bims-mitdis 2023-01-22 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2023–01–22
thirty-two papers selected by
Catalina Vasilescu, Helmholz Munich

Mitochondria regulate intracellular coenzyme Q transport and ferroptotic resistance via STARD7.
Tackling Inflammation at its Source in Heart Failure: Are Mitochondria the Key?
Lineage-Mismatched Mitochondrial Replacement in an Inducible Mitochondrial Depletion Model Effectively Restores the Original Proteomic Landscape of Recipient Cells.
Insulin Resistance in Mitochondrial Diabetes.
CoQ Regulates Brown Adipose Tissue Respiration and Uncoupling Protein 1 Expression.
[Thermosensibility and mitochondrial trifunctional protein deficiencies].
SERS uncovers the link between conformation of cytochrome c heme and mitochondrial membrane potential.
Isolation of Mitochondrial Lipids and Mass Spectrometric Analysis.
Novel insights into the involvement of mitochondrial fission/fusion in heart failure: From molecular mechanisms to targeted therapies.
Methods to Study Mitochondria: Techniques Used to Study the Effects of Age-Related Diseases Including Alzheimer's.
Emerging implications for ribosomes in proximity to mitochondria.
Emerging role of mitophagy in heart failure: from molecular mechanism to targeted therapy.
Cardiovascular Research in Friedreich Ataxia: Unmet Needs and Opportunities.
[The study of mitochondrial disorder pedigree associated with FASTKD2 variants and uniparental disomy].
Safety and Tolerability of Nicotinamide Riboside in Heart Failure With Reduced Ejection Fraction.
Exploring therapeutic strategies for infantile neuronal axonal dystrophy (INAD/PARK14).
Mitochondrial stress and mitokines in aging.
EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders.
NMN: The NAD Precursor at the Intersection Between Axon Degeneration and Anti-ageing Therapies.
Current development of patient-specific induced pluripotent stem cells harbouring mitochondrial gene mutations and their applications in the treatment of sensorineural hearing loss.
Circulating Mitochondrial DNA as a Diagnostic Biomarker for Predicting Disease Severity in Patients with Acute Pancreatitis.
Adult patient diagnosed with NADSYN1 associated congenital NAD deficiency and analysis of NAD levels to be published in: European Journal of Medical Genetics.
UK launches whole-genome sequencing pilot for babies.
Generation of two mother-child pairs of iPSCs from maternally inherited Leigh syndrome patients with m.8993 T > G and m.9176 T > G MT-ATP6 mutations.
Profiling the Mammalian Lipidome by Quantitative Shotgun Lipidomics.
An efficient genotyper and star-allele caller for pharmacogenomics.
OPA1 Dominant Optic Atrophy: Diagnostic Approach in the Pediatric Population.
Mono- and biallelic variant effects on disease at biobank scale.
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset.
Brain endothelium-derived extracellular vesicles containing amyloid-beta induce mitochondrial alterations in neural progenitor cells.
Linking genetic variants to cellular function and disease.
FinnGen provides genetic insights from a well-phenotyped isolated population.

Nat Cell Biol. 2023 Jan 19.

Mitochondria regulate intracellular coenzyme Q transport and ferroptotic resistance via STARD7.

Soni Deshwal, Mashun Onishi, Takashi Tatsuta, Tim Bartsch, Eileen Cors, Katharina Ried, Kathrin Lemke, Hendrik Nolte, Patrick Giavalisco, Thomas Langer.

Coenzyme Q (or ubiquinone) is a redox-active lipid that serves as universal electron carrier in the mitochondrial respiratory chain and antioxidant in the plasma membrane limiting lipid peroxidation and ferroptosis. Mechanisms allowing cellular coenzyme Q distribution after synthesis within mitochondria are not understood. Here we identify the cytosolic lipid transfer protein STARD7 as a critical factor of intracellular coenzyme Q transport and suppressor of ferroptosis. Dual localization of STARD7 to the intermembrane space of mitochondria and the cytosol upon cleavage by the rhomboid protease PARL ensures the synthesis of coenzyme Q in mitochondria and its transport to the plasma membrane. While mitochondrial STARD7 preserves coenzyme Q synthesis, oxidative phosphorylation function and cristae morphogenesis, cytosolic STARD7 is required for the transport of coenzyme Q to the plasma membrane and protects against ferroptosis. A coenzyme Q variant competes with phosphatidylcholine for binding to purified STARD7 in vitro. Overexpression of cytosolic STARD7 increases ferroptotic resistance of the cells, but limits coenzyme Q abundance in mitochondria and respiratory cell growth. Our findings thus demonstrate the need to coordinate coenzyme Q synthesis and cellular distribution by PARL-mediated STARD7 processing and identify PARL and STARD7 as promising targets to interfere with ferroptosis.

DOI: https://doi.org/10.1038/s41556-022-01071-y
JACC Basic Transl Sci. 2022 Dec;7(12): 1197-1199

Tackling Inflammation at its Source in Heart Failure: Are Mitochondria the Key?

Michael N Sack.



Keywords:  heart failure with reduced ejection fraction; mitochondrial function; nicotinamide adenine dinucleotide; nicotinamide riboside; sterile inflammation

DOI:  https://doi.org/10.1016/j.jacbts.2022.07.008
Adv Biol (Weinh). 2023 Jan 18. e2200246

Lineage-Mismatched Mitochondrial Replacement in an Inducible Mitochondrial Depletion Model Effectively Restores the Original Proteomic Landscape of Recipient Cells.

Fausto Capelluto, Hannah Alberico, Paula Ledo-Hopgood, Jonathan L Tilly, Dori C Woods.

