bims-mitdis 2022-01-30 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2022–01–30
thirty-two papers selected by
Catalina Vasilescu, University of Helsinki

Recent Advances in Modeling Mitochondrial Cardiomyopathy Using Human Induced Pluripotent Stem Cells.
Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria.
Into the matrix: current methods for mitochondrial translation studies.
Coordinated Translocation of Presequence-Containing Precursor Proteins Across Two Mitochondrial Membranes: Knowns and Unknowns of How TOM and TIM23 Complexes Cooperate With Each Other.
Cytosolic adaptation to mitochondria-induced proteostatic stress causes progressive muscle wasting.
Mitochondrial DNA variation across 56,434 individuals in gnomAD.
Dual role of Mic10 in mitochondrial cristae organization and ATP synthase-linked metabolic adaptation and respiratory growth.
Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review.
Targeted mitochondrial delivery: A therapeutic new era for disease treatment.
Severe metabolic acidosis with cardiac involvement in DNM1L-related mitochondrial encephalopathy.
Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) is a novel complex III specific assembly factor in mitochondria.
A relatively common hypomorphic variant in WARS2 causes monogenic disease.
Mitochondria and Viral Infection: Advances and Emerging Battlefronts.
Thymidine Kinase 2 and Mitochondrial Protein COX I in the Cerebellum of Patients with Spinocerebellar Ataxia Type 31 Caused by Penta-nucleotide Repeats (TTCCA)n.
Medium branched chain fatty acids improve the profile of tricarboxylic acid cycle intermediates in mitochondrial fatty acid β-oxidation deficient cells: A comparative study.
Mitochondrial genome-wide analysis of nuclear DNA methylation quantitative trait loci.
Elevated glutamate and decreased glutamine levels in the cerebrospinal fluid of patients with MELAS syndrome.
Mitochondria, energy, and metabolism in neuronal health and disease.
Lipid droplet-mitochondria coupling via Perilipin 5 augments respiratory capacity but is dispensable for FA oxidation.
Multi-omics analyses reveal early metabolic imbalance and mitochondrial stress in neonatal photoreceptors leading to cell death in Pde6brd1/rd1 mouse model of retinal degeneration.
Metabolic Disease, NAD Metabolism, Nicotinamide Riboside, and the Gut Microbiome: Connecting the Dots from the Gut to Physiology.
Epigenetics of Mitochondria-Associated Genes in Striated Muscle.
Targeting the Mitochondrial Permeability Transition Pore for Drug Discovery: Challenges and Opportunities.
Case Report: Whole Exome Sequencing Identifies Compound Heterozygous Variants in TSFM Gene Causing Juvenile Hypertrophic Cardiomyopathy.
Metabolic signatures of regulation by phosphorylation and acetylation.
Metabolism in Human Pluripotent Stem Cells and Cardiomyocytes for Regenerative Therapy.
Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice.
iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling.
GA4GH: International policies and standards for data sharing across genomic research and healthcare.
A genome-wide association study of serum proteins reveals shared loci with common diseases.
Coding and regulatory variants are associated with serum protein levels and disease.
LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis.

Front Cell Dev Biol. 2021 ;9 800529

Recent Advances in Modeling Mitochondrial Cardiomyopathy Using Human Induced Pluripotent Stem Cells.

Mario G Pavez-Giani, Lukas Cyganek.

  Around one third of patients with mitochondrial disorders develop a kind of cardiomyopathy. In these cases, severity is quite variable ranging from asymptomatic status to severe manifestations including heart failure, arrhythmias, and sudden cardiac death. ATP is primarily generated in the mitochondrial respiratory chain via oxidative phosphorylation by utilizing fatty acids and carbohydrates. Genes in both the nuclear and the mitochondrial DNA encode components of this metabolic route and, although mutations in these genes are extremely rare, the risk to develop cardiac symptoms is significantly higher in this patient cohort. Additionally, infants with cardiovascular compromise in mitochondrial deficiency display a worse late survival compared to patients without cardiac symptoms. At this point, the mechanisms behind cardiac disease progression related to mitochondrial gene mutations are poorly understood and current therapies are unable to substantially restore the cardiac performance and to reduce the disease burden. Therefore, new strategies are needed to uncover the pathophysiological mechanisms and to identify new therapeutic options for mitochondrial cardiomyopathies. Here, human induced pluripotent stem cell (iPSC) technology has emerged to provide a suitable patient-specific model system by recapitulating major characteristics of the disease in vitro, as well as to offer a powerful platform for pre-clinical drug development and for the testing of novel therapeutic options. In the present review, we summarize recent advances in iPSC-based disease modeling of mitochondrial cardiomyopathies and explore the patho-mechanistic insights as well as new therapeutic approaches that were uncovered with this experimental platform. Further, we discuss the challenges and limitations of this technology and provide an overview of the latest techniques to promote metabolic and functional maturation of iPSC-derived cardiomyocytes that might be necessary for modeling of mitochondrial disorders.

Keywords:  heteroplasmy; iPSC-derived cardiomyocytes; induced pluripotent stem cells (hiPSCs); mitochondrial cardiomyopathy; mitochondrial disease; mtDNA

DOI:  https://doi.org/10.3389/fcell.2021.800529
J Vis Exp. 2022 Jan 07.

Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria.

Ashley N Oliveira, Brandon J Richards, David A Hood.

Mitochondria are key metabolic and regulatory organelles that determine the energy supply as well as the overall health of the cell. In skeletal muscle, mitochondria exist in a series of complex morphologies, ranging from small oval organelles to a broad, reticulum-like network. Understanding how the mitochondrial reticulum expands and develops in response to diverse stimuli such as alterations in energy demand has long been a topic of research. A key aspect of this growth, or biogenesis, is the import of precursor proteins, originally encoded by the nuclear genome, synthesized in the cytosol, and translocated into various mitochondrial sub-compartments. Mitochondria have developed a sophisticated mechanism for this import process, involving many selective inner and outer membrane channels, known as the protein import machinery (PIM). Import into the mitochondrion is dependent on viable membrane potential and the availability of organelle-derived ATP through oxidative phosphorylation. Therefore its measurement can serve as a measure of organelle health. The PIM also exhibits a high level of adaptive plasticity in skeletal muscle that is tightly coupled to the energy status of the cell. For example, exercise training has been shown to increase import capacity, while muscle disuse reduces it, coincident with changes in markers of mitochondrial content. Although protein import is a critical step in the biogenesis and expansion of mitochondria, the process is not widely studied in skeletal muscle. Thus, this paper outlines how to use isolated and fully functional mitochondria from skeletal muscle to measure protein import capacity in order to promote a greater understanding of the methods involved and an appreciation of the importance of the pathway for organelle turnover in exercise, health, and disease.

DOI: https://doi.org/10.3791/63055
J Biochem. 2022 Jan 26. pii: mvac005. [Epub ahead of print]

Into the matrix: current methods for mitochondrial translation studies.

Antonios Apostolopoulos, Shintaro Iwasaki.

  In addition to the cytoplasmic translation system, eukaryotic cells house additional protein synthesis machinery in mitochondria. The importance of this in organello translation is exemplified by clinical pathologies associated with mutations in mitochondrial translation factors. Although a detailed understanding of mitochondrial translation has long been awaited, quantitative, comprehensive, and spatiotemporal measurements have posed analytic challenges. The recent development of novel approaches for studying mitochondrial protein synthesis has overcome these issues and expands our understanding of the unique translation system. Here, we review the current technologies for the investigation of mitochondrial translation and the insights provided by their application.

Keywords:  FUNCAT; Mitochondria; Mitoribosome; Ribosome profiling; Translation

DOI:  https://doi.org/10.1093/jb/mvac005
Front Physiol. 2021 ;12 806426

Coordinated Translocation of Presequence-Containing Precursor Proteins Across Two Mitochondrial Membranes: Knowns and Unknowns of How TOM and TIM23 Complexes Cooperate With Each Other.

