Functional metabolism of storage carbohydrates is vital to plants and animals. The water-soluble glycogen in animal cells and the amylopectin which is the major component of water-insoluble starch granules residing in plant plastids are chemically similar as they consist of α-1,6 branched α-1,4 glucan chains. Synthesis and degradation of transitory starch and of glycogen are accomplished by a set of enzymatic activities that to some extend are also similar in plants and animals. Chain elongation, branching, and debranching are achieved by synthases, branching enzymes, and debranching enzymes, respectively. Similarly, both types of polyglucans contain low amounts of phosphate esters whose abundance varies depending on species and organs. Starch is selectively phosphorylated by at least two dikinases (GWD and PWD) at the glucosyl carbons C6 and C3 and dephosphorylated by the phosphatase SEX4 and SEX4-like enzymes. In Arabidopsis insufficiency in starch phosphorylation or dephosphorylation results in largely impaired starch turnover, starch accumulation, and often in retardation of growth. In humans the progressive neurodegenerative epilepsy, Lafora disease, is the result of a defective enzyme (laforin) that is functional equivalent to the starch phosphatase SEX4 and capable of glycogen dephosphorylation. Patients lacking laforin progressively accumulate unphysiologically structured insoluble glycogen-derived particles (Lafora bodies) in many tissues including brain. Previous results concerning the carbon position of glycogen phosphate are contradictory. Currently it is believed that glycogen is esterified exclusively at the carbon positions C2 and C3 and that the monophosphate esters, being incorporated via a side reaction of glycogen synthase (GS), lack any specific function but are rather an enzymatic error that needs to be corrected. In this study a versatile and highly sensitive enzymatic cycling assay was established that enables quantification of very small G6P amounts in the presence of high concentrations of non-target compounds as present in hydrolysates of polysaccharides, such as starch, glycogen, or cytosolic heteroglycans in plants. Following validation of the G6P determination by analyzing previously characterized starches G6P was quantified in hydrolysates of various glycogen samples and in plant heteroglycans. Interestingly, glucosyl C6 phosphate is present in all glycogen preparations examined, the abundance varying between glycogens of different sources. Additionally, it was shown that carbon C6 is severely hyperphosphorylated in glycogen of Lafora disease mouse model and that laforin is capable of removing C6 phosphate from glycogen. After enrichment of phosphoglucans from amylolytically degraded glycogen, several techniques of two-dimensional NMR were applied that independently proved the existence of 6-phosphoglucosyl residues in glycogen and confirmed the recently described phosphorylation sites C2 and C3. C6 phosphate is neither Lafora disease- nor species-, or organ-specific as it was demonstrated in liver glycogen from laforin-deficient mice and in that of wild type rabbit skeletal muscle. The distribution of 6-phosphoglucosyl residues was analyzed in glycogen molecules and has been found to be uneven. Gradual degradation experiments revealed that C6 phosphate is more abundant in central parts of the glycogen molecules and in molecules possessing longer glucan chains. Glycogen of Lafora disease mice consistently contains a higher proportion of longer chains while most short chains were reduced as compared to wild type. Together with results recently published (Nitschke et al., 2013) the findings of this work completely unhinge the hypothesis of GS-mediated phosphate incorporation as the respective reaction mechanism excludes phosphorylation of this glucosyl carbon, and as it is difficult to explain an uneven distribution of C6 phosphate by a stochastic event. Indeed the results rather point to a specific function of 6-phosphoglucosyl residues in the metabolism of polysaccharides as they are present in starch, glycogen, and, as described in this study, in heteroglycans of Arabidopsis. In the latter the function of phosphate remains unclear but this study provides evidence that in starch and glycogen it is related to branching. Moreover a role of C6 phosphate in the early stages of glycogen synthesis is suggested. By rejecting the current view on glycogen phosphate to be a stochastic biochemical error the results permit a wider view on putative roles of glycogen phosphate and on alternative biochemical ways of glycogen phosphorylation which for many reasons are likely to be mediated by distinct phosphorylating enzymes as it is realized in starch metabolism of plants. Better understanding of the enzymology underlying glycogen phosphorylation implies new possibilities of Lafora disease treatment. / Pflanzen und Tiere speichern Glukose in hochmolekularen Kohlenhydraten, um diese bei Bedarf unter anderem zur Gewinnung von Energie zu nutzen. Amylopectin, der größte Bestandteil des pflanzlichen Speicherkohlenhydrats Stärke, und das tierische Äquivalent Glykogen sind chemisch betrachtet