Detection of Variants in Patients with Idiopathic Ventricular Fibrillation by Whole-exome Sequencing.

Ann Clin Lab Sci. 2018 Jul;48(4):427-434

Authors: Chang YS, Lee CC, Huang HY, Lin KH, Chen JY, Chang KC, Chang JG

Abstract
AIMS AND BACKGROUND: Idiopathic ventricular fibrillation (IVF) is a cause of sudden cardiac death (SCD). The frequency of mutations in disease-causing genes ranges, on average, between 16 and 48% in SCD cases. This study aimed to identify novel mutations in IVF patients without KCNQ1, KCNH2, and SCN5A mutations using whole-exome sequencing (WES).
METHODS: Genomic DNA extracted from peripheral blood samples obtained from five patients with IVF and WES was used to identify mutations associated with IVF. Candidate variants were validated by Sanger sequencing.
RESULTS: Four patients harbored suspected mutations in 100 inherited cardiomyopathy-and channelopathy-associated genes (e.g., TCAP, TTN, MYPN, CACNA1C, and TNNT2). All of these genetic variants have been given a dbSNP rs number; however, their clinical significance remains unknown. Bioinformatics tools predicted severe functional disruptions in the loci harboring these suspected mutations, suggesting their pivotal roles in IVF.
CONCLUSIONS: This study revealed the effectiveness of WES for IVF patients without KCNQ1, KCNH2, and SCN5A mutations. Although it is difficult to interpret broad WES results, the analysis can provide insight into the etiology of a heterogeneous disease.

PMID: 30143482 [PubMed - in process]

Research Techniques Made Simple: Genome-Wide Homozygosity/Autozygosity Mapping Is a Powerful Tool for Identifying Candidate Genes in Autosomal Recessive Genetic Diseases.

J Invest Dermatol. 2018 Sep;138(9):1893-1900

Authors: Vahidnezhad H, Youssefian L, Jazayeri A, Uitto J

Abstract
Homozygosity mapping (HM), also known as autozygosity mapping, was originally used to map genes underlying homozygous autosomal recessive Mendelian diseases in patients from closely genetically related populations, followed by Sanger sequencing. With the increase in use of next-generation sequencing approaches, such as whole-exome sequencing and whole-genome sequencing, together with advanced bioinformatics filtering approaches, HM is again emerging as a powerful method for the identification of genes involved in disease etiology. In addition to its usefulness for research, HM is effective in clinical genetic services, increasing the efficiency of molecular diagnostics. For autosomal recessive Mendelian disorders with extensive genetic heterogeneity, HM can reduce both cost and turnaround time of mutation detection in the context of next-generation sequencing and can obviate expensive screening, such as biochemical testing in the setting of metabolic genodermatoses or antigen mapping for epidermolysis bullosa. It is therefore important for dermatology clinicians and researchers to understand the processes, principal uses, and advantages and limitations of HM when ordering or performing genetic tests for patients affected by heritable skin disorders.

PMID: 30143075 [PubMed - in process]

Next-Generation Sequencing and Mutational Analysis: Implications for Genes Encoding LINC Complex Proteins.

Methods Mol Biol. 2018;1840:321-336

Authors: Nagy PL, Worman HJ

Abstract
Targeted panel, whole exome, or whole genome DNA sequencing using next-generation sequencing (NGS) allows for extensive high-throughput investigation of molecular machines/systems such as the LINC complex. This includes the identification of genetic variants in humans that cause disease, as is the case for some genes encoding LINC complex proteins. The relatively low cost and high speed of the sequencing process results in large datasets at various stages of analysis and interpretation. For those not intimately familiar with the process, interpretation of the data might prove challenging. This review lays out the most important and most commonly used materials and methods of NGS. It also discusses data analysis and potential pitfalls one might encounter because of peculiarities of the laboratory methodology or data analysis pipelines.

PMID: 30141054 [PubMed - in process]

Novel Variants Identified in Multiple Sclerosis Patients From Southern China.

