Splice Acceptor Site Mutation Research Articles

Functional Analyses of BTK Mutations in Follicular Lymphoma

Introduction: Follicular lymphoma (FL) constitutes the second most common non-Hodgkin's lymphoma in the Western world. Recently, novel mutations in the Bruton's Tyrosine Kinase (BTK) have been identified in FL (Krysiak et al, Blood 2017). Additional mutations in other components of BCR signaling pathways in FL have been reported as well but functional consequences have not been fully explored.Methods: Using a combination of WES on N=82 FLand BTK resequencing in an extended FL panel we uncovered novel BTK mutations in FL. These BTK mutations are all distinct from the previously identified mutations suggesting that a full complement of BTK mutations has not yet been identified. Using crispr-Cas9-mediated BTK gene targeting in multiple lymphoma cell lines, we generated novel BTK-/- null lines. We introduced all BTK mutations by site-directed mutagenesis into a reference BTK cDNA. Subsequently, we re-introduced HA-tagged wild type and mutated BTK constructs using lentiviral transduction into the BTK-/- cell lines and also into BTK-/- DT40 cells. We measured signal transduction pathway components following BCR cross linking. The location of BTK mutations was modeled onto a 3D-model assembled from various published BTK substructures.Results: Mutations in BTK are distributed along the entire length of the gene and are targeting the PH-, SH2- and catalytic domain, with the catalytic domain carrying the majority of BTK mutations. Interestingly, occasional frame shift mutations as reported and a splice acceptor site mutation by genetic criteria suggest gene inactivation. The 3D modeling data show that all BTK mutations are on the surface of the BTK protein within the various functional domains. The quantitation of BTK protein after reconstitution into various engineered BTK-/- cell lines uncovered lower steady state levels of various mutants especially for mutations targeting the catalytic domain. PLCγ2 remains the best studied BTK substrate and various sites have been reported to be phosphorylated by BTK in vivo (PLCγ2 amino acids 753, 759 and 1217). Following BCR crosslinking in engineered BTK-/- lymphoma cell lines we found only a modest reduction in the phosphorylation of PLCγ2 residue 759 or 1217 demonstrating that these sites are under the control of various tyrosine kinases and not exclusively targeted by BTK. After BCR crosslinking in the BTK-/- cells lines we detected a substantial increase in PLCy2 residues 759 or 1217 phosphorylation over baseline and this increase was abolished by ibrutinib pre-treatment. Therefore, PLCγ2 residue 759 or 1217 phosphorylation is due to multiple BCR stimulated and ibrutinib sensitive tyrosine kinases. In engineered BTK-/- lymphoma cell lines reconstituted with HA-tagged wild type and mutated BTK we did not detect major effects by the BTK mutants on the phosphorylation state of PLCγ2 residue 759 or 1217. In addition, phosphorylation of BTK at residue 223 (a major autophosphorylation site) was reduced or absent in multiple BTK mutants. Summarizing these findings, FL-associated BTK mutations do not activate the BTK kinase; instead, multiple BTK mutants are inactivating.Focusing on BCR-regulated signaling pathways, we measured ERK and AKT phosphorylation in the engineered BTK-/- lymphoma cell lines reconstituted with HA-tagged wild type and mutated BTK. Following BCR crosslinking, we detected increased p-AKT-473 phosphorylation in most BTK mutants in a total of 4 separate cell lines. In contrast, p-ERK was largely unaffected. Recent reports implicated AKT activation as a major factor in tonic BCR signaling in germinal center type DLBCL. We did not detect elevated AKT phosphorylation prior to BCR stimulation in our BTK reconstituted cell systems but an exaggerated response following BCR engagement. The effects of BTK mutations on protein-protein interactions within the BTK signalosome as well as effects on sensitivity to ibrutinib will be updated at the meeting.Conclusion : Our initial efforts at functional characterization of FL-associated BTK mutations uncovered that despite reduced stability and impaired catalytic activity most BTK mutations resulted in enhanced AKT activation following BCR crosslinking. Given the established pro-growth and pro-survival function of AKT, the data provide a clear reason why FL would select for such mutations. DisclosuresPhillips:Incyte: Other: Travel/Expenses; Pharmacyclics: Consultancy; KITE: Consultancy; Seattle Genetics: Consultancy. Malek:Abbvie: Equity Ownership; Janssen R&D: Honoraria, Research Funding; Pharmacyclics: Honoraria, Research Funding.

