Search Results (156)

Background/Objectives: Glioblastoma remains the most aggressive and lethal form of brain cancer, with no effective cure to date. The molecular mechanisms sustaining its development and relentless proliferation are still not fully understood. SETMAR, a protein lysine methyltransferase involved in various DNA repair and chromatin processes, has been reported as dysregulated in several cancers, including glioblastoma. Interestingly, S-SETMAR, a shorter isoform of SETMAR, has been suggested to antagonize the oncogenic properties of the full-length protein. Here, we explored the cellular and molecular consequences of S-SETMAR overexpression in glioblastoma cells. Methods: We compared native glioblastoma cells (8MGBA) with a recombinant 8MGBA line stably over-expressing αS-SETMAR, a stable form of S-SETMAR, using complementary cellular and molecular approaches. Results: Overexpression of αS-SETMAR markedly prolonged the cell cycle duration (from 27 to 37 h), leading to a significant decrease in cell proliferation. Unexpectedly, αS-SETMAR triggered genomic alterations characterized by an increased DNA content and extensive chromosomal instability, including aneuploidy, chromoanasynthesis-like rearrangements, and tripolar mitoses. Moreover, αS-SETMAR-expressing cells displayed heightened sensitivity to stress conditions mimicking chemotherapy and radiotherapy, resulting in increased apoptosis. Conclusions: Our findings identify αS-SETMAR as a dual modulator of glioblastoma cell fate—simultaneously slowing proliferation and promoting chromosomal instability while enhancing vulnerability to genotoxic stress. These results suggest that αS-SETMAR could serve as both a prognostic marker and a potential therapeutic tool in glioblastoma management. Full article

Background/Objectives: The tumour immune microenvironment (TIME) critically influences colorectal cancer (CRC) progression and therapeutic response, yet mechanisms shaping immune phenotypes remain unclear. Mucin-type O-glycosylation regulates tumour–immune interactions at the cell surface. Methods: We analysed O-glycosylation activity in 988 colorectal cancer (CRC) tumours derived from three independent cohorts: The Cancer Genome Atlas (TCGA-CRC, n = 534), the Clinical Proteomic Tumour Analysis Consortium (CPTAC2-CRC, n = 106), and the Sidra–Leiden University Medical Center (Sidra-LUMC, n = 348). O-glycosylation activity was quantified using a transcriptomic gene signature and single-sample gene set enrichment analysis (ssGSEA). Tumours were stratified into high and low O-glycosylation groups based on the median score, and associations with immune phenotypes, genomic alterations, and tumour functional states were assessed. Results: High O-glycosylation tumours exhibited an immune-desert phenotype with reduced immune-inflamed (p = 3.65 × 10⁻¹⁰) and immune-excluded (p = 0.0070) signatures alongside increased immune-desert scores (p = 0.0049) and reduced Siglec signalling (p = 8.14 × 10⁻⁵). O-glycosylation was associated with genomic stability, including lower TP53 mutation frequency (p = 0.0056), reduced aneuploidy (p = 0.0116), and decreased fraction of genome altered (p = 0.0309). High O-glycosylation tumours also showed upregulation of multidrug resistance programmes and reduced epithelial–mesenchymal transition (p = 0.0141) and proliferation (p = 0.0294). Conclusions: O-glycosylation defines a CRC subtype characterised by immune exclusion, genomic stability, and multidrug resistance, highlighting its potential as a biomarker and therapeutic target. Full article

