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26 pages, 6919 KB  
Article
Reticuline and Coclaurine Exhibit Vitamin D Receptor-Dependent Anticancer and Pro-Apoptotic Activities in the Colorectal Cancer Cell Line HCT116
by Hind A. Alghamdi, Sahar S. Alghamdi, Maryam Hassan Al-Zahrani, Thadeo Trivilegio, Sara Bahattab, Rehab AlRoshody, Yazeid Alhaidan, Rana A. Alghamdi and Sabine Matou-Nasri
Curr. Issues Mol. Biol. 2025, 47(10), 810; https://doi.org/10.3390/cimb47100810 - 1 Oct 2025
Abstract
Alkaloids have garnered significant interest as potential anticancer agents. Vitamin D receptor (VDR) plays a role in preventing the progression of colorectal cancer (CRC) and may be a crucial mediator of the anticancer effects produced by certain alkaloids. The search for novel anticancer [...] Read more.
Alkaloids have garnered significant interest as potential anticancer agents. Vitamin D receptor (VDR) plays a role in preventing the progression of colorectal cancer (CRC) and may be a crucial mediator of the anticancer effects produced by certain alkaloids. The search for novel anticancer drugs that induce VDR expression and act through the VDR could improve the clinical outcomes of CRC patients. The anticancer and pro-apoptotic effects of coclaurine and reticuline were investigated using CRISPR/Cas9-edited VDR/knockout (KO) and wild-type (WT) CRC HCT116 cell lines. Western blotting, RT-qPCR, confocal microscopy, cell viability, scratch assays, and flow cytometry were employed to assess VDR expression and cellular localization, cell growth, wound-healing, cytotoxicity, apoptotic status, cell cycle progression, and VDR-mediated gene expression. Coclaurine and reticuline dose-dependently inhibited HCT116-WT cell viability, decreased wound-healing, and increased VDR nuclear localization and gene expression while downregulating the oncogenic genes SNAIL1 and SNAIL2. Both alkaloids induced late apoptosis in HCT116-WT cells, increased the cleavage of PARP and caspase-3, and upregulated Bax and TP53 while decreasing BCL-2. Both alkaloids caused HCT116-WT cell growth arrest in the S-phase, which is associated with cyclin A1 overexpression. Coclaurine and reticuline lost their anticancer effects in HCT116-VDR/KO cells. Docking studies revealed that both alkaloids occupied the VDR’s active site. These findings demonstrate that coclaurine and reticuline exert anti-CRC and pro-apoptotic activities via the VDR, suggesting them as natural therapeutic candidates. The use of in vivo CRC models is needed to validate the anticancer activities of coclaurine and reticuline. Full article
(This article belongs to the Section Bioorganic Chemistry and Medicinal Chemistry)
14 pages, 8646 KB  
Article
UCHL1 Promotes Gastric Cancer Progression by Regulating CIP2A Degradation
by Ga-ye Lee, In-ho Jeong, Byung Sik Kim, Hee-Sung Kim and Peter Chang-Whan Lee
Pharmaceuticals 2025, 18(10), 1468; https://doi.org/10.3390/ph18101468 - 29 Sep 2025
Abstract
Background: Gastric cancer is one of the most prevalent malignancies worldwide and the fourth leading cause of cancer-related mortality. Protein ubiquitination and deubiquitination regulate protein stability as post-translational modifications, playing essential roles in tumorigenesis. Although UCHL1, a deubiquitinating enzyme (DUB), is implicated in [...] Read more.
