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Biomolecules
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Genetic and Genomic Biomarkers of Cancer
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Genetic and Genomic Biomarkers of Cancer

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biomarkers".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 7954

Special Issue Editor

Dr. Jianli Dong

E-Mail Website
Guest Editor
Department of Pathology, Sealy Center for Cancer Cell Biology, University of Texas Medical Branch, 5.202 John Sealy Annex, 301 University Boulevard, Galveston, TX 77555, USA
Interests: laboratory genetics and genomics; genetic and genomic biomarkers; cancer biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetic and genomic assays are increasingly being used in medical practice. Cancer genetic and genomic tests typically analyze nucleic acid-based biomarkers and can be diagnostic, prognostic, or predictive. Cancer diagnostic tests are used for cancer screening, diagnosis, subtyping, and staging; cancer prognostic tests reveal the nature course of cancer, disease outcome, and recurrence risk, whereas cancer predictive tests provide information on the likely response of a patient to a drug or therapy. Often, a single genetic or genomic oncology test can be applied to several clinical scenarios. Genetic and genomic tests are expected to have ever-increasing impact on the clinical management of cancer patients. For example, such tests are developed to select patients who will benefit from a targeted therapy, monitor the development of treatment resistance, assess recurrence following treatment, modify the dose of a therapeutic, and identify the pharmacogenetic risk of adverse drug reactions. This way, the optimal treatment is determined for every patient, non-effective treatments can be spared, and side-effects can be avoided, thus leading to personalized and precision cancer management.

This Special Issue aims to highlight recent advances made in the utility of genetic and genomic assays in medical oncology. I encourage basic, translational, and clinical researchers to present original research articles and reviews, emphasizing the current preclinical and clinical advancement of laboratory genetics and genomics in clinical oncology.

I look forward to receiving your contributions.

Dr. Jianli Dong
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. Biomolecules 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 2700 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

  • laboratory genetics and genomics
  • genetic and genomic biomarkers
  • diagnostic
  • prognostic
  • predictive
  • companion diagnosis
  • targeted therapy

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Published Papers (5 papers)

