1
|
Zhang X, Xing T, Zhao L, Zhang L, Gao F. Transcriptomic meta-analysis and exploration of differentially expressed gene functions in wooden breast myopathy of broilers. Poult Sci 2024; 103:104047. [PMID: 39068695 PMCID: PMC11332813 DOI: 10.1016/j.psj.2024.104047] [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: 04/18/2024] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/30/2024] Open
Abstract
Wooden breast (WB) myopathy is a common myopathy found in commercial broiler chickens worldwide. Although extensive research on WB has been conducted using transcriptomics, effectively screening and analyzing key target information remains a challenge. In this present study, 5 transcriptomic datasets obtained from the National Center for Biotechnology Information (NCBI) were used. A meta-analysis was conducted to identify meta-differentially expressed genes (meta-DEGs) involved in the response of broilers to WB myopathy. These meta-DEGs were further analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA), supplemented by protein-protein interaction (PPI) network construction to pinpoint hub genes. These analyses help to reveal key genes, pathways, and biological processes associated with WB myopathy. The results showed that 645 up-regulated and 99 down-regulated significant meta-DEGs (|log2FC| ≥0.6, P-Meta < 0.05, and present in at least 4 datasets) were identified. GO analysis showed that multiple fibrosis-related pathways/biological processes, such as cell adhesion, connective tissue development, and collagen-rich extracellular matrix, as well as calcium ion binding were significantly upregulated. PPI analysis identified TGFB3, COL1A1, COL1A2, and COL3A1 as central hub genes involved in the fibrotic processes. KEGG analysis revealed significant upregulation of apoptosis and lysosomal pathways, with an enrichment of Ca2+-related signals and lysosomal cathepsins within the apoptosis pathway. Additionally, GSEA indicated a suppression of the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain (ETC) in WB myopathy, with PPI analysis also identifying specific hub genes associated with these pathways. In conclusion, our comprehensive analysis of meta-DEGs elucidated key biological processes and pathways implicated in WB myopathy, including fibrosis, apoptosis, altered calcium signaling, and metabolic disruption. The identification of specific hub genes offers avenues for further investigation into the pathogenesis of this condition, potentially guiding targeted therapeutic strategies.
Collapse
Affiliation(s)
- Xinrui Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing 210095, People' s Republic of China
| | - Tong Xing
- College of Animal Science and Technology, Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing 210095, People' s Republic of China
| | - Liang Zhao
- College of Animal Science and Technology, Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing 210095, People' s Republic of China
| | - Lin Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing 210095, People' s Republic of China
| | - Feng Gao
- College of Animal Science and Technology, Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing 210095, People' s Republic of China.
| |
Collapse
|
2
|
Wang J, Xia YC, Tian BX, Li JT, Li HY, Dong H, Li XG, Yu H, Zhu YY, Ma J, Jiang YJ, Jin GZ. Novel quantitative immunohistochemistry method using histone H3, family 3B as the internal reference standard for measuring human epidermal growth factor receptor 2 expression in breast cancer. Cancer 2024; 130:1424-1434. [PMID: 38217532 DOI: 10.1002/cncr.35176] [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: 08/09/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND Immunohistochemistry (IHC) is an essential technique in surgical and clinical pathology for detecting diagnostic, prognostic, and predictive biomarkers for personalized cancer therapy. However, the lack of standardization and reference controls results in poor reproducibility, and a reliable tool for IHC quantification is urgently required. The objective of this study was to describe a novel approach in which H3F3B (histone H3, family 3B) can be used as an internal reference standard to quantify protein expression levels using IHC. METHODS The authors enrolled 89 patients who had human epidermal growth factor receptor 2 (HER2)-positive breast cancer (BC). They used a novel IHC-based assay to measure protein expression using H3F3B as the internal reference standard. H3F3B was uniformly expressed at the protein level in all tumor regions in cancer tissues. HER2 expression levels were measured with the H-score using HALO software. RESULTS Kaplan-Meier analysis indicated that, among patients who had HER2-positive BC in The Cancer Genome Atlas data set and the authors' data set, the subgroup with low HER2 expression had a significantly better prognosis than the subgroup with high HER2 expression. Furthermore, the authors observed that HER2 expression levels were precisely evaluated using the proposed method, which can classify patients who are at higher risk of HER2-positive BC to receive trastuzumab-based adjuvant therapy. Dual-color IHC with H3F3B is an excellent tool for internal and external quality control of HER2 expression assays. CONCLUSIONS The proposed IHC-based quantification method accurately assesses HER2 expression levels and provides insights for predicting clinical prognosis in patients with HER2-positive BC who receive trastuzumab-based adjuvant therapy.
