Who would benefit from exome sequencing?

Duodecim. 2017;133(5):481-8

Authors: Saarela J, Kettunen K

Abstract
Next-generation sequencing methods have revolutionized the possibilities for analyzing the human genome. Sequencing the exome, the protein-encoding portion of the genome, is used, in clinical medicine, especially in the diagnosis of rare hereditary diseases, congenital developmental disorders and cancer. Using exome sequencing as a diagnostic test is justified when the results could lead to an accurate diagnosis, significantly influence the treatment and genetic counseling. It is a reliable method for detecting single base mutations as minor deletions and insertions. However, with current methods the reliable analysis of larger changes in the number of copies, the length or repeats and areas present in multiple copies in the genome is challenging. Every human has many mutations in their exome, and distinguishing between insignificant and pathogenic mutations is thus a key challenge when interpreting the results of exome sequencing.

PMID: 29205997 [PubMed - indexed for MEDLINE]

Chromatin remodeling gene ARID2 targets cyclin D1 and cyclin E1 to suppress hepatoma cell progression.

Oncotarget. 2016 Jul 19;7(29):45863-45875

Authors: Duan Y, Tian L, Gao Q, Liang L, Zhang W, Yang Y, Zheng Y, Pan E, Li S, Tang N

Abstract
Exome and whole-genome sequencing studies have drawn attention to the role of somatic mutations in SWI/SNF chromatin remodeling complexes in the carcinogenesis of hepatocellular carcinoma (HCC). Here, we explored the molecular mechanisms underlying the biological roles of AT-rich interactive domain 2 (ARID2) in the pathogenesis of HCC. We found that ARID2 expression was significantly downregulated in HCC tissues compared with non-tumorous tissues. Restoration of ARID2 expression in hepatoma cells was sufficient to suppress cell proliferation and tumor growth in mice, whereas ARID2 knockdown contributed to the enhancement of cellular proliferation and tumorigenicity. Suppression of ARID2 expression accelerated G1/S transition associated with upregulation of cyclin D1, cyclin E1, CDK4, and phosphorylation of the retinoblastoma protein (Rb). Furthermore, we demonstrated that ARID2 physically interacts with E2F1 and decreases binding of E2F1/RNA Pol II to the promoters of CCND1 and CCNE1. Taken together, these results demonstrate that ARID2 suppresses tumor cell growth through repression of cyclin D1 and cyclin E1 expression, thereby retarding cell cycle progression and cell proliferation in hepatoma cells. These findings highlight the potential role of ARID2 as a tumor growth suppressor in HCC.

PMID: 27351279 [PubMed - indexed for MEDLINE]

A de novo nonsense mutation in ASXL3 shared by siblings with Bainbridge-Ropers syndrome.

Cold Spring Harb Mol Case Stud. 2018 Jan 05;:

Authors: Koboldt DC, Mihalic Mosher T, Kelly BJ, Sites E, Bartholomew D, Hickey SE, McBride K, Wilson RK, White P

Abstract
Two sisters (ages 16 y. and 15 y.) have been followed by our clinical genetics team for several years. Both girls have severe intellectual disability, hypotonia, seizures, and distinctive craniofacial features. The parents are healthy, and have no other children. Oligo array, fragile X testing, and numerous single-gene tests were negative. All four family members underwent research exome sequencing, which revealed a heterozygous nonsense mutation in ASXL3 (p.R1036X) that segregated with disease. Exome data and independent Sanger sequencing confirmed that the variant is de novo, suggesting possible germline mosaicism in one parent. The p.R1036X variant has never been observed in healthy human populations and has been previously reported as a pathogenic mutation. Truncating de novo mutations in ASXL3 cause Bainbridge-Ropers syndrome (BRS), a developmental disorder with similarities to Bohring-Optitz syndrome. Fewer than 30 BRS patients have been described in the literature; to our knowledge, this is the first report of the disorder in two related individuals. Our findings lend further support to intellectual disability, absent speech, autistic traits, hypotonia, and distinctive facial appearance as common emerging features of Bainbridge-Ropers syndrome.

