Anastasia Ricci, Federica Biancucci, Gianluca Morganti
et al.
Abstract Ataxia Telangiectasia is a rare neurodegenerative disease caused by biallelic mutations in the Ataxia Telangiectasia Mutated gene. No cure is currently available for these patients but positive effects on neurologic features in AT patients have been achieved by dexamethasone administration through autologous erythrocytes (EryDex) in phase II and phase III clinical trials, leading us to explore the molecular mechanisms behind the drug action. During these investigations new ATM variants, which originated from alternative splicing of ATM messenger, were discovered, and detected in vivo in the blood of AT patients treated with EryDex. Some of the new ATM variants, alongside an i n silico designed one, were characterized and examined in AT fibroblast cell lines. ATM variants were capable of rescuing ATM activity in AT cells, particularly in the nuclear role of DNA DSBs recognition and repair, and in the cytoplasmic role of modulating autophagy, antioxidant capacity and mitochondria functionality, all of the features that are compromised in AT but essential for neuron survival. These outcomes are triggered by the kinase and further functional domains of the tested ATM variants, that are useful for restoring cellular functionality. The in silico designed ATM variant eliciting most of the functionality recover may be exploited in gene therapy or gene delivery for the treatment of AT patients.
The time-dependent kinetics of formation and evolution of nano-size atomic clusters is investigated and illustrated with the nucleation dynamics of ion-seed Ar$_n$H$^+$ particles. The rates of growth and degradation of Ar-atomic shells around the seed ion are inferred from Molecular Dynamics (MD) simulations. Simulations of cluster formation have been performed with accurate quantum-mechanical binary interaction potentials. Both the nonequilibrium and equilibrium growth of Ar$_n$H$^+$ are investigated at different temperature and densities of the atomic gas and seed ions. Formation of Ar$_{n\leq 40}$ shells is the main mechanism which regulates the kinetics of nano-cluster growth and the diffusive fluctuations of the cluster size distribution. The time-evolution of the cluster intrinsic energy and cluster size distributions are analyzed at the non-thermal, quasi-equilibrium, and thermal equilibrium stages of Ar$_n$H$^+$ formation. We've determined the self-consistent model parameters for the temporal fluctuations of the cluster size and found coefficients of the diffusive growth mechanism describing the equilibrium distribution of nano-clusters. Nucleation of haze and nano-dust particles in astrophysical and atmospheric ionized gases are discussed.
F. Sampedro, J. Marín-Lahoz, S. Martínez-Horta
et al.
The C allele of the rs11136000 genetic variant of the clusterin gene has been associated with increased risk of Alzheimer's disease. However, a comprehensive characterization of the role of this genetic variant in early cognitive deterioration in PD is lacking.
Clusterin (CLU) is one of the risk genes most associated with late onset Alzheimer’s disease (AD), and several genetic variants in CLU are associated with AD risk. However, the functional role of known AD risk genetic variants in CLU has been little explored. We investigated the effect of an AD risk variant (rs7982) in the 5th exon of CLU on alternative splicing by using an integrative approach of brain-tissue-based RNA-Seq and whole genome sequencing data from Accelerating Medicines Partnership—Alzheimer’s Disease (AMP-AD). RNA-Seq data were generated from three regions in the temporal lobe of the brain—the temporal cortex, superior temporal gyrus, and parahippocampal gyrus. The rs7982 was significantly associated with intron retention (IR) of the 5th exon of CLU; as the number of alternative alleles (G) increased, the IR rates decreased more significantly in females than in males. Our results suggest a sex-dependent role of rs7982 in AD pathogenesis via splicing regulation.
