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Acta Neuropathologica Dec 2023Glioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to...
Glioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to specific treatments. Through prospective genomic profiling of 459 consecutive primary treatment-naïve IDH-wildtype glioblastomas in adults, we identified a unique subgroup (2%, 9/459) defined by somatic hypermutation and DNA replication repair deficiency due to biallelic inactivation of a canonical mismatch repair gene. The deleterious mutations in mismatch repair genes were often present in the germline in the heterozygous state with somatic inactivation of the remaining allele, consistent with glioblastomas arising due to underlying Lynch syndrome. A subset of tumors had accompanying proofreading domain mutations in the DNA polymerase POLE and resultant "ultrahypermutation". The median age at diagnosis was 50 years (range 27-78), compared with 63 years for the other 450 patients with conventional glioblastoma (p < 0.01). All tumors had histologic features of the giant cell variant of glioblastoma. They lacked EGFR amplification, lacked combined trisomy of chromosome 7 plus monosomy of chromosome 10, and only rarely had TERT promoter mutation or CDKN2A homozygous deletion, which are hallmarks of conventional IDH-wildtype glioblastoma. Instead, they harbored frequent inactivating mutations in TP53, NF1, PTEN, ATRX, and SETD2 and recurrent activating mutations in PDGFRA. DNA methylation profiling revealed they did not align with known reference adult glioblastoma methylation classes, but instead had unique globally hypomethylated epigenomes and mostly classified as "Diffuse pediatric-type high grade glioma, RTK1 subtype, subclass A". Five patients were treated with immune checkpoint blockade, four of whom survived greater than 3 years. The median overall survival was 36.8 months, compared to 15.5 months for the other 450 patients (p < 0.001). We conclude that "De novo replication repair deficient glioblastoma, IDH-wildtype" represents a biologically distinct subtype in the adult population that may benefit from prospective identification and treatment with immune checkpoint blockade.
Topics: Adult; Humans; Child; Middle Aged; Aged; Glioblastoma; Immune Checkpoint Inhibitors; Homozygote; Prospective Studies; Brain Neoplasms; Sequence Deletion; Mutation; Isocitrate Dehydrogenase
PubMed: 38079020
DOI: 10.1007/s00401-023-02654-1 -
Cellular Signalling Aug 2023EHMT1 is an epigenetic factor with histone methyltransferase activity that appears mutated in Kleefstra syndrome, a neurodevelopmental genetic disorder characterized by...
EHMT1 is an epigenetic factor with histone methyltransferase activity that appears mutated in Kleefstra syndrome, a neurodevelopmental genetic disorder characterized by developmental delay, intellectual disability, and autistic-like features. Despite recent progress in the study of the function of this gene and the molecular etiology of the disease, our knowledge of how EHMT1 haploinsufficiency causes Kleefstra syndrome is still very limited. Here, we show that EHMT1 depletion in RPE1 cells leads to alterations in the morphology and distribution of different subcellular structures, such as the Golgi apparatus, the lysosomes and different cell adhesion components. EHMT1 downregulation also increases centriolar satellites detection, which may indicate a role for EHMT1 in centrosome functioning. Furthermore, the migration process is also altered in EHMT1 depleted cells, which show reduced migration capacity. We consider that the described phenotypes could open new possibilities for understanding the functional impact of EHMT1 haploinsufficiency in Kleefstra syndrome, helping to elucidate the link between epigenetic regulation and the underlying cellular mechanisms that result in this neurodevelopmental disorder. This knowledge could be relevant not only for the treatment of this syndrome, but also for other neurodevelopmental conditions that could share similar deregulated cellular pathways.
Topics: Humans; Epigenesis, Genetic; Chromosome Deletion; Intellectual Disability; Craniofacial Abnormalities; Histone-Lysine N-Methyltransferase
PubMed: 37257768
DOI: 10.1016/j.cellsig.2023.110734 -
Frontiers in Cellular and Infection... 2023Banna virus (BAV), a potential pathogen that may cause human encephalitis, is the prototype species of genus within the family , and has been isolated from a variety of...
INTRODUCTION
Banna virus (BAV), a potential pathogen that may cause human encephalitis, is the prototype species of genus within the family , and has been isolated from a variety of blood-sucking insects and mammals in Asia.
METHODS
, , and were collected overnight in Yunnan, China, during 2016-2023 using light traps. Virus was isolated from these collected blood-sucking insects and grown using (C6/36) cells. Preliminary identification of the virus was performed by agarose gel electrophoresis (AGE). The full genome sequences of the BAVs were determined by full-length amplification of cDNAs (FLAC) and sequenced using next-generation sequencing.
