1
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Wang H, Wang Y, Zhang D, Li P. Circulating nucleosomes as potential biomarkers for cancer diagnosis and treatment monitoring. Int J Biol Macromol 2024; 262:130005. [PMID: 38331061 DOI: 10.1016/j.ijbiomac.2024.130005] [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: 11/29/2023] [Revised: 01/03/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Nucleosomes play a crucial role in regulating gene expression through their composition and post-translational modifications. When cells die, intracellular endonucleases are activated and cleave chromatin into oligo- and mono-nucleosomes, which are then released into the body fluids. Studies have shown that the levels of nucleosomes are increased in serum and plasma in various cancer types, suggesting that analysis of circulating nucleosomes can provide an initial assessment of carcinogenesis. However, it should be noted that elevated serum nucleosome levels may not accurately diagnose certain tumor types, as increased cell death may occur in different pathological conditions. Nevertheless, detection of circulating nucleosomes and their histone modifications, along with specific tumor markers, can help diagnose certain types of cancer. Furthermore, monitoring changes in circulating nucleosome levels during chemotherapy or radiotherapy in patients with malignancies can provide valuable insights into clinical outcomes and therapeutic efficacy. The utilization of circulating nucleosomes as biomarkers is an exciting and emerging area of research, with the potential for early detection of various diseases and monitoring of treatment response. Integrating nucleosome-based biomarkers with existing ones may improve the specificity and sensitivity of current assays, offering the possibility of personalized precision medical treatment for patients.
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Affiliation(s)
- Huawei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
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2
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Kehl A, Aupperle-Lellbach H, de Brot S, van der Weyden L. Review of Molecular Technologies for Investigating Canine Cancer. Animals (Basel) 2024; 14:769. [PMID: 38473154 DOI: 10.3390/ani14050769] [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: 12/21/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Genetic molecular testing is starting to gain traction as part of standard clinical practice for dogs with cancer due to its multi-faceted benefits, such as potentially being able to provide diagnostic, prognostic and/or therapeutic information. However, the benefits and ultimate success of genomic analysis in the clinical setting are reliant on the robustness of the tools used to generate the results, which continually expand as new technologies are developed. To this end, we review the different materials from which tumour cells, DNA, RNA and the relevant proteins can be isolated and what methods are available for interrogating their molecular profile, including analysis of the genetic alterations (both somatic and germline), transcriptional changes and epigenetic modifications (including DNA methylation/acetylation and microRNAs). We also look to the future and the tools that are currently being developed, such as using artificial intelligence (AI) to identify genetic mutations from histomorphological criteria. In summary, we find that the molecular genetic characterisation of canine neoplasms has made a promising start. As we understand more of the genetics underlying these tumours and more targeted therapies become available, it will no doubt become a mainstay in the delivery of precision veterinary care to dogs with cancer.
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Affiliation(s)
- Alexandra Kehl
- Laboklin GmbH & Co. KG, Steubenstr. 4, 97688 Bad Kissingen, Germany
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675 München, Germany
| | - Heike Aupperle-Lellbach
- Laboklin GmbH & Co. KG, Steubenstr. 4, 97688 Bad Kissingen, Germany
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675 München, Germany
| | - Simone de Brot
- Institute of Animal Pathology, COMPATH, University of Bern, 3012 Bern, Switzerland
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3
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Yamamoto T, Yamane H, Yokoshi N, Oka H, Ishihara H, Sugawara Y. Optical Imaging of a Single Molecule with Subnanometer Resolution by Photoinduced Force Microscopy. ACS Nano 2024; 18:1724-1732. [PMID: 38157420 PMCID: PMC10795473 DOI: 10.1021/acsnano.3c10924] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Visualizing the optical response of individual molecules is a long-standing goal in catalysis, molecular nanotechnology, and biotechnology. The molecular response is dominated not only by the electronic states in their isolated environment but also by neighboring molecules and the substrate. Information about the transfer of energy and charge in real environments is essential for the design of the desired molecular functions. However, visualizing these factors with spatial resolution beyond the molecular scale has been challenging. Here, by combining photoinduced force microscopy and Kelvin probe force microscopy, we have mapped the photoinduced force in a pentacene bilayer with a spatial resolution of 0.6 nm and observed its "multipole excitation". We identified the excitation as the result of energy and charge transfer between the molecules and to the Ag substrate. These findings can be achieved only by combining microscopy techniques to simultaneously visualize the optical response of the molecules and the charge transfer between the neighboring environments. Our approach and findings provide insights into designing molecular functions by considering the optical response at each step of layering molecules.
