1
|
Fang J, Wang Y, Li C, Liu W, Wang W, Wu X, Wang Y, Zhang S, Zhang J. A hypoxia-derived gene signature to suggest cisplatin-based therapeutic responses in patients with cervical cancer. Comput Struct Biotechnol J 2024; 23:2565-2579. [PMID: 38983650 PMCID: PMC11231957 DOI: 10.1016/j.csbj.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Cervical cancer remains a significant global public health concern, often exhibits cisplatin resistance in clinical settings. Hypoxia, a characteristic of cervical cancer, substantially contributes to cisplatin resistance. To evaluate the therapeutic efficacy of cisplatin in patients with cervical cancer and to identify potential effective drugs against cisplatin resistance, we established a hypoxia-inducible factor-1 (HIF-1)-related risk score (HRRS) model using clinical data from patients treated with cisplatin. Cox and LASSO regression analyses were used to stratify patient risks and prognosis. Through qRT-PCR, we validated nine potential prognostic HIF-1 genes that successfully predict cisplatin responsiveness in patients and cell lines. Subsequently, we identified fostamatinib, an FDA-approved spleen tyrosine kinase inhibitor, as a promising drug for targeting the HRRS-high group. We observed a positive correlation between the IC50 values of fostamatinib and HRRS in cervical cancer cell lines. Moreover, fostamatinib exhibited potent anticancer effects on high HRRS groups in vitro and in vivo. In summary, we developed a hypoxia-related gene signature that suggests cisplatin response prediction in cervical cancer and identified fostamatinib as a potential novel treatment approach for resistant cases.
Collapse
Affiliation(s)
- Jin Fang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Ying Wang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Chen Li
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Weixiao Liu
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Wannan Wang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Xuewei Wu
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Yang Wang
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Shuixing Zhang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| | - Jing Zhang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
- MOE Key Laboratory of Tumor Molecular Biology, The First Affiliated Hospital of Jinan University, Guangzhou 510613, China
| |
Collapse
|
2
|
Xie X, Zhang G, Liu N. Comprehensive analysis of abnormal methylation modification differential expression mRNAs between low-grade and high-grade intervertebral disc degeneration and its correlation with immune cells. Ann Med 2024; 56:2357742. [PMID: 38819022 PMCID: PMC11146251 DOI: 10.1080/07853890.2024.2357742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Intervertebral disc degeneration (IDD) is an important cause of low back pain. The aim of this study is to identify the potential molecular mechanism of abnormal methylation-modified DNA in the progression of IDD, hoping to contribute to the diagnosis and management of IDD. METHODS Low-grade IDD (grade I-II) and high-grade IDD (grade III-V) data were downloaded from GSE70362 and GSE129789 datasets. The abnormally methylated modified differentially expressed mRNAs (DEmRNAs) were identified by differential expression analysis (screening criteria were p < .05 and |logFC| > 1) and differential methylation analysis (screening criteria were p < .05 and |δβ| > 0.1). The classification models were constructed, and the receiver operating characteristic analysis was also carried out. In addition, functional enrichment analysis and immune correlation analysis were performed and the miRNAs targeted for the abnormally methylated DEmRNAs were predicted. Finally, expression validation was performed using real-time PCR. RESULTS Compared with low-grade IDD, seven abnormal methylation-modified DEmRNAs (AOX1, IBSP, QDPR, ABLIM1, CRISPLD2, ACTC1 and EMILIN1) were identified in high-grade IDD, and the classification models of random forests (RF) and support vector machine (SVM) were constructed. Moreover, seven abnormal methylation-modified DEmRNAs and classification models have high diagnostic accuracy (area under the curve [AUC] > 0.8). We also found that AUC values of single abnormal methylation-modified DEmRNA were all lower than those of RF and SVM classification models. Pearson correlation analysis found that macrophages M2 and EMILIN1 had significant negative correlation, while macrophages M2 and IBSP had significant positive correlation. In addition, four targeted relationship pairs (hsa-miR-4728-5p-QDPR, hsa-miR-4533-ABLIM1, hsa-miR-4728-5p-ABLIM1 and hsa-miR-4534-CRISPLD2) and multiple signalling pathways (for example, PI3K-AKT signalling pathway, osteoclast differentiation and calcium signalling pathway) were also identified that may be involved in the progression of IDD. CONCLUSION The identification of abnormal methylation-modified DEmRNAs and the construction of classification models in this study were helpful for the diagnosis and management of IDD progression.
Collapse
Affiliation(s)
- Xuehu Xie
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
| | - Guoqiang Zhang
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
| | - Ning Liu
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
| |
Collapse
|
3
|
Zhao Y, Yu ZM, Cui T, Li LD, Li YY, Qian FC, Zhou LW, Li Y, Fang QL, Huang XM, Zhang QY, Cai FH, Dong FJ, Shang DS, Li CQ, Wang QY. scBlood: A comprehensive single-cell accessible chromatin database of blood cells. Comput Struct Biotechnol J 2024; 23:2746-2753. [PMID: 39050785 PMCID: PMC11266868 DOI: 10.1016/j.csbj.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
The advent of single cell transposase-accessible chromatin sequencing (scATAC-seq) technology enables us to explore the genomic characteristics and chromatin accessibility of blood cells at the single-cell level. To fully make sense of the roles and regulatory complexities of blood cells, it is critical to collect and analyze these rapidly accumulating scATAC-seq datasets at a system level. Here, we present scBlood (https://bio.liclab.net/scBlood/), a comprehensive single-cell accessible chromatin database of blood cells. The current version of scBlood catalogs 770,907 blood cells and 452,247 non-blood cells from ∼400 high-quality scATAC-seq samples covering 30 tissues and 21 disease types. All data hosted on scBlood have undergone preprocessing from raw fastq files and multiple standards of quality control. Furthermore, we conducted comprehensive downstream analyses, including multi-sample integration analysis, cell clustering and annotation, differential chromatin accessibility analysis, functional enrichment analysis, co-accessibility analysis, gene activity score calculation, and transcription factor (TF) enrichment analysis. In summary, scBlood provides a user-friendly interface for searching, browsing, analyzing, visualizing, and downloading scATAC-seq data of interest. This platform facilitates insights into the functions and regulatory mechanisms of blood cells, as well as their involvement in blood-related diseases.
Collapse
Affiliation(s)
- Yu Zhao
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Zheng-Min Yu
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Ting Cui
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Li-Dong Li
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Yan-Yu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Feng-Cui Qian
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Li-Wei Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ye Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Qiao-Li Fang
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Xue-Mei Huang
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Qin-Yi Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Fu-Hong Cai
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Fu-Juan Dong
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - De-Si Shang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Chun-Quan Li
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Maternal and Child Health Care Hospital, National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Qiu-Yu Wang
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Maternal and Child Health Care Hospital, National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| |
Collapse
|
4
|
Song T, Wang R, Zhou X, Chen W, Chen Y, Liu Z, Men L. Metabolomics and molecular dynamics unveil the therapeutic potential of epalrestat in diabetic nephropathy. Int Immunopharmacol 2024; 140:112812. [PMID: 39094360 DOI: 10.1016/j.intimp.2024.112812] [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: 05/19/2024] [Revised: 07/12/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Diabetic nephropathy (DN) is one of the leading clinical causes of end-stage renal failure. The classical aldose reductase (AR) inhibitor epalrestat shows beneficial effect on renal dysfunction induced by DN, with metabolic profile and molecular mechanisms remains to be investigated further. In the current study, integrated untargeted metabolomics, network pharmacology and molecular dynamics approaches were applied to explore the therapeutic mechanisms of epalrestat against DN. Firstly, untargeted serum and urine metabolomics analysis based on UPLC-Q-TOF-MS was performed, revealed that epalrestat could regulate the metabolic disorders of amino acids metabolism, arachidonic acid metabolism, pyrimidine metabolism and citrate cycle metabolism pathways after DN. Subsequently, metabolomics-based network analysis was carried out to predict potential active targets of epalrestat, mainly involving AGE-RAGE signaling pathway, TNF signaling pathway and HIF-1 signaling pathway. Moreover, a 100 ns molecular dynamics approach was employed to validate the interactions between epalrestat and the core targets, showing that epalrestat could form remarkable tight binding with GLUT1 and NFκB than it with AR. Surface-plasmon resonance assay further verified epalrestat could bind GLUT1 and NFκB proteins specifically. Overall, integrated system network analysis not only demonstrated that epalrestat could attenuate DN induced metabolic disorders and renal injuries, but also revealed that it could interact with multi-targets to play a synergistic regulatory role in the treatment of DN.
Collapse
Affiliation(s)
- Tongtong Song
- College of Basic Medical Sciences, Jilin University, Changchun 130021, PR China
| | - Rongjin Wang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, PR China
| | - Xiaoyue Zhou
- The First Hospital of Jilin University, Changchun 130052, PR China
| | - Weijia Chen
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, PR China
| | - Ying Chen
- The First Hospital of Jilin University, Changchun 130052, PR China
| | - Zhongying Liu
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, PR China
| | - Lihui Men
- College of Basic Medical Sciences, Jilin University, Changchun 130021, PR China.
| |
Collapse
|
5
|
Chen JY, Li YF, Zhou Z, Jiang XM, Bi X, Yang MF, Zhao B. De novo mutations promote inflammation in children with STAT3 gain-of-function syndrome by affecting IL-1β expression. Int Immunopharmacol 2024; 140:112755. [PMID: 39098225 DOI: 10.1016/j.intimp.2024.112755] [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: 03/26/2024] [Revised: 07/09/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024]
Abstract
STAT3 gain-of-function syndrome, characterized by early-onset autoimmunity and primary immune regulatory disorder, remains poorly understood in terms of its immunological mechanisms. We employed whole-genome sequencing of familial trios to elucidate the pivotal role of de novo mutations in genetic diseases. We identified 37 high-risk pathogenic loci affecting 23 genes, including a novel STAT3 c.508G>A mutation. We also observed significant down-regulation of pathogenic genes in affected individuals, potentially associated with inflammatory responses regulated by PTPN14 via miR378c. These findings enhance our understanding of the pathogenesis of STAT3 gain-of-function syndrome and suggest potential therapeutic strategies. Notably, combined JAK inhibitors and IL-6R antagonists may offer promising treatment avenues for mitigating the severity of STAT3 gain-of-function syndrome.
Collapse
Affiliation(s)
- Ji-Yu Chen
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Yan-Fang Li
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Zhu Zhou
- Department of Nephrology, First Affiliated Hospital of Kunming Medical University, Yunnan Clinical Medical Research Center of Chronic Kidney Disease, Kunming 650032, Yunnan, China
| | - Xue-Mei Jiang
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Xin Bi
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Mi-Feng Yang
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Bo Zhao
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China.
| |
Collapse
|
6
|
Guo H, Zhang Y, Xiang X, Tang N, Gao W, Cui X. Single-cell RNA sequencing analysis provides novel insights into the role of apoptosis-related genes in muscle aging. Arch Gerontol Geriatr 2024; 125:105499. [PMID: 38852373 DOI: 10.1016/j.archger.2024.105499] [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: 04/05/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
OBJECTIVE This study employed a comprehensive single-cell analysis approach to explore the role of cell apoptosis-related genes in muscle aging. METHODS The single-cell RNA sequencing data from the GSE143704 dataset were used to identify distinct cell clusters and assess gene expression patterns related to apoptosis activation. The "limma" package was used to identify hub genes, after which we performed Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to identify relevant pathways. Additionally, Gene Set Enrichment Analysis(GSEA) and Gene Set Variation Analysis (GSVA) were used to uncover relevant biological pathways. The Receiver Operating Characteristic Curve (ROC) was used to evaluate the diagnostic value of the hub genes. Single-sample Gene Set Enrichment Analysis (ssGSEA) was used to analyze the immune cell infiltration levels. RESULTS Single-cell sequencing data from muscle aging patients allowed the identification of various cell types, including epithelial cells, adipocytes, and tissue-resident macrophages. By conducting a differential expression analysis that intersected active and nonactive apoptosis, as well as comparing elderly and young samples, a total of 22 hub genes were identified (p < 0.05). The 22 hub genes have discriminative ability as potential biomarkers for diagnosing muscle aging. The enrichment analysis indicated that these genes were closely associated with diverse pathways, including "response to UV-B" and "extracellular matrix organization" (p < 0.05). Furthermore, GSEA and GSVA indicated that multiple pathways emerged-for example, the "complement and coagulation cascades", "proteasome", "insulin signaling pathway", and "MAPK signaling pathway". Additionally, the analysis of immune cell infiltration revealed positive correlations between most of the hub genes and immune cells. CONCLUSION Our study identified 22 apoptosis-related genes involved in muscle aging and indicated their potential diagnostic value. These findings offer a novel perspective on the pathogenesis of muscle aging and present potential targets for therapeutic interventions.
Collapse
Affiliation(s)
- Hua Guo
- Department of General Medicine and Sleep Medicine Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University; Wuxi Medical Center, Nanjing Medical University Wuxi People's Hospital, Wuxi, Jiangsu Province, China
| | - Yunyun Zhang
- Department of General Medicine and Sleep Medicine Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University; Wuxi Medical Center, Nanjing Medical University Wuxi People's Hospital, Wuxi, Jiangsu Province, China
| | - Xin Xiang
- Nanjing Medical University, Nanjing, Jiangsu, China
| | - Na Tang
- Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Gao
- Department of Geriatrics, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China.
| | - Xiaochuan Cui
- Department of General Medicine and Sleep Medicine Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University; Wuxi Medical Center, Nanjing Medical University Wuxi People's Hospital, Wuxi, Jiangsu Province, China.
| |
Collapse
|
7
|
Roy R, Man E, Aldakhlallah R, Gonzalez K, Merritt L, Daisy C, Lombardo M, Yordanova V, Sun L, Isaac B, Rockowitz S, Lotz M, Pories S, Moses MA. Mammary adipocytes promote breast tumor cell invasion and angiogenesis in the context of menopause and obesity. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167325. [PMID: 38925485 DOI: 10.1016/j.bbadis.2024.167325] [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: 01/17/2024] [Revised: 06/03/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
The mechanism(s) underlying obesity-related postmenopausal (PM) breast cancer (BC) are not clearly understood. We hypothesized that the increased local presence of 'obese' mammary adipocytes within the BC microenvironment promotes the acquisition of an invasive and angiogenic BC cell phenotype and accelerates tumor proliferation and progression. BC cells, treated with primary mammary adipocyte secretome from premenopausal (Pre-M) and PM obese women (ObAdCM; obese adipocyte conditioned-media) upregulated the expression of several pro-tumorigenic factors including VEGF, lipocalin-2 and IL-6. Both Pre-M and PM ObAdCM stimulated endothelial cell recruitment and proliferation and significantly stimulated BC cell proliferation, migration and invasion. IL-6 and LCN2 induced STAT3/Akt signaling in BC cells and STAT3 inhibition abrogated the ObAdCM-stimulated BC cell proliferation and migration. Expression of proangiogenic regulators including VEGF, NRP1, NRP2, IL8RB, TGFβ2, and TSP-1 were found to be differentially regulated in mammary adipocytes from obese PM women. Comparative RNAseq indicated an upregulation of PI3K/Akt signaling, ECM-receptor interactions and lipid/fatty acid metabolism in PM versus Pre-M mammary adipocytes. Our results demonstrate that irrespective of menopausal status, cross-talk between obese mammary adipocytes and BC cells promotes tumor aggressiveness and suggest that targeting the LCN2/IL-6/STAT3 signaling axis may be a useful strategy in obesity-driven breast tumorigenesis.
