bims-mitdis 2021-04-04 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2021–04–04
34 papers selected by
Catalina Vasilescu, University of Helsinki

Whole genome and exome sequencing identify NDUFV2 mutations as a new cause of progressive cavitating leukoencephalopathy.
Selective packaging of mitochondrial proteins into extracellular vesicles prevents the release of mitochondrial DAMPs.
Unraveling the Link Between Mitochondrial Dynamics and Neuroinflammation.
Current and new Next-Generation Sequencing approaches to study mitochondrial DNA.
High dietary fat consumption impairs axonal mitochondrial function in vivo.
Role of Mitochondria in Viral Infections.
The Role of Mitochondria in Immune-Cell-Mediated Tissue Regeneration and Ageing.
ANT1 Activation and Inhibition Patterns Support the Fatty Acid Cycling Mechanism for Proton Transport.
Comprehensive identification of somatic nucleotide variants in human brain tissue.
Knock-Down of HDAC2 in Human Induced Pluripotent Stem Cell Derived Neurons Improves Neuronal Mitochondrial Dynamics, Neuronal Maturation and Reduces Amyloid Beta Peptides.
Opa1 relies on cristae preservation and ATP synthase to curtail reactive oxygen species accumulation in mitochondria.
Mitochondrial Mistranslation in Brain Provokes a Metabolic Response Which Mitigates the Age-Associated Decline in Mitochondrial Gene Expression.
VRK2 is involved in the innate antiviral response by promoting mitostress-induced mtDNA release.
Sorting sub-150-nm liposomes of distinct sizes by DNA-brick-assisted centrifugation.
Discovering the landscape of protein modifications.
Opportunities and challenges for the computational interpretation of rare variation in clinically important genes.
Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons.
Mitochondrial LonP1 protease is implicated in the degradation of unstable Parkinson's disease-associated DJ-1/PARK 7 missense mutants.
Progressive myoclonus epilepsies-Residual unsolved cases have marked genetic heterogeneity including dolichol-dependent protein glycosylation pathway genes.
Mitochondrial Syndromes Revisited.
Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism.
Stem Cell Metabolism and Diet.
Increased ROS-Mediated CaMKII Activation Contributes to Calcium Handling Abnormalities and Impaired Contraction in Barth Syndrome.
A novel oral nutritional supplement improves gait speed and mitochondrial functioning compared to standard care in older adults with (or at risk of) undernutrition: results from a randomized controlled trial.
A unified haplotype-based method for accurate and comprehensive variant calling.
Fabrication of 3D Cardiac Microtissue Arrays using Human iPSC-Derived Cardiomyocytes, Cardiac Fibroblasts, and Endothelial Cells.
Iron Deficiency without Anemia Decreases Physical Endurance and Mitochondrial Complex I Activity of Oxidative Skeletal Muscle in the Mouse.
Conserved role of ENDOG in promoting autophagy.
Generation of Human iPSC-derived Neural Progenitor Cells (NPCs) as Drug Discovery Model for Neurological and Mitochondrial Disorders.
The folate cycle enzyme MTHFD2 induces cancer immune evasion through PD-L1 up-regulation.
ASHLEYS: automated quality control for single-cell Strand-seq data.
Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment.
Using machine learning approaches for multi-omics data analysis: A review.
Serine metabolism antagonizes antiviral innate immunity by preventing ATP6V0d2-mediated YAP lysosomal degradation.

J Med Genet. 2021 Apr 02. pii: jmedgenet-2020-107383. [Epub ahead of print]

Whole genome and exome sequencing identify NDUFV2 mutations as a new cause of progressive cavitating leukoencephalopathy.

Zhimei Liu, Li Zhang, Changhong Ren, Manting Xu, Shufang Li, Rui Ban, Ye Wu, Ling Chen, Suzhen Sun, Matthias Elstner, Masaru Shimura, Minako Ogawa-Tominaga, Kei Murayama, Tieliu Shi, Holger Prokisch, Fang Fang.

   BACKGROUND: Progressive cavitating leukoencephalopathy (PCL) is thought to result from mutations in nuclear genes affecting mitochondrial function and energy metabolism. To date, mutations in two subunits of complex I, NDUFS1 and NDUFV1, have been reported to be related to PCL.
METHODS: Patients underwent clinical examinations, brain MRI, skin biopsy and muscle biopsy. Whole-genome or whole-exome sequencing was performed on the index patients from two unrelated families with PCL. The effects of the mutations were examined through complementation of the NDUFV2 mutation by cDNA expression.
RESULTS: The common clinical features of the patients in this study were recurring episodes of acute or subacute developmental regression that appeared in the first years of life, followed by gradual remissions and prolonged periods of stability. MRI showed leukoencephalopathy with multiple cavities. Three novel NDUFV2 missense mutations were identified in these families. Complex I deficiency was confirmed in affected individuals' fibroblasts and a muscle biopsy. Functional and structural analyses revealed that these mutations affect the structural stability and function of the NDUFV2 protein, indicating that defective NDUFV2 function is responsible for the phenotypes in these individuals.
CONCLUSIONS: Here, we report the clinical presentations, neuroimaging and molecular and functional analyses of novel mutations in NDUFV2 in two sibling pairs of two Chinese families presenting with PCL. We hereby expand the knowledge on the clinical phenotypes associated with mutations in NDUFV2 and the genotypes causative for PCL.

Keywords:  central nervous system diseases; diagnosis; genotype; neurodegenerative diseases; phenotype

DOI:  https://doi.org/10.1136/jmedgenet-2020-107383
Nat Commun. 2021 Mar 30. 12(1): 1971

Selective packaging of mitochondrial proteins into extracellular vesicles prevents the release of mitochondrial DAMPs.

Kiran Todkar, Lilia Chikhi, Véronique Desjardins, Firas El-Mortada, Geneviève Pépin, Marc Germain.

Most cells constitutively secrete mitochondrial DNA and proteins in extracellular vesicles (EVs). While EVs are small vesicles that transfer material between cells, Mitochondria-Derived Vesicles (MDVs) carry material specifically between mitochondria and other organelles. Mitochondrial content can enhance inflammation under pro-inflammatory conditions, though its role in the absence of inflammation remains elusive. Here, we demonstrate that cells actively prevent the packaging of pro-inflammatory, oxidized mitochondrial proteins that would act as damage-associated molecular patterns (DAMPs) into EVs. Importantly, we find that the distinction between material to be included into EVs and damaged mitochondrial content to be excluded is dependent on selective targeting to one of two distinct MDV pathways. We show that Optic Atrophy 1 (OPA1) and sorting nexin 9 (Snx9)-dependent MDVs are required to target mitochondrial proteins to EVs, while the Parkinson's disease-related protein Parkin blocks this process by directing damaged mitochondrial content to lysosomes. Our results provide insight into the interplay between mitochondrial quality control mechanisms and mitochondria-driven immune responses.

DOI: https://doi.org/10.1038/s41467-021-21984-w
Front Immunol. 2021 ;12 624919

Unraveling the Link Between Mitochondrial Dynamics and Neuroinflammation.

Lilian Gomes de Oliveira, Yan de Souza Angelo, Antonio H Iglesias, Jean Pierre Schatzmann Peron.

