000, Belgium
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15
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Xie Z, Liu J, Xie T, Liu P, Hui X, Zhang Q, Xiao X. Integration of proteomics and metabolomics reveals energy and metabolic alterations induced by glucokinase (GCK) partial inactivation in hepatocytes. Cell Signal 2024; 114:111009. [PMID: 38092300 DOI: 10.1016/j.cellsig.2023.111009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 01/01/2024]
Abstract
AIMS Glucokinase (GCK) acts as the glucose sensor in maintaining glucose homeostasis. The inactivating mutation of the GCK gene leads to glucokinase-maturity onset diabetes of the young (GCK-MODY). This study aims to gain further insights into the molecular alterations triggered by GCK partial inactivation in hepatocytes, potentially underlying the favorable prognosis of GCK-MODY. MAIN METHODS A GCK knockdown HepG2 cell model was established, and the integration of proteomics and metabolomics was used to gain a comprehensive understanding of the molecular pathway changes caused by GCK inactivation in the liver. KEY FINDINGS Proteomic analysis identified 257 differential proteins. KEGG pathway enrichment analysis showed that protein expression changes in the GCK knockdown group were significantly enriched in central carbon metabolism, the TCA cycle, amino acid metabolism and the oxidative phosphorylation pathway. Among them, enzymes in the TCA cycle (PC, IDH2, SDH) were significantly downregulated in GCK-knockdown group. Targeted metabolomics revealed that in the GCK knockdown hepatocytes, TCA cycle intermediates were significantly decreased, including pyruvate, oxaloacetate, citrate and succinic acid, and three metabolites increased including glycine, betaine and homocysteine. These metabolic alterations in turn reduced the accumulation of reactive oxygen species in GCK knockdown hepatocytes. Correlation analysis indicated that TCA cycle metabolites were positively correlated with proteins involved in the TCA cycle, carbon metabolism, glycolysis, Ras signaling, fibrosis and inflammation. SIGNIFICANCE In conclusion, GCK knockdown reduced TCA cycle flux and oxidative stress in hepatocytes by influencing the levels of key transcription factors and enzymes, providing a comprehensive understanding of the effects of GCK partial inactivation on liver metabolism and molecular mechanisms.
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Affiliation(s)
- Ziyan Xie
- China Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jieying Liu
- China Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China; Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Ting Xie
- China Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China; Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Peng Liu
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Xiangyi Hui
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Qian Zhang
- China Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xinhua Xiao
- China Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China.
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16
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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17
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Wishart DS, Kruger R, Sivakumaran A, Harford K, Sanford S, Doshi R, Khetarpal N, Fatokun O, Doucet D, Zubkowski A, Jackson H, Sykes G, Ramirez-Gaona M, Marcu A, Li C, Yee K, Garros C, Rayat D, Coleongco J, Nandyala T, Gautam V, Oler E. PathBank 2.0-the pathway database for model organism metabolomics. Nucleic Acids Res 2024; 52:D654-D662. [PMID: 37962386 PMCID: PMC10767802 DOI: 10.1093/nar/gkad1041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
PathBank (https://pathbank.org) and its predecessor database, the Small Molecule Pathway Database (SMPDB), have been providing comprehensive metabolite pathway information for the metabolomics community since 2010. Over the past 14 years, these pathway databases have grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in computing technology. This year's update, PathBank 2.0, brings a number of important improvements and upgrades that should make the database more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of primary or canonical pathways (from 1720 to 6951); (ii) a massive increase in the total number of pathways (from 110 234 to 605 359); (iii) significant improvements to the quality of pathway diagrams and pathway descriptions; (iv) a strong emphasis on drug metabolism and drug mechanism pathways; (v) making most pathway images more slide-compatible and manuscript-compatible; (vi) adding tools to support better pathway filtering and selecting through a more complete pathway taxonomy; (vii) adding pathway analysis tools for visualizing and calculating pathway enrichment. Many other minor improvements and updates to the content, the interface and general performance of the PathBank website have also been made. Overall, we believe these upgrades and updates should greatly enhance PathBank's ease of use and its potential applications for interpreting metabolomics data.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ray Kruger
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Aadhavya Sivakumaran
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Karxena Harford
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Selena Sanford
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Rahil Doshi
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Nitya Khetarpal
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Omolola Fatokun
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Daphnee Doucet
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Ashley Zubkowski
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Hayley Jackson
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Gina Sykes
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Miguel Ramirez-Gaona
- Department of Plant Breeding, Wageningen University and Research, 6708 PBWageningen, Gelderland, Netherlands
| | - Ana Marcu
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Carin Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Kristen Yee
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Christiana Garros
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Dorsa Yahya Rayat
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Jeanne Coleongco
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Tharuni Nandyala
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Eponine Oler
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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18
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Zhang W, Zhang M, Sun M, Hu M, Yu M, Sun J, Zhang X, Du B. Metabolomics-transcriptomics joint analysis: unveiling the dysregulated cell death network and developing a diagnostic model for high-grade neuroblastoma. Front Immunol 2024; 14:1345734. [PMID: 38239355 PMCID: PMC10794662 DOI: 10.3389/fimmu.2023.1345734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/14/2023] [Indexed: 01/22/2024] Open
Abstract
High-grade neuroblastoma (HG-NB) exhibits a significantly diminished survival rate in comparison to low-grade neuroblastoma (LG-NB), primarily attributed to the mechanism of HG-NB is unclear and the lacking effective therapeutic targets and diagnostic model. Therefore, the current investigation aims to study the dysregulated network between HG-NB and LG-NB based on transcriptomics and metabolomics joint analysis. Meanwhile, a risk diagnostic model to distinguish HG-NB and LG-NB was also developed. Metabolomics analysis was conducted using plasma samples obtained from 48 HG-NB patients and 36 LG-NB patients. A total of 39 metabolites exhibited alterations, with 20 showing an increase and 19 displaying a decrease in HG-NB. Additionally, transcriptomics analysis was performed on NB tissue samples collected from 31 HG-NB patients and 20 LG-NB patients. Results showed that a significant alteration was observed in a total of 1,199 mRNAs in HG-NB, among which 893 were upregulated while the remaining 306 were downregulated. In particular, the joint analysis of both omics data revealed three aberrant pathways, namely the cAMP signaling pathway, PI3K-Akt signaling pathway, and TNF signaling pathway, which were found to be associated with cell death. Notably, a diagnostic model for HG-NB risk classification was developed based on the genes MGST1, SERPINE1, and ERBB3 with an area under the receiver operating characteristic curve of 0.915. In the validation set, the sensitivity and specificity were determined to be 75.0% and 80.0%, respectively.
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Affiliation(s)
- Wancun Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Mengxin Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Meng Sun
- Henan Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Minghui Hu
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Muchun Yu
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Jushan Sun
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xianwei Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Bang Du
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
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19
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Yang Z, Chen W, Jia T, Shi H, Sun D. Integrated Transcriptomic and Metabolomic Analyses Identify Critical Genes and Metabolites Associated with Seed Vigor of Common Wheat. Int J Mol Sci 2023; 25:526. [PMID: 38203695 PMCID: PMC10779259 DOI: 10.3390/ijms25010526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Seed aging is a common physiological phenomenon during storage which has a great impact on seed quality. An in-depth analysis of the physiological and molecular mechanisms of wheat seed aging is of great significance for cultivating high-vigor wheat varieties. This study reveals the physiological mechanisms of wheat seed aging in two cultivars differing in seed vigor, combining metabolome and transcriptome analyses. Differences between cultivars were examined based on metabolomic differential analysis. Artificial aging had a significant impact on the metabolism of wheat seeds. A total of 7470 (3641 upregulated and 3829 downregulated) DEGs were detected between non-aging HT and LT seeds; however, 10,648 (4506 up and 6142 down) were detected between the two cultivars after aging treatment. Eleven, eight, and four key metabolic-related gene families were identified in the glycolysis/gluconeogenesis and TCA cycle pathways, starch and sucrose metabolism pathways, and galactose metabolism pathways, respectively. In addition, 111 up-regulated transcription factor genes and 85 down-regulated transcription factor genes were identified in the LT 48h group. A total of 548 metabolites were detected across all samples. Cultivar comparisons between the non-aged groups and aged groups revealed 46 (30 upregulated and 16 downregulated) and 62 (38 upregulated and 24 downregulated) DIMs, respectively. Network analysis of the metabolites indicated that glucarate O-phosphoric acid, L-methionine sulfoxide, isocitric acid, and Gln-Gly might be the most crucial DIMs between HT and LT. The main related metabolites were enriched in pathways such as glyoxylate and dicarboxylate metabolism, biosynthesis of secondary metabolites, fatty acid degradation, etc. However, metabolites that exhibited differences between cultivars were mainly enriched in carbon metabolism, the TCA cycle, etc. Through combined metabolome and transcriptome analyses, it was found that artificial aging significantly affected glycolysis/gluconeogenesis, pyruvate metabolism, and glyoxylate and dicarboxylate metabolism, which involved key genes such as ACS, F16P2, and PPDK1. We thus speculate that these genes may be crucial in regulating physiological changes in seeds during artificial aging. In addition, an analysis of cultivar differences identified pathways related to amino acid and polypeptide metabolism, such as cysteine and methionine metabolism, glutathione metabolism, and amino sugar and nucleotide sugar metabolism, involving key genes such as BCAT3, CHI1, GAUT1, and GAUT4, which may play pivotal roles in vigor differences between cultivars.
