Search Results (37)

Gastric cancer (GC) is characterized by heterogeneity and complexity and remains one of the leading causes of cancer-related deaths. The molecular mechanisms underlying carcinogenesis and the progression of GC have been central to scientific research and urgently need to be elucidated. With the potent development of next-generation sequencing technologies, a vast amount of bioinformatic data—including genomics, epigenomics, transcriptomics, proteomics, and metabolomics—has been accumulated, providing an extraordinary prospect to explore the heterogeneity and intricacy of GC. Nevertheless, the enormous amount of data created by bioinformatics analyses presents considerable analytical challenges. The application of artificial intelligence (AI), including machine learning and deep learning, has emerged as a powerful resolution to these challenges, obtaining useful information from exponential omics data, particularly in GC. The integration of AI with multi-omics approaches in GC research offers novel insights and powerful tools for gaining a deeper understanding of cancer’s complexities. This article reviews the latest research and progress of AI and bioinformatics analysis in GC oncology over the past several years, focusing on the landscape of GC carcinogenesis, progression, and metastasis. We also discuss the current challenges for improving performance and highlight future directions for more precise and effective treatments for GC patients. Full article

Human papillomavirus (HPV) integration is recognized as a hallmark event in cervical carcinogenesis. However, it does not represent a routine phase of the viral life cycle but rather a stochastic occurrence, often constituting a dead-end pathway for the virus. High-risk human papillomavirus (hr-HPV) exhibits a greater propensity for integration. The progression from initial infection to genomic integration constitutes a dynamic multi-step oncogenic process in the development of cervical cancer (CC). This process involves viral entry, immune evasion, persistent infection, and ultimately integration. This article innovatively provides a comprehensive overview of this multi-stage mechanism: HPV, via the L1/L2 proteins, mediates internalization and establishes infection. Subsequently, under the influence of factors such as the host’s genetic background, vaginal microbiota imbalance, and immune evasion, the host’s DNA damage response (DDR) pathways are activated. Viral DNA integrates into host genome vulnerable sites (e.g., 3q28 and 8q24) through microhomology-mediated end joining (MMEJ) or other alternative pathways. Following integration, the expression of viral oncogenes persists, triggering host genomic rearrangements, aberrant epigenetic modifications, and immune microenvironment remodeling, all of which collectively drive cervical cancer progression. The study further reveals the clinical potential of HPV integration as a highly specific molecular biomarker, offering new perspectives for precision screening and targeted therapy. This dynamic model deepens our understanding of the HPV carcinogenic mechanism and provides a theoretical basis for intervention strategies. Full article

After delivering my Keynote address to the young scientists at the International Gap Junction meeting, “International Colloquium on Gap Junctions and Cancer: Discussing how cellular communication modifies carcinogenesis and cancer treatment outcomes” (San Paulo, Brazil, 10–14 July 2023), I was asked to condense the talk into a manuscript covering the 50+ years of my scientific journey of basic biomedical research. While this journey had to omit so many important experiences, people and external events, I have tried to illustrate how my initial motivation, personal perspective of my abilities, and naïve goal as a young scientist did not prepare me for the non-linear path to where I ended. That path had many twists, turns, barriers, disappointments, surprises and wrong directions, as well as associations with co-workers, students and collaborators who afforded me with great wisdom, support and technical advice. In the history of science, few individuals have left their footprints in a straight path; however, my early education in human evolutionary genetics provided me a strong background framework, on which multiple other acquired disciplines, forced by circumstances along my uneven journey, allowed me to grow intellectually, as well as making me aware of my limitations. As my late mentor, Dr. Van Rensselaer Potter said: “… humility with responsibility”. At the completion of my experimental journey, I continued to reflect on the implied meanings of my and others’ results to view the current state of collected knowledge on global health issues as one of all scientists’ obligations, namely, to weigh the value and bioethical implications of our work to global society. “ Full article

