bims-camemi 2018-11-11 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2018–11–11
thirteen papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Bhlhe40 differentially regulates the function and number of peroxisomes and mitochondria in myogenic cells.
MDM2 and Mitochondrial Function: One Complex Intersection.
Peroxynitrite nitrates adenine nucleotide translocase and Voltage-Dependent Anion Channel 1 and alters their interactions and association with hexokinase II in mitochondria.
Rapid peroxynitrite reduction by human peroxiredoxin 3: Implications for the fate of oxidants in mitochondria.
Deficiency of the mitochondrial sulfide regulator ETHE1 disturbs cell growth, glutathione level and causes proteome alterations outside mitochondria.
Cancer-Associated Fibroblasts Modify Lung Cancer Metabolism involving ROS and TGF-β signaling.
Mitochondrial transplantation prolongs cold ischemia time in murine heart transplantation.
Mitochondrial Nucleoids: Superresolution microscopy analysis.
Calcium-independent phospholipase A2γ (iPLA2γ) and its roles in cellular functions and diseases.
Metabolomics of Ndufs4-/- skeletal muscle: Adaptive mechanisms converge at the ubiquinone-cycle.
Homocysteine and age-associated disorders.
Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination.
High Content, Phenotypic Assays and Screens for Compounds Modulating Cellular Processes in Primary Neurons.

Redox Biol. 2018 Oct 29. pii: S2213-2317(18)30815-2. [Epub ahead of print]20 321-333

Bhlhe40 differentially regulates the function and number of peroxisomes and mitochondria in myogenic cells.

Hsuan Chia Chang, Chien Han Kao, Shih Ying Chung, Wei Cheng Chen, Lulus Putri Aninda, Yi Huan Chen, Yi An Juan, Shen Liang Chen.

  PGC-1α is a key regulator of oxidative metabolism facilitating the expression of genes critical for the function and biogenesis of the two key oxidative organelles, mitochondria and peroxisomes, in skeletal muscle (SKM) and other organs. Our recent studies have found that the transcription factor Bhlhe40 negatively regulates PGC-1α gene expression and its coactivational activity, therefore, this factor should have profound influence on the biogenesis and metabolic activity of mitochondria and peroxisomes. Here we found that both the number and activity of peroxisomes were increased upon knockdown of Bhlhe40 expression but were repressed by its over-expression. Mitochondrial number and efficiency were significantly reduced by Bhlhe40 knockdown, resulting in the burst of ROS. Over-expression of a constitutively active PGC-1α-interactive domain (named as VBH135) of Bhlhe40 mimicked the effects of its knockdown on peroxisomes but simultaneously reduced ROS level. Furthermore, the efficiency, but not the number, of mitochondria was also increased by VBH135, suggesting differential regulation of peroxisomes and mitochondria by Bhlhe40. Unsaturated fatty acid oxidation, insulin response, and oxidative respiration were highly enhanced in Bhlhe40 knockdown or VBH135 over-expressed cells, suggesting the importance of Bhlhe40 in the regulation of unsaturated fatty acid and glucose oxidative metabolism. Expression profiling of genes important for either organelle also supports differential regulation of peroxisomes and mitochondria by Bhlhe40. These observations have established the important role of Bhlhe40 in SKM oxidative metabolism as the critical regulator of peroxisome and mitochondrion biogenesis and functions, and thus should provide a novel route for developing drugs targeting SKM metabolic diseases.

Keywords:  Bhlhe40; Oxidative metabolism; PGC-1α; Peroxisome; Skeletal muscle

DOI:  https://doi.org/10.1016/j.redox.2018.10.009
Biochem Pharmacol. 2018 Oct 31. pii: S0006-2952(18)30466-0. [Epub ahead of print]

MDM2 and Mitochondrial Function: One Complex Intersection.

Camila Rubio-Patiño, Andrew Paul Trotta, Jerry Edward Chipuk.

  Decades of research reveal that MDM2 participates in cellular processes ranging from macro-molecular metabolism to cancer signaling mechanisms. Two recent studies uncovered a new role for MDM2 in mitochondrial bioenergetics. Through the negative regulation of NDUFS1 (NADH:ubiquinone oxidoreductase 75 kDa Fe-S protein 1) and MT-ND6 (NADH dehydrogenase 6), MDM2 decreases the function and efficiency of Complex I (CI). These observations propose several important questions: (1) Where does MDM2 affect CI activity? (2) What are the cellular consequences of MDM2-mediated regulation of CI? (3) What are the physiological implications of these interactions? Here, we will address these questions and position these observations within the MDM2 literature.

