Biology subjects

Langer, T.

Publications and source records attributed to Langer, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Loss of CHCHD2 and CHCHD10 reveals differential vulnerability to bioenergetic failure in cardiac and skeletal muscle

Mutations in the mitochondrial proteins CHCHD2 and CHCHD10 cause severe neurodegenerative and neuromuscular disorders, yet their physiological functions remain poorly defined. CHCHD2 and CHCHD10 localize to the mitochondrial intermembrane space, where they assemble into a high-molecular-weight complex. Here, we generated Chchd2/Chchd10 double-knockout (DKO) mice to define the in vivo role of this complex. DKO mice developed reduced lean mass, progressive muscle weakness, and oxidative phosphorylation defects in both cardiac and skeletal muscle. Despite comparable bioenergetic impairment, CHCHD2-CHCHD10 deficiency elicited tissue-specific responses distinct from those induced by the disease-associated CHCHD10 S59L mutation. The heart accumulated enlarged mitochondria with disrupted ultrastructure and underwent adaptive proteomic remodeling that preserved myocardial contractility into adulthood. By contrast, skeletal muscle exhibited limited proteomic alterations, accompanied by profound changes in lipid composition, reduced expression of the myogenic regulators, and altered myofiber size. Mechanistically, depletion of CHCHD2 and CHCHD10 in primary satellite cells impaired proliferation and myogenic differentiation, suggesting that defective postnatal myogenesis contributes to the muscle growth defect in DKO mice. Together, these findings identify the CHCHD2-CHCHD10 complex as a critical regulator of mitochondrial integrity and demonstrate that its loss drives tissue-specific defects culminating in diverse pathological outcomes.

cell biology↗

bioRxiv2025

Mutant CHCHD10 disrupts cytochrome c oxidation and activates retrograde signaling in a model of cardiomyopathy.

Mutations in CHCHD10, a mitochondrial intermembrane space (IMS) protein implicated in proteostasis and cristae maintenance, cause multi-systemic mitochondrial disease. Heterozygous Chchd10 knock-in mice modeling the human CHCHD10S59L variant associated with Amyotrophic Lateral Sclerosis and Frontotemporal Dementia (ALS-FTD) develop a mitochondrial cardiomyopathy driven by CHCHD10 insolubility and aggregation, which is associated with chronic activation of the mitochondrial integrated stress response (mtISR). Here, we demonstrate that cardiac dysfunction in Chchd10S55L/+ mice carrying the orthologous pathogenic variant is associated with dual defects originating at the onset of disease: (1) early bioenergetic dysfunction linked to defects in the mitochondrial copper homeostasis and the oxidation of cytochrome c and (2) maladaptive mtISR signaling via the OMA1-DELE1-HRI axis. Using Oma1E324Q/E324Qknock-in mice, we show that the catalytic inactivation of the mitochondrial protease OMA1 in Chchd10S55L/+ mice delays cardiomyopathy onset without rescuing CHCHD10 insolubility, proteomic remodeling, cristae defects or OXPHOS impairment, demonstrating that mtISR can be uncoupled from the bioenergetic collapse triggered by mutant CHCHD10. Proteomic profiling of soluble and insoluble mitochondrial proteins in Chchd10S55L/+ mice reveals wide-spread disruptions of mitochondrial proteostasis, including IMS proteins involved in cytochrome c biogenesis. Defective respiration in mutant mitochondria could be rescued by the exogenous addition of cytochrome c, pinpointing IMS proteostasis disruption as a key pathogenic mechanism. Our work reveals that mutant CHCHD10 insolubility compromises metabolic resilience by impairing both mitochondrial bioenergetics and stress adaptation, offering new perspectives for the development of therapeutic targets.

cell biology↗

bioRxiv2025

OMA1-mediated cleavage of AIFM1 upon mitochondrial stress and suppression of cell growth through the control of OXPHOS activity

