Fabian Ille

Prof. Dr. Fabian Ille

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Research Focus & Metrics

Academic Career Length

9Years (2018-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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Journal Article
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SWSimon Wuest
Simon Wuest
MCMartina Caliò
Martina Caliò
TWTimon Wernas
Timon Wernas
STSamuel Tanner
Samuel Tanner
CGChristina Giger-Lange
Christina Giger-Lange
Marcel EgliMarcel Egli
Marcel Egli
Due to the limited self-repair capacity of articular cartilage, the surgical restoration of defective cartilage remains a major clinical challenge. The cell-based approach, which is known as autologous chondrocyte transplantation (ACT), has limited success, presumably because the chondrocytes acquire a fibroblast-like phenotype in monolayer culture. This unwanted dedifferentiation process is typically addressed by using three-dimensional scaffolds, pellet culture, and/or the application of exogenous factors. Alternative mechanical unloading approaches are suggested to be beneficial in preserving the chondrocyte phenotype. In this study, we examined if the random positioning machine (RPM) could be used to expand chondrocytes in vitro such that they maintain their phenotype. Bovine chondrocytes were exposed to (a) eight days in static monolayer culture; (b) two days in static monolayer culture, followed by six days of RPM exposure; and, (c) eight days of RPM exposure. Furthermore, the experiment was also conducted with the application of 20 mM gadolinium, which is a nonspecific ion-channel blocker. The results revealed that the chondrocyte phenotype is preserved when chondrocytes go into suspension and aggregate to cell clusters. Exposure to RPM rotation alone does not preserve the chondrocyte phenotype. Interestingly, the gene expression (mRNA) of the mechanosensitive ion channel TRPV4 decreased with progressing dedifferentiation. In contrast, the gene expression (mRNA) of the mechanosensitive ion channel TRPC1 was reduced around fivefold to 10-fold in all of the conditions. The application of gadolinium had only a minor influence on the results. This and previous studies suggest that the chondrocyte phenotype is preserved if cells maintain a round morphology and that the ion channel TRPV4 could play a key role in the dedifferentiation process.

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MCMartina Calio
Martina Calio
Benjamin GantenbeinBenjamin Gantenbein
Benjamin Gantenbein
Marcel EgliMarcel Egli
Marcel Egli
LPLucy Poveda
Lucy Poveda
FIFabian Ille
Fabian Ille
Intervertebral disc (IVD) degeneration and its medical consequences is still one of the leading causes of morbidity worldwide. To support potential regenerative treatments for degenerated IVDs, we sought to deconvolute the cell composition of the nucleus pulposus (NP) and the annulus fibrosus (AF) of bovine intervertebral discs. Bovine calf tails have been extensively used in intervertebral disc research as a readily available source of NP and AF material from healthy and young IVDs. We used single-cell RNA sequencing (scRNAseq) coupled to bulk RNA sequencing (RNAseq) to unravel the cell populations in these two structures and analyze developmental changes across the rostrocaudal axis. By integrating the scRNAseq data with the bulk RNAseq data to stabilize the clustering results of our study, we identified 27 NP structure/tissue specific genes and 24 AF structure/tissue specific genes. From our scRNAseq results, we could deconvolute the heterogeneous cell populations in both the NP and the AF. In the NP, we detected a notochordal-like cell cluster and a progenitor stem cell cluster. In the AF, we detected a stem cell-like cluster, a cluster with a predominantly fibroblast-like phenotype and a potential endothelial progenitor cluster. Taken together, our results illustrate the cell phenotypic complexity of the AF and NP in the young bovine IVDs.

29 March 2018 in npj Microgravity
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SWSimon Wuest
Simon Wuest
Benjamin GantenbeinBenjamin Gantenbein
Benjamin Gantenbein
FIFabian Ille
Fabian Ille
Marcel EgliMarcel Egli
Marcel Egli
Advances in electrophysiological experiments have led to the discovery of mechanosensitive ion channels (MSCs) and the identification of the physiological function of specific MSCs. They are believed to play important roles in mechanosensitive pathways by allowing for cells to sense their mechanical environment. However, the physiological function of many MSCs has not been conclusively identified. Therefore, experiments have been developed that expose cells to various mechanical loads, such as shear flow, membrane indentation, osmotic challenges and hydrostatic pressure. In line with these experiments, mechanical unloading, as experienced in microgravity, represents an interesting alternative condition, since exposure to microgravity leads to a series of physiological adaption processes. As outlined in this review, electrophysiological experiments performed in microgravity have shown an influence of gravity on biological functions depending on ion channels at all hierarchical levels, from the cellular level to organs. In this context, calcium signaling represents an interesting cellular pathway, as it involves the direct action of calcium-permeable ion channels, and specific gravitatic cells have linked graviperception to this pathway. Multiple key proteins in the graviperception pathways have been identified. However, measurements on vertebrae cells have revealed controversial results. In conclusion, electrophysiological experiments in microgravity have shown that ion-channel-dependent physiological processes are altered in mechanically unloaded conditions. Future experiments may provide a better understanding of the underlying mechanisms.

