A Systems Biology Approach Towards a Comprehensive Understanding of Ferroptosis

Abstract

Ferroptosis is a regulated cell death process characterized by iron ion catalysis and reactive oxygen species, leading to lipid peroxidation. This mechanism plays a crucial role in age-related diseases, including cancer and cardiovascular and neurological disorders. To better mimic iron-induced cell death, predict the effects of various elements, and identify drugs capable of regulating ferroptosis, it is essential to develop precise models of this process. Such drugs can be tested on cellular models. Systems biology offers a powerful approach to studying biological processes through modeling, which involves accumulating and analyzing comprehensive research data. Once a model is created, it allows for examining the system's response to various stimuli. Our goal is to develop a modular framework for ferroptosis, enabling the prediction and screening of compounds with geroprotective and antiferroptotic effects. For modeling and analysis, we utilized BioUML (Biological Universal Modeling Language), which supports key standards in systems biology, modular and visual modeling, rapid simulation, parameter estimation, and a variety of numerical methods. This combination fulfills the requirements for modeling complex biological systems. The integrated modular model was validated on diverse datasets, including original experimental data. This framework encompasses essential molecular genetic processes such as the Fenton reaction, iron metabolism, lipid synthesis, and the antioxidant system. We identified structural relationships between molecular agents within each module and compared them to our proposed system for regulating the initiation and progression of ferroptosis. Our research highlights that no current models comprehensively cover all regulatory mechanisms of ferroptosis. By integrating data on ferroptosis modules into an integrated modular model, we can enhance our understanding of its mechanisms and assist in the discovery of new treatment targets for age-related diseases. A computational model of ferroptosis was developed based on a modular modeling approach and included 73 differential equations and 93 species.

Keywords: ferroptosis; mathematical modeling; neurodegenerative diseases; systems biology.

Figure 1

Modular diagram of the ferroptosis model.

Figure 2

Fenton’s reaction module. c-Fe²⁺—cytoplasmic labile Fe²⁺ stock; c-Fe³⁺—cytoplasmic labile Fe³⁺ stock; m-Fe²⁺—mitochondrial labile Fe²⁺ stock; O*⁻—oxygen radical anion; H₂O₂—water; OH*—hydroxide radical.

Figure 3

Iron metabolism module. c-Fe²⁺—cytoplasmic labile Fe²⁺; c-Fe³⁺—cytoplasmic labile Fe³⁺; m-Fe²⁺—mitochondrial labile Fe²⁺; TF—transferrin; TFR1—transferrin receptor; STEAP3/4—six-transmembrane prostate epithelial antigen 3 metalloreductase; CP—ceruloplasmin; DMT1—solute carrier family 11 member 2; ZIP8/14—solute transporter family 39 member 8/member 14; FtMt—mitochondrial ferritin; MCU—Mitochondrial calcium uniporter [23,24,25].

Figure 4

Lipid synthesis module. LPCAT3—lysophosphatidylcholine acyltransferase 3; PE–PUFAs—phosphatidylethanolamine–polyunsaturated fatty acids; CoA—coenzyme A; LysoPE—lysophosphatidylethanolamine; PUFAs—polyunsaturated fatty acids; ACSL4—acyl–CoA synthetase long-chain family member 4 [29].

Figure 5

Lipid peroxidation module. PE-PUFAs—phosphatidylethanolamine–polyunsaturated fatty acids; PE-PUFAs-O-OH—PE-PUFAs hydroperoxide; PE-PUFAs-OH—PE-PUFAs alcohol; PE-PUFAs-O*—PE-PUFAs alkoxyl radical; PE-PUFAs-OO*—PE-PUFAs peroxyl radical; PE-PUFAs*—PE-PUFAs radical; O-PE-PUFAs-OO*—epoxyallylic PE-PUFAs peroxyl radicals; O-E-PUFAs-OOH—epoxyallilic PE-PUFAs hydroperoxide; LOXs—Lipoxygenases (mainly arachidonate 15–lipoxygenase and arachidonate 5–lipoxygenase) [39,40,41].

Figure 6

Pentose phosphate pathway module. PGD—phosphogluconate dehydrogenase; G6PD—glucose–6–phosphate dehydrogenase; NADPH—reduced nicotinamide adenine dinucleotide phosphate; NADP+—oxidized form of nicotinamide adenine dinucleotide phosphate.

Figure 7

Antioxidant system module. GPX4—glutathione peroxidase 4; GR—glutathione reductase; PE-PUFAs-O-OH—PE-PUFAs hydroperoxide; PE-PUFAs-OH—PE-PUFAs alcohol; PE-PUFAs-O*—PE-PUFAs alkoxyl radical; PE-PUFAs-OO*—PE-PUFAs peroxyl radical; GSH—glutathione; GSSG—glutathione disulfide [56]; aT-OH—a-tocopherol; O-PE-PUFAs-OO*—epoxyallylic PE-PUFAs peroxyl radicals; O-PE-PUFAs-OOH—epoxyallylic PE-PUFAs hydroperoxide.

Figure 8

GSH synthesis module. GSH—glutathione; GGT—gamma–glutamyl transpeptidase; AA—amino acid; GGCT—γ-glutamylcyclotransferase; y-glu-AA—γ-glutamyl amino acid [55,57,62]; GCL—glutamate cysteine ligase (catalytic (GCLC) and modifier (GCLM) subunit); SLC3A2—solute carrier family 3 member 2; SLC7A11—solute carrier family 7 member 11; system_Xc⁻—cystine/glutamate exchange transporter; TXNRD1—thioredoxin reductase 1; GCL—Glutamate cysteine ligase (catalytic (GCLC) and modifier (GCLM) subunit) [63]; GGC—gamma–glutamylcysteine; GSS—glutathione synthetase [64]; GGT—gamma–glutamyl transpeptidase.

Figure 9

Modeling results under normal conditions and during ferroptosis. c-Fe²⁺: The level of ferrous iron (Fe²⁺) slightly increases during ferroptosis. This aligns with the understanding that ferroptosis is associated with iron accumulation, which facilitates lipid peroxidation and contributes to oxidative damage, leading to cell death [8,70]. GSH (glutathione): There is a decrease in glutathione levels during ferroptosis. Glutathione is crucial in defending cells against oxidative stress, and its depletion leaves cells more susceptible to damage, thereby promoting ferroptosis [71,72]. OH· (hydroxyl radical): There is a significant increase in hydroxyl radicals. These radicals indicate heightened oxidative processes, which play a key role in the damage to cellular components during ferroptosis [73,74]. O₂⁻—superoxide anion: The level of superoxide anion also rises, suggesting an increase in oxidative stress and reactive oxygen species (ROS) production, further driving the cell towards ferroptotic death [75,76]. PUFA-OO· and PUFA-OOH (peroxides of polyunsaturated fatty acids): An increase in these markers points to enhanced lipid peroxidation, which is a central mechanism in ferroptosis. Lipid peroxides accumulate and contribute to membrane damage and cell death [77].

Figure 10

General scheme of the ferroptosis model (adapted from [14]).

Figure 11

Structural model development process.