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11 pages, 649 KB  
Article
Infrequent HPV Infection in Colorectal Neuroendocrine Carcinoma: Molecular and Histologic Characteristics
by Xi Wang, Minghao Zhong, Xuchen Zhang and Yuanxin Liang
Diagnostics 2025, 15(20), 2569; https://doi.org/10.3390/diagnostics15202569 - 12 Oct 2025
Abstract
Background/Objectives: Colorectal neuroendocrine carcinomas (NECs) are rare, aggressive tumors with poorly defined clinicopathologic and molecular features. Their biological behavior and optimal treatment strategies remain unclear. Additionally, a subset of anorectal NECs may be associated with high-risk human papillomavirus (HPV) infection, suggesting potential [...] Read more.
Background/Objectives: Colorectal neuroendocrine carcinomas (NECs) are rare, aggressive tumors with poorly defined clinicopathologic and molecular features. Their biological behavior and optimal treatment strategies remain unclear. Additionally, a subset of anorectal NECs may be associated with high-risk human papillomavirus (HPV) infection, suggesting potential heterogeneity in pathogenesis. Methods: We retrospectively reviewed 12 cases of colorectal NECs. Clinical outcomes, histologic morphology, immunohistochemistry, molecular profiling, including common oncogenic mutations, and HPV status were analyzed. Results: Seven cases demonstrated small cell NECs, and five showed large cell NECs. The majority of NECs (n = 9) arose in the rectum. TP53 mutations were the most common (75%), followed by KRAS, RB1, FBXW7, and BRAF mutations. One case demonstrated mismatch repair (MMR) deficiency. High-risk HPV was detected in one rectal NEC, which lacked common oncogenic mutations and was the only long-term survivor (54 months). p16 expression did not correlate consistently with HPV in situ hybridization (ISH) status. Among small cell NECs with follow-up, platinum-based chemotherapy resulted in significantly longer survival than FOLFOX (13.5 vs. 4 months, p = 0.0209). Conclusions: Colorectal NECs display histologic and molecular heterogeneity. The tumors of small cell NECs potentially benefit more from platinum-based chemotherapy. HPV-associated NECs may represent a distinct subset with better prognosis, but p16 is not a reliable surrogate marker. Routine subclassification into small vs. large cell types and comprehensive molecular profiling, including HPV testing, may aid clinical decision-making and prognostication. Full article
(This article belongs to the Special Issue Advances in Infectious Disease Diagnosis Technologies)
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18 pages, 1231 KB  
Article
Survival Outcomes and Prognostic Factors in Metastatic Unresectable Appendiceal Adenocarcinoma Treated with Palliative Systemic Chemotherapy: A 10-Year Retrospective Analysis from Australia
by Jirapat Wonglhow, Hui-Li Wong, Michael Michael, Alexander Heriot, Glen Guerra, Catherine Mitchell and Jeanne Tie
Cancers 2025, 17(20), 3297; https://doi.org/10.3390/cancers17203297 (registering DOI) - 11 Oct 2025
Abstract
Background: Appendiceal adenocarcinoma is a rare malignancy, and data guiding its systemic treatment in metastatic settings are limited. This study aimed to determine the clinical outcomes, treatment efficacy, biomarkers, and prognostic factors in patients with metastatic or unresectable appendiceal adenocarcinoma receiving palliative chemotherapy. [...] Read more.
Background: Appendiceal adenocarcinoma is a rare malignancy, and data guiding its systemic treatment in metastatic settings are limited. This study aimed to determine the clinical outcomes, treatment efficacy, biomarkers, and prognostic factors in patients with metastatic or unresectable appendiceal adenocarcinoma receiving palliative chemotherapy. Methods: We retrospectively reviewed patients with metastatic appendiceal adenocarcinoma who received first-line palliative systemic chemotherapy at the Peter MacCallum Cancer Centre between January 2015 and December 2024. Results: Of the 40 patients included, fluoropyrimidine-based doublet regimens were most commonly used (82.5%) in first-line setting, achieving an objective response rate of 39.4%. Median overall survival (OS) was 21.6 months, and median first-line progression-free survival (PFS) was 8.9 months. 22 patients (55.0%) received second-line treatment. Median OS and PFS were 21.6 and 8.9 months, respectively, among patients treated with oxaliplatin-based doublet regimens, and 66.4 and 10.8 months, respectively, among those treated with irinotecan-based doublet regimens. Molecular biomarker testing was performed in 35 patients (87.5%). KRAS and NRAS mutations were identified in 68.6% and 2.9% of tested patients, respectively. Factors associated with poorer OS included male sex, elevated carcinoembryonic antigen levels, and overweight status. Bevacizumab use was not clearly associated with survival. Conclusions: Palliative systemic chemotherapy, particularly fluoropyrimidine-based doublet regimens, appears to be a reasonable and effective treatment option for patients with advanced appendiceal adenocarcinoma. Although this study was underpowered for formal comparison, the numerically longer OS and PFS of irinotecan-based regimens are hypothesis-generating and support further prospective evaluation. Molecular profiling emphasizes the need for personalized targeted therapeutic strategies. The identified prognostic factors may help guide risk stratification and patient counseling for treatment planning. Full article
(This article belongs to the Special Issue Clinical Efficacy of Drug Therapy in Gastrointestinal Cancers)
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18 pages, 586 KB  
Article
Genetic Alteration Profiling in North Macedonian Lung Cancer Patients
by Aleksandar Eftimov, Rubens Jovanovic, Slavica Kostadinova Kunovska, Magdalena Bogdanovska Todorovska, Boro Ilievski, Panche Zdravkovski, Selim Komina, Blagica Krstevska, Simonida Crvenkova, Marija Simonovska and Gordana Petrushevska
Genes 2025, 16(10), 1177; https://doi.org/10.3390/genes16101177 - 10 Oct 2025
Viewed by 92
Abstract
Background/Objectives: Late diagnosis and inefficient treatment regimens lead to poor prognosis, with a low 5-year survival rate for both non-small-cell lung cancer (NSCLC) and small-cell lung cancer (SCLC). New targeted therapeutic agents can be developed and introduced only by first discovering new [...] Read more.