Front Neurol. 2018;9:582

Authors: Wang H, Pardeshi LA, Rong X, Li E, Wong KH, Peng Y, Xu RH

Abstract
Background: Multiple sclerosis (MS) is an autoimmune and demyelinating disease. Genome-wide association studies have shown that MS is associated with many genetic variants in some human leucocyte antigen genes and other immune-related genes, however, those studies were mostly specific to Caucasian populations. We attempt to address whether the same associations are also true for Asian populations by conducting whole-exome sequencing on MS patients from southern China. Methods: Genomic DNA was extracted from the peripheral blood mononucleocytes of 8 MS patients and 26 healthy controls and followed by exome sequencing. Results: In total, 41,227 variants were found to have moderate to high impact on their protein products. After filtering per allele frequencies according to known database, 17 variants with the allele frequency <1% or variants with undetermined frequency were identified to be unreported and have significantly different frequencies between the MS patients and healthy controls. After validation via Sanger sequencing, one rare variant located in exon 7 of TRIOBP (Chr22: 37723520G>T, Ala322Ser, rs201693690) was found to be a novel missense variant. Conclusion: MS in southern China may have association with unique genetic variants, our data suggest TRIOBP as a potential novel risk gene.

PMID: 30140248 [PubMed]

Personalized treatment based on mini patient-derived xenografts and WES/RNA sequencing in a patient with metastatic duodenal adenocarcinoma.

Cancer Commun (Lond). 2018 Aug 23;38(1):54

Authors: Zhao P, Chen H, Wen D, Mou S, Zhang F, Zheng S

Abstract
BACKGROUND: Treatment guidelines for a variety of cancers have been increasingly used in clinical practice, and have resulted in major improvement in patient outcomes. However, recommended regimens (even first-line treatments) are clearly not ideal for every patients. In the present study, we used mini patient-derived xenograft (mini-PDX) and next-generation sequencing to develop personalized treatment in a patient with metastatic duodenal adenocarcinoma.
METHODS: Resected metachronous metastatic tumor tissues were implanted into SCID mice to determine the sensitivity to a variety of drug regimens. Mutation profiles were assessed using both DNA whole-exome sequencing (DNA-WES) and RNA sequencing. The results of the analyses were used to select optimal treatment for the patient with metastatic duodenal adenocarcinoma.
RESULTS: Assessment with mini-PDX models took only 7 days. The results showed high sensitivity to S-1 plus cisplatin, gemcitabine plus cisplatin and everolimus alone. The patient received gemcitabine plus cisplatin initially, but the treatment was terminated due to toxicity. The patient was then switched to treatment with S-1 alone. The overall disease-free survival was 34 months. DNA-WES and RNA sequencing identified KRAS mutation (A146T), TP53 (C229Yfs*10) and RICTOR amplification in the metastatic duodenal adenocarcinoma. These findings provided further support to the results of the mini-PDX, and suggest mTOR inhibitors should be used if and when relapse eventually occurs in this patient.
CONCLUSIONS: Mini-PDX model combined with WES/RNA sequencing can rapidly assess drug sensitivity in cancer patients and reveal key genetic alterations. Further research on this technology for personalized therapy in patients with refractory malignant tumors is warranted.

PMID: 30139386 [PubMed - in process]

Rare PDCD11 variations are not associated with risk of schizophrenia in Japan.

Psychiatry Clin Neurosci. 2017 Nov;71(11):780-788

Authors: Hoya S, Watanabe Y, Hishimoto A, Nunokawa A, Kaneko N, Muratake T, Shinmyo N, Otsuka I, Okuda S, Inoue E, Igeta H, Shibuya M, Egawa J, Orime N, Sora I, Someya T

Abstract
AIM: Rare gene variations are thought to confer substantial risk for schizophrenia. We performed a three-stage study to identify rare variations that have a strong impact on the risk of developing schizophrenia.
METHODS: In the first stage, we prioritized rare missense variations using whole-exome sequencing (WES) data from three families, consisting of a proband, an affected sibling, and parents. In the second stage, we performed targeted resequencing of the PDCD11 coding region in 96 patients. In the third stage, we conducted an association study of rare PDCD11 variations with schizophrenia in a total of 1357 patients and 1394 controls.
RESULTS: Via WES, we identified two rare missense PDCD11 variations, p.(Asp961Asn) and p.(Val1240Leu), shared by two affected siblings within families. Targeted resequencing of the PDCD11 coding region identified three rare non-synonymous variations: p.(Asp961Asn), p.(Phe1835del), and p.(Arg1837His). The case-control study demonstrated no significant associations between schizophrenia and four rare PDCD11 variations: p.(Asp961Asn), p.(Val1240Leu), p.(Phe1835del), and p.(Arg1837His).
CONCLUSION: Our data do not support the role of rare PDCD11 variations in conferring substantial risk for schizophrenia in the Japanese population.