  Neuroinflammatory and neurodegenerative diseases are a major public health problem worldwide, especially with the increase of life-expectancy observed during the last decades. For many of these diseases, we still lack a full understanding of their etiology and pathophysiology. Nonetheless their association with mitochondrial dysfunction highlights this organelle as an important player during CNS homeostasis and disease. Markers of Parkinson (PD) and Alzheimer (AD) diseases are able to induce innate immune pathways induced by alterations in mitochondrial Ca2+ homeostasis leading to neuroinflammation. Additionally, exacerbated type I IFN responses triggered by mitochondrial DNA (mtDNA), failures in mitophagy, ER-mitochondria communication and mtROS production promote neurodegeneration. On the other hand, regulation of mitochondrial dynamics is essential for CNS health maintenance and leading to the induction of IL-10 and reduction of TNF-α secretion, increased cell viability and diminished cell injury in addition to reduced oxidative stress. Thus, although previously solely seen as power suppliers to organelles and molecular processes, it is now well established that mitochondria have many other important roles, including during immune responses. Here, we discuss the importance of these mitochondrial dynamics during neuroinflammation, and how they correlate either with the amelioration or worsening of CNS disease.

Keywords:  Alzheimer disease; Parkinson disease; mitochondria; multiple sclerosis; neurodegenerative diseases; neuroinflammation

DOI:  https://doi.org/10.3389/fimmu.2021.624919
J Mol Diagn. 2021 Mar 26. pii: S1525-1578(21)00066-0. [Epub ahead of print]

Current and new Next-Generation Sequencing approaches to study mitochondrial DNA.

Andrea Legati, Nadia Zanetti, Alessia Nasca, Camille Peron, Costanza Lamperti, Eleonora Lamantea, Daniele Ghezzi.

Mitochondria harbor multiple copies of a maternally inherited non-nuclear genome; point mutations, deletions, or depletion of the mitochondrial DNA have been associated with various human diseases. Different approaches have been used to investigate mitochondrial DNA defects: Sanger sequencing, Southern blot, long and quantitative PCR. All these technologies are inherently hampered by limitations in speed, throughput, sensitivity, and associated costs. Recently, Next Generation Sequencing has been introduced in this field and all its potential applications still need to be fully validated. Analysis of mitochondrial DNA from 16 control samples and 33 affected samples, previously investigated by traditional techniques, was performed. Different Next Generation Sequencing approaches were tested, using classical library preparation based on PCR amplifications and an innovative PCR-free protocol, defining their suitability and utility for: (i) generating full accurate mtDNA sequence, (ii) assessing heteroplasmy for single point mutations with high accuracy, (iii) detecting break positions and heteroplasmy of single large deletions. This study confirmed that PCR-based library preparations are appropriate for the first two points while showed that a new PCR-free method gave the best results for the third aim.

DOI: https://doi.org/10.1016/j.jmoldx.2021.03.002
J Neurosci. 2021 Mar 29. pii: JN-RM-1852-20. [Epub ahead of print]

High dietary fat consumption impairs axonal mitochondrial function in vivo.

Marija Sajic, Amy E Rumora, Anish A Kanhai, Giacomo Dentoni, Sharlini Varatharajah, Caroline Casey, Ryan D R Brown, Fabian Peters, Lucy M Hinder, Masha G Savelieff, Eva L Feldman, Kenneth J Smith.

Peripheral neuropathy (PN) is the most common complication of prediabetes and diabetes. PN causes severe morbidity for type 2 diabetes (T2D) and prediabetes patients, including limb pain followed by numbness resulting from peripheral nerve damage. PN in T2D and prediabetes is associated with dyslipidemia and elevated circulating lipids; however, the molecular mechanisms underlying PN development in prediabetes and T2D are unknown. Peripheral nerve sensory neurons rely on axonal mitochondria to provide energy for nerve impulse conduction under homeostatic conditions. Models of dyslipidemia in vitro demonstrate mitochondrial dysfunction in sensory neurons exposed to elevated levels of exogenous fatty acids. Herein, we evaluated the effect of dyslipidemia on mitochondrial function and dynamics in sensory axons of the saphenous nerve of a male high-fat diet (HFD)-fed murine model of prediabetes to identify mitochondrial alterations that correlate with PN pathogenesis in vivo We found that the HFD decreased mitochondrial membrane potential (MMP) in axonal mitochondria and reduced the ability of sensory neurons to conduct at physiological frequencies. Unlike mitochondria in control axons, which dissipated their MMP in response to increased impulse frequency (from 1 to 50 Hz), HFD mitochondria dissipated less MMP in response to axonal energy demand, suggesting a lack of reserve capacity. The HFD also decreased sensory axonal Ca2+ levels and increased mitochondrial lengthening and expression of PGC1α, a master regulator of mitochondrial biogenesis. Together, these results suggest that mitochondrial dysfunction underlies an imbalance of axonal energy and Ca2+ levels and impairs impulse conduction within the saphenous nerve in prediabetic PN.SIGNIFICANCE STATEMENT:Diabetes and prediabetes are leading causes of peripheral neuropathy (PN) worldwide. PN has no cure, but development in diabetes and prediabetes is associated with dyslipidemia, including elevated levels of saturated fatty acids. Saturated fatty acids impair mitochondrial dynamics and function in cultured neurons, indicating a role for mitochondrial dysfunction in PN progression; however, the effect of elevated circulating fatty acids on the peripheral nervous system in vivo is unknown. In this study, Sajic et al. identify early pathogenic events in sensory nerve axons of mice with high-fat diet-induced PN, including alterations in mitochondrial function, axonal conduction, and intra-axonal calcium, that provide important insight into potential PN mechanisms associated with prediabetes and dyslipidemia in vivo.

DOI: https://doi.org/10.1523/JNEUROSCI.1852-20.2021
Life (Basel). 2021 Mar 11. pii: 232. [Epub ahead of print]11(3):

Role of Mitochondria in Viral Infections.

Srikanth Elesela, Nicholas W Lukacs.

  Viral diseases account for an increasing proportion of deaths worldwide. Viruses maneuver host cell machinery in an attempt to subvert the intracellular environment favorable for their replication. The mitochondrial network is highly susceptible to physiological and environmental insults, including viral infections. Viruses affect mitochondrial functions and impact mitochondrial metabolism, and innate immune signaling. Resurgence of host-virus interactions in recent literature emphasizes the key role of mitochondria and host metabolism on viral life processes. Mitochondrial dysfunction leads to damage of mitochondria that generate toxic compounds, importantly mitochondrial DNA, inducing systemic toxicity, leading to damage of multiple organs in the body. Mitochondrial dynamics and mitophagy are essential for the maintenance of mitochondrial quality control and homeostasis. Therefore, metabolic antagonists may be essential to gain a better understanding of viral diseases and develop effective antiviral therapeutics. This review briefly discusses how viruses exploit mitochondrial dynamics for virus proliferation and induce associated diseases.

Keywords:  MAVS; MDA5; RIG-I; RSV; SARS CoV-2; influenza; innate immune response; mitochondria; mitochondrial dynamics; viral infections

DOI:  https://doi.org/10.3390/life11030232
Int J Mol Sci. 2021 Mar 06. pii: 2668. [Epub ahead of print]22(5):

The Role of Mitochondria in Immune-Cell-Mediated Tissue Regeneration and Ageing.

Yu-Jih Su, Pei-Wen Wang, Shao-Wen Weng.

