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New Diagnostic Tools and Biomarkers in Oncological Diseases: 2nd Edition
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New Diagnostic Tools and Biomarkers in Oncological Diseases: 2nd Edition

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: 20 March 2025 | Viewed by 7368

Special Issue Editor

Dr. Bruna Scaggiante

E-Mail Website
Guest Editor
Department of Life Sciences, University of Trieste, Valerio 28, 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.

More published papers can be found in the closed special issue: New Diagnostic Tools and Biomarkers in Oncological Diseases.

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.

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Keywords

  • oncologic diseases
  • biomarkers
  • liquid biopsy
  • miRNA
  • ncRNA
  • exosomes

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Published Papers (5 papers)

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15 pages, 3428 KiB  
Article
ddPCR Overcomes the CRISPR-Cas13a-Based Technique for the Detection of the BRAF p.V600E Mutation in Liquid Biopsies
by Irina Palacín-Aliana, Noemí García-Romero, Josefa Carrión-Navarro, Pilar Puig-Serra, Raul Torres-Ruiz, Sandra Rodríguez-Perales, David Viñal, Víctor González-Rumayor and Ángel Ayuso-Sacido
Int. J. Mol. Sci. 2024, 25(20), 10902; https://doi.org/10.3390/ijms252010902 - 10 Oct 2024
Viewed by 788
Abstract
The isolation of circulating tumoral DNA (ctDNA) present in the bloodstream brings about the opportunity to detect genomic aberrations from the tumor of origin. However, the low amounts of ctDNA present in liquid biopsy samples makes the development of highly sensitive techniques necessary [...] Read more.
The isolation of circulating tumoral DNA (ctDNA) present in the bloodstream brings about the opportunity to detect genomic aberrations from the tumor of origin. However, the low amounts of ctDNA present in liquid biopsy samples makes the development of highly sensitive techniques necessary to detect targetable mutations for the diagnosis, prognosis, and monitoring of cancer patients. Here, we employ standard genomic DNA (gDNA) and eight liquid biopsy samples from different cancer patients to examine the newly described CRISPR-Cas13a-based technology in the detection of the BRAF p.V600E actionable point mutation and appraise its diagnostic capacity with two PCR-based techniques: quantitative Real-Time PCR (qPCR) and droplet digital PCR (ddPCR). Regardless of its lower specificity compared to the qPCR and ddPCR techniques, the CRISPR-Cas13a-guided complex was able to detect inputs as low as 10 pM. Even though the PCR-based techniques have similar target limits of detection (LoDs), only the ddPCR achieved a 0.1% variant allele frequency (VAF) detection with elevated reproducibility, thus standing out as the most powerful and suitable tool for clinical diagnosis purposes. Our results also demonstrate how the CRISPR-Cas13a can detect low amounts of the target of interest, but its base-pair specificity failed in the detection of actionable point mutations at a low VAF; therefore, the ddPCR is still the most powerful and suitable technique for these purposes. Full article
(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases: 2nd Edition)
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13 pages, 2649 KiB  
Article
Serum Splicing Factor Proline- and Glutamine-Rich Is a Diagnostic Marker for Non-Small-Cell Lung Cancer and Other Solid Cancers
by Libang Yang, Adam Gilbertsen, Blake Jacobson, Robert Kratzke and Craig A. Henke
Int. J. Mol. Sci. 2024, 25(16), 8766; https://doi.org/10.3390/ijms25168766 - 12 Aug 2024
Viewed by 1135
Abstract
Cancer markers are measurable molecules in blood or tissues that are produced by tumor cells or immune cells in response to cancer progression. They play an important role in clinical diagnosis, prognosis, and therapy monitoring. Splicing factor proline- and glutamine-rich (SFPQ) plays an [...] Read more.
