Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (2,723)

Search Parameters:
Keywords = carcinoma biomarkers

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
25 pages, 1677 KiB  
Review
The Multifaceted Role of Growth Differentiation Factor 15 (GDF15): A Narrative Review from Cancer Cachexia to Target Therapy
by Daria Maria Filippini, Donatella Romaniello, Francesca Carosi, Laura Fabbri, Andrea Carlini, Raffaele Giusti, Massimo Di Maio, Salvatore Alfieri, Mattia Lauriola, Maria Abbondanza Pantaleo, Lorena Arribas, Marc Oliva, Paolo Bossi and Laura Deborah Locati
Biomedicines 2025, 13(8), 1931; https://doi.org/10.3390/biomedicines13081931 (registering DOI) - 8 Aug 2025
Abstract
Background: Growth Differentiation Factor 15 (GDF15) has emerged as a key biomarker and therapeutic target in oncology, with roles extending beyond cancer cachexia. Elevated GDF15 levels correlate with poor prognosis across several solid tumors, including colorectal, gastric, pancreatic, breast, lung, prostate, and head [...] Read more.
Background: Growth Differentiation Factor 15 (GDF15) has emerged as a key biomarker and therapeutic target in oncology, with roles extending beyond cancer cachexia. Elevated GDF15 levels correlate with poor prognosis across several solid tumors, including colorectal, gastric, pancreatic, breast, lung, prostate, and head and neck cancers. GDF15 modulates tumor progression through PI3K/AKT, MAPK/ERK, and SMAD2/3 signaling, thereby promoting epithelial-to-mesenchymal transition, metastasis, immune evasion, and chemoresistance via Nrf2 stabilization and oxidative stress regulation. Methods: We performed a narrative review of the literature focusing on the role of GDF15 in solid tumors, with a particular emphasis on head and neck cancers. Results: In head and neck squamous cell carcinoma (HNSCC), GDF15 overexpression is linked to aggressive phenotypes, radioresistance, poor response to induction chemotherapy, and failure of immune checkpoint inhibitors (ICIs). Similar associations are observed in colorectal, pancreatic, and prostate cancer, where GDF15 contributes to metastasis and therapy resistance. Targeting the GDF15-GFRAL axis appears therapeutically promising: the monoclonal antibody ponsegromab improved cachexia-related outcomes in the PROACC-1 trial, while visugromab combined with nivolumab enhanced immune response in ICI-refractory tumors. Conclusions: Further investigation is warranted to delineate the role of GDF15 across malignancies, refine patient selection, and evaluate combinatorial approaches with existing treatments. Full article
(This article belongs to the Special Issue Head and Neck Tumors, 4th Edition)
Show Figures

Figure 1

17 pages, 1865 KiB  
Article
Biomarkers in Renal Cell Carcinoma: A Systematic Review and Immunohistochemical Validation Study
by Brett Berezowski, Robert Boothe, Billy Chaplin, Sharon J. Del Vecchio, Zakariya Fares, Tyrone L. R. Humphries, Keng Lim Ng, Taylor Noonan, Hemamali Samaratunga, Aaron Urquhart, David A. Vesey, Simon T. Wood, Glenda C. Gobe and Robert J. Ellis
Cancers 2025, 17(15), 2588; https://doi.org/10.3390/cancers17152588 - 6 Aug 2025
Abstract
Background and Objectives: The worldwide incidence of renal cell carcinoma (RCC) rose by 22% between 2012 and 2022. In Australia, RCC accounted for 2.8% of all cancer diagnoses and contributing to 1.8% of cancer-related deaths. Identification of RCC biomarkers may aid in [...] Read more.
Background and Objectives: The worldwide incidence of renal cell carcinoma (RCC) rose by 22% between 2012 and 2022. In Australia, RCC accounted for 2.8% of all cancer diagnoses and contributing to 1.8% of cancer-related deaths. Identification of RCC biomarkers may aid in diagnosis and management. Methods: A systematic review of immunohistochemical markers of RCC studies published between 1990 and 2019 was undertaken to select candidate biomarkers of RCC. Immunohistochemical staining of 73 clear cell RCC tumors and paired normal tissue was undertaken using selected markers. Semi-quantitative and quantitative analysis of staining intensity between paired samples was undertaken to evaluate utility as potential biomarkers, using Chi-square tests and paired t-tests for analysis. As an exploratory analysis, staining intensity was also compared on clinical/demographic variables using linear and logistic regression. Results: There were 123 candidate biomarkers identified in 91 studies. Four candidate markers were selected for further investigation: aminopeptidase A (APA)/cluster of differentiation (CD)249, aminopeptidase N (APN)/CD13, gamma-glutamyl transferase (GGT), and neuron-specific enolase (NSE). APA, GGT, and APN all demonstrated reduced staining intensity in the tumor compared with normal tissue (p < 0.001 for all). NSE demonstrated a statistically significant increase in expression in tumor compared with normal tissue (p < 0.001), and this was more pronounced in patients aged >60 years (p = 0.038). Conclusions: The utility of APA, APN, and GGT as diagnostic biomarkers in clear cell RCC is limited. NSE may have some role as a biomarker for clear cell RCC, particularly among older patients; however, further investigation is required. Full article
(This article belongs to the Special Issue Optimizing Surgical Procedures and Outcomes in Renal Cancer)
Show Figures

