α-Synuclein Pathology in PRKN-Linked Parkinson's Disease: New Insights from a Blood-Based Seed Amplification Assay

Pathogenic variants in PRKN cause early-onset Parkinson's disease (PD), while the role of alpha-synuclein in PRKN-PD remains uncertain. One study performed a blood-based alpha-synuclein seed amplification assay (SAA) in PRKN-PD, not detecting seed amplification in 17 PRKN-PD patients. By applying a methodologically different SAA focusing on neuron-derived extracellular vesicles, we demonstrated alpha-synuclein seed amplification in 8 of 13 PRKN-PD patients, challenging the view of PRKN-PD as a non-synucleinopathy. Moreover, we performed blinded replication of the neuron-derived extracellular vesicles-dependent SAA in idiopathic PD patients and healthy controls. In conclusion, blood-based neuron-derived extracellular vesicles-dependent SAA represents a promising biomarker to elucidate the underpinnings of (monogenic) PD. ANN NEUROL 2024;95:1173-1177.

Recurrent de-novo gain-of-function mutation in SPTLC2 confirms dysregulated sphingolipid production to cause juvenile amyotrophic lateral sclerosis

BACKGROUND

Amyotrophic lateral sclerosis (ALS) leads to paralysis and death by progressive degeneration of motor neurons. Recently, specific gain-of-function mutations in SPTLC1 were identified in patients with juvenile form of ALS. SPTLC2 encodes the second catalytic subunit of the serine-palmitoyltransferase (SPT) complex.

METHODS

We used the GENESIS platform to screen 700 ALS whole-genome and whole-exome data sets for variants in SPTLC2. The de-novo status was confirmed by Sanger sequencing. Sphingolipidomics was performed using liquid chromatography and high-resolution mass spectrometry.

RESULTS

Two unrelated patients presented with early-onset progressive proximal and distal muscle weakness, oral fasciculations, and pyramidal signs. Both patients carried the novel de-novo SPTLC2 mutation, c.203T>G, p.Met68Arg. This variant lies within a single short transmembrane domain of SPTLC2, suggesting that the mutation renders the SPT complex irresponsive to regulation through ORMDL3. Confirming this hypothesis, ceramide and complex sphingolipid levels were significantly increased in patient plasma. Accordingly, excessive sphingolipid production was shown in mutant-expressing human embryonic kindney (HEK) cells.

CONCLUSIONS

Specific gain-of-function mutations in both core subunits affect the homoeostatic control of SPT. SPTLC2 represents a new Mendelian ALS gene, highlighting a key role of dysregulated sphingolipid synthesis in the pathogenesis of juvenile ALS. Given the direct interaction of SPTLC1 and SPTLC2, this knowledge might open new therapeutic avenues for motor neuron diseases.

Another de novo mutation in the SOD1 gene: the first Turkish patient with SOD1-His47Arg, a case report

Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease of motor neurons. Most ALS cases are considered sporadic due to the presence of a combination of environmental and complex genetic risk factors, while approximately 10% of cases have a family history. Pathogenic variants in the SOD1 gene are the second most frequent causative factor of genetics-based ALS worldwide, after C9ORF72 hexanucleotide repeat expansion. The De novo occurrence of pathogenic mutations in ALS-associated genes and its effect on disease progression have been studied previously, especially in the FUS gene. Recent studies have shown that a very small portion of SOD1 cases occurred de novo. Here, we present the first de novo case of the SOD1 His47Arg mutation in a young female patient with mild symptoms and, currently, a slow progression for 7 years.

Four Turkish families with hyperekplexia: A missense mutation and the exon 1-7 deletion in the GLRA1 gene

BACKGROUND

Hyperekplexia is a disease that progresses with excessive startle attacks and is included in the differential diagnosis of epilepsy and many movement disorders.

METHODS

The WES results were validated in available family members by Sanger sequencing, or in the case of deletion, PCR followed by agarose gel electrophoresis was performed.

RESULTS

WES analysis revealed the previously reported homozygous c.277C>T p.Arg93Trp variant in the GLRA1 gene (ENST00000455880.2) in Family 1. In all other three families, the previously reported homozygous deletion of exons 1-7 of the GLRA1 gene was identified using CNV analysis based on the WES data.

CONCLUSIONS

The homozygous exon1-7 deletion has been described several times in different populations and may be a founder mutation in the Kurdish people in Turkey. The family with Arg93Trp variant stems from the Black Sea region of Turkey where close consanguinity is common. These analyses are important to provide genetic counseling to families and for a better understanding of the pathophysiology of the disease.

Early-Onset Parkinson's Disease: A Novel Deletion Comprising the DJ-1 and TNFRSF9 Genes

Patients with mutations in DJ-1 have early-onset Parkinson's disease and slow progression. Here we describe a Turkish family with a large deletion in the neighboring genes DJ-1 (del exons 1-5) and TNFRSF9 (del exons 1-6), raising the question if TNFRSF9 is a possible disease modifier.

