bims-midhyp 2023-10-01 papers

bims-midhyp

Biomed News

on Mitochondrial dysfunction and hypoxia

Issue of 2023‒10‒01
twenty-one papers selected by
Alia Abukiwan, University of Heidelberg

Role of MicroRNAs in Regulation of Cellular Response to Hypoxia.
Early fate decision for mitochondrially encoded proteins by a molecular triage.
Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression.
Overexpression of KLF4 Suppresses Pulmonary Fibrosis through the HIF-1α/Endoplasmic Reticulum Stress Signaling Pathway.
TMEM135 links peroxisomes to the regulation of brown fat mitochondrial fission and energy homeostasis.
Multifaceted roles of mitochondrial dysfunction in diseases: from powerhouses to saboteurs.
Hypoxic regulation of hypoxia inducible factor 1 alpha via antisense transcription.
Oxidized Low-Density Lipoprotein Accumulation Suppresses Glycolysis and Attenuates the Macrophage Inflammatory Response by Diverting Transcription from the HIF-1α to the Nrf2 Pathway.
Mitochondrial proteome research: the road ahead.
Comprehensive metabolomics and transcriptomics analysis reveals protein and amino acid metabolic characteristics in liver tissue under chronic hypoxia.
Oxidative stress, tRNA metabolism and protein synthesis.
Extracellular vesicles set the stage for brain plasticity and recovery by multimodal signalling.
Inhaled nitric oxide testing in predicting prognosis in pulmonary hypertension due to left-sided heart diseases.
MRPS6 modulates glucose-stimulated insulin secretion in mouse islet cells through mitochondrial unfolded protein response.
Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer.
TRPV1 Channels Are New Players in the Reticulum-Mitochondria Ca2+ Coupling in a Rat Cardiomyoblast Cell Line.
The roles of intracellular proteolysis in cardiac ischemia-reperfusion injury.
The role of heat shock proteins in the pathogenesis of heart failure (Review).
TRIM25 targets p300 for degradation.
Conserved mechanisms of NuRD function in hematopoetic gene expression.
CTRP9 alleviates hypoxia/reoxygenation-induced human placental vascular endothelial cells impairment and mitochondrial dysfunction through activating AMPK/Nrf2 signaling.

Biochemistry (Mosc). 2023 Jun;88(6): 741-757

Role of MicroRNAs in Regulation of Cellular Response to Hypoxia.

Maria V Silina, Dzhuliia Sh Dzhalilova, Olga V Makarova.

  Hypoxia causes changes in transcription of the genes that contribute to adaptation of the cells to low levels of oxygen. The main mechanism regulating cellular response to hypoxia is activation of hypoxia-inducible transcription factors (HIF), which include several isoforms and control expression of more than a thousand genes. HIF activity is regulated at various levels, including by small non-coding RNA molecules called microRNAs (miRNAs). miRNAs regulate cellular response to hypoxia by influencing activation of HIF, its degradation, and translation of HIF-dependent proteins. At the same time, HIFs also affect miRNAs biogenesis. Data on the relationship of a particular HIF isoform with miRNAs are contradictory, since studies have been performed using different cell lines, various types of experimental animals and clinical material, as well as at different oxygen concentrations and durations of hypoxic exposure. In addition, HIF expression may be affected by the initial resistance of organisms to lack of oxygen, which has not been taken into account in the studies. This review analyzes the data on the effect of hypoxia on biogenesis and functioning of miRNAs, as well as on the effect of miRNAs on mRNAs of the genes involved in adaptation to oxygen deficiency. Understanding the mechanisms of relationship between HIF, hypoxia, and miRNA is necessary to develop new approaches to personalized therapy for diseases accompanied by oxygen deficiency.

Keywords:  HIF; hypoxia; microRNAs

DOI:  https://doi.org/10.1134/S0006297923060032
Mol Cell. 2023 Sep 21. pii: S1097-2765(23)00696-2. [Epub ahead of print]

Early fate decision for mitochondrially encoded proteins by a molecular triage.

Andreas Kohler, Andreas Carlström, Hendrik Nolte, Verena Kohler, Sung-Jun Jung, Sagar Sridhara, Takashi Tatsuta, Jens Berndtsson, Thomas Langer, Martin Ott.

  Folding of newly synthesized proteins poses challenges for a functional proteome. Dedicated protein quality control (PQC) systems either promote the folding of nascent polypeptides at ribosomes or, if this fails, ensure their degradation. Although well studied for cytosolic protein biogenesis, it is not understood how these processes work for mitochondrially encoded proteins, key subunits of the oxidative phosphorylation (OXPHOS) system. Here, we identify dedicated hubs in proximity to mitoribosomal tunnel exits coordinating mitochondrial protein biogenesis and quality control. Conserved prohibitin (PHB)/m-AAA protease supercomplexes and the availability of assembly chaperones determine the fate of newly synthesized proteins by molecular triaging. The localization of these competing activities in the vicinity of the mitoribosomal tunnel exit allows for a prompt decision on whether newly synthesized proteins are fed into OXPHOS assembly or are degraded.

