Metabolic Imaging & Tissue engineering Group News

  Increased micro- and nanoplastic (MNP) pollution and its poorly understood biomedical impact raises questions on their cell and tissue uptake mechanisms and effects on the absorptive tissues. Dmitriev’s team reports a new microscopy-based approach to perform dynamic imaging of dye-modified micro- and nanoplastics (MNP). When combined with stem cell-derived intestinal organoids, with controlled apical and basal polarity, this approach enables for sensitive detection and quantification of MNPs, their internalization and biological effects.  The work was published in Light: Science & Applications , big thanks to all collaborators and researchers involved, especially Irina, Hang (first 'big paper' in PhD) and Bert! We hope to get this research line funded and expand towards studying effects of MNPs on the brain, tooth development and other tissues! Press-release on Eurekalert (14-09-2025)  

  We collaborated with groups of Prof. Richard Hoogenboom and Prof. Devriendt (Ghent University) and tested application of poly(2-alkyl-2-oxazoline) hydrogels (PAOx) for 3D cell cultures of cancer and stem cells. We found that encapsulation of small intestinal organoids into PAOx hydrogels results in polarity reversion, i.e. transition from basal to apical-out phenotype. This is useful for studying drug delivery, nutrient absorption and host-microbiota interactions within this model.  This figure shows dramatic differences of mitochondrial polarisation (TMRM) and appearance (transmission light) in small intestinal organoids, observed after apical-out transition (PAOx), in contrast to conventional Matrigel-grown culture: Since the PAOx hydrogels can show variable mechanical properties, we tested if encapsulation into stiff and soft hydrogels can affect behaviour of cancer cells in 3D: indeed, with HCT116 spheroids we found that stiffness of the hydrogels affect cell migration f...

Wow, time really does fly! It's been a while since our previous update but by no means our team was idle.  End of 2024 was memorable with exciting conferences, including SPAOM 2024, Histochemical Society Annual online meeting 2024, FHERITALE consortium and others! We've received funding to study neurodevelopmental and neurodegenerative diseases (more news soon) so we can plan new & exciting research projects. Our team currently hosts 2 international researchers, Valerie Cote and Dr. Simone Perottoni, both learning and doing exciting science in FLIM, organoids and imaging of cancer cells / tissues. In addition, we are looking forward to host more of PhD students from FLIMagin3D consortium! Here are some recent publications, from our team and collaborative research projects: Sheehan A, Okkelman IA, Groslambert G, Bucher C, Dmitriev RI, Filatov MA: Optoelectronic Properties and Fluorescence Lifetime Imaging Application of Donor-Acceptor Dyads Derived From 2,6-DicarboxyBODIPY ...

ALERT: New publication from our group! Angela, Gabriele, Hang, Nore, Nina and Irina teamed up to produce a video protocol paper, focusing on comparing various multicellular spheroid formation methods, suitable for 'downstream' live multi-parameter fluorescence lifetime imaging microscopy (FLIM) and imaging cell oxygenation. This protocol is illustrated with examples of autofluorescence-based FLIM microscopy of NAD(P)H, oxygenation and cell death, as well as imaging of visible flavin-based cell autofluorescence, performed in tumour and stem cell-derived spheroids. The article is also a part of the Methods collection 'Quantitative Live Cell Imaging of 3D Models', which is going to expand in the future.    Link to the publication: https://www.jove.com/t/66845/production-multi-parameter-live-cell-fluorescence-lifetime-imaging The Methods Collection (Journal of Visualised Experiments, JOVE):  https://app.jove.com/methods-collections/902

It's been busy, it's been tough but it's been also fun! Our team has trained a number of MSc students, with excellent projects, spanning the scope from establishment of novel organoid models, to testing of mechanical properties of the hydrogel-producing biomaterials on the small intestinal epithelium organoids and FLIM analysis of neural ('brain') iPSC-derived organoids. Thanks to everyone involved! The end of year (June) was culminated in presenting of research at Ghent Gut Inflammation Group (Ruslan, Irina, Hang, Lenie) and participating (as instructors, Ruslan and Michele) in the FEBS course on Functional Imaging of cellular dynamics (Amsterdam, 9-15 June 2024)!         Stay tuned for more exciting news on our research!

(video: time lapse FLIM of endocytosis in human colon cancer cells using LysoSensor Green, (C) Dmitriev Lab, 2023) The period of ~October 2023 until ~May 2024 (almost complete academic year!) was too busy for publishing any updates but thanks for staying tuned (if you did so). Some key updates for this period: Successful start of FLIMagin3D project, with the 3 new PhD students (Hang, Michele and Gabriele) + visiting (via secondments) PhD students, joining our team to address challenges in multi-parameter FLIM of organoids and multicellular spheroids, advancing imaging & probes for cell oxygenation, FLIM-FRET, tissue mechanics and biofabricated inter-species communities. More about the FLIMagin3D can be found here:  https://www.flimagin3d.com/   Some visiting scientists with exciting projects, including Dr. A. Russegger, R. Harkhoe, partners from OsteoNet Horizon MSCA Staff Exchange network Our group (including the microscopes!) has relocated to the new 'The Core' / MREB3 r...

