Search Results (432)

Analysis of coding areas has long been used to study monogenic illnesses, but despite the extensive use of whole-exome sequencing (WES), up to half of suspected cases remain genetically unexplained. Variants outside coding areas can alter splicing, transcript stability, or gene regulation, compromising normal gene activity. These include mutations in noncoding RNAs, promoters, enhancers, deep intronic sequences, and untranslated regions (UTRs). Several well-known disorders have been linked to these mechanisms, including β-thalassemia caused by deep intronic mutations leading to aberrant splicing, familial hypercholesterolemia caused by promoter defects affecting LDLR expression, and inherited retinal diseases driven by noncoding variants influencing retinal gene regulation. These instances show that pathogenic variation is not limited to the exome and can have significant clinical implications. This review summarizes current understanding of noncoding and regulatory variants in monogenic diseases, discusses how they influence diagnosis and therapy, and highlights integrative approaches combining genomic, transcriptomic, and epigenomic data. Multi-layered research has increased diagnostic accuracy and unveiled new therapeutic potentials, although noncoding variations make the connection between genotype and phenotype more complex. Noncoding regions will need to be incorporated into standard diagnostic procedures to convert molecular insights into concrete therapeutic applications in the future. Predictive algorithms, patient-derived model systems, and functional validation testing will all help to simplify this process. Full article

Assisted reproductive technologies (ART) and, in particular, intracytoplasmic sperm injection (ICSI) transformed the management of male infertility by making fertility possible in previously untreatable cases. However, the bypassing of natural selection mechanisms at fertilization is fraught with the danger of transmission of genetic and epigenetic abnormalities. Male infertility is now a multifactorial disorder with notable contributions from single-gene defects, chromosomal abnormalities, and Y-chromosome microdeletions. The recent advances in next-generation sequencing and sperm omics have identified mutations and copy-number variations in genes critical for spermatogenesis, flagellar structure, and endocrine regulation. Along with these findings, an increasing body of evidence suggests that ART procedures can lead to a disruption of epigenetic reprogramming during gametogenesis and early embryogenesis, resulting in imprinting disorders and altered patterns of gene expression in the offspring. This review synthesizes recent progress in the molecular underpinnings of genetic and epigenetic hazards of ART, with an emphasis on clinical significance for reproductive counselling and ethical considerations for future generations. Full article

Morphoeic basal cell carcinoma (mBCC) has a higher risk of local recurrence than the more indolent nodular (nodBCC) subtype. Little is known about the genetic and molecular makeup of mBCC that determines its invasive behaviour: a comparison of mBCC with nodBCC was carried out. Whole-exome sequencing (WES) of 20 BCC tumours (10 eyelid morphoeic and 10 nodular) underwent driver gene detection using OncodriveFM and MutSigCV, followed by a randomisation analysis procedure. Samples underwent RNA sequencing, gene-set enrichment analysis and candidates verified by RT-PCR. PTCH1, FLNB, and double-knockdown human keratinocyte models were used to validate phenotype and gene expression. Hedgehog pathway analysis of 20 additional BCCs underwent immunostaining verification. Our analysis revealed FLNB as a potential driver with a mutational cluster in FLNB Filamin domain 24 and a 4-fold reduction in expression compared to normal eyelids in mBCC only. FLNB knockdown demonstrated an mBCC phenotype. Aberrant Gli2 dominant hedgehog (Hh) signalling was seen in mBCC on three molecular levels: mutational significance, transcriptome profile, and protein expression. Gli2-dominant Hh overexpression was seen in the tumour plus stroma of eyelid morphoeic but not nodular BCC. FLNB is a potential tumour suppressor, with its loss producing a morphoeic phenotype in vitro. Full article

