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Bi X, Czajkowsky DM, Shao Z, Ye J. Digital colloid-enhanced Raman spectroscopy by single-molecule counting. Nature 2024; 628:771-775. [PMID: 38632399 DOI: 10.1038/s41586-024-07218-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/21/2024] [Indexed: 04/19/2024]
Abstract
Quantitative detection of various molecules at very low concentrations in complex mixtures has been the main objective in many fields of science and engineering, from the detection of cancer-causing mutagens and early disease markers to environmental pollutants and bioterror agents1-5. Moreover, technologies that can detect these analytes without external labels or modifications are extremely valuable and often preferred6. In this regard, surface-enhanced Raman spectroscopy can detect molecular species in complex mixtures on the basis only of their intrinsic and unique vibrational signatures7. However, the development of surface-enhanced Raman spectroscopy for this purpose has been challenging so far because of uncontrollable signal heterogeneity and poor reproducibility at low analyte concentrations8. Here, as a proof of concept, we show that, using digital (nano)colloid-enhanced Raman spectroscopy, reproducible quantification of a broad range of target molecules at very low concentrations can be routinely achieved with single-molecule counting, limited only by the Poisson noise of the measurement process. As metallic colloidal nanoparticles that enhance these vibrational signatures, including hydroxylamine-reduced-silver colloids, can be fabricated at large scale under routine conditions, we anticipate that digital (nano)colloid-enhanced Raman spectroscopy will become the technology of choice for the reliable and ultrasensitive detection of various analytes, including those of great importance for human health.
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Affiliation(s)
- Xinyuan Bi
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Daniel M Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jian Ye
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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2
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Zhang L, Hu C, Xu Z, Li H, Ye B, Li X, Czajkowsky DM, Shao Z. Quantitative catalogue of mammalian mitotic chromosome-associated RNAs. Sci Data 2024; 11:43. [PMID: 38184632 PMCID: PMC10771512 DOI: 10.1038/s41597-023-02884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
The faithful transmission of a cell's identity and functionality to its daughters during mitosis requires the proper assembly of mitotic chromosomes from interphase chromatin in a process that involves significant changes in the genome-bound material, including the RNA. However, our understanding of the RNA that is associated with the mitotic chromosome is presently limited. Here, we present complete and quantitative characterizations of the full-length mitotic chromosome-associated RNAs (mCARs) for 3 human cell lines, a monkey cell line, and a mouse cell line derived from high-depth RNA sequencing (3 replicates, 47 M mapped read pairs for each replicate). Overall, we identify, on average, more than 20,400 mCAR species per cell-type (including isoforms), more than 5,200 of which are enriched on the chromosome. Notably, overall, more than 2,700 of these mCARs were previously unknown, which thus also expands the annotated genome of these species. We anticipate that these datasets will provide an essential resource for future studies to better understand the functioning of mCARs on the mitotic chromosome and in the cell.
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Affiliation(s)
- Le Zhang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chuansheng Hu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zeqian Xu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hua Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bishan Ye
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinhui Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Daniel M Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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3
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Li Y, Wang J, Chen X, Czajkowsky DM, Shao Z. Quantitative Super-Resolution Microscopy Reveals the Relationship between CENP-A Stoichiometry and Centromere Physical Size. Int J Mol Sci 2023; 24:15871. [PMID: 37958853 PMCID: PMC10649757 DOI: 10.3390/ijms242115871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Centromeric chromatin is thought to play a critical role in ensuring the faithful segregation of chromosomes during mitosis. However, our understanding of this role is presently limited by our poor understanding of the structure and composition of this unique chromatin. The nucleosomal variant, CENP-A, localizes to narrow regions within the centromere, where it plays a major role in centromeric function, effectively serving as a platform on which the kinetochore is assembled. Previous work found that, within a given cell, the number of microtubules within kinetochores is essentially unchanged between CENP-A-localized regions of different physical sizes. However, it is unknown if the amount of CENP-A is also unchanged between these regions of different sizes, which would reflect a strict structural correspondence between these two key characteristics of the centromere/kinetochore assembly. Here, we used super-resolution optical microscopy to image and quantify the amount of CENP-A and DNA within human centromere chromatin. We found that the amount of CENP-A within CENP-A domains of different physical sizes is indeed the same. Further, our measurements suggest that the ratio of CENP-A- to H3-containing nucleosomes within these domains is between 8:1 and 11:1. Thus, our results not only identify an unexpectedly strict relationship between CENP-A and microtubules stoichiometries but also that the CENP-A centromeric domain is almost exclusively composed of CENP-A nucleosomes.
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Affiliation(s)
- Yaqian Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
| | - Jiabin Wang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Daniel M. Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
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4
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Chen X, Li Y, Li X, Sun J, Czajkowsky DM, Shao Z. Quasi-equilibrium state based quantification of biological macromolecules in single-molecule localization microscopy. Methods Appl Fluoresc 2023; 11:047001. [PMID: 37647910 DOI: 10.1088/2050-6120/acf546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
The stoichiometry of molecular components within supramolecular biological complexes is often an important property to understand their biological functioning, particularly within their native environment. While there are well established methods to determine stoichiometryin vitro, it is presently challenging to precisely quantify this propertyin vivo,especially with single molecule resolution that is needed for the characterization stoichiometry heterogeneity. Previous work has shown that optical microscopy can provide some information to this end, but it can be challenging to obtain highly precise measurements at higher densities of fluorophores. Here we provide a simple approach using already established procedures in single-molecule localization microscopy (SMLM) to enable precise quantification of stoichiometry within individual complexes regardless of the density of fluorophores. We show that by focusing on the number of fluorophore detections accumulated during the quasi equilibrium-state of this process, this method yields a 50-fold improvement in precision over values obtained from images with higher densities of active fluorophores. Further, we show that our method yields more correct estimates of stoichiometry with nuclear pore complexes and is easily adaptable to quantify the DNA content with nanodomains of chromatin within individual chromosomes inside cells. Thus, we envision that this straightforward method may become a common approach by which SMLM can be routinely employed for the accurate quantification of subunit stoichiometry within individual complexes within cells.
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Affiliation(s)
- Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Yaqian Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xiaowei Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Jielin Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Daniel M Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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5
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Jiang HW, Chen H, Zheng YX, Wang XN, Meng Q, Xie J, Zhang J, Zhang C, Xu ZW, Chen ZQ, Wang L, Kong WS, Zhou K, Ma ML, Zhang HN, Guo SJ, Xue JB, Hou JL, Liu ZY, Niu WX, Wang FJ, Wang T, Li W, Wang RN, Dang YJ, Czajkowsky DM, Pei J, Dong JJ, Tao SC. Specific pupylation as IDEntity reporter (SPIDER) for the identification of protein-biomolecule interactions. Sci China Life Sci 2023; 66:1869-1887. [PMID: 37059927 PMCID: PMC10103678 DOI: 10.1007/s11427-023-2316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 04/16/2023]
Abstract
Protein-biomolecule interactions play pivotal roles in almost all biological processes. For a biomolecule of interest, the identification of the interacting protein(s) is essential. For this need, although many assays are available, highly robust and reliable methods are always desired. By combining a substrate-based proximity labeling activity from the pupylation pathway of Mycobacterium tuberculosis and the streptavidin (SA)-biotin system, we developed the Specific Pupylation as IDEntity Reporter (SPIDER) method for identifying protein-biomolecule interactions. Using SPIDER, we validated the interactions between the known binding proteins of protein, DNA, RNA, and small molecule. We successfully applied SPIDER to construct the global protein interactome for m6A and mRNA, identified a variety of uncharacterized m6A binding proteins, and validated SRSF7 as a potential m6A reader. We globally identified the binding proteins for lenalidomide and CobB. Moreover, we identified SARS-CoV-2-specific receptors on the cell membrane. Overall, SPIDER is powerful and highly accessible for the study of protein-biomolecule interactions.
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Affiliation(s)
- He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yun-Xiao Zheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xue-Ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qingfeng Meng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Xie
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jiong Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200240, China
| | - ChangSheng Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zhao-Wei Xu
- Key Laboratory of Gastrointestinal Cancer, Fujian Medical University, Ministry of Education, Fuzhou, 350122, China
| | - Zi-Qing Chen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08540, USA
| | - Lei Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei-Sha Kong
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kuan Zhou
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming-Liang Ma
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun-Biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing-Li Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhe-Yi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wen-Xue Niu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Fang-Jun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tao Wang
- Institute of Systems Biology, Shenzhen Bay Laboratory, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wei Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Rui-Na Wang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200240, China
| | - Yong-Jun Dang
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, Chongqing, 400016, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - JianFeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Jia-Jia Dong
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200240, China.
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China.
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6
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Wei Y, Xu Z, Hu M, Wu Z, Liu A, Czajkowsky DM, Guo Y, Shao Z. Time-resolved transcriptomics of mouse gastric pit cells during postnatal development reveals features distinct from whole stomach development. FEBS Lett 2023; 597:418-426. [PMID: 36285639 DOI: 10.1002/1873-3468.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/27/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
Abstract
Whole-organ transcriptomic analyses have emerged as a common method for characterizing developmental transitions in mammalian organs. However, it is unclear if all cell types in an organ follow the whole-organ defined developmental trajectory. Recently, a postnatal two-stage developmental process was described for the mouse stomach. Here, using laser capture microdissection to obtain in situ transcriptomic data, we show that mouse gastric pit cells exhibit four postnatal developmental stages. Interestingly, early stages are characterized by the up-regulation of genes associated with metabolism, a functionality not typically associated with pit cells. Hence, beyond revealing that not all constituent cells develop according to the whole-organ determined pathway, these results broaden our understanding of the pit cell phenotypic landscape during stomach development.
