Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer, with a rising global incidence. Neurotrophins (NTs) and their receptors, including TrkA and CD271, play key roles in epidermal homeostasis and tumor progression. We showed that CD271 expression and function are critical for low- to high-risk progression of cSCC, while TrkA is highly expressed in poorly differentiated tumors. Although NTRK fusions are recognized as oncogenic drivers, the functional impact of TrkA signaling in cSCC remains underexplored. In this study, we investigated the effects of TrkA inhibition, using both the pan-Trk inhibitor K252a and siRNA-mediated silencing, on cSCC cell lines. We evaluated cell growth and invasion in vitro, using 2D and 3D cultures, and in vivo using zebrafish xenografts. TrkA inhibition significantly reduced tumor growth and invasion, with efficacy comparable to standard chemotherapeutics (5-FU, cisplatin). Additionally, TrkA blockade downregulated mitogenic and invasive markers. Importantly, TrkA inhibition enhanced the response to photodynamic therapy in cSCC spheroids. In zebrafish, Trk-targeted interventions reduced metastatic dissemination. These findings highlight TrkA as a key regulator of cSCC survival and metastasis, suggesting its potential as a therapeutic target either alone or in combination with existing treatments.

Colorectal cancer (CRC) is the second leading cause of cancer-related mortality in the United States. Recent breakthroughs in research are highlighting the complex genetic and epigenetic alterations driving CRC progression. Among these, the ERK1/2 and PI3K pathways are central regulators of cellular proliferation, survival, and differentiation. The overactivation of these pathways is frequently observed in cancer and is associated with poor patient prognosis. Protein Arginine Methyltransferase 5 (PRMT5), a key epigenetic regulator, has been implicated in modulating the ERK1/2 and PI3K pathways in cancer. Previous studies, including those from our own group, are starting to suggest that targeting PRMT5 and the ERK1/2 and PI3K pathways may offer therapeutic benefits. Thus, we sought to provide further evidence of the relationship between PRMT5 and the ERK1/2 and PI3K pathways in CRC. Using patient tumor gene expression data and protein-protein interaction networks, we provide further evidence that PRMT5 is positively correlated with, and interacts with, the ERK1/2 and PI3K pathways in CRC. These findings are significant, as they further strengthen the case for the urgent need of additional research into therapeutic strategies targeting PRMT5 and the ERK1/2 and PI3K pathways in CRC.

Cutaneous T-Cell Lymphomas (CTCL) are a heterogenous group of T-cell malignancies in the skin and have poor treatment outcomes in advanced stages. CD5, a surface glycoprotein expressed on most mature T cells, has emerged as a promising target for chimeric antigen receptor (CAR) T-cell therapy in systemic T-cell lymphomas. However, its expression profile in CTCL and relevance for targeted therapy remain unclear. Notably, in CTCL, the cell surface expression of receptors, such as CD7 and CD26, tends to become downregulated on the surfaces of malignant T cells In this study, we analyzed single-cell RNA sequencing (scRNA-seq) data from patients at two institutions with mycosis fungoides (MF), the most common subtype of CTCL with a predominantly CD4 phenotype. We utilized 5 patch/plaque MF skin biopsies (majority from early-stage patients), 8 MF tumor biopsies (all from advanced-stage patients), and 8 healthy control biopsies to evaluate lesion-specific CD5 gene expression on CD4 T cells. We found that CD5 was significantly increased in malignant MF CD4 T cells compared to healthy control CD4 T cells (21.1% of MF CD4 T cells expressed CD5 vs. 5.2% of healthy control CD4 T cells, respectively). In subgroup analysis, patch/plaque stage MF biopsies showed higher expression of CD5 in CD4 T cells than tumor stage MF biopsies. Notably, 94.3% of malignant CD4+ T cells in tumor stage MF lesions exhibited complete CD5 loss compared to only 76.6% in patch-plaque MF lesions, suggesting antigen escape in tumor stage disease. These findings demonstrate that CD5 expression in CTCL is dynamic and varies based on lesion type. Our work suggests CD5 may be a viable therapeutic target in MF with patch/plaque presentations but may not be as effective in advanced stages of MF with tumor presentations. This work informs CD5 gene expression in MF based on clinical lesion type and further information is needed to clarify clinical implications as a future therapeutic target.

