Mechanobiology of nuclear import of transcription factors modeled within a bioengineered stem cell niche

Duration 1/05/2015 – 31/07/2020 – Funded by ERC-CoG-2014 – G.A. nr 646990

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Project abstract

Many therapeutic applications of stem cells require accurate control of their differentiation. To this purpose there is a major ongoing effort in the development of advanced culture substrates to be used as “synthetic niches” for the cells, mimicking the native ones. The goal of this project is to use a synthetic niche cell culture model to test my revolutionary hypothesis that in stem cell differentiation, nuclear import of gene-regulating transcription factors is controlled by the stretch of the nuclear pore complexes. If verified, this idea could lead to a breakthrough in bio-mimetic approaches to engineering stem cell differentiation.

I investigate this question specifically in mesenchymal stem cells (MSC), because they are adherent and highly mechano-sensitive to architectural cues of the microenvironment. To verify my hypothesis I will use a combined experimental-computational model of mechanotransduction. I will a) scale-up an existing three-dimensional synthetic niche culture substrate, fabricated by two-photon laser polymerization,  b) characterize the effect of tridimensionality on the differentiation fate of MSC cultured in the niches, c) develop a multiphysics/multiscale computational model of nuclear import of transcription factors within differentially-spread cultured cells, and d) integrate the numerical predictions with experimentally-measured import of fluorescently-labelled transcription factors.

This project requires the synergic combination of several advanced bioengineering technologies, including micro/nano fabrication and biomimetics. The use of two-photon laser polymerization for controlling the geometry of the synthetic cell niches is very innovative and will highly impact the fields of bioengineering and biomaterial technology. A successful outcome will lead to a deeper understanding of bioengineering methods to direct stem cell fate and have therefore a significant impact in tissue repair technologies and regenerative medicine.


Bianca Barzaghini obtained her M.Sc. in biomedical engineering in 2019 at Politecnico di Milano, Italy. Here, she is currently attending a PhD program in bioengineering focused on the ERC-funded project NICHOID, in collaboration with the Dr. Stephana Carelli lab at Università degli Studi of Milano. Her research is focused on the microfabrication of micro engineered stem cell niches by two-photon laser polymerization and their biological validation.

Francesca Donnaloja has obtained the Master Degree in Biomedical Engineering in December 2016, at Politecnico di Milano. She has developed her Bachelor thesis project at Ospedale San Raffaele in Milan where she analyzed tissue damage induced by lead extraction. The Master project thesis has involved Baxter company for the analysis of the adsorbent capacity of novel materials to be used in dyalisis process. She has worked as a consultant at EY company in the Life Sciences section. Currently she is a PhD student involved in the ERC-CoG NICHOID project with a reseach activity entitled “Modelling the molecular mechanics of the nuclear pore complex” at Politecnico di Milano.

Dr. Emanuela Jacchetti graduated in Physics at Università degli Studi di Milano where she completed her PhD in Physics, astrophysics and Applied Physics in 2009 with the thesis “Differentiation and cytoskeletal protein dynamics of PC12 cells cultured on nanostructured titanium dioxide surfaces”. Then she worked on the project “Characterization of cytoplasmic calcium kinetics induced in human Mesenchymal Stem Cell”, at Istituto di BioFisica-CNR and Centro di Biotecnologie Avanzate in Genoa. From 2010 to 2014 she was a post-doc researcher at NEST, Scuola Normale Superiore (Pisa) to design and develop micro/nano-structured substrates for cell differentiation and at Istituto di BioFisica – CNR (Pisa) to study the spectroscopic characterization of photochromic fluorescent protein and their use in high spatial resolution microscopy applied to cell systems. In 2015 she was employed at IRCCS San Raffaele Scientific Institute on the project “Development of high resolution microscopy for imaging and tracking individual transcription factors”. She has joined the Mechanobiology lab in 2015 and she is in charge of the activities related to high resolution imaging relevant to the project ERC-CoG NICHOID.

