scholarly journals Comparative proteome signatures of trace samples by multiplexed Data-Independent Acquisition

2021 ◽  
pp. 100177
Author(s):  
Claudia Ctortecka ◽  
Gabriela Krššáková ◽  
Karel Stejskal ◽  
Josef M. Penninger ◽  
Sasha Mendjan ◽  
...  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Leyla A. Erozenci ◽  
Sander R. Piersma ◽  
Thang V. Pham ◽  
Irene V. Bijnsdorp ◽  
Connie R. Jimenez

AbstractThe protein content of urinary extracellular vesicles (EVs) is considered to be an attractive non-invasive biomarker source. However, little is known about the consistency and variability of urinary EV proteins within and between individuals over a longer time-period. Here, we evaluated the stability of the urinary EV proteomes of 8 healthy individuals at 9 timepoints over 6 months using data-independent-acquisition mass spectrometry. The 1802 identified proteins had a high correlation amongst all samples, with 40% of the proteome detected in every sample and 90% detected in more than 1 individual at all timepoints. Unsupervised analysis of top 10% most variable proteins yielded person-specific profiles. The core EV-protein-interaction network of 516 proteins detected in all measured samples revealed sub-clusters involved in the biological processes of G-protein signaling, cytoskeletal transport, cellular energy metabolism and immunity. Furthermore, gender-specific expression patterns were detected in the urinary EV proteome. Our findings indicate that the urinary EV proteome is stable in longitudinal samples of healthy subjects over a prolonged time-period, further underscoring its potential for reliable non-invasive diagnostic/prognostic biomarkers.


2021 ◽  
Vol 22 (10) ◽  
pp. 5065
Author(s):  
Tatjana Vujić ◽  
Domitille Schvartz ◽  
Anton Iliuk ◽  
Jean-Charles Sanchez

Over the last decade, the knowledge in extracellular vesicles (EVs) biogenesis and modulation has increasingly grown. As their content reflects the physiological state of their donor cells, these “intercellular messengers” progressively became a potential source of biomarker reflecting the host cell state. However, little is known about EVs released from the human brain microvascular endothelial cells (HBMECs). The current study aimed to isolate and characterize EVs from HBMECs and to analyze their EVs proteome modulation after paraquat (PQ) stimulation, a widely used herbicide known for its neurotoxic effect. Size distribution, concentration and presence of well-known EV markers were assessed. Identification and quantification of PQ-exposed EV proteins was conducted by data-independent acquisition mass spectrometry (DIA-MS). Signature pathways of PQ-treated EVs were analyzed by gene ontology terms and pathway enrichment. Results highlighted that EVs exposed to PQ have modulated pathways, namely the ubiquinone metabolism and the transcription HIF-1 targets. These pathways may be potential molecular signatures of the PQ-induced toxicity carried by EVs that are reflecting their cell of origin by transporting with them irreversible functional changes.


2021 ◽  
Vol 11 (3) ◽  
pp. 1125
Author(s):  
Htet Myet Lynn ◽  
Pankoo Kim ◽  
Sung Bum Pan

In this report, the study of non-fiducial based approaches for Electrocardiogram(ECG) biometric authentication is examined, and several excessive techniques are proposed to perform comparative experiments for evaluating the best possible approach for all the classification tasks. Non-fiducial methods are designed to extract the discriminative information of a signal without annotating fiducial points. However, this process requires peak detection to identify a heartbeat signal. Based on recent studies that usually rely on heartbeat segmentation, QRS detection is required, and the process can be complicated for ECG signals for which the QRS complex is absent. Thus, many studies only conduct biometric authentication tasks on ECG signals with QRS complexes, and are hindered by similar limitations. To overcome this issue, we proposed a data-independent acquisition method to facilitate highly generalizable signal processing and feature learning processes. This is achieved by enhancing random segmentation to avoid complicated fiducial feature extraction, along with auto-correlation to eliminate the phase difference due to random segmentation. Subsequently, a bidirectional recurrent neural network (RNN) with long short-term memory (LSTM) deep networks is utilized to automatically learn the features associated with the signal and to perform an authentication task. The experimental results suggest that the proposed data-independent approach using a BLSTM network achieves a relatively high classification accuracy for every dataset relative to the compared techniques. Moreover, it exhibited a significantly higher accuracy rate in experiments using ECG signals without the QRS complex. The results also revealed that data-dependent methods can only perform well for specified data types and amendments of data variations, whereas the presented approach can also be considered for generalization to other quasi-periodical biometric signal-based classification tasks in future studies.


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