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Jaradi B, Das T, Koo KM. Design and Analytical Evaluation of a Rapid Plasma Screening Assay for Circulating Human Papillomavirus DNA via Thermostable Enzyme Chemistries. Anal Chem 2023; 95:11172-11180. [PMID: 37441723 DOI: 10.1021/acs.analchem.3c02528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Infection with oncogenic strains of human papillomavirus (HPV), such as HPV-16 and HPV-18, can lead to malignant progression and tumorigenesis. As an adjunct to traditional invasive tissue sampling methods, the use of modern thermostable enzyme chemistries can aid in the development of innovative assay workflows to extract and detect circulating HPV DNA (cHPV-DNA) in liquid biopsies. In this work, we first successfully generated a model system to replicate fragmented cHPV-DNA in human plasma. Using this model system, we designed a novel thermostable enzyme chemistry-based cHPV-DNA assay for rapid clinical HPV screening and robustly evaluated its analytical assay performance. Our findings demonstrated that the use of thermostable enzymes provided faster cHPV-DNA extraction and amplification, leading to an overall three-fold improvement in overall assay time as compared to the current standard assay workflow and achieving clinically relevant levels of analytical specificity, sensitivity, and precision for accurate cHPV-DNA detection with excellent 100% sensitivity and specificity in contrived human plasma specimens. In summary, we have devised a rapid laboratory workflow to facilitate the emerging use of liquid biopsies for minimally invasive, rapid, and scalable HPV DNA testing. With facile assay modifications, our thermostable enzyme-based cHPV-DNA assay can be utilized for the detection of other clinically high-risk HPV genotypes.
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Affiliation(s)
- Binny Jaradi
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, Brisbane, Queensland 4073, Australia
| | - Tulika Das
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, Brisbane, Queensland 4073, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kevin M Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, Brisbane, Queensland 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Herston, Queensland 4029, Australia
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2
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Dey S, Koo KM, Ahmed E, Trau M. Nanophotonic immunoarray with electrochemically roughened surfaces for handheld detection of secreted PD-L1 to predict immuno-oncology efficacy. Lab Chip 2023. [PMID: 37417778 DOI: 10.1039/d3lc00523b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The analysis of secreted protein biomarkers can be a useful non-invasive method of predicting or monitoring cancer therapeutic response. The increased level of soluble programmed cell death protein ligand 1 (sPD-L1) is a promising predictive biomarker for selecting patients who are likely to respond to immune checkpoint immunotherapy. The current established immunoassay for secreted protein analysis is enzyme-linked immunosorbent assay (ELISA). Yet, ELISA is generally still liable to limited detection sensitivity and restricted to bulky chromogenic readout equipment. Herein, we present a designed nanophotonic immunoarray sensor which achieved sPD-L1 analysis at high-throughput, enhanced detection sensitivity and portability. The key benefits of our nanophotonic immunoarray sensor are (i) high-throughput surface-enhanced Raman scattering (SERS) analysis of multiple samples on a singular platform; (ii) improved sPD-L1 detection sensitivity at 1 pg mL-1 (by two orders of magnitude as compared to ELISA) via electrochemically roughened gold sensor surfaces; (iii) fit for handheld SERS detection with miniaturized equipment footprint. We evaluated the analytical performance of the nanophotonic immunoarray sensor and successfully demonstrated quantitative sPD-L1 detection in a cohort of contrived human plasma samples.
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Affiliation(s)
- Shuvashis Dey
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD 4072, Australia.
| | - Kevin M Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, QLD 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Herston, QLD 4029, Australia.
| | - Emtiaz Ahmed
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD 4072, Australia.
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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3
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Tan TJ, Fink JL, Tay TK, Jaradi B, Stone N, Waring P, Koo KM, Tan PH, Tan DS, Dent RA. Exquisitely Platinum-Sensitive Triple-Negative Breast Cancer, Time for BRCA Methylation Testing? JCO Precis Oncol 2022; 6:e2200309. [DOI: 10.1200/po.22.00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Tira J. Tan
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - J. Lynn Fink
- XING Genomic Services, Brisbane, Australia
- The University of Queensland Diamantina Institute, Brisbane, Australia
| | - Timothy K. Tay
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | | | | | | | | | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Daniel S. Tan
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Rebecca A. Dent
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
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4
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Wang J, Koo KM, Trau M. Tetraplex Immunophenotyping of Cell Surface Proteomes via Synthesized Plasmonic Nanotags and Portable Raman Spectroscopy. Anal Chem 2022; 94:14906-14916. [PMID: 36256869 DOI: 10.1021/acs.analchem.2c02262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiplex immunophenotyping of cell surface proteomes is useful for cell characterization as well as providing valuable information on a patient's physiological or pathological state. Current methods for multiplex immunophenotyping of cell surface proteomes still have associated technical pitfalls in terms of limited multiplexing capability, challenging result interpretation, and large equipment footprint limited to use in a laboratory setting. Herein, we presented a portable surface-enhanced Raman spectroscopy (SERS) assay for multiplex cell surface immunophenotyping. We synthesized and functionalized customizable SERS nanotags for cell labeling and subsequent signal measurement using a portable Raman spectrometer. We extensively evaluated and validated the analytical assay performance of the portable SERS immunophenotyping assay in two different cellular models (red blood cells and breast cancer cells). In terms of analytical specificity, the cell surface immunophenotyping of both red blood cells and breast cancer cells correlated well with flow cytometry. The portable SERS immunophenotyping assay also has comparable analytical repeatability to flow cytometry, with coefficient of variation values of 21.89-23.33% and 6.88-17.32% for detecting red blood cells and breast cancer cells, respectively. The analytical detection limits were 77 cells/mL for red blood cells and 1-17 cells/mL for breast cancer cells. As an alternative to flow cytometry, the portable SERS immunophenotyping assay demonstrated excellent analytical assay performance and possessed advantages such as quick sample-to-result turnaround time, multiplexing capability, and small equipment footprint.
