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Dabrowski JK, Yang EJ, Crofts SJC, Hillary RF, Simpson DJ, McCartney DL, Marioni RE, Kirschner K, Latorre-Crespo E, Chandra T. Probabilistic inference of epigenetic age acceleration from cellular dynamics. NATURE AGING 2024; 4:1493-1507. [PMID: 39313745 PMCID: PMC11485233 DOI: 10.1038/s43587-024-00700-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/31/2024] [Indexed: 09/25/2024]
Abstract
The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological aging into a quantitative era; however, while current epigenetic clocks show strong predictive power, they are data-driven in nature and are not based on the underlying biological mechanisms driving methylation dynamics. We show that predictions of these clocks are susceptible to several confounding non-age-related phenomena that make interpretation of these estimates and associations difficult. To address these limitations, we developed a probabilistic model describing methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, which directly reflect perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias corresponds to global changes in methylation levels. Using data from 15,900 participants from the Generation Scotland study, we develop a robust inference framework and show that these are two distinct processes confounding current epigenetic predictors. Our results show improved associations of acceleration and bias with physiological traits known to impact healthy aging, such as smoking and alcohol consumption, respectively. Furthermore, a genome-wide association study of epigenetic age acceleration identified seven genomic loci.
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Affiliation(s)
- Jan K Dabrowski
- School of Informatics, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Emma J Yang
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Samuel J C Crofts
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kristina Kirschner
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Department of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Eric Latorre-Crespo
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.
- School of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Tamir Chandra
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
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Wu Y, Liu W, Li J, Shi H, Ma S, Wang D, Pan B, Xiao R, Jiang H, Liu X. Decreased Tiam1-mediated Rac1 activation is responsible for impaired directional persistence of chondrocyte migration in microtia. J Cell Mol Med 2024; 28:e18443. [PMID: 38837873 PMCID: PMC11149491 DOI: 10.1111/jcmm.18443] [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: 02/06/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 06/07/2024] Open
Abstract
The human auricle has a complex structure, and microtia is a congenital malformation characterized by decreased size and loss of elaborate structure in the affected ear with a high incidence. Our previous studies suggest that inadequate cell migration is the primary cytological basis for the pathogenesis of microtia, however, the underlying mechanism is unclear. Here, we further demonstrate that microtia chondrocytes show a decreased directional persistence during cell migration. Directional persistence can define a leading edge associated with oriented movement, and any mistakes would affect cell function and tissue morphology. By the screening of motility-related genes and subsequent confirmations, active Rac1 (Rac1-GTP) is identified to be critical for the impaired directional persistence of microtia chondrocytes migration. Moreover, Rho guanine nucleotide exchange factors (GEFs) and Rho GTPase-activating proteins (GAPs) are detected, and overexpression of Tiam1 significantly upregulates the level of Rac1-GTP and improves directional migration in microtia chondrocytes. Consistently, decreased expression patterns of Tiam1 and active Rac1 are found in microtia mouse models, Bmp5se/J and Prkralear-3J/GrsrJ. Collectively, our results provide new insights into microtia development and therapeutic strategies of tissue engineering for microtia patients.
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Affiliation(s)
- Yi Wu
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Wei Liu
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Jia Li
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Hang Shi
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Shize Ma
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Di Wang
- Department of Auricular Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Bo Pan
- Department of Auricular Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Ran Xiao
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- Key Laboratory of External Tissue and Organ Regeneration, Chinese Academy of Medical Sciences, Beijing, China
| | - Haiyue Jiang
- Department of Auricular Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xia Liu
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- Key Laboratory of External Tissue and Organ Regeneration, Chinese Academy of Medical Sciences, Beijing, China
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3
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Li T, Fan L, Jia Y, Xu C, Guo W, Wang Y, Li Y. Colorectal cancer cells with stably expressed SIRT3 demonstrate proliferating retardation by Wnt/β-catenin cascade inactivation. Clin Exp Pharmacol Physiol 2024; 51:e13856. [PMID: 38621772 DOI: 10.1111/1440-1681.13856] [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: 12/18/2023] [Revised: 02/24/2024] [Accepted: 03/04/2024] [Indexed: 04/17/2024]
Abstract
Colorectal cancer (CRC) is a typical and lethal digestive system malignancy. In this study, we investigated the effect of sirtuin 3 (SIRT3) expression, a fidelity mitochondrial protein, on the proliferation of CRC cells and the mechanisms involved. Using the University of Alabama at Birmingham Cancer Data Analysis Portal database and the Clinical Proteomic Tumour Analysis Consortium database, we discovered that low expression of SIRT3 in CRC was a negative factor for survival prognosis (P < .05). Meanwhile, SIRT3 expression was correlated with distant metastasis and tumour, node, metastasis stage of CRC patients (P < .05). Subsequently, we observed that CRC cells with stable SIRT3 expression exhibited a significant decrease in proliferative capacities both in vitro and in vivo, compared to their counterparts (P < .05). Further investigation using western blot, immunoprecipitation and TOPflash/FOPflash assay showed the mechanism of growth retardation of these cells was highly associated with the degradation of β-catenin in cytosol, and the localization of β-catenin/α-catenin complex in the nucleus. In conclusion, our findings suggest that the inhibition of CRC cell proliferation by SIRT3 is closely associated with the inactivation of the Wnt/β-catenin signalling pathway.
