Journal of Human Genetics最新文献

The 'thrifty' variant hypothesis, which posits that certain genetic adaptations promoting efficient energy storage during periods of food scarcity, has been invoked to explain the high prevalence of obesity in modern human populations. Although several candidate variants have been proposed, the timing and effects of these variants on body mass index (BMI) in specific populations remain poorly understood. In this study, we performed whole-genome sequencing of 22 Tongan individuals. A previous study identified the rs373863828-A variant in the CREBRF gene as a target of positive selection in Samoans based on iHS analysis. Here, we replicated this signal in Tongans, confirming that this variant has been subject to adaptive pressures more broadly across Polynesian populations. Using the CLUES program, we inferred the allele frequency trajectory of rs373863828-A in Tongans, revealing a marked increase over the past ~100 generations that temporally aligns with the period of Polynesian maritime expansion. The trajectory of the Polygenic Score (PS) showed an increase in the PS for BMI in ancestors of Tongans between 150 and 50 generations ago, followed by a recent decline. Analysis of polarized trait integrated haplotype scores detected significant polygenic selection favoring lower BMI in recent generations. Our findings suggest that the CREBRF variant underwent strong positive selection during oceanic dispersal, while numerous modest-effect variants collectively contributed to adaptation to food-limited environments during long sea voyages. More recently, however, selection pressures may have shifted toward lower BMI, indicating a potential evolutionary mismatch between past adaptations and modern environments.

Galactose, a monosaccharide, plays diverse biological roles in energy production, especially in the glycolysis and glycosylation of proteins and lipids. Galactose metabolism is mediated by the Leloir pathway, which comprises four key enzymes. Following lactose hydrolysis, galactose mutarotase (GALM) catalyzes the anomerization of β-D-galactose to α-D-galactose, providing a substrate for the downstream pathway. In 2019, GALM deficiency was defined as the fourth type of galactosemia. Affected individuals may develop cataracts similar to those observed in individuals with galactokinase deficiency, disrupting the subsequent steps in the Leloir pathway. However, cataracts generally occur less frequently and tend to be milder in patients with GALM deficiency, likely because of the partial compensation provided by spontaneous galactose mutarotation in aqueous solutions. Because lactose, the primary dietary source of galactose, is the predominant carbohydrate consumed until weaning, the timely initiation of lactose restriction can prevent or even reverse cataract formation. To date, other complications or adverse events, including those in heterozygous carriers of GALM variants, have not been clearly demonstrated. This review aims to synthesize current knowledge and findings of GALM deficiency on molecular mechanisms, clinical presentation, diagnostic approaches, carrier risk, and dietary management, with particular emphasis on cataract prevention and reversibility through early lactose restriction. By consolidating available evidence, we propose future research directions, with broader implications for newborn screening programs, clinical decision-making, and a deeper understanding of galactose metabolism.

Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder with broad clinical variability, making diagnosis in pediatric patients particularly challenging due to age-dependent penetrance and variable expressivity. In this study, we analyzed 536 unrelated Chinese children with clinical suspicion of NF1 using optimized whole-exome sequencing (WES) enhanced by targeted probe enrichment and exon-level copy number variation (CNV) analysis to investigate the molecular etiology and mutation spectrum. Pathogenic or likely pathogenic variants were identified in 288 patients (53.7%), including 271 with variants in the NF1 gene. These consisted of 197 distinct small sequence variants (SNVs) and 25 CNVs, of which 19 were large multigenic deletions, and 6 were intragenic. Notably, 62 of the NF1 SNVs were novel. The incorporation of exon-level CNV analysis and probe enrichment improved the diagnostic yield by 9.2% and 2.2%, respectively. Seven patients were found to have dual diagnoses involving NF1 and other genetic disorders, including six novel combinations. In addition, 17 were diagnosed with non-NF1 conditions such as RASopathies and cancer predisposition syndromes. Our findings highlight the value of optimized WES strategies in improving diagnostic accuracy and yield, particularly for pediatric patients with atypical clinical presentations. This study represents one of the most comprehensive assessments of NF1 molecular diagnostics in a Chinese pediatric population.