A novel pathogenic splice acceptor site germline mutation in intron 14 of the APC gene in a Chinese family with familial adenomatous polyposis.

Familial adenomatous polyposis (FAP) is an autosomal dominant precancerous condition, clinically characterized by the presence of multiple colorectal adenomas or polyps. Patients with FAP has a high risk of developing colorectal cancer (CRC) from these colorectal adenomatous polyps by the mean age of diagnosis at 40 years. Germline mutations of the APC gene cause familial adenomatous polyposis (FAP). Colectomy has recommended for the FAP patients with significant polyposis. Here, we present a clinical molecular study of a four generation Chinese family with FAP. Clinical diagnosis of FAP has been done according to the phenotype, family history and medical records. Patient's blood samples were collected and genomic DNA was extracted. In order to identify the pathogenic mutation underlying the disease phenotype targeted next-generation sequencing and confirmatory sanger sequencing has undertaken. Targeted next generation sequencing identified a novel heterozygous splice-acceptor site mutation [c.1744-1G>A] in intron 14 of APC gene, which is co-segregated with the FAP phenotypes in the proband and amongst all the affected family members. This mutation is not present in unaffected family members and in normal healthy controls of same ethnic origin. According to the LOVD database for Chinese colorectal cancer patients, in Chinese population, 60% of the previously reported APC gene mutations causes FAP, are missense mutations. This novel splice-acceptor site mutation causing FAP in this Chinese family expands the germline mutation spectrum of the APC gene in the Chinese population.

Expanding the genetic spectrum of ANOS1 mutations in patients with congenital hypogonadotropic hypogonadism.

What is the prevalence and functional consequence of ANOS1 (KAL1) mutations in a group of men with congenital hypogonadotropic hypogonadism (CHH)? Three of forty-two (7.1%) patients presented ANOS1 mutations, including a novel splice site mutation leading to exon skipping and a novel contiguous gene deletion associated with ichthyosis. CHH is characterized by lack of pubertal development and infertility, due to deficient production, secretion or action of GnRH, and can be associated with anosmia/hyposmia (Kallmann syndrome, KS) or with a normal sense of smell (normosmic CHH). Mutations in the anosmin-1 (ANOS1) gene are responsible for the X-linked recessive form of KS. This cross-sectional study included 42 unrelated men with CHH (20 with KS and 22 with normosmic CHH). Patients were screened for mutations in the ANOS1 gene by DNA sequencing. Identified mutations were further investigated by RT-PCR analysis and multiplex ligation-dependent probe amplification (MLPA) analysis. Hemizygous mutations were identified in three (7.1%) KS cases: a novel splice acceptor site mutation (c.542-1G>C), leading to skipping of exon 5 in the ANOS1 transcript in a patient with self-reported normosmia (but hyposmic upon testing); a recurrent nonsense mutation (c.571C>T, p.Arg191*); and a novel 4.8 Mb deletion involving ANOS1 and eight other genes (VCX3B, VCX2, PNPLA4, VCX, STS, HDHD1, VCX3A and NLGN4X) in KS associated with ichthyosis. Objective olfactory testing was not performed in all cases of self-reported normosmia and this may have underestimated the olfactory deficits. This study further expands the spectrum of known genetic defects associated with CHH and suggests that patients with self-reported normal olfactory function should not be excluded from ANOS1 genetic testing. This study was funded by the Portuguese Foundation for Science and Technology. The authors have no conflicts of interest. N/A.

IGHMBP2-related clinical and genetic features in a cohort of Chinese Charcot–Marie–Tooth disease type 2 patients

