Applications of single-cell RNA sequencing in drug discovery and development

Nature Reviews Drug Discovery, Journal Year: 2023, Volume and Issue: 22(6), P. 496 - 520

Published: April 28, 2023

Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods, together with associated computational tools and the growing availability of public data resources, are transforming drug discovery development. New opportunities emerging in target identification owing to improved disease understanding through cell subtyping, highly multiplexed functional genomics screens incorporating scRNA-seq enhancing credentialling prioritization. ScRNA-seq is also aiding selection relevant preclinical models providing new insights into mechanisms action. In clinical development, can inform decision-making via biomarker for patient stratification more precise monitoring response progression. Here, we illustrate how methods being applied key steps discuss ongoing challenges their implementation pharmaceutical industry. There have been significant recent advances development remarkable Ferran colleagues primarily pipeline, from decision-making. Ongoing potential future directions discussed.

Language: Английский

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Increasing the throughput of sensitive proteomics by plexDIA

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 41(1), P. 50 - 59

Published: July 14, 2022

Language: Английский

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Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments

Nature Methods, Journal Year: 2023, Volume and Issue: 20(3), P. 375 - 386

Published: March 1, 2023

Language: Английский

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Exploring functional protein covariation across single cells using nPOP

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: Dec. 16, 2022

Many biological processes, such as cell division cycle and drug resistance, are reflected in protein covariation across single cells. This can be quantified interpreted by single-cell mass spectrometry with sufficiently high throughput accuracy.

Language: Английский

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Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics

Nature Methods, Journal Year: 2023, Volume and Issue: 20(5), P. 714 - 722

Published: April 3, 2023

Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth protein quantification, especially for proteins modifications biological interest. Here, to simultaneously advance all these aims, we developed prioritized Single-Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands peptides across single cells (thus data completeness) while maximizing instrument time spent analyzing identifiable peptides, thus proteome depth. These strategies increased sensitivity, completeness coverage over twofold. The gains enabled quantifying variation in untreated lipopolysaccharide-treated primary macrophages. Within each condition, covaried within functional sets, including phagosome maturation proton transport, similarly both treatment conditions. This covariation is coupled phenotypic variability endocytic activity. also proteolytic products, suggesting a gradient cathepsin activities condition. freely available widely applicable, interest without sacrificing coverage. Support at http://scp.slavovlab.net/pSCoPE .

Language: Английский

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Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA

Journal of Proteome Research, Journal Year: 2023, Volume and Issue: 22(3), P. 697 - 705

Published: Feb. 3, 2023

Accurate protein quantification is key to identifying markers, regulatory relationships between proteins, and pathophysiological mechanisms. Realizing this potential requires sensitive deep analysis of a large number samples. Toward goal, proteomics throughput can be increased by parallelizing the both precursors samples using multiplexed data independent acquisition (DIA) implemented plexDIA framework: https://plexDIA.slavovlab.net. Here we demonstrate improved precisions retention time estimates within how enables more accurate quantification. has demonstrated multiplicative gains in throughput, these may substantially amplified improving multiplexing reagents, acquisition, interpretation. We discuss future directions for advancing plexDIA, which include engineering optimized mass-tags high-plexDIA, introducing isotopologous carriers, developing algorithms that utilize regular structures improve sensitivity, proteome coverage, quantitative accuracy. These advances will increase functional proteomic assays, including quantifying conformations, turnover dynamics, modifications states activities. The sensitivity assays extend single-cell analysis, thus enabling analysis.

Language: Английский

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Dynamics of Single-Cell Protein Covariation during Epithelial–Mesenchymal Transition

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: unknown

Published: April 25, 2024

Physiological processes, such as the epithelial–mesenchymal transition (EMT), are mediated by changes in protein interactions. These may be better reflected covariation within a cellular cluster than temporal dynamics of cluster-average abundance. To explore this possibility, we quantified proteins single human cells undergoing EMT. Covariation analysis data revealed that functionally coherent clusters dynamically changed their protein–protein correlations without concomitant were monotonic time and delineated modules functioning actin cytoskeleton organization, energy metabolism, transport. defined same point and, thus, reflect biological regulation masked dynamics. Thus, correlation across offers window into during physiological transitions.

Language: Английский

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Single‐cell proteomics by mass spectrometry: Advances and implications in cancer research

PROTEOMICS, Journal Year: 2024, Volume and Issue: 24(12-13)

Published: May 10, 2024

Abstract Cancer harbours extensive proteomic heterogeneity. Inspired by the prior success of single‐cell RNA sequencing (scRNA‐seq) in characterizing minute transcriptomics heterogeneity cancer, researchers are now actively searching for information regarding proteomics counterpart. Therefore recently, mass spectrometry (SCP) has rapidly developed into state‐of‐the‐art technology to cater need. This review aims summarize application SCP cancer research, while revealing current development progress technology. The also contribute ideas research gaps and future directions, ultimately promoting research.

Language: Английский

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The Current State of Single‐Cell Proteomics Data Analysis

Current Protocols, Journal Year: 2023, Volume and Issue: 3(1)

Published: Jan. 1, 2023

Sound data analysis is essential to retrieve meaningful biological information from single-cell proteomics experiments. This carried out by computational methods that are assembled into workflows, and their implementations influence the conclusions can be drawn data. In this work, we explore compare workflows have been used over last four years identify a profound lack of consensus on how analyze We highlight need for benchmarking standardization tools data, as well carefully designed Finally, cover current efforts aim fill gap, list remaining missing pieces, conclude with lessons learned replication published analyses. © 2023 Wiley Periodicals LLC.

Language: Английский

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Recent advances in microfluidics for single-cell functional proteomics

Lab on a Chip, Journal Year: 2023, Volume and Issue: 23(7), P. 1726 - 1751

Published: Jan. 1, 2023

This article covers exciting developments of recent microfluidics-based single-cell proteomics methods and their utilizations to tackle important biological questions for both basic translational research.

Language: Английский

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