bims-mitdis 2021-06-20 papers

bims-mitdis

Biomed News

on Mitochondrial Disorders

Issue of 2021‒06‒20
forty-four papers selected by
Catalina Vasilescu
University of Helsinki

Pathogenic variants in MRPL44 cause infantile cardiomyopathy due to a mitochondrial translation defect.
Human Pluripotent Stem Cells for High-Throughput Drug Screening and Characterization of Small Molecules.
Mitochondrial genome variations are associated with amyotrophic lateral sclerosis in patients from mainland China.
Stepwise maturation of the peptidyl transferase region of human mitoribosomes.
Stress granules inhibit fatty acid oxidation by modulating mitochondrial permeability.
VPS13D interacts with VCP/p97 and negatively regulates ER- mitochondrial interactions.
Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance.
Cellular mechanisms of mtDNA heteroplasmy dynamics.
Parkinson's disease-associated VPS35 mutant reduces mitochondrial membrane potential and impairs PINK1/Parkin-mediated mitophagy.
Cardiolipin Remodeling Defects Impair Mitochondrial Architecture and Function in a Murine Model of Barth Syndrome Cardiomyopathy.
Structural basis for late maturation steps of the human mitoribosomal large subunit.
Flavin Adenine Dinucleotide Depletion Caused by electron transfer flavoprotein subunit alpha Haploinsufficiency Leads to Hepatic Steatosis and Injury in Zebrafish.
Phenolic acid metabolites of polyphenols act as inductors for hormesis in C. elegans.
Molecular mechanisms underlying nucleotide repeat expansion disorders.
Mitochondrial noncoding RNAs: new wine in an old bottle.
Mitochondrial genetic variation in human bioenergetics, adaptation, and adult disease.
A unified framework identifies new links between plasma lipids and diseases from electronic medical records across large-scale cohorts.
Mitochondrial quality control: Epigenetic signatures and therapeutic strategies.
Bi-allelic variants in MTMR5/SBF1 cause Charcot-Marie-Tooth type 4B3 featuring mitochondrial dysfunction.
Loss of the long non-coding RNA OIP5-AS1 exacerbates heart failure in a sex-specific manner.
Mitochondrial CMPK2 mediates immunomodulatory and antiviral activities through IFN-dependent and IFN-independent pathways.
R1441G but not G2019S mutation enhances LRRK2 mediated Rab10 phosphorylation in human peripheral blood neutrophils.
Modifying splice site usage with ModCon: Maintaining the genetic code while changing the underlying mRNP code.
Nampt controls skeletal muscle development by maintaining Ca2+ homeostasis and mitochondrial integrity.
MicroRNAs Regulating Mitochondrial Function in Cardiac Diseases.
Schizosaccharomyces pombe Ppr10 and Mpa1 together mediate mitochondrial translational initiation.
Complex II subunit SDHD is critical for cell growth and metabolism, which can be partially restored with a synthetic ubiquinone analog.
Novel reporters of mitochondria-associated membranes (MAM), MAMtrackers, demonstrate MAM disruption as a common pathological feature in amyotrophic lateral sclerosis.
Regulation of mitochondrial function by noncoding RNAs in heart failure and its application in diagnosis and treatment.
Coenzyme Q10 supplementation - In ageing and disease.
Recent advances in functional annotation and prediction of the epitranscriptome.
The extensive and functionally uncharacterized mitochondrial phosphoproteome.
How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data.
Leber Hereditary Optic Neuropathy: Review of Treatment and Management.
Learning from massive testing of mitochondrial disorders: UPD explaining unorthodox transmission.
Induced pluripotent stem cell-derived motor neurons of CMT type 2 patients reveal progressive mitochondrial dysfunction.
Protective role of the mitochondrial fusion protein OPA1 in hypertension.
Impact of phosphorylation on thermal stability of proteins.
Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling.
Mapping the multiscale structure of biological systems.
Metabolon: a novel cellular structure that regulates specific metabolic pathways.
Intracellular monitoring of NADH release from mitochondria using a single functionalized nanowire electrode.
Predicting biological pathways of chemical compounds with a profile-inspired approach.
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics.

Mol Genet Metab. 2021 Jun 10. pii: S1096-7192(21)00721-6. [Epub ahead of print]

Pathogenic variants in MRPL44 cause infantile cardiomyopathy due to a mitochondrial translation defect.

Marisa W Friederich, Gabrielle C Geddes, Saskia B Wortmann, Ann Punnoose, Eric Wartchow, Kaz M Knight, Holger Prokisch, Geralyn Creadon-Swindell, Johannes A Mayr, Johan L K Van Hove.

  Cardiac dysfunction is a common phenotypic manifestation of primary mitochondrial disease with multiple nuclear and mitochondrial DNA pathogenic variants as a cause, including disorders of mitochondrial translation. To date, five patients have been described with pathogenic variants in MRPL44, encoding the ml44 protein which is part of the large subunit of the mitochondrial ribosome (mitoribosome). Three presented as infants with hypertrophic cardiomyopathy, mild lactic acidosis, and easy fatigue and muscle weakness, whereas two presented in adolescence with myopathy and neurological symptoms. We describe two infants who presented with cardiomyopathy from the neonatal period, failure to thrive, hypoglycemia and in one infant lactic acidosis. A decompensation of the cardiac function in the first year resulted in demise. Exome sequencing identified compound heterozygous variants in the MRPL44 gene including the known pathogenic variant c.467 T > G and two novel pathogenic variants. We document a combined respiratory chain enzyme deficiency with emphasis on complex I and IV, affecting heart muscle tissue more than skeletal muscle or fibroblasts. We show this to be caused by reduced mitochondrial DNA encoded protein synthesis affecting all subunits, and resulting in dysfunction of complex I and IV assembly. The degree of oxidative phosphorylation dysfunction correlated with the impairment of mitochondrial protein synthesis due to different pathogenic variants. These functional studies allow for improved understanding of the pathogenesis of MRPL44-associated mitochondrial disorder.

Keywords:  Cardiomyopathy; Combined deficiency; Genetic cause; Mitochondrial ribosome; Mitochondrial translation

DOI:  https://doi.org/10.1016/j.ymgme.2021.06.001
Methods Mol Biol. 2021 Jun 15.

Human Pluripotent Stem Cells for High-Throughput Drug Screening and Characterization of Small Molecules.

Seungmi Ryu, Pei-Hsuan Chu, Claire Malley, John Braisted, Pinar Ormanoglu, Ruili Huang, Misha Itkin, Zina Itkin, Paul Shinn, Carleen Klumpp-Thomas, Sam Michael, Carlos A Tristan, Anton Simeonov, Ilyas Singeç.

  Human pluripotent stem cells (hPSCs), such as induced pluripotent stem cells (iPSCs), hold great promise for drug discovery, toxicology studies, and regenerative medicine. Here, we describe standardized protocols and experimental procedures that combine automated cell culture for scalable production of hPSCs with quantitative high-throughput screening (qHTS) in miniaturized 384-well plates. As a proof of principle, we established dose-response assessments and determined optimal concentrations of 12 small molecule compounds that are commonly used in the stem cell field. Multi-parametric analysis of readouts from diverse assays including cell viability, mitochondrial membrane potential, plasma membrane integrity, and ATP production was used to distinguish normal biological responses from cellular stress induced by small molecule treatment. Collectively, the establishment of integrated workflows for cell manufacturing, qHTS, high-content imaging, and data analysis provides an end-to-end platform for industrial-scale projects and should leverage the drug discovery process using hPSC-derived cell types.

Keywords:  Cell viability; Dose–response curves; Embryonic stem cells; High-throughput screening; Induced pluripotent stem cells; Robotic cell culture; Small molecules; Toxicity

DOI:  https://doi.org/10.1007/7651_2021_394
J Neurol. 2021 Jun 15.

Mitochondrial genome variations are associated with amyotrophic lateral sclerosis in patients from mainland China.

Jie Ni, Zhen Liu, Yanchun Yuan, Wanzhen Li, Yiting Hu, Pan Liu, Xiaorong Hou, Xiangyu Zhu, Xuxiong Tang, Mingyu Liang, Siqi Zheng, Xuan Hou, Juan Du, Jianguang Tang, Hong Jiang, Lu Shen, Beisha Tang, Junling Wang.

  BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a late-onset neurodegenerative disorder. Mitochondrial dysfunction is involved in the complex pathophysiology of ALS; however, the role of mitochondrial DNA (mtDNA) variants in ALS is poorly understood. We aimed to elucidate the role of mtDNA variants in the pathogenesis of ALS.METHODS: The mitochondrial haplogroups of 585 ALS patients and 371 healthy controls were determined; 38 ALS patients and 42 controls underwent long-range polymerase chain reaction combined with next-generation sequencing technology to analyze whole mitochondrial genome variants.
RESULTS: A higher percentage of variants accumulated in ALS patients than in controls. Analysis of coding region variations that were further stratified by mtDNA genes revealed that nonsynonymous variants were more vulnerable in ALS patients than in controls, particularly in the ND4L, ND5, and ATP8 genes. Moreover, pathogenic nonsynonymous variants tended to over-represent in ALS patients. Unsurprisingly, nonsynonymous variants were not related to the phenotype. Haplogroup analysis did not found evidence of association between haplogroups with the risk of ALS, however, patients belonging to haplogroup Y and M7c were prone to develop later onset of ALS.
CONCLUSIONS: This is the first study to profile mtDNA variants in ALS patients from mainland China. Our results suggest that an increase in the number of nonsynonymous variants is linked to the pathogenesis of ALS. Moreover, haplogroup Y and M7c may modulate the clinical expression of ALS. Our findings provide independent, albeit limited, evidence for the role of mtDNA in the pathogenesis of ALS.

