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The Significance of Transcription Factors, miRNAs, and lncRNAs in Anticancer Drug Development, 2nd Edition

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Medicine".

Deadline for manuscript submissions: closed (31 March 2026) | Viewed by 7090

Special Issue Editors

Prof. Dr. Ru Chih C. Huang

E-Mail Website
Guest Editor
1. Department of Biology, Zanvyl Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218-2685, USA
2. National Academy of Inventors, Tampa, FL 33612, USA
3. Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
Interests: chromatin structure and function; tetra-O-methyl nordihydroguaiaretic acid (M4N, terameprocol); oncogenic development in humans; chemotherapeutic drug treatments; viral replication; gene functions
Special Issues, Collections and Topics in MDPI journals
Dr. Kotohiko Kimura

E-Mail Website
Guest Editor
Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218-2685, USA
Interests: anticancer drug; combination drug treatment; transcription factor; gene regulation; alternative splicing; cancer metabolism; mitochondria; apoptosis and hypoxia
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent progress in system biology has shown that several specific factors are part of a network functioning as a master regulator of cancer. These factors are usually transcription factors, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) in control of the expression of various genes playing important roles in the regulation of cancer development. This suggests that there may be a way to induce unfavorable effects in cancer development and progression by modulating the activity and/or expression of these specific factors. In this Special Issue, we will focus on studies that investigate the roles and mechanisms of transcription factors, miRNAs, and lncRNAs in the regulation of the expression of cancer-related genes and/or proteins and search for potential drugs that cause adverse effects against cancer by modulating the activity of these specific factors, thus manipulating the activity and/or expression of various cancer-related genes and/or proteins. In other words, this Special Issue focuses on the effort to discover potentially effective anticancer drugs by targeting transcription factors, miRNAs, and lncRNAs that function as master regulators of cancer.

You can read the publications in the first volume of our Special Issue at https://www.mdpi.com/journal/cimb/special_issues/X459J1D74V.

Prof. Dr. Ru Chih C. Huang
Dr. Kotohiko Kimura
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 250 words) can be sent to the Editorial Office for assessment.

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. Current Issues in Molecular Biology 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 2200 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

  • transcription factors
  • microRNAs (miRNAs)
  • long non-coding RNAs (lncRNAs)
  • anticancer drugs
  • cancer
  • coactivators

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Published Papers (4 papers)