PMID: 29305346 [PubMed - as supplied by publisher]

Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing.

Semin Fetal Neonatal Med. 2018 Jan 02;:

Authors: Hayward J, Chitty LS

Abstract
Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities. In addition, the transformation of prenatal genetic testing arising from the introduction of whole genome, exome and targeted NGS produces unprecedented volumes of data requiring complex analysis and interpretation. Now translating these technologies to the clinic has become the goal of clinical genomics, transforming modern healthcare and personalized medicine. The achievement of this goal requires the most progressive technological tools for rapid high-throughput data generation at an affordable cost. Furthermore, as larger proportions of patients with genetic disease are identified we must be ready to offer appropriate genetic counselling to families and potential parents. In addition, the identification of novel treatment targets will continue to be explored, which is likely to introduce ethical considerations, particularly if genome editing techniques are included in these targeted treatments and transferred into mainstream personalized healthcare. Here we review the impact of NGS technology to analyse cell-free DNA (cfDNA) in maternal plasma to deliver NIPD for monogenic disorders and allow more comprehensive investigation of the abnormal fetus through the use of exome sequencing.

PMID: 29305293 [PubMed - as supplied by publisher]

SNPitty: An intuitive web-application for interactive B-allele frequency and copy-number visualization of next-generation sequencing data.

J Mol Diagn. 2018 Jan 02;:

Authors: van Riet J, Krol NMG, Atmodimedjo PN, Brosens E, van IJcken WFJ, Jansen MPHM, Martens JWM, Looijenga LH, Jenster G, Dubbink HJ, Dinjens WNM, van de Werken HJG

Abstract
Exploration and visualization of next-generation sequencing data is crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions-of-interest coupled with dynamic heuristic filtering of genetic aberrations is however lacking. Therefore, we developed the web-application SNPitty that allows interactive visualization and interrogation of variant call format (VCF) files by utilizing B-allele frequencies of single nucleotide polymorphisms and single nucleotide variants, coverage metrics and copy-numbers analysis results. SNPitty displays variant alleles and allelic imbalances with a focus on loss of heterozygosity and copy number variation using genome-wide heterozygous markers and somatic mutations. In addition, SNPitty is capable of generating predefined reports that summarize and highlight disease-specific targets-of-interest.We validated SNPitty for diagnostic interpretation of somatic events by showcasing a serial dilution series of glioma tissue. Additionally, we demonstrate SNPitty in four cancer-related scenarios encountered in daily clinical practice and on whole-exome sequencing data of peripheral blood from a Down syndrome patient. SNPitty allows detection of loss of heterozygosity, chromosomal and gene amplifications, homozygous or heterozygous deletions, somatic mutations or any combination thereof in regions- or genes-of-interest. Furthermore, SNPitty can be used to distinguish molecular relationships between multiple tumors from a single patient. Based on these data, we demonstrate that SNPitty is robust and user-friendly in a wide range of diagnostic scenarios.https://bitbucket.org/ccbc/snpitty.

PMID: 29305224 [PubMed - as supplied by publisher]

Alternative Splicing in Genetic Diseases: Improved Diagnosis and Novel Treatment Options.

Int Rev Cell Mol Biol. 2018;335:85-141

Authors: Bergsma AJ, van der Wal E, Broeders M, van der Ploeg AT, Pim Pijnappel WWM