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Affiliation(s)
- Tatsuya Yamamoto
- Department
of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hidemasa Yamane
- Department
of Physics, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
- Osaka
Research Institute of Industrial Science and Technology, Izumi, Osaka 594-1157, Japan
| | - Nobuhiko Yokoshi
- Department
of Physics and Electronics, Osaka Metropolitan
University, Sakai, Osaka 599-8531, Japan
| | - Hisaki Oka
- Department
of Physics, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Hajime Ishihara
- Department
of Materials Engineering Science, Osaka
University, Toyonaka, Osaka 560-8531, Japan
| | - Yasuhiro Sugawara
- Department
of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
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4
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Tsoneva DK, Ivanov MN, Vinciguerra M. Liquid Liver Biopsy for Disease Diagnosis and Prognosis. J Clin Transl Hepatol 2023; 11:1520-1541. [PMID: 38161500 PMCID: PMC10752811 DOI: 10.14218/jcth.2023.00040] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 01/03/2024] Open
Abstract
Liver diseases are a major burden worldwide, the scope of which is expected to further grow in the upcoming years. Clinically relevant liver dysfunction-related blood markers such as alanine aminotransferase and aspartate aminotransferase have limited accuracy. Nowadays, liver biopsy remains the gold standard for several liver-related pathologies, posing a risk of complication due to its invasive nature. Liquid biopsy is a minimally invasive approach, which has shown substantial potential in the diagnosis, prognosis, and monitoring of liver diseases by detecting disease-associated particles such as proteins and RNA molecules in biological fluids. Histones are the core components of the nucleosomes, regulating essential cellular processes, including gene expression and DNA repair. Following cell death or activation of immune cells, histones are released in the extracellular space and can be detected in circulation. Histones are stable in circulation, have a long half-life, and retain their post-translational modifications. Here, we provide an overview of the current research on histone-mediated liquid biopsy methods for liver diseases, with a focus on the most common detection methods.
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Affiliation(s)
- Desislava K. Tsoneva
- Department of Medical Genetics, Medical University of Varna, Varna, Bulgaria
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, Varna, Bulgaria
| | - Martin N. Ivanov
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, Varna, Bulgaria
- Department of Anatomy and Cell Biology, Research Institute, Medical University of Varna, Varna, Bulgaria
| | - Manlio Vinciguerra
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, Varna, Bulgaria
- Faculty of Health, Liverpool John Moores University, Liverpool, United Kingdom
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5
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Challa K, Paysan D, Leiser D, Sauder N, Weber DC, Shivashankar GV. Imaging and AI based chromatin biomarkers for diagnosis and therapy evaluation from liquid biopsies. NPJ Precis Oncol 2023; 7:135. [PMID: 38092866 PMCID: PMC10719365 DOI: 10.1038/s41698-023-00484-8] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
Multiple genomic and proteomic studies have suggested that peripheral blood mononuclear cells (PBMCs) respond to tumor secretomes and thus could provide possible avenues for tumor prognosis and treatment evaluation. We hypothesized that the chromatin organization of PBMCs obtained from liquid biopsies, which integrates secretome signals with gene expression programs, provides efficient biomarkers to characterize tumor signals and the efficacy of proton therapy in tumor patients. Here, we show that chromatin imaging of PBMCs combined with machine learning methods provides such robust and predictive chromatin biomarkers. We show that such chromatin biomarkers enable the classification of 10 healthy and 10 pan-tumor patients. Furthermore, we extended our pipeline to assess the tumor types and states of 30 tumor patients undergoing (proton) radiation therapy. We show that our pipeline can thereby accurately distinguish between three tumor groups with up to 89% accuracy and enables the monitoring of the treatment effects. Collectively, we show the potential of chromatin biomarkers for cancer diagnostics and therapy evaluation.
