Cellular Cytosol Research Articles

Glucosamine and Silibinin Alter Cartilage Homeostasis through Glycosylation and Cellular Stresses in Human Chondrocyte Cells.

Osteoarthritis is more prevalent than any other form of arthritis and is characterized by the progressive mechanical deterioration of joints. Glucosamine, an amino monosaccharide, has been used for over fifty years as a dietary supplement to alleviate osteoarthritis-related discomfort. Silibinin, extracted from milk thistle, modifies the degree of glycosylation of target proteins, making it an essential component in the treatment of various diseases. In this study, we aimed to investigate the functional roles of glucosamine and silibinin in cartilage homeostasis using the TC28a2 cell line. Western blots showed that glucosamine suppressed the N-glycosylation of the gp130, EGFR, and N-cadherin proteins. Furthermore, both glucosamine and silibinin differentially decreased and increased target proteins such as gp130, Snail, and KLF4 in TC28a2 cells. We observed that both compounds dose-dependently induced the proliferation of TC28a2 cells. Our MitoSOX and DCFH-DA dye data showed that 1 µM glucosamine suppressed mitochondrial reactive oxygen species (ROS) generation and induced cytosol ROS generation, whereas silibinin induced both mitochondrial and cytosol ROS generation in TC28a2 cells. Our JC-1 data showed that glucosamine increased red aggregates, resulting in an increase in the red/green fluorescence intensity ratio, while all the tested silibinin concentrations increased the green monomers, resulting in decreases in the red/green ratio. We observed increasing subG1 and S populations and decreasing G1 and G2/M populations with increasing amounts of glucosamine, while increasing amounts of silibinin led to increases in subG1, S, and G2/M populations and decreases in G1 populations in TC28a2 cells. MTT data showed that both glucosamine and silibinin induced cytotoxicity in TC28a2 cells in a dose-dependent manner. Regarding endoplasmic reticulum stress, both compounds induced the expression of CHOP and increased the level of p-eIF2α/eIF2α. With respect to O-GlcNAcylation status, glucosamine and silibinin both reduced the levels of O-GlcNAc transferase and hypoxia-inducible factor 1 alpha. Furthermore, we examined proteins and mRNAs related to these processes. In summary, our findings demonstrated that these compounds differentially modulated cellular proliferation, mitochondrial and cytosol ROS generation, the mitochondrial membrane potential, the cell cycle profile, and autophagy. Therefore, we conclude that glucosamine and silibinin not only mediate glycosylation modifications but also regulate cellular processes in human chondrocytes.

Intracellular delivery strategies using membrane-interacting peptides and proteins.

While the cellular cytosol and organelles contain attractive targets for disease treatments, it remains a challenge to deliver therapeutic biomacromolecules to these sites. This is due to the selective permeability of the plasma and endosomal membranes, especially for large and hydrophilic therapeutic cargos such as proteins and nucleic acids. In response, many different delivery systems and molecules have been devised to help therapeutics cross these barriers to reach cytosolic targets. Among them are peptide and protein-based systems, which have several advantages over other natural and synthetic materials including their ability to interact with cell membranes. In this review, we will describe recent advances and current challenges of peptide and protein strategies that leverage cell membrane association and modulation to enable cytosolic delivery of biomacromolecule cargo. The approaches covered here include peptides and proteins derived from or inspired by natural sequences as well as those designed de novo for delivery function.

An ultra-sensitive platinized nanocavity electrode for analysis of cytosolic catecholamines in one living cell

The catecholamines, mainly dopamine (DA), are present in the cellular cytosol with low abundance, while, play key roles in various neurodegenerative disorders. Here, platinized nanocavity carbon electrodes are employed to analyze cytosolic catecholamines in a single living PC12 cell, which is not easily quantified using the classic electrodes. The confined structure and excellent conductivity in the platinized nanocavity accelerate the electron transfer of the DA, resulting in a low detection limit down to 50 nM. The sensitivity of DA detection is improved to be 10.73 pA mM−1 nm−1 in the response range of 50 nM–100 μM, which guarantees quantitative analysis of cytosolic catecholamines with low abundance. Eventually, the platinized nanocavity electrode is employed to detect cytosolic catecholamines in a single PC12 cell without an obvious interruption of cellular catecholamine level. The cytosolic catecholamines in a single PC12 cell is measured in situ to be 0.1 μM, which is achieved for the first time at the single cell level using the electrochemical method. The results demonstrate that the nanocavity electrode with a high sensitivity could offer a promising means to dynamically track catecholamines in a single cell.