PMID: 28657695 [PubMed - indexed for MEDLINE]

Distinct clinical and pathological features of melorheostosis associated with somatic MAP2K1 mutations.

J Bone Miner Res. 2018 Aug 23;:

Authors: Jha S, Fratzl-Zelman N, Roschger P, Papadakis GZ, Cowen EW, Kang H, Lehky TJ, Alter K, Deng Z, Ivovic A, Flynn L, Reynolds JC, Dasgupta A, Miettinen M, Lange E, Katz J, Klaushofer K, Marini JC, Siegel RM, Bhattacharyya T

Abstract
Melorheostosis is a rare hyperostotic disease of the long bones classically characterized by a "dripping candle-wax" radiographic appearance. We recently described somatic activating mutations in MAP2K1 as a cause of melorheostosis. Here, we report distinguishing characteristics of patients with MAP2K1-positive melorheostosis. Fifteen unrelated patients with radiographic appearance of melorheostosis underwent paired biopsies of affected and unaffected bone for whole exome sequencing, histology and cell culture. Eight patients with mutations in MAP2K1 in affected bone were compared to the seven MAP2K1-negative patients to identify distinguishing characteristics. Patients with MAP2K1-positive melorheostosis had a distinct phenotype with classic "dripping candle-wax" appearance on radiographs (p= 0.01), characteristic vascular lesions on skin overlying affected bone (p= 0.01) and higher prevalence of extra-osseous mineralization and joint involvement (p= 0.04 for both). Melorheostotic bone from both MAP2K1-positive and MAP2K1-negative patients showed two zones of distinct morphology - an outer segment of parallel layers of primary lamellar bone and a deeper zone of intensely remodeled highly porous osteonal-like bone. Affected bone from MAP2K1-positive patients showed excessive osteoid (p = 0.0012), increased number of osteoblasts (p = 0.012) and osteoclasts (p = 0.04) and increased vascularity on histology in comparison to paired unaffected bone which was not seen in affected bone in most MAP2K1-negative patients. The identification of a distinct phenotype of patients with MAP2K1-positive melorheostosis demonstrates clinical and genetic heterogeneity among patients with the disease. Further studies are needed to better understand the underlying pathophysiology and associated skin findings. This article is protected by copyright. All rights reserved.

PMID: 30138550 [PubMed - as supplied by publisher]

Prolactin-Secreting Lung Adenocarcinoma Metastatic to the Pituitary Mimicking a Prolactinoma: A Case Report.

Neurosurgery. 2018 Aug 20;:

Authors: Yao H, Rui W, Zhang Y, Liu Y, Lin S, Tang H, Zhao W, Wu Z

Abstract
BACKGROUND AND IMPORTANCE: Metastasis to the pituitary gland is uncommon in patients with systemic disseminated cancer. Individual articles have reported cases of pituitary metastasis mimicking a prolactinoma, but no case of a prolactin-secreting tumor metastasizing to the pituitary mimicking a prolactinoma has been reported so far.
CLINICAL PRESENTATION: This article reports a 67-yr-old man with a recent onset of headaches, ophthalmoplegia, hypopituitarism, and hyperprolactinemia who was initially diagnosed with prolactinoma and given bromocriptine in the local hospital. Because of vomiting after taking drugs, he was transferred to our hospital for further diagnosis and treatment. Serum prolactin was elevated up to 1022 ng/mL, and pituitary magnetic resonance imaging revealed a 2.9 × 2.8 × 2.3 cm sellar mass with pituitary apoplexy, for which endoscopic transsphenoidal surgery was performed. Postoperative pathology and western blotting disclosed a prolactin-positive metastatic lung adenocarcinoma. Whole exome sequencing revealed a number of gene mutations including KRAS, PIK3CA, ALK, and CTNNB1. The patient died of deterioration of the lung disease 3 mo after the initial diagnosis.
CONCLUSION: To the best of our knowledge, this is the first report of a prolactin-secreting tumor metastasizing to the pituitary mimicking a prolactinoma as confirmed by both immunohistochemistry and western blot. Prolactin secretion is rare and elusive, and may associate with specified gene mutations.