Keywords:  Amyotrophic lateral sclerosis; Long-range polymerase chain reaction; Mitochondrial DNA haplogroup; Mitochondrial DNA variation; Whole mitochondrial genome screening

DOI:  https://doi.org/10.1007/s00415-021-10659-7
Nat Commun. 2021 06 16. 12(1): 3671

Stepwise maturation of the peptidyl transferase region of human mitoribosomes.

Tea Lenarčič, Mateusz Jaskolowski, Marc Leibundgut, Alain Scaiola, Tanja Schönhut, Martin Saurer, Richard G Lee, Oliver Rackham, Aleksandra Filipovska, Nenad Ban.

Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.

DOI: https://doi.org/10.1038/s41467-021-23811-8
Cell Rep. 2021 Jun 15. pii: S2211-1247(21)00596-9. [Epub ahead of print]35(11): 109237

Stress granules inhibit fatty acid oxidation by modulating mitochondrial permeability.

Triana Amen, Daniel Kaganovich.

  The formation of stress granules (SGs) is an essential aspect of the cellular response to many kinds of stress, but its adaptive role is far from clear. SG dysfunction is implicated in aging-onset neurodegenerative diseases, prompting interest in their physiological function. Here, we report that during starvation stress, SGs interact with mitochondria and regulate metabolic remodeling. We show that SG formation leads to a downregulation of fatty acid β-oxidation (FAO) through the modulation of mitochondrial voltage-dependent anion channels (VDACs), which import fatty acids (FAs) into mitochondria. The subsequent decrease in FAO during long-term starvation reduces oxidative damage and rations FAs for longer use. Failure to form SGs, whether caused by the genetic deletion of SG components or an amyotrophic lateral sclerosis (ALS)-associated mutation, translates into an inability to downregulate FAO. Because metabolic dysfunction is a common pathological element of neurodegenerative diseases, including ALS, our findings provide a direction for studying the clinical relevance of SGs.

Keywords:  ALS; VDAC; fatty acid oxidation; lipid droplet; lipid metabolism; metabolic adaptation; mitochondria; porin; starvation; stress granule

DOI:  https://doi.org/10.1016/j.celrep.2021.109237
Mol Biol Cell. 2021 Jun 16. mbcE21030097

VPS13D interacts with VCP/p97 and negatively regulates ER- mitochondrial interactions.

Yuanjiao Du, Jingru Wang, Juan Xiong, Na Fang, Wei-Ke Ji.

Membrane contact sites (MCSs) between the endoplasmic reticulum (ER) and mitochondria are emerging as critical hubs for diverse cellular events, and alterations in the extent of these contacts are linked to neurodegenerative diseases. However, the mechanisms that control ER-mitochondrial interactions are so far elusive. Here, we demonstrate a key role of vacuolar protein sorting-associated protein 13D (VPS13D) in the negative regulation of ER-mitochondrial MCSs. VPS13D suppression results in extensive ER-mitochondrial tethering, a phenotype that can be substantially rescued by suppression of the tethering proteins VAPB and PTPIP51. VPS13D interacts with valosin-containing protein (VCP/p97) to control the level of ER-resident VAPB at contacts. VPS13D is required for the stability of p97. Functionally, VPS13D suppression leads to severe defects in the mitochondrial morphology, mitochondrial cellular distribution and mitochondrial DNA synthesis. Together our results suggest that VPS13D negatively regulates the ER-mitochondrial MCSs partially through its interactions with VCP/p97. [Media: see text].

DOI: https://doi.org/10.1091/mbc.E21-03-0097
Nat Commun. 2021 06 14. 12(1): 3607

Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance.

Ravi Kiran Koripella, Ayush Deep, Ekansh K Agrawal, Pooja Keshavan, Nilesh K Banavali, Rajendra K Agrawal.

Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRFmt) and a recycling-specific homolog of elongation factor G (EF-G2mt). These structures clarify an unusual role of a mitochondria-specific segment of RRFmt, identify the structural distinctions that confer functional specificity to EF-G2mt, and show that the deacylated tRNA remains with the dissociated 39S subunit, suggesting a distinct sequence of events in mitoribosome recycling. Furthermore, biochemical and structural analyses reveal that the molecular mechanism of antibiotic fusidic acid resistance for EF-G2mt is markedly different from that of mitochondrial elongation factor EF-G1mt, suggesting that the two human EF-Gmts have evolved diversely to negate the effect of a bacterial antibiotic.

DOI: https://doi.org/10.1038/s41467-021-23726-4
Crit Rev Biochem Mol Biol. 2021 Jun 13. 1-16

Cellular mechanisms of mtDNA heteroplasmy dynamics.

Claudia V Pereira, Bryan L Gitschlag, Maulik R Patel.

  Heteroplasmy refers to the coexistence of more than one variant of the mitochondrial genome (mtDNA). Mutated or partially deleted mtDNAs can induce chronic metabolic impairment and cause mitochondrial diseases when their heteroplasmy levels exceed a critical threshold. These mutant mtDNAs can be maternally inherited or can arise de novo. Compelling evidence has emerged showing that mutant mtDNA levels can vary and change in a nonrandom fashion across generations and amongst tissues of an individual. However, our lack of understanding of the basic cellular and molecular mechanisms of mtDNA heteroplasmy dynamics has made it difficult to predict who will inherit or develop mtDNA-associated diseases. More recently, with the advances in technology and the establishment of tractable model systems, insights into the mechanisms underlying the selection forces that modulate heteroplasmy dynamics are beginning to emerge. In this review, we summarize evidence from different organisms, showing that mutant mtDNA can experience both positive and negative selection. We also review the recently identified mechanisms that modulate heteroplasmy dynamics. Taken together, this is an opportune time to survey the literature and to identify key cellular pathways that can be targeted to develop therapies for diseases caused by heteroplasmic mtDNA mutations.

Keywords:  Heteroplasmy dynamics; mitochondria; mitochondrial genetics; mtDNA; selection

DOI:  https://doi.org/10.1080/10409238.2021.1934812
Transl Neurodegener. 2021 Jun 15. 10(1): 19

Parkinson's disease-associated VPS35 mutant reduces mitochondrial membrane potential and impairs PINK1/Parkin-mediated mitophagy.

Kai Yu Ma, Michiel R Fokkens, Fulvio Reggiori, Muriel Mari, Dineke S Verbeek.

  BACKGROUND: Mitochondrial dysfunction plays a prominent role in the pathogenesis of Parkinson's disease (PD), and several genes linked to familial PD, including PINK1 (encoding PTEN-induced putative kinase 1 [PINK1]) and PARK2 (encoding the E3 ubiquitin ligase Parkin), are directly involved in processes such as mitophagy that maintain mitochondrial health. The dominant p.D620N variant of vacuolar protein sorting 35 ortholog (VPS35) gene is also associated with familial PD but has not been functionally connected to PINK1 and PARK2.METHODS: To better mimic and study the patient situation, we used CRISPR-Cas9 to generate heterozygous human SH-SY5Y cells carrying the PD-associated D620N variant of VPS35. These cells were treated with a protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP) to induce the PINK1/Parkin-mediated mitophagy, which was assessed using biochemical and microscopy approaches.
RESULTS: Mitochondria in the VPS35-D620N cells exhibited reduced mitochondrial membrane potential and appeared to already be damaged at steady state. As a result, the mitochondria of these cells were desensitized to the CCCP-induced collapse in mitochondrial potential, as they displayed altered fragmentation and were unable to accumulate PINK1 at their surface upon this insult. Consequently, Parkin recruitment to the cell surface was inhibited and initiation of the PINK1/Parkin-dependent mitophagy was impaired.
CONCLUSION: Our findings extend the pool of evidence that the p.D620N mutation of VPS35 causes mitochondrial dysfunction and suggest a converging pathogenic mechanism among VPS35, PINK1 and Parkin in PD.

Keywords:  Mitochondrial membrane potential; Mitophagy; PINK1; Parkin; Parkinson’s disease; VPS35

DOI:  https://doi.org/10.1186/s40035-021-00243-4
Circ Heart Fail. 2021 Jun;14(6): e008289

Cardiolipin Remodeling Defects Impair Mitochondrial Architecture and Function in a Murine Model of Barth Syndrome Cardiomyopathy.

