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25th Anniversary of IJMS: Updates and Advances in Molecular Biology

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 January 2026) | Viewed by 9001

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Prof. Dr. Irmgard Tegeder

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Pharmazentrum Frankfurt, Department of Clinical Pharmacology, Goethe-University of Frankfurt, Theodor Stern Kai 7, Bd. 74, 4th Fl, 60590 Frankfurt am Main, Germany
Interests: nerve injury and neuropathic pain; neuroinflammation; glioblastoma; traumatic brain injury; redox signaling; endocannabinoids; lipidome and metabolome; progranulin; autophagy; neuropsychiatric diseases
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Dr. Antonio Ieni

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Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, Section of Pathology, University of Messina, 98125 Messina, Italy
Interests: molecular biology; pathology; epidermal growth factor receptors family; cancer
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Prof. Dr. Costantino Balestra

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Environmental, Occupational & Ageing Physiology Laboratory, Haute Ecole Bruxelles-Brabant (HE2B), Brussels, Belgium
Interests: integrative physiology; oxygen; challenging environments; hyperbaric; hypobaric; hyperoxia; hypoxia; normobaric oxygen paradox
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Special Issue Information

Dear Colleagues,

The last two decades have marked a revolutionary period in molecular biology, with foundational discoveries rapidly translating into clinical applications that are fundamentally reshaping our approach to complex human diseases. This Special Issue aims to bring together a collection of high-impact research and review articles that highlight the leading edge of molecular biology as it applies to oncology, (auto)immune diseases, and infectious diseases. We invite the submission of manuscripts that detail the profound impact of molecular techniques on personalized oncology. This includes research on the expanding applications of next-generation sequencing (NGS), including single-cell "omics" and the clinical utility of liquid biopsies for early cancer detection, prognostic stratification, and the real-time monitoring of therapeutic resistance. Furthermore, we encourage contributions that explore the frontier of molecular therapeutics, such as the application of CRISPR-Cas9 gene editing, RNAi-based strategies, and other innovations in cellular engineering aimed at creating curative cancer treatments.

In parallel, our understanding of immune disorders is being redefined through molecular investigation. We are seeking contributions that highlight the use of genome-wide association studies (GWAS) and other omics technologies in identifying genetic susceptibilities and disease-specific pathways. Of particular interest is research focused on the discovery and validation of novel molecular biomarkers for more precise diagnostics and the development of targeted therapies. This includes work on the role of immunogenetics, such as HLA genotyping, in predicting disease risk and tailoring patient treatment. The field of infectious diseases has also been fundamentally altered by molecular diagnostics, which have become a cornerstone of modern epidemiology. This Special Issue will welcome papers on the development of advanced diagnostic platforms, from refined PCR-based methods to the emergence of highly specific CRISPR-based tools for pathogen detection. We also solicit research leveraging NGS for pathogen or microbiome genomics, which is critical for robust epidemiological surveillance, tracking antimicrobial resistance, and achieving a deeper understanding of host-pathogen interactions at the molecular level. By bringing these interconnected fields together, this Special Issue will serve as an essential resource for clinicians and researchers, providing a comprehensive overview of the current and future state of molecularly informed medicine.

Prof. Dr. Irmgard Tegeder
Dr. Antonio Ieni
Prof. Dr. Costantino Balestra
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

next-generation sequencing (NGS)
CRISPR-Cas9
liquid biopsy
molecular diagnostics
personalized medicine
genome-wide association studies (GWAS)

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Published Papers (10 papers)

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Research

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14 pages, 2396 KB

Open AccessArticle

Prolonged Sample Storage Reshapes the m⁶A Methylation Landscape Through RNA Degradation

by Lingsong Yao, Zhiyu Liu, Ying Wang, Yuwei Yang, Yuqi Sheng, Qinyu Ge and Yunfei Bai

Int. J. Mol. Sci. 2026, 27(8), 3517; https://doi.org/10.3390/ijms27083517 - 15 Apr 2026