RESULTS
In this study, 13 strains BAV were isolated from , and . Their viral genome consisted of 12 segments of double-stranded RNA (dsRNA), and with three distinct distribution patterns. Sequence analysis showed that Seg-5 of four strains (SJ_M46, SJ_M49, JC_M19-13 and JC_C24-13) has 435 bases nucleotide sequence insertions in their ORF compared to other BAVs, resulting in the length of Seg-5 up to 2128 nt. There are 34 bases sequence deletion in Seg-9 of 3 strains (WS_T06, MS_M166 and MS_M140). Comparison of the coding sequences of VP1, VP2, VP5, VP9 and VP12 of the 13 BAV strains, the results show that VP1, VP2 and VP12 are characterised by high levels of sequence conservation, while VP9 is highly variable, under great pressure to adapt and may be correlated with serotype. While also variable, VP5 appears to be under less adaptive pressure than VP9. Additionally, phylogenetic analysis indicates that the 13 BAV strains locate in the same evolutionary cluster as BAVs isolated from various blood-sucking insects, and are clustered according to geographical distribution.
CONCLUSION
The data obtained herein would be beneficial for the surveillance of evolutionary characteristics of BAV in China and neighboring countries as well as extend the knowledge about its genomic diversity and geographic distribution.
Topics: Animals; Aedes; Ceratopogonidae; China; Coltivirus; Genome, Viral; Mammals; Phylogeny; Ticks
PubMed: 38035340
DOI: 10.3389/fcimb.2023.1283580 -
Cell Reports Aug 2023Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the...
Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the effect on spontaneous mutagenesis of three main TLS control mechanisms: REV1 and PCNA ubiquitylation that recruit TLS polymerases and PRIMPOL that creates post-replicative gaps. Using whole-genome sequencing of cultured human RPE-1 cell clones, we find that REV1 and Polymerase ζ are wholly responsible for one component of base substitution mutagenesis that resembles homologous recombination deficiency, whereas the remaining component that approximates oxidative mutagenesis is reduced in PRIMPOL cells. Small deletions in short repeats appear in REV1PCNA double mutants, revealing an alternative TLS mechanism. Also, 500-5,000 bp deletions appear in REV1 and REV3L mutants, and chromosomal instability is detectable in REV1PRIMPOL cells. Our results indicate that TLS protects the genome from deletions and large rearrangements at the expense of being responsible for the majority of spontaneous base substitutions.
PubMed: 37498746
DOI: 10.1016/j.celrep.2023.112887 -
BMC Medical Genomics Sep 2023To report novel pathogenic variants of X-linked genes in five Chinese families with early-onset high myopia (eoHM) by using whole-exome sequencing and analyzing the...
PURPOSE
To report novel pathogenic variants of X-linked genes in five Chinese families with early-onset high myopia (eoHM) by using whole-exome sequencing and analyzing the phenotypic features.
METHODS
5 probands with X-linked recessive related eoHM were collected in Ningxia Eye Hospital from January 2021 to June 2022. The probands and their family members received comprehensive ophthalmic examinations,and DNA was abstracted from patients and family members. Whole-exome sequencing was performed on probands to screen the causative variants, and all suspected pathogenic variants were determined by Sanger sequencing and co-segregation analysis was performed on available family members. The pathogenicity of novel variants was predicted using silico analysis and evaluated according to ACMG guidelines. RT-qPCR was used to detect differences in the relative mRNAs expression of candidate gene in mRNAs available with the proband and family members in the pedigree 2. The relationship between genetic variants and clinical features was analyzed.
RESULTS
All probands were male, and all pedigrees conformed to an X-linked recessive inheritance pattern. They were diagnosed with high myopia at their first visits between 4 and 7 years old. Spherical equivalent ranged between - 6.00D and - 11.00D.The five novel hemizygous variants were found in the probands, containing frameshift deletion variant c.797_801del (p.Val266Alafs*75) of OPN1LW gene in the pedigree 1, nonsense variant c.513G > A (p.Trp171Ter)of RP2 gene in the pedigree 2, missense variant c.98G > T (p.Cys33Phe) of GPR143 gene in the pedigree 3, frameshift deletion variant c.1876_1877del (p.Met626Valfs*22) of FRMD7 gene in the pedigree 4 and inframe deletion variant c.670_ 675del (p.Glu192_ Glu193del) of HMGB3 gene in the pedigree 5. All variants were classified as pathogenic or likely pathogenic by the interpretation principles of HGMD sequence variants and ACMG guidelines. In family 2, RT-qPCR showed that the mRNA expression of RP2 gene was lower in the proband than in other normal family members, indicating that such variant caused an effect on gene function at the mRNA expression level. Further clinical examination showed that pedigrees 1, 2, 3, and 4 were diagnosed as X-linked recessive hereditary eye disease with early-onset high myopia, including quiescent cone dysfunction, retinitis pigmentosa, ocular albinism, and idiopathic congenital nystagmus respectively. The pedigree 5 had eoHM in the right eye and ptosis in both eyes.