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Affiliation(s)
- Zhenrong Yang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Z.Y.); (T.J.); (H.S.)
| | - Weiguo Chen
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Tianxiang Jia
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Z.Y.); (T.J.); (H.S.)
| | - Huawei Shi
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Z.Y.); (T.J.); (H.S.)
| | - Daizhen Sun
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Z.Y.); (T.J.); (H.S.)
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20
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Na AY, Lee H, Min EK, Paudel S, Choi SY, Sim H, Liu KH, Kim KT, Bae JS, Lee S. Novel Time-dependent Multi-omics Integration in Sepsis-associated Liver Dysfunction. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1101-1116. [PMID: 37084954 PMCID: PMC11082264 DOI: 10.1016/j.gpb.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/03/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
The recently developed technologies that allow the analysis of each single omics have provided an unbiased insight into ongoing disease processes. However, it remains challenging to specify the study design for the subsequent integration strategies that can associate sepsis pathophysiology and clinical outcomes. Here, we conducted a time-dependent multi-omics integration (TDMI) in a sepsis-associated liver dysfunction (SALD) model. We successfully deduced the relation of the Toll-like receptor 4 (TLR4) pathway with SALD. Although TLR4 is a critical factor in sepsis progression, it is not specified in single-omics analyses but only in the TDMI analysis. This finding indicates that the TDMI-based approach is more advantageous than single-omics analyses in terms of exploring the underlying pathophysiological mechanism of SALD. Furthermore, TDMI-based approach can be an ideal paradigm for insightful biological interpretations of multi-omics datasets that will potentially reveal novel insights into basic biology, health, and diseases, thus allowing the identification of promising candidates for therapeutic strategies.
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Affiliation(s)
- Ann-Yae Na
- Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyojin Lee
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Eun Ki Min
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Sanjita Paudel
- Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - So Young Choi
- Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - HyunChae Sim
- Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kwang-Hyeon Liu
- Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ki-Tae Kim
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Jong-Sup Bae
- Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sangkyu Lee
- Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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21
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Ahmed E, Musio B, Todisco S, Mastrorilli P, Gallo V, Saponari M, Nigro F, Gualano S, Santoro F. Non-Targeted Spectranomics for the Early Detection of Xylella fastidiosa Infection in Asymptomatic Olive Trees, cv. Cellina di Nardò. Molecules 2023; 28:7512. [PMID: 38005234 PMCID: PMC10672767 DOI: 10.3390/molecules28227512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Olive quick decline syndrome (OQDS) is a disease that has been seriously affecting olive trees in southern Italy since around 2009. During the disease, caused by Xylella fastidiosa subsp. pauca sequence type ST53 (Xf), the flow of water and nutrients within the trees is significantly compromised. Initially, infected trees may not show any symptoms, making early detection challenging. In this study, young artificially infected plants of the susceptible cultivar Cellina di Nardò were grown in a controlled environment and co-inoculated with additional xylem-inhabiting fungi. Asymptomatic leaves of olive plants at an early stage of infection were collected and analyzed using nuclear magnetic resonance (NMR), hyperspectral reflectance (HSR), and chemometrics. The application of a spectranomic approach contributed to shedding light on the relationship between the presence of specific hydrosoluble metabolites and the optical properties of both asymptomatic Xf-infected and non-infected olive leaves. Significant correlations between wavebands located in the range of 530-560 nm and 1380-1470 nm, and the following metabolites were found to be indicative of Xf infection: malic acid, fructose, sucrose, oleuropein derivatives, and formic acid. This information is the key to the development of HSR-based sensors capable of early detection of Xf infections in olive trees.
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Affiliation(s)
- Elhussein Ahmed
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Via Orabona, 4, I-70125 Bari, Italy; (E.A.); (S.T.); (P.M.); (V.G.)
- International Centre for Advanced Mediterranean Agronomic Studies of Bari (CIHEAM Bari), Via Ceglie 9, 70010 Valenzano, Italy;
| | - Biagia Musio
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Via Orabona, 4, I-70125 Bari, Italy; (E.A.); (S.T.); (P.M.); (V.G.)
| | - Stefano Todisco
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Via Orabona, 4, I-70125 Bari, Italy; (E.A.); (S.T.); (P.M.); (V.G.)
| | - Piero Mastrorilli
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Via Orabona, 4, I-70125 Bari, Italy; (E.A.); (S.T.); (P.M.); (V.G.)
- Innovative Solutions S.r.l.—Spin-Off Company of Polytechnic University of Bari, Zona H 150/B, 70015 Noci, Italy
| | - Vito Gallo
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Via Orabona, 4, I-70125 Bari, Italy; (E.A.); (S.T.); (P.M.); (V.G.)
- Innovative Solutions S.r.l.—Spin-Off Company of Polytechnic University of Bari, Zona H 150/B, 70015 Noci, Italy
| | - Maria Saponari
- Istituto Per la Protezione Sostenibile Delle Piante, CNR, Via Amendola 122/D, I-70126 Bari, Italy;
| | - Franco Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona, 4, I-70125 Bari, Italy;
| | - Stefania Gualano
- International Centre for Advanced Mediterranean Agronomic Studies of Bari (CIHEAM Bari), Via Ceglie 9, 70010 Valenzano, Italy;
| | - Franco Santoro
- International Centre for Advanced Mediterranean Agronomic Studies of Bari (CIHEAM Bari), Via Ceglie 9, 70010 Valenzano, Italy;
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22
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Slocum RD, Mejia Peña C, Liu Z. Transcriptional reprogramming of nucleotide metabolism in response to altered pyrimidine availability in Arabidopsis seedlings. FRONTIERS IN PLANT SCIENCE 2023; 14:1273235. [PMID: 38023851 PMCID: PMC10652772 DOI: 10.3389/fpls.2023.1273235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In Arabidopsis seedlings, inhibition of aspartate transcarbamoylase (ATC) and de novo pyrimidine synthesis resulted in pyrimidine starvation and developmental arrest a few days after germination. Synthesis of pyrimidine nucleotides by salvaging of exogenous uridine (Urd) restored normal seedling growth and development. We used this experimental system and transcriptional profiling to investigate genome-wide responses to changes in pyrimidine availability. Gene expression changes at different times after Urd supplementation of pyrimidine-starved seedlings were mapped to major pathways of nucleotide metabolism, in order to better understand potential coordination of pathway activities, at the level of transcription. Repression of de novo synthesis genes and induction of intracellular and extracellular salvaging genes were early and sustained responses to pyrimidine limitation. Since de novo synthesis is energetically more costly than salvaging, this may reflect a reduced energy status of the seedlings, as has been shown in recent studies for seedlings growing under pyrimidine limitation. The unexpected induction of pyrimidine catabolism genes under pyrimidine starvation may result from induction of nucleoside hydrolase NSH1 and repression of genes in the plastid salvaging pathway, diverting uracil (Ura) to catabolism. Identification of pyrimidine-responsive transcription factors with enriched binding sites in highly coexpressed genes of nucleotide metabolism and modeling of potential transcription regulatory networks provided new insights into possible transcriptional control of key enzymes and transporters that regulate nucleotide homeostasis in plants.
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Affiliation(s)
- Robert D. Slocum
- Department of Biological Sciences, Goucher College, Towson, MD, United States
| | - Carolina Mejia Peña
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
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23
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Liu Z, Wang W, Li X, Zhao J, Zhu H, Que S, He Y, Xu J, Zhou L, Mardinoglu A, Zheng S. Multi-omics network analysis on samples from sequential biopsies reveals vital role of proliferation arrest for Macrosteatosis related graft failure in rats after liver transplantation. Genomics 2023; 115:110748. [PMID: 37984718 DOI: 10.1016/j.ygeno.2023.110748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/12/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
To investigate the molecular impact of graft MaS on post-transplant prognosis, based on multi-omics integrative analysis. Rats were fed by methionine-choline deficient diet (MCD) for MaS grafts. Samples were collected from grafts by sequential biopsies. Transcriptomic and metabolomic profilings were assayed. Post-transplant MaS status showed a close association with graft failure. Differentially expressed genes (DEGs) for in-vivo MaS were mainly enriched on pathways of cell cycle and DNA replication. Post-transplant MaS caused arrests of graft regeneration via inhibiting the E2F1 centered network, which was confirmed by an in vitro experiment. Data from metabolomics assays found insufficient serine/creatine which is located on one‑carbon metabolism was responsible for MaS-related GF. Pre-transplant MaS caused severe fibrosis in long-term survivors. DEGs for grafts from long-term survivors with pre-transplant MaS were mainly enriched in pathways of ECM-receptor interaction and focal adhesion. Transcriptional regulatory network analysis confirmed SOX9 as a key transcription factor (TF) for MaS-related fibrosis. Metabolomic assays found elevation of aromatic amino acid (AAA) was a major feature of fibrosis in long-term survivors. Graft MaS in vivo increased post-transplant GF via negative regulations on graft regeneration. Pre-transplant MaS induced severe fibrosis in long-term survivors via activations on ECM-receptor interaction and AAA metabolism.
