α-Actinin-4-Mediated FSGS: An Inherited Kidney Disease Caused by an Aggregated and Rapidly Degraded Cytoskeletal Protein

Focal segmental glomerulosclerosis (FSGS) is a common pattern of renal injury, seen as both a primary disorder and as a consequence of underlying insults such as diabetes, HIV infection, and hypertension. Point mutations in theα-actinin-4 gene ACTN4 cause an autosomal dominant form of human FSGS. We characterized the biological effect of these mutations by biochemical assays, cell-based studies, and the development of a new mouse model. We found that a fraction of the mutant protein forms large aggregates with a high sedimentation coefficient. Localization of mutant α-actinin-4 in transfected and injected cells, as well as in situ glomeruli, showed aggregates of the mutant protein. Video microscopy showed the mutant α-actinin-4 to be markedly less dynamic than the wild-type protein. We developed a “knockin” mouse model by replacing Actn4 with a copy of the gene bearing an FSGS-associated point mutation. We used cells from these mice to show increased degradation of mutant α-actinin-4, mediated, at least in part, by the ubiquitin–proteasome pathway. We correlate these findings with studies of α-actinin-4 expression in human samples. “Knockin” mice with a disease-associated Actn4 mutation develop a phenotype similar to that observed in humans. Comparison of the phenotype in wild-type, heterozygous, and homozygous Actn4 “knockin” and “knockout” mice, together with our in vitro data, suggests that the phenotypes in mice and humans involve both gain-of-function and loss-of-function mechanisms.     

Alpha-actinin-4-mediated FSGS: an inherited kidney disease caused by an aggregated and rapidly degraded cytoskeletal protein

Focal segmental glomerulosclerosis (FSGS) is a common pattern of renal injury, seen as both a primary disorder and as a consequence of underlying insults such as diabetes, HIV infection, and hypertension. Point mutations in the alpha-actinin-4 gene ACTN4 cause an autosomal dominant form of human FSGS. We characterized the biological effect of these mutations by biochemical assays, cell-based studies, and the development of a new mouse model. We found that a fraction of the mutant protein forms large aggregates with a high sedimentation coefficient. Localization of mutant alpha-actinin-4 in transfected and injected cells, as well as in situ glomeruli, showed aggregates of the mutant protein. Video microscopy showed the mutant alpha-actinin-4 to be markedly less dynamic than the wild-type protein. We developed a "knockin" mouse model by replacing Actn4 with a copy of the gene bearing an FSGS-associated point mutation. We used cells from these mice to show increased degradation of mutant alpha-actinin-4, mediated, at least in part, by the ubiquitin-proteasome pathway. We correlate these findings with studies of alpha-actinin-4 expression in human samples. "Knockin" mice with a disease-associated Actn4 mutation develop a phenotype similar to that observed in humans. Comparison of the phenotype in wild-type, heterozygous, and homozygous Actn4 "knockin" and "knockout" mice, together with our in vitro data, suggests that the phenotypes in mice and humans involve both gain-of-function and loss-of-function mechanisms.     

Chapter 4: Protein Interactions and Disease

Proteins do not function in isolation; it is their interactions with one another and also with other molecules (e.g. DNA, RNA) that mediate metabolic and signaling pathways, cellular processes, and organismal systems. Due to their central role in biological function, protein interactions also control the mechanisms leading to healthy and diseased states in organisms. Diseases are often caused by mutations affecting the binding interface or leading to biochemically dysfunctional allosteric changes in proteins. Therefore, protein interaction networks can elucidate the molecular basis of disease, which in turn can inform methods for prevention, diagnosis, and treatment. In this chapter, we will describe the computational approaches to predict and map networks of protein interactions and briefly review the experimental methods to detect protein interactions. We will describe the application of protein interaction networks as a translational approach to the study of human disease and evaluate the challenges faced by these approaches.

What to Learn in This Chapter

• Experimental and computational methods to detect protein interactions
• Protein networks and disease
• Studying the genetic and molecular basis of disease
• Using protein interactions to understand disease

This article is part of the “Translational Bioinformatics” collection for PLOS Computational Biology.