Marcel G Genge, Dejana Mokranjac.

  The vast majority of mitochondrial proteins are encoded in the nuclear genome and synthesized on cytosolic ribosomes as precursor proteins with specific mitochondrial targeting signals. Mitochondrial targeting signals are very diverse, however, about 70% of mitochondrial proteins carry cleavable, N-terminal extensions called presequences. These amphipathic helices with one positively charged and one hydrophobic surface target proteins to the mitochondrial matrix with the help of the TOM and TIM23 complexes in the outer and inner membranes, respectively. Translocation of proteins across the two mitochondrial membranes does not take place independently of each other. Rather, in the intermembrane space, where the two complexes meet, components of the TOM and TIM23 complexes form an intricate network of protein-protein interactions that mediates initially transfer of presequences and then of the entire precursor proteins from the outer to the inner mitochondrial membrane. In this Mini Review, we summarize our current understanding of how the TOM and TIM23 complexes cooperate with each other and highlight some of the future challenges and unresolved questions in the field.

Keywords:  TIM23 complex; TOM complex; TOM-TIM23 contacts; intermembrane space; mitochondria; precursor transfer; presequence pathway; protein translocation

DOI:  https://doi.org/10.3389/fphys.2021.806426
iScience. 2022 Jan 21. 25(1): 103715

Cytosolic adaptation to mitochondria-induced proteostatic stress causes progressive muscle wasting.

Xiaowen Wang, Frank A Middleton, Rabi Tawil, Xin Jie Chen.

  Mitochondrial dysfunction causes muscle wasting in many diseases and probably also during aging. The underlying mechanism is poorly understood. We generated transgenic mice with unbalanced mitochondrial protein loading and import, by moderately overexpressing the nuclear-encoded adenine nucleotide translocase, Ant1. We found that these mice progressively lose skeletal muscle. Ant1-overloading reduces mitochondrial respiration. Interestingly, it also induces small heat shock proteins and aggresome-like structures in the cytosol, suggesting increased proteostatic burden due to accumulation of unimported mitochondrial preproteins. The transcriptome of Ant1-transgenic muscles is drastically remodeled to counteract proteostatic stress, by repressing protein synthesis and promoting proteasomal function, autophagy, and lysosomal amplification. These proteostatic adaptations collectively reduce protein content thereby reducing myofiber size and muscle mass. Thus, muscle wasting can occur as a trade-off of adaptation to mitochondria-induced proteostatic stress. This finding could have implications for understanding the mechanism of muscle wasting, especially in diseases associated with Ant1 overexpression, including facioscapulohumeral dystrophy.

Keywords:  Biological sciences; Cell biology; Cellular physiology; Functional aspects of cell biology

DOI:  https://doi.org/10.1016/j.isci.2021.103715
Genome Res. 2022 Jan 24. pii: gr.276013.121. [Epub ahead of print]

Mitochondrial DNA variation across 56,434 individuals in gnomAD.

Genome Aggregation Database Consortium

Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three technical challenges: (i) detecting homoplasmic and heteroplasmic variants, present respectively in all or a fraction of mtDNA molecules, (ii) circular mtDNA genome, and (iii) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded contaminated samples, cell lines, and samples prone to NUMT misalignment due to few mtDNA copies. Furthermore, we report variants with heteroplasmy greater than 10%. We applied this pipeline to 56,434 whole genome sequences in the gnomAD v3.1 database that includes individuals of European (58%), African (25%), Latino (10%), and Asian (5%) ancestry. Our gnomAD v3.1 release contains population frequencies for 10,850 unique mtDNA variants at more than half of all mtDNA bases. We report frequencies within each nuclear ancestral population and mitochondrial haplogroup. Homoplasmic variants account for most variant calls (98%) and unique variants (85%). We observed that 1/250 individuals carry a pathogenic mtDNA variant with heteroplasmy above 10%. These mtDNA population allele frequencies are freely accessible and will aid in diagnostic interpretation and research studies.

DOI: https://doi.org/10.1101/gr.276013.121
Cell Rep. 2022 Jan 25. pii: S2211-1247(21)01805-2. [Epub ahead of print]38(4): 110290

Dual role of Mic10 in mitochondrial cristae organization and ATP synthase-linked metabolic adaptation and respiratory growth.

Heike Rampelt, Florian Wollweber, Mariya Licheva, Rinse de Boer, Inge Perschil, Liesa Steidle, Thomas Becker, Maria Bohnert, Ida van der Klei, Claudine Kraft, Martin van der Laan, Nikolaus Pfanner.

  Invaginations of the mitochondrial inner membrane, termed cristae, are hubs for oxidative phosphorylation. The mitochondrial contact site and cristae organizing system (MICOS) and the dimeric F1Fo-ATP synthase play important roles in controlling cristae architecture. A fraction of the MICOS core subunit Mic10 is found in association with the ATP synthase, yet it is unknown whether this interaction is of relevance for mitochondrial or cellular functions. Here, we established conditions to selectively study the role of Mic10 at the ATP synthase. Mic10 variants impaired in MICOS functions stimulate ATP synthase oligomerization like wild-type Mic10 and promote efficient inner membrane energization, adaptation to non-fermentable carbon sources, and respiratory growth. Mic10's functions in respiratory growth largely depend on Mic10ATPsynthase, not on Mic10MICOS. We conclude that Mic10 plays a dual role as core subunit of MICOS and as partner of the F1Fo-ATP synthase, serving distinct functions in cristae shaping and respiratory adaptation and growth.

Keywords:  ATP synthase; MICOS; Mic10; cristae organization; inner membrane; membrane architecture; membrane potential; metabolic adaptation; mitochondria; respiration

DOI:  https://doi.org/10.1016/j.celrep.2021.110290
EBioMedicine. 2022 Jan 24. pii: S2352-3964(22)00004-4. [Epub ahead of print]76 103815

Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review.

Alba Valiente-Pallejà, Juan Tortajada, Bengisu K Bulduk, Elisabet Vilella, Glòria Garrabou, Gerard Muntané, Lourdes Martorell.

   BACKGROUND: Mitochondrial DNA (mtDNA) encodes 37 genes necessary for synthesizing 13 essential subunits of the oxidative phosphorylation system. mtDNA alterations are known to cause mitochondrial disease (MitD), a clinically heterogeneous group of disorders that often present with neuropsychiatric symptoms. Understanding the nature and frequency of mtDNA alterations in health and disease could be a cornerstone in disentangling the relationship between biochemical findings and clinical symptoms of brain disorders. This systematic review aimed to summarize the mtDNA alterations in human brain tissue reported to date that have implications for further research on the pathophysiological significance of mtDNA alterations in brain functioning.
METHODS: We searched the PubMed and Embase databases using distinct terms related to postmortem human brain and mtDNA up to June 10, 2021. Reports were eligible if they were empirical studies analysing mtDNA in postmortem human brains.
FINDINGS: A total of 158 of 637 studies fulfilled the inclusion criteria and were clustered into the following groups: MitD (48 entries), neurological diseases (NeuD, 55 entries), psychiatric diseases (PsyD, 15 entries), a miscellaneous group with controls and other clinical diseases (5 entries), ageing (20 entries), and technical issues (5 entries). Ten entries were ascribed to more than one group. Pathogenic single nucleotide variants (pSNVs), both homo- or heteroplasmic variants, have been widely reported in MitD, with heteroplasmy levels varying among brain regions; however, pSNVs are rarer in NeuD, PsyD and ageing. A lower mtDNA copy number (CN) in disease was described in most, but not all, of the identified studies. mtDNA deletions were identified in individuals in the four clinical categories and ageing. Notably, brain samples showed significantly more mtDNA deletions and at higher heteroplasmy percentages than blood samples, and several of the deletions present in the brain were not detected in the blood. Finally, mtDNA heteroplasmy, mtDNA CN and the deletion levels varied depending on the brain region studied.
INTERPRETATION: mtDNA alterations are well known to affect human tissues, including the brain. In general, we found that studies of MitD, NeuD, PsyD, and ageing were highly variable in terms of the type of disease or ageing process investigated, number of screened individuals, studied brain regions and technology used. In NeuD and PsyD, no particular type of mtDNA alteration could be unequivocally assigned to any specific disease or diagnostic group. However, the presence of mtDNA deletions and mtDNA CN variation imply a role for mtDNA in NeuD and PsyD. Heteroplasmy levels and threshold effects, affected brain regions, and mitotic segregation patterns of mtDNA alterations may be involved in the complex inheritance of NeuD and PsyD and in the ageing process. Therefore, more information is needed regarding the type of mtDNA alteration, the affected brain regions, the heteroplasmy levels, and their relationship with clinical phenotypes and the ageing process.
FUNDING: Hospital Universitari Institut Pere Mata; Institut d'Investigació Sanitària Pere Virgili; Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación (PI18/00514).

