scholarly journals High-throughput single-EV liquid biopsy: Rapid, simultaneous, and multiplexed detection of nucleic acids, proteins, and their combinations

2020 ◽  
Vol 6 (47) ◽  
pp. eabc1204
Author(s):  
Jian Zhou ◽  
Zuoren Wu ◽  
Jie Hu ◽  
Dawei Yang ◽  
Xiaoyan Chen ◽  
...  

MicroRNAs (miRNAs), mRNA, and proteins in/on extracellular vesicles (EVs) represent potential cancer biomarkers. Concurrent detection of multiple biomarkers at a single-EV level would greatly improve prognosis and/or diagnosis and understanding of EV phenotypes, biogenesis, and functions. Here, we introduced a High-throughput Nano-bio Chip Integrated System for Liquid Biopsy (HNCIB) system for simultaneous detection of proteins and mRNA/miRNA in a single EV. Validated through systematic control experiments, HNCIB showed high reliability, sensitivity, and specificity. In a panel of 34 patients with lung adenocarcinoma (LUAD) and 35 healthy donors, HNCIB detected an up-regulated expression of programmed death-ligand 1 mRNA and protein and miR-21 in EVs derived from patients with LUAD compared to those from healthy donors. HNCIB has low sample requirement (~90 μl), fast assay time (~6 hours), and high throughput (up to 384 samples per assay) and would have great potential in the study of EVs and their clinical applications.

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Shahrzad Shadabi ◽  
Nargess Delrish ◽  
Mehdi Norouzi ◽  
Maryam Ehteshami ◽  
Fariba Habibian-Sezavar ◽  
...  

Abstract Background Human T-lymphotropic virus 1 (HTLV-1) infection may lead to the development of Adult T-cell leukemia/lymphoma (ATLL). To further elucidate the pathophysiology of this aggressive CD4+ T-cell malignancy, we have performed an integrated systems biology approach to analyze previous transcriptome datasets focusing on differentially expressed miRNAs (DEMs) in peripheral blood of ATLL patients. Methods Datasets GSE28626, GSE31629, GSE11577 were used to identify ATLL-specific DEM signatures. The target genes of each identified miRNA were obtained to construct a protein-protein interactions network using STRING database. The target gene hubs were subjected to further analysis to demonstrate significantly enriched gene ontology terms and signaling pathways. Quantitative reverse transcription Polymerase Chain Reaction (RTqPCR) was performed on major genes in certain pathways identified by network analysis to highlight gene expression alterations. Results High-throughput in silico analysis revealed 9 DEMs hsa-let-7a, hsa-let-7g, hsa-mir-181b, hsa-mir-26b, hsa-mir-30c, hsa-mir-186, hsa-mir-10a, hsa-mir-30b, and hsa-let-7f between ATLL patients and healthy donors. Further analysis revealed the first 5 of DEMs were directly associated with previously identified pathways in the pathogenesis of HTLV-1. Network analysis demonstrated the involvement of target gene hubs in several signaling cascades, mainly in the MAPK pathway. RT-qPCR on human ATLL samples showed significant upregulation of EVI1, MKP1, PTPRR, and JNK gene vs healthy donors in MAPK/JNK pathway. Discussion The results highlighted the functional impact of a subset dysregulated microRNAs in ATLL on cellular gene expression and signal transduction pathways. Further studies are needed to identify novel biomarkers to obtain a comprehensive mapping of deregulated biological pathways in ATLL.


2020 ◽  
Author(s):  
T.A. Hartjes ◽  
J.A. Slotman ◽  
M.S. Vredenbregt ◽  
N. Dits ◽  
R. Van der Meel ◽  
...  

AbstractExtracellular vesicles (EVs) reflect the cell of origin in terms of nucleic acids and protein content. They are found in biofluids and represent an ideal liquid biopsy biomarker source for many diseases. Unfortunately, clinical implementation is limited by available technologies for EV analysis. We have developed a simple, robust and sensitive microscopy-based high-throughput assay (EVQuant) to overcome these limitations and allow widespread use in the EV community. The EVQuant assay can detect individual immobilized EVs as small as 35 nm and determine their concentration in biofluids without extensive EV isolation or purification procedures. It can also identify specific EV subpopulations based on combinations of biomarkers and is used here to identify prostate-derived urinary EVs as CD9-/CD63+. Moreover, characterization of individual EVs allows analysis of their size distribution. The ability to identify, quantify and characterize EV (sub-)populations in high-throughput substantially extents the applicability of the EVQuant assay over most current EV quantification assays.


