Search Results (1,189)

Introduction: Epidermal growth factor receptor (EGFR) alterations exist in 15–50% of non-small cell lung cancer (NSCLC) diagnoses. Although effective therapeutics have been developed in the form of tyrosine kinase inhibitors (TKI), various mechanisms of resistance lead to treatment failure after exposure to EGFR TKI-based therapy. Of these, histologic transformation (HT) into small cell lung cancer (SCLC) represents approximately 14% of cases. Methods: Within a single institution, we retrospectively reviewed longitudinal data from both tissue and liquid biopsies of patients with histologic transformation after a diagnosis of EGFR-mutant NSCLC. We sought to further characterize the baseline and emergent genomic alterations after HT to SCLC in the context of TKI exposure, along with germline alterations that may contribute to lineage plasticity and outcomes. Results: Fifteen patients were included in our analysis. Of these, EGFR exon 19 deletions were the most frequent (n = 11, 73.3%), followed by L858R (n = 3, 20%) and L861Q (n = 1, 6.7%). The median time for transformation was 17 months (95%CI, 8.9–41.9 months). The median OS of our cohort was 51.6 months (95%CI, 26.3—NE) with a median OS post-transformation of 13.4 months. Recurrent genomic alterations included TP53, Rb1, PIK3CA, and BRAF. Germline testing revealed a pathogenic alteration in FBN1, with a recurrent variant of unknown significance (VUS) in PALLD. Conclusion: Post-transformation somatic mutation testing and germline testing at presentation revealed unique mutational profiles not previously reported in the setting of HT to SCLC. Further investigations are required to determine the optimal treatment and sequencing following HT. Full article

Background/Objectives: Gastric cancer (GC) remains a leading cause of cancer mortality worldwide. While most cases are sporadic, approximately 10% show familial clustering with only a minority explained by known hereditary syndromes. The remaining, termed familial non-hereditary gastric cancer (FNHGC), lack a defined high-penetrance germline mutation. This review aims to summarize current knowledge regarding the diagnosis, risk factors, molecular characteristics and management of FNHGC. Methods: A comprehensive narrative review of the literature was conducted focusing on epidemiologic, molecular and clinical studies addressing families with multiple GC cases but no identified germline mutation. Results: The etiology of FNHGC is multifactorial, and H. pylori, with its related chronic gastritis, is probably the key driver. Familial clustering likely occurs when combined with other elements such as genetic polymorphisms, shared exposures to risk factors or even epigenetic phenomena. Molecular profiling reveals distinct patterns in familial tumors such as more frequent microsatellite instability; somatic CDH1 promoter hypermethylation; and recurrent somatic mutations in TP53, RHOA and DNA repair genes. Current management focuses on genetic testing to rule out hereditary syndromes, endoscopic surveillance and mitigation of risk factors, with eradication of H. pylori paramount. Conclusions: FNHGC represents a distinct subgroup of GC characterized by a multifactorial etiology related to exposure to risk factors and genetic susceptibility although significant gaps remain in fully explaining the condition. Ongoing research holds promise to provide tools for better detection and prevention in order to reduce the burden of GC in familial settings. Full article