Ovarian cancer remains a formidable global health burden, characterized by frequent late-stage diagnosis and elevated mortality rates attributable to its elusive pathogenesis and the critical lack of reliable early-detection biomarkers. Emerging investigations into the gut–vaginal microbiome axis have unveiled novel pathogenic mechanisms and potential diagnostic targets in ovarian carcinogenesis. This comprehensive review systematically examines the compositional alterations in and functional interplay between vaginal and intestinal microbial communities in ovarian cancer patients. We elucidate three principal mechanistic pathways through which microbial dysbiosis may drive oncogenesis: (1) estrogen-mediated metabolic reprogramming via β-glucuronidase activity; (2) chronic activation of pro-inflammatory cascades (particularly NF-κB and STAT3 signaling); (3) epigenetic silencing of tumor suppressor genes through DNA methyltransferase modulation. We propose an integrative diagnostic framework synthesizing multi-omics data—incorporating microbial profiles, metabolic signatures, pathway-specific molecular alterations, established clinical biomarkers, and imaging findings—within a multifactorial etiological paradigm. This innovative approach aims to enhance early-detection accuracy through machine learning-enabled multidimensional pattern recognition. By bridging microbial ecology with tumor biology, this review provides novel perspectives for understanding ovarian cancer etiology and advancing precision oncology strategies through microbiome-targeted diagnostic innovations. Full article

Breast cancer remains a leading cause of malignancy-related mortality among women, with rising global incidence. While surgical intervention is effective for early-stage breast cancer, drug therapy is indispensable, particularly for triple-negative breast cancer, where treatment options are still limited. Actaea vaginata, a traditional Chinese medicinal herb, has been historically applied for inflammatory conditions, including pharyngitis and stomatitis. However, its antitumor potential remains under-reported. In this study, a cycloartane triterpene saponin, beesioside O (BO), was isolated from this plant. Its antitumor activity was evaluated in vitro. Its potential therapeutic mechanisms were elucidated through network pharmacology. BO exhibited substantial potency in inhibiting breast cancer cells. Network pharmacology analysis uncovered 179 potential pharmacological targets of BO, which were predominantly concentrated in pathways, such as pathways in cancer, the PI3K-Akt signaling pathway, and chemical carcinogenesis receptor activation. Molecular docking analysis indicated that STAT3 exhibited minimal binding energy with BO. Additionally, molecular dynamics simulations verified the conformational stability of the BO-STAT3 complex. Western blot analysis demonstrated that STAT3 was downregulated following administration. These results imply that BO may exhibit a multi-target, synergistic therapeutic effect against breast cancer, with STAT3 recognized as a pivotal target. This study demonstrates the potential of BO for development as a chemotherapeutic agent for breast cancer treatment. It lays the groundwork for further exploration of BO’s bioactivity and provides valuable insights into its molecular mechanisms in breast cancer therapy. Full article

Background: While miRNAs are increasingly recognized for their role in tumorigenesis, their involvement in head and neck cancer (HNC) remains insufficiently explored. Additionally, the carcinogenic mechanisms of areca nut, a major habitual carcinogen in Southeast Asia, are not well understood. Methods and results: This study adopts a systematic approach to identify miRNA profiles associated with areca nut-induced HNC. Using miRNA microarray analysis, we identified 292 miRNAs dysregulated in areca nut-treated HNC cells, with 136 upregulated and 156 downregulated. Bioinformatic analysis of the TCGA-HNSC dataset uncovered a set of 692 miRNAs relevant to HNC development, comprising 449 overexpressed and 243 underexpressed in tumor tissues. Integrating these datasets, we defined a signature of 84 miRNAs, including 39 oncogenic miRNAs (OncomiRs) and 45 tumor-suppressive miRNAs (TsmiRs), highlighting their pivotal role in areca nut-induced carcinogenesis. MultiMiR analysis identified 740 genes cross-regulated by eight hub TsmiRs, significantly impacting key cancer-related pathways (p53, PI3K-AKT, MAPK, and Ras) and critical oncogenic processes. Moreover, we validated miR-499a-5p as a vital regulator, demonstrating its ability to mitigate areca nut-induced cancer progression by reducing cell migration, invasion, and chemoresistance. Conclusions: Thus, this miRNA signature addresses a crucial gap in understanding the molecular underpinnings of areca nut-induced carcinogenesis and offers a promising platform for clinical applications in risk assessment, diagnosis, and prognosis of areca nut-associated malignancies. Full article