PMID: 30137505 [PubMed - as supplied by publisher]

Heterozygous Mutations in TBX1 as a Cause of Isolated Hypoparathyroidism.

J Clin Endocrinol Metab. 2018 Aug 20;:

Authors: Li D, Gordon CT, Oufadem M, Amiel J, Kanwar HS, Bakay M, Wang T, Hakonarson H, Levine MA

Abstract
Context: Most cases of autosomal dominant isolated hypoparathyroidism are caused by gain-of-function mutations in CASR or GNA11, or dominant negative mutations in GCM2 or PTH.
Objective: To identify the genetic etiology for dominantly transmitted isolated hypoparathyroidism in two multigenerational families with 14 affected family members.
Methods: We performed whole exome sequencing of DNA from two families and examined the consequences of mutations by minigene splicing assay.
Results: We discovered disease-causing mutations in both families. A novel splice-altering mutation in TBX1 (c.1009+1G>C), leading to skipping of exon 8 (101 bp), was identified in ten affected family members and five unaffected subjects of Family A, indicating reduced penetrance for this point mutation. Adjacent to the mutation identified in Family A, we identified another novel splice-altering mutation (c.1009+2T>C) that results in skipping of the same exon, in a second family from France (Family B), in which two subjects had isolated hypoparathyroidism while a third subject manifested the clinical triad of the 22q11.2 deletion syndrome, indicative of variable expressivity.
Conclusions: We report the first evidence that heterozygous TBX1 mutations can cause isolated hypoparathyroidism. This study adds knowledge to the increasingly expanding list of causative and candidate genes in isolated hypoparathyroidism.

PMID: 30137364 [PubMed - as supplied by publisher]

Evofosfamide for the treatment of human papillomavirus-negative head and neck squamous cell carcinoma.

JCI Insight. 2018 Aug 23;3(16):

Authors: Jamieson SM, Tsai P, Kondratyev MK, Budhani P, Liu A, Senzer NN, Chiorean EG, Jalal SI, Nemunaitis JJ, Kee D, Shome A, Wong WW, Li D, Poonawala-Lohani N, Kakadia PM, Knowlton NS, Lynch CR, Hong CR, Lee TW, Grénman RA, Caporiccio L, McKee TD, Zaidi M, Butt S, Macann AM, McIvor NP, Chaplin JM, Hicks KO, Bohlander SK, Wouters BG, Hart CP, Print CG, Wilson WR, Curran MA, Hunter FW

Abstract
Evofosfamide (TH-302) is a clinical-stage hypoxia-activated prodrug of a DNA-crosslinking nitrogen mustard that has potential utility for human papillomavirus (HPV) negative head and neck squamous cell carcinoma (HNSCC), in which tumor hypoxia limits treatment outcome. We report the preclinical efficacy, target engagement, preliminary predictive biomarkers and initial clinical activity of evofosfamide for HPV-negative HNSCC. Evofosfamide was assessed in 22 genomically characterized cell lines and 7 cell line-derived xenograft (CDX), patient-derived xenograft (PDX), orthotopic, and syngeneic tumor models. Biomarker analysis used RNA sequencing, whole-exome sequencing, and whole-genome CRISPR knockout screens. Five advanced/metastatic HNSCC patients received evofosfamide monotherapy (480 mg/m2 qw × 3 each month) in a phase 2 study. Evofosfamide was potent and highly selective for hypoxic HNSCC cells. Proliferative rate was a predominant evofosfamide sensitivity determinant and a proliferation metagene correlated with activity in CDX models. Evofosfamide showed efficacy as monotherapy and with radiotherapy in PDX models, augmented CTLA-4 blockade in syngeneic tumors, and reduced hypoxia in nodes disseminated from an orthotopic model. Of 5 advanced HNSCC patients treated with evofosfamide, 2 showed partial responses while 3 had stable disease. In conclusion, evofosfamide shows promising efficacy in aggressive HPV-negative HNSCC, with predictive biomarkers in development to support further clinical evaluation in this indication.

PMID: 30135316 [PubMed - as supplied by publisher]

[Genetic and biochemical features of the monogenic hereditary urolithiasis].

