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Harris AR, McGivern P, Gilbert F, Van Bergen N. Defining Biomarkers in Stem Cell-Derived Tissue Constructs for Drug and Disease Screening. Adv Healthc Mater 2024:e2401433. [PMID: 38741544 DOI: 10.1002/adhm.202401433] [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: 04/18/2024] [Revised: 04/24/2024] [Indexed: 05/16/2024]
Abstract
The development of stem cell-derived tissue constructs (SCTCs) for clinical applications, including regenerative medicine, drug and disease screening offers significant hope for detecting and treating intractable disorders. SCTCs display a variety of biomarkers that can be used to understand biological mechanisms, assess drug interactions, and predict disease. Although SCTCs can be derived from patients and share the same genetic make-up, they are nevertheless distinct from human patients in many significant ways, which can undermine the clinical significance of measurements in SCTCs. This study defines biomarkers, how they apply to SCTCs, and clarifies specific ethical issues associated with the use of SCTCs for drug and disease screening.
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Affiliation(s)
- Alexander R Harris
- Department of Biomedical Engineering, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Patrick McGivern
- School of Humanities and Social Inquiry, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Frederic Gilbert
- School of Humanities, University of Tasmania, Hobart, Tasmania, Australia
| | - Nicole Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3002, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3002, Australia
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2
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Choi S, Woo SH, Park I, Lee S, Yeo KI, Lee SH, Lee SY, Yang S, Lee G, Chang WJ, Bashir R, Kim YS, Lee SW. Cellular subpopulations identified using an ensemble average of multiple dielectrophoresis measurements. Comput Biol Med 2024; 170:108011. [PMID: 38271838 DOI: 10.1016/j.compbiomed.2024.108011] [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: 10/08/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
While the average value measurement approach can successfully analyze and predict the general behavior and biophysical properties of an isogenic cell population, it fails when significant differences among individual cells are generated in the population by intracellular changes such as the cell cycle, or different cellular responses to certain stimuli. Detecting such single-cell differences in a cell population has remained elusive. Here, we describe an easy-to-implement and generalizable platform that measures the dielectrophoretic cross-over frequency of individual cells by decreasing measurement noise with a stochastic method and computing ensemble average statistics. This platform enables multiple, real-time, label-free detection of individual cells with significant dielectric variations over time within an isogenic cell population. Using a stochastic method in combination with the platform, we distinguished cell subpopulations from a mixture of drug-untreated and -treated isogenic cells. Furthermore, we demonstrate that our platform can identify drug-treated isogenic cells with different recovery rates.
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Affiliation(s)
- Seungyeop Choi
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea; School of Biomedical Engineering, Korea University, Seoul, 02481, Republic of Korea; BK21 Four Institute of Precision Public Health, Korea University, Seoul, 02841, Republic of Korea
| | - Sung-Hun Woo
- Department of Biomedical Laboratory Science, Yonsei University, Wonju, 26493, Republic of Korea
| | - Insu Park
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Biomedical Engineering, Konyang University, Daejeon, 35365, Republic of Korea
| | - Sena Lee
- Department of Precision Medicine, Wonju College of Medicine, Yonsei University, Wonju, 26426, Republic of Korea
| | - Kang In Yeo
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea
| | - Sang Hyun Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea
| | - Sei Young Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea; Department of Medical Informatics and Biostatistics, Graduate School, Yonsei University, Wonju, 26426, Republic of Korea
| | - Sejung Yang
- Department of Precision Medicine, Wonju College of Medicine, Yonsei University, Wonju, 26426, Republic of Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Woo-Jin Chang
- Mechanical Engineering Department, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Rashid Bashir
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoon Suk Kim
- Department of Biomedical Laboratory Science, Yonsei University, Wonju, 26493, Republic of Korea.
| | - Sang Woo Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea.
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3
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Sjöblom A, Pehkonen H, Jouhi L, Monni O, Randén-Brady R, Karhemo PR, Tarkkanen J, Haglund C, Mattila P, Mäkitie A, Hagström J, Carpén T. Liprin-α1 Expression in Tumor-Infiltrating Lymphocytes Associates with Improved Survival in Patients with HPV-Positive Oropharyngeal Squamous Cell Carcinoma. Head Neck Pathol 2023; 17:647-657. [PMID: 37335526 PMCID: PMC10513983 DOI: 10.1007/s12105-023-01565-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/03/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Liprin-α1 is a scaffold protein involved in cell adhesion, motility, and invasion in malignancies. Liprin-α1 inhibits the expression of metastatic suppressor CD82 in cancers such as oral carcinoma, and the expression of these proteins has been known to correlate negatively. The role of these proteins has not been previously studied in human papillomavirus (HPV)-related head and neck cancers. Our aim was to assess the clinical and prognostic role of liprin-α1 and CD82 in HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) in comparison to HPV-negative OPSCC. METHODS The data included 139 OPSCC patients treated at the Helsinki University Hospital (HUS) during 2012-2016. Immunohistochemistry was utilized in HPV determination and in biomarker assays. Overall survival (OS) was used in the survival analysis. RESULTS Stronger expression of liprin-α1 in tumor-infiltrating lymphocytes (TILs) was linked to lower cancer stage (p < 0.001) and HPV positivity (p < 0.001). Additionally, we found an association between elevated expression of liprin-α1 and weak expression of CD82 in tumor cells (p = 0.029). In survival analysis, we found significant correlation between favorable OS and stronger expression of liprin-α1 in TILs among the whole patient cohort (p < 0.001) and among HPV-positive patients (p = 0.042). CONCLUSIONS Increased liprin-α1 expression in the TILs is associated with favorable prognosis in OPSCC, especially among HPV-positive patients.