Abstract
Alternative splicing is an important mechanism to regulate gene expression and to expand the repertoire of gene products in order to accommodate an increase in complexity of multicellular organisms. It needs to be precisely regulated, which is achieved via RNA structure, splicing factors, transcriptional regulation, and chromatin. Changes in any of these factors can lead to disease. These may include the core spliceosome, splicing enhancer/repressor sequences and their interacting proteins, the speed of transcription by RNA polymerase II, and histone modifications. While the basic principle of splicing is well understood, it is still very difficult to predict splicing outcome, due to the multiple levels of regulation. Current molecular diagnostics mainly uses Sanger sequencing of exons, or next-generation sequencing of gene panels or the whole exome. Functional analysis of potential splicing variants is scarce, and intronic variants are often not considered. This likely results in underestimation of the percentage of splicing variants. Understanding how sequence variants may affect splicing is not only crucial for confirmation of diagnosis and for genetic counseling, but also for the development of novel treatment options. These include small molecules, transsplicing, antisense oligonucleotides, and gene therapy. Here we review the current state of molecular mechanisms of splicing regulation and how deregulation can lead to human disease, diagnostics to detect splicing variants, and novel treatment options based on splicing correction.

PMID: 29305015 [PubMed - in process]

A recurrent de novo missense mutation in UBTF causes developmental neuroregression.

Hum Mol Genet. 2018 Jan 02;:

Authors: Toro C, Hori RT, Malicdan MCV, Tifft CJ, Goldstein A, Gahl WA, Adams DR, Harper F, Wolfe LA, Xiao J, Khan MM, Tian J, Hope KA, Reiter LT, Tremblay MG, Moss T, Franks AL, Balak C, C4RCD Research Group, LeDoux MS

Abstract
UBTF (upstream binding transcription factor) exists as two isoforms; UBTF1 regulates rRNA transcription by RNA polymerase 1, whereas UBTF2 regulates mRNA transcription by RNA polymerase 2. Herein, we describe 4 patients with very similar patterns of neuroregression due to recurrent de novo mutations in UBTF (GRCh37/hg19, NC_000017.10:g.42290219C>T, NM_014233.3:c.628G>A) resulting in the same amino acid change in both UBTF1 and UBTF2 (p.Glu210Lys [p.E210K]). Disease onset in our cohort was at 2.5 to 3 yrs and characterized by slow progression of global motor, cognitive and behavioral dysfunction. Notable early features included hypotonia with a floppy gait, high-pitched dysarthria and hyperactivity. Later features included aphasia, dystonia, and spasticity. Speech and ambulatory ability were lost by the early teens. Magnetic resonance imaging showed progressive generalized cerebral atrophy (supratentorial > infratentorial) with involvement of both gray and white matter. Patient fibroblasts showed normal levels of UBTF transcripts, increased expression of pre-rRNA and 18S rRNA, nucleolar abnormalities, markedly increased numbers of DNA breaks, defective cell-cycle progression, and apoptosis. Expression of mutant human UBTF1 in Drosophila neurons was lethal. Although no loss-of-function variants are reported in the Exome Aggregation Consortium (ExAC) database and Ubtf-/- is early embryonic lethal in mice, Ubtf+/- mice displayed only mild motor and behavioral dysfunction in adulthood. Our data underscore the importance of including UBTF E210K in the differential diagnosis of neuroregression and suggest that mainly gain-of-function mechanisms contribute to the pathogenesis of the UBTF E210K neuroregression syndrome.

PMID: 29300972 [PubMed - as supplied by publisher]

Genetic analysis of CHARGE syndrome identifies overlapping molecular biology.

Genet Med. 2018 Jan 04;:

Authors: Moccia A, Srivastava A, Skidmore JM, Bernat JA, Wheeler M, Chong JX, Nickerson D, Bamshad M, Hefner MA, Martin DM, Bielas SL

Abstract
PurposeCHARGE syndrome is an autosomal-dominant, multiple congenital anomaly condition characterized by vision and hearing loss, congenital heart disease, and malformations of craniofacial and other structures. Pathogenic variants in CHD7, encoding adenosine triphosphate-dependent chromodomain helicase DNA binding protein 7, are present in the majority of affected individuals. However, no causal variant can be found in 5-30% (depending on the cohort) of individuals with a clinical diagnosis of CHARGE syndrome.MethodsWe performed whole-exome sequencing (WES) on 28 families from which at least one individual presented with features highly suggestive of CHARGE syndrome.ResultsPathogenic variants in CHD7 were present in 15 of 28 individuals (53.6%), whereas 4 (14.3%) individuals had pathogenic variants in other genes (RERE, KMT2D, EP300, or PUF60). A variant of uncertain clinical significance in KDM6A was identified in one (3.5%) individual. The remaining eight (28.6%) individuals were not found to have pathogenic variants by WES.ConclusionThese results demonstrate that the phenotypic features of CHARGE syndrome overlap with multiple other rare single-gene syndromes. Additionally, they implicate a shared molecular pathology that disrupts epigenetic regulation of multiple-organ development.GENETICS in MEDICINE advance online publication, 4 January 2018; doi:10.1038/gim.2017.233.

