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Liu X, Zhang W, Gu J, Wang J, Wang Y, Xu Z. Single-cell SERS imaging of dual cell membrane receptors expression influenced by extracellular matrix stiffness. J Colloid Interface Sci 2024; 668:335-342. [PMID: 38678888 DOI: 10.1016/j.jcis.2024.04.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
Membrane receptors perform a diverse range of cellular functions, accounting for more than half of all drug targets. The mechanical microenvironment regulates cell behaviors and phenotype. However, conventional analysis methods of membrane receptors often ignore the effects of the extracellular matrix stiffness, failing to reveal the heterogeneity of cell membrane receptors expression. Herein, we developed an in-situ surface-enhanced Raman scattering (SERS) imaging method to visualize single-cell membrane receptors on substrates with different stiffness. Two SERS substrates, Au@4-mercaptobenzonitrile@Ag@Sgc8c and Au@4-pethynylaniline@Ag@SYL3c, were employed to specifically target protein tyrosine kinase-7 (PTK7) and epithelial cell adhesion molecule (EpCAM), respectively. The polyacrylamide (PA) gels with tunable stiffness (2.5-25 kPa) were constructed to mimic extracellular matrix. The simultaneous SERS imaging of dual membrane receptors on single cancer cells on substrates with different stiffness was achieved. Our findings reveal decreased expression of PTK7 and EpCAM on cells cultured on stiffer substrates and higher migration ability of the cells. The results elucidate the heterogeneity of membrane receptors expression of cells cultured on the substrates with different stiffness. This single-cell analysis method offers an in-situ platform for investigating the impacts of extracellular matrix stiffness on the expression of membrane receptors, providing insights into the role of cell membrane receptors in cancer metastasis.
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Affiliation(s)
- Xiaopeng Liu
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, PR China
| | - Wenshu Zhang
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, PR China
| | - Jiahui Gu
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, PR China
| | - Jie Wang
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, PR China
| | - Yue Wang
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, PR China
| | - Zhangrun Xu
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, PR China.
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Huang M, Tabib T, Khanna D, Assassi S, Domsic R, Lafyatis R. Single-cell transcriptomes and chromatin accessibility of endothelial cells unravel transcription factors associated with dysregulated angiogenesis in systemic sclerosis. Ann Rheum Dis 2024:ard-2023-225415. [PMID: 38754983 DOI: 10.1136/ard-2023-225415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVES Vasculopathy emerges early in systemic sclerosis (SSc) and links to endothelial cell (EC) injury and angiogenesis. Understanding EC transcriptomes and epigenomes is crucial for unravelling the mechanisms involved. METHODS Transcriptomes and chromatin accessibility were assessed by single-cell RNA sequencing and single-nucleus transposase-accessible chromatin sequencing. Immunofluorescent staining of skin and proteomics assay were employed to confirm the altered SSc EC phenotypes. Gain-of-function assay was used to evaluate the effects of ETS transcription factors on human dermal ECs (hDECs). RESULTS Both control and SSc ECs shared transcriptomic signatures of vascular linages (arterial, capillary and venous ECs) and lymphatic ECs. Arterial ECs in SSc showed reduced number and increased expression of genes associated with apoptosis. Two distinct EC subpopulations, tip and proliferating ECs, were markedly upregulated in SSc, indicating enhanced proangiogenic and proliferative activities. Molecular features of aberrant SSc-ECs were associated with disease pathogenesis and clinical traits of SSc, such as skin fibrosis and digital ulcers. Ligand-receptor analysis demonstrated altered intercellular networks of SSc EC subpopulations with perivascular and immune cells. Furthermore, the integration of open chromatin profiles with transcriptomic analysis suggested an increased accessibility of regulatory elements for ETS family transcription factors in SSc ECs. Overexpression of ETS genes in hDECs suggested ELK4, ERF and ETS1 may orchestrate arterial apoptosis and dysregulated angiogenesis in SSc. CONCLUSIONS This study unveils transcriptional and chromatin alterations in driving endovascular dysregulation in SSc, proposing ELK4, ERF and ETS1 as novel targets in ECs for addressing vascular complications in the condition.
