Abstract
In recent years, the advances in tissue engineering and regenerative medicine have resulted in introduction of novel 3D tissue models, materials and methods to the regular practice of cell biologists, material scientists and specialists from related areas. 3D tissue models allow mimicking in vivo cell and tissue organization. However, the efficient work in three dimensions has significant challenges, such as compatibility with conventional cell biology methods, live cell imaging and quantification readouts. Here, we briefly discuss the applicability of 3D tissue models to different live cell microscopy modalities and the available range of fluo- and phosphorescent probes and sensors allowing for multi-parametric imaging.
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References
Kleinman HK, Philp D, Hoffman MP (2003) Role of the extracellular matrix in morphogenesis. Curr Opin Biotechnol 14:526–532
Neelam S, Hayes PR, Zhang Q, Dickinson RB, Lele TP (2016) Vertical uniformity of cells and nuclei in epithelial monolayers. Sci Rep 6:19689
Fennema E, Rivron N, Rouwkema J, van Blitterswijk C, de Boer J (2013) Spheroid culture as a tool for creating 3D complex tissues. Trends Biotechnol 31:108–115
Fatehullah A, Tan SH, Barker N (2016) Organoids as an in vitro model of human development and disease. Nat Cell Biol 18:246–254
Yamada KM, Cukierman E (2007) Modeling tissue morphogenesis and cancer in 3D. Cell 130:601–610
Lozano E, Segarra M, García-Martínez A, Hernández-Rodríguez J, Cid MC (2008) Imatinib mesylate inhibits in vitro and ex vivo biological responses related to vascular occlusion in giant cell arteritis. Ann Rheum Dis 67:1581–1588
Arslan-Yildiz A, El Assal R, Chen P, Guven S, Inci F, Demirci U (2016) Towards artificial tissue models: past, present, and future of 3D bioprinting. Biofabrication 8:1758–5090
Marangoni E, Vincent-Salomon A, Auger N, Degeorges A, Assayag F, de Cremoux P et al (2007) A new model of patient tumor-derived breast cancer xenografts for preclinical assays. Clin Cancer Res 13:3989–3998
Costa EC, Gaspar VM, Coutinho P, Correia IJ (2014) Optimization of liquid overlay technique to formulate heterogenic 3D co-cultures models. Biotechnol Bioeng 111:1672–1685
Foty R (2011) A simple hanging drop cell culture protocol for generation of 3D spheroids. J Vis Exp 51:2720
Markovitz-Bishitz Y, Tauber Y, Afrimzon E, Zurgil N, Sobolev M, Shafran Y et al (2010) A polymer microstructure array for the formation, culturing, and high throughput drug screening of breast cancer spheroids. Biomaterials 31:8436–8444
Kenny PA, Lee GY, Myers CA, Neve RM, Semeiks JR, Spellman PT et al (2007) The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression. Mol Oncol 1:84–96
Luca AC, Mersch S, Deenen R, Schmidt S, Messner I, Schäfer K-L et al (2013) Impact of the 3D microenvironment on phenotype, gene expression, and EGFR inhibition of colorectal cancer cell lines. PLoS One 8:e59689
Härmä V, Virtanen J, Mäkelä R, Happonen A, Mpindi J-P, Knuuttila M et al (2010) A comprehensive panel of three-dimensional models for studies of prostate cancer growth, invasion and drug responses. PLoS One 5:e10431
Laurent J, Frongia C, Cazales M, Mondesert O, Ducommun B, Lobjois V (2013) Multicellular tumor spheroid models to explore cell cycle checkpoints in 3D. BMC Cancer 13:73
Hirschhaeuser F, Menne H, Dittfeld C, West J, Mueller-Klieser W, Kunz-Schughart LA (2010) Multicellular tumor spheroids: an underestimated tool is catching up again. J Biotechnol 148:3–15
