Gene Variants Research Articles

Cardiac Health, Type I Collagen, and Aging in the oim/oim Mouse Model of Osteogenesis Imperfecta (OI) and a Cohort of Adults with OI.

Osteogenesis imperfecta (OI) is a heritable connective tissue disorder with marked skeletal fragility and increased recognition as a pleiotropic type I collagenopathy. The impact of OI-causing gene variants on cardiac health and lifespan is just beginning to be understood. To begin to investigate cardiac manifestations of OI-causing type I collagen variants, we utilized the osteogenesis imperfecta murine (oim/oim) model to examine survival with increased age, as well as cardiac function and collagen expression at 4 and 18 months of age. We determined male oim/oim mice had 50% decreased survival by 18 months of age compared to wildtype (Wt) littermates. Cardiac magnetic resonance imaging and echocardiography revealed 18-month-old male oim/oim mice had increased left ventricular end-diastolic and end-systolic volumes concomitant with decreased function, as well as the presence of aortic stenosis in a subset of 4- and 18- month-old male oim/oim mice compared to Wt littermates. Female oim/oim survival and cardiac function were equivalent to their Wt counterparts. Cardiac evaluations of an adult OI patient cohort corroborated increased incidences of valvular dysfunction in the OI patient population with much of the male cohort also presenting with altered left ventricular function. Little is known concerning the impact of OI causing variants on patient cardiac health and the influence of sex and age. Using an OI mouse model, we determined that 18-month-old male oim/oim mice have cardiac dysfunction with decreased lifespan, confirming the need for further investigations to understand pleiotropic extra-skeletal manifestations and disease progression in osteogenesis imperfecta.

Chimeric CYP21A1P/CYP21A2 Genes in 21-Hydroxylase Deficiency Detected by Long-Read Sequencing and Phenotypes Correlation.

21-Hydroxylase deficiency (21-OHD) is caused by pathogenic variants in CYP21A2. High homology between CYP21A2 and its pseudogene CYP21A1P causes mismatches, leading to deletions and CYP21A1P/CYP21A2 chimeras. To detect chimeric CYP21A1P/CYP21A2 in 21-OHD patients using long-read sequencing (LRS) and analyze genotype-phenotype correlations. From 2015 to 2023, 869 21-OHD patients were enrolled at Peking Union Medical College Hospital, with 113 identified harboring CYP21A2 large deletion. Long-range PCR and LRS were used to identify the types of CYP21A1P/CYP21A2 chimeric. Haplotype analysis explored founder effects, and in vitro assays assessed the functional impact of novel mutations. Clinical data were retrospectively collected and patients were classified into 4 groups based on genotypes and residual enzyme activity to study genotype-phenotype correlations. Ten types of chimeric CYP21A1P/CYP21A2 genes were identified across 119 alleles, including a novel type, CH-10. The most common, CH-1, accounted for 50.4% of all types. Haplotype analysis of 24 SNPs within CYP21A1P/CYP21A2 CH-1 revealed 25 haplotypes, with haplotype 11 being the most prevalent. Variants p.L100P and p.L301V of CYP21A2 showed enzyme activities of 1.36 ± 0.44% or 1.63 ± 0.19% for 17-hydroxyprogesterone to 11-deoxycortisol, and 1.36 ± 0.58% or 3.99 ± 1.09% for progesterone to 11-deoxycorticosterone, respectively, linked to the simple virilizing type. Genotype-phenotype consistency rates were 78.6% to 84% across the 4 groups. LRS is a comprehensive genetic testing method for 21-OHD patients, effectively detecting both CYP21A2 gene variants and CYP21A1P/CYP21A2 chimeric gene types. This study expands the CYP21A2 variant spectrum by identifying a novel chimera. Haplotype analysis revealed diverse haplotypes for each chimeric gene type, suggesting the absence of a common founder effect. The strong genotype-phenotype correlation aids genetic counseling and supports personalized treatment.