IGHMBP2 mutations had been exclusively associated with spinal muscular atrophy with respiratory distress type I. However, increasing AR-CMT2S cases without respiratory failure caused by IGHMBP2 mutations have been reported in the past two years. We detected IGHMBP2 mutations in a cohort of Chinese CMT2 patients using genes panel testing, polymerase chain reaction and Sanger sequencing. We found four families with autosomal recessive IGHMBP2 mutations, and the frequency of IGHMBP2 mutations is 6.5% in CMT2 without dominant inheritance. We detected a homozygous variant c.1235 + 3A > G in Family 1, compound heterozygous variants c.1737C > A and c.2597_2598delAG in Family 2, compound heterozygous variants c.1489G > A and c.2356delG in Family 3, compound heterozygous variants c.1909C > T and c.1061-2A > G in Family 4. According to the standards and guidelines of the American College of Medical Genetics and Genomics, all the above variants were classified as pathogenic. Four mutations, c.1489G > A, c.2356delG, c.2597_2598delAG and c.1061-2A > G, are reported for the first time. The novel splice acceptor site mutation c.1061-2A > G resulted in deletion of 175 bp, and it was predicted to lead to a frameshift after codon 354 with a premature termination at codon 364. In conclusion, mutation screening of IGHMBP2 should be especially considered in AR-CMT2 and sporadic CMT2 patients.

A Novel Splice-Acceptor Site Mutation in GRN (c.709-2 A>T) Causes Frontotemporal Dementia Spectrum in a Large Family from Southern Italy

Heterozygous loss of function mutations in granulin represent a significant cause of frontotemporal lobar degeneration with ubiquitin and TDP-43 inclusions (FTLD-TDP). We report a novel GRN splice site mutation (c.709-2 A>T), segregating with frontotemporal dementia spectrum in a large family from southern Italy. The GRN c.709-2 A>T is predicted to result in the skipping of exon 8, leading to non-sense mediated mRNA decay. Moreover, the PGRN plasma levels in the GRN c.709-2 A>T carriers were significantly lower (24 ng/ml) compared to controls (142.7 ng/ml) or family members non-carriers (82.0 ng/ml) (p-value = 0.005, Kruskal Wallis), suggesting progranulin haploinsufficiency. We do not report any potential pathogenic GRN mutation in a follow-up cohort composed of 6 FTD families and 43 sporadic FTD cases, from the same geographic area. Our study suggests that GRN (c.709-2 A>T) is a novel and likely very rare cause of FTD in this Italian cohort. Finally, in line with previous studies, we show that GRN haploinsufficiency leads to a heterogeneous clinical picture, and plasma progranulin levels may be a reliable tool to identify GRN loss of function mutations. However, given that a) genetic and environmental factors, gender, and age may regulate PGRN plasma levels and b) plasma progranulin levels may not reflect PGRN levels in the central nervous system, we suggest that the measurement of progranulin in the plasma should always be coupled with genetic screening of GRN for mutations.

A novel splice acceptor site mutation (IVS11 G > A) of PEPD gene causing prolidase deficiency associated with hyperimmunoglobulinemia E

Prolidase deficiency is a rare, autosomal-recessive, inborn error of collagen metabolism. We report a 20-year old girl with prolidase deficiency, who presented with spontaneous, refractory, lower extremity ulceration, elevated immunoglobulin E levels (IgE) and normal intellect. Hyperimmunoglobulin E syndrome was considered as a possible diagnosis but Th1 and Th17 T cell subsets were normal. Thin layer chromatography for examination of amino acids in random urine sample revealed proline containing peptides. Prolidase enzyme activity was undetectable in dried blood spots as well as in plasma using glycylproline as substrate. Sequence analysis of PEPD gene revealed a single nucleotide substitution (G>A) at the splice acceptor consensus sequence of AG resulting in AA at 3′ of intron 11 in both the alleles leading to skipping of entire exon 12, frame shift and premature stop codon at 278.Comparative expression profile of selected inflammatory genes was carried out in the index patient with prolidase deficiency and high immunoglobulin E levels, another patient with hyperimmunoglobulin E syndrome and a normal control. Increased expression of IL-23 and TNF-α in prolidase deficient patient while IL-6 and TNF-a in hyperimmunoglobulinemia E patient was noted. This indicates a pro-inflammatory state in hyperimmunoglobulin E syndrome compared to the stable regulatory immunological state in prolidase deficiency. To the best of our knowledge, 819-1G>A is a novel mutation of PEPD gene in patients with prolidase deficiency and elevated immunoglobulin E levels.

A splice acceptor site mutation in TaGW2-A1 increases thousand grain weight in tetraploid and hexaploid wheat through wider and longer grains.