Background: Colorectal cancer is the third most diagnosed cancer and a leading cause of cancer-related deaths worldwide. Early detection significantly improves patient outcomes, yet many cases are identified only at late stages. The high molecular and genetic heterogeneity of colorectal cancer presents major challenges in accurate diagnosis, prognosis, and therapeutic stratification. Recent advances in gene expression profiling offer new opportunities to discover genes that play a role in colorectal cancer carcinogenesis and may contribute to early diagnosis, prognosis prediction, and the identification of novel therapeutic targets. Methods: This study involved 142 samples: 84 primary tumor samples, 27 liver metastases, and 31 adjacent non-tumor tissues serving as controls. RNA sequencing was performed on a subset of tissues (12 liver metastases and 3 adjacent non-tumor tissues) using a targeted RNA panel covering 395 cancer-related genes. Data processing and differential gene expression analysis were carried out using the DRAGEN RNA and DRAGEN Differential Expression tools. The expression of six genes involved in hypoxia and epithelial-to-mesenchymal transition (EMT) pathways (SLC16A3, ANXA2, P4HA1, SPP1, KRT19, and LGALS3) identified as significantly differentially expressed was validated across the whole cohort via quantitative real-time PCR. The relative expression levels were determined using the ΔΔct method and log2FC, and compared between different groups based on the sample type; clinical parameters; and mutational status of the genes KRAS, PIK3CA, APC, SMAD4, and TP53. Results: Our results suggest that the expression of all the validated genes is significantly altered in metastases compared to non-tumor control samples (p < 0.05). The most pronounced change occurred for the genes P4HA1 and SPP1, whose expression was significantly increased in metastases compared to non-tumor and primary tumor samples, as well as between clinical stages of CRC (p < 0.001). Furthermore, all genes, except for LGALS3, exhibited significantly altered expression between non-tumor samples and samples in stage I of the disease, suggesting that they play a role in the early stages of carcinogenesis (p < 0.05). Additionally, the results suggest the mutational status of the KRAS gene did not significantly affect the expression of any of the validated genes, indicating that these genes are not involved in the carcinogenesis of KRAS-mutated CRC. Conclusions: Based on our results, the genes P4HA1 and SPP1 appear to play a role in the progression and metastasis of colorectal cancer and are candidate genes for further investigation as potential biomarkers in CRC. Full article

Background: Wide application of genome sequencing technologies has highlighted extensive genetic diversity in Acute Myeloid Leukemia (AML), yet the specific roles of individual genes remain unclear. This systematic review and meta-analysis aims to provide robust evidence for the prognostic impact of somatic gene mutations in de novo AML patients, while also exploring the prevalence of these mutations. Methods: Eligible studies were identified from PubMed and Scopus, with a focus on those reporting the prognostic influence of somatic gene mutations on overall survival (OS) or relapse-free survival (RFS) when compared to wild-type carriers. We calculated the pooled prevalence with 95% confidence intervals to assess the frequency of these mutations, and the pooled Hazard Ratio (HR) to compare OS and RFS associated with specific gene mutations. Results: We evaluated 53 somatic gene mutations using 80 studies, involving 20,048 de novo AML patients. The analysis revealed that the most prevalent affected genes were NPM1 (27%), DNMT3A (26%), and FLT3-ITD (24%). Mutations in CSF3R, TET2, and TP53 were significantly associated with poorer OS or RFS (p < 0.05). Sensitivity analysis confirmed that ASXL1, DNMT3A, and RUNX1 mutations were consistently linked to inferior OS or RFS. In contrast, CEBPAdm mutations were associated with favorable OS [HR = 0.39 (0.30–0.50)] and RFS [HR = 0.44 (0.37–0.54)]. Subgroup analysis showed that FLT3-ITD mutations were consistently associated with worse OS or RFS across all subgroups, though no significant subgroup differences were noted. No significant impact on OS or RFS was observed for mutations in GATA2, FLT3-TKD, KRAS, NRAS, IDH1, and IDH2. Conclusions: These findings provide critical insights into AML prognosis, aiding clinical decision-making and improving risk stratification strategies. Full article