Improved Recombinant Adeno-Associated Viral Vector Production via Molecular Evolution of the Viral Rep Protein

In the dynamic field of gene therapy, recombinant adeno-associated viruses (rAAVs) have become leading viral vectors due to their safety, long-term expression, and wide-ranging cell and tissue tropism. With numerous FDA approvals and commercial products underscoring their potential, there is a critical need for efficient production processes to achieve high vector titers and quality. A major challenge in rAAV production is the efficient packaging of the genome into the viral capsid, with empty or partially filled capsids often representing over 90% of the produced material. To tackle this issue, we engineered the replication and packaging proteins of an AAV (Rep) to boost their functionality and improve vector titers. We subjected a complex Rep library derived from the AAV serotypes 1–13 to directed evolution in an AAV producer cell line. After each round of selection, single clones were analyzed, showing enrichment of specific hybrid Rep domains. Comparative analysis of these selected clones revealed considerable differences in their ability to package AAV2-based viral genomes, with hybrid Rep proteins achieving up to a 2.5-fold increase in packaging efficiency compared to their parental counterparts. These results suggest that optimizing rep gene variants through directed evolution is an effective strategy to enhance rAAV production efficiency.

ZEB2 Gene Pathogenic Variants Across Protein-Coding Regions and Impact on Clinical Manifestations: A Review

Mowat–Wilson syndrome (MWS) is a rare multi-system genetic disorder caused by variants in the Zinc Finger E-Box-Binding Homeobox 2 (ZEB2) gene. ZEB2 is an autosomal dominant gene containing ten exons within the canonical version transcript (Isoform: O60315-1). The ZEB2 gene encodes six functional domains and seven non-domain regions. This review provides a comprehensive summary of pathogenic variants and their associated MWS clinical characteristics, focusing on ZEB2 pathogenic variants, functional protein domains and non-domain regions with clinical features. A systematic literature search from 2001 to 2023 and of unpublished datasets found 191 individuals with reported clinical features and genotypic data. Genetic defects and clinical manifestations were examined that presumably impact on the structure and function of the ZEB2 gene, thereby causing multiple developmental defects with corresponding clinical presentation. This study found more nonsense ZEB2 variants observed within exon 8, which encodes four of the six protein domains: the CtBP-interacting domain (CID), homeodomain (HD), SMAD-binding domain (SMD or SBD) and part of the N-terminal zinc finger cluster (N-ZF), suggesting exon 8 plays a crucial role in this protein structure and function with multi-organ involvement. Exon 8 defects were found to be statistically more represented for gastrointestinal findings when compared to other exons, while frameshift defects were more often seen for the typical MWS face in non-domain protein regions. In contrast, nonsense or other types of variants in exons 3, 4 and 5 which encode only flanking non-domain regions were observed more often, compared with other exons excluding exon 8, to be specifically involved in the MWS facial gestalt, brain malformations, developmental delay and intellectual disability. Deleterious ZEB2 frameshift (45%) and nonsense (38%) gene variants were most often observed with deletions at 6% and missense at 5%. The genotype and clinical relationships in MWS can provide insights into prognosis, morbidity, clinical surveillance strategies and counseling of family members.

Association of functional variants in miRNA genes with the risk of coronary heart disease

Abstract Background Cardiovascular diseases, especially coronary heart disease (CHD), are currently the leading cause of mortality and morbidity. Environmental and genetic factors contribute to the pathophysiology of CHD. In this study, we investigated the associations of miRNA genes MIR222, MIR423, MIR4274, and MIR3117 with the pathogenesis of CHD. Methods Genetic inheritance models were applied to explore the association between these miRNA genes and CHD. Tetra-Primer Amplification Refractory Mutation System-Polymerase Chain Reaction (T-ARMS-PCR) was used for genotyping, and Sanger sequencing was applied for validation in selected cases. Results The codominant [χ2 = 8.058, 2; P value = 0.0178], and recessive (CC vs GC + GG) [OR = 0.4535 (0.2439–0.8669); P value = 0.0187] models demonstrated a statistically significant association between MIR222 (rs2858060) and CHD. Similarly, the co-dominant [χ2 = 6.105, 2, 2; P value = 0.0472], and additive [OR = 1.494 (1.024–2.211); P value = 0.0428] models revealed a significant association (P value < 0.05) between MIR423 (rs6505162) and CHD. In MIR4242, a novel triplet insertion (CAC) was identified exclusively in CHD samples, predicated to disrupt the stem-loop structure ofmiR-4274. However, MIR3117 showed no association with CHD, as confirmed by Sanger sequencing of 40 samples. Conclusion Our findings suggest that functional variants rs2858060, rs6505162, and a novel triplet insertion (CAC) in MIR222, MIR423, and MIR4274 respectively are strongly associated with CHD. These results underline the potential of miRNA gene variants as genetic biomarkers for CHD susceptibility.

