Splicing Endonuclease Subunit Research Articles

ALLELIC HETEROGENEITY IN COLGALT2 EXPRESSION CONTRIBUTES TO OSTEOARTHRITIS RISK THROUGH DECREASED DNA METHYLATION AT MULTIPLE ENHANCERS

Purpose: Genome wide association studies (GWAS) have identified over 100 single nucleotide polymorphisms (SNP) linked to osteoarthritis (OA). Many such SNPs contribute to disease risk by affecting the expression of their target genes, acting as expression quantitative trait loci (eQTL), or by affecting DNA methylation (DNAm), marking methylation QTLs (mQTL). Detection of these QTLs helps to uncover the mechanisms driving the genetic predisposition to OA. A recent GWAS reported a novel OA-risk signal marked by rs1046934 (A>C, minor allele frequency 0.34), located within TSEN15 (tRNA Splicing Endonuclease Subunit 15).

TSEN54 missense variant in Standard Schnauzers with leukodystrophy.

We report a hereditary leukodystrophy in Standard Schnauzer puppies. Clinical signs occurred shortly after birth or started at an age of under 4 weeks and included apathy, dysphoric vocalization, hypermetric ataxia, intension tremor, head tilt, circling, proprioceptive deficits, seizures and ventral strabismus consistent with a diffuse intracranial lesion. Magnetic resonance imaging revealed a diffuse white matter disease without mass effect. Macroscopically, the cerebral white matter showed a gelatinous texture in the centrum semiovale. A mild hydrocephalus internus was noted. Histopathologically, a severe multifocal reduction of myelin formation and moderate diffuse edema without inflammation was detected leading to the diagnosis of leukodystrophy. Combined linkage analysis and homozygosity mapping in two related families delineated critical intervals of approximately 29 Mb. The comparison of whole genome sequence data of one affected Standard Schnauzer to 221 control genomes revealed a single private homozygous protein changing variant in the critical intervals, TSEN54:c.371G>A or p.(Gly124Asp). TSEN54 encodes the tRNA splicing endonuclease subunit 54. In humans, several variants in TSEN54 were reported to cause different types of pontocerebellar hypoplasia. The genotypes at the c.371G>A variant were perfectly associated with the leukodystrophy phenotype in 12 affected Standard Schnauzers and almost 1000 control dogs from different breeds. These results suggest that TSEN54:c.371G>A causes the leukodystrophy. The identification of a candidate causative variant enables genetic testing so that the unintentional breeding of affected Standard Schnauzers can be avoided in the future. Our findings extend the known genotype-phenotype correlation for TSEN54 variants.

Low mutational load in pediatric medulloblastoma still translates into neoantigens as targets for specific T-cell immunotherapy

BackgroundMedulloblastoma is the most common malignant brain tumor in childhood and adolescence. Although some patients present with distinct genetic alterations, such as mutated TP53 or MYC amplification, pediatric medulloblastoma is a tumor entity with minimal mutational load and low immunogenicity. MethodsWe identified tumor-specific mutations using next-generation sequencing of medulloblastoma DNA and RNA derived from primary tumor samples from pediatric patients. Tumor-specific mutations were confirmed using deep sequencing and in silico analyses predicted high binding affinity of the neoantigen-derived peptides to the patients’ human leukocyte antigen molecules. Tumor-specific peptides were synthesized and used to induce a de novo T-cell response characterized by interferon gamma and tumor necrosis factor alpha release of CD8+ cytotoxic T cells in vitro. ResultsDespite low mutational tumor burden, at least two immunogenic tumor-specific peptides were identified in each patient. T cells showed a balanced CD4/CD8 ratio and mostly effector memory phenotype. Induction of a CD8-specific T-cell response was achieved for the neoepitopes derived from Histidine Ammonia-Lyase (HAL), Neuraminidase 2 (NEU2), Proprotein Convertase Subtilisin (PCSK9), Programmed Cell Death 10 (PDCD10), Supervillin (SVIL) and tRNA Splicing Endonuclease Subunit 54 (TSEN54) variants. ConclusionDetection of patient-specific, tumor-derived neoantigens confirms that even in tumors with low mutational load a molecular design of targets for specific T-cell immunotherapy is possible. The identified neoantigens may guide future approaches of adoptive T-cell transfer, transgenic T-cell receptor transfer or tumor vaccination.