ähnlich, denn sie bestehen aus verzweigten Ketten, deren Bausteine (Glukosylreste) auf identische Weise miteinander verbunden sind. Zudem kommen in beiden Kohlenhydraten kleine aber ähnliche Mengen von Phosphatgruppen vor, die offenbar eine tragende Rolle in Pflanzen und Tieren spielen. Ist in Pflanzen der Einbau oder die Entfernung von Phosphatgruppen in bzw. aus Stärke gestört, so ist oft der gesamte Stärkestoffwechsel beeinträchtigt. Dies zeigt sich unter anderem in der übermäßigen Akkumulation von Stärke und in Wachstumsverzögerungen der gesamten Pflanze. Beim Menschen und anderen Säugern beruht eine schwere Form der Epilepsie (Lafora disease) auf einer Störung des Glykogenstoffwechsels. Sie wird durch das erblich bedingte Fehlen eines Enzyms ausgelöst, das Phosphatgruppen aus dem Glykogen entfernt. Während die Enzyme, die für die Entfernung des Phosphats aus Stärke und Glykogen verantwortlich sind, hohe Ähnlichkeit aufweisen, ist momentan die Ansicht weit verbreitet, dass der Einbau von Phosphat in beide Speicherkohlenhydrate auf höchst unterschiedliche Weise erfolgt. In Pflanzen sind zwei Enzyme bekannt, die Phosphatgruppen an unterschiedlichen Stellen in Glukosylreste einbauen (Kohlenstoffatome 6 und 3). In Tieren soll eine seltene, unvermeidbare und zufällig auftretende Nebenreaktion eines Enzyms, das eigentlich die Ketten des Glykogens verlängert (Glykogen-Synthase), den Einbau von Phosphat bewirken, der somit als unwillkürlich gilt und weithin als „biochemischer Fehler“ (mit fatalen Konsequenzen bei ausbleibender Korrektur) betrachtet wird. In den Glukosylresten des Glykogens sollen ausschließlich die C-Atome 2 und 3 phosphoryliert sein. Die Ergebnisse dieser Arbeit zeigen mittels zweier unabhängiger Methoden, dass Glykogen auch am Glukosyl-Kohlenstoff 6 phosphoryliert ist, der Phosphatposition, die in der Stärke am häufigsten vorkommt. Die Tatsache, dass in dieser Arbeit Phosphat neben Stärke auch erstmals an Glukosylresten von anderen pflanzlichen Kohlenhydraten (wasserlösliche Heteroglykane) nachgewiesen werden konnte, lässt vermuten, dass Phosphorylierung ein generelles Phänomen bei Polysacchariden ist. Des Weiteren wiesen die Ergebnisse darauf hin, dass Phosphat im Glykogen, wie auch in der Stärke, einem bestimmten Zweck dient, der im Zusammenhang mit der Regulation von Kettenverzweigung steht, und dass kein zufälliges biochemisches Ereignis für den Einbau verantwortlich sein kann. Aufgrund der grundlegenden Ähnlichkeiten im Stärke- und Glykogenstoffwechsel, liegt es nahe, dass die Phosphorylierung von Glykogen, ähnlich der von Stärke, ebenfalls durch spezifische Enzyme bewirkt wird. Ein besseres Verständnis der Mechanismen, die der Glykogen-Phosphorylierung zugrunde liegen, kann neue Möglichkeiten der Behandlung von Lafora disease aufzeigen.

Lafora disease (LD) is an adolescent-onset autosomal recessive progressive myoclonus epilepsy. The main clinical symptoms of the disease are worsening seizures, neurodegeneration and usually death within ten years. No therapeutics or interventions exist for this devastating disease. Mutations in two genes, EPM2A (laforin) and EPM2B (malin) are causative of more than 90 percent of LD. The pathognomonic sign of LD is the presence of abnormal glycogen which precipitates and accumulates into starch-like masses called Lafora bodies (LB). There are two main hypotheses of LB formation. Glycogen is synthesized through the combined activities of glycogen synthase (GS) and branching enzyme (BE). One hypothesis is that LB form due to an overactivation of GS, causing a misbalance between synthesis and branching. Here, malin and laforin regulate levels of GS and other protein(s) involved in glycogen synthesis and when missing, result in their overaccumulation and thus overactivation of synthesis in relation to branching. The second hypothesis is based on evidence of increased phosphorylation of glycogen in LB. In this hypothesis, glycogen becomes abnormal because of the hyperphosphorylation, causing it to precipitate. Laforin is a glycogen phosphatase, and removes phosphate from glycogen. When missing, as in LD, glycogen becomes hyperphosphorylated and forms LB. A role for malin is less clear in this hypothesis. In this thesis, I identify and characterize a third gene, PRDM8, causing an early onset form of LD in a large consanguineous family. I show that it both interacts with laforin and malin and results in their relocation to the nucleus. I also characterize a laforin-interacting protein, Epm2aip1, finding an important role for this previously uncharacterized protein in glycogen metabolism. Epm2aip1-/- mice exhibit hepatic insulin resistance, decreased hepatic glycogen synthesis, increased liver fat, and resistance against obesity in adulthood. Epm2aip1 associates with glycogen synthase (GS), and its absence impairs the allosteric activation of GS by glucose-6-phosphate. Finally, I find that genetically removing PTG, an activator of GS, from mice with Lafora disease results in near-complete disappearance of LB, and resolution of the neurodegeneration and myoclonic epilepsy. This work has revealed a gateway to the treatment of this devastating and fatal disease.

