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Jolly A, Fanti AK, Kongsaysak-Lengyel C, Claudino N, Gräßer I, Becker NB, Höfer T. CycleFlow simultaneously quantifies cell-cycle phase lengths and quiescence in vivo. Cell Rep Methods 2022; 2:100315. [PMID: 36313807 PMCID: PMC9606136 DOI: 10.1016/j.crmeth.2022.100315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 07/25/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022]
Abstract
Populations of stem, progenitor, or cancer cells show proliferative heterogeneity in vivo, comprising proliferating and quiescent cells. Consistent quantification of the quiescent subpopulation and progression of the proliferating cells through the individual phases of the cell cycle has not been achieved. Here, we describe CycleFlow, a method that robustly infers this comprehensive information from standard pulse-chase experiments with thymidine analogs. Inference is based on a mathematical model of the cell cycle, with realistic waiting time distributions for the G1, S, and G2/M phases and a long-term quiescent G0 state. We validate CycleFlow with an exponentially growing cancer cell line in vitro. Applying it to T cell progenitors in steady state in vivo, we uncover strong proliferative heterogeneity, with a minority of CD4+CD8+ T cell progenitors cycling very rapidly and then entering quiescence. CycleFlow is suitable as a routine method for quantitative cell-cycle analysis.
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Affiliation(s)
- Adrien Jolly
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ann-Kathrin Fanti
- Division of Cellular Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | | | - Nina Claudino
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ines Gräßer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nils B. Becker
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Winokurow N, Schumacher S. A role for polycystin-1 and polycystin-2 in neural progenitor cell differentiation. Cell Mol Life Sci 2019; 76:2851-2869. [PMID: 30895336 DOI: 10.1007/s00018-019-03072-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/17/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
Abstract
Polycystin-1 (PC1) and polycystin-2 (PC2) are transmembrane proteins encoded by the Pkd1 and Pkd2 genes, respectively. Mutations in these genes are causative for the development of autosomal-dominant polycystic kidney disease. A prominent feature of this disease is an unbalanced cell proliferation. PC1 and PC2 physically interact to form a complex, which localizes to the primary cilia of renal epithelial cells. Recently, PC1 and PC2 have also been described to be present in primary cilia of radial glial cells (RGCs) and to contribute to the planar cell polarity of late RGCs and E1 ependymal cells. As neural progenitor cells (NPCs), early RGCs have to balance proliferation for expansion, or for self-renewal and differentiation to generate neurons. It is not known whether the polycystins play a role in this process. Here, we show that PC1 and PC2 are expressed in RGCs of the developing mouse cerebral cortex during neurogenesis. Loss-of-function analysis and cell-based assays reveal that a reduction of PC1 or PC2 expression leads to increased NPC proliferation, while the differentiation to neurons becomes impaired. The increased NPC proliferation is preceded by enhanced Notch signaling and accompanied by a rise in the number of symmetric cell divisions. The transcription factor STAT3 seems to be mechanistically important for polycystin signaling in NPCs as either STAT3 knockdown or inhibition of STAT3 function abrogates the increased proliferation driven by reduced polycystin expression. Our findings indicate that PC1 and PC2 are critical for maintaining a balance between proliferation and differentiation of NPCs.
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Affiliation(s)
- Natalie Winokurow
- Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Stefan Schumacher
- Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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Abstract
Small micromeres of the sea urchin are believed to be primordial germ cells (PGCs), fated to give rise to sperm or eggs in the adult. Sea urchin PGCs are formed at the fifth cleavage, undergo one additional division during blastulation, and migrate to the coelomic pouches of the pluteus larva. The goal of this chapter is to detail classical and modern techniques used to analyze primordial germ cell specification, gene expression programs, and cell behaviors in fixed and live embryos. The transparency of the sea urchin embryo enables both live imaging techniques and in situ RNA hybridization and immunolabeling for a detailed molecular characterization of these cells. Four approaches are presented to highlight small micromeres with fluorescent molecules for analysis by live and fixed cell microscopy: (1) small molecule dye accumulation during cleavage and blastula stages, (2) primordial germ cell targeted RNA expression using the Nanos untranslated regions, (3) fusing genes of interest with a Nanos2 targeting peptide, and (4) EdU and BrdU labeling. Applications of the live labeling techniques are discussed, including sorting by fluorescence-activated cell sorting for transcriptomic analysis, and, methods to image small micromere behavior in whole and dissociated embryos by live confocal microscopy. Finally, summary table of antibody and RNA probes as well as small molecule dyes to label small micromeres at a variety of developmental stages is provided.