Gene-replacement therapy in neurodevelopmental disorders: progress and challenges.

Heterozygous loss-of-function variants in the SLC6A1 gene, encoding GAT1, which is the main GABA transporter in the brain, lead to a broad spectrum of neuropsychiatric and neurodevelopmental disorders including epilepsy, developmental delay, intellectual disability, and autism. Gene-replacement strategies involving adeno-associated viruses (AAV) require the delivery of genes to specific types of neurons or areas in the brain, likely during certain developmental time points. In this issue of the JCI, Guo and colleagues from the Gray lab evaluated two promoters, three injection modalities, and various timing strategies for replacement of GAT1 via AAV type 9 in heterozygous and homozygous knockout mouse models. Intrathecal administration of vectors containing either promoter at postnatal day 5 achieved high expression and was the best tolerated approach. Notably, gene-replacement therapy failed at later disease stages, suggesting the importance of early gene reconstitution and confirming the importance of GABA metabolism in early brain development.

Progressive Retinal Degeneration and Juvenile Nephronophthisis in a Patient with Autosomal Recessive Ciliopathy: A Case Report

Introduction: Inherited retinal diseases (IRDs), particularly ciliopathies, often lead to irreversible blindness and are frequently accompanied by systemic manifestations such as nephronophthisis. Current treatment options are limited, necessitating the exploration of supplementary strategies to slow disease progression. Methods: We present a rare case from a retinal surgery clinic involving a 30-year-old male with autosomal recessive retinitis pigmentosa (ARRP) and juvenile nephronophthisis. Comprehensive ocular and genetic evaluations were conducted, followed by the implementation of nutritional interventions aimed at mitigating multi-systemic effects. Results: Genetic testing revealed pathogenic variants in CEP83, PCARE, and VPS13B genes, confirming the diagnosis of ARRP. Nutritional strategies, including omega-3 fatty acids, antioxidants, and tailored dietary modifications for renal health, were integrated alongside standard medical care. These interventions contributed to the stabilization of retinal degeneration and improved management of end-stage renal disease (ESRD). Conclusions: Integrating personalized nutritional strategies into the management of ciliopathies can enhance patient out-comes by addressing both ocular and systemic manifestations. These findings underscore the need for policy development around nutritional education and support for patients with inherited ciliopathies

Identification and functional analysis of a novel SMARCC2 splicing variant in a family with syndromic neurodevelopmental disorder

BackgroundTo determine the pathogenicity of a novel splicing variant in the SMARCC2 gene identified from a pair of adult male monozygotic twins with neurodevelopmental disorder, and to investigate the genotype-phenotype characteristics associated with SMARCC2 variants.MethodsWhole-exome sequencing (WES) was conducted on the proband, and candidate variants were validated using Sanger sequencing within the family. The effect of the identified splicing variant on SMARCC2 mRNA processing was analyzed using reverse transcription PCR (RT-PCR) and TA-clone sequencing using samples derived from the proband. The clinical features of the twins were collected and compared with the previously reported patients.ResultsThe twin adult males displayed comparable phenotypes, characterized by moderate developmental delay, intellectual and language delays, dense hair, craniofacial anomalies, scoliosis, cryptorchidism, hypotonia, behavioral abnormalities, allergic purpura and eczema, and drug allergies. WES unveiled a previously unreported heterozygous splice variant of the SMARCC2 gene (NM_003075.3: c.1496 + 1G > T). Sanger sequencing confirmed that the variant was de novo in both patients. TA-clone sequencing of the RT-PCR fragments showed that the canonical splicing variant resulted in two distinct aberrant splicing events in SMARCC2 mRNA. Specifically, approximately 80% of the mutant clones resulted from the in-frame insertion of 126 bases in intron 16, while the remaining 20% showed an in-frame deletion of exon 16 (c.1383_1496del). Crystal structure analysis showed that both in-frame alterations hindered the proper formation of the alpha helix structure within the SMARCC2 protein. An analysis of genotype-phenotype correlations indicated that our patients displayed neurological phenotypes of greater severity than those observed in patients with truncating variants, instead aligning more closely with the characteristics of the missense/in-frame variant group.ConclusionWe identified and reported a pair of twins suffering from syndromic neurodevelopmental disorders caused by a novel splicing variant of SMARCC2. Our findings further reinforce the notion that individuals harboring missense/in-frame variants in SMARCC2 are prone to experiencing more severe neurological phenotypes.