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Affiliation(s)
- Ying Wei
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Zeqian Xu
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Miaomiao Hu
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Zhongqin Wu
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Axian Liu
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Yan Guo
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Zhifeng Shao
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
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7
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Wang J, Qin Y, Kang Y, Li X, Wang Y, Li H, Czajkowsky DM, Shao Z. Temporal profiling with ultra-deep RRBS sequencing reveals the relative rarity of stably maintained methylated CpG sites in human cells. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1935-1938. [PMID: 36789696 PMCID: PMC10157517 DOI: 10.3724/abbs.2022185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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8
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Chen X, Li Y, Wang J, Sun J, Czajkowsky DM, Shao Z. Expansion microscopy with carboxylic trifunctional linkers. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1386-1389. [PMID: 36017892 PMCID: PMC9828645 DOI: 10.3724/abbs.2022113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Xuecheng Chen
- Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Yaqian Li
- State Key Laboratory for Oncogenes and Bio-ID CenterSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Jiabin Wang
- Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jielin Sun
- Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China,Correspondence address. Tel: +86-21-34206632; (J.S.) / Tel: +86-21-34206632; (D.C.) @sjtu.edu.cn
| | - Daniel M. Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID CenterSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200240China,Correspondence address. Tel: +86-21-34206632; (J.S.) / Tel: +86-21-34206632; (D.C.) @sjtu.edu.cn
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID CenterSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200240China
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Wang J, Hu C, Chen X, Li Y, Sun J, Czajkowsky DM, Shao Z. Single-Molecule Micromanipulation and Super-Resolution Imaging Resolve Nanodomains Underlying Chromatin Folding in Mitotic Chromosomes. ACS Nano 2022; 16:8030-8039. [PMID: 35485433 DOI: 10.1021/acsnano.2c01025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The folding of interphase chromatin into highly compact mitotic chromosomes is one of the most recognizable changes during the cell cycle. However, the structural organization underlying this drastic compaction remains elusive. Here, we combine several super resolution methods, including structured illumination microscopy (SIM), binding-activated localization microscopy (BALM), and atomic force microscopy (AFM), to examine the structural details of the DNA within the mitotic chromosome, both in the native state and after up to 30-fold extension using single-molecule micromanipulation. Images of native chromosomes reveal widespread ∼125 nm compact granules (CGs) throughout the metaphase chromosome. However, at maximal extensions, we find exclusively ∼90 nm domains (mitotic nanodomains, MNDs) that are unexpectedly resistant to extensive forces of tens of nanonewtons. The DNA content of the MNDs is estimated to be predominantly ∼80 kb, which is comparable to the size of the inner loops predicted by a recent nested loop model of the mitotic chromosome. With this DNA content, the total volume expected of the human genome assuming closely packed MNDs is nearly identical to what is observed. Thus, altogether, these results suggest that these mechanically stable MNDs, and their higher-order assembly into CGs, are the dominant higher-level structures that underlie the compaction of chromatin from interphase to metaphase.
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Affiliation(s)
- Jiabin Wang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaqian Li
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jielin Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Zhang X, Hu C, Huang C, Wei Y, Li X, Hu M, Li H, Wu J, Czajkowsky DM, Guo Y, Shao Z. Robust Acquisition of Spatial Transcriptional Programs in Tissues With Immunofluorescence-Guided Laser Capture Microdissection. Front Cell Dev Biol 2022; 10:853188. [PMID: 35399504 PMCID: PMC8990165 DOI: 10.3389/fcell.2022.853188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
The functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue, as local interactions precipitate intra-cellular events that often lead to changes in expression. However, our understanding of these processes in tissues, whether healthy or diseased, is limited at present owing to the difficulty in acquiring comprehensive transcriptional programs of spatially- and phenotypically-defined cells in situ. Here we present a robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to acquire finely resolved transcriptional programs with as few as tens of cells from snap-frozen or RNAlater-treated clinical tissues sufficient to resolve even isoforms. The protocol is optimized to protect the RNA with a small molecule inhibitor, the ribonucleoside vanadyl complex (RVC), which thereby enables the typical time-consuming immunostaining and laser capture steps of this procedure during which RNA is usually severely degraded in existing approaches. The efficacy of this approach is exemplified by the characterization of differentially expressed genes between the mouse small intestine lacteal cells at the tip versus the main capillary body, including those that function in sensing and responding to local environmental cues to stimulate intra-cellular signalling. With the extensive repertoire of specific antibodies that are presently available, our method provides an unprecedented capability for the analysis of transcriptional networks and signalling pathways during development, pathogenesis, and aging of specific cell types within native tissues.
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Affiliation(s)
- Xiaodan Zhang
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Wei
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Miaomiao Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Bio-X Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M. Czajkowsky
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Yan Guo
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Zhifeng Shao
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
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11
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Shen Y, Fei F, Zhong Y, Fan C, Sun J, Hu J, Gong B, Czajkowsky DM, Shao Z. Controlling Water Flow through a Synthetic Nanopore with Permeable Cations. ACS Cent Sci 2021; 7:2092-2098. [PMID: 34963901 PMCID: PMC8704043 DOI: 10.1021/acscentsci.1c01218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Indexed: 05/19/2023]
Abstract
There is presently intense interest in the development of synthetic nanopores that recapitulate the functional properties of biological water channels for a wide range of applications. To date, all known synthetic water channels have a hydrophobic lumen, and while many exhibit a comparable rate of water transport as biological water channels, there is presently no rationally designed system with the ability to regulate water transport, a critical property of many natural water channels. Here, we describe a self-assembling nanopore consisting of stacked macrocyclic molecules with a hybrid hydrophilic/hydrophobic lumen exhibiting water transport that can be regulated by alkali metal ions. Stopped-flow kinetic assays reveal a non-monotonic-dependence of transport on cation size as well as a strikingly broad range of water flow, from essentially none in the presence of the sodium ion to as high a flow as that of the biological water channel, aquaporin 1, in the absence of the cations. All-atom molecular dynamics simulations show that the mechanism underlying the observed sensitivity is the binding of cations to defined sites within this hybrid pore, which perturbs water flow through the channel. Thus, beyond revealing insights into factors that can modulate a high-flux water transport through sub-nm pores, the obtained results provide a proof-of-concept for the rational design of next-generation, controllable synthetic water channels.
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Affiliation(s)
- Yi Shen
- School
of Biomedical Engineering, Shanghai Jiao
Tong University, Shanghai 200240, China
| | - Fan Fei
- School
of Biomedical Engineering, Shanghai Jiao
Tong University, Shanghai 200240, China
| | - Yulong Zhong
- Department
of Chemistry, The State University of New
York at Buffalo, Buffalo, New York 14260, United States
| | - Chunhai Fan
- School
of Chemistry and Chemical Engineering, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Jielin Sun
- Shanghai
Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Jun Hu
- Key
Laboratory of Interfacial Physics and Technology, Shanghai Synchrotron
Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Bing Gong
- Department
of Chemistry, The State University of New
York at Buffalo, Buffalo, New York 14260, United States
| | - Daniel M. Czajkowsky
- School
of Biomedical Engineering, Shanghai Jiao
Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- School
of Biomedical Engineering, Shanghai Jiao
Tong University, Shanghai 200240, China
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12
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Alam MS, Czajkowsky DM. SARS-CoV-2 infection and oxidative stress: Pathophysiological insight into thrombosis and therapeutic opportunities. Cytokine Growth Factor Rev 2021; 63:44-57. [PMID: 34836751 PMCID: PMC8591899 DOI: 10.1016/j.cytogfr.2021.11.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023]
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic has presented unprecedented challenges to global health. Although the majority of COVID-19 patients exhibit mild-to-no symptoms, many patients develop severe disease and need immediate hospitalization, with most severe infections associated with a dysregulated immune response attributed to a cytokine storm. Epidemiological studies suggest that overall COVID-19 severity and morbidity correlate with underlying comorbidities, including diabetes, obesity, cardiovascular diseases, and immunosuppressive conditions. Patients with such comorbidities exhibit elevated levels of reactive oxygen species (ROS) and oxidative stress caused by an increased accumulation of angiotensin II and by activation of the NADPH oxidase pathway. Moreover, accumulating evidence suggests that oxidative stress coupled with the cytokine storm contribute to COVID-19 pathogenesis and immunopathogenesis by causing endotheliitis and endothelial cell dysfunction and by activating the blood clotting cascade that results in blood coagulation and microvascular thrombosis. In this review, we survey the mechanisms of how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces oxidative stress and the consequences of this stress on patient health. We further shed light on aspects of the host immunity that are crucial to prevent the disease during the early phase of infection. A better understanding of the disease pathophysiology as well as preventive measures aimed at lowering ROS levels may pave the way to mitigate SARS-CoV-2-induced complications and decrease mortality.