Key messageAcross 13 experiments thegw2-A1mutant allele shifts grain size distribution consistently across all grains significantly increasing grain weight (6.6 %), width (2.8 %) and length (2.1 %) in tetraploid and hexaploid wheat.There is an urgent need to identify, understand and incorporate alleles that benefit yield in polyploid wheat. The rice OsGW2 gene functions as a negative regulator of grain weight and width and is homologous to the wheat TaGW2 gene. Previously it was shown that transcript levels of the A-genome homoeologue, TaGW2-A1, are negatively associated with grain width in hexaploid wheat. In this study we screened the tetraploid Kronos TILLING population to identify mutants in TaGW2-A1. We identified a G to A transition in the splice acceptor site of exon 5 which leads to mis-splicing in TaGW2-A1. We backcrossed the mutant allele into tetraploid and hexaploid wheat and generated a series of backcross derived isogenic lines which were evaluated in glasshouse and field conditions. Across 13 experiments the GW2-A1 mutant allele significantly increased thousand grain weight (6.6 %), grain width (2.8 %) and grain length (2.1 %) in tetraploid and hexaploid wheat compared to the wild type allele. In hexaploid wheat, this led to an increase in spike yield since no differences were detected for spikelet or grain number between isogenic lines. The increase in grain width and length was consistent across grains of different sizes, suggesting that the effect of the mutation is stable across the ear and within spikelets. Differences in carpel size and weight between alleles were identified as early as 5 days before anthesis, suggesting that TaGW2-A1 acts on maternal tissue before anthesis to restrict seed size. A single nucleotide polymorphism marker was developed to aid the deployment of the mutant allele into breeding programmes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2686-2) contains supplementary material, which is available to authorized users.

Early Complement Component Deficiency in a Single-Centre Cohort of Pediatric Onset Lupus.

To assess complement levels C1q, C2, C3 and C4 in children with pediatric-onset lupus during the quiescent stage of disease. Thirty-four consecutive children with pediatric-onset SLE (onset below 12years), in the quiescent stage were enrolled for the study. Twenty-nine age and sex matched healthy children were also enrolled for the purpose of comparison. Complement C1q and C2 levels were estimated by enzyme-linked immunosorbent assay (ELISA) whereas C3 and C4 were measured by end-point nephelometry. Genetic mutation analysis and functional assessment of classical complement pathway by ELISA were carried out in children with depressed levels of these complements. The study protocol was approved by the Institute Thesis Committee and the Institute Ethics Committee. Mean complement C1q, C2, C3 and C4 levels were 50.32, 17.28, 1320 and 236mg/L respectively. Levels of complements were low in 7/34 children with SLE. An early age at onset, low anti-dsDNA titres and predominant skin manifestations were noted in children with decreased levels of complement C1q. Mutation analysis of C1qA gene revealed a homozygous nonsense mutation: C1QA (NM_015991) c.622C>T, p.Q208X in one child. A homozygous acceptor splice site mutation at the -2 position of intron2 of C1QA (c.164-2A>C) was detected in another child. The age at onset of disease was early in both these children, at 2.5 and 1.5years respectively. Children with inherited deficiency of C1q and other early complement components present with early onset lupus that has a distinct clinical and immunological profile.

A Novel SLC27A4 Splice Acceptor Site Mutation in Great Danes with Ichthyosis.

Ichthyoses are a group of various different types of hereditary disorders affecting skin cornification. They are characterized by hyperkeratoses of different severity levels and are associated with a dry and scaling skin. Genome-wide association analysis of nine affected and 13 unaffected Great Danes revealed a genome-wide significant peak on chromosome 9 at 57–58 Mb in the region of SLC27A4. Sequence analysis of genomic DNA of SLC27A4 revealed the non-synonymous SNV SLC27A4:g.8684G>A in perfect association with ichthyosis-affection in Great Danes. The mutant transcript of SLC27A4 showed an in-frame loss of 54 base pairs in exon 8 probably induced by a new splice acceptor site motif created by the mutated A- allele of the SNV. Genotyping 413 controls from 35 different breeds of dogs and seven wolves revealed that this mutation could not be found in other populations except in Great Danes. Affected dogs revealed high amounts of mutant transcript but only low levels of the wild type transcript. Targeted analyses of SLC27A4 protein from skin tissues of three affected and two unaffected Great Danes indicated a markedly reduced or not detectable wild type and truncated protein levels in affected dogs but a high expression of wild type SLC27A4 protein in unaffected controls. Our data provide evidence of a new splice acceptor site creating SNV that results in a reduction or loss of intact SLC27A4 protein and probably explains the severe skin phenotype in Great Danes. Genetic testing will allow selective breeding to prevent ichthyosis-affected puppies in the future.

