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Moldovan C, Onaciu A, Toma V, Munteanu RA, Gulei D, Moldovan AI, Stiufiuc GF, Feder RI, Cenariu D, Iuga CA, Stiufiuc RI. Current trends in luminescence-based assessment of apoptosis. RSC Adv 2023; 13:31641-31658. [PMID: 37908656 PMCID: PMC10613953 DOI: 10.1039/d3ra05809c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
Apoptosis, the most extensively studied type of cell death, is known to play a crucial role in numerous processes such as elimination of unwanted cells or cellular debris, growth, control of the immune system, and prevention of malignancies. Defective regulation of apoptosis can trigger various diseases and disorders including cancer, neurological conditions, autoimmune diseases and developmental disorders. Knowing the nuances of the cell death type induced by a compound can help decipher which therapy is more effective for specific diseases. The detection of apoptotic cells using classic methods has brought significant contribution over the years, but innovative methods are quickly emerging and allow more in-depth understanding of the mechanisms, aside from a simple quantification. Due to increased sensitivity, time efficiency, pathway specificity and negligible cytotoxicity, these innovative approaches have great potential for both in vitro and in vivo studies. This review aims to shed light on the importance of developing and using novel nanoscale methods as an alternative to the classic apoptosis detection techniques.
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Affiliation(s)
- Cristian Moldovan
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Department of Pharmaceutical Physics & Biophysics, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street No. 4-6 400349 Cluj-Napoca Romania
| | - Anca Onaciu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Valentin Toma
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Raluca A Munteanu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Diana Gulei
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Alin I Moldovan
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Gabriela F Stiufiuc
- Faculty of Physics, "Babes Bolyai" University Mihail Kogalniceanu Street No. 1 400084 Cluj-Napoca Romania
| | - Richard I Feder
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Diana Cenariu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Cristina A Iuga
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Pharmaceutical Analysis, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street 6 Cluj-Napoca 400349 Romania
| | - Rares I Stiufiuc
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Department of Pharmaceutical Physics & Biophysics, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street No. 4-6 400349 Cluj-Napoca Romania
- TRANSCEND Research Center, Regional Institute of Oncology 700483 Iasi Romania
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Guo M, Lu B, Gan J, Wang S, Jiang X, Li H. Apoptosis detection: a purpose-dependent approach selection. Cell Cycle 2021; 20:1033-1040. [PMID: 34000960 PMCID: PMC8208110 DOI: 10.1080/15384101.2021.1919830] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/13/2021] [Indexed: 01/20/2023] Open
Abstract
Apoptosis is closely associated with many diseases. Detection of apoptosis can be achieved by morphology, biochemistry, molecular biology, immunology, and other techniques. However, as technologies are increasingly used for the detection of apoptosis, many researchers are confused about how to choose a suitable method to detect apoptosis. Selection of a suitable detection method for apoptosis will help clinical diagnosis and prevention of diseases. This article reviews the selection of optimal apoptosis-detection methods based on research purposes and technique principles.
