Wednesday, 12 June 2019

Mitochondrial fusion supports increased oxidative phosphorylation during cell proliferation

https://elifesciences.org/articles/41351

Cong-Hui Yao, Rencheng Wang, Yahui Wang, Che-Pei Kung, Jason D Weber, Gary J Patti


  • The authors show that mouse fibroblasts increase oxidative phosphorylation by nearly x2, and mitochondrial coupling efficiency by ~30%, during proliferation. Both of these changes are supported by mitochondrial fusion.
  • Modulating mitochondrial fusion through Mfn2 levels caused modulation in proliferation rate. Decreases in fusion decreased OXPHOS but not ATP levels.
  • The authors suggest that cell proliferation requires increased OXPHOS supported by mitochondrial fusion.

Mammalian cell growth dynamics in mitosis

https://elifesciences.org/articles/44700

Teemu P Miettinen, Joon Ho Kang, Lucy F Yang, Scott R Manalis


  • The authors use a suspended microchannel resonator and protein synthesis assays to measure the accumulation of cell mass through the cell cycle, for single mammalian cells.
  • For various animal cell types, the growth rate in prophase (the first stage of the cell cycle) is comparable to or larger than interphase (the phase where DNA is copied) growth rates. Growth is only stopped in the metaphase-to-anaphase transition. 
  • The authors find that a range of mitotic arrest mechanisms inhibit cell growth. Their results counter the traditional idea that cell growth is negligible during mitosis.



Wednesday, 5 June 2019

Germline selection shapes human mitochondrial DNA diversity

https://science.sciencemag.org/content/364/6442/eaau6520.abstract

Wei Wei, Salih Tuna, Michael J. Keogh, Katherine R. Smith, Timothy J. Aitman, F. Lucy Raymond, Mark Caulfield, Ernest Turro, Patrick F. Chinnery and others


  • The authors analyse 1526 mother-offspring pairs from rare-disease patients in the 100,000 genomes project, to show that 45% of individuals display heteroplasmy at >1% variant allele frequency (VAF).
  • The authors define 3 kinds of variant: transmitted/inherited (present in both mother and offspring and heteroplasmic in at least one; transmitted = mother, inherited = offspring), lost (present in mother, absent in offspring) and de novo (present in offspring, absent in mother). Absence is defined as VAF < 1%.
  • Transmitted variants had a much larger heteroplasmic fraction than lost and de novo variants. 
  • Transmitted VAF correlates with inherited VAF (in logit-transformed space).
  • Heteroplasmy transmission/inheritance did not display a significantly skewed distribution in the inter-generational VAF shift, which is compatible with this set of mutations undergoing neutral drift.
  • The D-loop had an approximately 4 times higher inter-generational mutation rate per base pair than the rest of the mitochondrial genome, suggesting the existence of stronger selective pressures against mutation on the reset of the genome, or potentially an intrinsically lower de novo mutation rate.
  • tRNA, rRNA, and non-synonymous mutations tended to have a lower VAF than D-loop and synonymous mutations, suggesting the existence of selection.
  • The authors identified haplogroup-matched (92%) and haplogroup-mismatched (2.3%) groups within their dataset (6% could not be identified). Haplogroup mismatching arises from mixed-race ancestry. The heteroplasmic variants in the mismatched group were significantly more likely to match the ancestry of the nuclear genetic background than the mtDNA background on which the heteroplasmy occurred.

Monday, 3 June 2019

Epigenetic Control of Mitochondrial Fission Enables Self-Renewal of Stem-likeTumor Cells in Human Prostate Cancer

.https://www.ncbi.nlm.nih.gov/pubmed/31130467

Gianluca Civenni, Roberto Bosotti, Andrea Timpanaro, Ramiro Vàzquez, Jessica Merulla, Shusil Pandit, Simona Rossi, Domenico Albino, Sara Allegrini, Abhishek Mitra, Sarah N. Mapelli, Luca Vierling, Martina Giurdanella, Martina Marchetti, Alyssa Paganoni, Andrea Rinaldi, Marco Losa, Enrica Mira-Catò, Rocco D’Antuono, Diego Morone, Keyvan Rezai, Gioacchino D’Ambrosio, L’Houcine Ouafik, Sarah Mackenzie, Maria E. Riveiro, Esteban Cvitkovic, Giuseppina M. Carbone and Carlo V. Catapano

INTRODUCTION
  • Prostate cancer (PC) is the most common neoplasy in men and one of the main causes of cancer death in developed countries.
  • Cancer stem cells (CSCs) are a small subset of cancer cells with stem-cell like properties. They contribute to treatment failure and relapse. Understanding the mechanisms which regulate their self-renewal, differentiation and senescence could lead to new therapeutic strategies.
  • Mitochondrial reprogramming has important functions in CSCs. Mitochondrial dynamics control  asymmetric cell division, self-renewal, and the fate of stem cells. Fission and clearance of dysfunctional mitochondria avoid senescence and prevent stem cell exhaustion.
MAIN FINDINGS OF THE PAPER
  • The authors uncover a novel link between the protein BRD4, mitochondrial dynamics and self-renewal of CSCs.
  • Genetic knockdown of BRD4 or chemical inhibitors blocked mitochondrial fission and caused CSC exhaustion and loss of tumorigenic properties. This is mediated through the  inhibition of  mitochondrial fission factor (Mff) caused by BRD4 knockdown.
  • Evidence for this is that suppression of Mff transcription reproduced the effects of BRD4 knockdown, whereas ectopic expression of Mff rescued CSCs from exhaustion. Therefore the authors conclude that targeting mitochondrial plasticity in CSCs is a promising avenue for new and more effective therapies. 

Wednesday, 22 May 2019

Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000263

Natalya P. Degtyareva, Natalie Saini, Joan F. Sterling, Victoria C. Placentra, Leszek J. Klimczak, Dmitry A. Gordenin, Paul W. Doetsch


  • The authors report on the mutational spectra of redox stress in single-stranded DNA of budding yeast and in human mitochondrial DNA in the context of healthy aging, finding that the predominance of C>T transitions is a predominant feature in both.
  • The authors find that the frequencies of hydrogen peroxide-induced mutations in proof-reading deficient yeast mutants supports the conclusion that this form of mutagenesis is the result of direct damage to DNA, rather than misincorporation errors.
  • They propose that mutations may occur to the heavy strand of mtDNA when DNA replication starts at the light chain, temporarily making the displaced, heavy strand more vulnerable to damage.

An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482013/pdf/aav1110.pdf

John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K, Glöckner G


  • A long-standing debate in the field of mitochondrial physiology is the purpose of mitochondrial DNA. The "co-location for redox regulation" (CoRR) hypothesis states that mitochondrial genomes are necessary to provide local control of the electron transport chain.
  • The authors describe an aerobic eukaryotic parasite (Amoebophyra ceratii) with functional mitochondria, but have completely lost their mitochondrial genome, finding that all mitochondrial proteins appear to be lost or encoded in the nucleus. 
  • This finding challenges the CoRR hypothesis, and potentially suggests the possibility of complete transfer of the mitochondrial genome into the nuclear genome for more complex organisms.