Figure 1

23 pages, 1841 KiB  
Review
B Cell-Derived and Non-B Cell-Derived Free Light Chains: From Generation to Biological and Pathophysiological Roles
by Linyang Li, Huining Gu, Xiaoyan Qiu and Jing Huang
Int. J. Mol. Sci. 2025, 26(15), 7607; https://doi.org/10.3390/ijms26157607 - 6 Aug 2025
Abstract
Immunoglobulin light chains are essential components of intact immunoglobulins, traditionally believed to be produced exclusively by B cells. Physiologically, excess light chains not assembled into intact antibodies exist as free light chains (FLCs). Increasingly recognized as important biomarkers for diseases such as multiple [...] Read more.
Immunoglobulin light chains are essential components of intact immunoglobulins, traditionally believed to be produced exclusively by B cells. Physiologically, excess light chains not assembled into intact antibodies exist as free light chains (FLCs). Increasingly recognized as important biomarkers for diseases such as multiple myeloma, systemic amyloidosis, and light chain-related renal injuries, FLCs have also been shown in recent decades to originate from non-B cell sources, including epithelial and carcinoma cells. This review primarily focuses on novel non-B cell-derived FLCs, which challenge the conventional paradigms. It systematically compares B cell-derived and non-B cell-derived FLCs, analyzing differences in genetic features, physicochemical properties, and functional roles in both health and disease. By elucidating the distinctions and similarities in their nature as immune regulators and disease mediators, we highlight the significant clinical potential of FLCs, particularly non-B cell-derived FLCs, for novel diagnostic and therapeutic strategies. Full article
(This article belongs to the Section Molecular Biology)
Show Figures

Figure 1

10 pages, 826 KiB  
Article
Differential Associations of PIVKA-II with Epithelial and Mesenchymal Features in HCC and PDAC
by Farina Antonella, Cicolani Gaia, Viggiani Valentina, Maini Matteo, Angeloni Antonio and Anastasi Emanuela
Int. J. Mol. Sci. 2025, 26(15), 7581; https://doi.org/10.3390/ijms26157581 - 5 Aug 2025
Abstract
Hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC) are aggressive malignancies characterized by a poor prognosis and resistance to conventional therapies. Mounting evidence suggests the pivotal role of epithelial–mesenchymal transition (EMT) in tumor progression, metastasis, and therapeutic resistance in these cancers. Protein induced [...] Read more.
Hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC) are aggressive malignancies characterized by a poor prognosis and resistance to conventional therapies. Mounting evidence suggests the pivotal role of epithelial–mesenchymal transition (EMT) in tumor progression, metastasis, and therapeutic resistance in these cancers. Protein induced by vitamin K absence II (PIVKA-II)—a valuable HCC detector—has ultimately emerged as a potentially relevant biomarker in PDAC, serving as both a serum biomarker and a prognostic indicator. This study investigates the putative link between PIVKA-II expression and the EMT process in HCC and PDAC. Using a Western blot analysis and electrochemiluminescence immunoassay (ECLIA), we quantified PIVKA-II serum levels alongside two canonical EMT markers—Vimentin and E-cadherin—in selected cohorts. Emerging data suggest a dual, context-dependent role for PIVKA-II. Beyond its diagnostic value in both malignancies, its co-expression with EMT markers points to a potential mechanistic involvement in tumor invasiveness and phenotypic plasticity. Notably, the selective detection of E-cadherin in HCC implies limited EMT activation and a preservation of the epithelial phenotype, whereas the higher expression of Vimentin in PDAC reflects a more substantial shift toward EMT. We provide a comprehensive analysis of key molecular markers, their involvement in EMT-driven pathophysiological mechanisms, and their potential as novel diagnostic tools. Full article
(This article belongs to the Section Macromolecules)
Show Figures