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Affiliation(s)
- Mohammad Shah Alam
- Department of Anatomy and Histology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh.
| | - Daniel M Czajkowsky
- Bio-ID Centre, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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13
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Liu Y, Li H, Czajkowsky DM, Shao Z. Monocytic THP-1 cells diverge significantly from their primary counterparts: a comparative examination of the chromosomal conformations and transcriptomes. Hereditas 2021; 158:43. [PMID: 34740370 PMCID: PMC8569982 DOI: 10.1186/s41065-021-00205-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022] Open
Abstract
Immortalized cell lines have long been used as model systems to systematically investigate biological processes under controlled and reproducible conditions, providing insights that have greatly advanced cellular biology and medical sciences. Recently, the widely used monocytic leukemia cell line, THP-1, was comprehensively examined to understand mechanistic relationships between the 3D chromatin structure and transcription during the trans-differentiation of monocytes to macrophages. To corroborate these observations in primary cells, we analyze in situ Hi-C and RNA-seq data of human primary monocytes and their differentiated macrophages in comparison to that obtained from the monocytic/macrophagic THP-1 cells. Surprisingly, we find significant differences between the primary cells and the THP-1 cells at all levels of chromatin structure, from loops to topologically associated domains to compartments. Importantly, the compartment-level differences correlate significantly with transcription: those genes that are in A-compartments in the primary cells but are in B-compartments in the THP-1 cells exhibit a higher level of expression in the primary cells than in the THP-1 cells, and vice versa. Overall, the genes in these different compartments are enriched for a wide range of pathways, and, at least in the case of the monocytic cells, their altered expression in certain pathways in the THP-1 cells argues for a less immune cell-like phenotype, suggesting that immortalization or prolonged culturing of THP-1 caused a divergence of these cells from their primary counterparts. It is thus essential to reexamine phenotypic details observed in cell lines with their primary counterparts so as to ensure a proper understanding of functional cell states in vivo.
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Affiliation(s)
- Yulong Liu
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hua Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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14
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Shah Alam M, Czajkowsky DM, Aminul Islam M, Ataur Rahman M. The role of vitamin D in reducing SARS-CoV-2 infection: An update. Int Immunopharmacol 2021; 97:107686. [PMID: 33930705 PMCID: PMC8052476 DOI: 10.1016/j.intimp.2021.107686] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is having a disastrous impact on global health. Recently, several studies examined the potential of vitamin D to reduce the effects of SARS-CoV-2 infection by modulating the immune system. Indeed, vitamin D has been found to boost the innate immune system and stimulate the adaptive immune response against SARS-CoV-2 infection. In this review, we provide a comprehensive update of the immunological mechanisms underlying the positive effects of vitamin D in reducing SARS-CoV-2 infection as well as a thorough survey of the recent epidemiological studies and clinical trials that tested vitamin D as a potential therapeutic agent against COVID-19 infection. We believe that a better understanding of the histopathology and immunopathology of the disease as well as the mechanism of vitamin D effects on COVID-19 severity will ultimately pave the way for a more effective prevention and control of this global pandemic.
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Affiliation(s)
- Mohammad Shah Alam
- Department of Anatomy and Histology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.
| | - Daniel M Czajkowsky
- Bio-ID Centre, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Md Aminul Islam
- Department of Medicine, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md Ataur Rahman
- Department of Surgery and Radiology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
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15
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Zhang N, Li X, Czajkowsky DM, Zhang H, Alam MS, Shao Z. Efficient and Fast Immuno-Labeling of Clarified Tissues Using Low-Field Enhanced Diffusion. IEEE Trans Biomed Eng 2021; 68:3301-3307. [PMID: 33788676 DOI: 10.1109/tbme.2021.3070146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To alleviate the severe limitation of the prohibitively long process of immune-fluorescence labeling on the routine applications of revolutionary intact tissue clearing techniques in diverse biomedical arenas. METHODS We proposed an easily adaptable approach, electro-enhanced rapid staining (EERS), for highly efficient and fast immuno-labeling of thick clarified tissues. In EERS, an optimized and precisely controlled weak external electric field is engineered into a compact device to enable efficient and uniform transport of antibodies into clarified tissues while minimizing the detrimental effect of macromolecular crowding at the tissue-solution interface. RESULTS AND CONCLUSIONS The experimental results show that, with EERS, a current density of only ∼0.2 mA mm-2 is sufficient to achieve uniform labeling of clarified tissues of several millimeters thick in a few hours without detectable tissue damage. In addition, the amount of antibodies required is also several-fold lower than conventional immuno-labeling assays under comparable conditions. SIGNIFICANCE It is expected that the implementation of EERS in most laboratories should significantly expedite the application of tissue clearing in a broad range of research explorations, both basic and clinical.
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16
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Liu X, Sun Q, Wang Q, Hu C, Chen X, Li H, Czajkowsky DM, Shao Z. Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions. Genomics Proteomics Bioinformatics 2021; 20:101-109. [PMID: 33631432 PMCID: PMC9510857 DOI: 10.1016/j.gpb.2020.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/09/2020] [Accepted: 08/09/2020] [Indexed: 02/07/2023]
Abstract
Recent studies have characterized the genomic structures of many eukaryotic cells, often focusing on their relation to gene expression. However, these studies have largely investigated cells grown in 2D cultures, although the transcriptomes of 3D-cultured cells are generally closer to their in vivo phenotypes. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in higher-order genomic interactions, notably in compartment identity and strength as well as in topologically associating domain (TAD)–TAD interactions, but only minor differences are found at the TAD level. Our RNA-seq analysis reveals an up-regulated expression of genes involved in physiological hepatocyte functions in the 3D-cultured cells. These genes are associated with a subset of structural changes, suggesting that differences in genomic structure are critically important for transcriptional regulation. However, there are also many structural differences that are not directly associated with changes in gene expression, whose cause remains to be determined. Overall, our results indicate that growth in 3D significantly alters higher-order genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
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Affiliation(s)
- Xin Liu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiu Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Chuansheng Hu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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17
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Wang W, Zhang N, Du Y, Gao J, Li M, Lin L, Czajkowsky DM, Li X, Yang C, Shao Z. Three‐Dimensional Quantitative Imaging of Native Microbiota Distribution in the Gut. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Wei Wang
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Ni Zhang
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yahui Du
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Juan Gao
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Min Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Liyuan Lin
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Daniel M. Czajkowsky
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Xiaowei Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Chaoyong Yang
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
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18
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Sun Q, Perez-Rathke A, Czajkowsky DM, Shao Z, Liang J. High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis. Nat Commun 2021; 12:205. [PMID: 33420075 PMCID: PMC7794469 DOI: 10.1038/s41467-020-20490-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
Single-cell chromatin studies provide insights into how chromatin structure relates to functions of individual cells. However, balancing high-resolution and genome wide-coverage remains challenging. We describe a computational method for the reconstruction of large 3D-ensembles of single-cell (sc) chromatin conformations from population Hi-C that we apply to study embryogenesis in Drosophila. With minimal assumptions of physical properties and without adjustable parameters, our method generates large ensembles of chromatin conformations via deep-sampling. Our method identifies specific interactions, which constitute 5-6% of Hi-C frequencies, but surprisingly are sufficient to drive chromatin folding, giving rise to the observed Hi-C patterns. Modeled sc-chromatins quantify chromatin heterogeneity, revealing significant changes during embryogenesis. Furthermore, >50% of modeled sc-chromatin maintain topologically associating domains (TADs) in early embryos, when no population TADs are perceptible. Domain boundaries become fixated during development, with strong preference at binding-sites of insulator-complexes upon the midblastula transition. Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization.
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Affiliation(s)
- Qiu Sun
- Shanghai Center for System Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Alan Perez-Rathke
- Department of Bioengineering, University of Illinois at Chicago, SEO, MC-063, Chicago, IL, 60607-7052, USA
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhifeng Shao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, SEO, MC-063, Chicago, IL, 60607-7052, USA.
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19
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Wang W, Zhang N, Du Y, Gao J, Li M, Lin L, Czajkowsky DM, Li X, Yang C, Shao Z. Three‐Dimensional Quantitative Imaging of Native Microbiota Distribution in the Gut. Angew Chem Int Ed Engl 2020; 60:3055-3061. [DOI: 10.1002/anie.202010921] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/13/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Wei Wang
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Ni Zhang
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yahui Du
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Juan Gao
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Min Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Liyuan Lin
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Daniel M. Czajkowsky
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Xiaowei Li
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Chaoyong Yang
- Institute of Molecular Medicine (IMM) Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes & Related Genes and Bio-ID Center School of Biomedical Engineering Shanghai Jiao Tong University Shanghai 200240 China
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20
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Zhang Z, Wang Q, Liu Y, Sun Q, Li H, Czajkowsky DM, Shao Z. Massive reorganization of the genome during primary monocyte differentiation into macrophage. Acta Biochim Biophys Sin (Shanghai) 2020; 52:546-553. [PMID: 32324846 DOI: 10.1093/abbs/gmaa026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 12/20/2019] [Accepted: 02/24/2020] [Indexed: 12/13/2022] Open
Abstract
Monocyte-to-macrophage trans-differentiation has long been studied to better understand this immunological response and aspects of developmental processes more generally. A key question is the nature of the corresponding changes in chromatin conformation and its relationship to the transcriptome during this process. This question is especially intriguing since this trans-differentiation is not associated with progression through mitosis, often considered a necessary step for gross changes in chromosomal structure. Here, we characterized the transcriptional and genomic structural changes during macrophage development of primary human monocytes using RNA-seq and in situ Hi-C. We found that, during this transition, the genome architecture undergoes a massive remodeling to a degree not observed before between structured genomes, with changes in ~90% of the topologically associating domains (TADs). These changes in the TADs are associated with changed expression of immunological genes. These structural changes, however, differ extensively from those described recently in a study of the leukemia cell line, THP-1. Furthermore, up-regulation of the AP-1 family of genes that effected functionally important changes in the genomic structure during the differentiation of the THP-1 cells was not corroborated with the primary cells. Taken together, our results provide a comprehensive characterization of the changes in genomic structure during the monocyte-to-macrophage transition, establish a framework for the elucidation of processes underlying differentiation without proliferation, and demonstrate the importance of verifying with primary cells the mechanisms discovered with cultured cells.