  During tissue injury events, the innate immune system responds immediately to alarms sent from the injured cells, and the adaptive immune system subsequently joins in the inflammatory reaction. The control mechanism of each immune reaction relies on the orchestration of different types of T cells and the activators, antigen-presenting cells, co-stimulatory molecules, and cytokines. Mitochondria are an intracellular signaling organelle and energy plant, which supply the energy requirement of the immune system and maintain the system activation with the production of reactive oxygen species (ROS). Extracellular mitochondria can elicit regenerative effects or serve as an activator of the immune cells to eliminate the damaged cells. Recent clarification of the cytosolic escape of mitochondrial DNA triggering innate immunity underscores the pivotal role of mitochondria in inflammation-related diseases. Human mesenchymal stem cells could transfer mitochondria through nanotubular structures to defective mitochondrial DNA cells. In recent years, mitochondrial therapy has shown promise in treating heart ischemic events, Parkinson's disease, and fulminating hepatitis. Taken together, these results emphasize the emerging role of mitochondria in immune-cell-mediated tissue regeneration and ageing.

Keywords:  ageing; inflammation; mitochondria; regeneration

DOI:  https://doi.org/10.3390/ijms22052668
Int J Mol Sci. 2021 Mar 02. pii: 2490. [Epub ahead of print]22(5):

ANT1 Activation and Inhibition Patterns Support the Fatty Acid Cycling Mechanism for Proton Transport.

Jürgen Kreiter, Anne Rupprecht, Sanja Škulj, Zlatko Brkljača, Kristina Žuna, Denis G Knyazev, Sarah Bardakji, Mario Vazdar, Elena E Pohl.

  Adenine nucleotide translocase (ANT) is a well-known mitochondrial exchanger of ATP against ADP. In contrast, few studies have shown that ANT also mediates proton transport across the inner mitochondrial membrane. The results of these studies are controversial and lead to different hypotheses about molecular transport mechanisms. We hypothesized that the H+-transport mediated by ANT and uncoupling proteins (UCP) has a similar regulation pattern and can be explained by the fatty acid cycling concept. The reconstitution of purified recombinant ANT1 in the planar lipid bilayers allowed us to measure the membrane current after the direct application of transmembrane potential ΔΨ, which would correspond to the mitochondrial states III and IV. Experimental results reveal that ANT1 does not contribute to a basal proton leak. Instead, it mediates H+ transport only in the presence of long-chain fatty acids (FA), as already known for UCPs. It depends on FA chain length and saturation, implying that FA's transport is confined to the lipid-protein interface. Purine nucleotides with the preference for ATP and ADP inhibited H+ transport. Specific inhibitors of ATP/ADP transport, carboxyatractyloside or bongkrekic acid, also decreased proton transport. The H+ turnover number was calculated based on ANT1 concentration determined by fluorescence correlation spectroscopy and is equal to 14.6 ± 2.5 s-1. Molecular dynamic simulations revealed a large positively charged area at the protein/lipid interface that might facilitate FA anion's transport across the membrane. ANT's dual function-ADP/ATP and H+ transport in the presence of FA-may be important for the regulation of mitochondrial membrane potential and thus for potential-dependent processes in mitochondria. Moreover, the expansion of proton-transport modulating drug targets to ANT1 may improve the therapy of obesity, cancer, steatosis, cardiovascular and neurodegenerative diseases.

Keywords:  ADP/ATP carrier protein; arachidonic acid; fatty acid anion transport; long-chain fatty acids; mitochondrial transporter; proton transport

DOI:  https://doi.org/10.3390/ijms22052490
Genome Biol. 2021 Mar 29. 22(1): 92

Comprehensive identification of somatic nucleotide variants in human brain tissue.

Brain Somatic Mosaicism Network

BACKGROUND: Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells.
RESULTS: Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees.
CONCLUSIONS: This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.

DOI: https://doi.org/10.1186/s13059-021-02285-3
Int J Mol Sci. 2021 Mar 03. pii: 2526. [Epub ahead of print]22(5):

Knock-Down of HDAC2 in Human Induced Pluripotent Stem Cell Derived Neurons Improves Neuronal Mitochondrial Dynamics, Neuronal Maturation and Reduces Amyloid Beta Peptides.

Harald Frankowski, Fred Yeboah, Bonnie J Berry, Chizuru Kinoshita, Michelle Lee, Kira Evitts, Joshua Davis, Yoshito Kinoshita, Richard S Morrison, Jessica E Young.

  Histone deacetylase 2 (HDAC2) is a major HDAC protein in the adult brain and has been shown to regulate many neuronal genes. The aberrant expression of HDAC2 and subsequent dysregulation of neuronal gene expression is implicated in neurodegeneration and brain aging. Human induced pluripotent stem cell-derived neurons (hiPSC-Ns) are widely used models for studying neurodegenerative disease mechanisms, but the role of HDAC2 in hiPSC-N differentiation and maturation has not been explored. In this study, we show that levels of HDAC2 progressively decrease as hiPSCs are differentiated towards neurons. This suppression of HDAC2 inversely corresponds to an increase in neuron-specific isoforms of Endophilin-B1, a multifunctional protein involved in mitochondrial dynamics. Expression of neuron-specific isoforms of Endophilin-B1 is accompanied by concomitant expression of a neuron-specific alternative splicing factor, SRRM4. Manipulation of HDAC2 and Endophilin-B1 using lentiviral approaches shows that the knock-down of HDAC2 or the overexpression of a neuron-specific Endophilin-B1 isoform promotes mitochondrial elongation and protects against cytotoxic stress in hiPSC-Ns, while HDAC2 knock-down specifically influences genes regulating mitochondrial dynamics and synaptogenesis. Furthermore, HDAC2 knock-down promotes enhanced mitochondrial respiration and reduces levels of neurotoxic amyloid beta peptides. Collectively, our study demonstrates a role for HDAC2 in hiPSC-neuronal differentiation, highlights neuron-specific isoforms of Endophilin-B1 as a marker of differentiating hiPSC-Ns and demonstrates that HDAC2 regulates key neuronal and mitochondrial pathways in hiPSC-Ns.

Keywords:  endophilin-B1; hiPSCs; histone deacetylase 2; mitochondria; neuronal differentiation

DOI:  https://doi.org/10.3390/ijms22052526
Redox Biol. 2021 Mar 19. pii: S2213-2317(21)00092-6. [Epub ahead of print]41 101944

Opa1 relies on cristae preservation and ATP synthase to curtail reactive oxygen species accumulation in mitochondria.

Rubén Quintana-Cabrera, Israel Manjarrés-Raza, Carlos Vicente-Gutiérrez, Mauro Corrado, Juan P Bolaños, Luca Scorrano.

  Reactive oxygen species (ROS) are a common product of active mitochondrial respiration carried in mitochondrial cristae, but whether cristae shape influences ROS levels is unclear. Here we report that the mitochondrial fusion and cristae shape protein Opa1 requires mitochondrial ATP synthase oligomers to reduce ROS accumulation. In cells fueled with galactose to force ATP production by mitochondria, cristae are enlarged, ATP synthase oligomers destabilized, and ROS accumulate. Opa1 prevents both cristae remodeling and ROS generation, without impinging on levels of mitochondrial antioxidant defense enzymes that are unaffected by Opa1 overexpression. Genetic and pharmacologic experiments indicate that Opa1 requires ATP synthase oligomerization and activity to reduce ROS levels upon a blockage of the electron transport chain. Our results indicate that the converging effect of Opa1 and mitochondrial ATP synthase on mitochondrial ultrastructure regulate ROS abundance to sustain cell viability.