Biomed Khim. 2018 Aug;64(4):315-325

Authors: Mikhaylenko DS, Prosyannikov MY, Baranova A, Nemtsova MV

Abstract
Urolithiasis is a common urological problem. In most cases, this multifactorial pathology develops due to the combination of inherited low-penetrance gene variants and environment factors such as urinary tract infections and unbalanced diet. However, some cases are monogenic. These hereditary forms of urolithiasis manifest in childhood, and are characterized by multiple, bilateral and recurrent kidney stones and progress to chronic renal failure relatively early. Due to widening acceptance of exome and gene panel sequencing, substantially larger percentages of urolithiasis cases are now attributed to hereditary causes, up to 20% among patients of 18 years old or younger. Here we review genetic and biochemical mechanisms of urolithiasis, with an emphasis on its hereditary forms, including fermentopathies (primary hyperoxaluria, adenine phosphorobosyltransferase deficiency, phosphoribosyl-pyrophosphate-synthetase deficiency, xanthinuria, Lesch-Nihan syndrome) and these caused by membrane transport alterations (Dent's disease, familial hypomagnesia with hypercalciuria and nephrocalcinosis, hypophosphatemic urolithiasis, distal tubular acidosis, cystinuria, Bartter's syndrome). We suggest a comprehensive gene panel for NGS diagnostics of the hereditary urolithiasis. It is expected that accurate and timely diagnosis of hereditary forms of urolithiasis would enable the counselling of the carriers in affected families, and ensure personalized management of the patients with these conditions.

PMID: 30135278 [PubMed - in process]

Prevalence Estimates of Polycystic Kidney and Liver Disease by Population Sequencing.

J Am Soc Nephrol. 2018 Aug 22;:

Authors: Lanktree MB, Haghighi A, Guiard E, Iliuta IA, Song X, Harris PC, Paterson AD, Pei Y

Abstract
BACKGROUND: Estimating the prevalence of autosomal dominant polycystic kidney disease (ADPKD) is challenging because of age-dependent penetrance and incomplete clinical ascertainment. Early studies estimated the lifetime risk of ADPKD to be about one per 1000 in the general population, whereas recent epidemiologic studies report a point prevalence of three to five cases per 10,000 in the general population.
METHODS: To measure the frequency of high-confidence mutations presumed to be causative in ADPKD and autosomal dominant polycystic liver disease (ADPLD) and estimate lifetime ADPKD prevalence, we used two large, population sequencing databases, gnomAD (15,496 whole-genome sequences; 123,136 exome sequences) and BRAVO (62,784 whole-genome sequences). We used stringent criteria for defining rare variants in genes involved in ADPKD (PKD1, PKD2), ADPLD (PRKCSH, SEC63, GANAB, ALG8, SEC61B, LRP5), and potential cystic disease modifiers; evaluated variants for quality and annotation; compared variants with data from an ADPKD mutation database; and used bioinformatic tools to predict pathogenicity.
RESULTS: Identification of high-confidence pathogenic mutations in whole-genome sequencing provided a lower boundary for lifetime ADPKD prevalence of 9.3 cases per 10,000 sequenced. Estimates from whole-genome and exome data were similar. Truncating mutations in ADPLD genes and genes of potential relevance as cyst modifiers were found in 20.2 cases and 103.9 cases per 10,000 sequenced, respectively.
CONCLUSIONS: Population whole-genome sequencing suggests a higher than expected prevalence of ADPKD-associated mutations. Loss-of-function mutations in ADPLD genes are also more common than expected, suggesting the possibility of unrecognized cases and incomplete penetrance. Substantial rare variation exists in genes with potential for phenotype modification in ADPKD.

PMID: 30135240 [PubMed - as supplied by publisher]

A Cluster of Nucleotide-Binding Site-Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL.

Plant Genome. 2016 07;9(2):

Authors: Cantalapiedra CP, Contreras-Moreira B, Silvar C, Perovic D, Ordon F, Gracia MP, Igartua E, Casas AM

Abstract
Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus) conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig. Closer inspection of the region revealed a cluster of closely related NBS-LRR (nucleotide-binding site-leucine-rich repeat containing protein) genes. Large differences were found between the resistant lines and the reference genome of cultivar Morex, in the form of PAV (presence-absence variation) in the composition of the NBS-LRR cluster. Finally, a template-guided assembly was performed and subsequent expression analysis revealed that one of the new assembled candidate genes is transcribed. In summary, the results suggest that NBS-LRR genes, absent from the reference and the susceptible genotypes, could be functional and responsible for the powdery mildew resistance. The procedure followed is an example of the use of NGS (next-generation sequencing) tools to tackle the challenges of gene cloning when the target gene is absent from the reference genome.