Keywords:  assembly factors; complex assembly; m-AAA protease; mitochondria; mitoribosome; prohibitin; protein biogenesis; protein quality control; respiratory chain; translation

DOI:  https://doi.org/10.1016/j.molcel.2023.09.001
Nat Cell Biol. 2023 Sep 28.

Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression.

Nicholas J Kramer, Gyan Prakash, R Stefan Isaac, Karine Choquet, Iliana Soto, Boryana Petrova, Hope E Merens, Naama Kanarek, L Stirling Churchman.

Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed fluorescence-activated cell-sorting-based genome-wide screens analysing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. We identified genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6. We found that PREPL specifically impacts Complex IV biogenesis by acting at the intersection of mitochondrial lipid metabolism and protein synthesis, whereas NME6, an uncharacterized nucleoside diphosphate kinase, controls OXPHOS biogenesis through multiple mechanisms reliant on its NDPK domain. Firstly, NME6 forms a complex with RCC1L, which together perform nucleoside diphosphate kinase activity to maintain local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Secondly, NME6 modulates the activity of mitoribosome regulatory complexes, altering mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression.

DOI: https://doi.org/10.1038/s41556-023-01244-3
Int J Mol Sci. 2023 Sep 12. pii: 14008. [Epub ahead of print]24(18):

Overexpression of KLF4 Suppresses Pulmonary Fibrosis through the HIF-1α/Endoplasmic Reticulum Stress Signaling Pathway.

Shanchen Wei, Fei Qi, Yanping Wu, Xinmin Liu.

  The hypoxia-inducible factor-1α/endoplasmic reticulum stress signaling pathway (HIF-1α/ERS) has a crucial role in the pathogenetic mechanism of pulmonary fibrosis (PF). However, the upstream regulatory mediators of this pathway remain unclear. In the present study, by conducting bioinformatics analysis, we found that Krüppel-like factor 4 (KLF4) expression was decreased in the lung tissues of patients with idiopathic pulmonary fibrosis (IPF) as compared to that in patients with non-IPF. Furthermore, KLF4 expression was significantly reduced (p = 0.0331) in bleomycin-induced fibrotic HFL-1 cells. Moreover, in mice with bleomycin-induced PF, the degree of fibrosis was significantly reduced in mice overexpressing KLF4 as compared to that in wild-type mice. In mice and HFL-1 cells, KLF4 overexpression significantly reduced bleomycin-induced protein expression of HIF-1α (p = 0.0027) and ERS markers, particularly p-IRE1α (p = 0.0255) and ATF6 (p = 0.0002). By using the JASPAR database, we predicted that KLF4 has five binding sites for the HIF-1α promoter. The results of in vitro and in vivo studies suggest that KLF4 may inhibit PF through the HIF-1α/ERS pathway. This finding could guide the development of future therapies for PF and facilitate the identification of appropriate biomarkers for routine clinical diagnosis of PF.

Keywords:  HIF-1α; Krüppel-like factor 4; endoplasmic reticulum stress; pulmonary fibrosis

DOI:  https://doi.org/10.3390/ijms241814008
Nat Commun. 2023 Sep 29. 14(1): 6099

TMEM135 links peroxisomes to the regulation of brown fat mitochondrial fission and energy homeostasis.

Donghua Hu, Min Tan, Dongliang Lu, Brian Kleiboeker, Xuejing Liu, Hongsuk Park, Alexxai V Kravitz, Kooresh I Shoghi, Yu-Hua Tseng, Babak Razani, Akihiro Ikeda, Irfan J Lodhi.

Mitochondrial morphology, which is controlled by mitochondrial fission and fusion, is an important regulator of the thermogenic capacity of brown adipocytes. Adipose-specific peroxisome deficiency impairs thermogenesis by inhibiting cold-induced mitochondrial fission due to decreased mitochondrial membrane content of the peroxisome-derived lipids called plasmalogens. Here, we identify TMEM135 as a critical mediator of the peroxisomal regulation of mitochondrial fission and thermogenesis. Adipose-specific TMEM135 knockout in mice blocks mitochondrial fission, impairs thermogenesis, and increases diet-induced obesity and insulin resistance. Conversely, TMEM135 overexpression promotes mitochondrial division, counteracts obesity and insulin resistance, and rescues thermogenesis in peroxisome-deficient mice. Mechanistically, thermogenic stimuli promote association between peroxisomes and mitochondria and plasmalogen-dependent localization of TMEM135 in mitochondria, where it mediates PKA-dependent phosphorylation and mitochondrial retention of the fission factor Drp1. Together, these results reveal a previously unrecognized inter-organelle communication regulating mitochondrial fission and energy homeostasis and identify TMEM135 as a potential target for therapeutic activation of BAT.