PMID: 29300383 [PubMed - as supplied by publisher]

A homozygous founder missense variant in arylsulfatase G abolishes its enzymatic activity causing atypical Usher syndrome in humans.

Genet Med. 2018 Jan 04;:

Authors: Khateb S, Kowalewski B, Bedoni N, Damme M, Pollack N, Saada A, Obolensky A, Ben-Yosef T, Gross M, Dierks T, Banin E, Rivolta C, Sharon D

Abstract
PurposeWe aimed to identify the cause of disease in patients suffering from a distinctive, atypical form of Usher syndrome.MethodsWhole-exome and genome sequencing were performed in five patients from three families of Yemenite Jewish origin, suffering from distinctive retinal degeneration phenotype and sensorineural hearing loss. Functional analysis of the wild-type and mutant proteins was performed in human fibrosarcoma cells.ResultsWe identified a homozygous founder missense variant, c.133G>T (p.D45Y) in arylsulfatase G (ARSG). All patients shared a distinctive retinal phenotype with ring-shaped atrophy along the arcades engirdling the fovea, resulting in ring scotoma. In addition, patients developed moderate to severe sensorineural hearing loss. Both vision and hearing loss appeared around the age of 40 years. The identified variant affected a fully conserved amino acid that is part of the catalytic site of the enzyme. Functional analysis of the wild-type and mutant proteins showed no basal activity of p.D45Y.ConclusionHomozygosity for ARSG-p.D45Y in humans leads to protein dysfunction, causing an atypical combination of late-onset Usher syndrome. Although there is no evidence for generalized clinical manifestations of lysosomal storage diseases in this set of patients, we cannot rule out the possibility that mild and late-onset symptoms may appear.GENETICS in MEDICINE advance online publication, 4 January 2018; doi:10.1038/gim.2017.227.

PMID: 29300381 [PubMed - as supplied by publisher]

Mutations in EMT-Related Genes in ALK Positive Crizotinib Resistant Non-Small Cell Lung Cancers.

Cancers (Basel). 2018 Jan 04;10(1):

Authors: Wei J, van der Wekken AJ, Saber A, Terpstra MM, Schuuring E, Timens W, Hiltermann TJN, Groen HJM, van den Berg A, Kok K

Abstract
Crizotinib is an effective drug for patients with anaplastic lymphoma kinase (ALK)-positive non-small-cell lung cancer (NSCLC), but upon treatment, the tumors inevitably become crizotinib resistant in time. The resistance mechanisms are only partly understood. In this study, we aim to identify gene mutations associated with resistance in ALKpositive advanced non-squamous NSCLC treated with crizotinib. Four ALK positive patients with progressive disease following crizotinib treatment were identified with paired pre- and post-crizotinib tumor tissue from our previously published cohort. Somatic variants in these samples were detected by whole exome sequencing. In one of the four patients, an ALK-resistance associated mutation was identified. In the other three patients, no ALK-resistance associated mutations were present. In these patients we identified 89 relevant somatic mutations in 74 genes that were specific to the resistant tumors. These genes were enriched in 15 pathways. Four pathways, were related to epithelial-mesenchymal transition (EMT): proteoglycans in cancer, HIF-1 signaling, FoxO signaling pathway, and ECM-receptor interaction. Analysis of other EMT-related pathways revealed three additional genes with mutations specific to the crizotinib-resistant tumor samples. The enrichment of mutations in genes associated with EMT-related pathways indicates that loss of epithelial differentiation may represent a relevant resistance mechanism for crizotinib.

