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Lu J, Chen XZ, Liu Y, Liu YJ, Liu B. Trends in confinement-induced cell migration and multi-omics analysis. Anal Bioanal Chem 2024; 416:2107-2115. [PMID: 38135761 DOI: 10.1007/s00216-023-05109-4] [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: 10/14/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023]
Abstract
Cell migration is an essential manner of different cell lines that are involved in embryological development, immune responses, tumorigenesis, and metastasis in vivo. Physical confinement derived from crowded tissue microenvironments has pivotal effects on migratory behaviors. Distinct migration modes under a heterogeneous extracellular matrix (ECM) have been extensively studied, uncovering potential molecular mechanisms involving a series of biological processes. Significantly, multi-omics strategies have been launched to provide multi-angle views of complex biological phenomena, facilitating comprehensive insights into molecular regulatory networks during cell migration. In this review, we describe biomimetic devices developed to explore the migratory behaviors of cells induced by different types of confined microenvironments in vitro. We also discuss the results of multi-omics analysis of intrinsic molecular alterations and critical pathway dysregulations of cell migration under heterogeneous microenvironments, highlighting the significance of physical confinement-triggered intracellular signal transduction in order to regulate cellular behaviors. Finally, we discuss both the challenges and promise of mechanistic analysis in confinement-induced cell migration, promoting the development of early diagnosis and precision therapeutics.
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Affiliation(s)
- Jiayin Lu
- Department of ChemistryState Key Lab of Molecular Engineering of PolymersShanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological HospitalShanghai Xuhui Central Hospital, Zhongshan-Xuhui HospitalFudan University, Shanghai, China
| | - Xue-Zhu Chen
- Department of ChemistryState Key Lab of Molecular Engineering of PolymersShanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological HospitalShanghai Xuhui Central Hospital, Zhongshan-Xuhui HospitalFudan University, Shanghai, China
| | - Yixin Liu
- Department of ChemistryState Key Lab of Molecular Engineering of PolymersShanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological HospitalShanghai Xuhui Central Hospital, Zhongshan-Xuhui HospitalFudan University, Shanghai, China
| | - Yan-Jun Liu
- Department of ChemistryState Key Lab of Molecular Engineering of PolymersShanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological HospitalShanghai Xuhui Central Hospital, Zhongshan-Xuhui HospitalFudan University, Shanghai, China.
| | - Baohong Liu
- Department of ChemistryState Key Lab of Molecular Engineering of PolymersShanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological HospitalShanghai Xuhui Central Hospital, Zhongshan-Xuhui HospitalFudan University, Shanghai, China.
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2
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Jeffet J, Mondal S, Federbush A, Tenenboim N, Neaman M, Deek J, Ebenstein Y, Bar-Sinai Y. Machine-Learning-Based Single-Molecule Quantification of Circulating MicroRNA Mixtures. ACS Sens 2023; 8:3781-3792. [PMID: 37791886 PMCID: PMC10616852 DOI: 10.1021/acssensors.3c01234] [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: 06/20/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023]
Abstract
MicroRNAs (miRs) are small noncoding RNAs that regulate gene expression and are emerging as powerful indicators of diseases. MiRs are secreted in blood plasma and thus may report on systemic aberrations at an early stage via liquid biopsy analysis. We present a method for multiplexed single-molecule detection and quantification of a selected panel of miRs. The proposed assay does not depend on sequencing, requires less than 1 mL of blood, and provides fast results by direct analysis of native, unamplified miRs. This is enabled by a novel combination of compact spectral imaging and a machine learning-based detection scheme that allows simultaneous multiplexed classification of multiple miR targets per sample. The proposed end-to-end pipeline is extremely time efficient and cost-effective. We benchmark our method with synthetic mixtures of three target miRs, showcasing the ability to quantify and distinguish subtle ratio changes between miR targets.