Background: Non-invasive prenatal testing (NIPT) examines cell-free DNA (cfDNA) in maternal serum, which includes both maternal DNA and apoptotic placental DNA. The presence of multiple aneuploidies or widespread abnormal patterns of gains and losses across chromosomes in a structurally normal fetus has been linked to maternal cancer. Case Presentation: The patient was a 22-year-old G1P0 with a history of classical Hodgkin’s lymphoma in remission. Her NIPT collected at 14 weeks and 3 days was reported as a “no call”. A second NIPT at a different laboratory showed multiple chromosomal aneuploidies (trisomy 18, 21, and monosomy X) with normal fetal anatomy on ultrasound. The patient was asymptomatic and was referred to hematology–oncology specifically to address the concern that these NIPT results could be related to cancer recurrence. Imaging was deferred as she was already on an established surveillance protocol for her Hodgkin’s lymphoma. At 26 weeks of gestation, the patient presented with a cough and dyspnea. Chest x-ray raised concern for disease recurrence, and biopsy confirmed recurrent Hodgkin’s lymphoma. She received two cycles of ICE chemotherapy. Cesarean delivery at 34 weeks and 2 days was performed for non-reassuring fetal heart tones. She continued chemotherapy, followed by BEAM conditioning and autologous stem cell transplantation. Genetic testing of the neonate revealed a normal karyotype; the placenta karyotype yielded no interpretable results. Discussion and Conclusions: Certain patterns of abnormal NIPT results may be associated with maternal malignancy and warrant further investigation. The absence of standardized protocols for reporting such NIPT results can complicate timely interdisciplinary evaluation and treatment. However, diagnostic testing should be offered with a positive NIPT result, a no-call or test failure, and abnormal ultrasound results, even with a “low-risk” NIPT result. Full article

Background: Evaluation of chromosome aneuploidy and gene-level copy number alterations for diagnosis, prognosis, and therapeutic decision-making in solid tumors is the standard of care. Chromosomal microarray (CMA), next-generation sequencing (NGS), immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH) are the gold standard for detecting these variants in tumor tissue. In contrast to most solid tumors, cancers of the central nervous system (CNS) pose a unique challenge for effective detection via plasma due to the blood–brain barrier (BBB), with the additional challenges of brain biopsy or surgery being highly invasive and posing a significant risk to the patient. The Belay Ascent™ liquid biopsy test uses low-pass whole-genome sequencing (LP-WGS) to report on chromosome arm-level aneuploidy and gene-level copy number variants (CNVs) in cerebrospinal fluid (CSF) to inform diagnosis, prognosis, and therapeutic decision-making in CNS tumors. Methods: This study presents the equivalence of Ascent™ in detecting chromosome arm-level aneuploidy and gene-level CNVs using 48 tissue specimens followed by a clinical validation using a cohort of 32 CSF specimens with matched tissue-based tumor profiling information. Results: Equivalence of Ascent™ in detecting chromosome arm-level aneuploidy and gene-level CNVs using 48 tissue specimens was shown to have 100% and 97% positive percent agreement (PPA), respectively, compared to the gold standard of CMA/NGS. The validation cohort of 32 CSF specimens demonstrated 78% and 90% PPA for aneuploidy and gene-level CNVs, respectively. Clinical impact of Ascent™ was demonstrated, with 243 production cases able to inform the diagnosis and management of CNS tumors with high accuracy. Conclusions: Given the paucity of cells in CSF, limiting the use of karyotyping, CMA, IHC, and FISH, the Belay Ascent™ test provides a highly sensitive novel minimally invasive method for the evaluation of chromosome aneuploidy and gene-level CNVs in CSF. Full article

Lung cancer remains the leading cause of cancer-related mortality worldwide and is characterized by high aggressiveness and therapeutic resistance, partly driven by mitotic dysregulation. Key mitotic regulators, including kinases such as PLK1, AURKA, AURKB, and MPS1 and kinesins such as CENPE and Eg5, are frequently overexpressed in NSCLC and SCLC, contributing to chromosomal instability, aneuploidy, and highly proliferative tumor phenotypes. Although multiple inhibitors targeting these proteins have been developed, their clinical efficacy as monotherapies has been limited. This is largely due to insufficient target dependency, adaptive resistance mechanisms, mitotic slippage, activation of compensatory pathways, and dose-limiting toxicity. This review integrates current knowledge on the physiological roles of major mitotic regulators, their dysregulation in lung tumorigenesis, and the biological and pharmacological barriers that underlie the limited success of antimitotic drugs. We further highlight preclinical and clinical evidence supporting rational combination strategies designed to enhance the antitumor activity of mitotic inhibitors while minimizing toxicity. Together, these insights underscore the need for refined therapeutic approaches that better exploit vulnerabilities in mitotic control to improve outcomes for patients with lung cancer. Full article