Faculty team members:

Prof. Carmen Giordano

Prof. Josè Felix Rodriguez Matas

Prof. Roberto Fedele

Prof. Paolo Zunino

Former team members:

Lucia Boeri

Barbara Bonandrini

Alberto Garcia Gonzalez

Michele M. Nava

Marta Tunesi

Tommaso Zandrini




Musi CA, Colnaghi L, Giani A, Priori EC, Marchini G, Tironi M, Conci C, Cerullo G, Osellame R, Raimondi MT, Remuzzi A, Borsello T. Effect of 3D Synthetic Microscaffold Nichoid on the Morphology of Cultured Hippocampal Neurons and Astrocytes. Cells. 2022 Jun 23;11(13):2008. doi: 10.3390/cells11132008


Raimondi MT, Eaton SM, Nava MM, Laganà M, Cerullo G, Osellame R. Two-photon laser polymerization: from fundamentals to biomedical application in tissue engineering and regenerative medicine. J Appl Biomater Function Mater 2012, 10(1):55-65 DOI 10.5301/JABFM.2012.9278

(Invited Review) Nava MM, Raimondi MT, Pietrabissa R. Controlling self-renewal and differentiation of stem cells via mechanical cues. Journal of Biomedicine and Biotechnology. Epub 2012 Oct 2. 2012:797410, DOI 10.1155/2012/797410


Raimondi MT, Balconi G, Boschetti F, Di Metri A, Mohammed SAA, Quaglini V, Araneo L, Galvéz BG, Lupi M, Latini R, Remuzzi A. An opto-structural method to estimate the stress-strain field induced by cell contraction on substrates of controlled stiffness in vitro. J Appl Biomater Funct Mater. 2013 Dec 16;11(3):e143-50. DOI 10.5301/JABFM.2012.9773

Raimondi MT, Eaton SM, Laganà M, Aprile V, Nava MM, Cerullo G, Osellame R. Three-dimensional structural niches engineered via two-photon laser polymerization promote stem cell homing. Acta Biomater 2013, 9(1):4579–84. DOI 10.1016/j.actbio.2012.08.022


Nava MM, Raimondi MT, Pietrabissa R. Bio-chemo-mechanical models for nuclear deformation in adherent eukaryotic cells. Biomech Model Mechanobiol. 2014 Oct;13(5):929-43. DOI 10.1007/s10237-014-0558-8

Raimondi MT, Nava MM, Eaton SM, Bernasconi S, Vishnubhatla KC, Cerullo G, Osellame R. Optimization of femtosecond laser polymerized structural niches to control mesenchymal stromal cell fate in culture. Micromachines 2014, 5, 341-358; DOI 10.3390/mi5020341


Nava MM, Raimondi MT, Credi C, De Marco C, Turri S, Cerullo G, Osellame R. Interactions between structural and chemical biomimetism in synthetic stem cell niches. Biomedical Materials. 2015 Jan 16;10(1):015012. DOI 10.1088/1748-6041/10/1/015012


Nava MM, Fedele R, Raimondi MT. Computational prediction of strain-dependent diffusion of transcription factors through the cell nucleus. Biomech Model Mechanobiol. 2016 Aug;15(4):983-93. DOI 10.1007/s10237-015-0737-2

Garcia B, Rodriguez Matas JF, Raimondi MT. Modeling of the mechano-chemical behavior of the nuclear pore complex: current research and perspectives. Integrative Biology 2016, 8(10): 1011-1021. DOI 10.1039/c6ib00153j

Nava MM, Piuma A, Figliuzzi M, Cattaneo I, Bonandrini B, Zandrini T, Cerullo G, Osellame R, Remuzzi A, Raimondi MT. Two-photon polymerized “nichoid” substrates maintain function of pluripotent stem cells when expanded under feeder-free conditions. Stem Cell Research and Therapy. Sept 9, 2016. 7:Article 132. DOI 10.1186/s13287-016-0387-z