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Affiliation(s)
- Anni Sjöblom
- Department of Pathology, University of Helsinki and Helsinki University Hospital, PO Box 21, 00014 Helsinki, Finland
| | - Henna Pehkonen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lauri Jouhi
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Outi Monni
- Applied Tumor Genomics Research Program and Department of Oncology, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Reija Randén-Brady
- Department of Pathology, University of Helsinki and Helsinki University Hospital, PO Box 21, 00014 Helsinki, Finland
| | - Piia-Riitta Karhemo
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jussi Tarkkanen
- Department of Pathology, University of Helsinki and Helsinki University Hospital, PO Box 21, 00014 Helsinki, Finland
| | - Caj Haglund
- Research Programs Unit, Translational Cancer Medicine and Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Petri Mattila
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Antti Mäkitie
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska Hospital, Stockholm, Sweden
- Departments of Pathology and of Otorhinolaryngology, Head and Neck Surgery and Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaana Hagström
- Department of Pathology and Research Programs Unit, Translational Cancer Medicine, University of Helsinki, Helsinki, Finland
- Department of Oral Pathology and Oral Radiology, University of Turku, Turku, Finland
| | - Timo Carpén
- Departments of Pathology and of Otorhinolaryngology, Head and Neck Surgery and Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Neves Rebello Alves L, Dummer Meira D, Poppe Merigueti L, Correia Casotti M, do Prado Ventorim D, Ferreira Figueiredo Almeida J, Pereira de Sousa V, Cindra Sant'Ana M, Gonçalves Coutinho da Cruz R, Santos Louro L, Mendonça Santana G, Erik Santos Louro T, Evangelista Salazar R, Ribeiro Campos da Silva D, Stefani Siqueira Zetum A, Silva Dos Reis Trabach R, Imbroisi Valle Errera F, de Paula F, de Vargas Wolfgramm Dos Santos E, Fagundes de Carvalho E, Drumond Louro I. Biomarkers in Breast Cancer: An Old Story with a New End. Genes (Basel) 2023; 14:1364. [PMID: 37510269 PMCID: PMC10378988 DOI: 10.3390/genes14071364] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer is the second most frequent cancer in the world. It is a heterogeneous disease and the leading cause of cancer mortality in women. Advances in molecular technologies allowed for the identification of new and more specifics biomarkers for breast cancer diagnosis, prognosis, and risk prediction, enabling personalized treatments, improving therapy, and preventing overtreatment, undertreatment, and incorrect treatment. Several breast cancer biomarkers have been identified and, along with traditional biomarkers, they can assist physicians throughout treatment plan and increase therapy success. Despite the need of more data to improve specificity and determine the real clinical utility of some biomarkers, others are already established and can be used as a guide to make treatment decisions. In this review, we summarize the available traditional, novel, and potential biomarkers while also including gene expression profiles, breast cancer single-cell and polyploid giant cancer cells. We hope to help physicians understand tumor specific characteristics and support decision-making in patient-personalized clinical management, consequently improving treatment outcome.
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Affiliation(s)
- Lyvia Neves Rebello Alves
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Débora Dummer Meira
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Luiza Poppe Merigueti
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Matheus Correia Casotti
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Diego do Prado Ventorim
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo (Ifes), Cariacica 29150-410, ES, Brazil
| | - Jucimara Ferreira Figueiredo Almeida
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Valdemir Pereira de Sousa
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Marllon Cindra Sant'Ana
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Rahna Gonçalves Coutinho da Cruz
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Luana Santos Louro
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, ES, Brazil
| | - Gabriel Mendonça Santana
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, ES, Brazil
| | - Thomas Erik Santos Louro
- Escola Superior de Ciências da Santa Casa de Misericórdia de Vitória (EMESCAM), Vitória 29027-502, ES, Brazil
| | - Rhana Evangelista Salazar
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Danielle Ribeiro Campos da Silva
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Aléxia Stefani Siqueira Zetum
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Raquel Silva Dos Reis Trabach
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Flávia Imbroisi Valle Errera
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Flávia de Paula
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Eldamária de Vargas Wolfgramm Dos Santos
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Elizeu Fagundes de Carvalho
- Instituto de Biologia Roberto Alcântara Gomes (IBRAG), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20551-030, RJ, Brazil
| | - Iúri Drumond Louro
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
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Koyappayil A, Yagati AK, Lee MH. Recent Trends in Metal Nanoparticles Decorated 2D Materials for Electrochemical Biomarker Detection. BIOSENSORS 2023; 13:91. [PMID: 36671926 PMCID: PMC9855691 DOI: 10.3390/bios13010091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/27/2022] [Accepted: 01/01/2023] [Indexed: 05/29/2023]
Abstract
Technological advancements in the healthcare sector have pushed for improved sensors and devices for disease diagnosis and treatment. Recently, with the discovery of numerous biomarkers for various specific physiological conditions, early disease screening has become a possibility. Biomarkers are the body's early warning systems, which are indicators of a biological state that provides a standardized and precise way of evaluating the progression of disease or infection. Owing to the extremely low concentrations of various biomarkers in bodily fluids, signal amplification strategies have become crucial for the detection of biomarkers. Metal nanoparticles are commonly applied on 2D platforms to anchor antibodies and enhance the signals for electrochemical biomarker detection. In this context, this review will discuss the recent trends and advances in metal nanoparticle decorated 2D materials for electrochemical biomarker detection. The prospects, advantages, and limitations of this strategy also will be discussed in the concluding section of this review.