Lafora disease (LD) is an adolescent-onset autosomal recessive progressive myoclonus epilepsy. The main clinical symptoms of the disease are worsening seizures, neurodegeneration and usually death within ten years. No therapeutics or interventions exist for this devastating disease. Mutations in two genes, EPM2A (laforin) and EPM2B (malin) are causative of more than 90 percent of LD. The pathognomonic sign of LD is the presence of abnormal glycogen which precipitates and accumulates into starch-like masses called Lafora bodies (LB). There are two main hypotheses of LB formation. Glycogen is synthesized through the combined activities of glycogen synthase (GS) and branching enzyme (BE). One hypothesis is that LB form due to an overactivation of GS, causing a misbalance between synthesis and branching. Here, malin and laforin regulate levels of GS and other protein(s) involved in glycogen synthesis and when missing, result in their overaccumulation and thus overactivation of synthesis in relation to branching. The second hypothesis is based on evidence of increased phosphorylation of glycogen in LB. In this hypothesis, glycogen becomes abnormal because of the hyperphosphorylation, causing it to precipitate. Laforin is a glycogen phosphatase, and removes phosphate from glycogen. When missing, as in LD, glycogen becomes hyperphosphorylated and forms LB. A role for malin is less clear in this hypothesis. In this thesis, I identify and characterize a third gene, PRDM8, causing an early onset form of LD in a large consanguineous family. I show that it both interacts with laforin and malin and results in their relocation to the nucleus. I also characterize a laforin-interacting protein, Epm2aip1, finding an important role for this previously uncharacterized protein in glycogen metabolism. Epm2aip1-/- mice exhibit hepatic insulin resistance, decreased hepatic glycogen synthesis, increased liver fat, and resistance against obesity in adulthood. Epm2aip1 associates with glycogen synthase (GS), and its absence impairs the allosteric activation of GS by glucose-6-phosphate. Finally, I find that genetically removing PTG, an activator of GS, from mice with Lafora disease results in near-complete disappearance of LB, and resolution of the neurodegeneration and myoclonic epilepsy. This work has revealed a gateway to the treatment of this devastating and fatal disease.

Indiana University-Purdue University Indianapolis (IUPUI) / Glycogen, a branched polymer of glucose, serves as an osmotically neutral means of storing glucose. Covalent phosphate is a trace component of mammalian glycogen and has been a point of interest with respect to Lafora disease, a fatal form of juvenile myoclonus epilepsy. Mutations in either the EPM2A or EPM2B genes, which encode laforin and malin respectively, account for ~90% of disease cases. A characteristic of Lafora disease is the formation of Lafora bodies, which are mainly composed of an excess amount of abnormal glycogen that is poorly branched and insoluble. Laforin-/- and malin-/- knockout mice share several characteristics of the human disease, formation of Lafora bodies in various tissues, increased glycogen phosphorylation and development of neurological symptoms. The source of phosphate in glycogen has been an area of interest and here we provide evidence that glycogen synthase is capable of incorporating phosphate into glycogen. Mice lacking the glycogen targeting subunit PTG of the PP1 protein phosphatase have decreased glycogen stores in a number of tissues. When crossed with mice lacking either laforin or malin, the double knockout mice no longer over-accumulate glycogen, Lafora body formation is almost absent and the neurological disorders are normalized. Another question has been whether the abnormal glycogen in the Lafora disease mouse models can be metabolized. Using exercise to provoke glycogen degradation, we show that in laforin-/- and malin-/- mice the insoluble, abnormal glycogen appears to be metabolically inactive. These studies suggest that a therapeutic approach to Lafora disease may be to reduce the overall glycogen levels in cells so that insoluble, metabolically inert pools of the polysaccharide do not accumulate.