Aberrant expressions of apoptotic genes have been associated with papillary thyroid carcinoma (PTC) in the past, however, their prognostic role and utility as biomarkers remains poorly understood. In this study, we analysed 505 PTC patients by employing Cox-PH regression techniques, prognostic index models and machine learning methods to elucidate the relationship between overall survival (OS) of PTC patients and 165 apoptosis related genes. It was observed that nine genes (ANXA1, TGFBR3, CLU, PSEN1, TNFRSF12A, GPX4, TIMP3, LEF1, BNIP3L) showed significant association with OS of PTC patients. Five out of nine genes were found to be positively correlated with OS of the patients, while the remaining four genes were negatively correlated. These genes were used for developing risk prediction models, which can be utilized to classify patients with a higher risk of death from the patients which have a good prognosis. Our voting-based model achieved highest performance (HR = 41.59, p = 3.36x10-4, C = 0.84, logrank-p = 3.8x10-8). The performance of voting-based model improved significantly when we used the age of patients with prognostic biomarker genes and achieved HR = 57.04 with p = 10−4 (C = 0.88, logrank-p = 1.44x10-9). We also developed classification models that can classify high risk patients (survival ≤ 6 years) and low risk patients (survival > 6 years). Our best model achieved AUROC of 0.92. Further, the expression pattern of the prognostic genes was verified at mRNA level, which showed their differential expression between normal and PTC samples. Also, the immunostaining results from HPA validated these findings. Since these genes can also be used as potential therapeutic targets in PTC, we also identified potential drug molecules which could modulate their expression profile. The study briefly revealed the key prognostic biomarker genes in the apoptotic pathway whose altered expression is associated with PTC progression and aggressiveness. In addition to this, risk assessment models proposed here can help in efficient management of PTC patients.
Kelsey M. Sheard, Sarah Thibault-Sennett, Aditya Sen
et al.
Mitochondria perform a myriad of biochemical functions in the cell that integrate ATP production and metabolism. While mitochondria contain their own genome, mtDNA, it only encodes thirteen proteins required for oxidative phosphorylation, thus well over one thousand proteins required for all mitochondrial functions are encoded in the nucleus. One such protein is Drosophila Clueless (Clu), whose vertebrate homolog is Clustered mitochondria homolog (Cluh). Clu/Cluh is a ribonucleoprotein that binds mRNAs destined for import into mitochondria and is an essential protein that regulates cellular metabolism. Clu forms large particles in the cytoplasm, although how these particles relate to nutrition and metabolic stress is unknown. Using live-imaging, we show Clu particles are highly dynamic. Clu particles appear to be unique as they do not colocalize with many known cytoplasmic bodies. In addition, Clu particle formation is highly dependent on diet as ovaries from starved females no longer contain Clu particles and insulin is necessary and sufficient for Clu particle formation. Oxidative stress also disperses particle. Since Clu particles are only present under optimal conditions we are naming them bliss particles. These observations identify Clu particles as unique, stress-sensitive cytoplasmic ribonucleoprotein particles whose absence corresponds with altered mitochondrial function and localization.
Clusterin (CLU) is induced in many organs after tissue injury or remodeling. Recently, we show that CLU levels are increased in plasma and left ventricle (LV) after MI, however, the mechanisms involved are not yet elucidated. On the other hand, it has been shown that the activity of the protein degradation systems (PDS) is affected after MI with a decrease in ubiquitin proteasome system (UPS) and an increase in macroautophagy. The aim of this study was to decipher if the increased CLU levels after MI are in part due to the alteration of PDS activity. Rat neonate cardiomyocytes (NCM) were treated with different modulators of UPS and macroautophagy in order to decipher their role in CLU expression, secretion, and degradation. We observed that inhibition of UPS activity in NCM increased CLU mRNA levels, its intracellular protein levels (p-CLU and m-CLU) and its secreted form (s-CLU). Macroautophagy was also induced after MG132 treatment but is not active. The inhibition of macroautophagy induction in MG132-treated NCM increased CLU mRNA and m-CLU levels, but not s-CLU compared to NCM only treated by MG132. We also demonstrate that CLU can be degraded in NCM through proteasome and lysosome by a macroautophagy independent pathway. In another hand, CLU silencing in NCM has no effect either on macroautophagy or apoptosis induced by MG132. However, the overexpression of CLU secreted isoform in H9c2 cells, but not in NCM decreased apoptosis after MG132 treatment. Finally, we observed that increased CLU levels in hypertrophied NCM and in failing human hearts are associated with proteasome inhibition and macroautophagy alteration. All these data suggest that increased CLU expression and secretion after MI is, in part, due to a defect of UPS and macroautophagy activities in the heart and may have a protective effect by decreasing apoptosis induced by proteasome inhibition.