Viewed by 392

Abstract

N⁶-methyladenosine (m⁶A) is the most common internal modification in eukaryotic mRNA, essential for post-transcriptional regulation. MeRIP-seq is widely used for m⁶A profiling, but RNA degradation challenges accurate analysis. While the effects of sample handling on RNA are known, the impact of tissue sample storage durations on m⁶A remains unclear. We investigated how sample storage durations (0, 2, 12, 24, and 48 h at room temperature) affect RNA integrity, m⁶A peaks, and transcriptomes in mouse liver. RNA integrity declined with time, reducing m⁶A peak number and reproducibility. Prolonged storage diverged m⁶A profiles, increased unreported peaks, shifted RRACH motifs, and redistributed peaks to intergenic/intronic regions. Integrated data showed opposing changes in m⁶A and expression for some genes, suggesting storage degradation confounds epitranscriptomic interpretation. Sample storage durations are critical for m⁶A accuracy, emphasizing the need for standardized handling in MeRIP-seq studies. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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11 pages, 2508 KB

Open AccessArticle

Clinical Value of Neutrophil Gelatinase-Associated Lipocalin as a Non-Invasive Biomarker for Intestinal Ulcer in Behçet’s Syndrome: A Pilot Study

by Jing-Fen Ye, Yi-Xuan Zhang, Dan Hu, Jian-Fei Cai, Yu-Xin Liu, Li-Yang Zhang, Jun Zou and Jian-Long Guan

Int. J. Mol. Sci. 2026, 27(7), 3152; https://doi.org/10.3390/ijms27073152 - 31 Mar 2026

Viewed by 546

Abstract

Intestinal Behçet’s syndrome (BS) is a severe phenotype associated with high morbidity and mortality. Early identification of intestinal involvement in BS remains clinically challenging due to the lack of reliable biomarkers. Neutrophil gelatinase-associated lipocalin (NGAL) is abundantly secreted during intestinal inflammation and has been recognized as a promising inflammatory biomarker. This study was designed to investigate the clinical value of NGAL for predicting intestinal involvement in BS patients. BS patients who underwent colonoscopy for suspected intestinal lesions were enrolled and classified into intestinal BS and non-intestinal BS groups. Immunohistochemistry was performed to compare colonic mucosal NGAL expression among intestinal BS, non-intestinal BS, inflammatory bowel disease (IBD) patients, and healthy controls. Serum and fecal NGAL levels were also measured in intestinal BS, non-intestinal BS, and healthy controls. Intestinal mucosal NGAL expression was significantly elevated in both intestinal BS and IBD patients, with no significant difference between the two groups. Serum and fecal NGAL levels were both higher in intestinal BS patients than in healthy controls. Notably, only fecal NGAL was significantly increased in intestinal BS compared to non-intestinal BS (p < 0.001). Multivariate logistic regression analysis identified fecal NGAL as an independent predictive factor for intestinal involvement in BS (OR = 1.093, 95% CI: 1.017–1.174, p = 0.015), with superior predictive performance over conventional inflammatory markers. In conclusion, fecal NGAL serves as a non-invasive and promising biomarker for risk stratification of intestinal involvement in BS patients. Further large-scale prospective studies are required to verify these preliminary results. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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13 pages, 2340 KB

Open AccessArticle

Microbiome-Derived Indole-3-Lactic Acid Attenuates Cutibacterium Acnes-Induced Inflammation via the Aryl Hydrocarbon Receptor Pathway

by Sang Gyu Lee, Nam Hao Chau, Seoyoon Ham, Yujin Baek, Ngoc Ha Nguyen, Seon Hwa Kim and Young In Lee

Int. J. Mol. Sci. 2026, 27(3), 1131; https://doi.org/10.3390/ijms27031131 - 23 Jan 2026

Viewed by 1014

Abstract

Acne vulgaris is a chronic inflammatory dermatosis where conventional therapies often face limitations in efficacy and safety, necessitating the development of microbiome-targeted interventions. This study investigated the immunomodulatory potential of microbiome-derived tryptophan metabolites as a novel therapeutic strategy for Cutibacterium acnes (C. acnes)-induced inflammation, focusing on the aryl hydrocarbon receptor (AHR) pathway. We evaluated indole-3-lactic acid (ILA), indole-3-acrylic acid (IAA), and indole-3-propionic acid (IPA) in comparison to tapinarof, utilizing C. acnes-stimulated human epidermal keratinocytes and a C. acnes-induced acne mouse model. In vitro, ILA and IPA significantly suppressed C. acnes-driven inflammatory mediators, including Tumor Necrosis Factor-alpha (TNF-α), Interleukin (IL)-1β, and Cyclooxygenase-2 (COX2), whereas IAA demonstrated limited efficacy. In vivo, ILA treatment exhibited superior therapeutic activity, markedly reducing inflammatory cell infiltration, epidermal hyperplasia, and IL-1β expression. Transcriptomic analysis confirmed that ILA attenuates inflammatory signaling (e.g., IL-17 and TNF pathways) while upregulating AHR-responsive genes such as Cytochrome (CYP) 1A1 and CYP1B1. Collectively, these findings establish ILA as a potent postbiotic that mitigates cutaneous inflammation through selective activation of the AHR. Future studies should prioritize the clinical translation of ILA-based topical formulations, with rigorous evaluation of their efficacy and safety in well-designed human trials, to support their development as a non-antibiotic therapeutic alternative for acne management. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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22 pages, 8687 KB

