1
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Chan YT, Zhang C, Wu J, Lu P, Xu L, Yuan H, Feng Y, Chen ZS, Wang N. Biomarkers for diagnosis and therapeutic options in hepatocellular carcinoma. Mol Cancer 2024; 23:189. [PMID: 39242496 PMCID: PMC11378508 DOI: 10.1186/s12943-024-02101-z] [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: 07/30/2024] [Accepted: 08/23/2024] [Indexed: 09/09/2024] Open
Abstract
Liver cancer is a global health challenge, causing a significant social-economic burden. Hepatocellular carcinoma (HCC) is the predominant type of primary liver cancer, which is highly heterogeneous in terms of molecular and cellular signatures. Early-stage or small tumors are typically treated with surgery or ablation. Currently, chemotherapies and immunotherapies are the best treatments for unresectable tumors or advanced HCC. However, drug response and acquired resistance are not predictable with the existing systematic guidelines regarding mutation patterns and molecular biomarkers, resulting in sub-optimal treatment outcomes for many patients with atypical molecular profiles. With advanced technological platforms, valuable information such as tumor genetic alterations, epigenetic data, and tumor microenvironments can be obtained from liquid biopsy. The inter- and intra-tumoral heterogeneity of HCC are illustrated, and these collective data provide solid evidence in the decision-making process of treatment regimens. This article reviews the current understanding of HCC detection methods and aims to update the development of HCC surveillance using liquid biopsy. Recent critical findings on the molecular basis, epigenetic profiles, circulating tumor cells, circulating DNAs, and omics studies are elaborated for HCC diagnosis. Besides, biomarkers related to the choice of therapeutic options are discussed. Some notable recent clinical trials working on targeted therapies are also highlighted. Insights are provided to translate the knowledge into potential biomarkers for detection and diagnosis, prognosis, treatment response, and drug resistance indicators in clinical practice.
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Affiliation(s)
- Yau-Tuen Chan
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Cheng Zhang
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Junyu Wu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Pengde Lu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lin Xu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Hongchao Yuan
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yibin Feng
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Zhe-Sheng Chen
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA.
| | - Ning Wang
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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2
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Liu X, Wang DC, Powell CA, Wang X. Challenges of clinical translation from single-cell sequencing to measures in clinical biochemistry of haematology: Definition of immune cell identities. Clin Transl Med 2023; 13:e1401. [PMID: 37700496 PMCID: PMC10497804 DOI: 10.1002/ctm2.1401] [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: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/14/2023] Open
Abstract
Peripheral immune cells play important roles in the maintenance of systemic and microenvironmental hemostasis. Measurements of circulating blood cells by single-cell RNA sequencing (scRNA-seq) were proposed as one of the routine measures in clinical biochemistry of hematology. Out of translational challenges, defining precise identities of cell subsets and states is more difficult, due to the complexity of immune cell development, location, regulation, function, and metabolism. It is also a challenge to precisely interpret clinical significance and impact of each cell identity marker gene panel (ciMGPs). ciMGPs have potential to advance the understanding of systemic responses of the disease, identify disease-specific biomarkers, and to define cell heterogeneity. Recently, a large number of peripheral cell subsets and expending/activating states have been identified and validated for use in the fast developments in clinical single cell biomedicine. Defining specificity, measurability, and repeatability of cell subsets/states is important for translation of peripheral scRNA-seq in clinical hematology and biochemistry. The development of standard operating procedure and performance of clinical trials in large populations at various ages, diseases, and therapies will promote the clinical translation of ciMGPs to measures. Thus, defining cell subset/state identities will provide the multi-dimensional and comprehensive readouts of systemic immune cells, the precision monitoring of immune dynamics, and deeper-understanding of the disease and response to therapy.