Keywords:  Apoptosis; Bioenergetics; Complex I; Electron transport chain; MDM2; Mitochondria; Oncogene; Tumor suppressor; p53

DOI:  https://doi.org/10.1016/j.bcp.2018.10.032
Mitochondrion. 2018 Oct 31. pii: S1567-7249(18)30119-3. [Epub ahead of print]

Peroxynitrite nitrates adenine nucleotide translocase and Voltage-Dependent Anion Channel 1 and alters their interactions and association with hexokinase II in mitochondria.

Meiying Yang, Yanji Xu, James S Heisner, Jie Sun, David F Stowe, Wai-Meng Kwok, Amadou K S Camara.

  Cardiac ischemia and reperfusion (IR) injury induces excessive emission of deleterious reactive O2 and N2 species (ROS/RNS), including the non-radical oxidant peroxynitrite (ONOO-) that can cause mitochondria dysfunction and cell death. In this study, we explored whether IR injury in isolated hearts induces tyrosine nitration of adenine nucleotide translocase (ANT) and alters its interaction with the voltage-dependent anion channel 1 (VDAC1). We found that IR injury induced tyrosine nitration of ANT and that exposure of isolated cardiac mitochondria to ONOO- induced ANT tyrosine, Y81, nitration. The exposure of isolated cardiac mitochondria to ONOO- also led ANT to form high molecular weight proteins and dissociation of ANT from VDAC1. We also found that IR injury in isolated hearts, hypoxic injury in H9c2 cells, and ONOO- treatment of H9c2 cells and isolated mitochondria, each decreased mitochondrial bound-hexokinase II (HK II), which suggests that ONOO- caused HK II to dissociate from mitochondria. Moreover, we found that mitochondria exposed to ONOO- induced VDAC1 oligomerization which may decrease its binding with HK II. We have reported that ONOO- produced during cardiac IR injury induced tyrosine nitration of VDAC1, which resulted in conformational changes of the protein and increased channel conductance associated with compromised cardiac function on reperfusion. Thus, our results imply that ONOO- produced during IR injury and hypoxic stress impeded HK II association with VDAC1. ONOO- exposure nitrated mitochondrial proteins also led to cytochrome c (cyt c) release from mitochondria. In addition, in isolated mitochondria exposed to ONOO- or obtained after IR, there was significant compromise in mitochondrial respiration and delayed repolarization of membrane potential during oxidative (ADP) phosphorylation. Taken together, ONOO- produced during cardiac IR injury can nitrate tyrosine residues of two key mitochondrial membrane proteins involved in bioenergetics and energy transfer to contribute to mitochondrial and cellular dysfunction.

Keywords:  Adenine nucleotide translocase; Cardiac ischemia reperfusion injury; Hexokinase II; Mitochondria; Peroxynitrite; Tyrosine nitration; Voltage-Dependent Anion Channel 1

DOI:  https://doi.org/10.1016/j.mito.2018.10.002
Free Radic Biol Med. 2018 Nov 01. pii: S0891-5849(18)31280-2. [Epub ahead of print]

Rapid peroxynitrite reduction by human peroxiredoxin 3: Implications for the fate of oxidants in mitochondria.

María Inés De Armas, Romina Esteves, Nicolás Viera, Aníbal M Reyes, Mauricio Mastrogiovanni, Thiago G P Alegria, Luis E S Netto, Verónica Tórtora, Rafael Radi, Madia Trujillo.

  Mitochondria are main sites of peroxynitrite formation. While at low concentrations mitochondrial peroxynitrite has been associated with redox signaling actions, increased levels can disrupt mitochondrial homeostasis and lead to pathology. Peroxiredoxin 3 is exclusively located in mitochondria, where it has been previously shown to play a major role in hydrogen peroxide reduction. In turn, reduction of peroxynitrite by peroxiredoxin 3 has been inferred from its protective actions against tyrosine nitration and neurotoxicity in animal models, but was not experimentally addressed so far. Herein, we demonstrate the human peroxiredoxin 3 reduces peroxynitrite with a rate constant of 1 ×107M-1s-1 at pH 7.8 and 25°C. Reaction with hydroperoxides caused biphasic changes in the intrinsic fluorescence of peroxiredoxin 3: the first phase corresponded to the peroxidatic cysteine oxidation to sulfenic acid. Peroxynitrite in excess led to peroxiredoxin 3 hyperoxidation and tyrosine nitration, oxidative post-translational modifications that had been previously identified in vivo. A significant fraction of the oxidant is expected to react with CO2 and generate secondary radicals, which participate in further oxidation and nitration reactions, particularly under metabolic conditions of active oxidative decarboxylations or increased hydroperoxide formation. Our results indicate that both peroxiredoxin 3 and 5 should be regarded as main targets for peroxynitrite in mitochondria.

