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Lin P, Gan YB, He J, Lin SE, Xu JK, Chang L, Zhao LM, Zhu J, Zhang L, Huang S, Hu O, Wang YB, Jin HJ, Li YY, Yan PL, Chen L, Jiang JX, Liu P. Advancing skeletal health and disease research with single-cell RNA sequencing. Mil Med Res 2024; 11:33. [PMID: 38816888 PMCID: PMC11138034 DOI: 10.1186/s40779-024-00538-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Orthopedic conditions have emerged as global health concerns, impacting approximately 1.7 billion individuals worldwide. However, the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders. The advent of single-cell RNA sequencing (scRNA-seq) technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity. Nevertheless, investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges. In this comprehensive review, we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines. By utilizing these methodologies, crucial insights into the developmental dynamics, maintenance of homeostasis, and pathological processes involved in spine, joint, bone, muscle, and tendon disorders have been uncovered. Specifically focusing on the joint diseases of degenerative disc disease, osteoarthritis, and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension. These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.
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Grants
- 2022YFA1103202 National Key Research and Development Program of China
- 82272507 National Natural Science Foundation of China
- 32270887 National Natural Science Foundation of China
- 32200654 National Natural Science Foundation of China
- CSTB2023NSCQ-ZDJO008 Natural Science Foundation of Chongqing
- BX20220397 Postdoctoral Innovative Talent Support Program
- SFLKF202201 Independent Research Project of State Key Laboratory of Trauma and Chemical Poisoning
- 2021-XZYG-B10 General Hospital of Western Theater Command Research Project
- 14113723 University Grants Committee, Research Grants Council of Hong Kong, China
- N_CUHK472/22 University Grants Committee, Research Grants Council of Hong Kong, China
- C7030-18G University Grants Committee, Research Grants Council of Hong Kong, China
- T13-402/17-N University Grants Committee, Research Grants Council of Hong Kong, China
- AoE/M-402/20 University Grants Committee, Research Grants Council of Hong Kong, China
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Affiliation(s)
- Peng Lin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yi-Bo Gan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian He
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
- Pancreatic Injury and Repair Key Laboratory of Sichuan Province, the General Hospital of Western Theater Command, Chengdu, 610031, China
| | - Si-En Lin
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Jian-Kun Xu
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Liang Chang
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Li-Ming Zhao
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Sacramento, CA, 94305, USA
| | - Jun Zhu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liang Zhang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Sha Huang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ou Hu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ying-Bo Wang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Huai-Jian Jin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yang-Yang Li
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Pu-Lin Yan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Lin Chen
- Center of Bone Metabolism and Repair, State Key Laboratory of Trauma and Chemical Poisoning, Trauma Center, Research Institute of Surgery, Laboratory for the Prevention and Rehabilitation of Military Training Related Injuries, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian-Xin Jiang
- Wound Trauma Medical Center, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| | - Peng Liu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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Khan MZ, Chen W, Huang B, Liu X, Wang X, Liu Y, Chai W, Wang C. Advancements in Genetic Marker Exploration for Livestock Vertebral Traits with a Focus on China. Animals (Basel) 2024; 14:594. [PMID: 38396562 PMCID: PMC10885964 DOI: 10.3390/ani14040594] [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: 12/25/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
In livestock breeding, the number of vertebrae has gained significant attention due to its impact on carcass quality and quantity. Variations in vertebral traits have been observed across different animal species and breeds, with a strong correlation to growth and meat production. Furthermore, vertebral traits are classified as quantitative characteristics. Molecular marker techniques, such as marker-assisted selection (MAS), have emerged as efficient tools to identify genetic markers associated with vertebral traits. In the current review, we highlight some key potential genes and their polymorphisms that play pivotal roles in controlling vertebral traits (development, length, and number) in various livestock species, including pigs, donkeys, and sheep. Specific genetic variants within these genes have been linked to vertebral development, number, and length, offering valuable insights into the genetic mechanisms governing vertebral traits. This knowledge has significant implications for selective breeding strategies to enhance structural characteristics and meat quantity and quality in livestock, ultimately improving the efficiency and quality of the animal husbandry industry.