Genetic biomarkers have played a pivotal role in the classification, prognostication, and guidance of clinical cancer therapies. Large-scale and multi-dimensional analyses of entire cancer genomes, as exemplified by projects like The Cancer Genome Atlas (TCGA), have yielded an extensive repository of data that holds the potential to unveil the underlying biology of these malignancies. Mutations stand out as the principal catalysts of cellular transformation. Nonetheless, other global genomic processes, such as alterations in gene expression and chromosomal re-arrangements, also play crucial roles in conferring cellular immortality. The incorporation of multi-omics data specific to cancer has demonstrated the capacity to enhance our comprehension of the molecular mechanisms underpinning carcinogenesis. This report elucidates how the integration of comprehensive data on methylation, gene expression, and copy number variations can effectively facilitate the unsupervised clustering of cancer samples. We have identified regressors that can effectively classify tumor and normal samples with an optimal integration of RNA sequencing, DNA methylation, and copy number variation while also achieving significant $p$-values. Further, these regressors were trained using linear and logistic regression with $k$-means clustering. For comparison, we employed autoencoder- and stacking-based omics integration and computed silhouette scores to evaluate the clusters. The proof of concept is illustrated using liver cancer data. Our analysis serves to underscore the feasibility of unsupervised cancer classification by considering genetic markers beyond mutations, thereby emphasizing the clinical relevance of additional global cellular parameters that contribute to the transformative process in cells. This work is clinically relevant because changes in gene expression and genomic re-arrangements have been shown to be signatures of cellular transformation across cancers, as well as in liver cancers. Full article

The complex and multi-stage processes of carcinogenesis are accompanied by a number of phenomena related to the potential involvement of various chemopreventive factors, which include, among others, compounds of natural origin such as flavonols. The use of flavonols is not only promising but also a recognized strategy for cancer treatment. The chemopreventive impact of flavonols on cancer arises from their ability to act as antioxidants, impede proliferation, promote cell death, inhibit angiogenesis, and regulate the immune system through involvement in diverse forms of cellular death. So far, the molecular mechanisms underlying the regulation of apoptosis, autophagy, necroptosis, pyroptosis, ferroptosis, and cuproptosis occurring with the participation of flavonols have remained incompletely elucidated, and the results of the studies carried out so far are ambiguous. For this reason, one of the therapeutic goals is to initiate the death of altered cells through the use of quercetin, kaempferol, myricetin, isorhamnetin, galangin, fisetin, and morin. This article offers an extensive overview of recent research on these compounds, focusing particularly on their role in combating cancer and elucidating the molecular mechanisms governing apoptosis, autophagy, necroptosis, pyroptosis, ferroptosis, and cuproptosis. Assessment of the mechanisms underlying the anticancer effects of compounds in therapy targeting various types of cell death pathways may prove useful in developing new therapeutic regimens and counteracting resistance to previously used treatments. Full article

The vacuolar proton-translocating ATPase (V-ATPase) is a transmembrane multi-protein complex fundamental in maintaining a normal intracellular pH. In the tumoral contest, its role is crucial since the metabolism underlying carcinogenesis is mainly based on anaerobic glycolytic reactions. Moreover, neoplastic cells use the V-ATPase to extrude chemotherapy drugs into the extra-cellular compartment as a drug resistance mechanism. In glioblastoma (GBM), the most malignant and incurable primary brain tumor, the expression of this pump is upregulated, making it a new possible therapeutic target. In this work, the bafilomycin A1-induced inhibition of V-ATPase in patient-derived glioma stem cell (GSC) lines was evaluated together with temozolomide, the first-line therapy against GBM. In contrast with previous published data, the proposed treatment did not overcome resistance to the standard therapy. In addition, our data showed that nanomolar dosages of bafilomycin A1 led to the blockage of the autophagy process and cellular necrosis, making the drug unusable in models which are more complex. Nevertheless, the increased expression of V-ATPase following bafilomycin A1 suggests a critical role of the proton pump in GBM stem components, encouraging the search for novel strategies to limit its activity in order to circumvent resistance to conventional therapy. Full article