Background: Mortalin/GRP-75/mt-hsp70 is a mitochondrial chaperone protein, found in the cytoplasm, endoplasmic reticulum and cytoplasmic vesicles. It functions in many cellular processes such as mitochondrial biogenesis, intracellular trafficking, cell proliferation, signaling, immortalization and tumorigenesis. Thus, inhibition of mortalin is a promising avenue for cancer therapy. Previous studies in our lab have suggested that mortalin contributes to breast cancer development and progression. We showed that tumor extracellular vesicle secretion was decreased by knockdown of mortalin expression using HIV-1 Nef SMR peptides. Specifically, these peptides can block extracellular vesicle secretion and mediate cell cycle arrest in MDA-MB-231 and MCF-7 breast cancer cells. Aims: This study aims to investigate further the function and mechanism of interaction of PEG-SMR-CLU and SMR-CPP peptides with the chaperone protein mortalin and to explore the effect of SMR-derived peptides and mortalin expression on extracellular vesicle release and complement dependent cell toxicity in human breast cancer and leukemia cell lines. Results: Our results demonstrated additional effects reversing the tumorigenicity of these cells. First, the modified SMRwt peptides reduced the expression of the mesenchymal marker vimentin (VIM). Second, exposure to the SMRwt peptide inhibited mortalin and complement C9 expression in MDA-MB-231, MCF-7 breast cancer cells and K562 leukemia cells as measured by the Western blot analysis. Third, the SMRwt peptides blocked the cancer cells’ ability to release extracellular vesicles, which we observed blocked extracellular vesicle-mediated release of complement, re-establishing complements mediated cell death in those peptide-treated cells. Methods: We developed a series of peptides derived from the Secretion Modification Region (SMR) of HIV-1 Nef protein, modified by the addition of either a cell-penetrating peptide (CPP), a positively charged arginine-rich peptide derived from HIV-1 regulatory protein Tat, or a Clusterin-binding peptide (CLU), a molecular chaperone involved in protein secretion. Both CPP and CLU peptide sequences were added at the C-terminus of the Nef SMR peptide. The CLU-containing peptides were also modified with polyethylene glycol (PEG) to enhance solubility. After treatment of cells with the peptides, we used the MTT cell viability and complement-mediated cytotoxicity assays to confirm the inhibitory role of modified SMRwt peptides on the proliferation of MDA-MB-231 and MCF-7 breast cancer cells and K562 leukemia cells. Flow cytometry was used to determine complement mediated cell apoptosis and death. Western blot analysis was used to track SMR peptides impact on expression of mortalin, vimentin and complement C9 and to measure the expression of extracellular vesicle proteins. NanoSight analysis and acetylcholinesterase (AChE) assay were used for measuring extracellular vesicles particle size and concentration and acetylcholinesterase. Conclusions: Mortalin promotes cell proliferation, metastasis, angiogenesis, downregulate apoptotic signaling. Thus, mortalin is a potential therapeutic target for cancer immunotherapy. The novel SMRwt peptides antagonize the functions of mortalin, blocking tumor extracellular vesicle release and extracellular vesicle-mediated release of complement. This leads to decreases in breast cancer cell metastasis and allows standard treatment of these late stage tumor cells, thus having important clinical implications for late stage breast cancer chemotherapy. These findings support further investigation into the therapeutic value of the SMR peptide in cancer metastasis.
E. K. Anderson, A. F. Schmidt-May, P. K. Najeeb
et al.
