Mitochondrial leukoencephalopathies: A border zone between acquired and inherited white matter disorders in children?

Mult Scler Relat Disord. 2018 Feb;20:84-92

Authors: Bindu PS, Sonam K, Chiplunkar S, Govindaraj P, Nagappa M, Vekhande CC, Aravinda HR, Ponmalar JJ, Mahadevan A, Gayathri N, Bharath MS, Sinha S, Taly AB

Abstract
BACKGROUND: There is emerging evidence implicating mitochondrial dysfunction in the pathogenesis of acquired demyelinating disorders such as multiple sclerosis. On the other hand, some of the primary mitochondrial disorders such as mitochondrial leukoencephalopathies exhibit evidence of neuroinflammation on MRI. The inter-relationship between mitochondrial disorders and episodic CNS inflammation needs exploration because of the therapeutic implications.
OBJECTIVE: We sought to analyze the clinical course and MRI characteristics in a cohort of patients with mitochondrial leukoencephalopathy to determine features, if any, that mimic primary demyelinating disorders. Therapeutic implications of these findings are discussed.
PATIENTS AND METHODS: Detailed analysis of the clinical course, magnetic resonance imaging findings and therapeutic response was performed in 14 patients with mitochondrial leukoencephalopathy. The diagnosis was ascertained by clinical features, histopathology, respiratory chain enzyme assays and exome sequencing.
RESULTS: Fourteen patients [Age at evaluation: 2-7 yrs, M: F-1:1] were included in the study. The genetic findings included variations in NDUFA1 (1); NDUFV1 (4); NDUFS2 (2); LYRM (2);MPV17(1); BOLA3(2); IBA57(2). Clinical Features which mimicked acquired demyelinating disorder included acute onset focal deficits associated with encephalopathy [10/14, 71%], febrile illness preceding the onset [7/14, 50%] unequivocal partial or complete steroid responsiveness [11/11], episodic/ relapsing remitting neurological dysfunction [10/14, 71%] and a subsequent stable rather than a progressive course [12/14, 85%]. MRI characteristics included confluent white matter lesions [14/14, 100%], diffusion restriction [11/14,78.5%], contrast enhancement [13/13,100%], spinal cord involvement [8/13,61.5%], lactate peak on MRS [13/13] and white matter cysts [13/14, 92.8%].
CONCLUSION: Clinical presentations of mitochondrial leukoencephalopathy often mimic an acquired demyelinating disorder. The therapeutic implications of these observations require further exploration.

PMID: 29353736 [PubMed - indexed for MEDLINE]

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Whole genome sequencing of melanomas in adolescent and young adults reveals distinct mutation landscapes and the potential role of germline variants in disease susceptibility.

Int J Cancer. 2018 Sep 04;:

Authors: Wilmott JS, Johansson PA, Newell F, Waddell N, Ferguson P, Quek C, Patch AM, Nones K, Shang P, Pritchard AL, Kazakoff S, Holmes O, Leonard C, Wood S, Xu Q, Saw RPM, Spillane AJ, Stretch JR, Shannon KF, Kefford RF, Menzies AM, Long GV, Thompson JF, Pearson JV, Mann GJ, Hayward NK, Scolyer RA

Abstract
Cutaneous melanoma accounts for at least >10% of all cancers in adolescents and young adults (AYA, 15-30 years of age) in Western countries. To date, little is known about the correlations between germline variants and somatic mutations and mutation signatures in AYA melanoma patients that might explain why they have developed a cancer predominantly affecting those over 65 years of age. We performed genomic analysis of 50 AYA melanoma patients (onset 10-30 years, median 20); 25 underwent whole genome sequencing (WGS) of both tumour and germline DNA, exome data was retrieved from 12 TCGA AYA cases, and targeted DNA sequencing was conducted on 13 cases. The AYA cases were compared with WGS data from 121 adult cutaneous melanomas. Similar to mature adult cutaneous melanomas, AYA melanomas showed a high mutation burden and mutation signatures of ultraviolet radiation (UVR) damage. The frequencies of somatic mutations in BRAF (96%) and PTEN (36%) in the AYA WGS cohort were double the rates observed in adult melanomas (Q< 6.0x10-6 and 0.028, respectively). Furthermore, AYA melanomas contained a higher proportion of non-UVR related mutation signatures than mature adult melanomas as a proportion of total mutation burden (P=2.0x10-4 ). Interestingly, these non-UVR mutation signatures relate to APOBEC or mismatch repair pathways, and germline variants in related genes were observed in some of these cases. We conclude that AYA melanomas harbour some of the same molecular aberrations and mutagenic insults occurring in older adults, but in different proportions. Germline variants that may have conferred disease susceptibility correlated with somatic mutation signatures in a subset of AYA melanomas. This article is protected by copyright. All rights reserved.