Pancreatic cancer is one of the deadliest cancers, with a 5 year survival rate of around 10% globally. Although obesity is a modifiable risk factor for this cancer, the role of a high-fat diet (HFD) intake in pancreatic carcinogenesis, the effects of the dietary modification from an HFD to a low-fat diet, and the underlying molecular mechanisms of action are poorly defined. To contribute to understanding these relationships, we assessed the pancreatic global gene expression modulations using an LSL-Kras^G12D/+p48^Cre/+ (KC) mouse model. Five-week-old mice were fed an HFD (60% energy from fat) or a control diet (11% energy from fat) until 6 months old. In an additional group, the mice consumed an HFD until 3 months old, and then switched to a control diet for 3 months to evaluate the effects of a dietary change to a low-fat diet (DC). Pancreata were collected, RNA was extracted and sequenced, and bioinformatic analysis was performed to identify the biological functions affected by the diets. The HFD significantly modulated the expression of 2166 genes involved in regulating cellular metabolism (metabolic pathways, oxidative phosphorylation, and pancreatic secretion), cancer-specific functions (pathways in cancer and transcriptional misregulation in cancer), immune function (Th17, Th1, and Th2 cell differentiations) and cell signaling (cytokine–cytokine receptor interaction and chemokine signaling). The DC altered the expression of 988 genes more compared to that of the HFD, presenting an expression profile similar to the control diet. The modulated genes were linked with metabolic processes (pancreatic secretion, fat digestion, and absorption), cell signaling (chemokine signaling, NFκB, and TNF signaling pathways), and cancer-specific functions (proteoglycans in cancer and pathways in cancer). Over 800 genes, mainly linked with metabolic functions, were identified following both DC and HFD intake and presented opposing expression profiles, suggesting that a DC could counteract some nutrigenomic modulations prompted by an HFD. Moreover, this effect was mirrored in the pancreas and final body weights, with the DC mitigating the HFD-induced increases in both the parameters. In summary, we showed the multi-target mode of action of an HFD in the pancreas of KC mice accompanied by increases in pancreatic and body weights that were all neutralized by a 3-month-long switch to a low-fat diet. Further explorations of the possible regulators driving the observed multi-genomic effects are warranted. Full article

Cyclin D1, a critical cyclin-dependent kinase (CDK) 4/6-dependent regulator of G1/S transition, has attracted much interest as a therapeutic target. The cyclin D1 expression in small intestinal adenocarcinomas (SIACs) has not yet been comprehensively studied, owing to the rarity of this tumor. We investigated the clinicopathological and prognostic significance of the cyclin D1 expression in 232 surgically resected primary SIACs through a multi-institutional study. A high expression of cyclin D1 (cyclin D1^High) was detected in 145 SIAC cases (63%), which was significantly higher than that in normal small intestinal mucosa (11%). Cyclin D1^High was more commonly found in SIACs with a lower T-category and disease stage and KRAS mutation and predicted better patient survival. Multivariate analysis revealed that cyclin D1^High, the absence of retroperitoneal seeding and lymphovascular invasion, and the lower N-category were identified as independent prognostic indicators for patients with SIACs. Specifically, cyclin D1^High affected patient survival in the lower stage group (stages I and II). In conclusion, cyclin D1 was commonly overexpressed in SIACs, and cyclin D1^High acted as a favorable prognostic indicator in patients with SIACs. These findings in SIACs may, thus, be important to further comprehend the mechanism of cyclin D1 in carcinogenesis and to strategize appropriate patient therapies. Full article

Cervical carcinogenesis is the leading cause of cancer-related deaths in women, and the role of high-risk human papillomavirus (HR-HPV) as a possible risk factor in the development of this cancer is well recognized. Despite the availability of multi-therapeutic approaches, there is still major concern regarding the prevention of metastatic dissemination and excessive tissue injuries. Therefore, it is imperative to develop a safer and more efficient treatment modality. Ficus carica, a natural plant, has shown potential therapeutic properties through its fruit latex when applied to HPV-positive cervical cancer cell lines. However, the mechanisms of action of Ficus carica (fig) latex are not well understood. This study aims to provide a deeper insight into the biological activities of fig latex on human cervical cancer cell lines expressing high-risk HPV types 16 and 18. The data obtained from this study reveal that fig latex influences the expression of genes involved in “Class I MHC-mediated antigen presentation” as well as “Antigen processing: Ubiquitination and Proteasome degradation”. These genes play a crucial role in host immune surveillance and the resolution of infection. Notably, Western blot analysis corroborated these findings, demonstrating an increase in the expression of MHC class I in HeLa cells after fig latex treatment. Findings from this study suggest that fig latex may enhance T cell responses against oncogenic HPV, which could be beneficial for the clearance of early-stage cancer. Full article

Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three ”big omics”, based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein–protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses. Full article

