Search Results (191)

Background/Objectives: Acute myeloid leukemia (AML) with myelodysplasia-related gene mutations (AML-MR), often referred to as secondary AML (s-AML) or AML-MRC, is an aggressive form of leukemia that typically arises from an antecedent myelodysplastic syndrome (MDS) but may also originate de novo. It is characterized by mutations in key genes associated with MDS that include some epigenetic regulators (ASXL1 and EZH2), splicing factors (SF3B1, SRSF2, U2AF1, and ZRSR2), and transcription factors (BCOR, RUNX1, and STAG2). The main objective of this review paper consists of analyzing recent studies that have improved the criteria for the characterization, definition, and classification of AML-MR. Methods: An extensive search of the most recent literature on the topic was performed, selecting and critically analyzing the most relevant studies. Results. The studies carried out in the last few years have provided an extensive molecular characterization of AML-MR, supporting sounder criteria for identification and a better definition with respect to other AML subtypes, particularly with respect to TP53-mutant AML. Conclusions: A unifying classification of AML-MR is now possible, allowing its identification as a unique, well-defined, and separate entity. Full article

Background: Beta-thalassemia is a hereditary hematological illness in which beta-globin chain synthesis is missing or decreased, resulting in inefficient erythropoiesis, persistent hemolysis, and anemia. It is most frequently observed in populations with a high rate of consanguineous marriages; affordability becomes a limiting factor for families with low income. Methods: In this study, we optimized Sanger sequencing of the whole HBB gene covering all three coding exons, two introns, and 5′ and 3′ UTRs. Eleven families were enrolled from Fatimid Foundation Peshawar, Khyber Pakhtunkhwa, Pakistan, with a total of 16 transfusion-dependent patients. An index patient in each family was Sanger sequenced for the HBB gene (n = 11). The variants were classified as per ACMG 2015 guidelines. Results: Sequencing analysis revealed five homozygous pathogenic variations, including three frameshifts: c.27_28dupG (p.Ser10Valfs*14), c.17_18delCT (p.Pro6Argfs17), c.126_129delCTTT (p.Phe42Leufs*19), and two splice-sites (c.92+1G>A, and c.92+5G>C) in nine families. However, two families remained unresolved. The mutation, c.27_28dupG (p.Ser10Valfs*14), was observed in several pedigrees, indicating a probable founder effect or high allele frequency within the affected population. Conclusions: The majority of detected variations in this study were classified as disease-causing, which reside in the first two coding exons and intron-1 of the HBB gene, highlighting its functional importance in the Khyber Pakhtunkhwa population. We recommend performing Sanger sequencing of exon-1-intron-1-exon-2 of the HBB gene with the optimized primers of this study. Full article

Oncogenic viruses are responsible for between 12% and 20% of human cancers worldwide. They trigger tumorigenesis by integrating into host-cell genomes, altering cell cycle pathways, and evading immune detection. Oncoviral cancers exhibit low rates of mutation, implicating alternative splicing as an underappreciated alternative mechanism for oncogene and oncogenic pathway activation in oncoviral pathogenesis and progression. In order to create alternatively spliced viral proteins for replication and viral genome maintenance, oncoviruses take advantage of host-cell splicing machinery. Some of these proteins inhibit major host-cell tumor suppressors to promote the proliferation of DNA-damaged host-cells in order to facilitate persistent infection, whilst others interact with and de-regulate the expression and activity of host-cell splicing factors to alter host transcript splice site selection. The latter reprograms host-cell transcriptomes to express aberrant, sometimes oncogenic protein isoforms, which interact with oncoviral proteins to promote host-cell transformation and subsequent tumor progression to metastatic disease. In this article, we review oncovirus-induced alternative splicing as a fundamental, underappreciated, oncogenic and tumor-promoting mechanism. We present detailed descriptions of individual human oncoviruses. We compare how these oncoviruses hijack host-cell splicing mechanisms, how specific aberrant alternatively spliced host-cell protein isoforms, induced by oncoviruses, influence tumor pathogenesis and progression, organized with respect to the hallmarks of cancer, and provide a section on therapeutic perspectives. This approach not only crystallizes the complexity of how oncovirus-induced host-cell alternative splicing can influence cancer pathogenesis and progression but also reveals novel potential therapeutic opportunities. Full article

