Biology subjects

Suomalainen, A.

Publications and source records attributed to Suomalainen, A..

11 recordsLinked to original sources

bioRxiv2026

GDF15 modifies NAD+ salvage pathway and dampens immune response in mitochondrial disease

Mitochondrial integrated stress response (ISRmt) is a main mammalian metabolic stress pathway, with local ISRmt and a systemic response via circulating metabokines GDF15 and FGF21 as early signs of the response in mitochondrial diseases. FGF21 has been reported to regulate ISRmt progression and nutrient homeostasis, but the roles of GDF15 have remained unclear. Here, we explored the effects of inactivation of FGF21 or GDF15 or them together in Deletor mice. These mice endogenously activate the full ISRmt and metabokines as part of their mitochondrial muscle disease. GDF15 inactivity upregulated the skeletal muscle enzyme NMRK2, which converts nicotinamide riboside (NR) to nicotinamide mononucleotide (NMN) and NAD+. FGF21 was required for glutathione homeostasis. GDF15 inactivation also induced immune cell invasion in the muscle, aggravated by FGF21 loss, suggesting synergistic anti-inflammatory effects. Our findings indicate that in addition to their systemic effects, FGF21 and GDF15 are autocrine controllers of redox homeostasis in mitochondrial disease muscle.

cell biology↗

bioRxiv2026

Mitochondrial dysfunction reshapes methyl-group allocation inskeletal muscle

Mitochondria are central metabolic organelles with functions extending beyond energy production to anabolic and folate-mediated one-carbon (1C) metabolism. One-carbon metabolism supports methylation reactions that modify diverse targets including metabolites, nucleic acids, and chromatin, and has emerged as a contributor to mitochondrial disease-related stress responses. Here, we report tissue-specific remodeling of methylation events in response to mtDNA replication defect, using the deletor mice carrying a dominant mutation in Twinkle, the replicative helicase of mtDNA, causing adult-onset mitochondrial myopathy (MM) in humans and mice. In affected skeletal muscle, deletors show a distinct methylation signature, with increased creatine synthesis and reduced phosphatidylcholine production, two major consumers of S-adenosylmethionine-derived methyl groups. We further observed tissue-specific upregulation of selected RNA methylation marks and redistribution of the repressive histone mark H3K9me3, indicating coordinated remodeling of metabolic and epigenetic methylation pathways. Our evidence shows that a mtDNA replication defect remodels muscle-specific methylation signature of phospholipids, histones and RNA, identifying methylation remodeling as a key component of MM pathogenesis.

molecular biology↗

bioRxiv2026

Cell free-mtDNA release drives pyroptosis and inflammation in cell models carrying the mitochondrial m.3243A>G pathogenic variant

Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) syndrome is primarily caused by the heteroplasmic m.3243A>G/MT-TL1 pathogenic variant. Patients exhibit elevated circulating cell-free mtDNA (cf-mtDNA) in plasma, which acts as a damage-associated molecular pattern. Using patient-derived fibroblasts and neuronal progenitors, as well as transmitochondrial cytoplasmic hybrids (cybrids), we show that mutant cells release higher levels of cf-mtDNA than wild-type controls, demonstrating that the m.3243A>G pathogenic variant drives mtDNA release. Mechanistically, increased mitochondrial oxidative stress promotes mtDNA oxidation and fragmentation, leading to Ca2+ overload and subsequent mtDNA extrusion. This, in turn, triggers inflammasome activation and pyroptosis, resulting in the secretion of pro-inflammatory cytokines and the activation of innate immune pathways. Pharmacological inhibition of the Mitochondrial Calcium Uniporter (MCU) or Voltage-Dependent Anion Channel (VDAC) reduced mtDNA release, confirming their involvement. Overall, our findings reveal a previously unrecognized mechanism in MELAS linking mitochondrial dysfunction to innate immune activation, with potential implications for therapeutic intervention.