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Affiliation(s)
- Zhengtao Liu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China; NHC Key Laboratory of Combined Multi-Organ Transplantation, Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Shulan Hospital (Hangzhou), Hangzhou 310 000, China.
| | - Wenchao Wang
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Xiang Li
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Junsheng Zhao
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Hai Zhu
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Department of Hepatobiliary Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | | | - Yong He
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jun Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK; Science for Life Laboratory, KTH-Royal Institute of Technology, SE-17121 Stockholm, Sweden.
| | - Shusen Zheng
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China; NHC Key Laboratory of Combined Multi-Organ Transplantation, Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Shulan Hospital (Hangzhou), Hangzhou 310 000, China; Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
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24
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Boris V, Vanessa V. Molecular systems biology approaches to investigate mechanisms of gut-brain communication in neurological diseases. Eur J Neurol 2023; 30:3622-3632. [PMID: 37038632 DOI: 10.1111/ene.15819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND Whilst the incidence of neurological diseases is increasing worldwide, treatment remains mostly limited to symptom management. The gut-brain axis, which encompasses the communication routes between microbiota, gut and brain, has emerged as a crucial area of investigation for identifying new preventive and therapeutic targets in neurological disease. METHODS Due to the inter-organ, systemic nature of the gut-brain axis, together with the multitude of biomolecules and microbial species involved, molecular systems biology approaches are required to accurately investigate the mechanisms of gut-brain communication. High-throughput omics profiling, together with computational methodologies such as dimensionality reduction or clustering, machine learning, network inference and genome-scale metabolic models, allows novel biomarkers to be discovered and elucidates mechanistic insights. RESULTS In this review, the general concepts of experimental and computational methodologies for gut-brain axis research are introduced and their applications are discussed, mainly in human cohorts. Important aspects are further highlighted concerning rational study design, sampling procedures and data modalities relevant for gut-brain communication, strengths and limitations of methodological approaches and some future perspectives. CONCLUSION Multi-omics analyses, together with advanced data mining, are essential to functionally characterize the gut-brain axis and put forward novel preventive or therapeutic strategies in neurological disease.
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Affiliation(s)
- Vandemoortele Boris
- Laboratory for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Vermeirssen Vanessa
- Laboratory for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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25
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Juigné C, Becker E, Gondret F. Small networks of expressed genes in the whole blood and relationships to profiles in circulating metabolites provide insights in inter-individual variability of feed efficiency in growing pigs. BMC Genomics 2023; 24:647. [PMID: 37891507 PMCID: PMC10605982 DOI: 10.1186/s12864-023-09751-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Feed efficiency is a research priority to support a sustainable meat production. It is recognized as a complex trait that integrates multiple biological pathways orchestrated in and by various tissues. This study aims to determine networks between biological entities to explain inter-individual variation of feed efficiency in growing pigs. RESULTS The feed conversion ratio (FCR), a measure of feed efficiency, and its two component traits, average daily gain and average daily feed intake, were obtained from 47 growing pigs from a divergent selection for residual feed intake and fed high-starch or high-fat high-fiber diets during 58 days. Datasets of transcriptomics (60 k porcine microarray) in the whole blood and metabolomics (1H-NMR analysis and target gas chromatography) in plasma were available for all pigs at the end of the trial. A weighted gene co-expression network was built from the transcriptomics dataset, resulting in 33 modules of co-expressed molecular probes. The eigengenes of eight of these modules were significantly ([Formula: see text]) or tended to be ([Formula: see text]) correlated to FCR. Great homogeneity in the enriched biological pathways was observed in these modules, suggesting co-expressed and co-regulated constitutive genes. They were mainly enriched in genes participating to immune and defense-related processes, and to a lesser extent, to translation, cell development or learning. They were also generally associated with growth rate and percentage of lean mass. In the whole network, only one module composed of genes participating to the response to substances, was significantly associated with daily feed intake and body adiposity. The plasma profiles in circulating metabolites and in fatty acids were summarized by weighted linear combinations using a dimensionality reduction method. Close association was thus found between a module composed of co-expressed genes participating to T cell receptor signaling and cell development process in the whole blood and related to FCR, and the circulating concentrations of polyunsaturated fatty acids in plasma. CONCLUSION These systemic approaches have highlighted networks of entities driving key biological processes involved in the phenotypic difference in feed efficiency between animals. Connecting transcriptomics and metabolic levels together had some additional benefits.
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Affiliation(s)
- Camille Juigné
- PEGASE, INRAE, Institut Agro, Saint-Gilles, F-35590, France
- University Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, F-35000, France
| | - Emmanuelle Becker
- University Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, F-35000, France
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Vorperian SK, DeFelice BC, Buonomo JA, Chinchinian HJ, Gray IJ, Yan J, Mach KE, La V, Lee TJ, Liao JC, Lafayette R, Loeb GB, Bertozzi CR, Quake SR. Multiomics characterization of cell type repertoires for urine liquid biopsies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563226. [PMID: 37961398 PMCID: PMC10634682 DOI: 10.1101/2023.10.20.563226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Urine is assayed alongside blood in medicine, yet current clinical diagnostic tests utilize only a small fraction of its total biomolecular repertoire, potentially foregoing high-resolution insights into human health and disease. In this work, we characterized the joint landscapes of transcriptomic and metabolomic signals in human urine. We also compared the urine transcriptome to plasma cell-free RNA, identifying a distinct cell type repertoire and enrichment for metabolic signal. Untargeted metabolomic measurements identified a complementary set of pathways to the transcriptomic analysis. Our findings suggest that urine is a promising biofluid yielding prognostic and detailed insights for hard-to-biopsy tissues with low representation in the blood, offering promise for a new generation of liquid biopsies.
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Downing T, Angelopoulos N. A primer on correlation-based dimension reduction methods for multi-omics analysis. J R Soc Interface 2023; 20:20230344. [PMID: 37817584 PMCID: PMC10565429 DOI: 10.1098/rsif.2023.0344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/19/2023] [Indexed: 10/12/2023] Open
Abstract
The continuing advances of omic technologies mean that it is now more tangible to measure the numerous features collectively reflecting the molecular properties of a sample. When multiple omic methods are used, statistical and computational approaches can exploit these large, connected profiles. Multi-omics is the integration of different omic data sources from the same biological sample. In this review, we focus on correlation-based dimension reduction approaches for single omic datasets, followed by methods for pairs of omics datasets, before detailing further techniques for three or more omic datasets. We also briefly detail network methods when three or more omic datasets are available and which complement correlation-oriented tools. To aid readers new to this area, these are all linked to relevant R packages that can implement these procedures. Finally, we discuss scenarios of experimental design and present road maps that simplify the selection of appropriate analysis methods. This review will help researchers navigate emerging methods for multi-omics and integrating diverse omic datasets appropriately. This raises the opportunity of implementing population multi-omics with large sample sizes as omics technologies and our understanding improve.
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Affiliation(s)
- Tim Downing
- Pirbright Institute, Pirbright, Surrey, UK
- Department of Biotechnology, Dublin City University, Dublin, Ireland
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Joshi AD, Rahnavard A, Kachroo P, Mendez KM, Lawrence W, Julián-Serrano S, Hua X, Fuller H, Sinnott-Armstrong N, Tabung FK, Shutta KH, Raffield LM, Darst BF. An epidemiological introduction to human metabolomic investigations. Trends Endocrinol Metab 2023; 34:505-525. [PMID: 37468430 PMCID: PMC10527234 DOI: 10.1016/j.tem.2023.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
Metabolomics holds great promise for uncovering insights around biological processes impacting disease in human epidemiological studies. Metabolites can be measured across biological samples, including plasma, serum, saliva, urine, stool, and whole organs and tissues, offering a means to characterize metabolic processes relevant to disease etiology and traits of interest. Metabolomic epidemiology studies face unique challenges, such as identifying metabolites from targeted and untargeted assays, defining standards for quality control, harmonizing results across platforms that often capture different metabolites, and developing statistical methods for high-dimensional and correlated metabolomic data. In this review, we introduce metabolomic epidemiology to the broader scientific community, discuss opportunities and challenges presented by these studies, and highlight emerging innovations that hold promise to uncover new biological insights.
