Search Results (1,404)

Background: Seckel syndrome (SCKL) is a rare autosomal-recessive inherited disorder characterized by intrauterine and postnatal growth restriction, microcephaly, “bird-like” facial dysmorphisms, and mild-to-moderate intellectual disability (ID). CEP152 is one of the known causative genes, and pathogenic variants in CEP152 are responsible for SCKL5. To date, 18 CEP152 variants associated with SCKL5 have been reported in the peer-reviewed literature. According to the Human Gene Mutation Database (HGMD, version 2026.4), 51 CEP152 variants have been cataloged, including 28 disease-causing mutations (DMs) and 23 putative disease-causing mutations (DMs?). Methods: We conducted a retrospective analysis of a Chinese boy with suspected SCKL5 who was seen at our hospital in 2024, based on a review of his detailed clinical, genetic, and family history. Whole-exome sequencing (WES) followed by Sanger sequencing identified two novel CEP152 variants. A minigene splicing assay was performed to confirm the functional effect of the splice-site variant. We further analyzed the clinical phenotype of patients with SCKL5 carrying CEP152 variations based on the published literature. Results: Two novel compound heterozygous CEP152 (NM_014985.4) variants were identified: the paternal c.3661delA (p.(I1221Lfs*20)) and the maternal c.1577+3A>G. An in vitro minigene assay showed that c.1577+3A>G leads to aberrant splicing, including intron 12 retention (77 bp) and exon 12 skipping. Both splicing alterations introduce premature termination codons and are predicted to produce truncated protein. Conclusions: We discovered two novel CEP152 variants, c.3661delA and c.1577+3A>G, in a Chinese patient with SCKL5. Moreover, retention of intron 12 or exon 12 skipping due to the c.1577+3A>G variant was revealed by the minigene assay. These findings expand the variant and phenotypic spectrum of CEP152 and provide valuable insights for genetic counseling. Full article

Background: Hepatocellular carcinoma (HCC), the predominant type of liver cancer, exhibits a high mortality rate due to unclear molecular mechanisms and limited biomarkers. Accumulating evidence indicates that splicing factors (SFs) can promote tumor cell proliferation, invasion, metastasis, and drug resistance by altering the splicing patterns of target genes. However, the regulatory mechanisms underlying SF-mediated alternative splicing (AS) are highly intricate, and the specific functions and pathways of SFs in HCC initiation and progression remain to be further elucidated. Methods: First, Cox regression and LASSO regression analyses of splicing factors (SFs) were performed using the TCGA database, followed by validation using the ICGC dataset. The prognostic value of SFPQ was assessed with the Kaplan–Meier plotter. Next, the potential association of SFPQ with the immune microenvironment of HCC was explored using TIMER and CIBERSORT. In addition, we screened AS events associated with SFPQ expression in TCGA-LIHC, conducted GO/KEGG pathway enrichment analyses, and investigated the correlation between GTF2H3 percent spliced in index (PSI) values and clinicopathological features in HCC patients. Finally, the effect of targeting the exon 10- or exon 11-containing variants of GTF2H3 on HCC was examined at the cellular level. Results: LASSO regression analysis identified five key SFs significantly associated with HCC prognosis, including SFPQ, HTRA2, DAZAP1, PCBP2, and YBX1. Among these, SFPQ was determined as the most critical SF influencing HCC survival, and its overexpression was positively correlated with HCC progression. GO and KEGG analyses revealed that the pathways potentially associated with SFPQ include metabolic pathways, oxidative phosphorylation, mRNA surveillance pathway, and the PPAR signaling pathway. Furthermore, SFPQ expression was associated with the exclusion of exons 10 and 11 of the GTF2H3 gene. Computational analysis also suggested a potential link between SFPQ and immune cell infiltration. Targeting the exon 11-containing variant of GTF2H3 significantly reduced cell viability and migration of HCC cells. Conclusion: SFPQ expression is elevated in HCC and correlates with tumor aggressiveness and poor patient prognosis. Our findings suggest that SFPQ may influence HCC progression through its association with the GTF2H3 exon 10/11 ME event and the immune microenvironment. However, further experimental validation is required to confirm these mechanisms. Our findings suggest that SFPQ may serve as a promising biomarker and therapeutic candidate for HCC. Full article