Background/Objectives: Late diagnosis and inefficient treatment regimens lead to poor prognosis, with a low 5-year survival rate for both non-small-cell lung cancer (NSCLC) and small-cell lung cancer (SCLC). New targeted therapeutic agents can be developed and introduced only by first discovering new driver oncogenes and with a thorough investigation of the known driver genes. The aim of the current study is to investigate the prevalence of alterations in the eight most frequently altered genes in lung cancer—BRAF, EGFR, KRAS, ALK, ROS1, HER2, PD-L1 and PIK3CA. Methods: Real-time polymerase chain reaction (RT-PCR) was used to detect KRAS and EGFR mutations, multiplex PCR and microarray hybridization for KRAS/BRAF/PIK3CA mutations. Immunohistochemical analysis was performed for the detection of ALK, HER2/NEU, ROS-1 and PD-L1 alterations. Results: Overall, 221/603 patients (36.65%) had at least one genetic alteration, of which 22 patients (3.65%) had two genetic alterations and two patients had more than two genetic alterations. Additionally, 50 patients were identified with one or more KRAS mutations (8.29%), 45 patients with EGFR mutations (7.46%), and 1.82% with PIK3CA mutations and 0.66% with BRAF mutations. Furthermore, 50% of the co-occurring alterations were either on KRAS and PIK3CA genes (3/6), on KRAS and BRAF genes (2/6, 33.33%) or on EGFR and PIK3CA genes (1/6, 16.67%), and 10.45% of the patients exhibited PD-L1 overexpression, 5.31% ALK rearrangements, and 2.36% HER2/NEU expression, with no ROS-1 rearrangements detected. Conclusions: Comprehensive testing for somatic alterations in EGFR, BRAF, KRAS, and PIK3CA is significant in guiding therapeutic decisions in lung cancer management. Such testing should be routinely conducted to establish a thorough genetic profile of lung cancers in a manner that is both time-efficient and cost-effective. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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26 pages, 4125 KB  
Article
Enhanced Killing of Colon Cancer Cells by Mesoporous Silica Nanoparticles Loaded with Ellagic Acid
by Khaled AbouAitah, Amr Nassrallah, Ahmed A. F. Soliman, Anna Swiderska-Sroda, Tadeusz Chudoba, Julita Smalc-Koziorowska, Beom Soo Kim and Witold Łojkowski
Nanomaterials 2025, 15(20), 1547; https://doi.org/10.3390/nano15201547 - 10 Oct 2025
Viewed by 93
Abstract
Background: Natural compounds, including ellagic acid (ELG), are promising anticancer agents with low adverse effects. In this paper, we test in vitro the effectiveness of mesoporous silica nanoparticles (MSN) as an ELG carrier against colon cancer. Methods: We produced MSNs functionalized with triptycene [...] Read more.