A Splicing Reporter Tuned to Non-AG Acceptor Sites Reveals that Luteolin Enhances the Recognition of Non-canonical Acceptor Sites.

Removal of an intron requires precise recognition of the splice donor and acceptor sites located at the 5' and 3' termini of introns. Although the roles of these sequences differ, mutations in both sites easily block normal splicing and produce an aberrant mRNA. For example, many splice-site mutations occur in patients with inherited diseases. Several approaches have been evaluated to restore expression of a functional protein; however, because of the strict requirement for an AG dinucleotide at the 3' terminus of a U2-type intron, no method is available to correct splicing at a mutated sequence. To identify compounds that allow splicing at the non-AG acceptor site, in the present study we constructed a reporter gene with a modified polypyrimidine tract. However, the modified polypyrimidine tract mediated splicing at adjacent non-canonical acceptor sites, including the original mutated site. Further, we show that certain flavones such as luteolin and apigenin enhanced aberrant splicing at the non-canonical acceptor site of the reporter gene. These results suggest that the reporter gene and luteolin may be useful for further screening to identify molecules that correct aberrant splicing caused by a disease-associated splice acceptor site mutation.

Whole exome sequencing identifies mutations in Usher syndrome genes in profoundly deaf Tunisian patients.

Usher syndrome (USH) is an autosomal recessive disorder characterized by combined deafness-blindness. It accounts for about 50% of all hereditary deafness blindness cases. Three clinical subtypes (USH1, USH2, and USH3) are described, of which USH1 is the most severe form, characterized by congenital profound deafness, constant vestibular dysfunction, and a prepubertal onset of retinitis pigmentosa. We performed whole exome sequencing in four unrelated Tunisian patients affected by apparently isolated, congenital profound deafness, with reportedly normal ocular fundus examination. Four biallelic mutations were identified in two USH1 genes: a splice acceptor site mutation, c.2283-1G>T, and a novel missense mutation, c.5434G>A (p.Glu1812Lys), in MYO7A, and two previously unreported mutations in USH1G, i.e. a frameshift mutation, c.1195_1196delAG (p.Leu399Alafs*24), and a nonsense mutation, c.52A>T (p.Lys18*). Another ophthalmological examination including optical coherence tomography actually showed the presence of retinitis pigmentosa in all the patients. Our findings provide evidence that USH is under-diagnosed in Tunisian deaf patients. Yet, early diagnosis of USH is of utmost importance because these patients should undergo cochlear implant surgery in early childhood, in anticipation of the visual loss.

A Peruvian family with a novel PARK2 mutation: Clinical and pathological characteristics.

Mutations in PARK2 result in autosomal recessive young onset Parkinson's disease (YOPD). Although there have been a number of reports on the clinical characteristics of PARK2-related PD, there is limited information available on the associated neuropathologic changes. We describe the clinical and pathological characteristics of a Peruvian family with YOPD. The proband and one unaffected sibling were screened for PARK2 dosage and point mutations. One affected sibling had detailed neuropathologic examination. Instituto Nacional de Ciencias Neurologicas (INCN) in Lima, Peru. The proband and two of her four siblings developed YOPD and both parents were unaffected. The clinical course has been characterized by akinetic-rigid parkinsonism predominantly affecting the lower limbs and dyskinesias. Analysis of PARK2 showed that the proband is compound heterozygous for a novel acceptor splice site mutation in intron 5 (IVS5-1G>A) and an exon 7 deletion. Neuropathologic assessment of an affected sibling revealed severe neuronal loss in the substantia nigra (SN) and loss of tyrosine hydroxylase immunopositive fibers in the striatum. No Lewy body pathology was observed using standard histology or immunohistochemistry for α-synuclein. Consistent with most neuropathologic reports of patients with PARK2 mutations, we did not observe Lewy body inclusions, despite marked SN degeneration and severe dopaminergic denervation of the striatum. These data describe a novel splice site mutation and further extend the clinicopathological characterization of PARK2-associated PD.