DOI: https://doi.org/10.1038/s41467-023-41849-8
Arch Pharm Res. 2023 Sep 26.

Multifaceted roles of mitochondrial dysfunction in diseases: from powerhouses to saboteurs.

Surapriya Surendranath Prabhu, Aathira Sujathan Nair, Saiprabha Vijayakumar Nirmala.

  The fact that mitochondria play a crucial part in energy generation has led to the nickname "powerhouses" of the cell being applied to them. They also play a significant role in many other cellular functions, including calcium signalling, apoptosis, and the creation of vital biomolecules. As a result, cellular function and health as a whole can be significantly impacted by mitochondrial malfunction. Indeed, malignancies frequently have increased levels of mitochondrial biogenesis and quality control. Adverse selection exists for harmful mitochondrial genome mutations, even though certain malignancies include modifications in the nuclear-encoded tricarboxylic acid cycle enzymes that generate carcinogenic metabolites. Since rare human cancers with mutated mitochondrial genomes are often benign, removing mitochondrial DNA reduces carcinogenesis. Therefore, targeting mitochondria offers therapeutic options since they serve several functions and are crucial to developing malignant tumors. Here, we discuss the various steps involved in the mechanism of cancer for which mitochondria plays a significant role, as well as the role of mitochondria in diseases other than cancer. It is crucial to understand mitochondrial malfunction to target these organelles for therapeutic reasons. This highlights the significance of investigating mitochondrial dysfunction in cancer and other disease research.

Keywords:  Apoptosis; Carcinogenesis; Genome mutations; Mitochondrial dysfunction; Oncogenic signaling

DOI:  https://doi.org/10.1007/s12272-023-01465-y
J Biol Chem. 2023 Sep 23. pii: S0021-9258(23)02319-0. [Epub ahead of print] 105291

Hypoxic regulation of hypoxia inducible factor 1 alpha via antisense transcription.

Nicholas Downes, Henri Niskanen, Vanesa Tomas-Bosch, Mari Taipale, Mehvash Godiwala, Mari-Anna Väänänen, Tiia A Turunen, Einari Aavik, Nihay Laham-Karam, Seppo Ylä-Herttuala, Minna U Kaikkonen.

  Impaired oxygen homeostasis is a frequently encountered pathophysiological factor in multiple complex diseases, including cardiovascular disease and cancer. While the canonical hypoxia response pathway is well characterised, less is known about the role of non-coding RNAs in this process. Here, we investigated the nascent and steady-state non-coding transcriptional responses in endothelial cells and their potential roles in regulating the hypoxic response. Notably, we identify a novel antisense long non-coding RNA that convergently overlaps the majority of the HIF1A locus, which is expressed across several cell types and elevated in atherosclerotic lesions. The antisense (HIF1A-AS) is produced as a stable, unspliced and polyadenylated nuclear retained transcript. HIF1A-AS is highly induced in hypoxia by both HIF1A and HIF2A and exhibits anticorrelation with the coding HIF1A transcript and protein expression. We further characterized this functional relationship by CRISPR-mediated bimodal perturbation of the HIF1A-AS promoter. We provide evidence that HIF1A-AS represses the expression of HIF1a in cis by repressing transcriptional elongation and deposition of H3K4me3, and that this mechanism is dependent on the act of antisense transcription itself. Overall, our results indicate a critical regulatory role of antisense mediated transcription in regulation of HIF1A expression and cellular response to hypoxia.

Keywords:  HIF1a; Hypoxia; endothelial; lncRNA; transcriptional regulation

DOI:  https://doi.org/10.1016/j.jbc.2023.105291
J Immunol. 2023 Sep 27. pii: ji2300293. [Epub ahead of print]

Oxidized Low-Density Lipoprotein Accumulation Suppresses Glycolysis and Attenuates the Macrophage Inflammatory Response by Diverting Transcription from the HIF-1α to the Nrf2 Pathway.

Kenneth K Y Ting, Pei Yu, Riley Dow, Eric Floro, Hisham Ibrahim, Corey A Scipione, Sharon J Hyduk, Chanele K Polenz, Olga Zaslaver, Peer W F Karmaus, Michael B Fessler, Hannes L Röst, Michael Ohh, Sue Tsai, Daniel A Winer, Minna Woo, Jonathan Rocheleau, Jenny Jongstra-Bilen, Myron I Cybulsky.

