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New Diagnostic Tools and Biomarkers in Oncological Diseases

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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: closed (31 August 2023) | Viewed by 12442

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Special Issue Editor

Dr. Bruna Scaggiante

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Guest Editor

Department of Life Sciences, University of Trieste, Giorgeri 1, 34127 Trieste, Italy
Interests: biological fluids; cancer; cancer biomarkers; cfDI; cfDNA; cfNA; copy number variation; ctDNA; ddPCR; disease-free survival; epigenetic; epigenetic sequencing; exosome; extracellular vesicle; genotyping; liquid biopsy; miRNA; mRNA; mutation; ncRNA; next- generation sequencing; overall survival; progression-free survival; recurrence-free survival; whole-exome sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Personalized medicine has become a new paradigm for the treatment of a variety of diseases.

New diagnostic tools and biomarkers have transformed the understanding of oncologic diseases over the past decade and have helped to provide patients with the best screening, diagnosis, prognosis, therapy, and follow-up.

For example, liquid biopsy has great potential for precision medicine, especially in solid tumors, liquid biopsy is suitable for screening, diagnosis, prognosis, predictive value, and disease monitoring. In addition, other small molecules such as miRNA, ncRNA, and exosomes can be used for tumor diagnosis, prognosis, and therapy. Also, the new technologies and the high throughput facilities have substantially increased the sensitivity and rapidity of the oncological tests and other potential improvements are ongoing.

This Special Issue aims to publish the recent advances in the new diagnostic tools and biomarkers for oncological diseases. Original research and review articles are welcome in this Special Issue.

Dr. Bruna Scaggiante
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.

Published Papers (7 papers)

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Research

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14 pages, 813 KiB

Open AccessArticle

Selectivity of Exhaled Breath Biomarkers of Lung Cancer in Relation to Cancer of Other Localizations

by Elina M. Gashimova, Azamat Z. Temerdashev, Dmitry V. Perunov, Vladimir A. Porkhanov, Igor S. Polyakov and Ekaterina V. Dmitrieva

Int. J. Mol. Sci. 2023, 24(17), 13350; https://doi.org/10.3390/ijms241713350 - 28 Aug 2023

Cited by 1 | Viewed by 1044

Abstract

Lung cancer is a leading cause of death worldwide, mostly due to diagnostics in the advanced stage. Therefore, the development of a quick, simple, and non-invasive diagnostic tool to identify cancer is essential. However, the creation of a reliable diagnostic tool is possible only in case of selectivity to other diseases, particularly, cancer of other localizations. This paper is devoted to the study of the variability of exhaled breath samples among patients with lung cancer and cancer of other localizations, such as esophageal, breast, colorectal, kidney, stomach, prostate, cervix, and skin. For this, gas chromatography-mass spectrometry (GC-MS) was used. Two classification models were built. The first model separated patients with lung cancer and cancer of other localizations. The second model classified patients with lung, esophageal, breast, colorectal, and kidney cancer. Mann–Whitney U tests and Kruskal–Wallis H tests were applied to identify differences in investigated groups. Discriminant analysis (DA), gradient-boosted decision trees (GBDT), and artificial neural networks (ANN) were applied to create the models. In the case of classifying lung cancer and cancer of other localizations, average sensitivity and specificity were 68% and 69%, respectively. However, the accuracy of classifying groups of patients with lung, esophageal, breast, colorectal, and kidney cancer was poor. Full article

(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases)

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12 pages, 2631 KiB

Open AccessArticle

Methylation Profile of Small Breast Cancer Tumors Evaluated by Modified MS–HRM

by Aleksey M. Krasnyi, Alsu A. Sadekova, Vlada V. Kometova, Valeriy V. Rodionov, Ekaterina L. Yarotskaya and Gennadiy T. Sukhikh

Int. J. Mol. Sci. 2023, 24(16), 12660; https://doi.org/10.3390/ijms241612660 - 10 Aug 2023

Cited by 3 | Viewed by 1162

Abstract

The DNA methylation profile of breast cancer differs from that in healthy tissues and can be used as a diagnostic and prognostic biomarker. Aim of this study: To compare the levels of gene methylation in small malignant breast cancer tumors (<2 cm), in healthy tissue, and in fibroadenoma, and to evaluate the effectiveness of the modified Methylation Sensitive–High Resolution Melting (MS–HRM) method for this analysis. Analysis was performed using the modified MS–HRM method. For validation, the methylation levels of five genes were confirmed by pyrosequencing. The main study group included 96 breast cancer samples and the control group included 24 fibroadenoma samples and 24 healthy tissue samples obtained from patients with fibroadenoma. Breast cancer samples were divided into two subgroups (test set and validation set). The methylation of the following 15 genes was studied: MAST1, PRDM14, ZNF177, DNM2, SSH1, AP2M1, CACNA1E, CPEB4, DLGAP2, CCDC181, GCM2, ITPRIPL1, POM121L2, KCNQ1, and TIMP3. Significant differences in the validation set of samples were found for seven genes; the combination of the four genes GCM2, ITPRIPL1, CACNA1E, DLGAP2 (AUC = 0.99) showed the highest diagnostic value based on logistic regression for all breast cancer samples. Our modified MS–HRM method demonstrated that small breast cancer tumors have a specific DNA methylation profile that distinguishes them from healthy tissues and benign proliferative lesions. Full article

