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Liang Y, Jiang L, Hu M, Luo X, Cheng T, Wang Y. Tea tree oil inhibits hydrogen sulfide-induced oxidative damage in chicken lungs through CYP450s/ROS pathway. Poult Sci 2024; 103:103860. [PMID: 38795514 PMCID: PMC11153251 DOI: 10.1016/j.psj.2024.103860] [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: 03/09/2024] [Revised: 05/05/2024] [Accepted: 05/12/2024] [Indexed: 05/28/2024] Open
Abstract
A large amount of hydrogen sulfide (H2S) is produced in the process of chicken breeding, which can cause serious inflammation and oxidative damage to the respiratory system of chickens. Tea tree oil (TTO) has antioxidant and anti-inflammatory properties. No studies have been reported on the use of TTO in H2S-induced lung injury in chickens. Therefore, in this study, 240 one-day-old Roman pink laying hens were randomly and equally divided into 3 groups: control group (CON), H2S exposure group (AVG, containing H2S), and TTO treatment group (TTG, containing H2S and 0.02 mL/L TTO) to establish an experimental model of TTO treatment with H2S exposure for a period of 42 d. Hematoxylin and eosin (H&E) staining was used to detect lung histopathology. Gene expression profiles were analyzed using transcriptomics. The underlying mechanism of the amelioration of lung injury by TTO was further revealed by antioxidant enzyme assays and qRT-PCR. The results showed that H2S exposure induced significant gene expression of CYP450s (CYP1B1 and CYP1C1) (P < 0.05), and caused intense oxidative stress, apoptosis and inflammation compared with CON. TTO could reduce ROS production and enhance antioxidant capacity (SOD, CAT, T-AOC, and GSH-PX) by regulating the CYP450s/ROS pathway (P < 0.05). Compared with the control group, the treatment group showed significantly decreased expression of apoptotic (Caspase-8, Caspase-3, Bid and Fas) (P < 0.05) and inflammatory (IL-4, IL-16, NF-κB, TNF-α and IFN-γ) (P < 0.05) factors in the lung. This study revealed that TTO regulated CYP450s/ROS pathway to alleviate H2S-induced lung injury in chickens. These results enrich the theory of the action mechanism of TTO on H2S-exposed chicken lungs and are of great value for the treatment of H2S-exposed animals.
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Affiliation(s)
- Yilei Liang
- Biomass Center, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000
| | - Li Jiang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000
| | - Mao Hu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000
| | - Xuegang Luo
- Biomass Center, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000
| | - Tingting Cheng
- Biomass Center, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000
| | - Yachao Wang
- Biomass Center, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China, 621000.
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2
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Chu LX, Wang WJ, Gu XP, Wu P, Gao C, Zhang Q, Wu J, Jiang DW, Huang JQ, Ying XW, Shen JM, Jiang Y, Luo LH, Xu JP, Ying YB, Chen HM, Fang A, Feng ZY, An SH, Li XK, Wang ZG. Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine. Mil Med Res 2024; 11:31. [PMID: 38797843 PMCID: PMC11129507 DOI: 10.1186/s40779-024-00537-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Aging and regeneration represent complex biological phenomena that have long captivated the scientific community. To fully comprehend these processes, it is essential to investigate molecular dynamics through a lens that encompasses both spatial and temporal dimensions. Conventional omics methodologies, such as genomics and transcriptomics, have been instrumental in identifying critical molecular facets of aging and regeneration. However, these methods are somewhat limited, constrained by their spatial resolution and their lack of capacity to dynamically represent tissue alterations. The advent of emerging spatiotemporal multi-omics approaches, encompassing transcriptomics, proteomics, metabolomics, and epigenomics, furnishes comprehensive insights into these intricate molecular dynamics. These sophisticated techniques facilitate accurate delineation of molecular patterns across an array of cells, tissues, and organs, thereby offering an in-depth understanding of the fundamental mechanisms at play. This review meticulously examines the significance of spatiotemporal multi-omics in the realms of aging and regeneration research. It underscores how these methodologies augment our comprehension of molecular dynamics, cellular interactions, and signaling pathways. Initially, the review delineates the foundational principles underpinning these methods, followed by an evaluation of their recent applications within the field. The review ultimately concludes by addressing the prevailing challenges and projecting future advancements in the field. Indubitably, spatiotemporal multi-omics are instrumental in deciphering the complexities inherent in aging and regeneration, thus charting a course toward potential therapeutic innovations.
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Affiliation(s)
- Liu-Xi Chu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xin-Pei Gu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Ping Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Quan Zhang
- Integrative Muscle Biology Laboratory, Division of Regenerative and Rehabilitative Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Jia Wu
- Key Laboratory for Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Da-Wei Jiang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun-Qing Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China
| | - Xin-Wang Ying
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jia-Men Shen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi Jiang
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Hua Luo
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 324025, Zhejiang, China
| | - Jun-Peng Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi-Bo Ying
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao-Man Chen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ao Fang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zun-Yong Feng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.
| | - Shu-Hong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
| | - Xiao-Kun Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Zhou-Guang Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.