Keywords:  Bioenergetics; F(1)F(O)-ATP synthase; Mitochondrial cristae; Opa1; ROS; Ultrastructure

DOI:  https://doi.org/10.1016/j.redox.2021.101944
Int J Mol Sci. 2021 Mar 09. pii: 2746. [Epub ahead of print]22(5):

Mitochondrial Mistranslation in Brain Provokes a Metabolic Response Which Mitigates the Age-Associated Decline in Mitochondrial Gene Expression.

Dimitri Shcherbakov, Reda Juskeviciene, Adrián Cortés Sanchón, Margarita Brilkova, Hubert Rehrauer, Endre Laczko, Erik C Böttger.

  Mitochondrial misreading, conferred by mutation V338Y in mitoribosomal protein Mrps5, in-vivo is associated with a subtle neurological phenotype. Brain mitochondria of homozygous knock-in mutant Mrps5V338Y/V338Y mice show decreased oxygen consumption and reduced ATP levels. Using a combination of unbiased RNA-Seq with untargeted metabolomics, we here demonstrate a concerted response, which alleviates the impaired functionality of OXPHOS complexes in Mrps5 mutant mice. This concerted response mitigates the age-associated decline in mitochondrial gene expression and compensates for impaired respiration by transcriptional upregulation of OXPHOS components together with anaplerotic replenishment of the TCA cycle (pyruvate, 2-ketoglutarate).

Keywords:  aging; brain; metabolome; misreading; mitochondria

DOI:  https://doi.org/10.3390/ijms22052746
Cell Mol Immunol. 2021 Mar 30.

VRK2 is involved in the innate antiviral response by promoting mitostress-induced mtDNA release.

Wen-Rui He, Li-Bo Cao, Yu-Lin Yang, Duo Hua, Ming-Ming Hu, Hong-Bing Shu.

  Mitochondrial stress (mitostress) triggered by viral infection or mitochondrial dysfunction causes the release of mitochondrial DNA (mtDNA) into the cytosol and activates the cGAS-mediated innate immune response. The regulation of mtDNA release upon mitostress remains uncharacterized. Here, we identified mitochondria-associated vaccinia virus-related kinase 2 (VRK2) as a key regulator of this process. VRK2 deficiency inhibited the induction of antiviral genes and caused earlier and higher mortality in mice after viral infection. Upon viral infection, VRK2 associated with voltage-dependent anion channel 1 (VDAC1) and promoted VDAC1 oligomerization and mtDNA release, leading to the cGAS-mediated innate immune response. VRK2 was also required for mtDNA release and cGAS-mediated innate immunity triggered by nonviral factors that cause Ca2+ overload but was not required for the cytosolic nucleic acid-triggered innate immune response. Thus, VRK2 plays a crucial role in the mtDNA-triggered innate immune response and may be a potential therapeutic target for infectious and autoimmune diseases associated with mtDNA release.

Keywords:  Mita/Sting; cGAS; innate immune response; mitochondrial DNA; mitostress

DOI:  https://doi.org/10.1038/s41423-021-00673-0
Nat Chem. 2021 Mar 30.

Sorting sub-150-nm liposomes of distinct sizes by DNA-brick-assisted centrifugation.

Yang Yang, Zhenyong Wu, Laurie Wang, Kaifeng Zhou, Kai Xia, Qiancheng Xiong, Longfei Liu, Zhao Zhang, Edwin R Chapman, Yong Xiong, Thomas J Melia, Erdem Karatekin, Hongzhou Gu, Chenxiang Lin.

In cells, myriad membrane-interacting proteins generate and maintain curved membrane domains with radii of curvature around or below 50 nm. To understand how such highly curved membranes modulate specific protein functions, and vice versa, it is imperative to use small liposomes with precisely defined attributes as model membranes. Here, we report a versatile and scalable sorting technique that uses cholesterol-modified DNA 'nanobricks' to differentiate hetero-sized liposomes by their buoyant densities. This method separates milligrams of liposomes, regardless of their origins and chemical compositions, into six to eight homogeneous populations with mean diameters of 30-130 nm. We show that these uniform, leak-resistant liposomes serve as ideal substrates to study, with an unprecedented resolution, how membrane curvature influences peripheral (ATG3) and integral (SNARE) membrane protein activities. Compared with conventional methods, our sorting technique represents a streamlined process to achieve superior liposome size uniformity, which benefits research in membrane biology and the development of liposomal drug-delivery systems.

DOI: https://doi.org/10.1038/s41557-021-00667-5
Mol Cell. 2021 Mar 27. pii: S1097-2765(21)00210-0. [Epub ahead of print]

Discovering the landscape of protein modifications.

E Keith Keenan, Derek K Zachman, Matthew D Hirschey.

  Protein modifications modulate nearly every aspect of cell biology in organisms, ranging from Archaea to Eukaryotes. The earliest evidence of covalent protein modifications was found in the early 20th century by studying the amino acid composition of proteins by chemical hydrolysis. These discoveries challenged what defined a canonical amino acid. The advent and rapid adoption of mass-spectrometry-based proteomics in the latter part of the 20th century enabled a veritable explosion in the number of known protein modifications, with more than 500 discrete modifications counted today. Now, new computational tools in data science, machine learning, and artificial intelligence are poised to allow researchers to make significant progress in discovering new protein modifications and determining their function. In this review, we take an opportunity to revisit the historical discovery of key post-translational modifications, quantify the current landscape of covalent protein adducts, and assess the role that new computational tools will play in the future of this field.

Keywords:  amino acid; metabolism; post-translational modifications; protein acylation; protein modifications

DOI:  https://doi.org/10.1016/j.molcel.2021.03.015
Am J Hum Genet. 2021 Apr 01. pii: S0002-9297(21)00087-2. [Epub ahead of print]108(4): 535-548

Opportunities and challenges for the computational interpretation of rare variation in clinically important genes.

Gregory McInnes, Andrew G Sharo, Megan L Koleske, Julia E H Brown, Matthew Norstad, Aashish N Adhikari, Sheng Wang, Steven E Brenner, Jodi Halpern, Barbara A Koenig, David C Magnus, Renata C Gallagher, Kathleen M Giacomini, Russ B Altman.

Genome sequencing is enabling precision medicine-tailoring treatment to the unique constellation of variants in an individual's genome. The impact of recurrent pathogenic variants is often understood, however there is a long tail of rare genetic variants that are uncharacterized. The problem of uncharacterized rare variation is especially acute when it occurs in genes of known clinical importance with functionally consequential variants and associated mechanisms. Variants of uncertain significance (VUSs) in these genes are discovered at a rate that outpaces current ability to classify them with databases of previous cases, experimental evaluation, and computational predictors. Clinicians are thus left without guidance about the significance of variants that may have actionable consequences. Computational prediction of the impact of rare genetic variation is increasingly becoming an important capability. In this paper, we review the technical and ethical challenges of interpreting the function of rare variants in two settings: inborn errors of metabolism in newborns and pharmacogenomics. We propose a framework for a genomic learning healthcare system with an initial focus on early-onset treatable disease in newborns and actionable pharmacogenomics. We argue that (1) a genomic learning healthcare system must allow for continuous collection and assessment of rare variants, (2) emerging machine learning methods will enable algorithms to predict the clinical impact of rare variants on protein function, and (3) ethical considerations must inform the construction and deployment of all rare-variation triage strategies, particularly with respect to health disparities arising from unbalanced ancestry representation.