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Affiliation(s)
- Xuanqi Liu
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalShanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesFudan University Shanghai Medical College, Shanghai Institute of Clinical BioinformaticsShanghaiChina
| | - Diane C. Wang
- Department of Emergency MedicinePrincess Alexandra HospitalBrisbaneAustralia
| | - Charles A. Powell
- Division of PulmonaryDepartment of Critical Care and Sleep MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalShanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesFudan University Shanghai Medical College, Shanghai Institute of Clinical BioinformaticsShanghaiChina
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3
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Chen W, Xu D, Liu Q, Wu Y, Wang Y, Yang J. Unraveling the heterogeneity of cholangiocarcinoma and identifying biomarkers and therapeutic strategies with single-cell sequencing technology. Biomed Pharmacother 2023; 162:114697. [PMID: 37060660 DOI: 10.1016/j.biopha.2023.114697] [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: 02/21/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a common malignant tumor of the biliary tract that carries a high burden of morbidity and a poor prognosis. Due to the lack of precise diagnostic methods, many patients are often diagnosed at advanced stages of the disease. The current treatment options available are of varying efficacy, underscoring the urgency for the discovery of more effective biomarkers for early diagnosis and improved treatment. Recently, single-cell sequencing (SCS) technology has gained popularity in cancer research. This technology has the ability to analyze tumor tissues at the single-cell level, thus providing insights into the genomics and epigenetics of tumor cells. It also serves as a practical approach to study the mechanisms of cancer progression and to explore therapeutic strategies. In this review, we aim to assess the heterogeneity of CCA using single-cell sequencing technology, with the ultimate goal of identifying possible biomarkers and potential treatment targets.
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Affiliation(s)
- Wangyang Chen
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China
| | - Dongchao Xu
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China
| | - Qiang Liu
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China
| | - Yirong Wu
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China
| | - Yu Wang
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China.
| | - Jianfeng Yang
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Zhejiang Provincial Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research, Hangzhou, Zhejiang Province 310003, China.
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4
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Liu F, Liu X, Powell CA, Chen C, Zeng Y, Fang H, Wang X. Initiative of clinical single-cell biomedicine in clinical and translational medicine. Clin Transl Med 2023; 13:e1173. [PMID: 36629041 PMCID: PMC9832424 DOI: 10.1002/ctm2.1173] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 01/02/2023] [Indexed: 01/12/2023] Open
Abstract
With rapid developments of single-cell sequencing and multi/trans-omics, clinical single-cell biomedicine is a new and emergent discipline to integrate single-cell molecular and clinical phenomes and uncover new disease-specific diagnoses and therapy. The journal of Clinical and Translational Medicine (CTM) launches the first CTM initiative of clinical single-cell biomedicine (cscBioMed) to promote the discovery and development of single-cell-based biology and medicine, speed the translation from single-cell biology into clinical application, and improve early diagnosis and therapy for human diseases. The cscBioMed initiative is speeding translational processes from circulating single-cell RNA sequencing into routine measures in clinical biochemistry of haematology, from spatial transcriptomics into single-cell pathology, and from single-cell-based biomarkers and targets into clinical diagnostics and target drugs. With a clear goal, we expect that cscBioMed will benefit human health by establishing a clinical single-cell dynamic monitoring and early predicting system and by improving diagnosis and treatment.
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Affiliation(s)
- Fangming Liu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University Shanghai Medical College, Shanghai, China
| | - Xuanqi Liu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University Shanghai Medical College, Shanghai, China
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Chengshui Chen
- Quzhou People's Hospital, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Yiming Zeng
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, China
| | - Hao Fang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University Shanghai Medical College, Shanghai, China
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5
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Peethan A, M A, Chidangil S, George SD. Non-adhesive contrast substrate for single-cell trapping and Raman spectroscopic analysis. LAB ON A CHIP 2022; 22:4110-4117. [PMID: 36128986 DOI: 10.1039/d2lc00665k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Droplet splitting by exploiting tailored surface wettability is emerging as an important pathway to creating ultralow volumes of samples that can have applications in bioassays, tissue engineering, protein chips, and material synthesis. Reduction of droplet volumes enables the encapsulation of single biological cells which allows high throughput screening. In this work, we demonstrate a facile fabrication approach to create a non-adhesive contrast quartz substrate that allows droplet splitting under gravitational force and its utilization to trap single biological cells for Raman spectroscopic studies. The non-adhesive contrast surface is created by low-power continuous-wave laser-assisted removal of the region of interest from a biocompatible non-adhesive silicone oil grafted quartz substrate. For a given laser spot dimension, the hydrophilic zone dimension is controlled via irradiation with varying laser powers. The fabricated non-adhesive contrast surface can split a microliter droplet into pico- and sub-picolitre daughter droplets. By using the substrate, the trapping of a single polystyrene bead is demonstrated and the recording of Raman spectra is carried out. Additionally, the Raman spectra of two biological cells, yeast cells and human mononuclear cells (MNCs), from a daughter droplet are recorded independently and from a mixture of the solutions. This single-cell Raman analysis could find applications in cell identification and type discrimination, biochemical imaging, metabolic and functional characterization, and clinical and toxicity studies.
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Affiliation(s)
- Alina Peethan
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576104, India.
| | - Aravind M
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576104, India.
| | - Santhosh Chidangil
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576104, India.