cell biology↗

bioRxiv2025

NAD+ precursor treatment prevents cardiomyopathybut disrupts erythroid maturation in mitochondrial progeria

Nicotinamide adenine dinucleotide (NAD+) plays a central role in energy metabolism, and its decline is linked to various degenerative diseases. While NAD+ restoration holds therapeutic promise, its long term, tissue-specific consequences remain poorly understood. We investigated effects of nicotinamide riboside (NR) supplementation for "mutator" mice manifesting mitochondrial progeria. Our results reveal strikingly divergent outcomes: in proliferative bone marrow, NR-treated mutators show reductive stress with accumulation of NADH/NADPH, altered amino acid, nucleotide, folate levels and impaired heme biosynthesis. In blood, erythrocyte maturation defects are aggravated, exacerbating anemia. Conversely, in postmitotic cardiac tissue, NR enhanced contractility, reduces stress response markers and normalized metabolic profile. These findings indicate that while being beneficial for heart, chronic NAD+ boosting can compromise erythrocyte maturation in the context of mitochondrial disease. The data emphasize importance of evaluating systemic effects of NAD+ boosting therapies beyond the primary affected tissues and development of tissue-specific metabolic interventions for degenerative diseases. HighlightsO_LIChronic nicotinamide riboside supplementation exacerbates anemia and disrupts erythroid maturation in progeric mice. C_LIO_LIIn proliferative bone marrow cells, NR induces redox imbalance and drives profound metabolic dysregulation. C_LIO_LINR suppresses heme biosynthesis and iron transport pathways in the bone marrow. C_LIO_LIIn the heart, NR restores NAD+ levels, enhances cardiac function, and reduces metabolic stress. C_LI

physiology↗

bioRxiv2025

Nutrient-dependent pathology in mitochondrial hypertrophic cardiomyopathy model

ObjectiveMitochondrial translation defects are a major cause of early childhood hypertrophic cardiomyopathy (CMP). While the genetic basis of these disorders is being increasingly uncovered, the downstream molecular mechanisms driving disease pathogenesis remain poorly understood. In this study, we investigated the consequences of defects in mitochondrial ribosomal large subunit protein 44 (MRPL44), associated with infantile-onset CMP in human cardiomyocytes, in nutrient environments relevant to cardiac development. MethodsInduced pluripotent stem cell line with MRPL44 patient mutation and controls were differentiated to cardiomyocytes and grown in glucose or lipid-enriched medium reflecting prenatal or postnatal fuel preferences, respectively. Mitochondrial, lipid metabolic and cellular characteristics were studied by immunofluorescence and cellular transcriptome by RNA-sequencing. ResultsIn glucose-rich medium, patient-derived cardiomyocytes exhibit increased mitochondrial DNA (mtDNA) content and elevated mitochondrial transcripts. In contrast the lipid-enriched medium triggered both mitochondrial and endoplasmic reticulum -related stress responses, disrupted lipid and cholesterol homeostasis, accompanied by remodeling of the central biosynthetic pathway of one carbon metabolism. The cells accumulated lipids while also inducing lipid uptake and synthesis genes, suggesting maladaptive metabolic rewiring. ConclusionOur findings indicate that glucose and lipids, the latter being the postnatally favored cardiac fuel, exert remarkably different consequences in MRPL44 deficient cardiomyocytes. The lipid enriched medium elicited robust activation of metabolic stress responses, with chronic upregulation of anabolic biosynthesis pathways and lipid accumulation indicative of conflicting metabolic homeostasis. These observations provide a mechanistic basis for postnatal disease manifestation and highlight nutrient metabolism as a key driver in development of infantile-onset mitochondrial hypertrophic cardiomyopathy. HighlightsO_LIMRPL44 deficiency impairs mitochondrial translation but induces mtDNA replication and transcription in iPSC-derived cardiomyocytes. C_LIO_LIIn glucose conditions, MRPL44 mutant cardiomyocytes upregulate mitochondrial replication and transcription program, but not translation. C_LIO_LILipid-enriched nutrient conditions exacerbate disease phenotype, inducing mitochondrial and ER stress responses in MRPL44 deficiency. C_LIO_LIMitochondrial ribosome defect disrupts lipid homeostasis in cardiomyocytes causing impaired fatty acid oxidation, lipid accumulation and altered cholesterol metabolism. C_LI

molecular biology↗

bioRxiv2025

Dynamics of blood NAD and glutathione in health, disease, aging and under NAD-booster treatment