PMID: 29300322 [PubMed]

Cancer risk susceptibility loci in a Swedish population.

Oncotarget. 2017 Dec 15;8(66):110300-110310

Authors: Liu W, Jiao X, Thutkawkorapin J, Mahdessian H, Lindblom A

Abstract
A germline mutation in cancer predisposing genes is known to increase the risk of more than one tumor type. In order to find loci associated with many types of cancer, a genome-wide association study (GWAS) was conducted, and 3,555 Swedish cancer cases and 15,581 controls were analyzed for 226,883 SNPs. The study used haplotype analysis instead of single SNP analysis in order to find putative founder effects. Haplotype association studies identified seven risk loci associated with cancer risk, on chromosomes 1, 7, 11, 14, 16, 17 and 21. Four of the haplotypes, on chromosomes 7, 14, 16 and 17, were confirmed in Swedish familial cancer cases. It was possible to perform exome sequencing in one patient for each of those four loci. No clear disease-causing exonic mutation was found in any of the four loci. Some of the candidate loci hold several cancer genes, suggesting that the risk associated with one locus could involve more than one gene associated with cancer risk. In summary, this study identified seven novel candidate loci associated with cancer risk. It was also suggested that cancer risk at one locus could depend on multiple contributing risk mutations/genes.

PMID: 29299148 [PubMed]

Germline and somatic mutations in homologous recombination genes among Chinese ovarian cancer patients detected using next-generation sequencing.

J Gynecol Oncol. 2017 Jul;28(4):e39

Authors: Zhao Q, Yang J, Li L, Cao D, Yu M, Shen K, BGI Group

Abstract
OBJECTIVE: To define genetic profiling of homologous recombination (HR) deficiency in Chinese ovarian cancer patients.
METHODS: we have applied next-generation sequencing to detect deleterious mutations through all exons in 31 core HR genes. Paired whole blood and frozen tumor samples from 50 Chinese women diagnosed with epithelial ovarian carcinomas were tested to identify both germline and somatic variants.
RESULTS: Deleterious germline HR-mutations were identified in 36% of the ovarian cancer patients. Another 5 patients had only somatic mutations. BRCA2 was most frequently mutated. Three out of the 5 somatic mutations were in RAD genes and a wider distribution of other HR genes was involved in non-serous carcinomas. BRCA1/2-mutation carriers had favorable platinum sensitivity (relative risk, 1.57, p<0.05), resulting in a 100% remission probability and survival rate. In contrast, mutations in other HR genes predicted poor prognosis. However, multivariate analysis demonstrated that platinum sensitivity and optimal cytoreduction were the independent impact factors influencing survival (hazards ratio, 0.053) and relapse (hazards ratio, 0.247), respectively.
CONCLUSION: our results suggest that a more comprehensive profiling of HR defect than merely BRCA1/2 could help elucidate tumor heterogeneity and lead to better stratification of ovarian cancer patients for individualized clinical management.

PMID: 28541631 [PubMed - indexed for MEDLINE]

Psychosocial Profiles of Parents of Children with Undiagnosed Diseases: Managing Well or Just Managing?

J Genet Couns. 2018 Jan 02;:

Authors: McConkie-Rosell A, Hooper SR, Pena LDM, Schoch K, Spillmann RC, Jiang YH, Cope H, Undiagnosed Diseases Network, Palmer C, Shashi V

