Mutations in α-synuclein, TDP-43 and tau prolong protein half-life through diminished degradation by lysosomal proteases

BACKGROUND

Autosomal dominant mutations in α-synuclein, TDP-43 and tau are thought to predispose to neurodegeneration by enhancing protein aggregation. While a subset of α-synuclein, TDP-43 and tau mutations has been shown to increase the structural propensity of these proteins toward self-association, rates of aggregation are also highly dependent on protein steady state concentrations, which are in large part regulated by their rates of lysosomal degradation. Previous studies have shown that lysosomal proteases operate precisely and not indiscriminately, cleaving their substrates at very specific linear amino acid sequences. With this knowledge, we hypothesized that certain coding mutations in α-synuclein, TDP-43 and tau may lead to increased protein steady state concentrations and eventual aggregation by an alternative mechanism, that is, through disrupting lysosomal protease cleavage recognition motifs and subsequently conferring protease resistance to these proteins.

RESULTS

To test this possibility, we first generated comprehensive proteolysis maps containing all of the potential lysosomal protease cleavage sites for α-synuclein, TDP-43 and tau. In silico analyses of these maps indicated that certain mutations would diminish cathepsin cleavage, a prediction we confirmed utilizing in vitro protease assays. We then validated these findings in cell models and induced neurons, demonstrating that mutant forms of α-synuclein, TDP-43 and tau are degraded less efficiently than wild type despite being imported into lysosomes at similar rates.

CONCLUSIONS

Together, this study provides evidence that pathogenic mutations in the N-terminal domain of α-synuclein (G51D, A53T), low complexity domain of TDP-43 (A315T, Q331K, M337V) and R1 and R2 domains of tau (K257T, N279K, S305N) directly impair their own lysosomal degradation, altering protein homeostasis and increasing cellular protein concentrations by extending the degradation half-lives of these proteins. These results also point to novel, shared, alternative mechanism by which different forms of neurodegeneration, including synucleinopathies, TDP-43 proteinopathies and tauopathies, may arise. Importantly, they also provide a roadmap for how the upregulation of particular lysosomal proteases could be targeted as potential therapeutics for human neurodegenerative disease.

Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation

Cysteine side chains can exist in distinct oxidation states depending on the pH and redox potential of the environment, and cysteine oxidation plays important yet complex regulatory roles. Compared with the effects of post-translational modifications such as phosphorylation, the effects of oxidation of cysteine to sulfenic, sulfinic, and sulfonic acid on protein structure and function remain relatively poorly characterized. We present an analysis of the role of cysteine reactivity as a regulatory factor in proteins, emphasizing the interplay between electrostatics and redox potential as key determinants of the resulting oxidation state. A review of current computational approaches suggests underdeveloped areas of research for studying cysteine reactivity through molecular simulations.

Pyrvinium Pamoate and Structural Analogs Are Early Macrofilaricide Leads

Onchocerciasis and lymphatic filariasis are neglected tropical diseases caused by infection with filarial worms. Annual or biannual mass drug administration with microfilaricidal drugs that kill the microfilarial stages of the parasites has helped reduce infection rates and thus prevent transmission of both infections. However, success depends on high population coverage that is maintained for the duration of the adult worm's lifespan. Given that these filarial worms can live up to 14 years in their human hosts, a macrofilaricidal drug would vastly accelerate elimination efforts. Here, we have evaluated the repurposed drug pyrvinium pamoate as well as newly synthesized analogs of pyrvinium for their efficacy against filarial worms in vitro and in vivo. We found that pyrvinium pamoate, tetrahydropyrvinium and one of the analogs were highly potent in inhibiting worms in in vitro whole-worm screening assays, and that all three compounds reduced female worm fecundity and inhibited embryogenesis in the Brugia pahangi-gerbil in vivo model of infection.

The endosymbiont Wolbachia rebounds following antibiotic treatment

Antibiotic treatment has emerged as a promising strategy to sterilize and kill filarial nematodes due to their dependence on their endosymbiotic bacteria, Wolbachia. Several studies have shown that novel and FDA-approved antibiotics are efficacious at depleting the filarial nematodes of their endosymbiont, thus reducing female fecundity. However, it remains unclear if antibiotics can permanently deplete Wolbachia and cause sterility for the lifespan of the adult worms. Concerns about resistance arising from mass drug administration necessitate a careful exploration of potential Wolbachia recrudescence. In the present study, we investigated the long-term effects of the FDA-approved antibiotic, rifampicin, in the Brugia pahangi jird model of infection. Initially, rifampicin treatment depleted Wolbachia in adult worms and simultaneously impaired female worm fecundity. However, during an 8-month washout period, Wolbachia titers rebounded and embryogenesis returned to normal. Genome sequence analyses of Wolbachia revealed that despite the population bottleneck and recovery, no genetic changes occurred that could account for the rebound. Clusters of densely packed Wolbachia within the worm's ovarian tissues were observed by confocal microscopy and remained in worms treated with rifampicin, suggesting that they may serve as privileged sites that allow Wolbachia to persist in worms while treated with antibiotic. To our knowledge, these clusters have not been previously described and may be the source of the Wolbachia rebound.

