Homogeneous polymerase chain reaction nucleobase quenching assay to detect the 1-kbp deletion in CLN3 that causes Batten disease

A diagnostic confidence scheme for CLN3 disease

Over the past 20 years, diagnostic testing for genetic diseases has evolved, leading to variable diagnostic certainty for individuals included in long-term natural history studies. Using genotype and phenotype data from an ongoing natural history study of CLN3 disease, we developed a hierarchical diagnostic confidence scheme with three major classes: Definite, Probable, or Possible CLN3 disease. An additional level, CLN3 Disease PLUS, includes individuals with CLN3 disease plus an additional disorder with a separate etiology that substantially affects the phenotype. Within the Definite and Probable CLN3 disease classes, we further divided individuals into subclasses based on phenotype. After assigning participants to classes, we performed a blinded reclassification to assess the reliability of this scheme. A total of 134 individuals with suspected CLN3 disease were classified: 100 as Definite, 21 as Probable, and 7 as Possible. Six individuals were classified as CLN3-PLUS. Phenotypes included the classical juvenile-onset syndromic phenotype, a "vision loss only" phenotype, and an atypical syndromic phenotype. Some individuals were too young to fully classify phenotype. Test-retest reliability showed 96% agreement. We created a reliable diagnostic confidence scheme for CLN3 disease that has excellent face validity. This scheme has implications for clinical research in CLN3 and other rare genetic neurodegenerative disorders.

Establishment of a quenching probe method for detection of NPM1 mutations in acute myeloid leukemia cells

Nucleophosmin (NPM1) mutations, generally consisting of a four base-pair insertion, are present in ~60% of all cytogenetically normal acute myeloid leukemia (AML) cases. The mutation is clinically significant as an important prognostic factor. Direct sequencing is the current standard method of mutation detection, however, it is quite costly and time consuming. The present study aimed to establish a highly sensitive quenching probe (QP) method to detect NPM1 mutations efficiently. Melting curve analysis was performed using a QP, following polymerase chain reaction for amplification of the involved region of the gene. The curve derived from the fluorescent intensity with respect to the temperature of OCI/AML3, a heterozygous NPM1 mutant AML cell line, was W-shaped with melting peaks at 61°C and 68°C. That of M-07e, the homozygous wild type cell line, was V-shaped with a melting peak at 68°C. Thus, the curve derived from the mutant allele was easily discriminated from that of the wild-type allele. The mutant allele was detected in concentrations as low as 3% as determined by a subsequent sensitivity study. With a short testing time and a high sensitivity, this assay was applicable for NPM1-mutated AML patient samples and is appropriate for screening NPM1 mutations. It does require further examination as to whether it would be useful as a detection method for other mutant alleles since NPM1 mutations may consist of 61 known types of mutant sequences. To the best of our knowledge, this is the first report describing the QP method for the detection of NPM1 mutations.

Standardized assessment of seizures in patients with juvenile neuronal ceroid lipofuscinosis

AIM

To evaluate seizure phenomenology, treatment, and course in individuals with juvenile neuronal ceroid lipofuscinosis (JNCL).

METHOD

Data from an ongoing natural history study of JNCL were analyzed using cross-sectional and longitudinal methods. Seizures were evaluated with the Unified Batten Disease Rating Scale, a disease-specific quantitative assessment tool.

RESULTS

Eighty-six children (44 males, 42 females) with JNCL were assessed at an average of three annual visits (range 1-11). Eighty-six percent (n=74) experienced at least one seizure, most commonly generalized tonic-clonic, with mean age at onset of 9 years 7 months (SD 2y 10mo). Seizures were infrequent, typically occurring less often than once every 3 months, and were managed with one to two medications for most participants. Valproate (49%, n=36) and levetiracetam (41%, n=30) were the most commonly used seizure medications. Myoclonic seizures occurred infrequently (16%, n=14). Seizure severity did not vary by sex or genotype. Seizures showed mild worsening with increasing age.

INTERPRETATION

The neuronal ceroid lipofuscinoses (NCLs) represent a group of disorders unified by neurodegeneration and symptoms of blindness, seizures, motor impairment, and dementia. While NCLs are considered in the differential diagnosis of progressive myoclonus epilepsy, we show that myoclonic seizures are infrequent in JNCL. This highlights the NCLs as consisting of genetically distinct disorders with differing natural history.