Mitochondrial fragmentation drives selective removal of deleterious mtDNA in the germline

https://www.nature.com/articles/s41586-019-1213-4

Toby Lieber, Swathi P. Jeedigunta, Jonathan M. Palozzi, Ruth Lehmann & Thomas R. Hurd


  • The authors generate mutated fruit flies by transfering mitochondria from a wild-type strain of Drosophila yakuba into a strain of Drosophila melanogaster in which the mtDNA contain a temperature-sensitive mutation in Complex IV of the electron transport chain.
  • The authors designed fluorescent probes to specifically bind to the D-loop of either D. yakuba or D. melanogaster, allowing them to visualise heteroplasmy.
  • At 18C, the point mutation does not affect Complex IV activity, whereas at the inhibitory temperature of 29C, Complex IV activity is greatly reduced and is selected against 
  • Selection first manifests during oogenesis, where a reduction in mitofusins causes fragmentation of the mitochondrial network
  • The authors identify the proteins Atg1 and BNIP3  as necessary for the selective removal of mitochondria with mutated mtDNAs
  • A reduction in Atg1 or BNIP3 decreases the amount of wild-type mtDNA, suggesting a link between mitochondrial degradation and replication
  • At the restrictive temperature, selection occured in the germline but not in the somatic cells which surround the germline in the ovariole, and was largely absent in the male germ line (possibly because only female mtDNA is inherited)
  • Inhibiting cell death through over-expression of the cell-death inhibitor p35 did not block selection
  • Expression of the alternative oxidase protein (AOX) bypasses the function of complex IV and partially blocked selection, suggesting that the selection process senses defects in oxidative phosphorylation
  • The authors observed greater fragmentation in the germline mitochondria relative to the soma. Using photoactivatable GFP, the authors show that mitochondrial contents rarely pass from one mitochondrion to another, suggesting that the purpose of fragmentation is to reduce complementation so that the genotype of individual mitochondria may be sensed through their phenotype.
  • Reducing Mitofusin expression in somatic cells also induced selection
  • The authors inhibited the protein IF1, to allow ATP synthase to run in reverse and maintain mitochondrial membrane potential by burning ATP. In doing so, the authors did not observe statistically significant selection, which may suggest that membrane potential sensing is the mechanism by which mitochondria are selected.
  • Expression of a dominant-negative form of ATP synthase caused a reduction in mtDNA copy number of both mutants and wild-types

Friday, 10 May 2019

Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single cell resolution: a focus on aging and cancer

https://www.biorxiv.org/content/biorxiv/early/2019/03/16/579789.full.pdf

Ryan O’Hara, Enzo Tedone,, Andrew Ludlow, Ejun Huang, Beatrice Arosio, Daniela Mari, Jerry W. Shay


  • The authors develop a protocol to measure single-cell mtDNA copy number using digital droplet PCR
  • The authors find ~10-fold inter-cellular variability in mtDNA copy number (in an immortalised human cell line, H1299), which could not be fully explained by cell cycle variations.
  • The authors investigated how mtDNA copy number changes after stimulation of peripheral blood mononuclear cells (PBMCs, a heterogeneous cellular population largely consisting of T cells). Previous studies have shown a decline in mtDNA copy number with ageing in this cell population. The authors studied stimulated PBMCs in young, old, and healthy/frail centenarians. Healthy centenarians tended to have higher mtDNA copy number than frail, or ~70 year old, individuals.  

Tuesday, 23 April 2019

Intramitochondrial transfer and engineering of mammalian mitochondrial genomes in yeast

https://www.sciencedirect.com/science/article/pii/S1567724918300370?via%3Dihub

Yoon YG, Koob MD


  • The authors demonstrate that entire mouse mtDNA can be stably transferred to the mitochondrial network in yeast which have been depleted of their own native mtDNA.
  • The yeast cells which contained the full mouse mtDNA genome, replicated the mouse mtDNA molecules without detectable sequence alterations or rearrangements.

Mitochondria-specific drug release and reactive oxygen species burst induced by polyprodrug nanoreactors can enhance chemotherapy

https://www.nature.com/articles/s41467-019-09566-3

Zhang W, Hu X, Shen Q, Xing D
  • Many cancer cells over-produce reactive oxygen species by ~10-fold relative to normal cells, providing a biomarker for cancer cells.
  • The authors sought to design a chemical system which targets ROS-overproducing cells, and then further stimulate long-term ROS overproduction inside mitochondria, to induce apoptosis.

Mitochondrial Protein Synthesis and mtDNA Levels Coordinated through an Aminoacyl-tRNA Synthetase Subunit

https://www.cell.com/cell-reports/fulltext/S2211-1247(19)30329-8?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124719303298%3Fshowall%3Dtrue

Picchioni D, Antolin-Fontes A, Camacho N, Schmitz C, Pons-Pons A, Rodríguez-Escribà M, Machallekidou A, Güler MN, Siatra P, Carretero-Junquera M, Serrano A, Hovde SL, Knobel PA, Novoa EM, Solà-Vilarrubias M, Kaguni LS, Stracker TH, Ribas de Pouplana L


  • The authors investigate a signalling pathway which couples mtDNA translation to mtDNA copy number 
  • They identify a protein (SLIMP) which is essential for mitochondrial respiration, and is involved in tRNA-serine aminoacylation
  • SLIMP interacts with the protein LON, which degrades TFAM. TFAM is a protein involved in forming mtDNA-protein complexes known as nucleoids. Reduction in TFAM levels is associated with mtDNA depletion.
  • Hence mitochondrial translation is directly coupled to mtDNA copy number.

Thursday, 18 April 2019

Mitochondrial volume fraction controls translation of nuclear-encoded mitochondrial proteins

https://www.biorxiv.org/content/biorxiv/early/2019/01/25/529289.full.pdf

Tatsuhisa Tsuboi, Matheus P. Viana, Fan Xu, Jingwen Yu, Raghav Chanchani, Ximena G. Arceo, Evelina Tutucci, Joonhyuk Choi, Yang S. Chen, Robert H. Singer, Susanne M. Rafelski, Brian M. Zid

  • The authors investigate the physiological impact of nuclear-encoded mitochondrial mRNA localization to mitochondria in yeast
  • They observe that as yeast switches to oxidative metabolism, the cytoplasmic density of mitochondria increases (i.e. the ratio of mitochondrial volume to cytoplamic volume)
  • Increases in mitochondrial density drives the localisation of nuclear-encoded mitochondrial mRNAs to the mitochondrial surface, increasing mitochondrial protein production
  • Sequestering mRNAs away from the mitochondrial surface is sufficient to reduce mitochondrial protein production
  • This suggests that mitochondrial density is a physiologically important parameter, which is sensed to regulate mitochondrial gene expression via mRNA localisation.

Wednesday, 17 April 2019

A non‐death function of the mitochondrial apoptosis apparatus in immunity

http://emboj.embopress.org/content/early/2019/04/12/embj.2018100907

Dominik Brokatzky, Benedikt Dörflinger, Aladin Haimovici, Arnim Weber, Susanne Kirschnek, Juliane Vier, Arlena Metz, Julia Henschel, Tobias Steinfeldt, Ian E. Gentle and Georg Häcke

INTRODUCTION
Apoptosis mostly proceeds through mitochondria: the outer mitochondrial membrane is permeabilized, in a process called mitochondrial outer membrane permeabilization (MOMP). This releases cytochrome c to activate cytosolic caspases, which execute apoptosis through proteolysis of numerous substrates.