Abstract
Little is known about the psychosocial profiles of parents who have a child with an undiagnosed chronic illness. The National Institutes of Health Undiagnosed Diseases Network (UDN) evaluates individuals with intractable medical findings, with the objective of discovering the underlying diagnosis. We report on the psychosocial profiles of 50 parents whose children were accepted to one of the network's clinical sites. Parents completed questionnaires assessing anxiety, depression, coping self-efficacy, and health care empowerment at the beginning of their child's UDN clinical evaluation. Parents of undiagnosed children had high rates of anxiety and depression (~ 40%), which were significantly inversely correlated with coping self-efficacy, but not with health care empowerment. Coping self-efficacy, depressive, and anxiety symptoms were better in parents with older children and with longer duration of illness. Gender differences were identified, with mothers reporting greater health care engagement than fathers. Overall, our findings suggest that parents of children with undiagnosed diseases maintain positive coping self-efficacy and remain actively engaged in health care and to a lesser degree tolerance for uncertainty, but these come with a high emotional cost to the parents. As the parents' psychological needs may not be obvious, these should be ascertained and the requisite support provided.

PMID: 29297108 [PubMed - as supplied by publisher]

Whole-exome sequencing in evaluation of patients with venous thromboembolism.

Blood Adv. 2017 Jul 11;1(16):1224-1237

Authors: Lee EJ, Dykas DJ, Leavitt AD, Camire RM, Ebberink E, García de Frutos P, Gnanasambandan K, Gu SX, Huntington JA, Lentz SR, Mertens K, Parish CR, Rezaie AR, Sayeski PP, Cromwell C, Bar N, Halene S, Neparidze N, Parker TL, Burns AJ, Dumont A, Yao X, Chaar CIO, Connors JM, Bale AE, Lee AI

Abstract
Genetics play a significant role in venous thromboembolism (VTE), yet current clinical laboratory-based testing identifies a known heritable thrombophilia (factor V Leiden, prothrombin gene mutation G20210A, or a deficiency of protein C, protein S, or antithrombin) in only a minority of VTE patients. We hypothesized that a substantial number of VTE patients could have lesser-known thrombophilia mutations. To test this hypothesis, we performed whole-exome sequencing (WES) in 64 patients with VTE, focusing our analysis on a novel 55-gene extended thrombophilia panel that we compiled. Our extended thrombophilia panel identified a probable disease-causing genetic variant or variant of unknown significance in 39 of 64 study patients (60.9%), compared with 6 of 237 control patients without VTE (2.5%) (P < .0001). Clinical laboratory-based thrombophilia testing identified a heritable thrombophilia in only 14 of 54 study patients (25.9%). The majority of WES variants were either associated with thrombosis based on prior reports in the literature or predicted to affect protein structure based on protein modeling performed as part of this study. Variants were found in major thrombophilia genes, various SERPIN genes, and highly conserved areas of other genes with established or potential roles in coagulation or fibrinolysis. Ten patients (15.6%) had >1 variant. Sanger sequencing performed in family members of 4 study patients with and without VTE showed generally concordant results with thrombotic history. WES and extended thrombophilia testing are promising tools for improving our understanding of VTE pathogenesis and identifying inherited thrombophilias.

PMID: 29296762 [PubMed]

Neuropathology of childhood-onset basal ganglia degeneration caused by mutation of VAC14.

Ann Clin Transl Neurol. 2017 Dec;4(12):859-864

Authors: Stutterd C, Diakumis P, Bahlo M, Fanjul Fernandez M, Leventer RJ, Delatycki M, Amor D, Chow CW, Stephenson S, Meisler MH, Mclean C, Lockhart PJ

Abstract
Objective: To characterize the clinical features and neuropathology associated with recessive VAC14 mutations.
Methods: Whole-exome sequencing was used to identify the genetic etiology of a rapidly progressive neurological disease presenting in early childhood in two deceased siblings with distinct neuropathological features on post mortem examination.
Results: We identified compound heterozygous variants in VAC14 in two deceased siblings with early childhood onset of severe, progressive dystonia, and neurodegeneration. Their clinical phenotype is consistent with the VAC14-related childhood-onset, striatonigral degeneration recently described in two unrelated children. Post mortem examination demonstrated prominent vacuolation associated with degenerating neurons in the caudate nucleus, putamen, and globus pallidus, similar to previously reported ex vivo vacuoles seen in the late-endosome/lysosome of VAC14-deficient neurons. We identified upregulation of ubiquitinated granules within the cell cytoplasm and lysosomal-associated membrane protein (LAMP2) around the vacuole edge to suggest a process of vacuolation of lysosomal structures associated with active autophagocytic-associated neuronal degeneration.
Interpretation: Our findings reveal a distinct clinicopathological phenotype associated with recessive VAC14 mutations.

