Search Results (14,836)

Background: Circular RNAs (circRNAs) constitute an emerging research field, as these RNA molecules play a crucial role in cellular functions and the progression of various human pathologies. Little is known about alternative circularization leading to the formation of distinct circRNAs from the same primary transcript, the role of circRNAs with slightly different back-splice junctions (BSJs) resulting in very similar circRNA sequences—called circRNA isoforms—and the extent to which the same primary transcripts produce alternative circRNAs. In this study, we discovered alternative circRNAs produced by two apoptosis-related genes, BAX and BCL2L12, expressed in established human cell lines originating from myelodysplastic syndrome (MDS) and different types of acute myeloid leukemia (AML). Methods: After total RNA extraction from one MDS cell line and five AML cell lines, first-strand cDNA synthesis, and multiple nested PCRs with distinct sets of divergent primers (10 and 16 primer pairs for BAX and BCL2L12 circRNAs, respectively) annealing in each exon of BAX and BCL2L12 genes, amplicon libraries were prepared and sequenced by both nanopore sequencing and NGS. Detailed bioinformatic analysis was then performed, based on existing bioinformatic tools and our own algorithms. Results: Our approach led to the identification of 72 BAX circRNAs and 52 BCL2L12 circRNAs with distinct expression patterns in MDS and AML cell lines. Most of these circRNAs—either merely exonic or exonic–intronic—were detected for the very first time. Furthermore, several BAX circRNA isoforms were detected in a unique cell line. Moreover, the back-splice sites joined together to form the BSJ of each circRNA were non-canonical, in many cases. The identified circRNAs are predicted to sponge distinct sets of miRNAs, some of which are known to regulate the activity of pivotal pathways. Conclusions: Overall, our findings support the notion that alternative splicing and back-splicing lead to the production of tens of distinct circRNAs from the same human gene. Full article

Objectives: Lung adenocarcinoma (LUAD) is molecularly heterogeneous, and the prognostic relevance of fatty acid metabolism (FAM) remains incompletely defined. We aimed to develop a concise FAM-associated prognostic signature and examine its associations with the immune microenvironment and candidate therapeutic vulnerabilities. Methods: TCGA-LUAD transcriptomic and survival data were integrated with MSigDB FAM gene sets. Univariate Cox and elastic-net Cox regression were used to derive a risk score. The locked formula was evaluated in a Japanese cohort (GSE31210) and a U.S. cohort (GSE72094). Immune-infiltration algorithms as well as TIDE, GDSC2, and CPTAC data were used for exploratory immune, drug sensitivity, and protein-level analyses. Results: The six-gene signature comprised CYP4B1, ACOXL, DPEP2, HPGDS, CA4, and ALOX15. High-risk patients had shorter overall survival in the TCGA and both external cohorts (GSE31210, log-rank p = 0.0039; GSE72094, p < 0.0001). The risk score remained independently prognostic after adjustment for age, sex, and clinical stage. High-risk tumours showed lower immune and stromal signals, greater immune exclusion, and a lower TIDE-predicted ICB response proportion. GDSC2 analyses and expression comparisons identified associations with predicted drug sensitivity and lipogenic target expression. Five detectable signature proteins were less abundant in tumours in CPTAC data. Conclusions: This signature stratified patients by prognosis in two geographically distinct external cohorts and generated testable metabolic and immune hypotheses. Prospective validation, assay standardisation, and functional studies are required before clinical use. Full article