Background: Richter transformation (RT) is defined as the histologic transformation of Chronic Lymphocytic Leukemia (CLL) to either diffuse large B-cell lymphoma or Hodgkin lymphoma. Transformation into lymphoproliferative neoplasms with plasmablastic differentiation is exceptionally rare and poorly characterized. Case Presentation: We present the first case of a patient with CLL evolving into plasmablastic myeloma (PBM). A 62-year-old man with previously treated CLL developed thrombocytopenia and rapidly progressive acute kidney injury. Serum electrophoresis showed new IgA-λ protein (2.2 g/L) with λ and κ light chains at 3445.4 and 7.3 mg/L. Bone marrow examination showed extensive infiltration (>95%) by plasmablasts and mature plasma cells, with a consistent immunophenotype (CD38+, CD138+, MUM1+, CD19−, CD20−). In situ hybridization with EBER was negative. Mutation assessment by NGS demonstrated a TP53 mutation and FISH prob panel revealed a new del17p. Clonal relatedness was confirmed by shared IGHV somatic hypermutation using NGS. The patient was primary refractory to frontline myeloma therapy with Dara-VRd and succumbed rapidly to his disease. Discussion: This case illustrates an exceptionally rare form of RT. Recognition and incorporation in new classifications of plasmablastic RT as a distinct entity is critical, as its biology and resistance profile differ from classical RT. Full article

Background: Oncogenic fusions of MAML2 with CRTC1, CRTC3, YAP1, and NR1D1 retain the MAML2 transactivating domain (TAD) and are believed to drive aberrant gene transcription. While the oncogenic roles of these known fusions have been established, we aimed to identify novel MAML2 fusions across a range of human malignancies. Methods: DNA and RNA sequencing were performed on tumor samples submitted to Caris Life Sciences. MAML2 fusions were identified from RNA transcripts and filtered to include only known pathogenic fusions or recurrent, in-frame fusions containing a C-terminal MAML2 TAD. Fusion burden was defined as the number of unique fusion isoforms per sample. Results: Among 180,124 tumor samples, 143 specimens harbored MAML2 fusions with a MAML2 TAD: >50% of specimens harbored known fusions, but novel fusions with MTMR2 (31/143), SESN3 (11/143), CCDC82 (6/143), FAM76B (4/143), and ATXN3 (3/143) were also identified. Compared to the known fusions, the novel fusions generally had lower expressions (median: 8 vs. 13 junction reads/sample, p = 0.0064), higher fusion burdens (median: 6 vs. 2 unique fusion isoforms/sample, p < 0.0001), more frequent TP53 co-mutations (80% vs. 11.5%, p < 0.0001), and no clear association with the tissue of origin. Excluding ATXN3::MAML2, the novel fusion partners were located near MAML2 in the genome, likely arose from duplications or deletions, and occurred in samples harboring concurrent mutations. In contrast, ATXN3::MAML2 arose via interchromosomal translocation, occurred in samples with a low fusion burden, and was not associated with TP53 mutations. Conclusions: We identified novel MAML2 fusion partners, most of which likely represent passenger alterations, possibly arising from genomic instability or impaired p53 function. However, ATXN3::MAML2 fusions, previously reported in a pre-cancerous pancreatic disease case, may represent a pathogenic alteration warranting further investigation. Full article

Primary ovarian large cell neuroendocrine carcinoma is an extremely rare and aggressive gynecologic malignancy with poorly defined molecular characteristics and no standard treatment protocols. We present a case of pure ovarian LCNEC in a postmenopausal woman who underwent optimal cytoreductive surgery followed by platinum-based chemotherapy. Histopathologic and immunohistochemical analyses confirmed the diagnosis. Next-generation sequencing (NGS) revealed a pathogenic BRCA2 frameshift mutation (c.7177dupA), an ATM nonsense mutation, and Tier II mutations in TP53 and PTEN. The tumor exhibited homologous recombination deficiency (HRD), microsatellite instability-high (MSI-H), and an exceptionally high tumor mutational burden (TMB) of 277.49 mutations/Mb. These molecular alterations closely resemble those observed in high-grade neuroendocrine carcinomas of cervical and endometrial origin, suggesting a convergent genomic profile across gynecologic neuroendocrine carcinomas (NECs). Our findings underscore the potential of comprehensive genomic profiling in rare tumors such as ovarian LCNEC to refine diagnosis and identify candidates for biomarker-driven therapies, including PARP inhibitors and immune checkpoint inhibitors. This case supports the integration of molecular diagnostics into clinical practice and highlights the need for prospective studies incorporating molecular stratification to inform treatment strategies for rare and aggressive neuroendocrine tumors. Full article