PMID: 27898833 [PubMed - indexed for MEDLINE]

Reduced cerebrospinal fluid monoamines in Alexander's disease: a clue to a symptomatic therapy.

Eur J Neurol. 2018 Sep;25(9):e105-e106

Authors: Casarejos MJ, Lorenzo-Sanz G, Perez-Torres P, Mateo-Montero R, Villadoniga M, Belanger A, López-Viñas L, Bazán E, Braun J, Jimenez-Escrig A

PMID: 30134051 [PubMed - in process]

Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience.

Mol Genet Genomic Med. 2018 Aug 21;:

Authors: Porter KM, Kauffman TL, Koenig BA, Lewis KL, Rehm HL, Richards CS, Strande NT, Tabor HK, Wolf SM, Yang Y, Amendola LM, Azzariti DR, Berg JS, Bergstrom K, Biesecker LG, Biswas S, Bowling KM, Chung WK, Clayton EW, Conlin LK, Cooper GM, Dulik MC, Garraway LA, Ghazani AA, Green RC, Hiatt SM, Jamal SM, Jarvik GP, Goddard KAB, Wilfond BS, members of the CSER Actionability and Return of Results Working Group

Abstract
BACKGROUND: Clinical genome and exome sequencing (CGES) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X-linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed.
METHODS: Representatives from 11 projects in the clinical sequencing exploratory research (CSER) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project-specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects.
RESULTS: The proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results.
CONCLUSION: Future translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.

PMID: 30133189 [PubMed - as supplied by publisher]

NLRP3 expression in mesencephalic neurons and characterization of a rare NLRP3 polymorphism associated with decreased risk of Parkinson's disease.

NPJ Parkinsons Dis. 2018;4:24

Authors: von Herrmann KM, Salas LA, Martinez EM, Young AL, Howard JM, Feldman MS, Christensen BC, Wilkins OM, Lee SL, Hickey WF, Havrda MC

Abstract
Neuroinflammation is a well-characterized pathophysiology occurring in association with the progression of Parkinson's disease. Characterizing the cellular and molecular basis of neuroinflammation is critical to understanding its impact on the incidence and progression of PD and other neurologic disorders. Inflammasomes are intracellular pro-inflammatory pattern-recognition receptors capable of initiating and propagating inflammation. These cellular complexes are well characterized in the innate immune system and activity of the NLRP3 inflammasome has been reported in microglia. NLRP3 inflammasome activity has been associated with Alzheimer's disease, and recent reports, from our laboratory and others, indicate that Nlrp3 is required for neuroinflammation and nigral cell loss in animal models of PD. NLRP3 has not yet been characterized in PD patients. Here we characterize NLRP3 in PD using immunohistologic and genetic approaches. Histologic studies revealed elevated NLRP3 expression in mesencephalic neurons of PD patients. Analysis of exome sequencing data for genetic variation of NLRP3 identified multiple single-nucleotide polymorphisms (SNPs) including rs7525979 that was associated with a significantly reduced risk of developing PD. Mechanistic studies conducted in HEK293 cells indicated that the synonymous SNP, NLRP3 rs7525979, alters the efficiency of NLRP3 translation impacting NLRP3 protein stability, ubiquitination state, and solubility. These data provide evidence that dopaminergic neurons are a cell-of-origin for inflammasome activity in PD and are consistent with recent animal studies, suggesting that inflammasome activity may impact the progression of PD.