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Affiliation(s)
- Amit D Joshi
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin M Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wayne Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sachelly Julián-Serrano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Public Health, University of Massachusetts Lowell, Lowell, MA, USA
| | - Xinwei Hua
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Department of Cardiology, Peking University Third Hospital, Beijing, China
| | - Harriett Fuller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nasa Sinnott-Armstrong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Fred K Tabung
- The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH, USA
| | - Katherine H Shutta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Burcu F Darst
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Blutt SE, Coarfa C, Neu J, Pammi M. Multiomic Investigations into Lung Health and Disease. Microorganisms 2023; 11:2116. [PMID: 37630676 PMCID: PMC10459661 DOI: 10.3390/microorganisms11082116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Diseases of the lung account for more than 5 million deaths worldwide and are a healthcare burden. Improving clinical outcomes, including mortality and quality of life, involves a holistic understanding of the disease, which can be provided by the integration of lung multi-omics data. An enhanced understanding of comprehensive multiomic datasets provides opportunities to leverage those datasets to inform the treatment and prevention of lung diseases by classifying severity, prognostication, and discovery of biomarkers. The main objective of this review is to summarize the use of multiomics investigations in lung disease, including multiomics integration and the use of machine learning computational methods. This review also discusses lung disease models, including animal models, organoids, and single-cell lines, to study multiomics in lung health and disease. We provide examples of lung diseases where multi-omics investigations have provided deeper insight into etiopathogenesis and have resulted in improved preventative and therapeutic interventions.
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Affiliation(s)
- Sarah E. Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Josef Neu
- Department of Pediatrics, Section of Neonatology, University of Florida, Gainesville, FL 32611, USA;
| | - Mohan Pammi
- Department of Pediatrics, Section of Neonatology, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX 77030, USA
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Bahadoor A, Robinson KA, Loewen MC, Demissie ZA. Clonostachys rosea 'omics profiling: identification of putative metabolite-gene associations mediating its in vitro antagonism against Fusarium graminearum. BMC Genomics 2023; 24:352. [PMID: 37365507 DOI: 10.1186/s12864-023-09463-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Clonostachys rosea is an established biocontrol agent. Selected strains have either mycoparasitic activity against known pathogens (e.g. Fusarium species) and/or plant growth promoting activity on various crops. Here we report outcomes from a comparative 'omics analysis leveraging a temporal variation in the in vitro antagonistic activities of C. rosea strains ACM941 and 88-710, toward understanding the molecular mechanisms underpinning mycoparasitism. RESULTS Transcriptomic data highlighted specialized metabolism and membrane transport related genes as being significantly upregulated in ACM941 compared to 88-710 at a time point when the ACM941 strain had higher in vitro antagonistic activity than 88-710. In addition, high molecular weight specialized metabolites were differentially secreted by ACM941, with accumulation patterns of some metabolites matching the growth inhibition differences displayed by the exometabolites of the two strains. In an attempt to identify statistically relevant relationships between upregulated genes and differentially secreted metabolites, transcript and metabolomic abundance data were associated using IntLIM (Integration through Linear Modeling). Of several testable candidate associations, a putative C. rosea epidithiodiketopiperazine (ETP) gene cluster was identified as a prime candidate based on both co-regulation analysis and transcriptomic-metabolomic data association. CONCLUSIONS Although remaining to be validated functionally, these results suggest that a data integration approach may be useful for identification of potential biomarkers underlying functional divergence in C. rosea strains.
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Affiliation(s)
- Adilah Bahadoor
- Metrology Research Center, National Research Council Canada, 1200 Montreal Rd, Ottawa, ON, K1A 0R6, Canada
| | - Kelly A Robinson
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, ON, Canada
| | - Michele C Loewen
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, ON, Canada.
| | - Zerihun A Demissie
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, ON, Canada.
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Song J, Jiang Z, Wei X, Zhang Y, Bian B, Wang H, Gao W, Si N, Liu H, Cheng M, Zhao Z, Zhou Y, Zhao H. Integrated transcriptomics and lipidomics investigation of the mechanism underlying the gastrointestinal mucosa damage of Loropetalum chinense (R.Br.) and its representative component. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 114:154758. [PMID: 37001296 DOI: 10.1016/j.phymed.2023.154758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/23/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Loropetalum chinensis (R.Br) Oliv (Bhjm), a Chinese folk herbal medicine, was traditionally used in the treatment of wound bleeding and skin ulcers. A new drug named JIMUSAN granules used for gastrosia was developed by our group, and clinical trials have been approved. However, as the principal herb, the material basis and underlying mechanisms of Bhjm in attenuating gastrointestinal mucosa damage (GMD) remain to be systemically illuminated. PURPOSE An integrated strategy was used to explore the therapeutic effects and mechanisms of Bhjm and ellagic acid (EA) on GMD zebrafish, using network pharmacology, transcriptomics, lipidomics, and real-time quantitative PCR (RT-qPCR) verification. METHODS First, network pharmacological analysis was used to infer the major effective constituents and targets of Bhjm. Ultra high performance liquid chromatography-linear ion trap/orbitrap high resolution mass spectrometry (UHPLC-LTQ-Orbitrap HRMS) and ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) were employed to identify the chemical constituents and quantify the different types of constituents. Second, zebrafish model of GMD was established by using 2,4,6-trinitrobenzenesulfonic acid (TNBS) to evaluate the efficacy of Bhjm and EA. The potential mechanism was examined by integrated transcriptomics and lipidomics analysis. Finally, validation tests were implemented using RT-qPCR. RESULTS In this study, targets indentified by network pharmacology were related to inflammation and mucosal damage. Ten representative components that interacted with these targets were simultaneously determined by UHPLC-MS/MS. Sixty four compounds were identified or tentatively characterized, most of which were flavonoids and polyphenols. Bhjm and EA alleviated mucosal damage and reduced inflammation in a TNBS-induced zebrafish GMD model, indicating that EA was the main active compounds. Eight common differentially expressed genes were downregulated by Bhjm and EA, as determined by transcriptomics analysis. Lipidomics analysis confirmed 12 differential lipids, including phosphatidylcholine (PC) and triglyceride (TG). Further network enrichment analysis demonstrated that differential lipid metabolism was regulated by klf4 and hist1h2ba, and were validated by RT-qPCR. CONCLUSION In our study, the chemical profile of Bhjm was clarified. Moreover, the GMD repair effect and the mechanism of Bhjm and EA was comprehensively analyzed for the first time, involving inflammation and lipid metabolism. Collectively, these findings will be significantly helpful for deeply exploring the clinical application value of Bhjm.
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Affiliation(s)
- Jianfang Song
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Zhihong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Xiaolu Wei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yan Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baolin Bian
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hongjie Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenya Gao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Nan Si
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haoyuan Liu
- Beijing Gushen Life Health Science and Technology Co., Ltd, Beijing, China
| | - Meng Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | | | - Yanyan Zhou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Haiyu Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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Zheng L, Liu Q, Wu R, Zhu M, Dorjee T, Zhou Y, Gao F. The alteration of proteins and metabolites in leaf apoplast and the related gene expression associated with the adaptation of Ammopiptanthus mongolicus to winter freezing stress. Int J Biol Macromol 2023; 240:124479. [PMID: 37072058 DOI: 10.1016/j.ijbiomac.2023.124479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/20/2023]
Abstract
Ammopiptanthus mongolicus, an evergreen broad-leaved plant, can tolerate severe freezing stress (temperatures as low as -20 °C in winter). The apoplast is the space outside the plasma membrane that plays an important role in plant responses to environmental stress. Here, we investigated, using a multi-omics approach, the dynamic alterations in the levels of proteins and metabolites in the apoplast and related gene expression changes involved in the adaptation of A. mongolicus to winter freezing stress. Of the 962 proteins identified in the apoplast, the abundance of several PR proteins, including PR3 and PR5, increased significantly in winter, which may contribute to winter freezing-stress tolerance by functioning as antifreeze proteins. The increased abundance of the cell-wall polysaccharides and cell wall-modifying proteins, including PMEI, XTH32, and EXLA1, may enhance the mechanical properties of the cell wall in A. mongolicus. Accumulation of flavonoids and free amino acids in the apoplast may be beneficial for ROS scavenging and the maintenance of osmotic homeostasis. Integrated analyses revealed gene expression changes associated with alterations in the levels of apoplast proteins and metabolites. Our study improved the current understanding of the roles of apoplast proteins and metabolites in plant adaptation to winter freezing stress.