2021 ◽  
Author(s):  
Binfeng Yin ◽  
Xinhua Wan ◽  
Mingzhu Yang ◽  
Changcheng Qian ◽  
A S M Muhtasim Fuad Sohan

Abstract Background: Simultaneous and timely detection of C-reactive protein (CRP), procalcitonin (PCT), and interleukin-6 (IL-6) provides effective information for the accurate diagnosis of infections. Early diagnosis and classification of infections increase the cure rate while decreasing complications, which is significant for severe infections, especially for war surgery. However, traditional methods rely on laborious operations and bulky devices. On the other hand, point-of-care (POC) methods suffer from limited robustness and accuracy. Therefore, it is of urgent demand to develop POC devices for rapid and accurate diagnosis of infections to fulfill on-site militarized requirements.Methods: We developed a wave-shaped microfluidic chip (WMC) assisted multiplexed detection platform (WMC-MDP). WMC-MDP reduces detection time and improves repeatability through premixing of the samples and reaction of the reagents. We further combined the detection platform with the streptavidin-biotin (SA-B) amplified system to enhance the sensitivity while using chemiluminescence (CL) intensity as signal readout. We realized simultaneous detection of CRP, PCT, and IL-6 on the detection platform and evaluated the sensitivity, linear range, selectivity, and repeatability. Finally, we finished detecting 15 samples from volunteers and compared the results with commercial ELISA kits.Results: Detection of CRP, PCT, and IL-6 exhibited good linear relationships between CL intensities and concentrations in the range of 1.25-40 μg/mL, 0.4-12.8 ng/mL, and 50-1600 pg/mL. The limit of detection (LOD) of CRP, PCT, and IL-6 were 0.54 μg/mL, 0.11 ng/mL, and 16.25 pg/mL, respectively. WMC-MDP is capable of good adequate selectivity and repeatability. The whole detection procedure takes only 22 minutes that meets the requirements of a POC device. Results of 15 samples from volunteers were consistent with the results detected by commercial ELISA kits.Conclusion: WMC-MDP allows simultaneous, rapid, and sensitive detection of CRP, PCT, and IL-6 with satisfactory selectivity and repeatability, requiring minimal manipulation. However, WMC-MDP takes advantage of being a microfluidic device showing the coefficients of variation less than 10% enabling WMC-MDP to be a type of POCT. Therefore, WMC-MDP provides a promising alternative to point-of-care testing (POCT) of multiple biomarkers. We believe the practical application of WMC-MDP in militarized fields will revolutionize infection diagnosis for soldiers.


Gut ◽  
2015 ◽  
Vol 66 (3) ◽  
pp. 454-463 ◽  
Author(s):  
Daniele Mennonna ◽  
Cristina Maccalli ◽  
Michele C Romano ◽  
Claudio Garavaglia ◽  
Filippo Capocefalo ◽  
...  

ObjectivePatient-specific (unique) tumour antigens, encoded by somatically mutated cancer genes, generate neoepitopes that are implicated in the induction of tumour-controlling T cell responses. Recent advancements in massive DNA sequencing combined with robust T cell epitope predictions have allowed their systematic identification in several malignancies.DesignWe undertook the identification of unique neoepitopes in colorectal cancers (CRCs) by using high-throughput sequencing of cDNAs expressed by standard cancer cell cultures, and by related cancer stem/initiating cells (CSCs) cultures, coupled with a reverse immunology approach not requiring human leukocyte antigen (HLA) allele-specific epitope predictions.ResultsSeveral unique mutated antigens of CRC, shared by standard cancer and related CSC cultures, were identified by this strategy. CD8+and CD4+T cells, either autologous to the patient or derived from HLA-matched healthy donors, were readily expanded in vitro by peptides spanning different cancer mutations and specifically recognised differentiated cancer cells and CSC cultures, expressing the mutations. Neoepitope-specific CD8+T cell frequency was also increased in a patient, compared with healthy donors, supporting the occurrence of clonal expansion in vivo.ConclusionsThese results provide a proof-of-concept approach for the identification of unique neoepitopes that are immunogenic in patients with CRC and can also target T cells against the most aggressive CSC component.


