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Molecular Biomarkers of Tumors: Advancing Genetic Studies
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Molecular Biomarkers of Tumors: Advancing Genetic Studies

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular Genetics and Genetic Diseases".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 15986

Special Issue Editors

Dr. Sainan Wei

E-Mail Website
Guest Editor
Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
Interests: chromosomes; human genetics; genomics; genetic analysis; DNA sequencing; sequencing DNA; medical genetics; molecular genetics; mutation
Dr. Jing Di

E-Mail Website
Guest Editor
Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
Interests: investigating the interaction of Alzheimer's disease and sleep disruption in various mouse models, including use of novel noninvasive technologies, immunohistochemistry and metabolomics

Special Issue Information

Dear Colleagues,

We invite researchers and clinicians to contribute to the Special Issue of Biomedicine, dedicated to "Molecular Biomarkers of Tumors: Advancing Genetic Studies." This Special Issue aims to explore the latest developments in the realm of molecular biomarkers, with a specific focus on genetic investigations in tumors.

In the age of precision medicine, understanding the genetic landscape of tumors is crucial for accurate diagnosis, prognosis, and treatment decisions. This Special Issue will encompass a diverse range of topics related to molecular biomarkers, such as the identification and validation of novel genetic markers in various tumor types, genomic profiling to unravel tumor heterogeneity, and the application of molecular biomarkers for early detection and personalized therapeutic approaches.

We welcome original research articles and reviews that present cutting-edge discoveries, methodologies, and clinical applications in the field of molecular biomarkers in oncology. Additionally, studies addressing the challenges of translating genetic findings into clinical practice will be highly valued.

By fostering collaboration among multidisciplinary researchers, this Special Issue aims to advance our knowledge of tumor biology and personalized medicine. Ultimately, this knowledge will contribute to the development of more effective and targeted cancer therapies, enhancing patient outcomes and overall quality of life.

Dr. Sainan Wei
Dr. Jing Di
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. Biomedicines 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.

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Published Papers (10 papers)