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Affiliation(s)
- Lamei Zheng
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Qi Liu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Rongqi Wu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ming Zhu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tashi Dorjee
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yijun Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Fei Gao
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
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Yoosefzadeh Najafabadi M, Hesami M, Eskandari M. Machine Learning-Assisted Approaches in Modernized Plant Breeding Programs. Genes (Basel) 2023; 14:genes14040777. [PMID: 37107535 PMCID: PMC10137951 DOI: 10.3390/genes14040777] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
In the face of a growing global population, plant breeding is being used as a sustainable tool for increasing food security. A wide range of high-throughput omics technologies have been developed and used in plant breeding to accelerate crop improvement and develop new varieties with higher yield performance and greater resilience to climate changes, pests, and diseases. With the use of these new advanced technologies, large amounts of data have been generated on the genetic architecture of plants, which can be exploited for manipulating the key characteristics of plants that are important for crop improvement. Therefore, plant breeders have relied on high-performance computing, bioinformatics tools, and artificial intelligence (AI), such as machine-learning (ML) methods, to efficiently analyze this vast amount of complex data. The use of bigdata coupled with ML in plant breeding has the potential to revolutionize the field and increase food security. In this review, some of the challenges of this method along with some of the opportunities it can create will be discussed. In particular, we provide information about the basis of bigdata, AI, ML, and their related sub-groups. In addition, the bases and functions of some learning algorithms that are commonly used in plant breeding, three common data integration strategies for the better integration of different breeding datasets using appropriate learning algorithms, and future prospects for the application of novel algorithms in plant breeding will be discussed. The use of ML algorithms in plant breeding will equip breeders with efficient and effective tools to accelerate the development of new plant varieties and improve the efficiency of the breeding process, which are important for tackling some of the challenges facing agriculture in the era of climate change.
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Affiliation(s)
| | - Mohsen Hesami
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
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Patel JS, Selvaraj V, More P, Bahmani R, Borza T, Prithiviraj B. A Plant Biostimulant from Ascophyllum nodosum Potentiates Plant Growth Promotion and Stress Protection Activity of Pseudomonas protegens CHA0. PLANTS (BASEL, SWITZERLAND) 2023; 12:1208. [PMID: 36986897 PMCID: PMC10053968 DOI: 10.3390/plants12061208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Abiotic stresses, including salinity stress, affect numerous crops, causing yield reduction, and, as a result, important economic losses. Extracts from the brown alga Ascophyllum nodosum (ANE), and compounds secreted by the Pseudomonas protegens strain, CHA0, can mitigate these effects by inducing tolerance against salt stress. However, the influence of ANE on P. protegens CHA0 secretion, and the combined effects of these two biostimulants on plant growth, are not known. Fucoidan, alginate, and mannitol are abundant components of brown algae and of ANE. Reported here are the effects of a commercial formulation of ANE, fucoidan, alginate, and mannitol, on pea (Pisum sativum), and on the plant growth-promoting activity of P. protegens CHA0. In most situations, ANE and fucoidan increased indole-3-acetic acid (IAA) and siderophore production, phosphate solubilization, and hydrogen cyanide (HCN) production by P. protegens CHA0. Colonization of pea roots by P. protegens CHA0 was found to be increased mostly by ANE and fucoidan in normal conditions and under salt stress. Applications of P. protegens CHA0 combined with ANE, or with fucoidan, alginate, and mannitol, generally augmented root and shoot growth in normal and salinity stress conditions. Real-time quantitative PCR analyses of P. protegens revealed that, in many instances, ANE and fucoidan enhanced the expression of several genes involved in chemotaxis (cheW and WspR), pyoverdine production (pvdS), and HCN production (hcnA), but gene expression patterns overlapped only occasionally those of growth-promoting parameters. Overall, the increased colonization and the enhanced activities of P. protegens CHA0 in the presence of ANE and its components mitigated salinity stress in pea. Among treatments, ANE and fucoidan were found responsible for most of the increased activities of P. protegens CHA0 and the improved plant growth.
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Depuydt T, De Rybel B, Vandepoele K. Charting plant gene functions in the multi-omics and single-cell era. TRENDS IN PLANT SCIENCE 2023; 28:283-296. [PMID: 36307271 DOI: 10.1016/j.tplants.2022.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology.
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Affiliation(s)
- Thomas Depuydt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium; Ghent University, Bioinformatics Institute Ghent, Ghent, Belgium.
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Silva VNB, da Silva TLC, Ferreira TMM, Neto JCR, Leão AP, de Aquino Ribeiro JA, Abdelnur PV, Valadares LF, de Sousa CAF, Júnior MTS. Multi-omics Analysis of Young Portulaca oleracea L. Plants' Responses to High NaCl Doses Reveals Insights into Pathways and Genes Responsive to Salinity Stress in this Halophyte Species. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:1-21. [PMID: 36947413 PMCID: PMC9883379 DOI: 10.1007/s43657-022-00061-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 11/24/2022]
Abstract
Soil salinity is among the abiotic stressors that threaten agriculture the most, and purslane (Portulaca oleracea L.) is a dicot species adapted to inland salt desert and saline habitats that hyper accumulates salt and has high phytoremediation potential. Many researchers consider purslane a suitable model species to study the mechanisms of plant tolerance to drought and salt stresses. Here, a robust salinity stress protocol was developed and used to characterize the morphophysiological responses of young purslane plants to salinity stress; then, leaf tissue underwent characterization by distinct omics platforms to gain further insights into its response to very high salinity stress. The salinity stress protocol did generate different levels of stress by gradients of electrical conductivity at field capacity and water potential in the saturation extract of the substrate, and the morphological parameters indicated three distinct stress levels. As expected from a halophyte species, these plants remained alive under very high levels of salinity stress, showing salt crystal-like structures constituted mainly by Na+, Cl-, and K+ on and around closed stomata. A comprehensive and large-scale metabolome and transcriptome single and integrated analyses were then employed using leaf samples. The multi-omics integration (MOI) system analysis led to a data-set of 51 metabolic pathways with at least one enzyme and one metabolite differentially expressed due to salinity stress. These data sets (of genes and metabolites) are valuable for future studies aimed to deepen our knowledge on the mechanisms behind the high tolerance of this species to salinity stress. In conclusion, besides showing that this species applies salt exclusion already in young plants to support very high levels of salinity stress, the initial analysis of metabolites and transcripts data sets already give some insights into other salt tolerance mechanisms used by this species to support high levels of salinity stress. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00061-2.
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Affiliation(s)
- Vivianny Nayse Belo Silva
- Graduate Program of Plant Biotechnology, Federal University of Lavras, CP 3037, Lavras, MG 37200-000 Brazil
| | | | | | | | - André Pereira Leão
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF 70770‐901 Brazil
| | | | - Patrícia Verardi Abdelnur
- Institute of Chemistry, Federal University of Goiás, Campus Samambaia, Goiânia, GO 74690‐900 Brazil
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF 70770‐901 Brazil
| | | | | | - Manoel Teixeira Souza Júnior
- Graduate Program of Plant Biotechnology, Federal University of Lavras, CP 3037, Lavras, MG 37200-000 Brazil
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF 70770‐901 Brazil
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Duan Y, Yang H, Yang H, Wu Y, Fan S, Wu W, Lyu L, Li W. Integrative physiological, metabolomic and transcriptomic analysis reveals nitrogen preference and carbon and nitrogen metabolism in blackberry plants. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153888. [PMID: 36577314 DOI: 10.1016/j.jplph.2022.153888] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Nitrogen (N) is an indispensable element for plant growth and development. To understand the regulation of underlying carbon (C) and N metabolism in blackberry plants, we performed integrated analyses of the physiology, metabolome and transcriptome. Blackberry plants were subjected to no N, nitrate (NO3⁻)-N, ammonium (NH4+)-N and urea treatments. Our results showed that the NH4⁺-N treatment yielded higher values for the biomass, chlorophyll, antioxidants, N contents and antioxidant enzyme activities, as well as lower levels of free radicals and the C/N ratio compared with other treatments. Transcriptome analysis showed that different N forms significantly affected photosynthesis, flavonoid biosynthesis and the TCA cycle. Metabolome analysis indicated that the levels of lipids, carbohydrates, flavonoids and amino acids were markedly changed under different N treatments. Integrated transcriptomic and metabolomic data revealed that amino acids, including proline, arginine, L-isoleucine, L-aspartate, threonine, and L-glutamate, played important roles in maintaining normal plant growth by regulating N metabolism and amino acid metabolism. Overall, blackberry plants preferentially take up NH4⁺-N. Under the NH4⁺-N treatment, N assimilation was stronger, flavonoid biosynthesis was decreased, and the promoting influence of NH4⁺-N on N metabolism was better than that of NO3⁻-N. However, the NO3⁻-N treatment enhanced the C/N ratio, accelerated the process of C metabolism and increased the synthesis of flavonoids, thereby accelerating the flow of N metabolism to C metabolism. These results provide deeper insight into coordinating C and N metabolism and improving N use efficiency in blackberry plants.
