Background Cancer stem cells (CSCs) drive colorectal cancer (CRC) progression, metastasis, and therapy resistance, but their heterogeneity limits targeted treatment efficacy. Clarifying the stemness landscape and underlying mechanisms is crucial for developing effective CRC therapies.
Methods By integrating 10 ×single-cell data from GSE201348 and GSE161277, we constructed a single-cell atlas of nine primary CRC samples. CSCs were identified via scRNA-seq analyses. Using integrative bioinformatics tools, we identified ENY2 as a stemness-related marker and explored its potential role in CRC. We further compared genetic variants, immune infiltration, and drug sensitivity between high and low ENY2 expression groups.
Results Stem cell clusters (M0 and M7) in CRC were identified based on copy number variation, pseudotime trajectory, and CytoTRACE analyses. By integrating marker gene profiles, DEGs from GSE33113, CytoTRACE-based CSC genes, and prognostic genes from GSE17536, we identified two key stemness-related markers: ENY2 and PKM. ENY2 was prioritized for further analysis due to its limited investigation in CRC. Bioinformatic analyses revealed that ENY2 was significantly upregulated and associated with poor prognosis. Enrichment analyses indicated its involvement in MYC and E2F targets, G2M checkpoint, and EMT pathways. Drug sensitivity prediction suggested that high ENY2 expression may confer responsiveness to 5-fluorouracil, capecitabine, oxaliplatin, and 24 other potential agents.
Conclusions ENY2 may act as a key CSC-associated biomarker that promotes CRC tumorigenesis and metastasis via the EMT pathway, which enhance our understanding of CRC pathogenesis and highlight ENY2 as a potential target for diagnosis and therapy.
Chromosomal abnormalities play a significant role in reproductive issues and developmental disorders, yet information on their prevalence within the Turkish Cypriot population is limited. This study offers the first comprehensive cytogenetic evaluation of balanced chromosomal aberrations in 100 healthy Turkish Cypriot individuals of reproductive age. Structural abnormalities were detected in 4 % of participants, all of whom were female, including inversions, insertions, balanced translocations, and a derivative chromosome 22. The frequency of balanced translocations in this group was higher than global averages, highlighting important reproductive considerations for carriers. The observed sex-specific difference points to a complex interplay of genetic and epigenetic factors influencing chromosomal variation. To achieve accurate diagnosis and effective management, advanced molecular cytogenetic methods should be used alongside traditional karyotyping. Larger studies, especially those including male subjects, are needed to confirm these results and improve genetic counseling, risk assessment, and fertility treatment approaches tailored to this distinct population.
Glioblastoma (GB) remains the most aggressive and treatment-resistant primary brain tumor, characterized by extensive heterogeneity, therapeutic resistance, and dismal prognosis. In this comprehensive review, we aimed to synthesize emerging insights into the roles of non-coding RNAs (ncRNAs)—including microRNAs, long non-coding RNAs, circular RNAs, and PIWI-interacting RNAs—in the regulation of glioblastoma progression, resistance mechanisms, and potential therapeutic strategies. We critically evaluated the molecular functions of ncRNAs in key oncogenic processes such as proliferation, angiogenesis, epithelial-mesenchymal transition (EMT), and immune evasion. Additionally, we reviewed current detection methods, delivery technologies, and clinical trials targeting these ncRNAs. A central goal of this review was to bridge a notable gap in the literature by highlighting underrepresented ncRNA classes such as circRNAs and piRNAs, which exhibit regulatory complexity and potential as biomarkers and therapeutic agents in GB. We further discussed delivery challenges posed by the blood-brain barrier and explored promising nanocarrier and exosome-based approaches to enhance therapeutic targeting. Through curated case studies, we showcased the translational potential of targeting specific ncRNAs to reverse multiple resistance types and improve immunotherapy response. This review provides a consolidated framework for understanding the dynamic role of ncRNAs in glioblastoma and proposes an expanded toolkit for precision oncology approaches. Our findings not only underscore the therapeutic promise of ncRNAs but also call for future investigations into the lesser-known subclasses that could redefine the landscape of GB management.