Background: Natural compounds, including ellagic acid (ELG), are promising anticancer agents with low adverse effects. In this paper, we test in vitro the effectiveness of mesoporous silica nanoparticles (MSN) as an ELG carrier against colon cancer. Methods: We produced MSNs functionalized with triptycene (TRP) and loaded with ELG, further called MSNTRPELG nanoformulation. The nanoformulation contained over 11 wt.% TRP and approximately 25 wt.% ELG in the mesoporous structure and on the surface of particles. It was assessed for anticancer effects against two colon cancer cells: HCT-116 and HT-29 for treatment with up to 200 µM. Results: Comparing to free ELG, we have shown a three times higher cancer inhibition. The lowest IC50 values were for HCT-116 (88.1 ± 0.1 µM) and HT-29 (77.6 ± 0.1 µM). When treated with free ELG, the values were 187.1 ± 0.1 µM and 300.0 ± 0.1 µM, respectively. MSNTRPELG enhanced apoptosis primarily by activating caspase-3, p53, and Bax while downregulating Bcl-2 in HCT-116 and HT-29 cells. It also inhibited receptor tyrosine kinases (HER2 and VEGFR2). Preliminary Western blot observations suggest suppression of B-RAF, C-RAF, and K-RAS oncogenes, with stronger inhibition by the nanoformulation than by free ELG. Conclusions: This work highlights the potential of MSNs to enhance the efficacy of natural prodrugs, particularly ELG, in cancer therapy. Full article
(This article belongs to the Special Issue Metal Nanostructures in Biological Applications)
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20 pages, 1465 KB  
Review
The Genomic Topography of Appendiceal Cancers: Our Current Understanding, Clinical Perspectives, and Future Directions
by Daniel J. Gironda, Richard A. Erali, Steven D. Forsythe, Ashok K. Pullikuth, Rui Zheng-Pywell, Kathleen A. Cummins, Shay Soker, Xianyong Gui, Edward A. Levine, Konstantinos I. Votanopoulos and Lance D. Miller
Cancers 2025, 17(19), 3275; https://doi.org/10.3390/cancers17193275 - 9 Oct 2025
Viewed by 284
Abstract
Background/Objectives: Appendiceal cancer (AC) is a rare and understudied malignancy with limited genomic data available to guide clinical interventions. Historically treated as a subtype of colorectal cancer, AC is now recognized as a distinct disease with unique histologic subtypes and molecular features. [...] Read more.
Background/Objectives: Appendiceal cancer (AC) is a rare and understudied malignancy with limited genomic data available to guide clinical interventions. Historically treated as a subtype of colorectal cancer, AC is now recognized as a distinct disease with unique histologic subtypes and molecular features. This review aims to consolidate current genomic data across AC subtypes and explore the clinical relevance of recurrent mutations. Methods: A systematic literature review was performed in accordance with general Preferred Reporting Items for Systemic Reviews and Meta-Analyses (PRISMA) guidelines. Using search engines such as PubMed and Web of Science, we selected studies based on relevance to AC genomics using search terms such as “appendix cancer”, “appendiceal cancer”, “pseudomyxoma peritonei”, “sequencing”, “mutation”, and “genotype”. Results: AC comprises five major histologic subtypes—appendiceal neuroendocrine neoplasms (ANENs), mucinous appendiceal neoplasms (MANs), goblet cell adenocarcinomas (GCAs), colonic-type adenocarcinomas (CTAs) and signet ring cell adenocarcinomas (SRCs)—each with unique clinical behaviors and mutational profiles. Low-grade tumors, such as ANENs and MANs, frequently harbor KRAS and GNAS mutations, while high-grade subtypes, such as CTAs and SRCs, are enriched for TP53, APC, and SMAD gene alterations. GCA tumors exhibit a distinct mutational spectrum involving chromatin remodeling genes such as ARID1A and KMT2D. Compared to colorectal cancer, AC demonstrates lower frequencies of APC and TP53 mutations and a higher prevalence of GNAS mutations, consistent with a pathological divergence from CRC. Conclusions: The genomic heterogeneity of AC is commensurate with its histological complexity and has important implications for diagnosis, prognosis and treatment. While certain actionable mutations are present in a subset of tumors, large-scale genomic characterization efforts and development of subtype-specific models will be essential for advancing precision medicine in AC. Full article
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20 pages, 41804 KB  
Article
Immunophenotypic Panel for Comprehensive Characterization of Aggressive Thyroid Carcinomas
by Mihail Ceausu, Mihai Alin Publik, Dana Terzea, Carmen Adina Cristea, Dumitru Ioachim, Dana Manda and Sorina Schipor
Cells 2025, 14(19), 1554; https://doi.org/10.3390/cells14191554 - 6 Oct 2025
Viewed by 390
Abstract
Aggressive thyroid carcinomas—anaplastic (ATC) and poorly differentiated (PDTC)—are rare but highly lethal malignant entities. Their immunophenotypical characterization is still incomplete, and no standardized diagnostic algorithms have been used. Our study retrospectively analyzes 40 thyroidectomy cases as follows: 12 ATC and 28 PDTC from [...] Read more.