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Affiliation(s)
- Yongkang Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Haiyan Yang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, China.
| | - Hao Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, China
| | - Sufan Fan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.
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Pu Y, Wang C, Jiang Y, Wang X, Ai Y, Zhuang W. Metabolic profiling and transcriptome analysis provide insights into the accumulation of flavonoids in chayote fruit during storage. Front Nutr 2023; 10:1029745. [PMID: 36937343 PMCID: PMC10019507 DOI: 10.3389/fnut.2023.1029745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
Chayote (Sechium edulel) fruits are rich in flavonoids, folate, and low-calorie food. However, studies about the flavonoids and the corresponding regulatory mechanism of flavonoid synthesis in chayote fruits was still unclear. In present study, an integrated transcriptome and metabolite analysis of chayote fruits at three different storage stages were conducted to explore the flavonoid compositions and gene expression associated with flavonoid synthesis. Through the UPLC-MS/MS analysis, a total of 57 flavonoid compounds were detected. Of these, 42 flavonoid glycosides were significantly differential accumulation in chayote fruits at three different storage stages. Many genes associated with flavonoid synthesis were differentially expressed in chayote fruits at three different storage stages through RNA-seq analysis, including structural genes and some TFs. There was a high correlation between RNA-seq analysis and metabolite profiling, and the expression level of candidate genes in the flavonoid synthesis pathway were consistent with the dynamic changes of flavonoids. In addition, one R2R3-MYB transcription factor, FSG0057100, was defined as the critical regulatory gene of flavonoid synthesis. Furthermore, exogenous application of phenylalanine increased the total content of flavonoids and promoted some flavonoid biosynthesis-related gene expression in chayote fruits. The above results not only make us better understand the molecular mechanism of flavonoid synthesis in chayote fruits, but also contribute to the promotion and application of chayote products.
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Affiliation(s)
- YuTing Pu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Cheng Wang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - YongWen Jiang
- Tea Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - XiaoJing Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
- *Correspondence: XiaoJing Wang,
| | - YuJie Ai
- Tea Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
- YuJie Ai,
| | - WeiBing Zhuang
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Memorial Sun Yat-sen, Institute of Botany, Nanjing, China
- WeiBing Zhuang,
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Pollari M, Sipari N, Poque S, Himanen K, Mäkinen K. Effects of Poty-Potexvirus Synergism on Growth, Photosynthesis and Metabolite Status of Nicotiana benthamiana. Viruses 2022; 15:121. [PMID: 36680161 PMCID: PMC9867248 DOI: 10.3390/v15010121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Mixed virus infections threaten crop production because interactions between the host and the pathogen mix may lead to viral synergism. While individual infections by potato virus A (PVA), a potyvirus, and potato virus X (PVX), a potexvirus, can be mild, co-infection leads to synergistic enhancement of PVX and severe symptoms. We combined image-based phenotyping with metabolite analysis of single and mixed PVA and PVX infections and compared their effects on growth, photosynthesis, and metabolites in Nicotiana benthamiana. Viral synergism was evident in symptom severity and impaired growth in the plants. Indicative of stress, the co-infection increased leaf temperature and decreased photosynthetic parameters. In contrast, singly infected plants sustained photosynthetic activity. The host's metabolic response differed significantly between single and mixed infections. Over 200 metabolites were differentially regulated in the mixed infection: especially defense-related metabolites and aromatic and branched-chain amino acids increased compared to the control. Changes in the levels of methionine cycle intermediates and a low S-adenosylmethionine/S-adenosylhomocysteine ratio suggested a decline in the methylation potential in co-infected plants. The decreased ratio between reduced glutathione, an important scavenger of reactive oxygen species, and its oxidized form, indicated that severe oxidative stress developed during co-infection. Based on the results, infection-associated oxidative stress is successfully controlled in the single infections but not in the synergistic infection, where activated defense pathways are not sufficient to counter the impact of the infections on plant growth.
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Affiliation(s)
- Maija Pollari
- Department of Microbiology, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Nina Sipari
- Viikki Metabolomics Unit, Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Sylvain Poque
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Kristiina Himanen
- National Plant Phenotyping Infrastructure, HiLIFE, Biocenter Finland, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Kristiina Mäkinen
- Department of Microbiology, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
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Interdisciplinary Overview of Lipopeptide and Protein-Containing Biosurfactants. Genes (Basel) 2022; 14:genes14010076. [PMID: 36672817 PMCID: PMC9859011 DOI: 10.3390/genes14010076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Biosurfactants are amphipathic molecules capable of lowering interfacial and superficial tensions. Produced by living organisms, these compounds act the same as chemical surfactants but with a series of improvements, the most notable being biodegradability. Biosurfactants have a wide diversity of categories. Within these, lipopeptides are some of the more abundant and widely known. Protein-containing biosurfactants are much less studied and could be an interesting and valuable alternative. The harsh temperature, pH, and salinity conditions that target organisms can sustain need to be understood for better implementation. Here, we will explore biotechnological applications via lipopeptide and protein-containing biosurfactants. Also, we discuss their natural role and the organisms that produce them, taking a glimpse into the possibilities of research via meta-omics and machine learning.
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Quan L, Jia C, Guo Y, Chen Y, Wang X, Xu Q, Zhang Y. HNRNPA2B1-mediated m6A modification of TLR4 mRNA promotes progression of multiple myeloma. J Transl Med 2022; 20:537. [PMID: 36401285 PMCID: PMC9673362 DOI: 10.1186/s12967-022-03750-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Multiple myeloma (MM) is a malignancy of plasma cells that remains incurable. Toll-like receptor 4 (TLR4) acts as a stress-responsive signal, protecting mitochondria during proteasome inhibitor (PI) exposure, maintaining mitochondrial metabolism and increasing drug resistance in MM. However, the mechanism of TLR4 regulation remains elusive. AIMS The purpose of this study was to investigate the methylation pattern of multiple myeloma and its effect on the expression of HNRNPA2B1 and downstream targets. METHODS The methylation level in MM and normal bone marrow specimens was detected using a colorimetric assay. HNRNPA2B1 gene knockdown was achieved in RPMI 8226 MM cells via adenovirus transfection. CCK8 and flow cytometric assays were used to detect proliferation and apoptosis, respectively. Transcriptome sequencing and m6A methylation MeRIP sequencing were applied, and differentially expressed genes (DEGs) were detected. Three independent NCBI GEO datasets were applied to examine the effects of HNRNPA2B1 and TLR4 expression on MM patient survival. RESULTS HNRNPA2B1 promoted MM progression. Clinical data from database revealed that HNRNPA2B1 was adverse prognostic factor for survival among MM patients. Furthermore, transcriptome sequencing and methylation sequencing showed that HNRNPA2B1 recognized and was enriched at the m6A sites of TLR4 and TLR4 was down-regulated of both the m6A level and transcription level in HNRNPA2B1-knockdown MM cells. Moreover, TLR4 was an adverse survival prognostic factor based on database analysis. CONCLUSION Overall, our study implies that the RNA-binding protein HNRNPA2B1 increases cell proliferation and deregulates cell apoptosis in MM through TLR4 signaling. Our study suggests HNRNPA2B1 as a potential therapeutic target for MM.
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Affiliation(s)
- Lina Quan
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Chuiming Jia
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Yiwei Guo
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Yao Chen
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Xinya Wang
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Qiuting Xu
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
| | - Yu Zhang
- grid.412651.50000 0004 1808 3502Hematology Department, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang People’s Republic of China ,grid.410736.70000 0001 2204 9268Immunology Department, Harbin Medical University, Harbin, Heilongjiang People’s Republic of China
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Agamah FE, Bayjanov JR, Niehues A, Njoku KF, Skelton M, Mazandu GK, Ederveen THA, Mulder N, Chimusa ER, 't Hoen PAC. Computational approaches for network-based integrative multi-omics analysis. Front Mol Biosci 2022; 9:967205. [PMID: 36452456 PMCID: PMC9703081 DOI: 10.3389/fmolb.2022.967205] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/20/2022] [Indexed: 08/27/2023] Open
Abstract
Advances in omics technologies allow for holistic studies into biological systems. These studies rely on integrative data analysis techniques to obtain a comprehensive view of the dynamics of cellular processes, and molecular mechanisms. Network-based integrative approaches have revolutionized multi-omics analysis by providing the framework to represent interactions between multiple different omics-layers in a graph, which may faithfully reflect the molecular wiring in a cell. Here we review network-based multi-omics/multi-modal integrative analytical approaches. We classify these approaches according to the type of omics data supported, the methods and/or algorithms implemented, their node and/or edge weighting components, and their ability to identify key nodes and subnetworks. We show how these approaches can be used to identify biomarkers, disease subtypes, crosstalk, causality, and molecular drivers of physiological and pathological mechanisms. We provide insight into the most appropriate methods and tools for research questions as showcased around the aetiology and treatment of COVID-19 that can be informed by multi-omics data integration. We conclude with an overview of challenges associated with multi-omics network-based analysis, such as reproducibility, heterogeneity, (biological) interpretability of the results, and we highlight some future directions for network-based integration.