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Affiliation(s)
- Mengqi Huang
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dinesh Khanna
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Shervin Assassi
- Division of Rheumatology, The University of Texas Health Science Center, Houston, Texas, USA
| | - Robyn Domsic
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Sun Y, Liu Y, Li R, Zhang C, Wu M, Zhang X, Xu H, Zeng R, Zeng Y, Liu X. Direct visualization of immune status for tumor-infiltrating lymphocytes by rolling circle amplification. JOURNAL OF BIOPHOTONICS 2024; 17:e202300374. [PMID: 37885324 DOI: 10.1002/jbio.202300374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 10/28/2023]
Abstract
The immune status of tumor-infiltrating lymphocytes (TILs) is essential for the effectiveness of cancer immunotherapies. However, due to the diversity of immune status in TILs, cellular heterogeneity, and the applicability to the clinic, it is still lacking effective strategies to meet clinical needs. We developed a novel immuno-recognition-induced method based on rolling circle amplification (RCA), namely immunoRCA, to in situ visualize the immune status of TILs in actual clinical samples. This developed immunoRCA method, in which, feature mRNAs were used as the biomarkers for the immune status of TILs, has a low fluorescence background, high sensitivity, and specificity. The immunoRCA was able to efficiently evaluate the immune status of CD8+ T cells regulated by activating or inhibiting factors, track the T cell type and immune status during in vitro expansion, and in situ visualize the number, location, and immune status of TILs in clinical specimens.
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Affiliation(s)
- Yupeng Sun
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Yan Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, People's Republic of China
| | - Rui Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, People's Republic of China
| | - Cuilin Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Ming Wu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Xiaolong Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Haipo Xu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Rui Zeng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Yongyi Zeng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences, Fuzhou, People's Republic of China
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4
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Nogoceke R, Josino R, Robert AW, Stimamiglio MA. Evaluation of a Peptide Hydrogel as a Chondro-Instructive Three-Dimensional Microenvironment. Polymers (Basel) 2023; 15:4630. [PMID: 38139882 PMCID: PMC10747086 DOI: 10.3390/polym15244630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/16/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Articular cartilage injuries are inherently irreversible, even with the advancement in current therapeutic options. Alternative approaches, such as the use of mesenchymal stem/stromal cells (MSCs) and tissue engineering techniques, have gained prominence. MSCs represent an ideal source of cells due to their low immunogenicity, paracrine activity, and ability to differentiate. Among biomaterials, self-assembling peptide hydrogels (SAPH) are interesting given their characteristics such as good biocompatibility and tunable properties. Herein we associate human adipose-derived stem cells (hASCs) with a commercial SAPH, Puramatrix™, to evaluate how this three-dimensional microenvironment affects cell behavior and its ability to undergo chondrogenic differentiation. We demonstrate that the Puramatrix™ hydrogel comprises a highly porous matrix permissible for hASC adhesion and in vitro expansion. The morphology and cell growth dynamics of hASCs were affected when cultured on the hydrogel but had minimal alteration in their immunophenotype. Interestingly, hASCs spontaneously formed cell aggregates throughout culturing. Analysis of glycosaminoglycan production and gene expression revealed a noteworthy and donor-dependent trend suggesting that Puramatrix™ hydrogel may have a natural capacity to support the chondrogenic differentiation of hASCs. Altogether, the results provide a more comprehensive understanding of the potential applications and limitations of the Puramatrix™ hydrogel in developing functional cartilage tissue constructs.
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Affiliation(s)
| | | | - Anny Waloski Robert
- Stem Cells Basic Biology Laboratory, Instituto Carlos Chagas—ICC-FIOCRUZ/PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba 81350-010, Brazil; (R.N.); (R.J.)
| | - Marco Augusto Stimamiglio
- Stem Cells Basic Biology Laboratory, Instituto Carlos Chagas—ICC-FIOCRUZ/PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba 81350-010, Brazil; (R.N.); (R.J.)