Recently, it has been observed that apoptosis signaling may be initiated at a low level, in the absence of cell death. Only few mitochondria are permeabilized, and small amounts of cytochrome c are released, causing only limited caspase activation. Apoptosis appears to be triggered but then aborted before the point of no return. The process has been termed minority MOMP and the cell stays alive and can presumably repair any damage caused


MAIN FACTS OF THE PAPER
The author hypothesise that low-level (sub-lethal) “apoptosis” signaling (minority MOMP) can trigger cytokine secretion, causing inflammation and immune alert. Full apoptosis activates caspases that counteract this immune function. The small amounts of caspase activated during sub-lethal signaling following minority MOMP may however be too low to turn the signal off, resulting in cytokine secretion and immune activation.

Infecting HeLa cells by several agents, they tested this possibility and reported that human cells can react to low-level apoptosis induction with cytokine secretion. Minority MOMP was detected with all infectious agents tested. This suggests that minority MOMP is a very common occurrence during infection. In addition, the authors show that the ability of epithelial cells to fight the growth of parasites is decreased when proapoptotic signaling is deleted.


CONCLUSIONS
Their results suggest that mitochondria have a function in the detection of microbial infection and cell-autonomous immunity, through a sub-lethal (low-intensity) activation of the mitochondrial apoptosis apparatus.

They also report damage to the genomic DNA caused by the mitochondrial apoptosis signaling. Since MOMP seems like a frequent occurrence, this suggests that infection-associated damage to the genomic DNA is widespread. Therefore, this study also identifies DNA damage as a common occurrence during infection and indicate the possibility that infection-associated mutations, potentially leading to cancer, may be a side effect of this system of microbial detection.

Monday, 15 April 2019

Mitochondrial origins of fractional control in regulated cell death

https://www.nature.com/articles/s41467-019-09275-x.pdf

Luís C. Santos, Robert Vogel, Jerry E. Chipuk, Marc R. Birtwistle, Gustavo Stolovitzky & Pablo Meyer


  • The authors investigate cell-to-cell variability in cell death in response to TNF-related apoptosis inducing ligand (TRAIL), an apoptosis-inducing drug.
  • The authors find that with successively increasing doses of TRAIL, the probability distribution of mitochondrial density (which the authors define as MitoTracker Deep Red fluoresence intensity divided by forward scatter) becomes increasingly enriched for cells with high mitochondrial density -- suggesting that high cytoplasmic mitochondrial density is required for TRAIL resistance (in contrast to this)
  • The authors point out that the steepness of a dose-response curve is a measure of cell-to-cell variability in cellular sensitivity to a stimulus, and derive a formalism to convert a Hill function into a probability distribution over cellular stimulus thresholds for a binary response variable (such as cell death). They derive an approximate expansion of the sensitivity threshold in terms of the half maximal inhibitory concentration (IC50), and the log ratio of mitochondrial density to mean mitochondrial density. This results in an expression for the conditional probability of a cell being alive given a biological quantity of interest, e.g. mitochondrial density (see Eq 4)
  • The authors attribute this correlation to variable effective concentrations of pro-apoptotic proteins on the mitochondrial outer membrane
  • The authors suggest that anti-apoptotic Bcl-2 family proteins may increase the variance in cell death response, potentially enhancing resistance to treatment

Wednesday, 20 March 2019

NAD+ metabolism governs the proinflammatory senescence-associated secretome

https://www.nature.com/articles/s41556-019-0287-4

Nacarelli T, Lau L, Fukumoto T, Zundell J, Fatkhutdinov N, Wu S, Aird KM, Iwasaki O, Kossenkov AV, Schultz D, Noma KI, Baur JA, Schug Z, Tang HY, Speicher DW, David G, Zhang R

  • THe authors show that the enzyme nicotinamide phosphoribosyltransferase (NAMPT), which is a rate-limiting enzyme of the NAD+ salvage pathway, is involved in the senesence-associated secretory phenotype (SASP), independent of the senesence-associated growth arrest.
  • The signalling pathway the authors identify is promotes the SASP by enhancing glycolysis and mitochondrial respiration. 
  • The tumour-promoting effects of SASP suggests that anti-ageing dietary NAD+ augmentation should be administered with care.

The NAD-Booster Nicotinamide Riboside Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance

https://www.sciencedirect.com/science/article/pii/S1934590919300621

Vannini N, Campos V, Girotra M, Trachsel V, Rojas-Sutterlin S, Tratwal J, Ragusa S, Stefanidis E, Ryu D, Rainer PY, Nikitin G, Giger S, Li TY, Semilietof A, Oggier A, Yersin Y, Tauzin L, Pirinen E, Cheng WC, Ratajczak J, Canto C, Ehrbar M, Sizzano F, Petrova TV, Vanhecke D, Zhang L, Romero P, Nahimana A, Cherix S, Duchosal MA, Ho PC, Deplancke B, Coukos G, Auwerx J, Lutolf MP, Naveiras O

  • Boosting NAD+ via dietary supplementation of nicotinamide riboside (NR) in mice
    • Reduces mitochondrial activity in hematopoetic stem cells 
    • Increases mitophagy in HSCs (determined in the mitoQC mouse)
    • Reduces mitochondrial membrane potential (perhaps related to the increased mitophagy)
    • Leading to increased asymmetric division of mitochondria (quantified by TMRM/mitochondrial mass) in HSCs, resulting in expansion of the hematopoetic progenitor compartment.
  • NR supplementation enhanced survival and blood cell production following HSC transplantation.

Monday, 11 March 2019

Nuclear genetic regulation of the human mitochondrial transcriptome

https://elifesciences.org/articles/41927

Aminah T Ali, Lena Boehme, Guillermo Carbajosa, Vlad C Seitan, Kerrin S Small, Alan Hodgkinson

  • The authors analyse >11k RNA sequencing libraries across 36 tissue types and investigate the variability in transcription of the mitochondrial genome
  • The authors identify 64 nuclear genetic loci associated with expression of mitochondrially-encoded genes. 
  • The authors replicate ~21% of associations with independent tissue-matched datasets.

Systems biology identifies preserved integrity but impaired metabolism of mitochondria due to a glycolytic defect in Alzheimer’s disease neurons


Pierre Theurey, Niamh M. C. Connolly, Ilaria Fortunati, Emy Basso, Susette Lauwen, Camilla Ferrante, Catarina Moreira Pinho, Alvin Joselin,  Anna Gioran, Daniele Bano, David S. Park,  Maria Ankarcrona, Paola Pizzo,  Jochen H. M. Prehn

  • Many studies have focussed on the role of mitochondrial dysfunctions in Alzheimer's disease (AD), but most of them cannot tell whether mitochondrial defects are a cause or a consequence of AD.
  • The authors use a combined experimental and computational approach to study mitochondrial function in the neurons of a transgenic mouse model.
  • Experiments show that AD neurons have limited respiratory capacity. The computational model predicted that this could not be explained by any defect in the respiratory chain (RC),  but could be observed by simulating an impairment in the NADH flux to the RC.
  • The authors used NAD(P)H autofluorescence measurements to validate the computationally predicted mitochondrial NADH defect in transgenic AD neurons.
Additionally, the authors investigated the cause of these reduced NADH flux and the resulting  mitochondrial NAD(P)H dyshomeostasis.
  • Extracellular acidification experiments  measure the rate of excretion of lactic acid after its conversion from pyruvate, a product of glycolysis. These experiments  showed an impaired glycolytic flux in the transgenic AD neurons of the study.
  • The authors supplemented neurons with pyruvate (therefore bypassing glycolysis), and this suppressed the NAD(P)H  impairment and the mitochondrial defects.
  • This supports the hypothesis that a glycolytic defect is responsible for the unbalance of NAD(P)H observed in AD neurons.

