Biology subjects

Derua, R.

Publications and source records attributed to Derua, R..

8 recordsLinked to original sources

bioRxiv2025

Loss of PREPL alters lipid homeostasis due to mitochondrial defects

Loss of the prolyl endopeptidase-like (PREPL) protein causes congenital myasthenic syndrome-22 (CMS22), a rare neuromuscular and metabolic disorder. PREPL belongs to the serine hydrolase superfamily, but its physiological substrates remain unknown. Based on the predicted lipid binding pocket in its crystal structure and its in vitro esterase activity, we hypothesized that PREPL might act as a lipase in vivo and directly regulate lipid metabolism. To test this, we performed unbiased lipidomics in Prepl knockout (KO) mouse brains and CRISPR-Cas9-generated KO cell lines. Across tissue and cell types, global phospholipid composition was largely unchanged, with only modest, non-significant increases in lysophospholipids, arguing against a direct role of PREPL in (lyso)phospholipid turnover. In contrast, PREPL KO HEK293T cells exhibited a significant accumulation of triacylglycerols (TAGs) and an increased number of lipid droplets, indicating a selective shift toward lipid storage. Given the central role of peroxisomes in lipid metabolism, we assessed PREPL localization and examined peroxisome number, morphology, and levels of key peroxisomal proteins. PREPL did not localize to peroxisomes, and peroxisome number and proteins levels were largely unchanged. However, KO cells displayed elongated peroxisomes, a phenotype possibly linked to mitochondrial dysfunction. Indeed, previous studies have shown that PREPL localizes to mitochondria and is required for respiratory chain activity and oxidative phosphorylation. These mitochondrial defects are predicted to impair fatty acid {beta}-oxidation and disrupt redox balance, thereby promoting TAG synthesis and lipid droplet biogenesis as adaptive responses. Overall, our findings indicate that PREPL does not act as a canonical lipase but indirectly alters lipid homeostasis through its critical role in mitochondrial function. Elevated TAG levels and altered peroxisome morphology likely represent secondary consequences of impaired mitochondrial fatty acid metabolism in PREPL-deficient cells. These results establish a mechanistic link between mitochondrial dysfunction and lipid remodeling in PREPL deficiency, providing novel insights into the metabolic pathology of CMS22.

biochemistry↗

bioRxiv2024

The role of liprin-α1 phosphorylation in its liquid-liquid phase separation: regulation by PPP2R5D/PP2A holoenzyme

Liprin-1 is a widely expressed scaffolding protein responsible for regulating cellular processes such as focal adhesion, cell motility, and synaptic transmission. Liprin-1 interacts with many proteins including ELKS, GIT1, liprin-{beta}, and LAR-family receptor tyrosine protein phosphatase. Through these protein-protein interactions, liprin-1 assembles large higher-order molecular complexes; however, the regulation of this complex assembly/disassembly is unknown. Liquid-liquid phase separation (LLPS) is a process that concentrates proteins within cellular nano-domains to facilitate efficient spatiotemporal signaling in response to signaling cascades. While there is no report that liprin-1 spontaneously undergoes LLPS, we found that GFP-liprin-1 expressed in HEK293 cells occasionally forms droplet-like condensates. MS-based interactomics identified Protein Phosphatase 2A (PP2A)/B56{delta} (PPP2R5D) trimers as specific interaction partners of liprin-1 through a canonical Short Linear Interaction Motif (SLiM) in its N-terminal dimerization domain. Mutation of this SLiM nearly abolished PP2A interaction, and resulted in significantly increased LLPS. GFP-liprin-1 showed significantly increased droplet formation in HEK293 cells devoid of B56{delta} (PPP2R5D knockout), suggesting that PPP2R5D/PP2A holoenzyme inhibits liprin-1 LLPS. Guided by reported liprin-1 Ser/Thr phosphorylation sites, we found liprin-1 phospho-mimetic mutant at serine 763 (S763E) is sufficient to drive its LLPS. Domain mapping studies of liprin-1 indicated that the intrinsically disordered region, the N-terminal dimerization domain, and the SAM domains are all necessary for liprin-1 LLPS. Finally, expression of p.E420K, a human PPP2R5D variant causing Houge-Janssens Syndrome type 1 (also known as Jordans Syndrome), significantly compromised suppression of liprin-1 LLPS. Our work identified B56{delta}-PP2A holoenzyme as an inhibitor of liprin-1 LLPS via regulation at multiple phosphorylation sites.