Aberrant RNA splicing and metabolic reprogramming are defining hallmarks of cancer that were historically studied as parallel processes. Increasing evidence now reveals extensive crosstalk between these pathways, whereby RNA splicing reshapes metabolic circuits, and metabolic states reciprocally influence splice-site selection and spliceosome activity. In this review, we synthesize recent mechanistic insights into how splicing programs regulate metabolic adaptation across diverse cancer contexts. We discuss recurrent oncogenic mutations in spliceosomal components and dysregulation of RNA-binding proteins (RBPs) that drive alternative splicing events in key metabolic regulators, which promote metabolic plasticity required for tumor growth. We further examine how metabolites and nutrient-sensing pathways directly modulate splicing factor activity, spliceosome dynamics, and RNA processing. We also summarize a new mechanism of mitochondrial quality control mediated by retrograde signals from mitochondria to the spliceosome to enhance mitophagy of dysfunctional mitochondria. Full article

Neuroblastomas (NBs) are aggressive, therapy-resistant embryonal tumors of neural crest origin, which despite low mutational burdens exhibit high intra-tumoral heterogeneity characterized by adrenergic, noradrenergic, mesenchymal and cancer stem cell (CSC)-like subpopulations. These phenotypes exhibit interconverting plasticity that reflect both stage of transformation during sympathoadrenal development and conditions within the tumor microenvironment. Chemotherapeutic agents promote adrenergic-to-mesenchymal conversion in NBs, which underpins drug resistance, post-therapeutic relapse, metastatic progression, and the plateauing of responses to advances in multimodal therapy. Improved understanding of the molecular mechanisms that regulate NB phenotypic plasticity is essential for identifying novel prognostic markers and potential therapeutic targets. In this article, following introductions into NB, molecular regulation of NB phenotypic plasticity, and the NF-Y transcription factor and its role in development and differentiation, we focus on alternative NF-YAl, NF-YAs and NF-YAx splicing of the NF-Y subunit, NF-YA, and the potential influence that different NF-YA isoforms have on NF-Y function and the NF-Y-transcription factor networks that impact NB cell phenotypes. Particular attention is paid to the novel extra short-form NF-YAx isoform, originally detected as the exclusive NF-YA isoform in a non-MYCN amplified advanced stage 3 NB. This isoform is also induced by doxorubicin in non-Myc amplified SH-SY5Y NB cells and is involved in doxorubicin cytotoxicity. Despite high cytotoxicity, however, NF-YAx selects a resistant subpopulation with mesenchymal/neural crest stem cell-like identity, unveiling a doxorubicin-induced NF-YAx-dependent resistance mechanism, with potential to influence post-therapeutic relapse and disease progression. Therefore, evaluating alternative NF-YA splicing, and especially NF-YAx expression, in advanced stage and post-therapeutic relapsed NBs, may be of both prognostic and therapeutic significance. Full article

Background/Objectives: Autism spectrum disorder (ASD) is a neurodevelopmental disease with both clinical and genetic heterogeneity. Several loss-of-function variants in the chromodomain helicase DNA-binding protein 8 (CHD8) gene have been identified in individuals with ASD and/or developmental delay/intellectual disability. These are associated with specific clinical manifestations, including overgrowth, macrocephaly, sleep disturbance, and gastrointestinal problems. Methods: We performed clinical exome sequencing in a female patient with ASD and macrocephaly. RNA analysis from peripheral blood was carried out to investigate the functional effect of the identified variants. Results: We identified a novel maternally inherited CHD8 variant (c.5390+2T>C). Transcript analysis demonstrated that this variant disrupts the canonical splice donor in intron 30, causing splicing anomalies in the CHD7-binding domain of the CHD8 protein, resulting in a truncated inactive protein. Conclusions: In conclusion, this study identified a novel splice-site variant in the CHD8 gene with experimentally confirmed pathogenic effects on RNA splicing, expanding the mutational spectrum of CHD8-related neurodevelopmental disorders. The considerable intrafamilial phenotypic variability associated with CHD8 haploinsufficiency supports the presence of reduced penetrance and highlights the influence of modifying factors on the clinical expression of CHD8-related disorders. Full article