PMID: 29296614 [PubMed]

Arecoline N-Oxide Upregulates Caspase-8 Expression in Oral Hyperplastic Lesions of Mice.

J Agric Food Chem. 2017 Nov 29;65(47):10197-10205

Authors: Chang PY, Kuo TM, Chen PK, Lin YZ, Hua CH, Chen YC, Ko YC

Abstract
Areca nut is strongly associated with oral squamous cell carcinoma (OSCC) occurrence. Arecoline N-oxide (ANO), a metabolite of the areca alkaloid arecoline, exhibits an oral fibrotic effect in NOD/SCID mice. Caspase-8, a cysteine protease encoded by the CASP8 gene, is a central mediator in the extrinsic apoptotic pathway via death receptors. Deregulation of caspase-8 in OSCC has been reported. This study investigates the regulation of caspase-8 in ANO-induced oral squamous epithelial hyperplasia that represents the initial highly proliferative stage of oral carcinogenesis. CASP8 somatic mutations were identified from whole-exome sequencing of OSCC samples. Immunohistochemical staining showed upregulation of caspase-8 in ANO-induced hyperplasia of both NOD-SCID and C57BL/6 mice. Levels of expression of CASP8, APAF-1, BAX, and BAD increased in ANO-treated DOK cells. Co-localization of increased caspase-8 and PCNA levels was detected in ANO-induced hyperplastic lesions, whereas no co-localization among γ-H2A.X, caspase-3, and upregulated caspase-8 was observed. The findings indicate that upregulation of caspase-8 is involved in cell proliferation rather than apoptosis during the initial stage of ANO-mediated oral tumorigenesis.

PMID: 29092399 [PubMed - indexed for MEDLINE]

Familial Paroxysmal Kinesigenic Dyskinesia is associated with mutations in the KCNA1 gene.

Hum Mol Genet. 2017 Dec 27;:

Authors: Yin XM, Lin JH, Cao L, Zhang TM, Zeng S, Zhang KL, Tian WT, Hu ZM, Li N, Wang JL, Guo JF, Wang RX, Xia K, Zhang ZH, Yin F, Peng J, Liao WP, Yi YH, Liu JY, Yang ZX, Chen Z, Mao X, Yan XX, Jiang H, Shen L, Chen SD, Zhang LM, Tang BS

Abstract
Paroxysmal kinesigenic dyskinesia (PKD) is a heterogeneous movement disorder characterized by recurrent dyskinesia attacks triggered by sudden movement. PRRT2 has been identified as the first causative gene of PKD. However, it is only responsible for approximately half of affected individuals, indicating that other loci are most likely involved in the etiology of this disorder. To explore the underlying causative gene of PRRT2-negative PKD, we used a combination strategy including linkage analysis, whole-exome sequencing and copy number variations analysis to detect the genetic variants within a family with PKD. We identified a linkage locus on chromosome 12 (12p13.32-12p12.3) and detected a novel heterozygous mutation c.956 T>G (p.319 L>R) in the potassium voltage-gated channel subfamily A member 1, KCNA1. Whole-exome sequencing in another fifty-eight Chinese patients with PKD who lacked mutations in PRRT2 revealed another novel mutation in the KCNA1 gene [c.765 C>A (p.255 N>K)] within another family. Biochemical analysis revealed that the L319R mutant accelerated protein degradation via the proteasome pathway and disrupted membrane expression of the Kv1.1 channel. Electrophysiological examinations in transfected HEK293 cells showed that both the L319R and N255K mutants resulted in reduced potassium currents and respective altered gating properties, with a dominant negative effect on the Kv1.1 wild-type channel. Our study suggests that these mutations in KCNA1 cause the Kv1.1 channel dysfunction, which leads to familial PKD. The current study further extended the genotypic spectrum of this disorder, indicating that Kv1.1 channel dysfunction maybe one of the underlying defects in PKD.