- Centre of Excellence for Biophotonics, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sajan D George
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576104, India.
- Centre for Applied Nanosciences (CANs), Manipal Academy of Higher Education, Manipal, 576104, India
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6
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Goines S, Dick JE. Investigating the cytotoxic redox mechanism of PFOS within Hep G2 by hyperspectral-assisted scanning electrochemical microscopy. Analyst 2022; 147:4356-4364. [PMID: 36043461 PMCID: PMC10308698 DOI: 10.1039/d2an00904h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Perfluorooctane sulfonate (PFOS) is one of the most lethal per- and poly-fluoroalkyl substances (PFAS). Generally, exposure effects are studied through case-controlled studies, cohort studies, or cell assays. Unfortunately, most studies involving two-dimensional cell cultures require cell lysis or fixation. For in vitro studies, fluorescence microscopy has been useful, but methods to simultaneously discern phototoxic effects during an experiment are limited. Here, we use hepatocarcinoma (Hep G2) cells to examine the redox mechanism of PFOS cytotoxicity in vitro, while using hyperspectral-assisted scanning electrochemical microscopy (SECM) to differentiate between PFOS and redox mediator induced stress. Specifically, we correlate an increase in the electrochemical response of ferrocenemethanol oxidation with an increase in intracellular reactive oxygen species. Corresponding hyperspectral images of redox indicative-fluorophores implicate superoxide in the cytotoxic redox mechanism.
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Affiliation(s)
- Sondrica Goines
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey E Dick
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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7
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Liu X, Powell CA, Wang X. Forward single-cell sequencing into clinical application: Understanding of cancer microenvironment at single-cell solution. Clin Transl Med 2022; 12:e782. [PMID: 35474615 PMCID: PMC9042796 DOI: 10.1002/ctm2.782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 11/09/2022] Open
Abstract
Single‐cell RNA sequencing (scRNA‐seq) is considered an important approach to understand the molecular mechanisms of cancer microenvironmental functions and has the potential for clinical and translational discovery and development. The recent concerns on the impact of scRNA‐seq for clinical practice are whether scRNA can be applied as a routine measurement of clinical biochemistry to assist in clinical decision‐making for diagnosis and therapy. Pushing single‐cell sequencing into clinical application is one of the important missions for clinical and translational medicine (CTM), although there still are a large number of challenges to be overcome. The present Editorial as one of serials aims at overviewing the history of scRNA‐seq publications in CTM, sharing the understanding and consideration of the cancer microenvironment at the single‐cell solution and emphasising the objective of translating scRNA‐seq into clinical application. The dynamic characteristics and patterns of single‐cell identity, regulatory networks, and intercellular communication play decisive roles in the properties of the microenvironment, malignancy and migrative capacity of cancer cells, and defensive capacity of immune cells. The microenvironmental single‐cell transcriptomic profiles and cell clusters defined by scRNA‐seq have great value for exploring the molecular mechanisms of diseases and predicting cell sensitivities to therapy and patient prognosis.
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Affiliation(s)
- Xuanqi Liu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai Institute of Clinical Bioinformatics; Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai Institute of Clinical Bioinformatics; Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
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8
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Luo Q, Fu Q, Zhang X, Zhang H, Qin T. Application of Single-Cell RNA Sequencing in Pancreatic Cancer and the Endocrine Pancreas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:143-152. [PMID: 32949397 DOI: 10.1007/978-981-15-4494-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The pancreas is a complex organ composed of an endocrine (pancreatic islets) and an exocrine portion. This mixed cell population has resulted in an implacable barrier to exploring the detailed mechanism and function of each cell type in previous investigative approaches. In recent years, single-cell RNA sequencing (scRNA-seq) technologies have provided in-depth analysis of cell heterogeneity in the pancreas and in pancreatic cancer. It is especially effective in cell-type-specific molecule identification and detection of interactions between cancer cells and the stromal microenvironment. To date, numerous reports have described the application of scRNA-seq in studies of pancreatic islets and pancreatic cancer. The aim of this paper is to review recent advances of pancreatic transcriptomics and pancreatic cancer using scRNA-seq strategies.
