We performed whole exome sequencing of 250 unique tumor tissues from 30 multi-region sampled pancreatic cancer research autopsies from patients diagnosed with advanced-stage disease. Convergent evolution within the TGF-β pathway is a common feature of advanced-stage disease. However, SMAD4 inactivation is more common among de novo metastatic PDACs, whereas inactivation of TGF-β surface receptors is more common among locally advanced non-metastatic cancers. These differences in metastatic propensity were orthogonally validated in mice by orthotopic injections of PDAC organoids with SMAD4 versus TGFBR2 inactivation. No functionally deleterious driver gene mutations were identified that were attributed to treatment, although radiated PDACs had significantly greater genomic complexity and distinct mutational signatures compared to PDACs managed by chemotherapy. These findings provide a high-level profile of the genetic features distinguishing locally advanced from metastatic PDAC, potentially serving as a biomarker of borderline resectable or locally advanced PDACs most likely to benefit from neoadjuvant chemoradiation.

Lymphoid cancers of different types and subtypes are known to cluster in families. We hypothesize that there are shared susceptibility factors in families with these heterogenous lymphoid malignancies. Exome sequencing was performed on 100 individuals from 43 lymphoid cancer pedigrees. Variants from 37 families were ranked using the Weights-based vAriant Ranking in Pedigrees (WARP) pipeline. Six affected unrelated probands were used for interpretation only. We detected recurrent variants in the germline lymphoid cancer gene FAM160A1 in 4 (9%) of the 43 families, and variants in other genes involved in lymphoid cancers: NPAT, BCL9, HCLS1 and ID3. Variants in genes including BCL9, LEF1, TLE3, and KLHL12 involved in the WNT/β-catenin pathway were identified, representing a novel observation. Some variants appeared to segregate with specific types of lymphoid cancers; others were shared across different subtypes. Identifying factors predisposing to different types of lymphoid cancers will help understand the etiology of these neoplasms.

Immunodysregulation, Polyendocrinopathy, Enteropathy, and X-linked (IPEX) syndrome is a rare autoimmune disorder caused by mutations in the FOXP3 gene. Patients with IPEX frequently present with severe dermatitis, diabetes, and enteropathy. This study explores the efficacy of Dupilumab (an anti-IL-4Rα monoclonal antibody) in treating persistent, severe dermatitis in an IPEX patient refractory to conventional treatments like sirolimus. We conducted a clinical case study of a 2-year-old IPEX patient with refractory dermatitis. Whole-exome sequencing (WES) confirmed the FOXP3 mutation. Skin biopsies were analyzed for inflammatory gene expression by RNA sequencing and immunohistochemistry to characterize inflammatory pathways. Immune cell phenotyping was performed using flow cytometry pre- and post-treatment in peripheral blood mononuclear cells (PBMCs). The patient was treated with Dupilumab alongside sirolimus and prednisone. Clinical improvements were evaluated using the Eczema Area and Severity Index (EASI) score. Immunohistochemistry revealed elevated IL-13 expression. RNA sequencing of skin samples revealed upregulation of both Th1- and Th2-related genes, suggesting a dual inflammatory phenotype in IPEX dermatitis. The patient exhibited significant clinical improvement after 8 months of sustained Dupilumab therapy, with the EASI decreasing from 24.8 to 0.4. Flow cytometry demonstrated a reduction in Th1 and Th2 cell subsets post-treatment, accompanied by an increase in Treg and Th3 cell populations as well as enhanced expression of immunosuppressive markers such as CTLA-4 and CD39. Dupilumab appears promising as a therapeutic option for managing refractory dermatitis in IPEX, particularly by attenuating Th1/Th2 inflammation and promoting regulatory responses mediated by Treg and Th3 cells.