Three-dimensional microCT imaging of murine embryonic development from immediate post-implantation to organogenesis: application for phenotyping analysis of early embryonic lethality in mutant animals

In this work, we applied three-dimensional microCT imaging to study murine embryogenesis in the range from immediate post-implantation period (embryonic day 5.5) to mid-gestation (embryonic day 12.5) with the resolution up to 1.4 µm/voxel. Also, we introduce an imaging procedure for non-invasive volumetric estimation of an entire litter of embryos within the maternal uterine structures. This method allows for an accurate, detailed and systematic morphometric analysis of both embryonic and extra-embryonic components during embryogenesis. Three-dimensional imaging of unperturbed embryos was performed to visualize the egg cylinder, primitive streak, gastrulation and early organogenesis stages of murine development in the C57Bl6/N mouse reference strain. Further, we applied our microCT imaging protocol to determine the earliest point when embryonic development is arrested in a mouse line with knockout for tRNA splicing endonuclease subunit Tsen54 gene. Our analysis determined that the embryonic development in Tsen54 null embryos does not proceed beyond implantation. We demonstrated that application of microCT imaging to entire litter of non-perturbed embryos greatly facilitate studies to unravel gene function during early embryogenesis and to determine the precise point at which embryonic development is arrested in mutant animals. The described method is inexpensive, does not require lengthy embryos dissection and can be applicable for detailed analysis of mutant mice at laboratory scale as well as for high-throughput projects.

Autosomal-Recessive Mutations in the tRNA Splicing Endonuclease Subunit TSEN15 Cause Pontocerebellar Hypoplasia and Progressive Microcephaly

The tRNA splicing endonuclease is a highly evolutionarily conserved protein complex, involved in the cleavage of intron-containing tRNAs. In human it consists of the catalytic subunits TSEN2 and TSEN34, as well as the non-catalytic TSEN54 and TSEN15. Recessive mutations in the corresponding genes of the first three are known to cause pontocerebellar hypoplasia (PCH) types 2A-C, 4, and 5. Here, we report three homozygous TSEN15 variants that cause a milder version of PCH2. The affected individuals showed progressive microcephaly, delayed developmental milestones, intellectual disability, and, in two out of four cases, epilepsy. None, however, displayed the central visual failure seen in PCH case subjects where other subunits of the TSEN are mutated, and only one was affected by the extensive motor defects that are typical in other forms of PCH2. The three amino acid substitutions impacted the protein level of TSEN15 and the stoichiometry of the interacting subunits in different ways, but all resulted in an almost complete loss of invitro tRNA cleavage activity. Taken together, our results demonstrate that mutations in any known subunit of the TSEN complex can cause PCH and progressive microcephaly, emphasizing the importance of its function during brain development.

Safety Of a Gamma Globin Expressing Lentivirus Vector In a Non-Human Primate Model For Gene Therapy Of Sickle Cell Disease