Chronic myeloid leukaemia (CML) is the first clonal myeloproliferative disorder of pluripotent stem cells to be associated with a specific genetic abnormality, the Philadelphia chromosome, bearing the BCR-ABL1 fusion oncogene. Tyrosine kinase inhibitors are used as first-line treatment for the chronic phase of CML, although alternative treatments are necessary for resistant cases. Cannabidiol (CBD) is a major constituent of hemp oil that exerts a broad range of pharmacological effects in various malignancies. However, its molecular mechanisms in leukaemia remain unclear.
In the present study, Imatinib-sensitive K-562S cells were subjected to CBD treatment (IC50: 17.69 μM) for 4 and 12 h, followed by RNA sequencing to identify differentially expressed genes (DEGs). The subsequent transcriptomic profiling revealed 3518 DEGs at 12 h and 3433 DEGs at 4 h of treatment, including significant modulation of metallothionein-regulated oxidative stress responses (MT1, MT2, and SLC30A2) and p53-mediated apoptosis (TP53TG3, DDIT4, BBC3, CHAC1, NOXA1, and DAPK2). Additionally, the DEGs were enriched in alterations in immune signalling pathways—including type I interferon activation and PI3K-Akt-mTOR and Toll-like receptor signalling—crucial in leukaemia progression, as well as variations in lipid metabolism and mitochondrial homeostasis.
The results presented in this study validate the considerable potential of CBD to induce broad transcriptional and signalling alterations, related to immune modulation, apoptosis, and metabolic processes in K-562S cells. These findings provide novel insights into the therapeutic potential of CBD and lay the groundwork for further investigation into its precision applications in haematological malignancies.
Background Current targeted therapies for gastric cancer have limited efficacy, and recently discovered markers have not significantly improved survival rates in patients with gastric cancer. Therefore, it is imperative to identify more specific genes associated with the occurrence and progression of gastric cancer to achieve prevention and treatment. The aim of this study is to discover high-risk genes for gastric cancer by integrating single-cell transcriptomics and Mendelian randomization (MR) analysis.
Methods This study integrates gastric cancer genome-wide association study (GWAS) data, single-cell transcriptomics (sc-RNA-seq), and expression quantitative trait loci (eQTL) data for analysis, and employs two-sample MR to elucidate the causal relationships between genes and gastric cancer, thereby identifying high-risk genes for gastric cancer. Subsequently, in vitro cellular experiments are conducted to validate the transcriptional expression levels of these genes.
Results After quality control of the sc-RNA-seq data, we identified 2463 markers for gastric cancer cell subtypes. Subsequently, we utilized eQTL data and GWAS data for gastric cancer to perform MR analysis, yielding 149 genes with a causal relationship with gastric cancer. By applying log2FC filtering, we ultimately identified 5 high-risk gastric cancer genes: SORBS3, RMND5A, FBXO6, LPGAT1, and EPHB4. Finally, in vitro validation confirmed the differential expression of these 5 high-risk genes between normal gastric epithelial cell lines and gastric cancer cell lines.
Conclusions Our study reveals previously unattended high-risk gastric cancer genes, potentially offering new directions and evidence for the molecular diagnosis and treatment of gastric cancer.
Background Early-stage diagnosis, absence of specific reliable biomarkers, and better clinical management of colorectal cancer (CRC) remain major challenges. The Rspondin2 (RSPO2) gene is one of the most potent enablers of Wnt signaling, having contrasting aspects in tumor development and progression.
Aim We aimed to identify the role of RSPO2 as a molecular biomarker by evaluating its methylation and expression profiles in CRC tissue samples to identify biomarker potential.
Methodology Combined bisulfite restriction analysis (CoBRA) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to access the change in methylation pattern and expression profile of RSPO2 in 52 CRC tissue samples. DNA methylome and transcriptome profiling of CRC samples were hierarchically clustered, and prognostic utility was measured using a Kaplan-Meier (K-M) plot and univariate analysis.
Results RSPO2 was hypermethylated (33/52; 63.46 %) and significantly associated with early-stage (I+II, p = 0.04) CRC tissue and exhibited low RSPO2 expression (42/52; 80.76 %). Hierarchical clustering stratified the samples into two distinct clusters that share some significant clinical and molecular factors specific for cluster 1 such as LN status (p < 0.0001) and lymphovascular invasion (p = 0.0013) while staging (p < 0.0001) and RSPO2 methylation (p = 0.0402) in cluster 2, which are valuable for personalized medicine. K-M plot analysis showed that patients with low RSPO2 expression have poor disease-free survival but could not be a risk factor.
