bims-mikwok Biomed News
on Mitochondrial quality control
Issue of 2020‒11‒08
nineteen papers selected by
Avinash N. Mukkala
University of Toronto

  1. Redox Biol. 2020 Oct 23. pii: S2213-2317(20)30972-1. [Epub ahead of print]38 101767
    Wang Y, Zhu J, Liu Z, Shu S, Fu Y, Liu Y, Cai J, Tang C, Liu Y, Yin X, Dong Z.
      Sepsis is the major cause of acute kidney injury (AKI) associated with high mortality rates. Mitochondrial dysfunction contributes to the pathophysiology of septic AKI. Mitophagy is an important mitochondrial quality control mechanism that selectively eliminates damaged mitochondria, but its role and regulation in septic AKI remain largely unknown. Here, we demonstrate the induction of mitophagy in mouse models of septic AKI induced by lipopolysaccharide (LPS) treatment or by cecal ligation and puncture. Mitophagy was also induced in cultured proximal tubular epithelial cells exposed to LPS. Induction of mitophagy under these experimental setting was suppressed by pink1 or park2 knockout, indicating the role of the PINK1/PARK2 pathway of mitophagy in septic AKI. In addition, sepsis induced more severe kidney injury and cell apoptosis in pink1 or park2 knockout mice than in wild-type mice, suggesting a beneficial role of mitophagy in septic AKI. Furthermore, in cultured renal tubular cells treated with LPS, knockdown of pink1 or park2 inhibited mitochondrial accumulation of the autophagy adaptor optineurin (OPTN) and silencing Optn inhibited LPS-induced mitophagy. Taken together, these findings suggest that the PINK1/PARK2 pathway of mitophagy plays an important role in mitochondrial quality control, tubular cell survival, and renal function in septic AKI.
    Keywords:  Acute kidney injury; Mitophgay; Optineurin; PARK2; PINK1; Sepsis
  2. EMBO Rep. 2020 Nov 05. 21(11): e51652
    Aman Y, Cao S, Fang EF.
      Mitochondrial homeostasis is necessary for the maintenance of cellular function and neuronal survival. Mitochondrial quality is tightly regulated by mitophagy, in which defective/superfluous mitochondria are degraded and recycled. Here, Hara et al demonstrate that induction of mitophagy via iron depletion suppresses the development of hepatocellular carcinoma (HCC). This work suggests turning up mitophagy as a potential therapeutic strategy against liver cancer.
  3. Int J Mol Sci. 2020 Oct 31. pii: E8157. [Epub ahead of print]21(21):
    Giamogante F, Barazzuol L, Brini M, Calì T.
      Organelle intercommunication represents a wide area of interest. Over the last few decades, increasing evidence has highlighted the importance of organelle contact sites in many biological processes including Ca2+ signaling, lipid biosynthesis, apoptosis, and autophagy but also their involvement in pathological conditions. ER-mitochondria tethering is one of the most investigated inter-organelle communications and it is differently modulated in response to several cellular conditions including, but not limited to, starvation, Endoplasmic Reticulum (ER) stress, and mitochondrial shape modifications. Despite many studies aiming to understand their functions and how they are perturbed under different conditions, approaches to assess organelle proximity are still limited. Indeed, better visualization and characterization of contact sites remain a fascinating challenge. The aim of this review is to summarize strengths and weaknesses of the available methods to detect and quantify contact sites, with a main focus on ER-mitochondria tethering.
    Keywords:  ER–mitochondria tethering; SPLICS; organelle contact sites; split-GFP
  4. Annu Rev Physiol. 2020 Nov 03.
    Murphy E, Steenbergen C.