Background/Objectives: Pituitary neuroendocrine tumors (PitNETs) frequently exhibit invasive behaviors that complicate clinical treatment. While cyclin-dependent kinase 5 (CDK5) and lymphokine-activated killer T-cell-originated protein kinase (PBK, also known as PDZ-binding kinase) are implicated in tumor progression, their reciprocal regulatory mechanism remains unclear. This study aims to elucidate the CDK5-PBK interaction in PitNETs and identify potential therapeutic agents targeting this pathway. Methods: We utilized proximity labeling and phospho-specific assays to characterize the CDK5 and PBK interaction in PitNET cell lines. Immunohistochemical analysis was performed on patient tumor tissues to evaluate clinical relevance. Artificial intelligence (AI)-based virtual screening was employed to discover dual-target inhibitors. The therapeutic efficacy of the identified compound, proguanil hydrochloride, was subsequently evaluated using in vitro functional assays, alongside in vivo xenograft animal models. Results: We identified a mutual phosphorylation loop between CDK5 (at S159) and PBK (at T9) that activates insulin signaling, thereby promoting cellular proliferation and invasion in PitNETs. Patient tumor analysis revealed that the co-expression of phosphorylated CDK5 (S159) and PBK (T9) significantly correlates with tumor invasiveness (p < 0.001). Through AI screening, proguanil hydrochloride was identified as a candidate dual-target inhibitor. In vitro assays confirmed that it effectively reduces tumor cell growth, while in vivo xenograft studies validated its capacity to inhibit tumor progression. Conclusions: The CDK5-PBK mutual phosphorylation axis serves as a key driver of invasiveness in PitNETs. Proguanil hydrochloride represents a promising candidate dual-target therapeutic agent capable of disrupting this pathway to suppress tumor growth. Full article

Background: Germline PALB2 variants are associated with hereditary breast cancer risk, but their clinical impact in Central Asian populations remains largely uncharacterized. This case study aims to evaluate the clinical significance of PALB2 variants in two Kazakh women with early-onset breast cancer. Methods: Molecular genetic testing identified germline PALB2 pathogenic variants (NM_024675.4:c.18_22delGAAGC and NM_024675.4:c.1034T>G) in two Kazakh women with early-onset invasive ductal carcinoma. Clinical courses, treatment responses, and outcomes were followed. Results: Neither patient had a reported family history of breast or other malignancies. Patient 1, a 26-year-old pregnant woman, was diagnosed with stage IIIB luminal B, HER2-negative invasive ductal carcinoma and received neoadjuvant chemotherapy, radical surgery, radiotherapy, endocrine therapy, and subsequent treatment for metastatic disease. Despite an initial response, she developed extensive skeletal metastases and died from metastatic breast cancer. Patient 2, a 33-year-old woman, presented with de novo stage IV luminal B, HER2-negative invasive ductal carcinoma with hepatic metastases. Following multimodal treatment, including chemotherapy, surgery, radiotherapy, endocrine suppression, and systemic therapy for disease progression, she experienced further metastatic spread and ultimately died from breast cancer-related complications. Conclusions: Both patients exhibited aggressive clinical courses characterized by early disease onset, metastatic progression, and poor outcomes despite comprehensive treatment. These cases highlight the potential clinical significance of germline PALB2 variants in apparently sporadic breast cancer and underscore the importance of genetic testing, risk assessment, and genetic counselling in young breast cancer patients, particularly in underrepresented. Full article

Background. Bipolar disorder (BD) is characterized by circadian rhythm disruptions, contributing to mood instability and recurrence. These rhythms are regulated by clock genes in the suprachiasmatic nucleus, including the CLOCK 3111T/C (rs1801260) polymorphism that has been linked to delayed sleep phase, insomnia, and altered circadian expression. Both circadian disruption and adverse childhood experiences (ACEs) correlate with white matter (WM) abnormalities. We hypothesized that rs1801260 moderates ACE effects on WM microstructure in BD. Methods. We enrolled 137 BD patients in depressive episodes. Participants underwent 3T MRI, rs1801260 genotyping and completed the Childhood Trauma Questionnaire. Moderation (PROCESS) tested genotype–ACE interactions on whole-brain fractional anisotropy (FA), axial diffusivity (AD), mean diffusivity (MD), and radial diffusivity (RD) values; voxel-wise TBSS (FSL Randomize) localized effects, with sex-stratified and GLZ analyses for genotype–sex interactions. Results. Significant rs1801260 × ACE interactions emerged for FA and RD across physical abuse, physical neglect, and emotional neglect. Higher ACEs were associated with lower FA/higher RD only in CLOCK rs1801260*C carriers, mainly females. TBSS showed physical abuse × rs1801260 interaction in the corpus callosum, internal capsule and corona radiata. A GLZ model with separate slopes confirmed physical abuse × sex × rs1801260 interactions on FA/RD, with effects specific to female CLOCK rs1801260*C carriers but genotype-independent in males. Conclusions. rs1801260 moderates the impact of early-life stress on WM integrity in BD, particularly in emotion-regulation tracts, with CLOCK rs1801260*C carriers showing greater vulnerability. Effects are genotype-specific in females but genotype-independent in males, possibly reflecting sex-dimorphic neurodevelopment driven by estrogen–androgen modulation of clock genes, HPA axis, and myelination. Full article