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Research

13 pages, 1002 KB  
Article
Novel lncRNA Signature (UFC1/PTENP1) as a Molecular Biomarker for the Diagnosis and Prognosis of Hepatocellular Carcinoma in an Egyptian Cohort
by Marwa Hassan, Lobna Abdelsalam, Amal Kotb Behery and Rania Fathy Elnahas
Curr. Issues Mol. Biol. 2026, 48(4), 360; https://doi.org/10.3390/cimb48040360 - 29 Mar 2026
Viewed by 450
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of gene expression and play critical roles in cancer-related signaling networks. Dysregulation of antagonistic lncRNAs may contribute to hepatocarcinogenesis and disease progression. This study investigated the clinical significance and predictive value of two biologically antagonistic lncRNAs, [...] Read more.
Long non-coding RNAs (lncRNAs) are key regulators of gene expression and play critical roles in cancer-related signaling networks. Dysregulation of antagonistic lncRNAs may contribute to hepatocarcinogenesis and disease progression. This study investigated the clinical significance and predictive value of two biologically antagonistic lncRNAs, UFC1 and PTENP1, as circulating biomarkers for hepatocellular carcinoma (HCC) in an Egyptian cohort. Expression levels of these lncRNAs were quantified in 100 HCC patients and 100 age- and sex-matched healthy controls. UFC1 was significantly upregulated (~2.9-fold), while PTENP1 was markedly downregulated (~4-fold) in HCC patients, with a strong inverse correlation (r = −0.609, p < 0.001). Both lncRNAs demonstrated higher diagnostic accuracy compared to alpha-fetoprotein (AFP); combining them with AFP further enhanced overall performance. UFC1 expression was increased progressively with advancing fibrosis grade and Barcelona Clinic Liver Cancer (BCLC) stage, while PTENP1 levels diminished with BCLC stage. Logistic regression confirmed UFC1 as an independent risk factor and PTENP1 as a protective factor for HCC. In conclusion, the blood-based UFC1/PTENP1 panel exhibits promising diagnostic accuracy and is associated with disease severity, surpassing AFP. Their fibrosis-associated dysregulation suggests a role in early hepatocarcinogenesis. This antagonistic lncRNA signature represents a potential, non-invasive tool for HCC detection and risk stratification, meriting further clinical validation. Full article
(This article belongs to the Special Issue The Significance of Transcription Factors, miRNAs, and lncRNAs in Anticancer Drug Development, 2nd Edition)
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21 pages, 4447 KB  
Article
The Construction of ceRNA Regulatory Network Unraveled Prognostic Biomarkers and Repositioned Drug Candidates for the Management of Pancreatic Ductal Adenocarcinoma
by Busra Aydin, Keziban Okutan, Ozge Onluturk Aydogan, Raghu Sinha and Beste Turanli
Curr. Issues Mol. Biol. 2025, 47(7), 496; https://doi.org/10.3390/cimb47070496 - 27 Jun 2025
Viewed by 1552
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancer types due to its late diagnosis, low survival rates, and high frequency of metastasis. Considering the molecular mechanism of PDAC development has not been fully elucidated, this study aimed to shed more [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancer types due to its late diagnosis, low survival rates, and high frequency of metastasis. Considering the molecular mechanism of PDAC development has not been fully elucidated, this study aimed to shed more light on the molecular regulatory signatures of circular RNAs (circRNAs) in PDAC progression and provide a different perspective to identify potential biomarkers as well as discover candidate repositioned drug molecules for the prevention or treatment of PDAC with network-based integrative analysis. The mRNA, miRNA, and circRNA expression profiles of PDAC were obtained from nine microarray datasets. Differentially expressed genes (DEGs), microRNAs (DEmiRNAs), and circular RNAs (DEcircRNAs) were identified. The competing endogenous RNA (ceRNA; DEG–DEmiRNA–DEcircRNA) regulatory network was constructed, which included 12 DEcircRNAs, 64 DEGs, and 6 miRNAs specific to PDAC. The ADAM12, MET, QKI, SEC23A, and ZEB2 were identified as hub genes and demonstrated significant survival probability for PDAC. In addition to providing novel biomarkers for diagnosis that can be detected non-invasively, the secretion levels of hub genes-associated proteins were found in plasma, serum, and oral epithelium. The drug repositioning analysis revealed vorinostat, meclocycline sulfosalicylate, and trichostatin A, which exhibited significant binding affinities to the hub genes compared to their inhibitors via molecular docking analysis. Full article