Identification and reduction of sources of dietary lead in the United States

Lead, an environmental contaminant, originates from a variety of sources. For over two decades, the US Food and Drug Administration (FDA) has made a number of efforts to reduce dietary lead exposure of the general population, and especially of vulnerable subpopulations such as infants and children and, indirectly, the foetus. Through cooperation with infant food manufacturers, reductions of about 80-90% in the lead content of infant foods were achieved, primarily through eliminating the use of cans for infant food products and following good manufacturing practices. Another major reduction in dietary lead was realized by discontinuing the use of lead solder in domestically produced food cans. FDA has also taken steps to minimize or further reduce sources of lead in the diet from lead glazes on ceramicware, leaded crystalware, dietary supplements bottle water, and lead capsules on wine bottles. These actions have resulted in a considerable decrease in the exposure of the United States population to dietary lead.

FDA Total Diet Study, July 1986-April 1991, dietary intakes of pesticides, selected elements, and other chemicals

The U.S. Food and Drug Administration conducts the Total Diet Study to determine dietary intakes of selected pesticides, industrial chemicals, and elements (including radionuclides). This paper reports results for the sampling period July 1986 to April 1991. The study involves retail purchase of foods representative of the ¿total diet¿ of the U.S. population, preparation for ¿table-ready¿ consumption, and individual analyses of 234 items making up the diets of 8 population groups. The diets were based on 2 nationwide food consumption surveys. The data presented represent 21 food collections (also termed ¿market baskets¿) in regional metropolitan areas during the 5-year period. Dietary intakes of nearly 120 analytes are presented for 8 population groups, which range from infants to elderly adults. Intakes of selected population groups are compared with representative findings from earlier Total Diet Study sampling periods. As reported previously, average daily intakes are well below acceptable limits.

Dietary intakes of pesticides, selected elements, and other chemicals: FDA Total Diet Study, June 1984-April 1986

The U.S. Food and Drug Administration conducts the Total Diet Study to determine dietary intakes of selected pesticides, industrial chemicals, and elements (including radionuclides). The results reported here reflect the sampling period from June 1984 to April 1986. The study involves retail purchase of foods representative of the total diet of the U.S. population, preparation for table-ready consumption, and individual analyses of 234 items depicting the diets of 8 population groups. The diets were based on 2 nationwide food consumption surveys. The data presented represent 8 food collections (also termed "market baskets") in regional metropolitan areas during the 2-year period. Dietary intakes of over 90 analytes are presented for the 8 population groups, which range from infants to elderly adults. Intakes of selected population groups are compared with representative previous findings. As reported previously, average daily intakes are well below acceptable limits.

U.S. Food and Drug Administration monitoring of pesticide residues in infant foods and adult foods eaten by infants/children

The U.S. Food and Drug Administration uses 3 approaches to monitor pesticide residues in foods: regulatory monitoring, incidence/level monitoring, and the Total Diet Study. The results of monitoring infant foods and adult foods that may be eaten by infants/children under these 3 approaches are presented. Under regulatory monitoring, which is performed to enforce tolerances set by the U.S. Environmental Protection Agency (EPA), during fiscal years 1985-1991, over 10,000 such domestic and imported food samples were collected and analyzed, and under the Total Diet Study, in which pesticide residue intakes are estimated in foods prepared for consumption, the food items in 27 market baskets were analyzed. Under incidence/level monitoring, which is complementary to regulatory monitoring, over 4000 analyses were performed on infant foods and adult foods eaten by children. Fewer than 50 of the 10,000 regulatory samples had violative residues; nearly all of those were residues for which there was no tolerance for the particular commodity/pesticide combination. Under incidence/level monitoring and the Total Diet Study, the levels of pesticide residues found in infant foods and adult foods eaten by children were well below tolerances set by EPA.

Food and Drug Administration pesticide residue monitoring of foods: 1983-1986

Pesticide residues in foods are reported for the 4-year period 1982-1986 [fiscal years (FY) 83-86]. Results were summarized from the 2 complementary approaches that make up the Food and Drug Administration's (FDA) pesticide residue monitoring program. Under regulatory monitoring, which focuses on residues in raw agricultural commodities, a total of 49,055 samples (27,700 domestic and 21,355 import) that included fresh fruits and vegetables, grains and grain products, milk and dairy products, seafoods, and a variety of processed foods were analyzed. No residues were found in 60 and 48% of the domestic and import samples, respectively, compared with 55 and 44% in FY78-82. About 3% of the domestic and 5% of the import samples were violative. In FY78-82, about 3 and 7% were violative, respectively. The other FDA monitoring approach, the Total Diet Study, was revised in April 1982 to expand coverage of age/sex groups, use updated diets, and provide for analysis of individual foods. Results from monitoring under this modified approach and from regulatory monitoring continued to demonstrate that pesticide residues in the U.S. food supply were well below regulatory limits, and dietary intakes were many times lower than the Acceptable Daily Intakes established by international agencies.