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Affiliation(s)
- Maojuan Guo
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Bin Lu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jiali Gan
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shuangcui Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xijuan Jiang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Huhu Li
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Perišić Nanut M, Sabotič J, Švajger U, Jewett A, Kos J. Cystatin F Affects Natural Killer Cell Cytotoxicity. Front Immunol 2017; 8:1459. [PMID: 29180998 PMCID: PMC5693851 DOI: 10.3389/fimmu.2017.01459] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/18/2017] [Indexed: 01/21/2023] Open
Abstract
Cystatin F is a cysteine peptidase inhibitor which, unlike other cystatin family members, is targeted to endosomal/lysosomal compartments. It is synthesized as an inactive disulfide-linked dimer which is then converted to an active monomer by proteolytic cleavage of 15 N-terminal residues. Cystatin F has been suggested to regulate the cytotoxicity of natural killer (NK) cells by inhibiting the major granzyme convertases, cathepsins C and H. To test this hypothesis, we prepared variants of cystatin F and analyzed their uptake, subcellular trafficking, and peptidase inhibition, as well as their impact on the cytotoxicity of NK-92 cells and primary NK cells. The N-glycosylation pattern is responsible for the secretion, uptake, and subcellular sorting of cystatin F in HeLa and Hek293 cells, whereas the legumain binding site had no effect on these processes. Active, N-terminally truncated, monomeric cystatin F can also be internalized by recipient cells and targeted to endo/lysosomes, affecting also cells lacking the activating peptidase. Cystatin F mutants capable of cell internalization and trafficking through the endo/lysosomal pathway significantly decreased cathepsin C and H activities, both in situ, following transfection and in trans, using conditioned media. Further, incubation of IL-2 stimulated NK-92 and primary NK cells with full-length and N-terminally truncated cystatin F mutants led to suppression of their granule-mediated cytotoxicity. This effect was most significant with the N-terminally truncated mutants. These results suggest that cystatin F can be an important mediator within tumor microenvironment affecting the cytotoxicity of NK cells and consequently antitumor immune response.
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Affiliation(s)
| | - Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | | | - Anahid Jewett
- The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, Division of Oral Biology and Medicine, UCLA School of Dentistry, University of California-Los Angeles, Los Angeles, CA, United States
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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Leung ACS, Zhao E, Kwok RTK, Lam JWY, Leung CWT, Deng H, Tang BZ. An AIE-based bioprobe for differentiating the early and late stages of apoptosis mediated by H 2O 2. J Mater Chem B 2016; 4:5510-5514. [PMID: 32263348 DOI: 10.1039/c6tb01734g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A bioprobe, TPE-Zn2BDPA, with aggregation-induced emission characteristics was designed and synthesized to differentiate the early and late stages of apoptosis mediated by H2O2. TPE-Zn2BDPA does not respond to healthy cells, but it selectively lights up the membrane of apopotic cells in both stages with brighter fluorescence in the late apoptotic stage.
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Affiliation(s)
- Anakin C S Leung
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, Institute of Molecular Functional Materials, Division of Biomedical Engineering, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science & Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China.
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Wang H, Lööf S, Borg P, Nader GA, Blau HM, Simon A. Turning terminally differentiated skeletal muscle cells into regenerative progenitors. Nat Commun 2015; 6:7916. [PMID: 26243583 PMCID: PMC4765497 DOI: 10.1038/ncomms8916] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/24/2015] [Indexed: 01/09/2023] Open
Abstract
The ability to repeatedly regenerate limbs during the entire lifespan of an animal is restricted to certain salamander species among vertebrates. This ability involves dedifferentiation of post-mitotic cells into progenitors that in turn form new structures. A long-term enigma has been how injury leads to dedifferentiation. Here we show that skeletal muscle dedifferentiation during newt limb regeneration depends on a programmed cell death response by myofibres. We find that programmed cell death-induced muscle fragmentation produces a population of ‘undead' intermediate cells, which have the capacity to resume proliferation and contribute to muscle regeneration. We demonstrate the derivation of proliferating progeny from differentiated, multinucleated muscle cells by first inducing and subsequently intercepting a programmed cell death response. We conclude that cell survival may be manifested by the production of a dedifferentiated cell with broader potential and that the diversion of a programmed cell death response is an instrument to achieve dedifferentiation. Newts can regenerate amputated limbs via unknown mechanism involving dedifferentiation of cells in the stump into progenitors that contribute to the new appendages. Here the authors show that skeletal muscle dedifferentiation in regenerating newt limbs relies on a diverted programmed cell death response by myofibers.