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Affiliation(s)
- Tianyu Li
- Department of Pharmacology, School of Pharmaceutical Science, Capital Medical University, Beijing, China
| | - Leqi Fan
- Department of Pharmacology, School of Pharmaceutical Science, Capital Medical University, Beijing, China
| | - Yijiang Jia
- Department of Medicinal Chemistry, School of Pharmaceutical Science, Capital Medical University, Beijing, China
| | - Chen Xu
- Department of Pharmacology, School of Pharmaceutical Science, Capital Medical University, Beijing, China
| | - Wei Guo
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Yuji Wang
- Department of Medicinal Chemistry, School of Pharmaceutical Science, Capital Medical University, Beijing, China
| | - Ye Li
- Department of Pharmacology, School of Pharmaceutical Science, Capital Medical University, Beijing, China
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Tian Y, Lin J, Li X, Zhu G, Fan L, Lou S, Li D, Pan Y. Mechanical dissection and culture of mouse cranial neural crest cells. Birth Defects Res 2023; 115:417-429. [PMID: 36621938 DOI: 10.1002/bdr2.2148] [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: 10/10/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/10/2023]
Abstract
Owing to the contribution of cranial neural crest cells (CNCCs) to the majority of craniofacial structures, they have been studied extensively for the pathogenesis of craniofacial diseases. To investigate and summarize how to isolate and culture the CNCCs from wild-type mice, a literature search was performed in online databases (PubMed and Web of Science) using optimized keywords "mouse," "cranial neural crest cell" and "culture." The literature was checked by two investigators according to the screening and exclusion criteria. Initially, 197 studies were retrieved from PubMed and 169 from Web of Science, and after excluding replicate studies, 293 articles were considered. Finally, 17 studies met all the criteria and were included in this review. The results showed that obtaining purified stem cells and balancing the need to promote cell growth and prevent unwanted early cell differentiation were the two key points in the isolation and culture of CNCCs. However, no standard criteria are available for answering these questions. Thus, it is important to emphasize the necessity for standardization of CNCC isolation, culture, and identification in research on craniofacial diseases.
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Affiliation(s)
- Yu Tian
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, Jiangsu Province, China.,Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Junyan Lin
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, Jiangsu Province, China.,Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xiaofeng Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, Jiangsu Province, China.,Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Guirong Zhu
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, Jiangsu Province, China.,Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Liwen Fan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, Jiangsu Province, China.,Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, Jiangsu Province, China
| | - Shu Lou
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, Jiangsu Province, China.,Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, Jiangsu Province, China
| | - Dandan Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, Jiangsu Province, China.,Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, Jiangsu Province, China
| | - Yongchu Pan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, Jiangsu Province, China.,Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, Jiangsu Province, China
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Liao J, Huang Y, Wang Q, Chen S, Zhang C, Wang D, Lv Z, Zhang X, Wu M, Chen G. Gene regulatory network from cranial neural crest cells to osteoblast differentiation and calvarial bone development. Cell Mol Life Sci 2022; 79:158. [PMID: 35220463 PMCID: PMC11072871 DOI: 10.1007/s00018-022-04208-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/03/2022]
Abstract
Calvarial bone is one of the most complex sequences of developmental events in embryology, featuring a uniquely transient, pluripotent stem cell-like population known as the cranial neural crest (CNC). The skull is formed through intramembranous ossification with distinct tissue lineages (e.g. neural crest derived frontal bone and mesoderm derived parietal bone). Due to CNC's vast cell fate potential, in response to a series of inductive secreted cues including BMP/TGF-β, Wnt, FGF, Notch, Hedgehog, Hippo and PDGF signaling, CNC enables generations of a diverse spectrum of differentiated cell types in vivo such as osteoblasts and chondrocytes at the craniofacial level. In recent years, since the studies from a genetic mouse model and single-cell sequencing, new discoveries are uncovered upon CNC patterning, differentiation, and the contribution to the development of cranial bones. In this review, we summarized the differences upon the potential gene regulatory network to regulate CNC derived osteogenic potential in mouse and human, and highlighted specific functions of genetic molecules from multiple signaling pathways and the crosstalk, transcription factors and epigenetic factors in orchestrating CNC commitment and differentiation into osteogenic mesenchyme and bone formation. Disorders in gene regulatory network in CNC patterning indicate highly close relevance to clinical birth defects and diseases, providing valuable transgenic mouse models for subsequent discoveries in delineating the underlying molecular mechanisms. We also emphasized the potential regenerative alternative through scientific discoveries from CNC patterning and genetic molecules in interfering with or alleviating clinical disorders or diseases, which will be beneficial for the molecular targets to be integrated for novel therapeutic strategies in the clinic.