Clonal hematopoiesis refers to the clonal expansion of hematopoietic stem and progenitor cells, driven by somatic mutations. Major mutated genes in clonal hematopoiesis include genes involved in epigenetic regulation including DNA methylation and/or chromatin modification (e.g., DNMT3A, TET2, and ASXL1), tumor suppressors (e.g., TP53), signal transduction (e.g., JAK2), and RNA splicing (e.g., SF3B1 and SRSF2). Clonal hematopoiesis includes clonal hematopoiesis of indeterminate potential (CHIP), clonal cytopenia of unknown significance (CCUS), and myelodysplastic syndromes/neoplasms (MDS). CHIP occurs when the frequency of the variant allele equals or exceeds 2% (4% for X-linked genes in males) in the absence of cytopenias. CHIP is common among older persons and is associated with an increased risk of hematologic cancer. CHIP is also associated with an increased risk of atherosclerotic disease including acute myocardial infarction, stroke, cardiac failure, and abdominal aneurysm. Increasing evidence suggests that CHIP is associated with venous thromboembolic disease. Somatic mutations lead to proliferation of hematopoietic progenitor cells and their progeny, resulting in excessive activation of granulocytes and monocytes. It could be postulated that chronic inflammation caused by clonal expansion of myeloid cells carrying mutations in DNMT3A, TET2, and ASXL1 (“DTA”) genes may constitute an independent risk factor in clot formation and endothelial-cell damage. DTA mutations correlate with elevated proinflammatory cytokines such as IL-1β and IL-6 and enhanced activation of inflammasomes. Moreover, JAK2 mutations may have a direct role in the activation of platelets and coagulation. In vivo murine studies have demonstrated that activation of the JAK-STAT signaling pathway promotes neutrophil extracellular trap (NET) formation, contributing to a prothrombotic state. Insights from related clonal disorders such as paroxysmal nocturnal hemoglobinuria and the VEXAS syndrome support the concept that mutation-driven innate immune activation can directly perturb hemostatic balance. This review aims to summarize the association between clonal expansion of hematopoietic cells and thrombotic disease, and highlight how somatic mutations in hematopoietic cells may contribute to vascular disease and thrombogenesis. Full article

Congenital factor V (FV) deficiency is a rare autosomal recessive bleeding disorder caused by pathogenic variants in F5 gene and characterized by heterogeneous clinical manifestations. The aim of this study was to define the mutational spectrum of F5 in Russian patients with congenital FV deficiency. We analyzed 16 unrelated patients with different disease severity and 9 relatives from five families. All functionally relevant regions of F5 were examined by Sanger sequencing. Multiplex ligation-dependent probe amplification (MLPA) was used to detect large deletions and duplications. Whole-genome sequencing and functional cDNA analysis were performed in selected cases. This study represents the first description of the F5 mutational spectrum in a Russian cohort. We identified 12 novel variants and demonstrated the functional effect of two previously unreported variants located outside canonical splice-site dinucleotides, leading to aberrant splicing. Notably, the proportion of variants undetectable by routine diagnostic approaches was higher than that reported in other populations. No clear genotype–phenotype correlation was observed. Despite the limited sample size, our findings expand current knowledge of the molecular basis of congenital FV deficiency and may improve genetic diagnostics in Russia. Full article

Spinocerebellar Ataxia type 2 (SCA2) and Amyotrophic Lateral Sclerosis type 13 (ALS13) are triggered by polyglutamine expansion in Ataxin-2 (ATXN2). To understand these neurodegenerative disorders at the molecular level, the brains of 10-month-old Atxn2-CAG100-knockin mice were analyzed as microglial, astroglial and neuronal fractions via global RNA sequencing. Data were validated by comparison with the spinal cord oligonucleotide microarray profile or filtered by RNA-seq consistency. Here, we show that the mutation causes a massive inflammatory response in microglia and a reciprocal loss of neuronal transcripts in glial fractions, suggesting severe synapse loss. Beyond these general neurodegenerative signs, we identify pathognomonic changes in the machinery for protein translation and RNA splicing. Glial fractions showed upregulation of Gpnmb (to 2082%), Cst7, Clec7a, Axl, Csf1, Lgals3, Lgals3bp, Slc11a1, and Usp18 as an unspecific neuroinflammatory signature, versus downregulation of axonal Nefh (to <19%), and synaptic Scn4b, Camk2b, Rab15, and Grin1 mRNAs correlating with circuit disconnection. In all fractions, reductions in Kif5a, Rph3a, and Cplx1 were noted versus disease-specific inductions of ribosomal subunits, presumably mirroring the partial loss-of-function of ATXN2 as RNA translation modulator. Selective accumulations of embryonic factors Rnu1b2 and Eef1a1 versus downregulation of adult Eef1a2 specify the mutation impact on splicing and translation elongation. As a potential underpinning of toxic gain-of-function, the proteostasis transcript Rnf213 appeared increased in astroglial and microglial fractions. These transcriptome data suggest altered ribosomal and spliceosome machinery, with massive microgliosis versus mild astrogliosis, at the core of SCA2 and ALS13. Full article

