Systematic and Quantitative Investigation of Newly Synthesized Proteins Reveals Distinct Ion Homeostasis and Mitochondrial Changes between Cuproptosis and Ferroptosis in Human Cells

TL;DR

This study compares two types of metal-dependent cell death, cuproptosis and ferroptosis, by analyzing newly synthesized proteins to reveal differences in ion balance and mitochondrial changes.

Contribution

The study provides a systematic and quantitative comparison of newly synthesized proteins in cuproptosis and ferroptosis, uncovering distinct ion homeostasis and mitochondrial responses.

Findings

Cuproptosis involves elevated zinc ion homeostasis and ubiquitin-mediated mitophagy for damaged mitochondria.

Ferroptosis is linked to increased calcium-binding proteins and reduced RNA splicing-related proteins.

Both cell death types share mitochondrial dysfunction and suppressed gene expression.

Abstract

Dysregulated metal
ion metabolism and its connection to cell death
attract great attention in cell biology and biomedicine. There are
two major types of known metal ion-induced cell death so far. Well-documented
ferroptosis is an iron-dependent form of cell death driven by lipid
peroxidation, and the recently discovered cuproptosis is copper-dependent
cell death, possibly related to mitochondrial damage and cell stress.
Although some studies have suggested a possible link between cuproptosis
and ferroptosis, the cellular responses and mechanistic differences
between these two forms of metal ion-dependent cell death remain to
be explored. Here, we systematically and quantitatively analyzed newly
synthesized proteins (NSPs), which reflect rapid changes in gene expression,
in cells undergoing ferroptosis and cuproptosis through integrating
metabolic labeling, bioorthogonal chemistry, and multiplexed proteomics.
The results revealed that both types of cell death shared some common
features, such as mitochondrial disorder and gene expression suppression.
Furthermore, different changes between them were also uncovered. In
cuproptosis, proteins related to zinc ion homeostasis were elevated
because intracellular copper and zinc ions are cooperatively and competitively
involved in multiple biological processes, and excess copper ions
impact zinc ion homeostasis in cells. Moreover, damaged mitochondria
were found to be cleared mainly through ubiquitin-mediated mitophagy.
In contrast, ferroptosis is associated with an increased level of
calcium-binding proteins and a compensatory upregulation of key antioxidant
defense systems while concurrently showing a notable decrease in RNA
alternative splicing-related proteins. Taken together, a comprehensive
and comparative analysis of NSPs in cuproptosis and ferroptosis provides
us with a unique opportunity to understand the molecular mechanisms
of these two important forms of metal ion-dependent cell death.

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