Genetic mutations, altered RNA regulation, and protein aggregation are the main hallmarks of Parkinson’s disease (PD), a neurodegenerative disorder. Investigation into the molecular basis of the disease revealed that post-transcriptional regulation, specifically RNA processing, contributes to neuronal vulnerability in PD. Alterations in alternative splicing affecting genes involved in neuronal function and cellular homeostasis have been reported in PD, including SNCA, LRRK2, MAPT, PRKN, and BIN1. These alterations impact central neuronal pathways, including cytoskeletal maintenance, mitochondrial function, synaptic activity, oxidative stress, and intracellular trafficking. This review aims to provide an overview of alternative splicing in key PD gene transcripts, with a focus on their roles in pathogenesis and disease progression. Emerging data suggest that dysregulation of RNA binding proteins (RBPs) may influence RNA processing in PD. We will examine current evidence on the RNA regulatory networks in PD, highlighting the role of transcript isoforms and RBPs in neuronal dysfunction. Finally, we will discuss emerging experimental models such as 3D-brain organoids that offer new opportunities to investigate splicing regulation. Full article

Introduction: Congenital heart defects (CHD) occur in 1% of live births, with an estimated at least 33% of affected infants having genetic defects. It has become standard to screen children with CHD for genetic findings that could aid clinical decision-making, yet modern testing yields large volumes of information without understanding clinical utility. Genome-wide studies have identified associations between large copy number variants and neurocognitive outcomes in patients with CHD. Still, little research exists on the prognostic power of screening tests such as microarrays. The goal of this study was to determine if abnormal microarray results in infants with CHD were associated with worse clinical outcomes in the cardiac intensive care unit (CICU). Method: This was a single-center retrospective cohort study. The Society of Thoracic Surgery (STS) and Pediatric Cardiac Critical Care (PCICU) registries (PC4) were queried for all surgical admissions of neonates and infants between 1 January 2014 and 31 December 2019. Patient demographics, surgical details, and post-operative outcomes were collected for surgical admissions related to the patient’s index operation. A chart review was performed to ascertain microarray results, further genetic testing, and longitudinal outcomes. Patients without microarray results or long-term institutional follow-up were excluded. Wilcoxon rank-sum and chi-square tests were used to compare outcomes defined and collected in the PC4 registry between patients with normal and abnormal microarray results. Subgroup analysis was then performed using the same outcome measures to compare normal and abnormal microarray groups in children who required cardiac surgeries within 30 days of life and in children who presented with ventricular septal defect (VSD), atrioventricular septal defect (AVSD), aortic stenosis (AS), or Tetralogy of Fallot (TOF). Results: Of the 412 infants with surgical admissions to the CICU between 2014 and 2019, 43 infants had no longitudinal follow-up, and 65 infants had no microarray results. Three hundred and four infants were included in this study, of which 196 children had normal microarrays and 108 infants had abnormal microarrays. Both groups had similar distributions of gestational age and birth weight, but fundamental diagnoses and primary procedures differed significantly between groups (p < 0.005). STS score, deep hypothermic circulatory arrest (DHCA) time, and bypass time were each significantly lower in children with abnormal microarrays than in those with normal microarrays across the study. The patients with abnormal microarrays had a higher incidence of gastrostomy (G)-tube placement during their lifetime than infants with normal microarrays. On subgroup analysis, despite the differences in fundamental diagnoses and the fact that primary procedures differed significantly between normal and abnormal microarray groups that required cardiac surgery within 30 days of life, there were no detectable differences in the surgical and PCICU outcomes. DHCA time was once again significantly lower in the abnormal microarray subgroup in the second subgroup analysis. Conclusions: Our data indicate that microarray results have limited value in predicting immediate post-operative outcomes, but children with copy number variants should be included in future CHD research. Full article