CONCLUSION
In this paper,we are the first to report five novel hemizygous variants in OPN1LW, RP2, GPR143, FRMD7, HMGB3 genes are associated with eoHM. Our study extends the genotypic spectrums for eoHM and better assists ophthalmologists in assessing, diagnosing, and conducting genetic screening for eoHM.
Topics: Child; Child, Preschool; Humans; Male; Cytoskeletal Proteins; East Asian People; Genes, X-Linked; Membrane Proteins; Mutation; Myopia; Age of Onset; Exome Sequencing; Pedigree
PubMed: 37749571
DOI: 10.1186/s12920-023-01665-x -
Neuro-oncology Sep 2023
Topics: Humans; Glioma; Brain Neoplasms; Isocitrate Dehydrogenase; Mutation; Astrocytoma; Cyclin-Dependent Kinase Inhibitor p16
PubMed: 37329568
DOI: 10.1093/neuonc/noad095 -
BMC Plant Biology Jul 2023The structural basis of chloroplast and the regulation of chloroplast biogenesis remain largely unknown in maize. Gene mutations in these pathways have been linked to...
BACKGROUND
The structural basis of chloroplast and the regulation of chloroplast biogenesis remain largely unknown in maize. Gene mutations in these pathways have been linked to the abnormal leaf color phenotype observed in some mutants. Large scale structure variants (SVs) are crucial for genome evolution, but few validated SVs have been reported in maize and little is known about their functions though they are abundant in maize genomes.
RESULTS
In this research, a spontaneous maize mutant, pale green leaf-shandong (pgl-sd), was studied. Genetic analysis showed that the phenotype of pale green leaf was controlled by a recessive Mendel factor mapped to a 156.8-kb interval on the chromosome 1 delineated by molecular markers gy546 and gy548. There were 7 annotated genes in this interval. Reverse transcription quantitative PCR analysis, SV prediction, and de novo assembly of pgl-sd genome revealed that a 137.8-kb deletion, which was verified by Sanger sequencing, might cause the pgl-sd phenotype. This deletion contained 5 annotated genes, three of which, including Zm00001eb031870, Zm00001eb031890 and Zm00001eb031900, were possibly related to the chloroplast development. Zm00001eb031870, encoding a Degradation of Periplasmic Proteins (Deg) homolog, and Zm00001eb031900, putatively encoding a plastid pyruvate dehydrogenase complex E1 component subunit beta (ptPDC-E1-β), might be the major causative genes for the pgl-sd mutant phenotype. Plastid Degs play roles in protecting the vital photosynthetic machinery and ptPDCs provide acetyl-CoA and NADH for fatty acid biosynthesis in plastids, which were different from functions of other isolated maize leaf color associated genes. The other two genes in the deletion were possibly associated with DNA repair and disease resistance, respectively. The pgl-sd mutation decreased contents of chlorophyll a, chlorophyll b, carotenoids by 37.2%, 22.1%, and 59.8%, respectively, and led to abnormal chloroplast. RNA-seq revealed that the transcription of several other genes involved in the structure and function of chloroplast was affected in the mutant.
CONCLUSIONS
It was identified that a 137.8-kb deletion causes the pgl-sd phenotype. Three genes in this deletion were possibly related to the chloroplast development, which may play roles different from that of other isolated maize leaf color associated genes.
Topics: Zea mays; Plant Proteins; Chlorophyll A; Photosynthesis; Chlorophyll; Chloroplasts; Phenotype; Plant Leaves; Mutation; Gene Expression Regulation, Plant
PubMed: 37452313
DOI: 10.1186/s12870-023-04360-2 -
The Chinese Journal of Dental Research Mar 2024To analyse the aetiology and pathogenesis of Gorlin-Goltz syndrome (GS; also known as nevoid basal cell carcinoma syndrome [NBCCS] or basal cell nevus syndrome [BCNS])...
OBJECTIVE
To analyse the aetiology and pathogenesis of Gorlin-Goltz syndrome (GS; also known as nevoid basal cell carcinoma syndrome [NBCCS] or basal cell nevus syndrome [BCNS]) in a Chinese family.