Rapid plasma membrane isolation via intracellular polymerization-mediated biomolecular confinement

Plasma membrane isolation is a foundational process in membrane proteomic research, cellular vesicle studies, and biomimetic nanocarrier development, yet separation processes for this outermost layer are cumbersome and susceptible to impurities and low yield. Herein, we demonstrate that cellular cytosol can be chemically polymerized for decoupling and isolation of plasma membrane within minutes. A rapid, non-disruptive in situ polymerization technique is developed with cell membrane-permeable polyethyleneglycol-diacrylate (PEG-DA) and a blue-light-sensitive photoinitiator, lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP). The photopolymerization chemistry allows for precise control of intracellular polymerization and tunable confinement of cytosolic molecules. Upon cytosol solidification, plasma membrane proteins and vesicles are rapidly derived and purified as nucleic acids and intracellular proteins as small as 15 kDa are stably entrapped for removal. The polymerization chemistry and membrane derivation technique are broadly applicable to primary and fragile cell types, enabling facile membrane vesicle extraction from shorted-lived neutrophils and human primary CD8 T cells. The study demonstrates tunable intracellular polymerization via optimized live cell chemistry, offers a robust membrane isolation methodology with broad biomedical utility, and reveals insights on molecular crowding and confinement in polymerized cells. Statement of significanceIsolating the minute fraction of plasma membrane proteins and vesicles requires extended density gradient ultracentrifugation processes, which are susceptible to low yield and impurities. The present work demonstrates that the membrane isolation process can be vastly accelerated via a rapid, non-disruptive intracellular polymerization approach that decouples cellular cytosols from the plasma membrane. Following intracellular polymerization, high-yield plasma membrane proteins and vesicles can be derived from lysis buffer and sonication treatment, respectively. And the intracellular content entrapped within the polymerized hydrogel is readily removed within minutes. The technique has broad utility in membrane proteomic research, cellular vesicle studies, and biomimetic materials development, and the work offers insights on intracellular hydrogel-mediated molecular confinement.

Multi-view progression diagnosis of thyroid cancer by integrating platelet transcriptomes and blood routine tests

Thyroid cancer is the most common type of endocrine system cancer. The pre-cancer and early stages are usually benign or slowly growing, and do not need invasive treatments. This study investigated the challenging classification task of four classes of samples, i.e., normal controls (N), thyroid adenomas (TA), papillary thyroid cancers (PTC) and metastasized papillary thyroid cancers (MPTC). We proposed a multi-view progression diagnosis framework ThyroidBloodTest to integrate the two views of RNAseq platelet transcriptomes (View-T) and blood routine (View-B) features. Platelet transcriptome represented the molecular-level information, while the blood routine features were easy to obtain in the clinical practice. Eleven feature selection algorithms and seven classifiers were evaluated for both views. The experimental data suggested the importance of choosing appropriate data analysis algorithms and feature engineering techniques like principal component analysis (PCA). The best ThyroidBloodTest model achieved Acc = 0.8750 for the four-class classification of the N/TA/PTC/MPTC samples based on the integrated feature space of View-T and View-B. The cellular localization cytosol and three post-translational modification types acetylation/phosphorylation/ubiquitination were observed to be enriched in the proteins encoded by the View-T biomarkers. The numbers of different immune cells also contributed positively to the progression diagnosis of thyroid cancer. The proposed multi-view prediction model demonstrated the necessity of integrating both platelet transcriptomes and blood routine tests for the progression diagnosis of thyroid cancer.

The plant pathogenic bacterium Candidatus Liberibacter solanacearum induces calcium-regulated autophagy in midgut cells of its insect vector Bactericera trigonica.