Background/Objectives: Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) remains the predominant genotype circulating in China and continues to evolve through mutation and recombination. Although NSP1 is recognized as a multifunctional nonstructural protein involved in immune regulation, its genetic variation among PRRSV-2 strains circulating in China has not been comprehensively characterized. Methods: In this study, 425 complete NSP1 sequences, primarily representing PRRSV-2 strains circulating in China, were analyzed, and 48 representative strains were selected for pairwise percent-identity visualization. Results: Pairwise nucleotide identity among the 48 representative strains was found to range from 80.1% to 100.0%, with the lowest value detected between AHBZ and SD-R, whereas pairwise amino-acid identity ranged from 79.6% to 100.0%, with the lowest value detected between AHBZ and HNhx. Among the 425 aligned amino-acid sequences, 290 variable sites and 93 completely conserved sites were identified. The broad-lineage distribution was composed of Lineage 1 (n = 79), Lineage 3 (n = 4), Lineage 5 (n = 21), and Lineage 8 (n = 321). A global FEL dN/dS of approximately 0.2979 was estimated from 379 non-recombinant unique haplotypes, and seven high-confidence candidate positively selected sites—42, 239, 255, 302, 367, 370, and 378—were supported by MEME, FEL, and FUBAR. A descriptive lineage-biased pattern concentrated in Lineage 5 was observed for NSP1β Val19Ile, corresponding to full-length NSP1 V199I. Eight candidate recombination events were identified using RDP4, and six representative events were further examined using SimPlot. Conclusions: Overall, NSP1 was found to be under predominant purifying selection while retaining localized variability, lineage-biased residue patterns, and candidate recombination signals that should be interpreted cautiously and validated experimentally. Full article

Background/Objectives: Colorectal cancer (CRC) is molecularly heterogeneous, and the KRAS (Kirsten rat sarcoma viral oncogene homolog) genotype both governs eligibility for anti-EGFR (epidermal growth factor receptor) therapy and carries prognostic weight. Central Asian data are scarce: no Kazakhstani series has described the KRAS variant spectrum, linked it to survival, or reported mutation detection rates across specimen types and PCR platforms. Methods: We studied 332 patients with morphologically confirmed stage II–IV colorectal adenocarcinoma. KRAS status was determined in formalin-fixed paraffin-embedded (FFPE) tumor tissue by allele-specific real-time PCR (RT-PCR) covering six selected codon 12 and 13 variants. Overall survival (OS) was estimated by the Kaplan–Meier method for the whole cohort and with stage stratification. Separately, mutation detection rates were recorded in three non-overlapping groups of different patients: plasma RT-PCR on the Idylla platform (n = 30), plasma nanoplate digital PCR (dPCR) on QIAcuity One (n = 120), and a routine tissue RT-PCR series (546 evaluable of 550). Because these groups differed in patients, specimen type, and mutation panel, this comparison describes observed detection rates only and supports no inference about analytical sensitivity, specificity, or concordance. Results: KRAS was mutated in 149/332 tumors (44.9%); codon 12 supplied 80.5% of variants, led by G12D (32.2%), G12V (24.8%) and G13D (19.5%). Median OS did not differ between mutant and wild-type tumors (39.0 vs. 36.6 months; p = 0.40). Variant-level differences were directionally consistent, but none was significant, and all were exploratory and unadjusted for multiplicity. Observed detection rates were 40.3% for tissue RT-PCR (220/546), 13.3% for plasma RT-PCR (4/30; continuity-corrected p = 0.006 vs. tissue), and 50.8% for plasma dPCR (61/120; continuity-corrected p = 0.044, Pearson p = 0.034 vs. tissue). BRAF V600E was detected by plasma dPCR in 11/120 cases (9.1%). Conclusions: This first Kazakhstani series places KRAS frequency within the internationally reported range and shows that variant-level reporting reveals prognostic structure that a binary call conceals. The higher detection rate seen with plasma dPCR is hypothesis-generating, not evidence of platform superiority, and motivates a prospective paired-sample study with harmonized mutation panels. Full article

