Mitochondrial oxidation of the carbohydrate fuel is required for neural precursor/stem cell function and postnatal cerebellar development

Identification of 7 mitochondria-related genes as diagnostic biomarkers of MDD and their correlation with immune infiltration: New insights from bioinformatics analysis

BACKGROUND

Major depressive disorder (MDD) is one of the most prevalent and debilitating psychiatric disorders. It becomes more recognized that mitochondrial dysfunction contributes to the pathophysiology of depression. However, little research has systematically investigated the mitochondria-related biomarkers for MDD diagnosis. This study aimed to develop a novel diagnostic gene signature in MDD based on mitochondria-related genes.

METHOD

We identified the differentially expressed mitochondrial-related genes (DeMRGs) by combing the gene expression data of the GEO database with mitochondria-related gene lists obtained from the MitoCarta3.0 database. Next, three kinds of machine-learning algorithms were used to screen characteristic DeMRGs. Then, we constructed a multivariable diagnostic model based on these characteristic genes and evaluated the diagnostic ability of this model. Subsequently, the immune landscape of infiltrated immune cells between MDD patients and controls was evaluated by CIBERSORT. Using consensus clustering analysis, we divided MDD patients into different clusters based on the characteristic DeMRGs expression patterns. Finally, the variations in immune cell infiltration between different clusters, and the correlation between characteristic DeMRGs and immune cell infiltration were analyzed.

RESULTS

Seven characteristic genes, including PMPCB, MRPS28, LYRM2, MGST1, COX20, PTPMT1, and STX17, were identified from the 31 DeMRGs. Based on the seven characteristic genes, we successfully constructed a diagnostic model which had relatively good diagnostic performance and potential application in the clinical diagnosis of MDD. In addition, our results also imply an intimate and comprehensive association between the characteristic DeMRGs and immune infiltrating cells.

CONCLUSION

A novel mitochondria-related gene signature with a good diagnostic performance and a relationship with immune microenvironment were identified in major depressive disorder.

Mitochondrial metabolic flexibility is critical for CD8+ T cell antitumor immunity

Mitochondria use different substrates for energy production and intermediatory metabolism according to the availability of nutrients and oxygen levels. The role of mitochondrial metabolic flexibility for CD8+ T cell immune response is poorly understood. Here, we report that the deletion or pharmacological inhibition of protein tyrosine phosphatase, mitochondrial 1 (PTPMT1) significantly decreased CD8+ effector T cell development and clonal expansion. In addition, PTPMT1 deletion impaired stem-like CD8+ T cell maintenance and accelerated CD8+ T cell exhaustion/dysfunction, leading to aggravated tumor growth. Mechanistically, the loss of PTPMT1 critically altered mitochondrial fuel selection-the utilization of pyruvate, a major mitochondrial substrate derived from glucose-was inhibited, whereas fatty acid utilization was enhanced. Persistent mitochondrial substrate shift and metabolic inflexibility induced oxidative stress, DNA damage, and apoptosis in PTPMT1 knockout cells. Collectively, this study reveals an important role of PTPMT1 in facilitating mitochondrial utilization of carbohydrates and that mitochondrial flexibility in energy source selection is critical for CD8+ T cell antitumor immunity.

Targeting PDK2 rescues stress-induced impaired brain energy metabolism

Depression is a mental illness frequently accompanied by disordered energy metabolism. A dysregulated hypothalamus pituitary adrenal axis response with aberrant glucocorticoids (GCs) release is often observed in patients with depression. However, the associated etiology between GCs and brain energy metabolism remains poorly understood. Here, using metabolomic analysis, we showed that the tricarboxylic acid (TCA) cycle was inhibited in chronic social defeat stress (CSDS)-exposed mice and patients with first-episode depression. Decreased mitochondrial oxidative phosphorylation was concomitant with the impairment of the TCA cycle. In parallel, the activity of pyruvate dehydrogenase (PDH), the gatekeeper of mitochondrial TCA flux, was suppressed, which is associated with the CSDS-induced neuronal pyruvate dehydrogenase kinase 2 (PDK2) expression and consequently enhanced PDH phosphorylation. Considering the well-acknowledged role of GCs in energy metabolism, we further demonstrated that glucocorticoid receptors (GR) stimulated PDK2 expression by directly binding to its promoter region. Meanwhile, silencing PDK2 abrogated glucocorticoid-induced PDH inhibition, restored the neuronal oxidative phosphorylation, and improved the flux of isotope-labeled carbon (U-13C] glucose) into the TCA cycle. Additionally, in vivo, pharmacological inhibition and neuron-specific silencing of GR or PDK2 restored CSDS-induced PDH phosphorylation and exerted antidepressant activities against chronic stress exposure. Taken together, our findings reveal a novel mechanism of depression manifestation, whereby elevated GCs levels regulate PDK2 transcription via GR, thereby impairing brain energy metabolism and contributing to the onset of this condition.

