Quantitative proteomic mass spectrometry of protein kinases to determine dynamic heterogeneity of the human kinome DOI
Michael P. East, Robert W. Sprung, Denis O. Okumu

et al.

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

Published: Oct. 4, 2024

The kinome is a dynamic system of kinases regulating signaling networks in cells and dysfunction protein contributes to many diseases. Regulation the expression alters cellular responses environmental changes perturbations. We configured library 672 proteotypic peptides quantify >300 single LC-MS experiment using ten micrograms from human tissues including biopsies. This enables absolute quantitation kinase abundance at attomole-femtomole levels, requiring no enrichment less than starting flash-frozen formalin fixed paraffin embedded tissues. Breast cancer biopsies, organoids, cell lines were analyzed SureQuant method, demonstrating heterogeneity across within breast clinical subtypes. Kinome was coupled with nanoscale phosphoproteomics, providing feasible method for novel diagnosis understanding patient treatment.

Language: Английский

Hallmarks of sex bias in immuno-oncology: mechanisms and therapeutic implications DOI
Tong Xiao, Juyeun Lee, Timothy D. Gauntner

et al.

Nature reviews. Cancer, Journal Year: 2024, Volume and Issue: 24(5), P. 338 - 355

Published: April 8, 2024

Language: Английский

Citations

22
Advances in the understanding and therapeutic manipulation of cancer immune responsiveness: a Society for Immunotherapy of Cancer (SITC) review DOI Creative Commons

Alessandra Cesano,

Ryan C. Augustin, Luigi Barrea

et al.

Journal for ImmunoTherapy of Cancer, Journal Year: 2025, Volume and Issue: 13(1), P. e008876 - e008876

Published: Jan. 1, 2025

Cancer immunotherapy-including immune checkpoint inhibition (ICI) and adoptive cell therapy (ACT)-has become a standard, potentially curative treatment for subset of advanced solid liquid tumors. However, most patients with cancer do not benefit from the rapidly evolving improvements in understanding principal mechanisms determining responsiveness (CIR); including patient-specific genetically determined acquired factors, as well intrinsic biology. Though CIR is multifactorial, fundamental concepts are emerging that should be considered design novel therapeutic strategies related clinical studies. Recent advancements approaches to address limitations current treatments discussed here, specific focus on ICI ACT.

Language: Английский

Citations

2
Finding a needle in a haystack: functional screening for novel targets in cancer immunology and immunotherapies DOI Creative Commons

Yi Du,

Yang Yang, Bohao Zheng

et al.

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

Published: Jan. 25, 2025

Genome-wide functional genetic screening has been widely used in the biomedicine field, which makes it possible to find a needle haystack at level. In cancer research, gene mutations are closely related tumor development, metastasis, and recurrence, use of state-of-the-art powerful technologies, such as clustered regularly interspaced short palindromic repeat (CRISPR), search for most critical genes or coding products provides us with new possibility further refine mapping provide possibilities treatment patients. The CRISPR refined atlas provided Immunotherapy, highly promising method, validated clinic, but could only meet needs small proportion Finding immunotherapy targets is key future immunotherapy. Here, we revisit application immunology from different perspectives, selection diverse vitro vivo models potential immune checkpoints potentiating CAR-T cells. data will offer fresh therapeutic clues

Language: Английский

Citations

1
The interplay between autophagy and cGAS-STING signaling and its implications for cancer DOI Creative Commons
Maximilian Schmid, Patrick D. Fischer, Magdalena Engl

et al.

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 15

Published: April 10, 2024

Autophagy is an intracellular process that targets various cargos for degradation, including members of the cGAS-STING signaling cascade. senses cytosolic double-stranded DNA and triggers innate immune response through type I interferons. Emerging evidence suggests autophagy plays a crucial role in regulating fine-tuning signaling. Reciprocally, pathway can actively induce canonical as well non-canonical forms autophagy, establishing regulatory network feedback mechanisms alter both autophagic pathway. The crosstalk between impacts wide variety cellular processes such protection against pathogenic infections neurodegenerative disease, autoinflammatory disease cancer. Here we provide comprehensive overview involved signaling, with specific focus on interactions two pathways their importance

Language: Английский

Citations

7
Spatial oncology: Translating contextual biology to the clinic DOI
Dennis Gong,

Jeanna M Arbesfeld-Qiu,

Ella Perrault

et al.