Keywords:  Ageing; Mitochondrial DNA; Mitochondrial diseases; Neurological diseases; Postmortem; Psychiatric diseases

DOI:  https://doi.org/10.1016/j.ebiom.2022.103815
J Control Release. 2022 Jan 22. pii: S0168-3659(22)00039-6. [Epub ahead of print]

Targeted mitochondrial delivery: A therapeutic new era for disease treatment.

Ting Huang, Tianyuan Zhang, Jianqing Gao.

  As the major energy supplier in cells, mitochondria play a significant role in regulating cellular processes. The pathogenesis of various diseases is found to be associated with dysfunctional mitochondria, and supplement of functional mitochondria has been regarded as a potential therapeutic strategy. To achieve mitochondrial replenishment, transplantation of isolated mitochondria or utilization of cells as selective mitochondrial carrier have been developed. On the one hand, isolated mitochondria can be internalized into injured cells to restore impaired functions. On the other hand, the natural process of intercellular mitochondrial transfer can replace the dysfunctional mitochondria with functional mitochondria, providing a safe and effective way to rescue damaged tissues. Cell mediated mitochondrial transfer can serve as a promising targeted therapy with mitochondria being high-efficient biotherapeutics. In this review, we summarize the updated findings of mitochondrial delivery strategies, offering an overview of the role of mitochondria, mechanisms of intercellular mitochondrial transfer, therapeutic benefits, challenges and prospects of mitochondrial delivery. The understanding of mitochondrial delivery helps to improve the therapeutic outcomes of mitochondrial dysfunctional diseases in the future.

Keywords:  Delivery; Mitochondria; Regenerative potential; Stem cells; Transplantation

DOI:  https://doi.org/10.1016/j.jconrel.2022.01.025
Pediatr Int. 2022 Jan;64(1): e14879

Severe metabolic acidosis with cardiac involvement in DNM1L-related mitochondrial encephalopathy.

Yuya Kinoshita, Ken Momosaki, Shirou Matsumoto, Kei Murayama, Kimitoshi Nakamura.



Keywords:  DNM1L; metabolic acidosis; mitochondrial encephalopathy

DOI:  https://doi.org/10.1111/ped.14879
Mol Biol Cell. 2022 Jan 26. mbcE21030143

Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) is a novel complex III specific assembly factor in mitochondria.

Katarzyna Justyna Chojnacka, Praveenraj Elancheliyan, Ben Hur Marins Mussulini, Karthik Mohanraj, Sylvie Callegari, Aleksandra Gosk, Tomasz Banach, Tomasz Góral, Karolina Szczepanowska, Peter Rehling, Remigiusz Adam Serwa, Agnieszka Chacińska.

Assembly of the dimeric complex III (CIII2) in the mitochondrial inner membrane is an intricate process, in which several accessory proteins are involved as assembly factors. Despite numerous studies, this process is yet to be fully understood. Here we report the identification of human OCIAD2 (Ovarian Carcinoma Immunoreactive Antigen domain containing protein 2) protein as an assembly factor for CIII2. OCIAD2 was found deregulated in several carcinomas and also in some neurogenerative disorders, however its non-pathological role had not been elucidated. We have shown that OCIAD2 localizes to mitochondria and interacts with electron transport chain (ETC) proteins. Complete loss of OCIAD2 using gene editing in HEK293 cells resulted in abnormal mitochondrial morphology, a substantial decrease of both CIII2 and supercomplex III2+IV, and reduction in CIII enzymatic activity. Identification of OCIAD2 as a protein required for assembly of functional CIII2 provides a new insight into the biogenesis and architecture of the ETC. Elucidating the mechanism of OCIAD2 action is important both for the understanding of cellular metabolism and for an understanding of its role in malignant transformation.

DOI: https://doi.org/10.1091/mbc.E21-03-0143
Parkinsonism Relat Disord. 2022 Jan 19. pii: S1353-8020(22)00020-7. [Epub ahead of print]

A relatively common hypomorphic variant in WARS2 causes monogenic disease.

Andreea Ilinca, Efthymia Kafantari, Andreas Puschmann.



Keywords:  Common variants; Dystonia; Early-onset Parkinson disease; Hypomorphic variants; Mendelian disease; Mitochondrial disease; Myoclonus; Rare variants; WARS2 c.833T>G; WARS2 c.938A>T; WARS2 p.(Lys313Met); WARS2 p.(Val278Gly)

DOI:  https://doi.org/10.1016/j.parkreldis.2022.01.012
mBio. 2022 Jan 25. e0209621

Mitochondria and Viral Infection: Advances and Emerging Battlefronts.

Mahsa Sorouri, Tyron Chang, Dustin C Hancks.

  Mitochondria are dynamic organelles vital for energy production with now appreciated roles in immune defense. During microbial infection, mitochondria serve as signaling hubs to induce immune responses to counteract invading pathogens like viruses. Mitochondrial functions are central to a variety of antiviral responses including apoptosis and type I interferon signaling (IFN-I). While apoptosis and IFN-I mediated by mitochondrial antiviral signaling (MAVS) are well-established defenses, new dimensions of mitochondrial biology are emerging as battlefronts during viral infection. Increasingly, it has become apparent that mitochondria serve as reservoirs for distinct cues that trigger immune responses and that alterations in mitochondrial morphology may also tip infection outcomes. Furthermore, new data are foreshadowing pivotal roles for classic, homeostatic facets of this organelle as host-virus interfaces, namely, the tricarboxylic acid (TCA) cycle and electron transport chain (ETC) complexes like respiratory supercomplexes. Underscoring the importance of "housekeeping" mitochondrial activities in viral infection is the growing list of viral-encoded inhibitors including mimics derived from cellular genes that antagonize these functions. For example, virologs for ETC factors and several enzymes from the TCA cycle have been recently identified in DNA virus genomes and serve to pinpoint new vulnerabilities during infection. Here, we highlight recent advances for known antiviral functions associated with mitochondria as well as where the next battlegrounds may be based on viral effectors. Collectively, new methodology and mechanistic insights over the coming years will strengthen our understanding of how an ancient molecular truce continues to defend cells against viruses.

Keywords:  C15orf48; DAMP; MAVS; MISTR; NDUFA4; OXPHOS; TCA cycle; apoptosis; interferon; micropeptides; mimics; mitochondria; mitochondrial dynamics; mtDNA; mtROS; mtdsRNA; pyroptosis; supercomplexes; virologs; virus

DOI:  https://doi.org/10.1128/mbio.02096-21
Cerebellum. 2022 Jan 27.