DOI: https://doi.org/10.1016/j.ajhg.2021.03.003
Science. 2021 Apr 02. 372(6537): 91-94

Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons.

Dylan A Reid, Patrick J Reed, Johannes C M Schlachetzki, Ioana I Nitulescu, Grace Chou, Enoch C Tsui, Jeffrey R Jones, Sahaana Chandran, Ake T Lu, Claire A McClain, Jean H Ooi, Tzu-Wen Wang, Addison J Lana, Sara B Linker, Anthony S Ricciardulli, Shong Lau, Simon T Schafer, Steve Horvath, Jesse R Dixon, Nasun Hah, Christopher K Glass, Fred H Gage.

Neurons are the longest-lived cells in our bodies and lack DNA replication, which makes them reliant on a limited repertoire of DNA repair mechanisms to maintain genome fidelity. These repair mechanisms decline with age, but we have limited knowledge of how genome instability emerges and what strategies neurons and other long-lived cells may have evolved to protect their genomes over the human life span. A targeted sequencing approach in human embryonic stem cell-induced neurons shows that, in neurons, DNA repair is enriched at well-defined hotspots that protect essential genes. These hotspots are enriched with histone H2A isoforms and RNA binding proteins and are associated with evolutionarily conserved elements of the human genome. These findings provide a basis for understanding genome integrity as it relates to aging and disease in the nervous system.

DOI: https://doi.org/10.1126/science.abb9032
Sci Rep. 2021 Apr 01. 11(1): 7320

Mitochondrial LonP1 protease is implicated in the degradation of unstable Parkinson's disease-associated DJ-1/PARK 7 missense mutants.

Raúl Sánchez-Lanzas, José G Castaño.

DJ-1/PARK7 mutations are linked with familial forms of early-onset Parkinson's disease (PD). We have studied the degradation of untagged DJ-1 wild type (WT) and missense mutants in mouse embryonic fibroblasts obtained from DJ-1-null mice, an approach closer to the situation in patients carrying homozygous mutations. The results showed that the mutants L10P, M26I, A107P, P158Δ, L166P, E163K, and L172Q are unstable proteins, while A39S, E64D, R98Q, A104T, D149A, A171S, K175E, and A179T are as stable as DJ-1 WT. Inhibition of proteasomal and autophagic-lysosomal pathways had little effect on their degradation. Immunofluorescence and biochemical fractionation studies indicated that M26I, A107P, P158Δ, L166P, E163K, and L172Q mutants associate with mitochondria. Silencing of mitochondrial matrix protease LonP1 produced a strong reduction of the degradation of the mitochondrial-associated DJ-1 mutants A107P, P158Δ, L166P, E163K, and L172Q but not of mutant L10P. These results demonstrated a mitochondrial pathway of degradation of those DJ-1 missense mutants implicated in PD pathogenesis.

DOI: https://doi.org/10.1038/s41598-021-86847-2
Am J Hum Genet. 2021 Apr 01. pii: S0002-9297(21)00097-5. [Epub ahead of print]108(4): 722-738

Progressive myoclonus epilepsies-Residual unsolved cases have marked genetic heterogeneity including dolichol-dependent protein glycosylation pathway genes.

Carolina Courage, Karen L Oliver, Eon Joo Park, Jillian M Cameron, Kariona A Grabińska, Mikko Muona, Laura Canafoglia, Antonio Gambardella, Edith Said, Zaid Afawi, Betul Baykan, Christian Brandt, Carlo di Bonaventura, Hui Bein Chew, Chiara Criscuolo, Leanne M Dibbens, Barbara Castellotti, Patrizia Riguzzi, Angelo Labate, Alessandro Filla, Anna T Giallonardo, Geza Berecki, Christopher B Jackson, Tarja Joensuu, John A Damiano, Sara Kivity, Amos Korczyn, Aarno Palotie, Pasquale Striano, Davide Uccellini, Loretta Giuliano, Eva Andermann, Ingrid E Scheffer, Roberto Michelucci, Melanie Bahlo, Silvana Franceschetti, William C Sessa, Samuel F Berkovic, Anna-Elina Lehesjoki.

  Progressive myoclonus epilepsies (PMEs) comprise a group of clinically and genetically heterogeneous rare diseases. Over 70% of PME cases can now be molecularly solved. Known PME genes encode a variety of proteins, many involved in lysosomal and endosomal function. We performed whole-exome sequencing (WES) in 84 (78 unrelated) unsolved PME-affected individuals, with or without additional family members, to discover novel causes. We identified likely disease-causing variants in 24 out of 78 (31%) unrelated individuals, despite previous genetic analyses. The diagnostic yield was significantly higher for individuals studied as trios or families (14/28) versus singletons (10/50) (OR = 3.9, p value = 0.01, Fisher's exact test). The 24 likely solved cases of PME involved 18 genes. First, we found and functionally validated five heterozygous variants in NUS1 and DHDDS and a homozygous variant in ALG10, with no previous disease associations. All three genes are involved in dolichol-dependent protein glycosylation, a pathway not previously implicated in PME. Second, we independently validate SEMA6B as a dominant PME gene in two unrelated individuals. Third, in five families, we identified variants in established PME genes; three with intronic or copy-number changes (CLN6, GBA, NEU1) and two very rare causes (ASAH1, CERS1). Fourth, we found a group of genes usually associated with developmental and epileptic encephalopathies, but here, remarkably, presenting as PME, with or without prior developmental delay. Our systematic analysis of these cases suggests that the small residuum of unsolved cases will most likely be a collection of very rare, genetically heterogeneous etiologies.

Keywords:  dolichol-dependent glycosylation; epilepsy genetics; progressive myoclonus epilepsy; whole-exome sequencing

DOI:  https://doi.org/10.1016/j.ajhg.2021.03.013
J Clin Med. 2021 Mar 17. pii: 1249. [Epub ahead of print]10(6):

Mitochondrial Syndromes Revisited.

Daniele Orsucci, Elena Caldarazzo Ienco, Andrea Rossi, Gabriele Siciliano, Michelangelo Mancuso.

  In the last ten years, the knowledge of the genetic basis of mitochondrial diseases has significantly advanced. However, the vast phenotypic variability linked to mitochondrial disorders and the peculiar characteristics of their genetics make mitochondrial disorders a complex group of disorders. Although specific genetic alterations have been associated with some syndromic presentations, the genotype-phenotype relationship in mitochondrial disorders is complex (a single mutation can cause several clinical syndromes, while different genetic alterations can cause similar phenotypes). This review will revisit the most common syndromic pictures of mitochondrial disorders, from a clinical rather than a molecular perspective. We believe that the new phenotype definitions implemented by recent large multicenter studies, and revised here, may contribute to a more homogeneous patient categorization, which will be useful in future studies on natural history and clinical trials.

Keywords:  CPEO; Leigh syndrome; MELAS; MERRF; MNGIE; NARP; PEO; leber; mitochondrial myopathy; mtDNA

DOI:  https://doi.org/10.3390/jcm10061249
Nat Commun. 2021 Mar 31. 12(1): 1981

Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism.