The study shows that defects in glucose metabolism in vitro are detectable in neurons before the onset of any sign of pathology in transgenic AD mice.

Thursday, 7 March 2019

Cardiolipin remodeling by ALCAT1 links mitochondrial dysfunction to Parkinson’s diseases

https://onlinelibrary.wiley.com/doi/full/10.1111/acel.12941

Chengjie Song  Jun Zhang  Shasha Qi  Zhen Liu  Xiaoyang Zhang  Yue Zheng  John‐Paul Andersen  Weiping Zhang  Randy Strong  Paul Anthony Martinez  Nicolas Musi  Jia Nie Yuguang Shi
  • Parkinson's disease's (PD) causes remain elusive, but oxidative stress, mitochondrial dysfunction, and defective mitophagy are all considered as the primary pathogenic mechanisms.
  • Cardiolipin (CL) is a phospholipid which is almost exclusively located in the inner mitochondrial membrane, where it is biosynthesized.
  • ROS-induced damage of CL  is implicated in the pathogenesis of PD, but the mechanism remains unclear.
  • The authors induced PD in a mouse model, induced by MPTP (a chemical that caused PD when injected, and has been used to study disease models in various animal studies). They oxidative stress, mtDNA mutations, and mitochondrial dysfunction in the midbrain.
  • Then, they ablated  the ALCAT1 gene and treated mice with MPTP. This prevented MPTP‐induced neurotoxicity, apoptosis, and motor deficits and mitigated mitochondrial dysfunction.
  • Mitophagy, which removes dysfunctional mitochondria, is also compromised in PD. The pharmacological inhibition of ALCAT1 significantly improved mitophagy, by stimulating the recruitment of Parkin to dysfunctional mitochondria and their association.
  • These results show that ALCAT1 may be a promising drug target in the treatment of PD.

Wednesday, 6 March 2019

Alternative assembly of respiratory complex II connects energy stress to metabolic checkpoints

https://www.nature.com/articles/s41467-018-04603-z

Ayenachew Bezawork-Geleta, He Wen, LanFeng Dong, Bing Yan, Jelena Vider, Stepana Boukalova, Linda Krobova, Katerina Vanova, Renata Zobalova, Margarita Sobol, Pavel Hozak, Silvia Magalhaes Novais, Veronika Caisova, Pavel Abaffy, Ravindra Naraine, Ying Pang, Thiri Zaw, Ping Zhang, Radek Sindelka, Mikael Kubista, Steven Zuryn, Mark P. Molloy, Michael V. Berridge, Karel Pacak, Jakub Rohlena, Sunghyouk Park & Jiri Neuzil

  • The authors show that depletion of mtDNA causes a shift in CII assembly from its full tetrameric form to an alternative 100 kDa form
  • The authors suggest that cells may modulate their energy consumption by altering DNA synthesis and cell cycle progression. This modulation is mediated by the alternative form of CII

Monday, 4 March 2019

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

https://www.cell.com/cell/pdf/S0092-8674(19)30055-8.pdf

Leif S. Ludwig, Caleb A. Lareau, Jacob C. Ulirsch, Elena Christian, Christoph Muus, Lauren H. Li, Karin Pelka, Will Ge, Yaara Oren, Alison Brack, Travis Law, Christopher Rodman, Jonathan H. Chen, Genevieve M. Boland, Nir Hacohen, Orit Rozenblatt-Rosen, Martin J. Aryee, Jason D. Buenrostro, Aviv Regev, and Vijay G. Sankaran

INTRODUCTION
  • Lineage tracing involves inferring the developmental history of an organism, with respect to its ancestors. Since single cells divide and proliferate, an emerging field is the inference of lineages of single-cells.
  • In model organisms, this can be achieved through engineered genetic labels and single-cell RNA sequencing. These two approaches cannot be used together in humans, because of the genetic manipulations required to tag cells with heritable marks.
  • Therefore, to date lineage tracing studies in humans have relied on the detection of naturally occurring somatic mutations in the nuclear genome. However, these mutations have high error rates and their detection is costly and difficult to perform at scale.
  • The mitochondrial genome provides an attractive target for inferring cellular lineages for several reasons: 
    • MtDNA is large enough to show substantial levels of variation
    • It is short enough to be cost-effective for targetted sequencing: 18,000 mitochondrial genomes (17k bases) can be sequenced at 100-fold coverage for the same cost as a single nuclear genome (3.2bn bases) at 10-fold coverage. 
    • Its mutation rate is reported to be 10-100 times larger than the nuclear genome.
    • MtDNA is held in high copy number per cell (100-1000s), therefore less amplification is necessary.
    • Mutations in mtDNA often reach a variant allele fraction of ~100% due to partitioning noise, random genetic drift, and faster replication relative to nuclear DNA.
    • Existing methods (ATAC-seq and single-cell RNA-seq) can be used to detect mtDNA sequences and genetic variation.
MAIN FACTS OF THE PAPER
  • The authors established 65 individual sub-clonal populations, over 8 generation, in an immortalised cell line. They derived subclones (populations of cells derived from a single cell) from the parental colony at each generation, and performed bulk mitochondria individual cells’ l genome sequencing  through ATAC-seq. The authors used high-confidence mtDNA mutations to reconstruct clonal relations between the subpopulations, allowing them to predict the most recent common ancestor with >80% accuracy (See Fig 1C, 1E and 1F).
  • Since mtDNA is almost entirely transcribed, the authors hypothesized that single-cell RNA-seq would also be able to detect heteroplasmic mutations in mtDNA. The authors tested 6 protocols and found that full-length scRNA-seq methods showed better coverage of the mitochondrial genome than 3'-end-directed methods, with Smart-Seq2 having the best performance. 
    • The authors performed whole-genome sequencing and single-cell RNA-seq simultaneously for single cells using SIDR, finding that several mutations were highly heteroplasmic in RNA, but not present in the genome, suggesting: RNA editing, transcription errors or technical errors in sc-RNA seq (Fig 2B). 
  • To investigate inter- and intra-individual heterogeneity in mtDNA mutations, the authors analysed bulk RNA-seq data from 8.8k samples, spanning 49 tissues from at least 25 donors, as well as 426 donors with at least 10 tissues (GTEx project). 
    • The authors found 2.7k mutations that were tissue-specific within an individual donor at a minimum of 3% heteroplasmy 
    • Typically, ~25% of total mRNA originates from the mitochondrial genome across tissues, although this can be much larger in tissues such as the brain and heart. Tissues with a large proportion of mitochondrial mRNA tend to show very large variability -- see Fig 4B.
    • Mitochondrial mutations around 10% are not uncommon across the whole mitochondrial genome (Fig 4D) and somatic mtDNA mutations with levels as low as 5% heteroplasmy can be stably propagated and serve as clonal markers in primary human cells.
    • Every tissue had at least one tissue-specific mtDNA mutation across all individual donors, which likely arose via somatic mutation in a tissue-specific manner
  • The authors used primary hematopoietic stem cells from two individual donors, and found that the mtDNA mutation profile separates single cells according to their donor of origin, as well as their single-cell-derived colony of origin via highly heteroplasmic mtDNA mutations.
  • The authors performed bulk ATAC-seq and scRNA-seq on cells from colorectal adenocarcinoma primary tumor resection. Upon sequencing 238 cells, the authors found 12 distinct clusters of mtDNA mutations, suggesting clonal heterogeneity. 
  • The authors provide an improved mutation detection framework, where mutation are first identified through bulk sequencing, and then called in scRNA-seq data. 