PMID: 29294000 [PubMed - as supplied by publisher]

A rational approach to the use of sophisticated genetic analyses of pediatric stone disease.

Kidney Int. 2018 Jan;93(1):15-18

Authors: Langman CB

Abstract
Kidney stone disease in the childhood years has a genetic underpinning in some. The relationships between clinical phenotype, medical evaluation, and genetic etiologies were investigated using whole-exome sequencing by the Hildebrandt laboratory. At this time, a genetic evaluation of pediatric nephrolithiasis should be reserved for specific circumstances when clinical uncertainty of the reason for the presence of the stone or therapy is not satisfactory.

PMID: 29291816 [PubMed - in process]

Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder.

Am J Hum Genet. 2017 Dec 07;101(6):965-976

Authors: Falkenberg KD, Braverman NE, Moser AB, Steinberg SJ, Klouwer FCC, Schlüter A, Ruiz M, Pujol A, Engvall M, Naess K, van Spronsen F, Körver-Keularts I, Rubio-Gozalbo ME, Ferdinandusse S, Wanders RJA, Waterham HR

Abstract
Zellweger spectrum disorders (ZSDs) are autosomal-recessive disorders that are caused by defects in peroxisome biogenesis due to bi-allelic mutations in any of 13 different PEX genes. Here, we identified seven unrelated individuals affected with an apparent dominant ZSD in whom a heterozygous mutant PEX6 allele (c.2578C>T [p.Arg860Trp]) was overrepresented due to allelic expression imbalance (AEI). We demonstrated that AEI of PEX6 is a common phenomenon and is correlated with heterozygosity for a frequent variant in the 3' untranslated region (UTR) of the mutant allele, which disrupts the most distal of two polyadenylation sites. Asymptomatic parents, who were heterozygous for PEX c.2578C>T, did not show AEI and were homozygous for the 3' UTR variant. Overexpression models confirmed that the overrepresentation of the pathogenic PEX6 c.2578T variant compared to wild-type PEX6 c.2578C results in a peroxisome biogenesis defect and thus constitutes the cause of disease in the affected individuals. AEI promoting the overrepresentation of a mutant allele might also play a role in other autosomal-recessive disorders, in which only one heterozygous pathogenic variant is identified.

PMID: 29220678 [PubMed - indexed for MEDLINE]

Wiedemann-Steiner Syndrome With 2 Novel KMT2A Mutations.

J Child Neurol. 2017 Feb;32(2):237-242

Authors: Min Ko J, Cho JS, Yoo Y, Seo J, Choi M, Chae JH, Lee HR, Cho TJ

Abstract
Wiedemann-Steiner syndrome is a rare genetic disorder characterized by short stature, hairy elbows, facial dysmorphism, and developmental delay. It can also be accompanied by musculoskeletal anomalies such as muscular hypotonia and small hands and feet. Mutations in the KMT2A gene have only recently been identified as the cause of Wiedemann-Steiner syndrome; therefore, only 16 patients from 15 families have been described, and new phenotypic features continue to be added. In this report, we describe 2 newly identified patients with Wiedemann-Steiner syndrome who presented with variable severity. One girl exhibited developmental dysplasia of the hip and fibromatosis colli accompanied by other clinical features, including facial dysmorphism, hypertrichosis, patent ductus arteriosus, growth retardation, and borderline intellectual disability. The other patient, a boy, showed severe developmental retardation with automatic self-mutilation, facial dysmorphism, and hypertrichosis at a later age. Exome sequencing analysis of these patients and their parents revealed a de novo nonsense mutation, p.Gln1978*, of KMT2A in the former, and a missense mutation, p.Gly1168Asp, in the latter, which molecularly confirmed the diagnosis of Wiedemann-Steiner syndrome.

PMID: 27777327 [PubMed - indexed for MEDLINE]