Introduction. Over the past two decades, the αGal (Galα1–3Galβ1–4GlcNAc–R) epitope, a carbohydrate found in many non-primate mammals, has gained significant relevance in medicine due to its association with an increasing number of allergic reactions to animal-derived foods, drugs, and medical devices. Due to a mutated gene coding for α1,3-galactosyltransferase (α1–3GT), humans lack αGal and, therefore, naturally produce anti-α-Gal antibodies (IgM, IgA, and IgG), especially in the context of a xenotransplantation, which can lead to extreme immunological reactivity, including hyperacute rejection of the transplant. Recently, these uncontrollable immune reactions have driven demand for more accurate procedures to better detect αGal in animal-derived foods or bioprosthetics. The currently most widely used α-Gal-specific monoclonal antibody is an IgM antibody (clone M86), developed in Ggta1 KO mice and isolated from hybridoma tissue culture. As the IgM isotype has limited purification properties, specificity, and sensitivity, we aimed to produce a novel IgG antibody with high affinity and extensive applicability. Methods. An experimental murine IgG1 anti-αGal antibody (IgG-αGalomab) was developed by immunization of Ggta1 knockout (KO) mice, and its affinity was evaluated using ELISA, Western blot, flow cytometry, and immunohistochemistry/immunofluorescence. Results. Compared to IgM-M86, IgG-αGalomab demonstrated ~1200-fold higher binding potency and lower cross-reactivity with competitive molecules, i.e., bovine serum albumin, galactobiose, and lactose. Unlike IgM-M86, IgG-αGalomab showed an increasing affinity over time in the binding tests performed on xenogeneic tissues. Notably, high-affinity for αGal was detected by Western blot at high dilution [1:200,000] of IgG-αGalomab compared to IgM-M86 [1:1000]. By flow cytometry, specificity and dose-dependent response were confirmed using in vitro cultures of porcine and human fibroblasts. Finally, in immunofluorescence and immunohistochemistry analysis, αGal was demonstrated to be detectable by IgG-αGalomab at a dilution of [1:1000], while IgM-M86 was demonstrated to be detectable at [1:100]. Conclusions. Altogether, our newly developed antibody showed high sensitivity and specificity for α-Gal in various applications. Based on its potential binding capacity, IgG-αGalomab could have important applications in precision medicine for predicting, treating, and preventing immune-mediated phenomena of patients in different medical areas. Full article

Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality worldwide. While target therapies have changed the outcomes of patients harboring actionable mutations, resistance inevitably emerges. Circulating tumor DNA (ctDNA) offers a minimally invasive tool for capturing tumor evolution in real time. This approach enables the rapid detection of resistance mechanisms, complements or substitutes for tissue re-biopsy, and reduces the burden of invasive procedures for patients. In this review, we summarize the current evidence on the use of liquid biopsy to uncover resistance mechanisms in patients progressing on targeted therapies, with a focus on its role in dynamic tumor profiling and longitudinal disease monitoring. Full article

Background: Lymphatic malformations (LM) are rare congenital vascular anomalies caused by abnormal development and growth of lymphatic vessels. These malformations can lead to a wide range of symptoms, from mild swelling to more severe complications. Treatment options remain limited, especially for complex cases. Recent research has suggested that PIK3CA mutations play a key role in the pathogenesis of LM, potentially offering new possibilities for targeted treatment strategies. Methods: In this study, a cohort of 36 patients diagnosed with LM, Klippel-Trenaunay syndrome (KTS), and Proteus syndrome was analyzed. PIK3CA mutations were assessed in tissue samples obtained from the LM during clinically indicated procedures using digital droplet polymerase chain reaction (ddPCR), targeting five hotspots. Results: PIK3CA mutations were found in 18 patients (50%). The most frequent mutation was p.E542K (c.1624G>A), found in 19.44% of patients, followed by p.H1047R (c.3149A>G), p.E545K (c.1633G>A), and p.H1047L (c.3140A>T) each occurring in 11.11% of the cases. Mutations were more common in isolated LMs, with 63.16% of patients exhibiting PIK3CA mutations. Conclusions: PIK3CA mutations are common in LM, supporting the potential for targeted therapies like PI3K inhibitors in treating complex cases. This research highlights the importance of genetic analysis in the management of LM and offers a new therapeutic approach. Full article