Thymidine Kinase 2 and Mitochondrial Protein COX I in the Cerebellum of Patients with Spinocerebellar Ataxia Type 31 Caused by Penta-nucleotide Repeats (TTCCA)n.

Hanako Aoki, Miwa Higashi, Michi Okita, Noboru Ando, Shigeo Murayama, Kinya Ishikawa, Takanori Yokota.

  Spinocerebellar ataxia type 31 (SCA31), an autosomal-dominant neurodegenerative disorder characterized by progressive cerebellar ataxia with Purkinje cell degeneration, is caused by a heterozygous 2.5-3.8 kilobase penta-nucleotide repeat of (TTCCA)n in intron 11 of the thymidine kinase 2 (TK2) gene. TK2 is an essential mitochondrial pyrimidine-deoxyribonucleoside kinase. Bi-allelic loss-of-function mutations of TK2 lead to mitochondrial DNA depletion syndrome (MDS) in humans through severe (~ 70%) reduction of mitochondrial electron-transport-chain activity, and tk2 knockout mice show Purkinje cell degeneration and ataxia through severe mitochondrial cytochrome-c oxidase subunit I (COX I) protein reduction. To clarify whether TK2 function is altered in SCA31, we investigated TK2 and COX I expression in human postmortem SCA31 cerebellum. We confirmed that canonical TK2 mRNA is transcribed from exons far upstream of the repeat site, and demonstrated that an extended version of TK2 mRNA ("TK2-EXT"), transcribed from exons spanning the repeat site, is expressed in human cerebellum. While canonical TK2 was conserved among vertebrates, TK2-EXT was specific to primates. Reverse transcription-PCR demonstrated that both TK2 mRNAs were preserved in SCA31 cerebella compared with control cerebella. The TK2 proteins, assessed with three different antibodies including our original polyclonal antibody against TK2-EXT, were detected as ~ 26 kilodalton proteins on western blot; their levels were similar in SCA31 and control cerebella. COX I protein level was preserved in SCA31 compared to nuclear DNA-encoded protein. We conclude that the expression and function of TK2 are preserved in SCA31, suggesting a mechanism distinct from that of MDS.

Keywords:  Cytochrome-c oxidase (COX); Mitochondria; Mitochondrial DNA depletion syndrome (MDS); Purkinje cell; Spinocerebellar ataxia type 31 (SCA31); Thymidine kinase 2 (TK2)

DOI:  https://doi.org/10.1007/s12311-021-01364-2
J Inherit Metab Dis. 2022 Jan 25.

Medium branched chain fatty acids improve the profile of tricarboxylic acid cycle intermediates in mitochondrial fatty acid β-oxidation deficient cells: A comparative study.

Anuradha Karunanidhi, Clinton Van't Land, Dhivyaa Rajasundaram, Mateus Grings, Jerry Vockley, Al-Walid Mohsen.

  Inherited errors of mitochondrial fatty acid β-oxidation (FAO) are life threatening, even with optimum care. FAO is the major source of energy for heart and is critical for skeletal muscles especially during physiologic stress. Clinical trials revealed that triheptanoin (commercially known as DojolviTM ; C7G), improved heart function and decreased hypoglycemia in long chain FAO disorders, but other symptoms including rhabdomyolysis persisted, suggesting suboptimal tissue distribution/utilization of heptanoic acid (C7) conjugates and/or rapid liver breakdown. In this study medium branched chain fatty acids were tested as potential anaplerotic treatments in fibroblasts from patients deficient in very long chain acyl-CoA dehydrogenase (VLCAD), long chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD), trifunctional protein (TFP), and carnitine palmitoyltransferase II (CPT II). Cells were cultured to near confluency and treated with C7, 2,6-dimethylheptanoic acid (dMC7), 6-amino-2,4-dimethylheptanoic acid (AdMC7), or 4,8-dimethylnonanoic acid (dMC9) for 72 hours and targeted metabolomics performed. The profile of TCA cycle intermediates was improved in cells treated with these branched chain fatty acids compared to C7. Intracellular propionate was higher in AdMC7 treated cells compared to C7 in VLCAD, LCHAD, and TFP deficient cell lines. With AdMC7 treatment, succinate was higher in CPT II and VLCAD deficient cells, compared to C7. Malate and glutamate were consistently higher in AdMC7 treated VLCAD, LCHAD, TFP, and CPT II deficient cells compared to the C7 treatment. The results provide the impetus to further evaluate and consider branched chain fatty acids as viable anaplerotic therapy for fatty acid oxidation disorders and other diseases. This article is protected by copyright. All rights reserved.

Keywords:  CPT II deficiency; DojolviTM; LC-FAOD; LCHAD deficiency; MCT oil; TFP deficiency; VLCAD deficiency; long chain fatty acid oxidation disorders; medium branched chain fatty acids; triheptanoin

DOI:  https://doi.org/10.1002/jimd.12480
Hum Mol Genet. 2021 Nov 19. pii: ddab339. [Epub ahead of print]

Mitochondrial genome-wide analysis of nuclear DNA methylation quantitative trait loci.

Jaakko Laaksonen, Pashupati P Mishra, Ilkka Seppälä, Emma Raitoharju, Saara Marttila, Nina Mononen, Leo-Pekka Lyytikäinen, Marcus E Kleber, Graciela E Delgado, Maija Lepistö, Henrikki Almusa, Pekka Ellonen, Stefan Lorkowski, Winfried März, Nina Hutri-Kähönen, Olli Raitakari, Mika Kähönen, Jukka T Salonen, Terho Lehtimäki.

Mitochondria have a complex communication network with the surrounding cell and can alter nuclear DNA methylation (DNAm). Variation in the mitochondrial DNA (mtDNA) has also been linked to differential DNAm. Genome-wide association studies have identified numerous DNAm quantitative trait loci, but these studies have not examined the mitochondrial genome. Herein, we quantified nuclear DNAm from blood and conducted a mitochondrial genome-wide association study of DNAm, with an additional emphasis on sex- and prediabetes-specific heterogeneity. We used the Young Finns Study (n = 926) with sequenced mtDNA genotypes as a discovery sample and sought replication in the Ludwigshafen Risk and Cardiovascular Health study (n = 2317). We identified numerous significant associations in the discovery phase (P < 10-9), but they were not replicated when accounting for multiple testing. In total, 27 associations were nominally replicated with a P < 0.05. The replication analysis presented no evidence of sex- or prediabetes-specific heterogeneity. The 27 associations were included in a joint meta-analysis of the two cohorts, and 19 DNAm sites associated with mtDNA variants, while four other sites showed haplogroup associations. An expression quantitative trait methylation analysis was performed for the identified DNAm sites, pinpointing two statistically significant associations. This study provides evidence of a mitochondrial genetic control of nuclear DNAm with little evidence found for sex- and prediabetes-specific effects. The lack of a comparable mtDNA data set for replication is a limitation in our study and further studies are needed to validate our results.

DOI: https://doi.org/10.1093/hmg/ddab339
J Neurol. 2022 Jan 28.

Elevated glutamate and decreased glutamine levels in the cerebrospinal fluid of patients with MELAS syndrome.

María Paz Guerrero-Molina, Montserrat Morales-Conejo, Aitor Delmiro, María Morán, Cristina Domínguez-González, Elena Arranz-Canales, Ana Ramos-González, Joaquín Arenas, Miguel A Martín, Jesús González de la Aleja.