Ruofan Yu, Xiaohua Cao, Luyang Sun, Jun-Yi Zhu, Brian M Wasko, Wei Liu, Emeline Crutcher, Haiying Liu, Myeong Chan Jo, Lidong Qin, Matt Kaeberlein, Zhe Han, Weiwei Dang.

Histone acetylations are important epigenetic markers for transcriptional activation in response to metabolic changes and various stresses. Using the high-throughput SEquencing-Based Yeast replicative Lifespan screen method and the yeast knockout collection, we demonstrate that the HDA complex, a class-II histone deacetylase (HDAC), regulates aging through its target of acetylated H3K18 at storage carbohydrate genes. We find that, in addition to longer lifespan, disruption of HDA results in resistance to DNA damage and osmotic stresses. We show that these effects are due to increased promoter H3K18 acetylation and transcriptional activation in the trehalose metabolic pathway in the absence of HDA. Furthermore, we determine that the longevity effect of HDA is independent of the Cyc8-Tup1 repressor complex known to interact with HDA and coordinate transcriptional repression. Silencing the HDA homologs in C. elegans and Drosophila increases their lifespan and delays aging-associated physical declines in adult flies. Hence, we demonstrate that this HDAC controls an evolutionarily conserved longevity pathway.

DOI: https://doi.org/10.1038/s41467-021-22257-2
Curr Stem Cell Rep. 2020 Dec;6(4): 119-125

Stem Cell Metabolism and Diet.

Marine Barthez, Zehan Song, Chih Ling Wang, Danica Chen.

   Purpose of Review: Diet has profound impacts on health and longevity. Evidence is emerging to suggest that diet impinges upon the metabolic pathways in tissue-specific stem cells to influence health and disease. Here, we review the similarities and differences in the metabolism of stem cells from several tissues, and highlight the mitochondrial metabolic checkpoint in stem cell maintenance and aging. We discuss how diet engages the nutrient sensing metabolic pathways and impacts stem cell maintenance. Finally, we explore the therapeutic implications of dietary and metabolic regulation of stem cells.
Recent findings: Stem Cell transition from quiescence to proliferation is associated with a metabolic switch from glycolysis to mitochondrial OXPHOS and the mitochondrial metabolic checkpoint is critically controlled by the nutrient sensors SIRT2, SIRT3, and SIRT7 in hematopoietic stem cells. Intestine stem cell homeostasis during aging and in response to diet is critically dependent on fatty acid metabolism and ketone bodies and is influenced by the niche mediated by the nutrient sensor mTOR.
Summary: Nutrient sensing metabolic pathways critically regulate stem cell maintenance during aging and in response to diet. Elucidating the molecular mechanisms underlying dietary and metabolic regulation of stem cells provides novel insights for stem cell biology and may be targeted therapeutically to reverse stem cell aging and tissue degeneration.

Keywords:  SIRT2; SIRT3; SIRT7; calorie restriction; mTOR; stem cell metabolism

DOI:  https://doi.org/10.1007/s40778-020-00180-4
Circulation. 2021 Apr 01.

Increased ROS-Mediated CaMKII Activation Contributes to Calcium Handling Abnormalities and Impaired Contraction in Barth Syndrome.

Xujie Liu, Suya Wang, Xiaoling Guo, Yifei Li, Roza Ogurlu, Fujian Lu, Maksymilian Prondzynski, Sofia de la Serna Buzon, Qing Ma, Donghui Zhang, Gang Wang, Justin Cotton, Yuxuan Guo, Ling Xiao, David J Milan, Yang Xu, Michael Schlame, Vassilios J Bezzerides, William T Pu.

  Background: Mutations in tafazzin (TAZ), a gene required for biogenesis of cardiolipin, the signature phospholipid of the inner mitochondrial membrane, causes Barth syndrome (BTHS). Cardiomyopathy and risk of sudden cardiac death are prominent features of BTHS, but the mechanisms by which impaired cardiolipin biogenesis causes cardiac muscle weakness and arrhythmia are poorly understood. Methods: We performed in vivo electrophysiology to define arrhythmia vulnerability in cardiac specific TAZ knockout mice. Using cardiomyocytes derived from human induced pluripotent stem cells (iPSC-CMs) and cardiac specific TAZ knockout mice as model systems, we investigated the effect of TAZ inactivation on Ca2+ handling. Through genome editing and pharmacology, we defined a molecular link between TAZ mutation and abnormal Ca2+ handling and contractility. Results: A subset of mice with cardiac-specific TAZ inactivation developed arrhythmias including bidirectional ventricular tachycardia, atrial tachycardia, and complete atrioventricular block. Compared to WT, BTHS iPSC-CMs had increased diastolic Ca2+ and decreased Ca2+ transient amplitude. BTHS iPSC-CMs had higher levels of mitochondrial and cellular ROS than WT, which activated Ca2+/calmodulin-dependent protein kinase II (CaMKII). Activated CaMKII phosphorylated the cardiac ryanodine receptor (RYR2) on serine 2814, increasing Ca2+ leak through RYR2. Inhibition of this ROS-CaMKII-RYR2 pathway through pharmacological inhibitors or genome editing normalized aberrant Ca2+ handling in BTHS iPSC-CMs and improved their contractile function. Murine Taz knockout cardiomyocytes also exhibited elevated diastolic Ca2+ and decreased Ca2+ transient amplitude. These abnormalities were ameliorated by CaMKII or ROS inhibition. Conclusions: This study identified a molecular pathway that links TAZ mutation to abnormal Ca2+ handling and decreased cardiomyocyte contractility. This pathway may offer therapeutic opportunities to treat BTHS and potentially other diseases with elevated mitochondrial ROS production.

Keywords:  Barth syndrome; cardiolipin; iPSC-CM; mitochondrial disease cardiomyopathy

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.120.048698
Aging (Albany NY). 2021 Apr 02. 13

A novel oral nutritional supplement improves gait speed and mitochondrial functioning compared to standard care in older adults with (or at risk of) undernutrition: results from a randomized controlled trial.

Pol Grootswagers, Ellen Smeets, Antwi-Boasiako Oteng, Lisette de Groot.

  Undernutrition in older adults is mainly addressed by oral nutritional supplements, which do not affect physical functioning. In this study, we tested a novel oral nutritional supplement that included whey and casein protein, ursolic acid, free branch-chained amino acids and vitamin D against a standard supplement. We included older adults (>65y) with (or at risk of) undernutrition (n=82) and randomized them to 12 weeks of novel or standard supplement. Both groups showed significant increases in body mass. No within or between-group differences in lean body mass were observed. Fat mass increased significantly more in the standard than the novel supplement group (time*treatment effect P=0.045). The novel supplement group showed a larger improvement in walking performance on distances of 4m (treatment x time interaction P=0.048) and 400m (treatment x time interaction P=0.038) than the standard treatment group. Gene sets related to mitochondrial functioning and oxidative phosphorylation were upregulated in the novel supplement group and downregulated in the standard supplement group. We conclude that a 12-week intervention with the novel supplement improved walking performance both during short and long distance as compared to a standard supplement, which can largely be explained by increased mitochondrial functioning in the group receiving the novel supplement.

Keywords:  malnutrition; mitochondria; muscle; ursolic acid; walking performance

DOI:  https://doi.org/10.18632/aging.202912
Nat Biotechnol. 2021 Mar 29.