  In addition to critical roles in bioenergetics, mitochondria are key contributors to the regulation of many other functions in cells, ranging from steroidogenesis to apoptosis. Numerous studies further demonstrate that cell type-specific differences exist in mitochondria, with cells of a given lineage tailoring their endogenous mitochondrial population to suit specific functional needs. These findings, coupled with studies of the therapeutic potential of mitochondrial transplantation, provide a strong impetus to better understand how mitochondria can influence cell function or fate. Here an inducible mitochondrial depletion modelis used to study how cells lacking endogenous mitochondria respond, on a global protein expression level, to transplantation with lineage-mismatched (LM) mitochondria. It is shown that LM mitochondrial transplantation does not alter the proteomic profile in nonmitochondria-depleted recipient cells; however, enforced depletion of endogenous mitochondria results in dramatic changes in the proteomic landscape, which returns to the predepletion state following internalization of LM mitochondria. These data, derived from a cell system that can be rendered free of influence by endogenous mitochondria, indicate that transplantation of mitochondria-even from a source that differs significantly from the recipient cell population, effectively restores a normal proteomic landscape to cells lacking their own mitochondria.

Keywords:  Parkin; mitochondria; mitochondrial depletion; mitochondrial transplantation; proteomics

DOI:  https://doi.org/10.1002/adbi.202200246
Biomolecules. 2023 Jan 07. pii: 126. [Epub ahead of print]13(1):

Insulin Resistance in Mitochondrial Diabetes.

Chika Takano, Erika Ogawa, Satoshi Hayakawa.

  Mitochondrial diabetes (MD) is generally classified as a genetic defect of β-cells. The main pathophysiology is insulin secretion failure in pancreatic β-cells due to impaired mitochondrial ATP production. However, several reports have mentioned the presence of insulin resistance (IR) as a clinical feature of MD. As mitochondrial dysfunction is one of the important factors causing IR, we need to focus on IR as another pathophysiology of MD. In this special issue, we first briefly summarized the insulin signaling and molecular mechanisms of IR. Second, we overviewed currently confirmed pathogenic mitochondrial DNA (mtDNA) mutations from the MITOMAP database. The variants causing diabetes were mostly point mutations in the transfer RNA (tRNA) of the mitochondrial genome. Third, we focused on these variants leading to the recently described "tRNA modopathies" and reviewed the clinical features of patients with diabetes. Finally, we discussed the pathophysiology of MD caused by mtDNA mutations and explored the possible mechanism underlying the development of IR. This review should be beneficial to all clinicians involved in diagnostics and therapeutics related to diabetes and mitochondrial diseases.

Keywords:  insulin resistance; mitochondrial DNA mutation; mitochondrial diabetes; transfer RNA modopathy

DOI:  https://doi.org/10.3390/biom13010126
Antioxidants (Basel). 2022 Dec 22. pii: 14. [Epub ahead of print]12(1):

CoQ Regulates Brown Adipose Tissue Respiration and Uncoupling Protein 1 Expression.

Ching-Fang Chang, Amanda L Gunawan, Irene Liparulo, Peter-James H Zushin, Ambre M Bertholet, Yuriy Kirichok, Andreas Stahl.

  Coenzyme Q (CoQ, aka ubiquinone) is a key component of the mitochondrial electron transport chain (ETC) and membrane-incorporated antioxidant. CoQ10 deficiencies encompass a heterogeneous spectrum of clinical phenotypes and can be caused by hereditary mutations in the biosynthesis pathway or result from pharmacological interventions such as HMG-CoA Reductase inhibitors, and statins, which are widely used to treat hypercholesterolemia and prevent cardiovascular disease. How CoQ deficiency affects individual tissues and cell types, particularly mitochondrial-rich ones such as brown adipose tissue (BAT), has remained poorly understood. Here we show that pharmacological and genetic models of BAT CoQ deficiency show altered respiration that can only in part be explained by classical roles of CoQ in the respiration chain. Instead, we found that CoQ strongly impacts brown and beige adipocyte respiration via the regulation of uncoupling protein 1 (UCP1) expression. CoQ deficiency in BAT robustly decreases UCP1 protein levels and uncoupled respiration unexpectedly, resulting in increased inner mitochondrial membrane potential and decreased ADP/ATP ratios. Suppressed UCP1 expression was also observed in a BAT-specific in vivo model of CoQ deficiency and resulted in enhanced cold sensitivity. These findings demonstrate an as yet unappreciated role of CoQ in the transcriptional regulation of key thermogenic genes and functions.

Keywords:  Coenzyme Q; brown adipose tissue; mitochondrial function; thermogenesis

DOI:  https://doi.org/10.3390/antiox12010014
Med Sci (Paris). 2022 Dec;38 Hors série n° 1 42-43

[Thermosensibility and mitochondrial trifunctional protein deficiencies].

Gorka Fernández-Eulate.

DOI: https://doi.org/10.1051/medsci/2022181
Free Radic Biol Med. 2023 Jan 14. pii: S0891-5849(23)00021-7. [Epub ahead of print]

SERS uncovers the link between conformation of cytochrome c heme and mitochondrial membrane potential.

Nadezda A Brazhe, Evelina I Nikelshparg, Adil A Baizhumanov, Vera G Grivennikova, Anna A Semenova, Sergey M Novikov, Valentyn S Volkov, Aleksey V Arsenin, Dmitry I Yakubovsky, Andrey B Evlyukhin, Zhanna V Bochkova, Eugene A Goodilin, Georgy V Maksimov, Olga Sosnovtseva, Andrey B Rubin.

  The balance between the mitochondrial respiratory chain activity and the cell's needs in ATP ensures optimal cellular function. Cytochrome c is an essential component of the electron transport chain (ETC), which regulates ETC activity, oxygen consumption, ATP synthesis and can initiate apoptosis. The impact of conformational changes in cytochrome c on its function is not understood for lack of access to these changes in intact mitochondria. We have developed a novel sensor that uses unique properties of label-free surface-enhanced Raman spectroscopy (SERS) to identify conformational changes in heme of cytochrome c and to elucidate their role in functioning mitochondria. We verify that molecule bond vibrations assessed by SERS is a reliable indicator of the heme conformation during changes in the inner mitochondrial membrane potential and ETC activity. We have demonstrated that cytochrome c heme reversibly switches between planar and ruffled conformations in response to the inner mitochondrial membrane potential (ΔΨ) and H+ concentration in the intermembrane space to regulate the efficiency of the mitochondrial respiratory chain, thus, adjusting the mitochondrial respiration to the cell's consumption of ATP and the overall activity. We have found that under hypertensive conditions cytochrome c heme lose its sensitivity to ΔΨ that can affect the regulation of ETC activity. The ability of the proposed SERS-based sensor to track mitochondrial function opens wide perspectives on cell bioenergetics.