   BACKGROUND: Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome is a genetically heterogeneous disorder caused by mitochondrial DNA (mtDNA) mutations in the MT-TL1 gene. The pathophysiology of neurological manifestations is still unclear, but neuronal hyperexcitability and neuron-astrocyte uncoupling have been suggested. Glutamatergic neurotransmission is linked to glucose oxidation and mitochondrial metabolism in astrocytes and neurons. Given the relevance of neuron-astrocyte metabolic coupling and astrocyte function regulating energetic metabolism, we aimed to assess glutamate and glutamine CSF levels in MELAS patients.
METHODS: This prospective observational case-control study determined glutamate and glutamine CSF levels in patients with MELAS syndrome and compared them with controls. The plasma and CSF levels of the remaining amino acids and lactate were also determined.
RESULTS: Nine adult patients with MELAS syndrome (66.7% females mean age 35.8 ± 3.2 years) and 19 controls (63.2% females mean age 42.7 ± 3.8 years) were included. The CSF glutamate levels were significantly higher in patients with MELAS than in controls (18.48 ± 1.34 vs. 5.31 ± 1.09 μmol/L, p < 0.001). Significantly lower glutamine concentrations in patients with MELAS than controls were shown in CSF (336.31 ± 12.92 vs. 407.06 ± 15.74 μmol/L, p = 0.017). Moreover, the CSF levels of alanine, the branched-chain amino acids (BCAAs) and lactate were significantly higher in patients with MELAS.
CONCLUSIONS: Our results suggest the glutamate-glutamine cycle is altered probably due to metabolic imbalance, and as a result, the lactate-alanine and BCAA-glutamate cycles are upregulated. These findings might have therapeutic implications in MELAS syndrome.

Keywords:  Branched-chain amino acids; Glutamate; Glutamine; MELAS; Mitochondrial disease

DOI:  https://doi.org/10.1007/s00415-021-10942-7
FEBS Lett. 2022 Jan 28.

Mitochondria, energy, and metabolism in neuronal health and disease.

Diogo Trigo, Catarina Avelar, Miguel Fernandes, Juliana Sá, Odete da Cruz E Silva.

  Mitochondria are associated with various cellular activities critical to homeostasis, particularly in the nervous system. The plastic architecture of the mitochondrial network and its dynamic structure play crucial roles in ensuring that varying energetic demands are rapidly met to maintain neuronal and axonal energy homeostasis. Recent evidence associates ageing and neurodegeneration with anomalous neuronal metabolism, as age-dependent alterations of neuronal metabolism are now believed to occur prior to neurodegeneration. The brain has a high energy demand, which makes it particularly sensitive to mitochondrial dysfunction. Distinct cellular events causing oxidative stress or disruption of metabolism and mitochondrial homeostasis can trigger a neuropathology. This review explores the bioenergetic hypothesis for the neurodegenerative pathomechanisms, discussing factors leading to age-related brain hypometabolism and its contribution to cognitive decline. Recent research on the mitochondrial network in healthy nervous system cells, its response to stress and how it is affected by pathology, as well as current contributions to novel therapeutic approaches will be highlighted.

Keywords:  Alzheimer; Huntington; Parkinson; ROS; ageing; axon; mitochondria; mitophagy; neurodegeneration; neuron

DOI:  https://doi.org/10.1002/1873-3468.14298
J Lipid Res. 2022 Jan 20. pii: S0022-2275(22)00005-0. [Epub ahead of print] 100172

Lipid droplet-mitochondria coupling via Perilipin 5 augments respiratory capacity but is dispensable for FA oxidation.

Benedikt Kien, Stephanie Kolleritsch, Natalia Kunowska, Christoph Heier, Gabriel Chalhoub, Anna Tilp, Heimo Wolinski, Ulrich Stelzl, Guenter Haemmerle.

  Disturbances in lipid homeostasis can cause mitochondrial dysfunction and lipotoxicity. Perilipin 5 (PLIN5) decorates intracellular lipid droplets (LD) in oxidative tissues and controls triacylglycerol (TG) turnover via its interactions with Adipose triglyceride lipase (ATGL) and the ATGL co-activator Comparative gene identification-58 (CGI-58). Furthermore, PLIN5 anchors mitochondria to the LD membrane via the outermost part of the carboxyl-terminus. However, the role of this LD-mitochondria coupling (LDMC) in cellular energy catabolism is less established. In this study, we investigated the impact of PLIN5-mediated LDMC in comparison to disrupted LDMC on cellular TG homeostasis, FA oxidation, mitochondrial respiration and protein interaction. To do so, we established PLIN5 mutants deficient in LDMC whilst maintaining normal interactions with key lipolytic players. Radiotracer studies with cell lines stably overexpressing wild type or truncated PLIN5 revealed that LDMC has no significant impact on FA esterification upon lipid loading or TG catabolism during stimulated lipolysis. Moreover, we demonstrated that LDMC exerts a minor if any role in mitochondrial FA oxidation. In contrast, LDMC significantly improved the mitochondrial respiratory capacity and metabolic flexibility of lipid-challenged cardiomyocytes, which was corroborated by LDMC-dependent interactions of PLIN5 with mitochondrial proteins involved in mitochondrial respiration, dynamics and cristae organization. Taken together, this study suggests that PLIN5 preserves mitochondrial function by adjusting FA supply via the regulation of TG hydrolysis and that LDMC is a vital part of mitochondrial integrity.

Keywords:  Adipose-triglyceride lipase; Comparative gene identification-58; Lipid droplets; PLIN5; cardiovascular disease; fatty acid oxidation; lipid droplet-mitochondria coupling; lipolysis; lipotoxicity; mitochondrial respiration

DOI:  https://doi.org/10.1016/j.jlr.2022.100172
Hum Mol Genet. 2022 Jan 24. pii: ddac013. [Epub ahead of print]

Multi-omics analyses reveal early metabolic imbalance and mitochondrial stress in neonatal photoreceptors leading to cell death in Pde6brd1/rd1 mouse model of retinal degeneration.

Ke Jiang, Anupam Kumar Mondal, Yogita K Adlakha, Jessica Gumerson, Angel Aponte, Linn Gieser, Jung-Woong Kim, Alexis Boleda, Matthew J Brooks, Jacob Nellissery, Donald A Fox, Robert Balaban, Raul Covian, Anand Swaroop.

Retinal diseases exhibit extensive genetic heterogeneity and complex etiology with varying onset and severity. Mutations in over 200 genes can lead to photoreceptor dysfunction and/or cell death in retinal neurodegeneration. To deduce molecular pathways that initiate and/or drive cell death, we adopted a temporal multi-omics approach and examined molecular and cellular events in newborn and developing photoreceptors before the onset of degeneration in a widely-used Pde6brd1/rd1 (rd1) mouse, a model of autosomal recessive retinitis pigmentosa caused by PDE6B mutations. Transcriptome profiling of neonatal and developing rods from the rd1 retina revealed early downregulation of genes associated with anabolic pathways and energy metabolism. Quantitative proteomics of rd1 retina showed early changes in calcium signaling and oxidative phosphorylation, with specific partial bypass of complex I electron transfer, which precede the onset of cell death. Concurrently, we detected alterations in central carbon metabolism, including dysregulation of components associated with glycolysis, pentose phosphate and purine biosynthesis. Ex vivo assays of oxygen consumption and transmission electron microscopy validated early and progressive mitochondrial stress and abnormalities in mitochondrial structure and function of rd1 rods. These data uncover mitochondrial over-activation and related metabolic alterations as determinants of early pathology and implicate aberrant calcium signaling as an initiator of higher mitochondrial stress. Our studies thus provide a mechanistic framework with mitochondrial damage and metabolic disruptions as early drivers of photoreceptor cell death in retinal degeneration.

DOI: https://doi.org/10.1093/hmg/ddac013
mSystems. 2022 Jan 25. e0122321

Metabolic Disease, NAD Metabolism, Nicotinamide Riboside, and the Gut Microbiome: Connecting the Dots from the Gut to Physiology.

Anthony A Sauve.