Collapse
Affiliation(s)
- Roopali Roy
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School and Boston Children's Hospital, Boston, MA, USA.
| | - Emily Man
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA
| | - Rama Aldakhlallah
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA
| | | | - Lauren Merritt
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA
| | - Cassandra Daisy
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA
| | - Michael Lombardo
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School and Boston Children's Hospital, Boston, MA, USA
| | | | - Liang Sun
- Research Computing and Information Technology, Boston Children's Hospital, Boston, MA, USA
| | - Biju Isaac
- Research Computing and Information Technology, Boston Children's Hospital, Boston, MA, USA
| | - Shira Rockowitz
- Research Computing and Information Technology, Boston Children's Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Margaret Lotz
- Hoffman Breast Center, Mount Auburn Hospital, Cambridge, MA, USA
| | - Susan Pories
- Department of Surgery, Harvard Medical School and Boston Children's Hospital, Boston, MA, USA; Hoffman Breast Center, Mount Auburn Hospital, Cambridge, MA, USA
| | - Marsha A Moses
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School and Boston Children's Hospital, Boston, MA, USA.
| |
Collapse
|
8
|
Zhang Y, Tu J, Wang J, Dai T, Zheng L, Sun S, Tu C, Li H, Qian L. NFKBIE is a predictive factor of survival and is correlated with immune infiltration and antigen processing and presentation in hepatocellular carcinoma. Oncol Lett 2024; 28:480. [PMID: 39161335 PMCID: PMC11332585 DOI: 10.3892/ol.2024.14613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 02/21/2024] [Indexed: 08/21/2024] Open
Abstract
The important role of the nuclear factor κB (NFκB) pathway in tumour development has long been recognized; however, the role of the NFκB inhibitor family in liver cancer has not been elucidated. Hepatocellular carcinoma (HCC) is a serious public health burden with a high incidence, poor prognosis, and early detection, especially in Asia, where hepatitis is prevalent. In the present study, the mRNA expression level of the NFκB inhibitor family was assessed in HCC and normal tissues using the Metabolic Gene Rapid Visualizer, University of Alabama at Birmingham Cancer Data Analysis Portal, and the Tumor Immune Estimation Resource database (TIMER). Survival curves of nuclear factor of κ light polypeptide gene enhancer in B-cells inhibitor (NFKBI)E were obtained using the Kaplan-Meier method. Genes co-expressed with NFKBIE in HCC samples were studied using data from the LinkedOmics and the Hepatocellular Carcinoma Databases. Protein-protein interaction networks, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment pathway analyses were used to assess the NFKBIE mechanism in HCC. Using the TIMER database, the association between immune infiltration and NFKBIE was determined. RNA-sequencing (RNA-seq) was used to evaluate the function of NFKBIE in HCC and its impact on proliferation and migration. Western blotting was used to confirm the expression of NFKBIE in HCC cell lines. In addition, NFKBIE overexpression in HCC was demonstrated using tissue microarrays encompassing 80 pairs of HCC and normal liver tissues. NFKBIE was the only NFκB inhibitor with high expression and an improved prognosis in HCC compared with other NFκB inhibitors. NFKBIE was correlated with clinical characteristics, such as tumour grade, tumour protein P53 mutation status and tumour stage. Data obtained from Gene Set Cancer Analysis suggested that NFKBIE may inhibit the PI3K/AKT, RAS/MAPK, RTK and TSC/mTOR pathways. In addition, NFKBIE was significantly associated with B-cell immune infiltration and the RNA-seq data demonstrated that knockdown of NFKBIE significantly affected 'Antigen processing and presentation' and 'hepatocellular carcinoma' pathways. Immunohistochemistry of microarrays of tissue samples revealed that NFKBIE was overexpressed in several stages of HCC. Finally, inhibition of NFKBIE decreased the proliferation and migration of HCC cells. In conclusion, due to its prognostic value and overexpression in HCC, NFKBIE distinguished itself from other NFκB inhibitors. As such, it may provide a novel prognostic indicator and immunotherapeutic target for HCC.
Collapse
Affiliation(s)
- Yang Zhang
- Department of Comprehensive Surgery, The First Affiliated Hospital of University of Science and Technology of China West District, Hefei, Anhui 230031, P.R. China
| | - Jinqi Tu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui 241001, P.R. China
| | - Jian Wang
- Department of Comprehensive Surgery, The First Affiliated Hospital of University of Science and Technology of China West District, Hefei, Anhui 230031, P.R. China
| | - Tiancheng Dai
- Department of Medical Laboratory Technology, The First Clinical College of Anhui Medical University, Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Lin Zheng
- Department of Comprehensive Surgery, The First Affiliated Hospital of University of Science and Technology of China West District, Hefei, Anhui 230031, P.R. China
| | - Sinan Sun
- Department of Radiation Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230031, P.R. China
| | - Conyin Tu
- Department of Comprehensive Surgery, The First Affiliated Hospital of University of Science and Technology of China West District, Hefei, Anhui 230031, P.R. China
| | - Heng Li
- Department of Comprehensive Surgery, The First Affiliated Hospital of University of Science and Technology of China West District, Hefei, Anhui 230031, P.R. China
| | - Liting Qian
- Department of Radiation Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230031, P.R. China
| |
Collapse
|
9
|
Rojo MD, Bandyopadhyay I, Burke CM, Sturtz AD, Phillips ES, Matherne MG, Embrey SJ, LaRue R, Qiu Y, Schwertfeger KL, Machado HL. C/EBPβ deletion in macrophages impairs mammary gland alveolar budding during the estrous cycle. Life Sci Alliance 2024; 7:e202302516. [PMID: 39025525 PMCID: PMC11258408 DOI: 10.26508/lsa.202302516] [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: 12/08/2023] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
Macrophages have important roles in mammary gland development and tissue homeostasis, but the specific mechanisms that regulate macrophage function need further elucidation. We have identified C/EBPβ as an important transcription factor expressed by multiple macrophage populations in the normal mammary gland. Mammary glands from mice with C/EBPβ-deficient macrophages (Cebpb ΔM) show a significant decrease in alveolar budding during the diestrus stage of the reproductive cycle, whereas branching morphogenesis remains unchanged. Defects in alveolar budding were found to be the result of both systemic hormones and local macrophage-directed signals. RNA sequencing shows significant changes in PR-responsive genes and alterations in the Wnt landscape of mammary epithelial cells of Cebpb ΔM mice, which regulate stem cell expansion during diestrus. Cebpb ΔM macrophages demonstrate a shift from a pro-inflammatory to a tissue-reparative phenotype, and exhibit increased phagocytic capacity as compared to WT. Finally, Cebpb ΔM macrophages down-regulate Notch2 and Notch3, which normally promote stem cell expansion during alveolar budding. These results suggest that C/EBPβ is an important macrophage factor that facilitates macrophage-epithelial crosstalk during a key stage of mammary gland tissue homeostasis.
Collapse
Affiliation(s)
- Michelle D Rojo
- https://ror.org/04vmvtb21 Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Ishitri Bandyopadhyay
- https://ror.org/04vmvtb21 Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Caitlin M Burke
- https://ror.org/04vmvtb21 Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Alexa D Sturtz
- https://ror.org/04vmvtb21 Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Emily S Phillips
- https://ror.org/04vmvtb21 Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Megan G Matherne
- https://ror.org/04vmvtb21 Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samuel J Embrey
- https://ror.org/04vmvtb21 Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Rebecca LaRue
- Department of Laboratory Medicine and Pathology, Masonic Cancer Center, and Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Yinjie Qiu
- Department of Laboratory Medicine and Pathology, Masonic Cancer Center, and Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn L Schwertfeger
- Department of Laboratory Medicine and Pathology, Masonic Cancer Center, and Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Heather L Machado
- https://ror.org/04vmvtb21 Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
- Tulane Cancer Center, Louisiana Cancer Research Consortium, New Orleans, LA, USA
| |
Collapse
|
10
|
Zhang M, Ma J, Zeng FY, Hou XH. Network pharmacology combined with molecular docking revealed the potential targets of Coridius chinensis in prostate cancer treatment. World J Clin Cases 2024; 12:6094-6104. [DOI: 10.12998/wjcc.v12.i27.6094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/23/2024] [Accepted: 07/15/2024] [Indexed: 07/29/2024] Open
Abstract
BACKGROUND Prostate cancer (PCa) has high morbidity and mortality rates in elderly men. With a history of thousands of years, traditional Chinese medicine derived from insects could be an important source for developing cancer-targeted drugs to prevent tumorigenesis, enhance therapeutic effects, and reduce the risk of recurrence and metastasis. Multiple studies have shown that Coridius chinensis (Cc) has anticancer effects.
AIM To elucidate the mechanism of action of Cc against PCa via network pharmacology and molecular docking.
METHODS Potential targets for Cc and PCa were predicted using ChemDraw 19.0 software, the PharmMapper database and the GeneCards database. Then, the STRING database was used to construct the protein–protein interaction network. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and molecular docking analyses were subsequently conducted to identify the key targets, active ingredients and pathways involved.
RESULTS GO and KEGG analyses indicated that the PI3K-Akt signalling pathway was the critical pathway (P value < 1.0 × 10-8). Multiple targeting ingredients that can affect multiple pathways in PCa have been identified in Cc. Seven active compounds (asponguanosines A, asponguanine B, asponguanine C, aspongpyrazine A, N-acetyldopamine, aspongadenine B and aspongpyrazine B) were selected for molecular docking with 9 potential targets, and the results revealed that aspongpyrazine A and asponguanosine A are the main components by which Cc affects PCa (affinity<-5 kcal/mol, hydrogen bonding), but more studies are needed.
CONCLUSION We used network pharmacology to predict the bioactive components and important targets of Cc for the treatment of PCa, supporting the development of Cc as a natural anticancer agent.
Collapse
Affiliation(s)
- Mei Zhang
- School of Preclinical Medicine, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Jing Ma
- School of Preclinical Medicine, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Feng-Yin Zeng
- School of Preclinical Medicine, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Xiao-Hui Hou
- School of Preclinical Medicine, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| |
Collapse
|
11
|
Li J, Wu K, Liu X, Yang D, Xie J, Wang Y, Liu K, Wang Z, Liu W, Jiang L. Anti-Toxoplasma gondii effects of XYP1-derived peptides and regulatory mechanisms of XYP1. Parasit Vectors 2024; 17:376. [PMID: 39232817 DOI: 10.1186/s13071-024-06455-7] [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: 05/28/2024] [Accepted: 08/16/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Toxoplasmosis, caused by Toxoplasma gondii , poses serious health issues for humans and animals. Individuals with impaired immune systems are more susceptible to severe toxoplasmosis. Pregnant women infected by T. gondii can face the possibility of birth defects and miscarriages. While pyrimethamine and sulfadiazine are commonly used drugs in clinical practice, concerns over their side effects and resistance are on the rise. A spider peptide XYP1 isolated from Lycosa coelestis had potent anti-T. gondii effects, but it had a high synthesis cost and strong cytotoxicity. METHODS This study intended to modify XYP1 for producing derived peptides via amino acid truncation and substitution. The anti-T. gondii effect was evaluated by trypan blue staining assay and killing experiment of RH strain tachyzoites. The CCK8 and hemolysis assays were used to compare their safeties. The morphological changes of T. gondii were observed by scanning electron microscope and transmission electron microscope. In addition, the mechanism of XYP1 against T. gondii through RNA-sequencing was further explored. RESULTS In vivo and in vitro experiments revealed that XYP1-18 and XYP1-18-1 had excellent anti-T. gondii activity with lower cytotoxicity and hemolysis activity than XYP1. XYP1, XYP1-18, and XYP1-18-1 were able to disrupt the surface membrane integrity of T. gondii tachyzoites, forming pores and causing the disruption of organelles. Furthermore, RNA-sequencing analysis indicated that XYP1 could stimulate the host immune response to effectively eliminate T. gondii and lessen the host's inflammatory reaction. CONCLUSIONS XYP1-18 had lower cytotoxicity and hemolysis activity than XYP1, as well as significantly extending the survival time of the mice. XYP1 played a role in host inflammation and immune responses, revealing its potential mechanism. Our research provided valuable insights into the development and application of peptide-based drugs, offering novel strategies and directions for treating toxoplasmosis.
Collapse
Affiliation(s)
- Jing Li
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Kaijuan Wu
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Xiaohua Liu
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Dongqian Yang
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Jing Xie
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yixiao Wang
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Kang Liu
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Zheng Wang
- Department of Vascular Surgery, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Wei Liu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, China
| | - Liping Jiang
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China.
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, 410013, Hunan, China.
| |
Collapse
|
12
|
Vivier S, Bray F, Flament S, Guilbert L, Renaud F, Rolando C, Launay D, Dubucquoi S, Sobanski V. Analysis of Unfolded Protein Response Activation in Colon Adenocarcinoma Epithelial Cells: A Proteomic Study. Proteomics Clin Appl 2024:e202400008. [PMID: 39226110 DOI: 10.1002/prca.202400008] [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: 02/02/2024] [Revised: 07/26/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024]
Abstract
PURPOSE High throughput technologies have identified molecular patterns in colorectal cancer (CRC) cells, aiding in modeling responses to anti-cancer treatments. The different responses observed depend on the type of cancer, the tumour grade and the functional programme of the cancer cells. Recent studies suggest that the unfolded protein response (UPR), autophagy and apoptosis could be involved in treatment resistance mechanisms by interacting with the tumour microenvironment (TME). EXPERIMENTAL DESIGN We analysed by LC-MS/MS the proteome of two representative colon adenocarcinoma epithelial cell lines from different tumour grades (CCL-233 and CCL-221) at the basal state or after the UPR induction. RESULTS Cell lines expressed a different proteome on about 10% of their total proteins identified, especially on UPR, autophagy and apoptosis pathways proteins at basal state. After UPR induction, the proteome of the cells was modified with a greater adaptive response to cellular stress in CCL-221 cells where the UPR was strongly activated at the basal state. CONCLUSIONS AND CLINICAL RELEVANCE CRC cell lines at different tumour grades expressed different functional programmes at the proteomic level and were characterised by different responses to the UPR induction. This study suggests that baseline cancer cell stress status could have an impact on the efficiency of cancer therapies.
