Limits...
Autophagy capacity and sub-mitochondrial heterogeneity shape Bnip3-induced mitophagy regulation of apoptosis.

Choe SC, Hamacher-Brady A, Brady NR - Cell Commun. Signal (2015)

Bottom Line: Previously, we have shown that Bnip3-activated mitophagy prior to apoptosis induction can reduce mitochondrial activation of caspases, suggesting that a reduction to mitochondrial levels may be pro-survival.Our model identifies mechanisms and conditions that alter the mitophagy decision within mitochondrial subpopulations to an extent sufficient to shape cellular outcome to apoptotic stimuli.Overall, our modeling approach provides means to suggest new experiments and implement findings at multiple scales in order to understand how network topologies and subcellular heterogeneities can influence signaling events at individual organelle level, and hence, determine the emergence of heterogeneity in cellular decisions due the actions of the collective intra-cellular population.

View Article: PubMed Central - PubMed

Affiliation: Systems Biology of Cell Death Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany.

ABSTRACT

Background: Mitochondria are key regulators of apoptosis. In response to stress, BH3-only proteins activate pro-apoptotic Bcl2 family proteins Bax and Bak, which induce mitochondrial outer membrane permeabilization (MOMP). While the large-scale mitochondrial release of pro-apoptotic proteins activates caspase-dependent cell death, a limited release results in sub-lethal caspase activation which promotes tumorigenesis. Mitochondrial autophagy (mitophagy) targets dysfunctional mitochondria for degradation by lysosomes, and undergoes extensive crosstalk with apoptosis signaling, but its influence on apoptosis remains undetermined. The BH3-only protein Bnip3 integrates apoptosis and mitophagy signaling at different signaling domains. Bnip3 inhibits pro-survival Bcl2 members via its BH3 domain and activates mitophagy through its LC3 Interacting Region (LIR), which is responsible for binding to autophagosomes. Previously, we have shown that Bnip3-activated mitophagy prior to apoptosis induction can reduce mitochondrial activation of caspases, suggesting that a reduction to mitochondrial levels may be pro-survival. An outstanding question is whether organelle dynamics and/or recently discovered subcellular variations of protein levels responsible for both MOMP sensitivity and crosstalk between apoptosis and mitophagy can influence the cellular apoptosis decision event. To that end, here we undertook a systems biology analysis of mitophagy-apoptosis crosstalk at the level of cellular mitochondrial populations.

Results: Based on experimental findings, we developed a multi-scale, hybrid model with an individually adaptive mitochondrial population, whose actions are determined by protein levels, embedded in an agent-based model (ABM) for simulating subcellular dynamics and local feedback via reactive oxygen species signaling. Our model, supported by experimental evidence, identified an emergent regulatory structure within canonical apoptosis signaling. We show that the extent of mitophagy is determined by levels and spatial localization of autophagy capacity, and subcellular mitochondrial protein heterogeneities. Our model identifies mechanisms and conditions that alter the mitophagy decision within mitochondrial subpopulations to an extent sufficient to shape cellular outcome to apoptotic stimuli.

Conclusion: Overall, our modeling approach provides means to suggest new experiments and implement findings at multiple scales in order to understand how network topologies and subcellular heterogeneities can influence signaling events at individual organelle level, and hence, determine the emergence of heterogeneity in cellular decisions due the actions of the collective intra-cellular population.

No MeSH data available.