Mitochondrial proteases regulate the dynamic properties of organelle morphology and ensure functional plasticity at the cellular level. The metalloprotease OMA1 mediates constitutive and stress-inducible processing of its mitochondrial substrates, but the number of functionally characterized targets remains limited. Using multiproteomic and biochemical approaches, we demonstrated that the membrane-anchored inner membrane space (IMS) protein AIFM1 serves as a mitochondrial stress-responsive substrate of OMA1. OMA1 cleaves AIFM1 in the IMS under stress conditions with a kinetically slower reaction than that of its conventional substrate, dynamin-like GTPase OPA1. Membrane dislocation of cleaved AIFM1 in mitochondria reduces its binding to subunits of the oxidative phosphorylation machinery, leading to decreased respiratory activity and ultimately impaired cell growth. Mechanistically, we revealed that AIFM1 broadly safeguards the mitochondrial proteome under steady-state conditions by mediating the import of proteins, particularly respiratory complex I subunits, via the TIM23 complex. These findings reveal a previously unrecognized role for OMA1 in integrating mitochondrial stress sensing and cellular energetics by altering the AIFM1 topology.

cell biology↗

bioRxiv2025

Stress adaptation of mitochondrial protein import by OMA1-mediated degradation of DNAJC15

Mitochondria adapt to cellular stress to ensure cell survival. The stress-regulated mitochondrial peptidase OMA1 orchestrates these adaptive responses, which limit mitochondrial fusion and promote mitochondrial stress signaling and metabolic rewiring. Here, we show that cellular stress adaptation involves OMA1-mediated regulation of mitochondrial protein import and OXPHOS biogenesis. OMA1 cleaves the mitochondrial chaperone DNAJC15 and promotes its degradation by the m-AAA protease AFG3L2. Loss of DNAJC15 reduces the import of OXPHOS-related proteins via the TIMM23-TIMM17A protein translocase, limiting OXPHOS biogenesis under conditions of mitochondrial dysfunction. Non-imported mitochondrial preproteins accumulate at the endoplasmic reticulum and induce an ATF6-related unfolded protein response. Our results demonstrate stress-dependent changes in protein import specificity as part of the OMA1-mediated mitochondrial stress response and highlight the interdependence of proteostasis regulation between different organelles.

cell biology↗

bioRxiv2024

Prohibitin 2 is a Key Regulator of T Cell Proliferation, Differentiation, and Effector Functions in vivo

Prohibitin 2 (PHB2) is a highly conserved protein with essential roles in cell homeostasis and survival across different cell types. Previous studies have shown that the deletion of PHB2 results in an arrest in proliferation due to impaired mitochondrial function regulated by the dynamin-like GTPase OPA1. The function of PHB2 in immune cells remains unclear, however, some studies suggest that PHB2 plays a role in the cell membranes of B and T cells. In order to elucidate the role of PHB2 in immune cells, we generated PHB2-deficient T cells. Our findings reveal a pivotal role for PHB2 in the proliferation and differentiation of T cells. PHB2 deficiency inhibits T cell proliferation by inducing a cell cycle arrest at the G1 to S phase, thereby preventing the differentiation into effector T cells. Furthermore, in contrast to previous reports, T cells lacking PHB2 are more resistant to apoptosis. Metabolic analysis reveals that PHB2-deficient T cells fail to upregulate their glycolysis and oxidative phosphorylation upon activation, thus rendering them incapable to proliferate.

immunology↗

bioRxiv2024

AFG3L2-mediated proteolysis restricts mitochondrial biogenesis and gene expression in hypoxia

Mitochondria are metabolically rewired in hypoxia when cells switch to glycolytic growth. In addition to the well-established role of transcriptional and translational programs, there is increasing evidence that post-translational mechanisms contribute to the rapid adaptation of the mitochondrial proteome to hypoxia. Here, we have used a proteomic survey to define how the m-AAA protease AFG3L2, a proteolytic complex in the inner mitochondrial membrane, regulates mitochondrial proteostasis. Our experiments identify a broad spectrum of mitochondrial substrate proteins and show that AFG3L2 is activated in hypoxia along an HIF1-mTORC1 signaling axis. AFG3L2-mediated proteolysis restricts mitochondrial biogenesis and gene expression by degrading proteins, which are involved in mitochondrial protein import, mitochondrial transcription, mRNA processing, mRNA modification and stability, and RNA granule formation. Our experiments highlight the important contribution of proteolytic rewiring of the mitochondrial proteome for the adaptation to low oxygen tension and shed new light on the pathophysiology of several neurodegenerative disorders associated with mutations in AFG3L2.

cell biology↗

bioRxiv2024

The CHCHD2-CHCHD10 protein complex is modulated by mitochondrial dysfunction and alters lipid homeostasis in the mouse brain.

