Biology subjects

Lee, S. Y.

Publications and source records attributed to Lee, S. Y..

5 recordsLinked to original sources

bioRxiv2018

High-risk human papillomaviruses down-regulate expression of the Ste20 family kinase MST1 to inhibit the Hippo pathway and promote transformation

Human papillomaviruses (HPV) are a major cause of malignancy worldwide They are the aetiological agent of almost all cervical cancers and an increasing number of head and neck carcinomas. Deregulation of the Hippo pathway component YAP1 has recently been demonstrated to play a role in HPV-mediated cervical cancer, but whether other components of this pathway are implicated in the pathogenesis of this disease remains poorly understood.\n\nThe expression level and activation status of critical Hippo pathway components were analysed across multiple cytology samples from patients with cervical disease, as well as HPV positive (HPV+) and HPV negative (HPV-) cervical cancer cell lines using real time qPCR, western blot and immunohistochemistry. In parallel, we assessed the effects of MST1 and MST2 overexpression upon cervical cancer cell proliferation, migration and invasion. Finally, we interrogated the consequences of interrupted MST1 and MST2 function using a targeted small molecule inhibitor in tandem with kinase inactive MST mutants. Our analysis found that expression of the Ste20 kinase MST1 was decreased within both HPV+ primary patient samples and cervical cancer cell lines. This effect was mediated by the virus-coded oncoproteins E6 and E7, which impair MST1 transcription. Reintroduction of MST1, or its paralogue MST2, into HPV positive cervical cancer cells re-activated the Hippo pathway, leading to a reduction in cell proliferation, migration and invasion. Finally, using a small molecule inhibitor of MST1/2 or kinase inactive mutants of either protein, we demonstrated that this effect required the kinase function of MST1/2. Our results reveal that HPV down regulates MST1 expression to inactivate the Hippo pathway and so drive cells towards transformation.

microbiology↗

bioRxiv2018

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed.\n\nHere, we present memote (https://github.com/opencobra/memote) an open-source software containing a community-maintained, standardized set of metabolic model tests. The tests cover a range of aspects from annotations to conceptual integrity and can be extended to include experimental datasets for automatic model validation. In addition to testing a model once, memote can be configured to do so automatically, i.e., while building a GEM. A comprehensive report displays the models performance parameters, which supports informed model development and facilitates error detection.\n\nMemote provides a measure for model quality that is consistent across reconstruction platforms and analysis software and simplifies collaboration within the community by establishing workflows for publicly hosted and version controlled models.

systems biology↗

bioRxiv2018

Optimization of Tenocyte Lineage-related Factors from Tonsil-derived Mesenchymal Stem Cells using Response Surface Methodology

Researchers should consider various potential factors that affect tenogenic differentiation of mesenchymal stem cells (MSCs); however, this requires numerous experimental settings, which are associated with high cost and time. We aimed to assess the differential effects of transforming growth factor beta 3 (TGF-{beta}3) on the tenogenesis of tonsil-derived MSCs (T-MSCs) and bone marrow-derived MSCs (BM-MSCs) using design of experiments (DoE). Bone marrow and tonsillar tissue was collected from four patients; mononuclear cells were separated and treated with 5 and 10 ng/mL of TGF-{beta}3 with vehicle control. A full-factorial experimental design with a categorical factor of 0 was employed to study the effect of tension based on T-MSCs. Eighty-four trials were utilized, fitted with RSM, and then used to obtain mathematical prediction models. Exposure of T-MSCs and BM-MSCs to TGF-{beta}3 increased the expression of scleraxis (SCX), tenomodulin (TNMD), decorin, collagen I, and tenascin C. Expression of most of these factors reached a maxima after 2-3 days of treatment. Considering all of the tenocyte lineage-related factors that were assessed, the predicted value of the factors from T-MSCs was significantly induced at 2.7 ng/mL of TGF-{beta}3 during 2.5-day culture, whereas the predicted value of the factors from BM-MSCs was significantly induced during 2.3-day culture, regardless of TGF-{beta}3 concentration. This study demonstrated that tenogenic differentiation of T-MSCs and BM-MSCs under TGF-{beta}3 stimulation showed a similar culture time for peak expression of tenocyte-related mRNAs using RSM. This study suggests the potential of using the DoE approach for optimization of the culture protocol for tenogenesis of MSCs.

bioengineering↗

bioRxiv2018

Gradual repression of selenoprotein W ensures physiological bone remodelling

Selenoproteins containing selenium in the form of selenocysteine are critical for bone remodelling. However, their mechanism of action is not well understood. Here, we report the identification of selenoprotein W (SELENOW) through large-scale mRNA profiling of receptor activator of nuclear factor (NF)-{kappa}B ligand (RANKL)-induced osteoclast differentiation, as a protein that is downregulated via RANKL/RANK/tumour necrosis factor receptor-associated factor 6/p38 signalling. RNA sequencing analysis revealed that SELENOW regulates osteoclastogenic genes. SELENOW overexpression enhanced osteoclastogenesis in vitro via nuclear translocation of NF-{kappa}B and nuclear factor of activated T-cells cytoplasmic 1, whereas its loss suppressed osteoclast formation. SELENOW-deficient and SELENOW-overexpressing mice exhibited osteopetrosis and osteoporosis, respectively. Ectopic SELENOW expression stimulated cell-cell fusion critical for osteoclast maturation as well as bone resorption. Thus, RANKL-dependent repression of SELENOW maintains proper osteoclast differentiation and blocks osteoporosis caused by overactive osteoclasts. These findings demonstrate a biological link between selenium and bone metabolism.

physiology↗

bioRxiv2017

Holographic deep learning for rapid optical screening of anthrax spores

Establishing early warning systems for anthrax attacks is crucial in biodefense. Here we present an optical method for rapid screening of Bacillus anthracis spores through the synergistic application of holographic microscopy and deep learning. A deep convolutional neural network is designed to classify holographic images of unlabeled living cells. After training, the network outperforms previous techniques in all accuracy measures, achieving single-spore sensitivity and sub-genus specificity. The unique representation learning capability of deep learning enables direct training from raw images instead of manually extracted features. The method automatically recognizes key biological traits encoded in the images and exploits them as fingerprints. This remarkable learning ability makes the proposed method readily applicable to classifying various single cells in addition to B. anthracis, as demonstrated for the diagnosis of Listeria monocytogenes, without any modification. We believe that our strategy will make holographic microscopy more accessible to medical doctors and biomedical scientists for easy, rapid, and accurate diagnosis of pathogens, and facilitate exciting new applications.

microbiology↗