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Kanavarioti A, Rehman MH, Qureshi S, Rafiq A, Sultan M. High Sensitivity and Specificity Platform to Validate MicroRNA Biomarkers in Cancer and Human Diseases. Noncoding RNA 2024; 10:42. [PMID: 39051376 PMCID: PMC11270241 DOI: 10.3390/ncrna10040042] [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: 06/04/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
We developed a technology for detecting and quantifying trace nucleic acids using a bracketing protocol designed to yield a copy number with approximately ± 20% accuracy across all concentrations. The microRNAs (miRNAs) let-7b, miR-15b, miR-21, miR-375 and miR-141 were measured in serum and urine samples from healthy subjects and patients with breast, prostate or pancreatic cancer. Detection and quantification were amplification-free and enabled using osmium-tagged probes and MinION, a nanopore array detection device. Combined serum from healthy men (Sigma-Aldrich, St. Louis, MO, USA #H6914) was used as a reference. Total RNA isolated from biospecimens using commercial kits was used as the miRNA source. The unprecedented ± 20% accuracy led to the conclusion that miRNA copy numbers must be normalized to the same RNA content, which in turn illustrates (i) independence from age, sex and ethnicity, as well as (ii) equivalence between serum and urine. miR-21, miR-375 and miR-141 copies in cancers were 1.8-fold overexpressed, exhibited zero overlap with healthy samples and had a p-value of 1.6 × 10-22, tentatively validating each miRNA as a multi-cancer biomarker. miR-15b was confirmed to be cancer-independent, whereas let-7b appeared to be a cancer biomarker for prostate and breast cancer, but not for pancreatic cancer.
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Affiliation(s)
- Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA 95672, USA; (M.H.R.); (S.Q.); (A.R.); (M.S.)
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Quint I, Simantzik J, Kaiser L, Laufer S, Csuk R, Smith D, Kohl M, Deigner HP. Ready-to-use nanopore platform for label-free small molecule quantification: Ethanolamine as first example. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 55:102724. [PMID: 38007066 DOI: 10.1016/j.nano.2023.102724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/06/2023] [Accepted: 10/26/2023] [Indexed: 11/27/2023]
Abstract
In recent decades, nanopores have become a promising diagnostic tool. Protein and solid-state nanopores are increasingly used for both RNA/DNA sequencing and small molecule detection. The latter is of great importance, as their detection is difficult or expensive using available methods such as HPLC or LC-MS. DNA aptamers are an excellent detection element for sensitive and specific detection of small molecules. Herein, a method for quantifying small molecules using a ready-to-use sequencing platform is described. Taking ethanolamine as an example, a strand displacement assay is developed in which the target-binding aptamer is displaced from the surface of magnetic particles by ethanolamine. Non-displaced aptamer and thus the ethanolamine concentration are detected by the nanopore system and can be quantified in the micromolar range using our in-house developed analysis software. This method is thus the first to describe a label-free approach for the detection of small molecules in a protein nanopore system.
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Affiliation(s)
- Isabel Quint
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Strasse 17, Villingen-Schwenningen 78054, Germany; Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, Tuebingen 72076, Germany
| | - Jonathan Simantzik
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Strasse 17, Villingen-Schwenningen 78054, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Strasse 17, Villingen-Schwenningen 78054, Germany
| | - Stefan Laufer
- Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, Tuebingen 72076, Germany; Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | - Rene' Csuk
- Institute of Organic Chemistry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - David Smith
- Fraunhofer Institute IZI (Leipzig), Perlickstrasse 1, 04103 Leipzig, Germany
| | - Matthias Kohl
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Strasse 17, Villingen-Schwenningen 78054, Germany.
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Strasse 17, Villingen-Schwenningen 78054, Germany; EXIM Department, Fraunhofer Institute IZI (Leipzig), Schillingallee 68, 18057 Rostock, Germany; Faculty of Science, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, Tuebingen, 72076, Germany.
