Browsing by Author "Lin, Pei-Yi"

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An Informatics-assisted Label-free Approach for Personalized Tissue Membrane Proteomics: Case Study on Colorectal Cancer
(2011-04-01)
Han, Chia-Li
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Chen, Jinn-Shiun
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Chan, Err-Cheng
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Wu, Chien-Peng
;
Yu, Kun-Hsing
We developed a multiplexed label-free quantification strategy, which integrates an efficient gel-assisted digestion protocol, high-performance liquid chromatography tandem MS analysis, and a bioinformatics alignment method to determine personalized proteomic profiles for membrane proteins in human tissues. This strategy provided accurate (6% error) and reproducible (34% relative S. D.) quantification of three independently purified membrane fractions from the same human colorectal cancer (CRC) tissue. Using CRC as a model, we constructed the personalized membrane protein atlas of paired tumor and adjacent normal tissues from 28 patients with different stages of CRC. Without fractionation, this strategy confidently quantified 856 proteins (>= 2 unique peptides) across different patients, including the first and robust detection (Mascot score: 22,074) of the well-documented CRC marker, carcinoembryonic antigen 5 by a discovery-type proteomics approach. Further validation of a panel of proteins, annexin A4, neutrophils defensin A1, and claudin 3, confirmed differential expression levels and high occurrences (48-70%) in 60 CRC patients. The most significant discovery is the overexpression of stomatin-like 2 (STOML2) for early diagnostic and prognostic potential. Increased expression of STOML2 was associated with decreased CRC-related survival; the mean survival period was 34.77 +/- 2.03 months in patients with high STOML2 expression, whereas 53.67 +/- 3.46 months was obtained for patients with low STOML2 expression. Further analysis by ELISA verified that plasma concentrations of STOML2 in early-stage CRC patients were elevated as compared with those of healthy individuals (p < 0.001), suggesting that STOML2 may be a noninvasive serological biomarker for early CRC diagnosis. The overall sensitivity of STOML2 for CRC detection was 71%, which increased to 87% when combined with CEA measurements. This study demonstrated a sensitive, label-free strategy for differential analysis of tissue membrane proteome, which may provide a roadmap for the subsequent identification of molecular target candidates of multiple cancer types. Molecular & Cellular Proteomics 10: 10.1074/mcp.M110.003087, 1-15, 2011.
Capulet and Slingshot share overlapping functions during Drosophila eye morphogenesis
(1970-01-01)
Lin, Chiao-Ming
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Lin, Pei-Yi
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Li, Yu-Chiao
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Hsu, Jui-Chou
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生物科技學系
"Background: CAP/Capulet (Capt), Slingshot (Ssh) and Cofilin/Twinstar (Tsr) are actin-binding proteins that restrict actin polymerization. Previously, it was shown that low resolution analyses of loss-of-function mutations in capt, ssh and tsr all show ectopic F-actin accumulation in various Drosophila tissues. In contrast, RNAi depletion of capt, tsr and ssh in Drosophila S2 cells all affect actin-based lamella formation differently. Whether loss of these three related genes might cause the same effect in the same tissue remains unclear. Methods: Loss-of-function mutant clones were generated using the MARCM or EGUF system whereas overexpression clones were generated using the Flip-out system. Immunostaining were then performed in eye imaginal discs with clones. FRAP was performed in cultured eye discs. Results: Here, we compared their loss-of-function phenotype at single-cell resolution, using a sheet of epithelial cells in the Drosophila eye imaginal disc as a model system. Surprisingly, we found that capt and ssh, but not tsr, mutant cells within and posterior to the morphogenetic furrow (MF) shared similar phenotypes. The capt/ssh mutant cells possessed: (1) hexagonal cell packing with discontinuous adherens junctions; and (2) largely complementary accumulation of excessive phosphorylated myosin light chain (p-MLC) and F-actin rings at the apical cortex. We further showed that the capt/ssh mutant phenotypes depended on the inactivation of protein kinase A (PKA) and activation of Rho. Conclusions: Although Capt, Ssh and Tsr were reported to negatively regulate actin polymerization, we found that Capt and Ssh, but not Tsr, share overlapping functions during eye morphogenesis."