Collapse
Affiliation(s)
- Solange Vivier
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Fabrice Bray
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Stéphanie Flament
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Lucile Guilbert
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- Institut d'Immunologie, Centre de Biologie Pathologie, CHU Lille, Lille, Hauts-de-France, France
| | - Florence Renaud
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Christian Rolando
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - David Launay
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes et Auto-inflammatoires Systémiques Rares du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), Lille, Hauts-de-France, France
| | - Sylvain Dubucquoi
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- Institut d'Immunologie, Centre de Biologie Pathologie, CHU Lille, Lille, Hauts-de-France, France
| | - Vincent Sobanski
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes et Auto-inflammatoires Systémiques Rares du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), Lille, Hauts-de-France, France
- Institut Universitaire de France (IUF), Paris, France
| |
Collapse
|
13
|
Zhang L, Li Y, Fu C, Yang L, Li G, Wu Y, Tong H, Tian G, Wang K, Wang J, Ying X, Li Z. Exploration and validation of ceRNA regulatory networks in colorectal cancer based on associations whole transcriptome sequencing. Sci Rep 2024; 14:20446. [PMID: 39227669 DOI: 10.1038/s41598-024-71465-5] [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: 02/16/2024] [Accepted: 08/28/2024] [Indexed: 09/05/2024] Open
Abstract
Colorectal cancer (CRC) is a wide-spread gastrointestinal cancer that is associated with augmented morbidity and mortality, and we do not yet have a deep understanding of its epidemiology and carcinogenicity. The transcriptome can reveal the complexity and heterogeneity of tumors and uncover new biomarkers or treatment options. In this study, we identified messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), round RNAs (circRNAs), and microRNAs (miRNAs) using whole-transcriptome sequencing and generated competing endogenous RNA (ceRNA) modulatory axes. We conducted whole transcriptome sequencing on 10 CRC and para-cancer (CRCP) samples and discovered 2465 differentially expressed (DE) mRNAs (DEmRNAs), 77 DE miRNAs (DEmiRNAs). 2852 DE lncRNAs (DElncRNAs) and 1477 DE circRNAs (DEcircRNAs). In addition, utilizing co-DE analysis, we generated the ceRNA axis. Subsequently, we employed the ceRNA axis to identify essential genes and corresponding associations with lncRNAs, circRNAs, and miRNAs in CRC. ceRNA regulatory network including mRNA-miRNA-lncRNA and mRNA-miRNA-circRNA. These modulatory axes potentially modulate the positive regulation of smooth muscle contraction, melanosome, plasma membrane, integral plasma membrane component and so on. Finally, the results of RNA sequencing (RNA-SEQ) were combined with the TCGA and GEO databases, and the DEGs strongly correlated with the TCGA-COAD overall survival (OS) as estimated by univariate cox and logarithmic rank analyses were cross-analyzed, and the co-upregulated DEGs were screened. Among the many DEs, KPNA2 was chosen for additional analysis. Using invitro experimentations, western blot, CCK8, EdU and other experiments were performed to verify the results. We found siRNA-based KPNA2 depletion reduces bladder cancer cells' viability, migratory, and proliferative activities, which showed that the DEmRNA profiles were comparable to the sequencing information, confirming that the sequencing data were very reliable. These evidences highlight the ceRNA regulatory mechanisms in CRC and will aid future research into the molecular mechanisms behind colorectal cancer prevention and treatment.
Collapse
Affiliation(s)
- Lulu Zhang
- Medical research center, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Yulei Li
- Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Chao Fu
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - LiXia Yang
- Medical research center, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Gang Li
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Yiyang Wu
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Huanjun Tong
- Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Guojiang Tian
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Kaifang Wang
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau Special Adiministrative Region, China
| | - Jun Wang
- Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Xiaojiang Ying
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China.
| | - Zhenjun Li
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China.
| |
Collapse
|
14
|
Kim CY, Park Y, Namgung JY, Park Y, Park BY. The macroscale routing mechanism of structural brain connectivity related to body mass index. Hum Brain Mapp 2024; 45:e70019. [PMID: 39230183 DOI: 10.1002/hbm.70019] [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: 10/20/2023] [Revised: 08/05/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024] Open
Abstract
Understanding the brain's mechanisms in individuals with obesity is important for managing body weight. Prior neuroimaging studies extensively investigated alterations in brain structure and function related to body mass index (BMI). However, how the network communication among the large-scale brain networks differs across BMI is underinvestigated. This study used diffusion magnetic resonance imaging of 290 young adults to identify links between BMI and brain network mechanisms. Navigation efficiency, a measure of network routing, was calculated from the structural connectivity computed using diffusion tractography. The sensory and frontoparietal networks indicated positive associations between navigation efficiency and BMI. The neurotransmitter association analysis identified that serotonergic and dopaminergic receptors, as well as opioid and norepinephrine systems, were related to BMI-related alterations in navigation efficiency. The transcriptomic analysis found that genes associated with network routing across BMI overlapped with genes enriched in excitatory and inhibitory neurons, specifically, gene enrichments related to synaptic transmission and neuron projection. Our findings suggest a valuable insight into understanding BMI-related alterations in brain network routing mechanisms and the potential underlying cellular biology, which might be used as a foundation for BMI-based weight management.
Collapse
Affiliation(s)
- Chae Yeon Kim
- Department of Data Science, Inha University, Incheon, South Korea
| | - Yunseo Park
- Department of Data Science, Inha University, Incheon, South Korea
| | | | - Yeongjun Park
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Bo-Yong Park
- Department of Brain and Cognitive Engineering, Korea University, Seoul, South Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea
- Research Center for Small Businesses Ecosystem, Inha University, Incheon, South Korea
| |
Collapse
|
15
|
Hua W, Qi J, Zhou M, Han S, Xu X, Su J, Pan T, Wu D, Han Y. Overexpression of REC8 induces aberrant gamete meiotic division and contributes to AML pathogenesis - a multiplexed microarray analysis and mendelian randomization study. Ann Hematol 2024; 103:3563-3572. [PMID: 39012516 DOI: 10.1007/s00277-024-05882-x] [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: 03/08/2024] [Accepted: 07/04/2024] [Indexed: 07/17/2024]
Abstract
Acute myeloid leukemia (AML) is a notably lethal disease, characterized by malignant clonal proliferation of hematopoietic stem cells in the bone marrow. This study seeks to unveil potential therapeutic targets for AML, using a combined approach of microarray analysis and Mendelian randomization (MR). We collected data samples from the Gene Expression Omnibus (GEO) database and extracted pQTL data from genome-wide association studies (GWAS) to identify overlapping genes between the DEGs and GWAS data. Gene enrichment and pathway annotation analyses were performed on these genes. Furthermore, we validated gene expression levels and assessed their clinical relevance. By taking the intersection of these gene sets, we obtained a list of co-expressed genes, including four upregulated genes (REC8, TPM2, ZMIZ1, CD82) and two downregulated genes (IFNAR1, TMCO3). MR analysis demonstrated that genetically predicted protein levels of CD82, REC8, ZMIZ1, and TPM2 were significantly associated with increased odds of AML, while IFNAR1 and TMCO3 showed a protective effect. Gene ontology and KEGG pathway analyses revealed significant enrichment in functions related to female gamete generation, meiosis, p53 signaling pathway, and cardiac muscle contraction. Differences in immune cell profiles were observed between AML survivors and those with poor prognosis, including lower levels of neutrophils and higher levels of follicular helper T cells in the latter group. This study identifies a causal relationship between gene expression and AML and highlights the potential role of REC8 in leukemogenesis, possibly through its impact on gametocyte meiotic abnormalities. The findings provide new insights into the prevention and treatment of leukemia.
Collapse
Affiliation(s)
- Wenxi Hua
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jiaqian Qi
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Meng Zhou
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Shiyu Han
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaoyan Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Jinwen Su
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Tingting Pan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
| | - Yue Han
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
| |
Collapse
|
16
|
Barrios-Núñez I, Martínez-Redondo G, Medina-Burgos P, Cases I, Fernández R, Rojas A. Decoding functional proteome information in model organisms using protein language models. NAR Genom Bioinform 2024; 6:lqae078. [PMID: 38962255 PMCID: PMC11217674 DOI: 10.1093/nargab/lqae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/31/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested how two different machine learning-based methods performed when decoding functional information from the proteomes of selected model organisms. We found that protein language models are more precise and informative than deep learning methods for all the species tested and across the three gene ontologies studied, and that they better recover functional information from transcriptomic experiments. The results obtained indicate that these language models are likely to be suitable for large-scale annotation and downstream analyses, and we recommend a guide for their use.
Collapse
Affiliation(s)
- Israel Barrios-Núñez
- Computational Biology and Bioinformatics Group, Andalusian Center for Developmental Biology (CABD-CSIC), 41013 Sevilla, Spain
| | | | - Patricia Medina-Burgos
- Computational Biology and Bioinformatics Group, Andalusian Center for Developmental Biology (CABD-CSIC), 41013 Sevilla, Spain
| | - Ildefonso Cases
- Bioinformatics Unit, Andalusian Center for Developmental Biology (CABD-CSIC), 41013 Sevilla, Spain
| | - Rosa Fernández
- Metazoa Phylogenomics Lab, Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Ana M Rojas
- Computational Biology and Bioinformatics Group, Andalusian Center for Developmental Biology (CABD-CSIC), 41013 Sevilla, Spain
| |
Collapse
|
17
|
Huang Y, Shan X, Zhang C, Duan Y. Pseudomonas protegens volatile organic compounds inhibited brown rot of postharvest peach fruit by repressing the pathogenesis-related genes in Monilinia fructicola. Food Microbiol 2024; 122:104551. [PMID: 38839219 DOI: 10.1016/j.fm.2024.104551] [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: 01/28/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/07/2024]
Abstract
Brown rot, caused by Monilinia fructicola, is considered one of the devasting diseases of pre-harvest and post-harvest peach fruits, restricting the yield and quality of peach fruits and causing great economic losses to the peach industry every year. Presently, the management of the disease relies heavily on chemical control. In the study, we demonstrated that the volatile organic compounds (VOCs) of endophyte bacterial Pseudomonas protegens QNF1 inhibited the mycelial growth of M. fructicola by 95.35% compared to the control, thereby reducing the brown rot on postharvest fruits by 98.76%. Additionally, QNF1 VOCs severely damaged the mycelia of M. fructicola. RNA-seq analysis revealed that QNF1 VOCs significantly repressed the expressions of most of the genes related to pathogenesis (GO:0009405) and integral component of plasma membrane (GO:0005887), and further analysis revealed that QNF1 VOCs significantly altered the expressions of the genes involved in various metabolism pathways including Amino acid metabolism, Carbohydrate metabolism, and Lipid metabolism. The findings of the study indicated that QNF1 VOCs displayed substantial control efficacy by disrupting the mycelial morphology of M. fructicola, weakening its pathogenesis, and causing its metabolic disorders. The study provided a potential way and theoretical support for the management of the brown rot of peach fruits.
Collapse
Affiliation(s)
- Yonghong Huang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China; Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China; National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China; Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China.
| | - Xiaoying Shan
- College of Horticulture, Qingdao Agricultural University, Qingdao, China; Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China; National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China; Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Cuifang Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China; Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China; National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China; Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Yanxin Duan
- College of Horticulture, Qingdao Agricultural University, Qingdao, China; Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China; National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China; Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China.
| |
Collapse
|
18
|
Zhao R, Ran L, Yao H, He Y, Lu X, Zhu W, Zhang Y, Zhang T, Shi S, Luo Z, Zhang C. Moxibustion ameliorates ovarian function in premature ovarian insufficiency rats by activating cAMP/PKA/CREB to promote steroidogenesis in ovarian granulosa cells. J Steroid Biochem Mol Biol 2024; 242:106547. [PMID: 38754522 DOI: 10.1016/j.jsbmb.2024.106547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/05/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
Premature ovarian insufficiency (POI) presents a substantial challenge to women's physiological and psychological well-being. Hormone replacement therapy, as the preferred therapeutic approach, involves solely exogenous supplementation of estrogen. Moxibustion, a traditional Chinese external treatment, has been investigated in our previous studies. It not only improves hormone levels and clinical symptoms in POI patients but also safeguards ovarian reserve. This study aims to explore the regulatory mechanisms by which moxibustion modulates hormone levels and restores ovarian function in POI. A POI rat model was established using cyclophosphamide, and moxibustion treatment was applied at acupoints "CV4" and "SP6" for a total of four courses. Subsequently, ovaries from each group were subjected to transcriptome sequencing (Bulk RNA-seq). Target pathways and key genes were selected through enrichment analysis and GSVA scoring, with validation using various techniques including electron microscopy, ELISA, Western blot, and immunohistochemistry. The results demonstrated that moxibustion restored the estrous cycle in POI rats, improved sex hormone levels, reduced the number of atretic follicles, and increased the count of dominant follicles (P<0.05). Bulk RNA-seq analysis revealed that moxibustion downregulated pathways associated with ovarian dysfunction, infertility, and immune responses, upregulated pathways related to follicular development and ovarian steroidogenesis. Furthermore, our data confirmed that moxibustion significantly increased the number of ovarian granulosa cells (GCs) and upregulated the expression of proteins related to steroidogenesis in GCs, including FSHR, P450 arom, cAMP, PKA, and CREB (P<0.05), with no significant effect observed on proteins related to steroidogenesis in theca cells. These outcomes aligned with the RNA-seq results. In conclusion, these findings propose that moxibustion enhances steroidogenesis in GCs through the activation of the cAMP/PKA/CREB pathway, consequently improving impaired ovarian function in POI rats. This study provides robust evidence supporting moxibustion as a targeted intervention for treating POI by specifically regulating steroidogenesis in GCs.
Collapse
Affiliation(s)
- Rui Zhao
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Lingxiang Ran
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China; Department of Urology, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Hanyue Yao
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Yizhi He
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Xinru Lu
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Weina Zhu
- Central Laboratory, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China; Department of Biobank, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Yajie Zhang
- Central Laboratory, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China; Department of Biobank, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Tianyi Zhang
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Shijie Shi
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Zheng Luo
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China
| | - Cairong Zhang
- Department of Acupuncture and Moxibustion, Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China.
| |
Collapse
|
19
|
Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024; 25:639-657. [PMID: 38565962 PMCID: PMC11330371 DOI: 10.1038/s41576-024-00711-3] [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] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
Collapse
Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| |
Collapse
|
20
|
Zhao C, Chen J, Tian L, Wen Y, Wu M, Tang L, Zhou A, Xie W, Dong T. Gandouling ameliorates liver injury in Wilson's disease through the inhibition of ferroptosis by regulating the HSF1/HSPB1 pathway. J Cell Mol Med 2024; 28:e70018. [PMID: 39223962 PMCID: PMC11369335 DOI: 10.1111/jcmm.70018] [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: 05/04/2024] [Revised: 07/18/2024] [Accepted: 08/10/2024] [Indexed: 09/04/2024] Open
Abstract
Ferroptosis, an iron-dependent form of cell death, plays a crucial role in the progression of liver injury in Wilson's disease (WD). Gandouling (GDL) has emerged as a potential therapeutic agent for preventing and treating liver injury in WD. However, the precise mechanisms by which GDL mitigates ferroptosis in WD liver injury remain unclear. In this study, we discovered that treating Toxic Milk (TX) mice with GDL effectively decreased liver copper content, corrected iron homeostasis imbalances, and lowered lipid peroxidation levels, thereby preventing ferroptosis and improving liver injury. Bioinformatics analysis and machine learning algorithms identified Hspb1 as a pivotal regulator of ferroptosis. GDL treatment significantly upregulated the expression of HSPB1 and its upstream regulatory factor HSF1, thereby activating the HSF1/HSPB1 pathway. Importantly, inhibition of this pathway by NXP800 reversed the protective effects of GDL on ferroptosis in the liver of TX mice. In conclusion, GDL shows promise in alleviating liver injury in WD by inhibiting ferroptosis through modulation of the HSF1/HSPB1 pathway, suggesting its potential as a novel therapeutic agent for treating liver ferroptosis in WD.