      Mitochondria are responsible for ATP production but are also known as regulators of cell death, and mitochondrial matrix Ca2+ is a key modulator of both ATP production and cell death. Although mitochondrial Ca2+ uptake and efflux have been studied for over 50 years, it is only in the past decade that the proteins responsible for mitochondrial Ca2+ uptake and efflux have been identified. The identification of the mitochondrial Ca2+ uniporter (MCU) led to an explosion of studies identifying regulators of the MCU. The levels of these regulators vary in a tissue- and disease-specific manner, providing new insight into how mitochondrial Ca2+ is regulated. This review focuses on the proteins responsible for mitochondrial transport and what we have learned from mouse studies with genetic alterations in these proteins. Expected final online publication date for the Annual Review of Physiology, Volume 83 is February 10, 2021. Please see for revised estimates.
  5. Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30538-6. [Epub ahead of print]32(5): 889-900.e7
    Ludikhuize MC, Meerlo M, Gallego MP, Xanthakis D, Burgaya Julià M, Nguyen NTB, Brombacher EC, Liv N, Maurice MM, Paik JH, Burgering BMT, Rodriguez Colman MJ.
      Differential WNT and Notch signaling regulates differentiation of Lgr5+ crypt-based columnar cells (CBCs) into intestinal cell lineages. Recently we showed that mitochondrial activity supports CBCs, while adjacent Paneth cells (PCs) show reduced mitochondrial activity. This implies that CBC differentiation into PCs involves a metabolic transition toward downregulation of mitochondrial dependency. Here we show that Forkhead box O (FoxO) transcription factors and Notch signaling interact in determining CBC fate. In agreement with the organoid data, Foxo1/3/4 deletion in mouse intestine induces secretory cell differentiation. Importantly, we show that FOXO and Notch signaling converge on regulation of mitochondrial fission, which in turn provokes stem cell differentiation into goblet cells and PCs. Finally, scRNA-seq-based reconstruction of CBC differentiation trajectories supports the role of FOXO, Notch, and mitochondria in secretory differentiation. Together, this points at a new signaling-metabolic axis in CBC differentiation and highlights the importance of mitochondria in determining stem cell fate.
    Keywords:  FOXO; Notch; differentiation; intestine; metabolism; mitochondria; stem cells
  6. Cell Death Dis. 2020 Oct 31. 11(10): 940
    Hu C, Shu L, Huang X, Yu J, Li L, Gong L, Yang M, Wu Z, Gao Z, Zhao Y, Chen L, Song Z.
      Mitochondrial cristae are the main site for oxidative phosphorylation, which is critical for cellular energy production. Upon different physiological or pathological stresses, mitochondrial cristae undergo remodeling to reprogram mitochondrial function. However, how mitochondrial cristae are formed, maintained, and remolded is still largely unknown due to the technical challenges of tracking mitochondrial crista dynamics in living cells. Here, using live-cell Hessian structured illumination microscopy combined with transmission electron microscopy, focused ion beam/scanning electron microscopy, and three-dimensional tomographic reconstruction, we show, in living cells, that mitochondrial cristae are highly dynamic and undergo morphological changes, including elongation, shortening, fusion, division, and detachment from the mitochondrial inner boundary membrane (IBM). In addition, we find that OPA1, Yme1L, MICOS, and Sam50, along with the newly identified crista regulator ATAD3A, control mitochondrial crista dynamics. Furthermore, we discover two new types of mitochondrial crista in dysfunctional mitochondria, "cut-through crista" and "spherical crista", which are formed due to incomplete mitochondrial fusion and dysfunction of the MICOS complex. Interestingly, cut-through crista can convert to "lamellar crista". Overall, we provide a direct link between mitochondrial crista formation and mitochondrial crista dynamics.
  7. Sci Rep. 2020 Nov 03. 10(1): 18941
    Rohani A, Kashatus JA, Sessions DT, Sharmin S, Kashatus DF.