Background/Objectives: β-thalassemia major is a common inherited hemoglobin disorder caused by Hemoglobin Subunit Beta (HBB) mutations and often complicated by iron overload and oxidative stress. This study characterized the clinical, hematological, biochemical, and molecular profile of β-thalassemia major in Al-Diwaniyah, Iraq, focusing on HBB mutations and CAT promoter polymorphisms as oxidative modifiers. Methods: A retrospective case–control study included 100 transfusion-dependent patients and 50 healthy controls. Sociodemographic data, complete blood count, ferritin, lipid profile, catalase (CAT), and malondialdehyde (MDA) were assessed. HBB mutations, namely IVSI-1 (G>A), IVSI-6 (T>C), and CD39 (C>T), and CAT polymorphisms, namely rs1001179 (C>T) and rs7943316 (A>T), were genotyped. Results: Patients had high rates of family history (80%), consanguinity (80%), rural residence (74%), low education (60.6%), and poor socioeconomic status (71.4%). Compared with controls, they showed lower RBC, HGB, HCT, HDL, LDL, and CAT but higher ferritin, triglycerides, and MDA (all p < 0.001). Overall, 69% of patients carried at least one studied HBB mutations, while 31% remained uncharacterized. Mutant allele frequencies were 29% for IVSI-1 (A) and 25.5% each for IVSI-6 (C) and CD39 (T). The CAT polymorphism rs1001179 (C>T) was associated with disease risk (CT: 33% vs. 14%; OR = 3.25, p = 0.019), whereas rs7943316 (A>T) was not. IVS-I-1 (G>A)/CD39 (C>T) β⁰ mutations were associated with lower CAT activity (β = −0.205; p = 0.046). Conclusions: β-thalassemia in Al-Diwaniyah, Iraq, shows substantial clinical, genetic, and oxidative heterogeneity. Integrated HBB–CAT analysis may improve molecular diagnosis, risk stratification, and preventive strategies in high-consanguinity populations. Full article

Background: Soybean is an important crop with multiple uses for oil, food, and feed, providing 50% of the vegetable protein and 20% of the edible oil in the world. The WD40 family genes play crucial regulatory roles in growth, development, secondary metabolism, and stress responses. However, the definition of WD40 family genes in soybean remained unclear, which limited their application potential in genetic improvement. Methods: To identify soybean WD40 family members and screen candidate genes for breeding improvement, this study performed genome-wide identification of the soybean WD40 gene family via bioinformatic approaches based on the latest Williams 82 reference genome (Wm82.a6.v1). Meanwhile, the function of the family gene GmWD40-257 regulating seed quality was analyzed. Results: The results showed that a total of 458 GmWD40 genes were identified, which were distributed on the 20 chromosomes. Subcellular localization showed that most members were mainly concentrated in the nucleus, chloroplast, and cytoplasm. Phylogenetic tree analysis divided the 458 GmWD40 genes into eight groups. Synteny analysis identified 160 syntenic genes between soybean and Arabidopsis thaliana. Conserved motif analysis identified ten core motifs. The promoter regions of GmWD40 contained 19 types of cis-acting elements. Functional analysis revealed that the nonsense mutation of GmWD40-257 significantly reduced the content of oil, palmitic acid, oleic acid, linoleic acid, α-linolenic acid and soluble sugar, while significantly increasing the contents of protein, γ-tocopherol and δ-tocopherol. Conclusions: A total of 458 members of the WD40 gene family were identified in soybean. Among these, GmWD40-257 was found to positively regulate the contents of soybean oil, palmitic acid, oleic acid, linoleic acid, α-linolenic acid and soluble sugar, while negatively regulating the contents of soybean protein, γ-tocopherol and δ-tocopherol. Full article