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Affiliation(s)
| | | | - Min-Ho Lee
- School of Integrative Engineering, Chung-Ang University, 84 Heuseok-ro, Dongjak-Gu, Seoul 06974, Republic of Korea
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Mathews J, Amaravadi L, Eck S, Stevenson L, Wang YMC, Devanarayan V, Allinson J, Lundsten K, Gunsior M, Ni YG, Pepin MO, Gagnon A, Sheldon C, Trampont PC, Litwin V. Best practices for the development and fit-for-purpose validation of biomarker methods: a conference report. AAPS OPEN 2022. [DOI: 10.1186/s41120-021-00050-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractThis conference report summarized a full-day workshop, “best practices for the development and fit-for-purpose validation of biomarker methods,” which was held prior to the American Association of Pharmaceutical Scientists (AAPS) PharmSci360 Congress, San Antonio, TX, November 2019. The purpose of the workshop was to bring together thought leaders in biomarker assay development in order to identify which assay parameters and key statistical measures need to be considered when developing a biomarker assay. A diverse group of more than 40 scientists participated in the workshop. The workshop and subsequent working dinner stimulated robust discussion. While a consensus on best practices was not achieved, some common themes and major points to consider for biomarker assay development have been identified and agreed on. The focus of this conference report is to summarize the presentations and discussions which occurred at the workshop. Biomarker assay validation is a complex and an evolving area with discussions ongoing.
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From imaging a single cell to implementing precision medicine: an exciting new era. Emerg Top Life Sci 2021; 5:837-847. [PMID: 34889448 PMCID: PMC8786301 DOI: 10.1042/etls20210219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022]
Abstract
In the age of high-throughput, single-cell biology, single-cell imaging has evolved not only in terms of technological advancements but also in its translational applications. The synchronous advancements of imaging and computational biology have produced opportunities of merging the two, providing the scientific community with tools towards observing, understanding, and predicting cellular and tissue phenotypes and behaviors. Furthermore, multiplexed single-cell imaging and machine learning algorithms now enable patient stratification and predictive diagnostics of clinical specimens. Here, we provide an overall summary of the advances in single-cell imaging, with a focus on high-throughput microscopy phenomics and multiplexed proteomic spatial imaging platforms. We also review various computational tools that have been developed in recent years for image processing and downstream applications used in biomedical sciences. Finally, we discuss how harnessing systems biology approaches and data integration across disciplines can further strengthen the exciting applications and future implementation of single-cell imaging on precision medicine.
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8
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Yang M, Villarreal JC, Ariyasinghe N, Kruithoff R, Ros R, Ros A. Quantitative Approach for Protein Analysis in Small Cell Ensembles by an Integrated Microfluidic Chip with MALDI Mass Spectrometry. Anal Chem 2021; 93:6053-6061. [PMID: 33819014 PMCID: PMC8128341 DOI: 10.1021/acs.analchem.0c04112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing evidence has demonstrated that cells are individually heterogeneous. Advancing the technologies for single-cell analysis will improve our ability to characterize cells, study cell biology, design and screen drugs, and aid cancer diagnosis and treatment. Most current single-cell protein analysis approaches are based on fluorescent antibody-binding technology. However, this technology is limited by high background and cross-talk of multiple tags introduced by fluorescent labels. Stable isotope labels used in mass cytometry can overcome the spectral overlap of fluorophores. Nevertheless, the specificity of each antibody and heavy-metal-tagged antibody combination must be carefully validated to ensure detection of the intended target. Thus, novel single-cell protein analysis methods without using labels are urgently needed. Moreover, the labeling approach targets already known motifs, hampering the discovery of new biomarkers relevant to single-cell population variation. Here, we report a combined microfluidic and matrix-assisted laser desorption and ionization (MALDI) mass spectrometric approach for the analysis of protein biomarkers suitable for small cell ensembles. All necessary steps for cell analysis including cell lysis, protein capture, and digestion as well as MALDI matrix deposition are integrated on a microfluidic chip prior to the downstream MALDI-time-of-flight (TOF) detection. For proof of principle, this combined method is used to assess the amount of Bcl-2, an apoptosis regulator, in metastatic breast cancer cells (MCF-7) by using an isotope-labeled peptide as an internal standard. The proposed approach will eventually provide a new means for proteome studies in small cell ensembles with the potential for single-cell analysis and improve our ability in disease diagnosis, drug discovery, and personalized therapy.