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Affiliation(s)
- Qiankun Luo
- Department of Hepato-Biliary-Pancreatic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qiang Fu
- Department of Hepato-Biliary-Pancreatic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xu Zhang
- Department of Hepato-Biliary-Pancreatic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongwei Zhang
- Department of Hepato-Biliary-Pancreatic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Tao Qin
- Department of Hepato-Biliary-Pancreatic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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9
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Ferrara V, Zito G, Arrabito G, Cataldo S, Scopelliti M, Giordano C, Vetri V, Pignataro B. Aqueous Processed Biopolymer Interfaces for Single-Cell Microarrays. ACS Biomater Sci Eng 2020; 6:3174-3186. [PMID: 33463257 PMCID: PMC7997111 DOI: 10.1021/acsbiomaterials.9b01871] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Single-cell microarrays are emerging tools to unravel intrinsic diversity within complex cell populations, opening up new approaches for the in-depth understanding of highly relevant diseases. However, most of the current methods for their fabrication are based on cumbersome patterning approaches, employing organic solvents and/or expensive materials. Here, we demonstrate an unprecedented green-chemistry strategy to produce single-cell capture biochips onto glass surfaces by all-aqueous inkjet printing. At first, a chitosan film is easily inkjet printed and immobilized onto hydroxyl-rich glass surfaces by electrostatic immobilization. In turn, poly(ethylene glycol) diglycidyl ether is grafted on the chitosan film to expose reactive epoxy groups and induce antifouling properties. Subsequently, microscale collagen spots are printed onto the above surface to define the attachment area for single adherent human cancer cells harvesting with high yield. The reported inkjet printing approach enables one to modulate the collagen area available for cell attachment in order to control the number of captured cells per spot, from single-cells up to double- and multiple-cell arrays. Proof-of-principle of the approach includes pharmacological treatment of single-cells by the model drug doxorubicin. The herein presented strategy for single-cell array fabrication can constitute a first step toward an innovative and environmentally friendly generation of aqueous-based inkjet-printed cellular devices.
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Affiliation(s)
- Vittorio Ferrara
- Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Giovanni Zito
- Dipartimento di Promozione della Salute, Materno-Infantile, Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro" (ProMISE), Sezione di Malattie Endocrine, del Ricambio e della Nutrizione, Università di Palermo, Piazza delle Cliniche 2, 90127 Palermo, Sicilia, Italy
| | - Giuseppe Arrabito
- Dipartimento di Fisica e Chimica-Emilio Segrè, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Sebastiano Cataldo
- Dipartimento di Fisica e Chimica-Emilio Segrè, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Michelangelo Scopelliti
- Dipartimento di Fisica e Chimica-Emilio Segrè, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Carla Giordano
- Dipartimento di Promozione della Salute, Materno-Infantile, Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro" (ProMISE), Sezione di Malattie Endocrine, del Ricambio e della Nutrizione, Università di Palermo, Piazza delle Cliniche 2, 90127 Palermo, Sicilia, Italy
| | - Valeria Vetri
- Dipartimento di Fisica e Chimica-Emilio Segrè, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Bruno Pignataro
- Dipartimento di Fisica e Chimica-Emilio Segrè, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
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10
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Zeng Y, Wang X, Zhang J. Single-cell biomedicine: roles of single-cell nuclear elements. Cell Biol Toxicol 2020; 36:1-3. [PMID: 32008122 DOI: 10.1007/s10565-020-09515-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 01/24/2020] [Indexed: 12/17/2022]
Abstract
Single-cell biomedicine, a new merging discipline of cell biology and medicine to improve the life quality of patients, gains high priority in cell biology and toxicology. Single-cell nuclear elements are specially focused and headlined to understand regulatory mechanisms by which transcriptional factors, DNA elements, and genome organization interact with each other and contribute to the developmental evolution and dynamic formation of genotoxicity. Cell molecular phenomics, clonal genotypes, and structural metamorphoses during the cell cycle at single-cell level provide deep insights to understanding mechanism-based bridges between cell biology and toxicology, between cell sensitive and resistance, and between chronic diseases and cancer.
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Affiliation(s)
- Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Xiangdong Wang
- Centre for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University Shanghai Medical College, Shanghai, China.