Keywords:  Cytochrome c; Electron transport chain; Heme; Mitochondria; Surface-enhanced Raman spectroscopy

DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.01.013
Methods Mol Biol. 2023 ;2625 1-6

Isolation of Mitochondrial Lipids and Mass Spectrometric Analysis.

Alexa M Jauregui, Zoé M Cubero Cortés, Sean D Meehan, Sanjoy K Bhattacharya.

  Mitochondria participate in many important metabolic processes in the body. The lipid profile of mitochondria is especially important in membrane regulation and pathway signaling. The isolation and study of these lipids can provide unparalleled information about the mechanisms behind these cellular processes. In this chapter, we describe a protocol to isolate mitochondrial lipids from homogenized murine optic nerves. The lipid extraction was performed using butanol-methanol (BUME) and subsequently analyzed using liquid chromatography-mass spectrometry. Further analysis of the raw data was conducted using LipidSearch™ and MetaboAnalyst 4.0.

Keywords:  Lipidomics; Liquid chromatography; Mitochondrial lipids; Neurodegeneration; mass spectrometry

DOI:  https://doi.org/10.1007/978-1-0716-2966-6_1
Cell Stress Chaperones. 2023 Jan 18.

Novel insights into the involvement of mitochondrial fission/fusion in heart failure: From molecular mechanisms to targeted therapies.

Xinxin Liu, Chenchen Guo, Qiming Zhang.

  Mitochondria are dynamic organelles that alter their morphology through fission (fragmentation) and fusion (elongation). These morphological changes correlate highly with mitochondrial functional adaptations to stressors, such as hypoxia, pressure overload, and inflammation, and are important in the setting of heart failure. Pathological mitochondrial remodeling, characterized by increased fission and reduced fusion, is associated with impaired mitochondrial respiration, increased mitochondrial oxidative stress, abnormal cytoplasmic calcium handling, and increased cardiomyocyte apoptosis. Considering the impact of the mitochondrial morphology on mitochondrial behavior and cardiomyocyte performance, altered mitochondrial dynamics could be expected to induce or exacerbate the pathogenesis and progression of heart failure. However, whether alterations in mitochondrial fission and fusion accelerate or retard the progression of heart failure has been the subject of intense debate. In this review, we first describe the physiological processes and regulatory mechanisms of mitochondrial fission and fusion. Then, we extensively discuss the pathological contributions of mitochondrial fission and fusion to heart failure. Lastly, we examine potential therapeutic approaches targeting mitochondrial fission/fusion to treat patients with heart failure.

Keywords:  DRP1; Heart failure; MFN1/2; Mitochondrial fission; Mitochondrial fusion; OPA1

DOI:  https://doi.org/10.1007/s12192-023-01321-4
Curr Protoc. 2023 Jan;3(1): e631

Methods to Study Mitochondria: Techniques Used to Study the Effects of Age-Related Diseases Including Alzheimer's.

Javaria Baig, Jangampalli Adi Pradeepkiran, P Hemachandra Reddy.

  Various laboratories across the world have developed methods to study mitochondrial proteins/markers through extraction of mitochondrial RNA and protein to assess mitophagy/autophagy in Alzheimer's disease and other age-related diseases. Techniques outlined in this article include qRT-PCR, immunoblotting, immunofluorescence, transmission electron microscopy, Seahorse bioanalysis, staining for mitochondrial membrane potential, detection of mitophagy, and mitochondrial functional assays. Most of these techniques have been performed in vitro (in human and mouse neuronal cell lines transfected with mutant amyloid precursor protein or tau protein cDNAs) and in vivo (in brain tissues from different mouse models of Alzheimer's and other neurological diseases). Mitochondrial abnormalities in Alzheimer's disease have taken various forms, including excessive reactive oxygen species production, mitochondrial calcium dyshomeostasis, loss of ATP, defects in mitochondrial dynamics and transport, and mitophagy. Mitochondrial dysfunction is largely involved in aging; age-related diseases such as cancer, diabetes, and obesity; and neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, multiple sclerosis, and others. The goal of this article is to make protocols/methods available to students, scholars, and researchers of mitochondria in order to facilitate future mitochondrial studies. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Analyzing mitochondrial gene expression in mouse brain tissue and HT22 cells by qRT-PCR Basic Protocol 2: Analyzing protein expression in mouse brain tissue and HT22 cells by immunoblotting Basic Protocol 3: Immunofluorescence staining of cells and tissue sections Basic Protocol 4: Staining for mitochondrial membrane potential Basic Protocol 5: Assessing mitochondrial structure by transmission electron microscopy Basic Protocol 6: Methods for detecting mitophagy Basic Protocol 7: Bioenergetics assay via Seahorse Basic Protocol 8: Assays for mitochondrial function.

Keywords:  Alzheimer's disease; fluorescence; microscopy; mitochondria; mitochondrial function

DOI:  https://doi.org/10.1002/cpz1.631
Semin Cell Dev Biol. 2023 Jan 13. pii: S1084-9521(23)00003-4. [Epub ahead of print]

Emerging implications for ribosomes in proximity to mitochondria.

Bar Cohen, Adi Golani-Armon, Yoav S Arava.