Multi-scale comparison of the formation mechanisms in landscape genes of traditional villages

The relationship between traditional village landscape genes and the geographical environment is closely intertwined, exhibiting notable spatial differences and cultural characteristics during scale transformations. To effectively elucidate the formation mechanisms of these landscape genes, it is essential to construct a multi-scale analytical framework that integrates multiple dimensions. This paper address these challenges by expanding the sample selection range and combining both qualitative and quantitative analyses of landscape genes across various scales. Subjective judgments reveal that macro conditions influence microscopic responses, which, in turn impact outcomes at the micro level. Similarly, quantitative analyses underscore the significant role of geographic factors in shaping architectural patterns, illustrating the interplay of geographic, cultural, and economic factors across different dimensions. Convergence analysis challenges the simplistic correspondence between subjective judgment and quantitative findings, indicating that macro-level geographic environmental features may not exert as substantial an influence on micro-level architectural clusters as previously assumed. Instead, there are instances where the internal spatial structure of clusters may transcends geographic constraints. The research paradigm centered on landscape genes offers a valuable approach to identifying the factors contributing to spatial disparities in traditional villages and advancing our understanding of the processes and mechanisms governing landscape gene inheritance, expression, and variation.

Harnessing Non-standard Nucleic Acids for Highly Sensitive Icosaplex (20-Plex) Detection of Microbial Threats for Environmental Surveillance.

Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. Using parallelized multitarget TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay on wastewater, soil, and human stool samples, we found 90% agreement on positive calls and 89% agreement on negative calls. Additionally, we show how long-read and short-read sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish subspecies. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.

Systematic Review, Meta-Analysis, and Population Study to Determine the Biologic Sex Ratio in Dilated Cardiomyopathy.

Dilated cardiomyopathy (DCM) appears to be diagnosed twice as often in male than in female patients. This could be attributed to underdiagnosis in female patients or sex differences in susceptibility. Up to 30% of cases have an autosomal dominant monogenic cause, where equal sex prevalence would be expected. The aim of this systematic review, meta-analysis, and population study was to assess the sex ratio in patients with DCM, stratified by genetic status, and evaluate whether this is influenced by diagnostic bias. A literature search identified DCM patient cohorts with discernible sex ratios. Exclusion criteria were studies with a small (n<100), pediatric, or peripartum population. Meta-analysis and metaregression compared the proportion of female participants for an overall DCM cohort and the following subtypes: all genetic DCM, individual selected DCM genes (TTN and LMNA), and gene-elusive DCM. Population DCM sex ratios generated from diagnostic codes were also compared with those from sex-specific means using the UK Biobank imaging cohort; this established International Classification of Diseases, 10th revision-coded, novel imaging-first, and genotype-first-determined sex ratios. A total of 99 studies, with 37 525 participants, were included. The overall DCM cohort had a 0.30 female proportion (95% CI, 0.28-0.32), corresponding to a male:female ratio (M:F) of 2.38:1. This was similar to patients with an identified DCM variant (0.31 [95% CI, 0.26-0.36]; M:F 2.22:1; P=0.56). There was also no significant difference when compared with patients with gene-elusive DCM (0.30 [95% CI, 0.24-0.37]; M:F 2.29:1; P=0.81). Furthermore, the ratio within autosomal dominant gene variants was not significantly different for TTN (0.28 [95% CI, 0.22-0.36]; M:F 2.51:1; P=0.82) or LMNA (0.35 [95% CI, 0.27-0.44]; M:F 1.84:1; P=0.41). Overall, the sex ratio for DCM in people with disease attributed to autosomal dominant gene variants was similar to the all-cause group (0.34 [95% CI, 0.28-0.40]; M:F 1.98:1; P=0.19). In the UK Biobank (n=47 549), DCM defined by International Classification of Diseases, 10th revision, coding had 4.5:1 M:F. However, implementing sex-specific imaging-first and genotype-first diagnostic approaches changed this to 1.7:1 and 2.3:1, respectively. This study demonstrates that DCM is twice as prevalent in male patients. This was partially mitigated by implementing sex-specific DCM diagnostic criteria. The persistent male excess in genotype-positive patients with an equally prevalent genetic risk suggests additional genetic or environmental drivers for sex-biased penetrance. URL: https://www.crd.york.ac.uk/prospero; Unique identifier: CRD42023451944.