      Mitochondria are highly dynamic organelles that can exhibit a wide range of morphologies. Mitochondrial morphology can differ significantly across cell types, reflecting different physiological needs, but can also change rapidly in response to stress or the activation of signaling pathways. Understanding both the cause and consequences of these morphological changes is critical to fully understanding how mitochondrial function contributes to both normal and pathological physiology. However, while robust and quantitative analysis of mitochondrial morphology has become increasingly accessible, there is a need for new tools to generate and analyze large data sets of mitochondrial images in high throughput. The generation of such datasets is critical to fully benefit from rapidly evolving methods in data science, such as neural networks, that have shown tremendous value in extracting novel biological insights and generating new hypotheses. Here we describe a set of three computational tools, Cell Catcher, Mito Catcher and MiA, that we have developed to extract extensive mitochondrial network data on a single-cell level from multi-cell fluorescence images. Cell Catcher automatically separates and isolates individual cells from multi-cell images; Mito Catcher uses the statistical distribution of pixel intensities across the mitochondrial network to detect and remove background noise from the cell and segment the mitochondrial network; MiA uses the binarized mitochondrial network to perform more than 100 mitochondria-level and cell-level morphometric measurements. To validate the utility of this set of tools, we generated a database of morphological features for 630 individual cells that encode 0, 1 or 2 alleles of the mitochondrial fission GTPase Drp1 and demonstrate that these mitochondrial data could be used to predict Drp1 genotype with 87% accuracy. Together, this suite of tools enables the high-throughput and automated collection of detailed and quantitative mitochondrial structural information at a single-cell level. Furthermore, the data generated with these tools, when combined with advanced data science approaches, can be used to generate novel biological insights.
  8. Acta Histochem. 2020 Oct 28. pii: S0065-1281(20)30145-8. [Epub ahead of print]122(8): 151646
    Duranova H, Valkova V, Knazicka Z, Olexikova L, Vasicek J.
      Mitochondria are highly dynamic intracellular organelles with ultrastructural heterogeneity reflecting the behaviour and functions of the cells. The ultrastructural remodelling, performed by the counteracting active processes of mitochondrial fusion and fission, enables the organelles to respond to diverse cellular requirements and cues. It is also an important part of mechanisms underlying adaptation of mitochondria to pathophysiological conditions that challenge the cell homeostasis. However, if the stressor is constantly acting, the adaptive capacity of the cell can be exceeded and defective changes in mitochondrial morphology (indicating the insufficient functionality of mitochondria or development of mitochondrial disorders) may appear. Beside qualitative description of mitochondrial ultrastructure, stereological principles concerning the estimation of alterations in mitochondrial volume density or surface density are invaluable approaches for unbiased quantification of cells under physiological or pathophysiological conditions. In order to improve our understanding of cellular functions and dysfunctions, transmission electron microscopy (TEM) still remains a gold standard for qualitative and quantitative ultrastructural examination of mitochondria from various cell types, as well as from those experienced to different stimuli or toxicity-inducing factors. In the current study, general morphological and functional features of mitochondria, and their ultrastructural heterogeneity related to physiological and pathophysiological states of the cells are reviewed. Moreover, stereological approaches for accurate quantification of mitochondrial ultrastructure from electron micrographs taken from TEM are described in detail.
    Keywords:  Mitochondria; Mitochondrial dynamics; Stereological approaches; Surface density; Ultrastructural heterogeneity; Volume density
  9. Front Immunol. 2020 ;11 506275
    Jiangqiao Z, Tianyu W, Zhongbao C, Long Z, Jilin Z, Xiaoxiong M, Tao Q.
      Ubiquitin-specific peptidase 10 (USP10) protein is a deubiquitination enzyme involved in many important biological processes. However, the function of USP10 in hepatic ischaemic/reperfusion (I/R) injury remains unknown. The aim of this study was to explore the role of USP10 in hepatic I/R injury. USP10 Heterozygote mice and primary hepatocytes were used to construct hepatic I/R models. The effect of USP10 on hepatic I/R injury was examined via pathological and molecular analyses. Our results indicated that USP10 was significantly downregulated in the livers of mice after hepatic I/R injury and in hepatocytes subjected to hypoxia/reoxygenation stimulation. USP10 Heterozygote mice exhibited exacerbated hepatic I/R injury, as evidenced by enhanced liver inflammation via the NF-κB signalling pathway and increased hepatocyte apoptosis. Additionally, USP10 overexpression inhibited hepatocyte inflammation and apoptosis in hepatic I/R injury in vitro and in vivo. Mechanistically, our study demonstrated that USP10 knockdown exerted its detrimental effects on hepatic I/R injury by inducing activation of the transforming growth factor β-activated kinase 1 (TAK1)-JNK/p38 signalling pathways. TAK1 was required for USP10 function in hepatic I/R injury as TAK1 inhibition abolished USP10 function in vitro. In conclusion, our study demonstrated that USP10 plays a protective role in hepatic I/R injury by inhibiting the activation of the TAK1-JNK/p38 signalling pathways. Modulation of USP10/TAK1 might be a promising strategy to prevent this pathological process.