  Synthesis of all proteins in eukaryotic cells, apart from a few organellar proteins, is done by cytosolic ribosomes. Many of these ribosomes are localized in the vicinity of the functional site of their encoded protein, enabling local protein synthesis. Studies in various organisms and tissues revealed that such locally translating ribosomes are also present near mitochondria. Here, we provide a brief summary of evidence for localized translation near mitochondria, then present data suggesting that these localized ribosomes may enable local translational regulatory processes in response to mitochondria needs. Finally, we describe the involvement of such localized ribosomes in the quality control of protein synthesis and mitochondria. These emerging views suggest that ribosomes localized near mitochondria are a hub for a variety of activities with diverse implications on mitochondria physiology.

Keywords:  Localized translation; MitoRQC; Mitochondria; RNA binding proteins; Ribosomal quality control; Ribosomes; Translation regulation; mRNA localization

DOI:  https://doi.org/10.1016/j.semcdb.2023.01.003
Cell Cycle. 2023 Jan 19. 1-13

Emerging role of mitophagy in heart failure: from molecular mechanism to targeted therapy.

Yu Liu, Yizhou Wang, Yingfei Bi, Zhiqiang Zhao, Shuai Wang, Shanshan Lin, Zhihua Yang, Xianliang Wang, Jingyuan Mao.

  Heart failure is defined as a drop in heart's pump function, accounting for reduced blood output and venous stasis, and constitutes the end stage of various cardiovascular diseases. Although mild mitochondrial dysfunction may hinder cardiomyocyte metabolism and impair myocardial function, severe mitochondrial injury is accompanied by cardiomyocyte apoptosis, leading to irreversible damage of the heart. Selective autophagy of mitochondria, or mitophagy, serves to rapidly remove dysfunctional mitochondria and restore the health of the mitochondrial population within cells by allowing reutilization of degradative substrates such as amino acids, fatty acids, and nucleotides. Although mitophagy represents a protective program that prevents the accumulation of poorly structured or damaged mitochondria, excessive mitophagy leads to mitochondrial population decline, impaired oxidative phosphorylation, and decreased ATP production. In this review, we first discuss the molecular underpinnings of mitophagy and the roles of different mitophagy adaptors. Then, the multiple and complex influence of mitophagy on heart failure is summarized. Finally, novel pharmacological strategies targeting mitophagy to relieve heart failure are briefly summarized.

Keywords:  Bnip3; FUNDC1; Heart failure; Parkin; mitophagy

DOI:  https://doi.org/10.1080/15384101.2023.2167949
JACC Basic Transl Sci. 2022 Dec;7(12): 1267-1283

Cardiovascular Research in Friedreich Ataxia: Unmet Needs and Opportunities.

R Mark Payne.

  Friedreich Ataxia (FRDA) is an autosomal recessive disease in which a mitochondrial protein, frataxin, is severely decreased in its expression. In addition to progressive ataxia, patients with FRDA often develop a cardiomyopathy that can be hypertrophic. This cardiomyopathy is unlike the sarcomeric hypertrophic cardiomyopathies in that the hypertrophy is associated with massive mitochondrial proliferation within the cardiomyocyte rather than contractile protein overexpression. This is associated with atrial arrhythmias, apoptosis, and fibrosis over time, and patients often develop heart failure leading to premature death. The differences between this mitochondrial cardiomyopathy and the more common contractile protein hypertrophic cardiomyopathies can be a source of misunderstanding in the management of these patients. Although imaging studies have revealed much about the structure and function of the heart in this disease, we still lack an understanding of many important clinical and fundamental molecular events that determine outcome of the heart in FRDA. This review will describe the current basic and clinical understanding of the FRDA heart, and most importantly, identify major gaps in our knowledge that represent new directions and opportunities for research.

Keywords:  CMR, cardiac magnetic resonance; FDA, U.S. Food and Drug Administration; FRDA, Friedreich ataxia; Friedreich ataxia; GAA, triplet expansion in first intron of the Friedreich ataxia gene; HF, heart failure; LV, left ventricle; LVEF, left ventricular ejection fraction; LVMI, left ventricular mass index; RV, right ventricle; cardiomyopathy; frataxin; heart; mitochondria

DOI:  https://doi.org/10.1016/j.jacbts.2022.04.005
Zhonghua Yi Xue Za Zhi. 2023 Jan 17. 103(3): 171-177

[The study of mitochondrial disorder pedigree associated with FASTKD2 variants and uniparental disomy].

Y N Ma, L L Lin, Y Zhang, L Li, H R Wu, Y Xiao, H Pan, Y L Yang, Y Qi.

Objective: To analyse the genetic cause of a proband with mitochondrial disease caused by FASTKD2 gene variation and uniparental disomy. Methods: Detailed medical history of a child suspected "mitochondrial disease" were inquired in Peking University First Hospital on November 23, 2017. c.810_820dup homozygous variation in FASTKD2 gene was found by high-throughput sequencing, and her mother had heterozygous variation, but her father didn't have such variation, which didn't conform to the genetic law of variation. Further clinical examinations and molecular genetic tests were carried out. The venous blood of the child and her parents was drawn, and genomic DNA was extracted. Sanger sequencing, polymerase chain reaction (PCR) testing, short tandem repeat (STR) analysis, chromosome microarray analysis and loss of heterozygosity (LOH) genetic relationship analysis were performed on the proband and the parents to determine the variation. Results: The clinical manifestations, physical examination and laboratory examination of the child supported the diagnosis of mitochondrial disease. c.810_820dup(p.Ser274Phefs*8) homozygous variant in FASTKD2 gene was identified. Sanger sequencing indicated that the mother was a heterozygote of the variant, while the father had no such variation, which did not conform to the genetic law. PCR testing and Sanger sequencing review to eliminate sampling errors, PCR amplification and sequencing errors. Non-biological father was excluded by STR analysis. Three large segmental LOH of FASTKD2 gene were found by chromosome microarray analysis, then the LOH relative analysis verified the child was a mixed maternal uniparental disomy of chromosome 2. The child was diagnosed as mitochondrial disease caused by oxidative phosphorylation coupling defect of type 44. Conclusions: In this study, an autosomal recessive mitochondrial disease which does not conform to the genetic law was found, and it was confirmed that this mitochondrial disease family had both pathogenic variation and uniparental disomy phenomenon. It was diagnosed as mitochondrial disease caused by type 44 oxidative phosphorylation coupling defect.