A rare variant in the UQCRC1 gene, p.(Gly405Val) in three Austrian Parkinson's patients.

Variants in the UQCRC1 gene have been proposed to cause autosomal dominant Parkinson's disease with neuropathy. However, definitive confirmation of UQCRC1 as an authentic Parkinson's gene remains elusive, as follow-up studies have not yet provided conclusive evidence. 382 Austrian Parkinson's patients, particularly selected for familial and/or early onset cases, were Exome sequenced. We found three unrelated patients with a positive family history of the disease who shared the same rare missense variant in the UQCRC1 gene: c.1214G>T; p.(Gly405Val). The variant is very rare in the control population, with an allele frequency of 2×10-6 in the gnomAD database. None of the three patients carries a rare variant in a monogenic Parkinson's disease gene. We suggest that UQCRC1 p.(Gly405Val) probably contributes to the development of the disease in these three patients. Our findings provide further evidence that UQCRC1 is a 'bona fide' Parkinson's disease gene.

The interaction between the Circadian Locomotor Output Cycles Kaput and Melanocortin-4-receptor gene variants on obesity and parameters related to obesity.

Obesity is a multifactorial disease caused by an interaction between genetic, environmental and behavioral factors. Polymorphisms of the two genes Circadian Locomotor Output Cycles Kaput (CLOCK) rs1801260 and Melanocortin-4-receptor (MC4R) rs17782313, are associated with obesity. Knowledge is limited on the interaction between CLOCK, MC4R and obesity. The aim was to explore the interactions between the CLOCK and MC4R gene variants on markers related to obesity. There were 423 subjects with information on two genetic variants of two genes (CLOCK and MC4R). Their interaction was evaluated with: chronotype, sleeping duration, emotional eating, food timing, stress, dietary intake, appetite, physical activity (assessed by questionnaires), anthropometric measures of obesity (assessed by physical measurements), and also hormonal factors (assessed by ELISA). Generalized Linear Models were applied. Our results revealed that significant differences were observed between the genotypes of CLOCK rs1801260 for weight, Body Mass Index (BMI), Glucagon-like peptide-1 (GLP-1), cortisol, energy, fat, sleep duration, chronotype, appetite, depression, stress, emotional eating, physical activity, breakfast, lunch, and dinner time (p˂0.05). Also, significant differences were observed between the genotypes of MC4R rs17782313 for weight, BMI, Waist Circumference (WC), Waist to Hip Ratio (WHR), ghrelin, energy, carbohydrate, fat, appetite, depression, stress, breakfast time, and emotional eating (p˂0.05). Our findings also showed significant interactions between the CLOCK (CC)∗MC4R (CT) genotypes for higher appetite, stress and CLOCK (CT)∗ MC4R (CC) genotypes for higher fat and energy intake and CLOCK (CC)∗MC4R (CC) genotypes for higher weight, BMI, energy and fat intake, appetite, emotional eating, stress, ghrelin, cortisol and lower sleep duration and GLP-1 (p˂ 0.05). Due to the non-significance of the interaction in CLOCK (CT)∗ MC4R (CT) genotypes, it seems that the presence of a healthy arm in the CLOCK and MC4R polymorphism is necessary for the proper function of the genes. Thus, these results highlight that gene variants and their interaction should be considered in obesity assessment.

Retrospective Study of Genetic Testing Results Reveals Pathogenic Variants Beyond BRCA1/2 in Hereditary Breast and Ovarian Cancer Cases in New Brunswick: Implications for Future Care.