Aggressive thyroid carcinomas—anaplastic (ATC) and poorly differentiated (PDTC)—are rare but highly lethal malignant entities. Their immunophenotypical characterization is still incomplete, and no standardized diagnostic algorithms have been used. Our study retrospectively analyzes 40 thyroidectomy cases as follows: 12 ATC and 28 PDTC from 2014 to 2024 by evaluating clinical data, histopathological aspects, molecular analysis for presence of BRAFV600E and TERTC228/250T mutations, as well as immunohistochemical expression of BRAFV600E, total BRAF, K-RAS, TERT, PAX-8, TTF-1, P53, and Ki-67. BRAFV600E was present in 70% of cases, with higher prevalence in ATC. Total BRAF correlated positively with K-RAS and TERT and negatively with BRAFV600E. TERT abnormal expression was highly prevalent in over 90% of cases, while loss of TTF-1 and PAX-8 is associated with anaplastic transformation. Ki-67 proliferative index had significantly higher values in ATC, thus supporting its role as a marker for aggressiveness. On univariate analysis, higher Ki-67 indices and lymph node invasion are independent predictor factors for the presence of metastases. However, on multivariate analysis, they both lose significance. Upon multivariate analysis, loss of TTF-1 and tumor necrosis were significant predictors for anaplastic histotype. Specific BRAFV600E immunohistochemistry may be a good screening tool for the BRAFV600E mutation. Molecularly, there is a relatively frequent association of the BRAFV600E mutation and TERTC228, mainly in the PDTC subgroup. Patterns of marker expression suggest that BRAF or RAF activation with subsequent loss of TTF-1 or PAX-8, TERT upregulation, and TP53 alteration are frequent occurrences in aggressive thyroid carcinomas. The association between TTF-1 loss and anaplastic transformation, presence of necrosis alongside BRAFV600E, underlines their diagnostic potential in subclassifying aggressive thyroid carcinomas. Full article
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22 pages, 1864 KB  
Article
SPP1 as a Potential Stage-Specific Marker of Colorectal Cancer
by Eva Turyova, Peter Mikolajcik, Michal Kalman, Dusan Loderer, Miroslav Slezak, Maria Skerenova, Emile Johnston, Tatiana Burjanivova, Juraj Miklusica, Jan Strnadel and Zora Lasabova
Cancers 2025, 17(19), 3200; https://doi.org/10.3390/cancers17193200 - 30 Sep 2025
Viewed by 176
Abstract
Background: Colorectal cancer is the third most diagnosed cancer and a leading cause of cancer-related deaths worldwide. Early detection significantly improves patient outcomes, yet many cases are identified only at late stages. The high molecular and genetic heterogeneity of colorectal cancer presents major [...] Read more.
Background: Colorectal cancer is the third most diagnosed cancer and a leading cause of cancer-related deaths worldwide. Early detection significantly improves patient outcomes, yet many cases are identified only at late stages. The high molecular and genetic heterogeneity of colorectal cancer presents major challenges in accurate diagnosis, prognosis, and therapeutic stratification. Recent advances in gene expression profiling offer new opportunities to discover genes that play a role in colorectal cancer carcinogenesis and may contribute to early diagnosis, prognosis prediction, and the identification of novel therapeutic targets. Methods: This study involved 142 samples: 84 primary tumor samples, 27 liver metastases, and 31 adjacent non-tumor tissues serving as controls. RNA sequencing was performed on a subset of tissues (12 liver metastases and 3 adjacent non-tumor tissues) using a targeted RNA panel covering 395 cancer-related genes. Data processing and differential gene expression analysis were carried out using the DRAGEN RNA and DRAGEN Differential Expression tools. The expression of six genes involved in hypoxia and epithelial-to-mesenchymal transition (EMT) pathways (SLC16A3, ANXA2, P4HA1, SPP1, KRT19, and LGALS3) identified as significantly differentially expressed was validated across the whole cohort via quantitative real-time PCR. The relative expression levels were determined using the ΔΔct method and log2FC, and compared between different groups based on the sample type; clinical parameters; and mutational status of the genes KRAS, PIK3CA, APC, SMAD4, and TP53. Results: Our results suggest that the expression of all the validated genes is significantly altered in metastases compared to non-tumor control samples (p < 0.05). The most pronounced change occurred for the genes P4HA1 and SPP1, whose expression was significantly increased in metastases compared to non-tumor and primary tumor samples, as well as between clinical stages of CRC (p < 0.001). Furthermore, all genes, except for LGALS3, exhibited significantly altered expression between non-tumor samples and samples in stage I of the disease, suggesting that they play a role in the early stages of carcinogenesis (p < 0.05). Additionally, the results suggest the mutational status of the KRAS gene did not significantly affect the expression of any of the validated genes, indicating that these genes are not involved in the carcinogenesis of KRAS-mutated CRC. Conclusions: Based on our results, the genes P4HA1 and SPP1 appear to play a role in the progression and metastasis of colorectal cancer and are candidate genes for further investigation as potential biomarkers in CRC. Full article
(This article belongs to the Special Issue Colorectal Cancer Metastasis (Volume II))
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15 pages, 4739 KB  
Article
EC359 Enhances Trametinib Efficacy in Ras/Raf-Driven Ovarian Cancer by Suppressing LIFR Signaling
by William C. Arnold, Durga Meenakshi Panneerdoss, Baskaran Subramani, Megharani Mahajan, Behnam Ebrahimi, Paulina Ramirez, Bindu Santhamma, Suryavathi Viswanadhapalli, Edward R. Kost, Yidong Chen, Zhao Lai, Hareesh B. Nair, Ratna K. Vadlamudi and Yasmin A. Lyons
Biomolecules 2025, 15(10), 1396; https://doi.org/10.3390/biom15101396 - 30 Sep 2025
Viewed by 299
Abstract
Ovarian cancer (OCa) remains the most lethal gynecologic malignancy in the United States, with low-grade serous and mucinous subtypes frequently driven by KRAS mutations. These mutations activate downstream MAPK and PI3K/AKT signaling pathways, contributing to tumor progression and resistance to therapy. Although the [...] Read more.