Collapse
Affiliation(s)
- Chenling Zhao
- Department of NeurologyThe First Affiliated Hospital of Anhui University of Chinese MedicineHefeiChina
| | - Jie Chen
- Department of NeurologyThe First Affiliated Hospital of Anhui University of Chinese MedicineHefeiChina
| | - Liwei Tian
- Department of NeurologyThe First Affiliated Hospital of Anhui University of Chinese MedicineHefeiChina
| | - Yuya Wen
- Department of NeurologyThe First Affiliated Hospital of Anhui University of Chinese MedicineHefeiChina
| | - Mingcai Wu
- School of Basic Medical SciencesWannan Medical CollegeWuhuChina
| | - Lulu Tang
- Department of NeurologyThe First Affiliated Hospital of Anhui University of Chinese MedicineHefeiChina
- Key Laboratory of Xin'An MedicineMinistry of EducationHefeiChina
| | - An Zhou
- The Experimental Research CenterAnhui University of Chinese MedicineHefeiChina
| | - Wenting Xie
- Department of NeurologyThe First Affiliated Hospital of Anhui University of Chinese MedicineHefeiChina
- Key Laboratory of Xin'An MedicineMinistry of EducationHefeiChina
| | - Ting Dong
- Department of NeurologyThe First Affiliated Hospital of Anhui University of Chinese MedicineHefeiChina
- Key Laboratory of Xin'An MedicineMinistry of EducationHefeiChina
| |
Collapse
|
21
|
Xu S, Zheng Y, Ye M, Shen T, Zhang D, Li Z, Lu Z. Comprehensive pan-cancer analysis reveals EPHB2 is a novel predictive biomarker for prognosis and immunotherapy response. BMC Cancer 2024; 24:1064. [PMID: 39198775 PMCID: PMC11351591 DOI: 10.1186/s12885-024-12843-0] [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: 07/10/2024] [Accepted: 08/22/2024] [Indexed: 09/01/2024] Open
Abstract
PURPOSE Recent studies have increasingly linked Ephrin receptor B2 (EPHB2) to cancer progression. However, comprehensive investigations into the immunological roles and prognostic significance of EPHB2 across various cancers remain lacking. METHODS We employed various databases and bioinformatics tools to investigate the impact of EPHB2 on prognosis, immune infiltration, genome instability, and response to immunotherapy. Validation of the correlation between EPHB2 expression and M2 macrophages included analyses using bulk and single-cell transcriptomic datasets, spatial transcriptomics, and multi-fluorescence staining. Moreover, we performed cMap web tool to screen for EPHB2-targeted compounds and assessed their potential through molecular docking and dynamics simulations. Additionally, in vitro validation using lung adenocarcinoma (LUAD) cell lines was conducted to confirm the bioinformatics predictions about EPHB2. RESULTS EPHB2 dysregulation was observed across multiple cancer types, where it demonstrated significant diagnostic and prognostic value. Gene Set Enrichment Analysis (GSEA) indicated that EPHB2 is involved in enhancing cellular proliferation, invasiveness of cancer cells, and modulation of the anti-cancer immune response. Furthermore, it is emerged as a pan-cancer marker for M2 macrophage infiltration, supported by integrated analyses of transcriptomics and multiple fluorescence staining. In LUAD cells, knockdown of EPHB2 expression led to a decrease in both cell proliferation and migratory activity. CONCLUSION EPHB2 expression may serve as a pivotal indicator of M2 macrophage infiltration, offering vital insights into tumor dynamics and progression across various cancers, including lung adenocarcinoma, highlighting its significant prognostic and therapeutic potential for further exploration.
Collapse
Affiliation(s)
- Shengshan Xu
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China.
| | - Youbin Zheng
- Department of Radiology, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, Guangdong, China
| | - Min Ye
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Tao Shen
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Dongxi Zhang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Zumei Li
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Zhuming Lu
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China.
| |
Collapse
|
22
|
Wang J, Wang R, Luo F, Du W, Hou J, Chen G, Tang X, Wu J, Wang W, Huang B, Wang C, Yuan L. Comparative Morphological, Physiological, and Transcriptomic Analyses of Diploid and Tetraploid Wucai ( Brassica campestris L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:2341. [PMID: 39204777 PMCID: PMC11359193 DOI: 10.3390/plants13162341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/10/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Polyploid plants often exhibit superior yield, stress resistance, and quality. In this study, homologous tetraploid wucai (Brassica campestris L.) was successfully obtained by spraying seedling growth points with colchicine. The morphological, cytological, and physiological characteristics of diploid and tetraploid wucai were analyzed, and transcriptomic sequencing was performed at three stages of development. Tetraploid seedings grew slowly but exhibited darker leaves, enlarged organs and cells, increased stomatal volume, decreased stomatal density, improved nutritional content, and enhanced photosynthesis. Differentially expressed genes (DEGs) identified in diploid and tetraploid plants at three stages of development were enriched in different pathways. Notably, DEGs identified in the tetraploid plants were specifically enriched in starch and sucrose metabolism, pentose and glucuronate interconversions, and ascorbate and aldarate metabolism. In addition, we found that the light green module was most relevant to ploidy, and DEGs in this module were significantly enriched in the glycolysis/gluconeogenesis and TCA cycle pathways. The differential expression of key glycolysis-associated genes at different developmental stages may be the driver of the observed differences between diploid and tetraploid wucai. This study lays a technical foundation for the development of polyploid wucai germplasm resources as well as the breeding of new varieties with improved quality, yield, and stress resistance. It also provides a good empirical reference for the genetic breeding of closely related Brassica species.
Collapse
Affiliation(s)
- Jian Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Ruxi Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Fan Luo
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Wenjing Du
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Xiaoyan Tang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jianqiang Wu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Wenjie Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Bin Huang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (J.W.); (R.W.); (F.L.); (W.D.); (J.H.); (G.C.); (X.T.); (J.W.); (W.W.); (B.H.)
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| |
Collapse
|
23
|
Shubhanjali S, Mohapatra T, Khan R, Dixit M. Unveiling FRG1's DNA repair role in breast cancer. Sci Rep 2024; 14:19371. [PMID: 39169067 PMCID: PMC11339311 DOI: 10.1038/s41598-024-70368-9] [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: 10/16/2023] [Accepted: 08/16/2024] [Indexed: 08/23/2024] Open
Abstract
The FRG1(FSHD region gene 1) gene has emerged as a pivotal tumor suppressor in both breast and prostate cancer. HPF1 (Histone PARylation Factor 1), a gene crucial in the base excision repair (BER) mechanism for single-stranded DNA (ssDNA) lesions, showcases a robust correlation with FRG1. This implies that FRG1 might have the capacity to influence BER via HPF1, potentially playing a role in tumorigenesis. Using a comprehensive approach that integrates in-silico analyses involving differential gene expression, KEGG (Kyoto Encyclopedia of Genes and Genomes), GO (Gene Ontology), and STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) databases, we unravelled the intricate network of genes and pathways influenced by FRG1, which includes BER. Our linear regression analysis unveiled a positive relationship between FRG1 and key genes crucial for BER. Notably, breast cancer patients with low FRG1 expression exhibited a significantly higher frequency of mutation in TP53. To enhance the accuracy of our analysis, we conducted qRT-PCR assays, which demonstrated that FRG1 affects the transcription of DNA base excision repair genes, showing differential expression in breast cancer cells. Moreover, through the Alkaline Comet Assay, a technique that quantifies DNA damage at the single-cell level, we observed diminished DNA repair capabilities when FRG1 levels are low. Risk scores were calculated using the Cox regression coefficients, and we found notable differences in Overall Survival (OS) and mRNA expression of DEGs in the low and high-risk groups. In summary, our findings shed light on the pivotal role of FRG1 in maintaining DNA repair efficiency within breast cancer cells.
Collapse
Affiliation(s)
- Shubhanjali Shubhanjali
- School of Biological Sciences, National Institute of Science Education and Research, Room No. 204, PO: Jatani, Khurda, Bhubaneswar, Odisha, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Talina Mohapatra
- School of Biological Sciences, National Institute of Science Education and Research, Room No. 204, PO: Jatani, Khurda, Bhubaneswar, Odisha, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Rehan Khan
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Manjusha Dixit
- School of Biological Sciences, National Institute of Science Education and Research, Room No. 204, PO: Jatani, Khurda, Bhubaneswar, Odisha, 752050, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| |
Collapse
|
24
|
Lv W, Xie H, Wu S, Dong J, Jia Y, Ying H. Identification of key metabolism-related genes and pathways in spontaneous preterm birth: combining bioinformatic analysis and machine learning. Front Endocrinol (Lausanne) 2024; 15:1440436. [PMID: 39229380 PMCID: PMC11368757 DOI: 10.3389/fendo.2024.1440436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
Background Spontaneous preterm birth (sPTB) is a global disease that is a leading cause of death in neonates and children younger than 5 years of age. However, the etiology of sPTB remains poorly understood. Recent evidence has shown a strong association between metabolic disorders and sPTB. To determine the metabolic alterations in sPTB patients, we used various bioinformatics methods to analyze the abnormal changes in metabolic pathways in the preterm placenta via existing datasets. Methods In this study, we integrated two datasets (GSE203507 and GSE174415) from the NCBI GEO database for the following analysis. We utilized the "Deseq2" R package and WGCNA for differentially expressed genes (DEGs) analysis; the identified DEGs were subsequently compared with metabolism-related genes. To identify the altered metabolism-related pathways and hub genes in sPTB patients, we performed multiple functional enrichment analysis and applied three machine learning algorithms, LASSO, SVM-RFE, and RF, with the hub genes that were verified by immunohistochemistry. Additionally, we conducted single-sample gene set enrichment analysis to assess immune infiltration in the placenta. Results We identified 228 sPTB-related DEGs that were enriched in pathways such as arachidonic acid and glutathione metabolism. A total of 3 metabolism-related hub genes, namely, ANPEP, CKMT1B, and PLA2G4A, were identified and validated in external datasets and experiments. A nomogram model was developed and evaluated with 3 hub genes; the model could reliably distinguish sPTB patients and term labor patients with an area under the curve (AUC) > 0.75 for both the training and validation sets. Immune infiltration analysis revealed immune dysregulation in sPTB patients. Conclusion Three potential hub genes that influence the occurrence of sPTB through shadow participation in placental metabolism were identified; these results provide a new perspective for the development and targeting of treatments for sPTB.
Collapse
Affiliation(s)
- Wenqi Lv
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai, China
| | - Han Xie
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai, China
| | - Shengyu Wu
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai, China
| | - Jiaqi Dong
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai, China
| | - Yuanhui Jia
- Department of Clinical Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai, sChina
| | - Hao Ying
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai, China
- Department of Clinical Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai, sChina
| |
Collapse
|
25
|
Wang Y, Di Y, Li Y, Lu J, Ji B, Zhang Y, Chen Z, Chen S, Liu B, Tang R. Role of sphingolipid metabolism signaling in a novel mouse model of renal osteodystrophy based on transcriptomic approach. Chin Med J (Engl) 2024:00029330-990000000-01181. [PMID: 39149978 DOI: 10.1097/cm9.0000000000003261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Renal osteodystrophy (ROD) is a skeletal pathology associated with chronic kidney disease-mineral and bone disorder (CKD-MBD) that is characterized by aberrant bone mineralization and remodeling. ROD increases the risk of fracture and mortality in CKD patients. The underlying mechanisms of ROD remain elusive, partially due to the absence of an appropriate animal model. To address this gap, we established a stable mouse model of ROD using an optimized adenine-enriched diet and conducted exploratory analyses through ribonucleic acid sequencing (RNA-seq). METHODS Male 8-week-old C57BL/6J mice were randomly allocated into three groups: control group (n = 5), adenine and high-phosphate (HP) diet group (n = 20), and the optimized adenine-containing diet group (n = 20) for 12 weeks. We assessed the skeletal characteristics of model mice through blood biochemistry, microcomputed tomography (micro-CT), and bone histomorphometry. RNA-seq was utilized to profile gene expression changes of ROD. We elucidated the functions of differentially expressed genes (DEGs) using gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and gene set enrichment analysis (GSEA). DEGs were validated via quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS By the fifth week, adenine followed by an HP diet induced rapid weight loss and high mortality rates in the mouse group, precluding further model development. Mice with optimized adenine diet-induced ROD displayed significant abnormalities in serum creatinine and blood urea nitrogen levels, accompanied by pronounced hyperparathyroidism and hyperphosphatemia. The femur bone mineral density (BMD) of the model mice was lower than that of control mice, with substantial bone loss and cortical porosity. ROD mice exhibited substantial bone turnover with an increase in osteoblast and osteoclast markers. Transcriptomic profiling revealed 1907 genes with upregulated expression and 723 genes with downregulated expression in the femurs of ROD mice relative to those of control mice. Pathway analyses indicated significant enrichment of upregulated genes in the sphingolipid metabolism pathway. The significant upregulation of alkaline ceramidase 1 (Acer1), alkaline ceramidase 2 (Acer2), prosaposin-like 1 (Psapl1), adenosine A1 receptor (Adora1), and sphingosine-1-phosphate receptor 5 (S1pr5) were successfully validated in mouse femurs by qRT-PCR. CONCLUSIONS Optimized adenine diet mouse model may be a valuable proxy for studying ROD. RNA-seq analysis revealed that the sphingolipid metabolism pathway is likely a key player in ROD pathogenesis, thereby providing new avenues for therapeutic intervention.
Collapse
Affiliation(s)
- Yujia Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| | - Yan Di
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| | - Yongqi Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| | - Jing Lu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| | - Bofan Ji
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| | - Yuxia Zhang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| | - Zhiqing Chen
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| | - Sijie Chen
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| | - Bicheng Liu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu 210003, China
| | - Rining Tang
- Institute of Nephrology, NanJing LiShui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University School of Medicine, Nanjing, Jiangsu 211200, China
| |
Collapse
|
26
|
Gupta P, Jaiswal P. Transcriptional Modulation during Photomorphogenesis in Rice Seedlings. Genes (Basel) 2024; 15:1072. [PMID: 39202430 PMCID: PMC11353317 DOI: 10.3390/genes15081072] [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: 07/19/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. The study aims to reveal differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs), their light-induced alternative splicing, and their association with biological pathways. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of a successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data. This study provides insights on light-regulated gene expression and alternative splicing in rice.
Collapse
Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| |
Collapse
|
27
|
Massey S, Ang CS, Davidson NM, Quigley A, Rollo B, Harris AR, Kapsa RMI, Christodoulou J, J Van Bergen N. Novel CDKL5 targets identified in human iPSC-derived neurons. Cell Mol Life Sci 2024; 81:347. [PMID: 39136782 PMCID: PMC11335273 DOI: 10.1007/s00018-024-05389-8] [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: 03/26/2024] [Revised: 07/01/2024] [Accepted: 07/31/2024] [Indexed: 08/22/2024]
Abstract
CDKL5 Deficiency Disorder (CDD) is a debilitating epileptic encephalopathy disorder affecting young children with no effective treatments. CDD is caused by pathogenic variants in Cyclin-Dependent Kinase-Like 5 (CDKL5), a protein kinase that regulates key phosphorylation events in neurons. For therapeutic intervention, it is essential to understand molecular pathways and phosphorylation targets of CDKL5. Using an unbiased phosphoproteomic approach we identified novel targets of CDKL5, including GTF2I, PPP1R35, GATAD2A and ZNF219 in human iPSC-derived neuronal cells. The phosphoserine residue in the target proteins lies in the CDKL5 consensus motif. We validated direct phosphorylation of GTF2I and PPP1R35 by CDKL5 using complementary approaches. GTF2I controls axon guidance, cell cycle and neurodevelopment by regulating expression of neuronal genes. PPP1R35 is critical for centriole elongation and cilia morphology, processes that are impaired in CDD. PPP1R35 interacts with CEP131, a known CDKL5 phospho-target. GATAD2A and ZNF219 belong to the Nucleosome Remodelling Deacetylase (NuRD) complex, which regulates neuronal activity-dependent genes and synaptic connectivity. In-depth knowledge of molecular pathways regulated by CDKL5 will allow a better understanding of druggable disease pathways to fast-track therapeutic development.