Mutations in IDH1/2 are frequent in Acute Myeloid Leukemia (AML), defining a molecularly distinct subgroup with therapeutic implications due to the availability of specific inhibitors. Accurate monitoring of treatment response is crucial and Droplet Digital PCR (ddPCR) offers a sensitive approach for quantifying mutational burden in IDH-mutated AML. This study aimed to optimize and validate ddPCR assays specific for IDH1 R132 and IDH2 R172/R140 mutations for future use in Minimal Residual Disease (MRD) monitoring. Four ddPCR assays were set to evaluate the trend of IDH1/2 mutations in 191 diagnostic and follow-up samples. Each validation procedure included determining the limit of blank (LOB) and limit of detection (LOD) using titration series. Moreover, in AML harboring both IDH and NPM1 mutations, we performed generalized estimating equations (GEE) to assess the association between IDH fractional abundance and NPM1 RQ-Ratio across time points. Four IDH1/2 ddPCR assays were validated, demonstrating high sensitivity with limits of detection of 0.07% for IDH1 R132H, 0.1% for IDH2 R140Q and R172K, and 0.2% for IDH1 R132C. The method also exhibited excellent intra-run reproducibility, providing consistent results for patient follow-up. Comparison of IDH and NPM1 trends during follow-up revealed a statistically significant positive correlation, both in raw (β = 0.079, p = 0.001) and ranked data (β = 0.99, p = 0.004), suggesting a co-dynamic pattern potentially useful for surrogate monitoring. While our study cannot yet define the clinical role of IDH mutation assessment by ddPCR due to the lack of comparative follow-up studies, it establishes a solid methodological foundation for standardizing minimal residual disease evaluation via ddPCR, paving the way for future prospective validation.

Genistein has anti-cancer effects, but its molecular targets in gastric adenocarcinoma (GA) are unclear. This study used single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) to explore genistein's "drug-gene-cell" interactions in GA. GA- and genistein-related target genes were retrieved and intersected with differentially expressed genes identified from bulk transcriptomic data. Machine learning screened candidates, and survival analysis assessed prognosis. Molecular docking with genistein validated key genes, with molecular dynamics assessing binding stability. HSD17B1, EZH2, CCNB1, CCNB2, CDKN2A, and IGFBP6 were identified as key candidate genes with prognostic value for GA. Specifically, samples in the IGFBP6 high-expression group were associated with higher survival probability, whereas the opposite trend was observed for the other five genes. In addition, HSD17B1 was genistein's main target in GA treatment, showing a strong binding affinity with genistein (binding energy of -8.1 kcal/mol). scRNA-seq analysis indicated that HSD17B1 was predominantly expressed in epithelial cells and was significantly involved during their malignant transformation (confirmed by ST). This study identified HSD17B1 as a critical target gene for genistein in GA treatment, emphasizing its roles in the malignant transformation of epithelial cells, thus providing a theoretical foundation for understanding the therapeutic mechanism of genistein in GA.