     

An Age-Calibrated Definition of Chronic Kidney Disease: Rationale and Benefits

Defining chronic kidney disease (CKD) is the subject of intense debate in the current nephrology literature. The debate concerns the threshold value of estimated glomerular filtration rate (eGFR) used to make the diagnosis of CKD. Current recommendations argue that a universal threshold of 60 mL/min/1.73m² should be used. This threshold has been defended by epidemiological studies showing that the risk of mortality or end-stage renal disease increases with an eGFR below 60 mL/min/1.73m². However, a universal threshold does not take into account the physiologic decline in GFR with ageing nor does it account for the risk of mortality and end-stage renal disease being trivial with isolated eGFR levels just below 60 mL/min/1.73m² in older subjects and significantly increased with eGFR levels just above 60 mL/min/1.73m² among younger patients. Overestimation of the CKD prevalence in the elderly (medicalisation of senescence) and underestimation of CKD (potentially from treatable primary nephrologic diseases) in younger patients is of primary concern. An age-calibrated definition of CKD has been proposed to distinguish age-related from disease-related changes in eGFR. For patients younger than 40 years, CKD is defined by eGFR below 75 mL/min/1.73m². For patients with ages between 40 and 65 years, CKD is defined by 60 mL/min/1.73m². For subjects older than 65 years without albuminuria or proteinuria, CKD is defined by eGFR below 45 mL/min/1.73m².     

Human Brain βA4 Amyloid Protein Precursor of Alzheimer''s Disease: Purification and Partial Characterization

The major component of the amyloid deposition that characterizes Alzheimer's disease is the 4-kDa beta A4 protein, which is derived from a much larger amyloid protein precursor (APP). A procedure for the complete purification of APP from human brain is described. The same amino terminal sequence of APP was found in two patients with Alzheimer's disease and one control subject. Two major forms of APP were identified in human brain with apparent molecular masses of 100-110 kDa and 120-130 kDa. Soluble and membrane fractions of brain contained nearly equal amounts of APP in both humans and rats. Immunoprecipitation with carboxyl terminus-directed antibodies indicates that the soluble forms of APP are truncated. Carboxyl terminus truncation of membrane-associated forms of human brain APP was also found to occur during postmortem autolysis. The availability of purified human brain APP will facilitate the investigation of its normal function and the events that lead to its abnormal cleavage in patients with Alzheimer's disease.     

Inactivation of DNA-Dependent Protein Kinase by Protein Kinase Cδ: Implications for Apoptosis

Protein kinase Cδ (PKCδ) is proteolytically cleaved and activated at the onset of apoptosis induced by DNA-damaging agents, tumor necrosis factor, and anti-Fas antibody. A role for PKCδ in apoptosis is supported by the finding that overexpression of the catalytic fragment of PKCδ (PKCδ CF) in cells is associated with the appearance of certain characteristics of apoptosis. However, the functional relationship between PKCδ cleavage and induction of apoptosis is unknown. The present studies demonstrate that PKCδ associates constitutively with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). The results show that PKCδ CF phosphorylates DNA-PKcs in vitro. Interaction of DNA-PKcs with PKCδ CF inhibits the function of DNA-PKcs to form complexes with DNA and to phosphorylate its downstream target, p53. The results also demonstrate that cells deficient in DNA-PK are resistant to apoptosis induced by overexpressing PKCδ CF. These findings support the hypothesis that functional interactions between PKCδ and DNA-PK contribute to DNA damage-induced apoptosis.     

Pod Spot and Seed Blight: A New Disease of Mesquite Caused by Macrophomina phaseoVma

A new disease of pods and seeds of mequite caused by Macrophomina phaseolina is described from Northeastern Brazil. Affected pods showed a brown discolouration which often included pycnidia of the fungus. Infected seeds did not germmate.     