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Affiliation(s)
- Kiran Challa
- Mechano-Genomic Group, Division of Biology and Chemistry, Paul-Scherrer Institute, Villigen, Switzerland
| | - Daniel Paysan
- Mechano-Genomic Group, Division of Biology and Chemistry, Paul-Scherrer Institute, Villigen, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Dominic Leiser
- Center for Proton Therapy, Paul-Scherrer Institute, Villigen, Switzerland
| | - Nadia Sauder
- Center for Proton Therapy, Paul-Scherrer Institute, Villigen, Switzerland
| | - Damien C Weber
- Center for Proton Therapy, Paul-Scherrer Institute, Villigen, Switzerland.
- Department of Radio-Oncology, University Hospital Zurich, Zurich, Switzerland.
- Department of Radio-Oncology, University of Bern, Bern, Switzerland.
| | - G V Shivashankar
- Mechano-Genomic Group, Division of Biology and Chemistry, Paul-Scherrer Institute, Villigen, Switzerland.
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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6
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [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: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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7
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Erez N, Furth N, Fedyuk V, Wadden J, Aittaleb R, Schwark K, Niculcea M, Miclea M, Mody R, Franson A, Eze A, Nourmohammadi N, Nazarian J, Venneti S, Koschmann C, Shema E. Single-molecule systems for detection and monitoring of plasma circulating nucleosomes and oncoproteins in Diffuse Midline Glioma. bioRxiv 2023:2023.11.21.568019. [PMID: 38045418 PMCID: PMC10690213 DOI: 10.1101/2023.11.21.568019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The analysis of cell-free tumor DNA (ctDNA) and proteins in the blood of cancer patients potentiates a new generation of non-invasive diagnostics and treatment monitoring approaches. However, confident detection of these tumor-originating markers is challenging, especially in the context of brain tumors, in which extremely low amounts of these analytes circulate in the patient's plasma. Here, we applied a sensitive single-molecule technology to profile multiple histone modifications on millions of individual nucleosomes from the plasma of Diffuse Midline Glioma (DMG) patients. The system reveals epigenetic patterns that are unique to DMG, significantly differentiating this group of patients from healthy subjects or individuals diagnosed with other cancer types. We further develop a method to directly capture and quantify the tumor-originating oncoproteins, H3-K27M and mutant p53, from the plasma of children diagnosed with DMG. This single-molecule system allows for accurate molecular classification of patients, utilizing less than 1ml of liquid-biopsy material. Furthermore, we show that our simple and rapid detection strategy correlates with MRI measurements and droplet-digital PCR (ddPCR) measurements of ctDNA, highlighting the utility of this approach for non-invasive treatment monitoring of DMG patients. This work underscores the clinical potential of single-molecule-based, multi-parametric assays for DMG diagnosis and treatment monitoring.
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8
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Chen Z, Li C, Zhou Y, Yao Y, Liu J, Wu M, Su J. Liquid biopsies for cancer: From bench to clinic. MedComm (Beijing) 2023; 4:e329. [PMID: 37492785 PMCID: PMC10363811 DOI: 10.1002/mco2.329] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023] Open
Abstract
Over the past two decades, liquid biopsy has been increasingly used as a supplement, or even, a replacement to the traditional biopsy in clinical oncological practice, due to its noninvasive and early detectable properties. The detections can be based on a variety of features extracted from tumor‑derived entities, such as quantitative alterations, genetic changes, and epigenetic aberrations, and so on. So far, the clinical applications of cancer liquid biopsy mainly aimed at two aspects, prediction (early diagnosis, prognosis and recurrent evaluation, therapeutic response monitoring, etc.) and intervention. In spite of the rapid development and great contributions achieved, cancer liquid biopsy is still a field under investigation and deserves more clinical practice. To better open up future work, here we systematically reviewed and compared the latest progress of the most widely recognized circulating components, including circulating tumor cells, cell-free circulating DNA, noncoding RNA, and nucleosomes, from their discovery histories to clinical values. According to the features applied, we particularly divided the contents into two parts, beyond epigenetics and epigenetic-based. The latter was considered as the highlight along with a brief overview of the advances in both experimental and bioinformatic approaches, due to its unique advantages and relatively lack of documentation.