Iannetti L, D’Urso G, Conoscenti L, Cutrì E, Tuan R.S., Raimondi M.T., Gottardi R, Zunino P. Distributed and lumped parameter models for the characterization of high throughput bioreactors. PLOS ONE 11(9):e0162774. Sept 26, 2016. DOI 10.1371/journal.pone.0162774


Sacco R, Causin P, Lelli C, Raimondi MT. A Poroelastic Mixture Model of Mechanobiological Processes in Biomass Growth: Theory and Application to Tissue Engineering. Meccanica Nov 2017. 52(14): 3273:3297. DOI 10.1007/s11012-017-0638-9

Chierchia A, Chirico N, Boeri L, Raimondi I, Riva GA, Raimondi MT, Tunesi M, Giordano C, Forloni G, AlbaniD. Secretome released from hydrogel-embedded adipose mesenchymal stem cells protects against the Parkinson’s disease related toxin 6-hydroxydopamine, European Journal of Pharmaceutics and Biopharmaceutics 121 (2017) 113–120, DOI 10.1016 /j.ejpb.2017.09.014

Eghbali H, Nava MM, Leonardi G, Mohebbi-Kalhori D, Sebastiano R, Samimi A, Raimondi MT. An Experimental-Numerical Investigation on the Effects of the Macroporous Scaffold Geometry on Cell Culture Parameters. Int J Artif Organs 2017; 40(4):185-195. DOI 10.5301/ijao.5000554

Nava MM, Di Maggio N, Zandrini T, Cerullo G, Osellame R, Martin I, Raimondi MT. Synthetic niche substrates engineered via two-photon laser polymerization for the expansion of human mesenchymal stromal cells. J Tissue Eng Reg Med. 2017; 11(10): 2836–2845. DOI 10.1002/term.2187

Ricci D, Nava MM, Zandrini T, Cerullo G, Raimondi MT, Osellame R. Scaling-Up Techniques for the Nanofabrication of Cell Culture Substrates via Two-Photo Polymerization for Industrial-Scale Expansion of Stem Cells. Materials 2017, 10(1):Article 66. DOI:10.3390/ma10010066


Garcia A, Jacchetti E, Marotta R, Tunesi M, Rodriguez Matas JF, Raimondi MT. The Effect of Cell Morphology on the Permeability of the Nuclear Envelope to Diffusive Factors. Front Physiol. 2018 Jul 13;9:925. DOI 10.3389/fphys.2018.00925


Donnaloja F, Jacchetti E, Soncini M and Raimondi MT (2019). Mechanosensing at the Nuclear Envelope by Nuclear Pore Complex Stretch Activation and Its Effect in Physiology and Pathology. Front. Physiol. 2019 Jul 10:896. DOI

Boeri L, Albani D, Raimondi MT, Jacchetti E. Mechanical regulation of nucleocytoplasmic translocation in mesenchymal stem cells: characterization and methods for investigation. Biophys Rev. 2019 Oct;11(5):817-831. DOI


Steimberg, N., Bertero, A., Chiono, V., Dell’Era, P., Di Angelantonio, S., Hartung, T., Perego, S., Raimondi, M.T., Xinaris, C., Caloni, F., De Angelis, I., Alloisio, S. and Baderna, D. (2020) “iPS, organoids and 3D models as advanced tools for in vitro toxicology”, ALTEX – Alternatives to animal experimentation, 37(1), pp. 136-140. DOI

Boeri L, Jacchetti E, Soncini M, Negro A, Albani D, Raimondi MT. Advantages and limitations of a supernegative GFP in facilitating MyoD intracellular tracking. Methods Appl Fluoresc. 2020 Mar 13;8(2):025007. doi: 10.1088/2050-6120/ab797c

Donnaloja F, Jacchetti E, Soncini M, Raimondi MT. Natural and Synthetic Polymers for Bone Scaffolds Optimization. Polymers 2020, 12, 905; doi:10.3390/polym12040905

Conci C, Bennati L, Bregoli C, Buccino F, Danielli F, Gallan M, Gjini E, Raimondi MT. Tissue engineering and regenerative medicine strategies for the female breast. J Tissue Eng Regen Med. 2020 Feb;14(2):369-387. doi 10.1002/term.2999

Donnaloja F, Carnevali F, Jacchetti E, Raimondi MT.Lamin A/C Mechanotransduction in Laminopathies. Cells. 2020 May 24;9(5):E1306. doi: 10.3390/cells9051306.