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Koch C, Reilly-O'Donnell B, Gutierrez R, Lucarelli C, Ng FS, Gorelik J, Ivanov AP, Edel JB. Nanopore sequencing of DNA-barcoded probes for highly multiplexed detection of microRNA, proteins and small biomarkers. NATURE NANOTECHNOLOGY 2023; 18:1483-1491. [PMID: 37749222 PMCID: PMC10716039 DOI: 10.1038/s41565-023-01479-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/28/2023] [Indexed: 09/27/2023]
Abstract
There is an unmet need to develop low-cost, rapid and highly multiplexed diagnostic technology platforms for quantitatively detecting blood biomarkers to advance clinical diagnostics beyond the single biomarker model. Here we perform nanopore sequencing of DNA-barcoded molecular probes engineered to recognize a panel of analytes. This allows for highly multiplexed and simultaneous quantitative detection of at least 40 targets, such as microRNAs, proteins and neurotransmitters, on the basis of the translocation dynamics of each probe as it passes through a nanopore. Our workflow is built around a commercially available MinION sequencing device, offering a one-hour turnaround time from sample preparation to results. We also demonstrate that the strategy can directly detect cardiovascular disease-associated microRNA from human serum without extraction or amplification. Due to the modularity of barcoded probes, the number and type of targets detected can be significantly expanded.
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Affiliation(s)
- Caroline Koch
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Benedict Reilly-O'Donnell
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | | | - Carla Lucarelli
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Fu Siong Ng
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Julia Gorelik
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
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Maguire S, Guan S. Rolling circle reverse transcription enables high fidelity nanopore sequencing of small RNA. PLoS One 2022; 17:e0275471. [PMID: 36215256 PMCID: PMC9550094 DOI: 10.1371/journal.pone.0275471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/17/2022] [Indexed: 11/07/2022] Open
Abstract
Small RNAs (sRNAs) are an important group of non-coding RNAs that have great potential as diagnostic and prognostic biomarkers for treatment of a wide variety of diseases. The portability and affordability of nanopore sequencing technology makes it ideal for point of care and low resource settings. Currently sRNAs can't be reliably sequenced on the nanopore platform due to the short size of sRNAs and high error rate of the nanopore sequencer. Here, we developed a highly efficient nanopore-based sequencing strategy for sRNAs (SR-Cat-Seq) in which sRNAs are ligated to an adapter, circularized, and undergo rolling circle reverse transcription to generate concatemeric cDNA. After sequencing, the resulting tandem repeat sequences within the individual cDNA can be aligned to generate highly accurate consensus sequences. We compared our sequencing strategy with other sRNA sequencing methods on a short-read sequencing platform and demonstrated that SR-Cat-Seq can obtain low bias and highly accurate sRNA transcriptomes. Therefore, our method could enable nanopore sequencing for sRNA-based diagnostics and other applications.
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Affiliation(s)
- Sean Maguire
- New England Biolabs, Inc., Beverly, MA, United States of America
| | - Shengxi Guan
- New England Biolabs, Inc., Beverly, MA, United States of America
- * E-mail:
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Cai S, Pataillot-Meakin T, Shibakawa A, Ren R, Bevan CL, Ladame S, Ivanov AP, Edel JB. Single-molecule amplification-free multiplexed detection of circulating microRNA cancer biomarkers from serum. Nat Commun 2021; 12:3515. [PMID: 34112774 PMCID: PMC8192752 DOI: 10.1038/s41467-021-23497-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) play essential roles in post-transcriptional gene expression and are also found freely circulating in bodily fluids such as blood. Dysregulated miRNA signatures have been associated with many diseases including cancer, and miRNA profiling from liquid biopsies offers a promising strategy for cancer diagnosis, prognosis and monitoring. Here, we develop size-encoded molecular probes that can be used for simultaneous electro-optical nanopore sensing of miRNAs, allowing for ultrasensitive, sequence-specific and multiplexed detection directly in unprocessed human serum, in sample volumes as small as 0.1 μl. We show that this approach allows for femtomolar sensitivity and single-base mismatch selectivity. We demonstrate the ability to simultaneously monitor miRNAs (miR-141-3p and miR-375-3p) from prostate cancer patients with active disease and in remission. This technology can pave the way for next generation of minimally invasive diagnostic and companion diagnostic tests for cancer.