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Affiliation(s)
- Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 522000, China
| | | | | | | | | | | | | | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 522000, China
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Zhou G, Yan X, Chen Z, Zeng X, Wu F. ASPN Synergizes with HAPLN1 to Inhibit the Osteogenic Differentiation of Bone Marrow Mesenchymal Stromal Cells and Extracellular Matrix Mineralization of Osteoblasts. Orthop Surg 2023; 15:2423-2434. [PMID: 37427673 PMCID: PMC10475675 DOI: 10.1111/os.13803] [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: 10/14/2022] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023] Open
Abstract
OBJECTIVE Bone marrow mesenchymal stromal cells (BMSCs) are major sources of osteogenic precursor cells in bone remodeling, which directly participate in osteoporosis (OP) progression. However, the involved specific mechanisms of BMSCs in OP warrant mass investigations. Initially, our bioinformatics analysis uncovered the prominent up-regulation of Asporin (ASPN) and proteoglycan link protein 1 (HAPLN1) in osteoblasts (OBs) of OP patients and their possible protein interaction. Hence, this study aimed to explore the effects of ASPN and HAPLN1 on osteogenic differentiation of BMSCs, extracellular matrix (ECM) mineralization of OBs, and osteoclastogenesis, hoping to offer research basis for OP treatment. METHODS GSE156508 dataset was used for analysis and screening to acquire the differentially expressed genes in OBs of OP patients, followed by the predicative analysis via STRING. OP mouse models were induced by ovariectomy (OVX), and ASPN and HAPLN1 expression was determined. BMSCs and bone marrow macrophages (BMMs) were isolated from OVX mice and induced for osteogenic differentiation and osteoclastogenesis, respectively. After knockdown experiments, we assessed adipogenic differentiation and osteogenic differentiation in BMSCs. Osteogenic (OPN, OCN, and COL1A1) and osteoclast (Nfatc1 and c-Fos) marker protein expression was determined. The binding of ASPN to HAPLN1 was analyzed. RESULTS High expression of ASPN and HAPLN1 and their protein interaction were observed in OBs of OP patients via bioinformatics and in bone tissues of OVX mice. ASPN interacted with HAPLN1 in BMSCs of OVX mice. ASPN/HAPLN1 knockdown increased ALP, OPN, OCN, and COL1A1 protein expression and ECM mineralization in BMSCs while decreasing Nfatc1 and c-Fos expression in BMMs. These effects were aggravated by the simultaneous knockdown of ASPN and HAPLN1. CONCLUSION Our results indicate that ASPN synergises with HAPLN1 to suppress the osteogenic differentiation of BMSCs and ECM mineralization of OBs and promote the osteoclastogenesis in OP.
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Affiliation(s)
- Guohui Zhou
- Department of OrthopaedicsFirst People's Hospital of FuzhouFuzhouChina
| | - Xinmin Yan
- Department of OrthopaedicsFirst People's Hospital of FuzhouFuzhouChina
| | - Zhenfei Chen
- Hospital‐Acquired Infection Control DepartmentFirst People's Hospital of FuzhouFuzhouChina
| | - Xing Zeng
- Department of OrthopaedicsFirst People's Hospital of FuzhouFuzhouChina
| | - Fangqian Wu
- Department of Spine SurgeryFirst People's Hospital of FuzhouFuzhouChina
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Shi X, Li Y, Wang T, Ren W, Huang B, Wang X, Liu Z, Liang H, Kou X, Chen Y, Wang Y, Akhtar F, Wang C. Association of HOXC8 Genetic Polymorphisms with Multi-Vertebral Number and Carcass Weight in Dezhou Donkey. Genes (Basel) 2022; 13:2175. [PMID: 36421849 PMCID: PMC9691153 DOI: 10.3390/genes13112175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 08/09/2023] Open
Abstract
An increase in the number of vertebrae can significantly affect the meat production performance of livestock, thus increasing carcass weight, which is of great importance for livestock production. The homeobox gene C8 (HOXC8) has been identified as an essential candidate gene for regulating vertebral development. However, it has not been researched on the Dezhou donkey. This study aimed to verify the Dezhou donkey HOXC8 gene's polymorphisms and assess their effects on multiple vertebral numbers and carcass weight. In this study, the entire HOXC8 gene of the Dezhou donkey was sequenced, SNPs at the whole gene level were identified, and typing was accomplished utilizing a targeted sequencing genotype detection technique (GBTS). Then, a general linear model was used to perform an association study of HOXC8 gene polymorphism loci, multiple vertebral numbers, and carcass weight for screening candidate markers that can be used for molecular breeding of Dezhou donkeys. These findings revealed that HOXC8 included 12 SNPs, all unique mutant loci. The HOXC8 g.15179224C>T was significantly negatively associated with carcass weight (CW) and lumbar vertebrae length (LL) (p < 0.05). The g.15179674G>A locus was shown to be significantly positively associated with the number of lumbar vertebrae (LN) (p < 0.05). The phylogenetic tree constructed for the Dezhou donkey HOXC8 gene and seven other species revealed that the HOXC8 gene was highly conserved during animal evolution but differed markedly among distantly related animals. The results suggest that HOXC8 is a vital gene affecting multiple vertebral numbers and carcass weight in Dezhou donkeys, and the two loci g.15179224C>T and g.15179674G>A may be potential genetic markers for screening and breeding of new strains of high-quality and high-yielding Dezhou donkeys.