Background: Gastric cancer is one of the most prevalent malignancies worldwide and the fourth leading cause of cancer-related mortality. Protein ubiquitination and deubiquitination regulate protein stability as post-translational modifications, playing essential roles in tumorigenesis. Although UCHL1, a deubiquitinating enzyme (DUB), is implicated in the progression of several cancer types, its role in gastric cancer remains unclear. Methods: Kaplan–Meier analysis and gastric cancer patient tissues were used to assess UCHL1 expression. Cell viability assay, colony-forming assay, and transwell migration and invasion assay were performed to evaluate cell growth. Immunoprecipitation and Western blotting analyzed protein expression and interactions. Results: This study demonstrates that UCHL1 expression is markedly upregulated in gastric cancer tissues compared to normal tissues. Elevated UCHL1 expression is associated with poor patient prognosis, supporting its potential role as an oncogenic factor. Reduced UCHL1 expression suppressed cell proliferation, migration, and invasion in gastric cancer cell lines. As the underlying mechanism, we identified CIP2A, a known oncogenic regulator of c-Myc, as a downstream effector of UCHL1. UCHL1 knockdown reduced CIP2A protein levels via deubiquitination, attenuated c-Myc signaling, and decreased expression of key cell cycle regulators. Furthermore, UCHL1 knockdown significantly downregulated cyclin D1 expression, arresting the cell cycle in the G1 phase and inhibiting cell proliferation. Conclusions: Collectively, our findings reveal that UCHL1 promotes gastric cancer progression, highlighting it as a potential therapeutic target. Full article
(This article belongs to the Section Pharmacology)
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11 pages, 1809 KB  
Communication
Apoptosis, Cell Growth, and Glycogen Synthase Kinase 3β Phosphorylation in Caffeic Acid-Treated Human Malignant Melanoma Cells
by Yoon-Jin Lee, Ki Dam Kim, Min Hyuk Choi, Sukh Que Park, Yu Sung Choi, Youin Bae, Hae Seon Nam, Sang Han Lee and Moon Kyun Cho
Biomedicines 2025, 13(10), 2389; https://doi.org/10.3390/biomedicines13102389 - 29 Sep 2025
Abstract
Objectives: Caffeic acid (CA), a naturally occurring phenolic compound exhibiting antioxidant and anti-inflammatory effects, has demonstrated anticancer activity against several tumor types. Nevertheless, its involvement in melanoma and its effects on the GSK3β signaling pathway have not been fully elucidated. This study aimed [...] Read more.
Objectives: Caffeic acid (CA), a naturally occurring phenolic compound exhibiting antioxidant and anti-inflammatory effects, has demonstrated anticancer activity against several tumor types. Nevertheless, its involvement in melanoma and its effects on the GSK3β signaling pathway have not been fully elucidated. This study aimed to assess the expression of p-GSK3β in melanoma tissues and to evaluate the anti-melanoma efficacy of CA. Methods: Western blot analysis was performed to determine the expression levels of p-GSK3β in melanoma and normal skin samples. G361 melanoma cells were exposed to CA, after which cell viability, apoptotic induction, cell cycle distribution, and related signaling molecules were examined. Results: Significantly increased p-GSK3β levels were identified in melanoma tissues. CA exposure decreased cell viability, triggered apoptosis, and elevated p-GSK3β levels in G361 melanoma cells. Moreover, CA induced the upregulation of p53 and p21 while concomitantly downregulating cyclin D1 and Bcl-2. Conclusions: These results suggest that CA inhibits melanoma cell growth through activation of a pathway involving the tumor suppressor p53, rather than through modulation of GSK3β signaling. Full article
(This article belongs to the Special Issue Pathogenesis, Diagnosis and Treatment of Melanoma)
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17 pages, 1742 KB  
Article
Pinocembrin Downregulates Vascular Smooth Muscle Cells Proliferation and Migration Leading to Attenuate Neointima Formation in Balloon-Injured Rats
by Hyeonhwa Kim, Jihye Jung, Young-Bob Yu, Dong-Hyun Choi, Leejin Lim and Heesang Song
Biomolecules 2025, 15(9), 1325; https://doi.org/10.3390/biom15091325 - 17 Sep 2025
Viewed by 303
Abstract
The abnormal proliferation and migration of vascular smooth muscle cells (VSMCs) are a primary cause of cardiovascular diseases such as atherosclerosis and restenosis after angioplasty. Pinocembrin (5,7-dihydroxyflavanone, PCB), a natural flavonoid compound found abundantly in propolis, has been reported to have antibacterial, anti-inflammatory, [...] Read more.