Loss of Ptpmt1 limits mitochondrial utilization of carbohydrates and leads to muscle atrophy and heart failure in tissue-specific knockout mice

While mitochondria in different tissues have distinct preferences for energy sources, they are flexible in utilizing competing substrates for metabolism according to physiological and nutritional circumstances. However, the regulatory mechanisms and significance of metabolic flexibility are not completely understood. Here, we report that the deletion of Ptpmt1, a mitochondria-based phosphatase, critically alters mitochondrial fuel selection - the utilization of pyruvate, a key mitochondrial substrate derived from glucose (the major simple carbohydrate), is inhibited, whereas the fatty acid utilization is enhanced. Ptpmt1 knockout does not impact the development of the skeletal muscle or heart. However, the metabolic inflexibility ultimately leads to muscular atrophy, heart failure, and sudden death. Mechanistic analyses reveal that the prolonged substrate shift from carbohydrates to lipids causes oxidative stress and mitochondrial destruction, which in turn results in marked accumulation of lipids and profound damage in the knockout muscle cells and cardiomyocytes. Interestingly, Ptpmt1 deletion from the liver or adipose tissue does not generate any local or systemic defects. These findings suggest that Ptpmt1 plays an important role in maintaining mitochondrial flexibility and that their balanced utilization of carbohydrates and lipids is essential for both the skeletal muscle and the heart despite the two tissues having different preferred energy sources.

High SPATA18 Expression and its Diagnostic and Prognostic Value in Clear Cell Renal Cell Carcinoma

BACKGROUND SPATA18 (spermatogenesis-associated 18, also called Mieap) encodes a protein that can induce lysosome-like organelles within mitochondria, which plays an important role in tumor growth. We measured the expression of SPATA18 in ccRCC, and assessed its diagnostic and prognostic clinical value in patients with clear cell renal cell carcinoma (ccRCC). MATERIAL AND METHODS We analyzed SPATA18 expression using data from the TCGA-KIRC cohort, GEO database, and UALCAN database. Immunohistochemistry was carried out to verify the expression in the ccRCC patients. The diagnostic value of SPATA18expression was evaluated by a receiver operating characteristic (ROC) curve. The correlation between clinical characteristics and SPATA18 expression was calculated by chi-square test. The prognostic value of SPATA18 expression was assessed by Kaplan-Meier analysis and Cox analysis. We conducted gene set enrichment analysis (GSEA) using TCGA database. RESULTS SPATA18 gene exhibited a higher expression in ccRCC tissues than in normal tissues. SPATA18 showed a substantial diagnostic value in ccRCC. SPATA18 expression was correlated with histological grade, clinical stage, T classification, and distant metastasis of ccRCC. Furthermore, high SPATA18 expression was associated with favorable overall survival. Multivariate analysis showed that SPATA18 was an independent risk factor for ccRCC. Gene set enrichment analysis (GSEA) showed that B cell receptors, WNT targets, extracellular matrix, oxidative phosphorylation, calcium metabolism, iron uptake and transport, potassium channels, and insulin receptor were differently enriched in the phenotype that was negatively correlated with SPATA18. CONCLUSIONS Our study indicated that high SPATA18 expression in ccRCC was associated with a good prognosis, and it could be a positive prognostic biomarker for ccRCC.