Neurobehavioral features and natural history of juvenile neuronal ceroid lipofuscinosis (Batten disease)

Juvenile neuronal ceroid lipofuscinosis is a childhood-onset neurodegenerative disease with prominent symptoms comprising a pediatric dementia syndrome: intellectual decline, mood and behavioral impairments, and loss of adaptive skills. We review the history of neurobehavioral features in juvenile neuronal ceroid lipofuscinosis and the work of the University of Rochester Batten Center to characterize the extent and progression of neurobehavioral symptoms over the disease course, and discuss the relevance of neurobehavioral studies as an aid to understanding the clinical phenotype of juvenile Batten disease and potential targets for intervention.

Methodology of clinical research in rare diseases: development of a research program in juvenile neuronal ceroid lipofuscinosis (JNCL) via creation of a patient registry and collaboration with patient advocates

INTRODUCTION

Juvenile neuronal ceroid lipofuscinosis (JNCL; Batten disease) is a rare, inherited, fatal lysosomal storage childhood disorder. True for many rare diseases, there are no treatments that impact the course of JNCL. The University of Rochester Batten Center's (URBC) mission is to find treatments to slow, halt, or prevent JNCL.

OBJECTIVES

Our initial objective was to develop clinical research infrastructure preparatory to clinical trials, establish a JNCL research cohort, construct a disease-specific clinical outcome measure, and validate a non-invasive diagnostic sampling method. The long-term objective is to design and implement JNCL clinical trials.

METHODS

The Unified Batten Disease Rating Scale (UBDRS) was developed. The Batten Disease Support and Research Association (BDSRA) referred participants; annual BDSRA meetings provided a mobile research setting for registry enrollment and UBDRS piloting. Neuropsychological examinations were performed, enabling external validation of the UBDRS. Buccal epithelial cell collection for genotyping was introduced. Telemedicine for remote UBDRS assessment was piloted.

RESULTS

The registry enrolled 198 families representing 237 children with NCL. The UBDRS was piloted, was validated and has been used to collect natural history data from 120 subjects. Funding and regulatory approval were obtained for a recently launched phase II clinical trial. Several additional lines of inquiry were reported.

CONCLUSION

The registry and BDSRA collaboration have enabled development of a clinical rating scale, natural history and neuropsychological studies, and genetic studies for disease confirmation. This work highlights an approach for preparatory natural history research and infrastructure development needed to facilitate efficient implementation of clinical trials in rare diseases.

Diagnosis of neuronal ceroid lipofuscinosis: mutation detection strategies

The neuronal ceroid lipofuscinoses (NCL) are a group of rare genetically inherited neurodegenerative disorders in children. These diseases are classified by age of onset (congenital, infantile, late-infantile, juvenile and adult-onset) and by the gene bearing mutations (CLN10/CTSD, CLN1/PPT1, CLN2/TPP1, CLN3, CLN5, CLN6, CLN7/MFSD8 and CLN8). Enzyme activity assays are helpful in identifying several of these disorders; however confirmation of the mutation in the gene causing these diseases is vital for definitive diagnosis. There exists considerable heterogeneity in the NCLs as a whole and within each type of NCL both in phenotype (disease manifestation and progression) and genotype (type of mutation), which complicates NCL diagnosis. In order to streamline the diagnostic process, the age of symptom onset, geography and/or ethnicity, and enzyme activity may be considered together. However, these ultimately serve to guide targeting the correct route to genetic confirmation of an NCL through mutational analysis. Herein, an effective protocol to diagnose NCLs using these criteria is presented.

Females experience a more severe disease course in Batten disease

Juvenile neuronal ceroid lipofuscinosis (JNCL; CLN3 disease; Batten disease) is an autosomal recessive neurodegenerative disease of childhood. Symptoms typically present at school age with vision loss followed by progressive cognitive decline, motor dysfunction, seizures, and behavior problems. Studies on sex differences in JNCL have yielded mixed results, but parent anecdotes suggest that females experience a more precipitous disease course. Therefore, we sought to determine if sex-based differences exist in JNCL. We used data from the Unified Batten Disease Rating Scale (UBDRS), the Batten Disease Support and Research Association (BDSRA) database, and the PedsQL quality of life (QoL) survey to evaluate sex-based differences in functional independence and time from symptom onset to death. On average, females had JNCL symptom onset one year later and death one year earlier than did males. Despite a later age at onset, females had lower functional capability, earlier loss of independent function, and lower physical QoL. Future research in sex differences in JNCL may help to further understand the biological mechanisms underpinning the disease course and may point to targeted therapies.