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Affiliation(s)
- Jing Wang
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350007, P. R. China.,Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kevin M Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, Sinnamon Park, QLD 4073, Australia.,The University of Queensland Centre for Clinical Research (UQCCR), Herston, QLD 4029, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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5
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Velaga R, Koo KM, Mainwaring PN. Harnessing gene fusion-derived neoantigens for 'cold' breast and prostate tumor immunotherapy. Immunotherapy 2022; 14:1165-1179. [PMID: 36043380 DOI: 10.2217/imt-2022-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Breast and prostate cancers are generally considered immunologically 'cold' tumors due to multiple mechanisms rendering them unresponsive to immune checkpoint blockade therapies. With little success in garnering positive outcomes in modern immunotherapeutic clinical trials, it is prudent to re-examine the role of immunogenic neoantigens in these cold tumors. Gene fusions are driver mutations in hormone-driven cancers that can result in alternative mutation-specific neoantigens to promote immunotherapy sensitivity. This review focuses on 1) gene fusion formation mechanisms in neoantigen generation; 2) gene fusion neoantigens in cancer immunotherapeutic strategies and associated clinical trials; and 3) challenges and opportunities in computational and liquid biopsy technologies. This review is anticipated to initiate further research into gene fusion neoantigens of cold tumors for further experimental validation.
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Affiliation(s)
- Ravi Velaga
- Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Kevin M Koo
- XING Technologies Pty Ltd, Brisbane, QLD 4073, Australia.,The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD 4029, Australia
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6
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Koo KM, Trau M. Molecular locker probe enrichment of gene fusion variants from matched patient liquid biopsy specimens for magneto-bioelectrocatalytic nanosensing. Nanoscale 2022; 14:4225-4233. [PMID: 35234786 DOI: 10.1039/d1nr07845c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The accurate and sensitive analysis of recurrent gene fusion mutant variants in circulating tumor nucleic acids (NAs) of patient liquid biopsy samples is crucial for realizing clinical potential for cancer screening, diagnostics, and therapeutics. Gene fusion analysis is especially challenging in patient liquid biopsy samples because of trace biotarget levels in high non-target background of highly similar native and variant NA sequences. Herein, we describe accurate analysis of three prostate cancer gene fusion mutant variants in matched plasma and urine specimens from real cancer patients and healthy controls (n = 80) by (i) direct locker probe enrichment of multiple gene fusion mutant variants without tedious upstream sample processing; (ii) magneto-bioelectrocatalytic cycling readout using both NA-intercalating and freely diffusive redox probes for superior signal enhancement. For each mutant variant, an ultrabroad dynamic range (10-105 copies) was achieved with enhanced 10 copies (zmol) detection limit. With the combination of locker probe enrichment and magneto-bioelectrocatalytic cycling readout for NA mutant variant analysis, the potential of non-invasive liquid biopsies may be exploited for the benefit of cancer patients.
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Affiliation(s)
- Kevin M Koo
- The University of Queensland Centre for Clinical Research (UQCCR), QLD 4029, Australia.
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, QLD 4073, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia
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7
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Fitzpatrick KJ, Rohlf HJ, Sutherland TD, Koo KM, Beckett S, Okelo WO, Keyburn AL, Morgan BS, Drigo B, Trau M, Donner E, Djordjevic SP, De Barro PJ. Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains. ACS Sens 2021; 6:4283-4296. [PMID: 34874700 DOI: 10.1021/acssensors.1c01973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.
