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Song X, Yao Z, Zhang Z, Lyu S, Chen N, Qi X, Liu X, Ma W, Wang W, Lei C, Jiang Y, Wang E, Huang Y. Whole-genome sequencing reveals genomic diversity and selection signatures in Xia'nan cattle. BMC Genomics 2024; 25:559. [PMID: 38840048 PMCID: PMC11151506 DOI: 10.1186/s12864-024-10463-3] [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: 12/30/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data. RESULT The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1). CONCLUSION We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.
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Affiliation(s)
- Xingya Song
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Zhi Yao
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Shijie Lyu
- Institute of Animal Husbandry, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Xingshan Qi
- Biyang County Xiananniu Technology Development Co., Ltd, Zhumadian, 463700, People's Republic of China
| | - Xian Liu
- Henan Provincial Livestock Technology Promotion Station, Zhengzhou, 450008, Henan, People's Republic of China
| | - Weidong Ma
- Shaanxi Agricultural and Animal Husbandry Seed Farm, Shaanxi Fufeng, 722203, People's Republic of China
| | - Wusheng Wang
- Shaanxi Agricultural and Animal Husbandry Seed Farm, Shaanxi Fufeng, 722203, People's Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China.
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Yuan F, Wei J, Cheng Y, Wang F, Gu M, Li Y, Zhao X, Sun H, Ban R, Zhou J, Xia Z. SLAMF7 Promotes Foam Cell Formation of Macrophage by Suppressing NR4A1 Expression During Carotid Atherosclerosis. Inflammation 2024; 47:530-542. [PMID: 37971565 DOI: 10.1007/s10753-023-01926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/25/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
Macrophage-derived lipid-laden foam cells from the subendothelium play a crucial role in the initiation and progression of atherosclerosis. However, the molecule mechanism that regulates the formation of foam cells is not completely understood. Here, we found that SLAMF7 was upregulated in mice bone marrow-derived macrophages and RAW264.7 cells stimulated with oxidized low-density lipoprotein (ox-LDL). SLAMF7 promoted ox-LDL-mediated macrophage lipid accumulation and M1-type polarization. SLAMF7 deficiency reduced serum lipid levels and improved the lesions area of carotid plaque and aortic arch in high-fat diet-fed ApoE-/- mice. In response to ox-LDL, SLAMF7 downregulated NR4A1 and upregulated RUNX3 through transcriptome sequencing analysis. Overexpression NR4A1 reversed SLAMF7-induced lipid uptake and M1 polarization via inhibiting RUNX3 expression. Furthermore, RUNX3 enhanced foam cell formation and M1-type polarization. Taken together, the study suggested that SLAMF7 play contributing roles in the pro-atherogenic effects by regulating NR4A1-RUNX3.
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Affiliation(s)
- Fengjiao Yuan
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong, 252000, People's Republic of China
- Department of Neurology, Liaocheng People's Hospital, Shandong University, Jinan, Shandong, 250012, People's Republic of China
- Medical Integration and Practice Center, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Jianmei Wei
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong, 252000, People's Republic of China
| | - Yan Cheng
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong, 252000, People's Republic of China
| | - Feifei Wang
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong, 252000, People's Republic of China
| | - Mingliang Gu
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong, 252000, People's Republic of China
| | - Yanhui Li
- Department of Rehabilitation Medicine, Liaocheng Chinese Medicine Hospital, Liaocheng, Shandong, 252000, People's Republic of China
| | - Xin Zhao
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, 252000, People's Republic of China
| | - Hao Sun
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, 252000, People's Republic of China
| | - Ru Ban
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, 252000, People's Republic of China
| | - Jing Zhou
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, 250014, People's Republic of China.
| | - Zhangyong Xia
- Department of Neurology, Liaocheng People's Hospital, Shandong University, Jinan, Shandong, 250012, People's Republic of China.
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, 252000, People's Republic of China.
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Jacobs BM, Vickaryous N, Giovannoni G, Proitsi P, Waters S, Dobson R. Plasma proteomic profiles of UK Biobank participants with multiple sclerosis. Ann Clin Transl Neurol 2024; 11:698-709. [PMID: 38282238 DOI: 10.1002/acn3.51990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024] Open
Abstract
OBJECTIVE We aimed to describe plasma protein biomarkers of multiple sclerosis risk and to explore protein biomarkers of disease severity using radiological outcome measures. METHODS Multiple sclerosis cases and controls were identified in UK Biobank, a longitudinal cohort study of ~500,000 British adults. Plasma proteins were assayed in ~50,000 UK Biobank participants using the Olink proximity extension assay. We performed case-control association testing to examine the association between 2911 proteins and multiple sclerosis, using linear models adjusted for confounding covariates. Associations with radiological lesion burden and brain volume were determined in a subset of the cohort with available magnetic resonance imaging, using normalized T2-hyperintensity volume or whole brain volume as the outcome measure. RESULTS In total, 407 prevalent multiple sclerosis cases and 39,979 healthy controls were included. We discovered 72 proteins associated with multiple sclerosis at a Bonferroni-adjusted p value of 0.05, including established markers such as neurofilament light chain and glial fibrillary acidic protein. We observed a decrease in plasma Granzyme A, a marker of T cell and NK cell degranulation, which was specific to multiple sclerosis. Higher levels of plasma proteins involved in coagulation were associated with lower T2 lesion burden and preserved brain volume. INTERPRETATION We report the largest plasma proteomic screen of multiple sclerosis, replicating important known associations and suggesting novel markers, such as the reduction in granzyme A. While these findings require external validation, they demonstrate the power of biobank-scale datasets for discovering new biomarkers for multiple sclerosis.