Background Improving the diagnostic rate of genetic etiologies in pediatric drug-resistant epilepsy (DRE) is of critical importance, as it provides valuable guidance for clinical management in this challenging patient population. Methods In this study, matched tissue–blood whole-exome sequencing (WES) was performed on lesional brain tissue and peripheral blood from 21 patients diagnosed with DRE who had undergone resective epilepsy surgery, in order to assess its diagnostic yield. Results The final cohort therefore consisted of 21 pediatric patients with DRE. The patients’ ages ranged from 0.2 to 10.7 years, with a mean age of 5.2 years. Eleven were male and ten were female. Matched tissue-blood WES successfully identified the genetic etiology in six pediatric patients with drug-resistant epilepsy, yielding a diagnostic rate of 28.6% (6/21). This rate was higher than that achieved using blood-only WES (19.0%, 4/21) or clinical and imaging evaluations alone (9.5%, 2/21). Among these six positive cases: Patients 2 and 7 carried deletion and splice-site variants in the DEPDC5 gene, respectively, and these findings were detected in both blood and diseased brain tissue; Patients 14 and 20 both had missense variants in the TSC2 gene, detected in both blood and diseased brain tissue; Patients 8 and 16 had negative blood WES results, but somatic mosaic BRAF variants were detected in the diseased brain tissue, with mosaic levels of 20.2% and 13.5%, respectively. Conclusions Matched tissue–blood WES facilitates the diagnostic yield in pediatric drug-resistant epilepsy, highlighting its critical value in detecting genetic variants that may be missed by blood-only testing and providing essential support for precision diagnosis and therapy.

Hypospadias is a common congenital malformation of the male external genitalia, with severe cases presenting considerable surgical and long-term challenges. Despite the clinical importance of severe hypospadias demonstrated by prolonged hospital stays, repeated surgeries, and substantial costs, the genetic etiology of severe hypospadias remains incompletely understood, particularly in diverse populations. To determine the molecular basis, we performed whole-exome sequencing (WES) on 30 Chinese patients from southeastern China with confirmed 46,XY karyotypes. Our analysis identified clinically relevant genetic variants, including single-nucleotide variants (SNVs) and copy number variations (CNVs), with subsequent phenotypic correlation. Clinically relevant genetic variants were identified in 33.3% (10/30) of cases, including novel SNVs in gonadal regulators (nuclear receptor subfamily 5 group A member 1 [NR5A1] c.1344dupC/c.244+1G>T and SRY-box 3 [SOX3] c.1273G>C), morphogenetic modulators (GLI family zinc finger 3 [GLI3] c.4731delA and aristaless-related homeobox [mARX] c.644C>G), and syndromic genes (patched domain containing 1 [PTCHD1] c.667G>A and euchromatic histone lysine methyltransferase 1 [EHMT1] c.3081C>T). Additionally, recurrent CNVs at 22q12.3 and a novel CNV exon 18 deletion in myelin regulatory factor (MYRF) and 18q11.2 were identified. Mutation carriers showed a significantly higher frequency of cryptorchidism (40.0% vs 5.0%, P < 0.01) and a higher prevalence of ≥3 associated malformations (80.0% vs 35.0%, P < 0.05) than non-carriers, highlighting genotype-phenotype correlations. The 33.3% diagnostic yield tripled conventional estimates, demonstrating WES efficacy in identifying SNVs and CNVs in severe phenotypes. These findings reveal the genetic heterogeneity of severe hypospadias and support WES utility in uncovering novel variants and structural genomic alterations.

Background Autosomal recessive polycystic kidney disease (ARPKD) is an inherited renal disorder characterized by multiple renal cysts. This study aimed to investigate the pathogenesis of PKHD1 gene variants in a Chinese ARPKD pedigree and elucidate the mechanisms underlying the phenotypic heterogeneity in patients with PKHD1 mutations. Methods Clinical data and blood samples were collected from the proband and family members. Whole-exome sequencing (WES) and Sanger sequencing were performed. Conservative analysis and local secondary structure prediction of the mutation site were performed to evaluate the pathogenicity. The genotype-phenotype correlation of PKHD1 mutations was analyzed in combination with this pedigree. Results A pediatric patient with ARPKD was identified. Ultrasonography revealed bilateral renal enlargement with multiple cysts, accompanied by hepatic fibrosis. WES identified a novel compound heterozygous variant in the PKHD1 gene (c.5850_5851insTTCAT; p.Gly1951Phefs*25 and c.8710G &amp;gt; A; p.Glu2904Lys). Conservation analysis confirmed that both mutations occurred in conserved regions, indicating potential pathogenicity. Secondary structure prediction revealed that the p.Gly1951Phefs*25 frameshift mutation resulted in protein truncation and conformational changes, whereas the p.Glu2904Lys missense mutation caused drastic changes in amino acid polarity, impairing protein stability and function. Genotype-phenotype analysis of 605 PKHD1 mutations revealed a trend suggesting that hepatobiliary manifestations might present with less severe mutational burden compared to renal phenotypes, and mild homozygous missense mutations or heterozygous states may attenuate or eliminate renal phenotypes. Conclusion This study uncovered novel PKHD1 mutations in an ARPKD patient, expanding the pathogenic gene spectrum of ARPKD and providing insights for genetic counseling and prenatal diagnosis. Our findings also contribute to the understanding of genotype-phenotype correlations in PKHD1 mutation carriers and generate hypotheses regarding potential organ-specific thresholds for disease manifestation.