neuroscience↗

bioRxiv2024

ROSALIND protects the mitochondrial translational machinery from oxidative damage

Upregulation of mitochondrial respiration coupled with high ROS-scavenging capacity is a characteristic shared by drug-tolerant cells in several cancers. As translational fidelity is essential for cell fitness, protection of the mitochondrial and cytosolic ribosomes from oxidative damage is pivotal. While mechanisms for recognizing and repairing such damage exist in the cytoplasm, the corresponding process in the mitochondria remains unclear. By performing Ascorbate PEroXidase (APEX)-proximity ligation assay directed to the mitochondrial matrix followed by isolation and sequencing of RNA associated to mitochondrial proteins, we identified the nuclear-encoded lncRNA ROSALIND as an interacting partner of ribosomes. ROSALIND is upregulated in recurrent tumours and its expression can discriminate between responders and non-responders to immune checkpoint blockade in a melanoma cohort of patients. Featuring an unusually high G content, ROSALIND serves as a substrate for oxidation. Consequently, inhibiting ROSALIND leads to an increase in ROS and protein oxidation, resulting in severe mitochondrial respiration defects. This, in turn, impairs melanoma cell viability and increases immunogenicity both in vitro and ex vivo in preclinical humanized cancer models. These findings underscore the role of ROSALIND as a novel ROS buffering system, safeguarding mitochondrial translation from oxidative stress, and shed light on potential therapeutic strategies for overcoming cancer therapy resistance.

molecular biology↗

bioRxiv2023

TIPRL1 and its ATM-dependent phosphorylation promote radiotherapy resistance in head and neck cancer

TIPRL1 (target of rapamycin signaling pathway regulator-like 1) is a known interactor and inhibitor of protein phosphatases PP2A, PP4 and PP6 - all pleiotropic modulators of the DNA Damage Response (DDR). Here, we describe a new role for TIPRL1 in the radiotherapy (RT) response of Head and Neck Squamous Cell Carcinoma (HNSCC). TIPRL1 expression was found increased in tumor versus non- tumor tissue, with high tumoral TIPRL1 expression associating with lower locoregional control and decreased survival of RT-treated patients. TIPRL1 deletion in HNSCC cells resulted in increased RT sensitivity, a faster but prolonged cell cycle arrest, increased micronuclei formation and an altered proteome-wide DDR. Upon irradiation, ATM phosphorylates TIPRL1 at Ser265, contributing to TIPRL1-mediated RT resistance. Mass spectrometry analysis identified DNA-PKcs, RAD51 and nucleosomal histones as novel TIPRL1 interactors. Histone binding, although stimulated by RT, was adversely affected by TIPRL1 Ser265 phosphorylation. Our findings underscore a clinically relevant role for TIPRL1 and its ATM-dependent phosphorylation in RT resistance through modulation of DNA damage checkpoint activation and repair.

cancer biology↗

bioRxiv2021

Peroxisome-derived hydrogen peroxide can modulate the sulfenylation profiles of key redox signaling proteins

Ever since the first characterization of peroxisomes, a central theme has been their involvement in cellular hydrogen peroxide (H2O2) metabolism. While the reputation of H2O2 drastically changed from an exclusively toxic molecule to a signaling messenger, the regulatory role of peroxisomes in these signaling events is still largely underappreciated. This is mainly because the number of known protein targets of peroxisome-derived H2O2 is rather limited and testing of specific targets is predominantly based on knowledge previously gathered in related fields of research. To gain a broader and more systematic insight into the role of peroxisomes in redox signaling, an unbiased approach is urgently needed. To accomplish this goal, we have combined a previously developed cell system in which peroxisomal H2O2 production can be modulated with a yeast AP-1-like-based sulfenome mining strategy to inventory protein thiol targets of peroxisome-derived H2O2 in different subcellular compartments. Using this unbiased approach, we were able to identify specific and common targets of peroxisome-derived and exogenous H2O2 in peroxisomes, the cytosol, and mitochondria. We also observed that the sulfenylation kinetics profiles of key targets belonging to different protein families can vary considerably. In addition, we obtained compelling but indirect evidence that peroxisome-derived H2O2 may oxidize at least some of its targets through a redox relay mechanism. In conclusion, given that sulfenic acids function as key intermediates in H2O2 signaling, the findings presented in this study provide initial but critical insight into how peroxisomes may be integrated in the cellular H2O2 signaling network. HighlightsO_LIYAP1C-trapping is a robust tool to assess the peroxisomal H2O2-dependent sulfenome C_LIO_LIExogenous and peroxisome-derived H2O2 have both common and distinct targets C_LIO_LIANXA2, PRDX1, and SKP1 are major targets of peroxisome-derived H2O2 C_LIO_LIThe sulfenylation kinetics profiles of key redox-active proteins vary considerably C_LIO_LIProduction of H2O2 inside peroxisomes directly impacts the mitochondrial sulfenome C_LI