Conclusion RSPO2 may be a potential biomarker for early-stage detection and provide valuable insight into the diagnosis of patients with CRC.
Cancer remains a leading cause of morbidity and mortality worldwide, with nearly 10 million deaths reported in 2022. In the United States, more than 618,000 deaths are projected to occur in 2025. Traditional methods for identifying cancer types are often time-consuming, labor-intensive, and resource-demanding, highlighting the need for efficient alternatives. This study aimed to evaluate machine learning algorithms on RNA-seq gene expression data to identify statistically significant genes and classify cancer types. We retrieved the PANCAN RNA-seq dataset from the UCI Machine Learning Repository and assessed eight classifiers—Support Vector Machines, K-Nearest Neighbors, AdaBoost, Random Forest, Decision Tree, Quadratic Discriminant Analysis, Naïve Bayes, and Artificial Neural Networks. Model performance was validated using a 70/30 train-test split and 5-fold cross-validation. Among the tested models, the Support Vector Machine achieved the highest classification accuracy of 99.87 % under 5-fold cross-validation. These findings demonstrate the potential of machine learning to efficiently analyze RNA-seq data, facilitate biomarker discovery, and support the development of personalized cancer diagnostics and treatment strategies.
Severely infected patients produce large amounts of inflammatory cytokines, such as interleukin-6 (IL-6) and interleukin-1β (IL-1β), leading to a "cytokine storm", which is a clinically refractory condition. Because IL-6 and IL-1β differ significantly in gene family, chromosomal location, protein structure, and signaling pathways, existing techniques are ineffective at simultaneously removing cytokines. This work developed a novel blood purification material by chemically grafting histidine onto a polyvinylidene fluoride (PVDF) membrane. ATR-FTIR and XPS analyses confirmed the successful grafting of histidine onto the PVDF membrane. Following histidine grafting, the membrane’s adsorption capacity for IL-6 in aqueous solution increased with histidine concentration. The optimized histidine-grafted PVDF membrane achieved adsorption rates of (36 ± 4)% for IL-6 and (63 ± 5) % for IL-1β in plasma. Additionally, the histidine-grafted PVDF membrane demonstrated enhanced biocompatibility, exhibiting a low hemolysis rate, minimal adsorption of red blood cells and platelets, and anticoagulant properties without activating the coagulation cascade. This histidine-grafted PVDF membrane offers a promising new therapeutic strategy for treating severe infections and holds significant potential for clinical application.
Purpose Persistent toe walking in children is often considered idiopathic; however, increasing evidence suggests that alterations in the PMP22 gene—implicated in Charcot-Marie-Tooth disease type 1 A (CMT1A) and Hereditary Neuropathy with Liability to Pressure Palsies (HNPP)—may contribute to its pathogenesis. This study investigates the association between PMP22 variants (duplications, deletions, and point mutations) and toe walking in children, aiming to delineate their clinical and genetic characteristics.
Methods A retrospective analysis was performed on 22 pediatric patients (mean age: 7.7 years) with persistent toe walking and confirmed PMP22 variants identified through a 49-gene next-generation sequencing (NGS) panel. In selected cases, Multiplex Ligation-dependent Probe Amplification (MLPA) was applied to confirm copy number variations. Comprehensive clinical evaluations included musculoskeletal, neurological, and developmental assessments.
Results All identified variants demonstrated dominant inheritance. Pathogenic variants were present in 54.5 % of patients, likely pathogenic in 31.8 %, and variants of uncertain significance (VUS) in 13.6 %. Among pathogenic cases, most carried PMP22 duplications, one had a deletion, and the remainder harbored the missense variant p.(Thr118Met). The three VUS carriers exhibited comparatively milder phenotypes, such as muscle cramps, lumbar hyperlordosis, mild dorsiflexion restriction, hyporeflexia, pes cavus, and clinodactyly/brachydactyly; only one presented with tremor. Lumbar hyperlordosis (90.9 %) and pes cavus (90.9 %) were the most consistent findings.
Conclusions Persistent toe walking may represent an early sign of PMP22-related neuropathies rather than a benign idiopathic gait pattern. The predominance of PMP22 duplications and characteristic neuromuscular features highlight the clinical utility of integrating NGS and MLPA testing for accurate diagnosis, targeted management, and genetic counseling.