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Affiliation(s)
- Kira J. Fitzpatrick
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Hayden J. Rohlf
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Tara D. Sutherland
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Kevin M. Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, Queensland 4029, Australia
| | - Sam Beckett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Walter O. Okelo
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Anthony L. Keyburn
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, Victoria 3220, Australia
| | - Branwen S. Morgan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Steven P. Djordjevic
- Ithree Institute, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Paul J. De Barro
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health & Biosecurity, EcoSciences Precinct, Brisbane, Queensland 4001, Australia
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8
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Soda N, Gonzaga ZJ, Chen S, Koo KM, Nguyen NT, Shiddiky MJA, Rehm BHA. Bioengineered Polymer Nanobeads for Isolation and Electrochemical Detection of Cancer Biomarkers. ACS Appl Mater Interfaces 2021; 13:31418-31430. [PMID: 34185493 DOI: 10.1021/acsami.1c05355] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Early sensitive diagnosis of cancer is critical for enhancing treatment success. We previously bioengineered multifunctional core-shell structures composed of a poly-3-hydroxybutyrate (PHB) core densely coated with protein functions for uses in bioseparation and immunodiagnostic applications. Here, we report bioengineering of Escherichia coli to self-assemble PHB inclusions that codisplay a ferritin-derived iron-binding peptide and the protein A-derived antibody-binding Z domain. The iron-binding peptide mediated surface coating with a ferrofluid imparting superparamagnetic properties, while the Z domain remained accessible for binding of cancer biomarker-specific antibodies. We demonstrated that these nanobeads can specifically bind biomarkers in complex mixtures, enabling efficient magnetic separation toward enhanced electrochemical detection of cancer biomarkers such as methylated DNA and exosomes from cancer cells. Our study revealed that superparamagnetic core-shell structures can be derived from biological self-assembly systems for uses in sensitive and specific electrochemical detection of cancer biomarkers, laying the foundation for engineering advanced nanomaterials for diverse diagnostic approaches.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan, Queensland 4111, Australia
| | - Zennia Jean Gonzaga
- School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Shuxiong Chen
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Kevin M Koo
- The University of Queensland Centre for Clinical Research (UQCCR), Herston, Queensland 4029, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan, Queensland 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan, Queensland 4111, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
- Menzies Health Institute Queensland (MHIQ), Griffith University, Gold Coast, Queensland 4222, Australia
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9
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Singh K, Nalabotala R, Koo KM, Bose S, Nayak R, Shiddiky MJA. Separation of distinct exosome subpopulations: isolation and characterization approaches and their associated challenges. Analyst 2021; 146:3731-3749. [PMID: 33988193 DOI: 10.1039/d1an00024a] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Exosomes are nano-sized extracellular vesicles that serve as a communications system between cells and have shown tremendous promise as liquid biopsy biomarkers in diagnostic, prognostic, and even therapeutic use in different human diseases. Due to the natural heterogeneity of exosomes, there is a need to separate exosomes into distinct biophysical and/or biochemical subpopulations to enable full interrogation of exosome biology and function prior to the possibility of clinical translation. Currently, there exists a multitude of different exosome isolation and characterization approaches which can, in limited capacity, separate exosomes based on biophysical and/or biochemical characteristics. While notable reviews in recent years have reviewed these approaches for bulk exosome sorting, we herein present a comprehensive overview of various conventional technologies and modern microfluidic and nanotechnological advancements towards isolation and characterization of exosome subpopulations. The benefits and limitations of these different technologies to improve their use for distinct exosome subpopulations in clinical practices are also discussed. Furthermore, an overview of the most commonly encountered technical and biological challenges for effective separation of exosome subpopulations is presented.
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Affiliation(s)
- Karishma Singh
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh, Noida 201301, UP, India.
| | - Ruchika Nalabotala
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh, Noida 201301, UP, India.
| | - Kevin M Koo
- The University of Queensland Centre for Clinical Research (UQCCR), Herston, QLD 4029, Australia.
| | - Sudeep Bose
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida 201301, UP, India
| | - Ranu Nayak
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh, Noida 201301, UP, India.
| | - Muhammad J A Shiddiky
- School of Environment and Natural Sciences and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia.
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10
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Zeng Y, Koo KM, Shen AG, Hu JM, Trau M. Nucleic Acid Hybridization-Based Noise Suppression for Ultraselective Multiplexed Amplification of Mutant Variants. Small 2021; 17:e2006370. [PMID: 33325632 DOI: 10.1002/smll.202006370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/11/2020] [Indexed: 06/12/2023]
Abstract
The analysis of mutant nucleic acid (NA) variants can provide crucial clinical and biological insights for many diseases. Yet, existing analysis techniques are generally constrained by nonspecific "noise" signals from excessive wildtype background sequences, especially under rapid isothermal multiplexed target amplification conditions. Herein, the molecular hybridization chemistry between NA bases is manipulated to suppress noise signals and achieve ultraselective multiplexed detection of cancer gene fusion NA variants. Firstly, modified locked NA (LNA) bases are rationally introduced into oligonucleotide sequences as designed "locker probes" for high affinity hybridization to wildtype sequences, leading to enrichment of mutant variants for multiplexed isothermal amplification. Secondly, locker probes are coupled with a customized "proximity-programmed" (SERS) readout which allows precise control of hybridization-based plasmonic signaling to specifically detect multiple target amplicons within a single reaction. Moreover, the use of triple bond Raman reporters endows NA noise signal-free quantification in the Raman silent region (≈1800-2600 cm-1 ). With this dual molecular hybridization-based strategy, ultraselective multiplexed detection of gene fusion NA variants in cancer cellular models is actualized with successful noise suppression of native wildtype sequences. The distinct benefits of isothermal NA amplification and SERS multiplexing ability are simultaneously harnessed.