Open AccessArticle

Monopolar Radiofrequency for Facial Hyperpigmentation Treatment: An Integrated Retrospective Clinical Trial and Ex Vivo Study

by Yujin Baek, Ngoc Ha Nguyen, Seoyoon Ham, Wanjin Kim, Ju Hee Lee and Young In Lee

Int. J. Mol. Sci. 2026, 27(2), 761; https://doi.org/10.3390/ijms27020761 - 12 Jan 2026

Cited by 1 | Viewed by 1659

Abstract

Aging-associated facial hyperpigmentation is driven not only by enhanced melanogenesis but also by dermal senescence and deterioration of the dermal–epidermal junction. The purpose of this study was to evaluate whether monopolar radiofrequency (MRF) monotherapy can improve aging-related facial hyperpigmentation by simultaneously suppressing melanogenic signaling and restoring senescence-associated dermal alterations. We assumed that deep dermal heating induced by MRF would modulate fibroblast senescence and basement membrane integrity, thereby indirectly regulating melanocyte activity. In a retrospective review of 26 Asian women, MRF treatment significantly decreased multiple pigmentation parameters, including melanin level, hyperconcentration, and Hemi Melasma Area and Severity Index (hemi-MASI) scores, while concurrently reducing wrinkles, pores, and enhanced overall skin texture without inducing inflammation. Complementary ex vivo experiments using ultraviolet B (UVB)-irradiated human skin demonstrated that MRF markedly reduced pro-melanogenic markers (α-MSH, MC1R, MITF, TYR, TRP1/2), restored collagen type IV expression at the basement membrane, decreased senescence-associated genes (p16, p21), and upregulated protective heat shock proteins (HSP70/47). Together, these findings suggest that MRF improves aging-associated hyperpigmentation by both suppressing melanogenesis and rejuvenating the senescent dermal microenvironment. MRF may serve as an effective non-invasive treatment option for pigmentation disorders in aging skin. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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21 pages, 2670 KB

Open AccessArticle

Analysis of Photosynthetic Parameters, Yield, and Quality Correlations in Herbicide-Tolerant Transgenic Hybrid Cotton

by Ping He, Meiqi Liu, Haoyu Jiang, Zexing Zhang, Zitang Bian, Yongqiang Liu, Honglei Ma, Jianbo Zhu, Tianqi Jiao and Ruina Liu

Int. J. Mol. Sci. 2026, 27(1), 400; https://doi.org/10.3390/ijms27010400 - 30 Dec 2025

Cited by 1 | Viewed by 488

Abstract

Weed stress remains a major limiting factor in cotton production, and glyphosate-tolerant varieties provide an effective solution for chemical weed control. However, achieving a balance between herbicide tolerance and agronomic physiological traits remains challenging. In this study, three hybrid combinations were generated by crossing a glyphosate-tolerant cotton line (GGK2) with conventional elite lines and were comprehensively evaluated. Gene expression analysis revealed that the classical detoxification gene GAT was significantly downregulated in all hybrid combinations, whereas the expression of GR79-EPSPS, a gene associated with glutathione metabolism and oxidative stress response, was markedly elevated, particularly in the GGK2 × Y4 combination. This differential expression pattern suggests that GR79-EPSPS may compensate for the reduced function of GAT by conferring oxidative protection under herbicide stress. Physiological determination indicated that hybrid combinations with enhanced GR79-EPSPS expression, especially GGK2 × Y5, exhibited superior photosynthetic pigment composition and photosystem II (PSII) efficiency, validating the role of GR79-EPSPS in maintaining photosynthetic stability. Agronomic trait assessment demonstrated that GGK2 × Y4 achieved significant biomass accumulation and yield improvement through heterosis, although fiber quality improvement was limited. This study effectively enhanced the herbicide resistance of conventional cotton through crossbreeding and revealed that the interaction between GR79-EPSPS and GAT can improve cotton tolerance to herbicides, thereby providing a breeding strategy for developing cotton varieties with both herbicide tolerance and superior agronomic traits. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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18 pages, 14663 KB