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Affiliation(s)
- Zhenhui Chen
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Chenghao Li
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
| | - Yue Zhou
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Yinghao Yao
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Jiaqi Liu
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Min Wu
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
| | - Jianzhong Su
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
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9
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Xin L, Yue Y, Zihan R, Youbin C, Tianyu L, Rui W. Clinical application of liquid biopsy based on circulating tumor DNA in non-small cell lung cancer. Front Physiol 2023; 14:1200124. [PMID: 37351260 PMCID: PMC10282751 DOI: 10.3389/fphys.2023.1200124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Lung cancer is a widely occurring and deadly malignancy, with high prevalence rates in China and across the globe. Specifically, non-small cell lung cancer (NSCLC) represents about 85% of all lung cancer cases. The 5-year disease-free survival rate after surgery for stage IB-IIIB NSCLC patients (disease-free survival, DFS) has notably declined from 73% to 13%. Early detection of abnormal cancer molecules and subsequent personalized treatment plans are the most effective ways to address this problem. Liquid biopsy, surprisingly, enables safe, accurate, non-invasive, and dynamic tracking of disease progression. Among the various modalities, circulating tumor DNA (ctDNA) is the most commonly used liquid biopsy modality. ctDNA serves as a credible "liquid biopsy" diagnostic tool that, to a certain extent, overcomes tumor heterogeneity and harbors genetic mutations in malignancies, thereby providing early information on tumor genetic alterations. Despite considerable academic interest in the clinical significance of ctDNA, consensus on its utility remains lacking. In this review, we assess the role of ctDNA testing in the diagnosis and management of NSCLC as a reference for clinical intervention in this disease. Lastly, we examine future directions to optimize ctDNA for personalized therapy.
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Affiliation(s)
| | | | | | | | - Lu Tianyu
- *Correspondence: Wang Rui, ; Lu Tianyu,
| | - Wang Rui
- *Correspondence: Wang Rui, ; Lu Tianyu,
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10
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Wang J, Xia Q, Huang K, Yin L, Jiang H, Liu X, Wang X. Ultrafast Cancer Cells Imaging for Liquid Biopsy via Dynamic Self-Assembling Fluorescent Nanoclusters. Biosensors (Basel) 2023; 13:602. [PMID: 37366966 DOI: 10.3390/bios13060602] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Lung cancer-specific clinical specimens, such as alveolar lavage fluid, are typically identified by microscopic biopsy, which has limited specificity and sensitivity and is highly susceptible to human manipulation. In this work, we present an ultrafast, specific, and accurate cancer cell imaging strategy based on dynamically self-assembling fluorescent nanoclusters. The presented imaging strategy can be used as an alternative or a complement to microscopic biopsy. First, we applied this strategy to detect lung cancer cells, and established an imaging method that can rapidly, specifically, and accurately distinguish lung cancer cells (e.g., A549, HepG2, MCF-7, Hela) from normal cells (e.g., Beas-2B, L02) in 1 min. In addition, we demonstrated that the dynamic self-assembly process that fluorescent nanoclusters formed by HAuCl4 and DNA are first generated at the cell membrane and then gradually enter the cytoplasm of lung cancer cells in 10 min. In addition, we validated that our method enables the rapid and accurate imaging of cancer cells in alveolar lavage fluid samples from lung cancer patients, whereas no signal was observed in the normal human samples. These results indicate that the dynamic self-assembling fluorescent nanoclusters-based cancer cells imaging strategy could be an effective non-invasive technique for ultrafast and accurate cancer bioimaging during liquid biopsy, thus providing a safe and promising cancer diagnostic platform for cancer therapy.
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Affiliation(s)
- Jinpeng Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingxiu Xia
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Ke Huang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Hui Jiang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaohui Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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11
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Yang Q, Wang B, Zheng Q, Li H, Meng X, Zhou F, Zhang L. A Review of Gut Microbiota-Derived Metabolites in Tumor Progression and Cancer Therapy. Adv Sci (Weinh) 2023; 10:e2207366. [PMID: 36951547 DOI: 10.1002/advs.202207366] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/15/2023] [Indexed: 05/27/2023]
Abstract
Gut microbiota-derived metabolites are key hubs connecting the gut microbiome and cancer progression, primarily by remodeling the tumor microenvironment and regulating key signaling pathways in cancer cells and multiple immune cells. The use of microbial metabolites in radiotherapy and chemotherapy mitigates the severe side effects from treatment and improves the efficacy of treatment. Immunotherapy combined with microbial metabolites effectively activates the immune system to kill tumors and overcomes drug resistance. Consequently, various novel strategies have been developed to modulate microbial metabolites. Manipulation of genes involved in microbial metabolism using synthetic biology approaches directly affects levels of microbial metabolites, while fecal microbial transplantation and phage strategies affect levels of microbial metabolites by altering the composition of the microbiome. However, some microbial metabolites harbor paradoxical functions depending on the context (e.g., type of cancer). Furthermore, the metabolic effects of microorganisms on certain anticancer drugs such as irinotecan and gemcitabine, render the drugs ineffective or exacerbate their adverse effects. Therefore, a personalized and comprehensive consideration of the patient's condition is required when employing microbial metabolites to treat cancer. The purpose of this review is to summarize the correlation between gut microbiota-derived metabolites and cancer, and to provide fresh ideas for future scientific research.
