Study of a Swiss dopa-responsive dystonia family with a deletion in GCH1: redefining DYT14 as DYT5.

OBJECTIVE: To report the study of a multigenerational Swiss family with dopa-responsive dystonia (DRD). METHODS: Clinical investigation was made of available family members, including historical and chart reviews. Subject examinations were video recorded. Genetic analysis included a genome-wide linkage study with microsatellite markers (STR), GTP cyclohydrolase I (GCH1) gene sequencing, and dosage analysis. RESULTS: We evaluated 32 individuals, of whom 6 were clinically diagnosed with DRD, with childhood-onset progressive foot dystonia, later generalizing, followed by parkinsonism in the two older patients. The response to levodopa was very good. Two additional patients had late onset dopa-responsive parkinsonism. Three other subjects had DRD symptoms on historical grounds. We found suggestive linkage to the previously reported DYT14 locus, which excluded GCH1. However, further study with more stringent criteria for disease status attribution showed linkage to a larger region, which included GCH1. No mutation was found in GCH1 by gene sequencing but dosage methods identified a novel heterozygous deletion of exons 3 to 6 of GCH1. The mutation was found in seven subjects. One of the patients with dystonia represented a phenocopy. CONCLUSIONS: This study rules out the previously reported DYT14 locus as a cause of disease, as a novel multiexonic deletion was identified in GCH1. This work highlights the necessity of an accurate clinical diagnosis in linkage studies as well as the need for appropriate allele frequencies, penetrance, and phenocopy estimates. Comprehensive sequencing and dosage analysis of known genes is recommended prior to genome-wide linkage analysis

Intrinsic Subtype and Therapeutic Response Among HER2-Positive Breast Tumors from the NCCTG (Alliance) N9831 Trial

Background: Genomic data from human epidermal growth factor receptor 2–positive (HER2+) tumors were analyzed to assess the association between intrinsic subtype and clinical outcome in a large, well-annotated patient cohort

The G2019S LRRK2 Mutation is Rare in Korean Patients with Parkinson's Disease and Multiple System Atrophy

Background and Purpose The LRRK2 (PARK8; OMIM607060)substitution was recently identified as a causative mutation for Parkinson`s disease (PD). The pathologic heterogeneity of LRRK2-positive patients Suggests that mutation of the LRRK2 gene is associated with the pathogenesis of PD and Parkinson-plus disorders, such as multiple system atrophy (MSA). We previously reported that the G2019S LRRK2 mutation-which is the most common LRRK-2 mutation-was not found in a sample of 453 Korean PD patients. In the present study, we extended the screening for the G2019S Mutation to a larger group of PD and MSA patients. Methods We performed a genetic analysis of the G2019S mutation ill 877 patients with PD and 199 patients with MSA using a standard PCR and restriction digestion method. Results None of the subjects carried the G2019S mutation. Conclusions The results of the present study support that the G2019S Mutation is extremely rare in PD and is unlikely to be associated with MSA in the Korean population. J Clin Neurol 2009;5:29-32This study was in part supported by a grant of the Korea Health 21 R & D Project. Ministry of Health & Welfare, Republic of Korea (03-PJ10- PG13-GD01-0002).Lin CH, 2008, J BIOMED SCI, V15, P661, DOI 10.1007/s11373-008-9260-0Healy DG, 2008, LANCET NEUROL, V7, P583, DOI 10.1016/S1474-4422(08)70117-0CHO JW, 2008, J CLIN NEUROL, V4, P23Ozelius LJ, 2007, MOVEMENT DISORD, V22, P546, DOI 10.1002/mds.21343Cho JW, 2007, CAN J NEUROL SCI, V34, P53Punia S, 2006, NEUROSCI LETT, V409, P83, DOI 10.1016/j.neulet.2006.04.052Hardy J, 2006, ANN NEUROL, V60, P389, DOI 10.1002/ana.21022Zabetian CP, 2006, NEUROLOGY, V67, P697Tomiyama H, 2006, MOVEMENT DISORD, V21, P1102, DOI 10.1002/mds.20886Tan EK, 2006, MOVEMENT DISORD, V21, P997, DOI 10.1002/mds.20875Fung HC, 2006, MOVEMENT DISORD, V21, P880, DOI 10.1002/mds.20814Schapira AHV, 2006, NEUROLOGY, V66, pS10Infante J, 2006, NEUROSCI LETT, V395, P224, DOI 10.1016/j.neulet.2005.10.083Giasson BI, 2006, ANN NEUROL, V59, P315, DOI 10.1002/ana.20791Taylor JP, 2006, TRENDS MOL MED, V12, P76, DOI 10.1016/j.molmed.2005.12.004Ross OA, 2006, ANN NEUROL, V59, P388, DOI 10.1002/ana.20731Lesage S, 2006, NEW ENGL J MED, V354, P422Ozelius LJ, 2006, NEW ENGL J MED, V354, P424Goldwurm S, 2006, PARKINSONISM RELAT D, V12, P410, DOI 10.1016/j.parkreldis.2006.04.001Hernandez D, 2005, NEUROSCI LETT, V389, P137, DOI 10.1016/j.neulet.2005.07.044Farrer M, 2005, NEUROLOGY, V65, P738Tan EK, 2005, NEUROSCI LETT, V384, P327, DOI 10.1016/j.neulet.2005.04.103Gasser T, 2005, CURR OPIN NEUROL, V18, P363Funayama M, 2005, ANN NEUROL, V57, P918, DOI 10.1002/ana.20484Kachergus J, 2005, AM J HUM GENET, V76, P672Gilks WP, 2005, LANCET, V365, P415Lu CS, 2005, PARKINSONISM RELAT D, V11, P521, DOI 10.1016/j.parkreldis.2005.09.003Nichols WC, 2005, LANCET, V365, P410Paisan-Ruiz C, 2004, NEURON, V44, P595Zimprich A, 2004, NEURON, V44, P601Wszolek ZK, 2004, NEUROLOGY, V62, P1619Funayama M, 2002, ANN NEUROL, V51, P296, DOI 10.1002/ana.10113Autere JM, 2000, J NEUROL NEUROSUR PS, V69, P107Gilman S, 1999, J NEUROL SCI, V163, P94HUGHES AJ, 1992, J NEUROL NEUROSUR PS, V55, P181

Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations

KRAS mutations are highly prevalent in non-small cell lung cancer (NSCLC), and tumors harboring these mutations tend to be aggressive and resistant to chemotherapy. We used next-generation sequencing technology to identify pathways that are specifically altered in lung tumors harboring a KRAS mutation. Paired-end RNA-sequencing of 15 primary lung adenocarcinoma tumors (8 harboring mutant KRAS and 7 with wild-type KRAS) were performed. Sequences were mapped to the human genome, and genomic features, including differentially expressed genes, alternate splicing isoforms and single nucleotide variants, were determined for tumors with and without KRAS mutation using a variety of computational methods. Network analysis was carried out on genes showing differential expression (374 genes), alternate splicing (259 genes), and SNV-related changes (65 genes) in NSCLC tumors harboring a KRAS mutation. Genes exhibiting two or more connections from the lung adenocarcinoma network were used to carry out integrated pathway analysis. The most significant signaling pathways identified through this analysis were the NFκB, ERK1/2, and AKT pathways. A 27 gene mutant KRAS-specific sub network was extracted based on gene–gene connections from the integrated network, and interrogated for druggable targets. Our results confirm previous evidence that mutant KRAS tumors exhibit activated NFκB, ERK1/2, and AKT pathways and may be preferentially sensitive to target therapeutics toward these pathways. In addition, our analysis indicates novel, previously unappreciated links between mutant KRAS and the TNFR and PPARγ signaling pathways, suggesting that targeted PPARγ antagonists and TNFR inhibitors may be useful therapeutic strategies for treatment of mutant KRAS lung tumors. Our study is the first to integrate genomic features from RNA-Seq data from NSCLC and to define a first draft genomic landscape model that is unique to tumors with oncogenic KRAS mutations

Intrinsic Subtype and Therapeutic Response Among HER2-Positive Breast Tumors from the NCCTG (Alliance) N9831 Trial.

Background: Genomic data from human epidermal growth factor receptor 2-positive (HER2+) tumors were analyzed to assess the association between intrinsic subtype and clinical outcome in a large, well-annotated patient cohort. Methods: Samples from the NCCTG (Alliance) N9831 trial were analyzed using the Prosigna algorithm on the NanoString platform to define intrinsic subtype, risk of recurrence scores, and risk categories for 1392 HER2+ tumors. Subtypes were evaluated for recurrence-free survival (RFS) using Kaplan-Meier and Cox model analysis following adjuvant chemotherapy (n = 484) or chemotherapy plus trastuzumab (n = 908). All statistical tests were two-sided. Results: Patients with HER2+ tumors from N9831 were primarily scored as HER2-enriched (72.1%). These individuals received statistically significant benefit from trastuzumab (hazard ratio [HR] = 0.68, 95% confidence interval [CI] = 0.52 to 0.89, P = .005), as did the patients (291 of 1392) with luminal-type tumors (HR = 0.52, 95% CI = 0.32 to 0.85, P = .01). Patients with basal-like tumors (97 of 1392) did not have statistically significantly better RFS when treated with trastuzumab and chemotherapy compared with chemotherapy alone (HR = 1.06, 95% CI = 0.53 to 2.13, P = .87). Conclusions: The majority of clinically defined HER2-positive tumors were classified as HER2-enriched or luminal using the Prosigna algorithm. Intrinsic subtype alone cannot replace conventional histopathological evaluation of HER2 status because many tumors that are classified as luminal A or luminal B will benefit from adjuvant trastuzumab if that subtype is accompanied by HER2 overexpression. However, among tumors that overexpress HER2, we speculate that assessment of intrinsic subtype may influence treatment, particularly with respect to evaluating alternative therapeutic approaches for that subset of HER2-positive tumors of the basal-like subtype

Analysis of Nigerians with Apparently Sporadic Parkinson Disease for Mutations in LRRK2, PRKN and ATXN3