Lipid accumulation in macrophages (Mφs) is a hallmark of atherosclerosis, yet how lipid accumulation affects inflammatory responses through rewiring of Mφ metabolism is poorly understood. We modeled lipid accumulation in cultured wild-type mouse thioglycolate-elicited peritoneal Mφs and bone marrow-derived Mφs with conditional (Lyz2-Cre) or complete genetic deficiency of Vhl, Hif1a, Nos2, and Nfe2l2. Transfection studies employed RAW264.7 cells. Mφs were cultured for 24 h with oxidized low-density lipoprotein (oxLDL) or cholesterol and then were stimulated with LPS. Transcriptomics revealed that oxLDL accumulation in Mφs downregulated inflammatory, hypoxia, and cholesterol metabolism pathways, whereas the antioxidant pathway, fatty acid oxidation, and ABC family proteins were upregulated. Metabolomics and extracellular metabolic flux assays showed that oxLDL accumulation suppressed LPS-induced glycolysis. Intracellular lipid accumulation in Mφs impaired LPS-induced inflammation by reducing both hypoxia-inducible factor 1-α (HIF-1α) stability and transactivation capacity; thus, the phenotype was not rescued in Vhl-/- Mφs. Intracellular lipid accumulation in Mφs also enhanced LPS-induced NF erythroid 2-related factor 2 (Nrf2)-mediated antioxidative defense that destabilizes HIF-1α, and Nrf2-deficient Mφs resisted the inhibitory effects of lipid accumulation on glycolysis and inflammatory gene expression. Furthermore, oxLDL shifted NADPH consumption from HIF-1α- to Nrf2-regulated apoenzymes. Thus, we postulate that repurposing NADPH consumption from HIF-1α to Nrf2 transcriptional pathways is critical in modulating inflammatory responses in Mφs with accumulated intracellular lipid. The relevance of our in vitro models was established by comparative transcriptomic analyses, which revealed that Mφs cultured with oxLDL and stimulated with LPS shared similar inflammatory and metabolic profiles with foamy Mφs derived from the atherosclerotic mouse and human aorta.

DOI: https://doi.org/10.4049/jimmunol.2300293
Nat Rev Mol Cell Biol. 2023 Sep 29.

Mitochondrial proteome research: the road ahead.

Zakery N Baker, Patrick Forny, David J Pagliarini.

Mitochondria are multifaceted organelles with key roles in anabolic and catabolic metabolism, bioenergetics, cellular signalling and nutrient sensing, and programmed cell death processes. Their diverse functions are enabled by a sophisticated set of protein components encoded by the nuclear and mitochondrial genomes. The extent and complexity of the mitochondrial proteome remained unclear for decades. This began to change 20 years ago when, driven by the emergence of mass spectrometry-based proteomics, the first draft mitochondrial proteomes were established. In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. The creation of these compendia provided a systemic view of an organelle previously studied primarily in a reductionist fashion and has accelerated both basic scientific discovery and the diagnosis and treatment of human disease. Yet numerous challenges remain in understanding mitochondrial biology and translating this knowledge into the medical context. In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. We highlight the power of an enhanced map for systematically defining the functions of its members. Finally, we examine the utility of an expanded, functionally annotated mitochondrial proteome in a translational setting for aiding both diagnosis of mitochondrial disease and targeting of mitochondria for treatment.

DOI: https://doi.org/10.1038/s41580-023-00650-7
PLoS One. 2023 ;18(9): e0291798

Comprehensive metabolomics and transcriptomics analysis reveals protein and amino acid metabolic characteristics in liver tissue under chronic hypoxia.

Hong Liang, Kang Song.

At high altitudes, oxygen deprivation can cause pathophysiological changes. Liver tissue function is known to impact whole-body energy metabolism; however, how these functions are affected by chronic hypoxia remains unclear. We aimed to elucidate changing characteristics underlying the effect of chronic hypoxia on protein and amino acid metabolism in mouse livers. Mice were maintained in a hypobaric chamber simulating high altitude for 4 weeks. Livers were collected for metabolomic analysis via ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry. For transcriptomics analysis, we conducted RNA sequencing of hepatic tissues followed by Gene Ontology and KEGG pathway enrichment analyses. Chronic hypoxic exposure caused metabolic disorders of amino acids and their derivatives in liver tissue. We identified a number of metabolites with significantly altered profiles (including amino acids, peptides, and analogues), of which serine, phenylalanine, leucine, proline, aspartic acid, L-glutamate, creatine, 5-aminovaleric acid, L-hydroxyarginin, and g-guanidinobutyrate showed great potential as biomarkers of chronic hypoxia. A total of 2124 genes with significantly different expression levels were identified in hypoxic liver tissue, of which 1244 were upregulated and 880 were downregulated. We found pathways for protein digestion and absorption, arginine and proline metabolism, and mineral absorption related to amino acid metabolism were affected by hypoxia. Our findings surrounding the regulation of key metabolites and differentially expressed genes provide new insights into changes in protein and amino acid metabolism in the liver that result from chronic hypoxia.

DOI: https://doi.org/10.1371/journal.pone.0291798
Antioxid Redox Signal. 2023 Sep 28.

Oxidative stress, tRNA metabolism and protein synthesis.

Yasutoshi Akiyama, Pavel Ivanov.