DOI: https://doi.org/10.3760/cma.j.cn.112137-20220808-01708
JACC Basic Transl Sci. 2022 Dec;7(12): 1183-1196

Safety and Tolerability of Nicotinamide Riboside in Heart Failure With Reduced Ejection Fraction.

Dennis D Wang, Sophia E Airhart, Bo Zhou, Laura M Shireman, Siyi Jiang, Carolina Melendez Rodriguez, James N Kirkpatrick, Danny D Shen, Rong Tian, Kevin D O'Brien.

  The mitochondrial dysfunction characteristic of heart failure (HF) is associated with changes in intracellular nicotinamide adenine dinucleotide (NAD+) and NADH levels. Raising NAD+ levels with the NAD+ precursor, nicotinamide riboside (NR), may represent a novel HF treatment. In this 30-participant trial of patients with clinically stable HF with reduced ejection fraction, NR, at a dose of 1,000 mg twice daily, appeared to be safe and well tolerated, and approximately doubled whole blood NAD+ levels. Intraindividual NAD+ increases in response to NR correlated with increases in peripheral blood mononuclear cell basal (R 2 = 0.413, P = 0.003) and maximal (R 2 = 0.434, P = 0.002) respiration, and with decreased NLRP3 expression (R 2 = 0.330, P = 0.020). (Nicotinamide Riboside in Systolic Heart Failure; NCT03423342).

Keywords:  AE, adverse event; E/e′, ratio of the early transmitral flow velocity to the early diastolic tissue velocity; GLS, global longitudinal strain; HF, heart failure; HFrEF; HFrEF, heart failure with reduced rejection fraction; IL, interleukin; LV, left ventricular; NAD+; NAD+, nicotinamide adenine dinucleotide; NLRP3, NOD-like receptor family pyrin domain containing 3; NR; NR, nicotinamide riboside; PBMC, peripheral blood mononuclear cell; TNF, tumor necrosis factor; heart failure with reduced ejection fraction; mitochondrial dysfunction; nicotinamide adenine dinucleotide; nicotinamide riboside; sterile inflammation

DOI:  https://doi.org/10.1016/j.jacbts.2022.06.012
Elife. 2023 Jan 16. pii: e82555. [Epub ahead of print]12

Exploring therapeutic strategies for infantile neuronal axonal dystrophy (INAD/PARK14).

Guang Lin, Burak Tepe, Geoff McGrane, Regine C Tipon, Gist Croft, Leena Panwala, Amanda Hope, Agnes J H Liang, Zhongyuan Zuo, Seul Kee Byeon, Lily Wang, Akhilesh Pandey, Hugo J Bellen.

  Infantile Neuroaxonal Dystrophy (INAD) is caused by recessive variants in PLA2G6 and is a lethal pediatric neurodegenerative disorder. Loss of the Drosophila homolog of PLA2G6, leads to ceramide accumulation, lysosome expansion, and mitochondrial defects. Here, we report that retromer function, ceramide metabolism, the endolysosomal pathway, and mitochondrial morphology are affected in INAD patient-derived neurons. We show that in INAD mouse models the same features are affected in Purkinje cells, arguing that the neuropathological mechanisms are evolutionary conserved and that these features can be used as biomarkers. We tested 20 drugs that target these pathways and found that Ambroxol, Desipramine, Azoramide, and Genistein alleviate neurodegenerative phenotypes in INAD flies and INAD patient-derived NPCs. We also develop an AAV-based gene therapy approach that delays neurodegeneration and prolongs lifespan in an INAD mouse model.

Keywords:  D. melanogaster; human; mouse; neuroscience

DOI:  https://doi.org/10.7554/eLife.82555
Aging Cell. 2023 Jan 15. e13770

Mitochondrial stress and mitokines in aging.

Johannes Burtscher, Afsaneh Soltany, Nishant P Visavadiya, Martin Burtscher, Grégoire P Millet, Kayvan Khoramipour, Andy V Khamoui.

  Mitokines are signaling molecules that enable communication of local mitochondrial stress to other mitochondria in distant cells and tissues. Among those molecules are FGF21, GDF15 (both expressed in the nucleus) and several mitochondrial-derived peptides, including humanin. Their responsiveness to mitochondrial stress induces mitokine-signaling in response for example to exercise, following mitochondrial challenges in skeletal muscle. Such signaling is emerging as an important mediator of exercise-derived and dietary strategy-related molecular and systemic health benefits, including healthy aging. A compensatory increase in mitokine synthesis and secretion could preserve mitochondrial function and overall cellular vitality. Conversely, resistance against mitokine actions may also develop. Alterations of mitokine-levels, and therefore of mitokine-related inter-tissue cross talk, are associated with general aging processes and could influence the development of age-related chronic metabolic, cardiovascular and neurological diseases; whether these changes contribute to aging or represent "rescue factors" remains to be conclusively shown. The aim of the present review is to summarize the expanding knowledge on mitokines, the potential to modulate them by lifestyle and their involvement in aging and age-related diseases. We highlight the importance of well-balanced mitokine-levels, the preventive and therapeutic properties of maintaining mitokine homeostasis and sensitivity of mitokine signaling but also the risks arising from the dysregulation of mitokines. While reduced mitokine levels may impair inter-organ crosstalk, also excessive mitokine concentrations can have deleterious consequences and are associated with conditions such as cancer and heart failure. Preservation of healthy mitokine signaling levels can be achieved by regular exercise and is associated with an increased lifespan.

Keywords:  FGF21; GDF15; humanin; mitochondria-derived peptides; mitochondrial stress response; mitohormesis; mitokines

DOI:  https://doi.org/10.1111/acel.13770
J Med Genet. 2023 Jan 20. pii: jmedgenet-2022-108618. [Epub ahead of print]

EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders.