Keywords:  Peroxynitrite; kinetics; mitochondria; peroxiredoxin; sulfenic acid; tyrosine nitration

DOI:  https://doi.org/10.1016/j.freeradbiomed.2018.10.451
Biochim Biophys Acta Mol Basis Dis. 2018 Nov 02. pii: S0925-4439(18)30438-1. [Epub ahead of print]1865(1): 126-135

Deficiency of the mitochondrial sulfide regulator ETHE1 disturbs cell growth, glutathione level and causes proteome alterations outside mitochondria.

Navid Sahebekhtiari, Paula Fernandez-Guerra, Zahra Nochi, Jasper Carlsen, Peter Bross, Johan Palmfeldt.

  The mitochondrial enzyme ETHE1 is a persulfide dioxygenase essential for cellular sulfide detoxification, and its deficiency causes the severe and complex inherited metabolic disorder ethylmalonic encephalopathy (EE). In spite of well-described clinical symptoms of the disease, detailed cellular and molecular characterization is still ambiguous. Cellular redox regulation has been described to be influenced in ETHE1 deficient cells, and to clarify this further we applied image cytometry and detected decreased levels of reduced glutathione (GSH) in cultivated EE patient fibroblast cells. Cell growth initiation of the EE patient cells was impaired, whereas cell cycle regulation was not. Furthermore, Seahorse metabolic analyzes revealed decreased extracellular acidification, i. e. decreased lactate formation from glycolysis, in the EE patient cells. TMT-based large-scale proteomics was subsequently performed to broadly elucidate cellular consequences of the ETHE1 deficiency. More than 130 proteins were differentially regulated, of which the majority were non-mitochondrial. The proteomics data revealed a link between ETHE1-deficiency and down-regulation of several ribosomal proteins and LIM domain proteins important for cellular maintenance, and up-regulation of cell surface glycoproteins. Furthermore, several proteins of endoplasmic reticulum (ER) were perturbed including proteins influencing disulfide bond formation (e.g. protein disulfide isomerases and peroxiredoxin 4) and calcium-regulated proteins. The results indicate that decreased level of reduced GSH and alterations in proteins of ribosomes, ER and of cell adhesion lie behind the disrupted cell growth of the EE patient cells.

Keywords:  Ethylmalonic encephalopathy; Glutathione; Glycosylation; Mitochondrion; Redox regulation; Sulfide

DOI:  https://doi.org/10.1016/j.bbadis.2018.10.035
Free Radic Biol Med. 2018 Oct 31. pii: S0891-5849(18)31446-1. [Epub ahead of print]

Cancer-Associated Fibroblasts Modify Lung Cancer Metabolism involving ROS and TGF-β signaling.

Alberto Cruz-Bermúdez, Raquel Laza-Briviesca, Ramiro J Vicente-Blanco, Aránzazu García-Grande, Maria José Coronado, Sara Laine-Menéndez, Cristina Alfaro, Juan Cristobal Sanchez, Fernando Franco, Virginia Calvo, Atocha Romero, Paloma Martin-Acosta, Clara Salas, José Miguel Garcia, Mariano Provencio.