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Affiliation(s)
- Yi Zeng
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- XING Technologies Pty Ltd, Sinnamon Park, Brisbane, QLD, 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD, 4029, Australia
| | - Ai-Guo Shen
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
| | - Ji-Ming Hu
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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11
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Koo KM, Trau M. Direct Enhanced Detection of Multiple Circulating Tumor DNA Variants in Unprocessed Plasma by Magnetic-Assisted Bioelectrocatalytic Cycling. ACS Sens 2020; 5:3217-3225. [PMID: 32896119 DOI: 10.1021/acssensors.0c01512] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The detection of single-nucleotide variants (SNVs) in circulating tumor DNA (ctDNA) in liquid biopsies has increasingly been shown to exhibit unique benefits for early detection or minimal residual disease monitoring in cancer. Yet, current clinically validated assays for ctDNA SNV detection are challenged by (i) time-consuming and laborious spin column-based ctDNA purification protocols, (ii) limited detection specificity to discriminate between mutated SNVs from large excess of closely similar wild-type sequences, and (iii) insufficient detection sensitivity required for trace ctDNA target analysis in blood. Herein, a ctDNA assay is demonstrated to tackle these triple key issues by fusing magnetics for quick ctDNA enrichment directly from unprocessed blood, selected bioenzyme activities for rapid discrimination, and molecular amplification of target SNVs, and designed magnetic-assisted bioelectrocatalytic cycling of DNA-intercalating and freely diffusing redox probes for electrochemical signal intensification. The described ctDNA SNV assay enables the detection of clinically relevant ctDNA SNVs in melanoma (BRAFV600E, KITL576P, and NRASQ61K) from unprocessed plasma samples with unprecedented 0.005% detection sensitivity, ultrabroad dynamic range over four orders of magnitude, and excellent single-base specificity.
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Affiliation(s)
- Kevin M. Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Saint Lucia, QLD 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Saint Lucia, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Saint Lucia, QLD 4072, Australia
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12
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Dey S, Trau M, Koo KM. Surface-Enhanced Raman Spectroscopy for Cancer Immunotherapy Applications: Opportunities, Challenges, and Current Progress in Nanomaterial Strategies. Nanomaterials (Basel) 2020; 10:E1145. [PMID: 32545182 PMCID: PMC7353228 DOI: 10.3390/nano10061145] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 02/06/2023]
Abstract
Cancer immunotherapy encompasses a variety of approaches which target or use a patient's immune system components to eliminate cancer. Notably, the current use of immune checkpoint inhibitors to target immune checkpoint receptors such as CTLA-4 or PD-1 has led to remarkable treatment responses in a variety of cancers. To predict cancer patients' immunotherapy responses effectively and efficiently, multiplexed immunoassays have been shown to be advantageous in sensing multiple immunomarkers of the tumor microenvironment simultaneously for patient stratification. Surface-enhanced Raman spectroscopy (SERS) is well-regarded for its capabilities in multiplexed bioassays and has been increasingly demonstrated in cancer immunotherapy applications in recent years. This review focuses on SERS-active nanomaterials in the modern literature which have shown promise for enabling cancer patient-tailored immunotherapies, including multiplexed in vitro and in vivo immunomarker sensing and imaging, as well as immunotherapy drug screening and delivery.
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Affiliation(s)
- Shuvashis Dey
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Kevin M. Koo
- XING Technologies Pty Ltd., Brisbane, QLD 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD 4029, Australia
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13
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Koo KM, Mainwaring PN. The role of circulating tumor DNA testing in breast cancer liquid biopsies: getting ready for prime time. Breast Cancer Management 2020. [DOI: 10.2217/bmt-2020-0003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Kevin M Koo
- XING Technologies Pty Ltd, 4073, Brisbane, QLD, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), 4072, Brisbane, QLD, Australia
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Wang J, Koo KM, Wang Y, Trau M. Engineering State-of-the-Art Plasmonic Nanomaterials for SERS-Based Clinical Liquid Biopsy Applications. Adv Sci (Weinh) 2019; 6:1900730. [PMID: 31832306 PMCID: PMC6891916 DOI: 10.1002/advs.201900730] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/26/2019] [Indexed: 05/23/2023]
Abstract
Precision oncology, defined as the use of the molecular understanding of cancer to implement personalized patient treatment, is currently at the heart of revolutionizing oncology practice. Due to the need for repeated molecular tumor analyses in facilitating precision oncology, liquid biopsies, which involve the detection of noninvasive cancer biomarkers in circulation, may be a critical key. Yet, existing liquid biopsy analysis technologies are still undergoing an evolution to address the challenges of analyzing trace quantities of circulating tumor biomarkers reliably and cost effectively. Consequently, the recent emergence of cutting-edge plasmonic nanomaterials represents a paradigm shift in harnessing the unique merits of surface-enhanced Raman scattering (SERS) biosensing platforms for clinical liquid biopsy applications. Herein, an expansive review on the design/synthesis of a new generation of diverse plasmonic nanomaterials, and an updated evaluation of their demonstrated SERS-based uses in liquid biopsies, such as circulating tumor cells, tumor-derived extracellular vesicles, as well as circulating cancer proteins, and tumor nucleic acids is presented. Existing challenges impeding the clinical translation of plasmonic nanomaterials for SERS-based liquid biopsy applications are also identified, and outlooks and insights into advancing this rapidly growing field for practical patient use are provided.