A novel pathogenic variant in the 3' end of the AGTPBP1 gene gives rise to neurodegeneration without cerebellar atrophy: an expansion of the disease phenotype?

Childhood-onset neurodegeneration with cerebellar atrophy (CONDCA) is a recently described form of the large group of infantile hereditary lower motor neuron diseases (Teoh et al. 2017), resulting from biallelic damaging variants in the AGTPBP1 gene, first described by Shashi et al. in EMBO J 37(23):e100540, 2018. AGTPBP-related neurodegeneration is a severe neurodevelopmental disorder that progresses with global developmental delay and intellectual disability, often accompanied with peripheral nerve damage and lower motor degeneration and a fatal course in the early years of life. The encoded protein is ATP/GTP-Binding Protein1, also known as cytosolic carboxypeptidase 1 (CCP1) or nervous system nuclear protein induced by axotomy (NNA1). Here we report a consanguineous family with four offspring, two of whom are affected. The index patient is a 21-month-old male with global developmental delay and hypotonia. The proband's 17-year-old sister, diagnosed with cerebral palsy, had severe hypotonia accompanied by motor and cognitive retardation. WES analysis revealed a novel homozygous c.3293G > A variant in the AGTPBP1 gene with high pathogenicity scores. Targeted Sanger sequencing confirmed the variant in both affected children and in heterozygous form in the parents. The affected siblings present with hypotonia and motor and cognitive retardation, in line with the studies previously reported. However, in our patients, no signs of cerebellar atrophy in cranial MRI were present, so the acronym CONDCA is not applicable; lower motor neuron findings were also absent. The matching and distinguishing aspects of our patients will add to the present literature and expand our understanding of this rare genetic neurodegenerative disease of early childhood.

The Complex Genetic Landscape of Hereditary Ataxias in Turkey and Implications in Clinical Practice

BACKGROUND

The genetic and epidemiological features of hereditary ataxias have been reported in several populations; however, Turkey is still unexplored. Due to high consanguinity, recessive ataxias are more common in Turkey than in Western European populations.

OBJECTIVE

To identify the prevalence and genetic structure of hereditary ataxias in the Turkish population.

METHODS

Our cohort consisted of 1296 index cases and 324 affected family members. Polymerase chain reaction followed by Sanger sequencing or fragment analysis were performed to screen for the trinucleotide repeat expansions in families with a dominant inheritance pattern, as well as in sporadic cases. The expansion in the frataxin (FXN) gene was tested in all autosomal recessive cases and in sporadic cases with a compatible phenotype. Whole-exome sequencing was applied to 251 probands, selected based on the family history, age of onset, and phenotype.

RESULTS

Mutations in known ataxia genes were identified in 30% of 1296 probands. Friedreich's ataxia was found to be the most common recessive ataxia in Turkey, followed by autosomal recessive spastic ataxia of Charlevoix-Saguenay. Spinocerebellar ataxia types 2 and 1 were the most common dominant ataxias. Whole-exome sequencing was performed in 251 probands with an approximate diagnostic yield of 50%. Forty-eight novel variants were found in a plethora of genes, suggesting a high heterogeneity. Variants of unknown significance were discussed in light of clinical data.

CONCLUSION

With the large sample size recruited across the country, we consider that our results provide an accurate picture of the frequency of hereditary ataxias in Turkey. © 2021 International Parkinson and Movement Disorder Society.

A combined clinical and computational approach to understand the SOD1A4T-mediated pathogenesis of rapidly progressive familial amyotrophic lateral sclerosis

Here, we aim to provide a comprehensive clinical and biomolecular description of familial amyotrophic lateral sclerosis (fALS) in a 25-year-old female patient with respect to the SOD1^A4T genotype. The clinical diagnosis of the disease was based on family history, neurological examination, electroneurophysiological studies, and revised El Escorial criteria. The heterozygous presence of the A4T mutation in the proband was confirmed by PCR coupled with Sanger sequencing of exon 1 of the SOD1 gene. The mutation was introduced in silico into the three-dimensional structure of the native protein. After energy minimization and quality assessment, non-covalent interactions around threonine-4 and changes in protein stability were calculated computationally. The patient differed widely in age at onset, initial neurological symptoms and findings, and survival time from her kindred, in which several members are affected. SOD1^A4T-linked fALS in this case had bulbar involvement at onset, a combination of lower and upper motor neuron signs and showed rapid progression. Unlike alanine-4, threonine-4 failed to engage in hydrophobic interactions with the vicinal non-polar amino acids. The overall fold of the modeled SOD1^A4T mutant remained intact, but unfolding free energy estimations disclosed a decrease in the protein's stability. We report a phenotypically distinct patient with fALS due to the SOD1^A4T mutation and further expand the largest pedigree ever published for SOD1^A4T-linked fALS. Genotype‒phenotype correlation in fALS is complex, and it demands detailed clinical investigation and advanced scientific research. Awareness of the broadened phenotypic spectrum might potentially enhance the diagnosis and genetic counseling of fALS.

