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Genotyping and Prognostic Markers in Cancers
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Genotyping and Prognostic Markers in Cancers

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (15 December 2023) | Viewed by 22311

Special Issue Editors

Prof. Dr. Iuri Drumond Louro

E-Mail Website
Guest Editor
Center for Human and Molecular Genetics, Universidade Federal do Espírito Santo, Vitória 29500-000, Espírito Santo, Brazil
Interests: cancer genetics; tumor markers; genotyping; genetic identification; forensic DNA; population genetics
Dr. Débora Dummer Meira

E-Mail Website
Guest Editor
Center for Human and Molecular Genetics, Universidade Federal do Espírito Santo, Vitória 29500-000, Espírito Santo, Brazil
Interests: cancer genetics; tumor markers; genotyping

Special Issue Information

Dear Colleagues, 

In this Special Issue, Genotyping and Prognostic Markers in Cancers, we are seeking contributions from authors with expertise in diverse cancer types and their current and candidate diagnostic and prognostic markers. Cancer is a multistep and complex disease that arises by various mechanisms in different tissues, but some characteristics tend to be universal. The common features or abilities that most cancers must achieve to overcome natural biological defenses include the following. Most notably, immortality, which is vital in providing enough time for all other characteristics to appear. Avoiding immune destruction, apoptosis and antigrowth stimuli, as well as gaining cell cycle and survival independence from positive stimuli are key factors in tumor success. The promotion of tumor vasculature, genome instability, deregulation of cellular metabolism, inflammation, activation of invasion and metastasis, phenotypic plasticity, epigenetic reprogramming and, most recently, the presence of tumor senescent cells are all part of the cancer evolution. All these features are mediated by players and intracellular pathways that can be used in the battle against cancer. We hope to enlighten readers with diverse aspects of cancer markers and their utility in establishing an efficient protocol for cancer treatment.

Prof. Dr. Iuri Drumond Louro
Dr. Débora Dummer Meira
Guest Editors

Manuscript Submission Information

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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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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 molecular markers
  • prognostic markers
  • tumor prognosis
  • genotyping
  • cancer genetics

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Published Papers (6 papers)

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Research

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15 pages, 1868 KiB  
Article
Association of Genetic Markers with the Risk of Early-Onset Breast Cancer in Kazakh Women
by Liliya Skvortsova, Saltanat Abdikerim, Kanagat Yergali, Natalya Mit, Anastassiya Perfilyeva, Nazgul Omarbayeva, Aigul Zhunussova, Zulfiya Kachiyeva, Tolkyn Sadykova, Bakhytzhan Bekmanov, Dilyara Kaidarova, Leyla Djansugurova and Gulnur Zhunussova
Genes 2024, 15(1), 108; https://doi.org/10.3390/genes15010108 - 17 Jan 2024
Viewed by 2073
Abstract
Breast cancer is a global health problem. It is an age-dependent disease, but cases of early-onset breast cancer (eBC) are gradually increasing. There are many unresolved questions regarding eBC risk factors, mechanisms of development and screening. Only 10% of eBC cases are due [...] Read more.
Breast cancer is a global health problem. It is an age-dependent disease, but cases of early-onset breast cancer (eBC) are gradually increasing. There are many unresolved questions regarding eBC risk factors, mechanisms of development and screening. Only 10% of eBC cases are due to mutations in the BRCA1/BRCA2 genes, and 90% have a more complex genetic background. This poses a significant challenge to timely cancer detection in young women and highlights the need for research and awareness. Therefore, identifying genetic risk factors for eBC is essential to solving these problems. This study represents an association analysis of 144 eBC cases and 163 control participants to identify genetic markers associated with eBC risks in Kazakh women. We performed a two-stage approach in association analysis to assess genetic predisposition to eBC. First-stage genome-wide association analysis revealed two risk intronic loci in the CHI3L2 gene (p = 5.2 × 10−6) and MGAT5 gene (p = 8.4 × 10−6). Second-stage exonic polymorphisms haplotype analysis showed significant risks for seven haplotypes (p < 9.4 × 10−4). These results point to the importance of studying medium- and low-penetrant genetic markers in their haplotype combinations for a detailed understanding of the role of detected genetic markers in eBC development and prediction. Full article
(This article belongs to the Special Issue Genotyping and Prognostic Markers in Cancers)
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20 pages, 8689 KiB  
Article
High Expression of CDCA7 in the Prognosis of Glioma and Its Relationship with Ferroptosis and Immunity
by Yunhan Wang, Yu Zhao, Zongying Zhang, Jie Zhang, Qiuyun Xu, Xiaorong Zhou and Liming Mao
Genes 2023, 14(7), 1406; https://doi.org/10.3390/genes14071406 - 6 Jul 2023
Cited by 4 | Viewed by 2003
Abstract
CDCA7 is a copy number amplification gene that promotes tumorigenesis. However, the clinical relevance and potential mechanisms of CDCA7 in glioma are unclear. CDCA7 expression level data were obtained from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) databases, [...] Read more.
CDCA7 is a copy number amplification gene that promotes tumorigenesis. However, the clinical relevance and potential mechanisms of CDCA7 in glioma are unclear. CDCA7 expression level data were obtained from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) databases, and the enriched genes and related signaling pathways were explored. Data on genes in CDCA7-related signaling pathways and nine marker genes of ferroptosis were retrieved and a protein–protein interaction (PPI) network analysis was performed. The correlation of CDCA7 to ferroptosis and tumor infiltration of 22 kinds of human immune cells and the association between CDCA7 and immune checkpoint molecules were analyzed. CDCA7 was significantly increased in gliomas in comparison to healthy tissues. Gene Ontology (GO) and gene set enrichment analysis (GSEA) revealed the impact of CDCA7 expression on multiple biological processes and signaling pathways. CDCA7 may affect ferroptosis by interacting with genes in the cell cycle pathway and P53 pathway. The increase in CDCA7 was positively correlated with multiple ferroptosis suppressor genes and genes involved in tumor-infiltrating immune cells and immune checkpoint molecules in glioma. CDCA7 can be a new prognostic factor for glioma, which is closely related to ferroptosis, tumor immune cell infiltration, and immune checkpoint. Full article
(This article belongs to the Special Issue Genotyping and Prognostic Markers in Cancers)
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Review