Figure 1

23 pages, 1642 KiB  
Review
The Multifaceted Role of Autophagy in Nasopharyngeal Carcinoma: Translational Perspectives on Pathogenesis, Biomarkers, Treatment Resistance, and Emerging Therapies
by Abdul L. Shakerdi, Emma Finnegan, Yin-Yin Sheng and Graham P. Pidgeon
Cancers 2025, 17(15), 2577; https://doi.org/10.3390/cancers17152577 - 5 Aug 2025
Abstract
Background: Nasopharyngeal carcinoma (NPC) is an epithelial malignancy arising from the nasopharyngeal mucosa. Despite treatment advances such as the use of intensity-modulated radiotherapy and immune checkpoint inhibitors, resistance remains a significant clinical challenge. Many tumours are also diagnosed at an advanced stage associated [...] Read more.
Background: Nasopharyngeal carcinoma (NPC) is an epithelial malignancy arising from the nasopharyngeal mucosa. Despite treatment advances such as the use of intensity-modulated radiotherapy and immune checkpoint inhibitors, resistance remains a significant clinical challenge. Many tumours are also diagnosed at an advanced stage associated with poor prognosis. Objective: This review aims to explore the biological roles of autophagy in NPC, primarily highlighting its involvement in disease pathogenesis and treatment resistance. Methods: We performed a review of the recent literature examining the role of autophagy-related pathways in NPC pathogenesis, biomarker discovery, and therapeutic targeting. Results: Autophagy plays a dual role in NPC as it contributes to both tumour suppression and progression. It is involved in tumour initiation, metastasis, immune modulation, and treatment resistance. Autophagy-related genes such as SQSTM1, Beclin-1, and AURKA may serve as prognostic and therapeutic biomarkers. Various strategies are being investigated for their role to modulate autophagy using pharmacologic inhibitors, RNA interventions, and natural compounds. Conclusions: Further research into autophagy’s context-dependent roles in NPC may inform the development of personalised therapies and allow progress in translational and precision oncology. Full article
Show Figures

Figure 1

16 pages, 2235 KiB  
Article
Plasma Lysophosphatidylcholine Levels Correlate with Prognosis and Immunotherapy Response in Squamous Cell Carcinoma
by Tomoyuki Iwasaki, Hidekazu Shirota, Eiji Hishinuma, Shinpei Kawaoka, Naomi Matsukawa, Yuki Kasahara, Kota Ouchi, Hiroo Imai, Ken Saijo, Keigo Komine, Masanobu Takahashi, Chikashi Ishioka, Seizo Koshiba and Hisato Kawakami
Int. J. Mol. Sci. 2025, 26(15), 7528; https://doi.org/10.3390/ijms26157528 - 4 Aug 2025
Viewed by 253
Abstract
Cancer is a systemic disease rather than a localized pathology and is characterized by widespread effects, including whole-body exhaustion and chronic inflammation. A thorough understanding of cancer pathophysiology requires a systemic approach that accounts for the complex interactions between cancer cells and host [...] Read more.
Cancer is a systemic disease rather than a localized pathology and is characterized by widespread effects, including whole-body exhaustion and chronic inflammation. A thorough understanding of cancer pathophysiology requires a systemic approach that accounts for the complex interactions between cancer cells and host tissues. To explore these dynamics, we employed a comprehensive metabolomic analysis of plasma samples from patients with either esophageal or head and neck squamous cell carcinoma (SCC). Plasma samples from 149 patients were metabolically profiled and correlated with clinical data. Among the metabolites identified, lysophosphatidylcholine (LPC) emerged as the sole biomarker strongly correlated with prognosis. A significant reduction in plasma LPC levels was linked to poorer overall survival. Plasma LPC levels demonstrated minimal correlation with patient-specific factors, such as tumor size and general condition, but showed significant association with the response to immune checkpoint inhibitor therapy. Proteomic and cytokine analyses revealed that low plasma LPC levels reflected systemic chronic inflammation, characterized by high levels of inflammatory proteins, the cytokines interleukin-6 and tumor necrosis factor-α, and coagulation-related proteins. These findings indicate that plasma LPC levels may be used as reliable biomarkers for predicting prognosis and evaluating the efficacy of immunotherapy in patients with SCC. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors)
Show Figures