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Research

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15 pages, 8370 KiB  
Article
Unveiling DENND2D as a Novel Prognostic Biomarker for Prostate Cancer Recurrence: From Gene to Prognosis
by Chi-Fen Chang, Lih-Chyang Chen, Yei-Tsung Chen, Chao-Yuan Huang, Chia-Cheng Yu, Victor C. Lin, Te-Ling Lu, Shu-Pin Huang and Bo-Ying Bao
Biomedicines 2025, 13(1), 25; https://doi.org/10.3390/biomedicines13010025 - 26 Dec 2024
Viewed by 890
Abstract
Background: Prostate cancer is a major global health burden, with biochemical recurrence (BCR) following radical prostatectomy affecting 20–40% of patients and posing significant challenges to prognosis and treatment. Emerging evidence suggests a critical role for differentially expressed in normal and neoplastic cell ( [...] Read more.
Background: Prostate cancer is a major global health burden, with biochemical recurrence (BCR) following radical prostatectomy affecting 20–40% of patients and posing significant challenges to prognosis and treatment. Emerging evidence suggests a critical role for differentially expressed in normal and neoplastic cell (DENN) domain-containing genes in oncogenesis; however, their implications in prostate cancer and BCR risk remain underexplored. Methods: This study systematically evaluated 151 single-nucleotide polymorphisms in DENN domain-containing genes in 458 patients with prostate cancer and BCR, followed by validation in an independent cohort of 185 patients. Results: Multivariate Cox regression analyses identified DENND2D rs610261 G>A as significantly associated with improved BCR-free survival in both cohorts (adjusted hazard ratio = 0.39, 95% confidence interval = 0.23–0.66, p = 0.001). Functional analysis revealed rs610261’s regulatory potential, with the protective A allele correlating with increased DENND2D expression in various human tissues. Compared to normal prostate tissues, DENND2D expression was reduced in prostate cancer, with higher expression being linked to favorable patient prognosis (p = 0.03). Gene set enrichment analysis revealed an association between DENND2D expression and the negative regulation of MYC target genes, including MAD2L1, ERH, and CLNS1A, which are overexpressed in prostate cancer and associated with poor survival. Furthermore, the elevated DENND2D expression promotes immune infiltration in prostate cancer, supporting its role in immune modulation. Conclusions: DENND2D is a prognostic biomarker for BCR in prostate cancer and offers new avenues for personalized treatment strategies. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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20 pages, 3857 KiB  
Article
The Role of Sphingolipid Metabolism in Pregnancy-Associated Breast Cancer After Chemotherapy
by Victor Blokhin, Tatiana Zavarykina, Vasily Kotsuba, Maria Kapralova, Uliana Gutner, Maria Shupik, Elena Kozyrko, Evgenia Luzina, Polina Lomskova, Darya Bajgazieva, Svetlana Khokhlova and Alice Alessenko
Biomedicines 2024, 12(12), 2843; https://doi.org/10.3390/biomedicines12122843 - 13 Dec 2024
Viewed by 1240
Abstract
Background: The aim of our study was to determine the role of sphingolipids, which control proliferation and apoptosis, in the placenta of pregnant women with pregnancy-associated breast cancer (PABC) after chemotherapy compared with healthy patients. Methods: We analyzed (by the PCR method) the [...] Read more.
Background: The aim of our study was to determine the role of sphingolipids, which control proliferation and apoptosis, in the placenta of pregnant women with pregnancy-associated breast cancer (PABC) after chemotherapy compared with healthy patients. Methods: We analyzed (by the PCR method) the gene expression of key sphingolipid metabolism enzymes (sphingomyelinases (SMPD1 and SMPD3), acid ceramidase (ASAH1), ceramide synthases (CERS 1–6), sphingosine kinase1 (SPHK1), sphingosine-1-phosphate lyase 1 (SGPL1), and sphingosine-1-phosphate receptors (S1PR1, S1PR2, and S1PR3)) and the content of subspecies of ceramides, sphingosine, and sphingosine-1-phosphate in seven patients with PABC after chemotherapy and eight healthy pregnant women as a control group. Results: We found a significant increase in the expression of genes of acid ceramidase (ASAH1), sphingosine-1-phosphate lyase 1 (SGPL1), sphingosine kinase (SPHK1), and ceramide synthases (CERS 1-3, 5, 6) in the samples of patients with PABC during their treatment with cytostatic chemotherapy. The increase in the expression of the enzymes’ genes was not accompanied by changes in the content of the studied sphingolipids. Such significant changes in the expression of genes controlling the level of CER, sphingosine, and S1P may indicate their ability to initiate the metabolism of pro-apoptotic and anti-apoptotic sphingolipids in the placenta of pregnant women with cancer undergoing chemotherapy in order to maintain levels typical of the placenta of healthy women. Conclusions: Our results may indicate the promising mechanism of placenta protection during chemotherapy for pregnant women with breast cancer and, consequently, of the newborn. This protective effect of the placenta and especially for the newborn has been discovered for the first time and requires more careful study. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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11 pages, 2227 KiB  
Article
Prognostic Significance and Treatment Response Associations of Genetic Mutations in Chronic Myelomonocytic Leukemia: A Retrospective Cohort Study
by Jing Di, Leonard N. Yenwongfai, Talal Arshad, Bin Huang, Jaclyn K. McDowell, Eric B. Durbin, Reinhold Munker and Sainan Wei
Biomedicines 2024, 12(11), 2476; https://doi.org/10.3390/biomedicines12112476 - 28 Oct 2024
Viewed by 1228
Abstract
Background: This retrospective cohort study investigates the prognostic significance of genetic mutations in Chronic Myelomonocytic Leukemia (CMML) and their association with treatment responses among patients treated at a single institution, juxtaposed with a statewide dataset from Kentucky. Methods: The study includes 51 patients [...] Read more.
Background: This retrospective cohort study investigates the prognostic significance of genetic mutations in Chronic Myelomonocytic Leukemia (CMML) and their association with treatment responses among patients treated at a single institution, juxtaposed with a statewide dataset from Kentucky. Methods: The study includes 51 patients diagnosed with CMML under the World Health Organization criteria from January 2005 to December 2023. It examines their genomic profiles and subsequent survival outcomes. The analysis also categorizes patients into CMML-1 and CMML-2 subtypes and assesses survival differences between transformed and non-transformed cases. Results: Mutations in TET2, ASXL1, and SRSF2 were found to significantly influence survival, establishing their roles as critical prognostic markers. Additionally, the cohort from the University of Kentucky exhibited distinct survival patterns compared to the broader Kentucky state population, suggesting that demographic and treatment-related factors could underlie these variances. Conclusions: This research underscores the pivotal role of targeted genetic profiling in deciphering the progression of CMML and refining therapeutic strategies. The findings emphasize the necessity for advanced genetic screening in managing CMML to better understand individual prognoses and optimize treatment efficacy, thereby offering insights that could lead to personalized treatment approaches. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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21 pages, 18578 KiB  
Article
ABCG2 Gene Expression in Non-Small Cell Lung Cancer
by Agnieszka Jeleń, Marta Żebrowska-Nawrocka, Mariusz Łochowski, Dagmara Szmajda-Krygier and Ewa Balcerczak
Biomedicines 2024, 12(10), 2394; https://doi.org/10.3390/biomedicines12102394 - 19 Oct 2024
Viewed by 2507
Abstract
Background/Objectives: ATP-binding cassette subfamily G member 2 [ABCG2/breast cancer resistance protein (BCRP)] contributes to mechanisms of multidrug resistance (MDR) and is a marker of side population (SP) cells in human cancers. The primary objective of this study was to investigate the impact of [...] Read more.
