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Biomolecules
Special Issues
Emerging Biomarkers Discovery for Molecular Diagnostics
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Emerging Biomarkers Discovery for Molecular Diagnostics

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 6375

Special Issue Editors

Prof. Dr. Toshiyuki Kitoh

E-Mail Website
Guest Editor
Laboratory of Pediatrics, School of Pharmacy, Aichi-Gakuin University, 1-100 Kusumoto, Chikusa, Nagoya 464-8650, Japan
Interests: pediatrics; Kawasaki disease; pentraxin 3; soluble pattern-recognition molecule; cytokines; enzyme preparations; cell death; sensitivity prediction; amino acid requirement; selective toxicity; pediatric hematology/oncology; amino acid metabolism; anticancer drugs; pediatric leukemia; flow cytometry; immunohistochemistry; monoclonal antibodies; asparagine synthetase; l-asparaginase; selective toxicity to cancer cells
Dr. Masaki Shimizu

E-Mail Website
Guest Editor
Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University Hospital, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
Interests: pediatric rheumatology; autoinflammatory disease; cytokine; pediatric rheumatology; cytokinesis; Kawasaki disease; macrophage activation syndrome; juvenile idiopathic arthritis; systemic lupus erythematosus
Prof. Dr. Tadej Avĉin

E-Mail Website
Guest Editor
Department of Allergology, Rheumatology and Clinical Immunology, University Medical Centre Ljubljana, Bohoriceva 20, Sl-1525 Ljubljana, Slovenia
Interests: autoinflammatory diseases; systemic lupus erythematosus; antiphospholipid syndrome; pediatric rheumatology; autoimmunity; rheumatology

Special Issue Information

Dear Colleagues,

Biomarkers play a crucial role in the early detection, diagnosis, and treatment of diseases. With ongoing research and technological advancements, new biomarkers continue to be discovered and applied in practical settings. In recent years, the related field has experienced explosive growth, generating significant interest in this expanding field of personalized medicine. This Special Issue aims to explore the latest research findings and innovative approaches in this field to drive advancements in molecular diagnostics and facilitate the realization of personalized medicine.

We welcome submissions focusing on the mechanisms and applications of various types of biomarkers, including, but not limited to, genes, proteins, metabolites, and extracellular vesicles. We encourage contributions related to biomarker research in different diseases, such as cancer, cardiovascular diseases, neurological disorders, etc.

This Special Issue will cover, but is not limited to, the following topics:

  • Emerging biomarker discovery and identification;
  • Biomarkers in early disease detection and screening;
  • Biomarkers in disease diagnosis and classification;
  • Biomarkers for monitoring and prognosis evaluation;
  • The potential of biomarkers in personalized medicine;
  • Biomarkers in drug development and clinical trials;
  • The association between biomarkers and disease mechanisms;
  • The relationship between biomarkers and genetic variations;
  • Biomarkers in translational medicine;
  • Bioinformatics analysis and data mining of biomarkers.

We encourage researchers in this field to submit their research work, sharing their latest findings and innovative methods. This Special Issue is dedicated to advancing the field of molecular diagnostics and the realization of personalized medicine.

Please note that, as a journal of molecular science, clinical research is not the primary focus of Biomolecules. Studies involving molecular and cellular experiments, as well as preclinical research related to the aforementioned topics, are welcome.

Prof. Dr. Toshiyuki Kitoh
Dr. Masaki Shimizu
Prof. Dr. Tadej Avĉin
Guest Editors

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

  • emerging biomarkers
  • pre-clinical
  • molecular diagnostics
  • deep sequencing
  • omics
  • personalized medicine
  • precision medicine
  • targeted therapy
  • prognosis

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (6 papers)