Indiana University-Purdue University Indianapolis (IUPUI) / Glycogen is a highly branched polymer of glucose that functions to store glucose residues for future metabolic use. Skeletal muscle and liver comprise the largest glycogen reserves and play critical roles in maintaining whole body glucose homeostasis. In addition to glucose, glycogen contains small amounts of covalent phosphate of unknown function, origin and structure. Evidence to support the involvement of glycogen associated phosphate in glycogen metabolism comes from patients with Lafora Disease. Lafora disease is an autosomal recessive, fatal form of progressive myoclonus epilepsy. Approximately 90% of cases of Lafora disease are caused by mutations in either the EPM2A or EPM2B genes that encode, respectively, a dual specificity phosphatase called laforin and an E3 ubiquitin ligase called malin. Lafora patients accumulate intracellular inclusion bodies, known as Lafora bodies that are primarily composed of poorly branched, insoluble glycogen-like polymers. We have shown that laforin is a glycogen phosphatase capable of releasing phosphate from glycogen in vitro and that this activity is dependent on a functional carbohydrate binding domain. In studies of laforin knockout mice, we observed a progressive change in the properties and structure of glycogen that paralleled the formation of Lafora bodies. Glycogen isolated from these mice showed increased glycogen phosphate, up to 6-fold (p< 0.001) compared to WT, providing strong evidence that laforin acts as a glycogen phosphatase in vivo. Furthermore we have demonstrated that glycogen synthase introduces phosphate into glycogen during synthesis by transferring the beta-phosphate of UDP-glucose into the polymer and that laforin is capable of releasing the phosphate incorporated by glycogen synthase. Analysis of mammalian glycogen revealed the presence of covalently linked phosphate at the 2 hydroxyl and the 3 hydroxyl of glucose residues in the polysaccharide, providing the first direct evidence of the chemical nature of the phosphate linkage. We envision a glycogen damage/repair process, analogous to errors during DNA synthesis that are subsequently repaired. We propose that laforin action parallels that of DNA repair enzymes and Lafora disease results from the inability of the phosphatase to repair damaged glycogen, adding another biological polymer to the list of those prone to errors by their respective polymerizing enzymes.

Glycogen is the sole carbohydrate storage molecule found in mammalian cells and plays an important role in cellular metabolism in nearly all tissues, including the brain. Defects in glycogen metabolism underlie the glycogen storage diseases (GSDs), genetic disorders with variable clinical phenotypes depending on the mutation type and affected gene(s). Lafora disease (LD) is a fatal form of progressive myoclonus epilepsy and a non-classical GSD. LD typically manifests in adolescence with tonic-clonic seizures, myoclonus, and a rapid, insidious progression. Patients experience increasingly severe and frequent epileptic episodes, loss of speech and muscular control, disinhibited dementia, and severe cognitive decline; death usually ensues in the second decade of life. LD, like one- third of all epilepsy disorders, is intractable and resistant to antiseizure drugs. A hallmark of LD is the accumulation of intracellular, insoluble carbohydrate aggregates known as Lafora bodies (LBs) in brain, muscle, and other tissues. LBs are a type of polyglucosan body, an insoluble aggregate of aberrant glycogen found in some GSDs and neurodegenerative disorders. Like most GSDs, LD is an autosomal recessive genetic disorder. Approximately 50% of LD patients carry mutations in the epilepsy, progressive myoclonus 2A (EPM2A) gene encoding laforin, a glycogen phosphatase. Remaining patients carry mutations in EPM2B, the gene that encodes malin, an E3 ubiquitin ligase. Laforin and malin play important roles in glycogen metabolism. In the absence of either enzyme, glycogen transforms into an insoluble, hyperphosphorylated and aberrantly branched polysaccharide reminiscent of plant starch. This abnormal polysaccharide precipitates to form LBs and has pathological consequences in the brain. Since a definitive LD diagnosis requires genetic testing, whole exome sequencing has been increasingly used to diagnose LD. As a result, numerous cases of more slowly progressing or late-onset LD have been discovered that are associated with missense mutations in EPM2A or EPM2B. Over 50 EPM2A missense mutations have been described. These mutations map to many regions of the laforin X-ray crystal structure, suggesting they produce a spectrum of effects on laforin function. In the present work, a biochemical pipeline was developed to characterize laforin patient mutations. The mutations fall into distinct classes with mild, moderate or severe effects on laforin function, providing a biochemical explanation for less severe forms of LD. LBs drive LD pathology. As a result, LBs and glycogen metabolism have become therapeutic targets. Since LBs are starch-like, and starch is degraded by amylases, these enzymes are potential therapeutics for reducing LB loads in vivo. However, amylases are normally secreted enzymes. Degradation of intracellular LBs requires a cell-penetrating delivery platform. Herein, an antibody-enzyme fusion (AEF) technology was developed to degrade LBs in vitro, in situ in cell culture, and in vivo in LD mouse models. AEFs are a now putative precision therapy for LD, potentially the first therapeutic to provide a significant clinical benefit. Prior to this work, LD was considered a homogenous disorder and treatments were only palliative. The data herein support a spectrum of clinical progression, a potential therapy for LD, and mechanistic insights into LD pathophysiology. This work illustrates how personalized medicine, both in diagnosis and treatment, can be achieved through basic biochemical approaches to human disease.

