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Genomics and Proteomics of Cancer
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Genomics and Proteomics of Cancer

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

Deadline for manuscript submissions: closed (10 May 2025) | Viewed by 4954

Special Issue Editor

Dr. Raffaella Lazzarini

E-Mail Website
Guest Editor
Occupational Medicine, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, 60126 Ancona, Italy
Interests: cancer cell proteomic profile; new anticancer therapy; cancer related signaling pathways
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Carcinogenesis, tumor growth, and cancer progression are classified as complex multifactorial tissue-dependent processes. Furthermore, tumor growth and progression are primarily stimulated by genetic predispositions or environmental causes, or a combination of the two. Genetic and epigenetic modifications are important in many diseases, especially in cancer development where cells are able to proliferate and escape the mechanisms that normally control their survival and migration. Cancer cells show extensive alterations in protein expression levels and in protein phosphorylation. A complete characterization of the altered proteins in cancer versus normal cells can also help explain multidrug resistance, therapy-related side effects, and disease recurrence after therapy. Proteomic profile data can be used to elucidate cancer biology and metastasis processes in detail and drive the development of novel drug targets.

This Special Issue of IJMS focuses on the proteins involved in the signaling pathways implicated in cancer biogenesis and progress.

Dr. Raffaella Lazzarini
Guest Editor

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Keywords

  • cancer
  • carcinogenesis
  • genetic
  • epigenetic modification
  • protein expression
  • protein phosphorylation
  • proteomic

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Published Papers (4 papers)