The abnormal proliferation and migration of vascular smooth muscle cells (VSMCs) are a primary cause of cardiovascular diseases such as atherosclerosis and restenosis after angioplasty. Pinocembrin (5,7-dihydroxyflavanone, PCB), a natural flavonoid compound found abundantly in propolis, has been reported to have antibacterial, anti-inflammatory, antioxidant, and anticancer effects, and cardiac function improvement in ischemic heart disease. In this study, the protective effects of PCB against the migration and proliferation of VSMCs were investigated. MTT and BrdU assays were performed to estimate the cytotoxicity and cell proliferative activity of PCB, respectively. Rat aortic VSMC migrations and neointima formation were evaluated using wound healing, boyden chamber assays, and in balloon-injured (BI) rat, respectively. PCB suppressed the phosphorylated levels of p38 in PDGF-BB-induced VSMCs followed by reducing the expression of MMP2 and 9. PCB downregulated the expression levels of cell cycle regulatory proteins such as PCNA, CDK2, CDK4, and Cyclin D1. Furthermore, the phosphorylated levels of FAK at Y397 and Y925 sites and the expression levels of FAK-related proteins such as Integrin β1, Paxillin, Talin, and Vinculin were significantly reduced by PCB in PDGF-BB-induced VSMCs. The neointima formation was markedly decreased by PCB administration in the carotid artery of a balloon-injured rat. In conclusion, PCB inhibits the proliferation and migration of VSMCs by stimulation of PDGF-BB through the regulation of the p38 and FAK signaling pathway. Therefore, PCB may be a promising therapeutic candidate for preventing and treating cardiovascular diseases such as atherosclerosis and restenosis. Full article
(This article belongs to the Section Cellular Biochemistry)
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21 pages, 2836 KB  
Article
Single-Vesicle Molecular Profiling by dSTORM Imaging in a Liquid Biopsy Assay Predicts Early Relapse in Colorectal Cancer
by Gabriele Raciti, Giulia Cavallaro, Raffaella Giuffrida, Cristina Grange, Loredana Leggio, Marco Catania, Nunzio Iraci, Elena Bruno, Luca Antonio Giaimi, Sofia Paola Lombardo, Giulia Chisari, Marzia Mare, Enrica Deiana, Lorenzo Memeo, Benedetta Bussolati and Stefano Forte
Biomolecules 2025, 15(9), 1307; https://doi.org/10.3390/biom15091307 - 11 Sep 2025
Viewed by 441
Abstract
Background and Objectives: Colorectal cancer (CRC) is the third most diagnosed tumor type and the second leading cause of cancer-related mortality. Despite recent improvements in the clinical management of CRC patients both before and after surgery, disease recurrence remains common, with an incidence [...] Read more.
Background and Objectives: Colorectal cancer (CRC) is the third most diagnosed tumor type and the second leading cause of cancer-related mortality. Despite recent improvements in the clinical management of CRC patients both before and after surgery, disease recurrence remains common, with an incidence of about 20–30% within 5 years. Current tissue biopsy techniques are invasive and inadequate for assessing tumor heterogeneity or capturing real-time disease dynamics. In contrast, liquid biopsy offers a promising, minimally invasive alternative. This study aimed to evaluate extracellular vesicle (EV)-associated protein markers, detected through super-resolution microscopy, as potential indicators of recurrence in CRC patients. Methods: We employed a novel liquid biopsy approach based on the super-resolution imaging (dSTORM) of specific protein markers carried by EVs isolated from the plasma of CRC patients. We analyzed combinations of both surface and intravesicular proteins, including EpCAM, PD-L1, CD81, IL-6, and Cyclin D1. Results: Specific combinations of EV-associated markers were able to distinguish patients with recurrence from those without residual disease. Additionally, we observed correlations between some marker profiles and tumor stage or lymph node involvement. No association was found with mismatch repair system status. Conclusions: To our knowledge, this is the first study to propose the use of EV-bound proteins for recurrence detection in CRC using super-resolution microscopy within a liquid biopsy framework. These findings support the potential of this approach as a non-invasive tool for CRC monitoring. Full article
(This article belongs to the Special Issue Extracellular Vesicles and Their Roles in Cancer Progression)
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13 pages, 2846 KB  
Article
Insight into the Wnt Pathway in Sporadic Small Bowel Adenocarcinoma
by Takayoshi Nishimoto, Atsushi Tatsuguchi, Takeshi Yamada, Sho Kuriyama, Aitoshi Hoshimoto, Jun Omori, Naohiko Akimoto, Katya Gudis, Keigo Mitsui, Shu Tanaka, Shunji Fujimori, Tsutomu Hatori, Akira Shimizu and Masanori Atsukawa
Cancers 2025, 17(18), 2965; https://doi.org/10.3390/cancers17182965 - 10 Sep 2025
Viewed by 259
Abstract
Background/Objectives: The Wnt signaling pathway is pivotal in the adenoma–carcinoma sequence; however, its role in small bowel adenocarcinoma (SBA) remains insufficiently characterized. We analyzed the clinicopathological significance of Wnt pathway-related gene mutations and the expression of downstream or associated proteins in SBA. Methods: [...] Read more.