PMID: 30131971 [PubMed]

An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

NPJ Genom Med. 2018;3:21

Authors: Haghighi A, Krier JB, Toth-Petroczy A, Cassa CA, Frank NY, Carmichael N, Fieg E, Bjonnes A, Mohanty A, Briere LC, Lincoln S, Lucia S, Gupta VA, Söylemez O, Sutti S, Kooshesh K, Qiu H, Fay CJ, Perroni V, Valerius J, Hanna M, Frank A, Ouahed J, Snapper SB, Pantazi A, Chopra SS, Leshchiner I, Stitziel NO, Feldweg A, Mannstadt M, Loscalzo J, Sweetser DA, Liao E, Stoler JM, Nowak CB, Sanchez-Lara PA, Klein OD, Perry H, Patsopoulos NA, Raychaudhuri S, Goessling W, Green RC, Seidman CE, MacRae CA, Sunyaev SR, Maas RL, Vuzman D, Undiagnosed Diseases Network, Brigham and Women’s Hospital FaceBase Project, Brigham Genomic Medicine (BGM)

Abstract
Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs.

PMID: 30131872 [PubMed]

A non-functional galanin receptor-2 in a multiple sclerosis patient.

Pharmacogenomics J. 2018 Aug 22;:

Authors: Garcia-Rosa S, Trivella DB, Marques VD, Serafim RB, Pereira JG, Lorenzi JC, Molfetta GA, Christo PP, Olival GS, Marchitto VB, Brum DG, Sabedot TS, Noushmehr H, Farias AS, Santos LM, Nogueira-Machado JA, Souza JE, Romano CM, Conde RM, Santos AC, Guerreiro CT, Schreuder WH, Gleber-Netto FO, Amorim M, Valieris R, Silva ITD, Silva WA, Nunes DN, Oliveira PS, Valente V, Arruda MA, Hill SJ, Barreira AA, Dias-Neto E

Abstract
Multiple Sclerosis (MS) is an inflammatory neurodegenerative disease that affects approximately 2.5 million people globally. Even though the etiology of MS remains unknown, it is accepted that it involves a combination of genetic alterations and environmental factors. Here, after performing whole exome sequencing, we found a MS patient harboring a rare and homozygous single nucleotide variant (SNV; rs61745847) of the G-protein coupled receptor (GPCR) galanin-receptor 2 (GALR2) that alters an important amino acid in the TM6 molecular toggle switch region (W249L). Nuclear magnetic resonance imaging showed that the hypothalamus (an area rich in GALR2) of this patient exhibited an important volumetric reduction leading to an enlarged third ventricle. Ex vivo experiments with patient-derived blood cells (AKT phosphorylation), as well as studies in recombinant cell lines expressing the human GALR2 (calcium mobilization and NFAT mediated gene transcription), showed that galanin (GAL) was unable to stimulate cell signaling in cells expressing the variant GALR2 allele. Live cell confocal microscopy showed that the GALR2 mutant receptor was primarily localized to intracellular endosomes. We conclude that the W249L SNV is likely to abrogate GAL-mediated signaling through GALR2 due to the spontaneous internalization of this receptor in this patient. Although this homozygous SNV was rare in our MS cohort (1:262 cases), our findings raise the potential importance of impaired neuroregenerative pathways in the pathogenesis of MS, warrant future studies into the relevance of the GAL/GALR2 axis in MS and further suggest the activation of GALR2 as a potential therapeutic route for this disease.

PMID: 30131588 [PubMed - as supplied by publisher]

Prevention of lipid peroxidation-derived cyclic DNA adduct and mutation in high fat diet-induced hepatocarcinogenesis by Theaphenon E.

Cancer Prev Res (Phila). 2018 Aug 21;:

Authors: Coia H, Ma N, Hou Y, Dyba MD, Fu Y, Cruz MI, Benitez C, Graham GT, McCutcheon JN, Zheng YL, Sun B, Kallakury BVS, Ma J, Fang HB, Berry DL, Muralidaran V, Chung FL

