State Key Laboratory of Oncogenes and Related Genes

Shanghai, China

State Key Laboratory of Oncogenes and Related Genes

Shanghai, China
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Zhang Y.,State Key Laboratory of Oncogenes and Related Genes | Qiu Y.,Institute of Medical science and Translational Medicine Collaborative Innovation Center | Lin L.,State Key Laboratory of Oncogenes and Related Genes | Gu H.,State Key Laboratory of Oncogenes and Related Genes | And 4 more authors.
ACS Applied Materials and Interfaces | Year: 2017

Surface-enhanced Raman scattering (SERS) tags can be utilized as optical labeling nanoprobes similar to fluorescent dyes and quantum dots for bioimaging with additional advantages of fingerprint vibrational signals as unique optical codes and ultranarrow line widths for multiplexing. However, the development of the SERS imaging technique is much less well-established compared to the devlopment of fluorescence imaging mainly because of speed limitations. An effective strategy for improving the SERS imaging speed and simultaneously maintaining the photostability of SERS tags has not, to the best of our knowledge, been reported. In this work, mesoporous silica-(MS-) coated gap-enhanced Raman tags (GERTs) were designed with builtin Raman reporters for off-resonance near-infrared laser excitation and reduced photothermal effects, leading to ultraphotostability during laser irradiation. Additionally, they achieve large amplification of Raman signals by combining the chemical (CHEM) and electromagnetic (EM) enhancement effects due to the subnanometer core-shell junction, so SERS imaging can be performed in a dramatically reduced duration. With these unique structural and optical advantages, MS GERTs exhibit high storage, pH, serum, and photostabilities; strong Raman enhancements; and favorable biocompatibility. Therefore, MS GERTs achieve long-term cell imaging that can last for 30 min without being photobleached and also maintain decent imaging effects. Furthermore, MS GERTs enable continuous and stable imaging in living tissues for more than 30 min. With these advantages, MS GERTs might potentially have more biomedical applications. © 2017 American Chemical Society.

Tu S.,Shanghai JiaoTong University | Tu S.,State Key Laboratory of Oncogenes and Related Genes | Jiang H.-W.,Shanghai JiaoTong University | Jiang H.-W.,State Key Laboratory of Oncogenes and Related Genes | And 6 more authors.
Current Pharmaceutical Design | Year: 2014

Protein microarray technology is one of the most powerful tools presently available for proteomic studies. Numerous types of protein microarrays have been widely and successfully applied for both basic biological studies and clinical researches, including those designed to characterize protein-protein, protein-nucleic acid, protein-drug/small molecule and antibody-antigen interactions. In the past decade, a variety of protein microarrays have been developed, including those spotted with whole proteomes, smaller peptides, antibodies, and lectins. Featured as high-throughput, miniaturized, and capable of parallel analysis, the power of protein microarrays has already been demonstrated many times in both basic research and clinical applications. In this review, we have summarized the latest developments in the production and application of protein microarrays. We discuss several of the most important applications of protein microarray, ranging from proteome microarrays for large scale identification of protein-protein interactions to lectin microarrays for live cell surface glycan profiling, with special emphasis on their use in studies of drug mechanisms and biomarker discovery. Already with tremendous success, we envision protein microarrays will become an indispensible tool for any systems-wide studies, fostering the integration of basic research observations to clinically useful applications. © 2014 Bentham Science Publishers.

Li Y.,Shanghai JiaoTong University | Li Y.,State Key Laboratory of Oncogenes and Related Genes | Guo S.-J.,Shanghai JiaoTong University | Guo S.-J.,State Key Laboratory of Oncogenes and Related Genes | And 11 more authors.
Lab on a Chip - Miniaturisation for Chemistry and Biology | Year: 2011

Both basic research and clinical medicine have urgent demands for highly efficient strategies to simultaneously identify many different DNA sequences within a single tube. Effective and simultaneous amplification of multiple target sequences is a prerequisite for any successful multiple nucleic acid detection method. Multiplex PCR is one of the best choices for this purpose. However, due to the intrinsic interference and competition among primer pairs in the same tube, multiple rounds of highly empirical optimization procedures are usually required to establish a successful multiplex PCR reaction. To address this challenge, we report here a universal multiplex PCR strategy that is capable of over 100-plex amplification using a specially designed microarray in which hydrophilic microwells are patterned on a hydrophobic chip. On such an array, primer pairs tagged with a universal sequence are physically separated in individual hydrophilic microwells on an otherwise hydrophobic chip, enabling many unique PCR reactions to be proceeded simultaneously during the first step of the procedure. The PCR products are then isolated and further amplified from the universal sequences, producing a sufficient amount of material for analysis by conventional gel electrophoresis or DNA microarray technology. This strategy is abbreviated as "MPH&HPM" for "Multiplex PCR on a Hydrophobically and Hydrophilically Patterned Microarray". The feasibility of this method is first demonstrated by a multiplex PCR reaction for the simultaneous detection of eleven pneumonia-causing pathogens. Further, we demonstrate the power of this strategy with a highly successful 116-plex PCR reaction that required only little prior optimization. The effectiveness of the MPH&HPM strategy with clinical samples is then illustrated with the detection of deleted exons of the Duchenne Muscular Dystrophy (DMD) gene, the results are in excellent agreement with the clinical records. Because of its generality, simplicity, flexibility, specificity and capacity of more than 100-plex amplification, the MPH&HPM strategy should have broad applications in both laboratory research and clinical applications when multiplex nucleic acid analysis is required. © The Royal Society of Chemistry 2011.