Related in: MedlinePlus

Impact of mitophagy/apoptosis signaling and ROS production on homogeneous mitochondrial population. Autophagic vesicles are randomly distributed to cover 20 % of cell surface (AV = 75) with a population of 100 mitochondria seeded with equal initial content (Bnip3 = 1, Bcl2 = 1, Bax = 1). All simulations are run for 100 time steps and sample size of 50 runs. a In absence of tBid activation and with 20 % pre-activation of Bnip3 LIR activity, scatter points (blue) track mitochondrial content individually, with size and color depth indicating level of mitophagy potential at every time step. Total mitophagic content in mitochondrial population (blue line) indicates the population response. The population exhibits three phases (insets): activation of signaling pathways (light gray), competition to commit to a phenotype (dark gray), and a committed phase during which phenotype is executed (olive). Runs show cell-to-cell variability (blue shaded area). Tables indicate statistics of total mitophagy potential after 30 time steps around the time of phenotype commitment, with sample size of 50 runs. b With tBid activation at t = 5 following 20 % pre-activation of Bnip3 LIR activity shows total apoptotic potential (red line) and total mitophagy potential (blue line). Scatter points track mitochondrial content individually showing mitophagy (blue) or apoptosis (red) potential at every time step. (Inset top) Final phenotype of all mitochondria shows size of mitophagy (blue) and apoptosis (red) sub-populations, and consequent cytochrome c release (green). Tables show statistics after 50 time steps, sampled over 50 runs. c Example simulation images (at t = 30) of 20 % pre-activation of Bnip3 followed by tBid activation (at t = 5), showing mitochondrial sub-populations with mitophagy (blue) or apoptosis (red) phenotypes and cytochrome c release environment layer (green); merged (black background)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4528699&req=5

Fig3: Impact of mitophagy/apoptosis signaling and ROS production on homogeneous mitochondrial population. Autophagic vesicles are randomly distributed to cover 20 % of cell surface (AV = 75) with a population of 100 mitochondria seeded with equal initial content (Bnip3 = 1, Bcl2 = 1, Bax = 1). All simulations are run for 100 time steps and sample size of 50 runs. a In absence of tBid activation and with 20 % pre-activation of Bnip3 LIR activity, scatter points (blue) track mitochondrial content individually, with size and color depth indicating level of mitophagy potential at every time step. Total mitophagic content in mitochondrial population (blue line) indicates the population response. The population exhibits three phases (insets): activation of signaling pathways (light gray), competition to commit to a phenotype (dark gray), and a committed phase during which phenotype is executed (olive). Runs show cell-to-cell variability (blue shaded area). Tables indicate statistics of total mitophagy potential after 30 time steps around the time of phenotype commitment, with sample size of 50 runs. b With tBid activation at t = 5 following 20 % pre-activation of Bnip3 LIR activity shows total apoptotic potential (red line) and total mitophagy potential (blue line). Scatter points track mitochondrial content individually showing mitophagy (blue) or apoptosis (red) potential at every time step. (Inset top) Final phenotype of all mitochondria shows size of mitophagy (blue) and apoptosis (red) sub-populations, and consequent cytochrome c release (green). Tables show statistics after 50 time steps, sampled over 50 runs. c Example simulation images (at t = 30) of 20 % pre-activation of Bnip3 followed by tBid activation (at t = 5), showing mitochondrial sub-populations with mitophagy (blue) or apoptosis (red) phenotypes and cytochrome c release environment layer (green); merged (black background)

Mentions: To simulate mitophagy in a single cell, an initial level of AV = 75 was distributed to approximate a 20 % coverage of the total cell surface area. For a single cell, the scatter points (Figure 3a) represent the time-dependent evolution of each mitochondrion’s phenotype, with the size and color indicating the dominant phenotypes, either mitophagy (blue) or apoptosis (red). Notably, the agent-based simulation resulted in emergence of mitochondrial heterogeneity. The spread of the scatter points along the y-axis indicates the emergent variable response of the mitochondrial population to mitophagy activation. This variability arises from the heterogeneity in co-localization of mitochondria to AVs, as mitochondria in the vicinity of AVs are affected more potently, resulting in the variable degradation rate of the population (along x-axis). In comparison, an homogeneous distribution of AVs, where total AV content was spatially distributed equally, shows almost no variability in mitochondrial response (Additional file 6: Figure S6A), implicating the importance of heterogeneous AV localization.Fig. 3


Autophagy capacity and sub-mitochondrial heterogeneity shape Bnip3-induced mitophagy regulation of apoptosis.