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Affiliation(s)
- Joseph P Campanale
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.
| | - Amro Hamdoun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.
| | - Gary M Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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Abstract
Adult neurogenesis is the lifelong generation of new neurons that occurs into restricted regions of the adult mammalian brain, namely the dentate gyrus of the hippocampus and the olfactory bulb. In this chapter, we describe the procedures aimed to investigate adult neurogenesis in the murine brain. Specifically, we explain how to inject into animals exogenous markers of proliferation (i.e., BrdU) and prepare brain tissues to perform immunofluorescence reactions for neuronal markers in combination with BrdU staining. As BrdU is incorporated in the DNA during the S-phase of the cell cycle of proliferating cells and is then inherited by daughter cells, by coupling BrdU-immunoreactivity together with the immunolabeling for neuronal markers, we provide the general procedures that can be applied to identify adult-born neurons and to characterize their specific phenotypes in different brain regions, under physiological condition or in pathological states.
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Affiliation(s)
- Sara Bonzano
- Department of Life Sciences and Systems Biology (DBIOS), University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Turin, Italy
| | - Silvia De Marchis
- Department of Life Sciences and Systems Biology (DBIOS), University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy.
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Turin, Italy.
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Hughes BJ, Thomas J, Lynch AM, Borghoff SJ, Green S, Mensing T, Sarang SS, LeBaron MJ. Methyl isobutyl ketone-induced hepatocellular carcinogenesis in B6C3F 1 mice: A constitutive androstane receptor (CAR)-mediated mode of action. Regul Toxicol Pharmacol 2016; 81:421-429. [PMID: 27664318 DOI: 10.1016/j.yrtph.2016.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 08/22/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
Abstract
In a National Toxicology Program (NTP) chronic inhalation study with methyl isobutyl ketone (MIBK), increases in hepatocellular adenomas and hepatocellular adenomas and carcinomas (combined) were observed in male and female B6C3F1 mice at 1800 ppm. A DNA reactive Mode-of-Action (MOA) for this liver tumor response is not supported by the evidence as MIBK and its major metabolites lack genotoxicity in both in vitro and in vivo studies. Constitutive androstane receptor (CAR) nuclear receptor-mediated activation has been hypothesized as the MOA for MIBK-induced mouse liver tumorigenesis. To further investigate the MOA for MIBK-induced murine liver tumors, male and female B6C3F1, C57BL/6, and CAR/PXR Knockout (KO) mice were exposed to either 0 or 1800 ppm MIBK for 6 h/day, 5 days/week for a total of 10 days. On day 1, mice were implanted with osmotic mini-pumps containing 5-Bromo-2-deoxyuridine (BrdU) 1 h following exposure and humanely euthanized 1-3 h following the final exposure. B6C3F1 and C57BL/6 mice had statistically significant increases in liver weights compared to controls that corresponded with hepatocellular hypertrophy and increased mitotic figures. Hepatocellular proliferation data indicated induction of S-phase DNA synthesis in B6C3F1 and C57BL/6 mice exposed to 1800 ppm MIBK compared to control, and no increase was observed in MIBK exposed CAR/PXR KO mice. Liver gene expression changes indicated a maximally-induced Cyp2b10 (CAR-associated) transcript and a slight increase in Cyp3a11(PXR-associated) transcript in B6C3F1 and C57BL/6 mice exposed to 1800 ppm MIBK compared to controls, but not in Cyp1a1 (AhR-associated) or Cyp4a10 (PPAR-α-associated) transcripts. CAR/PXR KO mice exposed to 1800 ppm MIBK showed no evidence of activation of AhR, CAR, PXR or PPAR-α nuclear receptors via their associated transcripts. MIBK induced hepatic effects are consistent with a phenobarbital-like MOA where the initiating events are activation of the CAR and PXR nuclear receptors and resultant hepatocellular proliferation leading to rodent liver tumors.
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Affiliation(s)
- B J Hughes
- The Dow Chemical Company, Midland, MI, USA.
