Fluorescence Analysis of Circulating Exosomes for Breast Cancer Diagnosis Using a Sensor Array and Deep Learning

Abstract

Emerging liquid biopsy methods for investigating biomarkers in bodily fluids such as blood, saliva, or urine can be used to perform noninvasive cancer detection. However, the complexity and heterogeneity of exosomes require improved methods to achieve the desired sensitivity and accuracy. Herein, we report our study on developing a breast cancer liquid biopsy system, including a fluorescence sensor array and deep learning (DL) tool AggMapNet. In particular, we used a 12-unit sensor array composed of conjugated polyelectrolytes, fluorophore-labeled peptides, and monosaccharides or glycans to collect fluorescence signals from cells and exosomes. Linear discriminant analysis (LDA) processed the fluorescence spectral data of cells and cellderived exosomes, demonstrating successful discrimination between normal and different cancerous cells and 100% accurate classification of different BC cells. For heterogeneous plasma-derived exosome analysis, CNN-based DL tool AggMapNet was applied to transform the unordered fluorescence spectra into feature maps (Fmaps), which gave a straightforward visual demonstration of the difference between healthy donors and BC patients with 100% prediction accuracy. Our work indicates that our fluorescent sensor array and DL model can be used as a promising noninvasive method for BC diagnosis.

Artificial Intelligent Label-Free SERS Profiling of Serum Exosomes for Breast Cancer Diagnosis and Postoperative Assessment

“…Considerable efforts have been recently devoted to the development of biosensing platforms for quantitative analysis of exosomes, broadly divided into two categories. 11 One strategy is to target specific exosomal biomarkers, including Western blot, enzymelinked immunosorbent assay, reverse transcription-polymerase chain reaction, and emerging optical and electrochemical methods. 11,12 However, these methods face challenges in clinical practice due to the requirement of prior knowledge of existing biomarkers and delicate design of signal probes.…”

“…Another strategy is omics-based integrative analysis of exosomes, which provides comprehensive molecular profiles of exosomal proteins, nucleic acids, and metabolites typically extracted by microarrays and gas/liquid chromatography−mass spectrometry. 11,12 The clinical utility of omics-based profiling is also hindered by sophisticated instrumentation and complicated data set analysis. Surface-enhanced Raman spectroscopy (SERS) is a promising detection tool because it presents rich molecular information, ultrahigh sensitivity, narrow spectral bandwidths, powerful multiplex detection capability and negligible water interference.…”

“…Exosomes are a class of extracellular vesicles with approximately 30–150 nm in diameter, secreted by almost all living cells. , Exosomes carry invaluable molecular information (i.e., proteins, nucleic acids, lipids, metabolites, and small biomolecules) inherited from their parent cells, and are present in high abundance (>5 × 10 9 particles/mL) with superior stability in nearly all body fluids compared with other circulating biomarkers such as circulating tumor cells (∼1 cell per milliliter blood), protein and nucleic acid biomarkers. − These merits permit the utility of exosomes as promising circulating biomarkers for liquid biopsies of cancer. Considerable efforts have been recently devoted to the development of biosensing platforms for quantitative analysis of exosomes, broadly divided into two categories . One strategy is to target specific exosomal biomarkers, including Western blot, enzyme-linked immunosorbent assay, reverse transcription-polymerase chain reaction, and emerging optical and electrochemical methods. , However, these methods face challenges in clinical practice due to the requirement of prior knowledge of existing biomarkers and delicate design of signal probes.…”

Tumor-derived small extracellular vesicles: potential roles and mechanism in glioma

“…TEXs are rich in protein, miRNA, mRNA, DNA, and lipid contents and play an essential role in the early diagnosis, development, and treatment of tumors [138][139][140]. However, because of the differences in experimental materials and research methods, the detection of single exosome contents is prone to false-positive results.…”

Urine exosomes as biomarkers in bladder cancer diagnosis and prognosis: From functional roles to clinical significance

“…While the techniques are well-established, they are often laborious, costly and time consuming, limiting their application in clinical settings. Recently, several “lab-on-a-chip” fluorescent ( 70 ), magneto-electrochemical ( 71 ), nanoplasmonic ( 72 ) and cationic lipoplex nanoparticle ( 73 ) technologies have been developed for detection of proteins and miRNAs in exosomes from biological fluids. However, they either require pre-processed clinical specimens or involve intricate fabrications.…”