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New Insights into Proteomics in Disease
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New Insights into Proteomics in Disease

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

Deadline for manuscript submissions: closed (24 May 2024) | Viewed by 10134

Special Issue Editor

Dr. Ilaria Cicalini

E-Mail Website
Guest Editor
Department of Innovative Technologies in Medicine and Dentistry, Medicine and Aging Science, Analytical Biochemistry and Proteomics Unit, Center for Advanced Studies and Technology (CAST),“G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
Interests: proteomics; metabolomics; LC-MS/MS; bioanalytical mass spectrometry; lipidomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Omics strategies, especially those related to proteomics, are becoming a powerful tool for acquiring in-depth knowledge of biological systems and for studying the molecular basis of multifactorial diseases. Thus, understanding protein modifications will require the application of innovative approaches and their integration with new combined interdisciplinary methods.

Leading by Dr. Ilaria Cicalini and assisted by Dr. Maria Concetta Cufaro and Dr. Silvia Valentinuzzi (University “G. d’Annunzio” of Chieti-Pescara), this Special Issue aims to collect articles related to innovative high-throughput proteomics, bioinformatics, and related topics, providing new insights into the molecular aspects of human health in relation to personalized medicine. We invite authors to contribute original research papers, methods, and review articles that discuss new biological knowledge at the protein level through omics strategies, including (but not limited to):

  • proteomic characterization of normal and diseased tissues/cells/biofluids;
  • omics approaches and biomarker discovery;
  • new methods of protein analysis;
  • bioinformatics for omics data integration.

Dr. Ilaria Cicalini
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
  • disease biomarkers
  • data integration
  • bioinformatics
  • mass spectrometry
  • biochemical pathway
  • personalized medicine

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Published Papers (5 papers)