CONCLUSION AND OBSERVATIONS
  • A potential limitation of inferring cell lineage from mtDNA sequence data comes from horizontal transfer of mtDNA between cells. However, the authors show that horizontal transfer would have to be relatively large to confound their analysis.
  • Mapping the phenotypic impact of such genotypic diversity remains an open challenge.
  • The authors use techniques for which reads mapping to the  mitochondrial genome are usually considered an unwanted by-product. Using assays focussed on the mitochondrial genomescan reduce costs and increase coverage.

Wednesday, 20 February 2019

The exceptional longevity of the naked mole‐rat may be explained by mitochondrial antioxidant defenses


Daniel Munro, Cécile Baldy, Matthew E. Pamenter, Jason R. Treberg

TWO THEORIES OF AGEING
The oxidative damage theory of ageing postulates that  a slow and steady accumulation of oxidative damage to macromolecules, which increases with age, causes the decline of physiologic functions. The oxidative damage is caused by reactive oxygen species (ROS) of mitochondrial origin.

The mitochondrial oxidative stress hypothesis states that ageing is primarily driven by loss of mitochondrial function with time, caused by oxidative stress. This theory stems from the fact that ROS are mostly released inside mitochondria, therefore directly exposing them to damage.


THE PRESENT STUDY
Naked mole-rat (NMR) can live >30 years in lab conditions, with a very long healthy lifespan, in comparison to <4 years for mice. Studies have shown that NMRs are subject to extensive oxidative damage (evidence found in liver cells) and high ROS productions, as much as mice. Therefore, their longevity has been widely used to contradict the oxidative damage theory of ageing. The mitochondrial oxidative stress hypothesis cannot explain these observations.

The authors, writing in Aging Cell, showed that NMRs mitochondria are much more efficient than mice's in consuming ROS. They also find evidence that skeletal muscle and heart mitochondria of mice and NMRs produce similar quantities of ROS.  Therefore, the authors conclude that the marked difference in longevity between the two species is to be attributed to the much greater capacity of NMRs mitochondria to clean ROS.

This finding supports the mitochondrial oxidative stress hypothesis, without positing that NMRs mitochondria produce less ROS. Further research could tell whether other long-lived species share this greater mitochondrial detoxifying capacity.

Tuesday, 19 February 2019

Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance

Shankar Mukherji, Erin K O'Shea

https://elifesciences.org/articles/02678

  • Modelled the dynamics of organelle biogenesis, finding that fluctuations in organelle abundance depend strongly on the specific mechanisms that influence organelle number
  • Model predicts the experimentally measured size of the Golgi apparatus and vacuole abundance fluctuations
  • Work provides a general framework for exploring stochastic organelle biogenesis

Monday, 18 February 2019

Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence

https://www.sciencedirect.com/science/article/pii/S0092867419300510

Gabriel E. Neurohr, Rachel L. Terry, Jette Lengefeld, Megan Bonney, Gregory P. Brittingham, Fabien Moretto, Teemu P. Miettinen, Laura Pontano Vaites, Luis M. Soares, Joao A. Paulo, J. Wade Harper, Stephen Buratowski, Scott Manalis, Folkert J. van Werven, Liam J. Holt, Angelika Amon

  • Cells of a particular type tend to display a relatively narrow range of cell sizes (relative to the orders-of-magnitude difference in cell size between cells of different types). 
  • When cell cycle is blocked in budding yeast, cells continue to grow. The authors were able to reversibly arrest the cell cycle by perturbing a particular gene (CDC28), providing them with a x12-fold variation in cell volume. Note that denying these cells with glucose, or applying cyclohexamide, prevented the mutants from growing large.
  • When allowed to re-enter the cell cycle, larger cells proliferated more slowly, and delays cell cycle progression.
  • The authors observed that cell cycle regulators are produced at a lower rate in oversized cells (although the pool-size was comparable to normal cells).
  • When cells exceeded ~200 fL, cellular growth shifted from exponential to linear
  • In the linear growth regime, cell volume increased faster than total RNA and protein, suggesting dilution of cellular macro-molecules. Direct measurement of cellular density showed a 36% reduction in total cell density, largely explained by reductions in protein and RNA mass.
  •  Transcriptome and proteome analysis suggested that general transcription and translation machineries becomes limiting in large cells.
  • Using nocodazole to generate diploid cells, large diploid cells grew faster than large haploid cells, and also progressed faster through the cell cycle. The authors therefore suggest that the nDNA:(cytoplasmic volume) ratio is what limits cell growth in oversized cells.
  • The authors found that the majority of old yeast cells (>16 cell divisions) were >200 fL and display many of the phenotypes of oversized cells. 
  • Excessive increase in cell size was sufficient to reduce lifespan
  • The authors tested many of these observations in human fibroblasts.

Thoughts
----------------------
  • Some of the findings in here, especially relating to cellular growth rates, remind me of this
  • Quantifying single-cell mtDNA copy number in this system would be extremely interesting! 

Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows

Thorsten B. Blum, Alexander Hahn, Thomas Meier, Karen M. Davies, and Werner Kühlbrandt
 
  • ATP synthase is known to form dimers which form rows along curved ridges of mitochondrial cristae
  • It has been suggested previously through computer simulation that these rows of ATP synthase cause local curvature
  • This study shows experimentally, for the first time, that ATP synthase dimers spontaneously assemble into rows, and that these rows bend the membrane.
  • The authors suggest that assembly of ATP synthase dimers into rows is likely the first step in the formation of cristae

Friday, 8 February 2019

Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells

https://doi.org/10.1016/j.cmet.2018.10.014

Bajzikova M, Kovarova J, Coelho AR, Boukalova S, Oh S, Rohlenova K, Svec D, Hubackova S, Endaya B, Judasova K, Bezawork-Geleta A, Kluckova K, Chatre L, Zobalova R, Novakova A, Vanova K, Ezrova Z, Maghzal GJ, Magalhaes Novais S, Olsinova M, Krobova L, An YJ, Davidova E, Nahacka Z, Sobol M, Cunha-Oliveira T, Sandoval-Acuña C, Strnad H, Zhang T, Huynh T, Serafim TL, Hozak P, Sardao VA, Koopman WJH, Ricchetti M, Oliveira PJ, Kolar F, Kubista M, Truksa J, Dvorakova-Hortova K, Pacak K, Gurlich R, Stocker R, Zhou Y, Berridge MV, Park S, Dong L, Rohlena J, Neuzil J.