Choe SC, Hamacher-Brady A, Brady NR - Cell Commun. Signal (2015)

Impact of mitophagy/apoptosis signaling and ROS production on homogeneous mitochondrial population. Autophagic vesicles are randomly distributed to cover 20 % of cell surface (AV = 75) with a population of 100 mitochondria seeded with equal initial content (Bnip3 = 1, Bcl2 = 1, Bax = 1). All simulations are run for 100 time steps and sample size of 50 runs. a In absence of tBid activation and with 20 % pre-activation of Bnip3 LIR activity, scatter points (blue) track mitochondrial content individually, with size and color depth indicating level of mitophagy potential at every time step. Total mitophagic content in mitochondrial population (blue line) indicates the population response. The population exhibits three phases (insets): activation of signaling pathways (light gray), competition to commit to a phenotype (dark gray), and a committed phase during which phenotype is executed (olive). Runs show cell-to-cell variability (blue shaded area). Tables indicate statistics of total mitophagy potential after 30 time steps around the time of phenotype commitment, with sample size of 50 runs. b With tBid activation at t = 5 following 20 % pre-activation of Bnip3 LIR activity shows total apoptotic potential (red line) and total mitophagy potential (blue line). Scatter points track mitochondrial content individually showing mitophagy (blue) or apoptosis (red) potential at every time step. (Inset top) Final phenotype of all mitochondria shows size of mitophagy (blue) and apoptosis (red) sub-populations, and consequent cytochrome c release (green). Tables show statistics after 50 time steps, sampled over 50 runs. c Example simulation images (at t = 30) of 20 % pre-activation of Bnip3 followed by tBid activation (at t = 5), showing mitochondrial sub-populations with mitophagy (blue) or apoptosis (red) phenotypes and cytochrome c release environment layer (green); merged (black background)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4528699&req=5

Fig3: Impact of mitophagy/apoptosis signaling and ROS production on homogeneous mitochondrial population. Autophagic vesicles are randomly distributed to cover 20 % of cell surface (AV = 75) with a population of 100 mitochondria seeded with equal initial content (Bnip3 = 1, Bcl2 = 1, Bax = 1). All simulations are run for 100 time steps and sample size of 50 runs. a In absence of tBid activation and with 20 % pre-activation of Bnip3 LIR activity, scatter points (blue) track mitochondrial content individually, with size and color depth indicating level of mitophagy potential at every time step. Total mitophagic content in mitochondrial population (blue line) indicates the population response. The population exhibits three phases (insets): activation of signaling pathways (light gray), competition to commit to a phenotype (dark gray), and a committed phase during which phenotype is executed (olive). Runs show cell-to-cell variability (blue shaded area). Tables indicate statistics of total mitophagy potential after 30 time steps around the time of phenotype commitment, with sample size of 50 runs. b With tBid activation at t = 5 following 20 % pre-activation of Bnip3 LIR activity shows total apoptotic potential (red line) and total mitophagy potential (blue line). Scatter points track mitochondrial content individually showing mitophagy (blue) or apoptosis (red) potential at every time step. (Inset top) Final phenotype of all mitochondria shows size of mitophagy (blue) and apoptosis (red) sub-populations, and consequent cytochrome c release (green). Tables show statistics after 50 time steps, sampled over 50 runs. c Example simulation images (at t = 30) of 20 % pre-activation of Bnip3 followed by tBid activation (at t = 5), showing mitochondrial sub-populations with mitophagy (blue) or apoptosis (red) phenotypes and cytochrome c release environment layer (green); merged (black background)
Mentions: To simulate mitophagy in a single cell, an initial level of AV = 75 was distributed to approximate a 20 % coverage of the total cell surface area. For a single cell, the scatter points (Figure 3a) represent the time-dependent evolution of each mitochondrion’s phenotype, with the size and color indicating the dominant phenotypes, either mitophagy (blue) or apoptosis (red). Notably, the agent-based simulation resulted in emergence of mitochondrial heterogeneity. The spread of the scatter points along the y-axis indicates the emergent variable response of the mitochondrial population to mitophagy activation. This variability arises from the heterogeneity in co-localization of mitochondria to AVs, as mitochondria in the vicinity of AVs are affected more potently, resulting in the variable degradation rate of the population (along x-axis). In comparison, an homogeneous distribution of AVs, where total AV content was spatially distributed equally, shows almost no variability in mitochondrial response (Additional file 6: Figure S6A), implicating the importance of heterogeneous AV localization.Fig. 3

