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Cai J, Han R, Li J, Hao J, Zhao Z, Jing D. Exploring mechanobiology network of bone and dental tissue based on Natural Language Processing. J Biomech 2024; 174:112271. [PMID: 39159585 DOI: 10.1016/j.jbiomech.2024.112271] [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: 04/01/2024] [Revised: 07/04/2024] [Accepted: 08/08/2024] [Indexed: 08/21/2024]
Abstract
Bone and cartilage tissues are physiologically dynamic organs that are systematically regulated by mechanical inputs. At cellular level, mechanical stimulation engages an intricate network where mechano-sensors and transmitters cooperate to manipulate downstream signaling. Despite accumulating evidence, there is a notable underutilization of available information, due to limited integration and analysis. In this context, we conceived an interactive web tool named MechanoBone to introduce a new avenue of literature-based discovery. Initially, we compiled a literature database by sourcing content from Pubmed and processing it through the Natural Language Toolkit project, Pubtator, and a custom library. We identified direct co-occurrence among entities based on existing evidence, archiving in a relational database via SQLite. Latent connections were then quantified by leveraging the Link Prediction algorithm. Secondly, mechanobiological pathway maps were generated, and an entity-pathway correlation scoring system was established through weighted algorithm based on our database, String, and KEGG, predicting potential functions of specific entities. Additionally, we established a mechanical circumstance-based exploration to sort genes by their relevance based on big data, revealing the potential mechanically sensitive factors in bone research and future clinical applications. In conclusion, MechanoBone enables: 1) interpreting mechanobiological processes; 2) identifying correlations and crosstalk among molecules and pathways under specific mechanical conditions; 3) connecting clinical applications with mechanobiological processes in bone research. It offers a literature mining tool with visualization and interactivity, facilitating targeted molecule navigation and prediction within the mechanobiological framework of bone-related cells, thereby enhancing knowledge sharing and big data analysis in the biomedical realm.
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Affiliation(s)
- Jingyi Cai
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - RuiYing Han
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Junfu Li
- Glagow College, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Jin Hao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; ChohoTech Inc., Hangzhou 311100, China.
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Dian Jing
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.
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Duan SL, Jiang Y, Li GQ, Fu W, Song Z, Li LN, Li J. Research insights into the chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTM): their roles in various tumors. PeerJ 2024; 12:e16757. [PMID: 38223763 PMCID: PMC10787544 DOI: 10.7717/peerj.16757] [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: 05/17/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024] Open
Abstract
The chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing (CMTM) family includes CMTM1-8 and CKLF, and they play key roles in the hematopoietic, immune, cardiovascular, and male reproductive systems, participating in the physiological functions, cancer, and other diseases associated with these systems. CMTM family members activate and chemoattract immune cells to affect the proliferation and invasion of tumor cells through a similar mechanism, the structural characteristics typical of chemokines and transmembrane 4 superfamily (TM4SF). In this review, we discuss each CMTM family member's chromosomal location, involved signaling pathways, expression patterns, and potential roles, and mechanisms of action in pancreatic, breast, gastric and liver cancers. Furthermore, we discuss several clinically applied tumor therapies targeted at the CMTM family, indicating that CMTM family members could be novel immune checkpoints and potential targets effective in tumor treatment.