Although genetic factors contribute significantly to male infertility, the underlying mechanisms remain incompletely understood. Coiled-coil domain-containing protein 113 (CCDC113) encodes a coiled-coil domain-containing protein critical for the assembly of cilia and flagella. Using whole-exome sequencing, we identified biallelic CCDC113 mutations in two unrelated families affected by oligoasthenoteratozoospermia. The mutations (c.901A>C; p.K301Q and c.404A>C; p.E135A) cosegregated with infertility phenotypes and were associated with defective sperm flagella. Functional analyses demonstrated that these mutations led to less stable CCDC113 protein and severely disrupted axonemal structures in spermatozoa from our three human patients. We generated Ccdc113 knockout mice, which recapitulated the human infertility phenotypes, including abnormal sperm morphology, impaired motility, and defective spermatogenesis. Importantly, one patient achieved successful pregnancy by intracytoplasmic sperm injection, highlighting the translational potential of genetic diagnostics. These findings suggest that CCDC113 is essential for male fertility and contribute to the understanding of the genetic landscape of infertility, offering novel insights into its diagnosis and management.

Introduction Here, we present the results of a nationwide newborn screening (NBS) program in Russia, covering over 2.3 million newborns and employing TREC and KREC quantification to improve the identification of severe forms of T and/or B cell immunodeficiencies and enable early treatment initiation. Methods A two-tier PCR testing strategy was used to define the screen-positive cohort, followed by confirmatory flow cytometry and genetic diagnostics, including fluorescent in situ hybridization (FISH) and whole-exome sequencing (WES). Results A total of 191 patients were diagnosed with defined forms of primary immunodeficiencies (PID), encompassing several groups of inborn errors of immunity (IEI): severe combined immunodeficiency (SCID), agammaglobulinemia, combined immunodeficiency less severe than SCID, and syndromic forms of PID. The overall birth prevalence of severe forms of T and/or B cell immunodeficiencies was 1 in 12,298 live births (95%CI: 1:10,672–1:14,247), corresponding to 8.13 cases per 100,000 newborns (95%CI: 7.02–9.37). Although the positive predictive value of KREC-based screening was relatively low, its use enabled the detection of a substantial proportion of patients with syndromic forms of PID, including Nijmegen breakage syndrome and ataxia–telangiectasia, along with various forms of agammaglobulinemia. Interestingly, 16% of diagnosed newborns had a positive family history, often with previously undiagnosed affected siblings or parents. Additionally, a considerable number of newborns detected by NBS presented with syndromic disorders not currently classified as IEI, suggesting potential avenues for future expansion of the IEI list. Discussion Importantly, early diagnosis through NBS allowed for the timely initiation of disease-specific treatments, including hematopoietic stem cell transplantation (HSCT), immunoglobulin replacement therapy, and targeted immunosuppressive or supportive care strategies. Early intervention may reduce the risk of severe infections, improve neurodevelopmental outcomes, and prevent irreversible organ damage or malignancies in predisposed syndromes. Overall, our study demonstrates the effectiveness of large-scale implementation of TREC/KREC-based NBS in identifying a broad spectrum of immunodeficiencies and highlights future directions for improving NBS algorithms, follow-up protocols, and individualized medical management for affected infants.

Introduction: Diets–Jongmans syndrome is a rare neurodevelopmental disorder associated with heterozygous variants in KDM3B. The phenotypic spectrum continues to expand as additional individuals are identified. Case Presentation: We report an 8-year-old girl who presented with short stature, micrognathia, a pointed chin, and mild developmental delay. Exome sequencing (ES) revealed a novel likely pathogenic heterozygous nonsense variant, KDM3B (NM_016604.4)c.5068C&gt;T p.(Gln1690Ter), which was also detected in her mother. Biochemical evaluation revealed growth hormone deficiency, which was confirmed by two stimulation tests. Short stature without intellectual disability was noted in the mother, indicating intrafamilial phenotypic variability. Conclusion: This case represents the first molecularly confirmed Diets–Jongmans syndrome patient from Türkiye and adds further clinical observations regarding growth hormone deficiency in a patient with DIJOS.