Figure 1

12 pages, 463 KiB  
Article
Association Between BRAF V600E Allele Frequency and Aggressive Behavior in Papillary Thyroid Microcarcinoma
by Luiza Tatar, Saruchi Bandargal, Marc P. Pusztaszeri, Véronique-Isabelle Forest, Michael P. Hier, Jasmine Kouz, Raisa Chowdhury and Richard J. Payne
Cancers 2025, 17(15), 2553; https://doi.org/10.3390/cancers17152553 - 1 Aug 2025
Viewed by 208
Abstract
Background/Objectives: Papillary thyroid microcarcinoma (MPTC), a subset of papillary thyroid carcinoma (PTC), is increasingly detected with advanced imaging. While most MPTCs are indolent, some exhibit aggressive behavior, complicating clinical management. The BRAF V600E mutation, common in PTC, is linked to aggressive features, [...] Read more.
Background/Objectives: Papillary thyroid microcarcinoma (MPTC), a subset of papillary thyroid carcinoma (PTC), is increasingly detected with advanced imaging. While most MPTCs are indolent, some exhibit aggressive behavior, complicating clinical management. The BRAF V600E mutation, common in PTC, is linked to aggressive features, and its allele frequency (AF) may serve as a biomarker for tumor aggressiveness. This study explored the association between BRAF V600E AF and aggressive histopathological features in MPTC. Methods: Data from 1 January 2016 to 23 December 2023 were retrieved from two McGill University teaching hospitals. Inclusion criteria comprised patients aged ≥ 18 years with thyroid nodules ≤ 1 cm, documented BRAF V600E mutation and AF results, and available surgical pathology reports. Tumor aggressiveness was defined as the presence of lymph node metastasis, aggressive histological subtype (tall cell, hobnail, columnar, solid/trabecular or diffuse sclerosing), extra thyroidal extension, or extensive lymphovascular extension. Associations were explored using t-tests. Results: Among 1564 records, 34 met the inclusion criteria and were included in analyses. The mean BRAF V600E AF was significantly higher in aggressive tumors (23.58) compared to non-aggressive tumors (13.73) (95% CI: −18.53 to −1.16, p = 0.03). Although not statistically significant, trends were observed for higher BRAF V600E AF in tumors with lymph node metastasis (mean AF: 25.4) compared to those without (mean AF: 16.67, p = 0.08). No significant difference was noted in BRAF V600E AF by histological subtype (mean AF for aggressive: 19.57; non-aggressive: 19.15, p = 0.94). Conclusions: Elevated BRAF V600E AF is associated with aggressive behavior in MPTC, highlighting its potential as a biomarker to inform treatment strategies. Larger studies are warranted to validate these findings and enhance clinical management of MPTC patients. Full article
(This article belongs to the Special Issue Thyroid Cancer: Diagnosis, Prognosis and Treatment (2nd Edition))
Show Figures

Figure 1

15 pages, 1566 KiB  
Systematic Review
Diagnostic Accuracy of Insulinoma-Associated Protein 1 in Pulmonary Neuroendocrine Carcinomas: A Systematic Review and Meta-Analysis
by Risa Waki, Saya Haketa, Riona Aburaki and Nobuyuki Horita
Cancers 2025, 17(15), 2544; https://doi.org/10.3390/cancers17152544 - 31 Jul 2025
Viewed by 161
Abstract
Background and Objective: Insulinoma-associated protein 1 (INSM1) is a novel immunohistochemical marker with potential utility in identifying neuroendocrine differentiation in lung cancer. Unlike conventional neuroendocrine (NE) markers, INSM1 can potentially serve as a standalone diagnostic biomarker. This study presents the first meta-analysis assessing [...] Read more.
Background and Objective: Insulinoma-associated protein 1 (INSM1) is a novel immunohistochemical marker with potential utility in identifying neuroendocrine differentiation in lung cancer. Unlike conventional neuroendocrine (NE) markers, INSM1 can potentially serve as a standalone diagnostic biomarker. This study presents the first meta-analysis assessing the diagnostic accuracy of using INSM1 to distinguish LCNEC and SCLC from other lung cancer subtypes, addressing the variability across individual studies. Methods: A systematic review and meta-analysis were conducted to comprehensively evaluate the diagnostic performance of INSM1 in the pathological classification of lung cancer. The online databases PubMed, Web of Science, and Embase were systematically searched for data collection. Studies reporting the sensitivity and specificity of INSM1 in diagnosing LCNEC and SCLC were included. Pooled estimates were calculated using two models: the NSCLC model, which distinguishes LCNEC from other non-small cell lung cancers (NSCLCs), and the lung cancer model, which differentiates both LCNEC and SCLC from non-neuroendocrine (non-NE) lung cancer. Results: Fourteen studies comprising 3,218 specimens were included in this systematic review and meta-analysis. In the NSCLC model, INSM1 demonstrated a pooled sensitivity of 0.67 (95% CI: 0.61–0.73) and specificity of 0.97 (95% CI: 0.96–0.98), with an area under the curve (AUC) of 0.943. In the lung cancer model, the pooled sensitivity and specificity were 0.86 (95% CI: 0.84–0.88) and 0.97 (95% CI: 0.96–0.98), respectively, with an AUC of 0.974. Conclusions: INSM1 demonstrated excellent diagnostic accuracy and consistently high specificity for pulmonary neuroendocrine carcinomas, supporting its utility as a reliable standalone immunohistochemical marker with the potential to replace conventional NE markers in the pathological diagnosis of LCNEC and SCLC. Full article
(This article belongs to the Section Systematic Review or Meta-Analysis in Cancer Research)
Show Figures