Novel variants broaden the phenotypic spectrum of PLEKHG5-associated neuropathies

BACKGROUND AND PURPOSE

Pathogenic variants in PLEKHG5 have been reported to date to be causative in three unrelated families with autosomal recessive intermediate Charcot-Marie-Tooth disease (CMT) and in one consanguineous family with spinal muscular atrophy (SMA). PLEKHG5 is known to be expressed in the human peripheral nervous system, and previous studies have shown its function in axon terminal autophagy of synaptic vesicles, lending support to its underlying pathogenetic mechanism. Despite this, there is limited knowledge of the clinical and genetic spectrum of disease.

METHODS

We leverage the diagnostic utility of exome and genome sequencing and describe novel biallelic variants in PLEKHG5 in 13 individuals from nine unrelated families originating from four different countries. We compare our phenotypic and genotypic findings with a comprehensive review of cases previously described in the literature.

RESULTS

We found that patients presented with variable disease severity at different ages of onset (8-25 years). In our cases, weakness usually started proximally, progressing distally, and can be associated with intermediate slow conduction velocities and minor clinical sensory involvement. We report three novel nonsense and four novel missense pathogenic variants associated with these PLEKHG5-associated neuropathies, which are phenotypically spinal muscular atrophy (SMA) or intermediate Charcot-Marie-Tooth disease.

CONCLUSIONS

PLEKHG5-associated neuropathies should be considered as an important differential in non-5q SMAs even in the presence of mild sensory impairment and a candidate causative gene for a wide range of hereditary neuropathies. We present this series of cases to further the understanding of the phenotypic and molecular spectrum of PLEKHG5-associated diseases.

Phenotypic and genotypic features of patients diagnosed with ALS in the city of Sakarya, Turkey

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease leading to motor neuron damage. In this study, the clinical, demographic, and genetic features of ALS patients in the city of Sakarya, Turkey, were investigated. Patients with an established diagnosis of ALS according to the Awaji criteria were included. Age, sex, age at onset of ALS, initial complaints, consanguineous marriage, and genetic features were retrospectively investigated. Conventional genetic analysis and NGS were used for molecular evaluation of patients. A total of 55 probands (10 familial, 45 sporadic) in whom ALS was suspected due to their phenotypic features were included. Thirty-two patients were male (58.2%), and 23 were female (41.8%); their mean ages were 62.65 ± 13 years. The mean age of onset for 37 familial patients from 10 families was 49.9 years. Two cases had juvenile-onset. Fourteen (25.5%) bulbar-onset versus 40 (72.7%) limb-onset patients were detected; one patient had both. Six (10.9%) patients showed marked frontotemporal dementia. Twenty-nine (52.7%) patients died during the follow-up period. Genetic analysis identified causative variants in eleven cases, carrying variants in six different ALS genes (C9orf72, SOD1, VCP, SPG11, TBK1, and SH3TC2). Genetic investigations have revealed more than 40 genes to be involved in the pathogenesis of ALS. Our relatively small study cohort restricted to one province of Turkey, however, prone to migration, consists of 10/55 familial ALS cases, which harbor two rare (SH3TC2-p.Met523Thr and TBK1-p.Glu643del) and two novel (SPG11-p.Lys656Valfs*11 and VCP-p.Arg191Pro) mutations contributing to the literature.

A novel PNPLA6 mutation in a Turkish family with intractable Holmes tremor and spastic ataxia

Autosomal recessive cerebellar ataxias are a group of rare neurological diseases with a genetic origin. Recently, the mutations in the PNPLA6 gene were suggested to lead to ataxia and also to other specific syndromes such as Boucher-Neuhauser (ataxia, hypogonadism, and chorioretinal dystrophy) or Gordon-Holmes Syndromes (ataxia, hypogonadism, and brisk reflexes) within a broad spectrum of neurodegenerative diseases. Here we report three patients from a single-family with a novel pathogenic mutation in the PNPLA6 gene which led to predominantly spastic-ataxia, and intractable Holmes tremor. The PNPLA6-related disease should be considered in the differential diagnosis of spastic-ataxias even in the absence of chorioretinal dystrophy, and hypogonadotropic hypogonadism. Further studies should unravel the factors which account for the phenotypic variability present in patients with PNPLA6 gene mutations.

Human CRY1 variants associate with attention deficit/hyperactivity disorder

Attention deficit/hyperactivity disorder (ADHD) is a common and heritable phenotype frequently accompanied by insomnia, anxiety, and depression. Here, using a reverse phenotyping approach, we report heterozygous coding variations in the core circadian clock gene cryptochrome 1 in 15 unrelated multigenerational families with combined ADHD and insomnia. The variants led to functional alterations in the circadian molecular rhythms, providing a mechanistic link to the behavioral symptoms. One variant, CRY1Δ11 c.1657+3A>C, is present in approximately 1% of Europeans, therefore standing out as a diagnostic and therapeutic marker. We showed by exome sequencing in an independent cohort of patients with combined ADHD and insomnia that 8 of 62 patients and 0 of 369 controls carried CRY1Δ11. Also, we identified a variant, CRY1Δ6 c.825+1G>A, that shows reduced affinity for BMAL1/CLOCK and causes an arrhythmic phenotype. Genotype-phenotype correlation analysis revealed that this variant segregated with ADHD and delayed sleep phase disorder (DSPD) in the affected family. Finally, we found in a phenome-wide association study involving 9438 unrelated adult Europeans that CRY1Δ11 was associated with major depressive disorder, insomnia, and anxiety. These results defined a distinctive group of circadian psychiatric phenotypes that we propose to designate as "circiatric" disorders.