GWAS have generally focused on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we use whole-genome sequencing data to evaluate the contribution to and architecture of rare non-coding variants for three commonly studied anthropometric traits: height, BMI and waist-hip ratio adjusted for BMI. Analysing 447,461 individuals in the UK Biobank for discovery and 225,515 individuals in All of Us for replication, we identify 90 rare and low-frequency single variant associations, including two independent rare variants upstream of IGF2BP2 that substantially reduce waist-hip ratio adjusted for BMI, but have distinct effects on other adiposity traits. We further identify 135 coding variant aggregates. For example, UBR3 protein-truncating variants are associated with a 2.7 kg/m2 increase in BMI. We additionally identify 51 non-coding variant aggregate associations, including one in the 5'UTR of FGF18 associated with up to 6 cm effects on height. We show that 97% of rare variant associations occur near GWAS-identified loci, demonstrating convergence of rare and common variant associations. Finally, we show that ultra rare variants explain a small fraction of heritability compared to common variants for these traits, that heritability is largely shared across ancestries, and that it concentrates around common variant loci.

NLRP12 -associated autoinflammatory disease ( NLRP12 -AID) is a rare monogenic disorder. The p.Glu619Gln (c.1855G &amp;gt; C) variant in NLRP12 is classified as a variant of uncertain significance (VUS), with no previously reported clinical cases. We describe a 16-year-old Chinese girl with a 9-year history of periodic high fevers (&amp;gt;39 °C), cold-triggered urticarial rashes, and polyarticular arthralgia. Previous misdiagnoses included recurrent infections and juvenile idiopathic arthritis. Laboratory tests showed elevated levels of interleukin-6 (IL-6) and acute-phase reactants. A lymph node biopsy confirmed necrotizing lymphadenitis. Extensive testing ruled out infections, autoimmune diseases, and cancers. Whole-exome sequencing identified a heterozygous NLRP12 p.Glu619Gln variant. Structural analysis with AlphaFold2 predicted that the mutation causes local structural destabilization and impairs function. After treatment with baricitinib (2 mg/day), the patient experienced rapid symptom relief within 2 weeks, with IL-6 levels decreasing from 17.8 pg./mL to 2.1 pg./mL and maintained clinical control over 12 months of follow-up. This is the first reported case providing multiple lines of evidence linking the NLRP12 p.Glu619Gln VUS to a typical autoinflammatory profile. Characteristic symptoms, inflammatory markers, histopathology, and a notable response to JAK inhibition support the diagnosis. Our findings suggest reclassifying this variant as likely pathogenic and propose baricitinib as a targeted therapy for NLRP12 -AID.

Background Intellectual disorder, Type 98 (ID 98) is an X-linked disorder characterized by intellectual disability, epilepsy, and multisystem manifestations. This condition is caused by pathogenic variants in the NEXMIF gene through X-linked dominant inheritance. Case presentation We identified a novel hemizygous NEXMIF variant (c.1939_1942delinsAT, p.S647Ifs*3) in a 5-year-old male with severe intellectual disability via trio whole-exome sequencing. His mildly affected mother was a heterozygous carrier. Prenatal diagnosis for the mother’s subsequent pregnancy identified the same hemizygous variant in the male fetus. Following genetic counseling, the decision was made to terminate the pregnancy, thereby preventing the clinical manifestation of the disease in the offspring. Conclusion This report expands the NEXMIF mutational spectrum and underscores the critical role of genetic testing in achieving early diagnosis and informed reproductive counseling for families affected by this disorder.