The critical role of cardiolipin in metazoan differentiation, development, and maturation

Cardiolipins are phospholipids that are central to proper mitochondrial functioning. Because mitochondria play crucial roles in differentiation, development, and maturation, we would also expect cardiolipin to play major roles in these processes. Indeed, cardiolipin has been implicated in the mechanism of three human diseases that affect young infants, implying developmental abnormalities. In this review, we will: (1) Review the biology of cardiolipin; (2) Outline the evidence for essential roles of cardiolipin during organismal development, including embryogenesis and cell maturation in vertebrate organisms; (3) Place the role(s) of cardiolipin during embryogenesis within the larger context of the roles of mitochondria in development; and (4) Suggest avenues for future research.

Cardiolipin Regulates Mitochondrial Ultrastructure and Function in Mammalian Cells

Cardiolipin (CL) is a unique, tetra-acylated diphosphatidylglycerol lipid that mainly localizes in the inner mitochondria membrane (IMM) in mammalian cells and plays a central role in regulating mitochondrial architecture and functioning. A deficiency of CL biosynthesis and remodeling perturbs mitochondrial functioning and ultrastructure. Clinical and experimental studies on human patients and animal models have also provided compelling evidence that an abnormal CL content, acyl chain composition, localization, and level of oxidation may be directly linked to multiple diseases, including cardiomyopathy, neuronal dysfunction, immune cell defects, and metabolic disorders. The central role of CL in regulating the pathogenesis and progression of these diseases has attracted increasing attention in recent years. In this review, we focus on the advances in our understanding of the physiological roles of CL biosynthesis and remodeling from human patients and mouse models, and we provide an overview of the potential mechanism by which CL regulates the mitochondrial architecture and functioning.

BACH1-Hemoxygenase-1 axis regulates cellular energetics and survival following sepsis

Sepsis is a complex disease due to dysregulated host response to infection. Oxidative stress and mitochondrial dysfunction leading to metabolic dysregulation are among the hallmarks of sepsis. The transcription factor NRF2 (Nuclear Factor E2-related factor2) is a master regulator of the oxidative stress response, and the NRF2 mediated antioxidant response is negatively regulated by BTB and CNC homology 1 (BACH1) protein. This study tested whether Bach1 deletion improves organ function and survival following polymicrobial sepsis induced by cecal ligation and puncture (CLP). We observed enhanced post-CLP survival in Bach1-/- mice with a concomitantly increased liver HO-1 expression, reduced liver injury and oxidative stress, and attenuated systemic and tissue inflammation. After sepsis induction, the liver mitochondrial function was better preserved in Bach1-/- mice. Furthermore, BACH1 deficiency improved liver and lung blood flow in septic mice, as measured by SPECT/CT. RNA-seq analysis identified 44 genes significantly altered in Bach1-/- mice after sepsis, including HMOX1 and several genes in lipid metabolism. Inhibiting HO-1 activity by Zinc Protoporphyrin-9 worsened organ function in Bach1-/- mice following sepsis. We demonstrate that mitochondrial bioenergetics, organ function, and survival following experimental sepsis were improved in Bach1-/- mice through the HO-1-dependent mechanism and conclude that BACH1 is a therapeutic target in sepsis.

Uric Acid Enhances Neurogenesis in a Parkinsonian Model by Remodeling Mitochondria

Background

Adult neurogenesis is the process of generating new neurons to enter neural circuits and differentiate into functional neurons. However, it is significantly reduced in Parkinson’s disease (PD). Uric acid (UA), a natural antioxidant, has neuroprotective properties in patients with PD. This study aimed to investigate whether UA would enhance neurogenesis in PD.

Methods

We evaluated whether elevating serum UA levels in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced parkinsonian mouse model would restore neurogenesis in the subventricular zone (SVZ). For a cellular model, we primary cultured neural precursor cells (NPCs) from post-natal day 1 rat and evaluated whether UA treatment promoted cell proliferation against 1-methyl-4-phenylpyridinium (MPP⁺).

Results

Uric acid enhanced neurogenesis in both in vivo and in vitro parkinsonian model. UA-elevating therapy significantly increased the number of bromodeoxyuridine (BrdU)-positive cells in the SVZ of PD animals as compared to PD mice with normal UA levels. In a cellular model, UA treatment increased the expression of Ki-67. In the process of modulating neurogenesis, UA elevation up-regulated the expression of mitochondrial fusion markers.