Shao N.,Shanghai JiaoTong University | Shao N.,State Key Laboratory of Oncogenes and Related Genes | Jiang S.-M.,Shanghai JiaoTong University | Zhang M.,Shanghai JiaoTong University | And 13 more authors.
Analytical Chemistry | Year: 2014

The monitoring of genetically modified organisms (GMOs) is a primary step of GMO regulation. However, there is presently a lack of effective and high-throughput methodologies for specifically and sensitively monitoring most of the commercialized GMOs. Herein, we developed a multiplex amplification on a chip with readout on an oligo microarray (MACRO) system specifically for convenient GMO monitoring. This system is composed of a microchip for multiplex amplification and an oligo microarray for the readout of multiple amplicons, containing a total of 91 targets (18 universal elements, 20 exogenous genes, 45 events, and 8 endogenous reference genes) that covers 97.1% of all GM events that have been commercialized up to 2012. We demonstrate that the specificity of MACRO is ∼100%, with a limit of detection (LOD) that is suitable for real-world applications. Moreover, the results obtained of simulated complex samples and blind samples with MACRO were 100% consistent with expectations and the results of independently performed real-time PCRs, respectively. Thus, we believe MACRO is the first system that can be applied for effectively monitoring the majority of the commercialized GMOs in a single test. © 2013 American Chemical Society.

Deng R.-P.,Shanghai JiaoTong University | Deng R.-P.,State Key Laboratory of Oncogenes and Related Genes | He X.,Shanghai JiaoTong University | He X.,State Key Laboratory of Oncogenes and Related Genes | And 6 more authors.
Proteomics | Year: 2014

O-Linked β-N-acetylglucosamine (O-GlcNAcylation) is an important protein PTM, which is very abundant in mammalian cells. O-GlcNAcylation is catalyzed by O-GlcNAc transferase (OGT), whose substrate specificity is believed to be regulated through interactions with other proteins. There are a handful of known human OGT interactors, which is far from enough for fully elucidating the substrate specificity of OGT. To address this challenge, we used a human proteome microarray containing ~17 000 affinity-purified human proteins to globally identify OGT interactors and identified 25 OGT-binding proteins. Bioinformatics analysis showed that these interacting proteins play a variety of roles in a wide range of cellular functions and are highly enriched in intra-Golgi vesicle-mediated transport and vitamin biosynthetic processes. Combining newly identified OGT interactors with the interactors identified prior to this study, we have constructed the first OGT interactome. Bioinformatics analysis suggests that the OGT interactome plays important roles in protein transportation/localization and transcriptional regulation. The novel OGT interactors that we identified in this study could serve as a starting point for further functional analysis. Because of its high-throughput and parallel analysis capability, we strongly believe that protein microarrays could be easily applied for the global identification of regulators for other key enzymes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hu B.,Shanghai JiaoTong University | Niu X.,Shanghai JiaoTong University | Cheng L.,Shanghai JiaoTong University | Cheng L.,State Key Laboratory of Oncogenes and Related Genes | And 7 more authors.
Proteomics - Clinical Applications | Year: 2015

Cancer biomarkers are of potential use in early cancer diagnosis, anticancer therapy development, and monitoring the responses to treatments. Protein-based cancer biomarkers are major forms in use, as they are much easier to be monitored in body fluids or tissues. For cancer biomarker discovery, high-throughput techniques such as protein microarrays hold great promises, because they are capable of global unbiased monitoring but with a miniaturized format. In doing so, novel and cancer type specific biomarkers can be systematically discovered at an affordable cost. In this review, we give a relatively complete picture on protein microarrays applied to clinical samples for cancer biomarker discovery, and conclude this review with the future perspectives. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Xin A.-J.,Fudan University | Xin A.-J.,East China University of Science and Technology | Cheng L.,Shanghai JiaoTong University | Cheng L.,State Key Laboratory of Oncogenes and Related Genes | And 13 more authors.
Clinical Proteomics | Year: 2014