Open AccessArticle

A High-Multiplicity Baculovirus Method Enables Efficient Gene Delivery to Diverse Mammalian Cells In Vitro and to Multiple Organs In Vivo

by Min-Hsiu Wu, Song-Tay Lee, Tsung-Hsien Chang, Wei-Sheng Chao, Nan-Kai Lin and Shoa-Lin Lin

Int. J. Mol. Sci. 2026, 27(1), 389; https://doi.org/10.3390/ijms27010389 - 30 Dec 2025

Cited by 1 | Viewed by 609

Abstract

Recombinant baculovirus vectors are recognized as effective gene delivery systems for mammalian cells in vitro. However, their application in vivo has been limited due to inactivation by the host’s complement system. We developed a recombinant baculoviral vector derived from Autographa californica multiple nucleopolyhedrovirus (AcMNPV), incorporating both CMV-IE and polyhedron promoter-driven green fluorescence protein (EGFP) (vAcMBac-CMV-IE-EGFP). We then evaluated the transduction efficiency and safety of vAcMBac-CMV-IE-EGFP at a high multiplicity of infection (MOI) across five distinct cell lines and in Sprague Dawley (SD) rats. In vitro, Sf9, HepG2, and Vero E6 cells showed high transduction rates (95.52 ± 4.86%, 80.53 ± 3.31%, and 80.87 ± 2.50%, respectively), significantly outperforming the other cell types tested, and cell viability remained largely unaffected even at an MOI of 1000. In vivo, EGFP expression was observed in the heart, liver, spleen, lungs, and kidneys of SD rats after tail vein injection. Direct injection of vAcMBac-CMV-IE-EGFP into the rat striatum also resulted in strong EGFP signals in neural tissues. These results demonstrate that a high-MOI baculovirus infection can serve as a remarkably efficient and versatile platform for gene delivery across diverse mammalian cell types as well as in various organs and neural tissues in animal models. This robust method might hold significant promise for future gene therapy applications. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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18 pages, 1526 KB

Open AccessArticle

Searching for Innovative Functional Foods: Correlation Between Chemopreventive Potential and Bioactive Compounds Accumulation in Brassica Sprouts Grown Under Altered Gravity Conditions

by Marta Markiewicz, Agnieszka Galanty, Paweł Zagrodzki, Agata Kołodziejczyk and Paweł Paśko

Int. J. Mol. Sci. 2025, 26(23), 11287; https://doi.org/10.3390/ijms262311287 - 22 Nov 2025

Viewed by 694

Abstract

The main aim of this study was to evaluate the effect of space-like environment on the chemopreventive activity of Brassica sprouts against thyroid cancer cells in vitro. For this purpose the sprouts of broccoli, kale, kohlrabi, and Brussels sprouts were cultivated in darkness and in microgravity for 5–7 days. Then, the sprouts’ extracts were examined for cytotoxic and antiproliferative activity against thyroid cancer and normal cells. The tested microgravity environment stimulated the cytotoxic activity of kohlrabi sprouts, causing approximately 50% reduction in thyroid cancer cells’ viability, while at the same time increasing the viability of normal thyroid cells. Broccoli sprouts showed the strongest antiproliferative activity against normal thyroid cells, with the best effect visible for darkness conditions, which may contribute to the reduction of thyroid hyperplasia. Microgravity and darkness significantly enhanced the antiproliferative activity of kale, especially in 7-day-old sprouts (inhibition approximately 90%). The tested conditions also increased the antiproliferative activity of kohlrabi sprouts, but in the case of Brussels sprouts the effect was unfavorable. The study showed that microgravity and darkness conditions may have significant influence on the chemopreventive role of Brassica sprouts against thyroid cancer cells in vitro, especially in the case of broccoli and kohlrabi sprouts. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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13 pages, 1502 KB

Open AccessArticle

Transcription Factor EB (TFEB) Expression and Localization in the Third-Trimester Placenta

by Cinzia Giacometti, Alessandro Ambrosi, Serena Cavaliere, Anna Caliò, Daniele Mautone and Guido Martignoni

Int. J. Mol. Sci. 2025, 26(21), 10294; https://doi.org/10.3390/ijms262110294 - 22 Oct 2025

