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)  

      In our new study (collaboration between Ghent University and Rousselot BV) we report application of GelMA (gelatin methacryloyl) hydrogels with tuneable mechanical properties and added laminin to the culture of the small intestinal organoids. We found that mechanical properties alone are not sufficient for basement membrane support, resulting in polarity reversion, in contrast to the Matrigel-grown cultures. Altogether, observed polarity reversion phenomenon highlights importance of the further research in biochemical factors, directing cell polarity in the epithelial cells, while it also provides a tractable way for producing 'apical-out' organoids. Congratulations to Lenie (for her work on this MSc research project), Irina (for her supervision and driving force), Thomas and Ruben for expertise with gelatins and Bert for expertise with pig intestinal organoids. The work has been published in the Journal of Tissue Engineering (Open Access): https://journals.sagepub...

  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...

Our team is growing and we can present at the same time in two different places now! PhD candidate Nore Van Loon (joint project with FunGen lab, Prof. S. Vergult) gave a talk at the Methods and Applications of Fluorescence 2024 conference (8-11 September Valencia, Spain)! She presented her work in progress on using autofluorescence and fluorescent cholera toxin labelling to monitor differentiation of neural cells in human iPSC-derived 'brain' organoids. This work is a part of ongoing efforts of bringing together multi-omics approaches and advanced imaging of organoids to better understand aetiology of such neurodevelopmental disorders as FOXG1 syndrome, funded by the Special Research Fund at Ghent University (BOF) and Marguerite-Marie Delacroix foundation. At the same time, Prof. Ruslan Dmitriev travelled to Munster, Germany, to present an invited lecture on imaging oxygenation and cell metabolism in multicellular spheroids in 4th Inflammation & Imaging symposium! This l...

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...

We will attend and present at TERMIS-EU 2023 (Manchester, UK, 28-31 March 2023)! Prof. R. Dmitriev will co-chair (together with Prof. M. Monaghan, Trinity College Dublin) and present at the symposium ' Wanted: dead or alive? Quantitative microscopy of single-cell, spheroid and organoid cultures': Fluorescence Lifetime Imaging Microscopy (FLIM) to study niche-specific regions and metabolism in epithelial organoids More on the program and the event can be found 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.

From September 2020, Dr. Ruslan Dmitriev will start as Assistant Professor at Ghent University (Ghent, Belgium), where he will lead Group of Tissue engineering and Biomaterials (Faculty of Medicine and Health Sciences) .  This means that our group is moving to Ghent, an exciting new location, where we will grow and continue our research at the interface of cancer / stem cell biology, mitochondrial function, organoids, biosensors, FLIM and tissue engineering! More news on our blog & website function to follow.

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 .

During the ASCB-EMBO 2019 conference in Washington DC (December 2019) Dr. Ruslan Dmitriev was interviewed by Biotechniques journal about FLIM, organoids, challenges and career inspirations. Here's an interview: https://www.biotechniques.com/microscopy-imaging/ruslan-dmitriev-on-flim-and-intestinal-organoids/

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  

In year 2019 we achieved the following: - 1 PhD student successfully graduated ( Neil O'Donnell , 2014-2018) - We published 5 research articles on new pH-sensitive ( Analytical Chemistry ), redox-sensitive ( Dyes and Pigments ) and O2 sensing films ( Sensors and Actuators B ), new FLIM method of visualising mitochondrial membrane potential ( Cytometry A ) and a work on tissue engineering ( Xenotransplantation ) - Submitted 1 preprint ( BioRxiv ) on assessing metabolism in the intestinal organoids, together with 2 other articles under consideration, 1 book chapter for the book 'Intestinal stem cells' (Springer, 2020?). - We presented at ISSCR Organoids Amsterdam Symposium (poster), Sechenov Biomedical Summit (Invited talk, organised and chaired a session), ASCB-EMBO 2019 (talk and poster), visited Leica training center and University Tubingen with short-term collaborative visits, lectures and seminars. - 3 funding awards were secured: SFI Industry Fello...

Our Team will present at the American Society for Cell Biology / EMBO 2019 Annual Meeting! Dr. R. Dmitriev will give a short talk at the Microsymposium 17 (New perspectives in cell biology, Tuesday) entitled 'Multiplexed FLIM reveals dynamic stem cell niche metabolism in Lgr5-GFP intestinal organoids' and present a poster on the biosensor tissue engineering scaffold materials (P1629, Monday): These presentations will briefly summarise our main research efforts in designing novel imaging tools and their application in study of stem cell niche metabolism in organoids. R. Dmitriev has also received ASCB-EMBO postdoctoral Travel Award to attend this meeting. More info on this Meeting  and the  Program . Twitter