Genomics England Research Consortium

   BACKGROUND: Genomic variant prioritisation is one of the most significant bottlenecks to mainstream genomic testing in healthcare. Tools to improve precision while ensuring high recall are critical to successful mainstream clinical genomic testing, in particular for whole genome sequencing where millions of variants must be considered for each patient.
METHODS: We developed EyeG2P, a publicly available database and web application using the Ensembl Variant Effect Predictor. EyeG2P is tailored for efficient variant prioritisation for individuals with inherited ophthalmic conditions. We assessed the sensitivity of EyeG2P in 1234 individuals with a broad range of eye conditions who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we assessed the precision of EyeG2P in comparison with routine diagnostic approaches. For 10 additional individuals, we assessed the utility of EyeG2P for whole genome analysis.
RESULTS: EyeG2P had 99.5% sensitivity for genomic variants previously identified as clinically relevant through routine diagnostic analysis (n=1234 individuals). Prospectively, EyeG2P enabled a significant increase in precision (35% on average) in comparison with routine testing strategies (p<0.001). We demonstrate that incorporation of EyeG2P into whole genome sequencing analysis strategies can reduce the number of variants for analysis to six variants, on average, while maintaining high diagnostic yield.
CONCLUSION: Automated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders.

Keywords:  Eye Diseases; Genetic Variation; Genomics

DOI:  https://doi.org/10.1136/jmg-2022-108618
Neurosci Res. 2023 Jan 16. pii: S0168-0102(23)00004-4. [Epub ahead of print]

NMN: The NAD Precursor at the Intersection Between Axon Degeneration and Anti-ageing Therapies.

Andrea Loreto, Christina Antoniou, Elisa Merlini, Jonathan Gilley, Michael P Coleman.

  The past 20 years of research on axon degeneration has revealed fine details on how NAD biology controls axonal survival. Extensive data demonstrate that the NAD precursor NMN binds to and activates the pro-degenerative enzyme SARM1, so a failure to convert sufficient NMN into NAD leads to toxic NMN accumulation and axon degeneration. This involvement of NMN brings the axon degeneration field to an unexpected overlap with research into ageing and extending healthy lifespan. A decline in NAD levels throughout life, at least in some tissues, is believed to contribute to age-related functional decay and boosting NAD production with supplementation of NMN or other NAD precursors has gained attention as a potential anti-ageing therapy. Recent years have witnessed an influx of NMN-based products and related molecules on the market, sold as food supplements, with many people taking these supplements daily. While several clinical trials are ongoing to check the safety profiles and efficacy of NAD precursors, sufficient data to back their therapeutic use are still lacking. Here, we discuss NMN supplementation, SARM1 and anti-ageing strategies, with an important question in mind: considering that NMN accumulation can lead to axon degeneration, how is this compatible with its beneficial effect in ageing and are there circumstances in which NMN lementation could become harmful?

Keywords:  Ageing; Axon degeneration; Lifespan; NAM, NAD, SARM1; NMN; NMNAT; NR; Programmed axon death

DOI:  https://doi.org/10.1016/j.neures.2023.01.004
Hear Res. 2023 Jan 05. pii: S0378-5955(23)00001-1. [Epub ahead of print]429 108689

Current development of patient-specific induced pluripotent stem cells harbouring mitochondrial gene mutations and their applications in the treatment of sensorineural hearing loss.

Chao-Wen Chou, Yi-Chao Hsu.

  Of all the human body's sensory systems, the auditory system is perhaps its most intricate. Hearing loss can result from even modest damage or cell death in the inner ear, and is the most common form of sensory loss. Human hearing is made possible by the sensory epithelium, the lateral wall, and auditory nerves. The most prominent functional cells in the sensory epithelium are outer hair cells (OHCs), inner hair cells (IHCs), and supporting cells. Different sound frequencies are processed by OHCs and IHCs in different cochlear regions, with those in the apex responsible for low frequencies and those in the basal region responsible for high frequencies. Hair cells can be damaged or destroyed by loud noise, aging process, genetic mutations, ototoxicity, infection, and illness. As such, they are a primary target for treating sensorineural hearing loss. Other areas known to affect hearing include spiral ganglion neurons (SGNs) in the auditory nerve. Age-related degradation of HCs and SGNs can also cause hearing loss. The aim of this review is to introduce the roles of mitochondria in human auditory system and the inner ear's main cell types and cellular functions, before going on to detail the likely health benefits of iPSC technology. We posit that patient-specific iPSCs with mitochondrial gene mutations will be an important aspect of regenerative medicine and will lead to significant progress in the treatment of SNHL.

Keywords:  Heteroplasmy; Induced pluripotent stem cells; Mitochondria; hearing loss; mitochondrial DNA

DOI:  https://doi.org/10.1016/j.heares.2023.108689
Gastroenterology. 2023 Jan 17. pii: S0016-5085(23)00044-6. [Epub ahead of print]

Circulating Mitochondrial DNA as a Diagnostic Biomarker for Predicting Disease Severity in Patients with Acute Pancreatitis.

BIDMC Acute Pancreatitis Working Group

DOI: https://doi.org/10.1053/j.gastro.2023.01.013
Eur J Med Genet. 2023 Jan 14. pii: S1769-7212(23)00004-6. [Epub ahead of print] 104698

Adult patient diagnosed with NADSYN1 associated congenital NAD deficiency and analysis of NAD levels to be published in: European Journal of Medical Genetics.

Emilie Erbs, Claus Lohman Brasen, Allan Meldgaard Lund, Maria Rasmussen.