Collapse
Affiliation(s)
- Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Ching-Seng Ang
- The Bio21 Institute of Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Nadia M Davidson
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, 3052, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Anita Quigley
- Electrical and Biomedical Engineering, School of Engineering, RMIT University, Melbourne, VIC, Australia
- Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
- Centre for Clinical Neurosciences and Neurological Research, St. Vincent's Hospital Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
- Department of Medicine, St Vincent's Hospital Melbourne, The University of Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
| | - Ben Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Alexander R Harris
- Department of Biomedical Engineering, University of Melbourne, Melbourne, 3010, Australia
| | - Robert M I Kapsa
- Electrical and Biomedical Engineering, School of Engineering, RMIT University, Melbourne, VIC, Australia
- Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
- Centre for Clinical Neurosciences and Neurological Research, St. Vincent's Hospital Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
- Department of Medicine, St Vincent's Hospital Melbourne, The University of Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, 3052, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, 3052, Australia.
- Department of Paediatrics, University of Melbourne, c/o MCRI, 50 Flemington Road, Parkville, VIC, 3052, Australia.
| |
Collapse
|
28
|
Gao Y, Song B, Wang M, Yang F, Yu C, Chen H. Complete genome sequence of Erwinia amylovora PBI209 isolated from a necrotic flower of Pyrus sinkiangensis in China. Microbiol Resour Announc 2024; 13:e0029124. [PMID: 38967467 PMCID: PMC11320953 DOI: 10.1128/mra.00291-24] [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: 03/22/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024] Open
Abstract
Here, we report the complete genome sequence of Erwinia amylovora PBI209 that causes fire blight isolated from a necrotic flower of Pyrus sinkiangensis in Xinjiang, China. The genome consists of 3,800,955 bp, with 3,403 protein-coding genes and a guanine-cytosine content of 53.61%.
Collapse
Affiliation(s)
- Ya Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Song
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi, China
- Xinjiang Key Laboratory of Agricultural Biosafety Urumqi, Urumqi, China
| | - Meihong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
29
|
Zhou J, Huang M. Navigating the landscape of enzyme design: from molecular simulations to machine learning. Chem Soc Rev 2024; 53:8202-8239. [PMID: 38990263 DOI: 10.1039/d4cs00196f] [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: 07/12/2024]
Abstract
Global environmental issues and sustainable development call for new technologies for fine chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the alternative to the traditional organic synthesis. However, it is challenging to navigate the vast sequence space to identify those proteins with admirable biocatalytic functions. The recent development of deep-learning based structure prediction methods such as AlphaFold2 reinforced by different computational simulations or multiscale calculations has largely expanded the 3D structure databases and enabled structure-based design. While structure-based approaches shed light on site-specific enzyme engineering, they are not suitable for large-scale screening of potential biocatalysts. Effective utilization of big data using machine learning techniques opens up a new era for accelerated predictions. Here, we review the approaches and applications of structure-based and machine-learning guided enzyme design. We also provide our view on the challenges and perspectives on effectively employing enzyme design approaches integrating traditional molecular simulations and machine learning, and the importance of database construction and algorithm development in attaining predictive ML models to explore the sequence fitness landscape for the design of admirable biocatalysts.
Collapse
Affiliation(s)
- Jiahui Zhou
- School of Chemistry and Chemical Engineering, Queen's University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK.
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK.
| |
Collapse
|
30
|
Li X, Mao X, Jiang H, Xia C, Fu L, Gao W, Chen W, Li W, Wang P, Zhang Y, Xu H. Shirebi granules ameliorate acute gouty arthritis by inhibiting NETs-induced imbalance between immunity and inflammation. Chin Med 2024; 19:105. [PMID: 39123236 PMCID: PMC11312299 DOI: 10.1186/s13020-024-00962-6] [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: 02/29/2024] [Accepted: 06/17/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Acute gouty arthritis (AGA) is classified as 'arthritis' in traditional Chinese medicine (TCM) theory. Shirebi granules (SGs), derived from the classic prescription SiMiaoWan, exerts satisfying therapeutic efficacy in ameliorating AGA clinically. However, the underlying mechanisms of SGs against AGA remain unclarified. METHODS AGA-related biological processes, signal pathways and biomarker genes were mined from the GEO database through bioinformatics. SGs components were systematically recognized using the UPLC-Q-TOF-MS/MS. A correlation network was established based on the biomarker genes and the chemical components, from which the signal pathway used for further study was selected. Finally, we established an AGA model using SD rats injected with monosodium urate (MSU) in the ankle joint for experimental validation. A combination of behavioral tests, H&E, safranin O- fast green, western blotting, and immunofluorescence were employed to reveal the mechanism of action of SGs on AGA. RESULTS The deterioration of AGA was significantly related to the imbalance between immunity and inflammation, neutrophil chemotaxis and inflammatory factor activation. HDAC5, PRKCB, NFκB1, MPO, PRKCA, PIK3CA were identified to be the candidate targets of SGs against AGA, associated with neutrophil extracellular traps (NETs) signal pathway. Animal experiments demonstrated that SGs effectively repaired cartilage damage, blocked TLR4 activation, and inhibited the expression of NETs indicators and inflammatory factors. In addition, SGs prominently alleviated joint redness and swelling, improved joint dysfunction, inhibited inflammatory infiltration of AGA rats. CONCLUSION Our data reveal that SGs may effectively alleviate the disease severity of AGA by suppressing NETs-promoted imbalance between immunity and inflammation.
Collapse
Affiliation(s)
- Xin Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Xia Mao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Hong Jiang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Cong Xia
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Lu Fu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Wenjing Gao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Wenjia Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Weijie Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Ping Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Yanqiong Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China.
| | - Haiyu Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China.
| |
Collapse
|
31
|
Islamaj R, Lai PT, Wei CH, Luo L, Almeida T, Jonker RAA, Conceição SIR, Sousa DF, Phan CP, Chiang JH, Li J, Pan D, Meesawad W, Tsai RTH, Sarol MJ, Hong G, Valiev A, Tutubalina E, Lee SM, Hsu YY, Li M, Verspoor K, Lu Z. The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. Database (Oxford) 2024; 2024:baae069. [PMID: 39114977 PMCID: PMC11306928 DOI: 10.1093/database/baae069] [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: 03/19/2024] [Revised: 05/27/2024] [Accepted: 07/09/2024] [Indexed: 08/11/2024]
Abstract
The BioRED track at BioCreative VIII calls for a community effort to identify, semantically categorize, and highlight the novelty factor of the relationships between biomedical entities in unstructured text. Relation extraction is crucial for many biomedical natural language processing (NLP) applications, from drug discovery to custom medical solutions. The BioRED track simulates a real-world application of biomedical relationship extraction, and as such, considers multiple biomedical entity types, normalized to their specific corresponding database identifiers, as well as defines relationships between them in the documents. The challenge consisted of two subtasks: (i) in Subtask 1, participants were given the article text and human expert annotated entities, and were asked to extract the relation pairs, identify their semantic type and the novelty factor, and (ii) in Subtask 2, participants were given only the article text, and were asked to build an end-to-end system that could identify and categorize the relationships and their novelty. We received a total of 94 submissions from 14 teams worldwide. The highest F-score performances achieved for the Subtask 1 were: 77.17% for relation pair identification, 58.95% for relation type identification, 59.22% for novelty identification, and 44.55% when evaluating all of the above aspects of the comprehensive relation extraction. The highest F-score performances achieved for the Subtask 2 were: 55.84% for relation pair, 43.03% for relation type, 42.74% for novelty, and 32.75% for comprehensive relation extraction. The entire BioRED track dataset and other challenge materials are available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BC8-BioRED-track/ and https://codalab.lisn.upsaclay.fr/competitions/13377 and https://codalab.lisn.upsaclay.fr/competitions/13378. Database URL: https://ftp.ncbi.nlm.nih.gov/pub/lu/BC8-BioRED-track/https://codalab.lisn.upsaclay.fr/competitions/13377https://codalab.lisn.upsaclay.fr/competitions/13378.
Collapse
Affiliation(s)
- Rezarta Islamaj
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20894, United States
| | - Po-Ting Lai
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20894, United States
| | - Chih-Hsuan Wei
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20894, United States
| | - Ling Luo
- School of Computer Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian 116024, China
| | - Tiago Almeida
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Informatics Engineering of Aveiro (IEETA), University of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - Richard A A Jonker
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Informatics Engineering of Aveiro (IEETA), University of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - Sofia I R Conceição
- Departamento de Informática, Faculdade de Ciências da Universidade de Lisboa, Edifício C6 Campo Grande, Lisbon 1749-016, Portugal
| | - Diana F Sousa
- Departamento de Informática, Faculdade de Ciências da Universidade de Lisboa, Edifício C6 Campo Grande, Lisbon 1749-016, Portugal
| | - Cong-Phuoc Phan
- Department of Computer Science and Information Engineering, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan, Republic of China
| | - Jung-Hsien Chiang
- Department of Computer Science and Information Engineering, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan, Republic of China
| | - Jiru Li
- School of Computer Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian 116024, China
| | - Dinghao Pan
- School of Computer Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian 116024, China
| | - Wilailack Meesawad
- Department of Computer Science and Information Engineering, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan, Republic of China
| | - Richard Tzong-Han Tsai
- Department of Computer Science and Information Engineering, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan, Republic of China
- Research Center for Humanities and Social Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang District, Taoyuan City 115201, Taiwan, Republic of China
| | - M Janina Sarol
- School of Information Sciences, University of Illinois at Urbana-Champaign, 614 E. Daniel St, Champaign, IL 61820, United States
| | - Gibong Hong
- School of Information Sciences, University of Illinois at Urbana-Champaign, 614 E. Daniel St, Champaign, IL 61820, United States
| | - Airat Valiev
- Higher School of Economics University, 20 Myasnitskaya st, Moscow 101000, Russia
| | - Elena Tutubalina
- Higher School of Economics University, 20 Myasnitskaya st, Moscow 101000, Russia
- Kazan Federal University, 18 Kremlevskaya st, Kazan, Russia 420008, Russia
| | - Shao-Man Lee
- Miin Wu School of Computing, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan, Republic of China
| | - Yi-Yu Hsu
- Miin Wu School of Computing, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan, Republic of China
| | - Mingjie Li
- School of Computing Technologies, RMIT University, 124 La Trobe Street, Melbourne, Victoria 3000, Australia
| | - Karin Verspoor
- School of Computing Technologies, RMIT University, 124 La Trobe Street, Melbourne, Victoria 3000, Australia
| | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20894, United States
| |
Collapse
|
32
|
Wu X, Chen H, Ge Z, Luo B, Pan H, Shen Y, Xie Z, Zhou C. A novel mitochondria-related algorithm for predicting the survival outcomes and drug sensitivity of patients with lung adenocarcinoma. Front Mol Biosci 2024; 11:1397281. [PMID: 39184152 PMCID: PMC11342398 DOI: 10.3389/fmolb.2024.1397281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/26/2024] [Indexed: 08/27/2024] Open
Abstract
Background Mitochondria have always been considered too be closely related to the occurrence and development of malignant tumors. However, the bioinformatic analysis of mitochondria in lung adenocarcinoma (LUAD) has not been reported yet. Methods In the present study, we constructed a novel and reliable algorithm, comprising a consensus cluster analysis and risk assessment model, to predict the survival outcomes and tumor immunity for patients with terminal LUAD. Results Patients with LUAD were classified into three clusters, and patients in cluster 1 exhibited the best survival outcomes. The patients in cluster 3 had the highest expression of PDL1 (encoding programmed cell death 1 ligand 11) and HAVCR2 (encoding Hepatitis A virus cellular receptor 2), and the highest tumor mutation burden (TMB). In the risk assessment model, patients in the low-risk group tended to have a significantly better survival outcome. Furthermore, the risk score combined with stage could act as a reliable independent prognostic indicator for patients with LUAD. The prognostic signature is a novel and effective biomarker to select anti-tumor drugs. Low-risk patients tended to have a higher expression of CTLA4 (encoding cytotoxic T-lymphocyte associated protein 4) and HAVCR2. Moreover, patients in the high-risk group were more sensitive to Cisplatin, Docetaxel, Erlotinib, Gemcitabine, and Paclitaxel, while low-risk patients would probably benefit more from Gefitinib. Conclusion We constructed a novel and reliable algorithm comprising a consensus cluster analysis and risk assessment model to predict survival outcomes, which functions as a reliable guideline for anti-tumor drug treatment for patients with terminal LUAD.
Collapse
Affiliation(s)
- Xianqiao Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Hang Chen
- Department of Thoracic Surgery, Ningbo Medical Center LiHuiLi Hospital, Ningbo, Zhejiang, China
| | - Zhen Ge
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Binyu Luo
- Department of Thoracic Surgery, Ningbo Medical Center LiHuiLi Hospital, Ningbo, Zhejiang, China
| | - Hanbo Pan
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiming Shen
- Department of Otology and Skull Base Surgery, Eye Ear Nose and Throat Hospital, Fudan University, Shanghai, China
| | - Zuorun Xie
- Department of Thoracic Surgery, Ningbo Medical Center LiHuiLi Hospital, Ningbo, Zhejiang, China
| | - Chengwei Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| |
Collapse
|
33
|
Knoll R, Helbig ET, Dahm K, Bolaji O, Hamm F, Dietrich O, van Uelft M, Müller S, Bonaguro L, Schulte-Schrepping J, Petrov L, Krämer B, Kraut M, Stubbemann P, Thibeault C, Brumhard S, Theis H, Hack G, De Domenico E, Nattermann J, Becker M, Beyer MD, Hillus D, Georg P, Loers C, Tiedemann J, Tober-Lau P, Lippert L, Millet Pascual-Leone B, Tacke F, Rohde G, Suttorp N, Witzenrath M, Saliba AE, Ulas T, Polansky JK, Sawitzki B, Sander LE, Schultze JL, Aschenbrenner AC, Kurth F. The life-saving benefit of dexamethasone in severe COVID-19 is linked to a reversal of monocyte dysregulation. Cell 2024; 187:4318-4335.e20. [PMID: 38964327 DOI: 10.1016/j.cell.2024.06.014] [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: 07/24/2023] [Revised: 02/27/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
Dexamethasone is a life-saving treatment for severe COVID-19, yet its mechanism of action is unknown, and many patients deteriorate or die despite timely treatment initiation. Here, we identify dexamethasone treatment-induced cellular and molecular changes associated with improved survival in COVID-19 patients. We observed a reversal of transcriptional hallmark signatures in monocytes associated with severe COVID-19 and the induction of a monocyte substate characterized by the expression of glucocorticoid-response genes. These molecular responses to dexamethasone were detected in circulating and pulmonary monocytes, and they were directly linked to survival. Monocyte single-cell RNA sequencing (scRNA-seq)-derived signatures were enriched in whole blood transcriptomes of patients with fatal outcome in two independent cohorts, highlighting the potential for identifying non-responders refractory to dexamethasone. Our findings link the effects of dexamethasone to specific immunomodulation and reversal of monocyte dysregulation, and they highlight the potential of single-cell omics for monitoring in vivo target engagement of immunomodulatory drugs and for patient stratification for precision medicine approaches.