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Affiliation(s)
- Zhipeng Zhang
- State Key Laboratory for Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Wang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Yulong Liu
- State Key Laboratory for Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiu Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- State Key Laboratory for Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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21
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Shen Y, Zhong Y, Fei F, Sun J, Czajkowsky DM, Gong B, Shao Z. Ultrasensitive liposome-based assay for the quantification of fundamental ion channel properties. Anal Chim Acta 2020; 1112:8-15. [PMID: 32334685 DOI: 10.1016/j.aca.2020.03.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/16/2020] [Accepted: 03/22/2020] [Indexed: 10/24/2022]
Abstract
One of the most widely used approaches to characterize transmembrane ion transport through nanoscale synthetic or biological channels is a straightforward, liposome-based assay that monitors changes in ionic flux across the vesicle membrane using pH- or ion-sensitive dyes. However, failure to account for the precise experimental conditions, in particular the complete ionic composition on either side of the membrane and the inherent permeability of ions through the lipid bilayer itself, can prevent quantifications and lead to fundamentally incorrect conclusions. Here we present a quantitative model for this assay based on the Goldman-Hodgkin-Katz flux theory, which enables accurate measurements and identification of optimal conditions for the determination of ion channel permeability and selectivity. Based on our model, the detection sensitivity of channel permeability is improved by two orders of magnitude over the commonly used experimental conditions. Further, rather than obtaining qualitative preferences of ion selectivity as is typical, we determine quantitative values of these parameters under rigorously controlled conditions even when the experimental results would otherwise imply (without our model) incorrect behavior. We anticipate that this simply employed ultrasensitive assay will find wide application in the quantitative characterization of synthetic or biological ion channels.
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Affiliation(s)
- Yi Shen
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yulong Zhong
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, NY, 14260, United States
| | - Fan Fei
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jielin Sun
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bing Gong
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, NY, 14260, United States.
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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22
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Ni J, Hu C, Li H, Li X, Fu Q, Czajkowsky DM, Guo Y, Shao Z. Significant improvement in data quality with simplified SCRB-seq. Acta Biochim Biophys Sin (Shanghai) 2020; 52:457-459. [PMID: 32147694 DOI: 10.1093/abbs/gmaa007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/17/2019] [Accepted: 12/26/2019] [Indexed: 01/23/2023] Open
Affiliation(s)
- Jian Ni
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinhui Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiong Fu
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory for Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Guo
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory for Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory for Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
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23
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Liu W, Guo Y, Wang K, Zhou X, Wang Y, Lü J, Shao Z, Hu J, Czajkowsky DM, Li B. Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches. Nanoscale 2019; 11:17206-17210. [PMID: 31535117 DOI: 10.1039/c9nr05234h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Atomic force microscopy-based single-molecule-force spectroscopy is limited by low throughput. We introduce addressable DNA origami to study multiple target molecules. Six target DNAs that differed by only a single base-pair mismatch were clearly differentiated a rupture force of only 4 pN.
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Affiliation(s)
- Wenjing Liu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yourong Guo
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Kaizhe Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingfei Zhou
- School of Science, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Ying Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Junhong Lü
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jun Hu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China and School of Physical Science and Technology, Shanghai Tech University, Shanghai 201204, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bin Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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24
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Zhang J, Yang Y, Yang S, Song J, Wang Y, Liu X, Yang Q, Shen Y, Wang S, Yang H, Lü J, Li B, Fang H, Lal R, Czajkowsky DM, Hu J, Shi G, Zhang Y. Unconventional Atomic Structure of Graphene Sheets on Solid Substrates. Small 2019; 15:e1902637. [PMID: 31468738 DOI: 10.1002/smll.201902637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/25/2019] [Indexed: 06/10/2023]
Abstract
The atomic structure of free-standing graphene comprises flat hexagonal rings with a 2.5 Å period, which is conventionally considered the only atomic period and determines the unique properties of graphene. Here, an unexpected highly ordered orthorhombic structure of graphene is directly observed with a lattice constant of ≈5 Å, spontaneously formed on various substrates. First-principles computations show that this unconventional structure can be attributed to the dipole between the graphene surface and substrates, which produces an interfacial electric field and induces atomic rearrangement on the graphene surface. Further, the formation of the orthorhombic structure can be controlled by an artificially generated interfacial electric field. Importantly, the 5 Å crystal can be manipulated and transformed in a continuous and reversible manner. Notably, the orthorhombic lattice can control the epitaxial self-assembly of amyloids. The findings reveal new insights about the atomic structure of graphene, and open up new avenues to manipulate graphene lattices.
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Affiliation(s)
- Jinjin Zhang
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yizhou Yang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai, 200444, China
| | - Shuo Yang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Wang
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xiaoguo Liu
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Qingqing Yang
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yue Shen
- Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
| | - Shuo Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Haijun Yang
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Junhong Lü
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Bin Li
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Haiping Fang
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Ratnesh Lal
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hu
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Guosheng Shi
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai, 200444, China
| | - Yi Zhang
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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25
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Xu Z, Zhang H, Zhang X, Jiang H, Liu C, Wu F, Qian L, Hao B, Czajkowsky DM, Guo S, Xu Z, Bi L, Wang S, Li H, Tan M, Yan W, Feng L, Hou J, Tao SC. Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP. EMBO J 2019; 38:e100948. [PMID: 31418899 DOI: 10.15252/embj.2018100948] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/05/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis, and DNA supercoiling in many bacteria. Using an Escherichia coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Further, protein deacetylation assays showed that c-di-GMP inhibits the activity of CobB and thereby modulates the biogenesis of acetyl-CoA. Interestingly, we also found that one of the key enzymes directly involved in c-di-GMP production, DgcZ, is a substrate of CobB. Deacetylation of DgcZ by CobB enhances its activity and thus the production of c-di-GMP. Our work establishes a novel negative feedback loop linking c-di-GMP biogenesis and CobB-mediated protein deacetylation.
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Affiliation(s)
- Zhaowei Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hainan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xingrun Zhang
- MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Hewei Jiang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chengxi Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fanlin Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lili Qian
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bingbing Hao
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shujuan Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijing Xu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lijun Bi
- National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Shihua Wang
- School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Feng
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Jingli Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
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26
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Chen J, Zhu C, Wang C, Hu C, Czajkowsky DM, Guo Y, Liu B, Shao Z. Evidence for heightened genetic instability in precancerous spasmolytic polypeptide expressing gastric glands. J Med Genet 2019; 57:385-388. [PMID: 30877236 DOI: 10.1136/jmedgenet-2018-105752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 02/02/2019] [Accepted: 02/06/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Spasmolytic polypeptide-expressing metaplasia (SPEM) is present in more than 90% of resected gastric cancer tissues. However, although widely regarded as a pre-cancerous tissue, its genetic characteristics have not been well studied. METHODS Immunohistochemistry using Trefoil factor 2 (TFF2) antibodies was used to identify TFF2-positive SPEM cells within SPEM glands in the stomach of Helicobacter felis (H. felis) -infected mice and human clinical samples. Laser microdissection was used to isolate specific cells from both the infected mice and the human samples. The genetic instability in these cells was examined by measuring the lengths of microsatellite (MS) markers using capillary electrophoresis. Also, genome-wide genetic variations in the SPEM cells from the clinical sample was examined using deep whole-exome sequencing. RESULTS SPEM cells indeed exhibit not only heightened MS instability (MSI), but also genetic instabilities that extend genome-wide. Furthermore, surprisingly, we found that morphologically normal, TFF2-negative cells also contain a comparable degree of genomic instabilities as the co-resident SPEM cells within the SPEM glands. CONCLUSION These results, for the first time, clearly establish elevated genetic instability as a critical property of SPEM glands, which may provide a greater possibility for malignant clone selection. More importantly, these results indicate that SPEM cells may not be the sole origin of carcinogenesis in the stomach and strongly suggest the common progenitor of these cells, the stem cells, as the source of these genetic instabilities, and thus, potential key players in carcinogenesis.