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Affiliation(s)
- Heng Wang
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Sara Lööf
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Paula Borg
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Gustavo A Nader
- Department of Physiology and Pharmacology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, California 94305, United States
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
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Eckert MA, Vu PQ, Zhang K, Kang D, Ali MM, Xu C, Zhao W. Novel molecular and nanosensors for in vivo sensing. Am J Cancer Res 2013; 3:583-94. [PMID: 23946824 PMCID: PMC3741607 DOI: 10.7150/thno.6584] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/14/2013] [Indexed: 11/05/2022] Open
Abstract
In vivo sensors are an emerging field with the potential to revolutionize our understanding of basic biology and our treatment of disease. In this review, we highlight recent advances in the fields of in vivo electrochemical, optical, and magnetic resonance biosensors with a focus on recent developments that have been validated in rodent models or human subjects. In addition, we discuss major challenges in the development and translation of in vivo biosensors and present potential solutions to these problems. The field of nanotechnology, in particular, has recently been instrumental in driving the field of in vivo sensors forward. We conclude with a discussion of emerging paradigms and techniques for the development of future biosensors.
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Demchenko AP. Beyond annexin V: fluorescence response of cellular membranes to apoptosis. Cytotechnology 2012; 65:157-72. [PMID: 22797774 DOI: 10.1007/s10616-012-9481-y] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 06/24/2012] [Indexed: 02/07/2023] Open
Abstract
Dramatic changes in the structure of cell membranes on apoptosis allow easy, sensitive and non-destructive analysis of this process with the application of fluorescence methods. The strong plasma membrane asymmetry is present in living cells, and its loss on apoptosis is commonly detected with the probes interacting strongly and specifically with phosphatidylserine (PS). This phospholipid becomes exposed to the cell surface, and the application of annexin V labeled with fluorescent dye is presently the most popular tool for its detection. Several methods have been suggested recently that offer important advantages over annexin V assay with the ability to study apoptosis by spectroscopy of cell suspensions, flow cytometry and confocal or two-photon microscopy. The PS exposure marks the integrated changes in the outer leaflet of cell membrane that involve electrostatic potential and hydration, and the attempts are being made to provide direct probing of these changes. This review describes the basic mechanisms underlying the loss of membrane asymmetry during apoptosis and discusses, in comparison with the annexin V-binding assay, the novel fluorescence techniques of detecting apoptosis on cellular membrane level. In more detail we describe the detection method based on smart fluorescent dye F2N12S incorporated into outer leaflet of cell membrane and reporting on apoptotic cell transformation by easily detectable change of the spectral distribution of fluorescent emission. It can be adapted to any assay format.
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Affiliation(s)
- Alexander P Demchenko
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kiev, 01030, Ukraine,
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Traumatic alterations in GABA signaling disrupt hippocampal network activity in the developing brain. J Neurosci 2012; 32:4017-31. [PMID: 22442068 DOI: 10.1523/jneurosci.5139-11.2012] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Severe head trauma causes widespread neuronal shear injuries and acute seizures. Shearing of neural processes might contribute to seizures by disrupting the transmembrane ion gradients that subserve normal synaptic signaling. To test this possibility, we investigated changes in intracellular chloride concentration ([Cl(-)](i)) associated with the widespread neural shear injury induced during preparation of acute brain slices. In hippocampal slices and intact hippocampal preparations from immature CLM-1 mice, increases in [Cl(-)](i) correlated with disruption of neural processes and biomarkers of cell injury. Traumatized neurons with higher [Cl(-)](i) demonstrated excitatory GABA signaling, remained synaptically active, and facilitated network activity as assayed by the frequency of extracellular action potentials and spontaneous network-driven oscillations. These data support a more inhibitory role for GABA in the unperturbed immature brain, demonstrate the utility of the acute brain slice preparation for the study of the consequences of trauma, and provide potential mechanisms for both GABA-mediated excitatory network events in the slice preparation and early post-traumatic seizures.