Siting Zhu, Ze'e Chen, Mason Zhu, Ying Shen, Leonardo J Leon, Liguo Chi, Simone Spinozzi, Changming Tan, Yusu Gu, Anh Nguyen, Yi Zhou, Wei Feng, Frédéric M Vaz, Xiaohong Wang, Asa B Gustafsson, Sylvia M Evans, Ouyang Kunfu, Xi Fang.

  BACKGROUND: Cardiomyopathy is a major clinical feature in Barth syndrome (BTHS), an X-linked mitochondrial lipid disorder caused by mutations in Tafazzin (TAZ), encoding a mitochondrial acyltransferase required for cardiolipin remodeling. Despite recent description of a mouse model of BTHS cardiomyopathy, an in-depth analysis of specific lipid abnormalities and mitochondrial form and function in an in vivo BTHS cardiomyopathy model is lacking.METHODS: We performed in-depth assessment of cardiac function, cardiolipin species profiles, and mitochondrial structure and function in our newly generated Taz cardiomyocyte-specific knockout mice and Cre-negative control mice (n≥3 per group).
RESULTS: Taz cardiomyocyte-specific knockout mice recapitulate typical features of BTHS and mitochondrial cardiomyopathy. Fewer than 5% of cardiomyocyte-specific knockout mice exhibited lethality before 2 months of age, with significantly enlarged hearts. More than 80% of cardiomyocyte-specific knockout displayed ventricular dilation at 16 weeks of age and survived until 50 weeks of age. Full parameter analysis of cardiac cardiolipin profiles demonstrated lower total cardiolipin concentration, abnormal cardiolipin fatty acyl composition, and elevated monolysocardiolipin to cardiolipin ratios in Taz cardiomyocyte-specific knockout, relative to controls. Mitochondrial contact site and cristae organizing system and F1F0-ATP synthase complexes, required for cristae morphogenesis, were abnormal, resulting in onion-shaped mitochondria. Organization of high molecular weight respiratory chain supercomplexes was also impaired. In keeping with observed mitochondrial abnormalities, seahorse experiments demonstrated impaired mitochondrial respiration capacity.
CONCLUSIONS: Our mouse model mirrors multiple physiological and biochemical aspects of BTHS cardiomyopathy. Our results give important insights into the underlying cause of BTHS cardiomyopathy and provide a framework for testing therapeutic approaches to BTHS cardiomyopathy, or other mitochondrial-related cardiomyopathies.

Keywords:  Barth syndrome; cardiolipin; cardiomyopathy; mice; mitochondria

DOI:  https://doi.org/10.1161/CIRCHEARTFAILURE.121.008289
Nat Commun. 2021 06 16. 12(1): 3673

Structural basis for late maturation steps of the human mitoribosomal large subunit.

Miriam Cipullo, Genís Valentín Gesé, Anas Khawaja, B Martin Hällberg, Joanna Rorbach.

Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determine the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5, allowing us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis. Our structures provide essential insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16 S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangements leading to PTC formation. Moreover, our data reveal an unexpected involvement of the elongation factor mtEF-Tu in mt-LSU assembly, where mtEF-Tu interacts with GTPBP5, similar to its interaction with tRNA during translational elongation.

DOI: https://doi.org/10.1038/s41467-021-23617-8
Hepatol Commun. 2021 Jun;5(6): 976-991

Flavin Adenine Dinucleotide Depletion Caused by electron transfer flavoprotein subunit alpha Haploinsufficiency Leads to Hepatic Steatosis and Injury in Zebrafish.

Ki-Hoon Park, Monika Gooz, Zhi-Wei Ye, Jie Zhang, Gyda C Beeson, Don C Rockey, Seok-Hyung Kim.

The electron transfer flavoprotein (ETF) complex, made up of the ETF alpha subunit (ETFA), ETF beta subunit (ETFB), and ETF dehydrogenase (ETFDH), regulates fatty acid β-oxidation activity while scavenging leaked electrons through flavin adenine dinucleotide (FAD)/reduced form FAD (FADH2) redox reactions in mitochondria. Here, we hypothesized that ETF dysfunction-mediated FAD deficiency may result in increased mitochondrial oxidative stress and steatosis and subsequent liver injury. We report that etfa haploinsufficiency caused hyperlipidemia, hypercholesterolemia, and hepatic steatosis and injury in adult zebrafish. Further, etfa+/ - mutant livers had reduced levels of FAD and glutathione and an increase in reactive oxygen species. Because FAD depletion might be critical in the pathogenesis of the liver lesion identified in etfa+/ - mutants, we used riboflavin to elevate FAD levels in the liver and found that riboflavin supplementation significantly suppressed hepatic steatosis and injury in etfa+/ - mutants through suppression of oxidative stress and de novo lipogenesis in the liver. Additionally, we found that adenosine triphosphate-linked mitochondrial oxygen consumption and mitochondrial membrane potential were reduced in etfa+/ - primary hepatocytes and that riboflavin supplementation corrected these defects. Conclusion: FAD depletion caused by etfa haploinsufficiency plays a key role in hepatic steatosis and oxidative stress-mediated hepatic injury in adult zebrafish. This raises the possibility that people with ETFA haploinsufficiency have a high risk for developing liver disease.

DOI: https://doi.org/10.1002/hep4.1691
Mech Ageing Dev. 2021 Jun 14. pii: S0047-6374(21)00090-7. [Epub ahead of print] 111518

Phenolic acid metabolites of polyphenols act as inductors for hormesis in C. elegans.

Benjamin Dilberger, Selina Weppler, Gunter P Eckert.

  INTRODUCTION: Aging represents a major risk factors for metabolic diseases, such as diabetes, obesity, or neurodegeneration. Polyphenols and their metabolites, especially simple phenolic acids, gained growing attention as a preventive strategy against age-related, non-communicable diseases, due to their hormetic potential. Using Caenorhabditis elegans (C. elegans) we investigate the effect of protocatechuic, gallic and vanillic acid on mitochondrial function, health parameters, and the induction of potential hormetic pathways.METHODS: Lifespan, heat-stress resistance and chemotaxis of C. elegans strain P X 627, a specific model for aging, were assessed in 2-day and 10-day old nematodes. Mitochondrial membrane potential (ΔΨm) and ATP generation was measured. mRNA expression levels of longevity and energy metabolism-related genes were determined using qRT-PCR.
RESULTS: All phenolic acids were able to significantly increase the nematodes lifespan, heat-stress resistance and chemotaxis at micromolar concentrations. While ΔΨm was only affected by age, vanillic acid (VA) significantly decreased ATP concentrations in aged nematodes. Longevity pathways, were activated by all phenolic acids, while VA also induced glycolytic activity and response to cold.
CONCLUSION: While life- and health span parameters are positively affected by the investigated phenolic acids, the concentrations applied were unable to affect mitochondrial performance. Therefore we suggest a hormetic mode of action, especially by activation of the sirtuin-pathway.

Keywords:  C. elegans; Hormesis; Metabolites; Mitochondria; PX627; Polyphenols

DOI:  https://doi.org/10.1016/j.mad.2021.111518
Nat Rev Mol Cell Biol. 2021 Jun 17.

Molecular mechanisms underlying nucleotide repeat expansion disorders.

Indranil Malik, Chase P Kelley, Eric T Wang, Peter K Todd.

The human genome contains more than one million short tandem repeats, and expansion of a subset of these repeat tracts underlies more than 50 human disorders. In this Review, we discuss the four major mechanisms by which expansion of short tandem repeats causes disease: loss of function through transcription repression, RNA-mediated gain of function through gelation and sequestration of RNA-binding proteins, gain of function of canonically translated repeat-harbouring proteins, and repeat-associated non-AUG translation of toxic repeat peptides. Somatic repeat instability amplifies these mechanisms and influences both disease age of onset and tissue specificity of pathogenic features. We focus on the crosstalk between these disease mechanisms, and argue that they often synergize to drive pathogenesis. We also discuss the emerging native functions of repeat elements and how their dynamics might contribute to disease at a larger scale than currently appreciated. Lastly, we propose that lynchpins tying these disease mechanisms and native functions together offer promising therapeutic targets with potential shared applications across this class of human disorders.

DOI: https://doi.org/10.1038/s41580-021-00382-6
RNA Biol. 2021 Jun 10. 1-15

Mitochondrial noncoding RNAs: new wine in an old bottle.

Huixin Liang, Jiayu Liu, Shicheng Su, Qiyi Zhao.

  Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.

Keywords:  Mitochondria; mitochondrial circRNAs; mitochondrial long noncoding RNAs; mitochondrial microRNAs; mitochondrial noncoding RNAs

DOI:  https://doi.org/10.1080/15476286.2021.1935572
Am J Hum Biol. 2021 Jun 19. e23629

Mitochondrial genetic variation in human bioenergetics, adaptation, and adult disease.

Volney K Friedrich, Meagan A Rubel, Theodore G Schurr.