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Halder A, Biswas D, Chauhan A, Saha A, Auromahima S, Yadav D, Nissa MU, Iyer G, Parihari S, Sharma G, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors. Clin Proteomics 2023; 20:41. [PMID: 37770851 PMCID: PMC10540342 DOI: 10.1186/s12014-023-09426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Meningiomas are the most prevalent primary brain tumors. Due to their increasing burden on healthcare, meningiomas have become a pivot of translational research globally. Despite many studies in the field of discovery proteomics, the identification of grade-specific markers for meningioma is still a paradox and requires thorough investigation. The potential of the reported markers in different studies needs further verification in large and independent sample cohorts to identify the best set of markers with a better clinical perspective. METHODS A total of 53 fresh frozen tumor tissue and 51 serum samples were acquired from meningioma patients respectively along with healthy controls, to validate the prospect of reported differentially expressed proteins and claimed markers of Meningioma mined from numerous manuscripts and knowledgebases. A small subset of Glioma/Glioblastoma samples were also included to investigate inter-tumor segregation. Furthermore, a simple Machine Learning (ML) based analysis was performed to evaluate the classification accuracy of the list of proteins. RESULTS A list of 15 proteins from tissue and 12 proteins from serum were found to be the best segregator using a feature selection-based machine learning strategy with an accuracy of around 80% in predicting low grade (WHO grade I) and high grade (WHO grade II and WHO grade III) meningiomas. In addition, the discriminant analysis could also unveil the complexity of meningioma grading from a segregation pattern, which leads to the understanding of transition phases between the grades. CONCLUSIONS The identified list of validated markers could play an instrumental role in the classification of meningioma as well as provide novel clinical perspectives in regard to prognosis and therapeutic targets.
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Affiliation(s)
- Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Aparna Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Adrita Saha
- Motilal Nehru National Institute of Technology, Allahabad, 211004, UP, India
| | - Shreeman Auromahima
- Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Deeksha Yadav
- CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, New Delhi, 110025, India
| | - Mehar Un Nissa
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Gayatri Iyer
- Koita Centre for Digital Health, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Shashwati Parihari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Gautam Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai, India
| | | | - Graham Roy Ball
- Medical Technology Research Centre, Anglia Ruskin University, Cambridge Campus, East Rd, Cambridge, CB1 1PT, UK
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 185 Berry St., Suite 290, San Francisco, CA, 94107, USA.
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Yue X, Cui J, Sun Z, Liu L, Li Y, Shao L, Feng Q, Wang Z, Hambright WS, Cui Y, Huard J, Mu Y, Mu X. Nuclear softening mediated by Sun2 suppression delays mechanical stress-induced cellular senescence. Cell Death Discov 2023; 9:167. [PMID: 37198162 DOI: 10.1038/s41420-023-01467-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Abstract
Nuclear decoupling and softening are the main cellular mechanisms to resist mechanical stress-induced nuclear/DNA damage, however, its molecular mechanisms remain much unknown. Our recent study of Hutchinson-Gilford progeria syndrome (HGPS) disease revealed the role of nuclear membrane protein Sun2 in mediating nuclear damages and cellular senescence in progeria cells. However, the potential role of Sun2 in mechanical stress-induced nuclear damage and its correlation with nuclear decoupling and softening is still not clear. By applying cyclic mechanical stretch to mesenchymal stromal cells (MSCs) of WT and Zmpset24-/- mice (Z24-/-, a model for HGPS), we observed much increased nuclear damage in Z24-/- MSCs, which also featured elevated Sun2 expression, RhoA activation, F-actin polymerization and nuclear stiffness, indicating the compromised nuclear decoupling capacity. Suppression of Sun2 with siRNA effectively reduced nuclear/DNA damages caused by mechanical stretch, which was mediated by increased nuclear decoupling and softening, and consequently improved nuclear deformability. Our results reveal that Sun2 is greatly involved in mediating mechanical stress-induced nuclear damage by regulating nuclear mechanical properties, and Sun2 suppression can be a novel therapeutic target for treating progeria aging or aging-related diseases.