Quantifying physical decline in juvenile neuronal ceroid lipofuscinosis (Batten disease)

OBJECTIVE

To use the Unified Batten Disease Rating Scale (UBDRS) to measure the rate of decline in physical and functional capability domains in patients with juvenile neuronal ceroid lipofuscinosis (JNCL) or Batten disease, a neurodegenerative lysosomal storage disorder. We have evaluated the UBDRS in subjects with JNCL since 2002; during that time, the scale has been refined to improve reliability and validity. Now that therapies are being proposed to prevent, slow, or reverse the course of JNCL, the UBDRS will play an important role in quantitatively assessing clinical outcomes in research trials.

METHODS

We administered the UBDRS to 82 subjects with JNCL genetically confirmed by CLN3 mutational analysis. Forty-four subjects were seen for more than one annual visit. From these data, the rate of physical impairment over time was quantified using multivariate linear regression and repeated-measures analysis.

RESULTS

The UBDRS Physical Impairment subscale shows worsening over time that proceeds at a quantifiable linear rate in the years following initial onset of clinical symptoms. This deterioration correlates with functional capability and is not influenced by CLN3 genotype.

CONCLUSION

The UBDRS is a reliable and valid instrument that measures clinical progression in JNCL. Our data support the use of the UBDRS to quantify the rate of progression of physical impairment in subjects with JNCL in clinical trials.

Quantitative telemedicine ratings in Batten disease: implications for rare disease research

OBJECTIVE

To determine if remote administration of the Unified Batten Disease Rating Scale (UBDRS) Physical Impairment subscale by telemedicine is reliable and feasible across a broad range of disease severity.

METHODS

For the majority (n = 10) of subjects, the examination was performed by a nonphysician who had been trained to perform the examination but not to score the subjects. A trained rater scored the subjects via live video; a second trained rater performed a separate examination in person and scored that examination. For 3 telemedicine evaluations, examinations were performed and scored by a trained rater while a second trained rater simultaneously scored the subjects via live video. Reliability was determined by intraclass correlation coefficient (ICC).

RESULTS

Subjects (n = 13) represented a wide range of disease severity. Remote administration of the UBDRS Physical Impairment subscale had high interrater reliability across all subjects (ICC = 0.94). When only the subjects (n = 10) who had been examined by the nonphysician and scored remotely were included in the analysis, the reliability was unchanged (ICC = 0.95).

CONCLUSIONS

The UBDRS Physical Impairment subscale is reliable and feasible for remote administration. Telemedicine has the potential to be a useful tool in rare neurologic disease research and clinical assessment.

Parent-reported benefits of flupirtine in juvenile neuronal ceroid lipofuscinosis (Batten disease; CLN3) are not supported by quantitative data

Juvenile neuronal ceroid lipofuscinosis (JNCL; CLN3 disease; Batten disease) is an autosomal recessive neurodegenerative disease of childhood that typically presents at school age with vision loss followed by progressive cognitive decline, motor dysfunction, seizures, and behavior problems. No therapy has been shown to slow the progression of disease in JNCL patients, and all current treatments are symptomatic. Flupirtine has been shown in vitro to reduce apoptosis in CLN3 lymphocytes. Based on that preclinical study, several children with JNCL were given flupirtine by their parents. The purpose of this study was to determine if there was evidence of attenuated disease progression in any JNCL symptom domain. We administered a survey to parents of JNCL children to qualitatively assess flupirtine efficacy. We used the Unified Batten Disease Rating Scale (UBDRS) to determine specific aspects of disease progression and investigated three age-related factors: loss of independent ambulation, loss of intelligible speech, and loss of ability to perform independent activities of daily living. The median scores for the UBDRS physical, behavior, and capability subscales were determined in flupirtine-exposed subjects and compared to age-, sex-, and genotype-matched subjects who had never taken flupirtine. Twenty-one percent of survey responders reported administering flupirtine to their JNCL child, and 56% of these families perceived beneficial changes that they attributed to flupirtine. However, our quantitative, prospectively obtained data did not show any change in JNCL disease progression that could be attributed to flupirtine. This study highlights the need for prospective experimental therapeutic research.