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Affiliation(s)
- Mian Yang
- Department of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan City, Hubei Province, 430081, P.R.China
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe AZ, 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-7401, USA
| | - Nethmi Ariyasinghe
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
| | - Robert Ros
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe AZ, 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-7401, USA
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Miller AK, Brown JS, Basanta D, Huntly N. What Is the Storage Effect, Why Should It Occur in Cancers, and How Can It Inform Cancer Therapy? Cancer Control 2021; 27:1073274820941968. [PMID: 32723185 PMCID: PMC7658723 DOI: 10.1177/1073274820941968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Intratumor heterogeneity is a feature of cancer that is associated with progression, treatment resistance, and recurrence. However, the mechanisms that allow diverse cancer cell lineages to coexist remain poorly understood. The storage effect is a coexistence mechanism that has been proposed to explain the diversity of a variety of ecological communities, including coral reef fish, plankton, and desert annual plants. Three ingredients are required for there to be a storage effect: (1) temporal variability in the environment, (2) buffered population growth, and (3) species-specific environmental responses. In this article, we argue that these conditions are observed in cancers and that it is likely that the storage effect contributes to intratumor diversity. Data that show the temporal variation within the tumor microenvironment are needed to quantify how cancer cells respond to fluctuations in the tumor microenvironment and what impact this has on interactions among cancer cell types. The presence of a storage effect within a patient’s tumors could have a substantial impact on how we understand and treat cancer.
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Affiliation(s)
- Anna K Miller
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Joel S Brown
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David Basanta
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Nancy Huntly
- Ecology Center & Department of Biology, Utah State University, Logan, UT, USA
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Campos A, Freitas M, de Almeida AM, Martins JC, Domínguez-Pérez D, Osório H, Vasconcelos V, Reis Costa P. OMICs Approaches in Diarrhetic Shellfish Toxins Research. Toxins (Basel) 2020; 12:E493. [PMID: 32752012 PMCID: PMC7472309 DOI: 10.3390/toxins12080493] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Diarrhetic shellfish toxins (DSTs) are among the most prevalent marine toxins in Europe's and in other temperate coastal regions. These toxins are produced by several dinoflagellate species; however, the contamination of the marine trophic chain is often attributed to species of the genus Dinophysis. This group of toxins, constituted by okadaic acid (OA) and analogous molecules (dinophysistoxins, DTXs), are highly harmful to humans, causing severe poisoning symptoms caused by the ingestion of contaminated seafood. Knowledge on the mode of action and toxicology of OA and the chemical characterization and accumulation of DSTs in seafood species (bivalves, gastropods and crustaceans) has significantly contributed to understand the impacts of these toxins in humans. Considerable information is however missing, particularly at the molecular and metabolic levels involving toxin uptake, distribution, compartmentalization and biotransformation and the interaction of DSTs with aquatic organisms. Recent contributions to the knowledge of DSTs arise from transcriptomics and proteomics research. Indeed, OMICs constitute a research field dedicated to the systematic analysis on the organisms' metabolisms. The methodologies used in OMICs are also highly effective to identify critical metabolic pathways affecting the physiology of the organisms. In this review, we analyze the main contributions provided so far by OMICs to DSTs research and discuss the prospects of OMICs with regard to the DSTs toxicology and the significance of these toxins to public health, food safety and aquaculture.
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Affiliation(s)
- Alexandre Campos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Marisa Freitas
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
- ESS-P.Porto, School of Health, Polytechnic Institute of Porto. Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
| | - André M. de Almeida
- LEAF-Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal;
| | - José Carlos Martins
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Dany Domínguez-Pérez
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Hugo Osório
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
- Ipatimup—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro Reis Costa
- IPMA—Instituto Português do Mar da Atmosfera, Rua Alfredo Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal;
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11
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Kamies R, Martinez-Jimenez CP. Advances of single-cell genomics and epigenomics in human disease: where are we now? Mamm Genome 2020; 31:170-180. [PMID: 32270277 PMCID: PMC7368869 DOI: 10.1007/s00335-020-09834-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
Abstract
Cellular heterogeneity is revolutionizing the way to study, monitor and dissect complex diseases. This has been possible with the technological and computational advances associated to single-cell genomics and epigenomics. Deeper understanding of cell-to-cell variation and its impact on tissue function will open new avenues for early disease detection, accurate diagnosis and personalized treatments, all together leading to the next generation of health care. This review focuses on the recent discoveries that single-cell genomics and epigenomics have facilitated in the context of human health. It highlights the potential of single-cell omics to further advance the development of personalized treatments and precision medicine in cancer, diabetes and chronic age-related diseases. The promise of single-cell technologies to generate new insights about the differences in function between individual cells is just emerging, and it is paving the way for identifying biomarkers and novel therapeutic targets to tackle age, complex diseases and understand the effect of life style interventions and environmental factors.