OBJECTIVES: Mitochondria are critical for the survival of eukaryotic organisms due to their ability to produce cellular energy, which drives virtually all aspects of host biology. However, the effects of mitochondrial DNA (mtDNA) variation in relation to disease etiology and adaptation within contemporary global human populations remains incompletely understood.METHODS: To develop a more holistic understanding of the role of mtDNA diversity in human adaptation, health, and disease, we investigated mitochondrial biology and bioenergetics. More specifically, we synthesized details from studies of mitochondrial function and variation in the context of haplogroup background, climatic adaptation, and oxidative disease.
RESULTS: The majority of studies show that mtDNA variation arose during modern human dispersal around the world. Some of these variants appear to have been positively selected for their adaptiveness in colder climates, with these sequence changes having implications for tissue-specific function and thermogenic capacity. In addition, many variants modulating energy production are also associated with damaging metabolic byproducts and mitochondrial dysfunction, which, in turn, are implicated in the onset and severity of several different adult mitochondrial diseases. Thus, mtDNA variation that governs bioenergetics, metabolism, and thermoregulation may potentially have adverse consequences for human health, depending on the genetic background and context in which it occurs.
CONCLUSIONS: Our review suggests that the mitochondrial research field would benefit from independently replicating mtDNA haplogroup-phenotype associations across global populations, incorporating potentially confounding environmental, demographic, and disease covariates into studies of mtDNA variation, and extending association-based studies to include analyses of complete mitogenomes and assays of mitochondrial function.

DOI: https://doi.org/10.1002/ajhb.23629
Nat Genet. 2021 Jun 17.

A unified framework identifies new links between plasma lipids and diseases from electronic medical records across large-scale cohorts.

Yogasudha Veturi, Anastasia Lucas, Yuki Bradford, Daniel Hui, Scott Dudek, Elizabeth Theusch, Anurag Verma, Jason E Miller, Iftikhar Kullo, Hakon Hakonarson, Patrick Sleiman, Daniel Schaid, Charles M Stein, Digna R Velez Edwards, QiPing Feng, Wei-Qi Wei, Marisa W Medina, Ronald M Krauss, Thomas J Hoffmann, Neil Risch, Benjamin F Voight, Daniel J Rader, Marylyn D Ritchie.

Plasma lipids are known heritable risk factors for cardiovascular disease, but increasing evidence also supports shared genetics with diseases of other organ systems. We devised a comprehensive three-phase framework to identify new lipid-associated genes and study the relationships among lipids, genotypes, gene expression and hundreds of complex human diseases from the Electronic Medical Records and Genomics (347 traits) and the UK Biobank (549 traits). Aside from 67 new lipid-associated genes with strong replication, we found evidence for pleiotropic SNPs/genes between lipids and diseases across the phenome. These include discordant pleiotropy in the HLA region between lipids and multiple sclerosis and putative causal paths between triglycerides and gout, among several others. Our findings give insights into the genetic basis of the relationship between plasma lipids and diseases on a phenome-wide scale and can provide context for future prevention and treatment strategies.

DOI: https://doi.org/10.1038/s41588-021-00879-y
Neurochem Int. 2021 Jun 08. pii: S0197-0186(21)00141-8. [Epub ahead of print]148 105095

Mitochondrial quality control: Epigenetic signatures and therapeutic strategies.

Tanuja Ambekar, Jyoti Pawar, Ramdev Rathod, Monica Patel, Valencia Fernandes, Rahul Kumar, Shashi Bala Singh, Dharmendra Kumar Khatri.

  Mitochondria are semi-autonomous organelle staging a crucial role in cellular stress response, energy metabolism and cell survival. Maintaining mitochondrial quality control is very important for its homeostasis. Pathological conditions such as oxidative stress and neurodegeneration, disrupt this quality control, and involvement of genetic and epigenetic materials in this disruption have been reported. These regulatory factors trigger mitochondrial imbalance, as seen in many neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, and Huntington's disease. The dynamic regulatory pathways i.e. mitophagy, biogenesis, permeability pore transitioning, fusion-fission are affected as a consequence and have been reviewed in this article. Moreover, several epigenetic mechanisms such as DNA methylation and histone modulation participating in such neurological disorders have also been discussed. Apart from it, therapeutic approaches targeting mitochondrial quality control have been tremendously explored showing ameliorative effects for these diseases, and have been discussed here with a novel perspective.

Keywords:  Biogenesis; DNA methylation; Histone acetylation; Mitochondrial quality control; Mitophagy; Neurodegeneration

DOI:  https://doi.org/10.1016/j.neuint.2021.105095
BMC Med Genomics. 2021 Jun 12. 14(1): 157

Bi-allelic variants in MTMR5/SBF1 cause Charcot-Marie-Tooth type 4B3 featuring mitochondrial dysfunction.

Beatrice Berti, Giovanna Longo, Francesco Mari, Stefano Doccini, Ilaria Piccolo, Maria Alice Donati, Francesca Moro, Renzo Guerrini, Filippo M Santorelli, Vittoria Petruzzella.

  BACKGROUND: Charcot-Marie-Tooth disease (CMT) type 4B3 (CMT4B3) is a rare form of genetic neuropathy associated with variants in the MTMR5/SBF1 gene. MTMR5/SBF1 is a pseudophosphatase predicted to regulate endo-lysosomal trafficking in tandem with other MTMRs. Although almost ubiquitously expressed, pathogenic variants primarily impact on the peripheral nervous system, corroborating the involvement of MTMR5/SBF1 and its molecular partners in Schwann cells-mediated myelinization.CASE PRESENTATION: We report a case of severe CMT4B3 characterized by early-onset motor and axonal polyneuropathy in an Italian child in absence of any evidence of brain and spine MRI abnormalities or intellectual disability and with a biochemical profile suggestive of mitochondrial disease. Using an integrated approach combining both NGS gene panels and WES analysis, we identified two novel compound heterozygous missense variants in MTMR5/SBF1 gene, p.R763H (c.2291G > A) and p.G1064E (c.3194G > A). Studies in muscle identified partial defects of oxidative metabolism.
CONCLUSION: We describe the first case of an early onset severe polyneuropathy with motor and axonal involvement, due to recessive variants in the MTMR5/SBF1 gene, with no evidence of brain and spine MRI abnormalities, intellectual disability, no clinical and neurophysiological evidences of distal sensory impairment, and rapid neuromuscular deterioration. This report suggests that MTMR5/SBF1 should be considered in cases of infantile-onset CMT with secondary mitochondrial dysfunction.

Keywords:  Case report; Charcot-Marie-Tooth 4B3; MTMR5/SBF1; Mitochondrial diseases; Next-generation sequencing

DOI:  https://doi.org/10.1186/s12920-021-01001-1
iScience. 2021 Jun 25. 24(6): 102537

Loss of the long non-coding RNA OIP5-AS1 exacerbates heart failure in a sex-specific manner.

Aowen Zhuang, Anna C Calkin, Shannen Lau, Helen Kiriazis, Daniel G Donner, Yingying Liu, Simon T Bond, Sarah C Moody, Eleanor A M Gould, Timothy D Colgan, Sergio Ruiz Carmona, Michael Inouye, Thomas Q de Aguiar Vallim, Elizabeth J Tarling, Gregory A Quaife-Ryan, James E Hudson, Enzo R Porrello, Paul Gregorevic, Xiao-Ming Gao, Xiao-Jun Du, Julie R McMullen, Brian G Drew.

  Long non-coding RNAs (lncRNAs) have been demonstrated to influence numerous biological processes, being strongly implicated in the maintenance and physiological function of various tissues including the heart. The lncRNA OIP5-AS1 (1700020I14Rik/Cyrano) has been studied in several settings; however its role in cardiac pathologies remains mostly uncharacterized. Using a series of in vitro and ex vivo methods, we demonstrate that OIP5-AS1 is regulated during cardiac development in rodent and human models and in disease settings in mice. Using CRISPR, we engineered a global OIP5-AS1 knockout (KO) mouse and demonstrated that female KO mice develop exacerbated heart failure following cardiac pressure overload (transverse aortic constriction [TAC]) but male mice do not. RNA-sequencing of wild-type and KO hearts suggest that OIP5-AS1 regulates pathways that impact mitochondrial function. Thus, these findings highlight OIP5-AS1 as a gene of interest in sex-specific differences in mitochondrial function and development of heart failure.

Keywords:  Cardiovascular medicine; Molecular physiology; Transcriptomics

DOI:  https://doi.org/10.1016/j.isci.2021.102537
iScience. 2021 Jun 25. 24(6): 102498

Mitochondrial CMPK2 mediates immunomodulatory and antiviral activities through IFN-dependent and IFN-independent pathways.

Jenn-Haung Lai, De-Wei Wu, Chien-Hsiang Wu, Li-Feng Hung, Chuan-Yueh Huang, Shuk-Man Ka, Ann Chen, Zee-Fen Chang, Ling-Jun Ho.