Cancer markers are measurable molecules in blood or tissues that are produced by tumor cells or immune cells in response to cancer progression. They play an important role in clinical diagnosis, prognosis, and therapy monitoring. Splicing factor proline- and glutamine-rich (SFPQ) plays an important role in cancer growth and metastasis. SFPQ is not only more highly expressed in non-small-cell lung cancer (NSCLC) cells than it is in controls, but also highly expressed in cancer cells in patients with other solid cancers. Thus, a new enzyme-linked immunosorbent assay (ELISA) for detecting SFPQ was developed, in which the SFPQ protein is trapped by the first specific mAb coated on a microplate, and then recognized by a second specific mAb. This assay allows for the specific detection of SFPQ in the serum of patients with solid cancer. Regarding NSCLC, the serum SFPQ levels distinguished the non-cancer controls from the patients with NSCLC, with an area under the curve of 0.876, a sensitivity of 87%, and a specificity of 94%. The serum SFPQ levels were significantly elevated in the patients with NSCLC or other solid cancers. In conclusion, serum SFPQ could be a promising novel diagnostic biomarker for NSCLC and other malignancies. Full article
(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases: 2nd Edition)
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13 pages, 1131 KiB  
Article
Assessment of Untargeted Metabolomics by Hydrophilic Interaction Liquid Chromatography−Mass Spectrometry to Define Breast Cancer Liquid Biopsy-Based Biomarkers in Plasma Samples
by Carmen González Olmedo, Leticia Díaz Beltrán, Verónica Madrid García, José Luis Palacios Ferrer, Alicia Cano Jiménez, Rocío Urbano Cubero, José Pérez del Palacio, Caridad Díaz, Francisca Vicente and Pedro Sánchez Rovira
Int. J. Mol. Sci. 2024, 25(10), 5098; https://doi.org/10.3390/ijms25105098 - 7 May 2024
Viewed by 1865
Abstract
An early diagnosis of cancer is fundamental not only in regard to reducing its mortality rate but also in terms of counteracting the progression of the tumor in the initial stages. Breast cancer (BC) is the most common tumor pathology in women and [...] Read more.
An early diagnosis of cancer is fundamental not only in regard to reducing its mortality rate but also in terms of counteracting the progression of the tumor in the initial stages. Breast cancer (BC) is the most common tumor pathology in women and the second deathliest cancer worldwide, although its survival rate is increasing thanks to improvements in screening programs. However, the most common techniques to detect a breast tumor tend to be time-consuming, unspecific or invasive. Herein, the use of untargeted hydrophilic interaction liquid chromatography−mass spectrometry analysis appears as an analytical technique with potential use for the early detection of biomarkers in liquid biopsies from BC patients. In this research, plasma samples from 134 BC patients were compared with 136 from healthy controls (HC), and multivariate statistical analyses showed a clear separation between four BC phenotypes (LA, LB, HER2, and TN) and the HC group. As a result, we identified two candidate biomarkers that discriminated between the groups under study with a VIP > 1 and an AUC of 0.958. Thus, targeting the specific aberrant metabolic pathways in future studies may allow for better molecular stratification or early detection of the disease. Full article
(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases: 2nd Edition)
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14 pages, 933 KiB  
Article
The Usefulness of Vitamin K-Dependent Proteins in the Diagnosis of Colorectal Carcinoma
by Mirela-Georgiana Perné, Adela-Viviana Sitar-Tăut, Olga Hilda Orășan, Vasile Negrean, Călin Vasile Vlad, Teodora-Gabriela Alexescu, Mircea Vasile Milaciu, Lorena Ciumărnean, Răzvan Dan Togănel, Gabriel Emil Petre, Ioan Șimon and Alexandra Crăciun
Int. J. Mol. Sci. 2024, 25(9), 4997; https://doi.org/10.3390/ijms25094997 - 3 May 2024
Viewed by 1391
Abstract
Colorectal cancer (CRC) is one of the most common neoplasms in developed countries, with increasing incidence and mortality, even in young people. A variety of serum markers have been associated with CRC (CEA, CA 19-9), but neither should be used as a screening [...] Read more.