A unified haplotype-based method for accurate and comprehensive variant calling.

Daniel P Cooke, David C Wedge, Gerton Lunter.

Almost all haplotype-based variant callers were designed specifically for detecting common germline variation in diploid populations, and give suboptimal results in other scenarios. Here we present Octopus, a variant caller that uses a polymorphic Bayesian genotyping model capable of modeling sequencing data from a range of experimental designs within a unified haplotype-aware framework. Octopus combines sequencing reads and prior information to phase-called genotypes of arbitrary ploidy, including those with somatic mutations. We show that Octopus accurately calls germline variants in individuals, including single nucleotide variants, indels and small complex replacements such as microinversions. Using a synthetic tumor data set derived from clean sequencing data from a sample with known germline haplotypes and observed mutations in a large cohort of tumor samples, we show that Octopus is more sensitive to low-frequency somatic variation, yet calls considerably fewer false positives than other methods. Octopus also outputs realigned evidence BAM files to aid validation and interpretation.

DOI: https://doi.org/10.1038/s41587-021-00861-3
J Vis Exp. 2021 Mar 14.

Fabrication of 3D Cardiac Microtissue Arrays using Human iPSC-Derived Cardiomyocytes, Cardiac Fibroblasts, and Endothelial Cells.

Dilip Thomas, Hyeonyu Kim, Nicole Lopez, Joseph C Wu.

Generation of human cardiomyocytes (CMs), cardiac fibroblasts (CFs), and endothelial cells (ECs) from induced pluripotent stem cells (iPSCs) has provided a unique opportunity to study the complex interplay among different cardiovascular cell types that drives tissue development and disease. In the area of cardiac tissue models, several sophisticated three-dimensional (3D) approaches use induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) to mimic physiological relevance and native tissue environment with a combination of extracellular matrices and crosslinkers. However, these systems are complex to fabricate without microfabrication expertise and require several weeks to self-assemble. Most importantly, many of these systems lack vascular cells and cardiac fibroblasts that make up over 60% of the nonmyocytes in the human heart. Here we describe the derivation of all three cardiac cell types from iPSCs to fabricate cardiac microtissues. This facile replica molding technique allows cardiac microtissue culture in standard multi-well cell culture plates for several weeks. The platform allows user-defined control over microtissue sizes based on initial seeding density and requires less than 3 days for self-assembly to achieve observable cardiac microtissue contractions. Furthermore, the cardiac microtissues can be easily digested while maintaining high cell viability for single-cell interrogation with the use of flow cytometry and single-cell RNA sequencing (scRNA-seq). We envision that this in vitro model of cardiac microtissues will help accelerate validation studies in drug discovery and disease modeling.

DOI: https://doi.org/10.3791/61879
Nutrients. 2021 Mar 24. pii: 1056. [Epub ahead of print]13(4):

Iron Deficiency without Anemia Decreases Physical Endurance and Mitochondrial Complex I Activity of Oxidative Skeletal Muscle in the Mouse.

Emmanuel Rineau, Naïg Gueguen, Vincent Procaccio, Franck Geneviève, Pascal Reynier, Daniel Henrion, Sigismond Lasocki.

  Iron deficiency (ID), with or without anemia, is responsible for physical fatigue. This effect may be linked to an alteration of mitochondrial metabolism. Our aim was to assess the impact of ID on skeletal striated muscle mitochondrial metabolism. Iron-deficient non-anemic mice, obtained using a bloodletting followed by a low-iron diet for three weeks, were compared to control mice. Endurance was assessed using a one-hour submaximal exercise on a Rotarod device and activities of mitochondrial complexes I and IV were measured by spectrophotometry on two types of skeletal striated muscles, the soleus and the quadriceps. As expected, ID mice displayed hematologic markers of ID and reduced iron stores, although none of them were anemic. In ID mice, endurance was significantly reduced and activity of the respiratory chain complex I, normalized to citrate synthase activity, was significantly reduced in the soleus muscle but not in the quadriceps. Complex IV activities were not significantly different, neither in the soleus nor in the quadriceps. We conclude that ID without anemia is responsible for impaired mitochondrial complex I activity in skeletal muscles with predominant oxidative metabolism. These results bring pathophysiological support to explain the improved physical activity observed when correcting ID in human. Further studies are needed to explore the mechanisms underlying this decrease in complex I activity and to assess the role of iron therapy on muscle mitochondrial metabolism.

Keywords:  complex I; fatigue; iron deficiency; mitochondrial metabolism; physical capacity; striated skeletal muscle

DOI:  https://doi.org/10.3390/nu13041056
Autophagy. 2021 Mar 28. 1-2

Conserved role of ENDOG in promoting autophagy.

Jianshuang Li, Wenjun Wang, Qinghua Zhou.

  ENDOG (endonuclease G), a mitochondrial endonuclease, is known to participate in apoptosis and paternal mitochondria elimination. However, the role and underlying mechanism of ENDOG in regulating macroautophagy remain unclear. We recently reported that ENDOG released from mitochondria promotes autophagy during starvation, which we demonstrated is evolutionarily conserved across species by performing experiments in human cell lines, mice, Drosophila, and C. elegans. This study demonstrates that ENDOG can be phosphorylated by GSK3B, which enhances the interaction between ENDOG with YWHAG and leads to the release of TSC2 and PIK3C3 from YWHAG, followed by MTOR pathway suppression and autophagy initiation. Additionally, the endonuclease activity of ENDOG is essential for activating the DNA damage response and thus inducing autophagy. Consequently, this study uncovered an exciting new role for ENDOG as a crucial regulator of autophagy.

Keywords:  Autophagy; DNA damage response; ENDOG; MTOR; YWHAG

DOI:  https://doi.org/10.1080/15548627.2021.1907513
Bio Protoc. 2021 Mar 05. 11(5): e3939

Generation of Human iPSC-derived Neural Progenitor Cells (NPCs) as Drug Discovery Model for Neurological and Mitochondrial Disorders.

Annika Zink, Pawel Lisowski, Alessandro Prigione.

  The high attrition rate in drug development processes calls for additional human-based model systems. However, in the context of brain disorders, sampling live neuronal cells for compound testing is not applicable. The use of human induced pluripotent stem cells (iPSCs) has revolutionized the field of neuronal disease modeling and drug discovery. Thanks to the development of iPSC-based neuronal differentiation protocols, including tridimensional cerebral organoids, it is now possible to molecularly dissect human neuronal development and human brain disease pathogenesis in a dish. These approaches may allow dissecting patient-specific treatment efficacy in a disease-relevant cellular context. For drug discovery approaches, however, a highly reproducible and cost-effective cell model is desirable. Here, we describe a step-by-step process for generating robust and expandable neural progenitor cells (NPCs) from human iPSCs. NPCs generated with this protocol are homogeneous and highly proliferative. These features make NPCs suitable for the development of high-throughput compound screenings for drug discovery. Human iPSC-derived NPCs show a metabolism dependent on mitochondrial activity and can therefore be used also to investigate neurological disorders in which mitochondrial function is affected. The protocol covers all steps necessary for the preparation, culture, and characterization of human iPSC-derived NPCs. Graphic abstract: Schematic of the protocol for the generation of human iPSC-derived NPCs.