The highly conserved CHCHD2 and CHCHD10 are small mitochondrial proteins residing in the intermembrane space. Recently, mutations in the CHCHD2 and CHCHD10 genes have been linked to severe disorders, including Parkinsons disease and amyotrophic lateral sclerosis. In cultured cells, a small fraction of CHCHD2 and CHCHD10 oligomerize to form a high molecular weight complex of unknown function. Here, we generated a whole-body Chchd2 knockout mouse to investigate the in vivo role of CHCHD2 and its protein complex. We show that CHCHD2 is crucial for sustaining full motor capacity, normal striatal dopamine levels, and lipid homeostasis in the brain of adult male mice. We also demonstrate that in mouse tissues, CHCHD2 and CHCHD10 exist exclusively as a high molecular weight complex, whose levels are finely tuned under physiological conditions. In response to mitochondrial dysfunction, the abundance and size of the CHCHD2-CHCHD10 complex increases, a mechanism conserved across different tissues. Although the loss of CHCHD2 does not abolish CHCHD10 oligomerization, it enhances cell vulnerability to mitochondrial stress, suggesting that CHCHD2 is protective against mitochondrial damage. Our findings uncover the role of CHCHD2 in preserving tissue homeostasis and provide important insights into the involvement of the CHCHD2-CHCHD10 complex in human diseases.

neuroscience↗

bioRxiv2024

Systematic mapping of MCU-mediated mitochondrial calcium signaling networks

The Mitochondrial Ca2+ Uniporter Channel (MCUC) allows calcium entry into the mitochondrial matrix to regulate energy metabolism but also cell death. Although, several MCUC components have been identified, the molecular basis of mitochondrial Ca2+ signaling networks and their remodeling upon changes in uniporter activity have not been systematically assessed. Using an unbiased and quantitative proteomic approach, we map the MCUC interactome in HEK293 cells under physiological conditions and upon chronic loss or gain of mitochondrial Ca2+ uptake. Besides all previously known subunits of the uniporter, we identify 89 high-confidence interactors linking MCUC to several mitochondrial complexes and pathways, half of which are currently linked to metabolic, neurological, and immunological diseases. As a proof-of-concept, we validate EFHD1 as a binding partner of MCU, EMRE and MCUB with a MICU1-dependent inhibitory effect on Ca2+ uptake. To investigate compensatory mechanisms and functional consequences of mitochondrial Ca2+ dyshomeostasis, we systematically survey the MCU interactome upon silencing of EMRE, MCUB, MICU1 or MICU2. We observe profound changes in the MCU interconnectivity, whereby downregulation of EMRE reduces the number of MCU interactors of over 10-fold, while silencing of MCUB leads to a wider functional network linking MCU to mitochondrial stress response pathways and cell death. Altogether our study provides a comprehensive map of MCUC protein-protein interactions and a rich, high-confidence resource that can be explored to gain insights into the players and mechanisms involved in calcium signal transduction cascades and their relevance in human diseases.

cell biology↗

bioRxiv2023

CLUH maintains functional mitochondria and translation in motoneuronal axons and prevents peripheral neuropathy