Revisiting the complex architecture of ALS in Turkey: Expanding genotypes, shared phenotypes, molecular networks, and a public variant database

The last decade has proven that amyotrophic lateral sclerosis (ALS) is clinically and genetically heterogeneous, and that the genetic component in sporadic cases might be stronger than expected. This study investigates 1,200 patients to revisit ALS in the ethnically heterogeneous yet inbred Turkish population. Familial ALS (fALS) accounts for 20% of our cases. The rates of consanguinity are 30% in fALS and 23% in sporadic ALS (sALS). Major ALS genes explained the disease cause in only 35% of fALS, as compared with ~70% in Europe and North America. Whole exome sequencing resulted in a discovery rate of 42% (53/127). Whole genome analyses in 623 sALS cases and 142 population controls, sequenced within Project MinE, revealed well-established fALS gene variants, solidifying the concept of incomplete penetrance in ALS. Genome-wide association studies (GWAS) with whole genome sequencing data did not indicate a new risk locus. Coupling GWAS with a coexpression network of disease-associated candidates, points to a significant enrichment for cell cycle- and division-related genes. Within this network, literature text-mining highlights DECR1, ATL1, HDAC2, GEMIN4, and HNRNPA3 as important genes. Finally, information on ALS-related gene variants in the Turkish cohort sequenced within Project MinE was compiled in the GeNDAL variant browser (www.gendal.org).

The first biallelic missense mutation in the FXN gene in a consanguineous Turkish family with Charcot-Marie-Tooth-like phenotype

Charcot-Marie-Tooth (CMT) disease is the most common inherited neuropathy with a prevalence of 1 in 2500 individuals worldwide. Here, we report three Turkish siblings from consanguineous parents presenting with a CMT-like phenotype who carry a homozygous c.493C>T, p.Arg165Cys mutation in the FXN gene that is the only known causative gene for Friedreich's ataxia (FRDA). The identified missense mutation has been reported previously in two FRDA cases in compound heterozygosity with the common GAA repeat expansion in the first intron of the FXN gene. Analysis of skin biopsy samples from our family indicated that the mutation does not affect the expression levels of the frataxin, pointing to functional impairment of the corresponding protein. The CMT phenotype in the siblings was associated with visual impairment, optic nerve atrophy, and dysarthria. To the best of our knowledge, this family represents the first FXN missense mutation in homozygosity and challenges the notion that missense mutations have not been reported yet due to their embryonic lethality. Furthermore, this finding poses an interesting genetic overlap between autosomal recessive CMT and FRDA that we believe may have important implications on understanding the pathogenesis of these neurological disorders.

Phenotypic and Genotypic Analysis of Hereditary Ataxia Patients in Sakarya City, Turkey

Introduction

Hereditary ataxias are a group of heterogeneous diseases in regard to their clinical and genetic characteristics. Ataxia that progresses slowly may be accompanied by pyramidal and extrapyramidal findings, articulation disorders, ophthalmic movement disorders, neuropathic complaints, cognitive and behavioral abnormalies, and epilepsy. Definitive diagnosis in hereditary ataxias is based on molecular assays. History, clinical examination, laboratory and neuroimaging assist diagnosis. In our study, thirty-seven patients of suspected hereditary ataxia were examined with their clinical and genetic aspects, and the results compared with literature.

Method

Our study included 37 patients in 22 families who presented to our center between 2010-2016, and whose familial history and phenotypic features indicated hereditary ataxia. The patients were studied for clinical findings, family tree, neuroimaging, and laboratory findings. Advanced genetic investigations were performed on peripheral venous blood samples for hereditary ataxia.

Results

Of the 37 patients included in our study, 21 were females and 16 were males. Genetic analyses resulted in spinocerebellar ataxia (SCA) in four families (10 patients), Friedrich ataxia (FA) in three families (eight patients), and recessive ataxia due to point mutation in one family (two patients). SCA subtyping revealed SCA 1, 2, 6 and 8 in our patients. The remaining 16 patients included in our study could not be solved so far and are under investigation.

Conclusion

Hereditary ataxias are rare neurodegenerative disorders. Large genetic pool, ethnic and local differences complicate diagnosing even further. Our study contributes to the literature by reflecting phenotypic and genotypic characteristics of hereditary SCA patients in our region and reporting rare hereditary ataxia genotypes.