It is well known that cell surface glycans or glycocalyx play important roles in sperm motility, maturation and fertilization. A comprehensive profile of the sperm surface glycans will greatly facilitate both basic research (sperm glycobiology) and clinical studies, such as diagnostics of infertility. As a group of natural glycan binders, lectin is an ideal tool for cell surface glycan profiling. However, because of the lack of effective technology, only a few lectins have been tested for lectin-sperm binding profiles. To address this challenge, we have developed a procedure for high-Throughput probing of mammalian sperm with 91 lectins on lectin microarrays. Normal sperm from human, boar, bull, goat and rabbit were collected and analyzed on the lectin microarrays. Positive bindings of a set of ~50 lectins were observed for all the sperm of 5 species, which indicated a wide range of glycans are on the surface of mammalian sperm. Species specific lectin bindings were also observed. Clustering analysis revealed that the distances of the five species according to the lectin binding profiles are consistent with that of the genome sequence based phylogenetic tree except for rabbit. The procedure that we established in this study could be generally applicable for sperm from other species or defect sperm from the same species. We believe the lectin binding profiles of the mammalian sperm that we established in this study are valuable for both basic research and clinical studies. © 2014 Xin et al.; licensee BioMed Central Ltd.

Chen Y.,CAS Wuhan Institute of Hydrobiology | Chen Y.,University of Chinese Academy of Sciences | Yang L.-N.,University of Chinese Academy of Sciences | Yang L.-N.,Shanghai JiaoTong University | And 21 more authors.
Molecular and Cellular Proteomics | Year: 2013

Bcl2-associated athanogene 3(BAG3), a member of the BAG family of co-chaperones, plays a critical role in regulating apoptosis, development, cell motility, autophagy, and tumor metastasis and in mediating cell adaptive responses to stressful stimuli. BAG3 carries a BAG domain, a WW domain, and a proline-rich repeat (PXXP), all of which mediate binding to different partners. To elucidate BAG3's interaction network at the molecular level, we employed quantitative immunoprecipitation combined with knockdown and human proteome microarrays to comprehensively profile the BAG3 interactome in humans. We identified a total of 382 BAG3-interacting proteins with diverse functions, including transferase activity, nucleic acid binding, transcription factors, proteases, and chaperones, suggesting that BAG3 is a critical regulator of diverse cellular functions. In addition, we characterized interactions between BAG3 and some of its newly identified partners in greater detail. In particular, bioinformatic analysis revealed that the BAG3 interactome is strongly enriched in proteins functioning within the proteasome-ubiquitination process and that compose the proteasome complex itself, suggesting that a critical biological function of BAG3 is associated with the proteasome. Functional studies demonstrated that BAG3 indeed interacts with the proteasome and modulates its activity, sustaining cell survival and underlying resistance to therapy through the down-modulation of apoptosis. Taken as a whole, this study expands our knowledge of the BAG3 interactome, provides a valuable resource for understanding how BAG3 affects different cellular functions, and demonstrates that biologically relevant data can be harvested using this kind of integrated approach. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Zhou S.-M.,Shanghai JiaoTong University | Zhou S.-M.,State Key Laboratory of Oncogenes and Related Genes | Cheng L.,Shanghai JiaoTong University | Cheng L.,State Key Laboratory of Oncogenes and Related Genes | And 5 more authors.
Combinatorial Chemistry and High Throughput Screening | Year: 2011

Cell surfaces, especially mammalian cell surfaces, are heavily coated with complex poly- and oligosaccharides, and these glycans have been implicated in many functions, such as cell-to-cell communication, host-pathogen interactions and cell matrix interactions. Not surprisingly then, the aberrations of glycosylation are usually indicative of the onset of specific diseases, such as cancer. Therefore, glycans are expected to serve as important biomarkers for disease diagnosis and/or prognosis. Recent development of the lectin microarray technology has allowed researchers to profile the glycans in complex biological samples in a high throughput fashion. This relatively new tool is highly suitable for both live cell and cell lysate analyses and has the potential for rapid discovery of glycan-based biomarkers. In this review, we will focus on the basic concepts and the latest advances of lectin microarray technology. We will also emphasize the application of lectin microarrays for biomarker discovery, and then discuss the challenges faced by this technology and potential future directions. Based on the tremendous progress already achieved, it seems apparent that lectin microarrays will soon become an indispensible tool for glycosylation biomarker discovery. © 2011 Bentham Science Publishers Ltd.

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