  The effort to use nutrients as interventions to treat human disease has been important to medicine. A current example in this vein pertains to NAD+ boosters, such as nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN), which are in many clinical trials in a variety of disease conditions. Independent laboratories have shown that ingested NR (or NMN) has mitigating effects on metabolic syndrome in mice. V. V. Lozada-Fernández, O. deLeon, S. L. Kellogg, F. L. Saravia, et al. (mSystems 7:e00230-21, 2022, https://doi.org/10.1128/mSystems.00230-21) show that NR shifts gut microbiome contents and that the transplantation of an NR-conditioned microbiome by fecal transfer reproduces some effects of NR in mice on a high-fat diet. The involvement of the gut microbiome as a factor in NR effects is linked to changes to the gut microbiome and its activity to transform NR and downstream catabolites. This commentary draws attention to these findings and focuses on some puzzling aspects of NAD+ boosters, exploring the still murky interactions between NAD+ metabolism, energy homeostasis, and the gut microbiome.

Keywords:  NAD+; NAD+ metabolism; energy metabolism; metabolic syndrome; microbiome; nicotinamide riboside

DOI:  https://doi.org/10.1128/msystems.01223-21
Epigenomes. 2021 Dec 22. pii: 1. [Epub ahead of print]6(1):

Epigenetics of Mitochondria-Associated Genes in Striated Muscle.

Kenneth C Ehrlich, Hong-Wen Deng, Melanie Ehrlich.

  Striated muscle has especially large energy demands. We identified 97 genes preferentially expressed in skeletal muscle and heart, but not in aorta, and found significant enrichment for mitochondrial associations among them. We compared the epigenomic and transcriptomic profiles of the 27 genes associated with striated muscle and mitochondria. Many showed strong correlations between their tissue-specific transcription levels, and their tissue-specific promoter, enhancer, or open chromatin as well as their DNA hypomethylation. Their striated muscle-specific enhancer chromatin was inside, upstream, or downstream of the gene, throughout much of the gene as a super-enhancer (CKMT2, SLC25A4, and ACO2), or even overlapping a neighboring gene (COX6A2, COX7A1, and COQ10A). Surprisingly, the 3' end of the 1.38 Mb PRKN (PARK2) gene (involved in mitophagy and linked to juvenile Parkinson's disease) displayed skeletal muscle/myoblast-specific enhancer chromatin, a myoblast-specific antisense RNA, as well as brain-specific enhancer chromatin. We also found novel tissue-specific RNAs in brain and embryonic stem cells within PPARGC1A (PGC-1α), which encodes a master transcriptional coregulator for mitochondrial formation and metabolism. The tissue specificity of this gene's four alternative promoters, including a muscle-associated promoter, correlated with nearby enhancer chromatin and open chromatin. Our in-depth epigenetic examination of these genes revealed previously undescribed tissue-specific enhancer chromatin, intragenic promoters, regions of DNA hypomethylation, and intragenic noncoding RNAs that give new insights into transcription control for this medically important set of genes.

Keywords:  DNA methylation; PGC-1α/PPARGC1A; PRKN/PARK2; Parkinson’s disease; enhancer; epigenetics; heart; mitochondria; mitophagy; skeletal muscle

DOI:  https://doi.org/10.3390/epigenomes6010001
Mitochondrion. 2022 Jan 22. pii: S1567-7249(22)00006-X. [Epub ahead of print]

Targeting the Mitochondrial Permeability Transition Pore for Drug Discovery: Challenges and Opportunities.

Ibrahim Damilare Boyenle, Abdulquddus Kehinde Oyedele, Abdeen Tunde Ogunlana, Adeyemo Aishat Folashade, Sunday Faith Oyelere, Akinola Olateju Balkees, Temitope Isaac Adelusi, Leonard Ona Ehigie, Adeola Folashade Ehigie.

  Several drug targets have been amenable to drug discovery pursuit not until the characterization of the mitochondrial permeability transition pore (MPTP), a pore with an undefined molecular identity that forms on the inner mitochondrial membrane upon mitochondrial permeability transition (MPT) under the influence of calcium overload and oxidative stress. The opening of the pore which is presumed to cause cell death in certain human diseases also has implications under physiological parlance. The mitochondrial community has witnessed many protein candidates such as; voltage-dependent anion channel (VDAC), adenine nucleotide translocase (ANT), Mitochondrial phosphate carrier (PiC), Spastic Paralegin (SPG7), disordered proteins, and F1Fo ATPase. Also, different models for this pore have been postulated in the last six decades since it was characterized but genetic studies have cast out most of these candidates with only F1Fo ATPase currently under intense argument. Cyclophilin D (CyPD) remains the widely accepted positive regulator of the MPTP known to date, but no drug candidate has emerged as its inhibitor, raising concern issues for therapeutics. Thus, in this review, we discuss various models of MPTP reported with the hope of stimulating further research in this field. We went beyond the classical description of the MPTP to ascribe a 'two-edged sword property' to the pore for therapeutic function in human disease because its inhibition and activation have pharmacological relevance. We identified putative proteins upstream to CyPD that can regulate its activity and prevent cell deaths in neurodegenerative disease and ischemia-reperfusion injury.

Keywords:  Cyclophilin D; Ischemia Reperfusion Injury; Mitochondrial permeability transition pore (MPTP); Neurodegenerative disease; drug discovery; mitochondrial permeability transition (MPT)

DOI:  https://doi.org/10.1016/j.mito.2022.01.006
Front Cardiovasc Med. 2021 ;8 798985

Case Report: Whole Exome Sequencing Identifies Compound Heterozygous Variants in TSFM Gene Causing Juvenile Hypertrophic Cardiomyopathy.

UCLA Clinical Genomics Center

  We report a case of hypertrophic cardiomyopathy and lactic acidosis in a 3-year-old female. Cardiac and skeletal muscles biopsies exhibited mitochondrial hyperplasia with decreased complex IV activity. Whole exome sequencing identified compound heterozygous variants, p.Arg333Trp and p.Val119Leu, in TSFM, a nuclear gene that encodes a mitochondrial translation elongation factor, resulting in impaired oxidative phosphorylation and juvenile hypertrophic cardiomyopathy.

Keywords:  COXPD3; TSFM; hypertrophic cardiomyopathy; mitochondrial cardiomyopathy; mitochondrial hyperplasia; whole exome sequencing

DOI:  https://doi.org/10.3389/fcvm.2021.798985
iScience. 2022 Jan 21. 25(1): 103730

Metabolic signatures of regulation by phosphorylation and acetylation.

Kirk Smith, Fangzhou Shen, Ho Joon Lee, Sriram Chandrasekaran.

  Acetylation and phosphorylation are highly conserved posttranslational modifications (PTMs) that regulate cellular metabolism, yet how metabolic control is shared between these PTMs is unknown. Here we analyze transcriptome, proteome, acetylome, and phosphoproteome datasets in E. coli, S. cerevisiae, and mammalian cells across diverse conditions using CAROM, a new approach that uses genome-scale metabolic networks and machine learning to classify targets of PTMs. We built a single machine learning model that predicted targets of each PTM in a condition across all three organisms based on reaction attributes (AUC>0.8). Our model predicted phosphorylated enzymes during a mammalian cell-cycle, which we validate using phosphoproteomics. Interpreting the machine learning model using game theory uncovered enzyme properties including network connectivity, essentiality, and condition-specific factors such as maximum flux that differentiate targets of phosphorylation from acetylation. The conserved and predictable partitioning of metabolic regulation identified here between these PTMs may enable rational rewiring of regulatory circuits.

Keywords:  Metabolic flux analysis; Omics; Systems biology

DOI:  https://doi.org/10.1016/j.isci.2021.103730
Keio J Med. 2022 Jan 25.