(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases)

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17 pages, 2402 KiB

Open AccessArticle

Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection

by Silvia D’Ambrosi, Stavros Giannoukakos, Mafalda Antunes-Ferreira, Carlos Pedraz-Valdunciel, Jillian W. P. Bracht, Nicolas Potie, Ana Gimenez-Capitan, Michael Hackenberg, Alberto Fernandez Hilario, Miguel A. Molina-Vila, Rafael Rosell, Thomas Würdinger and Danijela Koppers-Lalic

Int. J. Mol. Sci. 2023, 24(5), 4881; https://doi.org/10.3390/ijms24054881 - 2 Mar 2023

Cited by 5 | Viewed by 2605

Abstract

Despite the diversity of liquid biopsy transcriptomic repertoire, numerous studies often exploit only a single RNA type signature for diagnostic biomarker potential. This frequently results in insufficient sensitivity and specificity necessary to reach diagnostic utility. Combinatorial biomarker approaches may offer a more reliable diagnosis. Here, we investigated the synergistic contributions of circRNA and mRNA signatures derived from blood platelets as biomarkers for lung cancer detection. We developed a comprehensive bioinformatics pipeline permitting an analysis of platelet-circRNA and mRNA derived from non-cancer individuals and lung cancer patients. An optimal selected signature is then used to generate the predictive classification model using machine learning algorithm. Using an individual signature of 21 circRNA and 28 mRNA, the predictive models reached an area under the curve (AUC) of 0.88 and 0.81, respectively. Importantly, combinatorial analysis including both types of RNAs resulted in an 8-target signature (6 mRNA and 2 circRNA), enhancing the differentiation of lung cancer from controls (AUC of 0.92). Additionally, we identified five biomarkers potentially specific for early-stage detection of lung cancer. Our proof-of-concept study presents the first multi-analyte-based approach for the analysis of platelets-derived biomarkers, providing a potential combinatorial diagnostic signature for lung cancer detection. Full article

(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases)

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17 pages, 2230 KiB

Open AccessArticle

Evaluation of the Small Heat Shock Protein Family Members HSPB2 and HSPB3 in Bladder Cancer Prognosis and Progression

by Despoina D. Gianniou, Aimilia D. Sklirou, Maria-Alexandra Papadimitriou, Katerina-Marina Pilala, Konstantinos Stravodimos, Margaritis Avgeris, Andreas Scorilas and Ioannis P. Trougakos

Int. J. Mol. Sci. 2023, 24(3), 2609; https://doi.org/10.3390/ijms24032609 - 30 Jan 2023

Viewed by 1789

Abstract

Bladder cancer (BlCa) represents the sixth most commonly diagnosed type of male malignancy. Due to the clinical heterogeneity of BlCa, novel markers would optimize treatment efficacy and improve prognosis. The small heat shock proteins (sHSP) family is one of the major groups of molecular chaperones responsible for the maintenance of proteome functionality and stability. However, the role of sHSPs in BlCa remains largely unknown. The present study aimed to examine the association between HSPB2 and HSPB3 expression and BlCa progression in patients, and to investigate their role in BlCa cells. For this purpose, a series of experiments including reverse transcription-quantitative PCR, Western blotting, MTT assay and flow cytometry were performed. Initial analyses revealed increased vs. human transitional carcinoma cells, expression levels of the HSPB2 and HSPB3 genes and proteins in high grade BlCa cell lines. Therefore, we then evaluated the clinical significance of the HSPB2 and HSPB3 genes expression levels in bladder tumor samples and matched adjusted normal bladder specimens. Total RNA from 100 bladder tumor samples and 49 paired non-cancerous bladder specimens were isolated, and an accurate SYBR-Green based real-time quantitative polymerase chain reaction (qPCR) protocol was developed to quantify HSPB2 and HSPB3 mRNA levels in the two cohorts of specimens. A significant downregulation of the HSPB2 and HSPB3 genes expression was observed in bladder tumors as compared to matched normal urothelium; yet, increased HSPB2 and HSPB3 levels were noted in muscle-invasive (T2–T4) vs. superficial tumors (TaT1), as well as in high-grade vs. low-grade tumors. Survival analyses highlighted the significantly higher risk for post-treatment disease relapse in TaT1 patients poorly expressing HSPB2 and HSPB3 genes; this effect tended to be inverted in advanced disease stages (muscle-invasive tumors) indicating the biphasic impact of HSPB2, HSPB3 genes in BlCa progression. The pro-survival role of HSPB2 and HSPB3 in advanced tumor cells was also evident by our finding that HSPB2, HSPB3 genes expression silencing in high grade BlCa cells enhanced doxorubicin toxicity. These findings indicate that the HSPB2, HSPB3 chaperone genes have a likely pro-survival role in advanced BlCa; thus, they can be targeted as novel molecular markers to optimize treatment efficacy in BlCa and to limit unnecessary interventions. Full article

(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases)

