Cerebellar ataxia and functional genomics: Identifying the routes to cerebellar neurodegeneration

Cerebellar ataxias are progressive neurodegenerative disorders characterized by atrophy of the cerebellum leading to motor dysfunction, balance problems, and limb and gait ataxia. These include among others, the dominantly inherited spinocerebellar ataxias, recessive cerebellar ataxias such as Friedreich's ataxia, and X-linked cerebellar ataxias. Since all cerebellar ataxias display considerable overlap in their disease phenotypes, common pathological pathways must underlie the selective cerebellar neurodegeneration. Therefore, it is important to identify the molecular mechanisms and routes to neurodegeneration that cause cerebellar ataxia. In this review, we discuss the use of functional genomic approaches including whole-exome sequencing, genome-wide gene expression profiling, miRNA profiling, epigenetic profiling, and genetic modifier screens to reveal the underlying pathogenesis of various cerebellar ataxias. These approaches have resulted in the identification of many disease genes, modifier genes, and biomarkers correlating with specific stages of the disease. This article is part of a Special Issue entitled: From Genome to Function.     

Missense mutations in the regulatory domain of PKC gamma: a new mechanism for dominant nonepisodic cerebellar ataxia

We report a nonepisodic autosomal dominant (AD) spinocerebellar ataxia (SCA) not caused by a nucleotide repeat expansion that is, to our knowledge, the first such SCA. The AD SCAs currently comprise a group of > or =16 genetically distinct neurodegenerative conditions, all characterized by progressive incoordination of gait and limbs and by speech and eye-movement disturbances. Six of the nine SCAs for which the genes are known result from CAG expansions that encode polyglutamine tracts. Noncoding CAG, CTG, and ATTCT expansions are responsible for three other SCAs. Approximately 30% of families with SCA do not have linkage to the known loci. We recently mapped the locus for an AD SCA in a family (AT08) to chromosome 19q13.4-qter. A particularly compelling candidate gene, PRKCG, encodes protein kinase C gamma (PKC gamma), a member of a family of serine/threonine kinases. The entire coding region of PRKCG was sequenced in an affected member of family AT08 and in a group of 39 unrelated patients with ataxia not attributable to trinucleotide expansions. Three different nonconservative missense mutations in highly conserved residues in C1, the cysteine-rich region of the protein, were found in family AT08, another familial case, and a sporadic case. The mutations cosegregated with disease in both families. Structural modeling predicts that two of these amino acid substitutions would severely abrogate the zinc-binding or phorbol ester-binding capabilities of the protein. Immunohistochemical studies on cerebellar tissue from an affected member of family AT08 demonstrated reduced staining for both PKC gamma and ataxin 1 in Purkinje cells, whereas staining for calbindin was preserved. These results strongly support a new mechanism for neuronal cell dysfunction and death in hereditary ataxias and suggest that there may be a common pathway for PKC gamma-related and polyglutamine-related neurodegeneration.     

Spinocerebellar ataxia type 6 and episodic ataxia type 2: differences and similarities between two allelic disorders

Spinocerebellar ataxia type 6 (SCA6) is one of three allelic disorders caused by mutations of CACNA1A gene, coding for the pore-forming subunit of calcium channel type P/Q. SCA6 is associated with small expansions of a CAG repeat at the 3' end of the gene, while point mutations are responsible for its two allelic disorders (Episodic Ataxia type 2 and Familial Hemiplegic Migraine). Genetic, clinical, pathological and pathophysiological data of SCA6 patients are reviewed and compared to those of other SCAs with expanded CAG repeats as well as to those of its allelic channelopathies, with particular reference to Episodic Ataxia type 2. Overall SCA6 appears to share features with both types of disorders, and the question as to whether it belongs to polyglutamine disorders or to channelopathies remains unanswered at present.     

