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Cancer Diagnosis and Treatment: Exploring Molecular Research
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Cancer Diagnosis and Treatment: Exploring Molecular Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (20 March 2025) | Viewed by 2913

Special Issue Editor

Prof. Dr. Kazuyuki Matsushita

E-Mail Website
Guest Editor
Department of Laboratory Medicine, Chiba University Hospital, Chiba, Japan
Interests: cancer; clinical laboratiry; molecular science; rare diases; ribosome

Special Issue Information

Dear Colleagues,

The new functions of transcription, splicing regulation, translation, and ribosomal control mechanisms are considered to be the therapeutic targets of cancer. These mechanisms are acquired and retained through evolution.

The developmental regulation of these cellular events and its induced RNA translation control are expected to introduce new possibilities for biological and medical applications in cancer research. There is also a report that the disruption of these molecular regulators can induce cancer as well as neural development disorders. There is no doubt that a greater understanding of the transcription, splicing regulation, associated RNA control, and translation with ribosomal synthesis mechanisms will help to advance cancer diagnosis and treatment.

Specific topics covered in this Special Issue include (but are not limited to) the following:

  • Alteration of gene transcription, splicing, ribosomal expression in cancer development;
  • Bio-targets and agents of novel mechanisms in gene transcription, splicing, ribosomal expression for cancer treatment;
  • Detection and screening of cancer;
  • Cellular research and biomarkers for molecular targets of cancer;
  • Epigenetics in cancer.

Dr. Kazuyuki Matsushita
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.

Keywords

  • cancer diagnosis
  • gene transcription
  • detection and screening of cancer
  • cancer epigenetics

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

Published Papers (4 papers)