  Lung cancer is a major public health problem due to its high incidence and mortality rate. The altered metabolism in lung cancer is key for the diagnosis and has implications on both, the prognosis and the response to treatments. Although Cancer-associated fibroblasts (CAFs) are one of the major components of the tumor microenvironment, little is known about their role in lung cancer metabolism. We studied tumor biopsies from a cohort of 12 stage IIIA lung adenocarcinoma patients and saw a positive correlation between the grade of fibrosis and the glycolysis phenotype (Low PGC-1α and High GAPDH/MT-CO1 ratio mRNA levels). These results were confirmed and extended to other metabolism-related genes through the in silico data analysis from 73 stage IIIA lung adenocarcinoma patients available in TCGA. Interestingly, these relationships are not observed with the CAFs marker α-SMA in both cohorts. To characterize the mechanism, in vitro co-culture studies were carried out using two NSCLC cell lines (A549 and H1299 cells) and two different fibroblast cell lines. Our results confirm that a metabolic reprogramming involving ROS and TGF-β signaling occurs in lung cancer cells and fibroblasts independently of α-SMA induction. Under co-culture conditions, Cancer-Associated fibroblasts increase their glycolytic ability. On the other hand, tumor cells increase their mitochondrial function. Moreover, the differential capability among tumor cells to induce this metabolic shift and also the role of the basal fibroblasts Oxphos Phosphorylation (OXPHOS) function modifying this phenomenon could have implications on both, the diagnosis and prognosis of patients. Further knowledge in the mechanism involved may allow the development of new therapies.

Keywords:  Cancer; Cancer Associated Fibroblasts Mitochondria; Metabolism; OXPHOS; Reverse Warburg effect

DOI:  https://doi.org/10.1016/j.freeradbiomed.2018.10.450
J Heart Lung Transplant. 2018 Sep 28. pii: S1053-2498(18)31690-5. [Epub ahead of print]

Mitochondrial transplantation prolongs cold ischemia time in murine heart transplantation.

Kamila Moskowitzova, Borami Shin, Kaifeng Liu, Giovanna Ramirez-Barbieri, Alvise Guariento, David Blitzer, Jerusha K Thedsanamoorthy, Rouan Yao, Erin R Snay, James A H Inkster, Arzoo Orfany, David Zurakowski, Douglas B Cowan, Alan B Packard, Gary A Visner, Pedro J Del Nido, James D McCully.

   BACKGROUND: Cold ischemia time (CIT) causes ischemia‒reperfusion injury to the mitochondria and detrimentally effects myocardial function and tissue viability. Mitochondrial transplantation replaces damaged mitochondria and enhances myocardial function and tissue viability. Herein we investigated the efficacy of mitochondrial transplantation in enhancing graft function and viability after prolonged CIT.
METHODS: Heterotopic heart transplantation was performed in C57BL/6J mice. Upon heart harvesting from C57BL/6J donors, 0.5 ml of either mitochondria (1 × 108 in respiration buffer; mitochondria group) or respiration buffer (vehicle group) was delivered antegrade to the coronary arteries via injection to the coronary ostium. The hearts were excised and preserved for 29 ± 0.3 hours in cold saline (4°C). The hearts were then heterotopically transplanted. A second injection of either mitochondria (1 × 108) or respiration buffer (vehicle) was delivered antegrade to the coronary arteries 5 minutes after transplantation. Grafts were analyzed for 24 hours. Beating score, graft function, and tissue injury were measured.
RESULTS: Beating score, calculated ejection fraction, and shortening fraction were significantly enhanced (p < 0.05), whereas necrosis and neutrophil infiltration were significantly decreased (p < 0.05) in the mitochondria group as compared with the vehicle group at 24 hours of reperfusion. Transmission electron microscopy showed the presence of contraction bands in vehicle but not in mitochondria grafts.
CONCLUSIONS: Mitochondrial transplantation prolongs CIT to 29 hours in the murine heart transplantation model, significantly enhances graft function, and decreases graft tissue injury. Mitochondrial transplantation may provide a means to reduce graft failure and improve transplantation outcomes after prolonged CIT.

Keywords:  cold ischemia time; heart transplantation; ischemia–reperfusion; mitochondria; mitochondrial transplantation

DOI:  https://doi.org/10.1016/j.healun.2018.09.025
Int J Biochem Cell Biol. 2018 Nov 01. pii: S1357-2725(18)30229-2. [Epub ahead of print]

Mitochondrial Nucleoids: Superresolution microscopy analysis.

Petr Ježek, Tomáš Špaček, Jan Tauber, Vojtěch Pavluch.