Background/Objectives: The Wnt signaling pathway is pivotal in the adenoma–carcinoma sequence; however, its role in small bowel adenocarcinoma (SBA) remains insufficiently characterized. We analyzed the clinicopathological significance of Wnt pathway-related gene mutations and the expression of downstream or associated proteins in SBA. Methods: Immunohistochemical staining for β-catenin, cyclin D1, c-Myc, E-cadherin, and Wnt5a was performed in 75 primary SBA surgical specimens. Targeted next-generation sequencing was conducted in 48 of these cases. Results: The genomic alterations in the Wnt pathway were identified as APC (14.6%) and CTNNB1 (8.3%), with no overlap between the two mutations. Aberrant (reduced membranous and/or nuclear) expression of β-catenin was observed in 37% of cases. Cyclin D1 and c-Myc were expressed in 60% and 41% of cases, respectively. Aberrant expression of β-catenin and/or Wnt5a was present in 60% of cases and was correlated with cyclin D1 and c-Myc expression. Mutations in APC and CTNNB1 were found in intestinal- and gastrointestinal-type SBAs, but were absent in gastric-type SBA. In intestinal-type SBA, the mutation frequency of APC and CTNNB1 was 39%, closely aligning with the 45% aberrant expression of β-catenin. Aberrant expression of β-catenin and/or Wnt5a, a ligand of the noncanonical Wnt pathway, was detected in 60% of cases and showed a correlation with both cyclin D1 and c-Myc expression. Conclusions: These findings suggest that both canonical and noncanonical Wnt pathway-related proteins are involved in SBA carcinogenesis and progression. Notably, the canonical Wnt pathway appears to play a predominant role in intestinal-type SBA. Full article
(This article belongs to the Special Issue Molecular Pathways in Cancers (2nd Edition))
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17 pages, 3933 KB  
Article
Estrogen-like Activity of Scrophularia buergeriana Root Extracts in MCF-7 Cells
by Hye-Yeong Song, Jinsu Choi, Eunwoo Jeong, Harang Park, Juyeong Moon, Min-ah Kim, Javokhir Rustamov, Hwan-Soo Yoo and Tack-Joong Kim
Biomedicines 2025, 13(9), 2151; https://doi.org/10.3390/biomedicines13092151 - 4 Sep 2025
Viewed by 484
Abstract
Background/Objectives: Estrogen deficiency-related menopause is associated with various physical and psychological symptoms. Although hormone replacement therapy (HRT) effectively alleviates these symptoms, its long-term use is associated with several side effects such as an increased risk of breast cancer and cardiovascular disease. Consequently, [...] Read more.
Background/Objectives: Estrogen deficiency-related menopause is associated with various physical and psychological symptoms. Although hormone replacement therapy (HRT) effectively alleviates these symptoms, its long-term use is associated with several side effects such as an increased risk of breast cancer and cardiovascular disease. Consequently, there is a growing interest in some plant-derived phytoestrogens that are considered safer alternatives to estrogen. Recent studies on Scrophularia buergeriana confirmed their anti-inflammatory and antioxidant properties; however, their effects on menopausal health remain unclear. Therefore, the aim of this study was to investigate the estrogen-like effects of S. buergeriana root (SB-R) extract, a potential phytoestrogen. Methods: Briefly, the MCF-7 cell line, a widely used in vitro model for assessing estrogen-like activity, was treated with SB-R extract and 17β-estradiol (E2; positive control) in the presence or absence of ICI 182,780 (Fulvestrant), an estrogen receptor antagonist. An E-screen assay and flow cytometry were performed to assess the effects of the treatments on cell proliferation and the cell cycle, respectively. Additionally, Western blotting and immunofluorescence assays were performed to elucidate the potential mechanisms underlying the estrogen-like effects of SB-R. Result: Treatment with SB-R extract promoted MCF-7 cell proliferation in a manner similar to E2. However, ICI 182,780 co-treatment inhibited the SB-R extract-induced increase in MCF-7 cell proliferation. Additionally, SB-R extract promoted cell cycle progression by increasing the proportion of cells in the S and G2/M phases. Moreover, Western blotting and immunofluorescence assays showed that SB-R extract increased the expression of estrogen receptor alpha (ERα). Furthermore, SB-R treatment activated downstream signaling pathways by enhancing AKT and ERK phosphorylation and upregulated the expression of cell cycle regulators, including cyclin D1, cyclin dependent kinase 4 (CDK4), cyclin E1, and cyclin dependent kinase 2 (CDK2). Conclusions: SB-R exhibits estrogen-like activity by activating ERα-mediated AKT and ERK pathways and thereby increasing the expression of proteins involved in cell cycle regulation. This makes it a promising phytoestrogen candidate and a safer alternative to conventional hormonal therapy for alleviating menopausal symptoms. Full article
(This article belongs to the Section Cell Biology and Pathology)
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15 pages, 2810 KB  
Article
The Anti-Tumor and Bortezomib-Sensitizing Effects of Apigenin in Multiple Myeloma
by Ye Chen, Lan Wu, Siyu Wang, Huihao Chen, Miaojun Chen, Yanfen Huang and Bin Ding
Curr. Issues Mol. Biol. 2025, 47(9), 717; https://doi.org/10.3390/cimb47090717 - 3 Sep 2025
Viewed by 724
Abstract
Multiple myeloma (MM) is a kind of plasma cell neoplasm, accounting for approximately 10% of hematologic malignancies, with a high mortality rate. Apigenin (APG), a flavonoid, has been reported to have antiviral, antibacterial, antioxidant, and anticancer properties. However, the impact of APG on [...] Read more.