| | - Jiaqiang Zhang
- Department of Anesthesiology and Perioperative Medicine, Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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11
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Nalbantoglu S, Karadag A. Introductory Chapter: Insight into the OMICS Technologies and Molecular Medicine. Mol Med 2019. [DOI: 10.5772/intechopen.86450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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12
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Antmen E, Demirci U, Hasirci V. Amplification of nuclear deformation of breast cancer cells by seeding on micropatterned surfaces to better distinguish their malignancies. Colloids Surf B Biointerfaces 2019; 183:110402. [DOI: 10.1016/j.colsurfb.2019.110402] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/21/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022]
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13
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Koshkin V, Kochmann S, Sorupanathan A, Peng C, Ailles LE, Liu G, Krylov SN. Cytometry of Reaction Rate Constant: Measuring Reaction Rate Constant in Individual Cells To Facilitate Robust and Accurate Analysis of Cell-Population Heterogeneity. Anal Chem 2019; 91:4186-4194. [PMID: 30829484 DOI: 10.1021/acs.analchem.9b00388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Robust and accurate analysis of cell-population heterogeneity is challenging but required in many areas of biology and medicine. In particular, it is pivotal to the development of reliable cancer biomarkers. Here, we prove that cytometry of reaction rate constant (CRRC) can facilitate such analysis when the kinetic mechanism of a reaction associated with the heterogeneity is known. In CRRC, the cells are loaded with a reaction substrate, and its conversion into a product is followed by time-lapse fluorescence microscopy at the single-cell level. A reaction rate constant is determined for every cell, and a kinetic histogram "number of cells versus the rate constant" is used to determine quantitative parameters of reaction-based cell-population heterogeneity. Such parameters include, for example, the number and sizes of subpopulations. In this work, we applied CRRC to a reaction of substrate extrusion from cells by ATP-binding cassette (ABC) transporters. This reaction is viewed as a potential basis for predictive biomarkers of chemoresistance in cancer. CRRC proved to be robust (insensitive to variations in experimental settings) and accurate for finding quantitative parameters of cell-population heterogeneity. In contrast, a typical nonkinetic analysis, performed on the same data sets, proved to be both nonrobust and inaccurate. Our results suggest that CRRC can potentially facilitate the development of reliable cancer biomarkers on the basis of quantitative parameters of cell-population heterogeneity. A plausible implementation scenario of CRRC-based development, validation, and clinical use of a predictor of ovarian cancer chemoresistance to its frontline therapy is presented.
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Affiliation(s)
| | | | | | | | - Laurie E Ailles
- Department of Medical Biophysics , University of Toronto , Toronto , Ontario N5G 1L7 , Canada
| | - Geoffrey Liu
- Department of Medicine, Medical Oncology , Princess Margaret Cancer Centre , Toronto , Ontario M5G 2M9 , Canada
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14
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Khatri I, Ganguly K, Sharma S, Carmicheal J, Kaur S, Batra SK, Bhasin MK. Systems Biology Approach to Identify Novel Genomic Determinants for Pancreatic Cancer Pathogenesis. Sci Rep 2019; 9:123. [PMID: 30644396 PMCID: PMC6333820 DOI: 10.1038/s41598-018-36328-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/05/2018] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a 5-year survival rate of <8%. Its dismal prognosis stems from inefficient therapeutic modalities owing to the lack of understanding about pancreatic cancer pathogenesis. Considering the molecular complexity and heterogeneity of PDAC, identification of novel molecular contributors involved in PDAC onset and progression using global "omics" analysis will pave the way to improved strategies for disease prevention and therapeutic targeting. Meta-analysis of multiple miRNA microarray datasets containing healthy controls (HC), chronic pancreatitis (CP) and PDAC cases, identified 13 miRNAs involved in the progression of PDAC. These miRNAs showed dysregulation in both tissue as well as blood samples, along with progressive decrease in expression from HC to CP to PDAC. Gene-miRNA interaction analysis further elucidated 5 miRNAs (29a/b, 27a, 130b and 148a) that are significantly downregulated in conjunction with concomitant upregulation of their target genes throughout PDAC progression. Among these, miRNA-29a/b targeted genes were found to be most significantly altered in comparative profiling of HC, CP and PDAC, indicating its involvement in malignant evolution. Further, pathway analysis suggested direct involvement of miRNA-29a/b in downregulating the key pathways associated with PDAC development and metastasis including focal adhesion signaling and extracellular matrix organization. Our systems biology data analysis, in combination with real-time PCR validation indicates direct functional involvement of miRNA-29a in PDAC progression and is a potential prognostic marker and therapeutic candidate for patients with progressive disease.
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Affiliation(s)
- Indu Khatri
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Koelina Ganguly
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sunandini Sharma
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joseph Carmicheal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sukhwinder Kaur
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA.
| | - Manoj K Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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15
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Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:149-158. [PMID: 29943302 DOI: 10.1007/978-981-13-0502-3_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The advent of single-cell omics technology has promoted our understanding of the genomic, epigenomic, and transcriptomic heterogeneity in individual cells. Compared to traditional sequencing studies using bulk cells, single-cell transcriptome technology is naturally more dynamic for in depth analysis of genomic variation resulting from cell division and is useful in unraveling the regulatory mechanisms of gene networks in many diseases. However, there are still some limitations of current single-cell RNA sequencing (scRNA-seq) protocols. Biases that arise during the RNA reverse transcription and cDNA pre-amplification steps are the most common problems and play pivotal roles in limiting the quantitative accuracy of scRNA-seq. In this review, we will describe how these biases emerge and impact scRNA-seq protocols. Moreover, we will introduce several current and convenient modified scRNA-seq methods that allow for bias to be decreased and estimated.