Liao J, Qian F, Tchabo N, Mhawech-Fauceglia P, Beck A, Qian Z et al (2014) Ovarian cancer spheroid cells with stem cell-like properties contribute to tumor generation, and chemotherapy resistance through hypoxia-resistant metabolism. PLoS One 9:e84941
Longati P, Jia X, Eimer J, Wagman A, Witt M-R, Rehnmark S et al (2013) 3D pancreatic carcinoma spheroids induce a matrix-rich, chemoresistant phenotype offering a better model for drug testing. BMC Cancer 13:95
Herrmann D, Conway JRW, Vennin C, Magenau A, Hughes WE, Morton JP et al (2014) Three-dimensional cancer models mimic cell–matrix interactions in the tumour microenvironment. Carcinogenesis 35:1671–1679
Dolznig H, Rupp C, Puri C, Haslinger C, Schweifer N, Wieser E et al (2011) Modeling colon adenocarcinomas in vitro a 3D co-culture system induces cancer-relevant pathways upon tumor cell and stromal fibroblast interaction. Am J Pathol 179:487–501
Bingle L, Lewis CE, Corke KP, Reed MWR, Brown NJ (2006) Macrophages promote angiogenesis in human breast tumour spheroids in vivo. Br J Cancer 94:101–107
Pampaloni F, Ansari N, Stelzer EHK (2013) High-resolution deep imaging of live cellular spheroids with light-sheet-based fluorescence microscopy. Cell Tissue Res 352:161–177
Dmitriev RI, Borisov SM, Düssmann H, Sun S, Müller BJ, Prehn J et al (2015) Versatile conjugated polymer nanoparticles for high-resolution O2 imaging in cells and 3D tissue models. ACS Nano 9:5275–5288
Jenkins J, Borisov SM, Papkovsky DB, Dmitriev RI (2016) Sulforhodamine nanothermometer for multiparametric fluorescence lifetime imaging microscopy. Anal Chem 88:10566–10572
König K, Uchugonova A, Gorjup E (2011) Multiphoton fluorescence lifetime imaging of 3D-stem cell spheroids during differentiation. Microsc Res Tech 74:9–17
Lancaster MA, Knoblich JA (2014) Organogenesis in a dish: modeling development and disease using organoid technologies. Science 345:1247125
Fujii M, Matano M, Nanki K, Sato T (2015) Efficient genetic engineering of human intestinal organoids using electroporation. Nat Protoc 10:1474–1485
Takasato M, Er PX, Chiu HS, Maier B, Baillie GJ, Ferguson C et al (2015) Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis. Nature 526:564–568
Lancaster MA, Renner M, Martin C-A, Wenzel D, Bicknell LS, Hurles ME et al (2013) Cerebral organoids model human brain development and microcephaly. Nature 501:373–379
Völkner M, Zschätzsch M, Rostovskaya M, Overall Rupert W, Busskamp V, Anastassiadis K et al (2016) Retinal organoids from pluripotent stem cells efficiently recapitulate retinogenesis. Stem Cell Rep 6:525–538
McCracken KW, Cata EM, Crawford CM, Sinagoga KL, Schumacher M, Rockich BE et al (2014) Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature 516:400–404
Dye BR, Hill DR, Ferguson MAH, Tsai Y-H, Nagy MS, Dyal R et al (2015) In vitro generation of human pluripotent stem cell derived lung organoids. elife 4:e05098
Guye P, Ebrahimkhani MR, Kipniss N, Velazquez JJ, Schoenfeld E, Kiani S et al (2016) Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6. Nat Commun 7:10243
Moreno EL, Hachi S, Hemmer K, Trietsch SJ, Baumuratov AS, Hankemeier T et al (2015) Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture. Lab Chip 15:2419–2428
Khademhosseini A, Eng G, Yeh J, Kucharczyk PA, Langer R, Vunjak-Novakovic G et al (2007) Microfluidic patterning for fabrication of contractile cardiac organoids. Biomed Microdevices 9:149–157