Figure 1

15 pages, 7649 KiB  
Article
S100A14 as a Potential Biomarker of the Colorectal Serrated Neoplasia Pathway
by Pierre Adam, Catherine Salée, Florence Quesada Calvo, Arnaud Lavergne, Angela-Maria Merli, Charlotte Massot, Noëlla Blétard, Joan Somja, Dominique Baiwir, Gabriel Mazzucchelli, Carla Coimbra Marques, Philippe Delvenne, Edouard Louis and Marie-Alice Meuwis
Int. J. Mol. Sci. 2025, 26(15), 7401; https://doi.org/10.3390/ijms26157401 - 31 Jul 2025
Viewed by 255
Abstract
Accounting for 15–30% of colorectal cancer cases, the serrated pathway remains poorly characterized compared to the adenoma–carcinoma sequence. It involves sessile serrated lesions as precursors and is characterized by BRAF mutations (BRAFV600E), CpG island hypermethylation, and microsatellite instability (MSI). Using label-free [...] Read more.
Accounting for 15–30% of colorectal cancer cases, the serrated pathway remains poorly characterized compared to the adenoma–carcinoma sequence. It involves sessile serrated lesions as precursors and is characterized by BRAF mutations (BRAFV600E), CpG island hypermethylation, and microsatellite instability (MSI). Using label-free proteomics, we compared normal tissue margins from patients with diverticular disease, sessile serrated lesions, low-grade adenomas, and high-grade adenomas. We identified S100A14 as significantly overexpressed in sessile serrated lesions compared to low-grade adenomas, high-grade adenomas, and normal tissues. This overexpression was confirmed by immunohistochemical scoring in an independent cohort. Gene expression analyses of public datasets showed higher S100A14 expression in BRAFV600E-mutated and MSI-H colorectal cancers compared to microsatellite stable BRAFwt tumors. This finding was confirmed by immunohistochemical scoring in an independent colorectal cancer cohort. Furthermore, single-cell RNA sequencing analysis from the Human Colon Cancer Atlas revealed that S100A14 expression in tumor cells positively correlated with the abundance of tumoral CD8+ cytotoxic T cells, particularly the CD8+ CXCL13+ subset, known for its association with a favorable response to immunotherapy. Collectively, our results demonstrate for the first time that S100A14 is a potential biomarker of serrated neoplasia and further suggests its potential role in predicting immunotherapy responses in colorectal cancer. Full article
(This article belongs to the Special Issue Molecular Diagnosis and Treatment of Colorectal Cancer)
Show Figures