  Mitochondria regulate the immune response after dengue virus (DENV) infection. Microarray analysis of genes identified the upregulation of mitochondrial cytidine/uridine monophosphate kinase 2 (CMPK2) by DENV infection. We used small interfering RNA-mediated knockdown (KD) and CRISPR-Cas9 knockout (KO) approaches, to investigate the role of CMPK2 in mouse and human cells. The results showed that CMPK2 was critical in DENV-induced antiviral cytokine release and mitochondrial oxidative stress and mitochondrial DNA release to the cytosol. The DENV-induced activation of Toll-like receptor (TLR)-9, inflammasome pathway, and cell migration was suppressed by CMPK2 depletion; however, viral production increased under CMPK2 deficiency. Examining mouse bone marrow-derived dendritic cells from interferon-alpha (IFN-α) receptor-KO mice and signal transducer and activator of transcription 1 (STAT1)-KO mice, we confirmed that CMPK2-mediated antiviral activity occurred in IFN-dependent and IFN-independent manners. In sum, CMPK2 is a critical factor in DENV-induced immune responses to determine innate immunity.

Keywords:  Immunology; Molecular biology; Virology

DOI:  https://doi.org/10.1016/j.isci.2021.102498
Acta Neuropathol. 2021 Jun 14.

R1441G but not G2019S mutation enhances LRRK2 mediated Rab10 phosphorylation in human peripheral blood neutrophils.

Ying Fan, Raja S Nirujogi, Alicia Garrido, Javier Ruiz-Martínez, Alberto Bergareche-Yarza, Elisabet Mondragón-Rezola, Ana Vinagre-Aragón, Ioana Croitoru, Ana Gorostidi Pagola, Laura Paternain Markinez, Roy Alcalay, Richard A Hickman, Jonas Düring, Sara Gomes, Neringa Pratuseviciute, Shalini Padmanabhan, Francesc Valldeoriola, Leticia Pérez Sisqués, Cristina Malagelada, Teresa Ximelis, Laura Molina Porcel, Maria José Martí, Eduardo Tolosa, Dario R Alessi, Esther M Sammler.

  Heterozygous gain-of-kinase function variants in LRRK2 (leucine-rich repeat kinase 2) cause 1-2% of all cases of Parkinson's disease (PD) albeit with incomplete and age-dependent penetrance. All pathogenic LRRK2 mutations reside within the two catalytic domains of LRRK2-either in its kinase domain (e.g. G2019S) with modest effect or its ROC-COR GTPase domain (e.g. R1441G/H) with large effect on LRRK2 kinase activity. We have previously reported assays to interrogate LRRK2 kinase pathway activity in human bio-samples measuring phosphorylation of its endogenous substrate Rab10, that mirrors LRRK2 kinase activation status. Here, we isolated neutrophils from fresh peripheral blood from 101 participants including 42 LRRK2 mutation carriers (21 with the G2019S and 21 with the R1441G mutations), 27 patients with idiopathic PD, and 32 controls. Using a dual approach, LRRK2 dependent Rab10 phosphorylation at Threonine 73 (pRab10Thr73) was measured by quantitative multiplexed immunoblotting for pRab10Thr73/total Rab10 as well as targeted mass-spectrometry for absolute pRab10Thr73 occupancy. We found a significant over fourfold increase in pRab10Thr73 phosphorylation in carriers of the LRRK2 R1441G mutation irrespective of clinical disease status. The effect of the LRRK2 G2019S mutation did not reach statistical significance. Furthermore, we show that LRRK2 phosphorylation at Serine 935 is not a marker for LRRK2 kinase activity in human neutrophils. When analysing pRab10Thr73 phosphorylation in post-mortem brain samples, we observed overall high variability irrespective of clinical and LRRK2 mutation status and attributed this mainly to the adverse effect of the peri- and post-mortem period on the stability of posttranslational modifications such as protein phosphorylation. Overall, in vivo LRRK2 dependent pRab10Thr73 phosphorylation in human peripheral blood neutrophils is a specific, robust and promising biomarker for significant LRRK2 kinase hyperactivation, as with the LRRK2 R1441G mutation. Additional readouts and/or assays may be needed to increase sensitivity to detect modest LRRK2 kinase activation, as with the LRRK2 G2019S mutation. Our assays could be useful for patient stratification and target engagement studies for LRRK2 kinase inhibitors.

Keywords:  Biomarkers; LRRK2; LRRK2 kinase inhibitors; Parkinson’s disease; Protein phosphorylation; RabGTPases

DOI:  https://doi.org/10.1007/s00401-021-02325-z
Comput Struct Biotechnol J. 2021 ;19 3069-3076

Modifying splice site usage with ModCon: Maintaining the genetic code while changing the underlying mRNP code.

Johannes Ptok, Lisa Müller, Philipp Niklas Ostermann, Anastasia Ritchie, Alexander T Dilthey, Stephan Theiss, Heiner Schaal.

  Codon degeneracy of amino acid sequences permits an additional "mRNP code" layer underlying the genetic code that is related to RNA processing. In pre-mRNA splicing, splice site usage is determined by both intrinsic strength and sequence context providing RNA binding sites for splicing regulatory proteins. In this study, we systematically examined modification of splicing regulatory properties in the neighborhood of a GT site, i.e. potential splice site, without altering the encoded amino acids. We quantified the splicing regulatory properties of the neighborhood around a potential splice site by its Splice Site HEXplorer Weight (SSHW) based on the HEXplorer score algorithm. To systematically modify GT site neighborhoods, either minimizing or maximizing their SSHW, we designed the novel stochastic optimization algorithm ModCon that applies a genetic algorithm with stochastic crossover, insertion and random mutation elements supplemented by a heuristic sliding window approach. To assess the achievable range in SSHW in human splice donors without altering the encoded amino acids, we applied ModCon to a set of 1000 randomly selected Ensembl annotated human splice donor sites, achieving substantial and accurate changes in SSHW. Using ModCon optimization, we successfully switched splice donor usage in a splice site competition reporter containing coding sequences from FANCA, FANCB or BRCA2, while retaining their amino acid coding information. The ModCon algorithm and its R package implementation can assist in reporter design by either introducing novel splice sites, silencing accidental, undesired splice sites, and by generally modifying the entire mRNP code while maintaining the genetic code.

Keywords:  A, adenine; F1, filial sequence 1; G, guanine; GA, genetic algorithm; HBS, HBond score; HBond score; HEXplorer score; HZEI, HEXplorer score; P1, parental sequence 1; SA, splice acceptor; SD, splice donor; SR proteins, serine- and arginine-rich proteins; SRP, splicing regulatory protein; SSHW, splice site HEXplorer weight; SW, sliding window; Splice donor; Splicing regulatory proteins; Splicing reporter; T, thymine; eGFP, enhanced green fluorescent protein; hnRNP, heterogeneous nuclear ribonucleoproteins; nt, nucleotides; pre-mRNA splicing; pre-mRNA, precursor messenger RNA; snRNA, small nuclear RNA

DOI:  https://doi.org/10.1016/j.csbj.2021.05.033
Mol Metab. 2021 Jun 10. pii: S2212-8778(21)00116-2. [Epub ahead of print] 101271

Nampt controls skeletal muscle development by maintaining Ca2+ homeostasis and mitochondrial integrity.

Astrid L Basse, Marianne Agerholm, Jean Farup, Emilie Dalbram, Joachim Nielsen, Niels Ørtenblad, Ali Altıntaş, Amy M Ehrlich, Thomas Krag, Santina Bruzzone, Morten Dall, Roldan M de Guia, Jonas B Jensen, Andreas B Møller, Anders Karlsen, Michael Kjær, Romain Barrès, John Vissing, Steen Larsen, Niels Jessen, Jonas T Treebak.

  OBJECTIVE: NAD+ is a co-factor and substrate for enzymes maintaining energy homeostasis. Nicotinamide phosphoribosyltransferase (NAMPT) controls NAD+ synthesis, and in skeletal muscle, NAD+ is important for muscle integrity. However, the underlying molecular mechanisms by which NAD+ synthesis affects muscle health remain poorly understood. Thus, the objective of the current study was to delineate the role of NAMPT-mediated NAD+ biosynthesis in skeletal muscle development and function.METHODS: To determine the role of Nampt in muscle development and function, we generated skeletal muscle-specific Nampt KO (SMNKO) mice. We performed a comprehensive phenotypic characterization of the SMNKO mice including metabolic measurements, histological examinations, and RNA sequencing analyses of skeletal muscle from SMNKO mice and WT littermates.
RESULTS: SMNKO mice are smaller, with phenotypic changes in skeletal muscle, including reduced fiber area and increased number of centralized nuclei. The majority of SMNKO mice die prematurely. Transcriptomic analysis identified that the gene encoding the mitochondrial permeability transition pore (mPTP) regulator Cyclophilin D (Ppif) is upregulated in skeletal muscle of SMNKO mice from 2 weeks of age, with associated increased sensitivity of mitochondria to Ca2+-stimulated mPTP opening. Treatment of SMNKO mice with the Cyclophilin D inhibitor, Cyclosporine A, increased membrane integrity, decreased the number of centralized nuclei, and increased survival.
CONCLUSION: Our study demonstrates that NAMPT is crucial for maintaining cellular Ca2+ homeostasis and skeletal muscle development, which is vital for juvenile survival.