    Keywords:  TAK1; USP10; ischaemic/reperfusion injury; liver; ubiquitination
  10. Cell Mol Neurobiol. 2020 Nov 07.
    Morisaki Y, Nakagawa I, Ogawa Y, Yokoyama S, Furuta T, Saito Y, Nakase H.
      Ischemic postconditioning (PostC) is known to reduce cerebral ischemia/reperfusion (I/R) injury; however, whether the opening of mitochondrial ATP-dependent potassium (mito-KATP) channels and mitochondrial permeability transition pore (mPTP) cause the depolarization of the mitochondrial membrane that remains unknown. We examined the involvement of the mito-KATP channel and the mPTP in the PostC mechanism. Ischemic PostC consisted of three cycles of 15 s reperfusion and 15 s re-ischemia, and was started 30 s after the 7.5 min ischemic load. We recorded N-methyl-D-aspartate receptors (NMDAR)-mediated currents and measured cytosolic Ca2+ concentrations, and mitochondrial membrane potentials in mouse hippocampal pyramidal neurons. Both ischemic PostC and the application of a mito-KATP channel opener, diazoxide, reduced NMDAR-mediated currents, and suppressed cytosolic Ca2+ elevations during the early reperfusion period. An mPTP blocker, cyclosporine A, abolished the reducing effect of PostC on NMDAR currents. Furthermore, both ischemic PostC and the application of diazoxide potentiated the depolarization of the mitochondrial membrane potential. These results indicate that ischemic PostC suppresses Ca2+ influx into the cytoplasm by reducing NMDAR-mediated currents through mPTP opening. The present study suggests that depolarization of the mitochondrial membrane potential by opening of the mito-KATP channel is essential to the mechanism of PostC in neuroprotection against anoxic injury.
    Keywords:  Ca2+; Ischemic postconditioning; Mitochondrial KATP channel; Mitochondrial permeability transition pore; NMDA receptor
  11. Biomed Pharmacother. 2020 Nov;pii: S0753-3322(20)30980-X. [Epub ahead of print]131 110787
    Ji Y, Yao J, He Y.
      AIM: Acute myocardial infarction (AMI) is one of the deadliest diseases worldwide. The search for countermeasures to reduce cardiomyocytes death in the infarcted area has always been the focus of research. Ubiquitin (UB) is a small polypeptide mainly involved in proteasome-mediated protein degradation in cells, whereas extracellular UB in body fluids can also function through its receptor CXC chemokine receptor type 4 (CXCR4). This study aimed to explore the functional roles of extracellular UB in cardiomyocytes during ischemia/hypoxia (I/H).METHODS: H9C2 cells were subjected to I/H treatment and cell injury was evaluated by cell viability, morphology changes and apoptosis rate. UB expression and levels of ubiquitinated proteins after I/H injury were measured. The effects of extracellular UB on I/H-induced cardiomyocytes apoptosis and the possible underlying mechanisms were studied.
    RESULTS: I/H injury induced the decrease of cell viability as well as enhanced impaired cell morphology and apoptosis rate in H9C2 cells. Levels of UB mRNA and ubiquitinated proteins were significantly up-regulated after I/H treatment, whereas the concentration of extracellular UB in the conditioned media did not show significant change and the intracellular mono-UB levels in cells were down-regulated. Extracellular UB treatment protected cardiomyocytes from I/H injury by inhibiting the overactivation of mitochondria-dependent apoptosis pathway and up-regulating autophagy level. Inhibition of CXCR4 receptor using AMD3100 abolished cardioprotective effects of extracellular UB.