Leishmaniasis continues to be a major neglected tropical disease, particularly in endemic areas where reliable diagnosis remains challenging. Many existing diagnostic methods are invasive, lack sufficient sensitivity, or require equipment and expertise that may not be available in resource-limited settings. Parasite-derived spliced leader (SL) RNA has recently gained attention as a promising molecular marker because it may enable the sensitive detection of viable Leishmania parasites and help track changes in infection over time. Extracellular vesicles (EVs) are also of growing interest because they protect and transport stable biomolecules that may provide valuable diagnostic information and influence interactions between the parasite and its host. In this proof-of-concept study, we evaluated the feasibility of detecting Leishmania-derived SL-RNA in EV-enriched preparations from experimental leishmaniasis model systems. EV-enriched preparations were isolated from parasite-conditioned media (PCM), infected THP-1 macrophage (I-MP) cell-conditioned medium (CCM), and serum from experimentally infected mice using a precipitation method. As a complementary isolation approach, additional preparations were isolated from PCM by ultracentrifugation. An aliquot of each preparation was analyzed by nanoparticle tracking analysis to determine particle size and concentration, and the remaining portion was used for RNA extraction. RNA was reverse transcribed into cDNA and analyzed for SL-RNA amplification using quantitative polymerase chain reaction (qPCR). SL-RNA amplification was successfully detected in PCM, I-MP CCM, and serum from experimentally infected mice, while uninfected controls showed no specific amplification. These findings were independently confirmed via ddPCR analysis. Notably, EV-enriched preparations from infected mice yielded a stronger SL-RNA signal than serum alone, highlighting the diagnostic potential of targeting SL-RNA in EV-enriched human clinical samples, particularly in low-burden infections. Although these findings support the feasibility of EV-associated SL-RNA as a molecular biomarker for Leishmania infection, clinical validation with human samples is required. Full article

Background/Objectives: Primary ciliary dyskinesia (PCD) caused by biallelic RSPH4A variants is enriched in the Puerto Rican population due to the founder allele c.921+3_921+6delAAGT, a 4-nucleotide deletion affecting the intron 6 splice donor. This study aimed to characterize the genotype–computed tomography (CT) phenotype associated with homozygosity for this founder variant and examine relationships among age, pulmonary function, and structural lung disease. Methods: We performed a cross-sectional analysis of 20 genetically confirmed patients homozygous for RSPH4A c.921+3_921+6delAAGT. Demographic characteristics, spirometry, and chest CT findings were evaluated. Structural disease burden was quantified using a Bhalla-style CT severity score, and regression analyses assessed associations among age, CT severity, sex, and forced expiratory volume in 1 s (FEV₁). Results: Mean FEV₁ was 48.9% predicted (range, 26–65%) and showed no measurable association with age (slope −0.02% per year; 95% CI, −0.26 to +0.22; p = 0.88). Bronchiectasis was multilobar, with right-middle-lobe involvement in 80% of patients. CT severity showed a modest cross-sectional increase with age, whereas FEV₁ remained relatively stable across age groups. In multivariable analysis, greater CT severity showed the strongest association with lower FEV₁ (β = −0.56% per CT point; 95% CI, −1.13 to +0.01; p = 0.07), although this association did not reach statistical significance. Conclusions: In this Puerto Rican RSPH4A founder cohort, substantial airflow obstruction was observed across the age spectrum, while structural CT abnormalities were greater in older patients despite relatively stable FEV₁. This cross-sectional dissociation suggests that spirometry alone may incompletely reflect structural disease burden. These findings support the complementary role of CT imaging in phenotypic characterization and longitudinal assessment of RSPH4A-related PCD and provide a rationale for earlier identification and future longitudinal studies. Full article