Abstract
Obesity is associated with cancer risk and its link with liver cancer is particularly strong. Obesity causes non-alcoholic fatty liver disease (NAFLD) that could progress to hepatocellular carcinoma (HCC). Chronic inflammation likely plays a key role. We carried out a bioassay in the high fat diet (HFD) fed C57BL/6J mice to provide insight into the mechanisms of obesity-related HCC by studying γ-OHPdG, a mutagenic DNA adduct derived from lipid peroxidation. In an 80-week bioassay, mice received a low fat diet (LFD), high fat diet (HFD) or HFD with 2% Theaphenon E (HFD+TE). HFD mice developed a 42% incidence of HCC and LFD mice a 16%. Remarkably, TE, a standardized green tea extract formulation, completely blocked HCC in HFD mice with a 0% incidence. γ-OHPdG measured in the hepatic DNA of mice fed HFD and HFD+TE showed its levels increased during early stages of NAFLD in HFD mice and the increases were significantly suppressed by TE, correlating with the tumor data. Whole exome sequencing showed an increased mutation load in the liver tumors of HFD mice with G>A and G>T as the predominant mutations, consistent with the report that γ-OHPdG induces G>A and G>T. Furthermore, the mutation loads were significantly reduced in HFD+TE mice, particularly G>T, the most common mutation in human HCC. These results demonstrate in a relevant model of obesity-induced HCC that γ-OHPdG formation during fatty liver disease may be an initiating event for accumulated mutations that leads to HCC and this process can be effectively inhibited by TE.

PMID: 30131435 [PubMed - as supplied by publisher]

Association of Breast and Ovarian Cancers With Predisposition Genes Identified by Large-Scale Sequencing.

JAMA Oncol. 2018 Aug 16;:

Authors: Lu HM, Li S, Black MH, Lee S, Hoiness R, Wu S, Mu W, Huether R, Chen J, Sridhar S, Tian Y, McFarland R, Dolinsky J, Tippin Davis B, Mexal S, Dunlop C, Elliott A

Abstract
Importance: Since the discovery of BRCA1 and BRCA2, multiple high- and moderate-penetrance genes have been reported as risk factors for hereditary breast cancer, ovarian cancer, or both; however, it is unclear whether these findings represent the complete genetic landscape of these cancers. Systematic investigation of the genetic contributions to breast and ovarian cancers is needed to confirm these findings and explore potentially new associations.
Objective: To confirm reported and identify additional predisposition genes for breast or ovarian cancer.
Design, Setting, and Participants: In this sample of 11 416 patients with clinical features of breast cancer, ovarian cancer, or both who were referred for genetic testing from 1200 hospitals and clinics across the United States and of 3988 controls who were referred for genetic testing for noncancer conditions between 2014 and 2015, whole-exome sequencing was conducted and gene-phenotype associations were examined. Case-control analyses using the Genome Aggregation Database as a set of reference controls were also conducted.
Main Outcomes and Measures: Breast cancer risk associated with pathogenic variants among 625 cancer predisposition genes; association of identified predisposition breast or ovarian cancer genes with the breast cancer subtypes invasive ductal, invasive lobular, hormone receptor-positive, hormone receptor-negative, and male, and with early-onset disease.
Results: Of 9639 patients with breast cancer, 3960 (41.1%) were early-onset cases (≤45 years at diagnosis) and 123 (1.3%) were male, with men having an older age at diagnosis than women (mean [SD] age, 61.8 [12.8] vs 48.6 [11.4] years). Of 2051 women with ovarian cancer, 445 (21.7%) received a diagnosis at 45 years or younger. Enrichment of pathogenic variants were identified in 4 non-BRCA genes associated with breast cancer risk: ATM (odds ratio [OR], 2.97; 95% CI, 1.67-5.68), CHEK2 (OR, 2.19; 95% CI, 1.40-3.56), PALB2 (OR, 5.53; 95% CI, 2.24-17.65), and MSH6 (OR, 2.59; 95% CI, 1.35-5.44). Increased risk for ovarian cancer was associated with 4 genes: MSH6 (OR, 4.16; 95% CI, 1.95-9.47), RAD51C (OR, not estimable; false-discovery rate-corrected P = .004), TP53 (OR, 18.50; 95% CI, 2.56-808.10), and ATM (OR, 2.85; 95% CI, 1.30-6.32). Neither the MRN complex genes nor CDKN2A was associated with increased breast or ovarian cancer risk. The findings also do not support previously reported breast cancer associations with the ovarian cancer susceptibility genes BRIP1, RAD51C, and RAD51D, or mismatch repair genes MSH2 and PMS2.
Conclusions and Relevance: The results of this large-scale exome sequencing of patients and controls shed light on both well-established and controversial non-BRCA predisposition gene associations with breast or ovarian cancer reported to date and may implicate additional breast or ovarian cancer susceptibility gene candidates involved in DNA repair and genomic maintenance.

PMID: 30128536 [PubMed - as supplied by publisher]