Non-human primates (NHPs) serve as indispensable models for aging research due to their evolutionary proximity to humans, conserved epigenetic mechanisms, and lifespans amenable to longitudinal investigation. This review synthesizes age-related epigenetic modifications in NHPs, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA regulation, and evaluates their alignment with human epigenetic markers. Epigenetic clocks developed on human data demonstrate robust predictive capacity in NHPs, and numerous age-associated methylation patterns are evolutionarily conserved. However, most epigenetic changes exhibit pronounced tissue specificity, with only a limited number of markers showing cross-tissue and cross-species consistency. Critical modulating factors such as sexual dimorphism, social hierarchy, environmental stressors, and early-life adversity significantly influence epigenetic aging trajectories. Current research remains restricted to a narrow subset of NHP taxa, predominantly macaques and baboons; expanding to include great apes would deepen our understanding of primate epigenetic aging. Advancing the field requires integrating multi-tissue, multi-species, and multi-omics approaches, including single-cell resolution analyses, to distinguish conserved mechanisms from lineage-specific adaptations. Such an integrative framework is essential for translating epigenetic discoveries into clinical interventions. By leveraging the unique advantages of NHPs, controlled interventional studies, longitudinal multi-tissue sampling, and causal mechanistic dissection, researchers can bridge basic discovery and therapeutic development. This approach promises to refine our understanding of aging biology and guide the rational design of next-generation therapeutics, from epigenetic modulators to lifestyle interventions, ultimately paving the way for personalized strategies that extend both lifespan and healthspan. Full article

Background/Objectives: Citrus sinensis, Olea europaea var. sylvestris, Populus nigra, Prunus dulcis, and Punica granatum are economically and medicinally important perennial plant species. Carotenoid cleavage oxygenase (CCO) genes encode key enzymes involved in carotenoid degradation and play essential roles in plant growth, development, and responses to environmental stresses. In this study, a comprehensive genome-wide comparative analysis of the CCO gene family was conducted in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum to investigate their structural diversity, evolutionary relationships, and potential biological functions. Methods: Chromosomal distribution, phylogenetic relationships, gene structure, conserved protein motifs, homology modeling, subcellular localization, cis-regulatory elements, and miRNA interactions were analyzed. Results: A total of 12, 23, 22, 11, and 17 CCO genes were identified in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum, respectively. Most CCO proteins were acidic, and genes were concentrated on specific chromosomes. Phylogenetic analysis grouped CCO genes into three main clades. Gene structure analysis revealed intronless and intron-containing genes of varying lengths. Some CCO proteins possessed all conserved motifs, while others lacked certain motifs or had multiple copies. β-sheets were the predominant secondary structural elements, and CCO proteins were predicted to be localized in chloroplasts, mitochondria, peroxisomes, the cytoplasm, and the nucleus. Stress-related cis-elements and miRNAs were identified. Conclusions: These findings provide valuable insights into the diversity and evolutionary characteristics of the CCO gene family and suggest that CCO genes may contribute to plant stress responses and metabolic processes. Overall, this study provides a comprehensive comparative analysis of the CCO gene family in these five perennial plant species and offers a valuable genomic resource for future functional characterization, comparative genomic studies, and molecular breeding applications. Full article

Background: Peanut (Arachis hypogaea) is a globally important legume crop with high nutritional and economic value. In the plant, the highly conserved 14-3-3 proteins participate in various biological functions. This study investigated the characterization and evolution of the 14-3-3 gene family in peanut and explores its potential roles in stress resistance. Methods: The 14-3-3 gene families in cultivated peanut and its ancestral species Arachis duranensis and Arachis ipaensis were identified and characterized via a genome-wide approach. We subsequently analyzed their structural features, conserved motifs, genomic distribution, phylogeny and promoter cis-acting elements. Results: A total of 22, 10, and 12 14-3-3 genes (also called general regulatory factors, GRFs) were identified in A. hypogaea, A. duranensis, and A. ipaensis, respectively. Cultivated peanut exhibits extensive genomic synteny with its progenitors, and segmental duplication appears to be a key mechanism underlying the expansion of this gene family. Moreover, according to cis-acting element prediction, these genes may contribute to stress tolerance under diverse environmental conditions. Conclusion: This comprehensive analysis enhances our understanding of the 14-3-3 (GRF) gene family in peanut and provides a valuable basis for further functional research on these genes. Full article