Medical bioremediation: prospects for the application of microbial catabolic diversity to aging and several major age-related diseases

Impact of Oxysterols in Age-Related Disorders and Strategies to Alleviate Adverse Effects

Oxysterols or cholesterol oxidation products are a class of molecules with the sterol moiety, derived from oxidative reaction of cholesterol through enzymatic and non-enzymatic processes. They are widely reported in animal-origin foods and prove significant involvement in the regulation of cholesterol homeostasis, lipid transport, cellular signaling, and other physiological processes. Reports of oxysterol-mediated cytotoxicity are in abundance and thus consequently implicated in several age-related and lifestyle disorders such as cardiovascular diseases, bone disorders, pancreatic disorders, age-related macular degeneration, cataract, neurodegenerative disorders such as Alzheimer's and Parkinson's disease, and some types of cancers. In this chapter, we attempt to review a selection of physiologically relevant oxysterols, with a focus on their formation, properties, and roles in health and disease, while also delving into the potential of natural and synthetic molecules along with bacterial enzymes for mitigating oxysterol-mediated cell damage.

Sharing of Genetic Association Signals by Age-Related Macular Degeneration and Alzheimer's Disease at Multiple Levels

Age-related macular degeneration and Alzheimer's disease are closely related complex diseases that may share overlapping pathogenesis in gene networks. This study was conducted to investigate the genetic factors shared by both diseases. We analyzed genome-wide association studies' summary statistics from both diseases using a new platform known as functional mapping and annotation (FUMA) and a co-localization analysis. We obtained disease-related gene expression profile data from the Gene Expression Omnibus and analyzed these data using weighted gene co-expression network analysis. FUMA analysis and Bayesian co-localization analysis showed that ten genes on chromosome 7, one pathway (complement and coagulation cascade), and forty-two biological processes were common for both diseases. Among these ten genes, two protein-coding genes, two pseudogenes, and two RNA genes were, for the first time, identified to be associated with both diseases. Weighted gene co-expression network analysis identified 19 age-related macular degeneration hub genes and 19 Alzheimer's disease hub genes and revealed that these two diseases shared nine pathways and 63 biological processes. Using FUMA, co-localization analysis, and weighted gene co-expression network analysis, 10 genes on chromosome 7, 10 pathways, and 105 biological processes were found to be associated with the two degenerative diseases. This suggests that these10 genes and the hub genes of these modules associated with the shared pathways are potential diagnostic markers for both diseases.

7-Ketocholesterol in disease and aging

7-Ketocholesterol (7KC) is a toxic oxysterol that is associated with many diseases and disabilities of aging, as well as several orphan diseases. 7KC is the most common product of a reaction between cholesterol and oxygen radicals and is the most concentrated oxysterol found in the blood and arterial plaques of coronary artery disease patients as well as various other disease tissues and cell types. Unlike cholesterol, 7KC consistently shows cytotoxicity to cells and its physiological function in humans or other complex organisms is unknown. Oxysterols, particularly 7KC, have also been shown to diffuse through membranes where they affect receptor and enzymatic function. Here, we will explore the known and proposed mechanisms of pathologies that are associated with 7KC, as well speculate about the future of 7KC as a diagnostic and therapeutic target in medicine.

Positive lysosomal modulation as a unique strategy to treat age-related protein accumulation diseases

Lysosomes are involved in degrading and recycling cellular ingredients, and their disruption with age may contribute to amyloidogenesis, paired helical filaments (PHFs), and α-synuclein and mutant huntingtin aggregation. Lysosomal cathepsins are upregulated by accumulating proteins and more so by the modulator Z-Phe-Ala-diazomethylketone (PADK). Such positive modulators of the lysosomal system have been studied in the well-characterized hippocampal slice model of protein accumulation that exhibits the pathogenic cascade of tau aggregation, tubulin breakdown, microtubule destabilization, transport failure, and synaptic decline. Active cathepsins were upregulated by PADK; Rab proteins were modified as well, indicating enhanced trafficking, whereas lysosome-associated membrane protein and proteasome markers were unchanged. Lysosomal modulation reduced the pre-existing PHF deposits, restored tubulin structure and transport, and recovered synaptic components. Further proof-of-principle studies used Alzheimer disease mouse models. It was recently reported that systemic PADK administration caused dramatic increases in cathepsin B protein and activity levels, whereas neprilysin, insulin-degrading enzyme, α-secretase, and β-secretase were unaffected by PADK. In the transgenic models, PADK treatment resulted in clearance of intracellular amyloid beta (Aβ) peptide and concomitant reduction of extracellular deposits. Production of the less pathogenic Aβ(1-38) peptide corresponded with decreased levels of Aβ(1-42), supporting the lysosome's antiamyloidogenic role through intracellular truncation. Amelioration of synaptic and behavioral deficits also indicates a neuroprotective function of the lysosomal system, identifying lysosomal modulation as an avenue for disease-modifying therapies. From the in vitro and in vivo findings, unique lysosomal modulators represent a minimally invasive, pharmacologically controlled strategy against protein accumulation disorders to enhance protein clearance, promote synaptic integrity, and slow the progression of dementia.