Figure 1

12 pages, 1065 KiB  
Article
Clinico-Morphological Correlations with Ki-67 and p53 Immunohistochemical Expression in High-Grade Gastrointestinal Neuroendocrine Neoplasms
by Alexandra Dinu, Mariana Aşchie, Mariana Deacu, Anca Chisoi, Manuela Enciu, Oana Cojocaru and Sabina E. Vlad
Gastrointest. Disord. 2025, 7(3), 51; https://doi.org/10.3390/gidisord7030051 - 30 Jul 2025
Viewed by 215
Abstract
Background/Objectives: The 2019 WHO classification redefined high-grade gastrointestinal neuroendocrine neoplasms (GI NENs), encompassing not only poorly differentiated neuroendocrine carcinomas (NECs), but also well-differentiated grade 3 neuroendocrine tumors (NETs G3). Since both subtypes share a Ki-67 index > 20%, distinguishing them based solely on [...] Read more.
Background/Objectives: The 2019 WHO classification redefined high-grade gastrointestinal neuroendocrine neoplasms (GI NENs), encompassing not only poorly differentiated neuroendocrine carcinomas (NECs), but also well-differentiated grade 3 neuroendocrine tumors (NETs G3). Since both subtypes share a Ki-67 index > 20%, distinguishing them based solely on morphology is challenging. Prior studies have shown TP53 alterations in NECs but not in NETs. This study aimed to evaluate clinico-morphological parameters and the immunohistochemical (IHC) expression of p53 in high-grade GI NENs to identify relevant correlations. Methods: Tumors were stratified by Ki-67 index into two groups: >20–50% and >50%. p53 IHC expression was assessed as “wild-type” (1–20% positive tumor cells) or “non-wild-type” (absence or >20% positivity). Correlations were analyzed between Ki-67, p53 status, and various pathological features. Results: Significant correlations were found between the Ki-67 index and maximum tumor size, pT stage, lymphovascular invasion, perineural infiltration, and diagnostic classification. Similarly, p53 immunohistochemical status was significantly associated with lymphovascular invasion, lymph node metastasis, and tumor classification (NET G3 versus NEC, including NEC components of MiNENs). Conclusions: The findings support the value of Ki-67 and p53 as complementary biomarkers in the pathological evaluation of high-grade GI NENs. Their significant associations with key morphological parameters support their utility in differentiating NETs G3 from NECs, particularly in cases showing overlapping histological features. The immunohistochemical profile of p53 may serve as a useful diagnostic adjunct in routine practice. Full article
Show Figures

Figure 1

17 pages, 7610 KiB  
Article
Metabolomic Profiling of Hepatitis B-Associated Liver Disease Progression: Chronic Hepatitis B, Cirrhosis, and Hepatocellular Carcinoma
by Junsang Oh, Kei-Anne Garcia Baritugo, Jayoung Kim, Gyubin Park, Ki Jun Han, Sangheun Lee and Gi-Ho Sung
Metabolites 2025, 15(8), 504; https://doi.org/10.3390/metabo15080504 - 29 Jul 2025
Viewed by 288
Abstract
Background/Objective: The hepatitis B virus (HBV) can cause chronic hepatitis B (CHB), which can rapidly progress into fatal liver cirrhosis (CHB-LC) and hepatocellular carcinoma (CHB-HCC). Methods: In this study, we investigated metabolites associated with distinct clinical stages of HBV infection for the identification [...] Read more.
Background/Objective: The hepatitis B virus (HBV) can cause chronic hepatitis B (CHB), which can rapidly progress into fatal liver cirrhosis (CHB-LC) and hepatocellular carcinoma (CHB-HCC). Methods: In this study, we investigated metabolites associated with distinct clinical stages of HBV infection for the identification of stage-specific serum metabolite biomarkers using 1H-NMR-based metabolomics. Results: A total of 64 serum metabolites were identified, among which six core discriminatory metabolites, namely isoleucine, tryptophan, histamine (for CHB), and pyruvate, TMAO, lactate (for CHB-HCC), were consistently significant across univariate and multivariate statistical analyses, including ANOVA with FDR, OPLS-DA, and VIP scoring. These metabolites were closely linked to key metabolic pathways, such as propanoate metabolism, pyruvate metabolism, and the Warburg effect. Conclusions: The findings suggest that these six core metabolites serve as potential stage-specific biomarkers for CHB, CHB-LC, and CHB-HCC, respectively, and offer a foundation for the future development of metabolomics-based diagnostic and therapeutic strategies. Full article
Show Figures