Strategies for human gene therapy trials targeting hematopoietic stem cells (HSCs) are complicated by studies in murine models due to differences in stem cell behavior, short life-span and limited HSCs that could be transduced and transplanted when studying safety of viral vectors. Recent reports on adverse genotoxic events with integrating viral vectors in clinical trials utilizing autologous gene corrected HSCs underscores the need for safer gene transfer vectors. Non-human primates are relevant models due to similarities in the behavior of hematopoietic stem/progenitor cells, global gene expression profile, ability to assess long-term engraftment of transduced cells and safety of gene-modified HSCs, and thus could relatively accurately predict risk of vector genotoxicity. As a preclinical step towards globin gene therapy for hemoglobinopathies, we used pigtailed macaque HSC transplantation (HSCT) model to ascertain long-term safety and stable transgene expression from sGbG, a lentiviral vector (LV) encoding human γ-globin coding sequences from a β-globin promoter and locus control region (LCR). We observed upregulation of endogenous macaque fetal hemoglobin post-HSCT, which decreased to minimal levels by two years post-HSCT, a well-documented phenomenon following HSCT in humans. However, fetal hemoglobin (HbF) (comprised of macaque α and human γ-globin) expression remained steady at 12-15% even after 700 days post-HSCT. At 2.5 years post-HSCT, the HbF expression in a macaque transplanted with HSCs gene-modified with sGbG was stable in the range of 13% vs. 0.1% for control macaque; the average vector copy ranged between 0.13 and 0.28 with stable gene marking during the analysis period. In order to evaluate the LV integration site clonal population in sGbG transduced macaque repopulating cells, modified genome sequencing PCR was performed on genomic DNA from white blood cells and PCR products were sequenced. The junction sequences were mapped to the rhesus macaque genome assembly. A total of 177 unique vector insertions were retrieved at 6 months post-HSCT (early) and 102 vector insertions at 2.5 years (late) post-HSCT respectively. The relative distribution of vector insertions into chromosomes revealed a slight over-representation into Chromosome 16, both at early and late time points. Analysis of distribution of LV integrations of with respect to transcription start sites (TSS) revealed no insertions within the 2.5kb region of TSS. The frequency of insertions was concentrated near the 10-50kb window of TSS both upstream (18.6%) and downstream (15.6%) respectively. Interestingly, among the retrieved insertion sites, only 10% (17 insertions) were common at both time points, while 90% of insertions were unique at each time point, suggesting clonal fluctuations, with multiple HSC clones contributing to hematopoiesis at an early time point, and unique, HSC clones emerged at a later time point. Comparison of the top ten most frequently detected insertion sites at both time points revealed one insertion at Chromosome 16 mapping to an intron of KIAA0195 (an uncharacterized protein expressed ubiquitously), retrieved at both time points contributed to 3.27% and 9.23% of gene modified cells at early and late time points, respectively. No insertions were near MDS/EVI1, PRDM16 or HMGA2 loci. Other oncogenes and cancer associated genes were in the vicinity of some integrants; however, there was no significant clustering of insertions in gene regions. To assess the effect of insertions on flanking gene expression or putative cancer associated genes, we performed mRNAseq on whole blood RNA from sGbG macaque and two control macaques. A comparative analysis of transcript levels of >30,000 genes revealed no difference in global gene expression profile, gene insertions and genes within 300kb region of the LV insertion sites. Importantly, transcript levels of the most abundant clone observed (KIAA0195, Chr16: 70791901) and flanking genes, the tRNA splicing endonuclease subunit SEN54 and CASK interacting protein 2 differed from two control macaques analyzed by <2 fold. In summary, long-term follow-up data from a macaque that received cells gene-modified with a human γ-globin LV reveal polyclonal reconstitution of transduced cells, HSC clonal fluctuation, and a normal transcriptional profile, suggesting low risk of genotoxicity from this vector.Arumugam P, Burtner C: Equal Contribution Disclosures:No relevant conflicts of interest to declare.

Classification, diagnosis and potential mechanisms in Pontocerebellar Hypoplasia

Pontocerebellar Hypoplasia (PCH) is group of very rare, inherited progressive neurodegenerative disorders with prenatal onset. Up to now seven different subtypes have been reported (PCH1-7). The incidence of each subtype is unknown. All subtypes share common characteristics, including hypoplasia/atrophy of cerebellum and pons, progressive microcephaly, and variable cerebral involvement. Patients have severe cognitive and motor handicaps and seizures are often reported. Treatment is only symptomatic and prognosis is poor, as most patients die during infancy or childhood. The genetic basis of different subtypes has been elucidated, which makes prenatal testing possible in families with mutations. Mutations in three tRNA splicing endonuclease subunit genes were found to be responsible for PCH2, PCH4 and PCH5. Mutations in the nuclear encoded mitochondrial arginyl- tRNA synthetase gene underlie PCH6. The tRNA splicing endonuclease, the mitochondrial arginyl- tRNA synthetase and the vaccinia related kinase1 are mutated in the minority of PCH1 cases. These genes are involved in essential processes in protein synthesis in general and tRNA processing in particular. In this review we describe the neuroradiological, neuropathological, clinical and genetic features of the different PCH subtypes and we report on in vitro and in vivo studies on the tRNA splicing endonuclease and mitochondrial arginyl-tRNA synthetase and discuss their relation to pontocerebellar hypoplasia.

TSEN54 mutations cause pontocerebellar hypoplasia type 5

Pontocerebellar hypoplasia (PCH) is a group of autosomal recessive neurodegenerative disorders characterized by prenatal onset of stunted brain growth and progressive atrophy predominantly affecting cerebellum, pons and olivary nuclei, and to a lesser extent also the cerebral cortex. Six subtypes (PCH1-6) were described and genes for four types (PCH1, 2, 4 and 6) were identified. Mutations in the tRNA splicing endonuclease subunit (TSEN) genes 54, 2 and 34 are found in PCH2 and PCH4. One family with severe prenatal onset of PCH has been the only representative of PCH5 published so far, and the molecular genetic status of PCH5 has not been ascertained until now. We screened the previously reported PCH5 family for mutations in the TSEN54 gene. The PCH5 patient was found to be the result of compound heterozygosity for the common TSEN54 mutation (p.A307S) plus a novel splice site mutation. The mutations associated with PCH5 are similar to what has been reported in PCH4. Thus, PCH5, PCH4 and PCH2 represent a spectrum of clinical manifestations caused by different mutations in the TSEN genes. We, therefore, propose to classify PCH2, PCH4 and PCH5 as TSEN mutation spectrum disorders.