Optimization of Bacteriocin Release Protein (BRP)-Mediated Protein Release by Escherichia coli: Random Mutagenesis of the pCloDF13-Derived BRP Gene To Uncouple Lethality and Quasi-Lysis from Protein Release

Bacteriocin release proteins (BRPs) can be used for the release of heterologous proteins from the Escherichia coli periplasm into the culture medium. However, high-level expression of BRP causes apparent lysis of the host cells in liquid cultures (quasi-lysis) and inhibition of growth on broth agar plates (lethality). To optimize BRP-mediated protein release, the pCloDF13 BRP gene was subjected to random mutagenesis by using PCR techniques. Mutated BRPs with a strongly reduced capacity to cause growth inhibition on broth agar plates were selected, analyzed by nucleotide sequencing, and further characterized by performing growth and release experiments in liquid cultures. A subset of these BRP derivatives did not cause quasi-lysis and had only a small effect on growth but still functioned in the release of the periplasmic protein β-lactamase and the periplasmic K88 molecular chaperone FaeE and in the release of the bacteriocin cloacin DF13 into the culture medium. These BRP derivatives can be more efficiently used for extracellular production of proteins by E. coli than can the original BRP.     

Mitochondrial Protein Acylation and Intermediary Metabolism: Regulation by Sirtuins and Implications for Metabolic Disease

The sirtuins are a family of NAD⁺-dependent protein deacetylases that regulate cell survival, metabolism, and longevity. Three sirtuins, SIRT3–5, localize to mitochondria. Expression of SIRT3 is selectively activated during fasting and calorie restriction. SIRT3 regulates the acetylation level and enzymatic activity of key metabolic enzymes, such as acetyl-CoA synthetase, long-chain acyl-CoA dehydrogenase, and 3-hydroxy-3-methylglutaryl-CoA synthase 2, and enhances fat metabolism during fasting. SIRT5 exhibits demalonylase/desuccinylase activity, and lysine succinylation and malonylation are abundant mitochondrial protein modifications. No convincing enzymatic activity has been reported for SIRT4. Here, we review the emerging role of mitochondrial sirtuins as metabolic sensors that respond to changes in the energy status of the cell and modulate the activities of key metabolic enzymes via protein deacylation.     

Metabolic Syndrome and Chronic Kidney Disease in an Adult Korean Population: Results from the Korean National Health Screening

Background

This study was aimed to examine the prevalence of metabolic syndrome (MS) and chronic kidney disease (CKD), and the association between MS and its components with CKD in Korea.

Methods

We excluded diabetes to appreciate the real impact of MS and performed a cross-sectional study using the general health screening data of 10,253,085 (48.86±13.83 years, men 56.18%) participants (age, ≥20 years) from the Korean National Health Screening 2011. CKD was defined as dipstick proteinuria ≥1 or an estimated glomerular filtration rate (eGFR) <60 ml/min/1.73 m².

Results

The prevalence of CKD was 6.15% (men, 5.37%; women, 7.15%). Further, 22.25% study population had MS (abdominal obesity, 27.98%; hypertriglyceridemia, 30.09%; low high-density cholesterol levels, 19.74%; high blood pressure, 43.45%; and high fasting glucose levels, 30.44%). Multivariate-adjusted analysis indicated that proteinuria risk increased in participants with MS (odds ratio [OR] 1.884, 95% confidence interval [CI] 1.867–1.902, P<0.001). The presence of MS was associated with eGFR<60 mL/min/1.73 m² (OR 1.364, 95% CI 1.355–1.373, P<0.001). MS individual components were also associated with an increased CKD risk. The strength of association between MS and the development of CKD increase as the number of components increased from 1 to 5. In sub-analysis by men and women, MS and its each components were a significant determinant for CKD.

Conclusions

MS and its individual components can predict the risk of prevalent CKD for men and women.     

Viral Load and a Locus on Chromosome 11 Affect the Late Clinical Disease Caused by Theiler’s Virus

Theiler's virus causes a persistent infection and a demyelinating disease of mice which is a model for multiple sclerosis. Susceptibility to viral persistence maps to several loci, including the interferon gamma locus. Inactivating the gene coding for the interferon gamma receptor makes 129/Sv mice susceptible to persistent infection and clinical disease, whereas inactivating the interferon gamma gene makes C57BL/6 mice susceptible to persistent infection but not to clinical disease. This difference in phenotype is due to the difference in genetic background. Clinical disease depends on high viral load and Tmevd5, a locus on chromosome 11. These results have consequences for the identification of viruses which might be implicated in multiple sclerosis.     