Background/Objectives: Endometrial cancer (EC) remains a significant clinical challenge due to increasing incidence and mortality, particularly among patients with TP53 gene mutations, which define a high-risk molecular subtype. This study aimed to characterize the clinicopathological and molecular features of a cohort of patients diagnosed with endometrial cancer and confirmed TP53 mutations. Methods: This retrospective single-center study analyzed 20 patients with histologically confirmed EC and pathogenic TP53 mutations treated at the Pomeranian Medical University Clinical Hospital No. 2 between January 2023 and March 2025. Clinical, histological, and molecular data—including FIGO stage, tumor grade, and coexisting mutations—were collected. Results: Patients had a mean age of 69.2 years and a mean BMI of 29.5 kg/m². The most common histological types were endometrioid (45%) and serous carcinoma (40%). Grade 3 tumors were found in 65% of cases, and 65% of patients exhibited lymphovascular space invasion. Notably, 30% of patients were upstaged under the FIGO 2023 classification when incorporating TP53 mutation status. Four patients had coexisting PIK3CA mutations. No significant differences were observed in BMI, endometrial thickness, or abnormal bleeding between histological subgroups. Conclusions: TP53-mutated endometrial cancers are associated with aggressive histopathological features and advanced staging. Molecular profiling, particularly TP53 mutation assessment, provides essential prognostic information and may inform personalized therapeutic strategies. Larger, multicenter studies are warranted to validate these findings and identify actionable molecular targets. Full article

Colorectal cancer (CRC) is driven by a complex spectrum of somatic mutations and structural variants that contribute to tumor heterogeneity and therapy resistance. In this study, we performed a comparative analysis of short-read Illumina and long-read Nanopore sequencing technologies across multiple CRC sample groups, encompassing diverse tissue morphologies. Our evaluation included general base-level metrics—such as nucleotide ratios, sequence match rates, and coverage—as well as variant calling performance, including variant allele frequency (VAF) distributions and pathogenic mutation detection rates. Focusing on clinically relevant genes (KRAS, BRAF, TP53, APC, PIK3CA, and others), we characterized platform-specific detection profiles and completed the ground truth validation of somatic KRAS and BRAF mutations. Structural variant (SV) analysis revealed Nanopore’s enhanced ability to resolve large and complex rearrangements, with consistently high precision across SV types, though recall varied by variant class and size. To enable direct comparison with the Illumina exome panel, we applied an exonic position reference file. To assess the impact of depth and PCR amplification, we completed an additional high-coverage Nanopore sequencing run. This analysis confirmed that PCR-free protocols preserve methylation signals more accurately, reinforcing Nanopore’s utility for integrated genomic and epigenomic profiling. Together, these findings underscore the complementary strengths of short- and long-read sequencing platforms in high-resolution cancer genomics, and we highlight the importance of coverage normalization, epigenetic fidelity, and rigorous benchmarking in variant discovery. Full article

The tumour suppressor protein p53 plays a central role in safeguarding genomic integrity through the regulation of DNA repair, cell cycle arrest, and apoptosis. Mutations in TP53, particularly within its DNA-binding domain, are among the most frequent genetic alterations in human cancers and are strongly associated with chemoresistance and poor prognosis. In this study, all TP53 mutations reported in the COSMIC database were systematically mapped onto all experimentally resolved TP53 three-dimensional structures available in the Protein Data Bank, supplemented with AlphaFold-predicted models to achieve full structural coverage. Mutations were classified according to their structural context—protein core, interface regions, ligand- and zinc-binding sites, and intrinsically disordered regions—and evaluated using complementary sequence- and structure-based predictive tools. The analysis revealed distinct mutational hotspots, differential distribution across structural regions, and context-dependent effects on stability and DNA-binding capacity. Notably, a subset of mutations exhibited consistent predictions of high destabilisation across all structural contexts, underscoring their potential as drivers of functional inactivation. By providing a comprehensive structural map of TP53 alterations, this work offers a valuable resource for understanding mutation-specific mechanisms of p53 dysfunction and for guiding the development of precision therapeutic strategies aimed at restoring its tumour-suppressive functions. Full article