Mechanically encoded single-photon sources: Stress-controlled excitonic fine structures of droplet epitaxial quantum dots
(2015-03-20)
Cheng, Shun-Jen
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Liao, Yu-Huai
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Lin, Pei-Yi
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電子物理學系
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Department of Electrophysics
We present numerical investigations based on the Luttinger-Kohn four-band k . p theory and, accordingly, establish a quantitatively valid model of the excitonic fine structures of droplet epitaxial GaAs/AlGaAs quantum dots under uniaxial stress control. In the formalisms, stressing a photoexcited quantum dot is equivalent creating a pseudomagnetic field that is directly coupled to the pseudospin of the exciton doublet and tunable to tailor the polarized fine structure of exciton. The latter feature is associated with the valence-band mixing of exciton, which is especially sensitive to external stress in inherently unstrained droplet epitaxial GaAs/AlGaAs quantum dots and allows us to mechanically design and prepare any desired exciton states of QD photon sources prior to the photon generation.
Novel transport function of adherens junction revealed by live imaging in Drosophila
(2015-08-07)
Li, Yu-Chiao
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Yang, Wen-Ting
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Cheng, Lien-Chieh
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Lin, Chiao-Ming
;
Ho, Yu-Huei
Adherens junctions are known for their role in mediating cell cell adhesion. DE-cadherin and Echinoid are the principle adhesion molecules of adherens junctions in Drosophila epithelia. Here, using live imaging to trace the movement of endocytosed Echinoid vesicles in the epithelial cells of Drosophila embryos, we demonstrate that Echinoid vesicles co-localize and move with Rab5-or Rab11-positive endosomes. Surprisingly, these Echinoid-containing endosomes undergo directional cell-to-cell movement, through adherens junctions. Consistent with this, cell-to-cell movement of Echinoid vesicles requires the presence of DE-cadherin at adherens junctions. Live imaging further revealed that Echinoid vesicles move along adherens junction-associated microtubules into adjacent cells, a process requiring a kinesin motor. Importantly, DE-cadherin- and EGFR-containing vesicles also exhibit intercellular movement. Together, our results unveil a transport function of adherens junctions. Furthermore, this adherens junctions-based intercellular transport provides a platform for the exchange of junctional proteins and signaling receptors between neighboring cells. (C) 2015 Elsevier Inc. All rights reserved.
Orientations of ZnO grown on GaN(10(1)over-bar1)
(2015-01-01)
Shih, Yi-Sen
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Lin, Pei-Yi
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Wei, Lin-Lung
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Chang, Li
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材料科學與工程學系
On semipolar GaN(10 (1) over bar1), epitaxial ZnO grown by chemical vapor deposition consists of two distinct orientations as evidenced by transmission electron microscopy and X-ray diffraction. The initially grown ZnO on GaN follows the GaN lattice with the epitaxial relationship of ZnO(10 (1) over bar1)//GaN(10 (1) over bar1) and ZnO GaN [1 (2) over bar 10](ZnO)//[1 (2) over bar 10](ZnO). The other oriented ZnO domains then grow on faceted (10 (1) over bar1) ZnO with ZnO(0002)//ZnO(10 (1) over bar1) and [(2) over bar 110](ZnO)//[1 (1) over bar0 (1) over bar](ZnO) with good coherency with the (10 (1) over bar1) -oriented grains. (C) 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression
(2020-07-09)
Chen, Yi-Ju
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Roumeliotis, Theodoros, I
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Chang, Ya-Hsuan
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Chen, Ching-Tai
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Han, Chia-Li
Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype of this demographically distinct disease, we performed a deep comprehensive proteogenomic study on a prospectively collected cohort in Taiwan, representing early stage, predominantly female, non-smoking lung adenocarcinoma. Integrated genomic, proteomic, and phosphoproteomic analysis delineated the demographically distinct molecular attributes and hallmarks of tumor progression. Mutational signature analysis revealed age- and gender-related mutagenesis mechanisms, characterized by high prevalence of APOBEC mutational signature in younger females and over-representation of environmental carcinogen-like mutational signatures in older females. A proteomics-informed classification distinguished the clinical characteristics of early stage patients with EGFR mutations. Furthermore, integrated protein network analysis revealed the cellular remodeling underpinning clinical trajectories and nominated candidate biomarkers for patient stratification and therapeutic intervention. This multi-omic molecular architecture may help develop strategies for management of early stage never-smoker lung adenocarcinoma.