Single‐cell proteomics differentiates Arabidopsis root cell types

New Phytologist, Journal Year: 2024, Volume and Issue: 244(5), P. 1750 - 1759

Published: June 24, 2024

Single-cell proteomics (SCP) is an emerging approach to resolve cellular heterogeneity within complex tissues of multi-cellular organisms. Here, we demonstrate the feasibility SCP on plant samples using model Arabidopsis thaliana. Specifically, focused examining isolated single cells from cortex and endodermis, which are two adjacent root cell types derived a common stem lineage. From 756 cells, identified 3763 proteins 1118 proteins/cell. Ultimately, focus 3217 quantified following stringent filtering. Of these, 596 whose expression enriched in either or endodermis able differentiate these closely related types. Collectivity, this study demonstrates that can neighboring with distinct functions, thereby facilitating identification biomarkers candidate enable functional genomics.

Language: Английский

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Single cell proteomics by mass spectrometry reveals deep epigenetic insight into the actions of an orphan histone deacetylase inhibitor

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 6, 2024

Abstract Epigenetic programming has been shown to play a role in nearly every human system and disease where anyone thought look. However, the levels of heterogeneity at which epigenetic or epiproteomic modifications occur single cell resolution across population remains elusive. While recent advances sequencing technology have allowed between 1 3 histone post-translational be analyzed each cell, over twenty separate chemical PTMs are known exist, allowing thousands possible combinations. Single proteomics by mass spectrometry (SCP) is an emerging hundreds proteins can directly quantified typical cells. As detected SCP heavily biased toward highest abundance, chromatin attractive target for analysis. To this end, I applied analysis cancer cells treated with mocetinostat, class specific deacetylase inhibitor. find that 16 confidently identified localized high site specificity In addition, abundance allows higher throughput methods utilized than previously described. quantitative accuracy suffers when analyzing more 700 per day, 9 measured even 3,500 10-fold greater any previous report. unbiased global approach herein identifies uncharacterized response drug through S100-A8/S100-A9 protein complex partners. This observed 1,000 study, regardless relative method utilized. limitations exist described herein, current technologies easily improve upon results presented here allow comprehensive performed lab. All raw processed data study made publicly available ProteomeXchange/MASSIVE repository as MSV000093434 graphic

Language: Английский

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Metabolomic, Proteomic, and Single-Cell Proteomic Analysis of Cancer Cells Treated with the KRAS^G12D Inhibitor MRTX1133

Journal of Proteome Research, Journal Year: 2023, Volume and Issue: 22(12), P. 3703 - 3713

Published: Nov. 20, 2023

Mutations in KRAS are common drivers of human cancers and often those with the poorest overall prognosis for patients. A recently developed compound, MRTX1133, has shown promise inhibiting activity KRASG12D mutant proteins, which is one main pancreatic cancer. To better understand mechanism action this I performed both proteomics metabolomics on four cancer cell lines. obtain increased granularity proteomic observations, single-cell was successfully two these Following quality filtering, a total 1498 single cells were analyzed. From cells, 3140 proteins identified approximately 953 quantified per cell. At 48 h treatment, distinct populations can be observed based level effectiveness drug decreasing abundance protein each respective cell, results that effectively masked bulk analysis. All mass spectrometry data processed publicly available at www.massive.ucsd.edu accessions PXD039597, PXD039601, PXD039600.

Language: Английский

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Single-cell proteomics differentiates Arabidopsis root cell types

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 10, 2024

Abstract Recently, major advances have enabled the exploration of cellular heterogeneity using single-cell proteomics. Here we examine feasibility proteomics on plant samples. We focus Arabidopsis thaliana , examining isolated single cells from cortex and endodermis, which are two adjacent root cell-types derived a common stem cell. From 756 identify 3,763 proteins 1,118 proteins/cell. Ultimately, 3,217 quantified following stringent filtering. Of these, identified 596 whose expression is enriched in either or endodermis able to differentiate these closely related cell-types. Collectivity, our findings underscore promise explore between individual cells.