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Affiliation(s)
- Jing Wang
- Centre for Personalized NanomedicineAustralian Institute for Bioengineering and Nanotechnology (AIBN)The University of QueenslandBrisbaneQLD4072Australia
| | - Kevin M. Koo
- Centre for Personalized NanomedicineAustralian Institute for Bioengineering and Nanotechnology (AIBN)The University of QueenslandBrisbaneQLD4072Australia
| | - Yuling Wang
- Department of Molecular SciencesARC Excellence Centre for Nanoscale BioPhotonicsFaculty of Science and EngineeringMacquarie UniversitySydneyNSW2109Australia
| | - Matt Trau
- Centre for Personalized NanomedicineAustralian Institute for Bioengineering and Nanotechnology (AIBN)The University of QueenslandBrisbaneQLD4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQLD4072Australia
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Li J, Koo KM, Wang Y, Trau M. Native MicroRNA Targets Trigger Self-Assembly of Nanozyme-Patterned Hollowed Nanocuboids with Optimal Interparticle Gaps for Plasmonic-Activated Cancer Detection. Small 2019; 15:e1904689. [PMID: 31724319 DOI: 10.1002/smll.201904689] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/19/2019] [Indexed: 05/28/2023]
Abstract
The modernized use of nucleic acid (NA) sequences to drive nanostructure self-assembly has given rise to a new class of designed nanomaterials with controllable plasmonic functionalities for broad surface-enhanced Raman scattering (SERS)-based bioanalysis applications. Herein, dual usage of microRNAs (miRNAs) as both valuable cancer biomarkers and direct self-assembly triggers is identified and capitalized upon for custom-designed plasmonic nanostructures. Through strict NA hybridization of miRNA targets, Au nanospheres selectively self-assemble onto hollowed Au/Ag alloy nanocuboids with ideal interparticle distances (≈2.3 nm) for optimal SERS signaling. The intrinsic material properties of the self-assembled nanostructures further elevate miRNA detection performance via nanozyme catalytic SERS signaling cascades. This enables fM-level miR-107 detection limit within a clinically-relevant range without any molecular target amplification. The miRNA-triggered nanostructure self-assembly approach is further applied in clinical patient samples, and showcases the potential of miR-107 as a non-invasive prostate cancer diagnostic biomarker. The use of miRNA targets to drive nanostructure self-assembly holds great promise as a practical tool for miRNA detection in disease applications.
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Affiliation(s)
- Junrong Li
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yuling Wang
- Department of Molecular Sciences, Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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16
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Dey S, Koo KM, Wang Z, Sina AAI, Wuethrich A, Trau M. An integrated multi-molecular sensor for simultaneous BRAF V600E protein and DNA single point mutation detection in circulating tumour cells. Lab Chip 2019; 19:738-748. [PMID: 30624446 DOI: 10.1039/c8lc00991k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The analysis of circulating cancer biomarkers in the form of liquid biopsies confers several potential benefits as compared to traditional surgical tissue sampling. As a common key anomaly strongly implicated across several cancer types, the BRAFV600E mutation is one of the most valuable oncogenic biomarkers available in liquid biopsies. Crucially, BRAFV600E is also an actionable mutation which could be arrested by clinically beneficial drug inhibitors. Yet, as is true for most single base disease mutations, current BRAFV600E detection in either its DNA or protein molecular state is still liable to false positive/negative outcomes, thus impacting patient treatment benefit. Here we present an integrated multi-molecular sensor (IMMS) for an entire sample-to-answer workflow from melanoma cell capture to simultaneous quantification of both intracellular BRAFV600E DNA and protein levels on a single platform. The IMMS combines (i) specific capture and release of circulating melanoma cells; (ii) electric field-induced cell lysis; (iii) simultaneous quantification of BRAFV600E DNA and protein levels. We investigated the IMMS system's analytical performance in cell capture, release and lysis, and intracellular BRAFV600E detection by ligase-mediated DNA amplification and antibody-based protein hybridization. As a proof-of-concept, we successfully demonstrated circulating BRAFV600E detection at both DNA and protein molecular levels in simulated melanoma plasma samples. With its capabilities in integrated and miniaturized analysis, the IMMS could lead the emergence of a new generation of multi-molecular lab-on-chip biosensors for enabling more accurate and extensive analysis of powerful circulating biomarkers in patient liquid biopsies.
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Affiliation(s)
- Shuvashis Dey
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD 4072, Australia.
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Koo KM, Dey S, Trau M. A Sample-to-Targeted Gene Analysis Biochip for Nanofluidic Manipulation of Solid-Phase Circulating Tumor Nucleic Acid Amplification in Liquid Biopsies. ACS Sens 2018; 3:2597-2603. [PMID: 30461262 DOI: 10.1021/acssensors.8b01011] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The use of circulating tumor nucleic acids (ctNA) in patient liquid biopsies for targeted genetic analysis is rapidly increasing in clinical oncology. Still, the call for an integrated methodology, which is both rapid and sensitive for analyzing trace ctNA amount in liquid biopsies, has unfortunately not been fully realized. Herein, we performed complex liquid biopsy sample-to-targeted genetic analysis on a biochip with a 50 copies-detection limit within 30 min. Our biochip uniquely integrated the following: (1) electrical lysis and release of cellular targets with minimal processing; (2) nanofluidic manipulation to accelerate molecular kinetics of solid-phase isothermal amplification; and (3) single-step capture and amplification of multiple NA targets prior to nanozyme-mediated electrochemical detection. Using prostate cancer liquid biopsies, we successfully demonstrated multifunctionality for cancer risk prediction; correlation of serum and urine analyses; and cancer relapse monitoring.