Transport and local translation of mRNAs in distal axonal compartments are essential for neuronal viability. Local synthesis of nuclear-encoded mitochondrial proteins protects mitochondria from damage during their long journey along the axon, however the regulatory factors involved are largely unknown. Here, we show that CLUH, a cytosolic protein that binds mRNAs encoding mitochondrial proteins, is essential for preventing axonal degeneration of spinal motoneurons and maintaining motor behavior in the mouse. We demonstrate that CLUH is enriched in the growth cone of developing spinal motoneurons and is required for their growth. The absence of CLUH affects the abundance of target mRNAs and the corresponding mitochondrial proteins more prominently in axons, leading to ATP deficits specifically in the growth cone. CLUH binds ribosomal subunits, translation initiation and ribosome recycling components, and preserves axonal translation. Overexpression of the ribosome recycling factor ABCE1 rescues the growth cone and translation defects in CLUH-deficient motoneurons. In conclusion, we demonstrate a role for CLUH in mitochondrial quality control and translational regulation in axons, which are essential for their development and long-term integrity and function.

cell biology↗

bioRxiv2023

Feasibility of improving manufacturability based on protein engineering

While bioactivity and a favorable safety profile for biotherapeutics is of utmost importance, manufacturability is also worth of consideration to ease the manufacturing process. Many biotherapeutics are typically expressed in mammalian cells. Process-related impurities or biological impurities like viruses and host cell proteins (HCP) are present in the harvest which have mostly acid isoelectric points and need to be removed to ensure safety for the patients. Therefore, during molecule design, an isoelectric point of the target molecule should preferably differ sufficiently from the isoelectric points of the impurities to enable an efficient and straightforward purification strategy. In this feasibility study we have evaluated the possibility to improve manufacturability by increasing the isoelectric point of the target protein. We have generated several variants of a GLP1-receptor-agonist-Fc-domain -FGF21 fusion protein and demonstrate that the critical anion exchange chromatography step can be run at high pH values with maximal product recovery theoretically allowing removal of HCP and viruses. Addressing the isoelectric point can be useful for an efficient process for removing HCP and viruses and this topic should be considered early in the research phase to ensure that other important molecule properties, e.g. safety, efficacy and expression yield are not impacted.

bioengineering↗

bioRxiv2023

De novo serine biosynthesis is protective in mitochondrial disease

Importance of serine as a metabolic regulator is well known in tumors and raising attention also in degenerative diseases. Recent data indicate that de novo serine biosynthesis is an integral component of metabolic response to mitochondrial disease, but the roles of the response have remained unknown. Here, we report that glucose-driven de novo serine biosynthesis maintains metabolic homeostasis in energetic stress. Pharmacological inhibition of the rate-limiting enzyme, phosphoglycerate dehydrogenase (PHGDH), aggravated mitochondrial muscle disease, suppressed oxidative phosphorylation and mitochondrial translation, altered whole-cell lipid profiles and enhanced mitochondrial integrated stress response (ISRmt), in vivo, in skeletal muscle and in cultured cells. Our evidence indicates that de novo serine biosynthesis is essential to maintain mitochondrial respiration, redox balance, and cellular lipid homeostasis in skeletal muscle with mitochondrial dysfunction. Our evidence implies that interventions activating de novo serine synthesis may protect against mitochondrial failure in the skeletal muscle. Bullet pointsO_LISerine becomes an essential amino acid in mitochondrial translation defects C_LIO_LIBlocking de novo serine biosynthesis promotes progression of mitochondrial disease C_LIO_LIDe novo serine biosynthesis maintains phospholipid homeostasis upon mitochondrial insult C_LIO_LISerine biosynthesis sustains redox-balance and mitochondrial translation in disease C_LI

cell biology↗

bioRxiv2022

Ribonucleotide synthesis by NME6 fuels mitochondrial gene expression

Replication and expression of the mitochondrial genome depend on the sufficient supply of nucleotide building blocks to mitochondria. Dysregulated nucleotide metabolism is detrimental to mitochondrial genomes and can result in instability of mitochondrial DNA and inflammation. Here, we report that a mitochondrial nucleoside diphosphate kinase, NME6, supplies mitochondria with ribonucleotides to drive the transcription of mitochondrial genes. Moreover, NME6 supports the maintenance of mitochondrial DNA when the access to cytosolic deoxyribonucleotides is limited. Perturbation of NME6 leads to the depletion of mitochondrial transcripts, destabilisation of the electron transport chain and impaired oxidative phosphorylation; deficiencies which are suppressed upon supplementation with pyrimidine ribonucleotides. Our work proposes NME6 and mitochondrial nucleotide metabolism to be untapped therapeutic targets in diseases associated with aberrant mitochondrial gene expression including cancer and autoimmune disorders.