Comparison of High vs. Normal/Low Protein Diets on Renal Function in Subjects without Chronic Kidney Disease: A Systematic Review and Meta-Analysis

Background

It was the aim of the present systematic review and meta-analysis to investigate the effects of high protein (HP) versus normal/low protein (LP/NP) diets on parameters of renal function in subjects without chronic kidney disease.

Methods

Queries of literature were performed using the electronic databases MEDLINE, EMBASE, and the Cochrane Trial Register until 27^th February 2014. Study specific weighted mean differences (MD) were pooled using a random effect model by the Cochrane software package Review Manager 5.1.

Findings

30 studies including 2160 subjects met the objectives and were included in the meta-analyses. HP regimens resulted in a significantly more pronounced increase in glomerular filtration rate [MD: 7.18 ml/min/1.73 m², 95% CI 4.45 to 9.91, p<0.001], serum urea [MD: 1.75 mmol/l, 95% CI 1.13 to 237, p<0.001], and urinary calcium excretion [MD: 25.43 mg/24h, 95% CI 13.62 to 37.24, p<0.001] when compared to the respective LP/NP protocol.

Conclusion

HP diets were associated with increased GFR, serum urea, urinary calcium excretion, and serum concentrations of uric acid. In the light of the high risk of kidney disease among obese, weight reduction programs recommending HP diets especially from animal sources should be handled with caution.     

运动与阿尔茨海默病：基于Tau蛋白翻译后修饰视角的研究述评

阿尔茨海默病（Alzheimer’s disease,AD）是一种与年龄有关的神经退行性疾病,严重危害老年人的身心健康,给社会带来巨大的经济压力。但目前其发病机制尚不完全明确,临床仍无根治的有效方法。Tau蛋白是一种微管相关蛋白质,能够参与维持微管相关结构稳定,具有可溶性且不会聚集。在AD病理状态下,病人脑内Tau蛋白结构和功能异常。异常的Tau蛋白聚集成不可溶的神经纤维缠结,损害微管运输能力,导致病人认知功能障碍。Tau蛋白结构和功能的改变是由多种翻译后修饰过程来调控的,即将特定的化学修饰基团与Tau蛋白N-端或C-端结合,直接改变蛋白质的性质和功能。AD病人脑内Tau蛋白的磷酸化、糖基化、乙酰化及SUMO化等多种翻译后修饰异常,与Tau蛋白的降解和毒性物质的聚集密切相关。本文综述近年来的研究后发现,运动可以通过改善Tau蛋白翻译后的某些异常修饰来预防和改善AD,主要作用方式如下：(1）运动可通过抑制GSK 3β和MAPK等蛋白激酶活性来抑制Tau蛋白的过度磷酸化,可能通过上调PP2A活性来促进Tau蛋白去磷酸化;(2）运动可通过提高GLUT1和GLUT3蛋白质水平,可能通过调节OGA和OGT活性平衡,提高蛋白质O-GlcNAc糖基化水平;(3）运动可能通过AMPK/mTORC1途径抑制p300以及激活SIRT1,降低Tau蛋白乙酰化水平;同时运动还可能通过抑制HDAC6,改善Tau蛋白KXGS基序异常乙酰化程度;(4）运动可能通过调节磷酸化与SUMO化共定位点,改善Tau蛋白异常SUMO化水平。     

Biochemical Changes in Terminal Root Galls Caused by an Ectoparasitic Nematode,Longidorus africanus: Phenols,Carbohydrates and Cytokinins

Biochemical changes occurred in roots of bur marigold and grapevine infected with Longidorus africanus. Phenols of infected root tips differed quantitatively from those of healthy root tips (optical density of 0.68 and 0.32, respectively). Column chromatography of the phenol extracts resulted in more fractions in the infected than in the healthy root extract. Of the enzymes involved in phenol metabolism, three were tested. No polyphenol oxidase activity was detected and no difference in catalase activity was found between healthy and infected roots. Peroxidase activity, however, was much higher in infected roots. The extra peroxidase was associated mainly with the cortical cells of the infected root tips.Galled roots contained twice the amount of simple sugars and inulin as did the healthy roots. A cytokinin-active fraction was found only in the noninfected roots.     