Breast cancer remains a major global health challenge. In 2022, there were an estimated 2.3 million new cases and 670,000 deaths among women worldwide. Hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) breast cancer accounts for approximately 70% of breast cancer diagnoses. The treatment landscape for advanced HR+)/HER2- breast cancer has been transformed by the introduction of CDK4/6 inhibitors in the first-line setting. However, therapeutic strategies following progression on CDK4/6 inhibitors remain heterogeneous and uncertainty exists in their optimal integration in clinical practice. This review aims to systematically examine available second-line and subsequent treatment options for HR+/HER2- metastatic breast cancer after progression on CDK4/6 inhibitors, with a focus on biomarker-driven strategies and emerging therapies. The therapeutic landscape beyond CDK4/6 inhibitors includes targeted agents guided by actionable biomarkers as well as novel selective estrogen receptor degraders (SERDs). In biomarker-unselected populations, options include CDK4/6 continuation strategies, endocrine monotherapy in selected cases, and cytotoxic therapy. The integration of molecular testing via next-generation sequencing has become standard of care in guiding these decisions. However, overlapping molecular alterations and a lack of consensus on treatment sequencing pose significant challenges. Prognostic factors such as circulating tumor DNA dynamics may further refine treatment personalization. Post-CDK4/6 therapy in HR+/HER2- metastatic breast cancer is an evolving and increasingly complex area of practice. Optimal treatment selection should be tailored to both tumor biology and patient-specific factors, supported by molecular testing and high-quality evidence.

Lung cancer remains the leading cause of cancer-related mortality worldwide, accounting for nearly 1.8 million deaths annually. The present study aimed to investigate the role of miR-28-5p and miR-708-5p in lung cancer and to analyze the relationship between target gene profiles and transcriptional factor regulation. Both miRNAs that share a common seed sequence were found to be overexpressed in a cohort of 32 paired tumor and adjacent normal tissue samples collected from patients diagnosed at advanced stages (III and IV) of disease. Data from the dbDEMC database revealed that miR-28-5p exhibited variable expression across lung cancer subtypes, whereas miR-708-5p showed consistent overexpression, reinforcing its potential clinical diagnostic significance. Using the TransmiR database, we identified complex TF-miRNA regulatory networks, with both shared and distinct transcription factors controlling miR-28-5p and miR-708-5p. Pathway enrichment analysis indicated that these miRNAs regulate several cancer-associated pathways, including ECM-receptor interaction, adherens junctions, and Hippo signaling. Overall, our findings suggest that miR-708-5p may have a potential clinical application in lung cancer.

Uveal melanoma (UM) is the most prevalent primary intraocular tumor in adults. Transcription factor ZEB1 is one of the potential master regulators of melanocytes plasticity, because it is recognized as a "driver" of epithelial-to-mesenchymal transitions (EMTs) in carcinomas. We studied the correlation of tumor invasiveness with ZEB1 status and vascular endothelial growth factor/its receptor (VEGF-A/VEGFR2) in UM cells, and also with melanocyte's differentiation rate. Eight UM cell cultures were characterized by melanosomes content using an ETM. ZEB1, VEGF-A and VEGFR2 levels in UM cells were detected by RT-PCR, Western blot, ELISA and flow cytometry. Effects of siRNA-dependent ZEB1 knockdown on UM cell proliferation and their sensitivity to the VEGF-A inhibitor Eylea (aflibercept) were tested by MTT and in a real-time proliferation assay. UMs with an invasive growth type can maintain a high degree of melanocyte differentiation. All ZEB1low cells were obtained from spindle cell tumors. The sensitivity of UM cells to Eylea inversely correlated with the level of the VEGFR2 receptor. ZEB1 knockdown completely blocked VEGF-A production while anti-VEGF treatment stimulated ZEB1 increase. In UM cell cultures, ZEB1 is a positive regulator of VEGF-A expression. In addition, there is probably a ZEB1 feedback loop that is sensitive to a drop in VEGF-A concentration. The data obtained allow us to consider ZEB1 silencing as an auxiliary link for a combined strategy of killing UM cells.