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Research

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15 pages, 3746 KiB  
Article
Growth Differentiation Factor 15 as a Biomarker for Risk Stratification in the Cardiothoracic Surgery Intensive Care Unit
by Ricardo Ferreira, Tiago R. Velho, Rafael Maniés Pereira, Dora Pedroso, Beatriz Draiblate, Susana Constantino, Ângelo Nobre, Ana G. Almeida, Luís F. Moita and Fausto Pinto
Biomolecules 2024, 14(12), 1593; https://doi.org/10.3390/biom14121593 - 13 Dec 2024
Viewed by 471
Abstract
Growth Differentiation Factor 15 (GDF15) is an emerging biomarker that significantly increases during acute stress responses, such as infections, and is moderately elevated in chronic and inflammation-driven conditions. While evidence suggests that high levels of GDF15 in cardiac surgery are associated with worse [...] Read more.
Growth Differentiation Factor 15 (GDF15) is an emerging biomarker that significantly increases during acute stress responses, such as infections, and is moderately elevated in chronic and inflammation-driven conditions. While evidence suggests that high levels of GDF15 in cardiac surgery are associated with worse outcomes, its utility as an evaluator of early postoperative complications remains unclear. This study aims to characterize the postoperative profile of GDF15 in patients undergoing isolated surgical aortic valve replacement, evaluating its association with short-term outcomes. Serum samples from patients undergoing cardiac surgery were collected preoperatively and at defined postoperative time points (1 h, 6 h, 12 h, 24 h, and 48 h) to measure GDF15 levels. GDF15 levels significantly increased after surgery, peaking at 6 h. A positive correlation was observed between GDF15 levels and both cardiopulmonary bypass and aortic cross-clamp times. Notably, patients who developed postoperative acute kidney injury (AKI) or required prolonged hemodynamic support had significantly higher GDF15 levels, with increased mechanical ventilation time and extended intensive care unit length of stay. Furthermore, GDF15 levels correlated with postoperative SOFA scores at 24 h after surgery. GDF15 may be a valuable biomarker for risk stratification and guiding therapeutic decisions in cardiac surgery patients. Higher GDF15 levels were significantly associated with prolonged hemodynamic support, postoperative AKI, and measures of illness severity. Full article
(This article belongs to the Special Issue Emerging Biomarkers Discovery for Molecular Diagnostics)
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16 pages, 2759 KiB  
Article
Dysregulation of MiR-21, MiR-221 and MiR-451 During Neoadjuvant Treatment of Breast Cancer: A Prospective Study
by Carine Bispo Patury, Brenda Luanny Maia Santos, Anna Lucia Carvalho Matos, José Slabi, Luciene Cristina Campos Gastalho and Carla Martins Kaneto
Biomolecules 2024, 14(12), 1580; https://doi.org/10.3390/biom14121580 - 11 Dec 2024
Viewed by 385
Abstract
Background: Breast cancer is highly heterogeneous disease in which different responses are observed to the same treatment for different subtypes and extents of similar diseases. Considering this scenario, the search for tumor biomarkers is indispensable, with current evidence suggesting that circulating microRNAs are [...] Read more.
Background: Breast cancer is highly heterogeneous disease in which different responses are observed to the same treatment for different subtypes and extents of similar diseases. Considering this scenario, the search for tumor biomarkers is indispensable, with current evidence suggesting that circulating microRNAs are viable biomarkers. This study evaluated the expression of miR-21, miR-221, miR-195, and miR-451 in patients with breast cancer undergoing neoadjuvant treatment at oncology outpatient facilities in Brazil. Methods: We conducted a prospective and observational study in which blood samples were collected for microRNA expression analysis, comparing control and breast cancer patients who were candidates for neoadjuvant treatment groups. The expression of microRNAs was investigated by qRT-PCR method. For parametric data analysis, one-way ANOVA with Tukey’s post hoc test was used. Results: Thirty-three participants (all female) were included in the control group and twenty-seven participants were included in the study group. The non-special subtype of breast cancer was found in 96% of the study group participants; 88.9% were locally advanced tumors (T3, T4), 40.7% were luminal tumors, 33.3% were HER-2-positive, and 26% were triple negative tumors. Expression analysis of microRNAs during neoadjuvant treatment, using miR-16 as a normalizer, showed higher expression levels of miR-21 and miR-221 at the end of treatment, and high expression levels for miR-451 were also observed at the beginning of treatment. Conclusion: This is the first study that evaluates the expression of microRNAs in the context of neoadjuvant treatment of breast cancer in the Brazilian population. Our results suggest that there is a deregulation of miR-21, miR-221, and miR-451 during neoadjuvant treatment in these patients. Full article
(This article belongs to the Special Issue Emerging Biomarkers Discovery for Molecular Diagnostics)
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23 pages, 10508 KiB  
Article
Plasma microRNA Environment Linked to Tissue Factor Pathway and Cancer-Associated Thrombosis: Prognostic Significance in Ovarian Cancer
by Valéria Tavares, Joana Savva-Bordalo, Mariana Rei, Joana Liz-Pimenta, Joana Assis, Deolinda Pereira and Rui Medeiros
Biomolecules 2024, 14(8), 928; https://doi.org/10.3390/biom14080928 - 31 Jul 2024
Viewed by 1481
Abstract
Ovarian cancer (OC) is a leading cause of death among gynaecological malignancies. The haemostatic system, which controls blood flow and prevents clotting disorders, paradoxically drives OC progression while increasing the risk of venous thromboembolism (VTE). MicroRNAs (miRNAs) have emerged as crucial in understanding [...] Read more.