Background/Objectives: Homologous recombination deficiency (HRD) is an important feature of breast cancer, but the relationship between alternative splicing (AS) of homologous recombination (HR) genes and HRD remains poorly characterized. The study investigated whether coordinated HR-gene AS is associated with genomic HRD and immune phenotypes. Methods: Using The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) cohort, we developed a normal-referenced, module-balanced HR splicing disruption score (HRSD) from 186 AS events across 49 HR genes. Associations with HRD were evaluated across molecularly restricted subsets and by multivariable analysis. HRD-associated splicing features were assessed across six immune phenotypes. A prioritized RAD54B alternative termination event was characterized further and independently evaluated in the Sweden Cancerome Analysis Network-Breast (SCAN-B) cohort. Results: HRSD was positively associated with genomic HRD (ρ = 0.338, p = 1.64 × 10⁻²¹) and remained significant after restriction for HRD-associated molecular features and exclusion of basal tumors. In multivariable models, each 1-SD increase in HRSD was independently associated with higher HRD scores (β = 3.17, p = 7.08 × 10⁻⁷) and HRD-high status (OR = 1.6, p = 0.001). HRD-associated splicing converged with immunoregulatory phenotypes, particularly regulatory T-cells and checkpoint activity. RAD54B alternative termination (RAD54B|AT|84553) was higher in HRD-high tumors (p = 3.42 × 10⁻¹⁴) and remained independently associated with immunoregulatory phenotypes after adjustment. SCAN-B analysis validated the terminal-exon structure and reproduced subtype-specific termination patterns. Conclusions: HR-associated AS represents a transcript-level dimension of HRD biology in breast cancer. RAD54B alternative termination may provide a candidate link between HRD-associated splicing and immunoregulatory phenotypes, warranting further functional investigation. Full article

Excessive telomere shortening contributes to pulmonary fibrosis (PF), with at least 30% of familial cases attributed to telomere biology disorders (TBDs). However, TBD-associated PF remains underdiagnosed because of unidentified disease-causing mutations and limited referral for telomere and genetic testing. Here, we combined telomeric restriction fragment analysis, telomere analysis by a long-read Nanopore sequencing method (NanoTelSeq), exome sequencing (ES), and optical genome mapping (OGM) to investigate the underlying cause of disease in a family affected by PF, microcephaly, and premature hair graying. We identified a familial balanced translocation associated with short telomeres, which involved a chromosome 3 breakpoint within the non-coding telomerase RNA component (TERC) gene, disrupting the 451-nucleotide telomerase RNA. Establishing the diagnosis enabled a TBD-tailored protocol and successful lung transplantation in the proband at age 49. These findings identified structural disruption of TERC as a previously unrecognized cause of TBD and broadened the genetic landscape of TBD beyond splicing, single nucleotide substitutions, and insertion/deletion variants. Furthermore, they demonatrate the importance of routine telomere length measurement alongside comprehensive genomic testing in familial PF. Full article

Background: Joubert syndrome (JS) is a genetically heterogeneous ciliopathy wherein non-canonical splice-site (NCSS) variants are frequently reported as variants of uncertain significance (VUS), complicating prenatal counseling. We aimed to clarify the clinical significance of an NCSS in CC2D2A through functional validation. Methods: Trio-WES was performed on a 13-year-old female proband with clinically diagnosed JS. Candidate variants were validated by Sanger sequencing and familial segregation. An in vitro minigene assay and RT-PCR on patient peripheral blood RNA were used to assess the splicing effect of c.439-5T>G. Variant classification followed the ACMG/AMP guidelines using the ClinGen quantitative Bayesian framework. Results: Compound heterozygous CC2D2A variants were identified: c.439-5T>G (maternal) and c.4732G>A (p.(Val1578Met), paternal); both were initially classified as VUS. Minigene analysis showed that c.439-5T>G caused aberrant splicing, retaining the intronic nucleotides c.439-4_439-1 (ATAG) at the exon 6–7 junction (r.438_439insauag) and introducing a frameshift and premature termination (p.(Pro147IlefsTer14)). Patient RNA confirmed this pattern. c.439-5T>G was reclassified as likely pathogenic (PVS1_VeryStrong + PM2_Supporting). c.4732G>A remained a VUS (PM3 + PM2_Supporting + PP3) on an independent allele basis; its trans configuration with the likely pathogenic allele supported a family-specific biallelic explanation but did not establish the pathogenicity of the missense allele. The fetus in a subsequent pregnancy was confirmed to carry both variants, establishing the compound heterozygous state. Conclusions: Minigene-based validation provided evidence to reclassify a CC2D2A NCSS from VUS to likely pathogenic, enabling variant-directed prenatal testing and informed reproductive counseling in this JS family. The paternal missense variant c.4732G>A (p.(Val1578Met)) remains a VUS; its trans configuration with the likely pathogenic allele supports, but does not establish, a biallelic explanation. This study illustrates how functional assays can clarify splicing variants that in silico predictions alone cannot reliably interpret. Full article

