Biology subjects

Kallijarvi, J.

Publications and source records attributed to Kallijarvi, J..

6 recordsLinked to original sources

bioRxiv2025

Hepatic gene replacement restores energy metabolism and doubles the survival in mouse model of GRACILE syndrome, a neonatal mitochondrial disease

Preclinical gene therapy studies of mitochondrial diseases remain limited due to their multisystemic manifestations and the scarcity of physiologically relevant animal models. Mutations in BCS1L, a nuclear gene encoding an assembly factor for mitochondrial complex III (CIII), are the most common cause of pediatric CIII deficiency. The most severe phenotype, GRACILE syndrome, is caused by a homozygous Finnish founder mutation (c.A232G, p.S78G). The corresponding Bcs1lp.S78G knock-in mouse model effectively recapitulates the human disease, with juvenile-onset hepatopathy, tubulopathy, growth restriction, segmental progeria, and short survival. Here, we performed recombinant adeno-associated virus (rAAV)-mediated gene replacement in this model, which features a postnatal presymptomatic window until weaning. A single intraperitoneal injection of rAAV encoding wild-type Bcs1l restored CIII assembly and activity in the liver, preventing hepatopathy. Hepatocyte-specific correction was sufficient to ameliorate hypoglycemia, improve growth, normalize systemic metabolism, and extend survival by nearly two-fold, despite persistent CIII deficiency in other tissues. Remarkably, liver-directed rescue also prevented skeletal muscle transcriptomic changes, particularly those linked to altered energy substrate utilization. These results underscore the central role of the liver in systemic energy homeostasis and growth regulation in multiorgan mitochondrial diseases and demonstrate the therapeutic potential of hepatocyte-directed gene replacement in phenotypes with prominent hepatopathy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/677965v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@b1cf50org.highwire.dtl.DTLVardef@1a1c2e2org.highwire.dtl.DTLVardef@101bdb6org.highwire.dtl.DTLVardef@14e11e3_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

physiology↗

bioRxiv2025

Evolutionarily conserved temperature dependency leads to loss of protein O-GlcNAc in mammalian hypothermia

O-N-acetylglucosaminylation (O-GlcNAcylation) is a conserved, non-canonical glycosylation of intracellular proteins suggested to regulate a wide spectrum of fundamental cell processes and stress responses. O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) add and remove, respectively, O-GlcNAc on protein serines and threonines. O-GlcNAcylation is thought to be primarily regulated by the availability of its substrate, UDP-GlcNAc, produced by the hexosamine biosynthetic pathway (HBP). We observed a body-wide loss of O-GlcNAcylated proteins in Bcs1l mutant mice, a model of mitochondrial complex III deficiency. UDP-GlcNAc precursors glutamine, UTP and acetyl-CoA were decreased in the mutant liver but, surprisingly, UDP-GlcNAc was not consistently decreased in the organs that showed low O-GlcNAc. Neither N-acetylglucosamine supplementation nor overexpression of the HBP rate-limiting enzyme GFPT1 restored the protein O-GlcNAc levels. The Bcs1l mutant mice become hypothermic and, interestingly, earlier evidence suggest that O-GlcNAcylation depends on ambient temperature in Drosophila embryos. We found that temperature determined O-GlcNAc abundance also in adult flies of tropical and boreal Drosophila species, in the poikilothermic vertebrate zebrafish, and in cultured mammalian cells. In cultured cells, the OGT-OGA protein ratio coincided with temperature and O-GlcNAc level, providing a regulatory mechanism. Pharmacological OGA inhibition decoupled the O-GlcNAc temperature dependency in cultured cells, as did an OGA null allele in Drosophila. In Bcs1l mutant mice, O-GlcNAc levels strongly correlated with body temperature. Increasing the mouse body temperature through transgenic expression of the heat-generating mitochondrial alternative oxidase (AOX) or housing at 35{degrees}C prevented the loss of O-GlcNAc. Pharmacological restoration of O-GlcNAc in the Bcs1l mutant mice produced minimal effects, suggesting that the bulk of O-GlcNAc is dispensable in mild hypothermia. Our findings imply an evolutionarily ancient role of protein O-GlcNAcylation in temperature adaptation and, instead of protein function-specific roles, argue for a global role of O-GlcNAc in temperature control of proteostasis.

physiology↗

bioRxiv2025

Parsing glomerular and tubular structure variability in high-throughput kidney organoid culture

