Multiplexed Data-Independent Acquisition (mDIA) to Profile Extracellular Vesicle Proteomes DOI Creative Commons
Yi‐Kai Liu,

Nathaniel Miller,

Marco Hadisurya

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Май 15, 2025

Extracellular vesicles (EVs) have gained increasing attention with their intriguing biological functions and molecular cargoes serving as potential biomarkers for various diseases, including cancers. A relatively lower abundance of EV proteins compared to cellular counterparts necessitates sensitive accurate quantitative proteomic strategies. Multiplexed proteomics combined data-independent acquisition (mDIA) has shown promise improving sensitivity quantification over traditional DDA label-free methods. Despite this, mDIA pipelines that utilize types spectral libraries search software suites not been thoroughly evaluated proteome samples. In this study, we aim establish a robust pipeline based on dimethyl labeling EVs. EVs were isolated using the extracellular vesicle total recovery purification (EVtrap) technique processed directly through an on-bead one-pot sample preparation workflow obtain digested peptides. We different pipelines, library-free library-based DIA timsTOF HT platform. Results showed DIA, project-specific generated from StageTip-based fractionation, outperformed other in protein identification quantification. demonstrated first time landscape changes caused by IDH1 mutation inhibitor treatment intrahepatic cholangiocarcinoma, highlighting utility EV-based biomarker discovery.

Язык: Английский

Revisiting the advance of age-dependent α-synuclein propagation and aggregation DOI Open Access
Dong‐Yan Song, Jiayi Li

Ageing and Neurodegenerative Diseases, Год журнала: 2025, Номер 5(1)

Опубликована: Фев. 22, 2025

Aging is a major risk factor for different neurodegenerative diseases (NDDs), including Parkinson’s disease (PD). In PD, one of the key neuropathological features cytoplasmic protein aggregation, named Lewy bodies (LBs) in cell body, and neurites (LNs) neuronal processes terminals. The α-synuclein (α-syn) has been found to be component LBs LNs, considered play central role their formation. α-Syn also increases healthy aging conditions. Evidence shown that promotes α-syn pathological aggregation propagation and, therefore, may induce aggravate PD pathogenesis. Here, we aim highlight recent advances age-related prion-like discuss subsequent consequences functions.

Язык: Английский

Процитировано

0

Role and Potential of Artificial Intelligence in Biomarker Discovery and Development of Treatment Strategies for Amyotrophic Lateral Sclerosis DOI Open Access
Y. Kitaoka, Toshihiro Uchihashi, Satoshi Kawata

и другие.

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(9), С. 4346 - 4346

Опубликована: Май 2, 2025

Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), present significant challenges owing to their complex pathologies and a lack of curative treatments. Early detection reliable biomarkers are critical but remain elusive. Artificial intelligence (AI) has emerged as transformative tool, enabling advancements in biomarker discovery, diagnostic accuracy, therapeutic development. From optimizing clinical-trial designs leveraging omics neuroimaging data, AI facilitates understanding disease treatment innovation. Notably, technologies such AlphaFold deep learning models have revolutionized proteomics neuroimaging, offering unprecedented insights into ALS pathophysiology. This review highlights the intersection ALS, exploring current state progress future prospects.

Язык: Английский

Процитировано

0

Multiplexed Data-Independent Acquisition (mDIA) to Profile Extracellular Vesicle Proteomes DOI Creative Commons
Yi‐Kai Liu,

Nathaniel Miller,

Marco Hadisurya

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Май 15, 2025

Extracellular vesicles (EVs) have gained increasing attention with their intriguing biological functions and molecular cargoes serving as potential biomarkers for various diseases, including cancers. A relatively lower abundance of EV proteins compared to cellular counterparts necessitates sensitive accurate quantitative proteomic strategies. Multiplexed proteomics combined data-independent acquisition (mDIA) has shown promise improving sensitivity quantification over traditional DDA label-free methods. Despite this, mDIA pipelines that utilize types spectral libraries search software suites not been thoroughly evaluated proteome samples. In this study, we aim establish a robust pipeline based on dimethyl labeling EVs. EVs were isolated using the extracellular vesicle total recovery purification (EVtrap) technique processed directly through an on-bead one-pot sample preparation workflow obtain digested peptides. We different pipelines, library-free library-based DIA timsTOF HT platform. Results showed DIA, project-specific generated from StageTip-based fractionation, outperformed other in protein identification quantification. demonstrated first time landscape changes caused by IDH1 mutation inhibitor treatment intrahepatic cholangiocarcinoma, highlighting utility EV-based biomarker discovery.

Язык: Английский

Процитировано

0