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Review

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26 pages, 2450 KiB

Open AccessReview

Next-Generation Sequencing and Triple-Negative Breast Cancer: Insights and Applications

by Domenico Tierno, Gabriele Grassi, Serena Scomersi, Marina Bortul, Daniele Generali, Fabrizio Zanconati and Bruna Scaggiante

Int. J. Mol. Sci. 2023, 24(11), 9688; https://doi.org/10.3390/ijms24119688 - 2 Jun 2023

Cited by 1 | Viewed by 2969

Abstract

The poor survival of triple-negative breast cancer (TNBC) is due to its aggressive behavior, large heterogeneity, and high risk of recurrence. A comprehensive molecular investigation of this type of breast cancer using high-throughput next-generation sequencing (NGS) methods may help to elucidate its potential progression and discover biomarkers related to patient survival. In this review, the NGS applications in TNBC research are described. Many NGS studies point to TP53 mutations, immunocheckpoint response genes, and aberrations in the PIK3CA and DNA repair pathways as recurrent pathogenic alterations in TNBC. Beyond their diagnostic and predictive/prognostic value, these findings suggest potential personalized treatments in PD -L1-positive TNBC or in TNBC with a homologous recombination deficit. Moreover, the comprehensive sequencing of large genomes with NGS has enabled the identification of novel markers with clinical value in TNBC, such as AURKA, MYC, and JARID2 mutations. In addition, NGS investigations to explore ethnicity-specific alterations have pointed to EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation as possible molecular signatures of African and African American TNBC. Finally, the development of long-read sequencing methods and their combination with optimized short-read techniques promise to improve the efficiency of NGS approaches for future massive clinical use. Full article

(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases)

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Other

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7 pages, 523 KiB

Open AccessCase Report

A Novel FLCN Variant in a Suspected Birt–Hogg–Dubè Syndrome Patient

by Erika Bandini, Valentina Zampiga, Ilaria Cangini, Mila Ravegnani, Valentina Arcangeli, Tania Rossi, Isabella Mammi, Francesca Schiavi, Stefania Zovato, Fabio Falcini, Daniele Calistri and Rita Danesi

Int. J. Mol. Sci. 2023, 24(15), 12418; https://doi.org/10.3390/ijms241512418 - 4 Aug 2023

Cited by 1 | Viewed by 1033

Abstract

Subjects with pathogenic (PV) and likely pathogenic (LPV) FLCN variants have an increased risk of manifesting benign and malignant disorders that are related to Birt–Hogg–Dubé syndrome (BHDS): an autosomal dominantly inherited disorder whose severity can vary significantly. Renal cell carcinoma (RCC) development in BHD (Birt–Hogg–Dubé) patients has a very high incidence; thus, identifying this rare syndrome at early stages and preventing metastatic spread is crucial. Over the last decade, the advancement of Next Generation Sequencing (NGS) and the implementation of multigene panels for hereditary cancer syndromes (HCS) have led to a subsequent focus on additional genes and variants, including those of uncertain significance (VUS). Here, we describe a novel FLCN variant observed in a subject manifesting disorders that were suspected to be related to BHDS and with a family history of multiple cancers. Full article

(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases)

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7 pages, 642 KiB

Open AccessBrief Report

IDO1 Protein Is Expressed in Diagnostic Biopsies from Both Follicular and Transformed Follicular Patients

by Marie Beck Hairing Enemark, Emma Frasez Sørensen, Trine Engelbrecht Hybel, Maja Dam Andersen, Charlotte Madsen, Kristina Lystlund Lauridsen, Bent Honoré, Francesco d’Amore, Trine Lindhardt Plesner, Stephen Jacques Hamilton-Dutoit and Maja Ludvigsen

Int. J. Mol. Sci. 2023, 24(8), 7314; https://doi.org/10.3390/ijms24087314 - 15 Apr 2023

Viewed by 1046

Abstract

Follicular lymphoma (FL) is a lymphoid neoplasia characterized by an indolent clinical nature. Despite generally favorable prognoses, early progression and histological transformation (HT) to a more aggressive lymphoma histology remain the leading causes of death among FL patients. To provide a basis for possible novel treatment options, we set out to evaluate the expression levels of indoleamine 2,3-dioxygenase 1 (IDO1), an immunoinhibitory checkpoint molecule, in follicular and transformed follicular biopsies. The expression levels of IDO1 were assessed using immunohistochemical staining and digital image analysis in lymphoma biopsies from 33 FL patients without subsequent HT (non-transforming FL, nt-FL) and 20 patients with subsequent HT (subsequently transforming FL, st-FL) as well as in paired high-grade biopsies from the time of HT (transformed FL, tFL). Despite no statistical difference in IDO1 expression levels seen between the groups, all diagnostic and transformed lymphomas exhibited positive expression, indicating its possible role in novel treatment regimens. In addition, IDO1 expression revealed a positive correlation with another immune checkpoint inhibitor, namely programmed death 1 (PD-1). In summary, we report IDO1 expression in all cases of FL and tFL, which provides the grounds for future investigations of anti-IDO1 therapy as a possible treatment for FL patients. Full article

(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases)

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