Background/Objectives: ATP-binding cassette subfamily G member 2 [ABCG2/breast cancer resistance protein (BCRP)] contributes to mechanisms of multidrug resistance (MDR) and is a marker of side population (SP) cells in human cancers. The primary objective of this study was to investigate the impact of ABCG2 gene expression on the non-small cell lung cancer (NSCLC) development, course of cancer disease, and patient prognosis using publicly available data. Obtained results were supplemented with assessment of ABCG2 expression in blood of NSCLC patients. Methods: The dataset of lung cancer was analyzed utilizing the TIMER 2.0, UALCAN, TNMplot, MEXPRESS, cBioPortal, MethSurv, KM Plotter, STRING, and ShinyGO 0.80 databases. Blood samples from 50 patients were assessed using the real-time PCR method. Results: The ABCG2 gene was expressed at a low level in NSCLC, and did not correlate with clinical aggressiveness of lung cancer. Higher ABCG2 expression improved overall survival, but only in LUAD. In addition, CpG sites located on the CpG island affecting the NSCLC patient’s prognosis were indicated. In the case of our own laboratory results, the study did not reveal any changes in the ABCG2 expression levels in blood collected from patients at different time points during the diagnostic–therapeutic procedure. In the in silico analysis, most ABCG2 protein interactors were associated with the development of drug resistance. Conclusions: ABCG2 appears to have a particularly significant impact on the survival of patients with lung cancer and on the effect of immunotherapy related to immune cell infiltration. Presented findings may support personalized medicine strategies based on bioinformatics findings. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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29 pages, 10607 KiB  
Article
Interplay of RNA m6A Modification-Related Geneset in Pan-Cancer
by Boyu Zhang, Yajuan Hao, Haiyan Liu, Jiarun Wu, Lu Lu, Xinfeng Wang, Akhilesh K. Bajpai and Xi Yang
Biomedicines 2024, 12(10), 2211; https://doi.org/10.3390/biomedicines12102211 - 27 Sep 2024
Cited by 2 | Viewed by 1281
Abstract
Background: N6-methyladenosine (m6A), is the most common modification found in mRNA and lncRNA in higher organisms and plays an important role in physiology and pathology. However, its role in pan-cancer has not been explored. Results: A total [...] Read more.
Background: N6-methyladenosine (m6A), is the most common modification found in mRNA and lncRNA in higher organisms and plays an important role in physiology and pathology. However, its role in pan-cancer has not been explored. Results: A total of 31 m6A modification regulators, including 12 writers, 2 erasers, and 17 readers are identified in the current study. The functional analysis of the regulators results in the enrichment of processes, primarily related to RNA modification and metabolism, and the PPI network reveals multiple interactions among the regulators. The mRNA expression analysis reveals a high expression for most of the regulators in pan-cancer. Most of the m6A regulators are found to be mutated across the cancers, with ZC3H13, VIRMA, and PRRC2A having a higher frequency rate. Significant correlations of the regulators with clinicopathological parameters, such as age, gender, tumor stage, and grade are identified in pan-cancer. The m6A regulators’ expression is found to have significant positive correlations with the miRNAs in pan-cancer. The expression pattern of the m6A regulators is able to classify the tumors into different subclusters as well as into high- and low-risk groups. These tumor groups show differential patterns in terms of their immune cell infiltration, tumor stemness score, genomic heterogeneity score, expression of immune regulatory/checkpoint genes, and correlations between the regulators and the drugs. Conclusions: Our study provide a comprehensive overview of the functional roles, genetic and epigenetic alterations, and prognostic value of the RNA m6A regulators in pan-cancer. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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11 pages, 5809 KiB  
Article
Prognostic Significance of VAV3 Gene Variants and Expression in Renal Cell Carcinoma
by Chi-Fen Chang, Bo-Ying Bao, Yu-Mei Hsueh, Pei-Ling Chen, Li-Hsin Chang, Chia-Yang Li, Jiun-Hung Geng, Te-Ling Lu, Chao-Yuan Huang and Shu-Pin Huang
Biomedicines 2024, 12(8), 1694; https://doi.org/10.3390/biomedicines12081694 - 30 Jul 2024
Cited by 1 | Viewed by 1654
Abstract
Renal cell carcinoma (RCC) is characterized by high mortality and morbidity rates. Vav guanine nucleotide exchange factors (VAVs), crucial for signal transduction between cell membrane receptors and intracellular mediators, have been implicated in carcinogenesis. However, their potential prognostic value in RCC remains unclear. [...] Read more.
Renal cell carcinoma (RCC) is characterized by high mortality and morbidity rates. Vav guanine nucleotide exchange factors (VAVs), crucial for signal transduction between cell membrane receptors and intracellular mediators, have been implicated in carcinogenesis. However, their potential prognostic value in RCC remains unclear. The impact of 150 common VAV polymorphisms on RCC risk and survival was investigated in a cohort of 630 individuals. Publicly available gene expression datasets were utilized to analyze VAV gene expression in relation to patient outcomes. The VAV3 rs17019888 polymorphism was significantly associated with RCC risk and overall survival after adjusting for false discovery rates. Expression quantitative trait loci analysis revealed that the risk allele of rs17019888 is linked to reduced VAV3 expression. Analysis of 19 kidney cancer gene expression datasets revealed lower VAV3 expression in RCC tissues compared to normal tissues, with higher expression correlating with better prognosis. Gene set enrichment analysis demonstrated that VAV3 negatively regulates the ubiquitin–proteasome system, extracellular matrix and membrane receptors, inflammatory responses, matrix metalloproteinases, and cell cycle pathways. Furthermore, elevated VAV3 expression was associated with increased infiltration of B cells, macrophages, and neutrophils into the RCC tumor microenvironment. Our findings suggest that VAV3 gene variants influence RCC risk and survival, contributing to a favorable prognosis in RCC. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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12 pages, 1965 KiB  
Article
Generation of a Specific Fluorescence In Situ Hybridization Test for the Detection of Ovarian Carcinoma Cells
by Amelie Limburg, Xueqian Qian, Bernice Brechtefeld, Nina Hedemann, Inken Flörkemeier, Christoph Rogmans, Leticia Oliveira-Ferrer, Nicolai Maass, Norbert Arnold, Dirk O. Bauerschlag and Jörg Paul Weimer
Biomedicines 2024, 12(6), 1171; https://doi.org/10.3390/biomedicines12061171 - 24 May 2024
Cited by 1 | Viewed by 1514
Abstract
Examinations of ovarian cancer cells require the ability to identify tumor cells. Array-based comparative genome hybridization (aCGH) on 30 ovarian carcinomas (OC) identified three genomic loci (8q24.23; 17p12; 18q22.3) over- or under-represented in OC. A fluorescence in situ hybridization (FISH) probe of these [...] Read more.
Examinations of ovarian cancer cells require the ability to identify tumor cells. Array-based comparative genome hybridization (aCGH) on 30 ovarian carcinomas (OC) identified three genomic loci (8q24.23; 17p12; 18q22.3) over- or under-represented in OC. A fluorescence in situ hybridization (FISH) probe of these three loci is intended to identify tumor cells by their signal pattern deviating from a diploid pattern. Human DNA from these three loci is isolated from bacterial artificial chromosomes (BAC), amplified and labeled with fluorescent dyes. After a standard FISH procedure, 71 OC suspensions from primary tumors, three OC cell lines, three lymphocyte suspensions, and one mesenchymal cell line LP-3 are analyzed with a fluorescence microscope. On average, 15% of the lymphocytes deviate from the expected diploid signal pattern, giving a cut-off of 36%. If this value is exceeded, tumor cells are detected. The mesenchymal cell line LP-3 shows only 21% as a negative control. The OC cell lines as positive controls exceed this value at 38%, 67%, and 54%. Of the 71 OC primary cultures, four cases fell below this cut-off as false negatives. In the two-sample t-test, the percentages of conspicuous signal patterns differ significantly. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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Review

