Kristina Gotovac

Convergence of miRNA expression profiling, α-synuclein interacton and GWAS in Parkinson's disease.

miRNAs were recently implicated in the pathogenesis of numerous diseases, including neurological disorders such as Parkinsons disease (PD). miRNAs are abundant in the nervous system, essential for efficient brain function and play important roles in neuronal patterning and cell specification. To further investigate their involvement in the etiology of PD, we conducted miRNA expression profiling in peripheral blood mononuclear cells (PBMCs) of 19 patients and 13 controls using microarrays. We found 18 miRNAs differentially expressed, and pathway analysis of 662 predicted target genes of 11 of these miRNAs revealed an over-representation in pathways previously linked to PD as well as novel pathways. To narrow down the genes for further investigations, we undertook a parallel approach using chromatin immunoprecipitation-sequencing (ChIP-seq) analysis to uncover genome-wide interactions of α-synuclein, a molecule with a central role in both monogenic and idiopathic PD. Convergence of ChIP-seq and miRNomics data highlighted the glycosphingolipid biosynthesis and the ubiquitin proteasome system as key players in PD. We then tested the association of target genes belonging to these pathways with PD risk, and identified nine SNPs in USP37 consistently associated with PD susceptibility in three genome-wide association studies (GWAS) datasets (0.46≤OR≤0.63) and highly significant in the meta-dataset (3.36×10−4<p<1.94×10−3). A SNP in ST8SIA4 was also highly associated with PD (p = 6.15×10−3) in the meta-dataset. These findings suggest that several miRNAs may act as regulators of both known and novel biological processes leading to idiopathic PD.

Personalized medicine in neurodegenerative diseases: how far away?

Neurodegenerative diseases are characterized by progressive dysfunction of the nervous system as a result of neuronal loss in the brain and spinal cord. Despite extensive research efforts aimed at development of new disease-modifying therapeutics, there is still no effective treatment to halt neurodegenerative processes. Thus, modification of current therapeutic and diagnostic research strategies is a goal of increasing urgency. The biggest limitation in neurodegenerative disease research is the lack of appropriate biomarkers. Discovery of universal biomarkers capable of diagnosing patients with neurodegenerative diseases, monitoring their response to therapy, and predicting disease progression seems to be a tall order. Instead, a combination of different methodologies in the discovery of biomarkers specific for each described aspect of the disease seems to be a more viable approach. Although application of personalized medicine in diagnosis and treatment of neurodegenerative diseases may seem far off, some recent developments, such as utilizing specific biological therapies in multiple sclerosis, microRNA profiling as a source of novel biomarkers in Parkinson’s disease, or combination of neuroimaging and proteomic analyses in diagnosis of Alzheimer’s disease patients, already point to the way clinical neurology may integrate new achievements in everyday practice. Combination of genomic, proteomic, glycomic, and metabolomic approaches may yield novel insights into molecular mechanisms of disease pathophysiology, which could then be integrated and translated into clinical neurology. Based on the developments during the past decade, it is feasible to predict that a personalized approach to treating neurological disorders will become more widely applicable in the coming years.

Aberrant expression of shared master-key genes contributes to the immunopathogenesis in patients with juvenile spondyloarthritis.