SIGNIFICANCE: Oxidative stress refers to excessive intracellular levels of reactive oxygen species (ROS) due to an imbalance between ROS production and antioxidant defense system. Under oxidative stress conditions, cells trigger various stress response pathways to protect themselves, among which repression of messenger RNA (mRNA) translation is one of the key hallmarks to promote cell survival. This regulation process minimizes cellular energy consumption, enabling cells to survive in adverse conditions and to promote recovery from stress-induced damage.RECENT ADVANCES: Recent studies suggest that transfer RNAs (tRNAs) play important roles in regulating translation as a part of stress response under adverse conditions. In particular, research relying on high-throughput techniques such as next-generation sequencing and mass spectrometry approaches have given us detailed information on the mechanisms such as an individual tRNA dynamics and crosstalk among posttranscriptional modifications.
CRITICAL ISSUES: Oxidative stress leads to dynamic tRNA changes including their localization, cleavage, and alteration of expression profiles and modification patterns. Growing evidence suggests that these changes not only are tightly regulated by stress response mechanisms, but also can directly fine-tune the translation efficiency, which contributes to cell or tissue-specific response to oxidative stress.
FUTURE DIRECTIONS: In this review, we describe recent advances in the understanding of the dynamic changes of tRNAs caused by oxidative stress. We also highlight the emerging roles of tRNAs in translation regulation under the condition. In addition, we discuss future perspectives in this research field.

DOI: https://doi.org/10.1089/ars.2022.0206
Brain. 2023 Sep 28. pii: awad332. [Epub ahead of print]

Extracellular vesicles set the stage for brain plasticity and recovery by multimodal signalling.

Dirk M Hermann, Luca Peruzzotti-Jametti, Bernd Giebel, Stefano Pluchino.

  Extracellular vesicles (EVs) are extremely versatile naturally occurring membrane particles that convey complex signals between cells. EVs of different cellular sources are capable of inducing striking therapeutic responses in neurological disease models. Differently from pharmacological compounds that act by modulating defined signalling pathways, EV-based therapeutics possess multiple abilities via a variety of effectors, thus allowing the modulation of complex disease processes that may have very potent effects on brain tissue recovery. When applied in vivo in experimental models of neurological diseases, EV-based therapeutics have revealed remarkable effects on immune responses, cell metabolism and neuronal plasticity. This multimodal modulation of neuroimmune networks by EVs profoundly influences disease processes in a highly synergistic and context-dependent way. Ultimately, the EV-mediated restoration of cellular functions helps to set the stage for neurological recovery. With this review we first outline the current understanding of the mechanisms of action of EVs, describing how EVs released from various cellular sources identify their cellular targets and convey signals to recipient cells. Then, mechanisms of action applicable to key neurological conditions, such as stroke, multiple sclerosis, and neurodegenerative diseases, are presented. Pathways that deserve attention in specific disease contexts are discussed. We subsequently showcase considerations about EV biodistribution and delineate genetic engineering strategies aiming at enhancing brain uptake and signalling. By sketching a broad view of EV-orchestrated brain plasticity and recovery, we finally define possible future clinical EV applications and propose necessary information to be provided ahead of clinical trials. Our goal is to provide a steppingstone that can be used to critically discuss EVs as next generation therapeutics for brain diseases.

Keywords:  cell metabolism; exosome; immune modulation; mitochondria; neuronal plasticity

DOI:  https://doi.org/10.1093/brain/awad332
ESC Heart Fail. 2023 Sep 29.

Inhaled nitric oxide testing in predicting prognosis in pulmonary hypertension due to left-sided heart diseases.

Taijyu Satoh, Nobuhiro Yaoita, Kotaro Nochioka, Shunsuke Tatebe, Hideka Hayashi, Saori Yamamoto, Haruka Sato, Hiroyuki Takahama, Hideaki Suzuki, Yosuke Terui, Kaito Yamada, Yusuke Yamada, Takumi Inoue, Tatsuo Aoki, Kimio Satoh, Koichiro Sugimura, Satoshi Miyata, Satoshi Yasuda.

  AIMS: The pathophysiology of pulmonary hypertension (PH) due to left-sided heart disease (Group 2 PH) is distinct from that of other groups of PH, yet there are still no approved therapies that selectively target pulmonary circulation. The increase in pulmonary capillary pressure due to left-sided heart disease is a trigger event for physical and biological alterations of the pulmonary circulation, including the nitric oxide (NO)-soluble guanylate cyclase-cyclic guanosine monophosphate axis. This study investigated inhaled NO vasoreactivity tests for patients with Group 2 PH and hypothesized that these changes may have a prognostic impact.METHODS AND RESULTS: This was a single-centre, retrospective study with a median follow-up of 365 days. From January 2011 to December 2015, we studied 69 patients with Group 2 PH [age, 61.5 ± 13.0 (standard deviation) years; male:female, 49:20; left ventricular ejection fraction, 50.1 ± 20.4%; mean pulmonary arterial pressure, ≥25 mmHg; and pulmonary arterial wedge pressure (PAWP), >15 mmHg]. No adverse events were observed after NO inhalation. Thirty-four patients with Group 2 PH showed increased PAWP (ΔPAWP: 3.26 ± 2.22 mmHg), while the remaining 35 patients did not (ΔPAWP: -2.11 ± 2.29 mmHg). Multivariate analysis revealed that increased PAWP was the only significant predictor of all-cause death or hospitalization for heart failure (HF) after 1 year (hazard ratio 4.35; 95% confidence interval, 1.27-14.83; P = 0.019). The acute response of PAWP to NO differed between HF with preserved and reduced ejection fractions.
CONCLUSIONS: Patients with Group 2 PH were tolerant of the inhaled NO test. NO-induced PAWP is a novel prognostic indicator.