Cell signalling by reactive lipid species: new concepts and molecular mechanisms

The process of lipid peroxidation is widespread in biology and is mediated through both enzymatic and non-enzymatic pathways. A significant proportion of the oxidized lipid products are electrophilic in nature, the RLS (reactive lipid species), and react with cellular nucleophiles such as the amino acids cysteine, lysine and histidine. Cell signalling by electrophiles appears to be limited to the modification of cysteine residues in proteins, whereas non-specific toxic effects involve modification of other nucleophiles. RLS have been found to participate in several physiological pathways including resolution of inflammation, cell death and induction of cellular antioxidants through the modification of specific signalling proteins. The covalent modification of proteins endows some unique features to this signalling mechanism which we have termed the 'covalent advantage'. For example, covalent modification of signalling proteins allows for the accumulation of a signal over time. The activation of cell signalling pathways by electrophiles is hierarchical and depends on a complex interaction of factors such as the intrinsic chemical reactivity of the electrophile, the intracellular domain to which it is exposed and steric factors. This introduces the concept of electrophilic signalling domains in which the production of the lipid electrophile is in close proximity to the thiol-containing signalling protein. In addition, we propose that the role of glutathione and associated enzymes is to insulate the signalling domain from uncontrolled electrophilic stress. The persistence of the signal is in turn regulated by the proteasomal pathway which may itself be subject to redox regulation by RLS. Cell death mediated by RLS is associated with bioenergetic dysfunction, and the damaged proteins are probably removed by the lysosome-autophagy pathway.     

Oxidants and human disease: some new concepts

Oxidant species such as superoxide radical (O.2-), hydrogen peroxide (H2O2), hydroxyl radical (HO.), and lipid peroxides (LOOH) are becoming increasingly implicated in human disease. However, the question of whether such oxidants are a major cause of tissue injury in human disease or are merely produced during such injury has been difficult to answer because of inadequate experimental techniques, and possibly because of an overemphasis on lipid peroxidation as a mechanism of oxidant injury. Recent developments in methodology, in our understanding of the primary mechanism of oxidant toxicity to cells, and in concepts of antioxidant protection are reviewed. Good evidence now exists for some role of oxidant damage to tissues in the pathology of several human diseases, including rheumatoid arthritis, reperfusion injury, immune injury to lung and kidney, and cerebral trauma or ischemia. These have led to promising suggestions for new therapeutic approaches.     

Antiarrhythmic drug therapy: new drugs and changing concepts

The effective treatment of life-threatening ventricular arrhythmias (VA) leading to sudden cardiac death remains a major health problem. Cellular electrophysiological techniques that have provided insight into the underlying mechanisms of these arrhythmias have also provided a convenient classification of antiarrhythmic drugs based on their dominant electrophysiological action. Traditional pharmacological approaches to the management of VA have involved primarily class I agents. Newer drugs in this class are potent conduction depressants (class IC agents), which, however, have been limited in their clinical impact on VA because of unwanted cardiac and extracardiac side effects. Other recent approaches include the introduction of class III agents, which are thought to interrupt primarily reentrant impulses by specific prolongation of action potential duration and refractoriness without compromising normal cardiac conduction. Newer approaches may also include drugs with greater specificity of action, agents with combinations of electrophysiological effects (class I/III, I/II), drugs exemplifying novel mechanisms of action such as anion antagonism (class V), and agents controlling sympathetic neural outflow. The growing awareness of the potential proarrhythmic effects of antiarrhythmic drugs has also become important in drug development and assessment, as emphasized by the search for improved methods of drug selection (e.g., programmed electrical stimulation). Finally, the desired characteristics of a new antiarrhythmic agent are presented as a goal for future drug development.     

The genus Malassezia: old facts and new concepts

Lipophilic yeasts are being considered as major opportunistic pathogens for a very long time. Most of the yeasts show an absolute requirement for long fatty acid chains and specific procedures are required for their isolation, conservation and identification. For that reason, the history of the nomenclature used for the Malassezia genus is quite complex. Before 1996, only 3 species were recognized: Malassezia furfur, M. pachydermatis and M. sympodialis. To date, the genus is composed of one non lipid-dependent species (M. pachydermatis) and 12 lipid-dependent species. No doubt that additional new taxa will be described in close future. Very recently the genome and secretory proteome of two Malassezia species was described. This analysis demonstrated the presence of multiple secreted lipases to aid in harvesting host lipids. It also revealed the presence of mating-type genes, providing an indication that Malassezia yeasts may be capable of sex.     

DNA methylation and epigenomics: new technologies and emerging concepts

A report of the Keystone Symposia joint meetings on DNA Methylation and Epigenomics held in Keystone, Colorado, USA, 29 March to 3 April, 2015.     