cell biology↗

bioRxiv2022

Metabolic rewiring of mitochondria in senescence revealed by time-resolved analysis of the mitochondrial proteome

Mitochondrial dysfunction and cellular senescence are hallmarks of aging. However, the relationship between these two phenomena remains incompletely understood. In this study, we investigated the rewiring of mitochondria upon development of the senescent state in human IMR90 fibroblasts. Determining the bioenergetic activities and abundance of mitochondria, we demonstrate that senescent cells accumulate mitochondria with reduced OXPHOS activity, resulting in an overall increase of mitochondrial activities in senescent cells. Time-resolved proteomic analyses revealed extensive reprogramming of the mitochondrial proteome upon senescence development and allowed the identification of metabolic pathways that are rewired with different kinetics upon establishment of the senescent state. Among the early-responding pathways, the degradation of branched-chain amino acid (BCAA) was increased, while the one carbon-folate metabolism was decreased. Late-responding pathways include lipid metabolism and mitochondrial translation. These signatures were confirmed by metabolic tracing experiments, highlighting metabolic rewiring as a central feature of mitochondria in cellular senescence. Together, our data provide an unprecedentedly comprehensive view on the metabolic status of mitochondria in senescent cells and reveal how the mitochondrial proteome adapts to the induction of senescence.

cell biology↗

bioRxiv2022

Improving Small Molecule pKa Prediction Using Transfer Learning with Graph Neural Networks

Enumerating protonation states and calculating micro-state pKa values of small molecules is an important yet challenging task for lead optimization and molecular modeling. Commercial and non-commercial solutions have notable limitations such as restrictive and expensive licenses, high CPU/GPU hour requirements, or the need for expert knowledge to set up and use. We present a graph neural network model that is trained on 714,906 calculated mico-state pKa predictions from molecules obtained from the ChEMBL database. The model is fine-tuned on a set of 5,994 experimental pKa values significantly improving its performance on two challenging test sets. Combining the graph neural network model with Dimorphite-DL, an open-source program for enumerating ionization states, we have developed the open-source Python package pkasolver, which is able to generate and enumerate protonation states and calculate micro-state pKa values with high accuracy.

biophysics↗

bioRxiv2021

Regulation of mitochondrial proteostasis by the proton gradient

Mitochondria adapt to different energetic demands reshaping their proteome. Mitochondrial proteases are emerging as key regulators of these adaptive processes. Here, we use a multi-proteomic approach to demonstrate regulation of the m-AAA protease AFG3L2 by the mitochondrial proton gradient, coupling mitochondrial protein turnover to the energetic status of mitochondria. We identify TMBIM5 (previously also known as GHITM or MICS1) as a Ca2+/H+ exchanger in the mitochondrial inner membrane, which binds to and inhibits the m-AAA protease. TMBIM5 ensures cell survival and respiration, allowing Ca2+ efflux from mitochondria and limiting mitochondrial hyperpolarization. Persistent hyperpolarization, however, triggers degradation of TMBIM5 and activation of the m-AAA protease. The m-AAA protease broadly remodels the mitochondrial proteome and mediates the proteolytic breakdown of respiratory complex I to confine ROS production and oxidative damage in hyperpolarized mitochondria. TMBIM5 thus integrates mitochondrial Ca2+ signaling and the energetic status of mitochondria with protein turnover rates to reshape the mitochondrial proteome and adjust the cellular metabolism.