Ovarian cancer (OC) is a leading cause of death among gynaecological malignancies. The haemostatic system, which controls blood flow and prevents clotting disorders, paradoxically drives OC progression while increasing the risk of venous thromboembolism (VTE). MicroRNAs (miRNAs) have emerged as crucial in understanding VTE pathogenesis. Exploring the connection between cancer and thrombosis through these RNAs could lead to novel biomarkers of cancer-associated thrombosis (CAT) and OC, as well as potential therapeutic targets for tumour management. Thus, this study examined the impact of eight plasma miRNAs targeting the tissue factor (TF) coagulation pathway—miR-18a-5p, -19a-3p, -20a-5p, -23a-3p, -27a-3p, -103a-3p, -126-5p and -616-3p—in 55 OC patients. Briefly, VTE occurrence post-OC diagnosis was linked to shorter disease progression time (log-rank test, p = 0.024) and poorer overall survival (OS) (log-rank test, p < 0.001). High pre-chemotherapy levels of miR-20a-5p (targeting coagulation factor 3 (F3) and tissue factor pathway inhibitor 2 (TFPI2)) and miR-616-3p (targeting TFPI2) predicted VTE after OC diagnosis (χ2, p < 0.05). Regarding patients’ prognosis regardless of VTE, miR-20a-5p independently predicted OC progression (adjusted hazard ratio (aHR) = 6.13, p = 0.005), while miR-616-3p significantly impacted patients’ survival (aHR = 3.72, p = 0.020). Further investigation is warranted for their translation into clinical practice. Full article
(This article belongs to the Special Issue Emerging Biomarkers Discovery for Molecular Diagnostics)
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13 pages, 618 KiB  
Article
Novel Plasma Biomarkers Associated with Future Peripheral Atherosclerotic Disease and Abdominal Aortic Aneurysm—Insights from Contemporary Prospective Studies from the Malmö Diet and Cancer Study
by Stefan Acosta, Shahab Fatemi, Moncef Zarrouk and Anders Gottsäter
Biomolecules 2024, 14(7), 844; https://doi.org/10.3390/biom14070844 - 13 Jul 2024
Cited by 1 | Viewed by 1091
Abstract
Introduction: The potential utility of inflammatory and hemodynamic plasma biomarkers for the prediction of incident lower extremity arterial disease (LEAD), carotid artery stenosis (CAS), isolated atherosclerotic disease without concomitant abdominal aortic aneurysm (AAA), and isolated AAA without concomitant atherosclerotic disease has not yet [...] Read more.
Introduction: The potential utility of inflammatory and hemodynamic plasma biomarkers for the prediction of incident lower extremity arterial disease (LEAD), carotid artery stenosis (CAS), isolated atherosclerotic disease without concomitant abdominal aortic aneurysm (AAA), and isolated AAA without concomitant atherosclerotic disease has not yet been integrated in clinical practice. The main objective of this prospective study was to find predictive plasma biomarkers for cardiovascular disease and to evaluate differences in plasma biomarker profiles between asymptomatic and symptomatic CAS, as well as between isolated atherosclerotic disease and isolated AAA. Methods: Blood samples collected at baseline from participants in the prospective Malmö Diet and Cancer study (MDCS) cardiovascular cohort (n = 5550 middle-aged individuals; baseline 1991–1994) were used for plasma biomarker analysis. Validation of each incident cardiovascular diagnosis was performed by random sampling. Cox regression analysis was used to calculate hazard ratios (HRs) per one standard deviation increment of each respective log-transformed plasma biomarker with 95% confidence intervals (CI). Results: Adjusted lipoprotein-associated phospholipase A2 (Lp-PLA2) activity (HR 1.33; CI 1.17–1.52) and mass (HR 1.20; CI 1.05–1.37), C-reactive protein (CRP) (HR 1.55; CI 1.36–1.76), copeptin (HR 1.46; CI 1.19–1.80), N-terminal pro-B-type natriuretic peptide (N-BNP) (HR 1.28; 1.11–1.48), and cystatin C (HR 1.19; 95% 1.10–1.29) were associated with incident symptomatic LEAD. Adjusted N-BNP (HR 1.59; CI 1.20–2.11), mid-regional proadrenomedullin (HR 1.40; CI 1.13–1.73), cystatin C (HR 1.21; CI 1.02–1.43), and CRP (HR 1.53; CI 1.13–1.73) were associated with incident symptomatic but not asymptomatic CAS. Adjusted HR was higher for Lp-PLA2 (mass) for incident isolated AAA compared to for isolated atherosclerotic disease. Conclusions: Plasma biomarker profile data support that subclinical vascular inflammation and cardiovascular stress seem to be relevant for the development of atherosclerotic disease and AAA. Full article
(This article belongs to the Special Issue Emerging Biomarkers Discovery for Molecular Diagnostics)
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11 pages, 591 KiB  
Article
Serum Neuron-Specific Enolase as a Biomarker of Neonatal Brain Injury—New Perspectives for the Identification of Preterm Neonates at High Risk for Severe Intraventricular Hemorrhage
by Dimitra Metallinou, Grigorios Karampas, Maria-Loukia Pavlou, Maria-Ioanna Louma, Aimilia Mantzou, Antigoni Sarantaki, Christina Nanou, Kleanthi Gourounti, Maria Tzeli, Nikoletta Pantelaki, Evangelos Tzamakos, Theodora Boutsikou, Aikaterini Lykeridou and Nicoletta Iacovidou
Biomolecules 2024, 14(4), 434; https://doi.org/10.3390/biom14040434 - 3 Apr 2024
Cited by 2 | Viewed by 1723
Abstract
Neonatal brain injury (NBI) is a critical condition for preterm neonates with potential long-term adverse neurodevelopmental outcomes. This prospective longitudinal case–control study aimed at investigating the levels and prognostic value of serum neuron-specific enolase (NSE) during the first 3 days of life in [...] Read more.
Neonatal brain injury (NBI) is a critical condition for preterm neonates with potential long-term adverse neurodevelopmental outcomes. This prospective longitudinal case–control study aimed at investigating the levels and prognostic value of serum neuron-specific enolase (NSE) during the first 3 days of life in preterm neonates (<34 weeks) that later developed brain injury in the form of either periventricular leukomalacia (PVL) or intraventricular hemorrhage (IVH) during their hospitalization. Participants were recruited from one neonatal intensive care unit, and on the basis of birth weight and gestational age, we matched each case (n = 29) with a neonate who had a normal head ultrasound scan (n = 29). We report that serum NSE levels during the first three days of life do not differ significantly between control and preterm neonates with NBI. Nevertheless, subgroup analysis revealed that neonates with IVH had significantly higher concentrations of serum NSE in comparison to controls and neonates with PVL on the third day of life (p = 0.014 and p = 0.033, respectively). The same pattern on the levels of NSE on the third day of life was also observed between (a) neonates with IVH and all other neonates (PVL and control; p = 0.003), (b) neonates with II–IV degree IVH and all other neonates (p = 0.003), and (c) between control and the five (n = 5) neonates that died from the case group (p = 0.023). We conclude that NSE could be an effective and useful biomarker on the third day of life for the identification of preterm neonates at high risk of developing severe forms of IVH. Full article
(This article belongs to the Special Issue Emerging Biomarkers Discovery for Molecular Diagnostics)
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Review