2011 ◽  
Vol 10 (1) ◽  
pp. 282 ◽  
Author(s):  
Céline Barnadas ◽  
David Kent ◽  
Lincoln Timinao ◽  
Jonah Iga ◽  
Laurie R Gray ◽  
...  

Lab on a Chip ◽  
2019 ◽  
Vol 19 (4) ◽  
pp. 674-681 ◽  
Author(s):  
Jinhyeok Jeon ◽  
Namhyun Choi ◽  
Hao Chen ◽  
Joung-Il Moon ◽  
Lingxin Chen ◽  
...  

We report a fully integrated SERS-based microdroplet platform for simultaneous detection of various concentrations of a reagent.


2020 ◽  
Vol 8 (Suppl 2) ◽  
pp. A9.2-A10
Author(s):  
O Braubach ◽  
M Gallina ◽  
B Remeniuk ◽  
C Wang ◽  
N Nikulina ◽  
...  

BackgroundMultiplexed immunofluorescence (mIF) allows the visualization of multiple biomarkers in a single tumor tissue section, while at the same time preserving the spatial biology of the tumor microenvironment (TMI). CO-Detection by indEXing (CODEX®) and Phenoptics™ platforms are complementary mIF technologies that span the full spectrum of cancer research, from discovery to translational and clinical research. CODEX® is ultra-high plex and allows imaging of up to 40 antigens on a single tissue section with single-cell resolution. Phenoptics™ is an established mIF platform that enables high-throughput whole slide multispectral image acquisition and tissue interrogation with up to 8 markers plus DAPI. Here we present a study that compares shared sets of immune and tumor markers between the CODEX® and Phenoptics™ platforms. This cross-platform comparison provides a conceptual framework for researchers to translate biomarker signatures from discovery to high-throughput translational studies.Materials and MethodsSerial sections of human formalin-fixed paraffin embedded non-small cell lung cancer (NSCLC) and tonsils were analyzed. An initial screen with a 28-plex CODEX® antibody panel revealed multiple biomarkers of interest, including CK, CD8, Ki67, PD-L1 and PD-1; all of these biomarkers showed abundant expression in the TMI. Building on this result, we next developed a 6-plex Opal™ Phenotpics™ panel. This panel was screened and analyzed via high-throughput whole slide scanning of sample tissues. Image processing and data analysis were conducted similarly for both datasets so that repeatability and consistency of measurements could be established.ResultsBoth CODEX® and Phenoptics™ detected the same cell phenotypes and displayed similar frequencies of cells expressing CK, CD8, Ki67, PD-L1 and PD-1 in serial sections of tonsil and NSCLC tissues. These observations were consistent and cross-validated in data from CODEX® and Phenoptics™ platforms. Crucially, this means that the two approaches can be made analytically equivalent, and hence, that they can be used in conjunction with each other as research progresses along the continuum from discovery to translational and clinical research.ConclusionsOur cross-platform comparison provides a conceptual framework for biomarkers discovered on the CODEX® platform to be translated to the Phenoptics™ platform for high-throughput translational studies. The resulting comprehensive phenotyping and quantification data retain spatial context and provide unprecedented insight into tumor biology.Abstract P01.04 Figure 1Disclosure InformationO. Braubach: A. Employment (full or part-time); Significant; Akoya Biosciences. M. Gallina: A. Employment (full or part-time); Significant; Akoya Biosciences. B. Remeniuk: A. Employment (full or part-time); Significant; Akoya Biosciences. C. Wang: A. Employment (full or part-time); Significant; Akoya Biosciences. N. Nikulina: A. Employment (full or part-time); Significant; Akoya Biosciences. R. Bashier: A. Employment (full or part-time); Significant; Akoya Biosciences. J. Kennedy-Darling: A. Employment (full or part-time); Significant; Akoya Biosciences. C. Hoyt: A. Employment (full or part-time); Significant; Akoya Biosciences.


Sign in / Sign up

Export Citation Format

Share Document