Zeno's paradox and the faith that technological game-changers are impossible

In their article in this issue, Olshansky and Carnes [Gerontology 2013;59:85-92] spell out in perhaps the most explicit terms yet a view which they have long espoused: that increases in longevity will inevitably slow down in decades to come, since the rate of biomedical progress that everyone agrees would be necessary to avoid such a slowdown is far too dramatic to be plausible. By doing so, they also betray more explicitly than ever before the flaws in their own logic. It is ironic that these flaws, unlike the work they critique, are actually quite closely analogous to the flaws in Zeno's paradox. Since others are offering their own comments on other parts of the article, I shall restrict my remarks on the article to those passages which refer specifically to my own work, together with the conclusion.

Mechanism of ceroid formation in atherosclerotic plaque: in situ studies using a combination of Raman and fluorescence spectroscopy

Accumulation of the lipid-protein complex ceroid is a characteristic of atherosclerotic plaque. The mechanism of ceroid formation has been extensively studied, because the complex is postulated to contribute to plaque irreversibility. Despite intensive research, ceroid deposits are defined through their fluorescence and histochemical staining properties, while their composition remains unknown. Using Raman and fluorescence spectral microscopy, we examine the composition of ceroid in situ in aorta and coronary artery plaque. The synergy of these two types of spectroscopy allows for identification of ceroid via its fluorescence signature and elucidation of its chemical composition through the acquisition of a Raman spectrum. In accordance with in vitro predictions, low density lipoprotein (LDL) appears within the deposits primarily in its peroxidized form. The main forms of modified LDL detected in both coronary artery and aortic plaques are peroxidation products from the Fenton reaction and myeloperoxidase-hypochlorite pathway. These two peroxidation products occur in similar concentrations within the deposits and represent ∼40 and 30% of the total LDL (native and peroxidized) in the aorta and coronary artery deposits, respectively. To our knowledge, this study is the first to successfully employ Raman spectroscopy to unravel a metabolic pathway involved in disease pathogenesis: the formation of ceroid in atherosclerotic plaque.

New strategies for enzyme replacement therapy for lysosomal storage diseases

Enzyme replacement therapy is an established means of treating lysosomal storage diseases. Infused enzymes are normally targeted to the lysosomes of affected cells by interactions with cell-surface receptors that recognize carbohydrate moieties such as mannose and mannose 6-phosphate on the enzymes. Therefore, we have investigated alternative strategies to deliver the lysosomal enzyme beta-glucuronidase in the enzyme-deficient mucopolysaccharidosis type VII mouse model. Here we summarize our recent efforts to use nontraditional ways to deliver beta-glucuronidase. First, we used a chimeric protein of the insulin-like growth factor II (IGF-II) fused to beta-glucuronidase to deliver enzyme via the IGF-II binding site on the bifunctional IGF-II/mannose 6-phosphate receptor. Second, we used the 11-amino-acid human immunodeficiency virus (HIV) Tat domain fused to beta-glucuronidase to mediate uptake by absorptive endocytosis. Interaction with heparan sulfate on the cell surface internalizes and delivers the Tat-tagged enzyme to the lysosome via plasma membrane recycling. Third, we created a chimeric beta-glucuronidase fused to the Fc portion of human immunoglobulin G (IgG) Fc, which was transported by the neonatal Fc receptor from the maternal circulation across the placenta to sites of storage in fetal tissues. Finally, periodate treatment was used to eliminate interaction with carbohydrate receptors, creating an enzyme with increased plasma half-life, resulting in transport across the blood-brain barrier and clearance of storage in neurons. These strategies for delivering lysosomal enzymes could also be used to target nonlysosomal proteins or enzymes identified for bioremediation of other conditions.