  The mitochondrion owns an autonomous genome. Double-stranded circular mitochondrial DNA (mtDNA) is organized in complexes with a packing/stabilizing transcription factor TFAM, having multiple roles, and proteins of gene expression machinery in structures called nucleoids. From hundreds to thousands nucleoids exist distributed in the matrix of mitochondrial reticulum network. A single mtDNA molecule contained within the single nucleoid is a currently preferred but questioned model. Nevertheless, mtDNA replication should lead transiently to its doubling within a nucleoid. However, nucleoid division has not yet been documented in detail. A 3D superresolution microscopy is required to resolve nucleoid biology occurring in ~100 nm space, having an advantage over electron microscopy tomography in resolving the particular protein components. We discuss stochastic vs. stimulated emission depletion microscopy yielding wide vs. narrow nucleoid size distribution, respectively. Nucleoid clustering into spheroids fragmented from the continuous mitochondrial network, likewise possible nucleoid attachment to the inner membrane is reviewed.

Keywords:  3D superresolution microscopy; TFAM; mtDNA; nucleoids

DOI:  https://doi.org/10.1016/j.biocel.2018.10.012
Biochim Biophys Acta Mol Cell Biol Lipids. 2018 Oct 31. pii: S1388-1981(18)30345-7. [Epub ahead of print]

Calcium-independent phospholipase A2γ (iPLA2γ) and its roles in cellular functions and diseases.

Shuntaro Hara, Emiko Yoda, Yuka Sasaki, Yoshihito Nakatani, Hiroshi Kuwata.

Calcium-independent phospholipase A2γ (iPLA2γ)/patatin-like phospholipase domain-containing lipase 8 (PNPLA8) is one of the iPLA2 enzymes, which do not require Ca2+ ion for their activity. iPLA2γ is a membrane-bound enzyme with unique features, including the utilization of four distinct translation initiation sites and the presence of mitochondrial and peroxisomal localization signals. This enzyme is preferentially distributed in the mitochondria and peroxisomes and is thought to be responsible for the maintenance of lipid homeostasis in these organelles. Thus, both the overexpression and the deletion of iPLA2γ in vivo caused mitochondrial abnormalities and dysfunction. Roles of iPLA2γ in lipid mediator production and cytoprotection against oxidative stress have also been suggested by in vitro and in vivo studies. The dysregulation of iPLA2γ can therefore be a critical factor in the development of many diseases, including metabolic diseases and cancer. In this review, we provide an overview of the biochemical properties of iPLA2γ and then summarize the current understanding of the in vivo roles of iPLA2γ revealed by knockout mouse studies.

DOI: https://doi.org/10.1016/j.bbalip.2018.10.009
Biochim Biophys Acta Mol Basis Dis. 2018 Oct 31. pii: S0925-4439(18)30437-X. [Epub ahead of print]1865(1): 98-106

Metabolomics of Ndufs4-/- skeletal muscle: Adaptive mechanisms converge at the ubiquinone-cycle.

Karin Terburgh, Zander Lindeque, Shayne Mason, Francois van der Westhuizen, Roan Louw.

  Leigh syndrome is one of the most common childhood-onset neurometabolic disorders resulting from a primary oxidative phosphorylation dysfunction and affecting mostly brain tissues. Ndufs4-/- mice have been widely used to study the neurological responses in this syndrome, however the reason why these animals do not display strong muscle involvement remains elusive. We combined biochemical strategies and multi-platform metabolomics to gain insight into the metabolism of both glycolytic (white quadriceps) and oxidative (soleus) skeletal muscles from Ndufs4-/- mice. Enzyme assays confirmed severely reduced (80%) CI activity in both Ndufs4-/- muscle types, compared to WTs. No significant alterations were evident in other respiratory chain enzyme activities; however, Ndufs4-/- solei displayed moderate decreases in citrate synthase (12%) and CIII (18%) activities. Through hypothesis-generating metabolic profiling, we provide the first evidence of adaptive responses to CI dysfunction involving non-classical pathways fueling the ubiquinone (Q) cycle. We report a respective 48 and 34 discriminatory metabolites between Ndufs4-/- and WT white quadriceps and soleus muscles, among which the most prominent alterations indicate the involvement of the glycerol-3-phosphate shuttle, electron transfer flavoprotein system, CII, and proline cycle in fueling the Q cycle. By restoring the electron flux to CIII via the Q cycle, these adaptive mechanisms could maintain adequate oxidative ATP production, despite CI deficiency. Taken together, our results shed light on the underlying pathogenic mechanisms of CI dysfunction in skeletal muscle. Upon further investigation, these pathways could provide novel targets for therapeutic intervention in CI deficiency and potentially lead to the development of new treatment strategies.