Introduction ARHGAP32 gene (Rho GTPase Activating Protein 32) encodes a Rho GTPase activating protein, which is vital for the regulation of synaptic plasticity and cytoskeletal dynamics. ARHGAP32 (11q24.3) has been implicated as a candidate gene for Autism Spectrum Disorder (ASD) in Jacobsen syndrome, where a 243-kb terminal deletion encompasses its locus. A unique patient with de novo (DN) likely gene-disruptive mutation of ARHGAP32 has been reported so far in the medical literature. The present study was undertaken to understand clinical, molecular, and neurobehavioral characteristics of ASD associated with a novel DN nonsense mutation in ARHGAP32 . Methods Clinical characterization included basal and follow-up assessment with standardized measures and comorbidities diagnosis. Trio exome sequencing analyses (WES) and variants annotation were performed. Results WES analyses of a 6-year-old female patient with idiopathic ASD revealed DN heterozygous nonsense variant in ARHGAP32 (NM_001378024.1: c.610C&amp;gt;T; NP_001364953.1: p.(Arg204Ter). The variant is predicted to introduce a premature stop codon, resulting in either a truncated protein or activation of nonsense-mediated mRNA decay, ultimately leading to loss of function. The patient presented with normative growth parameters and cranial measurements, with no congenital morphological anomalies. A diagnosis of idiopathic ASD was made at age 2. Developmental delays were observed, notably language regression beginning at 18 months, mild intellectual disability, and restricted interests accompanied by repetitive motor and verbal behaviors. Significant hyperactivity and attentional difficulties were observed. Over time, she exhibited borderline non-verbal cognitive functioning, persistent speech impairment, and was subsequently diagnosed with comorbid Attention Deficit Hyperactivity Disorder. Discussion This study identifies shared neurobehavioral features of idiopathic Autism Spectrum Disorder (ASD) associated with de novo LoF mutations in ARHGAP32 and reinforces the involvement of RhoGAP family proteins in neurodevelopmental disorders. Taken together with previous evidence, our data support the role of ARHGAP32 as a candidate gene for ASD, expanding the genetic spectrum.

To determine the cause of marked hypotonia and neonatal encephalopathy, mild anemia and thrombocytopenia, and nonspecific facial dysmorphism in a neonate after extensive neurological and biochemical evaluations, and karyotyping failed to establish the etiology. Whole exome sequencing (WES), single-nucleotide polymorphisms chromosomal microarray (SNPs CMA), and fluorescence in-situ hybridization (FISH) analysis were performed in the patient and the parents. WES did not show a candidate gene/diagnosis. Trio-CMA and FISH confirmed a de novo 8.9 Mb duplication of 11p15.4p15.5 and a 6.4 Mb deletion of 11q24.3q25 in the child, and that the duplicated 11p was of paternal origin, based on the SNPs analysis. On long-term follow-up, encephalopathy improved gradually, thrombocytopenia resolved, facial puffiness persisted, and developmental delay remained. The present patient represents the first case of de novo 11p duplication with 11q deletion and severe neonatal encephalopathy. The de novo chromosomal rearrangement could still have resulted from nonallelic homologous recombination, triggered by low-copy repeats (LCRs) at distal 11p and 11q during paternal meiosis, despite the lower LCR density. Alternatively, it may represent a random event, as it does not involve the recurrent deletion/duplication typically observed in regions with dense LCRs.

To explore genetic basis leading tomeiotic disruption in human gametogenesis via exome sequencing. This study included three consanguineous families with well-defined infertility phenotypes. Exome sequencing was performed for the index case in family 1 and for the trio (index with parents) in the other two families. Sanger sequencing was used for confirmation and family segregation analysis. Exome sequencing revealed homozygous loss-of-function variations in SPIDR, TOP6BL, and RAD51AP2 in families 1, 2, and 3, respectively. Segregation in individual families revealed that the parents were carriers, as were the fertile siblings in families 1 and 2. All three genes function in double-strand break formation or repair, identified variants may therefore impair, potentially preventing its completion and contributing to infertility in the index cases. Gene-disease relationships (GDR) were re-evaluated due to the addition of new patients and/or variants in the literature. Our findings provide additional evidence for the role of SPIDR, TOP6BL, and RAD51AP2 as genetic contributors to human infertility due to meiotic errors. For patients with a similar phenotype, genetic screening could be recommended, and the identification of pathogenic variations might help avoid unsuccessful fertility treatments. Additionally, in patients with molecular defects in DNA repair genes, chromosomal instability may increase the risk of cancer; therefore, long-term follow-up by a multidisciplinary team is recommended.