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. Full article

Obesity is a multifaceted disorder influenced by various factors, with heredity being a significant contributor. Bariatric surgery is the most effective long-term intervention for morbid obesity and associated comorbidities, while outcomes vary significantly across individuals. Recent studies indicate that genetic and molecular determinants, particularly alterations in the leptin–melanocortin signalling pathway involving the fat mass and obesity-associated gene (FTO), pro-opiomelanocortin (POMC), melanocortin 4 receptor (MC4R), leptin (LEP), and leptin receptor (LEPR), influence the efficacy of weight loss and metabolic adaptations post-surgery. This narrative review consolidates evidence from peer-reviewed papers available in PubMed and Scopus until July 2025. The emphasis was on novel research and systematic reviews examining genetic polymorphisms, gene–environment interactions, and outcomes following bariatric procedures such as Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG). Recent research emphasised the integration of genetic screening and precision medicine models into clinical bariatric workflows. Variants in FTO (e.g., rs9939609), MC4R (e.g., rs17782313), LEPR, and POMC are associated with diminished weight loss post-surgery, an increased likelihood of weight regain, and reduced metabolic enhancement. Patients with bi-allelic mutations in MC4R, POMC, or LEPR exhibited poor long-term outcomes despite receiving effective physical interventions. Furthermore, genes regulating mitochondrial metabolism (such as PGC1A), adipokine signalling (such as ADIPOQ), and glucose regulation (such as GLP1R) have been demonstrated to influence the body’s response to sugar and the extent of weight gain or loss. Two recent systematic reviews elucidate that candidate gene investigations are beneficial; however, larger genome-wide association studies (GWAS) and machine learning techniques are necessary to enhance predictive accuracy. Integrating genetic and molecular screening with bariatric surgery planning possesses significant therapeutic potential. Genotyping can assist in patient selection, procedural decisions, and medication additions, particularly for those with variants that influence appetite regulation or metabolic flexibility. Advancements in precision medicine, including the integration of polygenic risk scores, omics-based profiling, and artificial intelligence, will enhance the customisation of surgical interventions and extend the lifespan of individuals with severe obesity. The epigenetic regulators of energy balance DNA methylation, histone changes, and microRNAs that may affect individual differences in weight-loss patterns after bariatric surgery are also briefly contextualised. We discuss the concept that epigenetic modulation of gene expression, mediated by microRNAs in response to food and exercise, may account for variations in metabolic outcomes post-surgery. Full article

Genomic studies have provided key insights into the molecular pathogenesis of differentiated thyroid carcinoma (DTC), including the role of genes involved in the homologous recombination (HR) related to DNA repair and genomic stability. This research aimed to investigate the genetic landscape of HR genes in thyroid pathology, associated with recurrence risk and clinical prognosis. The study involved six individuals with thyroid conditions, including two patients diagnosed with papillary thyroid carcinoma (PTC) and four individuals with benign thyroid disease. The research material consisted of tumor samples collected during surgical procedures. Protein interactions were analyzed using the STRING database (string-db.org). Homologous recombination genes were sequenced using the HRR Panel vr1.0 on the MiSeq™ Sequencing System. Bioinformatics analysis revealed a relationship between BRAF mutations and HR gene defects in PTC. Mutations in BRCA1, BRCA2, and FANCA genes, typically associated with thyroid tumors, were identified in the tissue of papillary thyroid cancer (PTC). A statistically significant correlation was found between the FANCA gene mutation (rs7195066) and the recurrent course of the PTC. The preliminary findings suggest a potential role for non-pathogenic BARD1 mutations in follicular adenoma. No significant association was found between genes involved in homologous recombination repair and the incidence of papillary thyroid carcinoma, suggesting that these genes may not play a major role in the development of this type of thyroid cancer. Full article