Nicotinamide adenine dinucleotide (NAD) and glutathione are vital molecules that control redox-state, enzyme functions and metabolic flux in hundreds of cellular metabolic reactions. High NAD+ level occurs in fasting and has been associated with health outcomes in model systems, while low NAD+/NADH ratio occurs in specific diseases. Still, the normal, booster-treated or disease-related levels of NADs or glutathiones are not well known in humans. Here, we present a standardized technology for high-throughput quantitative measurement of NAD+, NADH, NADP+, NADPH, GSH and GSSG from a single whole-blood sample. In healthy population (n=299;18-70 year-olds) redox metabolites follow normal distribution in blood and remain unchanged during aging. NAD-boosting increased 4-6 fold the blood NAD+ depending on individual, pointing to need of personalized dose adjustment in treatment trials. In patients with cancer, diabetes or neurodegeneration, NADs and glutathiones showed disease-dependent "redox fingerprints". The evidence highlights the potential of redox profiling as an indicator of metabolic pathology and as a measure of treatment response.

pharmacology and toxicology↗

bioRxiv2022

Mitochondrial dysfunction triggers actin polymerization necessary for rapid glycolytic activation

Mitochondrial damage represents a dramatic change in cellular homeostasis, necessitating rapid responses. One rapid response is peri-mitochondrial actin polymerization, termed ADA (acute damage-induced actin). The consequences of ADA are not fully understood. Here we show that ADA is necessary for rapid glycolytic activation upon inhibition of mitochondrial ATP production in multiple cells, including mouse embryonic fibroblasts and effector CD8+ T lymphocytes, for which glycolysis is an important source of ATP and biosynthetic molecules. Treatments that induce ADA include CCCP, antimycin A, rotenone, oligomycin, and hypoxia. The Arp2/3 complex inhibitor CK666 or the mitochondrial sodium-calcium exchanger (NCLX) inhibitor CGP37157, applied simultaneously with the ADA stimulus, inhibit both ADA and the glycolytic increase within 5-min, suggesting that ADA is necessary for glycolytic stimulation. Two situations causing chronic reductions in mitochondrial ATP production, ethidium bromide treatment (to deplete mitochondrial DNA) and mutation to the NDUFS4 subunit of complex 1 of the electron transport chain, cause persistent peri-mitochondrial actin filaments of similar morphology to ADA. Both peri-mitochondrial actin loss and a 20% ATP decrease occur within 10 min of CK666 treatment in NDUFS4 knock-out cells. We propose that ADA is necessary for rapid glycolytic activation upon mitochondrial impairment, to re-establish ATP production.

cell biology↗

bioRxiv2022

Overactive mitochondrial DNA replisome causes neonatal heart failure via ferroptosis

Increasing mitochondrial DNA (mtDNA) replication and amount have been proposed as therapeutic approaches for mitochondrial dysfunction, but also as a mechanism of premature aging. We addressed this fascinating paradox by enhancing mtDNA replication via two mechanisms: increasing both mtDNA replication licensing and processivity. We crossed mice overexpressing Twinkle helicase (boosting mtDNA replication initiation) with mtDNA mutator mice (exonuclease-deficient mtDNA replicase, increasing mtDNA mutagenesis and replication processivity). The former model is asymptomatic by two years of age, whereas the latter manifests with progeroid symptoms at six months. Surprisingly, the double transgenics demonstrate postnatally halted growth and devastating cardiomyopathy, fatal within weeks. The mice show high mtDNA replication preventing cardiac maturation and the postnatal shift to oxidative metabolism, causing ferroptotic cardiomyocyte death. Our findings emphasize the critical importance of mtDNA replisome regulation for perinatal cardiac maturation. Furthermore, the data implicate ferroptosis as a cell death mechanism for neonatal mitochondrial cardiomyopathies.

