Genomic Characterization of Partial Tandem Duplication Involving the KMT2A Gene in Adult Acute Myeloid Leukemia.

BACKGROUND: Gene rearrangements affecting KMT2A are frequent in acute myeloid leukemia (AML) and are often associated with a poor prognosis. KMT2A gene fusions are often detected by chromosome banding analysis and confirmed by fluorescence in situ hybridization. However, small intragenic insertions, termed KMT2A partial tandem duplication (KMT2A-PTD), are particularly challenging to detect using standard molecular and cytogenetic approaches. METHODS: We have validated the use of a custom hybrid-capture-based next-generation sequencing (NGS) panel for comprehensive profiling of AML patients seen at our institution. This NGS panel targets the entire consensus coding DNA sequence of KMT2A. To deduce the presence of a KMT2A-PTD, we used the relative ratio of KMT2A exons coverage. We sought to corroborate the KMT2A-PTD NGS results using (1) multiplex-ligation probe amplification (MLPA) and (2) optical genome mapping (OGM). RESULTS: We analyzed 932 AML cases and identified 41 individuals harboring a KMT2A-PTD. MLPA, NGS, and OGM confirmed the presence of a KMT2A-PTD in 22 of the cases analyzed where orthogonal testing was possible. The two false-positive KMT2A-PTD calls by NGS could be explained by the presence of cryptic structural variants impacting KMT2A and interfering with KMT2A-PTD analysis. OGM revealed the nature of these previously undetected gene rearrangements in KMT2A, while MLPA yielded inconclusive results. MLPA analysis for KMT2A-PTD is limited to exon 4, whereas NGS and OGM resolved KMT2A-PTD sizes and copy number levels. CONCLUSIONS: KMT2A-PTDs are complex gene rearrangements that cannot be fully ascertained using a single genomic platform. MLPA, NGS panels, and OGM are complementary technologies applied in standard-of-care testing for AML patients. MLPA and NGS panels are designed for targeted copy number analysis; however, our results showed that integration of concurrent genomic alterations is needed for accurate KMT2A-PTD identification. Unbalanced chromosomal rearrangements overlapping with KMT2A can interfere with the diagnostic sensitivity and specificity of copy-number-based KMT2A-PTD detection methodologies.

Genetic variability in CHMP2B and frontotemporal dementia.

A nonsense/protein chain-terminating mutation in the CHMP2B gene has recently been reported as a cause of frontotemporal dementia (FTD) in the single large family known to show linkage to chromosome 3. Screening for mutations in this gene in a large series of FTD families and individual patients led to the identification of a protein-truncating mutation in 2 unaffected members of an Afrikaner family with FTD, but not in their affected relatives. The putative pathogenicity of CHMP2B mutations for dementia is discussed.

Childhood onset in familial prion disease with a novel mutation in the PRNP gene.

BACKGROUND: Up to 15% of cases of prion diseases are due to the autosomal dominant inheritance of coding PRNP mutations. OBJECTIVE: To describe the unique clinical and genetic findings in a family of East Indian origin with autosomal dominant inheritance of a novel PRNP mutation. DESIGN: Detailed neurological examination and sequencing analysis of the MAPT and PRNP genes. SETTING: Toronto Western Hospital, Toronto, Ontario. PATIENTS: Five available members of a family of East Indian origin with a rapidly progressive neurodegenerative disorder characterized by dementia, motor decline, and ataxia. RESULTS: We identified a novel Pro105Thr mutation in the PRNP gene in all of the 3 clinically affected family members but not in their unaffected relatives or normal controls. Although 5 of 6 affected family members had a relatively homogeneous phenotype and age at onset (range, 33-41 years), 1 of the 6 patients developed the disease at age 13 years. CONCLUSIONS: A novel mutation in the PRNP gene was identified in all of the available, clinically affected members of this family with a rapidly progressive neurodegenerative disease. To our knowledge, the propositus represents the youngest individual with inherited prion disease described to date.

Novel SPG6 mutation p.A100T in a Japanese family with autosomal dominant form of hereditary spastic paraplegia.

We describe a Japanese family in which inheritance of a novel mutation p.A100T in SPG6 resulted in an autosomal dominant form of hereditary spastic paraplegia (ADHSP). Clinical investigation showed a pure form of HSP. Our study demonstrates further allelic heterogeneity of SPG6.

Homozygous and heterozygous PINK1 mutations: considerations for diagnosis and care of Parkinson's disease patients.

The first mutations described in PINK1 were homozygous. More recently, heterozygous mutations have been reported but the role of heterozygosity in disease pathogenesis is still debated. We describe two unrelated cases with PINK1 mutations (homozygous nonsense and heterozygous missense) that highlight issues regarding the role of heterozygous mutations and the utility of genetic screening in patient care.

Wild-type PINK1 prevents basal and induced neuronal apoptosis, a protective effect abrogated by Parkinson disease-related mutations.

Mutations in the PTEN-induced kinase 1 (PINK1) gene have recently been implicated in autosomal recessive early onset Parkinson Disease (1, 2). To investigate the role of PINK1 in neurodegeneration, we designed human and murine neuronal cell lines expressing either wild-type PINK1 or PINK1 bearing a mutation associated with Parkinson Disease. We show that under basal and staurosporine-induced conditions, the number of terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling (TUNEL)-positive cells was lower in wild-type PINK1 expressing SH-SY5Y cells than in mock-transfected cells. This phenotype was due to a PINK1-mediated reduction in cytochrome c release from mitochondria, which prevents subsequent caspase-3 activation. We show that overexpression of wild-type PINK1 strongly reduced both basal and staurosporine-induced caspase 3 activity. Overexpression of wild-type PINK1 also reduced the levels of cleaved caspase-9, caspase-3, caspase-7, and activated poly(ADP-ribose) polymerase under both basal and staurosporine-induced conditions. In contrast, Parkinson disease-related mutations and a kinase-inactive mutation in PINK1 abrogated the protective effect of PINK1. Together, these results suggest that PINK1 reduces the basal neuronal pro-apoptotic activity and protects neurons from staurosporine-induced apoptosis. Loss of this protective function may therefore underlie the degeneration of nigral dopaminergic neurons in patients with PINK1 mutations.

