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Quantitative Proteomics in Precision Medicine
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Quantitative Proteomics in Precision Medicine

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 9371

Special Issue Editor

Dr. Maria Rosa Mazzoni

E-Mail Website
Guest Editor
Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
Interests: proteome; secretome; biomarkers; molecular mechanisms of diseases; GPCRs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Today, multi-omic approaches are frequently used to analyze the molecular signatures of various human pathologies. Indeed, pathological changes of cell and tissue functions come with deviations in the physiological protein profiles of healthy individuals. Quantitative and qualitative proteomics allow identification of those proteins and, thereafter, their signaling pathways, which play a role in disease development, leading to better comprehension of the pathogenetic mechanisms and to the design of novel therapeutic interventions. Disease-associated alterations of protein profiles also enable the identification of diagnostic, prognostic, monitoring, and therapeutic response biomarkers. Moreover, proteomics and genomics contribute to recognition of those pathological molecular changes, which are characteristic and specific to individual patients, thus paving the way to personalized therapies.  The latest improvements in mass spectrometry technologies and proteomic big data analyses have offered opportunities for quickly and effectively analyzing the proteome with high reproducibility, thus impacting the significance of proteomic studies in medicine.

We invite the submission of original research and review articles, with a focus on disease proteomics applied to molecular mechanisms, biomarkers, and novel drug target discoveries for designing personalized medicine approaches. Investigations of disease-associated changes of protein post-translational modifications (PTM) and multi-omic studies are also welcomed.   

Dr. Maria Rosa Mazzoni
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteomics
  • protein profiles
  • mass spectrometry technologies
  • proteomic big data analyses
  • molecular mechanisms
  • biomarkers
  • novel drug target discoveries
  • protein post-translational modifications
  • multi-omic studies

Published Papers (4 papers)

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Research

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18 pages, 2118 KiB  
Article
Tear Proteome Revealed Association of S100A Family Proteins and Mesothelin with Thrombosis in Elderly Patients with Retinal Vein Occlusion
by Alexander Stepanov, Svetlana A. Usharova, Kristina A. Malsagova, Larisa K. Moshetova, Ksenia I. Turkina, Arthur T. Kopylov and Anna L. Kaysheva
Int. J. Mol. Sci. 2022, 23(23), 14653; https://doi.org/10.3390/ijms232314653 - 24 Nov 2022
Cited by 1 | Viewed by 1388
Abstract
Tear samples collected from patients with central retinal vein occlusion (CRVO; n = 28) and healthy volunteers (n = 29) were analyzed using a proteomic label-free absolute quantitative approach. A large proportion (458 proteins with a frequency > 0.6) of tear proteomes was [...] Read more.
Tear samples collected from patients with central retinal vein occlusion (CRVO; n = 28) and healthy volunteers (n = 29) were analyzed using a proteomic label-free absolute quantitative approach. A large proportion (458 proteins with a frequency > 0.6) of tear proteomes was found to be shared between the study groups. Comparative proteomic analysis revealed 29 proteins (p < 0.05) significantly differed between CRVO patients and the control group. Among them, S100A6 (log (2) FC = 1.11, p < 0.001), S100A8 (log (2) FC = 2.45, p < 0.001), S100A9 (log2 (FC) = 2.08, p < 0.001), and mesothelin ((log2 (FC) = 0.82, p < 0.001) were the most abundantly represented upregulated proteins, and β2-microglobulin was the most downregulated protein (log2 (FC) = −2.13, p < 0.001). The selected up- and downregulated proteins were gathered to customize a map of CRVO-related critical protein interactions with quantitative properties. The customized map (FDR < 0.01) revealed inflammation, impairment of retinal hemostasis, and immune response as the main set of processes associated with CRVO ischemic condition. The semantic analysis displayed the prevalence of core biological processes covering dysregulation of mitochondrial organization and utilization of improperly or topologically incorrect folded proteins as a consequence of oxidative stress, and escalating of the ischemic condition caused by the local retinal hemostasis dysregulation. The most significantly different proteins (S100A6, S100A8, S100A9, MSLN, and β2-microglobulin) were applied for the ROC analysis, and their AUC varied from 0.772 to 0.952, suggesting probable association with the CRVO. Full article
(This article belongs to the Special Issue Quantitative Proteomics in Precision Medicine)
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Review