Ovarian cancer (OCa) remains the most lethal gynecologic malignancy in the United States, with low-grade serous and mucinous subtypes frequently driven by KRAS mutations. These mutations activate downstream MAPK and PI3K/AKT signaling pathways, contributing to tumor progression and resistance to therapy. Although the MEK inhibitor trametinib is used to target these pathways, its efficacy is limited in KRAS-mutant OCa due to compensatory activation of the leukemia inhibitory factor (LIF)/LIF receptor (LIFR) axis. In this study, we evaluated the therapeutic potential of combining trametinib with EC359, a selective LIFR inhibitor, in Ras/Raf-driven OCa models. EC359 significantly reduced cell viability, clonogenic survival, and induced cell death via ferroptosis in vitro. Mechanistic studies revealed that EC359 suppressed trametinib-induced activation of LIFR downstream signaling. RNA-seq analysis showed that combination therapy downregulated mitochondrial translation and MYC target genes while upregulating apoptosis-related genes. In vivo, EC359 and trametinib co-treatment significantly reduced tumor growth in xenograft and PDX models without inducing toxicity. Our studies identify LIFR signaling as a critical vulnerability in Ras/Raf-mutant and low grade serous OCa. Further, it provides strong preclinical rationale for EC359 and trametinib combination therapy as a new therapeutic strategy for treating Ras/Raf-driven OCa and low-grade serous OCa. Full article
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29 pages, 1226 KB  
Systematic Review
Impact of Somatic Gene Mutations on Prognosis Prediction in De Novo AML: Unraveling Insights from a Systematic Review and Meta-Analysis
by Amal Elfatih, Nisar Ahmed, Luma Srour, Idris Mohammed, William Villiers, Tara Al-Barazenji, Hamdi Mbarek, Susanna El Akiki, Puthen Veettil Jithesh, Mohammed Muneer, Shehab Fareed and Borbala Mifsud
Cancers 2025, 17(19), 3189; https://doi.org/10.3390/cancers17193189 - 30 Sep 2025
Viewed by 376
Abstract
Background: Wide application of genome sequencing technologies has highlighted extensive genetic diversity in Acute Myeloid Leukemia (AML), yet the specific roles of individual genes remain unclear. This systematic review and meta-analysis aims to provide robust evidence for the prognostic impact of somatic gene [...] Read more.
Background: Wide application of genome sequencing technologies has highlighted extensive genetic diversity in Acute Myeloid Leukemia (AML), yet the specific roles of individual genes remain unclear. This systematic review and meta-analysis aims to provide robust evidence for the prognostic impact of somatic gene mutations in de novo AML patients, while also exploring the prevalence of these mutations. Methods: Eligible studies were identified from PubMed and Scopus, with a focus on those reporting the prognostic influence of somatic gene mutations on overall survival (OS) or relapse-free survival (RFS) when compared to wild-type carriers. We calculated the pooled prevalence with 95% confidence intervals to assess the frequency of these mutations, and the pooled Hazard Ratio (HR) to compare OS and RFS associated with specific gene mutations. Results: We evaluated 53 somatic gene mutations using 80 studies, involving 20,048 de novo AML patients. The analysis revealed that the most prevalent affected genes were NPM1 (27%), DNMT3A (26%), and FLT3-ITD (24%). Mutations in CSF3R, TET2, and TP53 were significantly associated with poorer OS or RFS (p < 0.05). Sensitivity analysis confirmed that ASXL1, DNMT3A, and RUNX1 mutations were consistently linked to inferior OS or RFS. In contrast, CEBPAdm mutations were associated with favorable OS [HR = 0.39 (0.30–0.50)] and RFS [HR = 0.44 (0.37–0.54)]. Subgroup analysis showed that FLT3-ITD mutations were consistently associated with worse OS or RFS across all subgroups, though no significant subgroup differences were noted. No significant impact on OS or RFS was observed for mutations in GATA2, FLT3-TKD, KRAS, NRAS, IDH1, and IDH2. Conclusions: These findings provide critical insights into AML prognosis, aiding clinical decision-making and improving risk stratification strategies. Full article
(This article belongs to the Section Systematic Review or Meta-Analysis in Cancer Research)
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14 pages, 2878 KB  
Article
Effects of Tyrphostin A9 and Structurally Related Tyrphostins on Colorectal Carcinoma Cells
by Lubna H. Tahtamouni, Ayah Y. Almasri, Marya A. Hamad, Nour A. Hussein, Khaled M. Saleh, Salem R. Yasin, Rainer Schobert and Bernhard Biersack
Future Pharmacol. 2025, 5(4), 57; https://doi.org/10.3390/futurepharmacol5040057 - 29 Sep 2025
Viewed by 270
Abstract
Background/Objectives: Colorectal carcinoma (CRC) is among the most commonly diagnosed cancers in both men and women. Although CRC mortality is generally decreasing, new therapeutic options are needed for unresponsive subgroups of CRC patients. Methods: A series of known and new tyrphostin derivatives was [...] Read more.