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Affiliation(s)
- Rizqah Kamies
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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12
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Lam VK, Nguyen T, Bui V, Chung BM, Chang LC, Nehmetallah G, Raub CB. Quantitative scoring of epithelial and mesenchymal qualities of cancer cells using machine learning and quantitative phase imaging. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-17. [PMID: 32072775 PMCID: PMC7026523 DOI: 10.1117/1.jbo.25.2.026002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/30/2020] [Indexed: 05/07/2023]
Abstract
SIGNIFICANCE We introduce an application of machine learning trained on optical phase features of epithelial and mesenchymal cells to grade cancer cells' morphologies, relevant to evaluation of cancer phenotype in screening assays and clinical biopsies. AIM Our objective was to determine quantitative epithelial and mesenchymal qualities of breast cancer cells through an unbiased, generalizable, and linear score covering the range of observed morphologies. APPROACH Digital holographic microscopy was used to generate phase height maps of noncancerous epithelial (Gie-No3B11) and fibroblast (human gingival) cell lines, as well as MDA-MB-231 and MCF-7 breast cancer cell lines. Several machine learning algorithms were evaluated as binary classifiers of the noncancerous cells that graded the cancer cells by transfer learning. RESULTS Epithelial and mesenchymal cells were classified with 96% to 100% accuracy. Breast cancer cells had scores in between the noncancer scores, indicating both epithelial and mesenchymal morphological qualities. The MCF-7 cells skewed toward epithelial scores, while MDA-MB-231 cells skewed toward mesenchymal scores. Linear support vector machines (SVMs) produced the most distinct score distributions for each cell line. CONCLUSIONS The proposed epithelial-mesenchymal score, derived from linear SVM learning, is a sensitive and quantitative approach for detecting epithelial and mesenchymal characteristics of unknown cells based on well-characterized cell lines. We establish a framework for rapid and accurate morphological evaluation of single cells and subtle phenotypic shifts in imaged cell populations.
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Affiliation(s)
- Van K. Lam
- The Catholic University of America, Department of Biomedical Engineering, Washington, DC, United States
| | - Thanh Nguyen
- The Catholic University of America, Department of Electrical Engineering and Computer Science, Washington, DC, United States
| | - Vy Bui
- The Catholic University of America, Department of Electrical Engineering and Computer Science, Washington, DC, United States
| | - Byung Min Chung
- The Catholic University of America, Department of Biology, Washington, DC, United States
| | - Lin-Ching Chang
- The Catholic University of America, Department of Electrical Engineering and Computer Science, Washington, DC, United States
| | - George Nehmetallah
- The Catholic University of America, Department of Electrical Engineering and Computer Science, Washington, DC, United States
| | - Christopher B. Raub
- The Catholic University of America, Department of Biomedical Engineering, Washington, DC, United States
- Address all correspondence to Christopher B. Raub, E-mail:
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13
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Varsanik JS, Manak MS, Whitfield MJ, Hogan BJ, Su WR, Jiang CJ, Sant GR, Albala DM, Chander AC. Application of Artificial Intelligence/Machine Vision & Learning for the Development of a Live Single-cell Phenotypic Biomarker Test to Predict Prostate Cancer Tumor Aggressiveness. Rev Urol 2020; 22:159-167. [PMID: 33927573 PMCID: PMC8058915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To assess the usefulness and applications of machine vision (MV) and machine learning (ML) techniques that have been used to develop a single cell-based phenotypic (live and fixed biomarkers) platform that correlates with tumor biological aggressiveness and risk stratification, 100 fresh prostate samples were acquired, and areas of prostate cancer were determined by post-surgery pathology reports logged by an independent pathologist. The prostate samples were dissociated into single-cell suspensions in the presence of an extracellular matrix formulation. These samples were analyzed via live-cell microscopy. Dynamic and fixed phenotypic biomarkers per cell were quantified using objective MV software and ML algorithms. The predictive nature of the ML algorithms was developed in two stages. First, random forest (RF) algorithms were developed using 70% of the samples. The developed algorithms were then tested for their predictive performance using the blinded test dataset that contained 30% of the samples in the second stage. Based on the ROC (receiver operating characteristic) curve analysis, thresholds were set to maximize both sensitivity and specificity. We determined the sensitivity and specificity of the assay by comparing the algorithm-generated predictions with adverse pathologic features in the radical prostatectomy (RP) specimens. Using MV and ML algorithms, the biomarkers predictive of adverse pathology at RP were ranked and a prostate cancer patient risk stratification test was developed that distinguishes patients based on surgical adverse pathology features. The ability to identify and track large numbers of individual cells over the length of the microscopy experimental monitoring cycles, in an automated way, created a large biomarker dataset of primary biomarkers. This biomarker dataset was then interrogated with ML algorithms used to correlate with post-surgical adverse pathology findings. Algorithms were generated that predicted adverse pathology with >0.85 sensitivity and specificity and an AUC (area under the curve) of >0.85. Phenotypic biomarkers provide cellular and molecular details that are informative for predicting post-surgical adverse pathologies when considering tumor biopsy samples. Artificial intelligence ML-based approaches for cancer risk stratification are emerging as important and powerful tools to compliment current measures of risk stratification. These techniques have capabilities to address tumor heterogeneity and the molecular complexity of prostate cancer. Specifically, the phenotypic test is a novel example of leveraging biomarkers and advances in MV and ML for developing a powerful prognostic and risk-stratification tool for prostate cancer patients.
