RNA modifications in the tumor microenvironment: insights into the cancer-immunity cycle and beyond DOI Creative Commons
Yuan Ding, Cuicui Liu, Ke‐Da Yu

et al.

Experimental Hematology and Oncology, Journal Year: 2025, Volume and Issue: 14(1)

Published: April 2, 2025

Language: Английский

Mass-spectrometry-based proteomics: from single cells to clinical applications DOI
Tiannan Guo, Judith A. Steen, Matthias Mann

et al.

Nature, Journal Year: 2025, Volume and Issue: 638(8052), P. 901 - 911

Published: Feb. 26, 2025

Language: Английский

Citations

3
A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research DOI Creative Commons
Christian M. Beusch,

Ken Braesch-Andersen,

Ulrika Felldin

et al.

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: Jan. 17, 2025

Recent developments in mass spectrometry-based proteomics have established it as a robust tool for system-wide analyses essential pathophysiological research. While post-mortem samples are critical source these studies, our understanding of how body decomposition influences the proteome remains limited. Here, we revisited published data and conducted clinically relevant time-course experiment mice, revealing organ-specific regulation after death, with only fraction changes linked to protein autolysis. The liver spleen exhibit significant proteomic alterations within hours post-mortem, whereas heart displays modest changes. Additionally, subcellular compartmentalization leads an unexpected surge at earliest interval (PMI). comprehensive analysis semi-tryptic peptides, distinct consensus motifs different organs, indicating protease activity. In conclusion, findings emphasize importance considering PMI effects when designing may significantly overshadow impacts diseases. Preferably, should be taken operation room, especially studies including or trans-organ comparison. single-organ planning involve careful control PMI.

Language: Английский

Citations

1
Formaldehyde Fixation Helps Preserve the Proteome State during Single-Cell Proteomics Sample Processing and Analysis DOI
Ilaria Piga, Claire Koenig, Maico Lechner

et al.

Journal of Proteome Research, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 3, 2025

Mass spectrometry-based single-cell proteomics (SCP) is gaining momentum but remains limited to a few laboratories due the high costs and specialized expertise required. The ability send samples core facilities would benefit nonspecialist popularize SCP for biological applications. However, no methods have been tested in "freeze" proteome state while maintaining cell integrity transfer between or prolonged sorting using fluorescence-activated (FACS). This study evaluates whether short-term formaldehyde (FA) fixation can maintain states. We demonstrate that FA does not substantially affect protein recovery, even without heating strong detergents, maintains analytical depth compared with classical workflows. Fixation also preserves drug-induced specific perturbations of abundance during sample preparation analysis. Our findings suggest facilitate by enabling shipping sorting, potentially democratizing access technology expanding its application research, thereby accelerating discoveries biology personalized medicine.

Language: Английский

Citations

0
Entering the era of deep single-cell proteomics DOI
Ludwig Sinn, Vadim Demichev

Nature Methods, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

Language: Английский

Citations

0
Trends in Mass Spectrometry-Based Single-Cell Proteomics DOI

Ximena Sanchez-Avila,

Raphaela Menezes de Oliveira, Siqi Huang

et al.

Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: March 16, 2025

InfoMetrics Analytical ChemistryASAPArticle CiteCitationCitation and abstractCitation referencesMore citation options ShareShare onFacebookXWeChatLinkedInRedditEmailBlueskyJump toExpandCollapse ReviewMarch 16, 2025Trends in Mass Spectrometry-Based Single-Cell ProteomicsClick to copy article linkArticle link copied!Ximena Sanchez-AvilaXimena Sanchez-AvilaDepartment of Chemistry Biochemistry, Brigham Young University, Provo, Utah 84602, United StatesMore by Ximena Sanchez-AvilaView BiographyRaphaela M. de OliveiraRaphaela OliveiraDepartment Raphaela OliveiraView BiographySiqi HuangSiqi HuangDepartment Siqi HuangView BiographyChao WangChao WangDepartment Chao WangView Biographyhttps://orcid.org/0009-0008-6197-2985Ryan T. Kelly*Ryan KellyDepartment States*Email: [email protected]More Ryan KellyView Biographyhttps://orcid.org/0000-0002-3339-4443Other Access OptionsAnalytical ChemistryCite this: Anal. Chem. 2025, XXXX, XXX, XXX-XXXClick citationCitation copied!https://pubs.acs.org/doi/10.1021/acs.analchem.5c00661https://doi.org/10.1021/acs.analchem.5c00661Published March 2025 Publication History Received 28 January 2025Accepted February 2025Revised 23 2025Published online 16 2025review-article© American Chemical SocietyRequest reuse permissionsACS Publications© SocietySubjectswhat are subjects Article automatically applied from the ACS Subject Taxonomy describe scientific concepts themes article. Cells Isolation spectrometry Peptides proteins Sample preparation Note: In lieu an abstract, this is article's first page. Read To access article, please review available below. Get instant Purchase for 48 hours. Check out below using your ID or as a guest. Restore my guest Recommended through Your Institution You may have institution. institution does not content. Add change let them know you'd like include access. Through Recommend Name Loading Institutional Login Options... Change Explore subscriptions institutions Log with if you previously purchased it member benefits. hours $48.00 cart Checkout Cited By Click section linkSection copied!This has yet been cited other publications.Download PDF e-AlertsGet e-AlertsAnalytical copied!https://doi.org/10.1021/acs.analchem.5c00661Published 2025© permissionsArticle Views6Altmetric-Citations-Learn about these metrics closeArticle Views COUNTER-compliant sum full text downloads since November 2008 (both HTML) across all individuals. These regularly updated reflect usage leading up last few days.Citations number articles citing calculated Crossref daily. Find more information counts.The Altmetric Attention Score quantitative measure attention that research received online. Clicking on donut icon will load page at altmetric.com additional details score social media presence given how calculated.Recommended Articles

Language: Английский

Citations

0
Global analysis of protein turnover dynamics in single cells DOI Creative Commons
Pierre Sabatier, Maico Lechner, Ulises H. Guzmán

et al.

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Single-cell proteomics (SCPs) has advanced significantly, yet it remains largely unidimensional, focusing primarily on protein abundances. In this study, we employed a pulsed stable isotope labeling by amino acids in cell culture (pSILAC) approach to simultaneously analyze abundance and turnover single cells (SC-pSILAC). Using state-of-the-art SCP workflow, demonstrated that two SILAC labels are detectable from ∼4,000 proteins HeLa recapitulating known biology. We performed large-scale time-series SC-pSILAC analysis of undirected differentiation human induced pluripotent stem (iPSCs) encompassing 6 sampling times over 2 months analyzed >1,000 cells. Protein dynamics highlighted differentiation-specific co-regulation complexes with core histone turnover, discriminating dividing non-dividing Lastly, correlating diameter the individual showed histones some cell-cycle do not scale size. The method provides multidimensional view single-cell

Language: Английский

Citations

0
RNA modifications in the tumor microenvironment: insights into the cancer-immunity cycle and beyond DOI Creative Commons
Yuan Ding, Cuicui Liu, Ke‐Da Yu

et al.

Experimental Hematology and Oncology, Journal Year: 2025, Volume and Issue: 14(1)

Published: April 2, 2025

Language: Английский

Citations

0