   INTRODUCTION: Nicotinamide adenine dinucleotide (NAD) is an essential cosubstrate/coenzyme in multiple cellular redox processes and a substrate in several non-redox reactions. Since NADSYN1 encodes NAD synthetase 1, an enzyme in the NAD de novo synthesis pathway and the Preiss-Handler pathway biallelic pathogenic variants causes NAD deficiency. Szot et al. and Kortbawi et al. have reported a total of seven patients with NADSYN1 associated congenital NAD deficiency disorder with the oldest patient being seven years old.
PATIENT DATA: We present a male patient age 30 with a height of 130 cm and numerous skeletal malformations including segmentation defects of the spine, rib anomalies and unequal leg length as well as bilateral ptosis, cleft palate and asymmetric dysmorphic facial features. The patient underwent surgery for an aortic stenosis due to a bicuspid valve. No malformations of the kidneys or urinary tract were identified.
RESULTS: Trio exome sequencing revealed a homozygous missense variant in NADSYN1 c.1717G > A (p.Ala573Thr). Both parents were unaffected carriers of the variant. Analysis of NAD levels showed that the patient had a lower NAD pool compared to his unaffected siblings. The NAD pool rose approximately 25% after supplementation with nicotinamide, a NAD precursor for the salvage pathway.
CONCLUSION: The variant was previously reported in four patients and functional analyses by Szot et al. support the pathogenicity of the variant. We report an adult patient with NADSYN1 associated congenital NAD deficiency disorder and expand the phenotypic spectrum. We also present analysis of the NAD levels before and after supplementation with nicotinamide.

Keywords:  Congenital NAD deficiency Disorder; Congenital malformations; NAD; NADSYN1; VCRL

DOI:  https://doi.org/10.1016/j.ejmg.2023.104698
Nat Biotechnol. 2023 Jan;41(1): 4

UK launches whole-genome sequencing pilot for babies.

DOI: https://doi.org/10.1038/s41587-022-01644-0
Stem Cell Res. 2023 Jan 17. pii: S1873-5061(23)00016-8. [Epub ahead of print]67 103030

Generation of two mother-child pairs of iPSCs from maternally inherited Leigh syndrome patients with m.8993 T > G and m.9176 T > G MT-ATP6 mutations.

Marie-Thérèse Henke, Annika Zink, Sebastian Diecke, Alessandro Prigione, Markus Schuelke.

We generated two pairs of mother-child iPSCs lines for Maternally Inherited Leigh Syndrome (MILS) carrying the m.8993 T > G and m.9176 T > G mutations in the MT-ATP6 gene. We delivered reprogramming factors OCT4, SOX2, KLF4, and c-MYC via Sendai virus. All iPSCs lines had a normal karyotype, expressed pluripotency markers, and differentiated into the three germ layers. Both patient-iPSCs retained the same degrees of heteroplasmy as their source fibroblasts (>97.0 %). In maternal iPSCs, the heteroplasmy remained 0.0 % in the case of the m.8993 T > G mutation and dropped from 55.0 % to 1.0 % in the case of m.9176 T > G mutation.

DOI: https://doi.org/10.1016/j.scr.2023.103030
Methods Mol Biol. 2023 ;2625 89-102

Profiling the Mammalian Lipidome by Quantitative Shotgun Lipidomics.

Mads Møller Foged, Kenji Maeda, Mesut Bilgin.

  The emerging field of lipidomics presents the systems biology approach to identify and quantify the full lipid repertoire of cells, tissues, and organisms. The importance of the lipidome is demonstrated by a number of biological studies on dysregulation of lipid metabolism in human diseases such as cancer, diabetes, and neurodegenerative diseases. Exploring changes and regulations in the huge networks of lipids and their metabolic pathways requires a lipidomics methodology: advanced mass spectrometry that resolves the complexity of the lipidome. Here, we report a comprehensive protocol of quantitative shotgun lipidomics that enables identification and quantification of hundreds of molecular lipid species, covering a wide range of lipid classes, extracted from cultured mammalian cells.

Keywords:  Lipid extraction; Lipidome profiling; Lipidomics; Mammalian cells; Mass spectrometry; Quantification; Shotgun lipidomics; Systems biology

DOI:  https://doi.org/10.1007/978-1-0716-2966-6_8
Genome Res. 2023 Jan 19.

An efficient genotyper and star-allele caller for pharmacogenomics.

Ananth Hari, Qinghui Zhou, Nina Gonzaludo, John Harting, Stuart A Scott, Xiang Qin, Steve Scherer, S Cenk Sahinalp, Ibrahim Numanagić.

High-throughput sequencing provides sufficient means for determining genotypes of clinically important pharmacogenes that can be used to tailor medical decisions to individual patients. However, pharmacogene genotyping, also known as star-allele calling, is a challenging problem that requires accurate copy number calling, structural variation identification, variant calling, and phasing within each pharmacogene copy present in the sample. Here we introduce Aldy 4, a fast and efficient tool for genotyping pharmacogenes that uses combinatorial optimization for accurate star-allele calling across different sequencing technologies. Aldy 4 adds support for long reads and uses a novel phasing model and improved copy number and variant calling models. We compare Aldy 4 against the current state-of-the-art star-allele callers on a large and diverse set of samples and genes sequenced by various sequencing technologies, such as whole-genome and targeted Illumina sequencing, barcoded 10x Genomics, and Pacific Biosciences (PacBio) HiFi. We show that Aldy 4 is the most accurate star-allele caller with near-perfect accuracy in all evaluated contexts, and hope that Aldy remains an invaluable tool in the clinical toolbox even with the advent of long-read sequencing technologies.

DOI: https://doi.org/10.1101/gr.277075.122
Curr Issues Mol Biol. 2023 Jan 05. 45(1): 465-478

OPA1 Dominant Optic Atrophy: Diagnostic Approach in the Pediatric Population.

Natalia Arruti, Patricia Rodríguez-Solana, María Nieves-Moreno, Marta Guerrero-Carretero, Ángela Del Pozo, Victoria E F Montaño, Fernando Santos-Simarro, Emi Rikeros-Orozco, Luna Delgado-Mora, Elena Vallespín, Susana Noval.