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Affiliation(s)
- Jonathan Jeffet
- School
of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact
Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Nanoscience and Nanotechnology, Tel
Aviv University, Tel Aviv 6997801, Israel
| | - Sayan Mondal
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Nanoscience and Nanotechnology, Tel
Aviv University, Tel Aviv 6997801, Israel
| | - Amit Federbush
- School
of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact
Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Nadav Tenenboim
- School
of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact
Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Nanoscience and Nanotechnology, Tel
Aviv University, Tel Aviv 6997801, Israel
| | - Miriam Neaman
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Hematology, Tel Aviv Sourasky Medical
Center, Tel Aviv 6423906, Israel
| | - Jasline Deek
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Biomedical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Nanoscience and Nanotechnology, Tel
Aviv University, Tel Aviv 6997801, Israel
- Center
for AI & Data Science (TAD), Tel Aviv
University, Tel Aviv 6997801, Israel
| | - Yohai Bar-Sinai
- School
of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact
Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for AI & Data Science (TAD), Tel Aviv
University, Tel Aviv 6997801, Israel
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3
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Zhang P, Tong Y, Huang X, Chen Y, Li Y, Luan D, Li J, Wang C, Li P, Du L, Wang J. The Dual-Response-Single-Amplification Fluorescent Nanomachine for Tumor Imaging and Gastric Cancer Diagnosis. ACS NANO 2023; 17:16553-16564. [PMID: 37527488 DOI: 10.1021/acsnano.3c02148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Gastric cancer (GC) is one of the most common tumors worldwide and is the leading cause of tumor-related mortality. Traditional biomarkers and screening methods cannot meet the clinical demands. There is an urgent need for highly sensitive diagnostic markers as well as accurate quantification methods for early gastric cancer (EGC) screening. Here a dual-target cooperatively responsive fluorescent nanomachine by the innovative application of two targets─responsive strand migration system with a single-amplification-cycle element was developed for the simultaneous detection of GC biomarkers miR-5585-5p and PLS3 mRNA, which were selected by next-generation sequencing and RT-qPCR. It was also an RNA extraction-free, PCR-free, and nonenzymatic biosensor to achieve tumor cell imaging and serum diagnosis. Requiring only a 20 μL serum sample and 20 min incubation time, the nanomachine achieved an ultrasensitive detection limit of fM level with a broad linear range from fM to nM. More importantly, a higher AUC value (0.884) compared to the clinically used biomarker CA 72-4 was obtained by the nanomachine to distinguish GC patients successfully. Notably, for the key concerns of diagnosis of EGC patients, the nanomachine also achieved a satisfactory AUC value of 0.859. Taken together, this work has screened and obtained multiple biomarkers and developed a fluorescent nanomachine for combination diagnosis of GC, providing an ingenious design of a functionalized DNA nanomachine and a feasible strategy for the transformation of serum biomarkers into clinical diagnosis.
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Affiliation(s)
- Peng Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Yao Tong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Xiaowen Huang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China
| | - Yuqing Chen
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Yanru Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Dongrui Luan
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Peilong Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, China
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
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Liu Y, Li B, Liu B, Zhang K. Single-Particle Optical Imaging for Ultrasensitive Bioanalysis. BIOSENSORS 2022; 12:1105. [PMID: 36551072 PMCID: PMC9775667 DOI: 10.3390/bios12121105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The quantitative detection of critical biomolecules and in particular low-abundance biomarkers in biofluids is crucial for early-stage diagnosis and management but remains a challenge largely owing to the insufficient sensitivity of existing ensemble-sensing methods. The single-particle imaging technique has emerged as an important tool to analyze ultralow-abundance biomolecules by engineering and exploiting the distinct physical and chemical property of individual luminescent particles. In this review, we focus and survey the latest advances in single-particle optical imaging (OSPI) for ultrasensitive bioanalysis pertaining to basic biological studies and clinical applications. We first introduce state-of-the-art OSPI techniques, including fluorescence, surface-enhanced Raman scattering, electrochemiluminescence, and dark-field scattering, with emphasis on the contributions of various metal and nonmetal nano-labels to the improvement of the signal-to-noise ratio. During the discussion of individual techniques, we also highlight their applications in spatial-temporal measurement of key biomarkers such as proteins, nucleic acids and extracellular vesicles with single-entity sensitivity. To that end, we discuss the current challenges and prospective trends of single-particle optical-imaging-based bioanalysis.
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Affiliation(s)
- Yujie Liu
- Shanghai Institute of Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Binxiao Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Kun Zhang
- Shanghai Institute of Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
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5
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Fan Z, Li B, Wang YJ, Huang X, Li B, Wang S, Liu Y, Liu YJ, Liu B. Spatially resolved single-molecule profiling of microRNAs in migrating cells driven by microconfinement. Chem Sci 2022; 13:11197-11204. [PMID: 36320480 PMCID: PMC9517726 DOI: 10.1039/d2sc04132d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer cells utilize a range of migration modes to navigate through a confined tissue microenvironment in vivo, while regulatory roles of key microRNAs (miRNAs) remain unclear. Precisely engineered microconfinement and the high spatial-resolution imaging strategy offer a promising avenue for deciphering the molecular mechanisms that drive cell migration. Here, enzyme-free signal-amplification nanoprobes as an effective tool are developed for three-dimensional (3D) high-resolution profiling of key miRNA molecules in single migrating cells, where distinct migration modes are precisely driven by microconfinement-engineered microchips. The constructed nanoprobes exhibit intuitive and ultrasensitive miRNA characterization in vitro by virtue of a single-molecule imaging microscope, and the differential expression and intracellular locations in different cell lines are successfully monitored. Furthermore, 3D spatial distribution of miR-141 at high resolution in flexible phenotypes of migrating cells is reconstructed in the engineered biomimetic microenvironment. The results indicate that miR-141 may be involved in the metastatic transition from a slow to a fast migration state. This work offers a new opportunity for investigating regulatory mechanisms of intracellular key biomolecules during cell migration in biomimetic microenvironments, which may advance in-depth understanding of cancer metastasis in vivo. Spatially resolved profiling of miRNAs was realized in migrating cells using enzyme-free signal-amplification nanoprobes, in which distinct migration modes of single living cells are driven by precisely engineered microchips.![]()
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Affiliation(s)
- Zihui Fan
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Bin Li
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Ya-Jun Wang
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Xuedong Huang
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Binxiao Li
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Shurong Wang
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Yixin Liu
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Yan-Jun Liu
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Baohong Liu
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
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