Association of juvenile spondyloarthritis (jSpA) with the HLA-B27 genotype is well established, but there is little knowledge of other genetic factors with a role in the development of the disease. To date, only a few studies have tried to find those associated genes by obtaining expression profiles, but with inconsistent results due to various patient selection criteria and methodology. The aim of the present study was to identify and confirm gene signatures and novel biomarkers in highly homogeneous cohorts of untreated and treated patients diagnosed with jSpA and other forms of juvenile idiopathic arthritis (JIA) according to ILAR criteria. For the purposes of the research, total RNA was isolated from whole blood of 45 children with jSpA and known HLA genotype, 11 children with oligo- and polyarticular forms of JIA, as well as 12 age and sex matched control participants without diagnosis of inflammatory disease. DNA microarray gene expression was performed in 11 patients with jSpA and in four healthy controls, along with bioinformatical analysis of retrieved data. Carefully selected differentially expressed genes where analyzed by qRT-PCR in all participants of the study. Microarray results and bioinformatical analysis revealed 745 differentially expressed genes involved in various inflammatory processes, while qRT-PCR analysis of selected genes confirmed data universality and specificity of expression profiles in jSpA patients. The present study indicates that jSpA could be a polygenic disease with a possible malfunction in antigen recognition and activation of immunological response, migration of inflammatory cells and regulation of the immune system. Among genes involved in these processes TLR4, NLRP3, CXCR4 and PTPN12 showed almost consistent expression in study patients diagnosed with jSpA. Those genes and their products could therefore potentially be used as novel biomarkers, possibly predictive of disease prognosis and response to therapy, or even as a target for new therapeutic approaches.

Complex intrachromosomal rearrangement in 1q leading to 1q32.2 microdeletion: a potential role of SRGAP2 in the gyrification of cerebral cortex

BackgroundVan der Woude syndrome (MIM: 119300, VWS) is a dominantly inherited and the most common orofacial clefting syndrome; it accounts for ~2 % of all cleft lip and palate cases. Intellectual disability (ID) is characterized by significant limitations, both in intellectual functioning (cognitive deficit) and in adaptive behavior as expressed in conceptual, social and practical adaptive skills. Karyotyping has been the first standard test for the detection of genetic imbalance in patients with ID for more than 35 years. Advances in genetic diagnosis have laid chromosomal microarrays (CMA) as a new standard and first first-line test for diagnosis of patients with ID, as well as other conditions, such as autism spectrum disorders or multiple congenital anomalies.Case PresentationThe present case was initially studied due to unexplained cognitive deficit. Physical examination at the age of 18 years revealed cleft palate, lower lip pits and hypodontia, accompanied with other dysmorphic features and absence of speech. Brain MRI uncovered significantly reduced overall volume of gray matter and cortical gyrification. Banding cytogenetics revealed an indistinct intrachromosomal rearrangement in the long arm of one chromosome 1, and subsequent microarray analyses identified a 5.56 Mb deletion in 1q32.1-1q32.3, encompassing 52 genes; included were the entire IRF6 gene (whose mutations/deletions underlay VWS) and SRGAP2, a gene with an important role in neuronal migration during development of cerebral cortex. Besides, a duplication in 3q26.32 (1.9 Mb in size) comprising TBL1XR1 gene was identified. Multicolor banding for chromosome 1 and molecular cytogenetics applying a battery of locus-specific probes covering 1q32.1 to 1q44 characterized a four breakpoint-insertional-rearrangement-event, resulting in 1q32.1-1q32.3 deletion.ConclusionsConsidering that the human-specific three-fold segmental duplication of SRGAP2 gene evolutionary corresponds to the beginning of neocortical expansion, we hypothesize that aberrations in SRGAP2 are strong candidates underlying specific brain abnormalities, namely reduced volume of grey matter and reduced gyrification.

Vagus nerve stimulation in Lafora body disease.

Introduction Lafora body disease (LBD) is a rare autosomal recessive disorder characterized by progression to inexorable dementia and frequent occipital seizures, in addition to myoclonus and generalized tonic–clonic seizures (GTCSs). It belongs to the group of progressive myoclonus epilepsies (PMEs), rare inherited neurodegenerative diseases with great clinical and genetic differences, as well as poor prognosis. Since those patients have a pharmacoresistant disease, an adjunctive treatment option is vagus nerve stimulation (VNS). To date, there are four reported cases of the utility of VNS in PME — in Unverricht–Lundborg disease (ULD), myoclonic epilepsy with ragged-red fibers (MERRF), Gauchers disease, and in one case that remained unclassified. Case presentation A 19-year-old male patient had progressive myoclonus, GTCSs that often progressed to status epilepticus (SE), progressive cerebellar and extrapyramidal symptomatology, and dementia, and his disease was pharmacoresistant. We confirmed the diagnosis of LBD by genetic testing. After VNS implantation, in the one-year follow-up period, there was a complete reduction of GTCS and SE, significant regression of myoclonus, and moderate regression of cerebellar symptomatology. Conclusion To our knowledge, this is the first reported case of the utility of VNS in LBD. Vagus nerve stimulation therapy may be considered a treatment option for different clinical entities of PME. Further studies with a larger number of patients are needed.