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Affiliation(s)
- Jiangrong Chen
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaojie Wang
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Guo
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
| | - Bingya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
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27
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Chen J, Zhu C, Wang C, Zhang X, Ni J, Czajkowsky DM, Liu B, Guo Y. Discovery and genetic characterization of intestinal metaplasia in the Helicobacter felis-infected mouse model of gastric cancer. Acta Biochim Biophys Sin (Shanghai) 2019; 51:219-222. [PMID: 30576406 DOI: 10.1093/abbs/gmy160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/20/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jiangrong Chen
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chunchao Zhu
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaojie Wang
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaodan Zhang
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Ni
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Bingya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Guo
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory for Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai, China
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28
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Cheng L, Liu CX, Jiang S, Hou S, Huang JG, Chen ZQ, Sun YY, Qi H, Jiang HW, Wang JF, Zhou YM, Czajkowsky DM, Dai J, Tao SC. Cell Lysate Microarray for Mapping the Network of Genetic Regulators for Histone Marks. Mol Cell Proteomics 2018; 17:1720-1736. [PMID: 29871872 DOI: 10.1074/mcp.ra117.000550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/22/2018] [Indexed: 11/06/2022] Open
Abstract
Proteins, as the major executer for cell progresses and functions, its abundance and the level of post-translational modifications, are tightly monitored by regulators. Genetic perturbation could help us to understand the relationships between genes and protein functions. Herein, to explore the impact of the genome-wide interruption on certain protein, we developed a cell lysate microarray on kilo-conditions (CLICK) with 4837 knockout (YKO) and 322 temperature-sensitive (ts) mutant strains of yeast (Saccharomyces cerevisiae). Taking histone marks as examples, a general workflow was established for the global identification of upstream regulators. Through a single CLICK array test, we obtained a series of regulators for H3K4me3, which covers most of the known regulators in S. cerevisiae We also noted that several group of proteins are involved in negatively regulation of H3K4me3. Further, we discovered that Cab4p and Cab5p, two key enzymes of CoA biosynthesis, play central roles in histone acylation. Because of its general applicability, CLICK array could be easily adopted to rapid and global identification of upstream protein/enzyme(s) that regulate/modify the level of a protein or the posttranslational modification of a non-histone protein.
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Affiliation(s)
- Li Cheng
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China.,§Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Cheng-Xi Liu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Shuangying Jiang
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Sha Hou
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Jin-Guo Huang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zi-Qing Chen
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yang-Yang Sun
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Huan Qi
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - He-Wei Jiang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jing-Fang Wang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yi-Ming Zhou
- ¶Beijing NeoAntigen Biotechnology Co. Ltd, Beijing, 102206, PR China
| | - Daniel M Czajkowsky
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Junbiao Dai
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China;
| | - Sheng-Ce Tao
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China;
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29
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Fang K, Chen X, Li X, Shen Y, Sun J, Czajkowsky DM, Shao Z. Super-resolution Imaging of Individual Human Subchromosomal Regions in Situ Reveals Nanoscopic Building Blocks of Higher-Order Structure. ACS Nano 2018; 12:4909-4918. [PMID: 29715004 DOI: 10.1021/acsnano.8b01963] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It is widely recognized that the higher-order spatial organization of the genome, beyond the nucleosome, plays an important role in many biological processes. However, to date, direct information on even such fundamental structural details as the typical sizes and DNA content of these higher-order structures in situ is poorly characterized. Here, we examine the nanoscopic DNA organization within human nuclei using super-resolution direct stochastic optical reconstruction microscopy (dSTORM) imaging and 5-ethynyl-2'-deoxyuridine click chemistry, studying single fully labeled chromosomes within an otherwise unlabeled nuclei to improve the attainable resolution. We find that, regardless of nuclear position, individual subchromosomal regions consist of three different levels of DNA compaction: (i) dispersed chromatin; (ii) nanodomains of sizes ranging tens of nanometers containing a few kilobases (kb) of DNA; and (iii) clusters of nanodomains. Interestingly, the sizes and DNA content of the nanodomains are approximately the same at the nuclear periphery, nucleolar proximity, and nuclear interior, suggesting that these nanodomains share a roughly common higher-order architecture. Overall, these results suggest that DNA compaction within the eukaryote nucleus occurs via the condensation of DNA into few-kb nanodomains of approximately similar structure, with further compaction occurring via the clustering of nanodomains.
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30
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Jiang HW, Czajkowsky DM, Wang T, Wang XD, Wang JB, Zhang HN, Liu CX, Wu FL, He X, Xu ZW, Chen H, Guo SJ, Li Y, Bi LJ, Deng JY, Xie J, Pei JF, Zhang XE, Tao SC. Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis. EBioMedicine 2018; 30:225-236. [PMID: 29622495 PMCID: PMC5952411 DOI: 10.1016/j.ebiom.2018.03.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 12/26/2022] Open
Abstract
Owing to the spread of multidrug resistance (MDR) and extensive drug resistance (XDR), there is a pressing need to identify potential targets for the development of more-effective anti-M. tuberculosis (Mtb) drugs. PafA, as the sole Prokaryotic Ubiquitin-like Protein ligase in the Pup-proteasome System (PPS) of Mtb, is an attractive drug target. Here, we show that the activity of purified Mtb PafA is significantly inhibited upon the association of AEBSF (4-(2-aminoethyl) benzenesulfonyl fluoride) to PafA residue Serine 119 (S119). Mutation of S119 to amino acids that resemble AEBSF has similar inhibitory effects on the activity of purified Mtb PafA. Structural analysis reveals that although S119 is distant from the PafA catalytic site, it is located at a critical position in the groove where PafA binds the C-terminal region of Pup. Phenotypic studies demonstrate that S119 plays critical roles in the function of Mtb PafA when tested in M. smegmatis. Our study suggests that targeting S119 is a promising direction for developing an inhibitor of M. tuberculosis PafA. The pupylation activity of purified M. tuberculosis PafA is almost completely inhibited upon the association of AEBSF. The AEBSF binding site, Ser 119 plays critical roles in both the pupylation and depupylation activity of purified M. tuberculosis PafA. Disruption of purified M. tuberculosis PafA Ser 119 causes a dramatic reduction in Pup binding.
Drug-resistant tuberculosis is a major challenge worldwide, there is an urgent need to identify potential drug targets for developing more effective anti-tubercular drugs. M. tuberculosis ubiquitin-like protein ligase PafA is an attractive drug target, however, effective PafA inhibitors have not yet been identified. Here, we show that interruption of a single amino acid, S119, causes dramatic loss of PafA activity. S119 could thus serve as a promising precise target for developing M. tuberculosis PafA inhibitors.
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Affiliation(s)
- He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai 200240, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China; SZCDC-SUSTech Joint Key Laboratory for Tropical Diseases, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xu-De Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jia-Bin Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng-Xi Liu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan-Lin Wu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiang He
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Wei Xu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Jun Bi
- National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; TB Healthcare Biotechnology Co., Ltd., Foshan, Guangdong 528000, China; School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China
| | - Jiao-Yu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jin Xie
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jian-Feng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.
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31
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Wang Q, Sun Q, Czajkowsky DM, Shao Z. Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells. Nat Commun 2018; 9:188. [PMID: 29335463 PMCID: PMC5768742 DOI: 10.1038/s41467-017-02526-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/06/2017] [Indexed: 01/19/2023] Open
Abstract
Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D. melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified. The overwhelming majority of these TADs are demarcated by the insulator complexes, BEAF-32/CP190, or BEAF-32/Chromator, indicating that these proteins may play an analogous role in flies as that of CTCF/cohesin in mammals. Moreover, extended regions previously thought to be unstructured are shown to consist of small contiguous TADs, a property also observed in mammals upon re-examination. Altogether, our work demonstrates that fundamental features associated with the higher-order folding of the genome are conserved from insects to mammals.
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Affiliation(s)
- Qi Wang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Qiu Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China.
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China.
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32
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Wu FL, Liu Y, Jiang HW, Luan YZ, Zhang HN, He X, Xu ZW, Hou JL, Ji LY, Xie Z, Czajkowsky DM, Yan W, Deng JY, Bi LJ, Zhang XE, Tao SC. The Ser/Thr Protein Kinase Protein-Protein Interaction Map of M. tuberculosis. Mol Cell Proteomics 2017; 16:1491-1506. [PMID: 28572091 DOI: 10.1074/mcp.m116.065771] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/28/2017] [Indexed: 01/16/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions. Bioinformatics analysis showed that the interacting proteins reflect diverse functions, including roles in two-component system, transcription, protein degradation, and cell wall integrity. Functional investigations confirmed that PknG regulates cell wall integrity through key components of peptidoglycan (PG) biosynthesis, e.g. MurC. The global STPK-KPIs network constructed here is expected to serve as a rich resource for understanding the key signaling pathways in Mtb, thus facilitating drug development and effective control of Mtb.