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Research

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30 pages, 9550 KiB  
Article
Abnormal Histopathological Expression of Klotho, Ferroptosis, and Circadian Clock Regulators in Pancreatic Ductal Adenocarcinoma: Prognostic Implications and Correlation Analyses
by Cielo García-Montero, Oscar Fraile-Martinez, David Cobo-Prieto, Diego De Leon-Oliva, Diego Liviu Boaru, Patricia De Castro-Martinez, Leonel Pekarek, Raquel Gragera, Mauricio Hernández-Fernández, Luis G. Guijarro, María Del Val Toledo-Lobo, Laura López-González, Raul Díaz-Pedrero, Jorge Monserrat, Melchor Álvarez-Mon, Miguel A. Saez and Miguel A. Ortega
Biomolecules 2024, 14(8), 947; https://doi.org/10.3390/biom14080947 - 5 Aug 2024
Viewed by 1259
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an extremely lethal tumor with increasing incidence, presenting numerous clinical challenges. The histopathological examination of novel, unexplored biomarkers offers a promising avenue for research, with significant translational potential for improving patient outcomes. In this study, we evaluated the [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) is an extremely lethal tumor with increasing incidence, presenting numerous clinical challenges. The histopathological examination of novel, unexplored biomarkers offers a promising avenue for research, with significant translational potential for improving patient outcomes. In this study, we evaluated the prognostic significance of ferroptosis markers (TFRC, ALOX-5, ACSL-4, and GPX-4), circadian clock regulators (CLOCK, BMAL1, PER1, PER2), and KLOTHO in a retrospective cohort of 41 patients deceased by PDAC. Immunohistochemical techniques (IHC) and multiple statistical analyses (Kaplan–Meier curves, correlograms, and multinomial linear regression models) were performed. Our findings reveal that ferroptosis markers are directly associated with PDAC mortality, while circadian regulators and KLOTHO are inversely associated. Notably, TFRC emerged as the strongest risk marker associated with mortality (HR = 35.905), whereas CLOCK was identified as the most significant protective marker (HR = 0.01832). Correlation analyses indicate that ferroptosis markers are positively correlated with each other, as are circadian regulators, which also positively correlate with KLOTHO expression. In contrast, KLOTHO and circadian regulators exhibit inverse correlations with ferroptosis markers. Among the clinical variables examined, only the presence of chronic pathologies showed an association with the expression patterns of several proteins studied. These findings underscore the complexity of PDAC pathogenesis and highlight the need for further research into the specific molecular mechanisms driving disease progression. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers of Cancer)
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11 pages, 1151 KiB  
Article
Novel Semi-Nested Real-Time PCR Assay Leveraging Extendable Blocking Probes for Improved SHOX2 Methylation Analysis in Lung Cancer
by Ngoc Anh Phuong, Trang Thuy Dao, Phuong Bich Pham, Ung Dinh Nguyen, Ba Van Nguyen and Tho Huu Ho
Biomolecules 2024, 14(6), 729; https://doi.org/10.3390/biom14060729 - 19 Jun 2024
Cited by 1 | Viewed by 994
Abstract
Lung cancer is the leading cause of cancer deaths globally, necessitating effective early detection methods. Traditional diagnostics like low-dose computed tomography (LDCT) often yield high false positive rates. SHOX2 gene methylation has emerged as a promising biomarker. This study aimed to develop and [...] Read more.
Lung cancer is the leading cause of cancer deaths globally, necessitating effective early detection methods. Traditional diagnostics like low-dose computed tomography (LDCT) often yield high false positive rates. SHOX2 gene methylation has emerged as a promising biomarker. This study aimed to develop and validate a novel semi-nested real-time PCR assay enhancing sensitivity and specificity for detecting SHOX2 methylation using extendable blocking probes (ExBPs). The assay integrates a semi-nested PCR approach with ExBPs, enhancing the detection of low-abundance methylated SHOX2 DNA amidst unmethylated sequences. It was tested on spiked samples with varied methylation levels and on clinical samples from lung cancer patients and individuals with benign lung conditions. The assay detected methylated SHOX2 DNA down to 0.01%. Clinical evaluations confirmed its ability to effectively differentiate between lung cancer patients and those with benign conditions, demonstrating enhanced sensitivity and specificity. The use of ExBPs minimized non-target sequence amplification, crucial for reducing false positives. The novel semi-nested real-time PCR assay offers a cost-effective, highly sensitive, and specific method for detecting SHOX2 methylation, enhancing early lung cancer detection and monitoring, particularly valuable in resource-limited settings. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers of Cancer)
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13 pages, 2043 KiB  
Article
A Challenging Correlation between Tumor Cellularity and Somatic Variant Allele Fraction in Lung and Colorectal Cancers—Specimens of Low Tumor Percentage Should Be Analyzed with Caution
by Samaneh K. Zarabi, Lidong Zhai and Yu-Wei Cheng
Biomolecules 2024, 14(2), 168; https://doi.org/10.3390/biom14020168 - 31 Jan 2024
Viewed by 1802
Abstract
Background and aims: The percentage of tumor cells (tumor cellularity) in a cancerous tissue has been assumed to correlate with the variant allele fraction (VAF) of an identified pathogenic variant. Many laboratories use the tumor cellularity as part of a quality criteria for [...] Read more.
Background and aims: The percentage of tumor cells (tumor cellularity) in a cancerous tissue has been assumed to correlate with the variant allele fraction (VAF) of an identified pathogenic variant. Many laboratories use the tumor cellularity as part of a quality criteria for specimen processing and clinical reporting. However, a systematic study of such correlation has yet to be shown. We performed a relatively large-scale study to determine whether pathologist-estimated tumor cellularity is correlated with next-generation sequencing (NGS)-derived VAF. Materials and Methods: A total of 1511 non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) specimens, including formalin-fixed paraffin-embedded (FFPE) and fine needle aspirated (FNA) tissues, were analyzed by cancer hotspot NGS. For a given specimen, pathogenic variants of BRAF, EGFR, KRAS, and NRAS were identified and the determined VAFs were correlated with the corresponding tissue tumor cellularity. Results: The coefficient of determination R-squared (R2) values were calculated for each correlation. All R2 values were lower than 0.25, indicating poor correlations. Pathogenic variants were found, not uncommonly, in tumor specimens that carried 10% or lower tumor cellularity. There were no apparent differences of R2 values between the FFPE and FNA specimens. Conclusion: In both NSCLC and CRC, the lack of linear relationship between tumor cellularity and VAF was found across a wide range of tumor cell percentages. Caution should be used when using tumor cellularity to triage specimens for NGS testing. The tumor cellularity should be considered in relation to the limit of detection of the specific assay for the proper interpretation of a negative test result. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers of Cancer)
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Review