FDA Total Diet Study, April 1982-April 1984, dietary intakes of pesticides, selected elements, and other chemicals

The U.S. Food and Drug Administration conducts the Total Diet Study to determine dietary intakes of selected pesticides, industrial chemicals, and elements (including radionuclides). The current study, which reflects significant redesign implemented in April 1982, involves retail purchase of foods representative of the "total diet" of the U.S. population, preparation for "table-ready" consumption, and individual analyses of 234 items depicting the diets of 8 population groups. The dietary revision was based on 2 nationwide food consumption surveys. The data presented represent 8 food collections (also termed "market baskets") in regional metropolitan areas during the 2-year period. Dietary intakes of over 100 analytes are presented for the 8 population groups, which range from infants to elderly adults. Intakes of selected population groups are compared with representative previous findings. As in the past, average daily intakes are within acceptable limits.

History of the Food and Drug Administration's total diet study--1961 to 1987

The Total Diet Study provides the Food and Drug Administration with baseline information on the levels of pesticide residues, contaminants, and nutrient elements in the food supply and in the diets of specific age-sex groups. The study also identifies trends and changes in the levels of these substances in the food supply and in diets over time and thereby assists in identifying potential public health problems. This paper describes the evolution of the Total Diet Study from 1961 to 1987. Food collections, sites of analysis, diets, food commodity groups, analytes, analytical methodologies, data transfer, publication of results, notable results, resources, and advantages of the study are discussed.

Pesticides, selected elements, and other chemicals in infant and toddler total diet samples, October 1979-September 1980

The U.S. Food and Drug Administration (FDA) conducts Total Diet Studies to determine the dietary intake of selected pesticides, industrial chemicals, and elements (including radionuclides). These studies involve the retail purchase and analysis of foods representative of the diets of infants, toddlers, and adults. The individual food items are separated into a number of food groups, each of which is analyzed as a composite. This report summarizes the results for infant and toddler Total Diet samples collected in 10 cities between October 1979 and September 1980. The average concentration, range of concentrations, and calculated average daily intake of each chemical found are presented by food group. The average daily intakes of the chemicals are similar to those found in the several preceding years and generally are within acceptable limits. The results for samples collected during the same period that represent the adult diet are reported separately.

Pesticides, selected elements, and other chemicals in adult total diet samples, October 1979-September 1980

The U.S. Food and Drug Administration (FDA) conducts Total Diet Studies to determine the dietary intake of selected pesticides, industrial chemicals, and elements (including radionuclides). These studies involve the retail purchase and analysis of foods representative of the diets of infants, toddlers, and adults. The individual food items are separated into a number of food groups, each of which is analyzed as a composite. This report summarizes the results for adult Total Diet samples collected in 20 cities between October 1979 and September 1980. The average concentration, range of concentrations, and calculated average daily intake of each chemical found are presented by food group. The average daily intakes of the chemicals are similar to those found in the several preceding years and are within acceptable limits. The results for samples collected during the same period that represent the diets of infants and toddlers are reported separately.

Pesticides, selected elements, and other chemicals in infant and toddler total diet samples, October 1978-September 1979

The U.S. Food and Drug Administration (FDA) conducts Total Diet Studies to determine the dietary intake of selected pesticides, industrial chemicals, and elements (including radionuclides). These studies involve the retail purchase and analysis of foods representative of the diets of infants, toddlers, and adults. The individual food items are separated into a number of food groups, each of which is analyzed as a composite. This report summarizes the results for infant and toddler Total Diet samples collected in 10 cities between October 1978 and September 1979. The average concentration, range of concentrations, and calculated average daily intake of the chemicals found are presented by food group. The average daily intakes of the chemicals are similar to those found in the several preceding years and generally are within acceptable limits. The results for samples collected during the same period that represent the adult diet are reported separately.

Pesticides, selected elements, and other chemicals in adult total diet samples, October 1978-September 1979

The U.S. Food and Drug Administration (FDA) conducts Total Diet Studies to determine the dietary intake of selected pesticides, industrial chemicals, and elements (including radionuclides). These studies involve the retail purchase and analysis of foods representative of the diets of infants, toddlers, and adults. The individual food items are separated into a number of food groups, each of which is analyzed as a composite. This report summarizes the results for adult Total Diet samples collected in 20 cities between October 1978 and September 1979. The average concentration, range of concentrations, and calculated average daily intake of each chemical found are presented by food group. The average daily intakes of the chemicals are similar to those found in the several preceding years and are within acceptable limits. The results for samples collected during the same period that represent the diets of infants and toddlers are reported separately.