Keywords:  Drug discovery; Human iPSCs; Mitochondrial disorders; Neural progenitor cells; Neuronal disease modeling; Stem cell differentiation

DOI:  https://doi.org/10.21769/BioProtoc.3939
Nat Commun. 2021 03 29. 12(1): 1940

The folate cycle enzyme MTHFD2 induces cancer immune evasion through PD-L1 up-regulation.

Man Shang, Huijie Yang, Ran Yang, Tao Chen, Yuan Fu, Yeyi Li, Xianlong Fang, Kangjian Zhang, Jianju Zhang, Hui Li, Xueping Cao, Jinfa Gu, Jianwen Xiao, Qi Zhang, Xinyuan Liu, Qiujing Yu, Ting Wang.

Metabolic enzymes and metabolites display non-metabolic functions in immune cell signalling that modulate immune attack ability. However, whether and how a tumour's metabolic remodelling contributes to its immune resistance remain to be clarified. Here we perform a functional screen of metabolic genes that rescue tumour cells from effector T cell cytotoxicity, and identify the embryo- and tumour-specific folate cycle enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2). Mechanistically, MTHFD2 promotes basal and IFN-γ-stimulated PD-L1 expression, which is necessary for tumourigenesis in vivo. Moreover, IFN-γ stimulates MTHFD2 through the AKT-mTORC1 pathway. Meanwhile, MTHFD2 drives the folate cycle to sustain sufficient uridine-related metabolites including UDP-GlcNAc, which promotes the global O-GlcNAcylation of proteins including cMYC, resulting in increased cMYC stability and PD-L1 transcription. Consistently, the O-GlcNAcylation level positively correlates with MTHFD2 and PD-L1 in pancreatic cancer patients. These findings uncover a non-metabolic role for MTHFD2 in cell signalling and cancer biology.

DOI: https://doi.org/10.1038/s41467-021-22173-5
Bioinformatics. 2021 Apr 01. pii: btab221. [Epub ahead of print]

ASHLEYS: automated quality control for single-cell Strand-seq data.

Christina Eimer, Ashley D Sanders, Jan O Korbel, Tobias Marschall, Peter Ebert.

SUMMARY: Single-cell DNA template strand sequencing (Strand-seq) enables chromosome length haplotype phasing, construction of phased assemblies, mapping sister-chromatid exchange events and structural variant discovery. The initial quality control of potentially thousands of single-cell libraries is still done manually by domain experts. ASHLEYS automates this tedious task, delivers near-expert performance and labels even large data sets in seconds.
AVAILABILITY AND IMPLEMENTATION: github.com/friendsofstrandseq/ashleys-qc, MIT license.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btab221
Brain. 2021 Apr 01. pii: awab021. [Epub ahead of print]

Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment.

Takeshi Mizuguchi, Tomoko Toyota, Satoko Miyatake, Satomi Mitsuhashi, Hiroshi Doi, Yosuke Kudo, Hitaru Kishida, Noriko Hayashi, Rie S Tsuburaya, Masako Kinoshita, Tetsuhiro Fukuyama, Hiromi Fukuda, Eriko Koshimizu, Naomi Tsuchida, Yuri Uchiyama, Atsushi Fujita, Atsushi Takata, Noriko Miyake, Mitsuhiro Kato, Fumiaki Tanaka, Hiroaki Adachi, Naomichi Matsumoto.

  A pentanucleotide TTTCA repeat insertion into a polymorphic TTTTA repeat element in SAMD12 causes benign adult familial myoclonic epilepsy. Although the precise determination of the entire SAMD12 repeat sequence is important for molecular diagnosis and research, obtaining this sequence remains challenging when using conventional genomic/genetic methods, and even short-read and long-read next-generation sequencing technologies have been insufficient. Incomplete information regarding expanded repeat sequences may hamper our understanding of the pathogenic roles played by varying numbers of repeat units, genotype-phenotype correlations, and mutational mechanisms. Here, we report a new approach for the precise determination of the entire expanded repeat sequence and present a workflow designed to improve the diagnostic rates in various repeat expansion diseases.

Keywords:   SAMD12 ; Cas9-mediated enrichment; benign adult familial myoclonic epilepsy; long-read sequencing; repeat expansion

DOI:  https://doi.org/10.1093/brain/awab021
Biotechnol Adv. 2021 Mar 29. pii: S0734-9750(21)00045-8. [Epub ahead of print] 107739

Using machine learning approaches for multi-omics data analysis: A review.

Parminder S Reel, Smarti Reel, Ewan Pearson, Emanuele Trucco, Emily Jefferson.

  With the development of modern high-throughput omic measurement platforms, it has become essential for biomedical studies to undertake an integrative (combined) approach to fully utilise these data to gain insights into biological systems. Data from various omics sources such as genetics, proteomics, and metabolomics can be integrated to unravel the intricate working of systems biology using machine learning-based predictive algorithms. Machine learning methods offer novel techniques to integrate and analyse the various omics data enabling the discovery of new biomarkers. These biomarkers have the potential to help in accurate disease prediction, patient stratification and delivering of precision medicine. This review paper explores different integrative machine learning methods which have been used to provide an in-depth understanding of biological systems during normal physiological functioning and in the presence of a disease. It provides insight and recommendations for interdisciplinary professionals who envisage employing machine learning skills in multi-omics studies.

Keywords:  Machine Learning; Multi-omics; Predictive Modelling; Supervised Learning; Systems Biology; Unsupervised Learning

DOI:  https://doi.org/10.1016/j.biotechadv.2021.107739
Cell Metab. 2021 Mar 26. pii: S1550-4131(21)00113-3. [Epub ahead of print]

Serine metabolism antagonizes antiviral innate immunity by preventing ATP6V0d2-mediated YAP lysosomal degradation.

Long Shen, Penghui Hu, Yanan Zhang, Zemin Ji, Xiao Shan, Lina Ni, Na Ning, Jing Wang, He Tian, Guanghou Shui, Yukang Yuan, Guoli Li, Hui Zheng, Xiang-Ping Yang, Dandan Huang, Xiangling Feng, Mulin Jun Li, Zhe Liu, Ting Wang, Qiujing Yu.

  Serine metabolism promotes tumor oncogenesis and regulates immune cell functions, but whether it also contributes to antiviral innate immunity is unknown. Here, we demonstrate that virus-infected macrophages display decreased expression of serine synthesis pathway (SSP) enzymes. Suppressing the SSP key enzyme phosphoglycerate dehydrogenase (PHGDH) by genetic approaches or by treatment with the pharmaceutical inhibitor CBR-5884 and by exogenous serine restriction enhanced IFN-β-mediated antiviral innate immunity in vitro and in vivo. Mechanistic experiments showed that virus infection or serine metabolism deficiency increased the expression of the V-ATPase subunit ATP6V0d2 by inhibiting S-adenosyl methionine-dependent H3K27me3 occupancy at the promoter. ATP6V0d2 promoted YAP lysosomal degradation to relieve YAP-mediated blockade of the TBK1-IRF3 axis and, thus, enhance IFN-β production. These findings implicate critical functions of PHGDH and the key immunometabolite serine in blunting antiviral innate immunity and also suggest manipulation of serine metabolism as a therapeutic strategy against virus infection.

Keywords:  ATP6V0d2; H3K27me3; PHGDH; SAM; YAP; antiviral; serine metabolism

DOI:  https://doi.org/10.1016/j.cmet.2021.03.006