PMID: 30178487 [PubMed - as supplied by publisher]

Loss of protocadherin-12 leads to Diencephalic-Mesencephalic Junction Dysplasia syndrome.

Ann Neurol. 2018 Sep 03;:

Authors: Guemez-Gamboa A, Çağlayan AO, Stanley V, Gregor A, Zaki M, Saleem SN, Musaev D, McEvoy-Venneri J, Belandres D, Akizu N, Silhavy JL, Schroth J, Rosti RO, Copeland B, Lewis SM, Fang R, Issa MY, Per H, Gumus H, Bayram AK, Kumandas S, Akgumus GT, Erson-Omay EZ, Yasuno K, Bilguvar K, Gali H, Pillar N, Shomron N, Weissglas-Volkov D, Porat Y, Einhorn Y, Gabriel S, Ben-Zeev B, Gunel M, Gleeson JG

Abstract
Objective To identify causes of the autosomal recessive malformation diencephalic-mesencephalic junction dysplasia (DMJD) syndrome.
METHODS: Eight families with DMJD were studied by whole exome or targeted sequencing, with detailed clinical and radiological characterization. Patient-derived induced pluripotent stem cells were derived into neural precursor and endothelial cells to study gene expression.
RESULTS: All patients showed bi-allelic mutations in the non-clustered protocadherin-12 (PCDH12) gene. The characteristic clinical presentation included progressive microcephaly, craniofacial dysmorphism, psychomotor disability, epilepsy, and axial hypotonia with variable appendicular spasticity. Brain imaging showed brainstem malformations and with frequent thinned corpus callosum with punctate brain calcifications, reflecting expression of PCDH12 in neural and endothelial cells. These cells showed lack of PCDH12 expression and impaired neurite outgrowth.
INTERPRETATION: DMJD patients have bi-allelic mutations in PCDH12 and lack of protein expression. These patients present with characteristic microcephaly and frequent abnormal white matter tracts. Such pathogenic variants predict a poor outcome as a result of brainstem malformation and evidence of white matter tract defects, and should be added to the phenotypic spectrum associated with PCDH12-related conditions. This article is protected by copyright. All rights reserved.

PMID: 30178464 [PubMed - as supplied by publisher]

Genetic Determinants of IgA Nephropathy: Western Perspective.

Semin Nephrol. 2018 Sep;38(5):443-454

Authors: Neugut YD, Kiryluk K

Abstract
IgA nephropathy (IgAN) represents a genetically complex multifactorial trait. Its prevalence and clinical features vary geographically, and the disease has a range of clinical presentations that suggest multiple subtypes. Although familial aggregation of IgAN has been reported and prior linkage studies have highlighted significant locus heterogeneity, specific genetic variants underlying familial IgAN have not yet been defined. Population-based genome-wide association studies (GWAS) have discovered nearly 20 IgAN risk loci, providing novel insights into disease epidemiology and molecular mechanisms, shifting old paradigms of the disease pathogenesis. Follow-up fine-mapping studies have identified specific causal variants, and genotype-phenotype correlation studies have begun to delineate clinical consequences of GWAS risk alleles. The association between IgAN and galactose-deficient IgA1 (Gd-IgA1), a validated serum biomarker of IgAN, presented another avenue for genetic discovery because elevated serum levels of Gd-IgA1 are highly heritable. Recent GWAS for serum Gd-IgA1 levels provided novel insights into genetic regulation of this trait, but the genetic link between Gd-IgA1 and IgAN has not yet been established. In this review, we discuss these developments in the broader context of modern genetic approaches to complex traits, and provide our perspective on the critical challenges that need to be addressed to advance the field.

PMID: 30177016 [PubMed - in process]

Genomic case report of a low grade bladder tumor metastasis to lung.