| | - J Thomas
- The Dow Chemical Company, Midland, MI, USA
| | - A M Lynch
- American Chemistry Council, Washington, DC, USA
| | | | - S Green
- Eastman Chemical, Kingsport, TN, USA
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Shahriyari L, Komarova NL, Jilkine A. The role of cell location and spatial gradients in the evolutionary dynamics of colon and intestinal crypts. Biol Direct 2016; 11:42. [PMID: 27549762 PMCID: PMC4994304 DOI: 10.1186/s13062-016-0141-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/15/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colon and intestinal crypts serve as an important model system for adult stem cell proliferation and differentiation. We develop a spatial stochastic model to study the rate of somatic evolution in a normal crypt, focusing on the production of two-hit mutants that inactivate a tumor suppressor gene. We investigate the effect of cell division pattern along the crypt on mutant production, assuming that the division rate of each cell depends on its location. RESULTS We find that higher probability of division at the bottom of the crypt, where the stem cells are located, leads to a higher rate of double-hit mutant production. The optimal case for delaying mutations occurs when most of the cell divisions happen at the top of the crypt. We further consider an optimization problem where the "evolutionary" penalty for double-hit mutant generation is complemented with a "functional" penalty that assures that fully differentiated cells at the top of the crypt cannot divide. CONCLUSION The trade-off between the two types of objectives leads to the selection of an intermediate division pattern, where the cells in the middle of the crypt divide with the highest rate. This matches the pattern of cell divisions obtained experimentally in murine crypts. REVIEWERS This article was reviewed by David Axelrod (nominated by an Editorial Board member, Marek Kimmel), Yang Kuang and Anna Marciniak-Czochra. For the full reviews, please go to the Reviewers' comments section.
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Affiliation(s)
- Leili Shahriyari
- Mathematical Biosciences Institute, The Ohio State University, 1735 Neil Ave, Columbus, 43210, USA
| | - Natalia L Komarova
- Department of Mathematics, University of California Irvine, 340 Rowland Hall, Irvine, 92697, USA.
| | - Alexandra Jilkine
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, 153 Hurley Hall, Notre Dame, 46556, USA.
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Chugh RM, Chaturvedi M, Yerneni LK. An evaluation of the choice of feeder cell growth arrest for the production of cultured epidermis. Burns 2015; 41:1788-1795. [PMID: 26392024 DOI: 10.1016/j.burns.2015.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/04/2015] [Accepted: 08/10/2015] [Indexed: 11/27/2022]
Abstract
Growth arrested 3T3 cells have been used as feeder cells in human epidermal keratinocyte cultures to produce cultured epidermal autografts for the treatment of burns. The feeder cells were ideally growth-arrested by gamma-irradiation. Alternatively, growth arrest by mitomycin C treatment is a cost effective option. We compared the functional efficacy of these two approaches in keratinocyte cultures by colony forming efficiency, the net growth area of colonies, BrdU labeling and histological features of cultured epidermal sheets. The growth area estimation involved a semi-automated digital technique using the Adobe Photoshop and comprised of isolation and enumeration of red pixels in Rhodamine B-stained keratinocyte colonies. A further refinement of the technique led to the identification of critical steps to increasing the degree of accuracy and enabling its application as an extension of colony formation assay. The results on feeder cell functionality revealed that the gamma irradiated feeders influenced significantly higher colony forming efficiency and larger growth area than the mitomycin C treated feeders. The BrdU labeling study indicated significant stimulation of the overall keratinocyte proliferation by the gamma irradiated feeders. The cultured epidermal sheets produced by gamma feeders were relatively thicker than those produced by mitomycin C feeders. We discussed the clinical utility of mitomycin C feeders from the viewpoint of cost-effective burn care in developing countries.
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Affiliation(s)
- Rishi Man Chugh
- Cell Biology Laboratory, National Institute of Pathology (ICMR), New Delhi, India
| | - Madhusudan Chaturvedi
- Cell Biology Laboratory, National Institute of Pathology (ICMR), New Delhi, India; Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi, India
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Ohta G, Kobayashi M, Sakai H, Masegi T, Yanai T. Proliferative potential of a spinal nephroblastoma in a young dog. J Toxicol Pathol 2009; 22:79-82. [PMID: 22271979 PMCID: PMC3246021 DOI: 10.1293/tox.22.79] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2008] [Accepted: 11/04/2008] [Indexed: 12/04/2022] Open
Abstract
The proliferative potential of a spinal nephroblastoma was studied in a young dog. A 4-month-old, female golden retriever showed developing deterioration in her gait and subsequent paralysis of her hind legs. At necropsy, a well-demarcated grayish brown tumor mass was found in the lumbar spinal cord segments between L2 and L3. Histologically, a blastemal cell tumor with a tubule- or glomeruli-like structure was found to be infiltrating intradurally. Proliferating cells at the S-phase, assessed using the bromodeoxyuridine (BrdU) labeling method, were seen occasionally in the tubular cells and glomeruli-like structures and were frequently seen in the blastemal cells. Immunohistochemically, the tubular epithelial cells were positive for cytokeratin, and the blastemal cells were positive for vimentin. The present tumor showed a high potential for growth and invasion, which suggests that it the potential to expand into the adjacent spinal cord.
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Affiliation(s)
- George Ohta
- Department of Veterinary Pathology, Faculty of Applied Biological Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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