Cancer Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Language: Английский

Citations

6
A review of Ribosome profiling and tools used in Ribo-seq data analysis DOI Creative Commons

Mingso Sherma Limbu,

Tianze Xiong,

Sufang Wang

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 1912 - 1918

Published: April 22, 2024

Translational regulation plays the most critical role in gene expression. Ribosome profiling sequencing (Ribo-Seq) is one of methods to study translation and its regulation. It a high throughput technology based on deep sequencing, which targets ribosome protected mRNA fragments produce 'global snapshot' translatome. There has been an annual increase number publications incorporating Ribo-seq technology. Because importance, we used PubMed database conduct comprehensive bibliometric analysis Ribo-seq. We identified 2,744 published articles that utilized term 'Ribo-seq' between 2009 Jan 2024, 684 contained both RNA-seq terms. Based keywords correlation analysis, discovered primary focus lies areas translation, transcriptome, past few years other topics such as single-cell ribo-seq crispr within two years, reflecting current interests research. The data applications were also explored summarized, providing guide for researchers choose corresponding tools different types analysis. Overall, highlighted advances made by technologies, possibilities utilizing machine learning models unravel information from multi-omics data. integration with omics data, RNA-seq, essential understand expression complex biological systems.

Language: Английский

Citations

5
Mechanisms and technologies in cancer epigenetics DOI Creative Commons
Zaki A. Sherif, Olorunseun O. Ogunwobi, Habtom W. Ressom

et al.

Frontiers in Oncology, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 7, 2025

Cancer's epigenetic landscape, a labyrinthine tapestry of molecular modifications, has long captivated researchers with its profound influence on gene expression and cellular fate. This review discusses the intricate mechanisms underlying cancer epigenetics, unraveling complex interplay between DNA methylation, histone chromatin remodeling, non-coding RNAs. We navigate through tumultuous seas dysregulation, exploring how these processes conspire to silence tumor suppressors unleash oncogenic potential. The narrative pivots cutting-edge technologies, revolutionizing our ability decode epigenome. From granular insights single-cell epigenomics holistic view offered by multi-omics approaches, we examine tools are reshaping understanding heterogeneity evolution. also highlights emerging techniques, such as spatial long-read sequencing, which promise unveil hidden dimensions regulation. Finally, probed transformative potential CRISPR-based epigenome editing computational analysis transmute raw data into biological insights. study seeks synthesize comprehensive yet nuanced contemporary landscape future directions research.

Language: Английский

Citations

0
PhosNetVis: A web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data DOI Creative Commons

Osho Rawal,

Berk Turhan, Irene Font Peradejordi

et al.

Patterns, Journal Year: 2025, Volume and Issue: 6(1), P. 101148 - 101148

Published: Jan. 1, 2025

Language: Английский

Citations

0
Functional proteomics-based investigation of the cellular response to farnesyltransferase inhibition in lung cancer DOI Creative Commons
Yanbo Pan, Olena Berkovska, Soumitra Marathe

et al.

iScience, Journal Year: 2025, Volume and Issue: 28(2), P. 111864 - 111864

Published: Jan. 21, 2025

Farnesylation is a lipid post-translational modification of proteins crucial for protein membrane anchoring and cellular signaling. Farnesyltransferase inhibitors (FTIs), such as tipifarnib, are being tested in cancer therapy. However, the full impact FTIs on farnesylation substrates remains poorly understood, thus limiting their use precision medicine. In this study, we performed global proteomics analysis to investigate effects tipifarnib lung cell lines. Using metabolic labeling mass spectrometry, identified farnesylated mapped subcellular localization. We also analyzed tipifarnib-dependent relocalization proteome-wide changes. Key findings include potential therapeutic value NRAS-mutated melanoma GNAQ/GNA11-mutated uveal by inhibiting INPP5A farnesylation. Additionally, synergistic drug combination involving ferroptosis inducer discovered PTP4A1 regulator interferon Our data, covering 15,080 proteins, offer valuable insights future studies FTIs.

Language: Английский

Citations

0
Advancements in proteogenomics for preclinical targeted cancer therapy research DOI Creative Commons

Yuying Suo,

Yuanli Song, Yuqiu Wang

et al.

Biophysics Reports, Journal Year: 2025, Volume and Issue: 11(1), P. 56 - 56

Published: Jan. 1, 2025

Advancements in molecular characterization technologies have accelerated targeted cancer therapy research at unprecedented resolution and dimensionality. Integrating comprehensive multi-omic profiling of a tumor, proteogenomics, marks transformative milestone for preclinical research. In this paper, we initially provided an overview proteogenomics research, spanning genomics, transcriptomics, proteomics. Subsequently, the applications were introduced examined from different perspectives, including but not limited to genetic alterations, quantifications, single-cell patterns, post-translational modification levels, subtype signatures, immune landscape. We also paid attention combined multi-omics data analysis pan-cancer analysis. This paper highlights crucial role elucidating mechanisms tumorigenesis, discovering effective therapeutic targets promising biomarkers, developing subtype-specific therapies.

Language: Английский

Citations

0