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Affiliation(s)
- Qiqing Yang
- General Surgery, Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, 310058, China
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Bin Wang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qinghui Zheng
- General Surgery, Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, 310058, China
| | - Heyu Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xuli Meng
- General Surgery, Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, 310058, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, P. R. China
| | - Long Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
- International Biomed-X Research Center, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Center for Infection & Immunity of International Institutes of Medicine The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
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12
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Fisher IF, Shemer R, Dor Y. Epigenetic liquid biopsies: a novel putative biomarker in immunology and inflammation. Trends Immunol 2023; 44:356-364. [PMID: 37012121 DOI: 10.1016/j.it.2023.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Immune and inflammatory processes occurring within tissues are often undetectable by blood cell counts, standard circulating biomarkers, or imaging, representing an unmet biomedical need. Here, we outline recent advances indicating that liquid biopsies can broadly inform human immune system dynamics. Nucleosome-size fragments of cell-free DNA (cfDNA) released from dying cells into blood contain rich epigenetic information such as methylation, fragmentation, and histone mark patterns. This information allows to infer the cfDNA cell of origin, as well as pre-cell death gene expression patterns. We propose that the analysis of epigenetic features of immune cell-derived cfDNA can shed light on immune cell turnover dynamics in healthy people, and inform the study and diagnosis of cancer, local inflammation, infectious or autoimmune diseases, as well as responses to vaccination.
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Liu M, Yu L, Li Y, Ma Y, An S, Zheng J, Liu L, Lin K, Gao P. Bionic Plasmonic Nanoarrays Excited by Radially Polarized Vector Beam for Metal-Enhanced Fluorescence. Nanomaterials (Basel) 2023; 13:1237. [PMID: 37049330 PMCID: PMC10097346 DOI: 10.3390/nano13071237] [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] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/18/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Metal-enhanced fluorescence (MEF) is an important fluorescence technology due to its ability to significantly improve the fluorescence intensity. Here, we present a new MEF configuration of the bionic nanorod array illuminated by radially polarized vector beam (RVB). The bionic nanorod array is fabricated via a nanoimprinting method by using the wings of the Chinese cicada "meimuna mongolica" as bio-templates, and later coating gold film by ion sputtering deposition method. The MEF performance of the prepared substrate is tested by a home-made optical system. The experiment results show that, in the case of RVB excitation, the intensity of fluorescence is more than 10 times stronger with the nano-imprinted substrate than that with glass. Using the bionic nanoarray as a substrate, the intensity of fluorescence is ~2 times stronger via RVB than that by the linearly polarized beam. In addition, the prepared substrate is verified to have good uniformity.