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Affiliation(s)
- Kevin M. Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shuvashis Dey
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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18
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Affiliation(s)
- Jing Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kevin M. Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuling Wang
- Department of Molecular Sciences and ARC Centre of Excellence for Nanoscale BioPhotonics, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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19
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Koo KM, Wang J, Richards RS, Farrell A, Yaxley JW, Samaratunga H, Teloken PE, Roberts MJ, Coughlin GD, Lavin MF, Mainwaring PN, Wang Y, Gardiner RA, Trau M. Design and Clinical Verification of Surface-Enhanced Raman Spectroscopy Diagnostic Technology for Individual Cancer Risk Prediction. ACS Nano 2018; 12:8362-8371. [PMID: 30028592 DOI: 10.1021/acsnano.8b03698] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The use of emerging nanotechnologies, such as plasmonic nanoparticles in diagnostic applications, potentially offers opportunities to revolutionize disease management and patient healthcare. Despite worldwide research efforts in this area, there is still a dearth of nanodiagnostics which have been successfully translated for real-world patient usage due to the predominant sole focus on assay analytical performance and lack of detailed investigations into clinical performance in human samples. In a bid to address this pressing need, we herein describe a comprehensive clinical verification of a prospective label-free surface-enhanced Raman scattering (SERS) nanodiagnostic assay for prostate cancer (PCa) risk stratification. This contribution depicts a roadmap of (1) designing a SERS assay for robust and accurate detection of clinically validated PCa RNA targets; (2) employing a relevant and proven PCa clinical biomarker model to test our nanodiagnostic assay; and (3) investigating the clinical performance on independent training ( n = 80) and validation ( n = 40) cohorts of PCa human patient samples. By relating the detection outcomes to gold-standard patient biopsy findings, we established a PCa risk scoring system which exhibited a clinical sensitivity and specificity of 0.87 and 0.90, respectively [area-under-curve of 0.84 (95% confidence interval: 0.81-0.87) for differentiating high- and low-risk PCa] in the validation cohort. We envision that our SERS nanodiagnostic design and clinical verification approach may aid in the individualized prediction of PCa presence and risk stratification and may overall serve as an archetypical strategy to encourage comprehensive clinical evaluation of nanodiagnostic innovations.
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Affiliation(s)
- Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology , University of Queensland , Brisbane , QLD 4072 , Australia
| | - Jing Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology , University of Queensland , Brisbane , QLD 4072 , Australia
| | - Renée S Richards
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- QIMR Berghofer Medical Research Institute , Brisbane , QLD 4006 , Australia
| | - Aine Farrell
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
| | - John W Yaxley
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
| | - Hema Samaratunga
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- Aquesta Specialized Uropathology, Brisbane , QLD 4066 , Australia
- Princess Alexandra Hospital , Brisbane , QLD 4102 , Australia
| | - Patrick E Teloken
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
- Princess Alexandra Hospital , Brisbane , QLD 4102 , Australia
| | - Matthew J Roberts
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
| | - Geoffrey D Coughlin
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
| | - Martin F Lavin
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
| | - Paul N Mainwaring
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology , University of Queensland , Brisbane , QLD 4072 , Australia
| | - Yuling Wang
- Department of Molecular Sciences, Faculty of Science and Engineering , Macquarie University , Sydney , NSW 2109 , Australia
| | - Robert A Gardiner
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
- Edith Cowan University , Perth , WA 6027 , Australia
- Griffith University , Brisbane , QLD 4111 , Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology , University of Queensland , Brisbane , QLD 4072 , Australia
- School of Chemistry and Molecular Biosciences , University of Queensland , Brisbane , QLD 4072 , Australia
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Abstract
The concept of personalised diagnostics is to direct accurate clinical decisions based on an individual's unique disease molecular profile. Lab-on-a-chip (LOC) systems are prime personalised diagnostics examples which seek to perform an entire sample-to-outcome detection of disease nucleic acid (NA) biomarkers on a single miniaturised platform with minimal user handling. Despite the great potential of LOC devices in providing rapid, portable, and inexpensive personalised diagnosis at the point-of-care (POC), the translation of this technology into widespread use has still been hampered by the need for sophisticated and complex engineering. As an alternative miniaturised diagnostics platform free of precision fabrication, there have been recent developments towards a solution-based lab-in-a-drop (LID) system by which an entire laboratory-based diagnostics workflow could be downscaled and integrated within a singular fluid droplet for POC detection of NA biomarkers. In contrast to existing excellent reviews on miniaturised LOC fabrication and individual steps of NA biomarker sensing, we herein focus on miniaturised solution-based NA biosensing strategies suited for integrated LID personalised diagnostics development. In this review, we first evaluate the three fundamental bioassay steps for miniaturised NA biomarker detection: crude sample preparation, isothermal target amplification, and detection readout of amplicons. Then, we provide insights into research advancements towards a functional LID system which integrates all three of the above-mentioned fundamental steps. Finally, we discuss perspectives and future directions of LID diagnostic platforms in personalised medicine applications.
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Affiliation(s)
- Kevin M Koo
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia.