  A clinical and genetic study was conducted with pediatric patients and their relatives with optic atrophy 1 (OPA1) mutations to establish whether there is a genotype-phenotype correlation among the variants detected within and between families. Eleven children with a confirmed OPA1 mutation were identified during the study period. The main initial complaint was reduced visual acuity (VA), present in eight patients of the cohort. Eight of eleven patients had a positive family history of optic atrophy. The mean visual acuity at the start of the study was 0.40 and 0.44 LogMAR in the right and left eye, respectively. At the end of the study, the mean visual acuity was unchanged. Optical coherence tomography during the first visit showed a mean retinal nerve fiber layer thickness of 81.6 microns and 80.5 microns in the right and left eye, respectively; a mean ganglion cell layer of 52.5 and 52.4 microns, respectively, and a mean central macular thickness of 229.5 and 233.5 microns, respectively. The most common visual field defect was a centrocecal scotoma, and nine out of eleven patients showed bilateral temporal disc pallor at baseline. Sequencing of OPA1 showed seven different mutations in the eleven patients, one of which, NM_130837.3: c.1406_1407del (p.Thr469LysfsTer16), has not been previously reported. Early diagnosis of dominant optic atrophy is crucial, both for avoiding unnecessary consultations and/or treatments and for appropriate genetic counseling.

Keywords:  Kjer type; OPA1; dominant optic atrophy; mitochondrial neuropathies

DOI:  https://doi.org/10.3390/cimb45010030
Nature. 2023 Jan;613(7944): 519-525

Mono- and biallelic variant effects on disease at biobank scale.

FinnGen

Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics1. Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance2,3. Here we examine the homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. We find associations for homozygous genotypes across a broad spectrum of phenotypes, including known associations with retinal dystrophy and novel associations with adult-onset cataract and female infertility. Of the recessive disease associations that we identify, 13 out of 20 would have been missed by the additive model that is typically used in genome-wide association studies. We use these results to find many known Mendelian variants whose inheritance cannot be adequately described by a conventional definition of dominant or recessive. In particular, we find variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects. Similarly, we find presumed benign variants with disease effects. Our results show how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease.

DOI: https://doi.org/10.1038/s41586-022-05420-7
Cell Syst. 2023 Jan 18. pii: S2405-4712(22)00494-X. [Epub ahead of print]14(1): 58-71.e5

Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset.

Ryan Conrad, Kedar Narayan.

  Mitochondria are extremely pleomorphic organelles. Automatically annotating each one accurately and precisely in any 2D or volume electron microscopy (EM) image is an unsolved computational challenge. Current deep learning-based approaches train models on images that provide limited cellular contexts, precluding generality. To address this, we amassed a highly heterogeneous ∼1.5 × 106 image 2D unlabeled cellular EM dataset and segmented ∼135,000 mitochondrial instances therein. MitoNet, a model trained on these resources, performs well on challenging benchmarks and on previously unseen volume EM datasets containing tens of thousands of mitochondria. We release a Python package and napari plugin, empanada, to rapidly run inference, visualize, and proofread instance segmentations. A record of this paper's transparent peer review process is included in the supplemental information.

Keywords:  benchmark; crowdsourcing; deep learning; electron microscopy; image dataset; mitochondria; panoptic; segmentation; volume EM; volume electron miscroscopy

DOI:  https://doi.org/10.1016/j.cels.2022.12.006
Extracell Vesicles Circ Nucl Acids. 2022 ;3(4): 340-362

Brain endothelium-derived extracellular vesicles containing amyloid-beta induce mitochondrial alterations in neural progenitor cells.

Olivia M Osborne, Jennifer M Kowalczyk, Kelssey D Pierre Louis, Manav T Daftari, Brett M Colbert, Oandy Naranjo, Silvia Torices, Ibolya E András, Derek M Dykxhoorn, Michal Toborek.

   Aim: Elevated brain deposits of amyloid beta (Aβ40) contribute to neuropathology and cognitive dysfunction in Alzheimer's disease (AD). However, the role of the blood-brain barrier (BBB) as an interface for the transfer of Aβ40 from the periphery into the brain is not well characterized. In addition, a substantial population of neural progenitor cells (NPCs) resides in close proximity to brain capillaries that form the BBB. The aim of this study is to understand the impact of brain endothelium-derived extracellular vesicles (EV) containing Aβ40 on metabolic functions and differentiation of NPCs.
Methods: Endothelial EVs were derived from an in vitro model of the brain endothelium treated with 100 nM Aβ40 or PBS. We then analyzed the impact of these EVs on mitochondrial morphology and bioenergetic disruption of NPCs. In addition, NPCs were differentiated and neurite development upon exposure to EVs was assessed using the IncuCyte Zoom live cell imaging system.
Results: We demonstrate that physiological concentrations of Aβ40 can be transferred to accumulate in NPCs via endothelial EVs. This transfer results in mitochondrial dysfunction, disrupting crista morphology, metabolic rates, fusion and fission dynamics of NPCs, as well as their neurite development.
Conclusion: Intercellular transfer of Aβ40 is carried out by brain endothelium-derived EVs, which can affect NPC differentiation and induce mitochondrial dysfunction, leading to aberrant neurogenesis. This has pathological implications because NPCs growing into neurons are incorporated into cerebral structures involved in learning and memory, two common phenotypes affected in AD and related dementias.

Keywords:  Alzheimer’s disease; Blood-brain barrier; Seahorse; extracellular vesicle; mitochondrial bioenergetics; neural progenitor cell; neurogenesis

DOI:  https://doi.org/10.20517/evcna.2022.22
Nat Biotechnol. 2023 Jan;41(1): 21

Linking genetic variants to cellular function and disease.

Alexandra Despang.

DOI: https://doi.org/10.1038/s41587-022-01647-x
Nature. 2023 Jan;613(7944): 508-518

FinnGen provides genetic insights from a well-phenotyped isolated population.

FinnGen

Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10-11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.

DOI: https://doi.org/10.1038/s41586-022-05473-8