Drost J, van Jaarsveld RH, Ponsioen B, Zimberlin C, van Boxtel R, Buijs A et al (2015) Sequential cancer mutations in cultured human intestinal stem cells. Nature 521:43–47
Okkelman IA, Dmitriev RI, Foley T, Papkovsky DB (2016) Use of fluorescence lifetime imaging microscopy (FLIM) as a timer of cell cycle S phase. PLoS One 11:e0167385
Walsh AJ, Cook RS, Sanders ME, Aurisicchio L, Ciliberto G, Arteaga CL et al (2014) Quantitative optical imaging of primary tumor organoid metabolism predicts drug response in breast cancer. Cancer Res 74:5184–5194
van Duinen V, Trietsch SJ, Joore J, Vulto P, Hankemeier T (2015) Microfluidic 3D cell culture: from tools to tissue models. Curr Opin Biotechnol 35:118–126
Bhatia SN, Ingber DE (2014) Microfluidic organs-on-chips. Nat Biotechnol 32:760–772
Anderson JR, Chiu DT, Wu H, Schueller O, Whitesides GM (2000) Fabrication of microfluidic systems in poly (dimethylsiloxane). Electrophoresis 21:27–40
Hsiao AY, Y-S T, Tung Y-C, Sud S, Taichman RS, Pienta KJ et al (2009) Microfluidic system for formation of PC-3 prostate cancer co-culture spheroids. Biomaterials 30:3020–3027
Bhise NS, Manoharan V, Massa S, Tamayol A, Ghaderi M, Miscuglio M et al (2016) A liver-on-a-chip platform with bioprinted hepatic spheroids. Biofabrication 8:1758–5090
Au SH, Chamberlain MD, Mahesh S, Sefton MV, Wheeler AR (2014) Hepatic organoids for microfluidic drug screening. Lab Chip 14:3290–3299
Kim HJ, Ingber DE (2013) Gut-on-a-Chip microenvironment induces human intestinal cells to undergo villus differentiation. Integr Biol 5:1130–1140
Kim HJ, Huh D, Hamilton G, Ingber DE (2012) Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow. Lab Chip 12:2165–2174
Benam KH, Villenave R, Lucchesi C, Varone A, Hubeau C, Lee H-H et al (2016) Small airway-on-a-chip enables analysis of human lung inflammation and drug responses in vitro. Nat Methods 13:151–157
Huh D, Matthews BD, Mammoto A, Montoya-Zavala M, Hsin HY, Ingber DE (2010) Reconstituting organ-level lung functions on a chip. Science 328:1662–1668
Grosberg A, Alford PW, McCain ML, Parker KK (2011) Ensembles of engineered cardiac tissues for physiological and pharmacological study: heart on a chip. Lab Chip 11:4165–4173
Agarwal A, Goss JA, Cho A, McCain ML, Parker KK (2013) Microfluidic heart on a chip for higher throughput pharmacological studies. Lab Chip 13:3599–3608
Nieskens TT, Wilmer MJ (2016) Kidney-on-a-chip technology for renal proximal tubule tissue reconstruction. Eur J Pharmacol 790:46–56
Wilmer MJ, Ng CP, Lanz HL, Vulto P, Suter-Dick L, Masereeuw R (2016) Kidney-on-a-chip technology for drug-induced nephrotoxicity screening. Trends Biotechnol 34:156–170
Young EWK, Watson MWL, Srigunapalan S, Wheeler AR, Simmons CA (2010) Technique for real-time measurements of endothelial permeability in a microfluidic membrane chip using laser-induced fluorescence detection. Anal Chem 82:808–816
Ryu H, Oh S, Lee HJ, Lee JY, Lee HK, Jeon NL (2015) Engineering a blood vessel network module for body-on-a-chip applications. J Lab Autom 20:296–301
Kim S, Lee H, Chung M, Jeon NL (2013) Engineering of functional, perfusable 3D microvascular networks on a chip. Lab Chip 13:1489–1500
van der Helm MW, van der Meer AD, Eijkel JCT, van den Berg A, Segerink LI (2016) Microfluidic organ-on-chip technology for blood-brain barrier research. Tissue Barriers 4:e1142493
Benam KH, Dauth S, Hassell B, Herland A, Jain A, Jang K-J et al (2015) Engineered in vitro disease models. Annu Rev Pathol 10:195–262