molecular biology↗

bioRxiv2021

CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression

Proliferating cells undergo metabolic changes in synchrony with cell cycle progression and cell division. Mitochondria provide fuel, metabolites, and ATP during different phases of the cell cycle, however it is not completely understood how mitochondrial function and the cell cycle are coordinated. CLUH is a post-transcriptional regulator of mRNAs encoding mitochondrial proteins involved in oxidative phosphorylation and several metabolic pathways. Here, we show a role of CLUH in regulating the expression of astrin, which is involved in metaphase to anaphase progression, centrosome integrity, and mTORC1 inhibition. We find that CLUH binds both the SPAG5 mRNA and its product astrin, and controls the synthesis and the stability of the full-length astrin-1 isoform. We show that CLUH interacts with astrin-1 specifically during interphase. Astrin-depleted cells show mTORC1 hyperactivation and enhanced anabolism. On the other hand, cells lacking CLUH show decreased astrin levels and increased mTORC1 signaling, but cannot sustain anaplerotic and anabolic pathways. In absence of CLUH, cells fail to grow during G1, and progress faster through the cell cycle, indicating dysregulated matching of growth, metabolism and cell cycling. Our data reveal a role of CLUH in coupling growth signaling pathways and mitochondrial metabolism with cell cycle progression.

cell biology↗

bioRxiv2021

Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L

The transition between quiescence and activation in neural stem and progenitor cells (NSPCs) is coupled to reversible changes in energy metabolism with key implications for life-long NSPC self-renewal and neurogenesis. How this metabolic plasticity is ensured between NSPC activity states is unclear. We found that a state-dependent rewiring of the mitochondrial proteome by the peptidase YME1L is required to preserve NSPC self-renewal in the adult brain. YME1L-mediated proteome rewiring regulates the rate of fatty acid oxidation (FAO) for replenishing Krebs cycle intermediates and dNTP precursors, which are required to sustain NSPC amplification. Yme1l deletion irreversibly shifts the metabolic profile of NSPCs away from a FAO-dependent state resulting in defective self-renewal, premature differentiation and NSPC pool depletion. Our results disclose an important role for YME1L in coordinating the switch between metabolic states of NSPCs and suggest that NSPC fate is regulated by compartmentalized changes in protein network dynamics.

neuroscience↗

bioRxiv2021

High-throughput phenotypic screen for genetic modifiers in patient-derived OPA1 mutant fibroblasts identifies PGS1 as a functional suppressor of mitochondrial fragmentation

Mutations affecting the mitochondrial fusion protein Optic Atrophy 1 (OPA1) cause autosomal dominant optic atrophy (DOA) - one of the most common form of mitochondrial disease. The majority of patients develop isolated optic atrophy, but about 20% of OPA1 mutation carriers manifest more severe neurological deficits as part of a "DOA+" phenotype. OPA1 deficiency causes mitochondrial fragmentation and also disrupts cristae organization, oxidative phosphorylation, mitochondrial DNA (mtDNA) maintenance, and cell viability. It has not yet been established whether phenotypic severity can be modulated by genetic modifiers of OPA1. To better understand the genetic regulation of mitochondrial dynamics, we established a high-throughput imaging pipeline using supervised machine learning (ML) to perform unbiased, quantitative mitochondrial morphology analysis that was coupled with a bespoke siRNA library targeting the entire known mitochondrial proteome (1531 genes), providing a detailed phenotypic screening of human fibroblasts. In control fibroblasts, we identified known and novel genes whose depletion promoted elongation or fragmentation of the mitochondrial network. In DOA+ patient fibroblasts, we identified 91 candidate genes whose depletion prevents mitochondrial fragmentation, including the mitochondrial fission genes DNM1L, MIEF1, and SLC25A46, but also genes not previously linked to mitochondrial dynamics such as Phosphatidyl Glycerophosphate Synthase (PGS1), which belongs to the cardiolipin (CL) synthesis pathway. PGS1 depletion reduces CL content in mitochondria and rebalances mitochondrial dynamics in OPA1-deficient fibroblasts by inhibiting mitochondrial fission, which improves defective respiration, but does not rescue mtDNA depletion, cristae dysmorphology or apoptotic sensitivity. Our data reveal that the multifaceted roles of OPA1 in mitochondria can be functionally uncoupled by modulating mitochondrial lipid metabolism, providing novel insights into the cellular relevance of mitochondrial fragmentation. This study illustrates the power of a first-in-kind objective automated imaging approach to uncover genetic modifiers of mitochondrial disease through high-throughput phenotypic screening of patient fibroblasts.

cell biology↗