Keywords:  Heart failure with preserved ejection fraction; Heart failure with reduced ejection fraction; Inhaled nitric oxide vasoreactivity tests; Pulmonary hypertension

DOI:  https://doi.org/10.1002/ehf2.14515
Sci Rep. 2023 09 27. 13(1): 16173

MRPS6 modulates glucose-stimulated insulin secretion in mouse islet cells through mitochondrial unfolded protein response.

Danhong Lin, Jingwen Yu, Leweihua Lin, Qianying Ou, Huibiao Quan.

Lack of efficient insulin secretion from the pancreas can lead to impaired glucose tolerance (IGT), prediabetes, and diabetes. We have previously identified two IGT-associated single nucleotide polymorphisms (SNPs) rs62212118 and rs13052524 located at two overlapping genes: MRPS6 and SLC5A3. In this study, we show that MRPS6 but not SLC5A3 regulates glucose-stimulated insulin secretion (GSIS) in primary human β-cell and a mouse pancreatic insulinoma β-cell line. Data mining and biochemical studies reveal that MRPS6 is positively regulated by the mitochondrial unfolded protein response (UPRmt), but feedback inhibits UPRmt. Disruption of such feedback by MRPS6 knockdown causes UPRmt hyperactivation in high glucose conditions, hence elevated ROS levels, increased apoptosis, and impaired GSIS. Conversely, MRPS6 overexpression reduces UPRmt, mitigates high glucose-induced ROS levels and apoptosis, and enhances GSIS in an ATF5-dependent manner. Consistently, UPRmt up-regulation or down-regulation by modulating ATF5 expression is sufficient to decrease or increase GSIS. The negative role of UPRmt in GSIS is further supported by analysis of public transcriptomic data from murine islets. In all, our studies identify MRPS6 and UPRmt as novel modulators of GSIS and apoptosis in β-cells, contributing to our understanding of the molecular and cellular mechanisms of IGT, prediabetes, and diabetes.

DOI: https://doi.org/10.1038/s41598-023-43438-7
bioRxiv. 2023 Sep 16. pii: 2023.09.14.557228. [Epub ahead of print]

Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer.

Katherine A Alexander, Ruofan Yu, Nicolas Skuli, Nathan J Coffey, Son Nguyen, Christine Faunce, Hua Huang, Ian P Dardani, Austin L Good, Joan Lim, Catherine Li, Nicholas Biddle, Eric F Joyce, Arjun Raj, Daniel Lee, Brian Keith, M Celeste Simon, Shelley L Berger.

Nuclear speckles are membrane-less bodies within the cell nucleus enriched in RNA biogenesis, processing, and export factors. In this study we investigated speckle phenotype variation in human cancer, finding a reproducible speckle signature, based on RNA expression of speckle-resident proteins, across >20 cancer types. Of these, clear cell renal cell carcinoma (ccRCC) exhibited a clear correlation between the presence of this speckle expression signature, imaging-based speckle phenotype, and clinical outcomes. ccRCC is typified by hyperactivation of the HIF-2α transcription factor, and we demonstrate here that HIF-2α drives physical association of a select subset of its target genes with nuclear speckles. Disruption of HIF-2α-driven speckle association via deletion of its s peckle targeting m otifs (STMs)-defined in this study-led to defective induction of speckle-associating HIF-2α target genes without impacting non-speckle-associating HIF-2α target genes. We further identify the RNA export complex, TREX, as being specifically altered in speckle signature, and knockdown of key TREX component, ALYREF, also compromises speckle-associated gene expression. By integrating tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2α gene regulatory programs are impacted by specific manipulation of speckle phenotype and by abrogation of speckle targeting abilities of HIF-2α. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2α-regulated target genes that, in turn, influence patient outcomes. We also identify STMs in other transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation.HIGHLIGHTS: - Nuclear speckles shown to reproducibly vary in cancer, predicting patient survival in ccRCC- HIF-2α drives DNA/gene-speckle contacts dependent on identified speckle targeting motifs within HIF-2α- Putative speckle targeting motifs are highly enriched among regulators of gene expression- Partitioning of transcription factor functional programs may be a major biological function of nuclear speckles.