    CONCLUSION: The up-regulation of UB was suggested to be an adaptive response to resist I/H-induced cardiomyocytes apoptosis, and additional extracellular UB treatment might serve as a new potential therapeutic drug for AMI.
    Keywords:  Apoptosis; Autophagy; CXCR4; Extracellular ubiquitin; ischemia/hypoxia
  12. Mol Cell. 2020 Oct 26. pii: S1097-2765(20)30720-6. [Epub ahead of print]
    Adachi Y, Kato T, Yamada T, Murata D, Arai K, Stahelin RV, Chan DC, Iijima M, Sesaki H.
      Mitochondria are highly dynamic organelles that continuously grow, divide, and fuse. The division of mitochondria is crucial for human health. During mitochondrial division, the mechano-guanosine triphosphatase (GTPase) dynamin-related protein (Drp1) severs mitochondria at endoplasmic reticulum (ER)-mitochondria contact sites, where peripheral ER tubules interact with mitochondria. Here, we report that Drp1 directly shapes peripheral ER tubules in human and mouse cells. This ER-shaping activity is independent of GTP hydrolysis and located in a highly conserved peptide of 18 amino acids (termed D-octadecapeptide), which is predicted to form an amphipathic α helix. Synthetic D-octadecapeptide tubulates liposomes in vitro and the ER in cells. ER tubules formed by Drp1 promote mitochondrial division by facilitating ER-mitochondria interactions. Thus, Drp1 functions as a two-in-one protein during mitochondrial division, with ER tubulation and mechano-GTPase activities.
    Keywords:  Drp1; mitochondria; mitochondrial division; organelle contact sites; phosphaditic acid; the endoplasmic reticulum
  13. Redox Biol. 2020 Oct 16. pii: S2213-2317(20)30967-8. [Epub ahead of print]37 101762
    Rodríguez LR, Calap-Quintana P, Lapeña-Luzón T, Pallardó FV, Schneuwly S, Navarro JA, Gonzalez-Cabo P.
      Friedreich ataxia (FRDA) is a neurodegenerative disorder characterized by neuromuscular and neurological manifestations. It is caused by mutations in the FXN gene, which results in loss of the mitochondrial protein frataxin. Endoplasmic Reticulum-mitochondria associated membranes (MAMs) are inter-organelle structures involved in the regulation of essential cellular processes, including lipid metabolism and calcium signaling. In the present study, we have analyzed in both, unicellular and multicellular models of FRDA, calcium management and integrity of MAMs. We observed that function of MAMs is compromised in our cellular model of FRDA, which was improved upon treatment with antioxidants. In agreement, promoting mitochondrial calcium uptake was sufficient to restore several defects caused by frataxin deficiency in Drosophila Melanogaster. Remarkably, our findings describe for the first time frataxin as a member of the protein network of MAMs, where interacts with two of the main proteins implicated in endoplasmic reticulum-mitochondria communication. These results suggest a new role of frataxin, indicate that FRDA goes beyond mitochondrial defects and highlight MAMs as novel therapeutic candidates to improve patient's conditions.
    Keywords:  Calcium; Frataxin; Lipid peroxidation; MAMs; N-acetylcysteine; Vitamin E
  14. Ageing Res Rev. 2020 Oct 29. pii: S1568-1637(20)30338-X. [Epub ahead of print] 101203
    Sun-Wang JL, Ivanova S, Zorzano A.
      Dysregulated proteostasis is one of the hallmarks of ageing. Damaged proteins may impair cellular function and their accumulation may lead to tissue dysfunction and disease. This is why protective mechanisms to safeguard the cell proteome have evolved. These mechanisms consist of cellular machineries involved in protein quality control, including regulators of protein translation, folding, trafficking and degradation. In eukaryotic cells, protein degradation occurs via two main pathways: the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway. Although distinct pathways, they are not isolated systems and have a complementary nature, as evidenced by recent studies. These findings raise the question of how autophagy and the proteasome crosstalk. In this review we address how the two degradation pathways impact each other, thereby adding a new layer of regulation to protein degradation. We also analyze the implications of the UPS and autophagy in ageing.