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24 pages, 742 KiB  
Review
Molecular Biomarkers of Glioma
by Punsasi Rajakaruna, Stella Rios, Hana Elnahas, Ashley Villanueva, David Uribe, Sophia Leslie, Walaa A. Abbas, Larissa Barroso, Stephanie Oyervides, Michael Persans, Wendy Innis-Whitehouse and Megan Keniry
Biomedicines 2025, 13(6), 1298; https://doi.org/10.3390/biomedicines13061298 - 26 May 2025
Viewed by 633
Abstract
In this review, we discuss how mutations in glioma are associated with prognosis and treatment efficacy. A fascinating characteristic of glioma and all cancers is that while common growth and developmental pathways are altered, the characteristic mutations are distinct depending on the specific [...] Read more.
In this review, we discuss how mutations in glioma are associated with prognosis and treatment efficacy. A fascinating characteristic of glioma and all cancers is that while common growth and developmental pathways are altered, the characteristic mutations are distinct depending on the specific type of tumor with concomitant prognoses. Next-generation sequencing, precision medicine, and artificial intelligence are boosting the employment of molecular biomarkers in cancer diagnosis and treatment. Understanding the biological underpinnings of distinct mutations on critical signaling pathways is crucial for developing novel therapies for glioma. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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16 pages, 1245 KiB  
Review
Microsatellite Instability in Urine: Breakthrough Method for Bladder Cancer Identification
by Manuel Alejandro Rico-Méndez, María de la Luz Ayala-Madrigal, Anahí González-Mercado, Melva Gutiérrez-Angulo, Jorge Adrián Ramírez de Arellano Sánchez, Saul Armando Beltrán-Ontiveros, Betsabe Contreras-Haro, Itzae Adonai Gutiérrez-Hurtado and José Miguel Moreno-Ortiz
Biomedicines 2024, 12(12), 2726; https://doi.org/10.3390/biomedicines12122726 - 28 Nov 2024
Cited by 1 | Viewed by 1103
Abstract
Bladder cancer (BC) is the most common neoplasm of the urinary system and ranks tenth in global cancer incidence. Due to its high recurrence rate and the need for continuous monitoring, it is the cancer with the highest cost per patient. Cystoscopy is [...] Read more.
Bladder cancer (BC) is the most common neoplasm of the urinary system and ranks tenth in global cancer incidence. Due to its high recurrence rate and the need for continuous monitoring, it is the cancer with the highest cost per patient. Cystoscopy is the traditional method for its detection and surveillance; however, this is an invasive technique, while non-invasive methods, such as cytology, have a limited sensitivity. For this reason, new non-invasive strategies have emerged, analyzing useful markers for BC detection from urine samples. The identification of tumor markers is essential for early cancer detection and treatment. Urine analysis offers a non-invasive method to identify these markers. Microsatellite instability (MSI) has been proposed as a promising marker for tumor cell detection and guided targeted therapies. Therefore, this review aims to explore the evidence supporting the identification of MSI in exfoliated bladder tumor cells (EBTCs) in the urine, emphasizing its potential as a non-invasive and clinically effective alternative for tumor identification. Furthermore, establishing clinical guidelines is crucial for standardizing its application in oncological screening and validating its clinical utility. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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Other