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Affiliation(s)
- Fan-Lin Wu
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,§State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Liu
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,§State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,§State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi-Zhao Luan
- ¶State Key Lab of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yatsen University, Guangzhou 500040, China
| | - Hai-Nan Zhang
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,§State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiang He
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,§State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.,‖School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhao-Wei Xu
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,§State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing-Li Hou
- **Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Yun Ji
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhi Xie
- ¶State Key Lab of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yatsen University, Guangzhou 500040, China
| | - Daniel M Czajkowsky
- ‖School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Yan
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jiao-Yu Deng
- ‡‡State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Li-Jun Bi
- §§National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,¶¶School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China.,‖‖Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan 528000, China
| | - Xian-En Zhang
- §§National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; .,§State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.,‖School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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33
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Lai M, Li X, Li J, Hu Y, Czajkowsky DM, Shao Z. Improved clearing of lipid droplet-rich tissues for three-dimensional structural elucidation. Acta Biochim Biophys Sin (Shanghai) 2017; 49:465-467. [PMID: 28338831 DOI: 10.1093/abbs/gmx018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Indexed: 01/25/2023] Open
Affiliation(s)
- Mengjie Lai
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaowei Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jun Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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34
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Cao H, Shen Y, Sun Y, Tao SC, Czajkowsky DM, Shao Z. Toward the development of magnetic tweezers for high-throughput measurement of protein-protein interactions. Acta Biochim Biophys Sin (Shanghai) 2017; 49:468-470. [PMID: 28369167 DOI: 10.1093/abbs/gmx027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Haowen Cao
- School of Biomedical Engineering, Bio-ID Center,Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Shen
- School of Biomedical Engineering, Bio-ID Center,Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yangyang Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education), State Key Laboratory of Oncogenes and Related Genes, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), State Key Laboratory of Oncogenes and Related Genes, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Bio-ID Center,Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- School of Biomedical Engineering, Bio-ID Center,Shanghai Jiao Tong University, Shanghai 200240, China
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35
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Qin L, Zhang J, Sun J, Czajkowsky DM, Shao Z. Development of a low-noise cryogenic atomic force microscope for high resolution imaging of large biological complexes. Acta Biochim Biophys Sin (Shanghai) 2016; 48:859-61. [PMID: 27521793 DOI: 10.1093/abbs/gmw074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ling Qin
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinjin Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Jiading Campus , Shanghai 201800, China
| | - Jielin Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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36
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Li H, Hu C, Bai L, Li H, Li M, Zhao X, Czajkowsky DM, Shao Z. Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryos reveals hundreds of conserved translated sORFs. DNA Res 2016; 23:571-580. [PMID: 27559081 PMCID: PMC5144680 DOI: 10.1093/dnares/dsw040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022] Open
Abstract
There is growing recognition that small open reading frames (sORFs) encoding peptides shorter than 100 amino acids are an important class of functional elements in the eukaryotic genome, with several already identified to play critical roles in growth, development, and disease. However, our understanding of their biological importance has been hindered owing to the significant technical challenges limiting their annotation. Here we combined ultra-deep sequencing of ribosome-associated poly-adenylated RNAs with rigorous conservation analysis to identify a comprehensive population of translated sORFs during early Drosophila embryogenesis. In total, we identify 399 sORFs, including those previously annotated but without evidence of translational capacity, those found within transcripts previously classified as non-coding, and those not previously known to be transcribed. Further, we find, for the first time, evidence for translation of many sORFs with different isoforms, suggesting their regulation is as complex as longer ORFs. Furthermore, many sORFs are found not associated with ribosomes in late-stage Drosophila S2 cells, suggesting that many of the translated sORFs may have stage-specific functions during embryogenesis. These results thus provide the first comprehensive annotation of the sORFs present during early Drosophila embryogenesis, a necessary basis for a detailed delineation of their function in embryogenesis and other biological processes.
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Affiliation(s)
- Hongmei Li
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ling Bai
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingfa Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Zhao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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37
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Guo Y, Huang A, Hu C, Zhou Y, Zhang X, Czajkowsky DM, Li J, Cheng S, Shen R, Gu J, Liu B, Shao Z. Complex clonal mosaicism within microdissected intestinal metaplastic glands without concurrent gastric cancer. J Med Genet 2016; 53:643-6. [DOI: 10.1136/jmedgenet-2016-103872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/18/2016] [Indexed: 12/22/2022]
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38
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Zhang Y, Tang Y, Sun S, Wang Z, Wu W, Zhao X, Czajkowsky DM, Li Y, Tian J, Xu L, Wei W, Deng Y, Shi Q. Single-cell codetection of metabolic activity, intracellular functional proteins, and genetic mutations from rare circulating tumor cells. Anal Chem 2016; 87:9761-8. [PMID: 26378744 DOI: 10.1021/acs.analchem.5b01901] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The high glucose uptake and activation of oncogenic signaling pathways in cancer cells has long made these features, together with the mutational spectrum, prime diagnostic targets of circulating tumor cells (CTCs). Further, an ability to characterize these properties at a single cell resolution is widely believed to be essential, as the known extensive heterogeneity in CTCs can obscure important correlations in data obtained from cell population-based methods. However, to date, it has not been possible to quantitatively measure metabolic, proteomic, and genetic data from a single CTC. Here we report a microchip-based approach that allows for the codetection of glucose uptake, intracellular functional proteins, and genetic mutations at the single-cell level from rare tumor cells. The microchip contains thousands of nanoliter grooves (nanowells) that isolate individual CTCs and allow for the assessment of their glucose uptake via imaging of a fluorescent glucose analog, quantification of a panel of intracellular signaling proteins using a miniaturized antibody barcode microarray, and retrieval of the individual cell nuclei for subsequent off-chip genome amplification and sequencing. This approach integrates molecular-scale information on the metabolic, proteomic, and genetic status of single cells and permits the inference of associations between genetic signatures, energy consumption, and phosphoproteins oncogenic signaling activities in CTCs isolated from blood samples of patients. Importantly, this microchip chip-based approach achieves this multidimensional molecular analysis with minimal cell loss (<20%), which is the bottleneck of the rare cell analysis.
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Affiliation(s)
| | | | | | | | | | | | | | - Yan Li
- Shanghai Municipal Hospital of Traditional Chinese Medicine , Shanghai 200071, P.R. China
| | - Jianhui Tian
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine , Shanghai 200032, P.R. China
| | - Ling Xu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine , Shanghai 200032, P.R. China
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States
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39
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Meng Y, Yi X, Li X, Hu C, Wang J, Bai L, Czajkowsky DM, Shao Z. The non-coding RNA composition of the mitotic chromosome by 5'-tag sequencing. Nucleic Acids Res 2016; 44:4934-46. [PMID: 27016738 PMCID: PMC4889943 DOI: 10.1093/nar/gkw195] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/15/2016] [Indexed: 12/16/2022] Open
Abstract
Mitotic chromosomes are one of the most commonly recognized sub-cellular structures in eukaryotic cells. Yet basic information necessary to understand their structure and assembly, such as their composition, is still lacking. Recent proteomic studies have begun to fill this void, identifying hundreds of RNA-binding proteins bound to mitotic chromosomes. However, by contrast, there are only two RNA species (U3 snRNA and rRNA) that are known to be associated with the mitotic chromosome, suggesting that there are many mitotic chromosome-associated RNAs (mCARs) not yet identified. Here, using a targeted protocol based on 5'-tag sequencing to profile the mammalian mCAR population, we report the identification of 1279 mCARs, the majority of which are ncRNAs, including lncRNAs that exhibit greater conservation across 60 vertebrate species than the entire population of lncRNAs. There is also a significant enrichment of snoRNAs and specific SINE RNAs. Finally, ∼40% of the mCARs are presently unannotated, many of which are as abundant as the annotated mCARs, suggesting that there are also many novel ncRNAs in the mCARs. Overall, the mCARs identified here, together with the previous proteomic and genomic data, constitute the first comprehensive catalogue of the molecular composition of the eukaryotic mitotic chromosomes.