Bottom Line: Previously, we have shown that Bnip3-activated mitophagy prior to apoptosis induction can reduce mitochondrial activation of caspases, suggesting that a reduction to mitochondrial levels may be pro-survival.Our model identifies mechanisms and conditions that alter the mitophagy decision within mitochondrial subpopulations to an extent sufficient to shape cellular outcome to apoptotic stimuli.Overall, our modeling approach provides means to suggest new experiments and implement findings at multiple scales in order to understand how network topologies and subcellular heterogeneities can influence signaling events at individual organelle level, and hence, determine the emergence of heterogeneity in cellular decisions due the actions of the collective intra-cellular population.

View Article: PubMed Central - PubMed

Affiliation: Systems Biology of Cell Death Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany.

ABSTRACT

Background: Mitochondria are key regulators of apoptosis. In response to stress, BH3-only proteins activate pro-apoptotic Bcl2 family proteins Bax and Bak, which induce mitochondrial outer membrane permeabilization (MOMP). While the large-scale mitochondrial release of pro-apoptotic proteins activates caspase-dependent cell death, a limited release results in sub-lethal caspase activation which promotes tumorigenesis. Mitochondrial autophagy (mitophagy) targets dysfunctional mitochondria for degradation by lysosomes, and undergoes extensive crosstalk with apoptosis signaling, but its influence on apoptosis remains undetermined. The BH3-only protein Bnip3 integrates apoptosis and mitophagy signaling at different signaling domains. Bnip3 inhibits pro-survival Bcl2 members via its BH3 domain and activates mitophagy through its LC3 Interacting Region (LIR), which is responsible for binding to autophagosomes. Previously, we have shown that Bnip3-activated mitophagy prior to apoptosis induction can reduce mitochondrial activation of caspases, suggesting that a reduction to mitochondrial levels may be pro-survival. An outstanding question is whether organelle dynamics and/or recently discovered subcellular variations of protein levels responsible for both MOMP sensitivity and crosstalk between apoptosis and mitophagy can influence the cellular apoptosis decision event. To that end, here we undertook a systems biology analysis of mitophagy-apoptosis crosstalk at the level of cellular mitochondrial populations.

Results: Based on experimental findings, we developed a multi-scale, hybrid model with an individually adaptive mitochondrial population, whose actions are determined by protein levels, embedded in an agent-based model (ABM) for simulating subcellular dynamics and local feedback via reactive oxygen species signaling. Our model, supported by experimental evidence, identified an emergent regulatory structure within canonical apoptosis signaling. We show that the extent of mitophagy is determined by levels and spatial localization of autophagy capacity, and subcellular mitochondrial protein heterogeneities. Our model identifies mechanisms and conditions that alter the mitophagy decision within mitochondrial subpopulations to an extent sufficient to shape cellular outcome to apoptotic stimuli.

Conclusion: Overall, our modeling approach provides means to suggest new experiments and implement findings at multiple scales in order to understand how network topologies and subcellular heterogeneities can influence signaling events at individual organelle level, and hence, determine the emergence of heterogeneity in cellular decisions due the actions of the collective intra-cellular population.

No MeSH data available.


Related in: MedlinePlus