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Affiliation(s)
- Xianlin Yue
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jie Cui
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Zewei Sun
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Lei Liu
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ying Li
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Liwei Shao
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Qi Feng
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ziyue Wang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - William S Hambright
- Steadman Philippon Research Institute, Center for Regenerative Sports Medicine, Vail, CO, USA
| | - Yan Cui
- Department of Orthopaedic Surgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Johnny Huard
- Steadman Philippon Research Institute, Center for Regenerative Sports Medicine, Vail, CO, USA
| | - Yanling Mu
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.
| | - Xiaodong Mu
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.
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Khalilimeybodi A, Fraley S, Rangamani P. Mechanisms underlying divergent relationships between Ca 2+ and YAP/TAZ signalling. J Physiol 2023; 601:483-515. [PMID: 36463416 PMCID: PMC10986318 DOI: 10.1113/jp283966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Yes-associated protein (YAP) and its homologue TAZ are transducers of several biochemical and biomechanical signals, integrating multiplexed inputs from the microenvironment into higher level cellular functions such as proliferation, differentiation and migration. Emerging evidence suggests that Ca2+ is a key second messenger that connects microenvironmental input signals and YAP/TAZ regulation. However, studies that directly modulate Ca2+ have reported contradictory YAP/TAZ responses: in some studies, a reduction in Ca2+ influx increases the activity of YAP/TAZ, while in others, an increase in Ca2+ influx activates YAP/TAZ. Importantly, Ca2+ and YAP/TAZ exhibit distinct spatiotemporal dynamics, making it difficult to unravel their connections from a purely experimental approach. In this study, we developed a network model of Ca2+ -mediated YAP/TAZ signalling to investigate how temporal dynamics and crosstalk of signalling pathways interacting with Ca2+ can alter the YAP/TAZ response, as observed in experiments. By including six signalling modules (e.g. GPCR, IP3-Ca2+ , kinases, RhoA, F-actin and Hippo-YAP/TAZ) that interact with Ca2+ , we investigated both transient and steady-state cell response to angiotensin II and thapsigargin stimuli. The model predicts that stimuli, Ca2+ transients and frequency-dependent relationships between Ca2+ and YAP/TAZ are primarily mediated by cPKC, DAG, CaMKII and F-actin. Simulation results illustrate the role of Ca2+ dynamics and CaMKII bistable response in switching the direction of changes in Ca2+ -induced YAP/TAZ activity. A frequency-dependent YAP/TAZ response revealed the competition between upstream regulators of LATS1/2, leading to the YAP/TAZ non-monotonic response to periodic GPCR stimulation. This study provides new insights into underlying mechanisms responsible for the controversial Ca2+ -YAP/TAZ relationship observed in experiments. KEY POINTS: YAP/TAZ integrates biochemical and biomechanical inputs to regulate cellular functions, and Ca2+ acts as a key second messenger linking cellular inputs to YAP/TAZ. Studies have reported contradictory Ca2+ -YAP/TAZ relationships for different cell types and stimuli. A network model of Ca2+ -mediated YAP/TAZ signalling was developed to investigate the underlying mechanisms of divergent Ca2+ -YAP/TAZ relationships. The model predicts context-dependent Ca2+ transient, CaMKII bistable response and frequency-dependent activation of LATS1/2 upstream regulators as mechanisms governing the Ca2+ -YAP/TAZ relationship. This study provides new insights into the underlying mechanisms of the controversial Ca2+ -YAP/TAZ relationship to better understand the dynamics of cellular functions controlled by YAP/TAZ activity.