Prof. Ruslan Dmitriev and PhD candidate Angela Debruyne collaborated with TU Graz (Prof. S. Borisov) and University of Tubingen on the design of new type of the nanothermometer, based on organic Zr complexes and exhibiting long emission decay times. These materials open a new framework for microsecond-range emitting temperature-sensitive materials, providing better resolution and potential applications in imaging temperature gradients in multicellular spheroids, as we have demonstrated in the study. The research has been published in Advanced Optical Materials journal. Russegger A, Debruyne AC, Berrio DC, Fuchs S, Marzi J, Schenke-Layland K, Dmitriev RI, Borisov SM: Bright and Photostable TADF-Emitting Zirconium(IV) Pyridinedipyrrolide Complexes: Efficient Dyes for Decay Time-Based Temperature Sensing and Imaging . Advanced Optical Materials 2023,:2202720. If you are interested in our research in nanothermometry, expertise and dedicated nanosensors, do not hesitate to contact us. ...

Our lab has published a new protocol paper, this time with the video, in the Journal of Visualized Experiments (JoVE)! In this research method paper, we report the use of red/ near-infrared emitting biocompatible nanosensors to monitor oxygenation of the live multicellular spheroids (made of one or more cell types), together with the tracers of cell death. While this methodology is typically available only for users with 'high-end' PLIM microscopes and alike, we show that using of ratiometric readout with the red and near infrared emitting fluorescent nanosensors makes this possible on broadly available 'widefield' fluorescence microscope platforms. This method helps comparing oxygenation of spheroids, assessing this in a long-term and kinetic assays, comparing their variability and viability, essential in follow-up 3D printing applications. This is the first article in our collection ' Quantitative live cell imaging of 3D models' , guest-edited together with ...

Our team contributed to the database summarising features of multicellular spheroids, produced from cancer and non-transformed cells.  3D spheroid cell cultures often suffer from incomplete reporting, lab-to-lab variability and other factors, which can affect reproducibility of research. The multidisciplinary team led by Prof. Olivier De Wever (LECR, CRIG) performed analysis of factors affecting spheroid reproducibility - among the others, spheroid formation method and growth medium composition and glucose content were found to be among the most important. The work published in Nature Methods journal can be assessed here . The  News and Views  feature. Feel free to use the database ! https://www.mispheroid.org 

  We are not presenting this year and the TERMIS world congress is virtual but we are still participating! - Prof. Dmitriev will co-chair the session ET2.2. on ' Advanced spatiotemporal imaging in regenerative medicine' (November, 17th, 15.30-17.00). In this session, Prof. Michael Monaghan (Trinity College Dublin) is also going to talk about our recently published joint research on microfluidic-based perivascular stem cell niche modelling . Stay tuned!

Together with Prof. Margarida Barroso (Albany Medical College, NY) and Prof. Xavier Intes (Rensselaer Polytechnic Institute, NY) we wrote a review article summarising biological aspects of applications of the fluorescence (FLIM) and phosphorescence (PLIM) lifetime imaging microscopies.  We covered most of FLIM and PLIM applications, including FLIM-FRET, macro-FLI, O2 and metabolic imaging, monitoring virus entry into the cell, imaging in organoids and tissue engineering and other areas. In addition, we outlined broad applicability of this type of microscopies not only for cancer and stem research (biomedicine) but also for fungal, plant and other 'general biology' areas.  The review published in the Journal of Cell Science can be assessed here . Twitter link  and link2

Together with Prof. Margarida Barroso (Albany Medical College), we guest edit a collection of video protocols, hosted by the Journal of Visualised Experiments ( JoVE ), and  dedicated to the quantitative live cell imaging in 3D .  We expect bringing together some leaders and innovators in various aspects of the quantitative live fluorescence microscopies applied to ex vivo animal models, organoids and 3D engineered tissue blocks. The collection, which just has been started, can be assessed here .