High variability in stem cell research is a well-known limiting phenomenon, with technical variation across experiments and laboratories often surpassing variation caused by genotypic effects of induced pluripotent stem cell (iPSC) lines. Evaluation of kidney organoid protocols and culture conditions across laboratories remains scarce in the literature. We used the original air-medium interface protocol to evaluate kidney organoid success rate and reproducibility with several human iPSC lines, including a novel patient-derived GRACILE syndrome iPSC line. Organoid morphology was assessed with light microscopy and immunofluorescence-stained maturing glomerular and tubular structures. The protocol was further adapted to four microplate-based high-throughput approaches utilizing spheroid culture steps. Quantitative high-content screening analysis of the nephrin-positive podocytes and ECAD-positive tubular cells revealed that the choice of approach and culture conditions were significantly associated with structure development. The culture approach, iPSC line, experimental replication, and initial cell number explained 35-77% of the variability in the logit-transformed proportion of nephrin and ECAD-positive area, when fitted into multiple linear models. Our study highlights the benefits of high-throughput culture and multivariate techniques to better distinguishing sources of technical and biological variation in morphological analysis of organoids. Our microplate-based high-throughput approach is easily adaptable for other laboratories to combat organoid size variability.

developmental biology↗

bioRxiv2023

Quantification of all 12 canonical ribonucleotides by real-time fluorogenic in vitro transcription

Enzymatic methods to quantify deoxyribonucleoside triphosphates have existed for decades. In contrast, no general enzymatic method to quantify ribonucleoside triphosphates (rNTPs), which drive almost all cellular processes and serve as precursors of RNA, exists to date. ATP can be measured with an enzymatic luminometric method employing the firefly luciferase, but the quantification of the other ribonucleoside mono-, di-, and triphosphates is still a challenge for a non-specialized laboratory and practically impossible without chromatography equipment. To allow feasible quantification of ribonucleoside phosphates in any laboratory with typical molecular biology and biochemistry tools, we developed a robust microplate assay based on real-time detection of the Broccoli aptamer during in vitro transcription. The assay employs the bacteriophage T7 and SP6 RNA polymerases, two oligonucleotide templates encoding the 49-nucleotide Broccoli aptamer, and a high-affinity fluorogenic aptamer-binding dye to quantify each of the four canonical rNTPs. The inclusion of nucleoside mono- and diphosphate kinases in the assay reactions enabled the quantification of the mono- and diphosphate counterparts. The assay is inherently specific and tolerates concentrated tissue and cell extracts. In summary, we describe the first chromatography-free method to quantify ATP, ADP, AMP, GTP, GDP, GMP, UTP, UDP, UMP, CTP, CDP, and CMP in biological samples.

molecular biology↗

bioRxiv2023

Mitochondrial complex III deficiency drives c-MYC overexpression and illicit cell cycle entry leading to senescence and segmental progeria

Accumulating evidence suggests mitochondria as key modulators of normal and premature aging, yet whether primary deficiency of oxidative phosphorylation (OXPHOS) can cause progeroid disease remains unclear. Here, we show that mice with severe isolated respiratory complex III (CIII) deficiency display nuclear DNA damage, cell cycle arrest, aberrant mitoses, cellular senescence, and laminopathy-like nuclei in the affected organs such as liver and kidney, and a systemic phenotype strikingly resembling juvenile-onset laminopathic and DNA repair-deficient progeroid syndromes. Mechanistically, CIII deficiency triggered presymptomatic cancer-like c-MYC upregulation followed by excessive anabolic metabolism and illicit cell proliferation against lack of energy and biosynthetic precursors. CIII-independent coenzyme Q oxidation dampened mitochondrial integrated stress response and the c-MYC induction, suppressed the illicit proliferation, and prevented juvenile lethality despite that canonical OXPHOS-linked functions remained uncorrected. Inhibition of c-MYC by expression of a dominant-negative Omomyc protein relieved the DNA damage in CIII-deficient hepatocytes in vivo. Our results unequivocally connect primary OXPHOS deficiency to genomic instability and progeroid disease and suggest that targeting c-MYC and aberrant cell proliferation may provide novel therapeutic strategies in mitochondrial diseases.

pathology↗

bioRxiv2019

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye, and inhibitor-resistant high-fidelity DNA polymerase

Deoxyribonucleotide triphosphates (dNTPs) are vital for the biosynthesis and repair of DNA. Their cellular concentration peaks during the S phase of the cell cycle. In non-proliferating cells dNTP concentrations are low, making their reliable quantification from tissue samples of heterogeneous cellular composition challenging. Partly because of this, the current knowledge related to regulation of and disturbances in cellular dNTP concentrations derive from cell culture experiments with little corroboration at the tissue or organismal level. Here, we fill the methodological gap by presenting a simple non-radioactive microplate assay for the quantification of dNTPs with a minimum requirement of 10 to 30 mg of biopsy material. In contrast to published assays, this assay is based on long (~200 nucleotides) synthetic single-stranded DNA templates, an inhibitor-resistant high-fidelity DNA polymerase, and the double-stranded-DNA-binding EvaGreen dye. The assay quantifies reliably as little as 100 fmol of each of the four dNTPs. Importantly, the assay allowed measurement of minute dNTP concentrations in mouse liver, heart, and skeletal muscle.

molecular biology↗