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Affiliation(s)
- A. Khalilimeybodi
- Department of Mechanical and Aerospace Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla CA 92093
| | - S.I. Fraley
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla CA 92093
| | - P. Rangamani
- Department of Mechanical and Aerospace Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla CA 92093
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Xu H, Zheng Y, Chen D, Cheng Y, Fang X, Zhong C, Huang X, Huang Q, Xu J, Xu J, Xue C. Branch-Shaped Trapping Device Regulates Accelerated Catalyzed Hairpin Assembly and Its Application for MicroRNA In Situ Imaging. Anal Chem 2023; 95:1210-1218. [PMID: 36583970 DOI: 10.1021/acs.analchem.2c03956] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Enzyme-free DNA strand displacement process is often practical when detecting miRNAs expressed at low levels in living cells. However, the poor kinetics, tedious reaction period, and multicomponent system hamper its in vivo applications to a great extent. Herein, we design a branch-shaped trapping device (BTD)-based spatial confinement reactor and applied it for accelerated miRNA in situ imaging. The reactor consists of a pair of trapped probe-based catalyzed hairpin assembly (T-CHA) reactions attached around the BTD. The trapping device naturally offered CHA reactions a good spatial-confinement effect by integrating the metastable probes (MHPa and MHPb) of the traditional CHA with the four-branched arm of BTD, which greatly improved the localized concentration of probes and shortened their physical distance. The autonomous and progressive walk of miRNA on the four-arm nanoprobes via T-CHA can rapidly tie numerous four-arm nanoprobes into figure-of-eight nanoknots (FENs), yielding strong fluorescence that is proportional to the miRNA expression level. The unique nanoarchitecture of the FEN also benefits the restricted freedom of movement (FOM) in a confined cellular environment, which makes the system ideally suitable for in situ imaging of intracellular miRNAs. In vitro and in situ analyses also demonstrated that the T-CHA overall outperformed the dissociative probe-based CHA (D-CHA) in stability, reaction speed, and amplification sensitivity. The final application of the T-CHA-based four-arm nanoprobe for imagings of both cancer cells and normal cells shows the potential of the platform for accurately and timely revealing miRNA in biological systems.
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Affiliation(s)
- Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Yanhui Zheng
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Danlong Chen
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Yinghao Cheng
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiaojun Fang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Chunlian Zhong
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Xinmei Huang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Qi Huang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Jiawei Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chang Xue
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
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9
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Feng X, Zhao J, Li F, Aloufi BH, Alshammari AM, Ma Y. Weighted Gene Co-expression Network Analysis Revealed That CircMARK3 Is a Potential CircRNA Affects Fat Deposition in Buffalo. Front Vet Sci 2022; 9:946447. [PMID: 35873681 PMCID: PMC9302235 DOI: 10.3389/fvets.2022.946447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Buffalo meat is increasingly widely accepted for consumption as it shares several quality attributes with cattle meat (beef). Hence, there is a huge opportunity for growth in the buffalo meat industry. However, buffalo meat has relatively low intramuscular fat (IMF) content, affecting its flavor, tenderness and juiciness. As there is a dearth of information on factors that control fat deposition, this study was undertaken to provide new candidate factor associated with buffalo fat deposition. Circular RNA (circRNA) is a novel class of non-coding RNA with a closed-loop structure, and play an important role in fat deposition. Methods In this study, weighted gene co-expression network analysis (WGCNA) was used to construct a circRNA co-expression network and revealed a candidate circRNA that may affect the IMF deposition of buffalo as determined by RT-qPCR, semiquantitative PCR and gain-of-function experiments. Results Herein, WGCNA determined that one module (turquoise module) is significantly associated with the growth and development stages of buffalo. Further analysis revealed a total of 191 overlapping circRNAs among differentially expressed (DE) circRNAs and the co-expression module. A candidate circRNA was found, 21:6969877|69753491 (circRNA_ID), with a reported involvement in lipid metabolism. This circRNA is stably expressed and originates from the MARK3 gene, hence the name circMARK3. circMARK3 is highly expressed in adipose tissue and mature adipocytes and is located in the cytoplasm. Gain-of-function experiments demonstrated that circMARK3 promoted adipogenic differentiation of buffalo adipocytes and 3T3-L1 cells by up-regulating the expression levels of adipogenic marker genes PPARG, C/EBPα and FABP4. Conclusion These results indicate that circMARK3 is a potential factor that promotes fat deposition by regulating adipocyte differentiation and adipogenesis in buffalo.