  • The authors graft cancer cells lacking mtDNA (ρ0) onto mice, and show horizontal transfer of mtDNA into the cancer cells after a lag period. After the transfer of mtDNA, a tumour subsequently develops. 
  • The authors show that OXPHOS-derived ATP is not essential for tumorigenesis 
  • Pyrimidine biosynthesis is dependent on respiration, and is required for cell-cycle progression

Mitochondrial complex III is essential for suppressive function of regulatory T cells

https://doi.org/10.1038/s41586-018-0846-z

Samuel E. Weinberg, Benjamin D. Singer, Elizabeth M. Steinert, Carlos A. Martinez, Manan M. Mehta, Inmaculada Martínez-Reyes, Peng Gao, Kathryn A. Helmin, Hiam Abdala-Valencia, Laura A. Sena, Paul T. Schumacker, Laurence A. Turka & Navdeep S. Chandel

  • Regulatory T-cells (T-regs) are a sub-population of T cells (T cells being a kind of immune cell) which have immunosuppressive activities. They tend to down-regulate the induction and proliferation of effector T cells.
  • In this study, the authors ablate complex III in T-regs of mice, and show that this induces fatal inflammatory disease early in life. 
  • Mice lacking complex III in T-regs displayed a loss of ability to downregulate T-cell activity, without affecting T-reg proliferation and survival. 
  • Loss of complex III in T-regs was associated with increased DNA methylation

Friday, 25 January 2019

How mitochondria can vary, and consequences for human health


Mitochondria are components of the cell which are involved in generating “energy currency” molecules called ATP across much of complex life. Since many mitochondria exist within single cells (often hundreds or thousands), it is possible for the characteristics of individual mitochondria to vary within cells, and within tissues. This variation of mitochondrial characteristics can affect biological function and human health.

Since mitochondria possess their own, small, circular, DNA molecules (mtDNA), we can split mitochondrial characteristics into two categories: genetic and non-genetic. In our review, we discuss a number of aspects in which mitochondria vary, from both genetic and non-genetic perspectives. 



In terms of mitochondrial genetics, the amount of mtDNA per cell is variable. When a cell divides, its daughters receive a share of its parents mtDNA, but the split isn’t precisely 50/50, so cell division can cause variability in the number of mtDNAs per cell. As mtDNAs are replicated and degraded over time, errors in the copying process may give rise to mtDNA mutations, which may spread throughout a cell. Factors such as: the total amount, the rate of degradation/replication, the mean fraction of mutants, and the extent of fragmentation in the mitochondrial network, can all influence how variable the fraction of mutated mtDNAs becomes through time (see here for a preview of some upcoming work on this topic). The total amount, and mutated fraction of mtDNAs, are implicated in diseases such as neurodegeneration, as well as the ageing process.

Apart from genetic variations, there are many non-genetic features of mitochondria which also vary within and between cells. Changes in mtDNA sequence can change the amino-acid sequence of the proteins encoded by mtDNA, causing structural changes in the molecular machines which generate ATP. The shape of the membranes of mitochondria are also highly variable, and respond to mitochondrial activity through quantities such as pH, where mitochondrial activity itself may depend on mtDNA sequence. The previous two examples (mitochondrial protein and membrane structure) demonstrate how the genetic state of mitochondria may influence their non-genetic characteristics. Mitochondrial non-genetic characteristics may also influence the genetic state: for instance, mitochondrial membrane potential can influence the probability of a mitochondria being degraded, along with its mtDNA.

The inter-dependence of genetic and non-genetic characteristics demonstrate the complex feedback loops linking these two aspects of mitochondrial physiology. We suggest here that, since changes in mitochondrial genetics occur more slowly than most physical aspects of mitochondrial physiology, understanding mitochondrial genetics may be especially important in explaining phenomena such as ageing, which appears to be closely related to mitochondrial heterogeneity. You can freely access our work, which has recently been published in Frontiers in Genetics, as “Mitochondrial Heterogeneity” https://www.frontiersin.org/articles/10.3389/fgene.2018.00718/full Juvid, Iain and Nick.
 

Thursday, 24 January 2019

Investigating mitonuclear interactions in human admixed populations

https://www.nature.com/articles/s41559-018-0766-1

Arslan A. Zaidi & Kateryna D. Makova

  • The authors explore signatures of mitonuclear incompatibility and coevolution in six admixed human populations from the Americas
  • They hypothesize that incompatibility might arise between e.g. mtDNA origins of replication and nuclear-encoded mtDNA replication machinery and therefore, might lead to a decrease in mtDNA replication efficiency. The authors therefore predict that if mito/nuclear discordance is increased in admixed individuals, mtDNA copy number may consequently decrease.
  • Given two admixed human populations with different mitochondrial haplotypes, if all females are from population 1, and all males from population 2, inherited autosomal loci will be a mixture of the two populations whereas the mtDNA will be purely from population 1. This may place selection in favour of nuclear-encoded mitochondrial genes from population 1, and such progeny may suffer mito-nuclear mismatch (see Fig 1b). 
  • The authors found statistically significant negative correlation between mtDNA copy number and mitonuclear DNA discordance in admixed individuals, although the relationship was rather noisy (Fig 3a, R^2=0.04).
  • They find significant enrichment of ancestry at nuclear-encoded mitochondrial genes towards the source populations contributing the most prevalent mtDNA haplogroups, indicating compensatory selective effects.

Mitochondrial Populations Exhibit Differential Dynamic Responses to Increased Energy Demand during Exocytosis In Vivo

https://www.sciencedirect.com/science/article/pii/S2589004218302669

Natalie Porat-Shliom, Olivia J. Harding, Lenka Malec, Kedar Narayan, and Roberto Weigert

  • This study leverages in vivo visualisation of mitochondrial physiology in mouse salivary epithelium, in live animals through intravital microscopy (see here for further fascinating work in this system).
  • The authors generate videos of mitochondrial dynamics, at single cell resolution, in all 3 spatial dimensions.
  • The authors find evidence for two distinct mitochondrial populations existing within secretory cells: one juxtaposed to the plasma membrane, and another dispersed throughout the cytosol. These populations differ in their motility and propensity to undergo mitochondrial fusion/fission.
  • The authors found that increasing energy demand in these cells enhanced fusion and motility in central mitochondria

Wednesday, 23 January 2019

Memory of ancestral mitochondrial stress



Sarah-Lena Offenburg, Marcos Francisco Perez and Ben Lehner

A WORD ON EPIGENETIC MODIFICATIONS
There are two main types of epigenetic modifications, DNA methylation and histone modifications.
In DNA methylations, a methyl group is added to DNA. These reactions are catalysed by enzymes known as DNA methyltransferases. This modification result in the creation binding sites for other proteins, which bind and recruit or are associated with other proteins which can act on histones (determining histone modifications, see below).In eukaryotes, the most prevalent DNA methylation concerns cytosine nucleotides and gives origin to 5-methylcytosine.


Histone modifications affect the DNA-protein interactions, modifying the structure of chromatin (mixture of DNA and proteins which form chromosomes). This, in turn, alters the ability for a gene to be transcribed and expressed. 


THE RECENT FINDING
Dna methylation was thought to be absent in the roundworm C. elegans, since its genome does not contain 5-methylcytosine. Another methylation, N6-methyldeoxyadenine (6mA) was recently detected in C. elegans (and other species), but its functions remain elusive.

In a recent work, published in Nature Cell Biology, Ma et al. show that C. elegans can inherit resistance to stress and give evidence for the involvement of 6mA into this process.
The authors used antimycin, an antibiotic, to stress the mitochondria of the roundworm. The effect of antimycin is to inhibit the mitochondrial respiratory chain and that, in turn, slows down the development of worms. 

It was observed the progeny of animals exposed to the antibiotic developed faster when exposed to the same stressor. Unexposed offspring was protected up to four generations.
Interestingly, the resistance is not inherited through mitochondria themselves, since it can also be transmitted through male parents.
The authors found that the worms defective in a specific histone modification (H3K4me3) were unable to inherit resistance. A previous study in C. elegans showed a crosstalk between H3K4me3 and the methylation 6mA. Moreover, animals deficient in a known 6mA me methyltransferase were unable to transmit the resistance.
Open questions remain about the precise roles of 6mA and H3K4me3 in the observed phenomenon.