Viewed by 966

Abstract

Transcription factor EB (TFEB) is expressed at high levels in the trophoblast cells of the placenta, where it plays a critical role in regulating normal vascularization. Preeclampsia (PE) is a severe complication of pregnancy with a high incidence of maternal and fetal morbidity and mortality. Gestational diabetes (GD) is a metabolic disease that can affect placental villous maturation and villous vascularity. We analyzed the expression of three different antibodies: TFEB from Invitrogen (TFEB-INV), which detects endogenous levels of TFEB only when phosphorylated at Ser211; TFEB from Bethyl Labs (TFEB-B), which recognizes and binds E-box sequences; and TFEB from Santa Cruz (C-6) (TFEB-SC), which is specifically used for epitope mapping between 440 and 470. We evaluated the presence/absence of TFEB in six placental districts: syncytiotrophoblast (STB), cytotrophoblast (CTB), extravillous trophoblast (EVT), syncytial knots, stem villi vessels, and villous capillaries. TFEB-B was significantly expressed in the stem villi vessels, STB, and villi vessels of GD cases. The lack of TFEB expression in late-onset PE appears to corroborate the role of TFEB in vascular remodeling during placental development. The positive results in STB and vessels in GD cases, regardless of the histological diagnosis, may suggest that the expression of TFEB mitigates hypoxic injury via the Akt/mTOR pathway. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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Review

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20 pages, 1601 KB

Open AccessReview

Targeting DYRKs in Cardiovascular Diseases: From Biological Mechanisms to Therapeutic Translation

by Long Jiang, Siyu Peng, Junchen Ma, Tingfei Liu, Xiaoru Long, Lin Li and Huaying Wu

Int. J. Mol. Sci. 2026, 27(8), 3456; https://doi.org/10.3390/ijms27083456 - 12 Apr 2026

Viewed by 592

Abstract

Cardiovascular diseases (CVDs) remain the leading cause of mortality globally, characterized by myocardial injury, pathological structural remodeling, and progressive deterioration of cardiac function. Clinical manifestations include post-infarct functional impairment, pathological cardiac hypertrophy, interstitial fibrosis, malignant arrhythmias, and end-stage heart failure. Although the dual-specificity tyrosine-regulated kinase (DYRK) family has been extensively investigated in cancer and neurodegenerative disorders, emerging evidence highlights DYRKs as critical upstream regulators in a wide spectrum of cardiovascular pathological processes. However, current research is largely confined to individual isoforms or isolated signaling pathways, lacking systematic integration of isoform-specific functions, dose- and spatiotemporal-dependent effects, as well as bidirectional regulatory roles in chronic cardiac remodeling. This review systematically summarizes the molecular mechanisms of the DYRK family across major cardiovascular disease models, with particular emphasis on the functional specificity of distinct DYRK isoforms and their translational potential as therapeutic targets. We further provide an integrated theoretical framework to facilitate the development of isoform-selective, context-dependent precision therapies for cardiovascular diseases. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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26 pages, 1552 KB

Open AccessReview

The Influences of RARγ on the Behavior of Normal and Cancer Stem Cells

by Geoffrey Brown

Int. J. Mol. Sci. 2026, 27(3), 1291; https://doi.org/10.3390/ijms27031291 - 28 Jan 2026

Cited by 1 | Viewed by 869

Abstract

Retinoic acid receptor (RARγ) mRNA is expressed spatially and temporally during mouse embryogenesis and largely within stem and progenitor cells, indicating a role in organ formation. RARγ agonism promoted the maintenance of hematopoietic stem cells, and blocked stem cell development as shown for hematopoiesis, zebrafish development, and chondrogenesis. Transgene expression enhanced the generation of induced pluripotent stem cells, indicating a role in ground-state pluripotency. RARγ is oncogenic in acute myeloid leukemia, cholangiocarcinoma, and colorectal, head and neck, hepatocellular, ovarian, pancreatic, prostate, and renal cancers. RARγ agonism or overexpression enhanced the proliferation of cancer cells. Conversely, antagonism or inhibition of all-trans retinoic acid synthesis led to the death of cancer cells including cancer stem cells. The pathways regulated by RARγ, via canonical activation and repression of gene expression, include Wnt/β-catenin and Notch signaling. RARγ also acts as a co-factor to Smad3 and reduced or enhanced TGFβ-driven and Smad3-mediated events when liganded and non-liganded, respectively. Collectively the findings support the view that RARγ plays a crucial role in controlling stem and progenitor cell behavior. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Biology)

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