Objective: This study examined the frequency of entosis in solid tumors of various origins (colorectal cancer, breast cancer, and lung cancer) and its association with clinical and pathological characteristics. It also examined survival and copy number alterations (CNAs) in genes associated with stem cells. The aim was to assess the potential prognostic value of entotic events in tumors. Methods: A total of 238 patients were included: 96 with colorectal cancer (CRC), 45 with lung cancer (LC), and 97 with breast cancer (BC). Entotic cell-in-cell (CIC) structures were evaluated on hematoxylin–eosin–stained slides using Mackay’s criteria. A CIC frequency >0.1 per 20 high-power fields was considered positive. Clinicopathological parameters, overall survival (CRC), metastasis-free survival (LC and BC), and CNA profiles of stemness-related genes were analyzed. Amplifications of MAP1LC3A and other chromosomal loci were assessed. Results: CRC demonstrated the highest entosis rate, more than two-fold higher compared with BC and LC (p < 0.05). Entosis correlated with high tumor grade (G3) in CRC (p = 0.03). In LC, CIC-positive tumors were more frequent in patients with lymph-node metastases (p = 0.02), whereas in BC, the opposite trend was observed (p = 0.02). It was noted that in patients with stage III–IV LC, the frequency of entosis was significantly higher than in patients with stage I–II cancer (p = 0.03). CIC-positive status was associated with poorer overall survival in CRC (p = 0.03) and reduced metastasis-free survival in LC (p = 0.011). In breast cancer, no statistically significant survival differences were observed. Tumors harboring two or more stemness-gene amplifications showed significantly higher entosis frequency regardless of tumor site. A strong association was identified between entosis and MAP1LC3A amplification. Conclusions: Enosis is not a random morphological phenomenon but a process associated with unfavorable tumor characteristics, high malignancy, reduced survival, and amplification of stem cell-related genes. The results of this study confirm the working hypothesis that entosis may contribute to the emergence of aneuploid clones of tumor cells, including those containing amplifications of stem cell-associated genes. This positions entosis as a potential factor in tumor genetic heterogeneity, which is particularly important in the context of therapeutic selection pressure. The observed association between high entosis frequency and the presence of ≥2 stem cell gene amplifications, as well as its association with poor prognosis in colorectal and lung cancer, highlights its potential value as a prognostic indicator. Furthermore, MAP1LC3A amplification data may serve as a molecular marker of entotic activity and a potential therapeutic target. Full article

Background/Objectives: SETD2 is a dual-function methyltransferase important for methylation of histone H3 at lysine 36 and α-tubulin in spindle microtubules. Genetic inactivation of SETD2 during oncogenesis drives loss of H3K36me3, genomic instability, and cancer progression. This study asked if disruption of genomic stability was a canonical feature of SETD2 inactivation via different pathways. Methods: We evaluated the impact of EPZ-719, a pharmacologic SETD2 inhibitor, and an H3.3K36M mutant histone (“oncohistone”) that binds and sequesters SETD2, on methylation activity and genomic stability in human cell lines. SETD2 activity was measured using in vitro methylation assays, H3K36me3 loss confirmed by Western analysis, and mitotic defects, specifically micronuclei and chromatin bridges, quantified with cytogenetic analysis. Results: EPZ-719 caused a dose- and time-dependent reduction in SETD2 activity on both histone and tubulin substrates, accompanied by significant increases in chromatin bridges and micronuclei in retinal pigmented epithelial (RPE-1) and 786-O ccRCC cells. Similarly, oncohistone expression markedly decreased SETD2 function, as determined by H3K36me3 levels, and induced comparable mitotic defects in 786-O cells, and aneuploidy in two chondrocyte cell lines expressing the H3.3K36M oncohistone. Combining EPZ-719 with H3.3K36M expression did not exacerbate mitotic defects beyond either oncohistone or pharmacologic inhibition alone, consistent with inhibition of SETD2 as their shared underlying mechanism of action. Conclusions: Pharmacologic inhibition and oncohistone-mediated sequestration of SETD2 converge on the induction of mitotic defects, underscoring SETD2’s essential role in maintaining genomic stability. Identification of loss of genomic stability as a canonical feature of SETD2 inactivation points to a potential therapeutic liability associated with targeting SETD2 in cancers where it is overexpressed and reveals a mechanism that could contribute to the progression of cancers expressing oncohistone mutations. Full article