BMC Urol. 2018 Sep 03;18(1):74

Authors: Van Every MJ, Dancik G, Paramesh V, Gurda GT, Meier DR, Cash SE, Richmond CS, Guin S

Abstract
BACKGROUND: We present a rare case where distant metastasis of a low grade bladder tumor was observed. We carried out detailed genomic analysis and cell based experiments on patient tumor samples to study tumor evolution, possible cause of disease and provide personalized treatment strategies.
CASE PRESENTATION: A man with a smoking history was diagnosed with a low-grade urothelial carcinoma of the bladder and a concurrent high-grade upper urinary tract tumor. Seven years later he had a lung metastasis. We carried out exome sequencing on all the patient's tumors and peripheral blood (germline) to identify somatic variants. We constructed a phylogenetic tree to capture how the tumors are related and to identify somatic changes important for metastasis. Although distant metastasis of low-grade bladder tumor is rare, the somatic variants in the tumors and the phylogenetic tree showed that the metastasized tumor had a mutational profile most similar to the low grade urothelial carcinoma. The primary and the metastatic tumors shared several important mutations, including in the KMT2D and the RXRA genes. The metastatic tumor also had an activating MTOR mutation, which may be important for tumor metastasis. We developed a mutational signature to understand the biologic processes responsible for tumor development. The mutational signature suggests that the tumor mutations are associated with tobacco carcinogen exposure, which is concordant with the patient's smoking history. We cultured cells from the lung metastasis to examine proliferation and signaling mechanisms in response to treatment. The mTOR inhibitor Everolimus inhibited downstream mTOR signaling and induced cytotoxicity in the metastatic tumor cells.
CONCLUSION: We used genomic analysis to examine a rare case of low grade bladder tumor metastasis to distant organ (lung). Our analysis also revealed exposure to carcinogens found is tobacco as a possible cause in tumor development. We further validated that the patient might benefit from mTOR inhibition as a potential salvage therapy in an adjuvant or recurrent disease setting.

PMID: 30176882 [PubMed - in process]

Biallelic JAK1 mutations in immunodeficient patient with mycobacterial infection.

Nat Commun. 2016 12 23;7:13992

Authors: Eletto D, Burns SO, Angulo I, Plagnol V, Gilmour KC, Henriquez F, Curtis J, Gaspar M, Nowak K, Daza-Cajigal V, Kumararatne D, Doffinger R, Thrasher AJ, Nejentsev S

Abstract
Mutations in genes encoding components of the immune system cause primary immunodeficiencies. Here, we study a patient with recurrent atypical mycobacterial infection and early-onset metastatic bladder carcinoma. Exome sequencing identified two homozygous missense germline mutations, P733L and P832S, in the JAK1 protein that mediates signalling from multiple cytokine receptors. Cells from this patient exhibit reduced JAK1 and STAT phosphorylation following cytokine stimulations, reduced induction of expression of interferon-regulated genes and dysregulated cytokine production; which are indicative of signalling defects in multiple immune response pathways including Interferon-γ production. Reconstitution experiments in the JAK1-deficient cells demonstrate that the impaired JAK1 function is mainly attributable to the effect of the P733L mutation. Further analyses of the mutant protein reveal a phosphorylation-independent role of JAK1 in signal transduction. These findings clarify JAK1 signalling mechanisms and demonstrate a critical function of JAK1 in protection against mycobacterial infection and possibly the immunological surveillance of cancer.

PMID: 28008925 [PubMed - indexed for MEDLINE]

Rare disruptive mutations in ciliary function genes contribute to testicular cancer susceptibility.

Nat Commun. 2016 12 20;7:13840

Authors: Litchfield K, Levy M, Dudakia D, Proszek P, Shipley C, Basten S, Rapley E, Bishop DT, Reid A, Huddart R, Broderick P, Castro DG, O'Connor S, Giles RH, Houlston RS, Turnbull C

Abstract
Testicular germ cell tumour (TGCT) is the most common cancer in young men. Here we sought to identify risk factors for TGCT by performing whole-exome sequencing on 328 TGCT cases from 153 families, 634 sporadic TGCT cases and 1,644 controls. We search for genes that are recurrently affected by rare variants (minor allele frequency <0.01) with potentially damaging effects and evidence of segregation in families. A total of 8.7% of TGCT families carry rare disruptive mutations in the cilia-microtubule genes (CMG) as compared with 0.5% of controls (P=2.1 × 10-8). The most significantly mutated CMG is DNAAF1 with biallelic inactivation and loss of DNAAF1 expression shown in tumours from carriers. DNAAF1 mutation as a cause of TGCT is supported by a dnaaf1hu255h(+/-) zebrafish model, which has a 94% risk of TGCT. Our data implicate cilia-microtubule inactivation as a cause of TGCT and provide evidence for CMGs as cancer susceptibility genes.

PMID: 27996046 [PubMed - indexed for MEDLINE]

The severity of hereditary porphyria is modulated by the porphyrin exporter and Lan antigen ABCB6.