Our team has co-authored an article focused on studying oxygenation and cell metabolism in bioreactor mimicking perivascular stem cell niche ('niche-on-a-chip'). This study combines mathematical modelling of flow and oxygenation of mesenchymal stem cells with actual analysis of their metabolism via multiparameter analysis of NAD(P)H (two-photon FLIM), cell oxygenation (two-photon ratiometric fluorescence), mitochondrial polarisation and glucose transport. The study is a result of joint efforts of Politecnico di Milano, Trinity College Dublin, NUI Galway and Ghent Univeristy. The article published in Lab on a Chip journal can can be assessed here . Twitter link

Our new lab at the Ghent University is starting. We are proud to be a part of the Department of Human Structure and Repair. Feel free to visit our webpage at the University (UGent) website . We are still in the process of re-starting the research, buying / upgrading equipment & the infrastructure, getting to know people and initiating new collaborations. We have also joined Ghent Gut Inflammation Group (GGIG.be), feel free to visit our webpage . More news to follow soon.

Our team has contributed to the Intestinal Stem Cells book, edited by Prof. P. Ordonez-Moran and published by Springer. The long-awaited book has gathered a number of experts and pioneers in the fields of intestinal stem cell biology, organoids, tissue engineering and innovative methodologies to study them. Our book chapter, written in collaboration with Jens Puschhof (Prof. Hans Clevers lab) describes  applications of FLIM and 3D FLIM for visualising stem cell niche in the small intestinal organoids. We describe imaging of oxygenation, cell and redox metabolism, labelling cell proliferation, with particular attention to 3D FLIM and multiplexed detection. The chapter link . Twitter link Link to the whole book by chapters.

Our group published new research article, focused on further development of the 'biosensor scaffold' concept for advanced tissue engineering applications, such as imaging-assisted organoid engineering. Here, we collaborated with colleagues from Agilent Technologies and University of Tubingen (Laboratory of Professor Katja Schenke-Layland, Germany) to develop and functionally evaluate recombinant extracellular Ca2+-specific protein biosensors that can bind collagen- and cellulose-based tissue engineering scaffold materials. Using confocal and two-photon FLIM, and Matrigel-based 3D culture of mouse intestinal organoids, we evaluated performance of the collagen-binding biosensor and found that 3D culture of the intestinal epithelium can regulate extracellular Ca2+, potentially through the function of lipid droplets. The article published in ACS Applied Bio Materials journal can be assessed here . Twitter link . 

Dr. Ruslan Dmitriev  has co-authored a paper focused on molecular mechanisms of breast cancer and the role of mitochondrial function in thermogenesis. This work, which is a result of collaborative efforts  from Oxford University, Kyoto University, University College Cork and Sechenov Medical University research groups, has been recently published in Cancer & Metabolism journal. Full-text is available here . Twitter link .

Our recent collaborative work on pH-sensing DAOTA dyes (published in Analytical Chemistry in 2019) has been included into the virtual issue of ACS Sensors journal, celebrating 5 years and entitled 'Giants in sensing'. To reflect back to what we have published over the period of 2015-2020 with ACS journals, see the list below: Dmitriev RI , Borisov SM, Düssmann H, Sun S, Müller BJ, Prehn J, Baklaushev VP, Klimant I, Papkovsky DB: Versatile Conjugated Polymer Nanoparticles for High-Resolution O2 Imaging in Cells and 3D Tissue Models.  ACS Nano  2015,  9 (5), 5275-5288. Dmitriev RI , O’Donnell N, Papkovsky DB:   Metallochelate Coupling of Phosphorescent Pt-Porphyrins to Peptides, Proteins, and Self-Assembling Protein Nanoparticles .   Bioconjugate Chemistry   2016,   27 (2):439-445. Fomin M,  Dmitriev RI , Jenkins J, Papkovsky DB, Heindl D, König B: A Two-Acceptor Cyanine-Based Fluorescent Indicator ...

Dr. Ruslan Dmitriev  recently presented a talk at the Biophysical Society 2020 Annual Meeting, in San Diego Convention Center, California, USA. In his talk, Ruslan summarised recent group developments in a multiparameter imaging of stem cell metabolism in the small intestinal organoid model. He focused on measuring oxygenation of live intestinal organoids, assessing mitochondrial polarisation and combining O2 with NAD(P)H redox microscopy analyses. He also received  Travel Award from the Biophysical Society to attend this meeting. More information on the meeting can be found on Twitter .  The abstract of presentation published in Biophysical Journal supplement can be viewed here .

Our manuscript on analysis of Lgr5-GFP intestinal organoid metabolism by different methods (O2-PLIM, NAD(P)H-FLIM and XF assay) has been accepted for publication by Redox Biology journal . This is an excellent result of collaboration with Prof. Michael Monaghan group at Trinity College Dublin (NAD(P)H-FLIM), which enabled us to compare and efficiently use 2 different FLIM-PLIM imaging platforms available in Ireland. Combining these innovative experimental approaches enabled us to discover highly 'flexible' and dynamic ability of stem cells to respond to the nutrient availability in the growth media. The next stages of our research on stem cell niche metabolism promise to be even more exciting! More on this story: Preprint Pre-Lights Twitter1 Twitter2