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19 pages, 3888 KiB  
Review
Insights from a Computational-Based Approach for Analyzing Autophagy Genes across Human Cancers
by Alexis Germán Murillo Carrasco, Guilherme Giovanini, Alexandre Ferreira Ramos, Roger Chammas and Silvina Odete Bustos
Genes 2023, 14(8), 1550; https://doi.org/10.3390/genes14081550 - 28 Jul 2023
Cited by 3 | Viewed by 2037
Abstract
In the last decade, there has been a boost in autophagy reports due to its role in cancer progression and its association with tumor resistance to treatment. Despite this, many questions remain to be elucidated and explored among the different tumors. Here, we [...] Read more.
In the last decade, there has been a boost in autophagy reports due to its role in cancer progression and its association with tumor resistance to treatment. Despite this, many questions remain to be elucidated and explored among the different tumors. Here, we used omics-based cancer datasets to identify autophagy genes as prognostic markers in cancer. We then combined these findings with independent studies to further characterize the clinical significance of these genes in cancer. Our observations highlight the importance of innovative approaches to analyze tumor heterogeneity, potentially affecting the expression of autophagy-related genes with either pro-tumoral or anti-tumoral functions. In silico analysis allowed for identifying three genes (TBC1D12, KERA, and TUBA3D) not previously described as associated with autophagy pathways in cancer. While autophagy-related genes were rarely mutated across human cancers, the expression profiles of these genes allowed the clustering of different cancers into three independent groups. We have also analyzed datasets highlighting the effects of drugs or regulatory RNAs on autophagy. Altogether, these data provide a comprehensive list of targets to further the understanding of autophagy mechanisms in cancer and investigate possible therapeutic targets. Full article
(This article belongs to the Special Issue Genotyping and Prognostic Markers in Cancers)
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29 pages, 1822 KiB  
Review
Biomarkers in Breast Cancer: An Old Story with a New End
by Lyvia Neves Rebello Alves, Débora Dummer Meira, Luiza Poppe Merigueti, Matheus Correia Casotti, Diego do Prado Ventorim, Jucimara Ferreira Figueiredo Almeida, Valdemir Pereira de Sousa, Marllon Cindra Sant’Ana, Rahna Gonçalves Coutinho da Cruz, Luana Santos Louro, Gabriel Mendonça Santana, Thomas Erik Santos Louro, Rhana Evangelista Salazar, Danielle Ribeiro Campos da Silva, Aléxia Stefani Siqueira Zetum, Raquel Silva dos Reis Trabach, Flávia Imbroisi Valle Errera, Flávia de Paula, Eldamária de Vargas Wolfgramm dos Santos, Elizeu Fagundes de Carvalho and Iúri Drumond Louroadd Show full author list remove Hide full author list
Genes 2023, 14(7), 1364; https://doi.org/10.3390/genes14071364 - 28 Jun 2023
Cited by 31 | Viewed by 9416
Abstract
Breast cancer is the second most frequent cancer in the world. It is a heterogeneous disease and the leading cause of cancer mortality in women. Advances in molecular technologies allowed for the identification of new and more specifics biomarkers for breast cancer diagnosis, [...] Read more.
Breast cancer is the second most frequent cancer in the world. It is a heterogeneous disease and the leading cause of cancer mortality in women. Advances in molecular technologies allowed for the identification of new and more specifics biomarkers for breast cancer diagnosis, prognosis, and risk prediction, enabling personalized treatments, improving therapy, and preventing overtreatment, undertreatment, and incorrect treatment. Several breast cancer biomarkers have been identified and, along with traditional biomarkers, they can assist physicians throughout treatment plan and increase therapy success. Despite the need of more data to improve specificity and determine the real clinical utility of some biomarkers, others are already established and can be used as a guide to make treatment decisions. In this review, we summarize the available traditional, novel, and potential biomarkers while also including gene expression profiles, breast cancer single-cell and polyploid giant cancer cells. We hope to help physicians understand tumor specific characteristics and support decision-making in patient-personalized clinical management, consequently improving treatment outcome. Full article
