Am J Hum Genet. 2025 Sep 3:S0002-9297(25)00320-9. doi: 10.1016/j.ajhg.2025.08.010. Online ahead of print. ABSTRACT Microtubule-actin cross-linking factor 1 (MACF1) is a large protein of the spectraplakin family, which is essential for brain development. MACF1 interacts with microtubules through the growth arrest-specific 2 (Gas2)-related (GAR) domain. Heterozygous MACF1 missense variants affecting the zinc-binding residues in this domain result in a distinctive cortical and brain stem malformation. Evidence for other MACF1-associated disorders is still limited. Here, we present a cohort of 45 individuals with heterozygous or bi-allelic MACF1 variants to explore the phenotypic spectrum and assess possible pathogenic relevance. We observe that de novo heterozygous missense variants in the EF-hand domains also result in distinctive brain malformation and provide experimental evidence that variants in the EF-hand/GAR module increase microtubule binding, suggestive of a toxic gain of function. Notably, no phenotype-genotype correlation was possible for the remaining heterozygous variants in other domains. A clinical review of eight families with bi-allelic variants reveals a possible complex neurodevelopmental syndrome of the central and peripheral nervous systems. In these individuals, bi-allelic variants mostly affect the Plakin domain. Furthermore, RNA sequencing and chromatin immunoprecipitation (ChIP) analyses of human fetal brain tissue reveal five MACF1 isoforms with region-specific expression, differing in their exon 1 transcription start sites but splicing to a common exon 2. This differential expression explains the frontal-predominant lissencephaly in an individual with a homozygous stop-gain in exon 1 (MACF1-204: c.70C>T [p.Arg24∗]), as this isoform is preferentially expressed in the frontal cortex. We conclude that MACF1-related disorders are strictly linked to domain function and the level of transcript expression, explaining the observed wide clinical heterogeneity. PMID:40925378 | DOI:10.1016/j.ajhg.2025.08.010

Genet Med. 2026 Aug 25:102698. doi: 10.1016/j.gim.2026.102698. Online ahead of print. ABSTRACT PURPOSE: Prenatal opioid exposure has inconsistently been associated with congenital anomalies. In 2023, fentanyl was proposed as a human teratogen in ten infants with documented exposure and a consistent pattern of abnormalities. Disrupted cholesterol biosynthesis was proposed as the pathogenetic mechanism. METHODS: We evaluated 56 children aged 0-4 years with confirmed prenatal fentanyl exposure. We collected data on intrauterine exposures, dysmorphic features, congenital anomalies, neonatal course, feeding, growth and development, cholesterol precursors and genetic testing. We analyzed the role of co-exposures and specific features in predicting clinical and developmental outcomes. Associations between dysmorphology categories and outcomes were tested. Using diagnostic frameworks from fetal alcohol spectrum disorders, we evaluated criteria for a potential fetal fentanyl syndrome. RESULTS: Among the enrolled patients, microcephaly, failure to thrive, feeding difficulties, and gastrostomy placement were common. A distinctive pattern of craniofacial dysmorphology was identified. Developmental delays affected 47% of individuals, and autism or high risk was identified in 50% of those screened. Genetic testing was non-contributory. Elevated cholesterol precursors were seen in some when tested in the first weeks of life. Dysmorphology severity was associated with microcephaly, failure to thrive, hypotonia, and gastrostomy use. CONCLUSION: Prenatal fentanyl exposure was associated with a recognizable pattern of dysmorphology, growth restriction, impaired brain development, and neurodevelopmental deficits. These findings support fentanyl as a human teratogen. PMID:42639750 | DOI:10.1016/j.gim.2026.102698