molecular biology↗

bioRxiv2021

Mitochondrial dysfunction compromises ciliary homeostasis in astrocytes

Astrocytes, often considered as secondary responders to neurodegenerative processes, are emerging as primary drivers of brain disease. The underlying pathogenic mechanisms are, however, insufficiently understood. Here we show that pathogenesis of mitochondrial spongiotic encephalopathy, a severe manifestation of mitochondrial brain diseases, involves abnormal maintenance of the astrocytic primary cilium, a major signaling organelle of a cell. We show that progressive respiratory chain deficiency in astrocytes activates FOXJ1 and RFX transcription factors and master regulators of motile ciliogenesis. Consequently, a wide aberrant nuclear expression program with FOXJ1 and RFX target genes, encoding motile cilia components, is induced in astrocytes. While the affected astrocytes still retain a single cilium, these organelles elongate and become remarkably distorted. Multiciliated ventricle-lining ependymal cells show no overt cilia morphology defects despite similar mitochondrial dysfunction. We propose that the chronic activation of the integrated mitochondrial stress response (ISRmt), specifically induced in astrocytes, drives anabolic metabolism and promotes ciliary growth. Collectively, our evidence indicate that 1) an active signaling axis exists between astrocyte mitochondria and primary cilia; 2) ciliary signaling is part of ISRmt in astrocytes; 3) metabolic ciliopathy is a novel pathomechanism for mitochondria-related neurodegenerative diseases.

neuroscience↗

bioRxiv2019

Twinkle is not the mitochondrial DNA replicative helicase in C. elegans, but may have alternate mitochondrial functions

Dysfunction of mitochondrial DNA replication machinery is a common cause of mitochondrial diseases. The minimal mammalian replisome is made up of DNA polymerase gamma, replicative helicase Twinkle, and single-stranded DNA binding protein. The replisome is localized to the inner mitochondrial membrane and serves as the site of mitochondrial DNA replication and mitochondrial fission. Recently, a sequence homolog of Twinkle was uncovered in the nematode Caenorhabditis elegans. Here, we characterized this homolog, twnk-1, and report that twnk-1 does not function as the primary mitochondrial DNA replicative helicase in this species, as loss of twnk-1 does not result in reduce mitochondrial DNA levels, or result in other expected mitochondrial dysfunctions such as reduced oxygen consumption rates, increased sensitivity to metabolic perturbations, or reduced muscle function. Instead, twnk-1 mutants have increased mitochondrial DNA as they age, and exhibit phenotypes associated with mitochondrial stress, including reduced fecundity, an activation of the mitochondrial unfolded protein response, and mitochondrial fragmentation. Our results suggest in Caenorhabditis elegans, twnk-1 does not function as the mitochondrial DNA replicative helicase, but has an alternative function in regulating mitochondrial function.

molecular biology↗

bioRxiv2018

Quantitative solid-phase assay to measure deoxynucleoside triphosphate pools

Deoxyribonucleoside triphosphates (dNTPs) are the reduced nucleotides used as the building blocks and energy source for DNA replication and maintenance in all living systems. They are present in highly regulated amounts and ratios in the cell, and their balance has been implicated in the most important cell processes, from determining the fidelity of DNA replication to affecting cell fate. Furthermore, many cancer drugs target biosynthetic enzymes in dNTP metabolism, and mutations in genes directly or indirectly affecting these pathways are the cause of devastating diseases. The accurate and systematic measurement of these pools is key to understand the mechanisms behind these diseases and their treatment. We present a new method for measuring dNTP pools from biological samples, utilising the current state-of-the-art polymerase method, modified to a solid-phase setting and optimised for larger scale measurements.

biochemistry↗