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Blais DR, Nasheri N, McKay CS, Legault MC, Pezacki JP. Activity-based protein profiling of host-virus interactions. Trends Biotechnol 2011; 30:89-99. [PMID: 21944551 PMCID: PMC7114118 DOI: 10.1016/j.tibtech.2011.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 02/08/2023]
Abstract
Virologists have benefited from large-scale profiling methods to discover new host–virus interactions and to learn about the mechanisms of pathogenesis. One such technique, referred to as activity-based protein profiling (ABPP), uses active site-directed probes to monitor the functional state of enzymes, taking into account post-translational interactions and modifications. ABPP gives insight into the catalytic activity of enzyme families that does not necessarily correlate with protein abundance. ABPP has been used to investigate several viruses and their interactions with their hosts. Differential enzymatic activity induced by viruses has been monitored using ABPP. In this review, we present recent advances and trends involving the use of ABPP methods in understanding host–virus interactions and in identifying novel targets for diagnostic and therapeutic applications.
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Affiliation(s)
- David R. Blais
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Neda Nasheri
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Craig S. McKay
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
| | - Marc C.B. Legault
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
| | - John Paul Pezacki
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
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Abstract
In vivo imaging of apoptosis in a preclinical setting in anticancer drug development could provide remarkable advantages in terms of translational medicine. So far, several imaging technologies with different probes have been used to achieve this goal. Here we describe a bioluminescence imaging approach that uses a new formulation of Z-DEVD-aminoluciferin, a caspase 3/7 substrate, to monitor in vivo apoptosis in tumor cells engineered to express luciferase. Upon apoptosis induction, Z-DEVD-aminoluciferin is cleaved by caspase 3/7 releasing aminoluciferin that is now free to react with luciferase generating measurable light. Thus, the activation of caspase 3/7 can be measured by quantifying the bioluminescent signal. Using this approach, we have been able to monitor caspase-3 activation and subsequent apoptosis induction after camptothecin and temozolomide treatment on xenograft mouse models of colon cancer and glioblastoma, respectively. Treated mice showed more than 2-fold induction of Z-DEVD-aminoluciferin luminescent signal when compared to the untreated group. Combining D: -luciferin that measures the total tumor burden, with Z-DEVD-aminoluciferin that assesses apoptosis induction via caspase activation, we confirmed that it is possible to follow non-invasively tumor growth inhibition and induction of apoptosis after treatment in the same animal over time. Moreover, here we have proved that following early apoptosis induction by caspase 3 activation is a good biomarker that accurately predicts tumor growth inhibition by anti-cancer drugs in engineered colon cancer and glioblastoma cell lines and in their respective mouse xenograft models.
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Darzynkiewicz Z, Pozarowski P, Lee BW, Johnson GL. Fluorochrome-labeled inhibitors of caspases: convenient in vitro and in vivo markers of apoptotic cells for cytometric analysis. Methods Mol Biol 2011; 682:103-14. [PMID: 21057924 DOI: 10.1007/978-1-60327-409-8_9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Activation of caspases is a hallmark of apoptosis. Several methods, therefore, were developed to identify and count the frequency of apoptotic cells based on the detection of caspases activation. The method described in this chapter is based on the use of fluorochrome-labeled inhibitors of caspases (FLICA) applicable to fluorescence microscopy, and flow- and image-cytometry. Cell-permeant FLICA reagents tagged with carboxyfluorescein or sulforhodamine when applied to live cells in vitro or in vivo, exclusively label cells that are undergoing apoptosis. The FLICA labeling methodology is simple, rapid, robust, and can be combined with other markers of cell death for multiplexed analysis. Examples are presented on FLICA use in combination with a vital stain (propidium iodide), detection of the loss of mitochondrial electrochemical potential, and exposure of phosphatidylserine on the outer surface of plasma cell membrane using Annexin V fluorochrome conjugates. Following cell fixation and stoichiometric staining of cellular DNA, FLICA binding can be correlated with DNA ploidy, cell cycle phase, DNA fragmentation, and other apoptotic events whose detection requires cell permeabilization. The "time window" for the detection of apoptosis with FLICA is wider compared to that with the Annexin V binding, making FLICA a preferable marker for the detection of early phase apoptosis and more accurate for quantification of apoptotic cells.