Background/Objectives: Colorectal carcinoma (CRC) is among the most commonly diagnosed cancers in both men and women. Although CRC mortality is generally decreasing, new therapeutic options are needed for unresponsive subgroups of CRC patients. Methods: A series of known and new tyrphostin derivatives was tested for their efficacy against three CRC cell lines with varying KRAS, p53, and/or BRAF statuses. Growth inhibition, apoptosis induction, and inhibition of EGFR and VEGFR-2 were investigated. Results: Tyrphostin A9, the known RG13022-related tyrphostin 1a and its dichlorido(p-cymene)ruthenium(II) complex 1b, and the new SF5-substituted compounds 2a and 2b showed selective antiproliferative activity against KRAS-mutant HCT-116 CRC cells expressing wildtype p53, while p53-knockout HCT-116 and KRAS-wildtype BRAF/p53-mutant HT-29 CRC cells were distinctly less sensitive. In HCT-116 cells, only tyrphostin A9 increased mRNA expression of caspases 3 and 8, as well as the kinases MEK1 and MEK2, whereas 2a reduced caspase 8 mRNA levels. Tyrphostin A9 increased caspase 3 activity and induced apoptosis in HCT-116 p53-wildtype cells while simultaneously inhibiting the receptor tyrosine kinases EGFR and VEGFR-2 at low nanomolar concentrations. Conclusions: Tyrphostin A9 could be a promising therapeutic option for the treatment of KRAS-mutant CRC that expresses wildtype p53. Full article
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16 pages, 602 KB  
Article
KRAS G12C Mutation Predicts Improved Survival in NSCLC Patients Receiving Immunotherapy: Insights from a Real-World Cohort
by Aslı Geçgel, Buket Şahin Çelik, Pınar Peker, Zeynep Sıla Gökdere, Didem Koca, Burçak Karaca, Deniz Nart and Erdem Göker
J. Clin. Med. 2025, 14(19), 6826; https://doi.org/10.3390/jcm14196826 - 26 Sep 2025
Viewed by 310
Abstract
Background: KRAS mutations are among the most common oncogenic drivers in non-small cell lung cancer (NSCLC), with KRAS G12C emerging as a therapeutically targetable subtype. However, the prognostic relevance of KRAS G12C compared with non-G12C mutations in patients receiving immune checkpoint inhibitors (ICIs) [...] Read more.
Background: KRAS mutations are among the most common oncogenic drivers in non-small cell lung cancer (NSCLC), with KRAS G12C emerging as a therapeutically targetable subtype. However, the prognostic relevance of KRAS G12C compared with non-G12C mutations in patients receiving immune checkpoint inhibitors (ICIs) remains unclear. Methods: We retrospectively analyzed 80 NSCLC patients treated with ICIs between January 2020 and July 2024; data were censored on 3 July 2025. The cohort included 32 KRAS-mutant (20 G12C, 12 non-G12C) and 48 KRAS wild-type patients. Clinicopathological features, treatment details, and survival outcomes were collected. Overall survival (OS) and progression-free survival (PFS) were estimated using the Kaplan–Meier method, with group comparisons made using the log-rank test. Univariate and multivariate Cox regression analyses were conducted to identify independent prognostic factors. Results: Among 80 NSCLC patients treated with ICIs, the median OS and PFS were 14.3 and 8.2 months, respectively. Survival outcomes were comparable between KRAS-mutant and wild-type patients. Within the KRAS-mutant subgroup (n = 32), baseline characteristics were generally balanced between G12C (n = 20) and non-G12C (n = 12) cases, with non-significant trends toward higher metastatic burden and PD-L1 ≥ 50% in the G12C group. Median OS was significantly longer in G12C patients than in non-G12C patients (20.7 vs. 6.4 months; p = 0.021), whereas PFS did not differ significantly (10.2 vs. 3.7 months; p = 0.181). In multivariate analysis, non-G12C mutation independently predicted increased mortality risk (HR 3.35, 95% CI 1.26–8.89; p = 0.015). For PFS, recurrent disease status was associated with improved outcomes in univariate analysis (HR 0.30, 95% CI 0.09–0.94; p = 0.040), but no independent predictors were identified in multivariate modeling. Conclusions: In NSCLC patients treated with ICIs, the KRAS G12C mutation was associated with significantly improved OS compared with other KRAS subtypes, independent of clinicopathological characteristics. These findings suggest distinct biological behavior of KRAS variants in immunotherapy response and warrant further prospective validation. Full article
(This article belongs to the Section Oncology)
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38 pages, 578 KB  
Review
Next-Generation Sequencing: A Review of Its Transformative Impact on Cancer Diagnosis, Treatment, and Resistance Management
by Alexandru Isaic, Nadica Motofelea, Teodora Hoinoiu, Alexandru Catalin Motofelea, Ioan Cristian Leancu, Emanuela Stan, Simona R. Gheorghe, Alina Gabriela Dutu and Andreea Crintea
Diagnostics 2025, 15(19), 2425; https://doi.org/10.3390/diagnostics15192425 - 23 Sep 2025
Viewed by 908
Abstract
Background/Objectives: Next-Generation Sequencing (NGS) has transformed cancer diagnostics and treatment by enabling comprehensive genomic profiling of tumors. This review aims to summarize the current applications of NGS in oncology, highlighting its role in early detection, precision therapy, and disease monitoring. Methods: [...] Read more.