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Affiliation(s)
- Yicong Meng
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Xinhui Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Ling Bai
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
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40
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Tu S, Guo SJ, Chen CS, Liu CX, Jiang HW, Ge F, Deng JY, Zhou YM, Czajkowsky DM, Li Y, Qi BR, Ahn YH, Cole PA, Zhu H, Tao SC. YcgC represents a new protein deacetylase family in prokaryotes. eLife 2015; 4. [PMID: 26716769 PMCID: PMC4709262 DOI: 10.7554/elife.05322] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 10/28/2015] [Indexed: 01/08/2023] Open
Abstract
Reversible lysine acetylation is one of the most important protein posttranslational modifications that plays essential roles in both prokaryotes and eukaryotes. However, only a few lysine deacetylases (KDACs) have been identified in prokaryotes, perhaps in part due to their limited sequence homology. Herein, we developed a ‘clip-chip’ strategy to enable unbiased, activity-based discovery of novel KDACs in the Escherichia coli proteome. In-depth biochemical characterization confirmed that YcgC is a serine hydrolase involving Ser200 as the catalytic nucleophile for lysine deacetylation and does not use NAD+ or Zn2+ like other established KDACs. Further, in vivo characterization demonstrated that YcgC regulates transcription by catalyzing deacetylation of Lys52 and Lys62 of a transcriptional repressor RutR. Importantly, YcgC targets a distinct set of substrates from the only known E. coli KDAC CobB. Analysis of YcgC’s bacterial homologs confirmed that they also exhibit KDAC activity. YcgC thus represents a novel family of prokaryotic KDACs. DOI:http://dx.doi.org/10.7554/eLife.05322.001 After proteins have been made, they can be modified in several ways. For example, chemical tags called acetyl groups may be added to (and later removed from) the protein to regulate cell activities such as aging and metabolism. Enzymes are proteins that help catalyze the reactions that add or remove the acetyl tags on certain “substrate” proteins. In the bacteria species Escherichia coli, many enzymes that help to add acetyl groups to proteins have been discovered. However, only a single E. coli “deacetylase” enzyme that removes the acetyl group has been identified. Now, Tu, Guo, Chen et al. have devised a technique to identify new deacetylases, called the “clip-chip” approach. In this method, thousands of proteins that are potential deacetylases are arrayed on a glass slide, and substrate proteins are immobilized on another slide. The two slides are then clipped together face-to-face, allowing the potential enzymes to transfer to the substrate slide and interact with the substrates. Using this approach, Tu, Guo, Chen et al. identified a protein called YcgC as a deacetylase in bacteria. Further characterization experiments revealed that YcgC works in a different way to other known deacetylases, and that it targets different substrates to the previously known E. coli deacetylase. Tu, Guo, Chen et al. found that the equivalents of YcgC in other bacteria species are also deacetylases; these enzymes therefore represent a new deacetylase family. In the future, the clip-chip approach could be used to discover new members of other enzyme families. DOI:http://dx.doi.org/10.7554/eLife.05322.002
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Affiliation(s)
- Shun Tu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
| | - Cheng-Xi Liu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jiao-Yu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yi-Ming Zhou
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Bang-Ruo Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Young-Hoon Ahn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States.,The High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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41
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Czajkowsky DM, Sun J, Shao Z. Single molecule compression reveals intra-protein forces drive cytotoxin pore formation. eLife 2015; 4:e08421. [PMID: 26652734 PMCID: PMC4714976 DOI: 10.7554/elife.08421] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/12/2015] [Indexed: 11/13/2022] Open
Abstract
Perfringolysin O (PFO) is a prototypical member of a large family of pore-forming proteins that undergo a significant reduction in height during the transition from the membrane-assembled prepore to the membrane-inserted pore. Here, we show that targeted application of compressive forces can catalyze this conformational change in individual PFO complexes trapped at the prepore stage, recapitulating this critical step of the spontaneous process. The free energy landscape determined from these measurements is in good agreement with that obtained from molecular dynamics simulations showing that an equivalent internal force is generated by the interaction of the exposed hydrophobic residues with the membrane. This hydrophobic force is transmitted across the entire structure to produce a compressive stress across a distant, otherwise stable domain, catalyzing its transition from an extended to compact conformation. Single molecule compression is likely to become an important tool to investigate conformational transitions in membrane proteins. DOI:http://dx.doi.org/10.7554/eLife.08421.001 Proteins are made up of chains of amino acids that need to fold into intricate three-dimensional shapes to work correctly. But some proteins also have to change their shape drastically when they work. Mechanical forces that change the shape of a protein can therefore be used to determine how a protein folds and how it changes its structure when working. Although researchers have developed techniques to analyze the effect of force on single proteins, most studies carried out so far have investigated the effect of stretching (or tensile forces) to understand structural changes that naturally involve an extension within the protein. However, many proteins undergo structural changes that involve a compaction in their shape. How these changes occur remains poorly understood because, for these, methods to apply compressive forces to single proteins are required. Perfringolysin O (PFO for short) is a protein that is made by a bacterium that causes food poisoning in humans. PFO makes pores in the membrane that surrounds cells. This causes the cell’s contents to leak out, killing the cell. When inserting into the membrane, PFO changes from an elongated “prepore” state to a compact pore-forming state. Czajkowsky et al. now use a combination of single molecule techniques and computer simulations to investigate how PFO undergoes this compaction. Previous work had identified a mutant PFO protein that arrests at the prepore state. Applying a compressive force to the top of this prepore-trapped PFO as it sits on the membrane transmitted forces across the entire PFO protein. This ultimately produced a compressive force across a distant part of the protein that caused the protein to change from the elongated prepore state to the compact, pore-like shape. If a compressive force was not applied, the PFO protein remained in the prepore state. Czajkowsky et al. further found that this compressive force is naturally produced by distant water-repellent parts of the naturally occurring protein interacting with the cell membrane. Therefore, internal forces can transmit across proteins to drive shape changes in distant regions. In the future, the methods developed in this study could be applied to analyze other naturally occurring changes in proteins where shape compaction happens when working. DOI:http://dx.doi.org/10.7554/eLife.08421.002
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Affiliation(s)
- Daniel M Czajkowsky
- State Key Laboratory of Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jielin Sun
- State Key Laboratory of Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhifeng Shao
- State Key Laboratory of Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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Semblat JP, Ghumra A, Czajkowsky DM, Wallis R, Mitchell DA, Raza A, Rowe JA. Identification of the minimal binding region of a Plasmodium falciparum IgM binding PfEMP1 domain. Mol Biochem Parasitol 2015; 201:76-82. [PMID: 26094597 PMCID: PMC4539346 DOI: 10.1016/j.molbiopara.2015.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/22/2015] [Accepted: 06/08/2015] [Indexed: 11/29/2022]
Abstract
Many pathogens bind the Fc region of host immunoglobulin to evade immunity. We examined a Plasmodium falciparum IgM binding PfEMP1 domain TM284var1 DBL4ζ. We identified the minimal IgM binding region comprising subdomain 2 and flanking regions. Specific charged amino acids were mutated but did not markedly affect IgM binding. Existing models of PfEMP1-IgM interaction need to be revised.
Binding of host immunoglobulin is a common immune evasion mechanism demonstrated by microbial pathogens. Previous work showed that the malaria parasite Plasmodium falciparum binds the Fc-region of human IgM molecules, resulting in a coating of IgM on the surface of infected erythrocytes. IgM binding is a property of P. falciparum strains showing virulence-related phenotypes such as erythrocyte rosetting. The parasite ligands for IgM binding are members of the diverse P. falciparum Erythrocyte Membrane Protein One (PfEMP1) family. However, little is known about the amino acid sequence requirements for IgM binding. Here we studied an IgM binding domain from a rosette-mediating PfEMP1 variant, DBL4ζ of TM284var1, and found that the minimal IgM binding region mapped to the central region of the DBL domain, comprising all of subdomain 2 and adjoining parts of subdomains 1 and 3. Site-directed mutagenesis of charged amino acids within subdomain 2, predicted by molecular modelling to form the IgM binding site, showed no marked effect on IgM binding properties. Overall, this study identifies the minimal IgM binding region of a PfEMP1 domain, and indicates that the existing homology model of PfEMP1-IgM interaction is incorrect. Further work is needed to identify the specific interaction site for IgM within the minimal binding region of PfEMP1.
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Affiliation(s)
- Jean-Philippe Semblat
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Ashfaq Ghumra
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Russell Wallis
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Daniel A Mitchell
- Clinical Sciences Research Laboratories, Warwick Medical School, Coventry CV2 2DX, United Kingdom
| | - Ahmed Raza
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - J Alexandra Rowe
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom.
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Czajkowsky DM, Andersen JT, Fuchs A, Wilson TJ, Mekhaiel D, Colonna M, He J, Shao Z, Mitchell DA, Wu G, Dell A, Haslam S, Lloyd KA, Moore SC, Sandlie I, Blundell PA, Pleass RJ. Developing the IVIG biomimetic, hexa-Fc, for drug and vaccine applications. Sci Rep 2015; 5:9526. [PMID: 25912958 PMCID: PMC5224519 DOI: 10.1038/srep09526] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/26/2015] [Indexed: 12/20/2022] Open
Abstract
The remarkable clinical success of Fc-fusion proteins has driven intense investigation for even more potent replacements. Using quality-by-design (QbD) approaches, we generated hexameric-Fc (hexa-Fc), a ~20 nm oligomeric Fc-based scaffold that we here show binds low-affinity inhibitory receptors (FcRL5, FcγRIIb, and DC-SIGN) with high avidity and specificity, whilst eliminating significant clinical limitations of monomeric Fc-fusions for vaccine and/or cancer therapies, in particular their poor ability to activate complement. Mass spectroscopy of hexa-Fc reveals high-mannose, low-sialic acid content, suggesting that interactions with these receptors are influenced by the mannose-containing Fc. Molecular dynamics (MD) simulations provides insight into the mechanisms of hexa-Fc interaction with these receptors and reveals an unexpected orientation of high-mannose glycans on the human Fc that provides greater accessibility to potential binding partners. Finally, we show that this biosynthetic nanoparticle can be engineered to enhance interactions with the human neonatal Fc receptor (FcRn) without loss of the oligomeric structure, a crucial modification for these molecules in therapy and/or vaccine strategies where a long plasma half-life is critical.