Collapse
Affiliation(s)
- Jie Wang
- Department of Breast Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ye-Chen Xia
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bao-Xing Tian
- Department of Breast Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ju-Tang Li
- Department of Obstetrics and Gynecology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Heng-Yu Li
- Department of Thyroid and Breast Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Hui Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Xiao-Guang Li
- Department of General Surgery, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Hua Yu
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Yu-Yao Zhu
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jun Ma
- Department of General Practitioners, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying-Jie Jiang
- Department of Pathology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Guang-Zhi Jin
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Interventional Radiology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
3
|
Suzuki S, Tanaka S, Kametani Y, Umeda A, Nishinaka K, Egawa K, Okada Y, Obana M, Fujio Y. Runx1 is upregulated by STAT3 and promotes proliferation of neonatal rat cardiomyocytes. Physiol Rep 2023; 11:e15872. [PMID: 38040660 PMCID: PMC10691971 DOI: 10.14814/phy2.15872] [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: 08/14/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
Though it is well known that mammalian cardiomyocytes exit cell cycle soon after birth, the mechanisms that regulate proliferation remain to be fully elucidated. Recent studies reported that cardiomyocytes undergo dedifferentiation before proliferation, indicating the importance of dedifferentiation in cardiomyocyte proliferation. Since Runx1 is expressed in dedifferentiated cardiomyocytes, Runx1 is widely used as a dedifferentiation marker of cardiomyocytes; however, little is known about the role of Runx1 in the proliferation of cardiomyocytes. The purpose of this study was to clarify the functional significance of Runx1 in cardiomyocyte proliferation. qRT-PCR analysis and immunoblot analysis demonstrated that Runx1 expression was upregulated in neonatal rat cardiomyocytes when cultured in the presence of FBS. Similarly, STAT3 was activated in the presence of FBS. Interestingly, knockdown of STAT3 significantly decreased Runx1 expression, indicating Runx1 is regulated by STAT3. We next investigated the effect of Runx1 on proliferation. Immunofluorescence microscopic analysis using an anti-Ki-67 antibody revealed that knockdown of Runx1 decreased the ratio of proliferating cardiomyocytes. Conversely, Runx1 overexpression using adenovirus vector induced cardiomyocyte proliferation in the absence of FBS. Finally, RNA-sequencing analysis revealed that Runx1 overexpression induced upregulation of cardiac fetal genes and downregulation of genes associated with fatty acid oxidation. Collectively, Runx1 is regulated by STAT3 and induces cardiomyocyte proliferation by juvenilizing cardiomyocytes.
Collapse
Affiliation(s)
- Shota Suzuki
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
| | - Shota Tanaka
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
| | - Yusuke Kametani
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
| | - Ayaka Umeda
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
| | - Kosuke Nishinaka
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
| | - Kaho Egawa
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
| | - Yoshiaki Okada
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
- Center for Infectious Disease Education and Research (CiDER)Osaka UniversitySuita CityOsakaJapan
| | - Masanori Obana
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
- Center for Infectious Disease Education and Research (CiDER)Osaka UniversitySuita CityOsakaJapan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative (OTRI)Osaka UniversitySuita CityOsakaJapan
- Global Center for Medical Engineering and Informatics (MEI)Osaka UniversitySuita CityOsakaJapan
- Radioisotope Research Center, Institute for Radiation SciencesOsaka UniversitySuita CityOsakaJapan
| | - Yasushi Fujio
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical SciencesOsaka UniversitySuita CityOsakaJapan
- Center for Infectious Disease Education and Research (CiDER)Osaka UniversitySuita CityOsakaJapan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative (OTRI)Osaka UniversitySuita CityOsakaJapan
| |
Collapse
|
4
|
Li Y, Shen X. Cadmium Exposure Affects Serum Metabolites and Proteins in the Male Guizhou Black Goat. Animals (Basel) 2023; 13:2705. [PMID: 37684969 PMCID: PMC10487163 DOI: 10.3390/ani13172705] [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: 07/11/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Food safety and environmental pollution are the hotspots of general concern globally. Notably, long-term accumulation of trace toxic heavy metals, such as cadmium (Cd), in animals may endanger human health via the food chain. The mechanism of Cd toxicity in the goat, a popular farmed animal, has not been extensively investigated to date. Therefore, in this study, ten male goats (Nubian black goat × native black goat) were exposed to Cd via drinking water containing CdCl2 (20 mg Cd·kg-1·BW) for 30 days (five male goats per group). In this study, we used an integrated approach combining proteomics and metabolomics to profile proteins and metabolites in the serum of Cd-exposed goats. It was found that Cd exposure impacted the levels of 30 serum metabolites and 108 proteins. The combined proteomic and metabolomic analysis revealed that Cd exposure affected arginine and proline metabolism, beta-alanine metabolism, and glutathione metabolism. Further, antioxidant capacity in the serum of goats exposed to Cd was reduced. We identified CKM and spermidine as potential protein and metabolic markers, respectively, of early Cd toxicity in the goat. This study details approaches for the early diagnosis and prevention of Cd-poisoned goats.
Collapse
Affiliation(s)
- Yuanfeng Li
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
| | - Xiaoyun Shen
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| |
Collapse
|