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Research

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10 pages, 1100 KiB  
Article
Allele-Specific PCR for Detection of Missense Mutations in the Chimeric BCR::ABL1 Gene Causing Failure of Tyrosine Kinase Inhibitor Therapy in CML Patients
by Anastasia Skripkina, Irina Fevraleva, Elena Kuzmina, Bella Biderman, Elena Stepanova, Ekaterina Chelysheva, Anna Turkina and Andrey Sudarikov
Int. J. Mol. Sci. 2025, 26(8), 3728; https://doi.org/10.3390/ijms26083728 - 15 Apr 2025
Viewed by 162
Abstract
Missense mutations in the BCR::ABL1 kinase domain are found in approximately 12–80% of patients with chronic myeloid leukemia (CML). Clinically significant mutations include T315I, M244V, Y253H/F, E255K/V, V299L, and F359V. The aim of this study was to create a diagnostic system for rapid [...] Read more.
Missense mutations in the BCR::ABL1 kinase domain are found in approximately 12–80% of patients with chronic myeloid leukemia (CML). Clinically significant mutations include T315I, M244V, Y253H/F, E255K/V, V299L, and F359V. The aim of this study was to create a diagnostic system for rapid and inexpensive detection of the above mutations. We used genomic DNA and RNA from peripheral blood and bone marrow cells of 57 patients with a Ph-positive CML diagnosis established in the chronic phase. We have developed a method to detect mutations in the BCR::ABL1 gene based on allele-specific real-time polymerase chain reaction (AS-PCR). In parallel, we analyzed the RNA sequence of the protein kinase domain of the same samples by next-generation sequencing (NGS) covering the points of putative mutations. In this work, we compared the results obtained by both methods for mutation detection and variant allele frequency (VAF) estimation of mutated vs. normal alleles. The sensitivity and specificity of our diagnostic system were also evaluated. It was found that AS-PCR gives reliable results at VAF up to 0.01%. AS-PCR has high sensitivity and may serve as an alternative for the more time-consuming NGS in some cases, as well as for monitoring CML treatment and for analyzing archival material. Full article
(This article belongs to the Special Issue Cancer Diagnosis and Treatment: Exploring Molecular Research)
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16 pages, 1844 KiB  
Article
Exploring the Potential of Optical Genome Mapping in the Diagnosis and Prognosis of Soft Tissue and Bone Tumors
by Alejandro Berenguer-Rubio, Esperanza Such, Neus Torres Hernández, Paula González-Rojo, Álvaro Díaz-González, Gayane Avetisyan, Carolina Gil-Aparicio, Judith González-López, Nicolay Pantoja-Borja, Luis Alberto Rubio-Martínez, Soraya Hernández-Girón, María Soledad Valera-Cuesta, Cristina Ramírez-Fuentes, María Simonet-Redondo, Roberto Díaz-Beveridge, Carolina de la Calva, José Vicente Amaya-Valero, Cristina Ballester-Ibáñez, Alessandro Liquori, Francisco Giner and Empar Mayordomo-Arandaadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2025, 26(6), 2820; https://doi.org/10.3390/ijms26062820 - 20 Mar 2025
Viewed by 570
Abstract
Sarcomas are rare malignant tumors of mesenchymal origin with a high misdiagnosis rate due to their heterogeneity and low incidence. Conventional diagnostic techniques, such as Fluorescence In Situ Hybridization (FISH) and Next-Generation Sequencing (NGS), have limitations in detecting structural variations (SVs), copy number [...] Read more.
Sarcomas are rare malignant tumors of mesenchymal origin with a high misdiagnosis rate due to their heterogeneity and low incidence. Conventional diagnostic techniques, such as Fluorescence In Situ Hybridization (FISH) and Next-Generation Sequencing (NGS), have limitations in detecting structural variations (SVs), copy number variations (CNVs), and predicting clinical behavior. Optical genome mapping (OGM) provides high-resolution genome-wide analysis, improving sarcoma diagnosis and prognosis assessment. This study analyzed 53 sarcoma samples using OGM. Ultra-high molecular weight (UHMW) DNA was extracted from core and resection biopsies, and data acquisition was performed with the Bionano Saphyr platform. Bioinformatic pipelines identified structural variations, comparing them with known alterations for each sarcoma subtype. OGM successfully analyzed 62.3% of samples. Diagnostic-defining alterations were found in 95.2% of cases, refining diagnoses and revealing novel oncogenic and tumor suppressor gene alterations. The challenges included DNA extraction and quality issues from some tissue samples. Despite these limitations, OGM proved to be a powerful diagnostic and predictive tool for bone and soft tissue sarcomas, surpassing conventional methods in resolution and scope, enhancing the understanding of sarcoma genetics, and enabling better patient stratification and personalized therapies. Full article
(This article belongs to the Special Issue Cancer Diagnosis and Treatment: Exploring Molecular Research)
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22 pages, 41503 KiB  
Article
BAMBI Is a Prognostic Biomarker Associated with Macrophage Polarization, Glycolysis, and Lipid Metabolism in Hepatocellular Carcinoma
by Huijie Gao, Cuimin Hu, Qing Wu and Zhongze Fang
Int. J. Mol. Sci. 2024, 25(23), 12713; https://doi.org/10.3390/ijms252312713 - 26 Nov 2024
Viewed by 1140
Abstract
Hepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide. Affected patients have poor prognoses due to high rates of post-surgical recurrence and metastasis. Bone morphogenetic protein and activin membrane-bound inhibitor (BAMBI) reportedly contributes to the development and progression of [...] Read more.
Hepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide. Affected patients have poor prognoses due to high rates of post-surgical recurrence and metastasis. Bone morphogenetic protein and activin membrane-bound inhibitor (BAMBI) reportedly contributes to the development and progression of various human cancers. Thus far, there have been no comprehensive studies regarding the expression of BAMBI in HCC; similarly, no studies have investigated the prognostic significance of BAMBI and its associated mechanisms in HCC. In this study, we analyzed the expression profiles of BAMBI, along with its contributions to pathological findings, metastasis characteristics, and prognosis, in multiple human cancers. We found that upregulation of BAMBI was associated with poor prognosis in HCC. Next, we explored the associations of BAMBI with multiple cell signaling pathways, immune cells, and immune checkpoints in HCC. The results showed that BAMBI was associated with tumor proliferation, epithelial–mesenchymal transition (EMT) markers, glycolysis, fatty acid biosynthesis and degradation pathways, and immune checkpoint regulation in HCC. In vitro and in vivo experiments showed that BAMBI promoted polarization of M1 macrophages and is linked to the expression of key genes involved in glycolipid metabolism. Furthermore, protein–protein interaction analysis suggested that BAMBI plays multiple roles in HCC by regulating genes in the transforming growth factor (TGF)-β and Wnt signaling pathways. Our findings elucidated that BAMBI is a prognostic biomarker and is associated with macrophage polarization, glycolysis, and lipid metabolism in HCC. Full article
(This article belongs to the Special Issue Cancer Diagnosis and Treatment: Exploring Molecular Research)
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Review

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27 pages, 2453 KiB  
Review
Integrins in Cancer Drug Resistance: Molecular Mechanisms and Clinical Implications
by Yoshinobu Kariya and Michiru Nishita
Int. J. Mol. Sci. 2025, 26(7), 3143; https://doi.org/10.3390/ijms26073143 - 28 Mar 2025
Viewed by 286
Abstract
It is estimated that between 80 and 90% of mortality in cancer patients is directly or indirectly related to drug resistance. Consequently, overcoming drug resistance represents a significant challenge in the treatment of cancer. Integrins are transmembrane adhesion molecules that facilitate the linkage [...] Read more.
It is estimated that between 80 and 90% of mortality in cancer patients is directly or indirectly related to drug resistance. Consequently, overcoming drug resistance represents a significant challenge in the treatment of cancer. Integrins are transmembrane adhesion molecules that facilitate the linkage between the extracellular matrix (ECM) and the cytoskeleton, thereby enabling the activation of various cellular signaling pathways. Integrins are highly expressed in various cancers and contribute to cancer progression through invasion and metastasis. In addition, recent studies have revealed that integrins play a pivotal role in the development of drug resistance in cancer. This review will first provide an overview of integrin function and classification. It then discusses recent advances in understanding how integrins contribute to drug resistance in cancer, with a focus on ECM, drug transporters, the epithelial-to-mesenchymal transition (EMT), cancer stemness, PD-L1, and glycosylation. Finally, the potential applications of integrins as targets for therapeutic agents against drug-resistant cancers are also summarized. Full article
(This article belongs to the Special Issue Cancer Diagnosis and Treatment: Exploring Molecular Research)
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