Exome Sequencing Identifies a c.148-1G>C Mutation of TBX5 in a Holt-Oram Family with Unusual Genotype-Phenotype Correlations

Background/Aims: Congenital heart defects (CHD) can occur with upper limbs deformities. Holt-Oram syndrome is the main type of heart-hand syndromes, characterized by upper limb radial ray malformations, CHD and/or conduction abnormalities. Mutations of the TBX5 gene, most of which are found within the T-box domain, are one cause of the disease. We aimed to find the cause of the disease in a family with two children exhibiting symptoms of Holt-Oram syndrome while the parents tend to be normal. Methods: Chromosomal microarray analysis and exome sequencing were applied in the proband segments bearing the specific mutation and single nucleotide variants (SNVs) suspected of being involved in the disease were analyzed by polymerase chain reaction and direct sequencing. Results: A splice acceptor site mutation c.148-1G>C of TBX5 was detected in both the father and the proband. The mutation may result in an aberrant transcript which will most probably undergo nonsense-mediated decay (NMD) system resulting in haploinsufficiency of TBX5 protein. In the meantime, 3 candidated SNVs were detected. Conclusions: c.148-1G>C of TBX5 should be the pathogenic cause of the disease in this family. Works have been done to find a possible explanation of the unusual genotype-phenotype correlations in this family and further studies are still needed.

Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients.

BackgroundSplicing is more efficient when coupled with transcription and it has been proposed that nucleosomes enriched in exons are important for splice site recognition. Lynch syndrome is a familial cancer syndrome that can be caused by the autosomal dominant inheritance of splice site mutations in the MutL homolog 1 (MLH1) gene. To better understand the role of nucleosomes in splicing, we used MLH1 splice site mutations in Lynch syndrome cases as a model to investigate if abnormal splicing was associated with altered nucleosome positioning at exon-intron boundaries.FindingsNucleosome Occupancy and Methylome sequencing (NOMe-seq) was used to determine the allele-specific positioning of nucleosomes around heterozygous splice site mutations in lymphoblastoid cells lines (LCLs) derived from six Lynch syndrome patients. These mutations were previously shown to cause exon skipping in five of the six patients. Allele-specific high-resolution nucleosome mapping across exons and exon-intron boundaries revealed high levels of nucleosomes across all regions examined. Alleles containing donor or acceptor splice site mutations showed no consistent alteration in nucleosome positioning or occupancy.ConclusionNucleosomes were enriched at MLH1 exons in LCLs derived from Lynch syndrome patients, and in this model system the positioning of nucleosomes was unaltered at exon-intron boundaries containing splice site mutations. Thus, these splice site mutations alone do not significantly change the local organisation of nucleosomes.

Splice-acceptor site mutation in p53 gene of hu888 zebrafish line.

The p53 transcription factor is a key tumor suppressor and a central regulator of the stress response, which has been a subject of intense research for over 30 years. Recently, a zebrafish line which carries splice site mutation (G>T) in intron 8 of p53 gene (p53 hu888), encoding the p53 paralogue, was developed (The Zebrafish Mutation Project). To uncover molecular effects of the mutation, we raised hu888 zebrafish line to adulthood and analyzed DNA, mRNA data, and protein levels of p53 to assess their potential contribution in molecular mechanisms of the mutant fish. To obtain zebrafish individuals homozygous for the point mutation, p53 hu888 carriers were repeatedly incrossed but only heterozygous mutants (p53 hu888/+) or p53-wild type hu888 zebrafish (p53 +/+) were identified in their progeny. By evaluation of p53 expression changes in the liver of mutant and wild type hu888 zebrafish as well as of Tübingen reference strain, we demonstrated that two types of splicing occurred in each case: a classical one and the alternative splicing which involves the activation of cryptic splice-acceptor site in the exon 9 of zebrafish p53 pre-mRNA. The alternative splicing event results in a deletion 12 nucleotides in the mature mRNA, and produces a shortened variant of p53 protein. Interestingly, expression of p53 protein in liver of both heterozygous and wild type hu888 zebrafish was highly reduced compared to that in the reference strain.

A founder splice site mutation underlies glycogen storage disease type 3 in consanguineous Saudi families.

