LONP1 and ClpP cooperatively regulate mitochondrial proteostasis for cancer cell survival

Abstract

Mitochondrial proteases are key components in mitochondrial stress responses that maintain proteostasis and mitochondrial integrity in harsh environmental conditions, which leads to the acquisition of aggressive phenotypes, including chemoresistance and metastasis. However, the molecular mechanisms and exact role of mitochondrial proteases in cancer remain largely unexplored. Here, we identified functional crosstalk between LONP1 and ClpP, which are two mitochondrial matrix proteases that cooperate to attenuate proteotoxic stress and protect mitochondrial functions for cancer cell survival. LONP1 and ClpP genes closely localized on chromosome 19 and were co-expressed at high levels in most human cancers. Depletion of both genes synergistically attenuated cancer cell growth and induced cell death due to impaired mitochondrial functions and increased oxidative stress. Using mitochondrial matrix proteomic analysis with an engineered peroxidase (APEX)-mediated proximity biotinylation method, we identified the specific target substrates of these proteases, which were crucial components of mitochondrial functions, including oxidative phosphorylation, the TCA cycle, and amino acid and lipid metabolism. Furthermore, we found that LONP1 and ClpP shared many substrates, including serine hydroxymethyltransferase 2 (SHMT2). Inhibition of both LONP1 and ClpP additively increased the amount of unfolded SHMT2 protein and enhanced sensitivity to SHMT2 inhibitor, resulting in significantly reduced cell growth and increased cell death under metabolic stress. Additionally, prostate cancer patients with higher LONP1 and ClpP expression exhibited poorer survival. These results suggest that interventions targeting the mitochondrial proteostasis network via LONP1 and ClpP could be potential therapeutic strategies for cancer.

DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion

“…In contrast, depletion of POLγB leads to lower levels of POLγA, whereas depletion of POLγA has no discernible effect on POLγB. In this context, it should be noted that we cannot rule out that other proteases can contribute to POLγA degradation in vivo ( 49 ).…”

Mitochondrial ATP-Dependent Proteases—Biological Function and Potential Anti-Cancer Targets

“…Moreover, considering the overlapping function of ATP-dependent proteases, it is important to understand mechanisms of resistance to ClpXP inhibition and hyperactivation. Moreover, since recent studies suggest ClpXP and LonP1 synergistically regulate cancer cell survival [ 189 ], preclinical and clinical studies on combination therapy of ClpXP regulators and other mitoproteases regulators may provide even broader applications of ClpXP regulators in newly-diagnosed and relapsed cancers. Finally, more biological studies are needed to determine the mechanism of action of this protease.…”

Mitofusin-2 Down-Regulation Predicts Progression of Non-Muscle Invasive Bladder Cancer

“…ClpP has been found to be increased in several cancers including BC [19,[26][27][28][29] and its expression has been found to be associated with poor prognosis [26,27]. Moreover, ClpP silencing has been shown to inhibit proliferation, migration, invasion, as well as to promote cell apoptosis [26][27][28][29]. Nevertheless, to the best of our knowledge, the correlation between ClpP expression and clinical outcome has never been studied in BC.…”

“…ClpP is a mitochondrial serine protease that plays an important role in maintaining the integrity of the mitochondrial respiratory chain and optimizing mitochondrial function by removing damaged mitochondrial proteins [25]. ClpP is upregulated in many primary and metastatic human tumors [19,[26][27][28][29] and in some tumors is correlated with shortened survival [26]. Its overexpression is also associated with mitochondrial stress [28].…”

“…Its overexpression is also associated with mitochondrial stress [28]. Chemical or genetic inhibition of ClpP impairs oxidative phosphorylation (OXPHOS) and mitochondrial functionality leading to an anti-proliferative effect in different cell types relying on OXPHOS [26][27][28][29][30]. To date, overexpression of ClpP has been reported in BC tissue [26,29] but its potential prognostic and predictive role in BC is still to be determined.…”