We report the first experimental evidence of spontaneous electron emission from a homonuclear dimer anion through direct measurements of $\rm{Ag}_2^- \rightarrow \rm{Ag}_2 + \rm{e}^-$ decays on milliseconds and seconds time scales. This observation is very surprising as there is no avoided crossing between adiabatic energy curves to mediate such a process. The process is weak but yet dominates the decay signal after 100 ms when ensembles of internally hot Ag$_2^-$ ions are stored in the cryogenic ion-beam storage ring, DESIREE, for 10 seconds. The electron emission process is associated with an instantaneous, very large, reduction of the vibrational energy of the dimer system. This represents a dramatic deviation from a Born-Oppenheimer description of dimer dynamics.
We calculate the photoionization cross-section of a molecular endohedral. We limit ourselves to two-atomic molecules. The consideration is much more complex than for atomic endohedrals because the system even for almost spherical fullerenes has only cylindrical instead of spherical symmetry. On the other hand, molecular endohedral is more interesting since the interelectron interaction in molecules is relatively stronger than in similar atoms. We present here results of calculations of molecular hydrogen stuffed inside almost spherical fullerene. For comparison, we perform calculations also for atomic endohedral with Helium inside fullerene. The results are obtained both in the single-electron Hartree-Fock approximation and with account of multi-electron correlations in the frame of so-called random phase approximation with exchange. The presence of the fullerenes shell results in prominent oscillations in the endohedrals photoionization cross section. The role of interelectron correlations becomes clear by comparing HF and RPAE results for molecular and atomic endohedral on the one side with that for corresponding isolated molecule and atom on the other.
We analyze using Poisson equation the spatial distributions of the positive charge of carbon atomic nuclei shell and negative charge of electron clouds forming the electrostatic potential of the C60 fullerene shell as a whole. We consider also the case when an extra positive charge appears inside C60 in course of e.g. photoionization of an endohedral A@C. We demonstrate that frequently used radial square-well potential U(r) simulating the C60 shell leads to nonphysical charge densities of the shell in both cases - without and with an extra positive charge inside. We conclude that the square well U(r) modified by adding a Coulomb-potential-like term does not describe the interior polarization of the shell by the electric charge located in the center of the C60 shell. We suggest another model potential, namely that of hyperbolic cosine shape with properly adjusted parameters that is able to describe the monopole polarization of C60 shell. As a concrete illustration, we have calculated the photoionization cross-sections of H@C60 taking into account the monopole polarization of the shell in the frame of suggested model. We demonstrate that proper account of this polarization does not change the photoionization cross-section.
L. Nordestgaard, A. Tybjærg-Hansen, K. Rasmussen
et al.
BackgroundClusterin, also known as apolipoprotein J (apoJ), is one of the most abundantly expressed apolipoproteins in the brain after apolipoprotein E (apoE). Like the ε4 allele of the apolipoprotein E gene (APOE), the clusterin gene (CLU) is a risk locus for Alzheimer’s disease, and may play additional roles in atherosclerosis pathogenesis. We tested whether genetic variation in CLU was associated with either Alzheimer’s disease or atherosclerosis-related diseases.MethodsWe studied individual data on 103,987 participants from the Copenhagen General Population Study (CGPS) and the Copenhagen City Heart Study (CCHS). We genotyped a common CLU variant (rs9331896) and two common APOE variants (rs7412 and rs429358), defining the ε2, ε3, and ε4, alleles in CGPS and CCHS. All individuals in the CGPS and CCHS cohorts were followed from study inclusion to occurrence of event, death, emigration, or until 10 November 2014, whichever came first. Summary consortia data on 258,351 individuals from the International Genomics of Alzheimer’s Project (IGAP) and the Coronary Artery Disease Genome-wide Replication and Meta-analysis plus the Coronary Artery Disease (C4D) Genetics and 1000-Genomes-based genome-wide association studies (CARDIoGRAMplusC4D) were used in meta-analyses.ResultsIn CGPS and CCHS, multifactorially adjusted hazard ratios for Alzheimer’s disease, all dementia, vascular dementia, ischemic cerebrovascular disease, and ischemic heart disease were 1.18 (1.07–1.30), 1.09 (1.02–1.17), 0.96 (0.80–1.17), 1.02 (0.97–1.07), and 0.97 (0.93–1.01) per T allele, respectively. Multifactorially adjusted hazard ratios for Alzheimer’s disease and all dementia were 2.72 (2.45–3.01) and 2.21 (2.05–2.38) for the APOE ɛ4 allele. There was no interaction between rs9331896 in CLU and rs429358 (defining the ɛ4 allele) in APOE in predicting Alzheimer’s disease or all dementia (P = 0.39 and P = 0.21). In a meta-analysis including consortium data, the overall fixed- and random-effects odds ratios for Alzheimer’s disease per T allele were 1.16 (1.13–1.18) (I2 = 0.0%; P for heterogeneity = 0.89).ConclusionsA common variant in CLU was associated with a high risk of Alzheimer’s disease and all dementia in the general population but not with vascular dementia or ischemic vascular disease. Important novel aspects compared to previous studies are the incorporation of individual risk factor data, the exact causative ε4 allele, and several subtypes of dementia and atherosclerosis-related endpoints.