ERLIN1 mutations cause teenage-onset slowly progressive ALS in a large Turkish pedigree

Amyotrophic lateral sclerosis (ALS) is a late-onset motor neuron disease with mostly dominant inheritance and a life expectancy of 2-5 years; however, a quite common occurrence of atypical forms of the disease, due to recessive inheritance, has become evident with the use of NGS technologies. In this paper, we describe a family with close consanguinity for at least four generations, suffering from a slowly progressive form of ALS. Spastic walking is observed since teenage years, while bulbar symptoms start much later, at the fifth or sixth decade of life. Patients usually die because of respiratory failure. Using whole-exome sequencing, we identified a novel homozygous p.(Val94Ala) (c.281T>C) (NG_052910.1) (NM_006459) variation in the endoplasmic reticulum lipid raft associated protein 1 (ERLIN1) gene, which segregates with the disease in the family. Here we suggest that ERLIN1 variants, previously shown in juvenile hereditary spastic paraplegia cases, may also be the cause of a slowly progressive early-onset ALS, starting with upper motor neuron features and developing into classical ALS with the addition of lower motor neuron dysfunction. We also demonstrate that ATP-binding cassette subfamily C member 2 (ABCC2) gene, responsible for hyperbilirubinemia, is linked to ERLIN1.

Elevated Global DNA Methylation Is Not Exclusive to Amyotrophic Lateral Sclerosis and Is Also Observed in Spinocerebellar Ataxia Types 1 and 2

Adult-onset neurological disorders are caused and influenced by a multitude of different factors, including epigenetic modifications. Here, using an ELISA kit selected upon careful testing, we investigated global 5-methylcytosine (5-mC) levels in sporadic and familial amyotrophic lateral sclerosis (sALS and fALS), spinocerebellar ataxia types 1 and 2 (SCA1 and SCA2), Huntington's disease, Friedreich's ataxia, and myotonic dystrophy type 1. We report a significant elevation in global 5-mC levels of about 2-7% on average for sALS (p < 0.01 [F(1, 243) = 9.159, p = 0.0027]) and various forms of fALS along with SCA1 (p < 0.01 [F(1, 83) = 11.285], p = 0.0012) and SCA2 (p < 0.001 [F(1, 122) = 29.996, p = 0.0001]) when compared to age- and sex-matched healthy controls. C9orf72 expansion carrier ALS patients exhibit the highest global 5-mC levels along with C9orf72 promoter hypermethylation. We failed to measure global 5-hydroxymethylcytosine (5-hmC) levels in blood, probably due to the very low levels of 5-hmC and the limitations of the commercially available ELISA kits. Our results point towards a role for epigenetics modification in ALS, SCA1, and SCA2, and help conclude a dispute on the global 5-mC levels in sALS blood.

Search for SCA2 blood RNA biomarkers highlights Ataxin-2 as strong modifier of the mitochondrial factor PINK1 levels

Ataxin-2 (ATXN2) polyglutamine domain expansions of large size result in an autosomal dominantly inherited multi-system-atrophy of the nervous system named spinocerebellar ataxia type 2 (SCA2), while expansions of intermediate size act as polygenic risk factors for motor neuron disease (ALS and FTLD) and perhaps also for Levodopa-responsive Parkinson's disease (PD). In view of the established role of ATXN2 for RNA processing in periods of cell stress and the expression of ATXN2 in blood cells such as platelets, we investigated whether global deep RNA sequencing of whole blood from SCA2 patients identifies a molecular profile which might serve as diagnostic biomarker. The bioinformatic analysis of SCA2 blood global transcriptomics revealed various significant effects on RNA processing pathways, as well as the pathways of Huntington's disease and PD where mitochondrial dysfunction is crucial. Notably, an induction of PINK1 and PARK7 expression was observed. Conversely, expression of Pink1 was severely decreased upon global transcriptome profiling of Atxn2-knockout mouse cerebellum and liver, in parallel to strong effects on Opa1 and Ghitm, which encode known mitochondrial dynamics regulators. These results were validated by quantitative PCR and immunoblots. Starvation stress of human SH-SY5Y neuroblastoma cells led to a transcriptional phasic induction of ATXN2 in parallel to PINK1, and the knockdown of one enhanced the expression of the other during stress response. These findings suggest that ATXN2 may modify the known PINK1 roles for mitochondrial quality control and autophagy during cell stress. Given that PINK1 is responsible for autosomal recessive juvenile PD, this genetic interaction provides a concept how the degeneration of nigrostriatal dopaminergic neurons and the Parkinson phenotype may be triggered by ATXN2 mutations.