Conclusion

In MPTP-induced parkinsonian model, UA probably enhanced neurogenesis via regulating mitochondrial dynamics, promoting fusion machinery, and inhibiting fission process.

Neural stem cells derived from human midbrain organoids as a stable source for treating Parkinson's disease: Midbrain organoid-NSCs (Og-NSC) as a stable source for PD treatment

Successful clinical translation of stem cell-based therapy largely relies on the scalable and reproducible preparation of donor cells with potent therapeutic capacities. In this study, midbrain organoids were yielded from human pluripotent stem cells (hPSCs) to prepare cells for Parkinson's disease (PD) therapy. Neural stem/precursor cells (NSCs) isolated from midbrain organoids (Og-NSCs) expanded stably and differentiated into midbrain-type dopamine(mDA) neurons, and an unprecedentedly high proportion expressed midbrain-specific factors, with relatively low cell line and batch-to-batch variations. Single cell transcriptome analysis followed by in vitro assays indicated that the majority of cells in the Og-NSC cultures are ventral midbrain (VM)-patterned with low levels of cellular senescence/aging and mitochondrial stress, compared to those derived from 2D-culture environments. Notably, in contrast to current methods yielding mDA neurons without astrocyte differentiation, mDA neurons that differentiated from Og-NSCs were interspersed with astrocytes as in the physiologic brain environment. Thus, the Og-NSC-derived mDA neurons exhibited improved synaptic maturity, functionality, resistance to toxic insults, and faithful expressions of the midbrain-specific factors, in vitro and in vivo long after transplantation. Consequently, Og-NSC transplantation yielded potent therapeutic outcomes that are reproducible in PD model animals. Collectively, our observations demonstrate that the organoid-based method may satisfy the demands needed in the clinical setting of PD cell therapy.

Mitochondrial biogenesis in developing astrocytes regulates astrocyte maturation and synapse formation

The mechanisms controlling the post-natal maturation of astrocytes play a crucial role in ensuring correct synaptogenesis. We show that mitochondrial biogenesis in developing astrocytes is necessary for coordinating post-natal astrocyte maturation and synaptogenesis. The astrocytic mitochondrial biogenesis depends on the transient upregulation of metabolic regulator peroxisome proliferator-activated receptor gamma (PPARγ) co-activator 1α (PGC-1α), which is controlled by metabotropic glutamate receptor 5 (mGluR5). At tissue level, the loss or downregulation of astrocytic PGC-1α sustains astrocyte proliferation, dampens astrocyte morphogenesis, and impairs the formation and function of neighboring synapses, whereas its genetic re-expression is sufficient to restore the mitochondria compartment and correct astroglial and synaptic defects. Our findings show that the developmental enhancement of mitochondrial biogenesis in astrocytes is a critical mechanism controlling astrocyte maturation and supporting synaptogenesis, thus suggesting that astrocytic mitochondria may be a therapeutic target in the case of neurodevelopmental and psychiatric disorders characterized by impaired synaptogenesis.

Drosophila PTPMT1 Has a Function in Tracheal Air Filling

The fly trachea is the equivalent of the mammalian lung and is a useful model for human respiratory diseases. However, little is known about the molecular mechanisms underlying tracheal air filling during larval development. In this study, we discover that PTPMT1 has a function in tracheal air filling. PTPMT1 is a widely conserved, ubiquitously expressed mitochondrial phosphatase. To reveal PTPMT1's functions in genetically tractable invertebrates and whether those functions are tissue specific, we generate a Drosophila model of PTPMT1 depletion. We find that fly PTPMT1 mutants show impairments in tracheal air filling and subsequent activation of innate immune responses. On a cellular level, these defects are preceded by aggregation of mitochondria within the tracheal epithelial cells. Our work demonstrates a cell-type-specific role for PTPMT1 in fly tracheal epithelial cells to support air filling and to prevent immune activation. The establishment of this model will facilitate exploration of PTPMT1's physiological functions in vivo.