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16
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Darde TA, Chalmel F, Svingen T. Exploiting advances in transcriptomics to improve on human-relevant toxicology. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2019.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Pande P, Giambalvo M, Huang Z. Complementing preclinical safety assessments through genomic analyses. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Zeng Y, Chen X, Gao H, Wang X. An artificial intelligent single cell is part of the cell dream world. Cell Biol Toxicol 2018; 34:247-249. [PMID: 29777423 PMCID: PMC6021470 DOI: 10.1007/s10565-018-9433-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/09/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Xiaoyang Chen
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Hongzhi Gao
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
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19
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Wang, DC, Wang, W, Zhu, B, Wang X. Lung Cancer Heterogeneity and New Strategies for Drug Therapy. Annu Rev Pharmacol Toxicol 2018; 58:531-546. [PMID: 28977762 DOI: 10.1146/annurev-pharmtox-010716-104523] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Diane C. Wang,
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
| | - William Wang,
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
| | - Bijun Zhu,
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
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20
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Zeng Y, Chen X, Wang X. Roles of Single Cell Systems Biomedicine in Lung Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:177-185. [PMID: 29943305 DOI: 10.1007/978-981-13-0502-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Single cell sequencing is important to detect the gene heterogeneity between cells, as the part of single-cell systems biology which combines computational science, mathematical modelling and high-throughput technologies with biological function and organization in the cell. We initially arise the question how to integrate the outcomes of single-cell systems biology with clinical phenotype, interpret alterations of single-cell gene sequencing and function in patient response to therapies, and understand the significance of single-cell systems biology in the discovery and development of new molecular diagnostics and therapeutics. The present review furthermore focuses the significance of singe cell systems biology in respiratory diseases and calls the special attention from scientists who are working on single cell systems biology to improve the diagnosis and therapy for patients with lung diseases.
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Affiliation(s)
- Yiming Zeng
- Department of Respiratory Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Xiaoyang Chen
- Department of Respiratory Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiangdong Wang
- Department of Respiratory Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
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21
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Can the Single Cell Make Biomedicine Different? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:1-6. [PMID: 29943291 DOI: 10.1007/978-981-13-0502-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The single-cell as the basic unit of biological organs and tissues has recently been considered an important window to furthermore understand molecular mechanisms of organ function and biology. The current issue with a special focus on single cell biomedicine is the first effort to collect the evidence of disease-associated single cell research, define the significance of single cell biomedicine in the pathogenesis of diseases, value the correlation of single cell gene sequencing with disease-specific biomarkers, and monitor the dynamics of RNA processes and responses to microenvironmental changes and drug resistances.
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22
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Ellsworth DL, Blackburn HL, Shriver CD, Rabizadeh S, Soon-Shiong P, Ellsworth RE. Single-cell sequencing and tumorigenesis: improved understanding of tumor evolution and metastasis. Clin Transl Med 2017; 6:15. [PMID: 28405930 PMCID: PMC5389955 DOI: 10.1186/s40169-017-0145-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/21/2017] [Indexed: 02/06/2023] Open
Abstract
Extensive genomic and transcriptomic heterogeneity in human cancer often negatively impacts treatment efficacy and survival, thus posing a significant ongoing challenge for modern treatment regimens. State-of-the-art DNA- and RNA-sequencing methods now provide high-resolution genomic and gene expression portraits of individual cells, facilitating the study of complex molecular heterogeneity in cancer. Important developments in single-cell sequencing (SCS) technologies over the past 5 years provide numerous advantages over traditional sequencing methods for understanding the complexity of carcinogenesis, but significant hurdles must be overcome before SCS can be clinically useful. In this review, we: (1) highlight current methodologies and recent technological advances for isolating single cells, single-cell whole-genome and whole-transcriptome amplification using minute amounts of nucleic acids, and SCS, (2) summarize research investigating molecular heterogeneity at the genomic and transcriptomic levels and how this heterogeneity affects clonal evolution and metastasis, and (3) discuss the promise for integrating SCS in the clinical care arena for improved patient care.