Collapse
Affiliation(s)
- Rainer Knoll
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Elisa T Helbig
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kilian Dahm
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Translational Pediatrics, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Olufemi Bolaji
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frederik Hamm
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Oliver Dietrich
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Martina van Uelft
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics & Immunoregulation, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Sophie Müller
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics & Immunoregulation, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, University of Bonn, and West German Genome Center, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, University of Bonn, and West German Genome Center, Bonn, Germany
| | - Lev Petrov
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Benjamin Krämer
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, University of Bonn, and West German Genome Center, Bonn, Germany
| | - Paula Stubbemann
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany; BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sophia Brumhard
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Heidi Theis
- PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, University of Bonn, and West German Genome Center, Bonn, Germany
| | - Gudrun Hack
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Elena De Domenico
- PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, University of Bonn, and West German Genome Center, Bonn, Germany
| | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Matthias Becker
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Marc D Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, University of Bonn, and West German Genome Center, Bonn, Germany; Immunogenomics & Neurodegeneration, Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - David Hillus
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Georg
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Constantin Loers
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Janina Tiedemann
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lena Lippert
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Belén Millet Pascual-Leone
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gernot Rohde
- Department of Respiratory Medicine, Medical Clinic I, Goethe-Universität Frankfurt am Main, Frankfurt, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany; CAPNETZ STIFTUNG, 30625 Hannover, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany; CAPNETZ STIFTUNG, 30625 Hannover, Germany; German Center for Lung Research (DZL), Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany; CAPNETZ STIFTUNG, 30625 Hannover, Germany; German Center for Lung Research (DZL), Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany; Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics & Immunoregulation, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, University of Bonn, and West German Genome Center, Bonn, Germany
| | - Julia K Polansky
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; German Rheumatism Research Centre (DRFZ) Berlin, Berlin, Germany
| | - Birgit Sawitzki
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Leif E Sander
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Germany
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics & Immunoregulation, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, University of Bonn, and West German Genome Center, Bonn, Germany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
| | - Florian Kurth
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Germany
| |
Collapse
|
34
|
Loktionov AV, Kobzeva KA, Karpenko AR, Sergeeva VA, Orlov YL, Bushueva OY. GWAS-significant loci and severe COVID-19: analysis of associations, link with thromboinflammation syndrome, gene-gene, and gene-environmental interactions. Front Genet 2024; 15:1434681. [PMID: 39175753 PMCID: PMC11338913 DOI: 10.3389/fgene.2024.1434681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
Objective The aim of this study was to replicate associations of GWAS-significant loci with severe COVID-19 in the population of Central Russia, to investigate associations of the SNPs with thromboinflammation parameters, to analyze gene-gene and gene-environmental interactions. Materials and Methods DNA samples from 798 unrelated Caucasian subjects from Central Russia (199 hospitalized COVID-19 patients and 599 controls with a mild or asymptomatic course of COVID-19) were genotyped using probe-based polymerase chain reaction for 10 GWAS-significant SNPs: rs143334143 CCHCR1, rs111837807 CCHCR1, rs17078346 SLC6A20-LLZTFL1, rs17713054 SLC6A20-LLZTFL1, rs7949972 ELF5, rs61882275 ELF5, rs12585036 ATP11A, rs67579710 THBS3, THBS3-AS1, rs12610495 DPP9, rs9636867 IFNAR2. Results SNP rs17713054 SLC6A20-LZTFL1 was associated with increased risk of severe COVID-19 in the entire group (risk allele A, OR = 1.78, 95% CI = 1.22-2.6, p = 0.003), obese individuals (OR = 2.31, 95% CI = 1.52-3.5, p = 0.0002, (p bonf = 0.0004)), patients with low fruit and vegetable intake (OR = 1.72, 95% CI = 1.15-2.58, p = 0.01, (p bonf = 0.02)), low physical activity (OR = 1.93, 95% CI = 1.26-2.94, p = 0.0035, (p bonf = 0.007)), and nonsmokers (OR = 1.65, 95% CI = 1.11-2.46, p = 0.02). This SNP correlated with increased BMI (p = 0.006) and worsened thrombodynamic parameters (maximum optical density of the formed clot, D (p = 0.02), delayed appearance of spontaneous clots, Tsp (p = 0.02), clot size 30 min after coagulation activation, CS (p = 0.036)). SNP rs17078346 SLC6A20-LZTFL1 was linked with increased BMI (p = 0.01) and severe COVID-19 in obese individuals (risk allele C, OR = 1.72, 95% CI = 1.15-2.58, p = 0.01, (p bonf = 0.02)). SNP rs12610495 DPP9 was associated with increased BMI (p = 0.01), severe COVID-19 in obese patients (risk allele G, OR = 1.48, 95% CI = 1.09-2.01, p = 0.01, (p bonf = 0.02)), and worsened thrombodynamic parameters (time to the start of clot growth, Tlag (p = 0.01)). For rs7949972 ELF5, a protective effect against severe COVID-19 was observed in non-obese patients (effect allele T, OR = 0.67, 95% CI = 0.47-0.95, p = 0.02, (p bonf = 0.04)), improving thrombodynamic parameters (CS (p = 0.02), stationary spatial clot growth rates, Vst (p = 0.02)). Finally, rs12585036 ATP11A exhibited a protective effect against severe COVID-19 in males (protective allele A, OR = 0.51, 95% CI = 0.32-0.83, p = 0.004). SNPs rs67579710 THBS3, THBS3-AS1, rs17713054 SLC6A20-LZTFL1, rs7949972 ELF5, rs9636867 IFNAR2-were involved in two or more of the most significant G×G interactions (p perm ≤ 0.01). The pairwise combination rs67579710 THBS3, THBS3-AS1 × rs17713054 SLC6A20-LZTFL1 was a priority in determining susceptibility to severe COVID-19 (it was included in four of the top five most significant SNP-SNP interaction models). Conclusion Overall, this study represents a comprehensive molecular-genetic and bioinformatics analysis of the involvement of GWAS-significant loci in the molecular mechanisms of severe COVID-19, gene-gene and gene-environmental interactions, and provides evidence of their relationship with thromboinflammation parameters in patients hospitalized in intensive care units.
Collapse
Affiliation(s)
- Alexey Valerevich Loktionov
- Department of Anesthesia and Critical Care, Institute of Continuing Education, Kursk State Medical University, Kursk, Russia
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
| | - Ksenia Andreevna Kobzeva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
| | - Andrey Romanovich Karpenko
- Department of Anesthesia and Critical Care, Institute of Continuing Education, Kursk State Medical University, Kursk, Russia
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
| | - Vera Alexeevna Sergeeva
- Department of Anesthesia and Critical Care, Institute of Continuing Education, Kursk State Medical University, Kursk, Russia
| | - Yuriy Lvovich Orlov
- Institute of Biodesign and Complex Systems Modeling, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Olga Yurievna Bushueva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russia
| |
Collapse
|
35
|
Symeonides C, Vacy K, Thomson S, Tanner S, Chua HK, Dixit S, Mansell T, O'Hely M, Novakovic B, Herbstman JB, Wang S, Guo J, Chia J, Tran NT, Hwang SE, Britt K, Chen F, Kim TH, Reid CA, El-Bitar A, Bernasochi GB, Delbridge LMD, Harley VR, Yap YW, Dewey D, Love CJ, Burgner D, Tang MLK, Sly PD, Saffery R, Mueller JF, Rinehart N, Tonge B, Vuillermin P, Ponsonby AL, Boon WC. Male autism spectrum disorder is linked to brain aromatase disruption by prenatal BPA in multimodal investigations and 10HDA ameliorates the related mouse phenotype. Nat Commun 2024; 15:6367. [PMID: 39112449 PMCID: PMC11306638 DOI: 10.1038/s41467-024-48897-8] [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: 12/01/2022] [Accepted: 05/16/2024] [Indexed: 08/10/2024] Open
Abstract
Male sex, early life chemical exposure and the brain aromatase enzyme have been implicated in autism spectrum disorder (ASD). In the Barwon Infant Study birth cohort (n = 1074), higher prenatal maternal bisphenol A (BPA) levels are associated with higher ASD symptoms at age 2 and diagnosis at age 9 only in males with low aromatase genetic pathway activity scores. Higher prenatal BPA levels are predictive of higher cord blood methylation across the CYP19A1 brain promoter I.f region (P = 0.009) and aromatase gene methylation mediates (P = 0.01) the link between higher prenatal BPA and brain-derived neurotrophic factor methylation, with independent cohort replication. BPA suppressed aromatase expression in vitro and in vivo. Male mice exposed to mid-gestation BPA or with aromatase knockout have ASD-like behaviors with structural and functional brain changes. 10-hydroxy-2-decenoic acid (10HDA), an estrogenic fatty acid alleviated these features and reversed detrimental neurodevelopmental gene expression. Here we demonstrate that prenatal BPA exposure is associated with impaired brain aromatase function and ASD-related behaviors and brain abnormalities in males that may be reversible through postnatal 10HDA intervention.
Collapse
Grants
- This multimodal project was supported by funding from the Minderoo Foundation. Funding was also provided by the National Health and Medical Research Council of Australia (NHMRC), the NHMRC-EU partnership grant for the ENDpoiNT consortium, the Australian Research Council, the Jack Brockhoff Foundation, the Shane O’Brien Memorial Asthma Foundation, the Our Women’s Our Children’s Fund Raising Committee Barwon Health, The Shepherd Foundation, the Rotary Club of Geelong, the Ilhan Food Allergy Foundation, GMHBA Limited, Vanguard Investments Australia Ltd, and the Percy Baxter Charitable Trust, Perpetual Trustees, Fred P Archer Fellowship; the Scobie Trust; Philip Bushell Foundation; Pierce Armstrong Foundation; The Canadian Institutes of Health Research; BioAutism, William and Vera Ellen Houston Memorial Trust Fund, Homer Hack Research Small Grants Scheme and the Medical Research Commercialisation Fund. This work was also supported by Ms. Loh Kia Hui. This project received funding from a NHMRC-EU partner grant with the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement number: 825759 (ENDpoiNTs project). This work was also supported by NHMRC Investigator Fellowships (GTN1175744 to D.B, APP1197234 to A-L.P, and GRT1193840 to P.S). The study sponsors were not involved in the collection, analysis, and interpretation of data; writing of the report; or the decision to submit the report for publication.
Collapse
Affiliation(s)
- Christos Symeonides
- Minderoo Foundation, Perth, Australia
- Murdoch Children's Research Institute, Parkville, Australia
- Centre for Community Child Health, Royal Children's Hospital, Parkville, Australia
| | - Kristina Vacy
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
- School of Population and Global Health, The University of Melbourne, Parkville, Australia
| | - Sarah Thomson
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Sam Tanner
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Hui Kheng Chua
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
- The Hudson Institute of Medical Research, Clayton, Australia
| | - Shilpi Dixit
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Toby Mansell
- Murdoch Children's Research Institute, Parkville, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Australia
| | - Martin O'Hely
- Murdoch Children's Research Institute, Parkville, Australia
- School of Medicine, Deakin University, Geelong, Australia
| | - Boris Novakovic
- Murdoch Children's Research Institute, Parkville, Australia
- School of Medicine, Deakin University, Geelong, Australia
| | - Julie B Herbstman
- Columbia Center for Children's Environmental Health, Columbia University, New York, NY, USA
- Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Shuang Wang
- Columbia Center for Children's Environmental Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Jia Guo
- Columbia Center for Children's Environmental Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Jessalynn Chia
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Nhi Thao Tran
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
- The Ritchie Centre, Department of Obstetrics and Gynaecology, School of Clinical Sciences, Monash University, Clayton, Australia
| | - Sang Eun Hwang
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Kara Britt
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
- Breast Cancer Risk and Prevention Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Feng Chen
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Tae Hwan Kim
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Christopher A Reid
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Anthony El-Bitar
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Gabriel B Bernasochi
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
- Faculty Medicine, Dentistry & Health Sciences, University of Melbourne, Parkville, Australia
| | - Lea M Durham Delbridge
- Faculty Medicine, Dentistry & Health Sciences, University of Melbourne, Parkville, Australia
| | - Vincent R Harley
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
- Sex Development Laboratory, Hudson Institute of Medical Research, Clayton, Australia
| | - Yann W Yap
- The Hudson Institute of Medical Research, Clayton, Australia
- Sex Development Laboratory, Hudson Institute of Medical Research, Clayton, Australia
| | - Deborah Dewey
- Departments of Paediatrics and Community Health Sciences, The University of Calgary, Calgary, Canada
| | - Chloe J Love
- School of Medicine, Deakin University, Geelong, Australia
- Barwon Health, Geelong, Australia
| | - David Burgner
- Murdoch Children's Research Institute, Parkville, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Australia
- Department of General Medicine, Royal Children's Hospital, Parkville, Australia
- Department of Pediatrics, Monash University, Clayton, Australia
| | - Mimi L K Tang
- Murdoch Children's Research Institute, Parkville, Australia
- Faculty Medicine, Dentistry & Health Sciences, University of Melbourne, Parkville, Australia
| | - Peter D Sly
- School of Medicine, Deakin University, Geelong, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Australia
- WHO Collaborating Centre for Children's Health and Environment, Brisbane, Australia
| | | | - Jochen F Mueller
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, Australia
| | - Nicole Rinehart
- Monash Krongold Clinic, Faculty of Education, Monash University, Clayton, Australia
| | - Bruce Tonge
- Centre for Developmental Psychiatry and Psychology, Monash University, Clayton, Australia
| | - Peter Vuillermin
- Murdoch Children's Research Institute, Parkville, Australia
- School of Medicine, Deakin University, Geelong, Australia
- Barwon Health, Geelong, Australia
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Parkville, Australia
- Centre for Community Child Health, Royal Children's Hospital, Parkville, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Wah Chin Boon
- The Florey Institute of Neuroscience and Mental Health, Parkville, Australia.
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Australia.
| |
Collapse
|
36
|
Fierro-Monti I. RBPs: an RNA editor's choice. Front Mol Biosci 2024; 11:1454241. [PMID: 39165644 PMCID: PMC11333368 DOI: 10.3389/fmolb.2024.1454241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/25/2024] [Indexed: 08/22/2024] Open
Abstract
RNA-binding proteins (RBPs) play a key role in gene expression and post-transcriptional RNA regulation. As integral components of ribonucleoprotein complexes, RBPs are susceptible to genomic and RNA Editing derived amino acid substitutions, impacting functional interactions. This article explores the prevalent RNA Editing of RBPs, unravelling the complex interplay between RBPs and RNA Editing events. Emphasis is placed on their influence on single amino acid variants (SAAVs) and implications for disease development. The role of Proteogenomics in identifying SAAVs is briefly discussed, offering insights into the RBP landscape. RNA Editing within RBPs emerges as a promising target for precision medicine, reshaping our understanding of genetic and epigenetic variations in health and disease.