Childhood-onset movement disorders are clinically and genetically heterogeneous, with over 500 implicated genes. Standard clinical genetic testing, including exome sequencing, has limited sensitivity for certain variants, including repeat expansions, structural variants (SVs), copy number variants (CNVs), and deep intronic changes. We evaluated the diagnostic utility of short-read whole genome sequencing (srWGS) and, in selected cases, long-read genome sequencing (lrWGS) in a real-world cohort of children and young adults with early-onset progressive movement disorders and prior nondiagnostic genetic testing. One hundred individuals (<30 years) with progressive movement disorders with a suspected genetic etiology were recruited from a tertiary pediatric movement disorders program. All had prior nondiagnostic testing. SrWGS (Illumina NovaSeq 6000) assessed single nucleotide variants (SNVs), CNVs, SVs, and repeat expansions; lrWGS (Pacific Biosciences) was applied to select unsolved trios. Variants were reviewed by a multidisciplinary team using standard variant interpretation guidelines and phenotype correlation. A molecular diagnosis was achieved in 27% (27/100) of cases, and candidate variants were identified in an additional 33% (33/100). Among solved cases, 81.5% (22/27) were identified from exome-level data, while 18.5% (5/27) required genome-level analysis to detect variants such as repeat expansions in HTT and FXN, an intragenic duplication in MECP2, an Alu insertion in ATM, and a deletion in FA2H. Genome-level analysis contributed an additional diagnostic yield of 5% (5/100) only. Notably, in 33.3% (9/27) of solved cases, variants had been previously reported but not recognized as diagnostic. LrWGS of 14 unsolved trios did not yield additional diagnoses. SrWGS provided a modest incremental yield over exome sequencing in early-onset movement disorders, with most diagnoses achieved through reanalysis of exome-level data. Findings highlight the importance of iterative variant interpretation and the need for improved analytic pipelines to fully realize the potential of genome sequencing.

Background Glucose-6-phosphate dehydrogenase (G6PD) deficiency is traditionally recognized as a risk factor for drug- or infection-induced hemolytic anemia. Emerging evidence implicates potential roles of G6PD in neurodevelopment, yet its association with rare neurological disorders remains underexplored in population-based genetic studies, especially within the Chinese population. Methods We conducted a retrospective case-control study utilizing whole-exome sequencing (WES) data from a Chinese cohort. Six most prevalent pathogenic G6PD variants in China were screended in children with rare neurological disorders (n = 211) and in controls without neurological involvement (n = 202). Genotype and carrier frequency comparisons were performed. Stratified analyses were performed based on diagnostic certainty and the presence of de novo mutations. Multivariable logistic regression was employed to calculate sex-adjusted odds ratios (ORs) to control for potential sex-related confounding. Results After adjusting for sex, the overall carrier rate of pathogenic G6PD variants was significantly higher in patients with neurological disorders than in controls (adjusted OR = 2.44, 95% CI: 1.18–5.06, p = 0.014). Further comparisons across specific groups revealed distinct patterns: affected male patients had a higher carrier rate than their own unaffected fathers (OR = 2.30, 95% CI: 1.08–4.91, p = 0.043), and mothers of case patients showed a higher carrier rate than mothers of controls (OR = 2.03, 95% CI: 1.09–3.78, p = 0.030). The variants NM_001042351.3: c.1376G&amp;gt;T (G6PD Canton) and NM_001042351.3:c.1388G&amp;gt;A (G6PD Kaiping) were the most prevalent across all groups. Conclusion This population-based genetic analysis provides preliminary evidence that G6PD deficiency may be a underrecognized genetic risk factor for rare neurological disorders in Chinese children. The findings suggest a potential maternal genetic contribution and indicate that the phenotypic spectrum of G6PD deficiency may extend beyond hematological manifestations to include neurodevelopmental vulnerability. Important limitations include the lack of functional validation and the use of a clinical control group. Further prospective studies incorporating G6PD enzyme activity assessment and functional investigations are warranted to elucidate the underlying mechanisms.