Keywords:  Cyclophilin D; NAD(+); mitochondrial permeability transition pore (mPTP); myopathy; nicotinamide riboside; sarcopenia

DOI:  https://doi.org/10.1016/j.molmet.2021.101271
Front Pharmacol. 2021 ;12 663322

MicroRNAs Regulating Mitochondrial Function in Cardiac Diseases.

Guang-Qiong Zhang, Sheng-Quan Wang, Yan Chen, Ling-Yun Fu, Yi-Ni Xu, Ling Li, Ling Tao, Xiang-Chun Shen.

  Mitochondria are the key organelles that supply cellular energy. As the most active organ in the body, the energy required to maintain the mechanical function of the heart requires a high quantity of high-quality mitochondria in cardiomyocytes. MicroRNAs (miRNAs) are single-stranded noncoding RNAs, approximately 22 nt in length, which play key roles in mediating post-transcriptional gene silencing. Numerous studies have confirmed that miRNAs can participate in the occurrence and development of cardiac diseases by regulating mitochondrial function-related genes and signaling pathways. Therefore, elucidating the crosstalk that occurs between miRNAs and mitochondria is important for the prevention and treatment of cardiac diseases. In this review, we discuss the biogenesis of miRNAs, the miRNA-mediated regulation of major genes involved in the maintenance of mitochondrial function, and the effects of miRNAs on mitochondrial function in cardiac diseases in order to provide a theoretical basis for the clinical prevention and treatment of cardiac disease and the development of new drugs.

Keywords:  cardiac apoptosis; cardiac disease; cardiac hypertrophy; diabetic cardiomyopathy; heart failure; microRNAs; mitochondrial function

DOI:  https://doi.org/10.3389/fphar.2021.663322
J Biol Chem. 2021 Jun 10. pii: S0021-9258(21)00669-4. [Epub ahead of print] 100869

Schizosaccharomyces pombe Ppr10 and Mpa1 together mediate mitochondrial translational initiation.

Ying Luo, Yirong Wang, Ying Huang.

  Pentatricopeptide repeat (PPR) proteins are a large family of proteins that act primarily at different post-transcriptional steps of organellar gene expression. We have previously found that the Schizosaccharomyces pombe PPR protein Ppr10 interacts with mitochondrial translational activator Mpa1, and both are essential for mitochondrial protein synthesis. However, it is unclear how these two proteins function in mitochondrial protein synthesis in S. pombe. In this study, we further investigated the role of Ppr10 and Mpa1 in mitochondrial protein synthesis. Mitochondrial translational initiation requires two initiation factors, Mti2 and Mti3, which bind to the small subunit of the mitochondrial ribosome (mt-SSU) during the formation of the mitochondrial translational initiation complex. Using sucrose gradient sedimentation analysis, we found that disruption of ppr10, mpa1 or the PPR motifs in Ppr10 impairs the association of Mti2 and Mti3 with the mt-SSU, suggesting that both Ppr10 and Mpa1 may be required for the interaction of Mti2 and Mti3 with the mt-SSU during the assembly of mitochondrial translational initiation complex. Loss of Ppr10 perturbs the association of mitochondrially encoded cytochrome b (cob1) and cytochrome c oxidase subunit 1 (cox1) mRNAs with assembled mitochondrial ribosomes. Proteomic analysis revealed that a fraction of Ppr10 and Mpa1 copurified with a subset of mitoribosomal proteins. The PPR motifs of Ppr10 are necessary for its interaction with Mpa1 and that disruption of these PPR motifs impairs mitochondrial protein synthesis. Our results suggest that Ppr10 and Mpa1 function together to mediate mitochondrial translational initiation.

Keywords:  Mpa1; Mti2; Mti3; PPR motif; Ppr10; Schizosaccharomyces pombe; mitochondrial translation

DOI:  https://doi.org/10.1016/j.jbc.2021.100869
BMC Mol Cell Biol. 2021 Jun 12. 22(1): 35

Complex II subunit SDHD is critical for cell growth and metabolism, which can be partially restored with a synthetic ubiquinone analog.

Aloka B Bandara, Joshua C Drake, David A Brown.

  BACKGROUND: Succinate dehydrogenase (Complex II) plays a dual role in respiration by catalyzing the oxidation of succinate to fumarate in the mitochondrial Krebs cycle and transferring electrons from succinate to ubiquinone in the mitochondrial electron transport chain (ETC). Mutations in Complex II are associated with a number of pathologies. SDHD, one of the four subunits of Complex II, serves by anchoring the complex to the inner-membrane and transferring electrons from the complex to ubiquinone. Thus, modeling SDHD dysfunction could be a valuable tool for understanding its importance in metabolism and developing novel therapeutics, however no suitable models exist.RESULTS: Via CRISPR/Cas9, we mutated SDHD in HEK293 cells and investigated the in vitro role of SDHD in metabolism. Compared to the parent HEK293, the knockout mutant HEK293ΔSDHD produced significantly less number of cells in culture. The mutant cells predictably had suppressed Complex II-mediated mitochondrial respiration, but also Complex I-mediated respiration. SDHD mutation also adversely affected glycolytic capacity and ATP synthesis. Mutant cells were more apoptotic and susceptible to necrosis. Treatment with the mitochondrial therapeutic idebenone partially improved oxygen consumption and growth of mutant cells.
CONCLUSIONS: Overall, our results suggest that SDHD is vital for growth and metabolism of mammalian cells, and that respiratory and growth defects can be partially restored with treatment of a ubiquinone analog. This is the first report to use CRISPR/Cas9 approach to construct a knockout SDHD cell line and evaluate the efficacy of an established mitochondrial therapeutic candidate to improve bioenergetic capacity.

Keywords:  ATP synthesis; Apoptosis; CRISPR/Cas9; Complex II; Electron transport chain; Glycolysis; Idebenone; Krebs cycle; Necrosis; Oxygen consumption; ROS; Respiration; SDHD; Succinate dehydrogenase

DOI:  https://doi.org/10.1186/s12860-021-00370-w
FASEB J. 2021 Jul;35(7): e21688

Novel reporters of mitochondria-associated membranes (MAM), MAMtrackers, demonstrate MAM disruption as a common pathological feature in amyotrophic lateral sclerosis.

Shohei Sakai, Seiji Watanabe, Okiru Komine, Akira Sobue, Koji Yamanaka.

  The mitochondria-associated membrane (MAM) is a functional subdomain of the endoplasmic reticulum membrane that tethers to the mitochondrial outer membrane and is essential for cellular homeostasis. A defect in MAM is involved in various neurological diseases, including amyotrophic lateral sclerosis (ALS). Recently, we and others reported that MAM was disrupted in the models expressing several ALS-linked genes, including SOD1, SIGMAR1, VAPB, TARDBP, and FUS, suggesting that MAM disruption is deeply involved in the pathomechanism of ALS. However, it is still uncertain whether MAM disruption is a common pathology in ALS, mainly due to the absence of a simple, quantitative tool for monitoring the status of MAM. In this study, to examine the effects of various ALS-causative genes on MAM, we created the following two novel MAM reporters: MAMtracker-Luc and MAMtracker-Green. The MAMtrackers could detect MAM disruption caused by suppression of SIGMAR1 or the overexpression of ALS-linked mutant SOD1 in living cells. Moreover, the MAMtrackers have an advantage in their ability to monitor reversible changes in the MAM status induced by nutritional conditions. We used the MAMtrackers with an expression plasmid library of ALS-causative genes and noted that 76% (16/21) of the genes altered MAM integrity. Our results suggest that MAM disruption is a common pathological feature in ALS. Furthermore, we anticipate our MAMtrackers, which are suitable for high-throughput assays, to be valuable tools to understand MAM dynamics.

Keywords:  ER-mitochondria contact; amyotrophic lateral sclerosis (ALS); mitochondria-associated membrane (MAM); organelle; sigma-1 receptor (Sig1R)

DOI:  https://doi.org/10.1096/fj.202100137R
J Cardiovasc Pharmacol. 2021 Jun 08.

Regulation of mitochondrial function by noncoding RNAs in heart failure and its application in diagnosis and treatment.

Miaomiao Yang, Xinxing Wang, Tianhui Wang.

ABSTRACT: Heart failure (HF) is the terminal stage of multiple cardiovascular diseases. However, the pathogenesis of HF remains unclear, and prompt, appropriate diagnosis and treatment of HF are crucial. Cardiomyocytes isolated from HF subjects frequently present mitochondrial impairment and dysfunction. Many studies have suggested that the regulation by noncoding RNAs (ncRNAs) of mitochondria can affect the occurrence and progression of HF. The regulation by ncRNAs of myocardial mitochondria during HF and the recent applications of ncRNAs in the diagnosis and treatment of HF are summarized in this review that is intended to gain keen insights into the mechanisms of HF and more effective treatments.

DOI: https://doi.org/10.1097/FJC.0000000000001081
Mech Ageing Dev. 2021 Jun 12. pii: S0047-6374(21)00093-2. [Epub ahead of print]197 111521

Coenzyme Q10 supplementation - In ageing and disease.