Keywords:  Complex I deficiency; Metabolomics; Mitochondrial disease; Ndufs4 knockout mice; Skeletal muscle; Ubiquinone-cycle

DOI:  https://doi.org/10.1016/j.bbadis.2018.10.034
Ageing Res Rev. 2018 Nov 01. pii: S1568-1637(18)30077-1. [Epub ahead of print]

Homocysteine and age-associated disorders.

E A Ostrakhovitch, S Tabibzadeh.

  There are numerous theories of aging, a process which still seems inevitable. Aging leads to cancer and multi-systemic disorders as well as chronic diseases including those that impair the functions of endothelial cells, kidney and lung. Decline in age- associated cellular functions leads to neurodegeneration and cognitive decline that affect the quality of life. Accumulation of damage, mutations, metabolic changes, failure in cellular energy production and clearance of altered proteins over the lifetime, and hyperhomocysteinemia, ultimately result in tissue degeneration. Moreover, approximately 50% of people, aged 65 years and older develop hypertension and are at a high risk of developing cardiovascular insufficiency. Dysfunctional mitochondria in aging cardiomyocytes contribute to myocardial remodeling leading to heart failure. Osteoporosis is prevalent in the elderly, making them predisposed to vertebral deformities as well as fractures of the hip, wrist and spine. Genetic factors as well as better medical care, a well balanced diet, and lack of stress increases the life expectancy.

Keywords:  Age Associated Diseases; Aging; Homocysteine; Hyperhomocysteinemia; Metabolism

DOI:  https://doi.org/10.1016/j.arr.2018.10.010
BMC Evol Biol. 2018 Nov 03. 18(1): 162

Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination.

Shir Portugez, William F Martin, Einat Hazkani-Covo.

   BACKGROUND: Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts and nupts are classified as simple if they are composed of a single organelle fragment or as complex if they are composed of multiple fragments. Mosaic insertions are complex insertions composed of fragments of both mitochondrial and plastid DNA. Simple numts and nupts in eukaryotes have been extensively studied, their mechanism of insertion involves non-homologous end joining (NHEJ). Mosaic insertions have been less well-studied and their mechanisms of integration are unknown.
RESULTS: Here we estimated the number of nuclear mosaic insertions (numins) in nine plant genomes. We show that numins compose up to 10% of the total nuclear insertions of organelle DNA in these plant genomes. The NHEJ hallmarks typical for numts and nupts were also identified in mosaic insertions. However, the number of identified insertions that integrated via NHEJ mechanism is underestimated, as NHEJ signatures are conserved only in recent insertions and mutationally eroded in older ones. A few complex insertions show signatures of long homology that cannot be attributed to NHEJ, a novel observation that implicates gene conversion or single strand annealing mechanisms in organelle nuclear insertions.
CONCLUSIONS: The common NHEJ signature that was identified here reveals that, in plant cells, mitochondria and plastid fragments in numins must meet during or prior to integration into the nuclear genome.

Keywords:  Gene conversion; Mosaic insertions; Non-homologous end joining; Numins; Numts; Nupts

DOI:  https://doi.org/10.1186/s12862-018-1279-x
Methods Enzymol. 2018 ;pii: S0076-6879(18)30384-7. [Epub ahead of print]610 219-250

High Content, Phenotypic Assays and Screens for Compounds Modulating Cellular Processes in Primary Neurons.

Miklos Kepiro, Boglarka H Varkuti, Ronald L Davis.

  High content, phenotypic screens offer a powerful approach to systems biology at the cellular level. The approach employs cells carrying fluorescently labeled molecules or organelles in 384- or 1536-well microplates, and an automated confocal screening microscope for capturing images from each well. Although some specifics vary according to the assay type, each will apply some degree of image processing and feature extraction followed by a data analysis pipeline to identify the perturbations (small molecules, etc.) of interest. We describe and discuss the advantages and limitations of high content assays and screens using the specific example of assaying mitochondrial dynamics in primary neurons. We provide a detailed description of our culturing methods, imaging and data analysis techniques and provide an open source, ready to use CellProfiler pipeline for high-throughput image segmentation and quantification tool for mitochondrial parameters.

Keywords:  Automated image analysis; CellProfiler; High content phenotypic screen; Hit selection; Mitochondrial dynamics; Mitochondrial morphology; Pintool; Primary neurons

DOI:  https://doi.org/10.1016/bs.mie.2018.09.021