Medical bioremediation of age-related diseases

Catabolic insufficiency in humans leads to the gradual accumulation of a number of pathogenic compounds associated with age-related diseases, including atherosclerosis, Alzheimer's disease, and macular degeneration. Removal of these compounds is a widely researched therapeutic option, but the use of antibodies and endogenous human enzymes has failed to produce effective treatments, and may pose risks to cellular homeostasis. Another alternative is "medical bioremediation," the use of microbial enzymes to augment missing catabolic functions. The microbial genetic diversity in most natural environments provides a resource that can be mined for enzymes capable of degrading just about any energy-rich organic compound. This review discusses targets for biodegradation, the identification of candidate microbial enzymes, and enzyme-delivery methods.

Alzheimer's, atherosclerosis, and aggregates: a role for bacterial degradation

Several of the most prevalent and severe age-related diseases, notably Alzheimer's disease and atherosclerosis, feature the accumulation of non-degradable aggregates within the lysosomes of disease-affected cells. At an early point in disease progression, the breakdown of lysosomal contents by the resident catabolic enzymes stops working properly. A return of lysosomal enzymatic activity to pre-disease levels may restore aggregate elimination. In this review, a method of bioremediation-derived lysosomal enzyme enhancement is proposed, featuring the cellular introduction of microbial-isolated enzymes, or xenoenzymes. The benefits and challenges of using xenoenzymes to break down aggregates are discussed. As the size of our elderly population grows, the incidence of age-related diseases will increase, necessitating the exploration of radical, but potentially powerful, therapeutic strategies.

Engineering away lysosomal junk: medical bioremediation

Atherosclerosis, macular degeneration, and neurodegenerative diseases such as Alzheimer's disease, are associated with the intracellular accumulation of substances that impair cellular function and viability. Reversing this accumulation may be a valuable therapy, but the accumulating substances resist normal cellular catabolism. On the other hand, these substances are naturally degraded in the soil and water by microorganisms. Thus, we propose the concept of "medical bioremediation," which derives from the successful field of in situ environmental bioremediation of petroleum hydrocarbons. In environmental bioremediation, communities of microorganisms mineralize hydrophobic organics using a series of enzymes. In medical bioremediation, we hope to utilize one or several microbial enzymes to degrade the intracellular accumulators enough that they can be cleared from the affected cells. Here, we present preliminary, but promising results for the bacterial biodegradation of 7-ketocholesterol, the main accumulator of foam cells associated with atherosclerosis. In particular, we report on the isolation of several Nocardia strains able to biodegrade 7-ketocholesterol and as an ester of 7-ketocholoesterol. We also outline key intermediates in the biodegradation pathway, a key step towards identifying the key enzymes that may lead to a therapy.

Cellular therapy using microglial cells

Recent insights into the function and dysfunction of microglia may inform future therapies to combat neurodegeneration. We hypothesise how different aspects of microglial activity including migration, activation, oxidative response, phagocytosis, proteolysis, and replenishment could be targeted by novel therapeutic approaches. A combined approach is suggested, encompassing opsonization and anti-inflammatory strategies in conjunction with an engineering of microglial precursors. Xenoproteases for bioremediation could be used to enhance intracellular and extracellular proteolytic capacity. The capacity of microglial precursors to cross the blood-brain barrier and to home in on sites of neural damage and inflammation might prove to be particularly useful for future therapeutic strategies.

Free radicals in aging: causal complexity and its biomedical implications

Superoxide generated adventitiously by the mitochondrial respiratory chain can give rise to much more reactive radicals, resulting in random oxidation of all classes of macromolecules. Harman's 1956 suggestion that this process might drive aging has been a leading strand of biogerontological thinking since the discovery of superoxide dismutase. However, it has become apparent that the many downstream consequences of free radical damage can also be caused by processes not involving oxidation. Moreover, free radicals have been put to use by evolution to such an extent that their wholesale elimination would certainly be fatal. This multiplicity of parallel pathways and side-effects illustrates why attempts to postpone aging by "cleaning up" metabolism will surely fail for the foreseeable future: we simply understand metabolism too poorly. This has led me to pursue the alternative, "repair and maintenance" approach that sidesteps our ignorance of metabolism and may be feasible relatively soon.