Background and Objectives: Hereditary cancer predisposition is associated with pathogenic germline variants in numerous genes. Identification of inherited cancer susceptibility enables personalized screening, preventive interventions, and targeted therapies. It also facilitates cascade testing of relatives who may be at increased risk and benefit from tailored clinical management. We describe the first results of hereditary cancer patient identification, selection, and genetic testing at the University Hospital of Split. Materials and Methods: Next-generation sequencing and hereditary cancer gene panel analysis were performed in individuals who met the National Comprehensive Cancer Network clinical criteria for genetic testing at the University Hospital of Split between May 2025 and July 2026. A comprehensive cancer gene panel covering 101 genes was used. Results: A total of 297 individuals underwent genetic testing, including 268 (90.24%) females and 29 (9.76%) males. Of these, 138 (46.46%) were unaffected individuals who met testing criteria based on a family history of cancer. Among individuals with a personal history of malignancy, breast cancer was the most common diagnosis, occurring in 130 patients (43.77%). Pathogenic or likely pathogenic (P/LP) variants, as well as risk variants, were identified in 80 individuals (26.94%), including seven individuals carrying two P/LP variants. Variants were detected in 29 different genes, most frequently BRCA1 (n = 14), BRCA2 (n = 11), CHEK2 (n = 9) and PALB2 (n = 7). The detected variant types included frameshift (n = 30), missense (n = 22), nonsense (n = 21), splice-site variants (n = 4), start loss variants (n = 4), large deletions (n = 4), and in-frame deletions (n = 2). Conclusions: To our knowledge, this is the first study to report the results of panel germline testing for hereditary cancer syndromes in a Croatian population. These findings provide initial epidemiological data on the spectrum and distribution of P/LP variants. The relatively high detection rate may reflect the recent implementation of genetic testing and the careful selection of individuals with a strong clinical suspicion of hereditary cancer predisposition. Full article

Background/Objectives: Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline. Most AD cases are sporadic, with both environmental and genetic factors contributing to disease onset and progression. TREM2, an AD susceptibility gene, encodes a receptor protein expressed on the plasma membrane of microglia and macrophages. In addition to membrane-bound TREM2, soluble TREM2 (sTREM2) is also present in the brain. sTREM2 can be generated through two distinct mechanisms: proteolytic shedding of membrane-bound TREM2 and alternative splicing of TREM2 exon 4. Because the mechanisms regulating the latter pathway remain unclear, we investigated the molecular mechanisms underlying TREM2 exon 4 alternative splicing, with a particular focus on RNA-binding proteins (RBPs). Methods: We designed guide RNAs (gRNAs) targeting sequences within exon 4. The gRNAs and an exon 4 splicing reporter were transfected into HEK293-based cells with inducible dCasRx expression to identify regions containing cis-regulatory elements involved in exon 4 splicing. RBPs interacting with the candidate region were subsequently identified by RNA pulldown followed by LC–MS/MS analysis. Results: We identified regions within exon 4 containing putative cis-regulatory elements involved in its alternative splicing and found that CELF1, CELF2, and DDX41 interact with RNA containing one of these regions. Knockdown experiments indicated that these RBPs differentially regulate exon 4 splicing. Conclusions: Our findings suggest that TREM2 exon 4 alternative splicing is regulated by multiple cis-regulatory elements and RBPs, including CELF1, CELF2, and DDX41. Together with our previous identification of CELF1 and CELF2 as regulators of TREM2 exon 3 splicing, these findings suggest that CELF1 and CELF2 play complex roles in the regulation of TREM2 alternative splicing. Full article