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Affiliation(s)
- Francis E. Agamah
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jumamurat R. Bayjanov
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anna Niehues
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kelechi F. Njoku
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Michelle Skelton
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gaston K. Mazandu
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R. Chimusa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
| | - Peter A. C. 't Hoen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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Falcone M, Uribe AH, Papalazarou V, Newman AC, Athineos D, Stevenson K, Sauvé CEG, Gao Y, Kim JK, Del Latto M, Kierstead M, Wu C, Smith JJ, Romesser PB, Chalmers AJ, Blyth K, Maddocks ODK. Sensitisation of cancer cells to radiotherapy by serine and glycine starvation. Br J Cancer 2022; 127:1773-1786. [PMID: 36115879 PMCID: PMC9643498 DOI: 10.1038/s41416-022-01965-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Cellular metabolism is an integral component of cellular adaptation to stress, playing a pivotal role in the resistance of cancer cells to various treatment modalities, including radiotherapy. In response to radiotherapy, cancer cells engage antioxidant and DNA repair mechanisms which mitigate and remove DNA damage, facilitating cancer cell survival. Given the reliance of these resistance mechanisms on amino acid metabolism, we hypothesised that controlling the exogenous availability of the non-essential amino acids serine and glycine would radiosensitise cancer cells. METHODS We exposed colorectal, breast and pancreatic cancer cell lines/organoids to radiation in vitro and in vivo in the presence and absence of exogenous serine and glycine. We performed phenotypic assays for DNA damage, cell cycle, ROS levels and cell death, combined with a high-resolution untargeted LCMS metabolomics and RNA-Seq. RESULTS Serine and glycine restriction sensitised a range of cancer cell lines, patient-derived organoids and syngeneic mouse tumour models to radiotherapy. Comprehensive metabolomic and transcriptomic analysis of central carbon metabolism revealed that amino acid restriction impacted not only antioxidant response and nucleotide synthesis but had a marked inhibitory effect on the TCA cycle. CONCLUSION Dietary restriction of serine and glycine is a viable radio-sensitisation strategy in cancer.
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Affiliation(s)
- Mattia Falcone
- School of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Alejandro Huerta Uribe
- School of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
| | - Vasileios Papalazarou
- School of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
| | - Alice C Newman
- School of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
| | | | - Katrina Stevenson
- School of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
| | | | - Yajing Gao
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jin K Kim
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Del Latto
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Maria Kierstead
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chao Wu
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - J Joshua Smith
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Paul B Romesser
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Early Drug Development Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Anthony J Chalmers
- School of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
| | - Karen Blyth
- School of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Oliver D K Maddocks
- School of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK.
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Zhang F, Duan B, Zhou Z, Han L, Huang P, Ye Y, Wang Q, Huang F, Li J. Integration of metabolomics and transcriptomics to reveal anti-chronic myocardial ischemia mechanism of Gualou Xiebai decoction. JOURNAL OF ETHNOPHARMACOLOGY 2022; 297:115530. [PMID: 35830899 DOI: 10.1016/j.jep.2022.115530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Gualou Xiebai decoction (GLXB), a well-known classic traditional Chinese medicine formula, is a recorded and proven therapy for the management of cardiac diseases. However, its pharmacological characteristics and mechanism of action are unclear. MATERIALS AND METHODS The effects of GLXB and its mechanism of action in an isoprenaline-induced rat model of chronic myocardial ischemia (CMI) were investigated by incorporating metabonomics and transcriptomics. Meanwhile, the echocardiographic evaluation, histopathological analysis, serum biochemistry assay, TUNEL assay and western blot analysis were detected to revealed the protective effects of GLXB on CMI. RESULTS The results of echocardiographic evaluation, histopathological analysis and serum biochemistry assay revealed that GLXB had a significantly cardioprotective performance by reversing echocardiographic abnormalities, restoring pathological disorders and converting the serum biochemistry perturbations. Further, the omics analysis indicated that many genes and metabolites were regulated after modeling and GLXB administration, and maintained the marked "high-low" or "low-high" trends. Meanwhile, the results from integrated bioinformatics analysis suggested that the interaction network mainly consisted of amino acid and organic acid metabolism. The results of TUNEL assay and western blot analysis complemented the findings of integrated analysis of metabolomics and transcriptomics. CONCLUSION These findings suggested that GLXB has a curative effect in isoproterenol-induced CMI in rats. Integrated analysis based on transcriptomics and metabolomics studies revealed that the mechanism of GLXB in alleviating CMI was principally by the regulation of energy homeostasis and apoptosis, which was through a multi-component and multi-target treatment modality.
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Affiliation(s)
- Fengyun Zhang
- Pharmacy School, Hubei University of Chinese Medicine, Wuhan, 430065, China; Key Laboratory of Traditional Chinese Medicine Resource and Prescription, Ministry of Education, Wuhan, Hubei, 430061, China
| | - Bailu Duan
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Zhenxiang Zhou
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Lintao Han
- Pharmacy School, Hubei University of Chinese Medicine, Wuhan, 430065, China; Key Laboratory of Traditional Chinese Medicine Resource and Prescription, Ministry of Education, Wuhan, Hubei, 430061, China
| | - Ping Huang
- Key Laboratory of Traditional Chinese Medicine Resource and Prescription, Ministry of Education, Wuhan, Hubei, 430061, China; College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Yan Ye
- Pharmacy School, Hubei University of Chinese Medicine, Wuhan, 430065, China; Key Laboratory of Traditional Chinese Medicine Resource and Prescription, Ministry of Education, Wuhan, Hubei, 430061, China
| | - Qiong Wang
- Key Laboratory of Traditional Chinese Medicine Resource and Prescription, Ministry of Education, Wuhan, Hubei, 430061, China; College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Fang Huang
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Jingjing Li
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China.
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Leão AP, Bittencourt CB, Carvalho da Silva TL, Rodrigues Neto JC, Braga ÍDO, Vieira LR, de Aquino Ribeiro JA, Abdelnur PV, de Sousa CAF, Souza Júnior MT. Insights from a Multi-Omics Integration (MOI) Study in Oil Palm ( Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part Two-Drought. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202786. [PMID: 36297811 PMCID: PMC9611107 DOI: 10.3390/plants11202786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 06/09/2023]
Abstract
Drought and salinity are two of the most severe abiotic stresses affecting agriculture worldwide and bear some similarities regarding the responses of plants to them. The first is also known as osmotic stress and shows similarities mainly with the osmotic effect, the first phase of salinity stress. Multi-Omics Integration (MOI) offers a new opportunity for the non-trivial challenge of unraveling the mechanisms behind multigenic traits, such as drought and salinity resistance. The current study carried out a comprehensive, large-scale, single-omics analysis (SOA) and MOI studies on the leaves of young oil palm plants submitted to water deprivation. After performing SOA, 1955 DE enzymes from transcriptomics analysis, 131 DE enzymes from proteomics analysis, and 269 DE metabolites underwent MOI analysis, revealing several pathways affected by this stress, with at least one DE molecule in all three omics platforms used. Moreover, the similarities and dissimilarities in the molecular response of those plants to those two abiotic stresses underwent mapping. Cysteine and methionine metabolism (map00270) was the most affected pathway in all scenarios evaluated. The correlation analysis revealed that 91.55% of those enzymes expressed under both stresses had similar qualitative profiles, corroborating the already known fact that plant responses to drought and salinity show several similarities. At last, the results shed light on some candidate genes for engineering crop species resilient to both abiotic stresses.