BackgroundThe aims of this study were to analyse the serum concentrations of clusterin (CLU) in patients with hand osteoarthritis (OA) and in healthy controls, to compare CLU levels between patients with erosive and non-erosive disease, and to examine the association of CLU levels with clinical and laboratory parameters.MethodsA total of 135 patients with hand OA (81 with erosive and 54 with non-erosive disease) and 53 healthy individuals were included in this study. All patients underwent clinical and hand joint ultrasound examination. The Australian/Canadian (AUSCAN) hand osteoarthritis index, algofunctional index and a visual analogue scale (VAS) for the measurement of pain were assessed. Serum levels of CLU were measured by an enzyme-linked immunosorbent assay (ELISA).ResultsSerum levels of CLU were significantly lower in patients with hand OA than in control subjects (p < 0.0001). In addition, patients with erosive hand OA had significantly lower CLU levels than those with non-erosive disease (p = 0.044). Negative correlations between CLU levels and pain as assessed by the AUSCAN score and the VAS were found in patients with erosive hand OA (r = − 0.275; p = 0.013 and r = − 0.220; p = 0.049, respectively).ConclusionThe present study demonstrates that lower concentrations of CLU are found in hand OA patients than in healthy individuals, especially in those with erosive disease, and that CLU concentrations have a negative association with hand pain.
Pin Wai Koh, Tiem Leong Yoon, Thong Leng Lim
et al.
Structural and electronic properties of ternary clusters AlkTilNim, where k, l, and m are integers and k + l + m = 4 are investigated. These clusters are generated and studied by performing a two-stage density functional theory (DFT) calculations using the SWVN and B3LYP functional exchange correlations. In the first stage, an unbiased global search algorithm coupled with a DFT code with a light exchange-correlation and smaller basis sets are used to generate the lowest energy cluster structures. It is then followed by further optimization using another round of DFT calculation with heavy exchanged correlations and large basis set. Electronic properties of the structures obtained via the two-stage procedure are then studied via DFT calculations. The results are illustrated in the form of ternary diagram. Our DFT calculations find that the stability of the cluster increases with the increase in the number of nickel atoms inside the clusters. Our findings provide new insight into the ternary metallic cluster through the structure, stability, chemical order and electronic properties studies.
Depending on obstetric risk, maternity care may be provided in one of two locations at hospital level: a consultant-led unit (CLU) or a midwifery-led unit (MLU). Care in a MLU is sparsely provided in Ireland, comprising as few as two units out of a total 21 maternity units. Given its potential for greater efficiencies of care and cost-savings for the state, there has been an increased interest to expand MLUs in Ireland. Yet, very little is known about women's preferences for midwifery-led care, and whether they would utilise this service when presented with the choice of delivering in a CLU or MLU. This study seeks to involve women in the future planning of maternity care by investigating their preferences for care and subsequent motivations when choosing place of birth. Qualitative research is undertaken to explore maternal preferences for these different models of care. Women only revealed a preference for the MLU when co-located with a CLU due to its close proximity to medical services. However, the results suggest women do not have a clear preference for either model of care, but rather a hybrid model of care which encompasses features of both consultant- and midwifery-led care.