Shell and pearl coloration is an economically important trait in Pinctada fucata martensii, with the golden-lip phenotype associated with commercially valuable golden nacre. In this study, full-length transcriptome sequencing was used to characterize transcript-abundance and transcript-structure patterns in pooled mantle samples from golden- and silver-lip oysters, with one pooled Iso-Seq library generated for each tissue/color condition from three individuals. Among the analyzed mantle samples, the largest transcript-profile differences between the color-line libraries were observed in mantle pallial tissue. The ferritin heavy-chain gene fth1-a showed moderately higher normalized transcript abundance in the Y_MP library than in W_MP but did not meet the predefined twofold screening threshold for library-level abundance differences. RT-qPCR analysis of additional independent individuals showed significantly higher fth1-a expression in golden-lip oysters. A custom anti-PmFTH1-A antibody was evaluated by Western blotting, and immunofluorescence analysis detected PmFTH1-A immunoreactivity within the decalcified shell organic matrix. Candidate alternative-splicing and alternative-polyadenylation events were identified in transcripts associated with carotenoid-related processes and biomineralization. COL1A1 showed higher transcript abundance in Y_MP, and RT-qPCR analysis of additional individuals showed significantly higher COL1A1 expression in the golden-lip group. Additional library-level differences involved transcripts associated with immune and stress-response processes. Overall, this exploratory study identifies candidate transcriptional and transcript-structural differences between the analyzed golden- and silver-lip samples and provides independent experimental support for higher fth1-a and COL1A1 expression in golden-lip oysters. These candidates require functional investigation and validation in independently replicated populations before any evaluation as molecular markers for selective breeding. Full article

Sinanodonta woodiana is one of the most widely distributed freshwater bivalves in the world. However, the sexual dimorphism of this species remains poorly understood. In this study, gonads of clearly sexed S. woodiana were used to analyze steroid hormones, including estrone (E1), estradiol-17β (E2), estriol (E3), and testosterone (T), by liquid chromatography-mass spectrometry, followed by comparative transcriptome analysis. Compared with males, females showed no significant differences in E1 (p = 0.251), E3 (p = 0.136), or T (p = 0.917), whereas E2 concentration in females (15.2 ± 1.4 ng/g wet weight) was significantly higher than that in males (3.2 ± 1.7 ng/g wet weight) (p = 0.009). In addition, a total of 6716 differentially expressed genes (DEGs) were identified, including several sex-related genes such as forkhead box L2 (FOXL2), upregulated in females, and splicing factor 1 (SF1), upregulated in males. All DEGs were mainly enriched in biological processes such as metabolic process, cellular process, and single-organism process, as well as signaling pathways including neuroactive ligand–receptor interaction, glycosphingolipid biosynthesis—lacto and neolacto series, and oocyte meiosis. Our findings provide valuable information for sex identification of adult S. woodiana and offer candidate markers for future testing in juveniles, while also enhancing our understanding of its sex-specific gene-expression diversity. Full article

Nephronophthisis type 20 (NPHP20; MIM #617271) is a rare autosomal recessive disorder caused by biallelic pathogenic variants in MAPKBP1. Although traditionally considered a kidney-restricted disorder, recent findings suggest that MAPKBP1-related disease may be associated with a broader spectrum of extrarenal manifestations. However, the available evidence remains fragmented across gene-discovery studies, family reports, diagnostic sequencing cohorts, and functional investigations. This systematic review aimed to characterize the extrarenal manifestations of MAPKBP1-related disease and estimate their frequency. A secondary objective was to describe the spectrum of pathogenic or likely pathogenic MAPKBP1 variants and integrate clinical findings with current mechanistic models. Studies were eligible if they reported at least one patient with biallelic MAPKBP1 variants and provided clinical information relevant to the phenotype. PubMed, Embase, ClinVar, and Google Scholar were systematically searched from inception to August 2026. The methodological quality and risk of bias of included reports were assessed using the appropriate Joanna Briggs Institute (JBI) critical appraisal tools. All included reports were judged to be of high or moderate methodological quality. Only one paper was considered at high risk of bias, while the remaining articles or database entries had a moderate or low risk of bias. ClinVar entries were evaluated separately, with additional information obtained from the respective submitters when required. Clinical and molecular data were extracted and descriptively synthesized across included reports. The frequency of individual extrarenal manifestations was calculated based on the total number of identified patients while considering possible reporting biases. The search identified 154 records, including duplicates. After deduplication, 100 records underwent title and abstract screening and 32 full-text reports were assessed for eligibility. Nine articles met the inclusion criteria, comprising 16 patients; three additional patients were identified through ClinVar, yielding a total of 19 patients with MAPKBP1-related nephronophthisis included in the analysis. Most patients presented with at least one extrarenal manifestation, predominantly involving the skeletal system. Scoliosis was the most frequently reported extrarenal feature, occurring in eight of 19 genetically eligible patients. Other reported manifestations included short stature, patellar subluxation, long fingers or feet, craniofacial dysmorphisms, and cardiovascular abnormalities. The identified pathogenic or likely pathogenic MAPKBP1 variants were predominantly stop-gain, splice-site, and frameshift variants. The evidence was limited by the rarity of MAPKBP1-related disease, the small number of reported patients, heterogeneity in clinical assessment and reporting, and the predominance of observational and case-based evidence. This systematic review supports an expanding extrarenal phenotypic spectrum of MAPKBP1-related nephronophthisis, with skeletal abnormalities (e.g., scoliosis) representing a prominent feature. Further systematic phenotyping and genotyping of affected individuals are warranted to formally suggest multidisciplinary surveillance, to clarify genotype–phenotype correlations and to investigate the mechanisms underlying extrarenal disease. Registration: The review was prospectively registered in PROSPERO (CRD420261429078). Full article