Exploratory study of a KLK2 polymorphism as a prognostic marker in prostate cancer

OBJECTIVES

An association of a single nucleotide polymorphism (SNP) of the KLK2 gene (rs198977; c.748C>T; R250W) with risk for developing prostate cancer has been observed. We evaluated the role of R250W SNP for prognosis in prostate cancer.

METHODS

The c.748C>T SNP was genotyped from blood DNA of 182 patients after completing initial cancer treatments. For evaluating prognosis of genotype groups, associations were performed with Gleason score (GS) and biochemical recurrence free survival (bRFS) in patients demonstrating PSA-recurrence after initial cancer therapy.

RESULTS

Overall distribution of the CC, CT and TT genotypes for the SNP was 48%, 44% and 8%, respectively. The distribution of high (8-10), moderate (5-7) and low (2-4) GS among the genotype groups was 17%, 74% and 9% for CC group compared to 25%, 74% and 1% for the CT/TT (P=0.04). Median bRFS time for CT/TT group was 36.5 months compared to 44.5 months for the CC group (P=0.16), while genotype groups combined with morphology revealed significantly different bRFS (P=0.004).

CONCLUSIONS

This exploratory analysis in prostate cancer patients revealed the W allele of the KLK2 R250W SNP to be less likely associated with low GS morphology. Further studies will be needed to confirm this observation in larger cohorts.

[Genetics of neuronal ceroidlipofuscinoses. Aspects of genetic counseling]

Neuronal ceroid lipofuscinoses are autosomal recessive inherited disorders of neuronal cells. Neuronal ceroid lipofuscinoses belong to the lysosomal storage disorders and are characterized by accumulation of protein-lipid complexes in the lysosomal compartments of all somatic cells. This debris causes degenerative activities in the nervous system, especially in the cerebrum, the cerebellum and the afferent and efferent cranial nerves. With one exception of adult onset the disorder causes the loss of receptive, cognitive and control function in the first decade of life and an early death by the age of 20. Currently 10 loci are known which correlate to 8 genes. The genotype related phenotype and the correlated prognosis depend on the underlying gene and type of mutation. The genotype phenotype correlation is hampered by a lack of knowledge on the function of the mutant gene products. In this review we summarize the known genetic data on neuronal ceroid lipofuscinoses and comment on therapeutic approaches.

Genotype does not predict severity of behavioural phenotype in juvenile neuronal ceroid lipofuscinosis (Batten disease)

AIM

The primary aim of this investigation was to examine genotype and clinical phenotype differences in individuals with juvenile neuronal ceroid lipofuscinosis (JNCL) who were homozygous for a common disease-causing deletion or compound heterozygous. The secondary aim was to cross-validate the Child Behavior Checklist (CBCL) and the Unified Batten Disease Rating Scale (UBDRS), a disease-specific JNCL rating scale.

METHOD

Sixty individuals (28 males, 32 females; mean age 15y 1mo, SD 4y 9mo, range 5y 8mo--31y 1mo) with JNCL completed the UBDRS.

RESULTS

No significant genotype and clinical phenotype differences were identified when comparing individuals homozygous for the deletion with a heterogeneous group of compound heterozygous individuals. There were significant correlations among related behaviour items and scales on the CBCL and UBDRS (Spearman's rho ranging from 0.39 [p<0.05] to 0.72 [p<0.01]). Behaviour and physical function ratings were uncorrelated, supporting divergent validity of these two constructs in JNCL.

INTERPRETATION

Previous reports of genotype and clinical phenotype differences were unsupported in this investigation, which did not find differences between individuals homozygous or heterozygous for the CLN3 deletion. The CBCL, an already validated measure of behaviour problems, appears valid for use in JNCL and cross-validates well with the UBDRS.