Nat Commun. 2016 08 10;7:12353

Authors: Fukuda Y, Cheong PL, Lynch J, Brighton C, Frase S, Kargas V, Rampersaud E, Wang Y, Sankaran VG, Yu B, Ney PA, Weiss MJ, Vogel P, Bond PJ, Ford RC, Trent RJ, Schuetz JD

Abstract
Hereditary porphyrias are caused by mutations in genes that encode haem biosynthetic enzymes with resultant buildup of cytotoxic metabolic porphyrin intermediates. A long-standing open question is why the same causal porphyria mutations exhibit widely variable penetrance and expressivity in different individuals. Here we show that severely affected porphyria patients harbour variant alleles in the ABCB6 gene, also known as Lan, which encodes an ATP-binding cassette (ABC) transporter. Plasma membrane ABCB6 exports a variety of disease-related porphyrins. Functional studies show that most of these ABCB6 variants are expressed poorly and/or have impaired function. Accordingly, homozygous disruption of the Abcb6 gene in mice exacerbates porphyria phenotypes in the Fech(m1Pas) mouse model, as evidenced by increased porphyrin accumulation, and marked liver injury. Collectively, these studies support ABCB6 role as a genetic modifier of porphyria and suggest that porphyrin-inducing drugs may produce excessive toxicities in individuals with the rare Lan(-) blood type.

PMID: 27507172 [PubMed - indexed for MEDLINE]

Meta-analysis of exome array data identifies six novel genetic loci for lung function.

Wellcome Open Res. 2018;3:4

Authors: Jackson VE, Latourelle JC, Wain LV, Smith AV, Grove ML, Bartz TM, Obeidat M, Province MA, Gao W, Qaiser B, Porteous DJ, Cassano PA, Ahluwalia TS, Grarup N, Li J, Altmaier E, Marten J, Harris SE, Manichaikul A, Pottinger TD, Li-Gao R, Lind-Thomsen A, Mahajan A, Lahousse L, Imboden M, Teumer A, Prins B, Lyytikäinen LP, Eiriksdottir G, Franceschini N, Sitlani CM, Brody JA, Bossé Y, Timens W, Kraja A, Loukola A, Tang W, Liu Y, Bork-Jensen J, Justesen JM, Linneberg A, Lange LA, Rawal R, Karrasch S, Huffman JE, Smith BH, Davies G, Burkart KM, Mychaleckyj JC, Bonten TN, Enroth S, Lind L, Brusselle GG, Kumar A, Stubbe B, Understanding Society Scientific Group, Kähönen M, Wyss AB, Psaty BM, Heckbert SR, Hao K, Rantanen T, Kritchevsky SB, Lohman K, Skaaby T, Pisinger C, Hansen T, Schulz H, Polasek O, Campbell A, Starr JM, Rich SS, Mook-Kanamori DO, Johansson Å, Ingelsson E, Uitterlinden AG, Weiss S, Raitakari OT, Gudnason V, North KE, Gharib SA, Sin DD, Taylor KD, O'Connor GT, Kaprio J, Harris TB, Pederson O, Vestergaard H, Wilson JG, Strauch K, Hayward C, Kerr S, Deary IJ, Barr RG, de Mutsert R, Gyllensten U, Morris AP, Ikram MA, Probst-Hensch N, Gläser S, Zeggini E, Lehtimäki T, Strachan DP, Dupuis J, Morrison AC, Hall IP, Tobin MD, London SJ

Abstract
Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.

PMID: 30175238 [PubMed]

Two novel homozygous missense mutations identified in the BSND gene in Moroccan patients with Bartter's syndrome.

Int J Pediatr Otorhinolaryngol. 2018 Oct;113:46-50

Authors: Elrharchi S, Riahi Z, Salime S, Nahili H, Rouba H, Kabine M, Bonnet C, Petit C, Barakat A

Abstract
OBJECTIVES: Hearing loss (HL) is one of the most common sensorineural disorders. In the present study, we identified two novel missense mutations in BSND gene causing Bartter syndrome type IV which is a genetic disease with an autosomal recessive transmission, characterized by hypokalaemia, metabolic alkalosis, an elevation in plasma renin activity and hyperaldosteronism as well as sensorineural deafness.
METHODS: Whole-exome sequencing was performed to study the genetic causes of Hearing loss in two unrelated patients from two Moroccan families.
RESULTS: The two novel homozygous mutations p.Arg8Gly (c.22C > G), p.Thr36Asn (c.107C > A) in exon 1 of BSND gene which encodes barttin were identified in 7 patients belonging to two unrelated families originated from central region of Morocco.
CONCLUSION: We identified two novel missense mutations p.Arg8Gly and p.Thr36Asn in exon 1 of BSND gene; both mutations were described for the first time in Moroccan patients with Bartter syndrome type IV.