Esch EW, Bahinski A, Huh D (2015) Organs-on-chips at the frontiers of drug discovery. Nat Rev Drug Discov 14:248–260
Kondrashina AV, Papkovsky DB, Dmitriev RI (2013) Measurement of cell respiration and oxygenation in standard multichannel biochips using phosphorescent O2-sensitive probes. Analyst 138:4915–4921
Wikswo JP, Block FE III, Cliffel DE, Goodwin CR, Marasco CC, Markov DA et al (2013) Engineering challenges for instrumenting and controlling integrated organ-on-chip systems. IEEE Trans Biomed Eng 60:682–690
Tibbitt MW, Anseth KS (2009) Hydrogels as extracellular matrix mimics for 3D cell culture. Biotechnol Bioeng 103:655–663
Gulrez SKH, Al-Assaf S (2011) Hydrogels: methods of preparation, characterisation and applications. Intech, Rijeka
Meadhbh ÁB, Audrey R, Anne-laure G, Cyril DA, Steven N, Valerie T et al (2015) 3D cell culture and osteogenic differentiation of human bone marrow stromal cells plated onto jet-sprayed or electrospun micro-fiber scaffolds. Biomed Mater 10:045019
Danilevicius P, Georgiadi L, Pateman CJ, Claeyssens F, Chatzinikolaidou M, Farsari M (2015) The effect of porosity on cell ingrowth into accurately defined, laser-made, polylactide-based 3D scaffolds. Appl Surf Sci 336:2–10
Jenkins J, Dmitriev RI, Morten K, McDermott KW, Papkovsky DB (2015) Oxygen-sensing scaffolds for 3-dimensional cell and tissue culture. Acta Biomater 16:126–135
Place ES, George JH, Williams CK, Stevens MM (2009) Synthetic polymer scaffolds for tissue engineering. Chem Soc Rev 38:1139–1151
Shoulders MD, Raines RT (2009) Collagen structure and stability. Annu Rev Biochem 78:929–958
Artym VV, Matsumoto K (2010) Imaging cells in three-dimensional collagen matrix. Curr Protocol Cell Biol. Chapter:Unit-10.18:1–20
Yurchenco PD (2011) Basement membranes: cell scaffoldings and signaling platforms. Cold Spring Harb Perspect Biol 3. https://doi.org/10.1101/cshperspect.a004911
Kleinman HK, Martin GR (2005) Matrigel: basement membrane matrix with biological activity. Semin Cancer Biol 15:378–386
Benton G, Kleinman HK, George J, Arnaoutova I (2011) Multiple uses of basement membrane-like matrix (BME/Matrigel) in vitro and in vivo with cancer cells. Int J Cancer 128:1751–1757
Price KJ, Tsykin A, Giles KM, Sladic RT, Epis MR, Ganss R et al (2012) Matrigel basement membrane matrix influences expression of microRNAs in cancer cell lines. Biochem Biophys Res Commun 427:343–348
Dolega ME, Abeille F, Picollet-D'hahan N, Gidrol X (2015) Controlled 3D culture in Matrigel microbeads to analyze clonal acinar development. Biomaterials 52:347–357
Nyga A, Cheema U, Loizidou M (2011) 3D tumour models: novel in vitro approaches to cancer studies. J Cell Commun Signal 5:239
Abitbol T, Rivkin A, Cao Y, Nevo Y, Abraham E, Ben-Shalom T et al (2016) Nanocellulose, a tiny fiber with huge applications. Curr Opin Biotechnol 39:76–88
Pääkkö M, Ankerfors M, Kosonen H, Nykänen A, Ahola S, Österberg M et al (2007) Enzymatic hydrolysis combined with mechanical shearing and high-pressure homogenization for nanoscale cellulose fibrils and strong gels. Biomacromolecules 8:1934–1941
Lou YR, Kanninen L, Kuisma T, Niklander J, Noon LA, Burks D et al (2014) The use of nanofibrillar cellulose hydrogel as a flexible three-dimensional model to culture human pluripotent stem cells. Stem Cells Dev 23:380–392
Malinen MM, Kanninen LK, Corlu A, Isoniemi HM, Lou Y-R, Yliperttula ML et al (2014) Differentiation of liver progenitor cell line to functional organotypic cultures in 3D nanofibrillar cellulose and hyaluronan-gelatin hydrogels. Biomaterials 35:5110–5121