Advanced atherosclerotic foam cell formation has features of an acquired lysosomal storage disorder

Atherosclerosis is a disease of large- and medium-sized arteries. Complications from atherosclerosis remain a serious cause of morbidity and mortality in industrialized countries. The disease begins very early in life and effects most people in the West. However, because the progression of the disease is slow, symptoms usually do not occur until after the fifth decade of life. Because atherosclerosis is a ubiquitous occurrence throughout the world, as life expectancy is prolonged most populations will see increasing numbers of deaths from complications of atherosclerosis unless there are dramatic advances in treatment. Because it begins so early in life, current treatment is aimed at slowing or reversing the progression of the disease rather than eliminating the initiating steps. Changes in diet and exercise, cholesterol-lowering drugs, and improvements in surgical treatments have made significant inroads into prolonging life, but much work is still required. To proceed further, a better understanding is needed of the underlying causes of disease progression. In this regard, evidence is mounting that the foam cells of the lesion (a critical cell in atherosclerosis progression) exhibit characteristics of an acquired lysosomal storage disorder. In this review the evidence for this conclusion is reviewed and the ramifications of this conclusion are explored with regard to the understanding of disease progression mechanisms, possible improvements in treatment, and their role in increasing life expectancy.

SENS and the Polarization of Aging-Related Research

The second Strategies for Engineered Negligible Senescence conference (SENS II) featured some very provocative ideas. The explicit objective of extending human life span indefinitely has opened a large rift between the meeting's organizer and those who believe he is acting unscientifically, perhaps recklessly. Two SENS conference participants present their views on the divisive nature of SENS.

Appropriating microbial catabolism: A proposal to treat and prevent neurodegeneration

Intraneuronal, largely proteinaceous aggregates accumulate in all major neurodegenerative disorders. Lysosomal degradation of proteinaceous and other material declines early in such diseases. This suggests that intraneuronal aggregates consist of material which is normally broken down in the lysosome and thus accumulates when lysosomal degradation fails. This is plausible even though those aggregates are generally non-lysosomal, because lysosomal uptake may be affected. Thus, restoring lysosomal function might eliminate them--and without increasing the concentration of the soluble monomers or oligomers of which they are formed. This approach is therefore unlikely to be harmful and may well be beneficial. How might lysosomes be rejuvenated? Since lysosomal dysfunction is likely to be caused by intralysosomal material that is resistant to lysosomal degradation, normal function might be recovered by augmenting that function to cause the toxin to be degraded. Here, I describe how such augmentation might be achieved with microbial enzymes. Soil microbes display astonishing catabolic diversity, something exploited for decades in the bioremediation industry. Environments enriched in human remains impose selective pressure on the microbial population to evolve the ability to degrade any recalcitrant, energy-rich human material. Thus, microbes may exist that can degrade these lysosomal toxins. If so, it should be possible to isolate the genes responsible and modify them for therapeutic activity in the mammalian lysosome.

You don't need a weatherman: famines, evolution, and intervention into aging

Calorie restriction (CR) is the most robust available intervention into biological aging. Efforts are underway to develop pharmaceuticals that would replicate CR's anti-aging effects in humans ("CR mimetics"), on the assumption that the life- and healthspan-extending effects of CR in lower organisms will be proportionally extrapolable to humans (the "proportionality principle" (PP)). A recent argument from evolutionary theory (the "weather hypothesis" (WH)) suggests that CR (or its mimetics) will only provide 2-3 years of extended healthy lifespan in humans. The extension of healthy human lifespan that would be afforded by intervention into aging makes it crucial that resources for therapeutic development be optimally allocated; CR mimetics being the main direction being pursued for interventive biogerontology, this paper evaluates the challenge to the potential efficacy of CR mimetics posed by the WH, on a theoretical level and by reference to the available interspecies data on CR. Rodent data suggest that the anti-aging effects of CR continue to increase in inverse proportion to the degree of energy restriction imposed, well below the level that would be expected to be survivable under the conditions under which the mechanisms of CR evolved and are maintained in the wild. Moreover, the same increase in anti-aging effects continues well below the point at which it interferes with reproductive function. Both of these facts are in accordance with the predictions of evolutionary theory. Granted these facts, the interspecies data-including data available in humans-are consistent with the predictions of PP rather than those of the WH. This suggests that humans will respond to a high degree of CR (or its pharmaceutical simulation) with a proportional deceleration of aging, so that CR mimetics should be as effective in humans as CR itself is in the rodent model. Despite this fact, CR mimetics should not be the focus of biomedical gerontology, as strategies based on the direct targeting of the molecular lesions of aging are likely to lead to more rapidly developable and far more effective anti-aging biomedicines.