Head and neck squamous cell carcinoma (HNSCC) describes a heterogeneous group of human neoplasms of the head and neck with high rates of morbidity and mortality, constituting about 3% of all cancers and ~1.5% of all cancer deaths. HNSCC constituted the seventh most prevalent human malignancy and the most common human cancer in the world in 2020, according to multi-population observations conducted by the GLOBOCAN group. Since approximately 60–70% of patients present with stage III/IV neoplastic disease, HNSCC is still one of the leading causes of death in cancer patients worldwide, with an overall survival rate that is too low, not exceeding 40–60% of these patients. Despite the application of newer surgical techniques and the implementation of modern combined oncological treatment, the disease often follows a fatal course due to frequent nodal metastases and local neoplastic recurrences. The role of micronutrients in the initiation, development, and progression of HNSCC has been the subject of considerable research. Of particular interest has been vitamin D, the pleiotropic biologically active fat-soluble family of secosteroids (vitamin-D-like steroids), which constitutes a key regulator of bone, calcium, and phosphate homeostasis, as well as carcinogenesis and the further development of various neoplasms. Considerable evidence suggests that vitamin D plays a key role in cellular proliferation, angiogenesis, immunity, and cellular metabolism. A number of basic science, clinical, and epidemiological studies indicate that vitamin D has multidirectional biological effects and influences anti-cancer intracellular mechanisms and cancer risk, and that vitamin D dietary supplements have various prophylactic benefits. In the 20th century, it was reported that vitamin D may play various roles in the protection and regulation of normal cellular phenotypes and in cancer prevention and adjunctive therapy in various human neoplasms, including HNSCC, by regulating a number of intracellular mechanisms, including control of tumour cell expansion and differentiation, apoptosis, intercellular interactions, angio- and lymphogenesis, immune function, and tumour invasion. These regulatory properties mainly occur indirectly via epigenetic and transcriptional changes regulating the function of transcription factors, chromatin modifiers, non-coding RNA (ncRNAs), and microRNAs (miRs) through protein-protein interactions and signalling pathways. In this way, calcitriol enhances intercellular communication in cancer biology, restores the connection with the extracellular matrix, and promotes the epithelial phenotype; it thus counteracts the tumour-associated detachment from the extracellular matrix and inhibits the formation of metastases. Furthermore, the confirmation that the vitamin D receptor (VDR) is present in many human tissues confirmed the physiopathological significance of vitamin D in various human tumours. Recent studies indicate quantitative associations between exposure to vitamin D and the incidence of HNC, i.e., cancer risk assessment included circulating calcidiol plasma/serum concentrations, vitamin D intake, the presence of the VDR gene polymorphism, and genes involved in the vitamin D metabolism pathway. Moreover, the chemopreventive efficacy of vitamin D in precancerous lesions of the head and neck and their role as predictors of mortality, survival, and recurrence of head and neck cancer are also widely discussed. As such, it may be considered a promising potential anti-cancer agent for developing innovative methods of targeted therapy. The proposed review discusses in detail the mechanisms regulating the relationship between vitamin D and HNSCC. It also provides an overview of the current literature, including key opinion-forming systematic reviews as well as epidemiological, prospective, longitudinal, cross-sectional, and interventional studies based on in vitro and animal models of HNSCC, all of which are accessible via the PubMed/Medline/EMBASE/Cochrane Library databases. This article presents the data in line with increasing clinical credibility. Full article

Advances in molecular technologies and targeted therapeutics have accelerated the implementation of precision oncology, resulting in improved clinical outcomes in selected patients. The use of next-generation sequencing and assessments of immune and other biomarkers helps optimize patient treatment selection. In this review, selected precision oncology trials including the IMPACT, SHIVA, IMPACT2, NCI-MPACT, TAPUR, DRUP, and NCI-MATCH studies are summarized, and their challenges and opportunities are discussed. Brief summaries of the new ComboMATCH, MyeloMATCH, and iMATCH studies, which follow the example of NCI-MATCH, are also included. Despite the progress made, precision oncology is inaccessible to many patients with cancer. Some patients’ tumors may not respond to these treatments, owing to the complexity of carcinogenesis, the use of ineffective therapies, or unknown mechanisms of tumor resistance to treatment. The implementation of artificial intelligence, machine learning, and bioinformatic analyses of complex multi-omic data may improve the accuracy of tumor characterization, and if used strategically with caution, may accelerate the implementation of precision medicine. Clinical trials in precision oncology continue to evolve, improving outcomes and expediting the identification of curative strategies for patients with cancer. Despite the existing challenges, significant progress has been made in the past twenty years, demonstrating the benefit of precision oncology in many patients with advanced cancer. Full article