The JAK2 46/1 ("GGCC") haplotype is an inherited genetic variation within the Jak2 gene locus that has become a focal point in research related to oncogenesis, particularly in myeloproliferative neoplasms (MPNs). We conducted a narrative review of landmark discoveries in hematological malignancies and Jak2, focusing on its role in oncogenesis, risk stratification, and drug resistance in MPNs. This haplotype spans several polymorphisms within the Jak2 gene. It has been found to increase susceptibility to a variety of hematologic cancers, especially when linked with the somatic JAK2 V617F mutation, which results in the alteration of the JAK/STAT pathway, which is particularly essential for hematopoiesis. The "GGCC" part is characterized by four SNPs, with the G allele of the rs10974944 SNP in this haplotype correlated with MPNs progressing to myelofibrosis. Moreover, the G allele seems to be crucial for the predisposition to onco-drug resistance onset. To conclude, identifying the 46/1 haplotype in patients may not only enhance risk stratification for JAK2-driven cancers but also guide more effective, personalized therapeutic strategies to overcome resistance. Thus, this review aims to describe current knowledge about the JAK2 46/1 haplotype as a marker for diagnosis and the prediction of disease outcome.

We previously demonstrated that in BAP1-proficient pleural mesothelioma cells, CDKN2A is critical for mediating the response to selective EZH2 inhibition and highlighted a complex interplay between epigenetic regulation and the tumor immune microenvironment. In this study, we employed a quantitative proteomic mass spectrometry approach to assess alterations in protein expression following EZH2 inhibition in BAP1- and CDKN2A-proficient mesothelioma cells cultured as spheroids. Additionally, we analyzed extracellular vesicles (EVs), which were isolated through tangential flow filtration. Flow cytometric analysis and co-culture systems were used to characterize the effects of EVs on neutrophils. Upon EZH2 inhibition, we demonstrated RAB27b and CD63 upregulation and increased release of extracellular vesicles. We found that a brief exposure to EVs derived from EZH2 inhibitor-treated cells skewed naïve neutrophils toward a pro-tumor phenotype characterized by high levels of PD-L1 and MSLN (Mesothelin) expression on the surface. These EV-elicited neutrophils suppressed T cell proliferation while enhancing tumor cell growth. Moreover, we observed changes in the EV cargo derived from EZH2 inhibitor-treated spheroids. Our findings highlight the significant role of EVs in creating an immunosuppressive microenvironment, and underscore the urgent need for further investigation into the regulation of neutrophil biology and function in the PM.

Hepatocellular carcinoma continues to be a predominant contributor to oncological fatalities, characterized by restricted treatment alternatives. Although berberine exhibits anti-neoplastic capabilities, the underlying molecular pathways in hepatic malignancy require clarification. A comprehensive computational framework was established, incorporating transcriptomic data analysis, multiple machine learning methodologies, weighted gene co-expression network analysis (WGCNA), and molecular simulation techniques to elucidate berberine's therapeutic pathways. Transcriptomic datasets from the Cancer Genome Atlas (TCGA) underwent examination to detect differentially expressed genes (DEGs). Ten machine learning methodologies screened critical targets, subsequently validated through molecular docking and 100 ns molecular dynamics simulations. Transcriptomic examination revealed 531 DEGs (341 exhibiting upregulation, 190 demonstrating downregulation) alongside 173 putative berberine interaction targets, yielding 17 intersecting candidates. Machine learning approaches consistently recognized AURKA and CDK1 as principal targets, subsequently confirmed by WGCNA as central genes. Elevated expression of both targets demonstrated correlation with unfavorable survival outcomes (p < 0.05). Computational docking analysis demonstrated robust binding interactions (AURKA: -8.2 kcal/mol; CDK1: -8.4 kcal/mol), with interaction stability validated through molecular dynamics simulations. Functional enrichment analysis unveiled targeting of cell cycle modulation, chromosome segregation, and p53 signaling networks. Berberine manifests anti-hepatocellular carcinoma activities primarily via coordinated targeting of AURKA and CDK1, essential cell cycle modulators. These discoveries provide molecular insights supporting berberine's potential as adjunctive hepatic cancer therapy.