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Affiliation(s)
- Min Liu
- School of Physics, Xidian University, Xi’an 710071, China
- Guangzhou Institute of Technology, Xidian University, Guangzhou 510555, China
| | - Lan Yu
- School of Physics, Xidian University, Xi’an 710071, China
| | - Yanru Li
- School of Optoelectronic Engineering, Xidian University, Xi’an 710071, China
| | - Ying Ma
- School of Physics, Xidian University, Xi’an 710071, China
| | - Sha An
- School of Physics, Xidian University, Xi’an 710071, China
| | - Juanjuan Zheng
- School of Physics, Xidian University, Xi’an 710071, China
| | - Lixin Liu
- School of Optoelectronic Engineering, Xidian University, Xi’an 710071, China
| | - Ke Lin
- School of Physics, Xidian University, Xi’an 710071, China
| | - Peng Gao
- School of Physics, Xidian University, Xi’an 710071, China
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Shema E. A single-molecule liquid biopsy for cancer diagnosis. Nat Rev Cancer 2023; 23:271. [PMID: 36973406 DOI: 10.1038/s41568-023-00563-9] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Affiliation(s)
- Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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15
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Tsoneva DK, Ivanov MN, Conev NV, Manev R, Stoyanov DS, Vinciguerra M. Circulating Histones to Detect and Monitor the Progression of Cancer. Int J Mol Sci 2023; 24:ijms24020942. [PMID: 36674455 PMCID: PMC9860657 DOI: 10.3390/ijms24020942] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Liquid biopsies have emerged as a minimally invasive cancer detection and monitoring method, which could identify cancer-related alterations in nucleosome or histone levels and modifications in blood, saliva, and urine. Histones, the core component of the nucleosome, are essential for chromatin compaction and gene expression modulation. Increasing evidence suggests that circulating histones and histone complexes, originating from cell death or immune cell activation, could act as promising biomarkers for cancer detection and management. In this review, we provide an overview of circulating histones as a powerful liquid biopsy approach and methods for their detection. We highlight current knowledge on circulating histones in hematologic malignancies and solid cancer, with a focus on their role in cancer dissemination, monitoring, and tumorigenesis. Last, we describe recently developed strategies to identify cancer tissue-of-origin in blood plasma based on nucleosome positioning, inferred from nucleosomal DNA fragmentation footprint, which is independent of the genetic landscape.
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Affiliation(s)
- Desislava K. Tsoneva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Varna, 9000 Varna, Bulgaria
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
| | - Martin N. Ivanov
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
- Department of Anatomy and Cell Biology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
| | - Nikolay Vladimirov Conev
- Clinic of Medical Oncology, UMHAT “St. Marina”, 1 “Hristo Smirnenski” Blvd., 9000 Varna, Bulgaria
- Department of Propedeutics of Internal Diseases, Medical University of Varna, 9000 Varna, Bulgaria
| | - Rostislav Manev
- Clinic of Medical Oncology, UMHAT “St. Marina”, 1 “Hristo Smirnenski” Blvd., 9000 Varna, Bulgaria
- Department of Propedeutics of Internal Diseases, Medical University of Varna, 9000 Varna, Bulgaria
| | - Dragomir Svetozarov Stoyanov
- Clinic of Medical Oncology, UMHAT “St. Marina”, 1 “Hristo Smirnenski” Blvd., 9000 Varna, Bulgaria
- Department of Propedeutics of Internal Diseases, Medical University of Varna, 9000 Varna, Bulgaria
| | - Manlio Vinciguerra
- Department of Stem Cell Biology and Transplantology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
- Correspondence:
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Liu Y, Li B, Liu B, Zhang K. Single-Particle Optical Imaging for Ultrasensitive Bioanalysis. Biosensors (Basel) 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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Armeev GA, Gribkova AK, Shaytan AK. Nucleosomes and their complexes in the cryoEM era: Trends and limitations. Front Mol Biosci 2022; 9:1070489. [PMID: 36504712 PMCID: PMC9730872 DOI: 10.3389/fmolb.2022.1070489] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022] Open
Abstract
Twenty-five years have passed since the appearance of the first atomistic model of the nucleosome structure, and since then the number of new structures has gradually increased. With the advent of cryo-microscopy, the rate of accumulation of models has increased significantly. New structures are emerging with different histone variants and a variety of proteins that bind to nucleosomes. At the moment, there are more than four hundred structures containing nucleosomes in the Protein Data Bank. Many of these structures represent similar complexes, others differ in composition, conformation and quality. In this perspective, we investigate the diversity of known nucleosome structures, analyze data and model quality, variations in histone/DNA content of nucleosomes and spectrum of their interactors. We outline those parts of the nucleosome "structurome" that are already explored and those awaiting further exploration.
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Affiliation(s)
- Grigoriy A. Armeev
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,*Correspondence: Grigoriy A. Armeev, ; Alexey K. Shaytan,
| | - Anna K. Gribkova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey K. Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Computer Science, HSE University, Moscow, Russia,*Correspondence: Grigoriy A. Armeev, ; Alexey K. Shaytan,
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