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Affiliation(s)
- Sai-Li Duan
- Department of General Surgery, Xiangya Hospital Central South University, Changsha Province, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha Province, Hunan, China
| | - Yingke Jiang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha Province, Hunan, China
| | - Guo-Qing Li
- Xiangya School of Medicine, Central South University, Changsha Province, Hunan, China
| | - Weijie Fu
- Xiangya School of Medicine, Central South University, Changsha Province, Hunan, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha Province, Hunan, China
| | - Li-Nan Li
- Department of Oncology, The 1st Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jia Li
- Department of Oncology, The 1st Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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Cell surface markers for mesenchymal stem cells related to the skeletal system: A scoping review. Heliyon 2023; 9:e13464. [PMID: 36865479 PMCID: PMC9970931 DOI: 10.1016/j.heliyon.2023.e13464] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Multipotent mesenchymal stromal cells (MSCs) have been described as bone marrow stromal cells, which can form cartilage, bone or hematopoietic supportive stroma. In 2006, the International Society for Cell Therapy (ISCT) established a set of minimal characteristics to define MSCs. According to their criteria, these cells must express CD73, CD90 and CD105 surface markers; however, it is now known they do not represent true stemness epitopes. The objective of the present work was to determine the surface markers for human MSCs associated with skeletal tissue reported in the literature (1994-2021). To this end, we performed a scoping review for hMSCs in axial and appendicular skeleton. Our findings determined the most widely used markers were CD105 (82.9%), CD90 (75.0%) and CD73 (52.0%) for studies performed in vitro as proposed by the ISCT, followed by CD44 (42.1%), CD166 (30.9%), CD29 (27.6%), STRO-1 (17.7%), CD146 (15.1%) and CD271 (7.9%) in bone marrow and cartilage. On the other hand, only 4% of the articles evaluated in situ cell surface markers. Even though most studies use the ISCT criteria, most publications in adult tissues don't evaluate the characteristics that establish a stem cell (self-renewal and differentiation), which will be necessary to distinguish between a stem cell and progenitor populations. Collectively, MSCs require further understanding of their characteristics if they are intended for clinical use.
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Anderson PJ. Ex Vivo Culture of Human Cranial Suture Cells. Methods Mol Biol 2022; 2403:215-222. [PMID: 34913125 DOI: 10.1007/978-1-0716-1847-9_14] [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] [Indexed: 06/14/2023]
Abstract
The culture of human cranial suture cells, including their osteoblasts, is an important asset to developmental and molecular biologists to allow study the molecular biology ex vivo. The use of cell cultures by bone biologists to investigate pathological bone formation has been well established (Marie et al. Vitro Cell Dev Biol 25:373-380, 1989), and the use of cell culture techniques was subsequently applied to investigate craniosynostosis (Marie. J Bone Miner Res 9(12):1847-1850, 1994). Cell cultures from fused, fusing, and fused cranial sutures allow comparative studies of cellular behavior from sutures with pathological craniosynostosis and those with unaffected sutures (Coussens et al. J Cell Physiol 218(1):183-191, 2009; Coussens et al. Differentiation 76(5):531-545, 2008).In addition to using this limited human resource for primary investigations, these human cell studies may be targeted to complement and help verify the findings of investigative studies undertaken using the more readily accessible animal cranial sutures. It is important, however, to remember that there may be critical differences in the animal genome which could impact on cellular function.This chapter describes the techniques for human suture cell culture and storage which have been used successfully since 2005 in the craniosynostosis laboratories in Adelaide.
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Affiliation(s)
- Peter J Anderson
- Australian Craniofacial Unit, Women's and Children's Hospital, North Adelaide, SA, Australia.
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Li M, Luo F, Tian X, Yin S, Zhou L, Zheng S. Chemokine-Like Factor-Like MARVEL Transmembrane Domain-Containing Family in Hepatocellular Carcinoma: Latest Advances. Front Oncol 2020; 10:595973. [PMID: 33282744 PMCID: PMC7691587 DOI: 10.3389/fonc.2020.595973] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
Chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTMs) is a new gene family, consisting of CKLF and CMTM1 to CMTM8, which plays an important role in hematopoiesis system, autoimmune diseases, male reproduction etc. Abnormal expression of CMTMs is also associated with tumor genesis, development and metastasis. In this review, we briefly describe the characteristics of CMTM family, outline its functions in multiple kinds of carcinomas, and summarize the latest research on their roles in hepatocellular carcinoma which are mainly related to the expression, prognostic effect, potential functions, and mechanism of action. The CMTM family is expected to provide new ideas and targets for HCC diagnosis and treatment.
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Affiliation(s)
- Mengxia Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Fangzhou Luo
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Xinyao Tian
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Shengyong Yin
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, China.,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, China
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