Multiple myeloma (MM) is a kind of plasma cell neoplasm, accounting for approximately 10% of hematologic malignancies, with a high mortality rate. Apigenin (APG), a flavonoid, has been reported to have antiviral, antibacterial, antioxidant, and anticancer properties. However, the impact of APG on MM and bortezomib (BTZ) sensitization has not been investigated. The effects of APG on the proliferation, cell cycle, apoptosis, and oxidative stress of RPMI-8226 and U266 cells were investigated using CCK-8 assay, crystal violet staining, flow cytometry, Western blot, and PCR. It was observed that APG treatment increased the G1 phase cells, by which the expression of P21 increased, and the expression of CDK2 and Cyclin D1 decreased. Even though Necrostatin-1 (a potent necroptosis inhibitor) and Fer-1 (a ferroptosis inhibitor) could attenuate the effect of APG, the effect of Z-VAD-FMK (a pan-caspase inhibitor) was more significant. APG treatment increased the transcription of P53 and BAX, and the level of cleaved-PARP1 and cleaved-Caspase 3 in two MM cell strains. In addition, the APG application could dose-dependently increase the ROS, MDA, and GSSH levels, and decrease the GSH level in both cell strains, by which the transcription of GCLC, NQO1, GSTM2, NRF2, and GPX4 were attenuated. Finally, APG enhances the inhibitory effect of BTZ on MM cell growth. This study provides a potential therapeutic approach of APG on MM. Full article
(This article belongs to the Section Molecular Pharmacology)
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29 pages, 5540 KB  
Article
Scaffold-Hopping Design and Synthesis of Thieno[3,2-d]pyrimidines: Anticancer Activity, Apoptosis Induction, and In Silico Inhibition of CDKs
by Zukela Ruzi, Anvarjon Buronov, Lifei Nie, Azizbek Nasrullaev, Zarifa Murtazaeva, Rustamkhon Kuryazov, Jiangyu Zhao, Thomas Efferth, Haji Akber Aisa and Khurshed Bozorov
Int. J. Mol. Sci. 2025, 26(17), 8528; https://doi.org/10.3390/ijms26178528 - 2 Sep 2025
Viewed by 650
Abstract
Two series of tricyclic thieno[3,2-d]pyrimidines were synthesized, achieving yields of up to 97%. The tricyclic thieno[3,2-d]pyrimidines examined in this study are synthetic analogs of the deoxyvasicinone alkaloids, where the thiophene ring substitutes for the benzene ring. A systematic investigation [...] Read more.
Two series of tricyclic thieno[3,2-d]pyrimidines were synthesized, achieving yields of up to 97%. The tricyclic thieno[3,2-d]pyrimidines examined in this study are synthetic analogs of the deoxyvasicinone alkaloids, where the thiophene ring substitutes for the benzene ring. A systematic investigation was conducted on the scaffold-hopping strategy of these alkaloids, emphasizing the selective synthesis and anticancer properties of thieno[3,2-d]pyrimidines. The anticancer evaluation was performed on human cancer cell lines, specifically cervical HeLa and colon HT-29 carcinoma cells. Additional bioassays included cell migration analyses, cell cycle progression, apoptosis, and molecular docking analyses. Furthermore, molecular docking studies showed that the most active small molecule 6e is likely to disrupt the cell cycle process through targeting CDKs (Cyclin-dependent kinases), leading to the inhibition of tumor cell proliferation. Full article
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22 pages, 6033 KB  
Article
Survivin Is a Central Mediator of Cell Proliferation in HPV-Negative Head and Neck Squamous Cell Carcinoma
by Jing Zhu, Jianhong An, Erqiang Hu, Gregory Rosenblatt, Gabriela Berner, Aadita Roy, Nicole Kawachi, Nitisha Shrivastava, Vikas Mehta, Jeffrey E. Segall, Michael B. Prystowsky and Thomas J. Ow
Cancers 2025, 17(17), 2864; https://doi.org/10.3390/cancers17172864 - 31 Aug 2025
Viewed by 718
Abstract
Background/Objectives: HNSCC is a highly aggressive malignancy marked by the dysregulation of the cell cycle. In HPV HNSCC, mutations in the CDKN2A gene frequently result in the loss of the p16 protein, a key inhibitor of the cyclin D1/CDK4/6 complex. This loss [...] Read more.