    Keywords:  Ageing; UPS-autophagy crosstalk; autophagy; proteostasis; ubiquitin-proteasome system
  15. Cell Rep. 2020 Nov 03. pii: S2211-1247(20)31329-2. [Epub ahead of print]33(5): 108340
    Yang Y, Zhang G, Guo F, Li Q, Luo H, Shu Y, Shen Y, Gan J, Xu L, Yang H.
      Bioenergetic reprogramming during hypoxia adaption is critical to promote hepatocellular carcinoma (HCC) growth and progression. However, the mechanism underlying the orchestration of mitochondrial OXPHOS (oxidative phosphorylation) and glycolysis in hypoxia is not fully understood. Here, we report that mitochondrial UQCC3 (C11orf83) expression increases in hypoxia and correlates with the poor prognosis of HCC patients. Loss of UQCC3 impairs HCC cell proliferation in hypoxia in vitro and in vivo. Mechanistically, UQCC3 forms a positive feedback loop with mitochondrial reactive oxygen species (ROS) to sustain UQCC3 expression and ROS generation in hypoxic HCC cells and subsequently maintains mitochondrial structure and function and stabilizes HIF-1α expression to enhance glycolysis under hypoxia. Thus, UQCC3 plays an indispensable role for bioenergetic reprogramming of HCC cells during hypoxia adaption by simultaneously regulating OXPHOS and glycolysis. The positive feedback between UQCC3 and ROS indicates a self-modulating model within mitochondria that initiates the adaptation of HCC to hypoxic stress.
    Keywords:  ATP; HCC; HIF-1α; OXPHOS; ROS; UQCC3 (C11orf83); bioenergenesis; glycolysis; hypoxia; mitochondria
  16. FASEB J. 2020 Nov 01.
    Montes de Oca Balderas P, Matus Núñez M, Picones A, Hernández-Cruz A.
      Glutamate N-methyl-D-aspartate (NMDA) receptor (NMDAR) is critical for neurotransmission as a Ca2+ channel. Nonetheless, flux-independent signaling has also been demonstrated. Astrocytes express NMDAR distinct from its neuronal counterpart, but cultured astrocytes have no electrophysiological response to NMDA. We recently demonstrated that in cultured astrocytes, NMDA at pH6 (NMDA/pH6) acting through the NMDAR elicits flux-independent Ca2+ release from the Endoplasmic Reticulum (ER) and depletes mitochondrial membrane potential (mΔΨ). Here we show that Ca2+ release is due to pH6 sensing by NMDAR, whereas mΔΨ depletion requires both: pH6 and flux-dependent NMDAR signaling. Plasma membrane (PM) NMDAR guard a non-random distribution relative to the ER and mitochondria. Also, NMDA/pH6 induces ER stress, endocytosis, PM electrical capacitance reduction, mitochondria-ER, and -nuclear contacts. Strikingly, it also produces the formation of PM invaginations near mitochondria along with structures referred to here as PM-mitochondrial bridges (PM-m-br). These and earlier data strongly suggest PM-mitochondria communication. As proof of the concept of mass transfer, we found that NMDA/pH6 provoked mitochondria labeling by the PM dye FM-4-64FX. NMDA/pH6 caused PM depolarization, cell acidification, and Ca2+ release from most mitochondria. Finally, the MCU and microtubules were not involved in mΔΨ depletion, while actin cytoskeleton was partially involved. These findings demonstrate that NMDAR has concomitant flux-independent and flux-dependent actions in cultured astrocytes.
    Keywords:  NMDAR; astrocyte; calcium; flux-independent; mitochondria; organelle communication
  17. Ecol Evol. 2020 Oct;10(20): 11117-11132
    Dutheil JY, Münch K, Schotanus K, Stukenbrock EH, Kahmann R.