Genome-wide copy number variation in sporadic amyotrophic lateral sclerosis in the Turkish population: deletion of EPHA3 is a possible protective factor

The genome-wide presence of copy number variations (CNVs), which was shown to affect the expression and function of genes, has been recently suggested to confer risk for various human disorders, including Amyotrophic Lateral Sclerosis (ALS). We have performed a genome-wide CNV analysis using PennCNV tool and 733K GWAS data of 117 Turkish ALS patients and 109 matched healthy controls. Case-control association analyses have implicated the presence of both common (>5%) and rare (<5%) CNVs in the Turkish population. In the framework of this study, we identified several common and rare loci that may have an impact on ALS pathogenesis. None of the CNVs associated has been implicated in ALS before, but some have been reported in different types of cancers and autism. The most significant associations were shown for 41 kb and 15 kb intergenic heterozygous deletions (Chr11: 50,545,009–50,586,426 and Chr19: 20,860,930–20,875,787) both contributing to increased risk for ALS. CNVs in coding regions of the MAP4K3, HLA-B, EPHA3 and DPYD genes were detected however, after validation by Log R Ratio (LRR) values and TaqMan CNV genotyping, only EPHA3 deletion remained as a potential protective factor for ALS (p = 0.0065024). Based on the knowledge that EPHA4 has been previously shown to rescue SOD1 transgenic mice from ALS phenotype and prolongs survival, EPHA3 may be a promising candidate for therepuetic interventions.

Are alsin and spartin novel interaction partners?

Mutations in ALS2 gene/alsin are associated with recessive forms of motor neuron disorders including Juvenile Amyotrophic Lateral Sclerosis (JALS), Infantile-onset Ascending Hereditary Spastic Paraplegia (IAHSP) and Juvenile Primary Lateral Sclerosis (JPLS). In this study, we show that alsin and another MND-linked protein, spartin are related to each other both at mRNA and protein levels in Neuro2a cells. We observed significant alterations in spartin expression in alsin knock-down conditions. We further found that both proteins colocalize in N2a cells and spartin isoform-a precipitates with alsin in the same protein complex. In the light of these results we suggest that alsin and spartin may interact each other physically.

ATXN2 and its neighbouring gene SH2B3 are associated with increased ALS risk in the Turkish population

Expansions of the polyglutamine (polyQ) domain (≥ 34) in Ataxin-2 (ATXN2) are the primary cause of spinocerebellar ataxia type 2 (SCA2). Recent studies reported that intermediate-length (27-33) expansions increase the risk of Amyotrophic Lateral Sclerosis (ALS) in 1-4% of cases in diverse populations. This study investigates the Turkish population with respect to ALS risk, genotyping 158 sporadic, 78 familial patients and 420 neurologically healthy controls. We re-assessed the effect of ATXN2 expansions and extended the analysis for the first time to cover the ATXN2 locus with 18 Single Nucleotide Polymorphisms (SNPs) and their haplotypes. In accordance with other studies, our results confirmed that 31-32 polyQ repeats in the ATXN2 gene are associated with risk of developing ALS in 1.7% of the Turkish ALS cohort (p=0.0172). Additionally, a significant association of a 136 kb haplotype block across the ATXN2 and SH2B3 genes was found in 19.4% of a subset of our ALS cohort and in 10.1% of the controls (p=0.0057, OR: 2.23). ATXN2 and SH2B3 encode proteins that both interact with growth receptor tyrosine kinases. Our novel observations suggest that genotyping of SNPs at this locus may be useful for the study of ALS risk in a high percentage of individuals and that ATXN2 and SH2B3 variants may interact in modulating the disease pathway.

History and origin of beta-thalassemia in Turkey: sequence haplotype diversity of beta-globin genes

In the present study we report the sequence haplotypes associated with 22 beta-globin gene mutations present in Turkey. Nine nucleotide polymorphisms and an (AT)xTy motif located at the 5' end of the beta-globin gene form the sequence haplotypes that were investigated in 204 unrelated beta-thalassemia and wild-type chromosomes from Turkey. Twelve sequence haplotypes were observed in the chromosomes analyzed and haplotypic heterogeneity was found in the wild-type beta-globin genes. Samples from the Black Sea region demonstrated a remarkable level of haplotypic heterogeneity in contrast to the homogeneity present in Central Anatolian samples. Of the 22 beta-globin mutations analyzed, 18 were related with single sequence haplotypes. This simple association led to the attempt to determine the origin of these mutations by comparing their frequencies in Turkey with those in other countries and/or the world distribution of the haplotypes carrying them. However, the presence of several exceptions for the "one haplotype/one mutation" rule showed that the beta-globin gene cluster is far from static. Each of the IVS-I-110 (G-->A), Cd 39 (C-->T), IVS-I-6 (T-->C), and -30 (T-->A) beta-globin mutations was associated with a minimum of two sequence haplotypes. This fact is best explained by the likelihood of strong recombination mechanisms taking place, rather than by assuming multiple origins for each of these alleles. According to our results, malarial selection for the oldest beta-thalassemia allele in Anatolia (i.e., IVS-I-110 G-->A) may have occurred between 6500 and 2000 B.C. From that date on, most of the common beta-thalassemia mutations in Turkey were established, and by the 13th century A.D. most of them were brought to frequencies close to those observed at present.

Homozygous ß-Thalassemia Associated with Familial Mediterranean Fever in a Turkish Patient

We report here a ß- thalassemia major case (homozygous IVS-1-110 G-A) associated with Familial Mediterranean Fever (FMF) (homozygous 694 Met-Val). Our patient's clinical course revealed a possible synergistic effect between colchicine and desferrioxamine (DFO) However, this could be a only a coincidence, as under colchicine therapy, fever attacks may appear, this may be the topic of a further investigation.