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14
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Wang K, Xue Y, Peng Y, Pang X, Zhang Y, Ruiz-Ortega LI, Tian Y, Ngan AHW, Tang B. Elastic modulus and migration capability of drug treated leukemia cells K562. Biochem Biophys Res Commun 2019; 516:177-182. [PMID: 31204049 DOI: 10.1016/j.bbrc.2019.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 06/05/2019] [Indexed: 01/25/2023]
Abstract
Leukemia is a commonly seen disease caused by abnormal differentiation of hematopoietic stem cells and blasting in bone marrow. Despite drugs are used to treat the disease clinically, the influence of these drugs on leukemia cells' biomechanical properties, which are closely related to complications like leukostasis or infiltration, is still unclear. Due to non-adherent and viscoelastic nature of leukemia cells, accurate measurement of their elastic modulus is still a challenging issue. In this study, we adopted rate-jump method together with optical tweezers indentation to accurately measure elastic modulus of leukemia cells K562 after phorbol 12-myristate 13-acetate (PMA), all-trans retinoic acid (ATRA), Cytoxan (CTX), and Dexamethasone (DEX) treatment, respectively. We found that compared to control sample, K562 cells treated by PMA showed nearly a threefold increase in elastic modulus. Transwell experiment results suggested that the K562 cells treated with PMA have the lowest migration capability. Besides, it was shown that the cytoskeleton protein gene α-tubulin and vimentin have a significant increase in expression after PMA treatment by qPCR. The results indicate that PMA has a significant influence on protein expression, stiffness, and migration ability of the leukemia cell K562, and may also play an important role in the leukostasis in leukemia.
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Affiliation(s)
- Kui Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China; Department of Mechanical Engineering, University of Hong Kong, Hong Kong, PR China
| | - Yuntian Xue
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - Ying Peng
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - Xiangchao Pang
- College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, PR China
| | - Yuanjun Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - L I Ruiz-Ortega
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - Ye Tian
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - A H W Ngan
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong, PR China
| | - Bin Tang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, PR China.
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15
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Guerrini L, Alvarez-Puebla RA. Surface-Enhanced Raman Spectroscopy in Cancer Diagnosis, Prognosis and Monitoring. Cancers (Basel) 2019; 11:E748. [PMID: 31146464 PMCID: PMC6627759 DOI: 10.3390/cancers11060748] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 12/28/2022] Open
Abstract
As medicine continues to advance our understanding of and knowledge about the complex and multifactorial nature of cancer, new major technological challenges have emerged in the design of analytical methods capable of characterizing and assessing the dynamic heterogeneity of cancer for diagnosis, prognosis and monitoring, as required by precision medicine. With this aim, novel nanotechnological approaches have been pursued and developed for overcoming intrinsic and current limitations of conventional methods in terms of rapidity, sensitivity, multiplicity, non-invasive procedures and cost. Eminently, a special focus has been put on their implementation in liquid biopsy analysis. Among optical nanosensors, those based on surface-enhanced Raman scattering (SERS) have been attracting tremendous attention due to the combination of the intrinsic prerogatives of the technique (e.g., sensitivity and structural specificity) and the high degree of refinement in nano-manufacturing, which translate into reliable and robust real-life applications. In this review, we categorize the diverse strategic approaches of SERS biosensors for targeting different classes of tumor biomarkers (cells, nucleic acids and proteins) by illustrating key recent research works. We will also discuss the current limitations and future research challenges to be addressed to improve the competitiveness of SERS over other methodologies in cancer medicine.
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Affiliation(s)
- Luca Guerrini
- Department of Physical and Inorganic Chemistry and EMaS, Universitat Rovira I Virgili, Carrer de Marcel.lí Domingo s/n, 43007 Tarragona, Spain.
| | - Ramon A Alvarez-Puebla
- Department of Physical and Inorganic Chemistry and EMaS, Universitat Rovira I Virgili, Carrer de Marcel.lí Domingo s/n, 43007 Tarragona, Spain.
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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Ouellette SB. Landscape of granted US patents in personalized diagnostics for oncology from 2014 to 2018. Expert Opin Ther Pat 2019; 29:191-198. [PMID: 30712415 DOI: 10.1080/13543776.2019.1575809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Personalized diagnostic testing (PDx) is a key component of the precision medicine toolkit and has shown the most development in cancer applications. Recent changes in the regulatory and legal landscapes regarding PDx development and commercialization have brought uncertainties to both intellectual property strategies and business model development. While the regulatory and legal uncertainties have been well-documented, there has been little reported analysis of the recent patent landscape and movement of IP into the PDx market. Areas covered: This article provides a snapshot landscape analysis of cancer-associated PDx US granted patents from 2014 to 2018, with a focus on claim types, biomarkers, and associated detection strategies, and assignee-specific IP portfolio analyses. Expert opinion: Patent-driven research is commonplace in the legal world for performing patentability, clearance, and validity analyses. The results from this review show that patent-driven analysis is also insightful for understanding strategies to build IP portfolios around biomarker and detection platforms, identifying partners and competitors, and driving PDx technologies into the market. This information is an important source of business intelligence and can provide companies or investors with valuable information for making strategic decisions in developing and commercializing PDx technologies.