In mitotic cell division, cytokinesis is followed by abscission, the final separation of the cytoplasmic canal, to release the two genetically identical daughter cells; however, sometimes chromatin bridges connecting the daughter nuclei appear. Preserving intact chromatin bridges is crucial because their breakage can cause DNA damage, aneuploidy, and cancer predisposition. For this purpose, cells use two main mechanisms: first, they activate the abscission checkpoint, a mechanism that delays the final cut of the cytoplasmic canal to prevent chromatin bridge breakage and secondly, they form accumulations of actin (“actin patches”) at the base of the intercellular canal to stabilize chromatin bridges. Here, we highlight new findings from our laboratory on how human cells “sense” chromatin bridges and remodel the actin cytoskeleton to generate actin patches in cytokinesis. More specifically, we discuss findings showing that the nuclear membrane Sun1/2-Nesprin-2-LINC (linker of nucleoskeleton and cytoskeleton) complex promotes the generation of mechanical tension on daughter nuclei with chromatin bridges. This tension leads to accumulation of Sun1/2 and Nesprin-2, and cytoplasmic accumulation of PDZ RhoGEF (PDZ domain-containing Rho guanine nucleotide exchange factor) at the base of the intercellular canal. In turn, PDZ RhoGEF activates downstream RhoA-ROCK-LIMK-Cofilin and RhoA-mDia1 signaling pathways to promote actin patches and prevent chromatin bridge breakage in cytokinesis. Full article

Cerebrospinal fluid (CSF) liquid biopsy has been recently recommended by the National Comprehensive Cancer Network (NCCN) as a molecular diagnostic tool for central nervous system (CNS) lymphoma that offers a minimally invasive method to detect key biomarkers when traditional diagnostics are limited by sensitivity or feasibility. This brief report describes the clinical use of two novel CLIA/CAP-approved CSF liquid biopsy tests from Belay Diagnostics, Summit™ and Vantage™, to aid in the diagnosis and management of CNS lymphoma. Results from both tests were reviewed for 50 CSF samples in the context of clinical information provided with the test order. Summit™ and Vantage™ detected clinically significant alterations in CNS lymphoma-associated genes such as MYD88, CD79B, and TP53 as well as MGMT methylation when other modalities (e.g., CSF cytology, MRI, or brain biopsy) were inconclusive. In several cases of suspected secondary CNS lymphoma, Summit™ detected pathogenic genomic variants as well as mild to high levels of aneuploidy, suggesting CNS involvement. Belay testing impacted management in 41 of 50 (82%) cases by informing CNS lymphoma diagnosis, stratification, or progression as well as therapeutic response with an overall false negative rate of 18% (2/11). This report contributes to the growing body of literature that demonstrates how comprehensive molecular profiling of CSF enhances detection and characterization of CNS lymphoma and offers a promising adjunct to conventional diagnostics. Full article