Vitamin D and aging: old concepts and new insights

Aging is a complex biological process driven by a selective class of molecules and pathways that affect overall deterioration of physiological functions to increase the risk of age-related diseases. A role of vitamin D in mammalian aging is well documented. Since vitamin D has an essential role in bone formation and mineralization, its deficiency results in impaired bone mineralization, such as rickets in children, osteomalacia in adults and osteoporosis in the aged population. Vitamin D replacement therapy therefore is one of the most commonly prescribed treatments for the elderly. Recent studies using genetically altered mouse models, such as in Fgf-23^−/− and klotho mutant mice, that exhibit altered mineral ion metabolism due to high vitamin D activities showed features of premature aging that include atherosclerosis, emphysema, osteopenia/osteoporosis, hypogonadism, soft tissue calcifications and generalized atrophy of organs; the pathologic effects of vitamin D in these mouse models are obvious, as diminution or genetic ablation of the vitamin D pathway ameliorated most of the above-mentioned phenotypes, by reversing mineral ion metabolism, and the resultant effect being prolonged survival of the mutant mice. These in vivo mouse studies, although subject to further molecular characterization, add new insights into the role of vitamin D in aging.     

Past and present concepts in flow cytometry: a European perspective

The development of flow cytometric instrumentation, methods and research concepts in Europe has been a continuous driving force for the general scientific advancement in this area over the years. This review addresses early European concepts of continuing interest with regard to instrumentation, data analysis, clinical and eperimental DNA analysis, cell function and microbiology at their worldwide first appearence while flow cytometric immunology and immunophenotyping will be covered separately. Flow cytometry represents an efficient approach to the enormous complexity of molecular cell architecture and cell function by the analysis of apparent molecular cell phenotypes in heterogeneous cell samples. The present merger of flow and image cytometry into the method independent cytomics discipline increases the potential of cell analysis very significantly. It opens the way for predictive medicine as well as for predictive cytopathology and predictive cytology in everyday clinical and medical practice. Current progress is driven by joint advances in molecular fluorescence technologies and instrument development. This complements the analysis of genome sequence information in an efficient way.     

A paradoxical improvement of misreaching in optic ataxia: new evidence for two separate neural systems for visual localization

We tested a patient (A. T.) with bilateral brain damage to the parietal lobes, whose resulting 'optic ataxia' causes her to make large pointing errors when asked to locate single light emitting diodes presented in her visual field. We report here that, unlike normal individuals, A. T.'s pointing accuracy improved when she was required to wait for 5 s before responding. This counter-intuitive result is interpreted as reflecting the very brief time-scale on which visuomotor control systems in the superior parietal lobe operate. When an immediate response was required, A. T.'s damaged visuomotor system caused her to make large errors; but when a delay was required, a different, more flexible, visuospatial coding system--presumably relatively intact in her brain--came into play, resulting in much more accurate responses. The data are consistent with a dual processing theory whereby motor responses made directly to visual stimuli are guided by a dedicated system in the superior parietal and premotor cortices, while responses to remembered stimuli depend on perceptual processing and may thus crucially involve processing within the temporal neocortex.     

Refinement by linkage analysis in two large families of the candidate region of the third locus (SCA3) for autosomal dominant cerebellar ataxia type I

The autosomal dominant cerebellar ataxias (ADCA) are clinically and genetically heterogeneous. To date, several loci (SCAI-V) have been identified for ADCA type I. We have studied two large families from the northern part of The Netherlands with ADCA type I with a broad intra-familial variation of symptoms. In both families significant linkage is shown of the disease to the markers of the SCA3 locus on chromosome 14. Through recombinations, the candidate region for SCA3 could be refined to a 13-cM range between D14S256 and D14S81. No recombinations were detected with the markers D14S291 and D14S280, which suggests that the SCA3 gene lies close to these loci. This finding will benefit the individuals at risk in these two families who are seeking predictive testing or prenatal diagnosis.     

The plaza and the pendulum: two concepts of ecological science

This essay explores two strategies of inquiryin ecological science. Ecologists may regardthe sites they study either as contingentcollections of plants and animals, therelations of which are place-specific andidiosyncratic, or as structured systems andcommunites that are governed by general rules,forces, or principles. Ecologists who take thefirst approach rely on observation, induction,and experiment – a case-study or historicalmethod – to determine the causes of particularevents. Ecologists who take the secondapproach, seeking to explain by inferringevents from general patterns or principles,confront four conceptual obstacles which thisessay describes. Theory in ecology must (1)define and classify the object it studies,e.g., the ecosystem, and thus determine theconditions under which it remains the ``same'system through time and change. Ecologistsmust (2) find ways to reject as well as tocreate mathematical models of the ecosystem,possibly by (3) identifying efficient causes ofecosystem organization or design. Finally,ecologists will (4) show ecological theory canhelp solve environmental problems both inpristine and in human-dominated systems. Afailure to solve – or even to address – theseobstacles suggests that theoretical ecology maybecome a formal science that studies themathematical consequences of assumptionswithout regard to the relation of theseassumptions to the world.