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Affiliation(s)
- Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - Thomas Pataillot-Meakin
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, London, W12 0BZ, UK
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Akifumi Shibakawa
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Ren Ren
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - Charlotte L Bevan
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, London, W12 0BZ, UK.
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
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Kang ASW, Bernasconi JG, Jack W, Kanavarioti A. Ready-to-use nanopore platform for the detection of any DNA/RNA oligo at attomole range using an Osmium tagged complementary probe. Sci Rep 2020; 10:19790. [PMID: 33188229 PMCID: PMC7666163 DOI: 10.1038/s41598-020-76667-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
Nanopores can serve as single molecule sensors. We exploited the MinION, a portable nanopore device from Oxford Nanopore Technologies, and repurposed it to detect any DNA/RNA oligo (target) in a complex mixture by conducting voltage-driven ion-channel measurements. The detection and quantitation of the target is enabled by the use of a unique complementary probe. Using a validated labeling technology, probes are tagged with a bulky Osmium tag (Osmium tetroxide 2,2′-bipyridine), in a way that preserves strong hybridization between probe and target. Intact oligos traverse the MinION’s nanopore relatively quickly compared to the device’s acquisition rate, and exhibit count of events comparable to the baseline. Counts are reported by a publicly available software, OsBp_detect. Due to the presence of the bulky Osmium tag, probes traverse more slowly, produce multiple counts over the baseline, and are even detected at single digit attomole (amole) range. In the presence of the target the probe is “silenced”. Silencing is attributed to a 1:1 double stranded (ds) complex that does not fit and cannot traverse this nanopore. This ready-to-use platform can be tailored as a diagnostic test to meet the requirements for point-of-care cell-free tumor DNA (ctDNA) and microRNA (miRNA) detection and quantitation in body fluids.
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Affiliation(s)
- Albert S W Kang
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | - Janette G Bernasconi
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | | | - Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA.
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Konečná B, Radošinská J, Keményová P, Repiská G. Detection of disease-associated microRNAs - application for autism spectrum disorders. Rev Neurosci 2020; 31:757-769. [PMID: 32813679 DOI: 10.1515/revneuro-2020-0015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022]
Abstract
Autism spectrum disorders (ASD) diagnostic procedure still lacks a uniform biological marker. This review gathers the information on microRNAs (miRNAs) specifically as a possible source of biomarkers of ASD. Extracellular vesicles, and their subset of exosomes, are believed to be a tool of cell-to-cell communication, and they are increasingly considered to be carriers of such a marker. The interest in studying miRNAs in extracellular vesicles grows in all fields of study and therefore should not be omitted in the field of neurodevelopmental disorders. The summary of miRNAs associated with brain cells and ASD either studied directly in the tissue or biofluids are gathered in this review. The heterogeneity in findings from different studies points out the fact that unified methods should be established, beginning with the determination of the accurate patient and control groups, through to sample collection, processing, and storage conditions. This review, based on the available literature, proposes the standardized approach to obtain the results that would not be affected by technical factors. Nowadays, the method of high-throughput sequencing seems to be the most optimal to analyze miRNAs. This should be followed by the uniformed bioinformatics procedure to avoid misvalidation. At the end, the proper validation of the obtained results is needed. With such an approach as is described in this review, it would be possible to obtain a reliable biomarker that would characterize the presence of ASD.
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Affiliation(s)
- Barbora Konečná
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Jana Radošinská
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 813 72 Bratislava, Slovakia
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, 841 04 Bratislava, Slovakia
| | - Petra Keményová
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 813 72 Bratislava, Slovakia
| | - Gabriela Repiská
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 813 72 Bratislava, Slovakia
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