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18 pages, 1488 KiB  
Review
Research Progress of Liquid Biopsy Based on DNA Methylation in Tumor Diagnosis and Treatment
by Yunxia Bao, Xianzhao Wang, Bingjie Zeng, Yichun Shi, Yiman Huang, Yiwen Huang, Shuang Shang, Liang Shan and Lifang Ma
Biomolecules 2024, 14(12), 1634; https://doi.org/10.3390/biom14121634 - 19 Dec 2024
Viewed by 489
Abstract
Liquid biopsy has been gradually applied to the clinical diagnosis and treatment of tumors because of its non-invasive and real-time reflection of the tumor status, as well as the convenience of sample collection, which allows the detection of primary or metastatic malignant tumors [...] Read more.
Liquid biopsy has been gradually applied to the clinical diagnosis and treatment of tumors because of its non-invasive and real-time reflection of the tumor status, as well as the convenience of sample collection, which allows the detection of primary or metastatic malignant tumors and reflects the heterogeneity of the tumors. DNA methylation, which is a type of epigenetic modification, is essential in the progression of tumors. This review introduces the common DNA methylation analysis methods and discusses their advantages and disadvantages, focusing on the new progress of DNA methylation-based liquid biopsy in tumor diagnosis and treatment. Full article
(This article belongs to the Special Issue Emerging Biomarkers Discovery for Molecular Diagnostics)
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