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Affiliation(s)
| | | | | | | | - Ítalo de Oliveira Braga
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, MG, Brazil
| | - Letícia Rios Vieira
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, MG, Brazil
| | | | | | | | - Manoel Teixeira Souza Júnior
- Embrapa Agroenergia, Brasília 70770-901, DF, Brazil
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, MG, Brazil
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Singh KS, van der Hooft JJJ, van Wees SCM, Medema MH. Integrative omics approaches for biosynthetic pathway discovery in plants. Nat Prod Rep 2022; 39:1876-1896. [PMID: 35997060 PMCID: PMC9491492 DOI: 10.1039/d2np00032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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Perlo V, Furtado A, Botha FC, Margarido GRA, Hodgson‐Kratky K, Choudhary H, Gladden J, Simmons B, Henry RJ. Transcriptome and metabolome integration in sugarcane through culm development. Food Energy Secur 2022. [DOI: 10.1002/fes3.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Virginie Perlo
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
| | - Gabriel R. A. Margarido
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo São Paulo Brazil
| | - Katrina Hodgson‐Kratky
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
| | - Hemant Choudhary
- Joint BioEnergy Institute Emeryville CA USA
- Sandia National Laboratories Livermore CA USA
| | - John Gladden
- Joint BioEnergy Institute Emeryville CA USA
- Sandia National Laboratories Livermore CA USA
| | | | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
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Pranneshraj V, Sangha MK, Djalovic I, Miladinovic J, Djanaguiraman M. Lipidomics-Assisted GWAS (lGWAS) Approach for Improving High-Temperature Stress Tolerance of Crops. Int J Mol Sci 2022; 23:ijms23169389. [PMID: 36012660 PMCID: PMC9409476 DOI: 10.3390/ijms23169389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 11/25/2022] Open
Abstract
High-temperature stress (HT) over crop productivity is an important environmental factor demanding more attention as recent global warming trends are alarming and pose a potential threat to crop production. According to the Sixth IPCC report, future years will have longer warm seasons and frequent heat waves. Thus, the need arises to develop HT-tolerant genotypes that can be used to breed high-yielding crops. Several physiological, biochemical, and molecular alterations are orchestrated in providing HT tolerance to a genotype. One mechanism to counter HT is overcoming high-temperature-induced membrane superfluidity and structural disorganizations. Several HT lipidomic studies on different genotypes have indicated the potential involvement of membrane lipid remodelling in providing HT tolerance. Advances in high-throughput analytical techniques such as tandem mass spectrometry have paved the way for large-scale identification and quantification of the enormously diverse lipid molecules in a single run. Physiological trait-based breeding has been employed so far to identify and select HT tolerant genotypes but has several disadvantages, such as the genotype-phenotype gap affecting the efficiency of identifying the underlying genetic association. Tolerant genotypes maintain a high photosynthetic rate, stable membranes, and membrane-associated mechanisms. In this context, studying the HT-induced membrane lipid remodelling, resultant of several up-/down-regulations of genes and post-translational modifications, will aid in identifying potential lipid biomarkers for HT tolerance/susceptibility. The identified lipid biomarkers (LIPIDOTYPE) can thus be considered an intermediate phenotype, bridging the gap between genotype–phenotype (genotype–LIPIDOTYPE–phenotype). Recent works integrating metabolomics with quantitative genetic studies such as GWAS (mGWAS) have provided close associations between genotype, metabolites, and stress-tolerant phenotypes. This review has been sculpted to provide a potential workflow that combines MS-based lipidomics and the robust GWAS (lipidomics assisted GWAS-lGWAS) to identify membrane lipid remodelling related genes and associations which can be used to develop HS tolerant genotypes with enhanced membrane thermostability (MTS) and heat stable photosynthesis (HP).
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Affiliation(s)
- Velumani Pranneshraj
- Department of Biochemistry, Punjab Agricultural University, Ludhiana 141004, India
| | - Manjeet Kaur Sangha
- Department of Biochemistry, Punjab Agricultural University, Ludhiana 141004, India
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, 21000 Novi Sad, Serbia
- Correspondence: (I.D.); (M.D.)
| | - Jegor Miladinovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, 21000 Novi Sad, Serbia
| | - Maduraimuthu Djanaguiraman
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India
- Correspondence: (I.D.); (M.D.)
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Bittencourt CB, Carvalho da Silva TL, Rodrigues Neto JC, Vieira LR, Leão AP, de Aquino Ribeiro JA, Abdelnur PV, de Sousa CAF, Souza MT. Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity. PLANTS 2022; 11:plants11131755. [PMID: 35807707 PMCID: PMC9269341 DOI: 10.3390/plants11131755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022]
Abstract
Oil palm (Elaeis guineensis Jacq.) is the number one source of consumed vegetable oil nowadays. It is cultivated in areas of tropical rainforest, where it meets its natural condition of high rainfall throughout the year. The palm oil industry faces criticism due to a series of practices that was considered not environmentally sustainable, and it finds itself under pressure to adopt new and innovative procedures to reverse this negative public perception. Cultivating this oilseed crop outside the rainforest zone is only possible using artificial irrigation. Close to 30% of the world’s irrigated agricultural lands also face problems due to salinity stress. Consequently, the research community must consider drought and salinity together when studying to empower breeding programs in order to develop superior genotypes adapted to those potential new areas for oil palm cultivation. Multi-Omics Integration (MOI) offers a new window of opportunity for the non-trivial challenge of unraveling the mechanisms behind multigenic traits, such as drought and salinity tolerance. The current study carried out a comprehensive, large-scale, single-omics analysis (SOA), and MOI study on the leaves of young oil palm plants submitted to very high salinity stress. Taken together, a total of 1239 proteins were positively regulated, and 1660 were negatively regulated in transcriptomics and proteomics analyses. Meanwhile, the metabolomics analysis revealed 37 metabolites that were upregulated and 92 that were downregulated. After performing SOA, 436 differentially expressed (DE) full-length transcripts, 74 DE proteins, and 19 DE metabolites underwent MOI analysis, revealing several pathways affected by this stress, with at least one DE molecule in all three omics platforms used. The Cysteine and methionine metabolism (map00270) and Glycolysis/Gluconeogenesis (map00010) pathways were the most affected ones, each one with 20 DE molecules.
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Affiliation(s)
- Cleiton Barroso Bittencourt
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, Brazil; (C.B.B.); (T.L.C.d.S.); (L.R.V.)
| | - Thalliton Luiz Carvalho da Silva
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, Brazil; (C.B.B.); (T.L.C.d.S.); (L.R.V.)
| | | | - Letícia Rios Vieira
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, Brazil; (C.B.B.); (T.L.C.d.S.); (L.R.V.)
| | - André Pereira Leão
- Embrapa Agroenergia, Brasília 70770-901, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (P.V.A.)
| | | | | | | | - Manoel Teixeira Souza
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, Brazil; (C.B.B.); (T.L.C.d.S.); (L.R.V.)
- Embrapa Agroenergia, Brasília 70770-901, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (P.V.A.)
- Correspondence: ; Tel.: +55-61-3448-3210
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Combined Analysis of BSA-Seq Based Mapping, RNA-Seq, and Metabolomic Unraveled Candidate Genes Associated with Panicle Grain Number in Rice (Oryza sativa L.). Biomolecules 2022; 12:biom12070918. [PMID: 35883474 PMCID: PMC9313402 DOI: 10.3390/biom12070918] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 01/27/2023] Open
Abstract
Rice grain yield is a complex and highly variable quantitative trait consisting of several key components, including the grain weight, the effective panicles per unit area, and the grain number per panicle (GNPP). The GNPP is a significant contributor to grain yield controlled by multiple genes (QTL) and is crucial for improvement. Attempts have been made to find genes for this trait, which has always been a challenging and arduous task through conventional methods. We combined a BSA analysis, RNA profiling, and a metabolome analysis in the present study to identify new candidate genes involved in the GNPP. The F2 population from crossing R4233 (high GNPP) and Ce679 (low GNPP) revealed a frequency distribution fitting two segregated genes. Three pools, including low, middle, and high GNPP, were constructed and a BSA analysis revealed six candidate regions spanning 5.38 Mb, containing 739 annotated genes. Further, a conjunctive analysis of BSA-Seq and RNA-Seq showed 31 differentially expressed genes (DEGs) in the candidate intervals. Subsequently, a metabolome analysis showed 1024 metabolites, with 71 significantly enriched, including 44 up and 27 downregulated in Ce679 vs. R4233. A KEGG enrichment analysis of these 31 DEGs and 71 differentially enriched metabolites (DEMs) showed two genes, Os12g0102100 and Os01g0580500, significantly enriched in the metabolic pathways’ biosynthesis of secondary metabolites, cysteine and methionine metabolism, and fatty acid biosynthesis. Os12g0102100, which encodes for the alcohol dehydrogenase superfamily and a zinc-containing protein, is a novel gene whose contribution to the GNPP is not yet elucidated. This gene coding for mitochondrial trans-2-enoyl-CoA reductase is involved in the biosynthesis of myristic acid, also known as tetradecanoic acid. The Os01g0580500 coding for the enzyme 1-aminoclopropane-1-carboxylate oxidase (OsACO7) is responsible for the final step of the ethylene biosynthesis pathway through the conversion of 1-aminocyclopropane-1-carboxylic acid (ACC) into ethylene. Unlike Os12g0102100, this gene was significantly upregulated in R4233, downregulated in Ce679, and significantly enriched in two of the three metabolite pathways. This result pointed out that these two genes are responsible for the difference in the GNPP in the two cultivars, which has never been identified. Further validation studies may disclose the physiological mechanisms through which they regulate the GNPP in rice.
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