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Yang B, Yang Z. Deterministic and stochastic approaches to a minimal model for the transition from autophagy to apoptosis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:3207-3228. [PMID: 38454725 DOI: 10.3934/mbe.2024142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Autophagy and apoptosis are crucial cellular mechanisms. The cytoprotective function of autophagy is mediated by the negative regulation of apoptosis, which in turn inhibits autophagy. Although research into the molecular connection between autophagy and apoptosis is booming, the intricate regulatory mechanisms of this process are still not completely understood. Therefore, the objective of this study was to develop a minimal model to explore the transition from autophagy to apoptosis. This biological system was analyzed by comprehensively integrating both the deterministic and the stochastic dynamics of the cells. The system exhibited bistability, and the statistical properties of cells undergoing autophagy and apoptosis were analyzed at two different stress levels with varying noise strengths. Moreover, we investigated how noise affected the double negative feedback loops between autophagy and apoptosis and further triggered transitions at two different stress levels and initial conditions. Finally, the effect of noise on transition was comprehensively studied under continuous stress variations and the two different initial conditions, showing that stronger noise results in more randomness during the switching process. Our work may provide novel insights for further experiments and modeling.
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Affiliation(s)
- Bojie Yang
- School of Mathematical Sciences, Beihang University, Beijing 100191, China
| | - Zhuoqin Yang
- School of Mathematical Sciences, Beihang University, Beijing 100191, China
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Long AF, Stearns T. A not-so-simple twist of fate. Dev Cell 2021; 56:402-404. [PMID: 33621489 DOI: 10.1016/j.devcel.2021.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Multiciliated cells are considered terminally differentiated, yet tissues bearing them are remodeled during development and after injury. In this issue of Developmental Cell, Tasca et al. (2021) show that multiciliated epithelial cells are lost via two different Notch-dependent processes, apoptosis and transdifferentiation, during developmental remodeling of the Xenopus epidermis.
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Affiliation(s)
- Alexandra F Long
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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Yang S, Kam WR, Liu Y, Ding J, Li Y, Sullivan DA. Comparative influence of differentiation and proliferation on gene expression in human meibomian gland epithelial cells. Exp Eye Res 2021; 205:108452. [PMID: 33493473 DOI: 10.1016/j.exer.2021.108452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022]
Abstract
We recently discovered that by changing environmental signals, differentiated immortalized human meibomian gland epithelial cells (IHMGECs) de-differentiate into proliferating cells. We also discovered that following exposure to appropriate stimuli, these proliferative cells re-differentiate into differentiated IHMGECs. We hypothesize that this plasticity of differentiated and proliferative IHMGECs is paralleled by very significant alterations in cellular gene expression. To begin to test this hypothesis, we compared the gene expression patterns of IHMGECs during differentiation and proliferation. IHMGECs were cultured for four days in either differentiating or proliferating media. After four days of culture, cells were processed for the analysis of gene expression by using Illumina BeadChips and bioinformatic software. Our study identified significant differences in the expression of more than 9200 genes in differentiated and proliferative IHMGECs. Differentiation was associated with significant increases in the expression of specific genes (e.g. S100 calcium binding protein P; 7,194,386-fold upregulation) and numerous ontologies (e.g. 83 biological process [bp] ontologies with ≥100 genes were upregulated), such as those related to development, transport and lysosomes. Proliferation also led to a significant rise in specific gene expressions (e.g. cathelicidin antimicrobial peptide; 859,100-fold upregulation) and many ontologies (115 biological process [bp] ontologies with ≥100 genes were upregulated), with most of the highly significant ontologies related to cell cycle (z scores > 13.9). Our findings demonstrate that gene expression in differentiated and proliferative IHMGECs is extremely different. These results may have significant implications for the regeneration of HMGECs and the reversal of MG dropout in MG dysfunction.
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Affiliation(s)
- Shan Yang
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; Schepens Eye Research Institute of Massachusetts Eye and Ear, And Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
| | - Wendy R Kam
- Schepens Eye Research Institute of Massachusetts Eye and Ear, And Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Yang Liu
- Schepens Eye Research Institute of Massachusetts Eye and Ear, And Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Juan Ding
- Schepens Eye Research Institute of Massachusetts Eye and Ear, And Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; Department of Ophthalmology & Visual Sciences, UMass Memorial Medical Center, Worcester, MA, USA
| | - Ying Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China.
| | - David A Sullivan
- Schepens Eye Research Institute of Massachusetts Eye and Ear, And Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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Abstract
This Open Question article highlights current advances in the study of non-apoptotic roles of apoptotic proteins. Apoptosis is a highly regulated and energy-requiring process in which cells actively kill themselves. Apoptosis helps remove extra cells to sculpt organs during embryo development and culls damaged cells throughout the body. Apoptosis relies on evolutionarily conserved proteins that include a family of proteases called caspases. Caspases activity has long been considered a hallmark of apoptosis. Yet an emerging body of literature indicates that caspase activity is required for a number of non-lethal processes that range from sculpting cells, removing protein aggregates, changing cell identity during differentiation or de-differentiation, and rebuilding tissues. Failure in each of these processes is associated with human disease. This article is not meant to be an exhaustive review but an introduction to the subject for an educated public, with caspases as a gateway example. I propose that it is time to explore non-apoptotic roles of caspases and other apoptotic proteins, in order to better understand their non-apoptosis function and to leverage new knowledge into new therapies.
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Affiliation(s)
- Tin Tin Su
- Department of Molecular, Cellular and Developmental Biology. University of Colorado, 347 UCB, Boulder, CO 80309-0347, USA.,Molecular and Cellular Oncology Program, University of Colorado Comprehensive Cancer Center, Anschutz Medical Campus, 13001 E. 17th Pl., Aurora, CO 80045, USA
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A novel indirubin derivative that increases somatic cell plasticity and inhibits tumorigenicity. Bioorg Med Chem 2019; 27:2923-2934. [DOI: 10.1016/j.bmc.2019.05.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/25/2019] [Accepted: 05/16/2019] [Indexed: 01/26/2023]
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