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Research

18 pages, 5395 KiB  
Article
Platelet Proteome Reveals Novel Targets for Hypercoagulation in Pseudoexfoliation Syndrome
by Elif Ugurel, Ghazal Narimanfar, Neslihan Cilek, Cem Kesim, Cigdem Altan, Afsun Sahin and Ozlem Yalcin
Int. J. Mol. Sci. 2024, 25(3), 1403; https://doi.org/10.3390/ijms25031403 - 24 Jan 2024
Cited by 2 | Viewed by 1289
Abstract
Pseudoexfoliation syndrome (PEX) is characterized by the accumulation of abnormal extracellular matrix material in ocular and non-ocular tissues, including blood vessel walls. Clot-forming dysfunction might be responsible for venous thrombosis in PEX. We investigated global coagulation, the proteome, and functions of platelets in [...] Read more.
Pseudoexfoliation syndrome (PEX) is characterized by the accumulation of abnormal extracellular matrix material in ocular and non-ocular tissues, including blood vessel walls. Clot-forming dysfunction might be responsible for venous thrombosis in PEX. We investigated global coagulation, the proteome, and functions of platelets in PEX patients and aimed to determine prognostic biomarkers for thrombosis risk in PEX. Peripheral blood was collected from PEX and retinal vein occlusion (RVO) patients, and age–sex matched controls. Viscoelastic hemostasis was evaluated by rotational thromboelastometry (ROTEM). Platelet markers (CD41, CD42, CD61, and CD62p) and endothelial markers (P-selectin, E-selectin, and von Willebrand factor) were investigated by flow cytometry and ELISA, respectively. The platelet proteome was analyzed by 2D fluorescence difference gel electrophoresis followed by mass spectrometry. Clot formation time (CFT) is significantly reduced in PEX patients compared to the controls (p < 0.05). P-selectin levels were higher in PEX patients than in controls (p < 0.05); E-selectin and von Willebrand factor remained unchanged. The monitorization of CFT by ROTEM, and soluble P-selectin, may help assess thrombotic risk in PEX patients. Proteomic analysis revealed differential expression of Profilin-1 in platelets. Profilin-1 regulates the stability of actin-cytoskeleton and may contribute to impaired platelet hemostatic functions. Increased P-selectin levels together with impaired coagulation dynamics might be responsible for the thrombotic events in PEX disease. Full article
(This article belongs to the Special Issue New Insights into Proteomics in Disease)
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13 pages, 2340 KiB  
Article
Proteome Analysis of Serum Purified Using Solanum tuberosum and Lycopersicon esculentum Lectins
by Daisuke Nakajima, Ryo Konno, Yasuomi Miyashita, Masaki Ishikawa, Osamu Ohara and Yusuke Kawashima
Int. J. Mol. Sci. 2024, 25(2), 1315; https://doi.org/10.3390/ijms25021315 - 21 Jan 2024
Viewed by 2034
Abstract
Serum and plasma exhibit a broad dynamic range of protein concentrations, posing challenges for proteome analysis. Various technologies have been developed to reduce this complexity, including high-abundance depletion methods utilizing antibody columns, extracellular vesicle enrichment techniques, and trace protein enrichment using nanobead cocktails. [...] Read more.
Serum and plasma exhibit a broad dynamic range of protein concentrations, posing challenges for proteome analysis. Various technologies have been developed to reduce this complexity, including high-abundance depletion methods utilizing antibody columns, extracellular vesicle enrichment techniques, and trace protein enrichment using nanobead cocktails. Here, we employed lectins to address this, thereby extending the scope of biomarker discovery in serum or plasma using a novel approach. We enriched serum proteins using 37 different lectins and subjected them to LC–MS/MS analysis with data-independent acquisition. Solanum tuberosum lectin (STL) and Lycopersicon esculentum lectin (LEL) enabled the detection of more serum proteins than the other lectins. STL and LEL bind to N-acetylglucosamine oligomers, emphasizing the significance of capturing these oligomer-binding proteins when analyzing serum trace proteins. Combining STL and LEL proved more effective than using them separately, allowing us to identify over 3000 proteins from serum through single-shot proteome analysis. We applied the STL/LEL trace-protein enrichment method to the sera of systemic lupus erythematosus model mice. This revealed differences in >1300 proteins between the systemic lupus erythematosus model and control mouse sera, underscoring the utility of this method for biomarker discovery. Full article
(This article belongs to the Special Issue New Insights into Proteomics in Disease)
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24 pages, 7216 KiB  
Article
SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms
by Letícia Graziela Costa Santos, Vinícius da Silva Coutinho Parreira, Esdras Matheus Gomes da Silva, Marlon Dias Mariano Santos, Alexander da Franca Fernandes, Ana Gisele da Costa Neves-Ferreira, Paulo Costa Carvalho, Flávia Cristina de Paula Freitas and Fabio Passetti
Int. J. Mol. Sci. 2024, 25(2), 1183; https://doi.org/10.3390/ijms25021183 - 18 Jan 2024
Viewed by 1450
Abstract
SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to [...] Read more.
SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to aid with proteomic validation of splice variants absent from the reference UniProtKB/SwissProt database. We demonstrate the value of SpliceProt 2.0 to predict orthologous proteins between humans and murines based on transcript reconstruction, sequence annotation and detection at the transcriptome and proteome levels. In this release, the annotation data used in the reconstruction of transcripts based on the methodology of ternary matrices were acquired from new databases such as Ensembl, UniProt, and APPRIS. Another innovation implemented in the pipeline is the exclusion of transcripts predicted to be susceptible to degradation through the NMD pathway. Taken together, our repository and its applications represent a valuable resource for the proteogenomics community. Full article
(This article belongs to the Special Issue New Insights into Proteomics in Disease)
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19 pages, 2925 KiB  
Article
Integrative Multi-Omics Analysis of Oncogenic EZH2 Mutants: From Epigenetic Reprogramming to Molecular Signatures
by Julian Aldana, Miranda L. Gardner and Michael A. Freitas
Int. J. Mol. Sci. 2023, 24(14), 11378; https://doi.org/10.3390/ijms241411378 - 12 Jul 2023
Cited by 3 | Viewed by 2491
Abstract
Somatic heterozygous mutations in the active site of the enhancer of zeste homolog 2 (EZH2) are prevalent in diffuse large B-cell lymphoma (DLBCL) and acute myeloid leukemia (AML). The methyltransferase activity of EZH2 towards lysine 27 on histone H3 (H3K27) and non-histone proteins [...] Read more.
Somatic heterozygous mutations in the active site of the enhancer of zeste homolog 2 (EZH2) are prevalent in diffuse large B-cell lymphoma (DLBCL) and acute myeloid leukemia (AML). The methyltransferase activity of EZH2 towards lysine 27 on histone H3 (H3K27) and non-histone proteins is dysregulated by the presence of gain-of-function (GOF) and loss-of-function (LOF) mutations altering chromatin compaction, protein complex recruitment, and transcriptional regulation. In this study, a comprehensive multi-omics approach was carried out to characterize the effects of differential H3K27me3 deposition driven by EZH2 mutations. Three stable isogenic mutants (EZH2Y641F, EZH2A677G, and EZH2H689A/F667I) were examined using EpiProfile, H3K27me3 CUT&Tag, ATAC-Seq, transcriptomics, label-free proteomics, and untargeted metabolomics. A discrete set of genes and downstream targets were identified for the EZH2 GOF and LOF mutants that impacted pathways involved in cellular proliferation, differentiation, and migration. Disruption of protein networks and metabolic signatures able to sustain aberrant cell behavior was observed in response to EZH2 mutations. This systems biology-based analysis sheds light on EZH2-mediated cell transformative processes, from the epigenetic to the phenotypic level. These studies provide novel insights into aberrant EZH2 function along with targets that can be explored for improved diagnostics/treatment in hematologic malignancies with mutated EZH2. Full article
(This article belongs to the Special Issue New Insights into Proteomics in Disease)
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17 pages, 4991 KiB  
Article
Quantitative Proteomic and Phosphoproteomic Profiling of Lung Tissues from Pulmonary Arterial Hypertension Rat Model
by Ang Luo, Yangfan Jia, Rongrong Hao, Yafang Yu, Xia Zhou, Chenxin Gu, Meijuan Ren and Haiyang Tang
Int. J. Mol. Sci. 2023, 24(11), 9629; https://doi.org/10.3390/ijms24119629 - 1 Jun 2023
Cited by 1 | Viewed by 2081
Abstract
Pulmonary arterial hypertension (PAH) is a rare but fatal disease characterized by elevated pulmonary vascular resistance and increased pressure in the distal pulmonary arteries. Systematic analysis of the proteins and pathways involved in the progression of PAH is crucial for understanding the underlying [...] Read more.
Pulmonary arterial hypertension (PAH) is a rare but fatal disease characterized by elevated pulmonary vascular resistance and increased pressure in the distal pulmonary arteries. Systematic analysis of the proteins and pathways involved in the progression of PAH is crucial for understanding the underlying molecular mechanism. In this study, we performed tandem mass tags (TMT)-based relative quantitative proteomic profiling of lung tissues from rats treated with monocrotaline (MCT) for 1, 2, 3 and 4 weeks. A total of 6759 proteins were quantified, among which 2660 proteins exhibited significant changes (p-value < 0.05, fold change < 0.83 or >1.2). Notably, these changes included several known PAH-related proteins, such as Retnla (resistin-like alpha) and arginase-1. Furthermore, the expression of potential PAH-related proteins, including Aurora kinase B and Cyclin-A2, was verified via Western blot analysis. In addition, we performed quantitative phosphoproteomic analysis on the lungs from MCT-induced PAH rats and identified 1412 upregulated phosphopeptides and 390 downregulated phosphopeptides. Pathway enrichment analysis revealed significant involvement of pathways such as complement and coagulation cascades and the signaling pathway of vascular smooth muscle contraction. Overall, this comprehensive analysis of proteins and phosphoproteins involved in the development and progression of PAH in lung tissues provides valuable insights for the development of potential diagnostic and treatment targets for PAH. Full article
(This article belongs to the Special Issue New Insights into Proteomics in Disease)
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