Genes Dev. 2026 Aug 19. doi: 10.1101/gad.353355.125. Online ahead of print. ABSTRACT MYC-driven (MYC⁺) cancers are highly aggressive and often fatal. MYC dysregulation is a key event in these cancers, yet MYC overexpression alone is often insufficient to initiate or sustain tumorigenesis. Plasmocytoma variant translocation 1 (PVT1), a long noncoding RNA (lncRNA) adjacent to MYC on chromosome 8q24, is frequently co-amplified with MYC in many of these cancers. Our prior work showed that PVT1 potentiates MYC function, although the underlying mechanism has remained unclear. Here we show that, in addition to amplification with MYC, genomic rearrangements at PVT1 frequently involve unbalanced translocations that asymmetrically enrich 5′-PVT1 while depleting 3′-PVT1 The retained 5′-PVT1 region generates a circular RNA, CircPVT1, that encodes a novel protein we have named Firefox (FFX). We show that FFX is essential for MYC-mediated oncogenic signaling, as its depletion markedly reduces MYC protein abundance and transcriptional output. Mechanistically, FFX stimulates AKT-mTORC1 signaling and enhances cap-dependent translational and biosynthetic capacity, thereby establishing a self-reinforcing oncogenic circuit that amplifies MYC activity. Inducible depletion of FFX in vivo significantly impairs tumor growth in MYC⁺ xenograft models. These findings define FFX as a critical effector within the MYC-PVT1 locus and reveal a therapeutically actionable vulnerability in MYC⁺ cancers. PMID:42618323 | DOI:10.1101/gad.353355.125

Genes Dev. 2026 Aug 19. doi: 10.1101/gad.353356.125. Online ahead of print. ABSTRACT Genomic rearrangements can drive cancer through mechanisms that extend beyond classical oncogenic fusions such as BCR-ABL A substantial fraction of these events involve long noncoding RNAs (lncRNAs), yet their functional impact on tumorigenesis has remained largely opaque. The lncRNA plasmacytoma variant translocation 1 (PVT1), positioned adjacent to MYC at chromosome 8q24, is among the most frequently altered loci in MYC-driven (MYC⁺) cancers. We recently showed that PVT1 translocations produce a characteristic asymmetric architecture that preserves the 5′-PVT1 region, generating a circular RNA (CircPVT1) that encodes Firefox (FFX), a novel oncoprotein that activates AKT-mTORC1 signaling and cooperates with MYC. Here, we uncover a complementary and opposing function for the deleted 3′-PVT1 segment, which encodes a tumor-suppressive micropeptide we term Honeybadger (HNB). HNB binds KRAS and dampens RAS-MAPK signaling, and its loss derepresses this pathway and stabilizes MYC via Ser⁶² phosphorylation. Thus, a single class of structural alterations at PVT1 simultaneously installs FFX-mediated AKT-mTORC1 activation and removes HNB-mediated RAS-MAPK regulation, creating a dual mechanism that synergistically amplifies MYC output. This oncoprotein gain coupled with tumor-suppressor loss provides a mechanistic explanation for the particularly poor prognosis of PVT1-rearranged cancers and establishes PVT1 as a central regulatory hub in MYC⁺ malignancies. PMID:42618324 | DOI:10.1101/gad.353356.125

Nat Med. 2026 Jul 21. doi: 10.1038/s41591-026-04527-y. Online ahead of print. ABSTRACT SCN2A variants are among the most common genetic causes of developmental and epileptic encephalopathies (DEEs), which can present with uncontrolled seizures at birth and account for 1-2% of all epileptic encephalopathies. A substantial fraction of causal variants are gain-of-function or mixed-function variants associated with increased channel open probability or greater sodium current flux. Here two parallel n = 1 clinical studies were conducted in two patients (9-year-old and 14-year-old boys) with SCN2A-related DEE. Individualized allele-selective antisense oligonucleotides (ASOs) were designed to target heterozygous intronic single-nucleotide polymorphisms (SNPs) for decreased expression of mutant SCN2A transcript while preserving the wild-type copy. Primary endpoints included quantitative change from baseline in seizure frequency and neurodevelopment, including motor scores. Efficacy measures were also individualized to each patient’s phenotype, including refractory seizures, developmental delay, autism spectrum disorder, choreoathetosis and gastrointestinal dysfunction. Patients experienced a reduction in seizure frequency (26% and 90% in the two patients, respectively), decreased use of concomitant medications and improvement in neurodevelopmental skills. Both ASOs were well tolerated, with no ASO-related serious adverse events. Continued long-term follow-up of these preliminary positive safety and efficacy findings is needed to confirm the disease-modifying potential of these ASOs. Haplotype phasing in a separate cohort of infants with SCN2A-related disorder (SCN2A-RD), diagnosed by rapid whole-genome sequencing, identified 16% of patients with compatible SNPs. These data provide a pathway from n = 1 to n of more patients with SCN2A-RD and other monogenic disorders. ClinicalTrials.gov registration: NCT06314490 . PMID:42481851 | DOI:10.1038/s41591-026-04527-y