Collapse
|
37
|
Li Y, Cui Y, Wang Z, Wang L, Yu Y, Xiong Y. Development and validation of a hypoxia- and mitochondrial dysfunction- related prognostic model based on integrated single-cell and bulk RNA sequencing analyses in gastric cancer. Front Immunol 2024; 15:1419133. [PMID: 39165353 PMCID: PMC11333257 DOI: 10.3389/fimmu.2024.1419133] [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: 04/17/2024] [Accepted: 07/22/2024] [Indexed: 08/22/2024] Open
Abstract
Introduction Gastric cancer (GC) remains a major global health threat ranking as the fifth most prevalent cancer. Hypoxia, a characteristic feature of solid tumors, significantly contributes to the malignant progression of GC. Mitochondria are the major target of hypoxic injury that promotes mitochondrial dysfunction during the development of cancers including GC. However, the gene signature and prognostic model based on hypoxia- and mitochondrial dysfunction-related genes (HMDRGs) in the prediction of GC prognosis have not yet been established. Methods The gene expression profile datasets of stomach cancer patients were retrieved from The Cancer Genome Atlas and the Gene Expression Omnibus databases. Prognostic genes were selected using Least Absolute Shrinkage and Selection Operator Cox (LASSO-Cox) regression analysis to construct a prognostic model. Immune infiltration was evaluated through ESTIMATE, CIBERSORT, and ssGSEA analyses. Tumor immune dysfunction and exclusion (TIDE) and immunophenoscore (IPS) were utilized to explore implications for immunotherapy. Furthermore, in vitro experiments were conducted to validate the functional roles of HMDRGs in GC cell malignancy. Results In this study, five HMDRGs (ZFP36, SERPINE1, DUSP1, CAV1, and AKAP12) were identified for developing a prognostic model in GC. This model stratifies GC patients into high- and low-risk groups based on median risk scores. A nomogram predicting overall survival (OS) was constructed and showed consistent results with observed OS. Immune infiltration analysis indicated that individuals in the high-risk group tend to exhibit increased immune cell infiltration. Additionally, analysis of cancer immunotherapy responses revealed that high-risk group patients exhibit poorer responses to cancer immunotherapy compared to the low-risk group. Immunohistochemistry (IHC) staining indicated that the expression levels of HMDRGs were remarkably correlated with GC, of which, SERPINE1 displayed the most pronounced up-regulation, while ZFP36 exhibited the most notable down-regulation in GC patients. Furthermore, in vitro investigation validated that SERPINE1 and ZFP36 contribute to the malignant processes of GC cells correlated with mitochondrial dysfunction. Conclusions This study presents a novel and efficient approach to evaluate GC prognosis and immunotherapy efficacy, and also provides insights into understanding the pathogenesis of GC.
Collapse
Affiliation(s)
- Yirong Li
- Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Yue Cui
- Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Zhen Wang
- Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Liwei Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Yi Yu
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Yuyan Xiong
- Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| |
Collapse
|
38
|
van den Berg PF, Yousif LI, Markousis-Mavrogenis G, Shi C, Bracun V, Tromp J, de Wit S, Appels Y, Screever EM, Aboumsallem JP, Ouwerkerk W, van Veldhuisen DJ, Silljé HHW, Voors AA, de Boer RA, Meijers WC. Hallmarks of cancer in patients with heart failure: data from BIOSTAT-CHF. CARDIO-ONCOLOGY (LONDON, ENGLAND) 2024; 10:47. [PMID: 39103886 PMCID: PMC11299300 DOI: 10.1186/s40959-024-00246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 07/03/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Within cardio-oncology, emerging epidemiologic studies have demonstrated a bi-directional relationship between heart failure (HF) and cancer. In the current study, we aimed to further explore this relationship and investigate the underlying pathophysiological pathways that connect these two disease entities. METHODS We conducted a post-hoc analysis in which we identified 24 Gene Ontology (GO) processes associated with the hallmarks of cancer based on 92 biomarkers in 1960 patients with HF. We performed Spearman's correlations and Cox-regression analyses to evaluate associations with HF biomarkers, severity and all-cause mortality. RESULTS Out of a total of 24 GO processes, 9 biological processes were significantly associated with adverse clinical outcome. Positive regulation of mononuclear cell proliferation demonstrated the highest hazard for reaching the clinical endpoint, even after adjusting for confounders: all-cause mortality HR 2.00 (95% CI 1.17-3.42), p = 0.012. In contrast, negative regulation of apoptotic process was consistently associated with a lower hazard of reaching the clinical outcome, even after adjusting for confounders: all-cause mortality HR 0.74 (95% CI 0.59-0.95), p = 0.016. All processes significantly correlated with HF biomarkers, renal function and HF severity. CONCLUSIONS In patients with HF, GO processes associated with hallmarks of cancer are associated with HF biomarkers, severity and all-cause mortality.
Collapse
Affiliation(s)
- P F van den Berg
- Department of Cardiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - L I Yousif
- Department of Cardiology, Erasmus MC, Cardiovascular Institute, Thorax Center, Rotterdam, The Netherlands
| | - G Markousis-Mavrogenis
- Department of Cardiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - C Shi
- Department of Cardiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - V Bracun
- Department of Cardiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - J Tromp
- National Heart Centre Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - S de Wit
- Department of Cardiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Y Appels
- Department of Cardiology, Erasmus MC, Cardiovascular Institute, Thorax Center, Rotterdam, The Netherlands
| | - E M Screever
- Department of Cardiology, Erasmus MC, Cardiovascular Institute, Thorax Center, Rotterdam, The Netherlands
| | - J P Aboumsallem
- Department of Cardiology, Erasmus MC, Cardiovascular Institute, Thorax Center, Rotterdam, The Netherlands
| | - W Ouwerkerk
- Department of Dermatology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - D J van Veldhuisen
- Department of Cardiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - H H W Silljé
- Department of Cardiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - A A Voors
- Department of Cardiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - R A de Boer
- Department of Cardiology, Erasmus MC, Cardiovascular Institute, Thorax Center, Rotterdam, The Netherlands
| | - Wouter C Meijers
- Department of Cardiology, Erasmus MC, Cardiovascular Institute, Thorax Center, Rotterdam, The Netherlands.
- Department of Cardiology, Thorax Center, Erasmus University Medical Center, P.O. Box 2040, Rotterdam, 3000CA, The Netherlands.
| |
Collapse
|
39
|
Vicario R, Fragkogianni S, Weber L, Lazarov T, Hu Y, Hayashi SY, Craddock BP, Socci ND, Alberdi A, Baako A, Ay O, Ogishi M, Lopez-Rodrigo E, Kappagantula R, Viale A, Iacobuzio-Donahue CA, Zhou T, Ransohoff RM, Chesworth R, Abdel-Wahab O, Boisson B, Elemento O, Casanova JL, Miller WT, Geissmann F. A microglia clonal inflammatory disorder in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577216. [PMID: 38328106 PMCID: PMC10849735 DOI: 10.1101/2024.01.25.577216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer's Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.
Collapse
Affiliation(s)
- Rocio Vicario
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Stamatina Fragkogianni
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Leslie Weber
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Yang Hu
- Department of Physiology and Biophysics, Institute for Computational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Samantha Y. Hayashi
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Nicholas D. Socci
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Araitz Alberdi
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ann Baako
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Oyku Ay
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Estibaliz Lopez-Rodrigo
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Rajya Kappagantula
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Agnes Viale
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christine A. Iacobuzio-Donahue
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ting Zhou
- SKI Stem Cell Research Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | | | | | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| |
Collapse
|
40
|
Foda MY, Salem ML, AlAkwaa FM, El-Khawaga OY. Atorvastatin lowers breast cancer risk by reversing an early tumorigenic signature. Sci Rep 2024; 14:17803. [PMID: 39090164 PMCID: PMC11294600 DOI: 10.1038/s41598-024-67706-2] [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: 01/31/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
Breast cancer remains a significant health challenge with complex molecular mechanisms. While many studies have explored genetic markers in breast carcinogenesis, few have studied the potential impact of pharmacological interventions such as Atorvastatin on its genetic landscape. This study aimed to elucidate the molecular distinctions between normal and tumor-adjacent tissues in breast cancer and to investigate the potential protective role of atorvastatin, primarily known for its lipid-lowering effects, against breast cancer. Searching the Gene Expression Omnibus database identified two datasets, GSE9574 and GSE20437, comparing normal breast tissues with tumor-adjacent samples, which were merged, and one dataset, GSE63427, comparing paired pre- and post-treated patients with atorvastatin. Post-ComBat application showed merged datasets' consistency, revealing 116 DEGs between normal and tumor-adjacent tissues. Although initial GSE63427 data analysis suggested a minimal impact of atorvastatin, 105 DEGs post-treatment were discovered. Thirteen genes emerged as key players, both affected by Atorvastatin and dysregulated in tumor-adjacent tissues. Pathway analysis spotlighted the significance of these genes in processes like inflammation, oxidative stress, apoptosis, and cell cycle control. Moreover, there was a noticeable interaction between these genes and the immunological microenvironment in tumor-adjacent tissues, with Atorvastatin potentially altering the suppressive immune landscape to favor anti-tumor immunity. Survival analysis further highlighted the prognostic potential of the 13-gene panel, with 12 genes associated with improved survival outcomes. The 13-gene signature offers promising insights into breast cancer's molecular mechanisms and atorvastatin's potential therapeutic role. The preliminary findings advocate for an in-depth exploration of atorvastatin's impact on.
Collapse
Affiliation(s)
- Mohamed Y Foda
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Mohamed L Salem
- Immunology and Biotechnology Unit, Department of Zoology, Faculty of Science, and Center of Excellence in Cancer Research, Tanta University, Tanta, Egypt
| | - Fadhl M AlAkwaa
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Omali Y El-Khawaga
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
| |
Collapse
|
41
|
Beer MA, Trumbo DR, Rautsaw RM, Kozakiewicz CP, Epstein B, Hohenlohe PA, Alford RA, Schwarzkopf L, Storfer A. Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia. Mol Ecol 2024; 33:e17464. [PMID: 38994885 DOI: 10.1111/mec.17464] [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: 09/25/2023] [Revised: 06/09/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north-central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic-environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post-introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories.
Collapse
Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Daryl R Trumbo
- Department of Biology, Colorado State University Pueblo, Pueblo, Colorado, USA
| | - Rhett M Rautsaw
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Christopher P Kozakiewicz
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, Michigan, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Ross A Alford
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Lin Schwarzkopf
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| |
Collapse
|
42
|
Zhang X, Hu S, Xiang X, Li Z, Chen Z, Xia C, He Q, Jin J, Chen H. Bulk and single-cell transcriptome profiling identify potential cellular targets of the long noncoding RNA Gas5 in renal fibrosis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167206. [PMID: 38718848 DOI: 10.1016/j.bbadis.2024.167206] [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: 01/06/2024] [Revised: 04/05/2024] [Accepted: 04/27/2024] [Indexed: 05/18/2024]
Abstract
The long noncoding RNA growth arrest-specific 5 (lncRNA Gas5) is implicated in various kidney diseases. In this study, we investigated the lncRNA Gas5 expression profile and its critical role as a potential biomarker in the progression of chronic kidney disease. Subsequently, we assessed the effect of lncRNA Gas5 deletion on renal fibrosis induced by unilateral ureteral obstruction (UUO). The results indicated that loss of lncRNA Gas5 exacerbates UUO-induced renal injury and extracellular matrix deposition. Notably, the deletion of lncRNA Gas5 had a similar effect on control mice. The fibrogenic phenotype observed in mice lacking lncRNA Gas5 correlates with peroxisome proliferator-activated receptor (PPAR) signaling pathway activation and aberrant cytokine and chemokine reprogramming. Single-cell RNA sequencing analysis revealed key transcriptomic features of fibroblasts after Gas5 deletion, revealing heterogeneous cellular states suggestive of a propensity for renal fibrosis. Our findings indicate that lncRNA Gas5 regulates the differentiation and activation of immune cells and the transcription of key genes in the PPAR signaling pathway. These data offer novel insights into the involvement of lncRNA Gas5 in renal fibrosis, potentially paving the way for innovative diagnostic and therapeutic targets.
Collapse
Affiliation(s)
- Xiang Zhang
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Shouci Hu
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Xiaojun Xiang
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Zhiyu Li
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Zhejun Chen
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Cong Xia
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Qiang He
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Juan Jin
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Hongbo Chen
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China.
| |
Collapse
|
43
|
Li ZH, Pu XQ, Li SS, Dong XK, Zhang GQ, Wang Y, Liu JM. Neuroprotective Effect and Mechanism of Tanreqing Injection on Ischemic Stroke: Insights from Network Pharmacology and in vivo Experiments. Chin J Integr Med 2024; 30:713-720. [PMID: 38910191 DOI: 10.1007/s11655-024-3910-6] [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] [Accepted: 08/02/2023] [Indexed: 06/25/2024]
Abstract
OBJECTIVE To explore the neuroprotective effects and mechanism of Tanreqing Injection (TRQ) on treating ischemic stroke based on network pharmacology and in vivo experimental validation. METHODS The chemical compounds of TRQ were retrieved based on published data, with targets retrieved from PubChem, Therapeutic Target Database and DrugBank. Network visualization and analysis were performed using Cytoscape, with protein-protein interaction networks derived from the STRING database. Enrichment analysis was performed using Kyoto Encyclopedia of Genes Genomes pathway and Gene Ontology analysis. In in vivo experiments, the middle cerebral artery occlusion (MCAO) model was used. Infarct volume was determined by 2,3,5-triphenyltetrazolium hydrochloride staining and protein expressions were analyzed by Western blot. Molecular docking was performed to predict ligand-receptor interactions. RESULTS We screened 81 chemical compounds in TRQ and retrieved their therapeutic targets. Of the targets, 116 were therapeutic targets for stroke. The enrichment analysis showed that the apelin signaling pathway was a key pathway for ischemic stroke. Furthermore, in in vivo experiment we found that administering with intraperitoneal injection of 2.5 mL/kg TRQ every 6 h could significantly reduce the infarct volume of MCAO rats (P<0.05). In addition, protein levels of the apelin receptor (APJ)/phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway were increased by TRQ (P<0.05). In addition, 41 chemical compounds in TRQ could bind to APJ. CONCLUSIONS The neuroprotective effect of TRQ may be related to the APJ/PI3K/AKT signaling pathway. However, further studies are needed to confirm the findings.
Collapse
Affiliation(s)
- Zhong-Hao Li
- Department of Emergency, China-Japan Friendship Hospital, Beijing, 100029, China
- Department of Neurology, Beijing University of Chinese Medicine Dongfang Hospital, Beijing, 100078, China
| | - Xiao-Qi Pu
- Department of Radiology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Sha-Sha Li
- Graduate School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiao-Ke Dong
- Department of Neurology, Beijing Daxing District Hospital of Integrated Chinese and Western Medicine, Beijing, 100163, China
| | - Guo-Qiang Zhang
- Department of Emergency, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Yu Wang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jin-Min Liu
- Department of Neurology, Beijing University of Chinese Medicine Dongfang Hospital, Beijing, 100078, China
| |
Collapse
|
44
|
Andrew SC, Simonsen AK, Coppin CW, Arnold PA, Briceño VF, McLay TGB, Jackson CJ, Gallagher RV, Mokany K. Expression-environment associations in transcriptomic heat stress responses for a global plant lineage. Mol Ecol 2024; 33:e17473. [PMID: 39034607 DOI: 10.1111/mec.17473] [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: 04/08/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
The increasing frequency and severity of heatwaves will intensify stress on plants. Given regional variation in heatwave exposure and expected differences in thermal tolerance between species it is unlikely that all plant species will be affected equally by climate change. However, little is currently known about variation in the responses of plants to heat stress, or how those responses differ among closely related species adapted to different environments. Here we quantify the response of 17 Acacia species (175 RNA-seq libraries), from across Australia's diverse biomes, to a multi-day experimental heatwave treatment to identify variation in transcriptomic and physiological responses to heat stress. Genes with known heat response functions showed consistent responses across Acacia species. Up to 10% of all genes and over 100 gene families showed significant clinal variation in the magnitude of their expression plasticity across species. Specifically, gene families linked to the temperature stress response were overrepresented among significant relationships with home range temperature conditions. Gene expression responses seen on the first day of the heatwave were more frequently associated with home range climates, while expression responses by day four were more commonly related to photosystem II acclimation. Comparative transcriptomics on non-model species has the potential to provide key information on stress response plasticity, especially when linked with our understanding of model species. Our study indicates that the pressing challenge to identifying potentially vulnerable species to climate change could be benefited by the further exploration of clinal variation in transcriptome plasticity.