Biomarkers of aggression in dementia

Dementia is a clinical syndrome defined by progressive global impairment of acquired cognitive abilities. It can be caused by a number of underlying conditions. The most common types of dementia are Alzheimers disease (AD), frontotemporal dementia (FTD), vascular cognitive impairment (VCI) and dementia with Lewy bodies (DLB). Despite the fact that cognitive impairment is central to the dementia, noncognitive symptoms, most commonly described nowadays as neuropsychiatric symptoms (NPS) exist almost always at certain point of the illness. Aggression as one of the NPS represents danger both for patients and caregivers and the rate of aggression correlates with the loss of independence, cognitive decline and poor outcome. Therefore, biomarkers of aggression in dementia patients would be of a great importance. Studies have shown that different genetic factors, including monoamine signaling and processing, can be associated with various NPS including aggression. There have been significant and multiple neurotransmitter changes identified in the brains of patients with dementia and some of these changes have been involved in the etiology of NPS. Aggression specific changes have also been observed in neuropathological studies. The current consensus is that the best approach for development of such biomarkers may be incorporation of genetics (polymorphisms), neurobiology (neurotransmitters and neuropathology) and neuroimaging techniques.

Location Analysis and Expression Profiling Using Next-Generation Sequencing for Research in Neurodegenerative Diseases

Neurodegenerative diseases carry a huge burden in terms of human suffering and economic cost. In spite of advances in the fi eld of neurology, there is still no effective cure. A combination of novel genomic approaches and techniques such as chromatin immunoprecipitation sequencing (ChIP-seq) and RNA-seq that enable high-quality data could provide better understanding of transcriptional and epigenetic signatures useful for both biomarker development and drug discovery in neurodegenerative diseases. This chapter provides detailed protocols of the different steps required to generate a successful ChIP-seq and RNA-seq library. ChIP-seq protocol starts with cell collection and fi xation, chromatin preparation, immunoprecipitation, and fi nally library preparation. RNA-seq protocol described in this chapter starts with the isolation of peripheral blood mononuclear cells (PBMCs), RNA isolation from cells, and library preparation. The ChIP-seq protocol is optimized for human neuroglioma cells (H4), and RNA-seq protocol is optimized for PBMCs, but both protocols can be adapted to different cell types with minor modifi cations. The obtained libraries are suitable for sequencing on Illumina GAIIx platform.

TRP channels overexpression contributes to inflammasome activation in clavicular cortical hyperostosis

