Proteomics and Precision Medicine

Chen, Ding; Qin, Zhaoyu; Li, Yan; Shi, Wenhao; Zhan, Dongdong; Yang, Wenjun

doi:10.1002/smtd.201900075

Cited by 6 publications

(4 citation statements)

References 188 publications

(201 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Screening DNA-binding activity of TFs in GC can advance our understanding of GC heterogeneity. Despite the application of proteome profiling have made great progress in precision oncology, the existing strategies of quantifying the changes in TF activities have certain limitations 44 . The sub-proteome consisting of TFs is usually neglected in cancer proteomics because of low abundance of TFs.…”

Section: Resultsmentioning

confidence: 99%

Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer

Shi

Wang

et al. 2023

Nat Commun

View full text Add to dashboard Cite

Diffuse-type gastric cancer (DGC) and intestinal-type gastric cancer (IGC) are the major histological types of gastric cancer (GC). The molecular mechanism underlying DGC and IGC differences are poorly understood. In this research, we carry out multilevel proteomic analyses, including proteome, phospho-proteome, and transcription factor (TF) activity profiles, of 196 cases covering DGC and IGC in Chinese patients. Integrative proteogenomic analysis reveals ARIDIA mutation associated with opposite prognostic effects between DGC and IGC, via diverse influences on their corresponding proteomes. Systematical comparison and consensus clustering analysis identify three subtypes of DGC and IGC, respectively, based on distinct patterns of the cell cycle, extracellular matrix organization, and immune response-related proteins expression. TF activity-based subtypes demonstrate that the disease progressions of DGC and IGC were regulated by SWI/SNF and NFKB complexes. Furthermore, inferred immune cell infiltration and immune clustering show Th1/Th2 ratio is an indicator for immunotherapeutic effectiveness, which is validated in an independent GC anti-PD1 therapeutic patient group. Our multilevel proteomic analyses enable a more comprehensive understanding of GC and can further advance the precision medicine.

show abstract

Section: Resultsmentioning

confidence: 99%

Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer

Shi

Wang

et al. 2023

Nat Commun

View full text Add to dashboard Cite

show abstract

“…With the development of soft ionization techniques, it becomes possible to acquire the mass spectra of macromolecules, thus improving the analysis of peptides and glycopeptides as well. 36 Matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) are the two commonly used ionization techniques in glycoproteomics. 13 MALDI shows great performance in the fast analysis of simple samples, along with outstanding compatibility of salts.…”

Section: Ionizationmentioning

confidence: 99%

Progress of proteomics‐driven precision medicine: From a glycosylation view

Liang

Zhang

et al. 2022

Rapid Comm Mass Spectrometry

View full text Add to dashboard Cite

Currently, cancer is one of the leading causes of death worldwide, partially owing to the lack of early diagnosis methods and effective therapies. With the rapid development of various omics, the precision medicine strategy becomes a promising way to increase the survival rates by considering individual differences. Glycosylation is one of the most essential protein post-translational modifications and plays important roles in a variety of biological processes. Therefore, it is highly possible to acquire understanding of the molecular mechanisms as well as discover novel potential markers for diagnosis and prognosis based on glycoproteomics research. This review summarizes the recent glycoproteomics studies about N-glycosylation of several cancer types, mainly in the past 5 years. We also highlight corresponding mass spectrometry-based analytical methods to give a brief overview on the main techniques applied in glycoproteomics.

show abstract

“…Proteomics is the next likely candidate to be included in the precision medicine arsenal, for proteins represent intermediate phenotypes. In particular, proteins are products of gene expression and mediate biochemical activities of cells and tissues (Ding et al, 2019). Proteomics approaches could describe diseaserelated pathways; identify novel biomarkers for diagnostics; detect drug targets; and analyze physiological patterns on the transition for disease (Van Eyk and Snyder, 2018).…”

Section: Introductionmentioning

confidence: 99%

Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review

et al. 2021

View full text Add to dashboard Cite

Precision medicine as a framework for disease diagnosis, treatment, and prevention at the molecular level has entered clinical practice. From the start, genetics has been an indispensable tool to understand and stratify the biology of chronic and complex diseases in precision medicine. However, with the advances in biomedical and omics technologies, quantitative proteomics is emerging as a powerful technology complementing genetics. Quantitative proteomics provide insight about the dynamic behaviour of proteins as they represent intermediate phenotypes. They provide direct biological insights into physiological patterns, while genetics accounting for baseline characteristics. Additionally, it opens a wide range of applications in clinical diagnostics, treatment stratification, and drug discovery. In this mini-review, we discuss the current status of quantitative proteomics in precision medicine including the available technologies and common methods to analyze quantitative proteomics data. Furthermore, we highlight the current challenges to put quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data with genomics data for future applications in precision medicine.

show abstract

Proteomics and Precision Medicine

Cited by 6 publications

References 188 publications

Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer

Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer

Progress of proteomics‐driven precision medicine: From a glycosylation view

Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review

Contact Info

Product

Resources

About