Foot Drop Caused by Lumbar Degenerative Disease: Clinical Features,Prognostic Factors of Surgical Outcome and Clinical Stage

Objective

The purpose of this study was to analyze the clinical features and prognostic factors of surgical outcome of foot drop caused by lumbar degenerative disease and put forward the clinical stage.

Methods

We retrospectively reviewed 135 patients with foot drop due to lumbar degenerative disease. The clinical features and mechanism were analyzed. Age, sex, duration of palsy, preoperative muscle strength of tibialis anterior (TA), sensation defect of affected lower limb, affected foot, diagnosis and compressed nerve roots were recorded and compared with surgical outcome.

Results

Foot drop was observed in 8.1% of all inpatients of lumbar degenerative disease. L5 nerve root compression was observed in 126 of all 135 patients (93.3%). Single, double and triple roots compression was observed respectively in 43, 83, and 9 patients (31.9%, 61.5%, and 6.6%). But there was no significant relationship between preoperative muscle strength of TA and the number of compressed roots. The muscle strength of TA was improved in 113 (83.7%) patients after surgery, but it reached to >=4 in only 21 (15.6%) patients. Improvement of the muscle strength of TA was almost stable at the 6-month follow-up. At the last follow-up, the muscle strength of TA was 1, 2, 3, 4, 5 respectively in 28, 24, 62, 13, 8 patients. Multivariate logistic regression showed duration of palsy (p=0.0360, OR=2.543), preoperative muscle strength of TA (p=0.0064, OR=5.528) and age (p=0.0309, OR=3.208) were factors that influenced recovery following an operation.

Conclusions

L5 nerve root was most frequently affected. The muscle strength of TA improved in most patients after surgery, but few patients can get a good recovery from foot drop. Patients of shorter duration of palsy, better preoperative muscle strength of TA and younger age showed a better surgical outcome.     

Subcutaneous Phaeohyphomycosis Caused by <Emphasis Type="Italic">Exophiala oligosperma</Emphasis> in an Immunocompetent Host: Case Report and Literature Review

We report a case of subcutaneous infection caused by Exophiala oligosperma. Erythematous ulcerated plaque with exudate was major clinical features. Histopathological examination showed yeast-like cells and fungal hyphae. Mycological and molecular identification revealed E. oligosperma as etiologic agent. Local debridement and oral itraconazole were effective. To the best of our knowledge, this is the first report of phaeohyphomycosis caused by E. oligosperma in mainland China. This report highlights the potential role of E. oligosperma as an emerging cause of infection in immunocompetent patients.     

A Host Creates an Enemy‐free Space for Mistletoes by Reducing Seed Predation Caused by a Woodboring Beetle: A Hypothesis

Parasitic plants rely on host plants for nutrition. The number of host species varies largely between groups, from single species or genus to hundreds of species. Relative abundance of the host and evolutionary history are the main requisites for parasitic plants to develop specificity to abundant hosts. In the present study, we suggest a novel mechanism by which a hemiparasitic mistletoe can develop local specificity mediated by its host. First, we describe a novel interaction in which a woodboring beetle (Hypothenemus obscurus) preys on mistletoe seeds (Psittacanthus plagiophyllus) attached to tree branches. This beetle preys more frequently on seeds deposited on branches of non‐host species than on branches of its unique local host species (53 percent on average vs. 26 percent respectively). We hypothesize that local host specificity for this mistletoe could be partly mediated by beetle‐host incompatibility, since the host offers a predation‐free space in which mistletoes have better chances to grow. Furthermore, that the exceptional gum exudates produced by this unique host species minimize beetle attacks on branches, thus reducing predation of mistletoe seeds. This novel tritrophic interaction opens an avenue for research on macroscopic host‐specificity mechanisms that occur at the level of the host bark and that have been poorly studied by plant ecologists.