Hypertension is a major risk factor for heart failure. Acetylation of p53 is known to regulate its activities. We have previously identified that p53 acetylation is required for cardiac remodeling in a mouse model of pressure overload-induced heart failure. Acetylation mutant p53 (p53aceKO) mice have been shown to have the ability to regulate SIRT3 KO-induced cardiac fibrosis. In the present study, we hypothesized that p53aceKO mice would exhibit cardiac protection and blunt cardiac fibrosis when subjected to Ang-II-induced hypertension. Control and p53aceKO mice received either a micro-osmotic pump implant administering Ang-II for 28 days or a sham procedure. Blood pressure was measured weekly, and echocardiography was performed every two weeks. Mice were euthanized and hearts were processed for histological analysis. While both control and p53aceKO mice receiving Ang-II exhibit increased systolic and diastolic blood pressures, control mice also demonstrate increases in ejection fraction and fractional shortening compared to the sham, while p53aceKO mice do not. Furthermore, control mice receiving Ang-II exhibit decreased left ventricular diameter and volume at end-systole and end-diastole, as well as thickening of both the anterior and posterior walls, while p53aceKO mice exhibit no significant changes in any of these parameters. Additionally, p53aceKO mice do not exhibit the Ang-II infusion-induced cardiac fibrosis seen in control mice treated with Ang-II. Mutation of p53 acetylation is protective against Ang-II infusion-induced cardiac fibrosis and dysfunction in mice. Acetylated p53 may, therefore, be a novel therapeutic target to address complications in the heart associated with hypertension. Full article

The progression of pancreatic cancer (PC) is significantly influenced by the immune system. In the United States, PC is the third leading cause of cancer-related mortality. The high lethality of PC is attributed to its immunological advantage, which is facilitated by an immunosuppressive microenvironment, a low mutational burden, and minimal T-cell infiltration. Although immunotherapies, such as checkpoint blockades or genetically engineered T cells, have not yet demonstrated viability, there is a growing body of evidence suggesting that innovative combinations of conventional therapies and various procedures may lead to effective immunotherapy in the treatment of PC. This review focuses on the importance of the tumor microenvironment and the promising role of immunotherapies in PC. Full article

Background/Objectives: We have previously reported the engineering of a point-of-care (POC) system that fully automates the procedures for nucleic acid extraction and multiplexed real-time RT-PCR, with a major advantage of high-level multiplexing. In this study, we applied and validated the system in a respiratory tract infection setting. Methods: An automatic nested real-time RT-PCR assay was developed (POCm). It was a 40-plex assay that simultaneously detected 39 epidemiologically important respiratory pathogens in 1.5 h in the POC system. The analytical and clinical performance was evaluated. Results: The analytical sensitivities of the POCm assay were comparable to those of its single-plex counterparts performed manually on a bench-top. The minimum detectable concentrations ranged from 53 copies/mL to 5.3 × 10³ copies/mL for all pathogen targets except hCoV-NL63 (5.3 × 10⁴ copies/mL). The quantitative performance was demonstrated by the linear correlations between Ct values and input concentrations for all pathogen targets, with 24 of them demonstrating coefficients of correlation (r) greater than 0.9. The POCm assay was subsequently evaluated in 283 clinical samples. A high level of agreement (98.2–100%) was achieved for pathogen detection results between POCm and standard diagnostic methods. The POCm result was also fully concordant with the result of another commercial POC multiplex platform. For positive clinical samples, pairwise Ct values measured by POCm closely correlated with those of the bench-top reference method (r = 0.70). The feasibility of mutation genotyping of the viral subtype was further demonstrated. Conclusions: This study demonstrated the practicality of POCm for routine testing in clinical laboratories. Further clinical trials are being conducted to evaluate the clinical performance of the system. Full article

Inflammatory bowel disease (IBD) is an autoimmune condition with an increasing incidence worldwide, which manifests in two pathological forms: Crohn’s disease (CD) or ulcerative colitis (UC). Both cause chronic inflammation of the digestive tract, although they can present different locations and with different symptoms. To date, the pathogenesis of IBD remains unclear. One of the major complications of these diseases is colorectal cancer. Several studies have reported a correlation between chronic intestinal inflammation and an increased risk of malignancy. Persistent inflammation damages the intestinal mucosa and epithelial wall, altering gut permeability and the local microenvironment. Moreover, the heightened activity of the immune system leads to an increased production of reactive oxygen and nitrogen species (ROS and RNS), increasing the risk of DNA mutation and cell transformation. In addition, some current therapies used to treat IBD and induce remission may contribute to carcinogenesis or impair immune surveillance due to their immunosuppressive activity. The management of cancer risk for IBD patients remains a challenge, and existing screening methods are often invasive (endoscopies, biopsies), resulting in low patient compliance. To address this unmet clinical need, researchers have started using proteomics to identify novel biomarkers that could predict cancer risk in IBD patients in a non-invasive manner. This review aims to examine the current state of knowledge regarding the correlation between IBD and cancer, with a special focus on the biomarkers discovered through proteomic approaches, and their potential application in routine clinical screening. In our view, proteomics represents a powerful and rapidly evolving strategy for biomarker discovery, with the potential to complement or even replace invasive procedures. Its future clinical impact will rely on translating current research advances into robust and accessible diagnostic tools. Full article