METHODS
Whole-exome sequencing (WES) was performed on genomic DNA samples from the subjects in a family, followed by the investigation of pathogenesis via bioinformatic approaches and conformational analysis.
RESULTS
A novel heterozygous non-frameshift deletion patched 1 (PTCH1) [NM_000264: c.3512_3526del (p.1171_1176del)] was identified by WES and further validated by Sanger sequencing. Bioinformatic and conformational analysis showed that the mutation caused altered PTCH1 protein structure, which may be related to functional abnormalities.
CONCLUSION
This study expands the mutation spectrum of PTCH1 in GS and facilitates the early diagnosis and screening of GS. PTCH1 [c.3512_3526del (p.1171_1176del)] may cause structural abnormalities and functional disabilities, leading to GS in families.
Topics: Humans; Basal Cell Nevus Syndrome; Causality; Computational Biology; Mutation; East Asian People
PubMed: 38546523
DOI: 10.3290/j.cjdr.b5128601 -
Virus Genes Aug 2023The critical Epstein‒Barr virus (EBV)-encoded latent membrane protein 1 (LMP-1) and BamHI fragment H rightward open reading frame 1 (BHRF-1) genes affect EBV-mediated...
Genetic variability and mutation of Epstein‒Barr virus (EBV)-encoded LMP-1 and BHRF-1 genes in EBV-infected patients: identification of precise targets for development of personalized EBV vaccines.
The critical Epstein‒Barr virus (EBV)-encoded latent membrane protein 1 (LMP-1) and BamHI fragment H rightward open reading frame 1 (BHRF-1) genes affect EBV-mediated malignant transformation and virus replication during EBV infection. Therefore, these two genes are considered ideal targets for EBV vaccine development. However, gene mutations in LMP-1 and BHRF-1 in different cohorts may affect the biological functions of EBV, which would seriously hinder development of personalized vaccines for EBV. In the present study, by performing nested polymerase chain reaction (nested PCR) and DNA sequence techniques, we analyzed the nucleotide variability and phylogeny of LMP-1 containing a 30 bp deletion region (del-LMP-1) and BHRF-1 in EBV-infected patients (N = 382) and healthy persons receiving physical examination (N = 98; defined as the control group) in Yunnan Province, China. Three BHRF-1 subtypes were identified in this study: 79V88V, 79L88L, and 79V88L, with mutation frequencies of 58.59%, 24.24%, and 17.17%, respectively. Compared with the control group, the distribution of BHRF-1 subtypes of the three groups showed no significant difference, suggesting that BHRF-1 is highly conserved in EBV-related samples. In addition, a short fragment of del-LMP-1 was found in 133 cases, and the nucleotide variation rate was 87.50% (133/152). For del-LMP-1, a significant distribution in three groups was detected, as characterized by a high mutation rate. In conclusion, our study illustrates gene variability and mutations of EBV-encoded del-LMP-1 and BHRF-1 in clinical samples. Highly mutated LMP-1 might be associated with various types of EBV-related diseases, indicating that BHRF-1 combined with LMP-1 may be used as an ideal target for development of EBV personalized vaccines.
Topics: Humans; China; Epstein-Barr Virus Infections; Herpesvirus 4, Human; Mutation; Nucleotides; Vaccines; Viral Matrix Proteins; Viral Proteins
PubMed: 37243920
DOI: 10.1007/s11262-023-02006-x -
European Journal of Medical Genetics Jul 2023The manifestations of Phelan-McDermid syndrome (PMS) are complex, warranting expert and multidisciplinary care in all life stages. In the present paper we propose...
The manifestations of Phelan-McDermid syndrome (PMS) are complex, warranting expert and multidisciplinary care in all life stages. In the present paper we propose consensus recommendations on the organization of care for individuals with PMS. We indicate that care should consider all life domains, which can be done within the framework of the International Classification of Functioning, Disability and Health (ICF). This framework assesses disability and functioning as the outcome of the individual's interactions with other factors. The different roles within care, such as performed by a centre of expertise, by regional health care providers and by a coordinating physician are addressed. A surveillance scheme and emergency card is provided and disciplines participating in a multidisciplinary team for PMS are described. Additionally, recommendations are provided for transition from paediatric to adult care. This care proposition may also be useful for individuals with other rare genetic neurodevelopmental disorders.
Topics: Adult; Humans; Child; Consensus; Transition to Adult Care; Chromosome Disorders; Chromosome Deletion; Chromosomes, Human, Pair 22
PubMed: 37003574
DOI: 10.1016/j.ejmg.2023.104747