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Affiliation(s)
- Junguang Liao
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yuping Huang
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Qiang Wang
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Sisi Chen
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Chenyang Zhang
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Dan Wang
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Zhengbing Lv
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xingen Zhang
- Department of Orthopedics, Jiaxing Key Laboratory for Minimally Invasive Surgery in Orthopaedics & Skeletal Regenerative Medicine, Zhejiang Rongjun Hospital, Jiaxing, 314001, China
| | - Mengrui Wu
- Institute of Genetics, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Guiqian Chen
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
- Institute of Genetics, College of Life Science, Zhejiang University, Hangzhou, 310058, China.
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Huang Z, Yang R, Li R, Zuo Y, Gu F, He M, Bian Z. Mesenchymal Mycn participates in odontoblastic lineage commitment by regulating Krüppel-like Factor 4 (Klf4) in mice. Stem Cell Res Ther 2022; 13:78. [PMID: 35193672 PMCID: PMC8864903 DOI: 10.1186/s13287-022-02749-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/27/2022] [Indexed: 11/27/2022] Open
Abstract
Background Commitment of mouse dental papilla cells (mDPCs) to the odontoblast lineage is critical for dentin formation, and this biological process is regulated by a complex transcription factor network. The transcription factor Mycn is a proto-oncogene that plays an important role in tumorigenesis and normal embryonic development. An early study revealed that Mycn is exclusively expressed in dental mesenchymal cells at E15.5, which implies a potential role of Mycn in dentinogenesis. However, the role of Mycn in dentin formation remains elusive. Thus, it is of considerable interest to elucidate the role of Mycn in dentin formation. Methods Mycnfl/fl; Osr2IresCre (MycnOsr2) and Mycnfl/fl; K14Cre (MycnK14) transgenic mice were generated, and micro-CT scans were performed to quantitatively analyse the volumetric differences in the molars and incisors of the mutants and their littermates. Mycn was also knocked down in vitro, and alkaline phosphatase (ALP) and alizarin red staining (ARS) were conducted. Cleavage under targets and tagmentation (CUT&Tag) analysis and dual luciferase assays were performed to identify direct downstream targets of Mycn. Immunofluorescence and immunochemistry staining and western blotting (WB) were performed to analyse the expression levels of potential targets. Quantitative PCR, WB, ALP and ARS were performed to test the rescue efficiency. Results Mesenchymal ablation of Mycn (MycnOsr2) led to defective dentin formation, while epithelial deletion (MycnK14) had no obvious effects on tooth development. ALP and ARS staining revealed that the commitment capacity of mDPCs to the odontoblast lineage was compromised in MycnOsr2 mice. CUT&Tag analysis identified Klf4 as a potential direct target of Mycn, and a dual luciferase reporter assay verified that Mycn could bind to the promotor region of Klf4 and directly activate its transcription. Reciprocally, forced expression of Klf4 partially recovered the odontoblastic differentiation capacity of mDPCs with Mycn knockdown. Conclusions Our results elucidated that mesenchymal Mycn modulates the odontoblastic commitment of dental papilla cells by directly regulating Klf4. Our study illustrated the role of Mycn in dentin development and furthers our general comprehension of the transcription factor networks involved in the dentinogenesis process. Thus, these results may provide new insight into dentin hypoplasia and bioengineered dentin regeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02749-8.
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Affiliation(s)
- Zhuo Huang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Ruihuan Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Ruyi Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Yining Zuo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Fan Gu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Miao He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China.
| | - Zhuan Bian
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China.
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