Metabolism in Human Pluripotent Stem Cells and Cardiomyocytes for Regenerative Therapy.

Tomohiko C Umei, Shugo Tohyama.

  Pluripotent stem cells (PSCs), which include embryonic stem cells and induced pluripotent stem cells, have the potential for unlimited self-renewal and proliferation and the ability to differentiate into all three embryonic germ layers. Human PSCs (hPSCs) are used in drug discovery screening, disease models, and regenerative medicine. These cells maintain a transcriptional regulatory network based on a set of unique transcription factors to maintain their stem cell properties. Downstream of such transcriptional regulatory networks, various stem cell-specific metabolic programs are used to produce energy and metabolites as necessary. hPSCs and differentiated cells utilize different metabolic programs for self-renewal ability and maintenance of quiescence. Understanding the different metabolic features of hPSCs and differentiated cells can contribute to the development of technologies that are useful for regenerative medicine, such as the purification of differentiated cells. This review describes the unique metabolic programs active in hPSCs and their differences from somatic cells, with a focus on cardiomyocytes.

Keywords:  cardiomyocyte; metabolism; pluripotent stem cell; regenerative therapy

DOI:  https://doi.org/10.2302/kjm.2021-0015-IR
mSystems. 2022 Jan 25. e0023021

Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice.

Valery V Lozada-Fernández, Orlando deLeon, Stephanie L Kellogg, Fatima L Saravia, Matthew A Hadiono, Samantha N Atkinson, Justin L Grobe, John R Kirby.

  The gut microbiome plays an essential role in host energy homeostasis and influences the development of obesity and related conditions. Studies demonstrate that nicotinamide riboside (NR) supplementation for diet-induced obesity (DIO) reduces weight gain and increases energy expenditure in mice. NR is a vitamin B3 derivative and an NAD+ precursor with potential for treating human diseases arising from mitochondrial degeneration, including obesity and type 2 diabetes. Gut bacteria produce vitamin B3 in the colon and are capable of salvaging and metabolizing vitamin B3 and its derivatives. However, it is unknown how dietary supplementation of NR alters the microbiome and if those alterations contribute to deflection of weight gain. In this study, we fed C57BL/6J male mice a high-fat diet (HFD) supplemented with or without NR and performed a fecal material transfer (FMT) to establish a link between NR-conditioned microbiota and NR-induced deflection of weight gain. FMT from NR-treated donors to naive mice fed a HFD was sufficient to deflect weight gain by increasing energy expenditure. We also investigated the effects of NR on the microbiome by using metagenomics sequencing. We found that NR-treated mice displayed an altered gut microbial composition relative to controls and that fecal transplant resulted in a distinct functional metabolic profile characterized by enrichment of butyrate-producing Firmicutes. NR-treated donors and subsequent FMT recipients share a similar enrichment of metagenomic biomarkers relative to controls. These findings suggest that microbial factors contribute to the beneficial effects of dietary NR supplementation, which may be useful to enhance the therapeutic effects of NR. IMPORTANCE With obesity and type 2 diabetes (T2D) at epidemic levels, we need to understand the complex nature of these diseases to design better therapeutics. The underlying causes of both obesity and T2D are complex, but both are thought to develop, in part, based on contributions from the gut microbiota. Nicotinamide riboside is a gut-derived vitamin B3 derivative and NAD+ precursor which has the potential to treat and prevent metabolic disorders by ameliorating mitochondrial dysfunction. Understanding how NR affects the gut microbiome and whether NR-conditioned microbiota contributes to weight loss in the host would (i) improve diagnosis and treatments for obesity and other metabolic pathologies, (ii) tailor treatments to satisfy the needs of each individual moving toward the future of precision medicine, and (iii) benefit other scientific fields that currently investigate the effects of NR in other disease pathologies.

Keywords:  diet-induced obesity; energy expenditure; fecal material transfer; high-fat diet; nicotinamide riboside

DOI:  https://doi.org/10.1128/msystems.00230-21
Elife. 2022 Jan 25. pii: e70341. [Epub ahead of print]11

iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling.

Dongsheng Guo, Katelyn Daman, Jennifer Jc Chen, Meng-Jiao Shi, Jing Yan, Zdenka Matijasevic, Amanda M Rickard, Monica H Bennett, Alex Kiselyov, Haowen Zhou, Anne G Bang, Kathryn R Wagner, René Maehr, Oliver D King, Lawrence J Hayward, Charles P Emerson.

  Skeletal muscle myoblasts (iMyoblasts) were generated from human induced pluripotent stem cells (iPSCs) using an efficient and reliable transgene-free induction and stem cell selection protocol. Immunofluorescence, flow cytometry, qPCR, digital RNA expression profiling, and scRNA-Seq studies identify iMyoblasts as a PAX3+/MYOD1+ skeletal myogenic lineage with a fetal-like transcriptome signature, distinct from adult muscle biopsy myoblasts (bMyoblasts) and iPSC-induced muscle progenitors. iMyoblasts can be stably propagated for >12 passages or 30 population doublings while retaining their dual commitment for myotube differentiation and regeneration of reserve cells. iMyoblasts also efficiently xenoengrafted into irradiated and injured mouse muscle where they undergo differentiation and fetal-adult MYH isoform switching, demonstrating their regulatory plasticity for adult muscle maturation in response to signals in the host muscle. Xenograft muscle retains PAX3+ muscle progenitors and can regenerate human muscle in response to secondary injury. As models of disease, iMyoblasts from individuals with Facioscapulohumeral Muscular Dystrophy revealed a previously unknown epigenetic regulatory mechanism controlling developmental expression of the pathological DUX4 gene. iMyoblasts from Limb-Girdle Muscular Dystrophy R7 and R9 and Walker Warburg Syndrome patients modeled their molecular disease pathologies and were responsive to small molecule and gene editing therapeutics. These findings establish the utility of iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease pathogenesis and for the development of muscle stem cell therapeutics.

Keywords:  developmental biology; human; human ipsc myogenesis; iMyoblasts; mouse; muscle stem cells; regenerative medicine; stem cells; xenograft

DOI:  https://doi.org/10.7554/eLife.70341
Cell Genom. 2021 Nov 10. pii: 100029. [Epub ahead of print]1(2):