Background/Objectives: HNSCC is a highly aggressive malignancy marked by the dysregulation of the cell cycle. In HPV HNSCC, mutations in the CDKN2A gene frequently result in the loss of the p16 protein, a key inhibitor of the cyclin D1/CDK4/6 complex. This loss results in unchecked G1/S phase progression. The CDK4/6 inhibitor palbociclib has shown therapeutic potential in HPV HNSCC by inducing G1 phase arrest and reducing cell viability. In this study, we investigated the molecular mechanisms by which palbociclib affects cell viability in HPV HNSCC. Methods: Four HPV HNSCC cell lines were treated with palbociclib, and RNA sequencing was performed to assess changes in gene expression. Cell viability was measured using the MTT assay. To further investigate protein localization, interactions, and function, we used immunofluorescence staining, co-immunoprecipitation, small molecule inhibitors, and siRNA-mediated knockdown. Results: We demonstrate that palbociclib downregulates survivin, a protein that plays dual roles in mitosis and apoptosis, thereby inhibiting cell proliferation. We also found that survivin is overexpressed in HPV HNSCC. Inhibiting survivin dimerization using the compound LQZ-7i significantly reduces cell viability and promotes its export from the nucleus to the cytoplasm. Additionally, we identified USP1, a deubiquitinase, as both a downstream target of CDK4/6 and a key regulator of survivin stability. Inhibiting USP1 activity or silencing its expression significantly reduces survivin levels. Conclusions: Our findings highlight survivin as a critical mediator of cell proliferation in HPV HNSCC and suggest that targeting the CDK4/6-USP1-survivin axis may offer a promising therapeutic strategy. Full article
(This article belongs to the Special Issue Genetic Alterations and the Tumor Microenvironment)
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32 pages, 21476 KB  
Article
CDKL5 Deficiency Disorder: Revealing the Molecular Mechanism of Pathogenic Variants
by Shamrat Kumar Paul, Shailesh Kumar Panday, Luigi Boccuto and Emil Alexov
Int. J. Mol. Sci. 2025, 26(17), 8399; https://doi.org/10.3390/ijms26178399 - 29 Aug 2025
Viewed by 527
Abstract
Cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder, which is a developmental and epileptic encephalopathy occurring in 1 in every 40,000 to 60,000 live births, was the subject of this computational investigation. This study provided a comprehensive list of missense variants (156) seen in the [...] Read more.
Cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder, which is a developmental and epileptic encephalopathy occurring in 1 in every 40,000 to 60,000 live births, was the subject of this computational investigation. This study provided a comprehensive list of missense variants (156) seen in the human population within the CDKL5 protein. Furthermore, the list of CDKL5 binding partners was updated to include four new entries. Computational modeling resulted in 3D structure models of twenty-four CDKL5-target protein complexes. The CDKL5 stability changes upon the above-mentioned missense mutations that were modeled, and it was shown that the corresponding folding free energy changes (ΔΔGfolding) caused by pathogenic variants are much larger than the ΔΔGfolding caused by benign variants. The same observation was made for the binding free energy change (ΔΔGbinding). This resulted in a protocol that allowed for the reclassification of missense variants with unknown or conflicting significance into pathogenic or benign. It was demonstrated that such reclassification is more reliable than using leading tools for pathogenicity predictions, since the latter failed to correctly predict known pathogenic/benign variants. Furthermore, the study demonstrated that pathogenicity is linked with the disturbance of thermodynamics quantities such as ΔΔGfolding and ΔΔGbinding, paving the way for development of therapeutic solutions. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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24 pages, 9438 KB  
Article
Large-Scale Transcriptome Profiling and Network Pharmacology Analysis Reveal the Multi-Target Inhibitory Mechanism of Modified Guizhi Fuling Decoction in Prostate Cancer Cells
by Guochen Zhang, Lei Xiang, Qingzhou Li, Mingming Wei, Xiankuo Yu, Yan Luo, Jianping Chen, Xilinqiqige Bao, Dong Wang and Shiyi Zhou
Pharmaceuticals 2025, 18(9), 1275; https://doi.org/10.3390/ph18091275 - 27 Aug 2025
Viewed by 584
Abstract
Background: Prostate cancer (PCa) is the primary contributor to male cancer-related mortality and currently lacks effective treatment options. The Modified Guizhi Fuling Decoction (MGFD) is used in clinical practice to treat multiple tumors. This research focused on the mechanisms of action (MOA) in [...] Read more.