Murphy SV, Atala A (2014) 3D bioprinting of tissues and organs. Nat Biotechnol 32:773–785
Nadernezhad A, Khani N, Skvortsov GA, Toprakhisar B, Bakirci E, Menceloglu Y et al (2016) Multifunctional 3D printing of heterogeneous hydrogel structures. Sci Rep 6
Lee VK, Lanzi AM, Haygan N, Yoo S-S, Vincent PA, Dai G (2014) Generation of multi-scale vascular network system within 3D hydrogel using 3D bio-printing technology. Cell Mol Bioeng 7:460–472
Jung JW, Lee J-S, Cho D-W (2016) Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs. Sci Rep 6:21685
Zhao Y, Yao R, Ouyang L, Ding H, Zhang T, Zhang K et al (2014) Three-dimensional printing of Hela cells for cervical tumor model in vitro. Biofabrication 6:1758–5082
Seol YJ, Kang HW, Lee SJ, Atala A, Yoo JJ (2014) Bioprinting technology and its applications. Eur J Cardiothorac Surg 46:342–348
Gjorevski N, Sachs N, Manfrin A, Giger S, Bragina ME, Ordóñez-Morán P et al (2016) Designer matrices for intestinal stem cell and organoid culture. Nature 539:560–564
Sachs N, Tsukamoto Y, Kujala P, Peters PJ, Clevers H (2017) Intestinal epithelial organoids fuse to form self-organizing tubes in floating collagen gels. Development 144:1107–1112
Schnell U, Dijk F, Sjollema KA, Giepmans BNG (2012) Immunolabeling artifacts and the need for live-cell imaging. Nat Methods 9:152–158
Jamieson LE, Harrison DJ, Campbell CJ (2015) Chemical analysis of multicellular tumour spheroids. Analyst 140:3910–3920
Quaranta M, Borisov SM, Klimant I (2012) Indicators for optical oxygen sensors. Bioanal Rev 4:115–157
Berezin MY, Achilefu S (2010) Fluorescence lifetime measurements and biological imaging. Chem Rev 110:2641–2684
Swoger J, Pampaloni F, Stelzer EH (2014) Light-sheet-based fluorescence microscopy for three-dimensional imaging of biological samples. Cold Spring Harb Protoc 1:1–8
Helmchen F, Denk W (2005) Deep tissue two-photon microscopy. Nat Methods 2:932–940
Benninger RKP, Piston DW (2001) Two-photon excitation microscopy for the study of living cells and tissues. Curr Protocols Cell Biol. https://doi.org/10.1002/0471143030.cb0411s59
Hopt A, Neher E (2001) Highly nonlinear photodamage in two-photon fluorescence microscopy. Biophys J 80:2029–2036
Ustione A, Piston DW (2011) A simple introduction to multiphoton microscopy. J Microsc 243:221–226
Patterson GH, Piston DW (2000) Photobleaching in two-photon excitation microscopy. Biophys J 78:2159–2162
Huisken J, Swoger J, Del Bene F, Wittbrodt J, Stelzer EHK (2004) Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305:1007–1009
Santi PA (2011) Light sheet fluorescence microscopy. J Histochem Cytochem 59:129–138
Cella Zanacchi F, Lavagnino Z, Perrone Donnorso M, Del Bue A, Furia L, Faretta M et al (2011) Live-cell 3D super-resolution imaging in thick biological samples. Nat Methods 8:1047–1049
Patra B, Peng YS, Peng CC, Liao WH, Chen YA, Lin KH et al (2014) Migration and vascular lumen formation of endothelial cells in cancer cell spheroids of various sizes. Biomicrofluidics 8:052109
Marx V (2016) Microscopy: openSPIM 2.0. Nat Methods 13:979–982
Hell SW (2007) Far-field optical nanoscopy. Science 316:1153–1158
Hirvonen LM, Wicker K, Mandula O, Heintzmann R (2009) Structured illumination microscopy of a living cell. Eur Biophys J 38:807–812
Gustafsson MGL, Shao L, Carlton PM, Wang CJR, Golubovskaya IN, Cande WZ et al (2008) Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J 94:4957–4970
Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793–796
van de Linde S, Loschberger A, Klein T, Heidbreder M, Wolter S, Heilemann M et al (2011) Direct stochastic optical reconstruction microscopy with standard fluorescent probes. Nat Protoc 6:991–1009
Hess ST, Girirajan TPK, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91:4258–4272
Klar TA, Jakobs S, Dyba M, Egner A, Hell SW (2000) Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proc Natl Acad Sci U S A 97:8206–8210
Takasaki Kevin T, Ding Jun B, Sabatini BL (2013) Live-cell superresolution imaging by pulsed STED two-photon excitation microscopy. Biophys J 104:770–777
Specht EA, Braselmann E, Palmer AE (2016) A critical and comparative review of fluorescent tools for live cell imaging. Annu Rev Physiol 79:93–117
Niehorster T, Loschberger A, Gregor I, Kramer B, Rahn H-J, Patting M et al (2016) Multi-target spectrally resolved fluorescence lifetime imaging microscopy. Nat Methods 13:257–262
Giordano L, Shvadchak VV, Fauerbach JA, Jares-Erijman EA, Jovin TM (2012) Highly Solvatochromic 7-Aryl-3-hydroxychromones. J Phys Chem Lett 3:1011–1016
Shcheslavskiy VI, Neubauer A, Bukowiecki R, Dinter F, Becker W (2016) Combined fluorescence and phosphorescence lifetime imaging. Appl Phys Lett 108:091111
Papkovsky DB, Dmitriev RI (2013) Biological detection by optical oxygen sensing. Chem Soc Rev 42:8700–8732
Hirvonen LM, Fisher-Levine M, Suhling K, Nomerotski A (2017) Photon counting phosphorescence lifetime imaging with TimepixCam. Rev Sci Instrum 88:013104
Becker W (2012) Fluorescence lifetime imaging--techniques and applications. J Microsc 247:119–136
Blacker TS, Mann ZF, Gale JE, Ziegler M, Bain AJ, Szabadkai G et al (2014) Separating NADH and NADPH fluorescence in live cells and tissues using FLIM. Nat Commun 5:3936
Chudakov DM, Lukyanov S, Lukyanov KA (2005) Fluorescent proteins as a toolkit for in vivo imaging. Trends Biotechnol 23:605–613
Mishin AS, Belousov VV, Solntsev KM, Lukyanov KA (2015) Novel uses of fluorescent proteins. Curr Opin Chem Biol 27:1–9
Nothdurft R, Sarder P, Bloch S, Culver J, Achilefu S (2012) Fluorescence lifetime imaging microscopy using near-infrared contrast agents. J Microsc 247:202–207
Wolfbeis OS (2015) An overview of nanoparticles commonly used in fluorescent bioimaging. Chem Soc Rev 44:4743–4768
Ma N, Digman MA, Malacrida L, Gratton E (2016) Measurements of absolute concentrations of NADH in cells using the phasor FLIM method. Biomed Opt Express 7:2441–2452
Blacker TS, Duchen MR (2016) Investigating mitochondrial redox state using NADH and NADPH autofluorescence. Free Radic Biol Med 100:53–65
Cannon TM, Shah AT, Skala MC (2017) Autofluorescence imaging captures heterogeneous drug response differences between 2D and 3D breast cancer cultures. Biomed Opt Express 8:1911–1925
Mongeon R, Venkatachalam V, Yellen G (2016) Cytosolic NADH-NAD(+) redox visualized in brain slices by two-photon fluorescence lifetime biosensor imaging. Antioxid Redox Signal 25:553–563
Wagener KC, Kolbrink B, Dietrich K, Kizina KM, Terwitte LS, Kempkes B et al (2016) Redox indicator mice stably expressing genetically encoded neuronal roGFP: versatile tools to decipher subcellular redox dynamics in neuropathophysiology. Antioxid Redox Signal 25:41–58
Dmitriev RI, Papkovsky DB (2015) Intracellular probes for imaging oxygen concentration: how good are they? Methods Appl Fluoresc 3:034001