Myopathy, lactic acidosis, and sideroblastic anemia type 1 (MLASA1) is an extremely rare mitochondrial disorder caused by biallelic pathogenic variants in PUS1, which encodes a mitochondrial tRNA pseudouridine synthase essential for mitochondrial protein synthesis. We describe two affected siblings presenting with progressive myopathy, lactic acidosis, sideroblastic anemia, short stature, developmental delay, and mild cognitive impairment. Depth-based copy number variation analysis of whole-exome sequencing data revealed a novel homozygous multi-exonic deletion in PUS1. The deletion breakpoints were defined by Sanger sequencing as a 9964 bp deletion spanning part of intron 3 through exons 4-6 and extending into the 3' untranslated region, resulting in complete loss of the C-terminal coding region. Skeletal muscle histology demonstrated ragged red fibers, whereas immunohistochemistry showed a selective and near-complete loss of NDUFB8, indicating impaired assembly of respiratory chain complex I. A systematic review of previously reported MLASA1 cases revealed marked clinical heterogeneity, including frequent developmental delay, dysmorphic features, and multi-organ involvement. These findings expand the genotypic and phenotypic landscape of MLASA1 and highlight the diagnostic value of copy number variation analysis in unresolved mitochondrial disorders. The impairment of complex I underscores the particular vulnerability of translation-dependent respiratory chain components in PUS1-related diseases.

AKT1 (Protein Kinase B alpha) is a serine/threonine kinase that plays a pivotal role in regulating various cellular processes. To elucidate the role of the AKT1 gene in signaling pathways, this study generated AKT1 knockout (KO) HT-1080 cells using the CRISPR/Cas9 system. Gene-editing efficiency was validated through Sanger DNA sequencing and insertion/deletion (InDel) analysis. Quantitative real-time PCR and Western blot analyses were performed to evaluate the expression levels of AKT1 mRNA and protein, as well as to examine the expression of AKT1 downstream effectors: mTOR, BCL-2, and FOXO1. The AKT1 single-guide RNA sequence was successfully cloned into the CRISPR/Cas9 vector, leading to the establishment of AKT1 KO cells. InDel analysis identified eight editing types, with two dominant populations. The expression levels of AKT1 mRNA and protein were significantly reduced in the KO cells. The expression levels of mTOR, BCL-2, and FOXO1 were significantly altered in the KO cells compared to normal cells. These findings highlight the impact of AKT1 disruption on signaling pathways and provide fundamental insights into the regulatory role of the AKT1 gene.

Inborn errors of metabolism (IEMs) lead to early-onset neurodegenerative disorders often caused by mitochondrial dysfunction. In this study, we identified a homozygous frameshift mutation (c.283dupG; p.Cys65LeufsTer13) in SLC27A3, identified through exome sequencing in a 2-month-old female proband presenting with developmental regression, hypotonia, seizure, feeding difficulty, and bilateral putaminal lesions on brain magnetic resonance imaging (MRI). The mutation results in a truncated, non-functional protein and complete loss of SLC27A3 expression in proband-derived fibroblasts. Results show the absence of SLC27A3 and aberrant mitochondrial morphology with clumped networks. Metabolic profiling showed elevated acyl-carnitine levels in the cytosol of proband cells, indicative of disrupted fatty acid oxidation. Additionally, mitochondrial respiratory chain activity was significantly reduced, and flow cytometry revealed increased cell death in mutant cells compared to controls. Protein-protein interaction analysis revealed SLC27A3 networks linked to fatty acid metabolism, ER-associated degradation (ERAD), and ion transport. GO enrichment demonstrated strong associations with transporter activity, protein homeostasis, and ER-mitochondrial membrane networks. Regional expression profiling showed high SLC27A3 transcript levels in the basal ganglia, correlating with the observed neuropathology. These findings position SLC27A3 as a critical lipid transporter involved in neuronal energy metabolism and proteostasis, and implicate its loss in mitochondrial encephalopathy. This study expands the genotypic and phenotypic spectrum of metabolic neurodevelopmental disorders and highlights the importance of fatty acid transport proteins in mitochondrial health and brain development. Our findings propose SLC27A3 as a novel candidate gene for early-onset mitochondrial disorders.