DOI: https://doi.org/10.1101/2023.09.14.557228
Cells. 2023 09 20. pii: 2322. [Epub ahead of print]12(18):

TRPV1 Channels Are New Players in the Reticulum-Mitochondria Ca2+ Coupling in a Rat Cardiomyoblast Cell Line.

Nolwenn Tessier, Mallory Ducrozet, Maya Dia, Sally Badawi, Christophe Chouabe, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux, Fabien Van Coppenolle, Sylvie Ducreux.

  The Ca2+ release in microdomains formed by intercompartmental contacts, such as mitochondria-associated endoplasmic reticulum membranes (MAMs), encodes a signal that contributes to Ca2+ homeostasis and cell fate control. However, the composition and function of MAMs remain to be fully defined. Here, we focused on the transient receptor potential vanilloid 1 (TRPV1), a Ca2+-permeable ion channel and a polymodal nociceptor. We found TRPV1 channels in the reticular membrane, including some at MAMs, in a rat cardiomyoblast cell line (SV40-transformed H9c2) by Western blotting, immunostaining, cell fractionation, and proximity ligation assay. We used chemical and genetic probes to perform Ca2+ imaging in four cellular compartments: the endoplasmic reticulum (ER), cytoplasm, mitochondrial matrix, and mitochondrial surface. Our results showed that the ER Ca2+ released through TRPV1 channels is detected at the mitochondrial outer membrane and transferred to the mitochondria. Finally, we observed that prolonged TRPV1 modulation for 30 min alters the intracellular Ca2+ equilibrium and influences the MAM structure or the hypoxia/reoxygenation-induced cell death. Thus, our study provides the first evidence that TRPV1 channels contribute to MAM Ca2+ exchanges.

Keywords:  Ca2+ homeostasis; ER–mitochondria contact sites; H9c2; TRP channels; TRPV1; hypoxia–reoxygenation

DOI:  https://doi.org/10.3390/cells12182322
Basic Res Cardiol. 2023 Sep 28. 118(1): 38

The roles of intracellular proteolysis in cardiac ischemia-reperfusion injury.

Bridgette Hartley, Wesam Bassiouni, Richard Schulz, Olivier Julien.

  Ischemic heart disease remains a leading cause of human mortality worldwide. One form of ischemic heart disease is ischemia-reperfusion injury caused by the reintroduction of blood supply to ischemic cardiac muscle. The short and long-term damage that occurs due to ischemia-reperfusion injury is partly due to the proteolysis of diverse protein substrates inside and outside of cardiomyocytes. Ischemia-reperfusion activates several diverse intracellular proteases, including, but not limited to, matrix metalloproteinases, calpains, cathepsins, and caspases. This review will focus on the biological roles, intracellular localization, proteolytic targets, and inhibitors of these proteases in cardiomyocytes following ischemia-reperfusion injury. Recognition of the intracellular function of each of these proteases includes defining their activation, proteolytic targets, and their inhibitors during myocardial ischemia-reperfusion injury. This review is a step toward a better understanding of protease activation and involvement in ischemic heart disease and developing new therapeutic strategies for its treatment.

Keywords:  Intracellular protease; Ischemic heart disease; Protease; Protease inhibitors

DOI:  https://doi.org/10.1007/s00395-023-01007-z
Int J Mol Med. 2023 Nov;pii: 106. [Epub ahead of print]52(5):

The role of heat shock proteins in the pathogenesis of heart failure (Review).

Anastasia Pavlovna Sklifasovskaya, Mikhail Blagonravov, Anna Ryabinina, Vyacheslav Goryachev, Sergey Syatkin, Sergey Chibisov, Karina Akhmetova, Daniil Prokofiev, Enzo Agostinelli.

  The influence of heat shock proteins (HSPs) on protein quality control systems in cardiomyocytes is currently under investigation. The effect of HSPs on the regulated cell death of cardiomyocytes (CMCs) is of great importance, since they play a major role in the implementation of compensatory and adaptive mechanisms in the event of cardiac damage. HSPs mediate a number of mechanisms that activate the apoptotic cascade, playing both pro‑ and anti‑apoptotic roles depending on their location in the cell. Another type of cell death, autophagy, can in some cases lead to cell death, while in other situations it acts as a cell survival mechanism. The present review considered the characteristics of the expression of HSPs of different molecular weights in CMCs in myocardial damage caused by heart failure, as well as their role in the realization of certain types of regulated cell death.

Keywords:  apoptosis; autophagy; heart failure; heat shock proteins; myocardium; regulated cell death

DOI:  https://doi.org/10.3892/ijmm.2023.5309
Life Sci Alliance. 2023 Dec;pii: e202301980. [Epub ahead of print]6(12):

TRIM25 targets p300 for degradation.