Background: Prostate cancer (PCa) is the primary contributor to male cancer-related mortality and currently lacks effective treatment options. The Modified Guizhi Fuling Decoction (MGFD) is used in clinical practice to treat multiple tumors. This research focused on the mechanisms of action (MOA) in MGFD that inhibit PCa. Methods: The impact of MGFD on PCa cells (PC3 and DU145) was examined via Cell Counting Kit-8, wound healing assays, and transwell assays. To determine the MOA, high-throughput sequencing based high-throughput screening (HTS2) was utilized along with network pharmacology. Results: The findings indicated that MGFD suppressed the proliferation, migration, and invasion of PCa cells. We then utilized the HTS2 assay to generate 270 gene expression profiles from PCa cells perturbed by MGFD. Large-scale transcriptional analysis highlighted three pathways closely associated with PCa: the TNF signaling pathway, cellular senescence, and FoxO signaling pathway. Through the combination of network pharmacology and bioinformatics, we discovered four primary targets through which MGFD acts on PCa: AKT serine/threonine kinase 1 (AKT1), Caspase-8 (CASP8), Cyclin-Dependent Kinase 1 (CDK1), and Cyclin D1 (CCND1). Finally, molecular docking demonstrated that the potential bioactive compounds baicalein, quercetin, and 5-[[5-(4-methoxyphenyl)-2-furyl] methylene] barbituric acid strongly bind to CDK1, AKT1, and CASP8, respectively. Conclusions: This research shows that MGFD displays encouraging anticancer effects via various mechanisms. Its multi-target activity profile underscores its promise as a potential therapeutic option for PCa treatment and encourages additional in vivo validation studies. Full article
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24 pages, 872 KB  
Article
The Roles of PD-L1, Ki-67, P53, and Cyclin D1 in PitNETs: Diagnostic and Prognostic Implications in a Series of 74 Patients
by Anna Krzentowska, Beata Biesaga, Ryszard Czepko, Anna Merklinger-Gruchała, Dariusz Adamek, Małgorzata Jasińska, Barbara Pluta, Wiktoria Michalska, Katarzyna Wróblewska, Filip Janczy and Filip Gołkowski
Int. J. Mol. Sci. 2025, 26(16), 7830; https://doi.org/10.3390/ijms26167830 - 13 Aug 2025
Viewed by 454
Abstract
Pituitary neuroendocrine tumors (PitNETs), also known as pituitary adenomas, are rare tumors that are usually benign. At present, the WHO PitNET classification based on transcription factors is in force. A problem is caused by invasive tumors and silent tumors which, despite a lack [...] Read more.
Pituitary neuroendocrine tumors (PitNETs), also known as pituitary adenomas, are rare tumors that are usually benign. At present, the WHO PitNET classification based on transcription factors is in force. A problem is caused by invasive tumors and silent tumors which, despite a lack of obvious clinical symptoms, tend to behave aggressively. Factors influencing the clinical course of these tumors are currently being sought. The aim of our study was to assess the expression of programmed death-ligand 1 (PD-L1) and proliferation biomarkers (Ki-67, cyclin D1, and P53) in PitNETs depending on the transcription factor and adenoma subtype. The analysis was performed in seventy-four patients operated on in a single neurosurgical center for pituitary tumors. Immunohistochemistry was performed for transcription factors and biomarkers—PD-L1, Ki-67, P53, and cyclin D1—in tissue microarray format. Membranous expression of PD-L1 was scored as 0 (no expression) and ≥1%. Nuclear expression of Ki-67 was scored at <3% and ≥3%, and the expression of P53 and cyclin D1 was scored at <10% and ≥10%. The following tumors expressed PD-L1 at ≥1%: gonadotroph, 21 (28.4%); corticotroph, 5 (6.7%); gonadotroph/lactotroph, 2 (2.7%); null cell adenoma, 3 (4.0%); multiple synchronous PitNET, 2 (2.7%); immature PIT-1 tumor, 1 (1.3%); mature PIT-1 tumor, 1 (1.5%). Ki-67 ≥ 3% was found in the following PitNETs: gonadotroph, 3 (4.0%); corticotroph, 2 (2.7%); lactotroph, 1 (1.3%); multiple synchronous PitNET, 1 (1.3%); immature PIT-1 tumor, 1 (1.3%); and mature PIT-1 tumor, 1 (1.3%). Patients with Ki-67 ≥ 3% were statistically significantly younger (p = 0.03). All tumors (100%) with a combination of cyclin D1 ≥ 10% and P53 < 10% were invasive on the Hardy scale. Of the four factors, PD-L1 increased the odds of invasiveness the most (adjusted OR = 2.35; 95% CI: 0.56–9.90). PD-L1 expression was present in some types of PitNETs. PD-L1 expression may help in identifying null cell adenomas. High cyclin D1 with low P53 may indicate greater tumor invasiveness. Full article
(This article belongs to the Special Issue Biomarkers in Cancer Immunology)
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27 pages, 11354 KB  
Article
Tetraarsenic Hexoxide Enhanced the Anticancer Effects of Artemisia annua L. Polyphenols by Inducing Autophagic Cell Death and Apoptosis in Oxalplatin-Resistant HCT116 Colorectal Cancer Cells
by Eun Joo Jung, Hye Jung Kim, Sung Chul Shin, Gon Sup Kim, Jin-Myung Jung, Soon Chan Hong, Choong Won Kim and Won Sup Lee
Int. J. Mol. Sci. 2025, 26(16), 7661; https://doi.org/10.3390/ijms26167661 - 8 Aug 2025
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Abstract
It was reported that polyphenols extracted from Korean Artemisia annua L. (pKAL) have higher anticancer effects in oxaliplatin-resistant (OxPt-R) HCT116 cells than in HCT116 cells. In this study, it was tested whether and how As4O6 enhances anticancer effects of pKAL [...] Read more.