PMID: 30174009 [PubMed - in process]

A balanced translocation disrupting SCN5A in a family with Brugada syndrome and sudden cardiac death.

Heart Rhythm. 2018 Aug 28;:

Authors: Yeates L, Ingles J, Gray B, Singarayar S, Sy RW, Semsarian C, Bagnall RD

Abstract
BACKGROUND: Brugada Syndrome (BrS) is a primary arrhythmia syndrome affecting 1 in 2000 of the general population. Genetic testing identifies pathogenic variants in the sodium voltage-gated channel α-subunit 5 gene (SCN5A) in up to 25% of familial BrS. Balanced translocations, which involve the exchange of the ends of two different chromosomes, are found in approximately 1 in 500 people and are usually benign, and only rarely reported to cause arrhythmogenic disorders.
OBJECTIVE: Identify the genetic mechanism underlying a family with BrS, sick sinus syndrome, cardiac hypertrophy, sudden cardiac death, and multiple miscarriages.
METHODS: We clinically evaluated family members with an electrocardiogram, 2D echocardiogram, and provocation testing with Ajmaline challenge. Cytogenetic testing included karyotype and fluorescent in-situ hybridisation (FISH) analysis. We performed gene panel, exome, and genome sequencing analysis.
RESULTS: Sequencing of 128 cardiac genes, and exome sequencing, of a family with BrS, sick sinus syndrome, cardiac hypertrophy, sudden cardiac death, and multiple miscarriages did not find a pathogenic variant. Karyotype and FISH analysis identified a balanced translocation breaking the SCN5A gene on chromosome 3 and the multiple chromosome maintenance 10 gene (MCM10) on chromosome 10 t(3;10)(p22.2;p13). We characterised both translocation breakpoint junctions using genome sequencing and found no regions of sequence homology.
CONCLUSIONS: A balanced translocation breaking SCN5A is a novel mechanism underlying disease in a family with BrS, sick sinus syndrome, cardiac hypertrophy, and sudden cardiac death. Genome sequencing can identify rare chromosomal aberrations causing inherited diseases that may otherwise be missed using gene panel and exome sequencing-based approaches.

PMID: 30170230 [PubMed - as supplied by publisher]

Hypomorphic CARD11 mutations associated with diverse immunologic phenotypes with or without atopic disease.

J Allergy Clin Immunol. 2018 Aug 28;:

Authors: Dorjbal B, Stinson JR, Ma CA, Weinreich MA, Miraghazadeh B, Hartberger JM, Frey-Jakobs S, Weidinger S, Moebus L, Franke A, Schäffer AA, Bulashevska A, Fuchs S, Ehl S, Limaye S, Arkwright PD, Briggs TA, Langley C, Bethune C, Whyte AF, Alachkar H, Nejentsev S, DiMaggio T, Nelson CG, Stone KD, Nason M, Brittain EH, Oler AJ, Veltri DP, Leahy TR, Conlon N, Poli MC, Borzutzky A, Cohen JI, Davis J, Lambert MP, Romberg N, Sullivan KE, Paris K, Freeman AF, Lucas L, Chandrasakan S, Savic S, Hambleton S, Patel SY, Jordan MB, Theos A, Lebensburger J, Atkinson TP, Torgerson TR, Chinn IK, Milner JD, Grimbacher B, Cook MC, Snow AL

Abstract
BACKGROUND: CARD11 encodes a scaffold protein in lymphocytes that links antigen receptor engagement with downstream signaling to NF-κB, JNK, and mTORC1. Germline CARD11 mutations cause several distinct primary immune disorders in humans, including SCID (biallelic null mutations), B cell Expansion with NF-κB and T cell Anergy (BENTA; heterozygous, gain-of-function mutations), and severe atopic disease (loss-of-function, heterozygous, dominant interfering mutations), which has focused attention on CARD11 mutations discovered by whole exome sequencing.
OBJECTIVES: To determine the molecular actions of an extended allelic series of CARD11, and to characterize the expanding range of clinical phenotypes associated with heterozygous CARD11 loss-of-function alleles.
METHODS: Cell transfections and primary T cell assays were utilized to evaluate signaling and function of CARD11 variants.
RESULTS: Here we report on an expanded cohort of patients harboring novel heterozygous CARD11 mutations that extend beyond atopy to include other immunologic phenotypes not previously associated with CARD11 mutations. In addition to (and sometimes excluding) severe atopy, heterozygous missense and indel mutations in CARD11 presented with immunologic phenotypes similar to those observed in STAT3-LOF, DOCK8 deficiency, common variable immune deficiency (CVID), neutropenia, and immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX)-like syndrome. Pathogenic variants exhibited dominant negative activity, and were largely confined to the CARD or coiled-coil domains of the CARD11 protein.
CONCLUSION: These results illuminate a broader phenotypic spectrum associated with CARD11 mutations in humans, and underscore the need for functional studies to demonstrate that rare gene variants encountered in expected and unexpected phenotypes must nonetheless be validated for pathogenic activity.