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

Heidi L Rehm, Angela J H Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, Lawrence J Babb, Maxmillian P Barkley, Michael Baudis, Michael J S Beauvais, Tim Beck, Jacques S Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K Bonfield, Tiffany F Boughtwood, Guillaume Bourque, Sarion R Bowers, Anthony J Brookes, Michael Brudno, Matthew H Brush, David Bujold, Tony Burdett, Orion J Buske, Moran N Cabili, Daniel L Cameron, Robert J Carroll, Esmeralda Casas-Silva, Debyani Chakravarty, Bimal P Chaudhari, Shu Hui Chen, J Michael Cherry, Justina Chung, Melissa Cline, Hayley L Clissold, Robert M Cook-Deegan, Mélanie Courtot, Fiona Cunningham, Miro Cupak, Robert M Davies, Danielle Denisko, Megan J Doerr, Lena I Dolman, Edward S Dove, L Jonathan Dursi, Stephanie O M Dyke, James A Eddy, Karen Eilbeck, Kyle P Ellrott, Susan Fairley, Khalid A Fakhro, Helen V Firth, Michael S Fitzsimons, Marc Fiume, Paul Flicek, Ian M Fore, Mallory A Freeberg, Robert R Freimuth, Lauren A Fromont, Jonathan Fuerth, Clara L Gaff, Weiniu Gan, Elena M Ghanaim, David Glazer, Robert C Green, Malachi Griffith, Obi L Griffith, Robert L Grossman, Tudor Groza, Jaime M Guidry Auvil, Roderic Guigó, Dipayan Gupta, Melissa A Haendel, Ada Hamosh, David P Hansen, Reece K Hart, Dean Mitchell Hartley, David Haussler, Rachele M Hendricks-Sturrup, Calvin W L Ho, Ashley E Hobb, Michael M Hoffman, Oliver M Hofmann, Petr Holub, Jacob Shujui Hsu, Jean-Pierre Hubaux, Sarah E Hunt, Ammar Husami, Julius O Jacobsen, Saumya S Jamuar, Elizabeth L Janes, Francis Jeanson, Aina Jené, Amber L Johns, Yann Joly, Steven J M Jones, Alexander Kanitz, Kazuto Kato, Thomas M Keane, Kristina Kekesi-Lafrance, Jerome Kelleher, Giselle Kerry, Seik-Soon Khor, Bartha M Knoppers, Melissa A Konopko, Kenjiro Kosaki, Martin Kuba, Jonathan Lawson, Rasko Leinonen, Stephanie Li, Michael F Lin, Mikael Linden, Xianglin Liu, Isuru Udara Liyanage, Javier Lopez, Anneke M Lucassen, Michael Lukowski, Alice L Mann, John Marshall, Michele Mattioni, Alejandro Metke-Jimenez, Anna Middleton, Richard J Milne, Fruzsina Molnár-Gábor, Nicola Mulder, Monica C Munoz-Torres, Rishi Nag, Hidewaki Nakagawa, Jamal Nasir, Arcadi Navarro, Tristan H Nelson, Ania Niewielska, Amy Nisselle, Jeffrey Niu, Tommi H Nyrönen, Brian D O'Connor, Sabine Oesterle, Soichi Ogishima, Vivian Ota Wang, Laura A D Paglione, Emilio Palumbo, Helen E Parkinson, Anthony A Philippakis, Angel D Pizarro, Andreas Prlic, Jordi Rambla, Augusto Rendon, Renee A Rider, Peter N Robinson, Kurt W Rodarmer, Laura Lyman Rodriguez, Alan F Rubin, Manuel Rueda, Gregory A Rushton, Rosalyn S Ryan, Gary I Saunders, Helen Schuilenburg, Torsten Schwede, Serena Scollen, Alexander Senf, Nathan C Sheffield, Neerjah Skantharajah, Albert V Smith, Heidi J Sofia, Dylan Spalding, Amanda B Spurdle, Zornitza Stark, Lincoln D Stein, Makoto Suematsu, Patrick Tan, Jonathan A Tedds, Alastair A Thomson, Adrian Thorogood, Timothy L Tickle, Katsushi Tokunaga, Juha Törnroos, David Torrents, Sean Upchurch, Alfonso Valencia, Roman Valls Guimera, Jessica Vamathevan, Susheel Varma, Danya F Vears, Coby Viner, Craig Voisin, Alex H Wagner, Susan E Wallace, Brian P Walsh, Marc S Williams, Eva C Winkler, Barbara J Wold, Grant M Wood, J Patrick Woolley, Chisato Yamasaki, Andrew D Yates, Christina K Yung, Lyndon J Zass, Ksenia Zaytseva, Junjun Zhang, Peter Goodhand, Kathryn North, Ewan Birney.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

DOI: https://doi.org/10.1016/j.xgen.2021.100029
Nat Commun. 2022 Jan 25. 13(1): 480

A genome-wide association study of serum proteins reveals shared loci with common diseases.

Alexander Gudjonsson, Valborg Gudmundsdottir, Gisli T Axelsson, Elias F Gudmundsson, Brynjolfur G Jonsson, Lenore J Launer, John R Lamb, Lori L Jennings, Thor Aspelund, Valur Emilsson, Vilmundur Gudnason.

With the growing number of genetic association studies, the genotype-phenotype atlas has become increasingly more complex, yet the functional consequences of most disease associated alleles is not understood. The measurement of protein level variation in solid tissues and biofluids integrated with genetic variants offers a path to deeper functional insights. Here we present a large-scale proteogenomic study in 5,368 individuals, revealing 4,035 independent associations between genetic variants and 2,091 serum proteins, of which 36% are previously unreported. The majority of both cis- and trans-acting genetic signals are unique for a single protein, although our results also highlight numerous highly pleiotropic genetic effects on protein levels and demonstrate that a protein's genetic association profile reflects certain characteristics of the protein, including its location in protein networks, tissue specificity and intolerance to loss of function mutations. Integrating protein measurements with deep phenotyping of the cohort, we observe substantial enrichment of phenotype associations for serum proteins regulated by established GWAS loci, and offer new insights into the interplay between genetics, serum protein levels and complex disease.

DOI: https://doi.org/10.1038/s41467-021-27850-z
Nat Commun. 2022 Jan 25. 13(1): 481

Coding and regulatory variants are associated with serum protein levels and disease.

Valur Emilsson, Valborg Gudmundsdottir, Alexander Gudjonsson, Thorarinn Jonmundsson, Brynjolfur G Jonsson, Mohd A Karim, Marjan Ilkov, James R Staley, Elias F Gudmundsson, Lenore J Launer, Jan H Lindeman, Nicholas M Morton, Thor Aspelund, John R Lamb, Lori L Jennings, Vilmundur Gudnason.

Circulating proteins can be used to diagnose and predict disease-related outcomes. A deep serum proteome survey recently revealed close associations between serum protein networks and common disease. In the current study, 54,469 low-frequency and common exome-array variants were compared to 4782 protein measurements in the serum of 5343 individuals from the AGES Reykjavik cohort. This analysis identifies a large number of serum proteins with genetic signatures overlapping those of many diseases. More specifically, using a study-wide significance threshold, we find that 2021 independent exome array variants are associated with serum levels of 1942 proteins. These variants reside in genetic loci shared by hundreds of complex disease traits, highlighting serum proteins' emerging role as biomarkers and potential causative agents of a wide range of diseases.

DOI: https://doi.org/10.1038/s41467-022-28081-6
Proc Natl Acad Sci U S A. 2022 Feb 01. pii: e2119767119. [Epub ahead of print]119(5):

LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis.

Li Lin, Yufeng Zhang, Weizhou Qian, Yao Liu, Yingkun Zhang, Fanghe Lin, Cenxi Liu, Guangxing Lu, Di Sun, Xiaoxu Guo, YanLing Song, Jia Song, Chaoyong Yang, Jin Li.

  Single-cell RNA-sequencing (scRNA-seq) has become a powerful tool for biomedical research by providing a variety of valuable information with the advancement of computational tools. Lineage analysis based on scRNA-seq provides key insights into the fate of individual cells in various systems. However, such analysis is limited by several technical challenges. On top of the considerable computational expertise and resources, these analyses also require specific types of matching data such as exogenous barcode information or bulk assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) data. To overcome these technical challenges, we developed a user-friendly computational algorithm called "LINEAGE" (label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis). Aiming to screen out endogenous markers of lineage located on mitochondrial reads from label-free scRNA-seq data to conduct lineage inference, LINEAGE integrates a marker selection strategy by feature subspace separation and de novo "low cross-entropy subspaces" identification. In this process, the mutation type and subspace-subspace "cross-entropy" of features were both taken into consideration. LINEAGE outperformed three other methods, which were designed for similar tasks as testified with two standard datasets in terms of biological accuracy and computational efficiency. Applied on a label-free scRNA-seq dataset of BRAF-mutated cancer cells, LINEAGE also revealed genes that contribute to BRAF inhibitor resistance. LINEAGE removes most of the technical hurdles of lineage analysis, which will remarkably accelerate the discovery of the important genes or cell-lineage clusters from scRNA-seq data.

Keywords:  BRAF inhibitor resistance; lineage analysis; single-cell RNA-seq

DOI:  https://doi.org/10.1073/pnas.2119767119