Dmitriev RI, Kondrashina AV, Koren K, Klimant I, Zhdanov AV, Pakan JM et al (2014) Small molecule phosphorescent probes for O2 imaging in 3D tissue models. Biomater Sci 2:853–866
Dmitriev RI, Okkelman IA, Foley T, Papkovsky DB (2017) Live cell microscopy of intestinal organoid oxygenation. FASEB J 31:590.1
Zhdanov AV, Okkelman IA, Golubeva AV, Doerr B, Hyland NP, Melgar S et al (2017) Quantitative analysis of mucosal oxygenation using ex vivo imaging of healthy and inflamed mammalian colon tissue. Cell Mol Life Sci 74:141–151
Zhdanov AV, Golubeva AV, Okkelman IA, Cryan JF, Papkovsky DB (2015) Imaging of oxygen gradients in giant umbrella cells: an ex vivo PLIM study. Am J Phys 309:C501–C5C9
Dmitriev RI, Papkovsky DB (2015) Multi-parametric O2 imaging in three-dimensional neural cell models with the phosphorescent probes. In: Lossi L, Merighi A (eds) Neuronal cell death: methods and protocols. Springer New York, New York, NY, pp 55–71
Zhdanov AV, Okkelman IA, Collins FWJ, Melgar S, Papkovsky DB (2015) A novel effect of DMOG on cell metabolism: direct inhibition of mitochondrial function precedes HIF target gene expression. Biochim Biophys Acta 1847:1254–1266
Roussakis E, Li Z, Nichols AJ, Evans CL (2015) Oxygen-sensing methods in biomedicine from the macroscale to the microscale. Angew Chem Int Ed 54:8340–8362
Yazgan G, Dmitriev RI, Tyagi V, Jenkins J, Rotaru G-M, Rottmar M et al (2017) Steering surface topographies of electrospun fibers: understanding the mechanisms. Sci Rep 7:158
Poëa-Guyon S, Pasquier H, Mérola F, Morel N, Erard M (2013) The enhanced cyan fluorescent protein: a sensitive pH sensor for fluorescence lifetime imaging. Anal Bioanal Chem 405:3983–3987
Tantama M, Hung YP, Yellen G (2011) Imaging intracellular pH in live cells with a genetically-encoded red fluorescent protein sensor. J Am Chem Soc 133:10034–10037
Aigner D, Dmitriev R, Borisov S, Papkovsky D, Klimant I (2014) pH-sensitive perylene bisimide probes for live cell fluorescence lifetime imaging. J Mater Chem B 2:6792–6801
Hille C, Berg M, Bressel L, Munzke D, Primus P, Löhmannsröben H-G et al (2008) Time-domain fluorescence lifetime imaging for intracellular pH sensing in living tissues. Anal Bioanal Chem 391:1871
Kuchibhotla KV, Lattarulo CR, Hyman BT, Bacskai BJ (2009) Synchronous hyperactivity and intercellular calcium waves in astrocytes in Alzheimer mice. Science 323:1211–1215
Wilms CD, Schmidt H, Eilers J (2006) Quantitative two-photon Ca2+ imaging via fluorescence lifetime analysis. Cell Calcium 40:73–79
Wilms CD, Eilers J (2007) Photo-physical properties of Ca2+−indicator dyes suitable for two-photon fluorescence-lifetime recordings. J Microsc 225:209–213
Rinnenthal JL, Börnchen C, Radbruch H, Andresen V, Mossakowski A, Siffrin V et al (2013) Parallelized TCSPC for dynamic intravital fluorescence lifetime imaging: quantifying neuronal dysfunction in neuroinflammation. PLoS One 8:e60100
Heim N, Garaschuk O, Friedrich MW, Mank M, Milos RI, Kovalchuk Y et al (2007) Improved calcium imaging in transgenic mice expressing a troponin C-based biosensor. Nat Methods 4:127–129
Sotelo-Hitschfeld T, Niemeyer MI, Mächler P, Ruminot I, Lerchundi R, Wyss MT et al (2015) Channel-mediated lactate release by K+-stimulated astrocytes. J Neurosci 35:4168
San Martín A, Ceballo S, Ruminot I, Lerchundi R, Frommer WB, Barros LF (2013) A genetically encoded FRET lactate sensor and its use to detect the warburg effect in single cancer cells. PLoS One 8:e57712