BACKGROUND AND OBJECTIVESGlycogen storage disease type 3 (GSD III) is an autosomal recessive disorder caused by genetic mutations in the gene AGL. AGL encodes amylo-α-1, 6-glucosidase, 4-α-glucanotransferase, a glycogen debranching enzyme. GSD III is characterized by fasting hypoglycemia, hepatomegaly, growth retardation, progressive myopathy, and cardiomyopathy due to storage of abnormally structured glycogen in both skeletal and cardiac muscles and/or liver. The aim of this study is to detect mutations underlying GSD III in Saudi patients.DESIGN AND SETTINGSA cross-sectional clinical genetic study of 5 Saudi consanguineous families examined at the metabolic clinic of the Madinah Maternity and Children Hospital.PATIENTS AND METHODSWe present a biochemical and molecular analysis of 5 consanguineous Saudi families with GSD III. DNA was isolated from the peripheral blood of 31 individuals, including 12 patients, and the AGL gene was sequenced bidirectionally. DNA sequences were compared with the AGL reference sequence from the ensemble genome browser.RESULTSGenotyping and sequence analysis identified a homozygous intronic splice acceptor site mutation (IVS32-12A>G) in 4 families perfectly segregating with the phenotype. Complementary (c)DNA sequence analysis of the AGL gene revealed an 11-bp sequence insertion between exon 32 and exon 33 due to the creation of a new 3′ splice site. The predicted mutant enzyme was truncated by 112 carboxyl-terminal amino acids as a result of premature termination.CONCLUSIONHaplotype analysis revealed that the mutation arises as a result of founder effect, not an independent event. This is the first report of a genetic mutation in the AGL gene from Saudi Arabia. Screening for this mutation can improve genetic counseling and prenatal diagnosis of GSD III in Saudi Arabia.

Clinical investigation and mutation analysis of ECM1 gene in a family with lipoid proteinosis

Objective To report a family with lipoid proteinosis (LP) from Shandong province and to analyze mutations in the extracellular matrix protein 1 (ECM1) gene in this family.Methods Eight members in a threegeneration family with LP were clinically investigated,and two patients were identified to suffer from LP,including the proband (Ⅲ 1) and her mother (Ⅱ 2).Both of the patients presented with papules on the palpebral margin,short and thick lingual frenum,and hoarseness.Indirect laryngoscopy showed infiltrating and thickening of the vocal cord.Pathological examination of lesions on the palpebral margin and laryngeal mucosa revealed deposits of hyaline-like material in the dermis,which was strongly positive for periodic acid-Schiff (PAS) staining and resistant to diastase digestion.The pathological diagnosis was LP.Blood samples were collected from all the family members and 100 ethnically matched,unrelated and unaffected Chinese human controls followed by DNA extraction.PCR and sequencing were performed to detect the ECM1 gene,and nested PCR followed by agarose gel electrophoresis to analyze mutations in the coding region of the ECM1 gene.Results Both of the two patients were compound heterozygotes.Three missense mutations,incluing p.P169T,p.A44T and p.R392W,were found in the ECM1 gene of the affected mother,with p.P169T in one allele and p.A44T as well as p.R392W in the other.The girl patient inheried the missence mutation p.P169T from her mother and a synonymous mutation c.879G ＞ A from her father (Ⅱ 1).Nested PCR showed that the c.978G ＞ A mutation generated a splice-acceptor site AG,which leaded to a splicing defect.Conclusion A novel synonymous splice-acceptor site mutation c.879G ＞ A in the ECM1 gene is identified in the family with LP. Key words: Lipoid proteinosis of Urbach and Wiethe; Extracellular matrix proteins; Mutation

Mutations in Pseudohypoparathyroidism 1a and Pseudopseudohypoparathyroidism in Ethnic Chinese