Language: Английский

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The G1/S transition in mammalian stem cellsin vivois autonomously regulated by cell size

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 11, 2024

Cell growth and division must be coordinated to maintain a stable cell size, but how this coordination is implemented in multicellular tissues remains unclear. In unicellular eukaryotes, autonomous size control mechanisms couple with little extracellular input. However, we do not know if operate the same way or whether cycle progression are separately controlled by cell-extrinsic signals. Here, address question tracking single epidermal stem cells growing adult mice. We find that cell-autonomous mechanism, dependent on RB pathway, sets timing of S phase entry based cell's current size. Cell-extrinsic variations cellular microenvironment affect rates coupling. Our work reassesses long-standing models regulation within complex metazoan identifies as critical mechanism regulating divisions

Language: Английский

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Cell shapes decode molecular phenotypes in image-based spatial proteomics

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: May 16, 2025

The diversity of cellular and tissue structures can arise from a few basic cell shapes, which undergo various transformations based on biophysical constraints cytoskeletal organization. While geometry has been linked with selected biological processes such as polarity, signaling or morphogenesis, the orchestration whole proteome in association to shape is still poorly understood. In this study, using more than 1 million images single cells stained for 11,998 proteins across 10 lines Human Protein Atlas database, we performed an integrated analysis organelle, pathway protein levels 2D shapespace. We found that nuclear shapes exist shared continuum. also subcellular organelle topology varies lines, but remains robust within each line's At level, different same cycle phase might be preparing fates, many non-cell expressed shape-based abundance variation. Using coordinate framework defined by shape, could analyze distribution shift spatial localization under drug perturbation.

Language: Английский

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Too big not to fail: emerging evidence for size‐induced senescence

FEBS Journal, Journal Year: 2023, Volume and Issue: 291(11), P. 2291 - 2305

Published: Nov. 20, 2023

Cellular senescence refers to a permanent and stable state of cell cycle exit. This process plays an important role in many cellular functions, including tumor suppression. It was first noted that is associated with increased size the early 1960s; however, how this contributes exit poorly understood until recently. In review, we discuss new findings identify as not only consequence but also cause We highlight recent insights into alters normal physiology creates homeostatic imbalances contribute induction. Finally, focus on potential clinical implications these context arrest‐causing cancer therapeutics speculate changes may impact outcomes patients treated drugs.

Language: Английский

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Understanding theory, literary theory and literary criticism

International Journal of Research in English, Journal Year: 2024, Volume and Issue: 6(1), P. 62 - 64

Published: Jan. 1, 2024

The term theory derives from the Greek word theorein, meaning 'to look at.' provides reader with a set of frameworks through which they would be able to analyses world around them. has been appropriately described as an amalgamation intellectual history, morality, philosophy, social beliefs, etc., studied together but not following perspective literary productivity. Further, acts tool for readers and understand work literature. A Literary Theory enables relationship between author thematic aspects within texts. Whereas, in Criticism, critic conveys appeal, relevance importance readers. Here, criticism means explanation, elucidation, evaluation, assessment, discussing positive literature co-relating one another This paper aims study significance understanding terms theory, criticism. Through practical application criticism, can intentionally participate endless conversation about concepts ourselves, culture, society role texts reshaping concepts. will help origin, need difference before studying interpreting also try emphasise significant contributions classical thinkers, who are now being ignored considered inadequate beneath glittering personality modern theorists.

Language: Английский

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RUCova: Removal of Unwanted Covariance in mass cytometry data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 28, 2024

High dimensional mass cytometry is confounded by unwanted covariance due to variations in cell size and staining efficiency, making analysis interpretation challenging. We present RUCova, a novel method designed address confounding factors data. RUCova removes using multivariate linear regression on Surrogates of Unwanted Covariance (SUCs), Principal Component Analysis (PCA). exemplify the use show that it effectively while preserving genuine biological signals. Our results demonstrate efficacy elucidating complex data patterns, facilitating identification activated signalling pathways, improving classification important populations. By providing robust framework for normalization interpretation, enhances accuracy reliability analyses, contributing advancements our understanding cellular biology disease mechanisms. The R package available https://github.com/molsysbio/RUCova . Detailed documentation, data, code required reproduce are https://doi.org/10.5281/zenodo.10913464 Supplementary material: Available at bioRxiv.

Language: Английский

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Metabolomic, proteomic and single cell proteomic analysis of cancer cells treated with the KRAS^G12Dinhibitor MRTX1133

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 23, 2023

Mutations in KRAS are common drivers of human cancers and often those with the poorest overall prognosis for patients. A recently developed compound, MRTX1133, has shown promise inhibiting activity

Language: Английский

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