Background/Objectives: Next-Generation Sequencing (NGS) has transformed cancer diagnostics and treatment by enabling comprehensive genomic profiling of tumors. This review aims to summarize the current applications of NGS in oncology, highlighting its role in early detection, precision therapy, and disease monitoring. Methods: We conducted a comprehensive review of the recent literature, focusing on the application of NGS in cancer care. Results: NGS enables high-resolution genomic profiling, identifying actionable mutations (e.g., EGFR, KRAS, and ALK) and immunotherapy biomarkers (e.g., PD-L1, TMB, and MSI), guiding personalized treatment selection and improving outcomes in advanced malignancies. Liquid biopsy enhances diagnostic accessibility and enables real-time monitoring of minimal residual disease and treatment resistance. Despite these advances, widespread clinical adoption remains constrained by technical limitations (e.g., coverage uniformity and sample quality), economic challenges (high costs and complex reimbursement), and interpretative issues, including the management of variants of uncertain significance (VUSs). Conclusions: NGS is central to precision oncology, enabling molecularly driven cancer care. Integration with artificial intelligence, single-cell sequencing, spatial transcriptomics, multi-omics, and nanotechnology promises to overcome current limitations, advancing personalized treatment strategies. Standardization of workflows, cost reduction, and improved bioinformatics expertise are critical for its full clinical integration. Full article
29 pages, 23285 KB  
Article
Methodological Comparison of Short-Read and Long-Read Sequencing Methods on Colorectal Cancer Samples
by Nikolett Szakállas, Alexandra Kalmár, Kristóf Róbert Rada, Marianna Kucarov, Tamás Richárd Linkner, Barbara Kinga Barták, István Takács and Béla Molnár
Int. J. Mol. Sci. 2025, 26(18), 9254; https://doi.org/10.3390/ijms26189254 - 22 Sep 2025
Viewed by 418
Abstract
Colorectal cancer (CRC) is driven by a complex spectrum of somatic mutations and structural variants that contribute to tumor heterogeneity and therapy resistance. In this study, we performed a comparative analysis of short-read Illumina and long-read Nanopore sequencing technologies across multiple CRC sample [...] Read more.
Colorectal cancer (CRC) is driven by a complex spectrum of somatic mutations and structural variants that contribute to tumor heterogeneity and therapy resistance. In this study, we performed a comparative analysis of short-read Illumina and long-read Nanopore sequencing technologies across multiple CRC sample groups, encompassing diverse tissue morphologies. Our evaluation included general base-level metrics—such as nucleotide ratios, sequence match rates, and coverage—as well as variant calling performance, including variant allele frequency (VAF) distributions and pathogenic mutation detection rates. Focusing on clinically relevant genes (KRAS, BRAF, TP53, APC, PIK3CA, and others), we characterized platform-specific detection profiles and completed the ground truth validation of somatic KRAS and BRAF mutations. Structural variant (SV) analysis revealed Nanopore’s enhanced ability to resolve large and complex rearrangements, with consistently high precision across SV types, though recall varied by variant class and size. To enable direct comparison with the Illumina exome panel, we applied an exonic position reference file. To assess the impact of depth and PCR amplification, we completed an additional high-coverage Nanopore sequencing run. This analysis confirmed that PCR-free protocols preserve methylation signals more accurately, reinforcing Nanopore’s utility for integrated genomic and epigenomic profiling. Together, these findings underscore the complementary strengths of short- and long-read sequencing platforms in high-resolution cancer genomics, and we highlight the importance of coverage normalization, epigenetic fidelity, and rigorous benchmarking in variant discovery. Full article
(This article belongs to the Section Molecular Oncology)
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15 pages, 1778 KB  
Article
Novel Organomineral Complex with Prolonged Antitumor Action
by Olga Ilinskaya, Galina Yakovleva, Pavel Zelenikhin, Alexey Kolpakov, William Kurdy, Mikhail Glukhov, Igor Sedov and Sergey Kharintsev
Int. J. Mol. Sci. 2025, 26(18), 9205; https://doi.org/10.3390/ijms26189205 - 20 Sep 2025
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Abstract
Blocking the MAPK pathway is a strategy to stop cancer cells proliferation. Despite all the successes, the acquisition of drug resistance by cells, as well as the mutational status of the downstream protein KRAS, reduces the tumor response to therapy. Ribonuclease binase from [...] Read more.