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Affiliation(s)
- Benjamin M Jacobs
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
- Department of Neurology, Royal London Hospital, London, UK
| | - Nicola Vickaryous
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Gavin Giovannoni
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
- Department of Neurology, Royal London Hospital, London, UK
| | - Petroula Proitsi
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Sheena Waters
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Ruth Dobson
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
- Department of Neurology, Royal London Hospital, London, UK
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Zhang J, Feng S, Chen M, Zhang W, Zhang X, Wang S, Gan X, Zheng Y, Wang G. Identification of potential crucial genes shared in psoriasis and ulcerative colitis by machine learning and integrated bioinformatics. Skin Res Technol 2024; 30:e13574. [PMID: 38303405 PMCID: PMC10835022 DOI: 10.1111/srt.13574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Mounting evidence suggest that there are an association between psoriasis and ulcerative colitis (UC), although the common pathogeneses are not fully understood. Our study aimed to find potential crucial genes in psoriasis and UC through machine learning and integrated bioinformatics. METHODS The overlapping differentially expressed genes (DEGs) of the datasets GSE13355 and GSE87466 were identified. Then the functional enrichment analysis was performed. The overlapping genes in LASSO, SVM-RFE and key module in WGCNA were considered as potential crucial genes. The receiver operator characteristic (ROC) curve was used to estimate their diagnostic confidence. The CIBERSORT was conducted to evaluate immune cell infiltration. Finally, the datasets GSE30999 and GSE107499 were retrieved to validate. RESULTS 112 overlapping DEGs were identified in psoriasis and UC and the functional enrichment analysis revealed they were closely related to the inflammatory and immune response. Eight genes, including S100A9, PI3, KYNU, WNT5A, SERPINB3, CHI3L2, ARNTL2, and SLAMF7, were ultimately identified as potential crucial genes. ROC curves showed they all had high confidence in the test and validation datasets. CIBERSORT analysis indicated there was a correlation between infiltrating immune cells and potential crucial genes. CONCLUSION In our study, we focused on the comprehensive understanding of pathogeneses in psoriasis and UC. The identification of eight potential crucial genes may contribute to not only understanding the common mechanism, but also identifying occult UC in psoriasis patients, even serving as therapeutic targets in the future.
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Affiliation(s)
- Jing Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Shuo Feng
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Minfei Chen
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Wen Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Xiu Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Shengbang Wang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Xinyi Gan
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Yan Zheng
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Guorong Wang
- The First Department of General Surgerythe Third Affiliated Hospital and Shaanxi Provincial People's HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
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Chu E, Wu J, Kang SS, Kang Y. SLAMF7 as a Promising Immunotherapeutic Target in Multiple Myeloma Treatments. Curr Oncol 2023; 30:7891-7903. [PMID: 37754488 PMCID: PMC10529721 DOI: 10.3390/curroncol30090573] [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: 07/20/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023] Open
Abstract
Multiple myeloma (MM) is a common hematological malignancy that has fostered several new therapeutic approaches to combat newly diagnosed or relapsed MM. While the field has advanced over the past 2 decades, the majority of patients will develop resistance to these treatments, causing the need for new therapeutic targets. SLAMF7 is an attractive therapeutic target in multiple myeloma, and a monoclonal antibody that targets SLAMF7 has shown consistent beneficial outcomes in clinical trials to date. In this review, we will focus on the structure and regulation of SLAMF7 and its mechanism of action. The most recent clinical trials will be reviewed to further understand the clinical implications and improve the prognosis of MM. Furthermore, the efficacy of anti-SLAMF7 monoclonal antibodies combined with standard therapies and possible resistance mechanisms will be discussed. This review aimed to provide a detailed summary of the role of SLAMF7 in the pathogenesis of patients with MM and the rationale for further investigation into SLAMF7-mediated molecular pathways associated with MM development.
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Affiliation(s)
- Emily Chu
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (E.C.); (J.W.)
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA
| | - Jian Wu
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (E.C.); (J.W.)
| | - Stacey S. Kang
- College of Arts and Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA;
| | - Yubin Kang
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (E.C.); (J.W.)
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