Background: Terminal erythroid differentiation (TED) is the maturation process of proerythroblasts into enucleated erythrocytes. Animal models are essential for studying red blood cell disorders.
Methods: We isolated erythroblasts at different TED stages from mouse bone marrow using FACS and performed integrated multi-omics analyses.
Results: We developed a stage-specific transcriptome and proteome profile, enhancing murine TED databases. The most significant changes occurred during the transition from proerythroblasts to basophilic erythroblasts, characterized by immune function suppression and activation of erythroid processes. Global gene and protein expression dynamics showed that orthochromatic erythroblasts exit the cell cycle, with transcription cofactors histone deacetylase 1(HDAC1), histone deacetylase 2(HDAC2), and cell division control protein 6 homolog (CDC6), playing key roles in cell cycle regulation. Additionally, autophagy was initiated at the basophilic stage, indicated by increased autophagy-related gene (ATG) mRNA levels and activation of autophagy marker proteins like microtubule associated protein 1 light chain 3 beta (LC3-I), optineurin (OPTN), and ATGs, including Atg7, Atg4b, Atg3, and Atg2b.
Conclusions: Overall, we have generated a foundational murine transcriptome and proteome dataset, providing insights into the functional dynamics and regulatory mechanisms of terminal erythroid differentiation.
Objective This study aimed to evaluate the association of single nucleotide polymorphisms (SNPs) in IKZF1, ARID5B, and CEBPE with acute lymphoblastic leukemia (ALL) susceptibility in Chinese children.
Methods A case-control study was conducted involving 360 ALL patients and 398 healthy controls. Nine SNPs were genotyped, and their associations with ALL risk were analyzed using logistic regression under various genetic models. Multifactor dimensionality reduction (MDR) analysis was employed to investigate SNP-SNP interactions.
Results Seven of the nine SNPs were significantly associated with ALL susceptibility. Specifically, IKZF1 SNPs (rs11980379, rs4132601, rs10272724) and a CEBPE SNP (rs4982731) were associated with an increased risk of ALL. In contrast, ARID5B SNPs (rs10994982, rs10821938) and another CEBPE SNP (rs2144827) were associated with a reduced risk. Stratified analyses revealed age- and sex-specific associations. MDR analysis identified significant SNP-SNP interactions, with a robust four-SNP model (rs10994982, rs2144827, rs10272724, rs10821938) showing the best predictive performance for ALL risk.
Conclusion Specific SNPs in IKZF1, ARID5B, CEBPE and their interactions are associated with childhood ALL susceptibility in Chinese populations, providing references for ALL risk stratification.
Objective To characterize the clinical features of a fetus with postaxial polydactyly caused by a de novo PRKACB gene variant and to perform a genetic analysis.
Methods A pregnant woman who presented to Zhejiang Provincial People's Hospital on 4 December 2024 was enrolled in this study. Fetal clinical data were collected, and genomic DNA was extracted from the fetus and both parents. Clinical whole-exome sequencing (WES) was performed on the trio (fetus and both parents). Candidate variants were identified and validated by Sanger sequencing, followed by bioinformatics analysis. This study was approved by the Medical Ethics Committee of Zhejiang Provincial People’s Hospital (approval number: QT2025076).
Results Prenatal ultrasonography revealed bilateral postaxial polydactyly and several fetal biometric measurements that were inconsistent with gestational age. The clinical diagnoses were intrauterine growth restriction and polydactyly. WES identified a de novo heterozygous variant (c.802 G>A; p.Asp268Asn) in exon 8 of the fetal PRKACB gene (NM_182948.4). According to the ACMG variant-classification guidelines, this variant was interpreted as likely pathogenic (PS2_Moderate, PM1, PM2_Supporting and PP3). AlphaFold-based structural prediction indicated that the PRKACB p.Asp268Asn substitution resulted in the loss of two hydrogen bonds, thereby altering the protein's three-dimensional conformation and affecting structural stability.
Conclusion The PRKACB gene c.802 G>A (p.Asp268Asn) variant is a potential genetic cause of bilateral postaxial polydactyly in the fetus. Identification of this variant expands the known mutational spectrum of PRKACB gene and provides an important reference for genetic counselling and prenatal diagnosis.