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Affiliation(s)
- Zbigniew Darzynkiewicz
- Department of Pathology, New York Medical College, Brander Cancer Research Institute, Valhalla, NY, USA
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12
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Qian Y, Wei C, Eun-Hyung Lee F, Campbell J, Halliley J, Lee JA, Cai J, Kong YM, Sadat E, Thomson E, Dunn P, Seegmiller AC, Karandikar NJ, Tipton CM, Mosmann T, Sanz I, Scheuermann RH. Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data. CYTOMETRY PART B-CLINICAL CYTOMETRY 2010; 78 Suppl 1:S69-82. [PMID: 20839340 DOI: 10.1002/cyto.b.20554] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Advances in multiparameter flow cytometry (FCM) now allow for the independent detection of larger numbers of fluorochromes on individual cells, generating data with increasingly higher dimensionality. The increased complexity of these data has made it difficult to identify cell populations from high-dimensional FCM data using traditional manual gating strategies based on single-color or two-color displays. METHODS To address this challenge, we developed a novel program, FLOCK (FLOw Clustering without K), that uses a density-based clustering approach to algorithmically identify biologically relevant cell populations from multiple samples in an unbiased fashion, thereby eliminating operator-dependent variability. RESULTS FLOCK was used to objectively identify seventeen distinct B-cell subsets in a human peripheral blood sample and to identify and quantify novel plasmablast subsets responding transiently to tetanus and other vaccinations in peripheral blood. FLOCK has been implemented in the publically available Immunology Database and Analysis Portal-ImmPort (http://www.immport.org)-for open use by the immunology research community. CONCLUSIONS FLOCK is able to identify cell subsets in experiments that use multiparameter FCM through an objective, automated computational approach. The use of algorithms like FLOCK for FCM data analysis obviates the need for subjective and labor-intensive manual gating to identify and quantify cell subsets. Novel populations identified by these computational approaches can serve as hypotheses for further experimental study.
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Affiliation(s)
- Yu Qian
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Jaramillo-Lambert A, Harigaya Y, Vitt J, Villeneuve A, Engebrecht J. Meiotic errors activate checkpoints that improve gamete quality without triggering apoptosis in male germ cells. Curr Biol 2010; 20:2078-89. [PMID: 20970339 DOI: 10.1016/j.cub.2010.10.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 09/08/2010] [Accepted: 10/04/2010] [Indexed: 10/18/2022]
Abstract
BACKGROUND Meiotic checkpoints ensure the production of gametes with the correct complement and integrity of DNA; in metazoans, these pathways sense errors and transduce signals to trigger apoptosis to eliminate damaged germ cells. The extent to which checkpoints monitor and safeguard the genome differs between sexes and may contribute to the high frequency of human female meiotic errors. In the C. elegans female germline, DNA damage, chromosome asynapsis, and/or unrepaired meiotic double-strand breaks (DSBs) activate checkpoints that induce apoptosis; conversely, male germ cells do not undergo apoptosis. RESULTS Here we show that the recombination checkpoint is in fact activated in male germ cells despite the lack of apoptosis. The 9-1-1 complex and the phosphatidylinositol 3-kinase-related protein kinase ATR, sensors of DNA damage, are recruited to chromatin in the presence of unrepaired meiotic DSBs in both female and male germlines. Furthermore, the checkpoint kinase CHK-1 is phosphorylated and the p53 ortholog CEP-1 induces expression of BH3-only proapoptotic proteins in germlines of both sexes under activating conditions. The core cell death machinery is expressed in female and male germlines; however, CED-3 caspase is not activated in the male germline. Although apoptosis is not triggered, checkpoint activation in males has functional consequences for gamete quality, because there is reduced viability of progeny sired by males with a checkpoint-activating defect in the absence of checkpoint function. CONCLUSIONS We propose that the recombination checkpoint functions in male germ cells to promote repair of meiotic recombination intermediates, thereby improving the fidelity of chromosome transmission in the absence of apoptosis.
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Affiliation(s)
- Aimee Jaramillo-Lambert
- Department of Molecular and Cellular Biology, Genetics Graduate Group, University of California, Davis, Davis, CA 95616, USA
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