Background/Objectives: Squamous cell carcinoma of the nail unit (SCCNU) is a rare yet often underrecognized malignancy that can lead to delayed diagnosis and significant functional morbidity. This review aims to comprehensively summarize the current understanding of SCCNU, focusing on its clinical, dermoscopic, and molecular features, diagnostic approaches, and evolving management strategies, including the role of emerging technologies and immunotherapy. Methods: A detailed literature review was conducted using peer-reviewed publications, case series, and institutional guidelines related to SCCNU. Emphasis was placed on studies addressing clinical presentation, dermoscopic patterns, molecular pathology, histologic subtypes, imaging, biopsy techniques, staging systems, and both conventional and novel therapeutic approaches. Comparative analyses of histopathological variants and diagnostic algorithms were included. Results: SCCNU presents in patients with diverse clinical manifestations, often mimicking benign nail disorders, leading to diagnostic delays. Dermoscopy improves lesion visualization, revealing features such as vascular changes and onycholysis. Histologically, SCCNU exhibits two main subtypes: basaloid (HPV-related) and keratinizing (HPV-negative) types. Molecular analyses have identified TP53 as the most frequently mutated gene, with additional alterations in HRAS, BRAF, and TERT. Imaging modalities such as MRI and LC-OCT aid in staging and surgical planning. Management is centered on complete excision—often via Mohs micrographic surgery—while topical, intralesional, and HPV-directed therapies are under investigation. Immunohistochemical markers (p16, Ki-67, AE1/AE3) and neoadjuvant immunotherapy represent promising adjuncts. Conclusions: Early diagnosis through non-invasive imaging, improved molecular characterization, and personalized treatment strategies are essential to advancing care in SCCNU. Future directions include clinical trials evaluating immunotherapy, vaccine strategies, and precision-guided surgical approaches to preserve function and minimize recurrence. Full article

Background: Cholangiocarcinoma (CCA) is a highly heterogeneous malignancy arising from the biliary epithelium, with an increasing incidence and poor prognosis worldwide. Recent advances in next-generation sequencing have revealed a variety of genomic alterations―such as FGFR2 fusions, IDH1 mutations, and ERBB2 amplification―that may serve as therapeutic targets. However, the influence of underlying etiologic factors, including chronic liver and biliary diseases, on the molecular landscape of CCA remains unclear. Objective: This review aimed to synthesize the current knowledge on the genomic and molecular alterations of CCA in the context of diverse etiologic factors, including hepatitis B virus, hepatitis C virus, primary sclerosing cholangitis (PSC), primary biliary cholangitis, metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-related liver disease (ALD), and liver fluke infection. Main findings: Certain backgrounds, such as PSC and liver fluke infection, are associated with distinct molecular signatures (e.g., TP53, SMAD4, KRAS, and ERBB2 alterations), whereas others, such as MASLD or ALD, show limited and inconsistent genomic data. Targetable alterations―including FGFR2 fusions, IDH1 mutations, and ERBB2 amplification―are heterogeneously distributed across etiologies and anatomical subtypes. Molecular targeted therapies such as FGFR and IDH1 inhibitors have shown clinical benefits in selected patients. Conclusions: A better understanding of how chronic liver and biliary diseases shape the genomic landscape of CCA will inform the development of personalized treatments, surveillance strategies, and preventive approaches. Large-scale etiology-stratified genomic studies integrating multiomics and real-world clinical data are urgently needed to advance precision oncology in CCA. Full article