It was reported that polyphenols extracted from Korean Artemisia annua L. (pKAL) have higher anticancer effects in oxaliplatin-resistant (OxPt-R) HCT116 cells than in HCT116 cells. In this study, it was tested whether and how As4O6 enhances anticancer effects of pKAL in HCT116 and HCT116-OxPt-R colorectal cancer cells. The CCK-8 assay, phase-contrast microscopy, and colony formation assay revealed that As4O6 enhanced anticancer effects of pKAL, with induction of nuclear deformity and intracytoplasmic vesicle formation in both cells. Western blot analysis revealed that co-treatment with As4O6 and pKAL significantly decreased the expression of NF-kB, EGFR, cyclin D1, CD44, and β-catenin, and upregulated the expression of p62 and LC3B in both cells. It also induced the activation of caspase-8 and γ-H2AX and the cleavage of β-catenin, PARP1, lamin A/C, and p62. These phenomena were inhibited by wortmannin, and further suppressed by co-treatment of wortmannin with an ROS inhibitor, N-acetyl cysteine. This study suggests that As4O6 enhanced the anticancer effects of pKAL by inducing autophagic cell death accompanied by apoptosis in both parental HCT116 and HCT116-OxPt-R cells. It also suggests that ROS generation and the downregulation of AKT, NF-κB p65, cyclin D1, EGFR, and β-catenin may play an important role in the As4O6-enhanced anticancer effect of pKAL. Full article
(This article belongs to the Special Issue Enhanced Anticancer Properties of Natural Products)
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Article
CTCF Represses CIB2 to Balance Proliferation and Differentiation of Goat Myogenic Satellite Cells via Integrin α7β1–PI3K/AKT Axis
by Changliang Gong, Huihui Song, Zhuohang Hao, Zhengyi Zhang, Nanjian Luo and Xiaochuan Chen
Cells 2025, 14(15), 1199; https://doi.org/10.3390/cells14151199 - 5 Aug 2025
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Abstract
Skeletal muscle development is a critical economic trait in livestock, governed by myogenic satellite cell regulation. Integrins mediate mechanical anchorage to the ECM and enable ECM–intracellular signaling. CIB2, as an EF-hand-domain protein involved in mechanotransduction, shows significant developmental regulation in goat muscle. [...] Read more.
Skeletal muscle development is a critical economic trait in livestock, governed by myogenic satellite cell regulation. Integrins mediate mechanical anchorage to the ECM and enable ECM–intracellular signaling. CIB2, as an EF-hand-domain protein involved in mechanotransduction, shows significant developmental regulation in goat muscle. Although the role of CIB2 in skeletal muscle growth is poorly characterized, we observed pronounced developmental upregulation of IB2 in postnatal goat muscle. CIB2 expression increased >20-fold by postnatal day 90 (P90) compared to P1, sustaining elevation through P180 (p < 0.05). Functional investigations indicated that siRNA-mediated knockdown of CIB2 could inhibit myoblast proliferation by inducing S-phase arrest (p < 0.05) and downregulating the expression of CDK4/Cyclin D/E. Simultaneously, CIB2 interference treatment was found to decrease the proliferative activity of goat myogenic satellite cells, yet it significantly promoted differentiation by upregulating the expression of MyoD/MyoG/MyHC (p < 0.01). Mechanistically, CTCF was identified as a transcriptional repressor binding to an intragenic region of the CIB2 gene locus (ChIP enrichment: 2.3-fold, p < 0.05). Knockdown of CTCF induced upregulation of CIB2 (p < 0.05). RNA-seq analysis established CIB2 as a calcium signaling hub: its interference activated IL-17/TNF and complement cascades, while overexpression suppressed focal adhesion/ECM–receptor interactions and enriched neuroendocrine pathways. Collectively, this study identifies the CTCF-CIB2–integrin α7β1–PI3K/AKT axis as a novel molecular mechanism that regulates the balance of myogenic fate in goats. These findings offer promising targets for genomic selection and precision breeding strategies aimed at enhancing muscle productivity in ruminants. Full article
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