Graphical abstract

27 pages, 5430 KiB  
Article
Gene Monitoring in Obesity-Induced Metabolic Dysfunction in Rats: Preclinical Data on Breast Neoplasia Initiation
by Francisco Claro, Joseane Morari, Camila de Angelis, Emerielle Cristine Vanzela, Wandir Antonio Schiozer, Lício Velloso and Luis Otavio Zanatta Sarian
Int. J. Mol. Sci. 2025, 26(15), 7296; https://doi.org/10.3390/ijms26157296 - 28 Jul 2025
Viewed by 310
Abstract
Obesity and metabolic dysfunction are established risk factors for luminal breast cancer, yet current preclinical models inadequately recapitulate the complex metabolic and immune interactions driving tumorigenesis. To develop and characterize an immunocompetent rat model of luminal breast cancer induced by chronic exposure to [...] Read more.
Obesity and metabolic dysfunction are established risk factors for luminal breast cancer, yet current preclinical models inadequately recapitulate the complex metabolic and immune interactions driving tumorigenesis. To develop and characterize an immunocompetent rat model of luminal breast cancer induced by chronic exposure to a cafeteria diet mimicking Western obesogenic nutrition, female rats were fed a cafeteria diet or standard chow from weaning. Metabolic parameters, plasma biomarkers (including leptin, insulin, IGF-1, adiponectin, and estrone), mammary gland histology, tumor incidence, and gene expression profiles were longitudinally evaluated. Gene expression was assessed by PCR arrays and qPCR. A subgroup underwent dietary reversal to assess the reversibility of molecular alterations. Cafeteria diet induced significant obesity (mean weight 426.76 g vs. 263.09 g controls, p < 0.001) and increased leptin levels without altering insulin, IGF-1, or inflammatory markers. Histological analysis showed increased ductal ectasia and benign lesions, with earlier fibroadenoma and luminal carcinoma development in diet-fed rats. Tumors exhibited luminal phenotype, low Ki67, and elevated PAI-1 expression. Gene expression alterations were time point specific and revealed early downregulation of ID1 and COX2, followed by upregulation of MMP2, THBS1, TWIST1, and PAI-1. Short-term dietary reversal normalized several gene expression changes. Overall tumor incidence was modest (~12%), reflecting early tumor-promoting microenvironmental changes rather than aggressive carcinogenesis. This immunocompetent cafeteria diet rat model recapitulates key metabolic, histological, and molecular features of obesity-associated luminal breast cancer and offers a valuable platform for studying early tumorigenic mechanisms and prevention strategies without carcinogen-induced confounders. Full article
(This article belongs to the Special Issue Genomic Research in Carcinogenesis, Cancer Progression and Recurrence)
Show Figures

Figure 1

16 pages, 2293 KiB  
Article
BIM-Ken: Identifying Disease-Related miRNA Biomarkers Based on Knowledge-Enhanced Bio-Network
by Yanhui Zhang, Kunjie Dong, Wenli Sun, Zhenbo Gao, Jianjun Zhang and Xiaohui Lin
Genes 2025, 16(8), 902; https://doi.org/10.3390/genes16080902 - 28 Jul 2025
Viewed by 214
Abstract
The identification of microRNA (miRNA) biomarkers is crucial in advancing disease research and improving diagnostic precision. Network-based analysis methods are powerful for identifying disease-related biomarkers. However, it is a challenge to generate a robust molecular network that can accurately reflect miRNA interactions and [...] Read more.
The identification of microRNA (miRNA) biomarkers is crucial in advancing disease research and improving diagnostic precision. Network-based analysis methods are powerful for identifying disease-related biomarkers. However, it is a challenge to generate a robust molecular network that can accurately reflect miRNA interactions and define reliable miRNA biomarkers. To tackle this issue, we propose a disease-related miRNA biomarker identification method based on the knowledge-enhanced bio-network (BIM-Ken) by combining the miRNA expression data and prior knowledge. BIM-Ken constructs the miRNA cooperation network by examining the miRNA interactions based on the miRNA expression data, which contains characteristics about the specific disease, and the information of the network nodes (miRNAs) is enriched by miRNA knowledge (i.e., miRNA-disease associations) from databases. Further, BIM-Ken optimizes the miRNA cooperation network using the well-designed GAE (graph auto-encoder). We improve the loss function by introducing the functional consistency and the difference prompt, so as to facilitate the optimized network to keep the intrinsically important characteristics of the miRNA data about the specific disease and the prior knowledge. The experimental results on the public datasets showed the superiority of BIM-Ken in classification. Subsequently, BIM-Ken was applied to analyze renal cell carcinoma data, and the defined key modules demonstrated involvement in the cancer-related pathways with good discrimination ability. Full article
(This article belongs to the Section Bioinformatics)
Show Figures