Whole-genome duplication, or tetraploidization, occurs in cells, tissues, or entire organisms. In human cancers, tetraploidization promotes aneuploidy and genomic instability, accelerating tumor progression, metastasis, and drug resistance. These adaptations demand metabolic rewiring, including mitochondrial plasticity. Here, we investigate the relationship between mitochondrial quantity/activity, including the mitochondrial transmembrane potential, the intracellular calcium, and the oxidative stress in diploid versus tetraploid cancer cells (colon, sarcoma, liver) and fungal and yeast models (C. albicans diploid/tetraploid strains; S. cerevisiae haploid/diploid/tetraploid strains). We demonstrate that tetraploid cells, whether from human carcinomas or yeast, exhibit consistently enlarged cell size, elevated mitochondrial content, and heightened metabolic activity compared to diploids. Our findings underscore mitochondrial adaptation as a hallmark of tetraploidization, offering novel therapeutic targets for chromosomally unstable tumors. Full article

High-grade serous ovarian cancer (HGSOC) is the most common (~80%) and lethal ovarian cancer subtype in the United States, characterized by TP53 mutations and DNA repair defects causing chromosomal instability (CIN). KIF18A is an essential cytoskeletal motor protein for cell division in CIN+ cancer cells, but it is not necessary for cell division in normal cells. Therefore, KIF18A represents a promising target for therapeutic interventions in CIN+ cancers. We investigated the use of a novel KIF18A inhibitor ATX020, for selectively targeting CIN+ HGSOC cells using growth inhibition assays, invasion assays, immunoassays, cell cycle analysis, and immunofluorescence techniques. Using DepMap and flow cytometry, we classified a panel of HGSOC cell lines based on aneuploidy scores (AS) and ploidy levels and identified a correlation between these classifications and sensitivity against ATX020. ATX020 induced cytotoxicity through mitotic arrest and DNA damage, and reduced tumor growth in HGSOC with high aneuploidy scores (AS). Mechanistically, ATX020 blocks KIF18A’s plus-end movement on spindle fibers, increasing spindle length, resulting in chromosomal mis-segregation, aneuploidy, and DNA damage. Our findings suggest that ATX020 inhibits CIN+ HGSOC cells mainly by inducing mitotic arrest and DNA damage, disrupting KIF18A’s function crucial for mitosis. Full article

Background and Objectives: Endometriosis has been shown to be associated with an increased cancer risk, and apoptosis may be important in the pathophysiology of endometriosis. To date, it remains unclear whether the tissue cell surface apoptosis marker (annexin V) is an important parameter in terms of cancer and endometriosis. This retrospective study aimed to compare endometriosis cases and ovarian cancer cases in terms of apoptosis and cell proliferation markers’ levels. Materials and Methods: In total, 65 (30 ovarian endometrioma, 35 ovarian carcinoma) paraffin blocks were taken for flow cytometric analysis. The flow cytometry analysis markers and annexin V staining levels were compared. Results: The G2/M stage cell ratio, S-phase fraction, proliferative index, aneuploidy cell ratio, and annexin V apoptotic index ratio were found to be statistically significantly lower in the endometrioma group compared to the carcinoma group. However, the G0/G1 phase cell ratio was found to be higher in the endometrioma group. According to the correlation analysis results, annexin V expression level showed a positive correlation with the G2/M cell ratio and S-phase fraction, while it showed a negative correlation with the G0/G1 level. In addition, as the apoptotic index increased, the cell aneuploidy rate also increased, which was statistically significant. When the apoptotic index was used to distinguish between endometrioma and ovarian cancer (cutoff value 16.05%), the sensitivity was found to be 94.3%, and the specificity was found to be 80%, which was statistically significant for cases below the cutoff value to be accepted as endometrioma. Conclusions: Apoptosis was reduced in endometriosis cases. The cell DNA activity was altered in endometriosis cases, as in cancer cases. Flow cytometric analysis can be used in the diagnosis of endometriosis even in paraffin-embedded tissues. The flow cytometric annexin V analysis provided results in an average of 30 min, making it a promising and highly sensitive differential diagnostic marker to distinguish between endometriosis and ovarian cancer. Full article