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Affiliation(s)
- Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Jinhui Zhao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Fen Li
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Bandar Hamad Aloufi
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | | | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, China
- *Correspondence: Yun Ma
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Smaluch K, Wollenhaupt B, Steinhoff H, Kohlheyer D, Grünberger A, Dusny C. Assessing the growth kinetics and stoichiometry of Escherichia coli at the single-cell level. Eng Life Sci 2022; 23:e2100157. [PMID: 36619887 PMCID: PMC9815083 DOI: 10.1002/elsc.202100157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/17/2022] [Accepted: 04/16/2022] [Indexed: 01/11/2023] Open
Abstract
Microfluidic cultivation and single-cell analysis are inherent parts of modern microbial biotechnology and microbiology. However, implementing biochemical engineering principles based on the kinetics and stoichiometry of growth in microscopic spaces remained unattained. We here present a novel integrated framework that utilizes distinct microfluidic cultivation technologies and single-cell analytics to make the fundamental math of process-oriented biochemical engineering applicable at the single-cell level. A combination of non-invasive optical cell mass determination with sub-pg sensitivity, microfluidic perfusion cultivations for establishing physiological steady-states, and picoliter batch reactors, enabled the quantification of all physiological parameters relevant to approximate a material balance in microfluidic reaction environments. We determined state variables (biomass concentration based on single-cell dry weight and mass density), biomass synthesis rates, and substrate affinities of cells grown in microfluidic environments. Based on this data, we mathematically derived the specific kinetics of substrate uptake and growth stoichiometry in glucose-grown Escherichia coli with single-cell resolution. This framework may initiate microscale material balancing beyond the averaged values obtained from populations as a basis for integrating heterogeneous kinetic and stoichiometric single-cell data into generalized bioprocess models and descriptions.
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Affiliation(s)
- Katharina Smaluch
- Department of Solar Materials – Microscale Analysis and EngineeringHelmholtz‐Centre for Environmental Research – UFZ LeipzigLeizpigGermany
| | - Bastian Wollenhaupt
- Microscale BioengineeringIBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
| | - Heiko Steinhoff
- Multiscale BioengineeringFaculty of TechnologyBielefeld UniversityBielefeldGermany
| | - Dietrich Kohlheyer
- Microscale BioengineeringIBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
| | - Alexander Grünberger
- Multiscale BioengineeringFaculty of TechnologyBielefeld UniversityBielefeldGermany
| | - Christian Dusny
- Department of Solar Materials – Microscale Analysis and EngineeringHelmholtz‐Centre for Environmental Research – UFZ LeipzigLeizpigGermany
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11
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Rolling Circle Replication for Biosensing, Bioimaging, and Biomedicine. Trends Biotechnol 2021; 39:1160-1172. [PMID: 33715868 DOI: 10.1016/j.tibtech.2021.02.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022]
Abstract
Rolling circle replication (RCR), including rolling circle amplification (RCA) and rolling circle transcription (RCT), is an isothermal enzymatic reaction. Because of its high amplification efficiency, RCR is a powerful biosensing tool for detecting biomolecules. In recent years, RCR has also been extended to the field of bioimaging to better understand biological pathways. Furthermore, RCR provides a simple technique to design and generate DNA/RNA structures with unique advantages in delivering drugs and enhanced targeting ability. In this review, we introduce the fundamentals of RCR and describe the most recent advances in RCR-based detection methods and delivery vehicles for biosensing, bioimaging, and biomedicine. Finally, some challenges and further opportunities of RCR-based biotechnology are discussed.
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12
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Zhang K, Deng R, Gao H, Teng X, Li J. Lighting up single-nucleotide variation in situ in single cells and tissues. Chem Soc Rev 2020; 49:1932-1954. [PMID: 32108196 DOI: 10.1039/c9cs00438f] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to 'see' genetic information directly in single cells can provide invaluable insights into complex biological systems. In this review, we discuss recent advances of in situ imaging technologies for visualizing the subtlest sequence alteration, single-nucleotide variation (SNV), at single-cell level. The mechanism of recently developed methods for SNV discrimination are summarized in detail. With recent developments, single-cell SNV imaging methods have opened a new door for studying the heterogenous and stochastic genetic information in individual cells. Furthermore, SNV imaging can be used on morphologically preserved tissue, which can provide information on histological context for gene expression profiling in basic research and genetic diagnosis. Moreover, the ability to visualize SNVs in situ can be further developed into in situ sequencing technology. We expect this review to inspire more research work into in situ SNV imaging technologies for investigating cellular phenotypes and gene regulation at single-nucleotide resolution, and developing new clinical and biomedical applications.