In Canada, founder variants in breast cancer susceptibility genes have been identified in populations residing in Québec and Newfoundland, thus demonstrating the value in characterizing the genetic profile of local populations for better clinical management. New Brunswick has a diverse, yet genetically unexplored population that includes founder Irish and Acadian ancestry, among others, and we hypothesized that this population could demonstrate potential enrichments for variants in breast cancer genes. Health records were retrospectively analyzed for 445 cases referred to the genetics clinic in Moncton, New Brunswick, their molecular results were summarized and compared to allele frequencies from similar studies in Canada. No ethnic or age-related correlation for specific variants could be identified. However, BRCA1/2 variant frequency was lower than expected in the study group and variants in other susceptibility genes such as ATM and CHEK2 were higher when compared to similar studies. This study demonstrates a distinct profile in hereditary breast cancer genetics in a previously uncharacterized population, thus adding to existing knowledge of population genetics in Atlantic Canada.

A Novel Compound Heterozygous Variant in the ABHD12 Gene Cause PHARC Syndrome in a Chinese Family: The Proband Presenting New Genotype and Phenotype.

PHARC syndrome, a rare autosomal recessive neurodegenerative disorder caused by mutations in the ABHD12 gene, is characterized by demyelinating polyneuropathy, hearing loss, ataxia, retinitis pigmentosa (RP), and early-onset cataracts. If patients are first diagnosed in the ophthalmology department, they are easily misdiagnosed as having RP or Usher syndrome. This study aimed to identify the genetic etiology and determine the clinical diagnosis of a Chinese family with suspected PHARC syndrome. Comprehensive ophthalmic examinations and systemic evaluations were conducted to confirm the phenotype. The genotype was identified through Whole Exome Sequencing (WES), and the current literature was reviewed understand better manifestations of PHARC syndrome related to pathogenic variants. The principal symptoms of the proband comprised profound sensorineural hearing loss since childhood, severe visual impairment, congenital cataracts, cone-rod dystrophy, and ataxia. WES revealed that the proband carried a compound heterozygous variant in the ABHD12 gene: M1, a known nonsense variation c.477G > A (p.Trp159Ter); and M2, a novel copy number variant with a deletion of approximately 18.10 Kbp in chromosome 20p11.21 (seq[GRCh38]del(20) (p11.21)chr20:g. 25302218_25320318del), covering exons 4-12 of the ABHD12 gene. The literature review indicated that there were 65 patients with PHARC from 30 different families. All clinical information of the described patients with PHARC syndrome and all known mutations associated with the disease to date were compiled. This study expands the spectrum of pathogenic variants and phenotype for PHARC syndrome and suggests genetic testing is necessary for a definitive diagnosis of PHARC syndrome.

Two Different NF1 Pathogenic Variants in a Family With Neurofibromatosis Type 1.

Neurofibromatosis type 1 (NF1) is a genetic disorder with an incidence of approximately one in 3,000. More than half of the patients have new de novo pathogenic variants of the NF1 gene. In most family cases, all family members share an identical NF1-variant. The aim of the study was to investigate the very rare phenomenon of de novo variants in cases of familial neurofibromatosis type 1 and highlight its implications for genetic testing and counseling. Patients underwent clinical examination in our NF outpatient clinic and genetic testing for the NF1-gene was performed by targeted sequencing. All family members were profiled by short-tandem repeat marker analysis. Additionally, a probability calculation was performed for this extremely rare event. In one NF1 family consisting of mother, father, and two sons, two different pathogenic variants of the NF1 gene were found. The father and one son share one NF1-variant and the other son carries a different de novo NF1-variant. Neither of these two NF1-variants was found in the unaffected mother. Short-tandem repeat analysis confirmed the paternity and revealed that the two sons inherited two different NF1-alleles from their father. The probability of two different NF1-variants occurring in one family is calculated as 1:9,000,000. Two different NF1-variants in one family is an extremely rare phenomenon: yet its occurrence is not impossible and therefore should be considered in genetic diagnosis and counselling. For an offspring with the indication for neurofibromatosis type 1, but lacking the familial pathogenic variant, a screening of the whole NF1-gene is necessary to detect potential new pathogenic variants and for exact diagnosis.

Variants in Chromatin Remodeling Genes Are Involved in Patients With Chiari Malformation Type 1.