The involvement of mitochondria is important because C. elegans may be exposed to bacteria-induced mitochondrial stress in its natural habitat, which makes the finding more relevant. The inheritance of this stress resistance is one of the few documented cases of a trans-generational memory of a kind of stimulus which can occur in nature.

Thursday, 17 January 2019

Quantitative 3D Mapping of the Human Skeletal Muscle Mitochondrial Network

https://www.cell.com/cell-reports/fulltext/S2211-1247(19)30018-X

Amy E. Vincent, Kathryn White, Tracey Davey, Jonathan Philips, R. Todd Ogden, Conor Lawess, Charlotte Warren, Matt G. Hall, Yi Shiau Ng, Gavin Falkous, Thomas Holden, David Deehan, Robert W. Taylor, Doug M. Turnbull,
and Martin Picard

  • The authors investigate morphological differences of mitochondria in muscle between mice, humans and humans with mitochondrial disease.
  • In all human and mouse muscle fibres analysed, the authors confirmed that the mitochondrial network is largely composed of distinct organelles, typically no more than a few microns in length. 
  • The authors quantify "mitochondrial complexity" by taking the ratio of surface area to volume. Intuitively, a more "complex" organelle will have a higher surface area for a fixed volume, due to greater invagination. Naively taking the ratio yields a quantity with dimensions, so the authors raise the surface area to the power 3/2 to yield a dimensionless quantity. Phenomenologically, the authors find that squaring their metric increases its dynamic range. They name the resultant quantity the "mitochondrial complexity index" (MCI), which scales as MCI ~ SA^3/V^2 (SA=surface area, V=volume).
  • The authors use a further metric, the "mitochondrial branching index" (MBI) which measured anisotropy. MBI > 1 denotes more branching in the transverse plane than the longitudinal direction of a muscle fibre. 
  • The authors find that humans have smaller muscle mitochondria than mice, with comparable MCI.
  • The authors found that, within cells, there is a large variability in mitochondrial volume and MCI (CV between 50-100%), although inter-cellular variability was smaller (CV < 50%). The authors also observed inter-individual variability in these metrics (CV ~ 50%).
  • The authors studied a trio of genetically related patients carrying a tRNA-lys mutation at 40% (asymptomatic), 63% (mild myopathy) and 97% (severe myopathy). The patients with mild/severe myopathy had smaller mitochondria and lower MCI.
  • Uncovering the correlation with single-cell heteroplasmy, respiratory chain function, and morphology remains a challenge for future studies.

Friday, 11 January 2019

Age-related declines in α-Klotho drive progenitor cell mitochondrial dysfunction and impaired muscle regeneration

A. Sahu, H. Mamiya, S. N. Shinde, A. Cheikhi, L. L. Winter, N. V. Vo, D. Stolz, V. Roginskaya, W. Y. Tang, C. St. Croix, L. H. Sanders, M. Franti, B. Van Houten, T. A. Rando, A. Barchowsky & F. Ambrosio

https://www.nature.com/articles/s41467-018-07253-3

  • Aged muscle shows a decreased capacity to repair itself after acute injury.   Muscle stem cells (MuSCs) mediate muscle repair, which become activated when muscles are injured. MuSCs show increased apoptosis, decreased proliferation, impairment of mitophagy, senescence, and decreased resistance to stress, with age.
  • The gene Klotho encodes a membrane-bound, circulating, hormonal protein in mice and humans; its deficiency is associated with ageing phenotypes including: decreased activity, gait disturbance, cognitive impairment, sarcopenia, and impaired wound repair. Declines in α-Klotho in tissues such as the skin, small intestine, and kidney, have been associated with senescence and stem cell dysfunction.
  • In young skeletal muscle, the authors show that the α-Klotho promoter is transiently demethylated under acute muscle injury, which is associated with increased expression. In aged tissue, α-Klotho shows no significant change in methylation in response to muscle injury, and no significant expression. 
  • Knockdown of α-Klotho in young animals results in an aged phenotype, with aberrant mitochondrial ultrastructure, decreased mitochondrial bioenergetics, mtDNA damage (perhaps mediated through cardiolipin peroxidation), and senescence.
  • Sytematic delivery of exogenous α-Klotho to aged mice rejuvenates muscle progenitor stem cell (MPC) bioenergetics, enhances myofiber regeneration, and muscle function after acute injury.   

Thoughts
---------------------

In Figure 6a, the authors show that when aged  MPC are isolated from old mice, and cultured with α-Klotho for 48h, the authors observe a decreased number of mtDNA lesions relative to cells which are not treated with α-Klotho (a difference of about 1 mutation per molecule of mtDNA). This is a pretty huge number of mutations over 48 hrs! It would be fascinating to infer the mtDNA mutation rate from these data.

Thursday, 10 January 2019

MITO-Tag Mice enable rapid isolation and multimodal profiling of mitochondria from specific cell types in vivo

Erol C. Bayraktar, Lou Baudrier, Ceren Özerdem, Caroline A. Lewis, Sze Ham Chan, Tenzin Kunchok, Monther Abu-Remaileh, Andrew L. Cangelosi, David M. Sabatini, Kıvanç Birsoy, and Walter W. Chen

https://www.pnas.org/content/116/1/303?ijkey=eedc3db1701d7607eb1389c8dc45fe6c9903294c&keytype2=tf_ipsecsha

  • The authors establish MITO-Tag mice, which allow cell type specific isolation of mitochondria from different tissues. These mice express a mitochondrially-localised epitope, whose expression is driven by a Cre-recombinase. Therefore, mice engineered such that Cre-recombinase is under the control of a promoter which is active in a particular cell type, allows isolation of mitochondria from particular cell types via immunoprecipitation.
  • Purified mitochondria can be subsequently analysed through e.g. proteomic, lipidomic, and metabolomic analyses. The authors demonstrate this for hepatocytes.

Mind your mouse strain

José Antonio Enríquez
 
https://www.nature.com/articles/s42255-018-0018-3

  • Many commonly used inbred mouse strains carry random mutations which can affect the interpretation of results derived from these strains
  • Mice of a single strain is still susceptible to random genetic drift. Whilst some animal providers have implemented a genetic stability program, this is not common practice across all animal facilities in research institutions
  • The most commonly used lab strain is BL6. There are two prominent mutations which are likely present in all substrains (Cdh23, causing age-related hearing loss, and COX7A2L which involves mitochondrial supercomplex formation). 
  • It is important to be aware of the nuclear genetic differences between substrains because they can result in different molecular and phenotypic signatures.
  • Correct reporting of animal substrains may go some way towards explaining contradictory observations between laboratories when they occur

Monday, 7 January 2019

Reversing wrinkled skin and hair loss in mice by restoring mitochondrial function

https://www.nature.com/articles/s41419-018-0765-9

Bhupendra Singh, Trenton R. Schoeb, Prachi Bajpai, Andrzej Slominski & Keshav K. Singh

  • The authors created an inducible mouse expressing a dominant negative mutant of POLG1 which induces mtDNA depletion (approximately x2 depletion) in the whole animal (mtDNA-depleter mouse). 
  • The depletion of mtDNA caused widespread reduction in activity of components of the electron transport chain.
  • Skin wrinkles and hair loss were amongst the earliest and most predominant phenotypic changes, along with a reduction in body weight and height, and skin inflammation
  • The authors induced mtDNA depletion for 2 months, resulting in the above phenotypes, then restored mtDNA copy number. After 1 month at normal mtDNA copy number, skin wrinkles and hair loss reverted, and the animals displayed relatively normal cutaneous structures. Skin inflammation reduced, although was not returned fully to wild-type levels. 
  • This study is further evidence for the causal role of mtDNA perturbations in mammalian ageing, and is amongst the first studies to demonstrate that mtDNA-induced ageing may be reversible.