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Baul S, Tanvir Ahmed K, Jiang Q, Wang G, Li Q, Yong J, Zhang W. Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks. Brief Bioinform 2024; 25:bbae316. [PMID: 38960406 PMCID: PMC11221891 DOI: 10.1093/bib/bbae316] [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: 02/23/2024] [Revised: 06/04/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024] Open
Abstract
Spatial transcriptomics data play a crucial role in cancer research, providing a nuanced understanding of the spatial organization of gene expression within tumor tissues. Unraveling the spatial dynamics of gene expression can unveil key insights into tumor heterogeneity and aid in identifying potential therapeutic targets. However, in many large-scale cancer studies, spatial transcriptomics data are limited, with bulk RNA-seq and corresponding Whole Slide Image (WSI) data being more common (e.g. TCGA project). To address this gap, there is a critical need to develop methodologies that can estimate gene expression at near-cell (spot) level resolution from existing WSI and bulk RNA-seq data. This approach is essential for reanalyzing expansive cohort studies and uncovering novel biomarkers that have been overlooked in the initial assessments. In this study, we present STGAT (Spatial Transcriptomics Graph Attention Network), a novel approach leveraging Graph Attention Networks (GAT) to discern spatial dependencies among spots. Trained on spatial transcriptomics data, STGAT is designed to estimate gene expression profiles at spot-level resolution and predict whether each spot represents tumor or non-tumor tissue, especially in patient samples where only WSI and bulk RNA-seq data are available. Comprehensive tests on two breast cancer spatial transcriptomics datasets demonstrated that STGAT outperformed existing methods in accurately predicting gene expression. Further analyses using the TCGA breast cancer dataset revealed that gene expression estimated from tumor-only spots (predicted by STGAT) provides more accurate molecular signatures for breast cancer sub-type and tumor stage prediction, and also leading to improved patient survival and disease-free analysis. Availability: Code is available at https://github.com/compbiolabucf/STGAT.
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Affiliation(s)
- Sudipto Baul
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, United States
| | - Khandakar Tanvir Ahmed
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, United States
| | - Qibing Jiang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, United States
| | - Guangyu Wang
- Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, United States
| | - Qian Li
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN 38105, United States
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, United States
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, United States
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Ji K, Zhong J, Cui L, Wang X, Chen LN, Wen B, Yang F, Deng W, Pan X, Wang L, Bao J, Chen Y, Liu H. Exploring myometrial microenvironment changes at the single-cell level from nonpregnant to term pregnant states. Physiol Genomics 2024; 56:32-47. [PMID: 37955337 PMCID: PMC11281821 DOI: 10.1152/physiolgenomics.00067.2023] [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: 07/10/2023] [Revised: 10/23/2023] [Accepted: 11/12/2023] [Indexed: 11/14/2023] Open
Abstract
The microenvironment and cell populations within the myometrium play crucial roles in maintaining uterine structural integrity and protecting the fetus during pregnancy. However, the specific changes occurring at the single-cell level in the human myometrium between nonpregnant (NP) and term pregnant (TP) states remain unexplored. In this study, we used single-cell RNA sequencing (scRNA-Seq) and spatial transcriptomics (ST) to construct a transcriptomic atlas of individual cells in the myometrium of NP and TP women. Integrated analysis of scRNA-Seq and ST data revealed spatially distinct transcriptional characteristics and examined cell-to-cell communication patterns based on ligand-receptor interactions. We identified and categorized 87,845 high-quality individual cells into 12 populations from scRNA-Seq data of 12 human myometrium tissues. Our findings demonstrated alterations in the proportions of five subpopulations of smooth muscle cells in TP. Moreover, an increase in monocytic cells, particularly M2 macrophages, was observed in TP myometrium samples, suggesting their involvement in the anti-inflammatory response. This study provides unprecedented single-cell resolution of the NP and TP myometrium, offering new insights into myometrial remodeling during pregnancy.NEW & NOTEWORTHY Using single-cell RNA sequencing and spatial transcriptomics, the myometrium was examined at the single-cell level during pregnancy. We identified spatially distinct cell populations and observed alterations in smooth muscle cells and increased M2 macrophages in term pregnant women. These findings offer unprecedented insights into myometrial remodeling and the anti-inflammatory response during pregnancy. The study advances our understanding of pregnancy-related myometrial changes.
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Affiliation(s)
- Kaiyuan Ji
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Junmin Zhong
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Long Cui
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xiaodi Wang
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Li-Na Chen
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Bolun Wen
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Fan Yang
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Wenfeng Deng
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xiuyu Pan
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lele Wang
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Junjie Bao
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - YunShan Chen
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Huishu Liu
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
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