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Research

18 pages, 3099 KiB  
Article
Proteomic Characterization of Human Peripheral Blood Mononuclear Cells Exposed to a 50 Hz Magnetic Field
by Massimo Bracci, Raffaella Lazzarini, Francesco Piva, Matteo Giulietti, Elena Marinelli Busilacchi, Elisa Rossi, Fabio Di Criscio, Lory Santarelli and Antonella Poloni
Int. J. Mol. Sci. 2025, 26(13), 6035; https://doi.org/10.3390/ijms26136035 - 24 Jun 2025
Viewed by 132
Abstract
Exposure to extremely low-frequency magnetic fields (ELF-MF) can induce biological alterations in human cells, including peripheral blood mononuclear cells (PBMCs). However, the molecular mechanisms and key regulatory factors underlying this cellular response remain largely unknown. In this study, we analyzed the proteomic profiles [...] Read more.
Exposure to extremely low-frequency magnetic fields (ELF-MF) can induce biological alterations in human cells, including peripheral blood mononuclear cells (PBMCs). However, the molecular mechanisms and key regulatory factors underlying this cellular response remain largely unknown. In this study, we analyzed the proteomic profiles of PBMCs isolated from three human subjects. PBMCs were exposed to 50 Hz, 1 mT of ELF-MF for 24 h and compared to unexposed PBMCs from the same individuals. ELF-MF exposure altered the expression levels of several PBMC proteins without affecting cell proliferation, cell viability, or cell cycle progression. A total of 51 proteins were upregulated, 36 of which were intercorrelated and associated with the Cellular Metabolic Process (GO:0044237) and Metabolic Process (GO:0008152). Among them, solute carrier family 25 member 4 (SLC25A4), which catalyzes the exchange of cytoplasmic ADP for mitochondrial ATP across the inner mitochondrial membrane, was consistently upregulated in all ELF-MF–exposed samples. Additionally, 67 proteins were downregulated, many of which are linked to T cell costimulation (GO:0031295), Cell activation (GO:0001775), and Immune system processes (GO:0002376) included ASPSCR1, PCYT1A, PCYT2, QRAS, and REPS1. In conclusion, ELF-MF exposure induces metabolic reprogramming in human PBMCs, characterized by the upregulation of mitochondrial proteins and downregulation of immune-activation-related proteins, without compromising cell viability or proliferation. Full article
(This article belongs to the Special Issue Genomics and Proteomics of Cancer)
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20 pages, 3312 KiB  
Article
Integrated Plasma and Tumor Proteomics of Nasopharyngeal Carcinoma in a Moroccan Cohort
by Ayman Reffai, Michelle Hori, Ravali Adusumilli, Abel Bermudez, Houssam Haddad, Nezha Tawfiq, Sharon Pitteri, Mohcine Bennani Mechita and Parag Mallick
Int. J. Mol. Sci. 2025, 26(12), 5771; https://doi.org/10.3390/ijms26125771 - 16 Jun 2025
Viewed by 152
Abstract
Nasopharyngeal carcinoma (NPC) is a multifactorial disease mainly affecting the Southeast Asian and North African populations. Critically, there is a dearth of available circulating biomarkers for NPC. Additionally, as of this writing, there have been no prior plasma proteomics studies on NPC in [...] Read more.
Nasopharyngeal carcinoma (NPC) is a multifactorial disease mainly affecting the Southeast Asian and North African populations. Critically, there is a dearth of available circulating biomarkers for NPC. Additionally, as of this writing, there have been no prior plasma proteomics studies on NPC in the Moroccan population. Accordingly, there has been no integrated analysis of tumor and plasma for NPC in the Moroccan sub-population. Label-free proteomics analysis was conducted on 25 samples of Moroccan origin (10 NPC samples and 15 healthy control samples). Each sample was depleted of albumin, fractionated into eight fractions, and then analyzed using Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS). A total of 291 proteins and 2702 unique peptides were identified across all samples. In total, 16 proteins were differentially expressed (DEPs) between NPC cases and healthy individuals. Of these, three showed prognostic significance, while four demonstrated diagnostic potential. A pathway analysis showed significantly enriched terms related to the immune response and chronic inflammation, revealing acute-phase proteins as differentially expressed. The investigation of patients with early and advanced stages of NPC revealed two DEPs, while four additional DEPs were identified across the three defined clusters of NPC. Across all comparisons, DEPs, such as H2A, IGHG2, SERPINA3, SAA1, CRP, PIGR, and APOA2, have shown potential as biomarkers for NPC, with several being identified for the first time. We additionally compared the plasma proteomic profile of NPC with the tumor proteomic profile, highlighting that deeper proteomics analysis of plasma may be required to quantify additional putative biomarkers that may be shed from the tumor into the blood. Our research presents the first plasma proteomic profile of NPC in Morocco and North Africa, identifying proteins that might ultimately have diagnostic and prognostic potential. Full article
(This article belongs to the Special Issue Genomics and Proteomics of Cancer)
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22 pages, 10922 KiB  
Article
TMEM160 Promotes Tumor Growth in Lung Adenocarcinoma and Cervical Adenocarcinoma Cell Lines
by Gloria Angelina Herrera-Quiterio, Heriberto Abraham Valencia-González, Karen Griselda de la Cruz-López, Diana Lashidua Fernández-Coto, Jeovanis Gil, György Marko-Varga, Josué Morales-Gálvez, Nilda C. Sánchez, Rubén Rodríguez-Bautista, Alejandro Avilés-Salas, Oscar Arrieta, Alejandro García-Carrancá and Sergio Encarnación-Guevara
Int. J. Mol. Sci. 2025, 26(3), 1097; https://doi.org/10.3390/ijms26031097 - 27 Jan 2025
Viewed by 1344
Abstract
The Chromosome-Centric Human Proteome Project (C-HPP) is an international initiative. It aims to create a protein list expressed in human cells by each chromosomal and mitochondrial DNA to enhance our understanding of disease mechanisms, akin to the gene list generated by the Human [...] Read more.
The Chromosome-Centric Human Proteome Project (C-HPP) is an international initiative. It aims to create a protein list expressed in human cells by each chromosomal and mitochondrial DNA to enhance our understanding of disease mechanisms, akin to the gene list generated by the Human Genome Project. Transmembrane protein 160 (TMEM160) is a member of the transmembrane proteins (TMEM) family. TMEM proteins have been implicated in cancer-related processes, including cell proliferation, migration, epithelial-mesenchymal transition, metastasis, and resistance to chemotherapy and radiotherapy. This study aimed to investigate the role of TMEM160 in non-small cell lung cancer and cervical cancer using cell lines, clinical samples, and xenograft studies. Our findings demonstrated that TMEM160 knockdown decreased the proliferation of lung and cervical cancer cell lines. We observed that TMEM160 is localized in the nucleus and cytoplasm and dynamic localization during mitosis of cancer cells and discovered a novel interaction between TMEM160 and nuclear proteins such as NUP50. Furthermore, the TMEM160 interactome was enriched in processes associated with apical junctions, xenobiotic metabolism, glycolysis, epithelial-mesenchymal transition, reactive oxygen species, UV response DNA, the P53 pathway, and the mitotic spindle. This study provides an initial understanding of the function of TMEM160 in lung and cervical cancer progression and clarifies the need to continue investigating the participation of TMEM160 in these cancers. Full article
(This article belongs to the Special Issue Genomics and Proteomics of Cancer)
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39 pages, 21725 KiB  
Article
Unveiling the Dynamics behind Glioblastoma Multiforme Single-Cell Data Heterogeneity
by Marcos Guilherme Vieira Junior , Adriano Maurício de Almeida Côrtes, Flávia Raquel Gonçalves Carneiro, Nicolas Carels and Fabrício Alves Barbosa da Silva
Int. J. Mol. Sci. 2024, 25(9), 4894; https://doi.org/10.3390/ijms25094894 - 30 Apr 2024
Cited by 2 | Viewed by 2207
Abstract
Glioblastoma Multiforme is a brain tumor distinguished by its aggressiveness. We suggested that this aggressiveness leads single-cell RNA-sequence data (scRNA-seq) to span a representative portion of the cancer attractors domain. This conjecture allowed us to interpret the scRNA-seq heterogeneity as reflecting a representative [...] Read more.
Glioblastoma Multiforme is a brain tumor distinguished by its aggressiveness. We suggested that this aggressiveness leads single-cell RNA-sequence data (scRNA-seq) to span a representative portion of the cancer attractors domain. This conjecture allowed us to interpret the scRNA-seq heterogeneity as reflecting a representative trajectory within the attractor’s domain. We considered factors such as genomic instability to characterize the cancer dynamics through stochastic fixed points. The fixed points were derived from centroids obtained through various clustering methods to verify our method sensitivity. This methodological foundation is based upon sample and time average equivalence, assigning an interpretative value to the data cluster centroids and supporting parameters estimation. We used stochastic simulations to reproduce the dynamics, and our results showed an alignment between experimental and simulated dataset centroids. We also computed the Waddington landscape, which provided a visual framework for validating the centroids and standard deviations as characterizations of cancer attractors. Additionally, we examined the stability and transitions between attractors and revealed a potential interplay between subtypes. These transitions might be related to cancer recurrence and progression, connecting the molecular mechanisms of cancer heterogeneity with statistical properties of gene expression dynamics. Our work advances the modeling of gene expression dynamics and paves the way for personalized therapeutic interventions. Full article
(This article belongs to the Special Issue Genomics and Proteomics of Cancer)
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