Chiari malformation type 1 (CMI) is defined by the herniation of cerebellar tonsils of 5 mm or more, with possible neurological consequences, including compression of the neural tissue and/or anomalies in cerebral spinal fluid circulation. The etiology of CMI is not fully elucidated, with both genetic and environmental factors being involved. Several genes and pathways involved in bone development are pointed out like genes of the WNT, FGF, and BMP signaling pathways. More recently, the crucial role played by chromatin remodeling genes in the pathogenesis of CMI has increasingly emerged. In this paper, we discuss a familial case of CMI and a single patient, harboring variants in chromatin remodeling genes, identified by whole exome sequencing. The first is a family with three affected members and one sibling with a cerebellar tonsil herniation of < 5 mm. The three CMI patients harbor a heterozygous missense variant in the SETD2 gene, whose truncating variants are responsible for Luscan-Lumish syndrome. A second variant in HP1BP3, a gene not previously associated with human pathology, with evidence of skeletal anomalies in mice models, was found in the three patients and also in the girl with a herniation of < 5 mm. The second case is a proband with a de novo variant in KMT2A, associated with Wiedemann-Steiner syndrome, in which anomalies of the craniocervical junction are described. We highlight the importance of chromatin remodeling genes in both isolated and syndromic CMI and suggest the potential role of HP1BP3 as a possible modifier gene in CMI pathogenesis, even if this association needs to be further clarified.

The novel p.A30G SNCA pathogenic variant in Greek patients with familial and sporadic Parkinson's disease.

The p.A53T variant in the SNCA gene was considered, until recently, to be the only SNCA variant causing familial Parkinson's disease (PD) in the Greek population. We identified a novel heterozygous p.A30G (c.89 C>G) SNCA pathogenic variant in five affected individuals of three Greek families, leading to autosomal dominant PD. This study aims to further explore the presence and phenotypic expression of this variant in the Greek PD population. Restriction fragment length polymorphism (RFLPs) was used for genotyping of 664 Greek PD cases. Detailed clinical information was obtained for the carriers and p.A30G-positive samples underwent haplotype analysis. We identified 10 additional p.A30G-positive PD patients (1.5%), of whom 4 were sporadic cases (0.9%). They manifested typical Parkinsonian motor dysfunction, with a mean age of onset of 51.7 years (range: 33-62) and a broad spectrum of non-motor symptoms. The absence of affected first degree relatives in four out of ten index cases, and the presence of a phenocopy in an additional family, suggest that the p.A30G variant manifests reduced penetrance. The common haplotype among the p.A30G carriers confirmed a founder effect. Furthermore, two asymptomatic carriers were identified, with possible premotor manifestations. These findings underscore that the p.A30G SNCA pathogenic variant represents an important, albeit rare, cause of genetic PD in the Greek population. This is the first time in which a genetic synucleinopathy, with a variant in the SNCA gene, is clearly linked to an appreciable frequency of sporadic PD in a particular population.

Effect of homologous recombination deficiency on survival in patients with metastatic colorectal cancer with KRAS mutations.