(This article belongs to the Special Issue The Significance of Transcription Factors, miRNAs, and lncRNAs in Anticancer Drug Development, 2nd Edition)
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23 pages, 2076 KB  
Article
Regulatory Roles of miR-155-5p, miR-21-5p, miR-93-5p, and miR-140-5p in Breast Cancer Progression
by Mai S. Degheidy, Amany A. Abou-Elalla, Mahmoud M. Kamel, Shaimaa Abdel-Ghany, Borros Arneth and Hussein Sabit
Curr. Issues Mol. Biol. 2025, 47(5), 377; https://doi.org/10.3390/cimb47050377 - 20 May 2025
Cited by 8 | Viewed by 2743
Abstract
Breast cancer (BC) remains the leading cause of cancer-related morbidity and mortality worldwide, necessitating innovative approaches to improve diagnosis, prognosis, and treatment. This case-control study, aimed to evaluate the expression profiles of specific microRNAs (miRNAs)—miR-155-5p, miR-21-5p, miR-93-5p, and miR-140-5p—in 50 female BC patients [...] Read more.
Breast cancer (BC) remains the leading cause of cancer-related morbidity and mortality worldwide, necessitating innovative approaches to improve diagnosis, prognosis, and treatment. This case-control study, aimed to evaluate the expression profiles of specific microRNAs (miRNAs)—miR-155-5p, miR-21-5p, miR-93-5p, and miR-140-5p—in 50 female BC patients treated with paclitaxel (PTX) compared to 50 healthy controls. miRNA expression was analyzed using qPCR. The study revealed significant up regulation of these miRNAs in BC patients, with miR-155-5p and miR-21-5p demonstrating the highest diagnostic accuracy (AUC = 0.890 and 0.863, respectively). These miRNAs are implicated in key oncogenic processes, including tumor growth, angiogenesis, metastasis, and chemoresistance, highlighting their potential as non-invasive biomarkers for BC diagnosis and prognosis. Additionally, the study identified significant differences in demographic and biochemical parameters between BC patients and controls, such as lower hemoglobin and RBC counts in patients, indicative of cancer-related anemia, and elevated AST levels. The findings underscore the importance of miRNAs in BC biology and their potential to guide personalized therapeutic strategies. Validation in larger cohorts is recommending and exploring miRNA-based interventions to improve patient outcomes and overcome chemoresistance in BC. Full article
(This article belongs to the Special Issue The Significance of Transcription Factors, miRNAs, and lncRNAs in Anticancer Drug Development, 2nd Edition)
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19 pages, 2190 KB  
Article
Evaluation of the Expression of IDO and PTEN in Human Kidney Cancer
by Gábor Kónya, Zsuzsanna Szabó, Nikoletta Dobos, József Király, Krisztián Szegedi, Anna Vass, Ákos Steli, Csaba Szász, Balázs Dezső, Barbara Zsebik and Gábor Halmos
Curr. Issues Mol. Biol. 2025, 47(5), 359; https://doi.org/10.3390/cimb47050359 - 13 May 2025
Cited by 1 | Viewed by 1863
Abstract
Immunotherapy has become one of the primary forms of cancer treatment. The inhibition of immune checkpoint molecules, including indoleamine 2,3-dioxygenase (IDO), is a promising approach for immunotherapy. Phosphatase and tensin homolog (PTEN) is well known as a tumor suppressor that antagonizes oncogenic signaling [...] Read more.
Immunotherapy has become one of the primary forms of cancer treatment. The inhibition of immune checkpoint molecules, including indoleamine 2,3-dioxygenase (IDO), is a promising approach for immunotherapy. Phosphatase and tensin homolog (PTEN) is well known as a tumor suppressor that antagonizes oncogenic signaling molecules/pathways and plays a key role in the prognosis and (immuno)therapy of the disease. In this study, twenty healthy and tumorous renal tissue pairs were investigated, and the mRNA (RT-qPCR) and protein (Western blot) expression of IDO and PTEN were analyzed. In two cancer cell lines (CAKI-2; A-498), the protein of IDO and PTEN was measured followed by IDO induction with interferon alpha-2 (IFN-α2). According to our results, a significantly higher mRNA expression of IDO and PTEN was found in tumorous tissues compared to the adjacent healthy kidney specimens. The mRNA expression of IDO and PTEN showed a positive correlation in 80% of the sample pairs. Western blot results confirmed the protein expression of both IDO and PTEN. In the cell lines, immunocytochemistry showed that IDO is inducible with IFN-α2. In summary, our results suggest that IDO expression may play a role in the development of renal cancer, and IDO as well as PTEN might be potential biomarkers for patients with RCC. Full article
(This article belongs to the Special Issue The Significance of Transcription Factors, miRNAs, and lncRNAs in Anticancer Drug Development, 2nd Edition)
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