Lafora disease (LD) is a rare yet invariably fatal form of epilepsy characterized by progressive degeneration of the central nervous and motor systems and accumulation of insoluble glucans within cells. LD results from mutation of either the phosphatase laforin, an enzyme that dephosphorylates cellular glycogen, or the E3 ubiquitin ligase malin, the binding partner of laforin. Currently, there are no therapeutic options for LD, or reported methods by which the specific activity of glucan phosphatases such as laforin can be easily measured. To facilitate our translational studies, we developed an assay with which the glucan phosphatase activity of laforin as well as emerging members of the glucan phosphatase family can be characterized. We then adapted this assay for the detection of endogenous laforin activity from human and mouse tissue. This laforin bioassay will prove useful in the detection of functional laforin in LD patient tissue following the application of therapies to LD patients. We subsequently developed an in vitro readthrough reporter system in order to assess the efficacy of aminoglycosides in the readthrough of laforin and malin nonsense mutations. We found that although several laforin and malin nonsense mutations exhibited significant drug-induced readthrough, the location of the epitope tag used to detect readthrough products dramatically affected our readthrough results. Cell lines established from LD patients with nonsense mutations are thus required to accurately assess the efficacy of aminoglycosides as a therapeutic option for LD. Using hydrogen-deuterium exchange mass spectrometry (DXMS), we then gained insight into the molecular etiology of several point mutations in laforin that cause LD. We identified a novel motif in the phosphatase domain of laforin that shares homology with glycosyl hydrolases (GH) and appears to play a role in the interaction of laforin with glucans. We studied the impact of the Y294N and P301L LD mutations within this GH motif on glucan binding. Surprisingly, these mutations did not reduce glucan binding as expected, rather enhancing the binding of laforin to glucans. These findings elucidate the mechanism by which laforin interacts with and acts upon glucan substrates, providing a target for the development of therapeutic compounds.

Indiana University-Purdue University Indianapolis (IUPUI) / Lafora disease is a neurodegenerative disorder caused by mutations in either the EPM2A or the EPM2B gene that encode a glycogen phosphatase, laforin and an E3 ubiquitin ligase, malin, respectively. A hallmark of the disease is accumulation of insoluble, poorly branched, hyperphosphorylated glycogen in brain, muscle and heart. The laforin-malin complex has been proposed to play a role in the regulation of glycogen metabolism and protein degradation/quality control. We evaluated three arms of protein quality control (the autophagolysosomal pathway, the ubiquitin-proteasomal pathway, and ER stress response) in embryonic fibroblasts from Epm2a-/-, Epm2b-/- and Epm2a-/- Epm2b-/- mice. There was an mTOR-dependent impairment in autophagy, decreased proteasomal activity but an uncompromised ER stress response in the knockout cells. These defects may be secondary to the glycogen overaccumulation. The absence of malin, but not laforin, decreased the level of LAMP1, a marker of lysosomes, suggesting a malin function independent of laforin, possibly in lysosomal biogenesis and/or lysosomal glycogen disposal. To understand the physiological role of malin, an unbiased diGly proteomics approach was developed to search for malin substrates. Ubiquitin forms an isopeptide bond with lysine of the protein upon ubiquitination. Proteolysis by trypsin cleaves the C-terminal Arg-Gly-Gly residues in ubiquitin and yields a diGly remnant on the peptides. These diGly peptides were immunoaffinity purified using anti-diGly antibody and then analyzed by mass spectrometry. The mouse skeletal muscle ubiquitylome was studied using diGly proteomics and we identified 244 nonredundant ubiquitination sites in 142 proteins. An approach for differential dimethyl labeling of proteins with diGly immunoaffinity purification was also developed. diGly peptides from skeletal muscle of wild type and Epm2b-/- mice were immunoaffinity purified followed by differential dimethyl labeling and analyzed by mass spectrometry. About 70 proteins were identified that were present in the wild type and absent in the Epm2b-/- muscle tissue. The initial results identified 14 proteins as potential malin substrates, which would need validation in future studies.