The CACNA1H gene, which encodes the T-type calcium channel Cav3.2, is known to confer susceptibility to childhood absence epilepsy (CAE) and has been implicated in various neurological disorders. However, its pathogenic significance, especially in childhood intractable epilepsies, has not been comprehensively explored. We performed whole-exome sequencing on a 4-year-old boy diagnosed with epilepsy with myoclonic-atonic seizures (EMAtS), and identified two missense variants in CACNA1H. One was a novel variant, p.D949H, inherited from the father, while the other was a known variant, p.R788C, inherited from the mother. Because the latter was previously reported to alter Cav3.2 channel function and contribute to the pathogenesis of CAE and idiopathic generalized epilepsy, we evaluated the former's functional impact using two-electrode voltage clamp analysis in Xenopus laevis oocytes. While the current-voltage relationship of the D949H mutant channel was not significantly different from that of the wild-type channel, the time constant of recovery from inactivation was significantly prolonged in the D949H variant (671.7 ± 52.0 ms vs. 455.5 ± 28.2 ms), indicating moderately impaired properties of the mutant. Notably, neither the D949H nor the R788C variant was associated with epilepsy in either parent, suggesting that these variants were not sufficient to cause epilepsy on their own, and that the compound heterozygous state of CACNA1H contributed to the EMAtS phenotype in the proband. Our findings highlight the genetic complexity of EMAtS and underscore the importance of accumulated functional impacts of modifier variants in severe epileptic diseases, even when individual variants are not pathogenic.

Thyroid hormones are central to regulating metabolism, growth, and development, yet their complex interactions with socioeconomic, metabolic, and genetic factors remain understudied in diverse populations. We compared thyroid profiles - free triiodothyronine (FT3), free thyroxine (FT4), and thyroid-stimulating hormone (TSH) in Indian adolescents with anthropometric traits, metabolic markers, and socioeconomic status (SES). We observed that adolescents from higher SES backgrounds exhibited greater metabolic dysregulation, altered thyroid profiles, and abnormalities in lipid and adipokine levels. Subclinical (16.1%) and clinical hypothyroidism (1.1%) were found to be prevalent in this population but were not associated with obesity. Instead, they showed links with dyslipidemia and altered adipokine profiles. To investigate the genetic basis of thyroid traits, we conducted an exome-wide association study (ExWAS, N = 4324), and a two-staged genome-wide association study (GWAS, N = 4854). The ExWAS revealed two novel loci for TSH (GYS2 and CEP162) and fifteen novel loci for FT4, including ZNF467, P3H3, CRLF3, SPATA2L, MEFV, THNSL2, COL27A1, COL28A1, IGSF3, ZNF732, MOG, GABBR1, HPF1, LOC440563, and SPEG. The GWAS identified novel associations at near-genome-wide significance for TSH (ACTL7B) and FT4 (LINC00648, YTHDC1, and C2CD4B). We also replicated established associations in FOXE1 and IGFBP5. Our findings suggest that SES, metabolic health, and genetics jointly influence thyroid function in Indian adolescents. The identification of population-specific loci emphasizes the importance of ancestry-informed genetic studies and supports the development of precision interventions to enhance pediatric thyroid health.

Tenascin-R (TNR) is an extracellular matrix glycoprotein that is essential for the formation of perineuronal nets in the central nervous system and is critical for neurite outgrowth, synaptic plasticity, and neural stem cell proliferation and differentiation. Biallelic TNR variants were reported to cause neurodevelopmental disorders with developmental delay, hypotonia, spasticity, and a variety of motor abnormalities. Here, we describe two Japanese siblings sharing novel compound heterozygous TNR missense variants (NM_003285.3:c.[1783 G > A];[3766 C > T] p.[(Asp595Asn)];[(Arg1256Cys)]) identified by exome and Sanger sequencing. The elder brother had dystonia, while the younger sister was asymptomatic except for adult-onset restless legs syndrome. Their development and intellect were normal. A total of 15 patients, including 13 previously reported patients, showed diverse phenotypic variability and severity, even among individuals sharing the same variants, indicating variable expressivity and reduced penetrance possibly influenced by genetic or environmental modifiers. Our findings extend the clinical spectrum of TNR-related disease and highlight the need for further accumulation of clinical cases and functional studies to understand genotype-phenotype correlations and the pathogenesis of diseases.