27 September 2025 in Computer Methods and Programs in Biomedicine Update
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Open access
FGFabian Gröger
Fabian Gröger
LALudovic Amruthalingam
Ludovic Amruthalingam
SLSimone Lionetti
Simone Lionetti
Alexander NavariniAlexander Navarini
Alexander Navarini
FIFabian Ille
Fabian Ille
MPMarc Pouly
Marc Pouly

Verified
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ACAlessandra Cazzaniga
Alessandra Cazzaniga
FIFabian Ille
Fabian Ille
SWSimon Wuest
Simon Wuest
CHCarsten Haack
Carsten Haack
AKAdrian Koller
Adrian Koller
JMJeanette Maier
Jeanette Maier
We introduce a new benchtop microgravity simulator (MGS) that is scalable and easy to use. Its working principle is similar to that of random positioning machines (RPM), commonly used in research laboratories and regarded as one of the gold standards for simulating microgravity. The improvement of the MGS concerns mainly the algorithms controlling the movements of the samples and the design that, for the first time, guarantees equal treatment of all the culture flasks undergoing simulated microgravity. Qualification and validation tests of the new device were conducted with human bone marrow stem cells (bMSC) and mouse skeletal muscle myoblasts (C2C12). bMSC were cultured for 4 days on the MGS and the RPM in parallel. In the presence of osteogenic medium, an overexpression of osteogenic markers was detected in the samples from both devices. Similarly, C2C12 cells were maintained for 4 days on the MGS and the rotating wall vessel (RWV) device, another widely used microgravity simulator. Significant downregulation of myogenesis markers was observed in gravitationally unloaded cells. Therefore, similar results can be obtained regardless of the used simulated microgravity devices, namely MGS, RPM, or RWV. The newly developed MGS device thus offers easy and reliable long-term cell culture possibilities under simulated microgravity conditions. Currently, upgrades are in progress to allow real-time monitoring of the culture media and liquids exchange while running. This is of particular interest for long-term cultivation, needed for tissue engineering applications. Tissue grown under real or simulated microgravity has specific features, such as growth in three-dimensions (3D). Growth in weightlessness conditions fosters mechanical, structural, and chemical interactions between cells and the extracellular matrix in any direction.

16 October 2025 in JOR SPINE
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ASAnja Stirnimann
Anja Stirnimann
LSLeon Schlagenhof
Leon Schlagenhof
Benjamin GantenbeinBenjamin Gantenbein
Benjamin Gantenbein
FIFabian Ille
Fabian Ille
Background: Intervertebral disc (IVD) degeneration (IDD) contributes to global disability and involves incompletely understood molecular processes. Recent advances in omics technologies help to unravel the complex biology of IDD and develop novel therapies. Methods: This narrative review explores how omics approaches—particularly RNA sequencing—have advanced our understanding of IVD biology and how these findings contribute to leveraging the intrinsic regenerative potential of the IVD, with a specific focus on nucleus pulposus progenitor cells (NPPCs). Relevant literature addressing transcriptomic, genomic, proteomic, metabolomic, and epigenetic data, as well as emerging mult‐iomics approaches, was summarized. Results: Single‐omics studies have provided insight into cellular heterogeneity, gene expression changes, genetic susceptibility loci, proteomic changes, metabolic alterations, and epigenetic regulation. Further, they have highlighted key pathways associated with extracellular matrix remodeling, inflammation, and progenitor cell depletion in IDD. Inconsistencies between TEK (the gene encoding TIE2) mRNA levels and TIE2 (Angiopoietin‐1 receptor) protein expression, discussed in this review, emphasize the limitations of single‐omics analyses and underscore the need for multi‐omics studies, which are currently underrepresented in the field. By enabling a system‐level understanding, multi‐omics offers a comprehensive framework to decode the networks driving IDD and identify biomarkers and therapeutic targets to restore disc function and reduce pain. Conclusions: Although NPPCs hold promise for IVD regeneration, translational challenges such as cell survival and efficacy persist. Omics‐informed insights into the IVD microenvironment may support the development of combinatorial strategies, including co‐delivery of modulators to enhance NPPC survival and the effectiveness of therapies.