Background Clavicular cortical hyperostosis (CCH) is a sterile inflammatory bone disorder of unknown etiology clinically characterized by pain and/or swelling of the clavicle. It has been regarded as a variant of chronic nonbacterial/recurrent multifocal osteomyelitis (CNO/CRMO) but due to lack of other inflammatory sites and recurrence it could also be regarded as a separate disease in the spectrum [1]. Objectives Identification of specific gene expression patterns in CCH patients. Methods Total RNA was isolated from whole blood of 18 new-onset, untreated CCH patients and 8 healthy controls. DNA microarray gene expression was preformed in 5 CCH and 4 control patients along with bioinformatical analysis of retrieved data. Carefully selected differentially expressed genes (TRPM2, TRPM3, TRPM7, CASP2, MEFV, STAT3, EIF5A, ERBB2, TLR4, NLRP3, CD24, MYST3) where analyzed by qRT-PCR in all participants of the study. Results Microarray results and bioinformatical analysis revealed 974 differentially expressed genes, while qRT-PCR analysis showed significantly higher expression of TRPM3 and TRPM7, and lower expression of ERBB2. Conclusions Microarray data analysis reveled that majority of differentially expressed genes in CCH patients are involved in various inflammatory processes, while qRT-PCR analysis confirmed statistically significant expression change of 3 genes. Among them, TRPM3 and TRPM7 are members of transient receptor potential (TRP) gene superfamily, which encodes proteins that act as multimodal sensor cation channels for a wide variety of stimuli, one of which is environmental temperature that in the case of CCH could be elicited by overuse of sterno-clavicular joint (SCJ) [2]. Upon stimulation, TRP channels transduce electrical and/or Ca2+ signals. Dysfunctions in Ca2+ signaling due to altered TRP channel function can have strong effects on a variety of cellular and systemic processes, including the activation and the regulation of the inflammasomes, which are reported to be involved in CRMO pathogenesis [3,4]. ERBB2, third gene with significant expression change, belongs to a family of genes that encodes for widely expressed cell surface growth factor receptors. Recently it has been shown that ErbB activation promotes protective cellular outcomes during inflammation, hence lower expression of this gene could cause damage due to inflammation [5]. Based on the results of these and previous studies, we hypothesize that CCH could be an autoinflammatory disease induced by SCJ overuse, TRP channel overexpression, inflammasome activation and reduced protection during inflammation. References Borzutzky A, Stern S, Reiff A, et al. Pediatric chronic nonbacterial osteomyelitis. Pediatrics. 2012 Nov; 130(5):e1190-1197. Shimizu S, Takahashi N, Mori Y. TRPs as chemosensors (ROS, RNS, RCS, gasotransmitters). Handbook of experimental pharmacology. 2014; 223:767-794. Latz E, Xiao TS, Stutz A. Activation and regulation of the inflammasomes. Nature reviews Immunology. 2013 Jun; 13(6):397-411. Scianaro R, Insalaco A, Bracci Laudiero L, et al. Deregulation of the IL-1beta axis in chronic recurrent multifocal osteomyelitis. Pediatric rheumatology online journal. 2014; 12:30. Frey MR, Brent Polk D. ErbB receptors and their growth factor ligands in pediatric intestinal inflammation. Pediatric research. 2014 Jan; 75(1-2):127-132. Disclosure of Interest None declared

Potential biomarkers and therapeutic targets in juvenile spondyloarthritis patients

To understand disease mechanism and close the gap between genotype and phenotype, majority of studies today use the high-throughput methods that allow us to study genes on a global scale. One of these methods is expression profiling which generates a “snapshot” of cellular activity at the time of analysis, telling us exactly what processes are occurring. By comparing disease and control samples it is possible to elucidate the processes contributing to disease and how they are altered. To date a number of disparate expression profiling studies in patients diagnosed with spondyloarthritis (SpA) have been undertaken, but results of these studies were often inconsistent. To the best of our knowledge, there has been no expression profiling study with RNA isolated from whole blood in a cohort of patients diagnosed with juvenile spondyloarthritis (jSpA) using ILAR criteria for enthesitis related arthritis (ErA), with known HLA genotype and calculated odds ratio (OR) for disease development. Further on, there was no study in which expression of selected genes was independently confirmed in new cohorts of untreated and treated patients diagnosed with jSpA, as well as with other forms of juvenile idiopathic arthritis (JIA).

PReS-FINAL-2151: HLA B27/B7, TLR-4, NLRP3, CXCR4 AND PTPN12: the shared genetic master-key genes leading to development of undifferentiated spondyloarthritis/era in children

Enthestis related arthritis (era) represent an undifferentiated form of spondyloarthritis (spa), distinguishing it from other subtypes of JIA for optimum treatment and outcome, as well as for studies aimed at understanding genetic predisposition and pathogenesis. Majority of these studies focused on genome associations within MHC, only few searched for connections outside of this region and only some analyzed transcriptome of era patients. Our preliminary results of gene expression profiling in PBMC of 11 new onset and untreated patients diagnosed with era, identified 744 differentially expressed genes.