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10 pages, 5608 KiB  
Case Report
NSD3::NUTM1 Fusion Sarcoma Mimicking Malignant Peripheral Nerve Sheath Tumor with Prolonged Survival
by Jing Di, Ali M. Alhaidary, Chi Wang, Jinge Liu, Sainan Wei, Joseph Valentino and Therese J. Bocklage
Biomedicines 2024, 12(8), 1709; https://doi.org/10.3390/biomedicines12081709 - 1 Aug 2024
Viewed by 1858
Abstract
Nuclear Protein in Testis (NUT)-rearranged tumors comprise predominantly NUT carcinoma but also include certain lymphomas, leukemias, skin appendage tumors, and sarcomas. Although histologically diverse, all are genetically identified by oncogenic rearrangement in the NUTM1 gene. Many fusion partners occur, and NSD3 is NUT [...] Read more.
Nuclear Protein in Testis (NUT)-rearranged tumors comprise predominantly NUT carcinoma but also include certain lymphomas, leukemias, skin appendage tumors, and sarcomas. Although histologically diverse, all are genetically identified by oncogenic rearrangement in the NUTM1 gene. Many fusion partners occur, and NSD3 is NUT carcinoma’s third most common partner. Herein, we present a case of a 26-year-old man with an NSD3::NUTM1 fusion sarcoma. The patient presented at the age of 13 months with a scalp nodule. Over the next 24 years, he experienced five local recurrences and ultimately expired of a rapidly progressive recurrence. His treatment included surgical resections, radiation, and various chemotherapies. Deceptively, the clinical presentation and histopathology aligned with a malignant peripheral nerve sheath tumor, a diagnosis rendered at initial resection with concurrence by a national soft tissue tumor expert. The patient’s exceptionally long survival could be due to NSD3 as the fusion partner, aided by the initial small tumor size and young patient age. Thus, this case expands NUT fusion sarcomas’ histologic and immunohistochemical profile to include mimicking a malignant peripheral nerve sheath tumor (MPNST). Additionally, it indicates that the NSD3::NUTM1 fusion can drive sarcoma genesis. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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