The optical response of skin tissue in the near-ultraviolet to short-wave infrared band (350–2350 nm) contains rich physiological information such as hemodynamics, hydration status, and lipid metabolism. However, due to limitations in detector technology, conventional spectroscopic systems often use a single type of detector: silicon-based CCD (effective wavelength ≤ 1100 nm) captures visible blood features but cannot cover the long-wave vibration bands of water/lipids, while InGaAs (effective wavelength ≥ 900 nm) is sensitive to long-wave water/lipid absorption but misses the strong blood absorption in the visible region. This spectral detector segmentation leads to a separation of blood features from tissue background signals. In addition, traditional single source-probe distance measurement only probes one depth and cannot observe tissue information at different depths by varying the source-probe distance. This study employs a dual-spectrometer splicing architecture to achieve seamless continuous spectral measurement across 350–2350 nm by amplitude registration and normalization in the overlapping region. Using the thumb, palm, and arm as representative sites, we systematically analyzed spectral differences under varying vascular densities and fat backgrounds and successfully extracted absorption features of major chromophores including blood, water, and lipids. The results showed that the dual-spectrometer splicing method achieved smooth transitions in the overlapping region across different sites, validating its reliability. Spectral differences across sites were mainly characterized by hemoglobin absorption features in the visible region and water/lipid vibrational absorption features in the short-wave infrared region. These findings demonstrate the feasibility of dual-spectrometer splicing for broadband tissue spectral acquisition, enabling simultaneous capture of multi-component signals, and providing a new technical approach for non-invasive tissue composition analysis. Full article

Alternative splicing (AS) is a significant post-transcriptional regulatory mechanism that facilitates environmental adaptation in fungi. However, the conservation of this mechanism and its host specificity during the infection of various hosts by B. cinerea remain ambiguous. This study utilized strand-specific RNA sequencing to perform a comparative analysis of genome-wide AS patterns during the infection of tomato and strawberry by B. cinerea. A comparative analysis identified a total of 1714 AS events and 1130 associated genes across the two hosts, alongside a significant number of host-specific events. Common alternatively spliced genes were predominantly enriched in processes related to gene expression regulation and signal transduction, whereas host-specific genes displayed distinct functional enrichment characteristics and temporal dynamics in their Percent Spliced In (PSI) patterns. Notably, introns linked to AS were generally longer than those associated with constitutive splicing and predominantly featured canonical GT-AG splice boundaries. Furthermore, the magnitude of PSI changes in host-specific events was greater than that observed in common events. This study reveals that B. cinerea exhibits both conserved and host-dependent AS regulatory programs, providing new insights into its post-transcriptional regulatory plasticity during the infection of various plant hosts. Full article

Lesion-mimic mutants provide tractable systems for linking metabolic disruption to cell death and immunity in plants. OsPHD1 encodes a plastidial UDP-glucose/UDP-galactose 4-epimerase, and its disruption causes a lesion-mimic phenotype in the rice mutant lm212. Here, we compared the leaf transcriptomes of lm212 and wild-type plants by RNA sequencing and identified 999 differentially expressed genes. Enriched functions included redox regulation, cell-wall organization, plant–pathogen interaction, MAPK signaling, glutathione metabolism, phenylpropanoid biosynthesis and alpha-linolenic acid metabolism. Alternative-splicing analysis revealed gene-dependent changes, and selected intron-retention events were supported by genome-browser inspection and isoform-specific RT-qPCR. Together, our findings associate OsPHD1 disruption with coordinated transcriptional and post-transcriptional differences and identify candidate pathways potentially related to lesion formation and defense responses in rice. Full article