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Wang J, Koo KM, Wee EJH, Wang Y, Trau M. A nanoplasmonic label-free surface-enhanced Raman scattering strategy for non-invasive cancer genetic subtyping in patient samples. Nanoscale 2017; 9:3496-3503. [PMID: 28240336 DOI: 10.1039/c6nr09928a] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Simple nucleic acid detection methods could facilitate the progress of disease diagnostics for clinical uses. An attractive strategy is label-free surface-enhanced Raman scattering (SERS) due to its capability of providing structural fingerprinting of analytes that are close to or on nanomaterial surfaces. However, current label-free SERS approaches for DNA/RNA biomarker detection are limited to short and synthetic nucleic acid targets and have not been fully realized in clinical samples due to two possible reasons: (i) low target copies in limited patient samples and (ii) poor capability in identifying specific biomarkers from complex samples. To resolve these limitations and enable label-free SERS for clinical applications, we herein present a novel strategy based on multiplex reverse transcription-recombinase polymerase amplification (RT-RPA) to enrich multiple RNA biomarkers, followed by label-free SERS with multivariate statistical analysis to directly detect, identify and distinguish between these long amplicons (∼200 bp). As a proof-of-concept clinical demonstration, we employed this strategy for non-invasive subtyping of prostate cancer (PCa). In a training cohort of 43 patient urinary samples, we achieved 93.0% specificity, 95.3% sensitivity, and 94.2% accuracy. We believe that our proposed assay could pave the way for simple and direct label-free SERS detection of multiple long nucleic acid sequences in patient samples, and thus facilitate rapid cancer molecular subtyping for personalized therapies.
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Affiliation(s)
- Jing Wang
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Kevin M Koo
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Eugene J H Wee
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Yuling Wang
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia. and School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
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Koo KM, Wee EJ, Trau M. High-speed biosensing strategy for non-invasive profiling of multiple cancer fusion genes in urine. Biosens Bioelectron 2017; 89:715-720. [DOI: 10.1016/j.bios.2016.11.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 11/29/2022]
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Koo KM, Wee EJH, Mainwaring PN, Wang Y, Trau M. Toward Precision Medicine: A Cancer Molecular Subtyping Nano-Strategy for RNA Biomarkers in Tumor and Urine. Small 2016; 12:6233-6242. [PMID: 27717152 DOI: 10.1002/smll.201602161] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/26/2016] [Indexed: 06/06/2023]
Abstract
Cancer is a heterogeneous disease which manifests as different molecular subtypes due to the complex nature of tumor initiation, progression, and metastasis. The concept of precision medicine aims to exploit this cancer heterogeneity by incorporating diagnostic technology to characterize each cancer patient's molecular subtype for tailored treatments. To characterize cancer molecular subtypes accurately, a suite of multiplexed bioassays have currently been developed to detect multiple oncogenic biomarkers. Despite the reliability of current multiplexed detection techniques, novel strategies are still needed to resolve limitations such as long assay time, complex protocols, and difficulty in interpreting broad overlapping spectral peaks of conventional fluorescence readouts. Herein a rapid (80 min) multiplexed platform strategy for subtyping prostate cancer tumor and urine samples based on their RNA biomarker profiles is presented. This is achieved by combining rapid multiplexed isothermal reverse transcription-recombinase polymerase amplification (RT-RPA) of target RNA biomarkers with surface-enhanced Raman spectroscopy (SERS) nanotags for "one-pot" readout. This is the first translational application of a RT-RPA/SERS-based platform for multiplexed cancer biomarker detection to address a clinical need. With excellent sensitivity of 200 zmol (100 copies) and specificity, we believed that this platform methodology could be a useful tool for rapid multiplexed subtyping of cancers.
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Affiliation(s)
- Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD, 4072, Australia
| | - Eugene J H Wee
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD, 4072, Australia
| | - Paul N Mainwaring
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD, 4072, Australia
| | - Yuling Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD, 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, 4072, Australia
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Koo KM, Carrascosa LG, Shiddiky MJA, Trau M. Amplification-Free Detection of Gene Fusions in Prostate Cancer Urinary Samples Using mRNA-Gold Affinity Interactions. Anal Chem 2016; 88:6781-8. [PMID: 27299694 DOI: 10.1021/acs.analchem.6b01182] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A crucial issue in present-day prostate cancer (PCa) detection is the lack of specific biomarkers for accurately distinguishing between benign and malignant cancer forms. This is causing a high degree of overdiagnosis and overtreatment of otherwise clinically insignificant cases. As around half of all malignant PCa cases display a detectable gene fusion mutation between the TMPRSS2 promoter sequence and the ERG coding sequence (TMPRSS2:ERG) in urine, noninvasive screening of TMPRSS2:ERG mRNA in patient urine samples could improve the specificity of current PCa diagnosis. However, current gene fusion detection methodologies are largely dependent on RNA enzymatic amplification, which requires extensive sample manipulation, costly labels for detection, and is prone to bias/artifacts. Herein we introduce the first successful amplification-free electrochemical assay for direct detection of TMPRSS2:ERG mRNA in PCa urinary samples by selectively isolating and adsorbing TMPRSS2:ERG mRNA onto bare gold electrodes without requiring any surface modification. We demonstrated excellent limit-of-detection (10 cells) and specificity using PCa cell line models, and showcased clinical utility by accurately detecting TMPRSS2:ERG in a collection of 17 urinary samples obtained from PCa patients. Furthermore, these results were validated with the current gold standard reverse transcription (RT)-PCR approach with 100% concordance.