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Yu H, Tang D, Wu H, Li C, Lu Y, He F, Zhang X, Yang Y, Shi W, Hu W, Zeng Z, Dai W, Ou M, Dai Y. Integrated single-cell analyses decode the developmental landscape of the human fetal spine. iScience 2022; 25:104679. [PMID: 35832888 PMCID: PMC9272381 DOI: 10.1016/j.isci.2022.104679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
The spine has essential roles in supporting body weight, and passaging the neural elements between the body and the brain. In this study, we used integrated single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing analyses to reveal the cellular heterogeneity, lineage, and transcriptional regulatory network of the developing human spine. We found that EPYC + HAPLN1+ fibroblasts with stem cell characteristics could differentiate into chondrocytes by highly expressing the chondrogenic markers SOX9 and MATN4. Neurons could originate from neuroendocrine cells, and MEIS2 may be an essential transcription factor that promotes spinal neural progenitor cells to selectively differentiate into neurons during early gestation. Furthermore, the interaction of NRP2_SEMA3C and CD74_APP between macrophages and neurons may be essential for spinal cord development. Our integrated map provides a blueprint for understanding human spine development in the early and midgestational stages at single-cell resolution and offers a tool for investigating related diseases. scRNA-seq and scATAC-seq analyses reveal the developmental landscape of the fetal spine Chondrocytes may originate from EPYC + HAPLN1+ fibroblasts with stem cell characteristics Neurons may originate from neuroendocrine cells with regulation by MEIS2
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Affiliation(s)
- Haiyan Yu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China.,Department of Pharmacy, Shenzhen Pingshan District People's Hospital, Pingshan General Hospital of Southern Medical University, Shenzhen, Guangdong 518118, P.R. China
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Hongwei Wu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Chunhong Li
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yongping Lu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China.,Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Fang He
- Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China
| | - Xiaogang Zhang
- Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China
| | - Yane Yang
- Shenzhen Far East Women & Children Hospital, Shenzhen 518000, Guangdong, China
| | - Wei Shi
- Department of Obstetrics and Gynecology, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Wenlong Hu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Zhipeng Zeng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX 78721, USA
| | - Minglin Ou
- Central Laboratory, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Lingui District, Guilin 541000, China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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Zagoskin MV, Wang J, Neff AT, Veronezi GMB, Davis RE. Small RNA pathways in the nematode Ascaris in the absence of piRNAs. Nat Commun 2022; 13:837. [PMID: 35149688 PMCID: PMC8837657 DOI: 10.1038/s41467-022-28482-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Small RNA pathways play key and diverse regulatory roles in C. elegans, but our understanding of their conservation and contributions in other nematodes is limited. We analyzed small RNA pathways in the divergent parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that associate with secondary 5’-triphosphate 22-24G-RNAs. These small RNAs target repetitive sequences or mature mRNAs and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Even in the absence of a piRNA pathway, Ascaris CSR-1 may still function to “license” as well as fine-tune or repress gene expression. Ascaris ALG-4 and its associated 26G-RNAs target and likely repress specific mRNAs during testis meiosis. Ascaris WAGO small RNAs demonstrate target plasticity changing their targets between repeats and mRNAs during development. We provide a unique and comprehensive view of mRNA and small RNA expression throughout spermatogenesis. Overall, our study illustrates the conservation, divergence, dynamics, and flexibility of small RNA pathways in nematodes. The parasitic nematode Ascaris lacks piRNAs. Here the authors compare Argonaute proteins and small RNAs from C. elegans and Ascaris, expanding our understanding of the conservation, divergence, and flexibility of Argonautes and small RNA pathways in nematodes.
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Affiliation(s)
- Maxim V Zagoskin
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA. .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA. .,UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA.
| | - Ashley T Neff
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.
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Chen L, Fan R, Tang F. Advanced Single-cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:343-345. [PMID: 34923125 PMCID: PMC8864189 DOI: 10.1016/j.gpb.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Affiliation(s)
- Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China.
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