Juvenile neuronal ceroid lipofuscinosis (JNCL) and the eye

Juvenile neuronal ceroid lipofuscinoses, or Batten disease, is the most common type of NCL in the United States and Europe. This devastating disorder presents with vision failure and progresses to include seizures, motor dysfunction, and dementia. Death usually occurs in the third decade, but some patients die before age twenty. Though the mechanism of visual failure remains poorly understood, recent advances in molecular genetics have improved diagnostic testing and suggested possible therapeutic strategies. The ophthalmologist plays a crucial role in both early diagnosis and documentation of progression of juvenile neuronal ceroid lipofuscinoses. We update Batten disease research, particularly as it relates to the eye, and present various theories on the pathophysiology of retinal degeneration.

Rapid method for detection of mutations in the nucleophosmin gene in acute myeloid leukemia

Mutations in exon 12 of the nucleophosmin gene (NPM1) that cause the encoded protein to abnormally relocate to the cytoplasm are found at diagnosis in about 50% of karyotypically normal acute myeloid leukemias and are associated with a more favorable outcome. We have devised a PCR-based assay for NPM1 exon 12 mutations using differential melting of an oligo probe labeled with a fluorescent dye. The nucleobase quenching (NBQ) phenomenon was used to detect probe hybridization, and an oligonucleotide containing locked nucleic acid (LNA) nucleotides was used as a PCR clamp to suppress amplification of the normal sequence and enhance the analytical sensitivity of the assay. After the NBQ assay, the specimens with a mutation were removed from the capillary and sequenced to identify the mutation. The use of the LNA clamp facilitates interpretation of the mutant sequence because of the lower intensity of the overlapping normal sequence. Analysis of a series of 70 patient specimens revealed 17 positive for an NPM1 mutation and 53 negatives. All of the NBQ results (positives and negatives) were confirmed with other methods. The analytical sensitivity of the NBQ assay is variable depending on the concentration of the PCR clamp and other parameters. Using a 100 nmol/L concentration of the LNA clamp, NPM1 mutations were detectable in a 10-fold excess of wild-type DNA. This assay may be valuable for screening disease specimens.

Neuropsychological symptoms of juvenile-onset batten disease: experiences from 2 studies

Juvenile neuronal ceroid lipofuscinosis (Batten disease) is a progressive and fatal autosomal-recessive inherited lysosomal storage disorder of childhood. Core symptoms include vision loss, seizures, and mental and motor decline. This article presents data from 2 studies of neuropsychological function in juvenile neuronal ceroid lipofuscinosis. In the first cross-sectional pilot study, 15 children with genetic or clinicopathologic confirmation of juvenile neuronal ceroid lipofuscinosis completed a brief test of attention (mean age = 14.3 +/- 2.9 years, range = 8.75-18.74 years; 7 males, 8 females). Average attention performances were significantly below age-expected normative data. A second longitudinal study was then initiated to study neuropsychological function in greater depth, including change in function over time. The authors have enrolled 18 children to date (mean age = 12.88 +/- 3.59 years, range = 6.26-18.65; 11 males, 7 females). Of these, 5 children have completed a second (annual) re-evaluation. Results thus far indicate significant impairment in domains of auditory attention, memory, estimated verbal intellectual function, and verbal fluency. Neuropsychological impairment was significantly correlated with disease duration and with motor function as assessed by a disease-specific clinical neurologic rating scale. There was no significant difference between males and females in neuropsychological test performance. Neuropsychological function was worse among children with a positive seizure history. Juvenile neuronal ceroid lipofuscinosis-affected children exhibited significant and pervasive impairments on tests of auditory attention, verbal memory and repetition, verbal fluency, and an estimate of verbal intellectual ability. Preliminary follow-up data from an annual reassessment showed progressive declines in cognitive function, in particular on a task of working memory. Neuropsychological deficits are pervasive and progressive. Future research will focus on clarifying the relationship among disease duration, motor function, and neuropsychological performances, including the relative sensitivity of neuropsychological testing at different stages of motor impairment or disease duration.