      Homing endonucleases (HE) are enzymes capable of cutting DNA at highly specific target sequences, the repair of the generated double-strand break resulting in the insertion of the HE-encoding gene ("homing" mechanism). HEs are present in all three domains of life and viruses; in eukaryotes, they are mostly found in the genomes of mitochondria and chloroplasts, as well as nuclear ribosomal RNAs. We here report the case of a HE that accidentally integrated into a telomeric region of the nuclear genome of the fungal maize pathogen Ustilago maydis. We show that the gene has a mitochondrial origin, but its original copy is absent from the U. maydis mitochondrial genome, suggesting a subsequent loss or a horizontal transfer from a different species. The telomeric HE underwent mutations in its active site and lost its original start codon. A potential other start codon was retained downstream, but we did not detect any significant transcription of the newly created open reading frame, suggesting that the inserted gene is not functional. Besides, the insertion site is located in a putative RecQ helicase gene, truncating the C-terminal domain of the protein. The truncated helicase is expressed during infection of the host, together with other homologous telomeric helicases. This unusual mutational event altered two genes: The integrated HE gene subsequently lost its homing activity, while its insertion created a truncated version of an existing gene, possibly altering its function. As the insertion is absent in other field isolates, suggesting that it is recent, the U. maydis 521 reference strain offers a snapshot of this singular mutational event.
    Keywords:  gene birth; gene transfer; homing endonuclease; intron; mitochondrion
  18. Sci Rep. 2020 Nov 04. 10(1): 19027
    Lunde A, Glover JC.
      Differential fluorescence labeling and multi-fluorescence imaging followed by colocalization analysis is commonly used to investigate cellular heterogeneity in situ. This is particularly important when investigating the biology of tissues with diverse cell types. Object-based colocalization analysis (OBCA) tools can employ automatic approaches, which are sensitive to errors in cell segmentation, or manual approaches, which can be impractical and tedious. Here, we present a novel set of tools for OBCA using a semi-automatic approach, consisting of two ImageJ plugins, a Microsoft Excel macro, and a MATLAB script. One ImageJ plugin enables customizable processing of multichannel 3D images for enhanced visualization of features relevant to OBCA, and another enables semi-automatic colocalization quantification. The Excel macro and the MATLAB script enable data organization and 3D visualization of object data across image series. The tools are well suited for experiments involving complex and large image data sets, and can be used in combination or as individual components, allowing flexible, efficient and accurate OBCA. Here we demonstrate their utility in immunohistochemical analyses of the developing central nervous system, which is characterized by complexity in the number and distribution of cell types, and by high cell packing densities, which can both create challenging situations for OBCA.
  19. Proc Natl Acad Sci U S A. 2020 Nov 03. pii: 202007827. [Epub ahead of print]
    Giarmarco MM, Brock DC, Robbings BM, Cleghorn WM, Tsantilas KA, Kuch KC, Ge W, Rutter KM, Parker ED, Hurley JB, Brockerhoff SE.
      Cone photoreceptors in the retina are exposed to intense daylight and have higher energy demands in darkness. Cones produce energy using a large cluster of mitochondria. Mitochondria are susceptible to oxidative damage, and healthy mitochondrial populations are maintained by regular turnover. Daily cycles of light exposure and energy consumption suggest that mitochondrial turnover is important for cone health. We investigated the three-dimensional (3D) ultrastructure and metabolic function of zebrafish cone mitochondria throughout the day. At night retinas undergo a mitochondrial biogenesis event, corresponding to an increase in the number of smaller, simpler mitochondria and increased metabolic activity in cones. In the daytime, endoplasmic reticula (ER) and autophagosomes associate more with mitochondria, and mitochondrial size distribution across the cluster changes. We also report dense material shared between cone mitochondria that is extruded from the cell at night, sometimes forming extracellular structures. Our findings reveal an elaborate set of daily changes to cone mitochondrial structure and function.
    Keywords:  circadian; mitochondria; photoreceptors; retina; zebrafish