Background: Heterogeneous nuclear ribonucleoprotein L-like (HNRNPLL) is an RNA-binding protein involved in alternative splicing and immune regulation; however, its role in liver hepatocellular carcinoma (LIHC) remains unclear. Methods: We performed integrative multi-omics analyses using data from TCGA, GEO, and the Human Protein Atlas to evaluate the expression patterns, prognostic value, and potential biological functions of HNRNPLL. Functional enrichment and immune-related analyses were conducted to explore associated pathways. Experimental validation was performed in LIHC cell lines using Western blotting, RT-qPCR, CCK-8, colony formation, and Transwell assays, along with a xenograft mouse model. Results: HNRNPLL was significantly upregulated in LIHC at both transcriptomic and proteomic levels and was associated with advanced clinicopathological features and poor overall survival. Multivariate Cox regression analysis identified HNRNPLL as an independent prognostic factor. Enrichment analyses suggested that HNRNPLL-related genes are mainly involved in cell cycle regulation, mitotic progression, epithelial–mesenchymal transition, and immune-related pathways. In addition, HNRNPLL expression was correlated with immune cell infiltration, tumor mutational burden, microsatellite instability, ferroptosis-related genes, and m6A methylation regulators. Functional experiments demonstrated that HNRNPLL knockdown suppressed proliferation, migration, and invasion of liver cancer cells and inhibited tumor growth in vivo. Conclusions: These findings suggest that HNRNPLL may act as a potential regulator of LIHC progression and is associated with tumor-related biological processes and immune features. HNRNPLL may serve as a candidate biomarker for prognosis and a potential therapeutic target in LIHC, although further mechanistic studies are required. Full article

Endometriosis is a chronic, estrogen-dependent inflammatory disorder that is increasingly recognized as a systemic condition with profound implications for female reproductive potential. In addition to pelvic distortion and impaired folliculogenesis, growing evidence indicates that intrinsic alterations in oocyte morphology, mitochondrial function, and developmental competence contribute to infertility. The disease is driven by a multifactorial interplay of somatic mutations, epigenetic remodeling, immune dysregulation, and aberrant steroid signaling, which together create a pro-inflammatory, oxidative, and fibrotic microenvironment. Elevated cytokines, reactive oxygen species, and disrupted granulosa-cell function within the follicular niche impair meiotic progression, cytoplasmic maturation, and mitochondrial integrity, potentially accelerating oocyte aging and diminishing reproductive longevity. Epigenetic and post-transcriptional disturbances—including altered DNA methylation, histone modifications, and RNA-splicing defects—further reinforce estrogen dominance, progesterone resistance, and impaired decidualization, with downstream consequences for ovarian–endometrial communication. Although morphological abnormalities have been documented in oocytes from women with endometriosis, clinical outcomes remain heterogeneous, highlighting the need for integrative models that connect molecular alterations to functional reproductive endpoints. A deeper understanding of these mechanisms is essential for identifying biomarkers of oocyte competence and modifiable strategies—ranging from nutritional optimization to reduction of environmental risk factors—in clinical care to safeguard the reproductive potential of women with endometriosis. Full article

Genome-wide studies have identified significant allelic associations between genetic variants in or near the IKZF1 gene and multiple autoimmune disorders. IKZF1, encoding the transcription factor IKAROS, produces at least 10 distinct transcripts. To explore the impact of alternative splicing of IKZF1 on the function of mature T cells and the risk of autoimmunity, we generated a panel of human T-cell clones with truncating mutations in IKZF1 exons 4, 6, or both. Differences in gene expression, chromatin accessibility, and protein abundance among clones were assessed by RNA-seq, ATAC-seq, and immunoblotting. Clones with single targeting events clustered separately from double-targeted clones on multiple parameters, but overall, clone responses were highly heterogeneous. Perturbation of IKZF1 splicing resulted in significant differences in expression and chromatin accessibility of other autoimmunity-associated genes and elicited compensatory expression changes in other IKAROS family members. Our results suggest that even modest alterations of IKZF1 splicing can have significant effects on gene expression and function in mature T cells, potentially contributing to autoimmunity in susceptible individuals. Full article