Blocking the MAPK pathway is a strategy to stop cancer cells proliferation. Despite all the successes, the acquisition of drug resistance by cells, as well as the mutational status of the downstream protein KRAS, reduces the tumor response to therapy. Ribonuclease binase from Bacillus pumilus is among the agents that block this pathway through direct interaction with EGFR and RAS. The present study is aimed at the design, optimization, and characterization of a novel complex based on antitumor binase immobilized on microgranular clinoptilolite-containing rock to ensure its prolonged release in the gastrointestinal tract. A set of modern methods including transmission electron microscopy, scanning electron microscopy, and computed tomography was used to characterize the granularity, porosity and elemental composition of the carrier. The size of binase particles, measured by atomic force microscopy at 7 nm, allows enzyme penetration into meso- and macropores of the carrier. Calorimetric results confirm that binase is stable at high temperatures, even exceeding those in the body, and retains catalytic activity in the model fluids of the gastrointestinal tract. The parameters for processing a natural clinoptilolite-containing rock and the conditions for binase sorption were selected. The gradual release of the enzyme from the carrier lasts over 20 h, which provides cytotoxicity towards human adenocarcinoma cells during movement through the gastrointestinal tract. Thus, for the first time a promising long-acting complex with antitumor and detoxifying properties was successfully created. Full article
(This article belongs to the Section Molecular Oncology)
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11 pages, 230 KB  
Article
Factors Associated with the Detection of Actionable Genomic Alterations Using Liquid Biopsy in Biliary Tract Cancer
by Hiroshi Shimizu, Rei Suzuki, Hiroyuki Asama, Kentaro Sato, Kento Osawa, Rei Ohira, Keisuke Kudo, Mitsuru Sugimoto and Hiromasa Ohira
Cancers 2025, 17(18), 3071; https://doi.org/10.3390/cancers17183071 - 19 Sep 2025
Viewed by 359
Abstract
Background: Blood-based comprehensive genomic profiling (CGP), a form of liquid biopsy, is often used for biliary tract cancer (BTC) when tissue-based CGP (tissue CGP) is unavailable, despite lower detection rates. This study explored factors linked to detecting actionable genomic alterations to optimize [...] Read more.
Background: Blood-based comprehensive genomic profiling (CGP), a form of liquid biopsy, is often used for biliary tract cancer (BTC) when tissue-based CGP (tissue CGP) is unavailable, despite lower detection rates. This study explored factors linked to detecting actionable genomic alterations to optimize its use. Methods: We retrospectively analyzed BTC cases in Japan’s C-CAT (June 2019–January 2025), restricting panel comparisons to FoundationOne® CDx (F1; n = 5019) and FoundationOne® Liquid CDx (F1L; n = 1550). Missing covariates were handled by multiple imputations (m = 20). Between-panel balance used 1:1 propensity-score matching (caliper 0.2). Outcomes were modeled with logistic regression. Targets included MSI-H, TMB-H, FGFR2/RET/NTRK fusions, BRAF V600E, KRAS G12C, IDH1 mutations, and ERBB2 amplification. An exploratory analysis stratified results by the number of prespecified enrichment factors (0–4). Liquid biopsy was performed using plasma-based comprehensive genomic profiling assays (FoundationOne® Liquid). Results: Missingness was low; after matching (n = 1549 per group) covariates were well balanced (all|SMD|≤0.05). Detection of any actionable alteration was lower with F1L than F1 (16.8% vs. 24.8%; OR 0.61, 95% CI 0.49–0.75; p < 0.001). F1L also had lower TMB-H (OR 0.62, 0.43–0.90; p = 0.01) and ERBB2 amplification (OR 0.42, 0.31–0.57; p < 0.001), with no significant differences for MSI-H, IDH1, KRAS G12C, or BRAF V600E. Within F1L, non-perihilar location (OR 2.05), liver (1.90), lymph-node (1.41), and lung metastases (1.52) predicted detection of actionable genomic alterations. F1L detection increased from 5.8% (zero factors) to 32.8% (four factors), approximating tissue at three factors. Conclusions: The utility of liquid biopsy can be maximized by carefully selecting samples on the basis of conditions that increase the detection rate. Full article
(This article belongs to the Section Cancer Informatics and Big Data)
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