Shimolina LE, Izquierdo MA, López-Duarte I, Bull JA, Shirmanova MV, Klapshina LG et al (2017) Imaging tumor microscopic viscosity in vivo using molecular rotors. Sci Rep 7:41097
Brand MD, Nicholls DG (2011) Assessing mitochondrial dysfunction in cells. Biochem J 435:297–312
Foster KA, Galeffi F, Gerich FJ, Turner DA, Müller M (2006) Optical and pharmacological tools to investigate the role of mitochondria during oxidative stress and neurodegeneration. Prog Neurobiol 79:136–171
Kalyanaraman B, Darley-Usmar V, Davies KJA, Dennery PA, Forman HJ, Grisham MB et al (2012) Measuring reactive oxygen and nitrogen species with fluorescent probes: challenges and limitations. Free Radic Biol Med 52:1–6
Jenkins J, Papkovsky DB, Dmitriev RI (2016) The Ca2+/Mn2+-transporting SPCA2 pump is regulated by oxygen and cell density in colon cancer cells. Biochem J 473:2507–2518
Dmitriev RI, Borisov SM, Jenkins J, Papkovsky DB (2015) Multi-parametric imaging of tumor spheroids with ultra-bright and tunable nanoparticle O2 probes. Proc SPIE 9328:932806–932808
Lowell BB, Spiegelman BM (2000) Towards a molecular understanding of adaptive thermogenesis. Nature 404:652–660
Bal NC, Maurya SK, Sopariwala DH, Sahoo SK, Gupta SC, Shaikh SA et al (2012) Sarcolipin is a newly identified regulator of muscle-based thermogenesis in mammals. Nat Med 18:1575–1579
Fedorenko A, Lishko PV, Kirichok Y (2012) Mechanism of fatty-acid-dependent UCP1 uncoupling in brown fat mitochondria. Cell 151:400–413
Zhou H, Sharma M, Berezin O, Zuckerman D, Berezin MY (2016) Nanothermometry: from microscopy to thermal treatments. ChemPhysChem 17:27–36
Repasky EA, Evans SS, Dewhirst MW (2013) Temperature matters! and why it should matter to tumor immunologists. Cancer Immunol Res 1:210–216
Lukinavičius G, Blaukopf C, Pershagen E, Schena A, Reymond L, Derivery E et al (2015) SiR-Hoechst is a far-red DNA stain for live-cell nanoscopy. Nat Commun 6:8497
Laviv T, Kim BB, Chu J, Lam AJ, Lin MZ, Yasuda R (2016) Simultaneous dual-color fluorescence lifetime imaging with novel red-shifted fluorescent proteins. Nat Methods 13:989–992
Weber P, Schickinger S, Wagner M, Angres B, Bruns T, Schneckenburger H (2015) Monitoring of apoptosis in 3D cell cultures by FRET and light sheet fluorescence microscopy. Int J Mol Sci 16:5375
Nobis M, McGhee EJ, Morton JP, Schwarz JP, Karim SA, Quinn J et al (2013) Intravital FLIM-FRET imaging reveals dasatinib-induced spatial control of src in pancreatic cancer. Cancer Res 73:4674–4686
Matano M, Date S, Shimokawa M, Takano A, Fujii M, Ohta Y et al (2015) Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids. Nat Med 21:256–262
Görlitz F, Kelly DJ, Warren SC, Alibhai D, West L, Kumar S et al (2017) Open source high content analysis utilizing automated fluorescence lifetime imaging microscopy. J Vis Exp 119:55119
Acknowledgments
This work was supported by Science Foundation Ireland (SFI) grant 13/SIRG/2144. We thank Prof. D. Papkovsky for useful comments on the manuscript.
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O’Donnell, N., Dmitriev, R.I. (2017). Three-Dimensional Tissue Models and Available Probes for Multi-Parametric Live Cell Microscopy: A Brief Overview. In: Dmitriev, R. (eds) Multi-Parametric Live Cell Microscopy of 3D Tissue Models. Advances in Experimental Medicine and Biology, vol 1035. Springer, Cham. https://doi.org/10.1007/978-3-319-67358-5_4
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DOI: https://doi.org/10.1007/978-3-319-67358-5_4
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