Seham Elabd, Eleonora Pauletto, Valeria Solozobova, Nils Eickhoff, Nuno Padrao, Wilbert Zwart, Christine Blattner.

p300 is an important transcriptional co-factor. By stimulating the transfer of acetyl residues onto histones and several key transcription factors, p300 enhances transcriptional initiation and impacts cellular processes including cell proliferation and cell division. Despite its importance for cellular homeostasis, its regulation is poorly understood. We show that TRIM25, a member of the TRIM protein family, targets p300 for proteasomal degradation. However, despite TRIM25's RING domain and E3 activity, degradation of p300 by TRIM25 is independent of TRIM25-mediated p300 ubiquitination. Instead, TRIM25 promotes the interaction of p300 with dynein, which ensures a microtubule-dependent transport of p300 to cellular proteasomes. Through mediating p300 degradation, TRIM25 affects p300-dependent gene expression.

DOI: https://doi.org/10.26508/lsa.202301980
Enzymes. 2023 ;pii: S1874-6047(23)00012-4. [Epub ahead of print]53 7-32

Conserved mechanisms of NuRD function in hematopoetic gene expression.

Jonathan Lenz, Alexander Brehm.

  The Nucleosome Remodeling and Deacetylating Complex (NuRD) is ubiquitously expressed in all metazoans. It combines nucleosome remodeling and histone deacetylating activities to generate inaccessible chromatin structures and to repress gene transcription. NuRD is involved in the generation and maintenance of a wide variety of lineage-specific gene expression programs during differentiation and in differentiated cells. A close cooperation with a large number of lineage-specific transcription factors is key to allow NuRD to function in many distinct differentiation contexts. The molecular nature of this interplay between transcription factors and NuRD is complex and not well understood. This review uses hematopoiesis as a paradigm to highlight recent advances in our understanding of how transcription factors and NuRD cooperate at the molecular level during differentiation. A comparison of vertebrate and invertebrate systems serves to identify the conserved and fundamental concepts guiding functional interactions between transcription factors and NuRD. We also discuss how the transcription factor-NuRD axis constitutes a potential therapeutic target for the treatment of hemoglobinopathies.

Keywords:  Chromatin; Differentiation; Evolutionary conservation; FOG1; GATA transcription factors; Gene regulation; Hematopoiesis; Nucleosome Remodeling and Decetylating (NuRD) complex; Nucleosome remodeling; Protein interaction

DOI:  https://doi.org/10.1016/bs.enz.2023.07.006
Tissue Cell. 2023 Sep 12. pii: S0040-8166(23)00205-7. [Epub ahead of print]85 102217

CTRP9 alleviates hypoxia/reoxygenation-induced human placental vascular endothelial cells impairment and mitochondrial dysfunction through activating AMPK/Nrf2 signaling.

Lin Zhu, Shaolei Chen, Xulei Dai.

  BACKGROUND: Pregnancy-induced hypertension (PIH) is associated with significant maternal and fetal mortality. The present study is aimed at exploring the molecular mechanism of C1q/TNF-related protein 9 (CTRP9) in PIH.METHODS: Human placental vascular endothelial cells (HPVECs) underwent hypoxia/reoxygenation (H/R) to construct an in vitro PIH cellular model. Cell transfection was conducted to over-express CTRP9. The expression level of CTRP9 was determined by western blot and quantitative real-time PCR. CCK-8, flow cytometry, wound-healing and tube formation assays were conducted to assess cell viability, apoptosis, migration and angiogenesis, respectively. Mitochondrial membrane potential (∆ψm) was evaluated adopting JC-1 staining. Mitochondrial ROS and copy number (mtDNA) were examined using superoxide indicator and real-time PCR, respectively. Then, HPVECs were pre-treated with Compound C (CC), the inhibitor of AMPK, for regulatory mechanism research.
RESULTS: CTRP9 was downregulated in HPVECs exposed to H/R induction. CTRP9 overexpression retards H/R-mediated cell viability loss and apoptosis, impaired migration and angiogenesis of HPVECs. Meanwhile, CTRP9 overexpression alleviates H/R-mediated mitochondrial dysfunction in HPVECs by enhancing mitochondrial ∆ψm, reducing mitochondrial ROS generation and increasing mtDNA copies. In addition, CTRP9 activated AMPK/Nrf2 signaling in H/R-mediated HPVECs, and additional treatment of CC greatly weakened the functional effects of CTRP9 in H/R-mediated HPVECs.
CONCLUSION: Our results suggested that CTRP9 protected against H/R-mediated HPVECs injuries dependent on AMPK/Nrf2 signaling and could be applied as a potential therapy for PIH.

Keywords:  AMPK; C1q/TNF-related protein 9; Human placental vascular endothelial cells; Hypoxia/reoxygenation; Mitochondrial dysfunction

DOI:  https://doi.org/10.1016/j.tice.2023.102217