(This article belongs to the Special Issue Genotyping and Prognostic Markers in Cancers)
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14 pages, 2061 KiB  
Review
The Role of Death-Associated Protein Kinase-1 in Cell Homeostasis-Related Processes
by Lilian Makgoo, Salerwe Mosebi and Zukile Mbita
Genes 2023, 14(6), 1274; https://doi.org/10.3390/genes14061274 - 16 Jun 2023
Cited by 2 | Viewed by 1717
Abstract
Tremendous amount of financial resources and manpower have been invested to understand the function of numerous genes that are deregulated during the carcinogenesis process, which can be targeted for anticancer therapeutic interventions. Death-associated protein kinase 1 (DAPK-1) is one of the [...] Read more.
Tremendous amount of financial resources and manpower have been invested to understand the function of numerous genes that are deregulated during the carcinogenesis process, which can be targeted for anticancer therapeutic interventions. Death-associated protein kinase 1 (DAPK-1) is one of the genes that have shown potential as biomarkers for cancer treatment. It is a member of the kinase family, which also includes Death-associated protein kinase 2 (DAPK-2), Death-associated protein kinase 3 (DAPK-3), Death-associated protein kinase-related apoptosis-inducing kinase 1 (DRAK-1) and Death-associated protein kinase-related apoptosis-inducing kinase 2 (DRAK-2). DAPK-1 is a tumour-suppressor gene that is hypermethylated in most human cancers. Additionally, DAPK-1 regulates a number of cellular processes, including apoptosis, autophagy and the cell cycle. The molecular basis by which DAPK-1 induces these cell homeostasis-related processes for cancer prevention is less understood; hence, they need to be investigated. The purpose of this review is to discuss the current understanding of the mechanisms of DAPK-1 in cell homeostasis-related processes, especially apoptosis, autophagy and the cell cycle. It also explores how the expression of DAPK-1 affects carcinogenesis. Since deregulation of DAPK-1 is implicated in the pathogenesis of cancer, altering DAPK-1 expression or activity may be a promising therapeutic strategy against cancer. Full article
(This article belongs to the Special Issue Genotyping and Prognostic Markers in Cancers)
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17 pages, 961 KiB  
Review
Breast Cancer with Brain Metastasis: Molecular Insights and Clinical Management
by Mariia Ivanova, Francesca Maria Porta, Federica Giugliano, Chiara Frascarelli, Elham Sajjadi, Konstantinos Venetis, Giulia Cursano, Giovanni Mazzarol, Elena Guerini-Rocco, Giuseppe Curigliano, Carmen Criscitiello and Nicola Fusco
Genes 2023, 14(6), 1160; https://doi.org/10.3390/genes14061160 - 26 May 2023
Cited by 12 | Viewed by 4286
Abstract
Breast cancer is the most frequently diagnosed malignancy worldwide and the leading cause of cancer-related death among women. Brain metastases are a primary contributor to mortality, as they often go undetected until late stages due to their dormant nature. Moreover, the clinical management [...] Read more.
Breast cancer is the most frequently diagnosed malignancy worldwide and the leading cause of cancer-related death among women. Brain metastases are a primary contributor to mortality, as they often go undetected until late stages due to their dormant nature. Moreover, the clinical management of brain metastases is complicated by the relevant issue of blood-brain barrier penetration. The molecular pathways involved in the formation, progression, and colonization of primary breast tumors and subsequent brain metastases are diverse, posing significant hurdles due to the heterogeneous nature of breast cancer subtypes. Despite advancements in primary breast cancer treatments, the prognosis for patients with brain metastases remains poor. In this review, we aim to highlight the biological mechanisms of breast cancer brain metastases by evaluating multi-step genetic pathways and to discuss currently available and emerging treatment strategies to propose a prospective overview of the management of this complex disease. Full article
(This article belongs to the Special Issue Genotyping and Prognostic Markers in Cancers)
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