Cisplatin is a widely used antineoplastic agent whose therapeutic efficacy is often limited by its adverse effects on the central nervous system. In this exploratory study, we characterized the transcriptomic impact of a cumulative cisplatin regimen on the male Wistar rat brain using microarray technology. Differentially expressed genes were identified, and their functional roles were investigated through enrichment analyses (KEGG) and Gene Ontology (GO), and the construction of protein-protein interaction (PPI) networks. Our results revealed significant alterations in pathways related to synaptic signaling, neuroplasticity, and cellular metabolism. To generate translational hypotheses, these findings were subsequently correlated in silico with public human lower-grade glioma (LGG) datasets, which suggested a potential association between key cisplatin-regulated genes and clinical prognosis and immune cell infiltration patterns. This manuscript does not include RT-qPCR (or Western blot) validation; results should be interpreted as hypothesis-generating and require orthogonal confirmation. These findings provide a comprehensive transcriptomic map of cisplatin-induced neurotoxicity, offering novel insights into its underlying molecular mechanisms and identifying a rich set of candidate targets for future neuroprotective strategies.

Non-small cell lung cancer (NSCLC) is a severe disease with a very poor prognosis. Some 30-80% of patients with NSCLC die within five years of cancer diagnosis. The main factors contributing to this condition are the lack of effective markers for diagnosing cancer at an early stage, as well as the complexity of the biological processes involved in tumorigenesis and progression. The development of knowledge regarding all aspects of NSCLC has provided information used in the detection, systemic anticancer therapy and monitoring of NSCLC, which has a significant impact on prognosis and quality of life. NSCLCs release various biological substances into the bloodstream. Liquid biopsies allow for the analysis of tumor components in body fluids, and the usefulness of these biopsy tests as a substitute for tumor tissue is increasing. In this article, we critically review the available literature on microRNAs, circulating cell-free DNA (cfDNA), tumor-educated platelets (TEPs), circulating tumor cells (CTCs), circulating extracellular vesicles (EVs), and metabolomic and proteomic markers in the diagnosis and monitoring of NSCLC. However, the usefulness of these new markers in clinical practice has significant limitations.

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. In Mexico, its higher incidence and lower survival suggest a role for epigenetic factors like DNA methylation (DNAme). We conducted an epigenome-wide association study (EWAS) to define the methylation landscape and identify the profiles associated with ALL and relapse. Bone marrow or peripheral blood samples from pediatric ALL patients at diagnosis and controls without ALL were analyzed using an Infinium MethylationEPIC v2.0 array. Differential methylation was assessed using the ChAMP package. We identified a significant hypermethylated profile in ALL patients compared to controls. Probes in MAD1L1 and RPTOR contained the most differentially methylated CpG sites. Key affected pathways included proliferation, neurotransmission, and neuronal signaling. Survival analysis revealed that hypomethylation of four specific CpGs-cg01052776 (RNH1), cg20747787, cg05001671, and cg01767116 (FBXL22)-was significantly associated with an increased risk of relapse, highlighting their potential as prognostic biomarkers. This study underscores the importance of epigenetic mechanisms in pediatric ALL.

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited treatment options, prompting extensive research into novel therapeutics. This study presents a comprehensive molecular characterization of usnic acid in TNBC using transcriptomic, proteomic, and in vivo analyses.

Despite a specific histone mutation defining the unique genetic makeup, diffuse midline gliomas are heterogeneous tumors with a wide range of morphologic and molecular spectrum. We investigated the feasibility of using hyperpolarized carbon-13(13C) MR metabolic imaging to differentiate distinctive molecular features from two H3K27M-mutant, biopsy-originated diffuse midline glioma xenografts. 13C MR metabolic imaging data were acquired on a 3T scanner from 12 rats that had been implanted with SF8628 or SF7761 diffuse midline glioma cells in brainstem, following injection of hyperpolarized [1-13C]pyruvate. Despite the two tumors' similar appearance of T2-hyperintensity throughout the cerebellum and pons without contrast enhancement, 13C metabolic imaging data revealed that SF8627 had significantly higher ratios of lactate to pyruvate, lactate to total carbon, and normalized lactate than SF7761. Elevated lactate levels in SF8628 were associated with large amounts of lactate dehydrogenase (LDH)-A and carbonic anhydrase-IX staining in SF8628 compared to SF7761, which implied that the highly hypoxic condition in SF8628 appeared to contribute to the high level of LDH-A enzyme activity, which, in turn, induced the large conversion from hyperpolarized pyruvate to lactate. Our findings suggest that this advanced metabolic imaging technique may be used for the noninvasive characterization of molecular hypoxia and lactate dehydrogenase-A activity in these pediatric brainstem gliomas.