Collapse
Affiliation(s)
- Samuel C Andrew
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Anna K Simonsen
- Department of Biological Sciences, Florida International University, Miami, Florida, USA
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Chris W Coppin
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Pieter A Arnold
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Verónica F Briceño
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Todd G B McLay
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Chris J Jackson
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Rachael V Gallagher
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Karel Mokany
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| |
Collapse
|
45
|
Bao HF, She CH, Hou CC, Ji DN, Hu D, Zou J, Shen Y, Jian LL, Cai JF, Ye JF, Luo D, Ma HF, Guan JL. PLK1-activating IFI16-STING-TBK1 pathway induces apoptosis of intestinal epithelial cells in patients with intestinal Behçet's syndrome. FEBS J 2024; 291:3432-3453. [PMID: 38676954 DOI: 10.1111/febs.17147] [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: 07/21/2023] [Revised: 12/28/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024]
Abstract
Inflammatory signals from immunological cells may cause damage to intestinal epithelial cells (IECs), resulting in intestinal inflammation and tissue impairment. Interferon-γ-inducible protein 16 (IFI16) was reported to be involved in the pathogenesis of Behçet's syndrome (BS). This study aimed to investigate how inflammatory cytokines released by immunological cells and IFI16 participate in the pathogenesis of intestinal BS. RNA sequencing and real-time quantitative PCR (qPCR) showed that the positive regulation of tumor necrosis factor-α (TNF-α) production in peripheral blood mononuclear cells (PBMCs) of intestinal BS patients may be related to the upregulation of polo like kinase 1 (PLK1) in PBMCs (P = 0.012). The plasma TNF-α protein level in intestinal BS was significantly higher than in healthy controls (HCs; P = 0.009). PBMCs of intestinal BS patients and HCs were co-cultured with human normal IECs (NCM460) to explore the interaction between immunological cells and IECs. Using IFI16 knockdown, PBMC-NCM460 co-culture, TNF-α neutralizing monoclonal antibody (mAb), stimulator of interferon genes (STING) agonist 2'3'-cGAMP, and the PLK1 inhibitor SBE 13 HCL, we found that PLK1 promotes the secretion of TNF-α from PBMCs of intestinal BS patients, which causes overexpression of IFI16 and induces apoptosis of IECs via the STING-TBK1 pathway. The expressions of IFI16, TNF-α, cleaved caspase 3, phosphorylated STING (pSTING) and phosphorylated tank binding kinase 1 (pTBK1) in the intestinal ulcer tissue of BS patients were significantly higher than that of HCs (all P < 0.05). PLK1 in PBMCs of intestinal BS patients increased TNF-α secretion, inducing IEC apoptosis via activation of the IFI16-STING-TBK1 pathway. PLK1 and the IFI16-STING-TBK1 pathway may be new therapeutic targets for intestinal BS.
Collapse
Affiliation(s)
- Hua-Fang Bao
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Chun-Hui She
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Cheng-Cheng Hou
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Da-Nian Ji
- Department of Gastrointestinal Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Dan Hu
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Jun Zou
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Yan Shen
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Lei-Lei Jian
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Jian-Fei Cai
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Jing-Fen Ye
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Dan Luo
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Hai-Fen Ma
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Jian-Long Guan
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| |
Collapse
|
46
|
Kim IB, Kim MH, Jung S, Kim WK, Lee J, Ju YS, Webster MJ, Kim S, Kim JH, Kim HJ, Kim J, Kim S, Lee JH. Low-level brain somatic mutations in exonic regions are collectively implicated in autism with germline mutations in autism risk genes. Exp Mol Med 2024; 56:1750-1762. [PMID: 39085355 DOI: 10.1038/s12276-024-01284-1] [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: 12/09/2023] [Revised: 04/15/2024] [Accepted: 05/12/2024] [Indexed: 08/02/2024] Open
Abstract
Low-level somatic mutations in the human brain are implicated in various neurological disorders. The contribution of low-level brain somatic mutations to autism spectrum disorder (ASD), however, remains poorly understood. Here, we performed high-depth exome sequencing with an average read depth of 559.3x in 181 cortical, cerebellar, and peripheral tissue samples to identify brain somatic single nucleotide variants (SNVs) in 24 ASD subjects and 31 controls. We detected ~2.4 brain somatic SNVs per exome per single brain region, with a variant allele frequency (VAF) as low as 0.3%. The mutational profiles, including the number, signature, and type, were not significantly different between the ASD patients and controls. Intriguingly, when considering genes with low-level brain somatic SNVs and ASD risk genes with damaging germline SNVs together, the merged set of genes carrying either somatic or germline SNVs in ASD patients was significantly involved in ASD-associated pathophysiology, including dendrite spine morphogenesis (p = 0.025), mental retardation (p = 0.012), and intrauterine growth retardation (p = 0.012). Additionally, the merged gene set showed ASD-associated spatiotemporal expression in the early and mid-fetal cortex, striatum, and thalamus (all p < 0.05). Patients with damaging mutations in the merged gene set had a greater ASD risk than did controls (odds ratio = 3.92, p = 0.025, 95% confidence interval = 1.12-14.79). The findings of this study suggest that brain somatic SNVs and germline SNVs may collectively contribute to ASD-associated pathophysiology.
Collapse
Affiliation(s)
- Il Bin Kim
- Department of Psychiatry, CHA Gangnam Medical Center, CHA University School of Medicine, Seoul, 06135, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Myeong-Heui Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Saehoon Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Maree J Webster
- Stanley Medical Research Institute, Laboratory of Brain Research, 9800 Medical Center Drive, Suite C-050, Rockville, MD, 20850, USA
| | - Sanghyeon Kim
- Stanley Medical Research Institute, Laboratory of Brain Research, 9800 Medical Center Drive, Suite C-050, Rockville, MD, 20850, USA
| | - Ja Hye Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hyun Jung Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Junho Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- SoVarGen, SoVarGen, Inc., Daejeon, 34141, Republic of Korea.
| |
Collapse
|
47
|
Lee HU, Shim S, Chung MN, Lee T, Park W, Kim TH, Lee KH, Woo KS, Nam SS, Kim MY, Lee SH. Transcriptomic analysis for the gamma-ray-induced sweetpotato mutants with altered stem growth pattern. Front Genet 2024; 15:1419399. [PMID: 39144719 PMCID: PMC11322061 DOI: 10.3389/fgene.2024.1419399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/11/2024] [Indexed: 08/16/2024] Open
Abstract
Introduction Sweetpotato faces breeding challenges due to physiological and genomic issues. Gamma radiation is a novel approach for inducing genetic variation in crops. We analyzed the transcriptomic changes in gamma ray-induced sweetpotato mutants with altered stem development compared with those in the wild-type 'Tongchaeru' cultivar. Methods RNA sequencing analyses were performed to identify changes in the expression of genes related to stem development. Results Transcriptomic analysis identified 8,931 upregulated and 6,901 downregulated genes, including the upregulation of the auxin-responsive SMALL AUXIN UP RNA (SAUR) and three PHYTOCHROME INTERACTING FACTOR 4 (PIF4) genes. PIF4 is crucial for regulating the expression of early auxin-responsive SAUR genes and stem growth in Arabidopsis thaliana. In the mutant, several genes related to stem elongation, including PIF4 and those involved in various signaling pathways such as auxin and gibberellin, were upregulated. Discussion Our results suggest that gamma ray-induced mutations influence auxin-dependent stem development by modulating a complex regulatory network involving the expression of PIF4 and SAUR genes, and other signaling pathways such as gibberellin and ethylene signaling genes. This study enhances our understanding of the regulatory mechanisms underlying stem growth in sweetpotato, providing valuable insights for genomics-assisted breeding efforts.
Collapse
Affiliation(s)
- Hyeong-Un Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Sangrea Shim
- Department of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Mi Nam Chung
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Taeyoung Lee
- Bioinformatics Institute, Macrogen Inc., Seoul, Republic of Korea
| | - Won Park
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Tae Hwa Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Kyo Hwui Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Koan Sik Woo
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Sang-Sik Nam
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Moon Young Kim
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Suk-Ha Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
48
|
Ning DS, Zhou ZQ, Zhou SH, Chen JM. Identification of macrophage differentiation related genes and subtypes linking atherosclerosis plaque processing and metabolic syndrome via integrated bulk and single-cell sequence analysis. Heliyon 2024; 10:e34295. [PMID: 39130409 PMCID: PMC11315131 DOI: 10.1016/j.heliyon.2024.e34295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 08/13/2024] Open
Abstract
Metabolic syndrome(MS) is a separate risk factor for the advancement of atherosclerosis(AS) plaque but mechanism behind this remains unclear. There may be a significant role for the immune system in this process. This study aims to identify potential diagnostic genes in MS patients at a higher risk of developing and progressing to AS. Datasets were retrevied from gene expression omnibus(GEO) database and differentially expressed genes were identified. Hub genes, immune cell dysregulation and AS subtypes were identified using a conbination of muliple bioinformatic analysis, machine learning and consensus clustering. Diagnostic value of hub genes was estimated using a nomogram and ROC analysis. Finally, enrichment analysis, competing endogenous RNA(ceRNA) network, single-cell RNA(scRNA) sequencing analysis and drug-protein interaction prediction was constructed to identify the functional roles, potential regulators and distribution for hub genes. Four hub genes and two macrophage-related subtypes were identified. Their strong diagnostic value was validated and functional process were identified. ScRNA analysis identified the macrophage differentiation regulation function of F13A1. CeRNA network and drug-protein binding modes revealed the potential therapeutic method. Four immune-correlated hub genes(F13A1, MMRN1, SLCO2A1 and ZNF521) were identified with their diagnostic value being assesed, which F13A1 was found strong correlated with macrophage differentiation and could be potential diagnostic and therapeutic marker for AS progression in MS patients.
Collapse
Affiliation(s)
- Da-Sheng Ning
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, PR China
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
- Southern China Key Laboratory of Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, PR China
| | - Zi-Qing Zhou
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, PR China
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
- Southern China Key Laboratory of Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, PR China
| | - Shu-Heng Zhou
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, PR China
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
- Southern China Key Laboratory of Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, PR China
| | - Ji-Mei Chen
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, PR China
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
- Southern China Key Laboratory of Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, PR China
| |
Collapse
|
49
|
Akki AJ, Patil SA, Hungund S, Sahana R, Patil MM, Kulkarni RV, Raghava Reddy K, Zameer F, Raghu AV. Advances in Parkinson's disease research - A computational network pharmacological approach. Int Immunopharmacol 2024; 139:112758. [PMID: 39067399 DOI: 10.1016/j.intimp.2024.112758] [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: 06/17/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Parkinson's disease (PD), the second most prevalent neurodegenerative disorder, is projected to see a significant rise in incidence over the next three decades. The precise treatment of PD remains a formidable challenge, prompting ongoing research into early diagnostic methodologies. Network pharmacology, a burgeoning field grounded in systems biology, examines the intricate networks of biological systems to identify critical signal nodes, facilitating the development of multi-target therapeutic molecules. This approach systematically maps the components of Parkinson's disease, thereby reducing its complexity. In this review, we explore the application of network pharmacology workflows in PD, discuss the techniques employed in this field, and evaluate the current advancements and status of network pharmacology in the context of Parkinson's disease. The comprehensive insights will pave newer paths to explore early disease biomarkers and to develop diagnosis with a holistic in silico, in vitro, in vivo and clinical studies.
Collapse
Affiliation(s)
- Ali Jawad Akki
- Faculty of Science and Technology, BLDE (Deemed-to-be University), Vijayapura 586 103, India
| | - Shruti A Patil
- Faculty of Science and Technology, BLDE (Deemed-to-be University), Vijayapura 586 103, India
| | - Sphoorty Hungund
- Faculty of Science and Technology, BLDE (Deemed-to-be University), Vijayapura 586 103, India
| | - R Sahana
- Department of Computer Science and Engineering, RV Institute of Technology and Management, 560 076 Bengaluru, India
| | - Malini M Patil
- Department of Computer Science and Engineering, RV Institute of Technology and Management, 560 076 Bengaluru, India.
| | - Raghavendra V Kulkarni
- Faculty of Science and Technology, BLDE (Deemed-to-be University), Vijayapura 586 103, India
| | - K Raghava Reddy
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 12 2006, Australia
| | - Farhan Zameer
- Department of Dravyaguna (Ayurveda Pharmacology), Alva's Ayurveda Medical College, and PathoGutOmics Laboratory, ATMA Research Centre, Dakshina Kannada 574 227, India.
| | - Anjanapura V Raghu
- Department of Basic Sciences, Faculty of Engineering and Technology, CMR University, 562149 Bangalore, India.
| |
Collapse
|
50
|
Gong J, Preminger Z, Steptoe A, Fancourt D. Protein signatures associated with loneliness and social isolation: plasma proteome analyses in the English Longitudinal Study of Ageing, with causal evidence from Mendelian randomization. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.25.24310989. [PMID: 39211870 PMCID: PMC11361243 DOI: 10.1101/2024.07.25.24310989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The understanding of biological pathways related to loneliness and social isolation remains incomplete. Cutting-edge population-based proteomics offers opportunities to uncover novel biological pathways linked to social deficits. This study employed a proteome-wide and data-driven approach to estimate the cross-sectional associations between objective measures of social connections (i.e., social isolation) and subjective measures (i.e., loneliness) with protein abundance, using the English Longitudinal Study of Ageing. Greater social isolation was associated with higher levels of 11 proteins (TNFRSF10A, MMP12, TRAIL-R2, SKR3, TNFRSF11A, VSIG2, PRSS8, FGFR2, KIM1, REN, and NEFL) after minimal adjustments; and three proteins were significantly associated after full adjustments (TNFRSF10A, TNFRSF11A, and HAOX1). Findings from two-sample Mendelian randomization indicated that a lower frequency of in-person social contact with friends or family causally increased levels of TNFRSF10A, TRAIL-R2, TNFRSF11A, and KIM1, and decreased the level of NEFL. The study also highlighted several enriched biological pathways, including necrosis and cell death regulation, dimerization of procaspase-8, and inhibition of caspase-8 pathways, which have previously not been linked to social deficits. These findings could help explain the relationship between social deficits and disease, confirming the importance of continuing to explore novel biological pathways associated with social deficits.
Collapse
|