A rare mutation [IVS-I-130 (G-A)] in a Turkish beta-thalassemia major patient

Here we describe the identification of the rare beta-thalassemia mutation IVS-I-130 (G-A) for the first time in Turkey. The hematological evaluation of the patient showed classical signs of beta-thalassemia major requiring regular blood transfusions every 30-35 days. DNA analysis was carried out using reverse dot-blot hybridization and restriction endonuclease digestion, as well as genomic sequencing. The patient was found to be heterozygous for the IVS-I-6 (T-C) and IVS-I-130 (G-A) mutations. In order to deduce a possible origin for the IVS-I-130 (G-A) mutation, the sequence polymorphisms in the DNA of the patient and her family were characterized. The method included the analysis of nine polymorphic nucleotides and the hypervariable microsatellite of composite sequence (AT)(x)T(y) 5' to the beta-globin gene by DNA sequencing. The sequence haplotype (HT4) carrying the IVS-I-130 (G-A) mutation is also observed in Algeria. This favors a Northeastern African origin for this allele. The observed results agree well with a recent introduction of this mutation to Turkey from Egypt toward the end of the 19th century.

Identification of the Chinese IVS-II-654 (C-->T) beta-thalassemia mutation in an immigrant Turkish family: recurrence or migration?

In this study we describe the Chinese IVS-II-654 (C-->T) beta-thalassemia mutation for the first time in an immigrant Turkish family living in Istanbul and originating from Xanthe, Greece. Four members of the family, representing 3 generations, are heterozygous for this mutation. A detailed family history demonstrated a Greek origin for members of 5 generations with no records of migration or consanguineous marriages. Analysis of polymorphic nucleotides located at the 5' end of the beta-globin chromosomes bearing the IVS-II-654 mutation in the family described carried the (AT)9(T)5 type of microsatellite sequence and the ACATCCCCA haplotype. These 2 haplotype components favor a non-Eastern Asian origin for this chromosome, hence suggesting an independent origin for the IVS-II-654 mutation described in this family.

HbS/beta(del)-thalassemia associated with high levels of hemoglobins A2 and F in a Turkish family

Beta-thalassemia and sickle cell disease (SCD) are common disorders in Turkey. Compound heterozygosity for these two disorders (betaS/beta-thalassemia) is encountered frequently. In this report we present hematological and molecular data of two Turkish siblings with betaS/beta(del)-thalassemia caused by a 290 base pair (bp) deletion and associated with increased levels of hemoglobin A2 (HbA2) and hemoglobin F (HbF). Clinical analysis of the two patients showed a mild course of the disease. Haplotypic factors involved in increasing the levels of HbF were analyzed. The two patients showed no changes from the normal sequences at the XmnI site of Ggamma-globin promoter and the (AT)xTy microsatellite 5' to the beta-globin mRNA cap site. The removal of the region between positions -125 to +78 relative to the beta-globin gene mRNA cap site by the 290 bp deletion is thought to allow the beta-locus control region to interact with the promoters of the delta- and gamma-globin genes, leading to increased HbA2 and HbF levels.

Molecular and population genetic analyses of beta-thalassemia in Turkey

In this report we describe the molecular analysis of 795 chromosomes derived from unrelated Turkish beta-thalassemia and sickle cell anemia carriers identified in hematology clinics in Istanbul, Ankara, Izmir, Adana, and Antalya. The determination of the molecular pathology of 754 beta-thalassemia and 42 abnormal hemoglobin genes and analysis of the frequency distribution in six distinct regions of Turkey was accomplished. The experimental strategy, based on PCR amplification of the beta-globin gene, included dot-blot hybridization with 18 probes specific for the Mediterranean populations, denaturing gradient gel electrophoresis, and genomic sequencing. When the regional results are compared with the overall frequency of mutations in the country, it is observed that the frequencies in the western and southern parts of Turkey are in good accordance with the overall distribution, whereas the northern and eastern parts have a more region/population-specific profile with some rare mutations having a significantly high occurrence in these regions. Further evaluation of the data with respect to region- or population-dependent differences will contribute to a better understanding of the mechanisms leading to the marked genetic heterogeneity in Turkey, but could also be extremely valuable in facilitating rapid identification of mutations in families at risk for different hemoglobinopathies.

Genotype-phenotype analysis in HbS-beta-thalassemia

Genotypes and phenotypes were studied in 31 Turkish HbS-beta-thalassemia patients. In 19 patients the beta-thalassemia mutations were beta+ and in 12 the beta 0 phenotype. The IVSI-110 mutation was found in 45% of the patients. IVSI-1, beta 39, IVSII-1 and FSC8 are the genotypes associated with beta 0-thalassemia. Hematological data were evaluated at the time of diagnosis and 4 years after diagnosis. The mean HbF value was 13 +/- 7.8% at diagnosis and 9.7 +/- 7.8% 4 years later. A significant negative correlation was observed between the age of the patients and the HbF value (p < 0.05). No statistically significant differences were observed between the mean of hematological parameters in beta(+)- and beta 0-thalassemia patients except for the mean HbF value which were 10.7 +/- 6.9 and 15.9 +/- 7.7% in beta(+)- and beta 0-thalassemia, respectively (p < 0.05). The study indicated that beta-thalassemia mutations in trans to the HbS mutation do not exert any beneficial effect on the manifestation of the disease.