Figure 1

34 pages, 11716 KiB  
Article
UPLC-MS/MS Metabolomics Reveals Babao Dan’s Mechanisms in MASH Treatment with Integrating Network Pharmacology and Molecular Docking
by Shijiao Zhang, Yanding Su, Ao Han, He Qi, Jiade Zhao and Xiangjun Qiu
Pharmaceuticals 2025, 18(8), 1111; https://doi.org/10.3390/ph18081111 - 25 Jul 2025
Viewed by 243
Abstract
Background: Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive disease that easily develops into cirrhosis and hepatocellular carcinoma, but its pathogenesis is not clear, and most therapeutic drugs have obvious limitations. However, Babao Dan (BBD) has a good therapeutic effect on liver disease, [...] Read more.
Background: Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive disease that easily develops into cirrhosis and hepatocellular carcinoma, but its pathogenesis is not clear, and most therapeutic drugs have obvious limitations. However, Babao Dan (BBD) has a good therapeutic effect on liver disease, but its treatment mechanism is still to be studied. Therefore, we further investigated the mechanism of BBD in treating MASH. Methods: We predicted BBD-related targets through network pharmacology and further verified the binding ability of BBD-related targets through molecular docking. We also detected relevant indicators before and after model treatment, as well as metabolomics analysis and identification of the mechanism of action of BBD on MASH. Results: Through network pharmacology methods, 158 key cross targets and the top 10 core targets were identified, and it was determined that the PI3K-AKT signaling pathway plays an important regulatory role in the treatment of MASH with BBD. The molecular docking results indicate that the representative compounds quercetin and 17 Beta Estradiol have good binding activity with five core targets. Metabolomics has identified four metabolic biomarkers, such as Piceid, and it is determined that the key pathway for BBD treatment of MASH is the bile secretion pathway. Conclusions: BBD effectively treats MASH by modulating Piceid and other biomarkers, targeting ESR1 and other core proteins via quercetin and 17-beta-estradiol, and regulating the PI3K-AKT and bile secretion pathways to alleviate liver injury. Full article
(This article belongs to the Section Pharmacology)
Show Figures

Graphical abstract

17 pages, 440 KiB  
Review
Diagnosis and Management of Upper Tract Urothelial Carcinoma: A Review
by Domenique Escobar, Christopher Wang, Noah Suboc, Anishka D’Souza and Varsha Tulpule
Cancers 2025, 17(15), 2467; https://doi.org/10.3390/cancers17152467 - 25 Jul 2025
Viewed by 500
Abstract
Background/Objectives: Upper tract urothelial carcinoma (UTUC) is a rare and biologically distinct subset of urothelial malignancies, comprising approximately 5–10% of urothelial cancers. UTUC presents unique diagnostic and therapeutic challenges, with both a higher likelihood of invasive disease at presentation and a less favorable [...] Read more.
Background/Objectives: Upper tract urothelial carcinoma (UTUC) is a rare and biologically distinct subset of urothelial malignancies, comprising approximately 5–10% of urothelial cancers. UTUC presents unique diagnostic and therapeutic challenges, with both a higher likelihood of invasive disease at presentation and a less favorable prognosis compared to urothelial carcinoma of the bladder. Current treatment strategies for UTUC are largely derived from bladder cancer studies, underscoring the need for UTUC-directed research. This review provides a comprehensive overview of UTUC, encompassing diagnostic approaches, systemic and intraluminal therapies, surgical management, and future directions. Methods: A narrative review was conducted synthesizing evidence from guideline-based recommendations, retrospective and prospective clinical studies, and ongoing trials focused on UTUC. Results: Neoadjuvant cisplatin-based chemotherapy is increasingly preferred in UTUC due to the risk of postoperative renal impairment that may preclude adjuvant cisplatin use. Surgical management includes kidney-sparing approaches and radical nephroureterectomy (RNU), with selection guided by tumor risk and patient comorbidities. While endoscopic management (EM) preserves renal function, it carries a higher recurrence and surveillance burden; RNU remains standard for high-risk cases. Systemic therapy for advanced and metastatic UTUC mirrors that of bladder urothelial carcinoma. Enfortumab vedotin (EV) plus pembrolizumab showed superior efficacy over chemotherapy in the EV-302 trial, with improved response rate, progression-free survival, and overall survival across subgroups, including UTUC. For patients ineligible for EV, the CheckMate-901 study supported first-line chemoimmunotherapy with gemcitabine, cisplatin, and nivolumab. Further systemic therapy strategies include maintenance avelumab post-chemotherapy (JAVELIN Bladder 100), targeted therapies such as erdafitinib (THOR trial), and trastuzumab deruxtecan (DESTINY-PanTumor02) in FGFR2/3-altered and HER2-positive disease, respectively. Conclusions: Historically, the therapeutic landscape of UTUC has been extrapolated from bladder cancer; however, ongoing research specific to UTUC is deriving more precise regimens involving the use of immune checkpoint inhibitors, antibody–drug conjugates, and biomarker-driven therapies. Full article
(This article belongs to the Special Issue Upper Tract Urothelial Carcinoma: Current Knowledge and Perspectives)
Show Figures

Figure 1

Back to TopTop