Raimondi MT,  Donnaloja F,  Barzaghini B, Bocconi A, Conci C, Parodi V, Jacchetti E, Carelli S. Bioengineering tools to speed up the discovery and preclinical testing of vaccines for SARS-CoV-2 and therapeutic agents for COVID-19. Theranostics 2020; 10(16):7034-7052. doi:10.7150/thno.47406. Available from: doi:10.7150/thno.47406

Rey F, Barzaghini B, Nardini A, Bordoni M, Zuccotti GV, Cereda C, Raimondi MT, Carelli S. Advances in Tissue Engineering and Innovative Fabrication Techniques for 3-D-Structures: Translational Applications in Neurodegenerative Diseases. Cells. 2020 Jul 7;9(7):E1636. doi: 10.3390/cells9071636.

Remuzzi A, Bonandrini B, Tironi M, Longaretti L, Figliuzzi M, Conti S, Zandrini T, Osellame R, Cerullo G, Raimondi MT. Effect of the 3D artificial Nichoid on the morphology and mechanobiological response of mesenchymal stem cells cultured in vitro. Cells 2020, 9, 1873; doi:10.3390/cells9081873

Rey F, Pandini C, Barzaghini B, Messa L, Giallongo T, Pansarasa O, Gagliardi S, Brilli M, Zuccotti GV, Cereda C, Raimondi MT, Carelli S. Dissecting the Effect of a 3D Microscaffold on the Transcriptome of Neural Stem Cells with Computational Approaches: A Focus on Mechanotransduction. Int J Mol Sci. 2020 Sep 15;21(18):E6775. doi: 10.3390/ijms21186775

Parodi V, Jacchetti E, Osellame R, Cerullo G, Polli D and Raimondi MT. (2020) Nonlinear Optical Microscopy: From Fundamentals to Applications in Live Bioimaging. Front. Bioeng. Biotechnol. 8:585363. doi: 10.3389/fbioe.2020.585363odi


Carelli S, Giallongo T, Rey F, Barzaghini B, Zandrini T, Pulcinelli A, Nardomarino R, Cerullo G, Osellame R, Cereda C, Zuccotti GV, Raimondi MT. Neural precursors cells expanded in a 3D micro-engineered niche present enhanced therapeutic efficacy in vivo. Nanotheranostics 2021; 5(1):8-26. doi:10.7150/ntno.50633

Jacchetti E, Nasehi R, Boeri L, Parodi V, Negro A, Albani D, Osellame R, Cerullo G, Matas JFR, Raimondi MT. The nuclear import of the transcription factor MyoD is reduced in mesenchymal stem cells grown in a 3D micro-engineered niche. Sci Rep. 2021 Feb 4;11(1):3021. doi: 10.1038/s41598-021-81920-2

Perottoni S, Neto NGB, Di Nitto C, Dmitriev RI, Raimondi MT, Monaghan MG. Intracellular label-free detection of mesenchymal stem cell metabolism within a perivascular niche-on-a-chip. Lab on a Chip. Feb 2020. doi:10.1039/d0lc01034k

Raimondi MT, Barzaghini B, Bocconi A, Conci C, Martinelli C, Nardini A, Testa C, Carelli S, Cerullo G, Chirico G, Gottardi R, Osellame R, Remuzzi A, Laganà M, Jacchetti E, Micro structured tools for cell modeling in the fourth dimension, Proc. SPIE 11786, Optical Methods for Inspection, Characterization, and Imaging of Biomaterials V, 117861T (20 June 2021); doi: 10.1117/12.259332