Front Neurol. 2026 Jul 16;17:1793300. doi: 10.3389/fneur.2026.1793300. eCollection 2026. ABSTRACT BH4 deficiencies may occur with or without hyperphenylalaninemia (HPA). If identified early through neonatal screening for PKU, the clinical follow-up aims to prevent the onset of typical disease symptoms. In contrast, for the conditions not associated with HPA, diagnosis usually occurs once symptoms manifest, and follow-up focuses on monitoring the treatment’s effectiveness in restoring normal neurological function. Except for pterin-4-alpha-carbinolamine dehydratase defect (PCCDd), the core symptoms and natural course of these diseases involve neurodevelopmental impairment and movement disorders. Current information on clinical follow-up and outcome comes from retrospective observational studies, with standardized measures used in only a few of them. Serial clinical observations focusing on the two most consistent areas of neurological impairment are the best predictors of outcome and the main follow-up targets. Available clinical data, often aggregating early- and late-treated patients, show that the best clinical outcome occurs in autosomal dominant guanosine triphosphate cyclohydrolase I deficiency (AD-GTPCHd). In contrast, for recessive conditions, prognosis is variably associated with both the timing of treatment (autosomal recessive [AR]-GTPCHd, 6-pyruvoyltetrahydropterin synthase [PTPS]d, sepiapterin [SR]d, q-dihydropyridine reductase [DHPR]d) and the severity of metabolic derangement (AR-GTPCHd, PTPSd). Neurocognitive, psychiatric, and sleep disorders are currently underestimated and can occur in children and adults, affecting social adaptation and quality of life. Among metabolic alterations, blood Phe levels, when altered, warrant regular monitoring. CSF evaluation can be considered in subjects unresponsive to treatment or with an unexpected clinical course. CSF 5-MTHF monitoring should be reserved for patients with DHPRd experiencing neurological deterioration and seizures. Monitoring prolactin levels, when altered, may assist in personalizing pharmacological treatment. Serum magnesium and glucose are metabolic markers that should be assessed in PDCCd. Brain MRI monitoring is recommended for patients experiencing unusual courses, epilepsy, and neurological deterioration (particularly in PTPSd and DHPRd). A DAT scan is advised for those with AD-GTPCH who present or develop Parkinsonism, and EEG monitoring should be conducted for every patient with epilepsy or suspected seizures. For future clinical studies, it is mandatory that the clinical assessment adopt standardized tools that score impairment across neurological and behavioral domains, taking the patient’s age into account. SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=1144143, identifier (CRD420251144143). PMID:42534655 | PMC:PMC13422167 | DOI:10.3389/fneur.2026.1793300

Clin Ther. 2026 Jun 9:S0149-2918(26)00188-8. doi: 10.1016/j.clinthera.2026.05.025. Online ahead of print. NO ABSTRACT PMID:42264972 | DOI:10.1016/j.clinthera.2026.05.025

Nat Commun. 2026 May 30. doi: 10.1038/s41467-026-73455-9. Online ahead of print. ABSTRACT Primary mitochondrial diseases (PMDs) affect approximately 1 in 4300 individuals and cause early-onset neuromuscular and multisystem dysfunction with reduced lifespan. They result from pathogenic variants in mitochondrial or nuclear DNA that impair oxidative phosphorylation. Cytochrome c oxidase (COX; complex IV) deficiency is a well-established cause of PMD, leading to a broad spectrum of phenotypes. COXFA4 (cytochrome c oxidase subunit FA4), formerly NDUFA4, is a nuclear-encoded COX subunit, but its role in disease remains poorly defined. We report the largest genetically confirmed cohort of COXFA4-related PMD to date, comprising 13 individuals from 12 families with biallelic pathogenic COXFA4 variants. All present with Leigh-like encephalopathy and complete loss of COXFA4 protein; however, patient-derived fibroblasts retain residual COX activity, with upregulation of COXFA4L2 (cytochrome c oxidase subunit FA4-like 2), a poorly characterised paralog. Here, we show that COXFA4 is a late-stage COX assembly subunit and identify a paralog-mediated compensatory mechanism with translational potential. PMID:42218136 | DOI:10.1038/s41467-026-73455-9