Myeloid neoplasms (MNs) with germline predisposition represent a distinct, increasingly recognized category in the WHO classification, encompassing myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) arising in the context of an inherited genetic alteration or mutation. While often presenting at a younger age or with characteristic cytopenias with or without organ dysfunction, some can manifest in adulthood, highlighting the need for vigilance regardless of age or family history. Key predisposing genes include transcription factors (e.g., RUNX1, CEBPA) and genes involved in RNA splicing and telomere biology disorders. Identification of these germline mutations is critical as MNs with germline predisposition dictate specific therapeutic strategies—particularly for hematopoietic stem cell transplantation (HSCT)—and require genetic counseling and surveillance for at-risk relatives. Accurate diagnosis often requires non-hematopoietic germline DNA testing, which provides important biological insights into the development of different myeloid neoplasms and directs personalized patient care. Full article

Monogenic forms of severe early-onset obesity often involve genetic disruptions in the hypothalamic leptin-melanocortin pathway. Pathogenic variants in the SIM1 gene, a key transcription factor required for the development of the paraventricular nucleus, are a known cause of Prader–Willi-like syndrome, characterized by hyperphagia, severe obesity, and developmental delay. We performed targeted next-generation sequencing of 52 obesity-associated genes on a cohort of pediatric patients with severe early-onset obesity. Identified variants were analyzed for population frequency and predicted pathogenicity using in silico tools. The structural impact of the novel missense variants was assessed using protein domain modeling with AlphaFold3. We identified five rare SIM1 variants in eleven patients. Four were heterozygous nonsynonymous variants: one frameshift in the bHLH domain (p.Ser18Ter), one frameshift in the Per-ARNT-Sim domain (p.His143Ter), and two missense variants, p.Pro30Ala and p.Ser663Leu. Structural modeling suggested that the missense variants are likely to disrupt critical protein–protein interactions. The fifth variant was a synonymous change, c.1173G>A, p.(Ser391Ser), which was detected in five unrelated patients. Bioinformatic analysis predicted that this variant could alter splicing. Structural modeling suggested that the missense variants interfere with SIM1 function. This study expands the mutational spectrum of SIM1-linked monogenic obesity, reporting novel likely pathogenic frameshift variants, a missense variant, and a recurrent synonymous variant with a potential splice-site effect. The majority of the variants are predicted to affect the SIM1 protein. Our findings strengthen the critical role of the SIM1 gene in hypothalamic development and energy homeostasis. The results underscore the importance of including the SIM1 gene in genetic testing panels for children with severe obesity and hyperphagia, enabling precise diagnosis and potential future personalized management. Functional in vitro or in vivo validation of these variants is required to confirm their pathogenicity. Full article

Retinitis pigmentosa (RP) represents a genetically heterogeneous group of inherited retinal dystrophies characterized by progressive photoreceptor degeneration and irreversible vision loss. Among the diverse pathogenic mechanisms, dysregulation of alternative splicing has emerged as a pivotal driver, particularly in RP cases caused by mutations in splicing factors or cis-regulatory elements. Alternative splicing governs transcript diversity and fine-tunes gene expression, with more than 95% of human multi-exon genes undergoing this process. Disruption of precise splicing patterns in the retina—an organ with exceptionally high transcriptional complexity—leads to widespread mis-splicing of photoreceptor-specific genes, triggering retinal dysfunction and cell death. This review synthesizes current understanding of alternative splicing-related mechanisms in RP, integrating molecular insights from splicing-factor mutations, retina-specific splice isoforms, and their downstream cellular consequences. We also evaluate therapeutic strategies targeting splicing dysregulation, including antisense oligonucleotides (ASOs), modified U1 snRNA, spliceosome-mediated RNA trans-splicing (SMaRT), and genome editing, emphasizing translational potential and clinical challenges. Finally, we highlight key research gaps and propose future directions for splicing-centered precision medicine in RP. Full article