PMID: 30170123 [PubMed - as supplied by publisher]

Rare coding variant analysis in a large cohort of Ashkenazi Jewish families with inflammatory bowel disease.

Hum Genet. 2018 Aug 22;:

Authors: Schiff ER, Frampton M, Ben-Yosef N, Avila BE, Semplici F, Pontikos N, Bloom SL, McCartney SA, Vega R, Lovat LB, Wood E, Hart A, Israeli E, Crespi D, Furman MA, Mann S, Murray CD, Segal AW, Levine AP

Abstract
Rare variants are thought to contribute to the genetics of inflammatory bowel disease (IBD), which is more common amongst the Ashkenazi Jewish (AJ) population. A family-based approach using exome sequencing of AJ individuals with IBD was employed with a view to identify novel rare genetic variants for this disease. Exome sequencing was performed on 960 Jewish individuals including 513 from 199 multiplex families with up to eight cases. Rare, damaging variants in loci prioritized by linkage analysis and those shared by multiple affected individuals within the same family were identified. Independent evidence of association of each variant with disease was assessed. A number of candidate variants were identified, including in genes involved in the immune system. The ability to achieve statistical significance in independent case/control replication data was limited by power and was only achieved for variants in the well-established Crohn's disease gene, NOD2. This work demonstrates the challenges of identifying disease-associated rare damaging variants from exome data, even amongst a favorable cohort of familial cases from a genetic isolate. Further research of the prioritized rare candidate variants is required to confirm their association with the disease.

PMID: 30167848 [PubMed - as supplied by publisher]

IDENTIFYING NEW SUDDEN DEATH GENES.

Trans Am Clin Climatol Assoc. 2018;129:183-184

Authors: London B, Greiner AM, Mehdi H, Gutmann R

Abstract
Inherited conditions that lead to cardiac arrhythmias and sudden cardiac death remain an important cause of morbidity and mortality. Identifying the genes responsible for these rare conditions can provide insights into the more common and heritable forms of sudden cardiac death seen in patients with structural heart disease. We and others have used candidate gene approaches and positional cloning in large families to show that mutations in ion channels and ion channel related proteins cause familial arrhythmia syndromes including long QT and Brugada syndromes. The genes responsible for many familial arrhythmia syndromes and the vast majority of the predisposition to common arrhythmias remain unknown. Using whole exome sequencing in families with Brugada syndrome and idiopathic ventricular fibrillation, we now seek to identify mutations in genes previously not thought to play a significant role in the heart.

PMID: 30166713 [PubMed - in process]

ATR inhibition is a promising radiosensitizing strategy for triple negative breast cancer.

Mol Cancer Ther. 2018 Aug 30;:

Authors: Tu X, Kahila MM, Zhou Q, Yu J, Kalari KR, Wang L, Harmsen WS, Yuan J, Boughey JC, Goetz MP, Sarkaria JN, Lou Z, Mutter RW

Abstract
Triple negative breast cancer (TNBC) is characterized by elevated locoregional recurrence risk despite aggressive local therapies. New tumor-specific radiosensitizers are needed. We hypothesized that the ATR inhibitor, VX-970, would preferentially radiosensitize TNBC. Non-cancerous breast epithelial and TNBC cell lines were investigated in clonogenic survival, cell cycle, and DNA damage signaling and repair assays. In addition, patient-derived xenograft (PDX) models generated prospectively as part of a neoadjuvant chemotherapy study from either baseline tumor biopsies or surgical specimens with chemoresistant residual disease were assessed for sensitivity to fractionated radiotherapy, VX-970, or the combination. To explore potential response biomarkers, exome sequencing was assessed for germ-line and/or somatic alterations in homologous recombination (HR) genes and other alterations associated with ATR inhibitor sensitivity. VX-970 preferentially inhibited ATR-Chk1-CDC25a signaling, abrogated the radiotherapy-induced G2/M checkpoint, delayed resolution of DNA double strand breaks and reduced colony formation after radiotherapy in TNBC cells relative to normal-like breast epithelial cells. In vivo, VX-970 did not exhibit significant single agent activity at the dose administered even in the context of genomic alterations predictive of ATR inhibitor responsiveness, but significantly sensitized TNBC PDXs to radiotherapy. Exome sequencing and functional testing demonstrated that combination therapy was effective in both HR proficient and deficient models. PDXs established from patients with chemoresistant TNBC were also highly radiosensitized. In conclusion, VX-970 is a tumor specific radiosensitizer for TNBC. Patients with residual TNBC after neoadjuvant chemotherapy, a subset at particularly high risk of relapse, may be ideally suited for this treatment intensification strategy.