Rare beta-thalassemia mutation in a Turkish patient: FSC-36/37 (-T)

We describe the rare beta-thalassemia mutation at codons 36/37 (-T) for the first time in Turkey. The propositus is a Turkish patient with beta-thalassemia major who originated in Adana but now resides in Istanbul. Molecular analysis revealed a compound heterozygosity for the common eastern Mediterranean mutation IVS-I-110 (G-A) along with mutation FSC-36/37 (-T). The FSC-36/37 (-T) mutation could have arisen somewhere in the region, including northern Iran and the inaccessible mountainous region of eastern Anatolia. The mutation could have followed two migration routes during the time of Ottoman rule, the first being to Azerbaijan and the second, probably a more recent one, passing through southeastern Anatolia and reaching southern Bulgaria.

Prenatal diagnosis of beta-thalassaemia and sickle cell anaemia in Turkey

This paper reports our experience of molecular analysis and diagnosis of beta-thalassaemia and sickle cell anaemia (HbS) in 70 prospective parents of Turkish descent and their fetuses. Molecular screening was carried out by allele-specific oligonucleotide (ASO) hybridization of amplified DNA to the 12 most common mutations in the Turkish population. By using this approach, we were able to define the mutation in 95 per cent of chromosomes investigated. Genomic sequencing led to the additional detection of three rare mutations: Cd 44 (-C), IVS-I-5 (G-C), and IVS-I-116 (T-G). All diagnoses were successfully accomplished and no misdiagnosis occurred. Consanguineous marriage appears to contribute significantly to the frequency of affected births in Turkey. Out of the 14 homozygous fetuses, six were the result of close consanguinity. This study indicates that fetal diagnosis of beta-thalassaemia and HbS may be obtained in practically all cases, even in a heterogeneous population like the Turkish population, when early methods of fetal sampling are combined with polymerase chain reaction (PCR)-based techniques. Until gene therapy becomes a reality, the only approaches to the control of haemoglobinopathies are prevention and avoidance. The most relevant and common aspects of the programmes, which have been very effective in reducing the birth rate of beta-thalassaemia major in several at-risk areas of the Mediterranean basin, are the continuous educational campaigns directed at the population at large, the voluntary basis, and non-directive counselling. The most important challenge for the eradication of the haemoglobinopathies in Turkey is the organization of a nation-wide and comprehensive genetic preventive programme based on DNA technology.

Imerslund-Gräsbeck syndrome coexisting with beta-thalassemia trait

A 9-year-old female patient with Imerslund-Gräsbeck syndrome and heterozygosity for beta-thalassemia is presented. At admission the hemoglobin (Hb) was 7.2 g/dL; reticulocytes, 0.2%; red blood cell count (RBC), 2.3 x 10(12)/L; mean corpuscular volume (MCV), 80 fL; hemoglobin A2 (HbA2), 4.3%; fetal hemoglobin intervening sequence (IVS) (HbF), 1.9%. In the bone marrow aspiration smear, megaloblastic changes were observed; the Schilling test was compatible with malabsorption. DNA analysis revealed the presence of heterozygosity for the IVS-I-110 type of beta-thalassemia mutation. Five months after treatment with vitamin B12, Hb was found to be 12.8 g/dL; RBC, 5 x 10(12)/L; MCV, 63 fL.

The molecular basis of β-thalassemia in Turkey

By using oligonucleotide hybridization, restriction endonuclease analysis and direct sequencing of amplified genomic DNA, we have been able to characterize 18 different mutations in the beta-globin genes of 161 beta-thalassemia homozygotes and 107 beta-thalassemia heterozygotes from Turkey (429 beta-thalassemia chromosomes). Previous studies dealing with beta-thalassemia in Mediterranean countries have shown that, in most Mediterranean populations, only a few mutations are prevalent. In contrast, beta-thalassemia in Turkey does not seem to be associated with a few predominant mutations. The six most frequent alleles, IVS-I-110 (G----A), IVS-I-6(T----C), FSC-8 (-AA), IVS-I-1(G----A), -30(T----A) and FSC-5 (-CT), account for only 69.3% of the disease genes; indeed, all 26 mutations assayed represent 85.8% of the disease genes, confirming the considerable molecular heterogeneity of beta-thalassemia among Turks, and indicating the possible presence of rare, previously undefined, mutations in the population. Two mutations observed in this study, IVS-I-116 (T----G) and Cd44(-C), have not been reported in the Turkish population to date. Since preventive medical services, such as genetic counseling and prenatal diagnosis, are greatly improved by detailed knowledge of the molecular pathology of beta-thalassemia, we strongly believe that the presented data will facilitate the intended establishment of a prenatal diagnosis center, based on DNA analysis, in Turkey.