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Affiliation(s)
- Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 P. R. China
| | - Jan Terje Andersen
- Centre for Immune Regulation (CIR) and Department of Immunology, Oslo University Hospital Rikshospitalet, P.O. Box 4956, Oslo N-0424, Norway
| | - Anja Fuchs
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy J Wilson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Mekhaiel
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jianfeng He
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 P. R. China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 P. R. China
| | - Daniel A Mitchell
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry CV2 2DX, UK
| | - Gang Wu
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7
| | - Anne Dell
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7
| | - Stuart Haslam
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7
| | - Katy A Lloyd
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Shona C Moore
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Inger Sandlie
- 1] Centre for Immune Regulation (CIR) and Department of Immunology, Oslo University Hospital Rikshospitalet, P.O. Box 4956, Oslo N-0424, Norway [2] CIR and Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Patricia A Blundell
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Richard J Pleass
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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Zhou SM, Cheng L, Guo SJ, Wang Y, Czajkowsky DM, Gao H, Hu XF, Tao SC. Lectin RCA-I specifically binds to metastasis-associated cell surface glycans in triple-negative breast cancer. Breast Cancer Res 2015; 17:36. [PMID: 25848723 PMCID: PMC4384317 DOI: 10.1186/s13058-015-0544-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 03/02/2015] [Indexed: 01/09/2023] Open
Abstract
Introduction Triple-negative breast cancer (TNBC) patients often face a high risk of early relapse characterized by extensive metastasis. Previous works have shown that aberrant cell surface glycosylation is associated with cancer metastasis, suggesting that altered glycosylations might serve as diagnostic signatures of metastatic potential. To address this question, we took TNBC as an example and analyzed six TNBC cell lines, derived from a common progenitor, that differ in metastatic potential. Methods We used a microarray with 91 lectins to screen for altered lectin bindings to the six TNBC cell lines. Candidate lectins were then verified by lectin-based flow cytometry and immunofluorescent staining assays using both TNBC/non-TNBC cancer cells. Patient-derived tissue microarrays were then employed to analyze whether the staining of Ricinus communis agglutinin I (RCA-I), correlated with TNBC severity. We also carried out real-time cell motility assays in the presence of RCA-I. Finally, liquid chromatography-mass spectrometry/tandem spectrometry (LC-MS/MS) was employed to identify the membrane glycoproteins recognized by RCA-I. Results Using the lectin microarray, we found that the bindings of RCA-I to TNBC cells are proportional to their metastatic capacity. Tissue microarray experiments showed that the intensity of RCA-I staining is positively correlated with the TNM grades. The real-time cell motility assays clearly demonstrated RCA-I inhibition of adhesion, migration, and invasion of TNBC cells of high metastatic capacity. Additionally, a membrane glycoprotein, POTE ankyrin domain family member F (POTEF), with different galactosylation extents in high/low metastatic TNBC cells was identified by LC-MS/MS as a binder of RCA-I. Conclusions We discovered RCA-I, which bound to TNBC cells to a degree that is proportional to their metastatic capacities, and found that this binding inhibits the cell invasion, migration, and adhesion, and identified a membrane protein, POTEF, which may play a key role in mediating these effects. These results thus indicate that RCA-I-specific cell surface glycoproteins may play a critical role in TNBC metastasis and that the extent of RCA-I cell binding could be used in diagnosis to predict the likelihood of developing metastases in TNBC patients. Electronic supplementary material The online version of this article (doi:10.1186/s13058-015-0544-9) contains supplementary material, which is available to authorized users.
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Czajkowsky DM, Sun J, Shao Z. Illuminated up close: near-field optical microscopy of cell surfaces. Nanomedicine: Nanotechnology, Biology and Medicine 2015; 11:119-25. [DOI: 10.1016/j.nano.2014.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/10/2014] [Indexed: 01/22/2023]
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Deng Y, Zhang Y, Sun S, Wang Z, Wang M, Yu B, Czajkowsky DM, Liu B, Li Y, Wei W, Shi Q. An integrated microfluidic chip system for single-cell secretion profiling of rare circulating tumor cells. Sci Rep 2014; 4:7499. [PMID: 25511131 PMCID: PMC4266859 DOI: 10.1038/srep07499] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/27/2014] [Indexed: 02/08/2023] Open
Abstract
Genetic and transcriptional profiling, as well as surface marker identification of single circulating tumor cells (CTCs) have been demonstrated. However, quantitatively profiling of functional proteins at single CTC resolution has not yet been achieved, owing to the limited purity of the isolated CTC populations and a lack of single-cell proteomic approaches to handle and analyze rare CTCs. Here, we develop an integrated microfluidic system specifically designed for streamlining isolation, purification and single-cell secretomic profiling of CTCs from whole blood. Key to this platform is the use of photocleavable ssDNA-encoded antibody conjugates to enable a highly purified CTC population with <75 ‘contaminated' blood cells. An enhanced poly-L-lysine barcode pattern is created on the single-cell barcode chip for efficient capture rare CTC cells in microchambers for subsequent secreted protein profiling. This system was extensively evaluated and optimized with EpCAM-positive HCT116 cells seeded into whole blood. Patient blood samples were employed to assess the utility of the system for isolation, purification and single-cell secretion profiling of CTCs. The CTCs present in patient blood samples exhibit highly heterogeneous secretion profile of IL-8 and VEGF. The numbers of secreting CTCs are found not in accordance with CTC enumeration based on immunostaining in the parallel experiments.
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Affiliation(s)
- Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Shuai Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Zhihua Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Minjiao Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Beiqin Yu
- Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M Czajkowsky
- 1] Center for Bio-Detection and Bio-Instrumentation, Shanghai Jiao Tong University, Shanghai, China [2] School of Biomedicial Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Bingya Liu
- 1] Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China [2] Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Li
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai, China
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Qihui Shi
- 1] Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China [2] State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China [3] Center for Bio-Detection and Bio-Instrumentation, Shanghai Jiao Tong University, Shanghai, China [4] School of Biomedicial Engineering, Shanghai Jiao Tong University, Shanghai, China
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Yang L, Czajkowsky DM, Sun J, Hu J, Shao Z. Anomalous surface fatigue in a nano-layered material. Adv Mater 2014; 26:6478-6482. [PMID: 25163860 DOI: 10.1002/adma.201401906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/18/2014] [Indexed: 06/03/2023]
Abstract
Nanoscale materials fatigue within a single 7 Å layer of a 2D nano-layered material, muscovite mica, resembles fatigue in macroscopic systems except for two remarkable properties: first, there is an Å-scale precision in the depth of the damage and second, there are sharply defined "magical" stresses, beyond yield, at which the surface remains intact regardless of the number of applications of stress.
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Affiliation(s)
- Liu Yang
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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Wu N, Czajkowsky DM, Zhang J, Qu J, Ye M, Zeng D, Zhou X, Hu J, Shao Z, Li B, Fan C. Molecular Threading and Tunable Molecular Recognition on DNA Origami Nanostructures. J Am Chem Soc 2013; 135:12172-5. [DOI: 10.1021/ja403863a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Na Wu
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Daniel M. Czajkowsky
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinjin Zhang
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jianxun Qu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming Ye
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dongdong Zeng
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xingfei Zhou
- Physics Department, Ningbo University, Zhejiang 315211, China
| | - Jun Hu
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Zhifeng Shao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bin Li
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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Shen Y, Czajkowsky DM, Li X, Sun J, Hu J, Shao Z. A novel electromagnetic apparatus for rapid multiplex single molecule force spectroscopy. J Nanosci Nanotechnol 2013; 13:1232-1236. [PMID: 23646609 DOI: 10.1166/jnn.2013.6099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Single-molecule force spectroscopy has revolutionized our ability to probe the details of molecular structures and interactions, but the numbers of individual measurements required for achieving a statistically reliable result can sometimes prove daunting. To overcome this problem, a number of instruments have recently been developed that are capable of monitoring the behavior of tens of individual biomolecules simultaneously. In this work, we have constructed a novel electromagnetic apparatus for multiplex single molecule force measurements utilizing magnetic microspheres. In this system, the magnetic field is generated with an electron-lens of an electron microscope mated with a high voltage flash light circuit to rapidly attain a stable magnetic field. We show that this instrument can generate a uniform magnetic force of up to -20 pN within 5 ms, over a region spanning 1 mm. The successful application of this apparatus to the force-dependent extension of dsDNA fully validates this approach. Furthermore, the lens-like design of the pole piece is fully compatible with optical imaging, thus allowing for the integration of single molecule fluorescence capabilities that should make this system a particularly powerful apparatus for multi-dimensional characterization of fast processes within interacting single molecules.
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Affiliation(s)
- Yi Shen
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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Czajkowsky DM, Hu J, Shao Z, Pleass RJ. Fc-fusion proteins: new developments and future perspectives. EMBO Mol Med 2012; 4:1015-28. [PMID: 22837174 PMCID: PMC3491832 DOI: 10.1002/emmm.201201379] [Citation(s) in RCA: 316] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/29/2012] [Accepted: 06/15/2012] [Indexed: 12/25/2022] Open
Abstract
Since the first description in 1989 of CD4-Fc-fusion antagonists that inhibit human immune deficiency virus entry into T cells, Fc-fusion proteins have been intensely investigated for their effectiveness to curb a range of pathologies, with several notable recent successes coming to market. These promising outcomes have stimulated the development of novel approaches to improve their efficacy and safety, while also broadening their clinical remit to other uses such as vaccines and intravenous immunoglobulin therapy. This increased attention has also led to non-clinical applications of Fc-fusions, such as affinity reagents in microarray devices. Here we discuss recent results and more generally applicable strategies to improve Fc-fusion proteins for each application, with particular attention to the newer, less charted areas.
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Affiliation(s)
- Daniel M Czajkowsky
- Key Laboratory of Systems Biomedicine (Ministry of Education) & State Key Laboratory of Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai, P. R. China
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