Many cutaneous adnexal tumors share molecular alterations with other homologous neoplasms occurring in salivary glands. Polymorphous adenocarcinoma (PAC) is a rare salivary gland tumor, usually associated with alterations in the PRKD gene family. In this report, we describe a primary cutaneous sweat gland adenocarcinoma of the scalp occurring in a 65-year-old female. Morphological features of the carcinoma were reminiscent of salivary gland PAC. Tumor cells were CK7+ S100+ SOX10+ p63 focally positive and p40-. Whole-transcriptome sequencing of the lesion showed the presence of an in-frame ATL2::PRKD3 fusion. PRKD1, 2 or 3 fusions are characteristic of the cribriform subtype of PAC (cribriform adenocarcinoma of salivary gland, CASG). No past history of salivary gland tumor nor existing salivary gland tumor was retrieved in the patient. After complete excision of the tumor, the patient has been in complete remission for 17 months. This case suggests that a subset of adnexal adenocarcinomas of not otherwise specified type (NOS) may carry PRKD alteration and may constitute the cutaneous counterpart of salivary gland PAC/CASG. This finding argues in favor of a more systematic molecular exploration of adnexal adenocarcinomas NOS for better classification and prognosis.

There is a need to improve the translation of gastric cancer molecular classification schemes, such as those proposed by the Cancer Genome Atlas (TCGA) and Tumour Microenvironment score (TME), to clinical specimens and three-dimensional organoid culture models. In this study, we validate a 107-gene Nanostring assay informed by previously established machine learning models using a prospective cohort of gastric adenocarcinoma tumours and tumour-organoid pairs. Thirty-eight gastric adenocarcinoma specimens and twelve parent tumour-tumour organoid pairs were assigned TCGA and TME subtypes using gene expression measured by our custom Nanostring gene set. Subtypes were validated using gold-standard tests for Epstein-Barr virus (EBV) and microsatellite instability (MSI). Molecular subtype scores were compared to known clinicopathologic characteristics. The correlation between dose-response and molecular subtypes using an organoid drug assay and the Cancer Cell Line Encyclopedia (CCLE) was investigated. TCGA and TME subtypes were successfully applied to all specimens. The relationship of molecular subtype scores in our population compared to public cohorts was statistically identical for Lauren Class and Signet Ring status. Our method achieved 100% accuracy in labeling EBV and MSI subtypes. We identified 81.8% and 63.6% concordance between parent tumour-tumour organoid pairs for TME and TCGA subtypes, respectively. No significant correlation was identified between dose response to chemotherapy and molecular subtype scores. Analysis of the CCLE identified promising personalized therapy candidates for each molecular subtype. Our 107-gene Nanostring test successfully assigns TCGA and TME molecular subtypes to clinical tumour and tumour organoid samples for use in future study.

Ossifying fibromyxoid tumor (OFMT) is an extremely rare mesenchymal tumor of uncertain differentiation having a potential for local recurrences and metastasis. OFMT can be classified as typical, atypical, and malignant tumors based on nuclear grade, cellularity, and mitotic rate. However, predicting the biological behavior remains challenging. We report one of these challenging cases of OFMT with metastases after 19 years. The primary tumor did not show morphologic characteristics of malignancy. We performed targeted RNA sequencing, copy number variation (CNV) analysis on all lesions and additional DNA methylation profiling.

Gastric cancer (GC) ranks as the third leading reason of cancer-associated deaths worldwide. This study investigates the mechanism by which the m6A methyltransferase methyltransferase-like 14 (METTL14) enhances ferroptosis and inhibits GC progression through regulation of sirtuin 5 (SIRT5).