The 2021 WHO classification of brain tumours revolutionised the oncological field by emphasising the role of molecular, genetic and pathogenetic advances in classifying brain tumours. In this context, incidental gliomas have been increasingly identified due to the widespread performance of standard and advanced MRI sequences and represent a diagnostic and therapeutic challenge. The impactful decision to perform a surgical procedure deeply relies on the non-invasive identification of features or parameters that may correlate with brain tumour genetic profile and grading. Therefore, it is paramount to reach an early and proper diagnosis through neuroradiological techniques, such as MRI. Standard MRI sequences are the cornerstone of diagnosis, while consolidated and emerging roles have been awarded to advanced sequences such as Diffusion-Weighted Imaging/Apparent Diffusion Coefficient (DWI/ADC), Perfusion-Weighted Imaging (PWI), Magnetic Resonance Spectroscopy (MRS), Diffusion Tensor Imaging (DTI) and functional MRI (fMRI). The current novelty relies on the application of AI in brain neuro-oncology, mainly based on radiomics and radiogenomics models, which enhance standard and advanced MRI sequences in predicting glioma genetic status by identifying the mutation of multiple key biomarkers deeply impacting patients’ diagnosis, prognosis and treatment, such as IDH, EGFR, TERT, MGMT promoter, p53, H3-K27M, ATRX, Ki67 and 1p19. AI-driven models demonstrated high accuracy in glioma detection, grading, prognostication, and pre-surgical planning and appear to be a promising frontier in the neuroradiological field. On the other hand, standardisation challenges in image acquisition, segmentation and feature extraction variability, data scarcity and single-omics analysis, model reproducibility and generalizability, the black box nature and interpretability concerns, as well as ethical and privacy challenges remain key issues to address. Future directions, rooted in enhanced standardisation and multi-institutional validation, advancements in multi-omics integration, and explainable AI and federated learning, may effectively overcome these challenges and promote efficient AI-based models in glioma management. The aims of our multidisciplinary review are to: (1) extensively present the role of standard and advanced MRI sequences in the differential diagnosis of iLGGs as compared to HGGs (High-Grade Gliomas); (2) give an overview of the current and main applications of AI tools in the differential diagnosis of iLGGs as compared to HGGs (High-Grade Gliomas); (3) show the role of MRI, radiomics and radiogenomics in unravelling glioma genetic profiles. Standard and advanced MRI, radiomics and radiogenomics are key to unveiling the grading and genetic profile of gliomas and supporting the pre-operative planning, with significant impact on patients’ differential diagnosis, prognosis prediction and treatment strategies. Today, neuroradiologists are called to efficiently use AI tools for the in vivo, non-invasive, and comprehensive assessment of gliomas in the path towards patients’ personalised medicine. Full article

The majority of the challenges faced in power system engineering are presented as constrained optimization functions, which are frequently characterized by their complicated architectures. Metaheuristics are mathematical techniques used to solve complicated optimization problems. One such technique, Artificial Rabbits Optimization (ARO), has been designed to address global optimization challenges. However, ARO has limitations in terms of search functionality, restricting its efficiency in dealing with constrained optimization environments. To improve ARO’s compatibility with a variety of challenging problems, this work proposes implementing the Cauchy mutation operator into the position-updating procedure during the exploration stage. Furthermore, a novel multi-mode control parameter is developed to facilitate a smooth transition between exploration and exploitation phases. The enhancements may boost the performance and serve as an effective optimization tool for tackling complex engineering tasks. The improved version is known as Cauchy Artificial Rabbits Optimization (CARO). The proposed CARO’s performance is evaluated using eleven power system challenges as part of the CEC2020 competition’s test set of real-world constrained problems. The experimental results demonstrate the practical applicability of the proposed CARO in engineering applications and provide areas for future investigation. Full article