Genome Med. 2026 May 28. doi: 10.1186/s13073-026-01676-0. Online ahead of print. ABSTRACT BACKGROUND: Extrachromosomal DNA (ecDNA) is a structural variant linked to poor prognosis in pediatric cancers. Patient-derived xenograft (PDX) models are crucial tools for cancer research, as they are believed to recapitulate the molecular features and intratumoral heterogeneity in patient tumors. However, ecDNA demonstrates unique evolutionary dynamics under selective pressure, and its behavior during PDX development remains largely uncharacterized. This study investigates the fidelity of PDX models in representing ecDNA from primary tumors. By analyzing ecDNA sequence composition and copy number conservation across pediatric solid cancers, we assess how well PDX models recapitulate the ecDNA landscape observed in human tumors. METHODS: AmpliconArchitect was used to analyze whole-genome sequencing (WGS) of 338 PDX models and 127 corresponding primary tumors. ecDNA status, sequence, copy number, and associated genes were compared between PDX models and their matched human tumors. Additionally, multiome RNA and ATAC single-cell sequencing of a PDX tumor enabled comparison of ecDNA intratumoral heterogeneity relative to similar data from the primary tumor. RESULTS: ecDNA in PDX models largely recapitulated oncogene amplifications observed in human tumors, with MYCN being the most frequently amplified. ecDNA status remained unchanged for a majority of the PDX models (105/127, 83%) compared to primary tumors, with 20% of previously ecDNA-negative cases acquiring ecDNA during PDX development. Consequently, ecDNA was more prevalent in the PDX models than in their corresponding human tumors (McNemar’s test, p = 0.00086). Detailed examination of ecDNA sequences in tumor-PDX pairs showed substantial conservation (67% with > 90% sequence overlap) but variable breakpoint concordance. Single-cell analysis demonstrated that rare ecDNA-positive cells from the primary tumor preferentially drive PDX tumor development. CONCLUSION: This study highlights the prevalence, oncogenic content, and conservation of ecDNA in PDX models relative to pediatric patient tumors. We observed that ecDNA frequently recapitulates oncogene amplifications found in human cancers, is generally preserved during PDX establishment, and reflects subtype-specific patterns across tumor types. These findings support the utility of PDX models in studying ecDNA biology in pediatric cancer progression and therapy. Longitudinal sampling during PDX tumor growth and under therapeutic pressure could provide insights into molecular evolution, clonal selection, and ecDNA-driven therapy resistance. PMID:42210429 | DOI:10.1186/s13073-026-01676-0

Clin Ther. 2026 May 28:S0149-2918(26)00184-0. doi: 10.1016/j.clinthera.2026.05.020. Online ahead of print. ABSTRACT Genomic sequencing (GS) in the neonatal period has advanced over the past several years. Results are available within days in many centers and cost-effectiveness and utility data continue to accumulate. Though less prevalent in clinical practice, prenatal GS is also demonstrating increasing evidence of efficacy. Clearly, information on a genetic disorder’s presence or absence is very useful for families and providers, both during pregnancy and postnatally in the intensive care units. Precision therapies for genetic disorders continue to advance in the pediatric space and, in some instances, are being considered for prenatal therapy. Despite caring for the same families along a continuum of care, prenatal and neonatal discussions about genomic sequencing are often siloed. We urge providers in the prenatal and neonatal spaces to align genomic medicine service delivery and consider offering GS prenatally or, at least, prenatally coordinating postnatal rapid GS in the third trimester to facilitate rapid diagnosis and patient-centered care. PMID:42209309 | DOI:10.1016/j.clinthera.2026.05.020