Multilocus pathogenic variation—when multiple genetic disorders coexist in a single individual—remains rare but is increasingly recognized in the era of genomic medicine. Reporting such cases is essential for improving diagnostic accuracy, refining clinical management, and informing genetic counseling. We describe a pediatric case with a complex phenotype resulting from the coexistence of two distinct genetic diagnoses—cerebrotendinous xanthomatosis (CTX), a rare autosomal recessive lipid storage disorder caused by biallelic mutations in the CYP27A1 gene and Klinefelter syndrome a common sex chromosome aneuploidy occurring in approximately 1 in 600 males, characterized by hypogonadism, gynecomastia, pubertal delay, infertility, micrognathia, and neurodevelopmental challenges—and an additional incidental finding with clinical relevance. The patient was born to consanguineous parents, presented with neurological symptoms, gastrointestinal dysfunction, endocrine abnormalities, and dysmorphic features. Trio-based exome sequencing identified a homozygous pathogenic variant in CYP27A1 consistent with CTX, while conventional G-banded karyotyping revealed a 47,XXY chromosomal pattern, confirming Klinefelter syndrome. Additionally, a heterozygous pathogenic variant in BRCA2 was incidentally detected, associated with hereditary cancer predisposition. The overlapping manifestations of CTX and Klinefelter syndrome produced a non-classical presentation that delayed diagnosis. Although the BRCA2 variant did not contribute to the current phenotype, it has important implications for future cancer surveillance and family risk assessment. This case underscores the importance of combining classical cytogenetic and modern genomic methods to elucidate complex phenotypes, particularly in consanguineous populations, and highlights the need for the multidisciplinary management of patients with multilocus or incidental findings. Full article

A woman in her 40s with a history of ER/PR+, HER2-negative breast cancer presented with a seizure three years after mastectomy. Magnetic resonance imaging (MRI) revealed a right caudate head mass, which was concerning for either high-grade glioma or metastatic disease, but biopsy was deemed too high risk. Cerebrospinal fluid (CSF) tumor-derived DNA (tDNA) analysis by next-generation sequencing (NGS) was ordered, revealing a gain-of-function variant in PIK3CA, ERBB2 copy number gain, and high aneuploidy, findings consistent with breast cancer brain metastasis. Based on these results, the patient was treated with stereotactic radiosurgery (SRS) followed by trastuzumab deruxtecan, a HER2-targeted therapy. This case highlights the diagnostic and therapeutic value of CSF tDNA analysis in central nervous system (CNS) lesions when biopsy is not feasible. The report also illustrates how clonal evolution, such as acquired ERBB2 amplification, can occur in metastatic disease and influence treatment decisions. Full article

Chromosome transmission fidelity is vital for organism fitness. Yet, extrinsic and intrinsic changes can affect this process, leading to aneuploidy, the loss/gain of chromosomes, which is a hallmark of cancer. Here, using a haploid fission yeast Schizosaccharomyces pombe strain with a segmental aneuploidy, we assayed genome stability under different temperatures and altered gene dosage. We find that S. pombe genome stability is temperature-dependent and is unexpectedly modulated by intracellular levels of inorganic polyphosphate polymers (polyP). The vtc4⁺ gene, encoding a subunit of the polyP-generating VTC complex, is present twice due to the segmental aneuploidy resulting in a gene-dosage-coupled increase in polyP. Using strains with different amounts of polyP, we find a direct negative correlation between polyP and chromosome segregation fidelity. PolyP modulates the function of the conserved CCAN kinetochore subcomplex, as the abnormal growth phenotype caused by the mutant CCAN protein Fta2-291 was rescued in the absence of polyP, while extra polyP had the opposite effect. Importantly, this appears to occur in part by modulation of the nucleolin Gar2. Gar2 is the functional homolog of the Saccharomyces cerevisiae Nsr1 protein, whose function is modulated by posttranslational polyP-mediated polyphosphorylation. Thus, polyP modulates genome stability, linking cellular metabolism to chromosome transmission fidelity. Full article