Several genetic variations have been associated with Parkinson disease in different populations over the past few years. Although a considerable number of worldwide populations have been screened for these variants, results from Sub-Saharan populations are very scarce in the literature. In the present report we have screened a cohort of Parkinson disease patients (n = 57) and healthy controls (n = 51) from Nigeria for mutations in the genes PRKN, LRRK2 and ATXN3. No pathogenic mutations were found in any of the genes. Hence, common pathogenic mutations in these genes, observed in several different populations, are not a frequent cause of Parkinson disease in Nigeria

Syndromic Approach to Parkinson's Disease: Role of Functional Imaging

Current evidence from monogenic Parkinson's disease (PD) supports the view that PD is a clinical syndrome, rather than a single disease entity, and that the heterogeneity of PD indeed reflects different pathogenesis. Recent developments in functional imaging have enabled the in vivo assessment of cellular and molecular pathology of PD with respect to temporal and topographical patterns. We propose that this new technology will be useful for linking monogenic and sporadic PD, and thus, for classifying PD based on the pathogenesis. It will be also useful in clinico-genetic studies exploring susceptibility factors and at-risk groups, which are important for neuroprotective treatment when it becomes available

LRRK2 deficiency induced mitochondrial Ca2+ efflux inhibition can be rescued by Na+/Ca2+/Li+ exchanger upregulation

Variants of leucine-rich repeat kinase 2 (lrrk2) are associated with an increased risk in developing Parkinson’s disease (PD). Mitochondrial dysfunction and specifically mitochondrial Ca2+ handling has been linked to the pathogenesis of PD. Here we describe for the second time a mitochondrial Ca2+ efflux deficiency in a model displaying alterations in a PD-associated risk protein. LRRK2 deletion, inhibition and mutations led to an impaired mitochondrial Ca2+ extrusion via Na+/Ca2+/Li+ exchanger (NCLX) which in turn lowered mitochondrial permeability transition pore (PTP) opening threshold and increased cell death. The mitochondrial membrane potential was found not to be the underlying cause for the Ca2+ extrusion deficiency. NCLX activity was rescued by a direct (phosphomimetic NCLX mutant) and indirect (protein kinase A) activation which in turn elevated the PTP opening threshold. Therefore, at least two PD-associated risk protein pathways appear to converge on NCLX controlling mitochondrial Ca2+ extrusion and therefore mitochondrial health. Since mitochondrial Ca2+ overload has been described in many neurological disorders this study warrants further studies into NCLX as a potential therapeutic target

Identification of Allele-Specific RNAi Effectors Targeting Genetic Forms of Parkinson's Disease

Parkinson's disease (PD) is a progressive neurological disorder affecting an estimated 5–10 million people worldwide. Recent evidence has implicated several genes that directly cause or increase susceptibility to PD. As well as advancing understanding of the genetic aetiology of PD these findings suggest new ways to modify the disease course, in some cases through genetic manipulation. Here we generated a ‘walk-through’ series of RNA Pol III-expressed shRNAs targeting both the α-synuclein A30P and LRRK2 G2019S PD-associated mutations. Allele-specific discrimination of the α-synuclein A30P mutation was achieved with alignments at position 10, 13 and 14 in two model systems, including a heterozygous model mimicking the disease setting, whilst 5′RACE was used to confirm stated alignments. Discrimination of the most common PD-linked LRRK2 G2019S mutation was assessed in hemizygous dual-luciferase assays and showed that alignment of the mutation opposite position 4 of the antisense species produced robust discrimination of alleles at all time points studied. Discrimination at this position was subsequently confirmed using siRNAs, where up to 10-fold discrimination was seen. The results suggest that RNAi-mediated silencing of PD-associated autosomal dominant genes could be a novel therapeutic approach for the treatment of the relevant clinical cases of PD in future

Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia.

No treatment for frontotemporal dementia (FTD), the second most common type of early-onset dementia, is available, but therapeutics are being investigated to target the 2 main proteins associated with FTD pathological subtypes: TDP-43 (FTLD-TDP) and tau (FTLD-tau). Testing potential therapies in clinical trials is hampered by our inability to distinguish between patients with FTLD-TDP and FTLD-tau. Therefore, we evaluated truncated stathmin-2 (STMN2) as a proxy of TDP-43 pathology, given the reports that TDP-43 dysfunction causes truncated STMN2 accumulation. Truncated STMN2 accumulated in human induced pluripotent stem cell-derived neurons depleted of TDP-43, but not in those with pathogenic TARDBP mutations in the absence of TDP-43 aggregation or loss of nuclear protein. In RNA-Seq analyses of human brain samples from the NYGC ALS cohort, truncated STMN2 RNA was confined to tissues and disease subtypes marked by TDP-43 inclusions. Last, we validated that truncated STMN2 RNA was elevated in the frontal cortex of a cohort of patients with FTLD-TDP but not in controls or patients with progressive supranuclear palsy, a type of FTLD-tau. Further, in patients with FTLD-TDP, we observed significant associations of truncated STMN2 RNA with phosphorylated TDP-43 levels and an earlier age of disease onset. Overall, our data uncovered truncated STMN2 as a marker for TDP-43 dysfunction in FTD