cell biology↗

bioRxiv2020

The IRE1 Inhibitor KIRA6 Curtails The Inflammatory Trait Of Immunogenic Anticancer Treatments By Targeting HSP60 Independent Of IRE1

Cellular stress evoked by immunogenic anticancer treatments engaging the unfolded protein response (UPR) can elicit inflammation with conflicting therapeutic outcomes. To define cell-autonomous mechanisms coupling the UPR to molecular mediators of inflammation, we profiled the transcriptome of cancer cells responding to immunogenic or weakly immunogenic-treatments. Bioinformatics-driven pathway analysis indicated that immunogenic treatments instigated NF-{kappa}B/AP-1-inflammatory pathways, which were abolished by the IRE1-kinase inhibitor KIRA6. Cell-free fractions of chemotherapy and KIRA6 co-treated cancer cells were deprived of pro-inflammatory/chemoattractant factors and failed to mobilize innate immune cells. Strikingly, these potent KIRA6 anti-inflammatory effects were found to be independent of IRE1. Generation of a KIRA6-clickable photoaffinity probe, mass spectrometry and co-immunoprecipitation analysis identified cytosolic HSP60 as a KIRA6 off-target in the NF-{kappa}B pathway. In sum, our study unravels that inflammation evoked by immunogenic treatments is curtailed by KIRA6 independently of IRE1 and further suggests great caution in interpreting the anti-inflammatory action of IRE1 chemical inhibitors.

cancer biology↗

bioRxiv2020

Lipidomic profiling of clinical prostate cancer reveals targetable alterations in lipid composition

Dysregulated lipid metabolism is a prominent feature of prostate cancer that is driven by androgen receptor (AR) signaling. Herein, we used quantitative mass spectrometry to define the "lipidome" in prostate tumors with matched benign tissues (n=21), independent tissues (n=47), and primary prostate explants cultured with a clinical AR antagonist, enzalutamide (n=43). Significant differences in lipid composition were detected and spatially visualized in tumors compared to matched benign samples. Notably, tumors featured higher proportions of monounsaturated lipids overall and elongated fatty acid chains in phosphatidylinositol and phosphatidylserine lipids. Significant associations between lipid profile and malignancy were validated in unmatched samples, and PL composition was characteristically altered in patient tissues that responded to AR inhibition. Importantly, targeting of altered tumor-related lipid features, via inhibition of acetyl CoA carboxylase 1, significantly reduced cellular proliferation in tissue explants (n=13). This first characterization of the prostate cancer lipidome in clinical tissues revealed enhanced fatty acid synthesis, elongation and desaturation as tumor-defining features, with potential for therapeutic targeting.

cancer biology↗

bioRxiv2018

Structures of the heart specific SERCA2a Ca2+-ATPase

The isoform 2a of sarco/endoplasmic reticulum Ca2+-ATPase (SERCA2a) performs active reuptake of cytoplasmic Ca2+ and is a major regulator of cardiac muscle contractility. Dysfunction or dysregulation of SERCA2a is associated with heart failure, while restoring its function is considered as a therapeutic strategy to restore cardiac performance, but its structure was not yet determined. Based on native, active protein purified from pig ventricular muscle, we present the first crystal structures of SERCA2a that were determined in the CPA-stabilized and H+-occluded [H2-3]E2-AlF4 - (3.3 [A]) form, arranged as parallel dimers, and the Ca2+-occluded [Ca2]E1-ATP (4.0 [A]) form. We compare these new structures to similar forms of the skeletal muscle SERCA1a and address structural, functional and regulatory differences. We show that the isoform specific motifs of SERCA2a allow a distinct regulation by post-translational modifications and affect the dynamic behavior, which may explain specific properties and regulation.

biochemistry↗