Background/Objectives: Developmental biologist Conrad Waddington proposed that evolution is shaped not only by genetic mutations and natural selection but also by environmentally responsive developmental mechanisms. Building on this premise, the epigenetic regulation of three master genes central to mammalian embryogenesis—OCT4, SOX2, and hTERT—focusing on their intragenic CpG islands (iCpGIs), which are crucial for transcriptional control and chromatin state modulation, were investigated. Methods: By performing a phylo-epigenetic comparison across 12 primate species, strong conservation of CpG-rich regions, punctuated by lineage-specific CpG transitions, particularly CpG→TpG and CpG→CpA was identified. Results: These mutational patterns align with methylation-dependent deamination mechanisms and highlight iCpGIs as evolutionarily constrained, epigenetically plastic elements. Notably, CpG variation alone recapitulated known primate phylogenies, suggesting that methylation-sensitive sites within iCpGIs encode both developmental and evolutionary information. Conclusions: It is proposed that such sites are prone to Environmentally Determined Epimutations (EDEMs)—methylation-driven, nutrition-sensitive changes that persist across generations and modulate gene regulatory capacity. This integrative framework advances Waddington’s concept of canalization by providing a molecular mechanism through which environmental factors can reshape developmental trajectories and contribute to evolutionary innovation. Full article

CAR-T therapy has transformed the treatment of relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL), particularly in pediatric and young adult patients. Many studies report one-year overall survival rates of between 60% and 80% following therapy. Event-free survival rates at one year are around 50–70%, with 40–50% of patients in remission after two years. Despite these impressive results, disease relapse remains a problem. Future CAR-T cell platforms should target multiple antigens, and the optimal design of such constructs must be determined. Modern trials should explore the role of CAR-T cell therapy as a consolidation treatment for patients with high-risk ALL, including those with persistent minimal residual disease at the end of induction/consolidation therapy, an IKZF1-positive gene expression profile, or a TP53 mutation or Ph-like gene expression profile. Improving the efficiency of gene-editing methods could lead to higher success rates in creating CAR-T cells, as well as reducing manufacturing time and costs. Producing universal CAR-T cells from healthy donors could significantly reduce production time and costs. These issues underscore the dynamic and evolving nature of B-ALL research. Ongoing studies and clinical trials are addressing many of these challenges in order to improve outcomes for B-ALL patients and expand the applications of CAR-T cell therapy. Full article

Background: Endometrial cancer (EC) is one of the most common gynecologic malignancies, with a rising incidence worldwide. The Cancer Genome Atlas (TCGA) classifies EC into four molecular subtypes, among which the high-copy number subtype is characterized by TP53 mutations and associated with poor prognosis. However, this subtype remains understudied. IL4I1, an immunoregulatory enzyme implicated in various cancers, has emerged as a potential biomarker for tumor progression. This study aimed to explore IL4I1 as a prognostic marker in P53-mutant EC and to identify its potential as a therapeutic target. Methods: We retrospectively analyzed clinical data from 495 EC patients and selected 33 P53-mutant cases using Sanger sequencing and immunohistochemistry. Tumor tissues were collected via laser capture microdissection, stratified by five-year survival outcomes. IL4I1 expression was assessed through 4D label-free proteomics, immunohistochemistry, and Western blotting. TCGA data were used to validate expression patterns and prognostic significance. Functional analyses were performed using IL4I1-knockout P53-mutant EC cell lines generated via CRISPR/Cas9, followed by phenotypic assays and xenograft models. Results: IL4I1 was significantly upregulated in deceased patients and correlated with immune microenvironment alterations in TCGA data. Knockout of IL4I1 inhibited proliferation, migration, and invasion in vitro and tumor growth in vivo. Conclusions: IL4I1 is a key player in the aggressiveness of P53-mutant EC. It holds promise as a prognostic biomarker and may serve as a novel target for precision therapies in this high-risk EC subtype. Full article