I’m a Research Fellow at Nanyang Technological University, School of Biological Scientist. I study unfolded protein response in wound healing, and several others, using bioinformatics tools.
As a self-taught, nascent bioinformatician, I try to use cutting-edge tools to interrogate metabolic diseases at the bulk and single-cell transcriptomics resolution.
I look forward to integrating other types of data (ChIP-seq, ATAC-seq, etc.) to extract more insights on how diseases progress.
Ethos of transparency, research integrity and keen collaboration in early career research.
Metabolic diseases often share common traits, including accumulation of unfolded proteins in the endoplasmic reticulum (ER). Upon ER stress, the unfolded protein response (UPR) is activated to limit cellular damage which weakens with age. Here, we show that Caenorhabditis elegans fed a bacterial diet supplemented high glucose at day 5 of adulthood (HGD-5) extends their lifespan, whereas exposed at day 1 (HGD-1) experience shortened longevity. We observed a metabolic shift only in HGD-1, while glucose and infertility synergistically prolonged the lifespan of HGD-5, independently of DAF-16. Notably, we identified that UPR stress sensors ATF-6 and PEK-1 contributed to the longevity of HGD-5 worms, while ire-1 ablation drastically increased HGD-1 lifespan. Together, we postulate that HGD activates the otherwise quiescent UPR in aged worms to overcome ageing-related stress and restore ER homeostasis. In contrast, young animals subjected to HGD provokes unresolved ER stress, conversely leading to a detrimental stress response.
@article{Beaudoin2022,author={Beaudoin-Chabot, C. and Wang, L. and Celik, C. and Abdul Khalid, A. T. and Thalappilly, S. and Xu, S. and Koh, J. H. and Lim, V. W. X. and Low, A. D. and Thibault, G.},title={The unfolded protein response reverses the effects of glucose on lifespan in chemically-sterilized C. elegans},journal={Nature Communications},volume={13},number={1},pages={5889},issn={2041-1723 (Electronic) 2041-1723 (Linking)},doi={10.1038/s41467-022-33630-0},year={2022},type={Journal Article},}
The endoplasmic reticulum (ER) is a complex and dynamic organelle that regulates many cellular pathways, including protein synthesis, protein quality control, and lipid synthesis. When one or multiple ER roles are dysregulated and saturated, the ER enters a stress state, which, in turn, activates the highly conserved unfolded protein response (UPR). By sensing the accumulation of unfolded proteins or lipid bilayer stress (LBS) at the ER, the UPR triggers pathways to restore ER homeostasis and eventually induces apoptosis if the stress remains unresolved. In recent years, it has emerged that the UPR works intimately with other cellular pathways to maintain lipid homeostasis at the ER, and so does at cellular levels. Lipid distribution, along with lipid anabolism and catabolism, are tightly regulated, in part, by the ER. Dysfunctional and overwhelmed lipid-related pathways, independently or in combination with ER stress, can have reciprocal effects on other cellular functions, contributing to the development of diseases. In this review, we summarize the current understanding of the UPR in response to proteotoxic stress and LBS and the breadth of the functions mitigated by the UPR in different tissues and in the context of diseases.
@article{Celik2023,author={Celik, C. and Lee, S. Y. T. and Yap, W. S. and Thibault, G.},title={Endoplasmic reticulum stress and lipids in health and diseases},journal={Progress in Lipid Research},volume={89},pages={101198},issn={1873-2194 (Electronic) 0163-7827 (Linking)},doi={10.1016/j.plipres.2022.101198},year={2023},type={Journal Article},}
Neuronal IRE-1 coordinates an organism-wide cold stress response by regulating fat metabolism
R. Dudkevich, J. H. Koh, C. Beaudoin-Chabot, C. Celik, I. Lebenthal-Loinger, S. Karako-Lampert, S. Ahmad-Albukhari, G. Thibault, and S. Henis-Korenblit
Cold affects many aspects of biology, medicine, agriculture, and industry. Here, we identify a conserved endoplasmic reticulum (ER) stress response, distinct from the canonical unfolded protein response, that maintains lipid homeostasis during extreme cold. We establish that the ER stress sensor IRE-1 is critical for resistance to extreme cold and activated by cold temperature. Specifically, neuronal IRE-1 signals through JNK-1 and neuropeptide signaling to regulate lipid composition within the animal. This cold-response pathway can be bypassed by dietary supplementation with unsaturated fatty acids. Altogether, our findings define an ER-centric conserved organism-wide cold stress response, consisting of molecular neuronal sensors, effectors, and signaling moieties, which control adaptation to cold conditions in the organism. Better understanding of the molecular basis of this stress response is crucial for the optimal use of cold conditions on live organisms and manipulation of lipid saturation homeostasis, which is perturbed in human pathologies.
@article{Dudkevich2022,author={Dudkevich, R. and Koh, J. H. and Beaudoin-Chabot, C. and Celik, C. and Lebenthal-Loinger, I. and Karako-Lampert, S. and Ahmad-Albukhari, S. and Thibault, G. and Henis-Korenblit, S.},title={Neuronal IRE-1 coordinates an organism-wide cold stress response by regulating fat metabolism},journal={Cell Reports},volume={41},number={9},pages={111739},issn={2211-1247 (Electronic)},doi={10.1016/j.celrep.2022.111739},year={2022},type={Journal Article},}
Mesenchymal stem cell (MSC) chondrogenesis is modulated by diverse biophysical cues. We have previously shown that brief, low-amplitude pulsed electromagnetic fields (PEMFs) differentially enhance MSC chondrogenesis in scaffold-free pellet cultures versus conventional tissue culture plastic (TCP), indicating an interplay between magnetism and micromechanical environment. Here, we examined the influence of PEMF directionality over the chondrogenic differentiation of MSCs laden on electrospun fibrous scaffolds of either random (RND) or aligned (ALN) orientations. Correlating MSCs’ chondrogenic outcome to pFAK activation and YAP localisation, MSCs on the RND scaffolds experienced the least amount of resting mechanical stress and underwent greatest chondrogenic differentiation in response to brief PEMF exposure (10 min at 1 mT) perpendicular to the dominant plane of the scaffolds (Z-directed). By contrast, in MSC-impregnated RND scaffolds, greatest mitochondrial respiration resulted from X-directed PEMF exposure (parallel to the scaffold plane), and was associated with curtailed chondrogenesis. MSCs on TCP or the ALN scaffolds exhibited greater resting mechanical stress and accordingly, were unresponsive, or negatively responsive, to PEMF exposure from all directions. The efficacy of PEMF-induced MSC chondrogenesis is hence regulated in a multifaceted manner involving focal adhesion dynamics, as well as mitochondrial responses, culminating in a final cellular response. The combined contributions of micromechanical environment and magnetic field orientation hence will need to be considered when designing magnetic exposure paradigms.
@article{Celik2021,author={Celik, C. and Franco-Obregón, A. and Lee, E. H. and Hui, J. H. and Yang, Z.},title={Directionalities of magnetic fields and topographic scaffolds synergise to enhance MSC chondrogenesis},journal={Acta Biomaterialia},volume={119},pages={169-183},issn={1878-7568 (Electronic) 1742-7061 (Linking)},doi={10.1016/j.actbio.2020.10.039},year={2021},type={Journal Article},}
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