Jan Aaseth, Jan Alexander, Urban Alehagen.

  Coenzyme Q10 (CoQ10) is an essential component of the mitochondrial electron transport chain. It is also an antioxidant in cellular membranes and lipoproteins. All cells produce CoQ10 by a specialized cytoplasmatic-mitochondrial pathway. CoQ10 deficiency can result from genetic failure or ageing. Some drugs including statins, widely used by inter alia elderly, may inhibit endogenous CoQ10 synthesis. There are also chronic diseases with lower levels of CoQ10 in tissues and organs. High doses of CoQ10 may increase both circulating and intracellular levels, but there are conflicting results regarding bioavailability. Here, we review the current knowledge of CoQ10 biosynthesis and primary and acquired CoQ10 deficiency, and results from clinical trials based on CoQ10 supplementation. There are indications that supplementation positively affects mitochondrial deficiency syndrome and some of the symptoms of ageing. Cardiovascular disease and inflammation appear to be alleviated by the antioxidant effect of CoQ10. There is a need for further studies and well-designed clinical trials, with CoQ10 in a formulation of proven bioavailability, involving a greater number of participants undergoing longer treatments in order to assess the benefits of CoQ10 treatment in neurodegenerative disorders, as well as in metabolic syndrome and its complications.

Keywords:  Ageing; Cardiovascular disease; Coenzyme Q(10); Neurodegenerative disease; Physiological function

DOI:  https://doi.org/10.1016/j.mad.2021.111521
Comput Struct Biotechnol J. 2021 ;19 3015-3026

Recent advances in functional annotation and prediction of the epitranscriptome.

Song-Yao Zhang, Shao-Wu Zhang, Teng Zhang, Xiao-Nan Fan, Jia Meng.

  RNA modifications, in particular N 6-methyladenosine (m6A), participate in every stages of RNA metabolism and play diverse roles in essential biological processes and disease pathogenesis. Thanks to the advances in sequencing technology, tens of thousands of RNA modification sites can be identified in a typical high-throughput experiment; however, it remains a major challenge to decipher the functional relevance of these sites, such as, affecting alternative splicing, regulation circuit in essential biological processes or association to diseases. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, we review here recent progress in functional annotation and prediction of RNA modification sites from a bioinformatics perspective. The review covers naïve annotation with associated biological events, e.g., single nucleotide polymorphism (SNP), RNA binding protein (RBP) and alternative splicing, prediction of key sites and their regulatory functions, inference of disease association, and mining the diagnosis and prognosis value of RNA modification regulators. We further discussed the limitations of existing approaches and some future perspectives.

Keywords:  Bioinformatics approaches; Functional epitranscriptome; Future perspective; RNA modification; Recent advances

DOI:  https://doi.org/10.1016/j.csbj.2021.05.030
J Biol Chem. 2021 Jun 15. pii: S0021-9258(21)00680-3. [Epub ahead of print] 100880

The extensive and functionally uncharacterized mitochondrial phosphoproteome.

Natalie M Niemi, David J Pagliarini.

  More than half a century ago, reversible protein phosphorylation was first linked to mitochondrial metabolism through the regulation of pyruvate dehydrogenase. Since this discovery, the number of identified mitochondrial protein phosphorylation sites has increased by orders of magnitude, driven largely by technological advances in mass spectrometry-based phosphoproteomics. However, the majority of these modifications remain uncharacterized, rendering their function and relevance unclear. Nonetheless, recent studies have shown that disruption of resident mitochondrial protein phosphatases causes substantial metabolic dysfunction across organisms, suggesting that proper management of mitochondrial phosphorylation is vital for organellar and organismal homeostasis. While these data suggest that phosphorylation within mitochondria is of critical importance, significant gaps remain in our knowledge of how these modifications influence organellar function. Here, we curate publicly available datasets to map the extent of protein phosphorylation within mammalian mitochondria and to highlight the known functions of mitochondrial-resident phosphatases. We further propose models by which phosphorylation may affect mitochondrial enzyme activities, protein import and processing, and overall organellar homeostasis.

Keywords:  mitochondria; phosphoproteomics; protein kinase; protein phosphatase; protein phosphorylation

DOI:  https://doi.org/10.1016/j.jbc.2021.100880
Front Mol Biosci. 2021 ;8 647277

How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data.

Lea D Schlieben, Holger Prokisch, Vicente A Yépez.

  Rare diseases, although individually rare, collectively affect approximately 350 million people worldwide. Currently, nearly 6,000 distinct rare disorders with a known molecular basis have been described, yet establishing a specific diagnosis based on the clinical phenotype is challenging. Increasing integration of whole exome sequencing into routine diagnostics of rare diseases is improving diagnostic rates. Nevertheless, about half of the patients do not receive a genetic diagnosis due to the challenges of variant detection and interpretation. During the last years, RNA sequencing is increasingly used as a complementary diagnostic tool providing functional data. Initially, arbitrary thresholds have been applied to call aberrant expression, aberrant splicing, and mono-allelic expression. With the application of RNA sequencing to search for the molecular diagnosis, the implementation of robust statistical models on normalized read counts allowed for the detection of significant outliers corrected for multiple testing. More recently, machine learning methods have been developed to improve the normalization of RNA sequencing read count data by taking confounders into account. Together the methods have increased the power and sensitivity of detection and interpretation of pathogenic variants, leading to diagnostic rates of 10-35% in rare diseases. In this review, we provide an overview of the methods used for RNA sequencing and illustrate how these can improve the diagnostic yield of rare diseases.

Keywords:  RNA sequencing; aberrant expression; aberrant splicing; machine learning; mono-allelic expression; rare disorders; statistical models

DOI:  https://doi.org/10.3389/fmolb.2021.647277
Front Neurol. 2021 ;12 651639

Leber Hereditary Optic Neuropathy: Review of Treatment and Management.

Rabih Hage, Catherine Vignal-Clermont.

  Leber hereditary optic neuropathy (LHON) is a maternally inherited mitochondrial disease that specifically targets the retinal ganglion cells by reducing their ability to produce enough energy to sustain. The mutations of the mitochondrial DNA that cause LHON are silent until an unknown trigger causes bilateral central visual scotoma. After the onset of loss of vision, most patients experience progressive worsening within the following months. Few of them regain some vision after a period of ~1 year. Management of LHON patients has been focused on understanding the triggers of the disease and its pathophysiology to prevent the onset of visual loss in a carrier. Medical treatment is recommended once visual loss has started in at least one eye. Research evaluated drugs that are thought to be able to restore the mitochondrial electron transport chain of the retinal ganglion cells. Significant advances were made in evaluating free radical cell scavengers and gene therapy as potential treatments for LHON. Although encouraging the results of clinical trial have been mixed in stopping the worsening of visual loss. In patients with chronic disease of over 1 year, efficient treatment that restores vision is yet to be discovered. In this review, we summarize the management strategies for patients with LHON before, during, and after the loss of vision, explain the rationale and effectiveness of previous and current treatments, and report findings about emerging treatments.

Keywords:  Leber's optic neuropathy; gene therapy; idebenone; mitochondrial disease; visual loss

DOI:  https://doi.org/10.3389/fneur.2021.651639
J Med Genet. 2021 Jun 16. pii: jmedgenet-2020-107644. [Epub ahead of print]

Learning from massive testing of mitochondrial disorders: UPD explaining unorthodox transmission.

Deborah Tolomeo, Anna Rubegni, Claudia Nesti, Melissa Barghigiani, Roberta Battini, Francesca D'Amore, Stefano Doccini, Maria Alice Donati, Daniele Galatolo, Sabrina Giglio, Silvia Guarducci, Marilena Pantaleo, Rosa Pasquariello, Elena Procopio, Francesca Pochiero, Alessandra Tessa, Filippo M M Santorelli.



Keywords:  DNA; genetics; sequence analysis

DOI:  https://doi.org/10.1136/jmedgenet-2020-107644
Brain. 2021 Jun 15. pii: awab226. [Epub ahead of print]

Induced pluripotent stem cell-derived motor neurons of CMT type 2 patients reveal progressive mitochondrial dysfunction.

Jonas Van Lent, Peter Verstraelen, Bob Asselbergh, Elias Adriaenssens, Ligia Mateiu, Christophe Verbist, Vicky De Winter, Kristel Eggermont, Ludo Van Den Bosch, Winnok H De Vos, Vincent Timmerman.