Colorectal cancer (CRC) is one of the most common neoplasms in developed countries, with increasing incidence and mortality, even in young people. A variety of serum markers have been associated with CRC (CEA, CA 19-9), but neither should be used as a screening tool for the diagnosis or evolution staging of CRC. The sensitivity and specificity of these markers are not as good as is required, so new ones need to be found. Matrix Gla protein and PIVKA II are involved in carcinogenesis, but few studies have evaluated their usefulness in predicting the presence and severity of CRC. Two hundred patients were divided into three groups: 80 patients were included in the control group; 80 with CRC and without hepatic metastasis were included in Group 1; 40 patients with CRC and hepatic metastasis were included in Group 2. Vitamin K-dependent proteins (VKDPs) levels in plasma were determined. Patients with CRC without methastasis (Group 1) and CRC patients with methastasis (Group 2) presented significantly higher values of CEA, CA 19-9, PIVKA II (310.05 ± 38.22 vs. 430.13 ± 122.13 vs. 20.23 ± 10.90), and ucMGP (14,300.00 ± 2387.02 vs. 13,410.52 ± 2243.16 vs. 1780.31 ± 864.70) compared to control group (Group 0). Interestingly, Group 1 presented the greatest PIVKA II values. Out of all the markers, significant differences between the histological subgroups were found only for ucMGP, but only in non-metastatic CRC. Studying the discrimination capacity between the patients with CRC vs. those without, no significant differences were found between the classical tumor markers and the VKDP AUROC curves (PIVKA II and ucMGP AUROCs = 1). For the metastatic stage, the sensitivity and specificity of the VKDPs were lower in comparison with those of CA 19-9 and CEA, respectively (PIVKA II AUROC = 0.789, ucMGP AUROC = 0.608). The serum levels of these VKDPs are significantly altered in patients with colorectal carcinoma; it is possible to find additional value of these in the early stages of the disease. Full article
(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases: 2nd Edition)
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13 pages, 3658 KiB  
Article
Identification of Serum Biomarkers to Monitor Therapeutic Response in Intestinal-Type Gastric Cancer
by Laura F. Dagley, Jumana Yousef, Adele Preaudet, Andrea Loving, Andrew I. Webb, Matthias Ernst and Tracy L. Putoczki
Int. J. Mol. Sci. 2024, 25(6), 3129; https://doi.org/10.3390/ijms25063129 - 8 Mar 2024
Viewed by 1374
Abstract
There are a limited number of clinically useful serum biomarkers to predict tumor onset or treatment response in gastric cancer (GC). For this reason, we explored the serum proteome of the gp130Y757F murine model of intestinal-type gastric cancer (IGC). We identified 30 [...] Read more.
There are a limited number of clinically useful serum biomarkers to predict tumor onset or treatment response in gastric cancer (GC). For this reason, we explored the serum proteome of the gp130Y757F murine model of intestinal-type gastric cancer (IGC). We identified 30 proteins with significantly elevated expression in early gp130Y757F IGC and 12 proteins that were significantly elevated in late gp130Y757F IGC compared to age- and gender-matched wild-type mice. Within these signatures, there was an overlap of 10 proteins commonly elevated in both early- and late-stage disease. These results highlight the potential to identify serum biomarkers of disease stage. Since IGC in the gp130Y757F model can be reversed following therapeutic inhibition of Interleukin (IL)-11, we explored whether the protein signatures we identified could be used to monitor tumor regression. We compared two different therapeutic modalities and found 5 proteins to be uniquely differentially expressed between control animals and animals halfway through treatment, with 10 differentially expressed at the end of treatment. Our findings highlight the potential to identify reliable biomarkers to track IGC tumor regression in response to treatment. Full article
(This article belongs to the Special Issue New Diagnostic Tools and Biomarkers in Oncological Diseases: 2nd Edition)
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