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22 pages, 851 KiB  
Review
The Role of Proteomics and Phosphoproteomics in the Discovery of Therapeutic Targets and Biomarkers in Acquired EGFR-TKI-Resistant Non-Small Cell Lung Cancer
by Sutpirat Moonmuang, Apichat Tantraworasin, Santhasiri Orrapin, Sasimol Udomruk, Busyamas Chewaskulyong, Dumnoensun Pruksakorn and Parunya Chaiyawat
Int. J. Mol. Sci. 2023, 24(5), 4827; https://doi.org/10.3390/ijms24054827 - 2 Mar 2023
Cited by 2 | Viewed by 2684
Abstract
The discovery of potent EGFR-tyrosine kinase inhibitors (EGFR-TKIs) has revolutionized the treatment of EGFR-mutated lung cancer. Despite the fact that EGFR-TKIs have yielded several significant benefits for lung cancer patients, the emergence of resistance to EGFR-TKIs has been a substantial impediment to improving [...] Read more.
The discovery of potent EGFR-tyrosine kinase inhibitors (EGFR-TKIs) has revolutionized the treatment of EGFR-mutated lung cancer. Despite the fact that EGFR-TKIs have yielded several significant benefits for lung cancer patients, the emergence of resistance to EGFR-TKIs has been a substantial impediment to improving treatment outcomes. Understanding the molecular mechanisms underlying resistance is crucial for the development of new treatments and biomarkers for disease progression. Together with the advancement in proteome and phosphoproteome analysis, a diverse set of key signaling pathways have been successfully identified that provide insight for the discovery of possible therapeutically targeted proteins. In this review, we highlight the proteome and phosphoproteomic analyses of non-small cell lung cancer (NSCLC) as well as the proteome analysis of biofluid specimens that associate with acquired resistance in response to different generations of EGFR-TKI. Furthermore, we present an overview of the targeted proteins and potential drugs that have been tested in clinical studies and discuss the challenges of implementing this discovery in future NSCLC treatment. Full article
(This article belongs to the Special Issue Quantitative Proteomics in Precision Medicine)
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29 pages, 3081 KiB  
Review
Using the Proteomics Toolbox to Resolve Topology and Dynamics of Compartmentalized cAMP Signaling
by Duangnapa Kovanich, Teck Yew Low and Manuela Zaccolo
Int. J. Mol. Sci. 2023, 24(5), 4667; https://doi.org/10.3390/ijms24054667 - 28 Feb 2023
Cited by 4 | Viewed by 1919
Abstract
cAMP is a second messenger that regulates a myriad of cellular functions in response to multiple extracellular stimuli. New developments in the field have provided exciting insights into how cAMP utilizes compartmentalization to ensure specificity when the message conveyed to the cell by [...] Read more.
cAMP is a second messenger that regulates a myriad of cellular functions in response to multiple extracellular stimuli. New developments in the field have provided exciting insights into how cAMP utilizes compartmentalization to ensure specificity when the message conveyed to the cell by an extracellular stimulus is translated into the appropriate functional outcome. cAMP compartmentalization relies on the formation of local signaling domains where the subset of cAMP signaling effectors, regulators and targets involved in a specific cellular response cluster together. These domains are dynamic in nature and underpin the exacting spatiotemporal regulation of cAMP signaling. In this review, we focus on how the proteomics toolbox can be utilized to identify the molecular components of these domains and to define the dynamic cellular cAMP signaling landscape. From a therapeutic perspective, compiling data on compartmentalized cAMP signaling in physiological and pathological conditions will help define the signaling events underlying disease and may reveal domain-specific targets for the development of precision medicine interventions. Full article
(This article belongs to the Special Issue Quantitative Proteomics in Precision Medicine)
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Other

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11 pages, 1836 KiB  
Brief Report
Quantification of Farnesylated Progerin in Hutchinson-Gilford Progeria Patient Cells by Mass Spectrometry
by Emilio Camafeita, Inmaculada Jorge, José Rivera-Torres, Vicente Andrés and Jesús Vázquez
Int. J. Mol. Sci. 2022, 23(19), 11733; https://doi.org/10.3390/ijms231911733 - 3 Oct 2022
Cited by 1 | Viewed by 2661
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare fatal disorder characterized by premature aging and death at a median age of 14.5 years. The most common cause of HGPS (affecting circa 90% of patients) is a de novo heterozygous synonymous single-base substitution (c.1824C>T; p.G608G) [...] Read more.
Hutchinson-Gilford progeria syndrome (HGPS) is a rare fatal disorder characterized by premature aging and death at a median age of 14.5 years. The most common cause of HGPS (affecting circa 90% of patients) is a de novo heterozygous synonymous single-base substitution (c.1824C>T; p.G608G) in the LMNA gene that results in the accumulation of progerin, an aberrant form of lamin A that, unlike mature lamin A, remains permanently farnesylated. The ratio of progerin to mature lamin A correlates with disease severity in HGPS patients, and can be used to assess the effectiveness of therapies aimed at lessening aberrant splicing or progerin farnesylation. We recently showed that the endogenous content of lamin A and progerin can be measured by mass spectrometry (MS), providing an alternative to immunological methods, which lack the necessary specificity and quantitative accuracy. Here, we present the first non-immunological method that reliably quantifies the levels of wild-type lamin A and farnesylated progerin in cells from HGPS patients. This method, which is based on a targeted MS approach and the use of isotope-labeled internal standards, could be applied in ongoing clinical trials evaluating the efficacy of drugs that inhibit progerin farnesylation. Full article
(This article belongs to the Special Issue Quantitative Proteomics in Precision Medicine)
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