PMID: 30166399 [PubMed - as supplied by publisher]

Non-HFE mutations in haemochromatosis in China: combination of heterozygous mutations involving HJV signal peptide variants.

J Med Genet. 2018 Aug 30;:

Authors: Lv T, Zhang W, Xu A, Li Y, Zhou D, Zhang B, Li X, Zhao X, Wang Y, Wang X, Duan W, Wang Q, Xu H, Zheng J, Zhao R, Zhu L, Dong Y, Lu L, Chen Y, Long J, Zheng S, Wang W, You H, Jia J, Ou X, Huang J

Abstract
INTRODUCTION: Hereditary haemochromatosis (HH) caused by a homozygous p.C282Y mutation in haemochromatosis (HFE) gene has been well documented. However, less is known about the causative non-HFE mutation. We aimed to assess mutation patterns of haemochromatosis-related genes in Chinese patients with primary iron overload.
METHODS: Patients were preanalysed for mutations in the classic HH-related genes: HFE, HJV, HAMP, TFR2 and SLC40A1. Whole exome sequencing was conducted for cases with variants in HJV signal peptide region. Representative variants were analysed for biological function.
RESULTS: None of the cases analysed harboured the HFE p.C282Y; however, 21 of 22 primary iron-overload cases harboured at least one non-synonymous variant in the non-HFE genes. Specifically, p.E3D or p.Q6H variants in the HJV signal peptide region were identified in nine cases (40.9%). In two of three probands with the HJV p.E3D, exome sequencing identified accompanying variants in BMP/SMAD pathway genes, including TMPRSS6 p.T331M and BMP4 p.R269Q, and interestingly, SUGP2 p.R639Q was identified in all the three cases. Pedigree analysis showed a similar pattern of combination of heterozygous mutations in cases with HJV p.E3D or p.Q6H, with SUGP2 p.R639Q or HJV p.C321X being common mutation. In vitro siRNA interference of SUGP2 showed a novel role of downregulating the BMP/SMAD pathway. Site-directed mutagenesis of HJV p.Q6H/p.C321X in cell lines resulted in loss of membrane localisation of mutant HJV, and downregulation of p-SMAD1/5 and HAMP.
CONCLUSION: Compound heterozygous mutations of HJV or combined heterozygous mutations of BMP/SMAD pathway genes, marked by HJV variants in the signal peptide region, may represent a novel aetiological factor for HH.

PMID: 30166352 [PubMed - as supplied by publisher]

Mutational Landscape of Ovarian Adult Granulosa Cell Tumors from Whole Exome and Targeted TERT Promoter Sequencing.

Mol Cancer Res. 2018 Aug 30;:

Authors: Alexiadis M, Rowley SM, Chu S, Leung DTH, Stewart CJR, Amarasinghe KC, Campbell IG, Fuller PJ

Abstract
Adult granulosa cell tumor (aGCT), the most common malignant ovarian sex cord-stromal tumor, is characterized by the forkhead transcription factor FOXL2 p.C134W somatic mutation. Late recurrences are relatively common but the molecular mechanisms of relapse or aggressive behavior are not known. The mutational landscape of FOXL2 p.C134W mutation positive tumors (n=22) was determined using whole exome sequencing (WES). An average of 64 coding and essential splice-site variants was identified per tumor. As the TERT promoter region is poorly covered by the WES, targeted sequencing identified the TERT -124C>T promoter mutation as the only recurrent mutation (~40% of cases). Pathway analysis suggested an association with DNA replication/repair and the epidermal growth factor receptor (EGFR) family canonical pathways. Copy number analysis confirmed that gains of chromosomes 12 and 14 occur in ~30% of aGCT and loss of chromosome 22 occurs in ~40% of cases. In summary, exome-wide analysis of the mutational landscape of aGCT revealed that, except for the TERT promoter mutation, recurrence and/or aggressive behavior is not defined by activation or loss of specific genes.
IMPLICATIONS: This study found that although aGCTs are defined by the presence of a common FOXL2 gene mutation, recurrence and/or aggressive behavior cannot be attributed to subsequent mutation of specific gene(s) or pathways; however, there is a high frequency of the TERT -124C>T promoter mutation which is associated with more aggressive disease.