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Affiliation(s)
- Darrell L. Ellsworth
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, 620 Seventh Street, Windber, PA 15963 USA
| | - Heather L. Blackburn
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, 620 Seventh Street, Windber, PA 15963 USA
| | - Craig D. Shriver
- Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Rockville Pike, Bethesda, MD 20889 USA
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23
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Zhang L, Wang W, Zhu B, Wang X. Regulatory Roles of Mitochondrial Ribosome in Lung Diseases and Single Cell Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:183-200. [PMID: 29178077 DOI: 10.1007/978-981-10-6674-0_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mitochondria have the most vital processes in eukaryotic cells to produce ATP composed of polypeptides that are produced via ribosomes, as oxidative phosphorylation. Initially, studies regarding human mitochondrial ribosomes were performed in the model system, bovine mitochondrial ribosome, to investigate how ribosomes are biosynthesized and evolved as well as what their structure and function are. Advances in X-ray crystallography have led to dramatic progresses in structural studies of the ribosome. In recent years, there has been a growing interest in the properties of the mitochondrial ribosome. Although one of its main functions is the production of ATP, it was also linked to multiple diseases. A key area that remains unexplored and requires investigation and exploration is how mitochondrial ribosomal RNA (mt-rRNA) variations can affect the mitochondrial ribosomes in developing disease. This review summarizes the structure, elements, functions, and regulatory roles in associated diseases. With the continuous development of technology, studies on the mechanism of mitochondrial ribosome related diseases are crucial, in order to identify methods of prevention and treatment of these disorders.
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Affiliation(s)
- Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China
| | - William Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China
| | - Bijun Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China.
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24
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Shi L, Zhu B, Xu M, Wang X. Selection of AECOPD-specific immunomodulatory biomarkers by integrating genomics and proteomics with clinical informatics. Cell Biol Toxicol 2017; 34:109-123. [DOI: 10.1007/s10565-017-9405-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 07/06/2017] [Indexed: 12/14/2022]
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25
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Wang W, Gao D, Wang X. Can single-cell RNA sequencing crack the mystery of cells? Cell Biol Toxicol 2017; 34:1-6. [DOI: 10.1007/s10565-017-9404-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/28/2017] [Indexed: 12/15/2022]
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26
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27
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Qian M, Zhu B, Wang X, Liebman M. Drug resistance in ALK-positiveNon-small cell lungcancer patients. Semin Cell Dev Biol 2017; 64:150-157. [DOI: 10.1016/j.semcdb.2016.09.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023]
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28
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Wang DC, Shi L, Zhu Z, Gao D, Zhang Y. Genomic mechanisms of transformation from chronic obstructive pulmonary disease to lung cancer. Semin Cancer Biol 2017; 42:52-59. [DOI: 10.1016/j.semcancer.2016.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/08/2016] [Indexed: 01/17/2023]
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29
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Epithelial Mitochondrial Dysfunction in Lung Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:201-217. [DOI: 10.1007/978-981-10-6674-0_14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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30
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Wang DC, Wang X. Tomorrow's genome medicine in lung cancer. Semin Cancer Biol 2016; 42:39-43. [PMID: 27840277 DOI: 10.1016/j.semcancer.2016.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/08/2016] [Indexed: 02/03/2023]
Abstract
Tomorrow's genome medicine in lung cancer should focus more on the homogeneity and heterogeneity of lung cancer which play an important role in the development of drug resistance, genetic complexity, as well as confusion and difficulty of early diagnosis and therapy. Chromosome positioning and repositioning may contribute to the sensitivity of lung cancer cells to therapy, the heterogeneity associated with drug resistance, and the mechanism of lung carcinogenesis. The CCCTC-binding factor plays critical roles in genome topology and function, increased risk of carcinogenicity, and potential of lung cancer-specific mediations. Chromosome reposition in lung cancer can be regulated by CCCTC binding factor. Single-cell gene sequencing, as part of genome medicine, was paid special attention in lung cancer to understand mechanical phenotypes, single-cell biology, heterogeneity, and chromosome positioning and function of single lung cancer cells. We at first propose to develop an intelligent single-cell robot of human cells to integrate together systems information of molecules, genes, proteins, organelles, membranes, architectures, signals, and functions. It can be a powerful automatic system to assist clinicians in the decision-making, molecular understanding, risk analyzing, and prognosis predicting.
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Affiliation(s)
- Diane C Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Shanghai, China.