An inactivating mutation in the GNAS gene causes either pseudohypoparathyroidism 1a (PHP1A) when it is maternally inherited or pseudopseudohypoparathyroidism (PPHP) when it is paternally inherited. We investigated clinical manifestations and mutations of the GNAS gene in ethnic Chinese patients with PHP1A or PPHP. Seven patients from 5 families including 4 girls and 2 boys with PHP1A and 1 girl with PPHP were studied. All PHP1A patients had mental retardation. They were treated with calcitriol and CaCO3 with regular monitoring of serum Ca levels, urinary Ca/Cr ratios, and renal sonography. Among them, 5 patients also had primary hypothyroidism suggesting TSH resistance. One female patient had a renal stone which was treated with extracorporeal shockwave lithotripsy. She had an increased urinary Ca/Cr ratio of 0.481 mg/mg when the stone was detected. We detected mutations using PCR and sequencing as well as analysed a splice acceptor site mutation using RT-PCR, sequencing, and minigene construct. We detected 5 mutations: c.85C>T (Q29*), c.103C>T (Q35*), c.840-2A>G (R280Sfs*21), c.1027_1028delGA (D343*), and c.1174G>A (E392K). Mutations c.840-2A>G and c.1027_1028delGA were novel. The c.840-2A>G mutation at the splice acceptor site of intron 10 caused retention of intron 10 in the minigene construct but skipping of exon 11 in the peripheral blood cells. The latter was the most probable mechanism which caused a frameshift, changing Arg to Ser at residue 280 and invoking a premature termination of translation at codon 300 (R280Sfs*21). Five GNAS mutations in ethnic Chinese with PHP1A and PPHP were reported. Two of them were novel. Mutation c.840-2A>G destroyed a spice acceptor site and caused exon skipping. Regular monitoring and adjustment in therapy are mandatory to achieve optimal therapeutic effects and avoid nephrolithiasis in patients with PHP1A.

Translation of branched-chain aminotransferase-1 transcripts is impaired in cells haploinsufficient for ribosomal protein genes

Diamond-Blackfan anemia (DBA) is a bone marrow failure syndrome linked to mutations in ribosomal protein (RP) genes that result in the impaired proliferation of hematopoietic progenitor cells. The etiology of DBA is not completely understood; however, the ribosomal nature of the genes involved has led to speculation that these mutations may alter the landscape of messenger RNA (mRNA) translation. Here, we performed comparative microarray analysis of polysomal mRNA transcripts isolated from lymphoblastoid cell lines derived from DBA patients carrying various haploinsufficient mutations in either RPS19 or RPL11. Different spectrums of changes were observed depending on the mutant gene, with large differences found in RPS19 cells and very few in RPL11 cells. However, we find that the small number of altered transcripts in RPL11 overlap for the most part with those altered in RPS19 cells. We show specifically that levels of branched-chain aminotransferase-1 (BCAT1) transcripts are significantly decreased on the polysomes of both RPS19 and RPL11 cells and that translation of BCAT1 protein is especially impaired in cells with small RP gene mutations, and we provide evidence that this effect may be due in part to the unusually long 5'UTR of the BCAT1 transcript. The BCAT1 enzyme carries out the final step in the biosynthesis and the first step of degradation of the branched-chain amino acids leucine, isoleucine, and valine. Interestingly, several animal models of DBA have reported that leucine ameliorates the anemia phenotypes generated by RPS19 loss. Our study suggests that RP mutations affect the synthesis of specific proteins involved in regulating amino acid levels that are important for maintaining the normal proliferative capacity of hematopoietic cells.

Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients

BackgroundSplicing is more efficient when coupled with transcription and it has been proposed that nucleosomes enriched in exons are important for splice site recognition. Lynch syndrome is a familial cancer syndrome that can be caused by the autosomal dominant inheritance of splice site mutations in the MutL homolog 1 (MLH1) gene. To better understand the role of nucleosomes in splicing, we used MLH1 splice site mutations in Lynch syndrome cases as a model to investigate if abnormal splicing was associated with altered nucleosome positioning at exon-intron boundaries.FindingsNucleosome Occupancy and Methylome sequencing (NOMe-seq) was used to determine the allele-specific positioning of nucleosomes around heterozygous splice site mutations in lymphoblastoid cells lines (LCLs) derived from six Lynch syndrome patients. These mutations were previously shown to cause exon skipping in five of the six patients. Allele-specific high-resolution nucleosome mapping across exons and exon-intron boundaries revealed high levels of nucleosomes across all regions examined. Alleles containing donor or acceptor splice site mutations showed no consistent alteration in nucleosome positioning or occupancy.ConclusionNucleosomes were enriched at MLH1 exons in LCLs derived from Lynch syndrome patients, and in this model system the positioning of nucleosomes was unaltered at exon-intron boundaries containing splice site mutations. Thus, these splice site mutations alone do not significantly change the local organisation of nucleosomes.