Neuroblastoma (NBL) is a pediatric malignancy with poor prognosis in high-risk cases. This study explores the function of albumin conformation factor 1 (ACF1) in NBL progression and delves into the underpinning mechanism. Exome and transcriptome sequencing were applied to analyze ACF1 mutations/expression in NBL tissues versus controls. ACF1 was knocked down in NBL cell lines (KELLY, BE2C, N2a) for in vitro assays (viability, proliferation, migration, apoptosis, therapy sensitivity) or in vivo xenograft/metastasis models with radiation/cisplatin. Mechanisms were probed via RNA-sequencing, chromatin immunoprecipitation, luciferase assays, co-immunoprecipitation, and immunofluorescence assays. Expression patterns and the correlations between ACF1, GCLM, and NAA20 were detected in human NBL tissue microarrays. ACF1 mutations and elevated expression correlated with advanced tumor staging, high-risk factors, and unfavorable prognosis in NBL datasets and TMAs. ACF1 knockdown suppressed NBL cell proliferation, mobility, and in vivo tumor growth/metastasis, while enhancing cisplatin/radiation sensitivity and apoptosis. Mechanistically, ACF1 knockdown reduced GCLM transcription via decreased H3K27ac/H3K4me3/Myc at its promoter, elevating lipid peroxidation and lowering glutathione (GSH) levels. Lactate induced ACF1 lactylation and nuclear translocation, promoted by NAA20 interaction (enhanced by lactate). NAA20 knockdown phenocopied ACF1 effects, rescued by GCLM overexpression. NAA20 and GCLM were upregulated in NBL datasets/TMAs. This study suggests that the NAA20-mediated ACF1 lactylation drives GCLM-dependent GSH synthesis, promoting NBL cell growth and metastasis. Targeting this axis may improve therapy response.

MKRN3 gene loss-of-function mutations cause central precocious puberty (CPP), whereas its deletion in Prader-Willi syndrome (PWS) paradoxically leads to hypogonadism. The mechanistic basis for these opposing reproductive phenotypes remains largely unclear. We performed whole-exome sequencing in 98 Chinese CPP patients along with a systematic review of previously reported MKRN3 pathogenic and likely pathogenic variants to summarize genotype-phenotype correlations. Subsequently, genome-wide DNA methylation profiling was performed in CPP patients with the MKRN3 pathogenic variant, and the results were compared with those of patients with PWS, idiopathic CPP, and healthy controls. A pathogenic frameshift MKRN3 variant [c.476dupC (p.Ala159fs*15)], representing the first frameshift mutation reported within the inter-C3H1 hotspot region in an Asian cohort, was identified. Patients with severe MKRN3 variants exhibited significantly earlier pubertal onset (5.80 vs. 7.50years, P = 0.029) and higher GnRH-stimulated peak LH levels (34.55 vs. 11.00IU/L, P = 0.047) than those with missense mutations. Methylation analysis revealed no differences in MKRN3 but identified 18,609 differentially methylated positions between MKRN3-CPP and PWS. Key findings included hypermethylation of IGSF10 (Δβ = 0.37), ZC3H18 (Δβ = 0.27), SH3RF3 (Δβ = 0.36), and PTH1R (Δβ = 0.28), alongside hypomethylation of MAGEL2 (Δβ = - 0.19), and PTPA (Δβ = - 0.23), where Δβ represents the difference in DNA methylation β values between groups. We identified a first frameshift pathogenic variant localized to the inter-C3H1 region in Asia, further confirming its functional significance. Our study suggests an epigenetic framework that could potentially explain how divergent pubertal phenotypes in MKRN3 deficiency might arise from dysregulated epigenetic programming of downstream neuroendocrine pathways.

Objective This study aimed to uncover the genetic variations and their corresponding clinical features in a Chinese family affected by epidermolysis bullosa (EB). Methods We enrolled a Chinese family clinically diagnosed with EB and conducted whole-exome sequencing on the proband to identify genetic variations. I-TASSER and PyMOL software were used to examine the structural and functional implications of the identified mutant proteins. Results The study identified an autosomal-dominant form of epidermolysis bullosa simplex (EBS) in the family, attributed to a novel missense variation c.A527G (D176G) in the ITGB4 gene. By bioinformatics analyses, we found that the wild-type D176 forms one hydrogen bond with a distance of 3.1 Å from F201, one hydrogen bond with a distance of 2.7 Å from K177, and two hydrogen bonds with a distance of 3.2 Å from Y304; however, the mutant G176 only forms one hydrogen bond with F201 at a distance of 3.2 Å. Conclusions This study confirms the dominant mode of inheritance of the missense ITGB4 mutation observed in EB. The novel missense variation c.A527G (D176G) in ITGB4 involves a transition from a polar to non-polar amino acid and a decrease in intermolecular hydrogen bonding, which was associated with EB development.