Homogeneous PCR nucleobase quenching assays to detect four mutations that cause neuronal ceroid lipofuscinosis: T75P and R151X in CLN1, and IVS5-1G>C and R208X in CLN2

The neuronal ceroid lipofuscinoses (NCLs) are a family of autosomal recessive lysosomal storage diseases characterized by progressive epilepsy, dementia and visual loss. The juvenile form of the disease (onset age 4-8 years with visual loss) is usually caused by mutations in the CLN3 gene, but some cases have been shown to be due to specific mutations in the CLN1 or CLN2 genes, which are usually associated with NCL with onset in infancy or late infancy, respectively. The CLN1 mutations T75P and R151X, and the CLN2 mutations R208X and IVS5-1G>C, are found in many NCL patients with a juvenile presentation that is not due to CLN3 mutation. We have developed and validated a set of assays for these mutations using PCR followed by differential melting of a fluorescently labeled oligo probe, on a Roche LightCycler platform. The nucleobase quenching phenomenon was used to detect probe hybridization. The tests were validated using alternate assays: PCR followed by allele specific restriction enzyme digestion for the CLN1 mutations, and PCR followed by sequencing for the CLN2 mutations. The homogeneous PCR method gave 100% concordance of results with the alternate methods. This new assay, combined with a test for the common 1 kbp deletion in the CLN3 gene, provides a set of DNA-based assays suitable for detection of the most common mutations causing NCL with onset in the juvenile age range.

Standardized assessment of behavior and adaptive living skills in juvenile neuronal ceroid lipofuscinosis

We obtained information about the behavioral, psychiatric, and functional status of 26 children (13 males, 13 females) with juvenile neuronal ceroid lipofuscinosis (JNCL; mean age 12y 3mo [SD 3y 4mo]; range 6y 9mo to 18y 8mo). Twenty-five children had visual impairment and 18 were known to have a positive seizure history before enrollment. Parents completed the Child Behavior Checklist, Scales of Independent Behavior - Revised, and a structured interview to assess obsessive-compulsive symptoms. Participants exhibited a broad range of behavioral and psychiatric problems, rated as occurring frequently and/or as severe in more than half of the sample. Males and females did not differ with regard to the number of behavioral and psychiatric problems. Children were also limited in their ability to perform activities of daily living, including self-care, hygiene, socialization, and other age-appropriate tasks. Results provide a quantitative baseline for behavioral and psychiatric problems and functional level in JNCL, against which further decline can be measured. Longitudinal assessment of behavioral and psychiatric symptoms and functional abilities is continuing and will provide much-needed data on the natural history of JNCL.

Novel CLN3 mutation predicted to cause complete loss of protein function does not modify the classical JNCL phenotype

Juvenile Neuronal Ceroid Lipofuscinosis (JNCL), or Batten disease, is a childhood neurodegenerative disease that is characterized clinically by progressive visual loss, seizures, dementia, and motor incoordination. Children affected with this disease tend to develop normally for the first 5 years of life. However, once disease onset occurs, they decline rapidly and die in their late 20s to early 30s. Though this represents the typical disease course, the onset and severity of disease symptoms can vary. This variability is presumed to be the result of both differences in the causative genetic mutation in the CLN3 gene as well as environmental influences. Most cases of JNCL are caused by a 1 kb deletion in the CLN3 gene, resulting in a frameshift mutation predicted to leave the first 153 amino acids of the CLN3 protein intact, followed by the addition of 28 novel amino acids. Here we report the discovery of a novel mutation identified as a G to T transversion at nucleotide 49 (G49T) in exon 2 of CLN3, introducing a premature stop codon (E17X) near the N-terminus. This mutation represents the most 5' mutation described to date. The patient examined in this study was heterozygous for the common 1 kb deletion and E17X. She had classical disease progression, suggesting that this mutation in CLN3 mimics the more prevalent 1 kb deletion and that progression of JNCL is predominantly the result of loss of CLN3 function.

Homogeneous amplification nucleobase quenching assay to detect the E474Q LCHAD deficiency mutation

Long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) deficiency is a rare and potentially fatal autosomal recessive disorder of fatty acid metabolism. Early institution of dietary therapy is essential and places a premium on rapid diagnosis. Pregnancy with an LCHAD-deficient fetus is often complicated in the third trimester by liver disease, particularly acute fatty liver of pregnancy. All cases of isolated LCHAD deficiency have at least one copy of the E474Q mutation in the gene encoding the alpha-subunit of the mitochondrial trifunctional protein. Previously published methods for detecting this mutation are based upon allele-specific restriction enzyme digestion of a DNA fragment generated by PCR, followed by gel electrophoresis to resolve the products. We have developed a faster and less expensive assay for the E474Q mutation using PCR followed directly by differential melting of a fluorescently labeled oligodeoxyribonucleotide probe, using nucleobase quenching to detect probe hybridization.