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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: 10 May 2025 | Viewed by 4119

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

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

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

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Published Papers (2 papers)

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Research

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 1082
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 2077
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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