Characterization of a cyclooxygenase-2-765G-->C promoter polymorphism in human neural cells.

Direct sequencing of the human cyclooxygenase-2 gene promoter revealed a common single nucleotide substitution, cyclooxygenase-2-765G-->C, in 24.5% of the populations analyzed. This change introduced a 20 base pair polypyrimidine/polypurine element and a partial recognition feature for RXRalpha, the 9-cis retinoic acid receptor, into the polymorphic promoter. Cyclooxygenase-2-765G-->C constructs, when transfected into human neural cells, exhibited a 1.4-fold higher level of basal expression, while the proinflammatory factors interleukin-1beta and 9-cis retinoic acid synergistically induced polymorphic promoter activity 2.4-fold over wild type. These results suggest that under specific conditions of cellular stress, a common variation in cyclooxygenase-2 promoter structure may enhance cyclooxygenase-2 transcription, and this may contribute to the proliferation of an inflammatory response in brain cells.

Analysis of the glucocerebrosidase gene in Parkinson's disease.

Parkinson's disease (PD) is a common progressive neurodegenerative disorder characterized clinically by a combination of motor symptoms. Identifying novel PD genetic risk factors is important for understanding its pathogenesis. A recent study suggested that up to 21% of subjects with PD may have mutations in the glucocerebrosidase (GBA) gene. We investigated the GBA gene for mutations in 88 PD cases and 122 normal controls and detected the presence of heterozygous GBA mutations in 5 PD cases and in 1 control. Sequencing of the entire open reading frame of the GBA gene in a subset of 25 cases with early-onset PD (<50 years of age) uncovered no additional mutations. Our results demonstrate a marginally significant association of GBA mutations with PD and suggest that variations in the GBA gene may constitute a rare susceptibility factor for PD (P = 0.048).

Analysis of the PINK1 gene in a large cohort of cases with Parkinson disease.

BACKGROUND: Mutations in the PTEN-induced kinase (PINK1) gene located within the PARK6 locus on chromosome 1p35-p36 have recently been identified in patients with recessive early-onset Parkinson disease. OBJECTIVE: To assess the prevalence of PINK1 mutations within a series of early- and late-onset Parkinson disease patients living in North America. DESIGN: All coding exons of the PINK1 gene were sequenced in a series of 289 Parkinson disease patients and 80 neurologically normal control subjects; the mutation frequencies were evaluated in additional controls (100 white and 50 Filipino subjects). RESULTS: We identified 27 variants, including the first reported compound heterozygous mutation (Glu240Lys and Leu489Pro) and a homozygous Leu347Pro mutation in 2 unrelated young-onset Parkinson disease patients. CONCLUSION: Autosomal recessive mutations in PINK1 are a rare cause of young-onset Parkinson disease.

Novel PS1 mutation in a Bavarian kindred with familial Alzheimer disease.

We describe a novel Leu174Arg PS1 mutation in two members of a Bavarian family which were initially diagnosed with frontotemporal dementia. Intriguingly, there is the possibility that there is an 18th century founder effect and that this family is related to original kindreds with familial Alzheimer disease described in the early 20th century.

Genetic association study of PINK1 coding polymorphisms in Parkinson's disease.

Parkinson's disease (PD) is the most common neurodegenerative movement disorder with a substantial genetic component (which is more pronounced in earlier onset cases). In addition to three well-confirmed PD genes (SNCA, parkin and DJ-1), mutations in the PTEN Induced Kinase (PINK1) gene have recently been identified in families with recessive early onset PD. We tested the hypothesis that three common coding variations (Leu63Leu, Ala340Thr and Asn521Thr) could increase the risk of PD. We performed a case control association study in a series of 91 PD cases (Caucasian of Canadian origin) and 182 normal controls. The patients were largely pre-selected for having an early age of onset (<50 years) and/or a positive family history. Our results did not reveal any evidence of association between PD and any of the three SNPs at the allelic or genotypic levels (p > 0.25). Furthermore, we did not detect a modifying effect for any genotype upon the age of onset in the PD group (p > 0.19). Nevertheless, it remains to be evaluated whether PINK1 variations contribute to the risk of common late onset sporadic PD.

Clinical findings in a large family with a parkin ex3delta40 mutation.

OBJECTIVE: To describe a large consanguineous family in which inheritance of a 438- to 477-base pair deletion in exon 3 (Ex3Delta40) in the parkin gene resulted in parkinsonism (age range at onset, 24-32 years). DESIGN: Fifty-two family members underwent genetic analysis. MAIN OUTCOME MEASURE: Two clinical examiners blinded to genetic status evaluated 21 family members, including all mutation carriers (4 homozygous and 12 heterozygous individuals; 5 family members did not have the mutation). RESULTS: In this family, the parkin Ex3Delta40 mutation is recessive; only homozygotes manifest symptoms of early-onset levodopa-responsive parkinsonism, including resting tremor, dystonia, and slow progression, with the caveat that presymptomatic signs of dopaminergic loss in heterozygotes must be excluded by fluorodopa F 18 with positron emission tomography. This contrasts with the autosomal dominant pattern of inheritance of parkinsonism described in families with the same mutation. CONCLUSION: In families with a dominant inheritance, an additional genetic or environmental cause must coexist with the Ex3Delta40 mutation.