  Axonal Charcot-Marie-Tooth neuropathies (CMT type 2) are caused by inherited mutations in various genes functioning in different pathways. The type of genes and multiplicity of mutations reflect the clinical and genetic heterogeneity in CMT2 disease, which complicates the diagnosis and has halted therapy development. Here, we used CMT2 patient-derived pluripotent stem cells (iPSCs) to identify common hallmarks of axonal degeneration shared by different CMT2 subtypes. We compared the cellular phenotypes of neurons differentiated from CMT2 patient iPSCs with those from healthy controls and a CRISPR/Cas9-corrected isogenic line. Our results demonstrate neurite network alterations along with extracellular electrophysiological abnormalities in the differentiated motor neurons. Progressive deficits in mitochondrial and lysosomal trafficking, as well as in mitochondrial morphology, were observed in all CMT2 patient lines. Differentiation of the same CMT2 iPSC-lines into peripheral sensory neurons, only gave rise to cellular phenotypes in subtypes with sensory involvement, supporting the notion that some gene mutations predominantly affect motor neurons. We revealed a common mitochondrial dysfunction in CMT2-derived motor neurons, supported by alterations in the expression pattern and oxidative phosphorylation, which could be recapitulated in the sciatic nerve tissue of a symptomatic mouse model. Inhibition of a dual leucine zipper kinase (DLK) could partially ameliorate the mitochondrial disease phenotypes in CMT2 subtypes. Altogether, our data reveals shared cellular phenotypes across different CMT2 subtypes and suggests that targeting such common pathomechanisms could allow the development of a uniform treatment for CMT2.

Keywords:  Charcot-Marie-Tooth neuropathy; dual leucine kinase inhibitor; iPSC-derived motor and sensory neurons; mitochondrial dysfunction; phenotyping

DOI:  https://doi.org/10.1093/brain/awab226
FASEB J. 2021 Jul;35(7): e21678

Protective role of the mitochondrial fusion protein OPA1 in hypertension.

Pauline Robert, Phuc Minh Chau Nguyen, Alexis Richard, Céline Grenier, Arnaud Chevrollier, Mathilde Munier, Linda Grimaud, Coralyne Proux, Tristan Champin, Eric Lelièvre, Emmanuelle Sarzi, Emilie Vessières, Samir Henni, Delphine Prunier, Pascal Reynier, Guys Lenaers, Céline Fassot, Daniel Henrion, Laurent Loufrani.

  Hypertension is associated with excessive reactive oxygen species (ROS) production in vascular cells. Mitochondria undergo fusion and fission, a process playing a role in mitochondrial function. OPA1 is essential for mitochondrial fusion. Loss of OPA1 is associated with ROS production and cell dysfunction. We hypothesized that mitochondria fusion could reduce oxidative stress that defect in fusion would exacerbate hypertension. Using (a) Opa1 haploinsufficiency in isolated resistance arteries from Opa1+/- mice, (b) primary vascular cells from Opa1+/- mice, and (c) RNA interference experiments with siRNA against Opa1 in vascular cells, we investigated the role of mitochondria fusion in hypertension. In hypertension, Opa1 haploinsufficiency induced altered mitochondrial cristae structure both in vascular smooth muscle and endothelial cells but did not modify protein level of long and short forms of OPA1. In addition, we demonstrated an increase of mitochondrial ROS production, associated with a decrease of superoxide dismutase 1 protein expression. We also observed an increase of apoptosis in vascular cells and a decreased VSMCs proliferation. Blood pressure, vascular contractility, as well as endothelium-dependent and -independent relaxation were similar in Opa1+/- , WT, L-NAME-treated Opa1+/- and WT mice. Nevertheless, chronic NO-synthase inhibition with L-NAME induced a greater hypertension in Opa1+/- than in WT mice without compensatory arterial wall hypertrophy. This was associated with a stronger reduction in endothelium-dependent relaxation due to excessive ROS production. Our results highlight the protective role of mitochondria fusion in the vasculature during hypertension by limiting mitochondria ROS production.

Keywords:  Opa1; hypertension; mitochondria; oxidative stress; vascular function

DOI:  https://doi.org/10.1096/fj.202000238RRR
Nat Methods. 2021 Jun 17.

Impact of phosphorylation on thermal stability of proteins.

Clément M Potel, Nils Kurzawa, Isabelle Becher, Athanasios Typas, André Mateus, Mikhail M Savitski.

DOI: https://doi.org/10.1038/s41592-021-01177-5
Nat Commun. 2021 06 16. 12(1): 3672

Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling.

Hauke S Hillen, Elena Lavdovskaia, Franziska Nadler, Elisa Hanitsch, Andreas Linden, Katherine E Bohnsack, Henning Urlaub, Ricarda Richter-Dennerlein.

Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint.

DOI: https://doi.org/10.1038/s41467-021-23702-y
Cell Syst. 2021 Jun 16. pii: S2405-4712(21)00198-8. [Epub ahead of print]12(6): 622-635

Mapping the multiscale structure of biological systems.

Leah V Schaffer, Trey Ideker.

  Biological systems are by nature multiscale, consisting of subsystems that factor into progressively smaller units in a deeply hierarchical structure. At any level of the hierarchy, an ever-increasing diversity of technologies can be applied to characterize the corresponding biological units and their relations, resulting in large networks of physical or functional proximities-e.g., proximities of amino acids within a protein, of proteins within a complex, or of cell types within a tissue. Here, we review general concepts and progress in using network proximity measures as a basis for creation of multiscale hierarchical maps of biological systems. We discuss the functionalization of these maps to create predictive models, including those useful in translation of genotype to phenotype, along with strategies for model visualization and challenges faced by multiscale modeling in the near future. Collectively, these approaches enable a unified hierarchical approach to biological data, with application from the molecular to the macroscopic.

Keywords:  community detection; hierarchical models; multiscale; network biology; networks; structural biology; structure; systems biology

DOI:  https://doi.org/10.1016/j.cels.2021.05.012
Cancer Commun (Lond). 2021 Jun;41(6): 439-441

Metabolon: a novel cellular structure that regulates specific metabolic pathways.

Tian Tian, Jun Fan, Shannon Elisabeth Elf.

This manuscript of research highlight focused on one paper recently published in Nature Metabolism entitled "Mitochondrial Long Non-coding RNA GAS5 Tunes TCA Metabolism in Response to Nutrient Stress" from Lin Aifu's group in Zhejiang University. In this manuscript, we discussed the novel findings in Lin's paper and concluded that the metabolon is emerging as a novel cellular structure that regulates specific metabolic pathways.

DOI: https://doi.org/10.1002/cac2.12154
Chem Sci. 2020 Aug 04. 11(33): 8771-8778

Intracellular monitoring of NADH release from mitochondria using a single functionalized nanowire electrode.

Hong Jiang, Yu-Ting Qi, Wen-Tao Wu, Ming-Yong Wen, Yan-Ling Liu, Wei-Hua Huang.

Mitochondria are the powerhouse of cells, and also their suicidal weapon store. Mitochondrial dysfunction can cause the opening of the mitochondrial permeability transition pore (mPTP) and nicotinamide adenine dinucleotide (NADH) release from mitochondria, eventually leading to the disruption of energy metabolism and even cell death. Hence, NADH is often considered a marker of mitochondrial function, but in situ monitoring of NADH release from mitochondria in single living cells remains a great challenge. Herein, we develop a functionalized single nanowire electrode (NWE) for electrochemical detection of NADH release from intracellular mitochondria by modifying conductive polymer (poly(3,4-ethylendioxythiophene), PEDOT)-coated carbon nanotubes (CNTs) on the surface of a SiC@C nanowire. The positively charged PEDOT facilitates the accumulation of negatively charged NADH at the electrode surface and CNTs promote electron transfer, thus endowing the NWE with high sensitivity and selectivity. Further studies show that resveratrol, a natural product, specifically induced NADH release from mitochondria of MCF-7 cancer cells rather than non-cancerous MCF-10 A cells, indicating the potential therapeutic effects of resveratrol in cancer treatment. This work provides an efficient method to monitor mitochondrial function by in situ electrochemical measurement of NADH release, which will be of great benefit for physiological and pathological studies.

DOI: https://doi.org/10.1039/d0sc02787a
BMC Bioinformatics. 2021 Jun 12. 22(1): 320

Predicting biological pathways of chemical compounds with a profile-inspired approach.

Javier Lopez-Ibañez, Florencio Pazos, Monica Chagoyen.

BACKGROUND: Assignment of chemical compounds to biological pathways is a crucial step to understand the relationship between the chemical repertory of an organism and its biology. Protein sequence profiles are very successful in capturing the main structural and functional features of a protein family, and can be used to assign new members to it based on matching of their sequences against these profiles. In this work, we extend this idea to chemical compounds, constructing a profile-inspired model for a set of related metabolites (those in the same biological pathway), based on a fragment-based vectorial representation of their chemical structures.RESULTS: We use this representation to predict the biological pathway of a chemical compound with good overall accuracy (AUC 0.74-0.90 depending on the database tested), and analyzed some factors that affect performance. The approach, which is compared with equivalent methods, can in addition detect those molecular fragments characteristic of a pathway.
CONCLUSIONS: The method is available as a graphical interactive web server http://csbg.cnb.csic.es/iFragMent .

DOI: https://doi.org/10.1186/s12859-021-04252-y
Nat Rev Genet. 2021 Jun 18.

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics.

Sophia K Longo, Margaret G Guo, Andrew L Ji, Paul A Khavari.

Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.

DOI: https://doi.org/10.1038/s41576-021-00370-8