252 Background: Metastatic colorectal cancer (mCRC) patients exhibit intertumoral genetic heterogeneity, making it difficult to apply precision medicine. In the molecular genetic profile of mCRC, there are relatively few other gene alterations that significantly impact treatment decisions beyond KRAS and MSI status. We aim to investigate the prognostic impact of Homologous recombination deficiency (HRD)-related genetic alterations in mCRC patients, focusing on how mutation status influences on patient outcomes. Methods: The analysis included 364 mCRC patients who underwent comprehensive genomic profiling at Korea University Anam Hospital from Sep. 2016 to Dec. 2020. HRD was defined by the presence of pathogenic variants in genes including ATM, ATR, BARD1, BRCA1/2, BRIP1, CDK12, CHEK2, FANCA, MRE11A, PALB2, RAD50/51. Overall survival (OS) and progression-free survival (PFS) were evaluated using the Kaplan-Meier method. Multivariate Cox proportional hazards regression analyses were performed to assess the independent impact of HRD status. Results: Of the total cohort, 181 of patients (49.78%) harbored KRAS mutations. HRD gene mutations were identified in 38 of patients (10.4%) of patients, predominantly in ATM, BRCA 1/2, ARID1A genes. KRAS-HRD co-mutations were present in 18 of patients (4.7%). There is no significant difference in HRD status between the KRAS mutant and wild-type groups (p=0.73). While first-line treatment PFS was independent of KRAS mutational status (wt 10.8 vs. mut 9.6 months, p=0.31), it was significantly associated with HRD gene mutation status (16.2 vs. 10.6 months, p=0.001). OS was similar with KRAS mutations (34.7 vs. 32.9 months, p=0.72) and HRD mutations (34.7 vs. 39.1 months, p=0.73). However, patients with both KRAS and HRD mutations had significantly worse OS compared to those with either KRAS and HRD mutation (21.3 vs. 36.7 vs. 65.3 months, p=0.034, &lt;0.001). A multivariate analysis was performed to evaluate factors affecting OS in mCRC patients. Among the variables, metastasectomy, which 44% of patients underwent, had a significantly low HR (=0.28) and would contributed to more favorable outcomes when evaluating OS. Neither KRAS nor HRD mutation alone was a significant prognostic factor, but their co-mutation was significantly associated with poor survival (HR=2.39, p=0.048). Conclusions: Poor OS in patients with KRAS-HRD co-mutations, despite metastasectomy, highlights the need for additional treatment strategies beyond surgery. Future studies with larger sample sizes and analyses stratified by metastasectomy status are necessary to strengthen these findings. Variables HR (95% CI) p-value Metastasis site Liver 2.16 (1.60 – 2.92) &lt; 0.001 Peritoneum 1.52 (1.01 – 2.11) 0.013 Bone 1.69 (0.96 – 2.97) 0.067 Metastasectomy 0.28 (0.47 – 0.74) &lt; 0.001 KRAS 1.03 (0.77 – 1.37) 0.826 HRD 0.75 (0.40 – 1.41) 0.367 Co-mutation 2.39 (1.01 – 5.66) 0.048

Exploration of novel biomarkers and novel therapies for immune checkpoint inhibitors (ICIs) in genetic variants of esophageal squamous cell carcinoma (ESCC): A study of 1,059 Japanese cases.

495 Background: In Japan, cancer genome profiling (CGP) tests will be covered by insurance in 2019, and more than 1,000 ESCC cases have been accumulated in the national database. ICIs are currently the key drugs for esophageal cancer, and MSI and TMB status can work as biomarkers for ICIs in solid tumors. Therefore, to improve the prognosis of esophageal squamous cell carcinoma (ESCC), we aim to search for gene variants that may predict the efficacy of ICIs and explore the possibility of new treatment from genetic data accumulated in the Japanese nation-wide C-CAT database. Methods: We retrospectively analyzed 1,059 ESCC cases from C-CAT data accumulated from June 2019 to February 2024. We used the registered clinical and genetic information to examine gene variants and carcinogenic pathways that could serve as biomarkers for ICIs. Results: Of the 1059, 152 (14.4%) had TMB-H and 3 (0.3%) had MSI-H, with a median TMB of 5.0 Muts/Mb (range: 0-268). XPO1 and TP53 were found to be positively and negatively correlated as genes affecting TTF in nivolumab monotherapy (FDR P value &lt; 0.01). TMB has the potential to be a biomarker for ICI, but TMB was significantly higher in the group with variants in the ARID family ( ARID2 , ARID1A plus ARID5B ) (median TMB 5.0 vs 8.0 Muts/Mb, P&lt;0.001). In addition, 709 patients (66.9%) had any variants in three pathways (TP53, RTK and cell cycle), which are thought to be involved in the carcinogenesis of ESCC. PIK/Akt/mTOR and epigenetic modulation pathways were also found to be abnormal in many cases, and abnormalities in the epigenetic modification pathway were found to contribute significantly to TMB-H (FDR P value&lt;0.01, Logarithmic value=19.2). Conclusions: This is the first case-specific report on the relationship between mutations in the ARID family and TMB in ESCC and the signalling pathways leading to carcinogenesis. In the present study, the association between the ARID family and TMB, and between abnormalities in the epigenetic modification pathway and TMB, which has been previously reported in other cancer types but not in esophageal cancer, suggests that multiple pathological mutations including these may be new biomarkers for ICI in 1059 Japanese patients. Furthermore, multiple pathways are often involved in ESCC carcinogenesis at the same time, and a separate, combined approach that takes these into account may be necessary in the development of new drugs.