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Affiliation(s)
- Steven B Ouellette
- a Biotechnology & Pharmaceuticals Group , Global Prior Art, Inc , Boston , MA , USA
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17
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An Integrative Data Mining and Omics-Based Translational Model for the Identification and Validation of Oncogenic Biomarkers of Pancreatic Cancer. Cancers (Basel) 2019; 11:cancers11020155. [PMID: 30700038 PMCID: PMC6407035 DOI: 10.3390/cancers11020155] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 12/20/2022] Open
Abstract
Substantial alterations at the multi-omics level of pancreatic cancer (PC) impede the possibility to diagnose and treat patients in early stages. Herein, we conducted an integrative omics-based translational analysis, utilizing next-generation sequencing, transcriptome meta-analysis, and immunohistochemistry, combined with statistical learning, to validate multiplex biomarker candidates for the diagnosis, prognosis, and management of PC. Experiment-based validation was conducted and supportive evidence for the essentiality of the candidates in PC were found at gene expression or protein level by practical biochemical methods. Remarkably, the random forests (RF) model exhibited an excellent diagnostic performance and LAMC2, ANXA2, ADAM9, and APLP2 greatly influenced its decisions. An explanation approach for the RF model was successfully constructed. Moreover, protein expression of LAMC2, ANXA2, ADAM9, and APLP2 was found correlated and significantly higher in PC patients in independent cohorts. Survival analysis revealed that patients with high expression of ADAM9 (Hazard ratio (HR)OS = 2.2, p-value < 0.001), ANXA2 (HROS = 2.1, p-value < 0.001), and LAMC2 (HRDFS = 1.8, p-value = 0.012) exhibited poorer survival rates. In conclusion, we successfully explore hidden biological insights from large-scale omics data and suggest that LAMC2, ANXA2, ADAM9, and APLP2 are robust biomarkers for early diagnosis, prognosis, and management for PC.
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18
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Albala D, Manak MS, Varsanik JS, Rashid HH, Mouraviev V, Zappala SM, Ette E, Kella N, Rieger-Christ KM, Sant GR, Chander AC. Clinical Proof-of-concept of a Novel Platform Utilizing Biopsy-derived Live Single Cells, Phenotypic Biomarkers, and Machine Learning Toward a Precision Risk Stratification Test for Prostate Cancer Grade Groups 1 and 2 (Gleason 3 + 3 and 3 + 4). Urology 2018; 124:198-206. [PMID: 30312670 DOI: 10.1016/j.urology.2018.09.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/05/2018] [Accepted: 06/14/2018] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To examine the ability of a novel live primary-cell phenotypic (LPCP) test to predict postsurgical adverse pathology (P-SAP) features and risk stratify patients based on SAP features in a blinded study utilizing radical prostatectomy (RP) surgical specimens. METHODS Two hundred fifty-one men undergoing RP were enrolled in a prospective, multicenter (10), and proof-of-concept study in the United States. Fresh prostate samples were taken from known areas of cancer in the operating room immediately after RP. Samples were shipped and tested at a central laboratory. Utilizing the LPCP test, a suite of phenotypic biomarkers was analyzed and quantified using objective machine vision software. Biomarkers were objectively ranked via machine learning-derived statistical algorithms (MLDSA) to predict postsurgical adverse pathological features. Sensitivity and specificity were determined by comparing blinded predictions and unblinded RP surgical pathology reports, training MLDSAs on 70% of biopsy cells and testing MLDSAs on the remaining 30% of biopsy cells across the tested patient population. RESULTS The LPCP test predicted adverse pathologies post-RP with area under the curve (AUC) via receiver operating characteristics analysis of greater than 0.80 and distinguished between Prostate Cancer Grade Groups 1, 2, and 3/Gleason Scores 3 + 3, 3 + 4, and 4 + 3. Further, LPCP derived-biomarker scores predicted Gleason pattern, stage, and adverse pathology with high precision-AUCs>0.80. CONCLUSION Using MLDSA-derived phenotypic biomarker scores, the LPCP test successfully risk stratified Prostate Cancer Grade Groups 1, 2, and 3 (Gleason 3 + 3 and 7) into distinct subgroups predicted to have surgical adverse pathologies or not with high performance (>0.85 AUC).
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Affiliation(s)
- David Albala
- Department of Urology, Crouse Hospital, Syracuse, NY; Associated Medical Professionals of New York, Syracuse, NY.
| | | | | | - Hani H Rashid
- University of Rochester Medical Center School of Medicine and Dentistry, Rochester, NY
| | | | - Stephen M Zappala
- Department of Urology, Tufts University School of Medicine, Boston, MA; Andover Urology, Andover, MA
| | | | | | | | - Grannum R Sant
- Department of Urology, Tufts University School of Medicine, Boston, MA
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Live-cell phenotypic-biomarker microfluidic assay for the risk stratification of cancer patients via machine learning. Nat Biomed Eng 2018; 2:761-772. [PMID: 30854249 DOI: 10.1038/s41551-018-0285-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The risk stratification of prostate cancer and breast cancer tumours from patients relies on histopathology, selective genomic testing, or on other methods employing fixed formalin tissue samples. However, static biomarker measurements from bulk fixed-tissue samples provide limited accuracy and actionability. Here, we report the development of a live-primary-cell phenotypic-biomarker assay with single-cell resolution, and its validation with prostate cancer and breast cancer tissue samples for the prediction of post-surgical adverse pathology. The assay includes a collagen-I/fibronectin extracellular-matrix formulation, dynamic live-cell biomarkers, a microfluidic device, machine-vision analysis and machine-learning algorithms, and generates predictive scores of adverse pathology at the time of surgery. Predictive scores for the risk stratification of 59 prostate cancer patients and 47 breast cancer patients, with values for area under the curve in receiver-operating-characteristic curves surpassing 80%, support the validation of the assay and its potential clinical applicability for the risk stratification of cancer patients.
