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Special Issue "Proteomics and Its Applications in Disease 2.0"

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Dear Colleagues,

This Special Issue is a continuation of our previous successful Special Issue “Proteomics and Its Applications in Disease”.

Recent advances in mass spectrometry-based technologies, e.g., data-independent acquisition (DIA), ion mobility spectrometry (IMS), and multiple reaction monitoring (MRM), have provided superior sensitivity, reproducibility, and throughput in proteomics analysis. This allows researchers to explore diseases by assessing a deeper proteome in a relatively short time with high reproducibility and fewer missing data. No doubt, the applications of proteomics research in diseases not only provide new insights into disease mechanisms, but also novel disease biomarkers and therapeutic targets.

In this Special Issue, we invite you to contribute original research and review articles which focus on (but are not limited to) the following topics related to the applications of proteomics in diseases: disease biomarker (discovery and validation), molecular mechanisms (signaling pathway) of disease, new drug targets, the role of post-translational modifications in disease, targeted proteomics, multi-omics studies, proteomic studies on in vitro cell disease models, animal disease models, or patient cohort studies.

Prof. Dr. Lei Zhou
Dr. Qingsong Lin
Dr. Chuen Lam
Guest Editors

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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.

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Research

Open AccessArticle

Inhibition of HSP90 in Driver Oncogene-Defined Lung Adenocarcinoma Cell Lines: Key Proteins Underpinning Therapeutic Efficacy

Ángela Marrugal

Irene Ferrer

Álvaro Quintanal-Villalonga

and

Int. J. Mol. Sci. 2023, 24(18), 13830; https://doi.org/10.3390/ijms241813830 - 07 Sep 2023

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Abstract

The use of 90 kDa heat shock protein (HSP90) inhibition as a therapy in lung adenocarcinoma remains limited due to moderate drug efficacy, the emergence of drug resistance, and early tumor recurrence. The main objective of this research is to maximize treatment efficacy in lung adenocarcinoma by identifying key proteins underlying HSP90 inhibition according to molecular background, and to search for potential biomarkers of response to this therapeutic strategy. Inhibition of the HSP90 chaperone was evaluated in different lung adenocarcinoma cell lines representing the most relevant molecular alterations (EGFR mutations, KRAS mutations, or EML4-ALK translocation) and wild-type genes found in each tumor subtype. The proteomic technique iTRAQ was used to identify proteomic profiles and determine which biological pathways are involved in the response to HSP90 inhibition in lung adenocarcinoma. We corroborated the greater efficacy of HSP90 inhibition in EGFR mutated or EML4-ALK translocated cell lines. We identified proteins specifically and significantly deregulated after HSP90 inhibition for each molecular alteration. Two proteins, ADI1 and RRP1, showed independently deregulated molecular patterns. Functional annotation of the altered proteins suggested that apoptosis was the only pathway affected by HSP90 inhibition across all molecular subgroups. The expression of ADI1 and RRP1 could be used to monitor the correct inhibition of HSP90 in lung adenocarcinoma. In addition, proteins such as ASS1, ITCH, or UBE2L3 involved in pathways related to the inhibition of a particular molecular background could be used as potential response biomarkers, thereby improving the efficacy of this therapeutic approach to combat lung adenocarcinoma. Full article

(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)

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Open AccessArticle

Differential Responses of Retinal Neurons and Glia Revealed via Proteomic Analysis on Primary and Secondary Retinal Ganglion Cell Degeneration

and

Int. J. Mol. Sci. 2023, 24(15), 12109; https://doi.org/10.3390/ijms241512109 - 28 Jul 2023

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Abstract

To explore the temporal profile of retinal proteomes specific to primary and secondary retinal ganglion cell (RGC) loss. Unilateral partial optic nerve transection (pONT) was performed on the temporal side of the rat optic nerve. Temporal and nasal retinal samples were collected at 1, 4 and 8 weeks after pONT (n = 4 each) for non-biased profiling with a high-resolution hybrid quadrupole time-of-flight mass spectrometry running on label-free SWATH^TM acquisition (SCIEX). An information-dependent acquisition ion library was generated using ProteinPilot 5.0 and OneOmics cloud bioinformatics. Combined proteome analysis detected 2531 proteins with a false discovery rate of <1%. Compared to the nasal retina, 10, 25 and 61 significantly regulated proteins were found in the temporal retina at 1, 4, and 8 weeks, respectively (p < 0.05, FC ≥ 1.4 or ≤0.7). Eight proteins (ALDH1A1, TRY10, GFAP, HBB-B1, ALB, CDC42, SNCG, NEFL) were differentially expressed for at least two time points. The expressions of ALDH1A1 and SNCG at nerve fibers were decreased along with axonal loss. Increased ALDH1A1 localization in the inner nuclear layer suggested stress response. Increased GFAP expression demonstrated regional reactivity of astrocytes and Muller cells. Meta-analysis of gene ontology showed a pronounced difference in endopeptidase and peptidase inhibitor activity. Temporal proteomic profiling demonstrates established and novel protein targets associated with RGC damage. Full article

(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)

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