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Affiliation(s)
- Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Hua Gao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and Department of Pathogeny Biology, Medical College, Zhengzhou University, Zhengzhou 450001, China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
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13
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Lv J, Dong Y, Gu Z, Yang D. Programmable DNA Nanoflowers for Biosensing, Bioimaging, and Therapeutics. Chemistry 2020; 26:14512-14524. [DOI: 10.1002/chem.202002242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/02/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Jigang Lv
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Yuhang Dong
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Zi Gu
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Dayong Yang
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
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14
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Gao H, Zhang K, Teng X, Li J. Rolling circle amplification for single cell analysis and in situ sequencing. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115700] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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15
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Huang Q, Mao S, Khan M, Li W, Zhang Q, Lin JM. Single-cell identification by microfluidic-based in situ extracting and online mass spectrometric analysis of phospholipids expression. Chem Sci 2019; 11:253-256. [PMID: 34040719 PMCID: PMC8132990 DOI: 10.1039/c9sc05143k] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022] Open
Abstract
This work describes a microfluidic system for in situ extraction of a single-cell and its phosphatidylcholine analysis through mass spectrometry. This approach uncovered cellular heterogeneity among seemingly identical cells and provided a new platform for identification and classification of cells.
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Affiliation(s)
- Qiushi Huang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Sifeng Mao
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Mashooq Khan
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Weiwei Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Qiang Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
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16
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Sun Y, Deng R, Ren X, Zhang K, Li J. 2D Gelatin Methacrylate Hydrogels with Tunable Stiffness for Investigating Cell Behaviors. ACS APPLIED BIO MATERIALS 2018; 2:570-576. [DOI: 10.1021/acsabm.8b00712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yupeng Sun
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Xiaojun Ren
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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17
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Sun Y, Zhang K, Deng R, Ren X, Wu C, Li J. Tunable stiffness of graphene oxide/polyacrylamide composite scaffolds regulates cytoskeleton assembly. Chem Sci 2018; 9:6516-6522. [PMID: 30310582 PMCID: PMC6115675 DOI: 10.1039/c8sc02100g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/30/2018] [Indexed: 12/31/2022] Open
Abstract
Graphene oxide/polyacrylamide composite scaffolds with tunable stiffness are designed and fabricated to investigate the effect of extracellular matrix (ECM) stiffness on cytoskeleton assembly and specific gene expression during cell growth.
The stiffness of the extracellular matrix (ECM) not only provides mechanical resistance to support the cellular shape, but also plays significant roles in many cell functions. However, it's difficult to utilize traditional substrate materials to investigate cell behaviors under physical microenvironments due to their unphysiological stiffness or intrinsic secondary effects. Herein, a stiffness-tunable graphene oxide/polyacrylamide composite scaffold was fabricated to investigate the effect of substrate stiffness on cytoskeleton assembly and specific gene expression during cell growth. In the composite structure, the polyacrylamide (PAAm) hydrogel plays an exceptional role in controlling the substrate stiffness; in contrast, graphene oxide (GO) sheets not only provide permissive surfaces for cell adhesion and growth, but also effectively eliminate the secondary effects of the PAAm hydrogel. It's found that substrate stiffness could affect cell morphology and cytoskeleton assembly via specific genetic pathways. Therefore, the composite structure can be considered an attractive candidate as a scaffold and provides potential to elucidate the disease association of ECMs.
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Affiliation(s)
- Yupeng Sun
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
- China
| | - Kaixiang Zhang
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
- China
| | - Ruijie Deng
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
- China
| | - Xiaojun Ren
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
- China
| | - Can Wu
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
- China
| | - Jinghong Li
- Department of Chemistry
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
- China
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