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20
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Her NG, Oh JW, Oh YJ, Han S, Cho HJ, Lee Y, Ryu GH, Nam DH. Potent effect of the MDM2 inhibitor AMG232 on suppression of glioblastoma stem cells. Cell Death Dis 2018; 9:792. [PMID: 30022047 PMCID: PMC6052082 DOI: 10.1038/s41419-018-0825-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023]
Abstract
Testing new ways to identify untapped opportunities for glioblastoma therapies remains highly significant. Amplification and overexpression of MDM2 gene is frequent in glioblastoma and disrupting the MDM2-p53 interaction is a promising strategy to treat the cancer. RG7112 is the first-in class inhibitor and recently discovered AMG232 is the most potent MDM2 inhibitor known to date. Here, we compared the effects of these two clinical MDM2 inhibitors in six glioblastoma cell lines and ten patient-derived glioblastoma stem cells. Targeted sequencing of the TP53, MDM2 genes and whole transcriptome analysis were conducted to verify genetic status associated with sensitivity and resistance to the drugs. Although TP53 wild-type glioblastoma cell lines are similarly sensitive to AMG232 and RG7112, we found that four TP53 wild-type out of ten patient-derived glioblastoma cells are much more sensitive to AMG232 than RG7112 (average IC50 of 76 nM vs. 720 nM). Among these, 464T stem cells containing MDM2 gene amplification were most sensitive to AMG232 with IC50 of 5.3 nM. Moreover, AMG232 exhibited higher selectivity against p53 wild-type cells over p53 mutant stem cells compared to RG7112 (average selectivity of 512-fold vs. 16.5-fold). Importantly, we also found that AMG232 is highly efficacious in three-dimensional (3D) tumor spheroids growth and effectively inhibits the stemness-related factors, Nestin and ZEB1. Our data provide new evidence that glioblastoma stem cells have high susceptibility to AMG232 suggesting the potential clinical implications of MDM2 inhibition for glioblastoma treatment. These will facilitate additional preclinical and clinical studies evaluating MDM2 inhibitors in glioblastoma and direct further efforts towards developing better MDM2-targeted therapeutics.
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Affiliation(s)
- Nam-Gu Her
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea
| | - Jeong-Woo Oh
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea.,Department of Health Sciences & Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, 06351, Korea
| | - Yun Jeong Oh
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea
| | - Suji Han
- Department of Health Sciences & Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, 06351, Korea
| | - Hee Jin Cho
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea
| | - Yeri Lee
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea
| | - Gyu Ha Ryu
- Office of R&D Strategy & Planning, Samsung Medical Center, Seoul, 06351, Korea.
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea. .,Department of Health Sciences & Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, 06351, Korea. .,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University, Seoul, 06351, Korea.
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21
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Zhang Y, Wang Z, Wu L, Zong S, Yun B, Cui Y. Combining Multiplex SERS Nanovectors and Multivariate Analysis for In Situ Profiling of Circulating Tumor Cell Phenotype Using a Microfluidic Chip. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1704433. [PMID: 29665274 DOI: 10.1002/smll.201704433] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/17/2018] [Indexed: 05/22/2023]
Abstract
Isolating and in situ profiling the heterogeneous molecular phenotype of circulating tumor cells are of great significance for clinical cancer diagnosis and personalized therapy. Herein, an on-chip strategy is proposed that combines size-based microfluidic cell isolation with multiple spectrally orthogonal surface-enhanced Raman spectroscopy (SERS) analysis for in situ profiling of cell membrane proteins and identification of cancer subpopulations. With the developed microfluidic chip, tumor cells are sieved from blood on the basis of size discrepancy. To enable multiplex phenotypic analysis, three kinds of spectrally orthogonal SERS aptamer nanovectors are designed, providing individual cells with composite spectral signatures in accordance with surface protein expression. Next, to statistically demultiplex the complex SERS signature and profile the cellular proteomic phenotype, a revised classic least square algorithm is employed to obtain the 3D phenotypic information at single-cell resolution. Combined with categorization algorithm partial least square discriminate analysis, cells from different human breast cancer subtypes can be reliably classified with high sensitivity and selectivity. The results demonstrate that this platform can identify cancer subtypes with the spectral information correlated to the clinically relevant surface receptors, which holds great potential for clinical cancer diagnosis and precision medicine.
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Affiliation(s)
- Yizhi Zhang
- Advanced Photonics Center, Southeast University, Nanjing, 210096, China
| | - Zhuyuan Wang
- Advanced Photonics Center, Southeast University, Nanjing, 210096, China
| | - Lei Wu
- Advanced Photonics Center, Southeast University, Nanjing, 210096, China
| | - Shenfei Zong
- Advanced Photonics Center, Southeast University, Nanjing, 210096, China
| | - Binfeng Yun
- Advanced Photonics Center, Southeast University, Nanjing, 210096, China
| | - Yiping Cui
- Advanced Photonics Center, Southeast University, Nanjing, 210096, China
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