Clinical, neuroradiological and genetic findings in pontocerebellar hypoplasia

Pontocerebellar hypoplasia is a group of autosomal recessive neurodegenerative disorders with prenatal onset. The common characteristics are cerebellar hypoplasia with variable atrophy of the cerebellum and the ventral pons. Supratentorial involvement is reflected by variable neocortical atrophy, ventriculomegaly and microcephaly. Mutations in the transfer RNA splicing endonuclease subunit genes (TSEN54, TSEN2, TSEN34) were found to be associated with pontocerebellar hypoplasia types 2 and 4. Mutations in the mitochondrial transfer RNA arginyl synthetase gene (RARS2) were associated with pontocerebellar hypoplasia type 6. We studied a cohort of 169 patients from 141 families for mutations in these genes, of whom 106 patients tested positive for mutations in one of the TSEN genes or the RARS2 gene. In order to delineate the neuroradiological and clinical phenotype of patients with mutations in these genes, we compared this group with 63 patients suspected of pontocerebellar hypoplasia who were negative on mutation analysis. We found a strong correlation (P < 0.0005) between TSEN54 mutations and a dragonfly-like cerebellar pattern on magnetic resonance imaging, in which the cerebellar hemispheres are flat and severely reduced in size and the vermis is relatively spared. Mutations in TSEN54 are clinically associated with dyskinesia and/or dystonia and variable degrees of spasticity, in some cases with pure generalized spasticity. Nonsense or splice site mutations in TSEN54 are associated with a more severe phenotype of more perinatal symptoms, ventilator dependency and early death. In addition, we present ten new mutations in TSEN54, TSEN2 and RARS2. Furthermore, we show that pontocerebellar hypoplasia type 1 together with elevated cerebrospinal fluid lactate may be caused by RARS2 mutations.

Achieving Specific RNA Cleavage Activity by an Inactive Splicing Endonuclease Subunit Through Engineered Oligomerization

Protein–protein interaction is a common strategy exploited by enzymes to control substrate specificity and catalytic activities. RNA endonucleases, which are involved in many RNA processing and regulation processes, are prime examples of this. How the activities of RNA endonucleases are tightly controlled such that they act on specific RNA is of general interest. We demonstrate here that an inactive RNA splicing endonuclease subunit can be switched “on” solely by oligomerization. Furthermore, we show that the mode of assembly correlates with different RNA specificities. The recently identified splicing endonuclease homolog from Sulfolobus solfataricus, despite possessing all of the putatively catalytic residues, has no detectable RNA cleavage activity on its own but is active upon mixing with its structural subunit. Guided by the previously determined three-dimensional structure of the catalytic subunit, we altered its sequence such that it could potentially self-assemble thereby enabling its catalytic activity. We present the evidence for the specific RNA cleavage activity of the engineered catalytic subunit and for its formation of a functional tetramer. We also identify a higher order oligomer species that possesses distinct RNA cleavage specificity from that of previously characterized RNA splicing endonucleases.

Three-dimensional Structure Determined for a Subunit of Human tRNA Splicing Endonuclease (Sen15) Reveals a Novel Dimeric Fold

Splicing of eukaryal intron-containing tRNAs requires the action of the heterotetrameric splicing endonuclease, which is composed of two catalytic subunits, Sen34 and Sen2, and two structural subunits, Sen15 and Sen54. Here we report the solution structure of the human tRNA splicing endonuclease subunit HsSen15. To facilitate the structure determination, we removed the disordered 35 N-terminal and 14 C-terminal residues of the full-length protein to produce HsSen15(36–157). The structure of HsSen15(36–157), the first for a subunit of a eukaryal splicing endonuclease, revealed that the protein possesses a novel homodimeric fold. Each monomer consists of three α-helices and a mixed antiparallel/parallel β-sheet, arranged in a topology similar to that of the C-terminal domain of Methanocaldococcus jannaschii endonuclease. The dimeric interface is dominated by a β-barrel structure, formed by face-to-face packing of two, three-stranded β-sheets. Each of the β-sheets results from reciprocal parallel pairing of one β-strand from one subunit with two other β-strands from the symmetric subunit. The structural model provides insights into the functional assembly of the human tRNA splicing endonuclease.