Thursday, 8 November 2018

Are you TORCing tau me? Amyloid‐β blocks the conversation between lysosomes and mitochondria

http://emboj.embopress.org/content/early/2018/11/02/embj.2018100839

Juan Carlos Polanco, Jürgen Götz


INTRODUCTION
This EMBO News&views paper is about recent progress on how amyloid‐β (Aβ) and tau exacerbate Alzheimer's disease (AD) at a subcellular level.
A link has been established between type 2 diabetes and AD: insulin dysregulation occurs in brain tissue from AD patients and mouse models for AD.

mTOR (the protein kinase mammalian target of rapamycin) is a key molecule in the insulin signalling: its hyperactivation mediates insulin resistance, which is one cause of type 2 diabetes.

AD is characterized by the aggregation of two molecules: the peptide amyloid‐β (Aβ) and the protein tau, which impair neuronal function. This accumulation has been linked to lysosomal dysfunction.

Lysosomes and mitochondria both malfunction in various human diseases. This makes sense in the light of the discovery of mitochondria–lysosome membrane contact sites. This could mean that these two organelles also cooperate in physiological conditions.


RECENT DEVELOPMENTS
In the same issue of EMBO, Norambuena et al provide evidence that oligomeric forms of Aβ (Aβos) disrupt the functional crosstalk between lysosomes and mitochondria, thereby contributing to the early stages of AD.

It was already known that mitochondrial dysfunction impairs lysosomal structure and function in a manner that depends on the levels of mitochondrial ROS.

Norambuena et al have provided evidence that that there is also an opposite information flow, with mitochondria receiving signals from lysosomes. This mechanism is dependent on mTORC1, a multiprotein signalling complex nucleated by mTOR and bound to the cytosolic side of lysosomes. This mTORC1 was shown to be activated by insulin and amino acids, leading to what the authors have called “nutrient‐induced mitochondrial activation (NiMA)”,

This lysosomal signalling was strongly inhibited by Aβos and was found to depend on the activation of mTORC1 by a mechanism that requires tau. Indeed, NiMA was not blocked by Aβos in tau knockout neurons.


This reinforces the view that tau facilitates the formation of signalling complexes affecting neuronal function. Future research could be targeted at the isolation and characterization of these putative complexes.

Thursday, 18 October 2018

Metformin Targets Mitochondrial Electron Transport to Reduce Air-Pollution-Induced Thrombosis


Saul Soberanes, Alexander V. Misharin,  Amit Jairaman, Luisa Morales-Nebreda, Alexandra C. McQuattie-Pimentel, Takugo Cho, Robert B. Hamanaka, Angelo Y. Meliton, James M. Walter, Ching-I Chen,  Monica Chi, Stephen Chiu, Francisco J. Gonzalez-Gonzalez, Matthew Antalek, Hiam Adbala-Valencia, Sergio E. Chiarella, Kaitlyn A. Sun, Parker S. Woods, Andrew J. Ghio, Manu Jain, Harris Perlman, Karen M. Ridge, Richard I. Morimoto, Jacob I. Sznajder, William E. Balch, Sangeeta M. Bhorade, Ankit Bharat, Murali Prakriya, Navdeep S. Chandel, Go¨ khan M. Mutlu  and G.R. Scott Budinger.

Intro: a word on macrophages.
Macrophages (big eaters, from Greek μακρός and φαγείν) are a type of white blood cell, of the immune system, that engulfs and digests cellular debris, foreign substances, microbes, cancer cells, and anything else that does not have the type of proteins specific to healthy body cells on its surface, in a process called phagocytosis. They are large phagocytes found essentially in every tissue, where they patrol for potential pathogens.

An alveolar macrophage (or dust cell) is a type of macrophage found in the pulmonary alveolus, near the pneumocytes, but separated from the wall.

The study
While air pollution exposure is associated with a variety of poor health outcomes, the major driver of mortality is an increased risk of death attributable to ischemic cardiovascular events, primarily heart attacks and ischemic/thrombotic strokes.

Urban PM air pollution induces the release of pro-inflammatory cytokines, including interleukin-6 (IL-6) from alveolar macrophages. Alveolar macrophage-produced IL-6 enters the circulation to induce the transcription of several coagulation factors in the liver, and augments the tendency toward arterial thrombosis in a murine model of stroke. This phenomenon was not observed in mice lacking IL-6.

Key findings of this model were recently confirmed in humans in an interventional trial of filtered air compared with ambient air conducted in a region of China with high levels of ambient PM.

Accordingly, molecules that can attenuate IL-6 release in response to PM predicted to lower the risk of arterial thrombosis in exposed populations.

Soberanes et al., find that metformin can attenuate PM-induced IL-6 release from alveolar macrophages in mice and reduce the resulting increase in the risk of arterial thrombosis.

The link to mitochondria
In alveolar macrophages from mice and humans, PM-induced mitochondrial ROS generation caused endoplasmic reticulum calcium store depletion, and the opening of store-operated calcium channels, which augmented IL-6 release.

Metformin acted as a complex I inhibitor in alveolar macrophages to reduce mitochondrial ROS from complex III of the mitochondrial electron transport chain in response to PM. That’s the mechanism behind his effectiveness in limiting IL-6 release in from alveolar macrophages.

Thursday, 27 September 2018

Mutations of mitochondrial DNA are not major contributors to aging of fruit flies

http://www.pnas.org/content/early/2018/09/21/1721683115.long

Timo E. S. Kauppila, Ana Bratic, Martin Borch Jensen, Francesca Baggio, Linda Partridge, Heinrich Jasper, Sebastian Grönke, and Nils-Göran Larsson
 
  • The authors engineered fruit flies expressing mutant versions of mitochondrial DNA polymerase as a means to introduce mtDNA mutations. This model is analogous to the 'mutator mouse', which shows premature ageing phenotypes.
  • The authors did not observe an increase in levels of somatic mtDNA mutations with age in the thorax of these mutant fruit flies, suggesting low mtDNA turnover (relative to total lifespan) in this tissue. However, old female flies tranmit more mtDNA mutations than young female flies, suggesting that mtDNA mutations may accumulate in proliferative tissues such as the female gonads.
  • Moderately increasing the somatic mtDNA mutation load did not have any impact on fly lifespan or physiology
  • Even after multiple generations, flies showed high tolerance to mtDNA mutations. The authors suggest this is likely due to the relatively large mtDNA genetic bottleneck during fly development
  • Very high levels of mtDNA mutation caused sensitivity to mechanical and starvation stress, intestinal stem cell dysfunction, and reduced lifespan
  • Flies with 9.7×10−4 mutations per bp had similar lifespans to WT flies, whereas mice with 2.1×10−4 mutations per bp display shortened lifespan.