PMID: 30166312 [PubMed - as supplied by publisher]

Elucidating the molecular pathogenesis of glioma: integrated germline and somatic profiling of a familial glioma case series.

Neuro Oncol. 2018 Aug 24;:

Authors: Jacobs DI, Fukumura K, Bainbridge MN, Armstrong GN, Tsavachidis S, Gu X, Doddapaneni HV, Hu J, Jayaseelan JC, Muzny DM, Huse JT, Bondy ML

Abstract
Background: The genomic characterization of sporadically arising gliomas has delineated molecularly and clinically distinct subclasses of disease. However, less is known about the molecular nature of gliomas that are familial in origin. We performed molecular subtyping of 163 tumor specimens from individuals with a family history of glioma and integrated germline and somatic genomic data to characterize the pathogenesis of 20 tumors in additional detail.
Methods: Immunohistochemical analyses were performed on formalin-fixed, paraffin-embedded tumor sections to determine molecular subtypes of glioma. For 20 cases, tumor DNA was exome sequenced on an Illumina HiSeq 2000 platform and copy number profiling was performed on the Illumina HumanOmniExpress BeadChip. Genotypes at glioma risk polymorphisms were determined from germline DNA profiled on the Illumina Infinium OncoArray and deleterious germline mutations were identified from germline sequencing data.
Results: All 3 molecular subtypes of sporadic glioma were represented in the overall case series, including molecular glioblastoma (n = 102), oligodendroglioma (n = 21), and astrocytoma (n = 20). Detailed profiling of 20 of these cases showed characteristic subtype-specific alterations at frequencies comparable to sporadic glioma cases. All 20 cases had alterations in genes regulating telomere length. Frequencies of common glioma risk alleles were similar to those among sporadic cases, and correlations between risk alleles and same-gene somatic mutations were not observed.
Conclusions: This study illustrates that the molecular characteristics of familial tumors profiled largely recapitulate what is known about sporadic glioma and that both germline and somatic molecular features target common core pathways involved in gliomagenesis.

PMID: 30165405 [PubMed - as supplied by publisher]

No major role for rare plectin variants in arrhythmogenic right ventricular cardiomyopathy.

PLoS One. 2018;13(8):e0203078

Authors: Hoorntje ET, Posafalvi A, Syrris P, van der Velde KJ, Bolling MC, Protonotarios A, Boven LG, Amat-Codina N, Groeneweg JA, Wilde AA, Sobreira N, Calkins H, Hauer RNW, Jonkman MF, McKenna WJ, Elliott PM, Sinke RJ, van den Berg MP, Chelko SP, James CA, van Tintelen JP, Judge DP, Jongbloed JDH

Abstract
AIMS: Likely pathogenic/pathogenic variants in genes encoding desmosomal proteins play an important role in the pathophysiology of arrhythmogenic right ventricular cardiomyopathy (ARVC). However, for a substantial proportion of ARVC patients, the genetic substrate remains unknown. We hypothesized that plectin, a cytolinker protein encoded by the PLEC gene, could play a role in ARVC because it has been proposed to link the desmosomal protein desmoplakin to the cytoskeleton and therefore has a potential function in the desmosomal structure.
METHODS: We screened PLEC in 359 ARVC patients and compared the frequency of rare coding PLEC variants (minor allele frequency [MAF] <0.001) between patients and controls. To assess the frequency of rare variants in the control population, we evaluated the rare coding variants (MAF <0.001) found in the European cohort of the Exome Aggregation Database. We further evaluated plectin localization by immunofluorescence in a subset of patients with and without a PLEC variant.
RESULTS: Forty ARVC patients carried one or more rare PLEC variants (11%, 40/359). However, rare variants also seem to occur frequently in the control population (18%, 4754/26197 individuals). Nor did we find a difference in the prevalence of rare PLEC variants in ARVC patients with or without a desmosomal likely pathogenic/pathogenic variant (14% versus 8%, respectively). However, immunofluorescence analysis did show decreased plectin junctional localization in myocardial tissue from 5 ARVC patients with PLEC variants.
CONCLUSIONS: Although PLEC has been hypothesized as a promising candidate gene for ARVC, our current study did not show an enrichment of rare PLEC variants in ARVC patients compared to controls and therefore does not support a major role for PLEC in this disorder. Although rare PLEC variants were associated with abnormal localization in cardiac tissue, the confluence of data does not support a role for plectin abnormalities in ARVC development.

PMID: 30161220 [PubMed - in process]