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31
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Wang L, Wang H, Song D, Xu M, Liebmen M. New strategies for targeting drug combinations to overcome mutation-driven drug resistance. Semin Cancer Biol 2016; 42:44-51. [PMID: 27840276 DOI: 10.1016/j.semcancer.2016.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/08/2016] [Indexed: 12/12/2022]
Abstract
Targeted therapies are suggested as an effective alternative for patients with cancer that harbor mutations, but treatment outcomes are frequently limited by primary or acquired drug resistance. The present review describes potential mechanisms of primary or acquired drug resistances to provide a resource for considering how to be overcome. We focus on strategies of targeted drug combinations to minimize the development of drug resistance within the context how resistance develops. Strategies benefit from the combined use of "omics" technologies, i.e., high-throughput functional genomics data, pharmacogenomics, or genome-wide CRISPR-Cas9 screening, to analyze and design targeted drug combinations for mutation-driven drug resistance. We also introduce new insights towards pathway-centric combined therapies as an alternative to overcome the heterogeneity and benefit patient prognoses.
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Affiliation(s)
- Linyan Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Biomedical Research Center, Shanghai, China.
| | - Haiyun Wang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Dongli Song
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Biomedical Research Center, Shanghai, China
| | - Menglin Xu
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Biomedical Research Center, Shanghai, China
| | - Michael Liebmen
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Biomedical Research Center, Shanghai, China.
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32
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Hou J, Zhang Y, Zhu Z. Gene heterogeneity in metastasis of colorectal cancer to the lung. Semin Cell Dev Biol 2016; 64:58-64. [PMID: 27590223 DOI: 10.1016/j.semcdb.2016.08.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 08/30/2016] [Indexed: 12/21/2022]
Abstract
Colorectal cancer (CRC) as a heterogeneous disease, is one of the most common and serious cancers with high metastases and mortality. Lung is one of the most common sites of CRC metastases with high heterogeneity between cells, pathways, or molecules. The present review will focus on potential roles of gene heterogeneity in KRAS pathway in the development of CRC metastasis to lung and clinical therapies, which would lead to better understanding of the metastatic control and benefit to the treatment of metastases. KRAS is the central relay for pathways originating at the epidermal growth factor receptor (EGFR) family. KRAS mutation exists in about 40% CRC, associated with higher cumulative incidence of CRC lung metastasis, and acts as an independent predictor of metastasis to lung. Mutations in KRAS can lead to poor response of patients to panitumumab, and inferior progression-free survival. However, most patients with KRAS wild-type tumors still do not respond, which indicates other mutations. Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutation was associated with lung metastases in metastatic colorectal cancer. PIK3CA mutation in exon 20 was found to be correlated with patient survival in the metastatic setting after the treatment with cetuximab and chemotherapy. The heterogeneity of KRAS pathway was found in the phosphatase and tensin homologue deleted on chromosome ten loss, disheveled binding antagonist of beta catenin 2 overexpression and increased dual-specificity protein phosphatase 4 expression of CRC lung metastasis.
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Affiliation(s)
- Jiayun Hou
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Biomedical Research Center, Shanghai, China
| | - Yong Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Biomedical Research Center, Shanghai, China.
| | - Zhitu Zhu
- Jinzhou Hospital of Jinzhou Medical University, JinZhou, China.
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33
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Bergau N, Navarette Santos A, Henning A, Balcke GU, Tissier A. Autofluorescence as a Signal to Sort Developing Glandular Trichomes by Flow Cytometry. FRONTIERS IN PLANT SCIENCE 2016; 7:949. [PMID: 27446176 PMCID: PMC4923063 DOI: 10.3389/fpls.2016.00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/14/2016] [Indexed: 05/04/2023]
Abstract
The industrial relevance of a number of metabolites produced in plant glandular trichomes (GTs) has spurred research on these specialized organs for a number of years. Most of the research, however, has focused on the elucidation of secondary metabolite pathways and comparatively little has been undertaken on the development and differentiation of GTs. One way to gain insight into these developmental processes is to generate stage-specific transcriptome and metabolome data. The difficulty for this resides in the isolation of early stages of development of the GTs. Here we describe a method for the separation and isolation of intact young and mature type VI trichomes from the wild tomato species Solanum habrochaites. The final and key step of the method uses cell sorting based on distinct autofluorescence signals of the young and mature trichomes. We demonstrate that sorting by flow cytometry allows recovering pure fractions of young and mature trichomes. Furthermore, we show that the sorted trichomes can be used for transcript and metabolite analyses. Because many plant tissues or cells have distinct autofluorescence components, the principles of this method can be generally applicable for the isolation of specific cell types without prior labeling.
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Affiliation(s)
- Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | | | - Anja Henning
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | - Gerd U. Balcke
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
- *Correspondence: Alain Tissier,
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