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Affiliation(s)
- Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Laura G Carrascosa
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Muhammad J A Shiddiky
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland , Brisbane, Queensland 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane, Queensland 4072, Australia
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Koo KM, Wee EJ, Trau M. Colorimetric TMPRSS2-ERG Gene Fusion Detection in Prostate Cancer Urinary Samples via Recombinase Polymerase Amplification. Am J Cancer Res 2016; 6:1415-24. [PMID: 27375789 PMCID: PMC4924509 DOI: 10.7150/thno.15250] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/27/2016] [Indexed: 12/01/2022] Open
Abstract
TMPRSS2 (Exon 1)-ERG (Exon 4) is the most frequent gene fusion event in prostate cancer (PC), and is highly PC-specific unlike the current serum prostate specific antigen (PSA) biomarker. However, TMPRSS2-ERG levels are currently measured with quantitative reverse-transcription PCR (RT-qPCR) which is time-consuming and requires costly equipment, thus limiting its use in clinical diagnostics. Herein, we report a novel rapid, cost-efficient and minimal-equipment assay named “FusBLU” for detecting TMPRSS2-ERG gene fusions from urine. TMPRSS2-ERG mRNA was amplified by isothermal reverse transcription-recombinase polymerase amplification (RT-RPA), magnetically-isolated, and detected through horseradish peroxidase (HRP)-catalyzed colorimetric reaction. FusBLU was specific for TMPRSS2-ERG mRNA with a low visual detection limit of 105 copies. We also demonstrated assay readout versatility on 3 potentially useful platforms. The colorimetric readout was detectable by naked eye for a quick yes/no evaluation of gene fusion presence. On the other hand, a more quantitative TMPRSS2-ERG detection was achievable by absorbance/electrochemical measurements. FusBLU was successfully applied to 12 urinary samples and results were validated by gold-standard RT-qPCR. We also showed that sediment RNA was likely the main source of TMPRSS2-ERG mRNA in urinary samples. We believe that our assay is a potential clinical screening tool for PC and could also have wide applications for other disease-related fusion genes.
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26
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Koo KM, Carrascosa LG, Shiddiky MJA, Trau M. Poly(A) Extensions of miRNAs for Amplification-Free Electrochemical Detection on Screen-Printed Gold Electrodes. Anal Chem 2016; 88:2000-5. [PMID: 26814930 DOI: 10.1021/acs.analchem.5b04795] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Current amplification-based microRNA (miRNA) detection approaches are limited by the small sizes of miRNAs as well as amplification bias/artifacts. Herein, we report on an amplification-free miRNA assay based on elevated affinity interaction between polyadenylated miRNA and bare gold electrode. The poly(A) extension on the 3' ends of magnetically isolated miRNA targets facilitated high adsorption efficiency onto gold electrode surfaces for electrochemical detection without any cumbersome electrode surface functionalization procedures. The assay showed excellent detection sensitivity (10 fM) and specificity and was demonstrated for quantitative miR-107 detection in human cancer cell lines and clinical urine samples. We believe our assay could be useful as an amplification-free alternative for miRNA detection.
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Affiliation(s)
- Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Laura G Carrascosa
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Muhammad J A Shiddiky
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland , Brisbane, Queensland 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane, Queensland 4072, Australia
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Wee EJ, Koo KM, Mainwaring PN, Trau M. Towards rapid and cost-effective point-of-care detection of TMPRSS2:ERG fusion transcripts in urine via a novel methodology. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.11063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Eugene J.H. Wee
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, Brisbane, Australia
| | - Kevin M Koo
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, Brisbane, Australia
| | | | - Mattias Trau
- Centre for Personalised Nanomedicine, AIBN University of Queensland, Brisbane, Australia
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Koo KM, Ibn Sina AA, Carrascosa LG, Shiddiky MJA, Trau M. eMethylsorb: rapid quantification of DNA methylation in cancer cells on screen-printed gold electrodes. Analyst 2014; 139:6178-84. [DOI: 10.1039/c4an01641f] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A simple, sensitive and inexpensive electrochemical method has been reported to detect regional DNA methylation by using differential adsorption affinity of DNA bases to gold.
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Affiliation(s)
- Kevin M. Koo
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
| | - Abu Ali Ibn Sina
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
| | - Laura G. Carrascosa
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
| | - Muhammad J. A. Shiddiky
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
- School of Chemistry and Molecular Biosciences
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Wee EJH, Rauf S, Koo KM, Shiddiky MJA, Trau M. μ-eLCR: a microfabricated device for electrochemical detection of DNA base changes in breast cancer cell lines. Lab Chip 2013; 13:4385-91. [PMID: 24061339 DOI: 10.1039/c3lc50528f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microfabricated devices for the electrochemical detection of single DNA base changes in cancer cell lines are highly desirable due to the inherent advantages such as portability, simplicity, and the rapid and inexpensive nature of electrochemical readout methods. Moreover, molecular sensors that use microscale-footprint working electrodes have shown high signal-to-noise ratio. Herein we report a microdevice-based electrochemical assay (μ-eLCR) measuring ligase chain reaction (LCR)-amplified long and short "knife" motifs which reflect the presence or absence of a DNA base change of interest in a target sequence. This μ-eLCR approach has higher sensitivity (4.4 to 10 fold improvement over macrodisk electrodes) and good reproducibility (%RSD 6.5%, n = 12) for the detection of LCR-amplified DNA bases. The devices also exhibited excellent sensitivity for the detection of DNA methylation (C to T base change in a locus associated with cancer metastasis) in two cell lines and serum derived DNA samples. We believe that the μ-eLCR device may be a useful diagnostic tool for inexpensive and rapid detection of single DNA base change applications such as DNA methylation and single nucleotide polymorphism (SNP) detection.
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Affiliation(s)
- Eugene J H Wee
- Centre for Biomarker Research and Development, Australian Institute for Bioengineering and Nanotechnology (AIBN), Brisbane, QLD 4072, Australia.
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