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20 pages, 904 KiB  
Review
Evaluating Circulating Biomarkers for Diagnosis, Prognosis, and Tumor Monitoring in Pediatric Sarcomas: Recent Advances and Future Directions
by Joaquín J. Maqueda, Alessandra De Feo and Katia Scotlandi
Biomolecules 2024, 14(10), 1306; https://doi.org/10.3390/biom14101306 - 16 Oct 2024
Viewed by 901
Abstract
Pediatric sarcomas present a significant challenge in oncology. There is an urgent need for improved therapeutic strategies for high-risk patients and better management of long-term side effects for those who survive the disease. Liquid biopsy is emerging as a promising tool to optimize [...] Read more.
Pediatric sarcomas present a significant challenge in oncology. There is an urgent need for improved therapeutic strategies for high-risk patients and better management of long-term side effects for those who survive the disease. Liquid biopsy is emerging as a promising tool to optimize treatment in these patients by offering non-invasive, repeatable assessments of disease status. Circulating biomarkers can provide valuable insights into tumor genetics and treatment response, potentially facilitating early diagnosis and dynamic disease monitoring. This review examines the potential of liquid biopsies, focusing on circulating biomarkers in the most common pediatric sarcomas, i.e., osteosarcoma, Ewing sarcoma, and rhabdomyosarcoma. We also highlight the current research efforts and the necessary advancements required before these technologies can be widely adopted in clinical practice. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers of Cancer)
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21 pages, 1861 KiB  
Review
Circular RNAs in Breast Cancer: An Update
by Haolin Bao, Jiehan Li, Qihang Zhao, Qingling Yang and Yi Xu
Biomolecules 2024, 14(2), 158; https://doi.org/10.3390/biom14020158 - 29 Jan 2024
Cited by 1 | Viewed by 1951
Abstract
Breast cancer (BC), characterized by high heterogeneity, is the most commonly reported malignancy among females across the globe. Every year, many BC patients die owing to delayed diagnosis and treatment. Increasing researches have indicated that aberrantly expressed circular RNAs (circRNAs) are implicated in [...] Read more.
Breast cancer (BC), characterized by high heterogeneity, is the most commonly reported malignancy among females across the globe. Every year, many BC patients die owing to delayed diagnosis and treatment. Increasing researches have indicated that aberrantly expressed circular RNAs (circRNAs) are implicated in the tumorigenesis and progression of various tumors, including BC. Hence, this article provides a summary of the biogenesis and functions of circRNAs, as well as an examination of how circRNAs regulate the progression of BC. Moreover, circRNAs have aroused incremental attention as potential diagnostic and prognostic biomarkers for BC. Exosomes enriched with circRNAs can be secreted into the tumor microenvironment to mediate intercellular communication, affecting the progression of BC. Detecting the expression levels of exosomal circRNAs may provide reference for BC diagnosis and prognosis prediction. Illuminating insights into the earlier diagnosis and better treatment regimens of BC will be potentially available following elucidation of deeper regulatory mechanisms of circRNAs in this malignancy. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers of Cancer)
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