Autophagy plays an important role against pathogen infection in many organisms; however, little has been done with regard to vector-borne plant and animal pathogens, that sometimes replicate and cause deleterious effects in their vectors. Candidatus Liberibacter solanacearum (CLso) is a fastidious gram-negative phloem-restricted plant pathogen and vectored by the carrot psyllid, Bactericera trigonica. The plant disease caused by this bacterium is called carrot yellows and has recently gained much importance due to worldwide excessive economical losses. Here, we demonstrate that calcium ATPase, cytosolic calcium, and most importantly Beclin-1 have a role in regulating autophagy and its association with Liberibacter inside the psyllid. The presence of CLso generates reactive oxygen species and induces the expression of detoxification enzymes in the psyllid midguts, a main site for bacteria transmission. CLso also induces the expression of both sarco/endoplasmic reticulum Ca2+pump (SERCA) and 1,4,5-trisphosphate receptors (ITPR) in midguts, resulting in high levels of calcium in the cellular cytosol. Silencing these genes individually disrupted the calcium levels in the cytosol and resulted in direct effects on autophagy and subsequently on Liberibacter persistence and transmission. Inhibiting Beclin1-phosphorylation through different calcium-induced kinases altered the expression of autophagy and CLso titers and persistence. Based on our results obtained from the midgut, we suggest the existence of a direct correlation between cytosolic calcium levels, autophagy, and CLso persistence and transmission by the carrot psyllid. IMPORTANCE Plant diseases caused by vector-borne Liberibacter species are responsible for the most important economic losses in many agricultural sectors. Preventing these diseases relies mostly on chemical sprays against the insect vectors. Knowledge-based interference with the bacteria-vector interaction remains a promising approach as a sustainable solution. For unravelling how Liberibacter exploits molecular pathways in its insect vector for transmission, here, we show that the bacterium manipulates calcium levels on both sides of the endoplasmic reticulum membrane, resulting in manipulating autophagy. Silencing genes associated with these pathways disrupted the calcium levels in the cytosol and resulted in direct effects on autophagy and Liberibacter transmission. These results demonstrate major pathways that could be exploited for manipulating and controlling the disease transmission.

Direct Measurements of FLASH-Induced Changes in Intracellular Oxygenation

The goal of our study was to characterize the dynamics of intracellular oxygen during application of radiation at conventional (CONV) and FLASH dose rates and obtain evidence for or against the oxygen depletion hypothesis as a mechanism of the FLASH effect. The measurements were performed by the phosphorescence quenching method using probe Oxyphor PtG4, which was delivered into the cellular cytosol by electroporation. Intracellular radiochemical oxygen depletion (ROD) g-value for a dose rate of 100 Gy/s in the normoxic range was found to be 0.58 ± 0.03 μM/Gy. Intracellular ROD g-values for FLASH and CONV dose rates in the normoxic range were found to be nearly equal. As in solution-based studies, intracellular ROD was found to exhibit strong dependence on oxygen concentration in the range of 0 to ∼40 μM [O2]. Depletion of oxygen in cells in vitro by a clinical dose of proton radiation delivered as FLASH is unable to produce a transient state of hypoxia and, therefore, unable to induce radioprotection. The difference between ROD g-values for FLASH and CONV dose rates, detected previously in solutions-based experiments, disappears when measurements are conducted inside cells. Understanding this phenomenon should provide additional insight into the role of oxygen in FLASH radiation therapy and help to decipher the mechanism of the FLASH effect.

The Impact of Ca2+ on Intracellular Distribution of Hemoglobin in Human Erythrocytes.

The membrane-bound hemoglobin (Hb) fraction impacts red blood cell (RBC) rheology and metabolism. Therefore, Hb-RBC membrane interactions are precisely controlled. For instance, the signaling function of membrane-bound deoxy-Hb and the structure of the docking sites in the cytosolic domain of the anion exchanger 1 (AE-1) protein are well documented; however, much less is known about the interaction of Hb variants with the erythrocyte's membrane. Here, we identified factors other than O2 availability that control Hb abundance in the membrane-bound fraction and the possible variant-specific binding selectivity of Hb to the membrane. We show that depletion of extracellular Ca2+ by chelators, or its omission from the extracellular medium, leads to membrane-bound Hb release into the cytosol. The removal of extracellular Ca2+ further triggers the redistribution of HbA0 and HbA2 variants between the membrane and the cytosol in favor of membrane-bound HbA2. Both effects are reversible and are no longer observed upon reintroduction of Ca2+ into the extracellular medium. Fluctuations of cytosolic Ca2+ also impact the pre-membrane Hb pool, resulting in the massive transfer of Hb to the cellular cytosol. We hypothesize that AE-1 is the specific membrane target and discuss the physiological outcomes and possible clinical implications of the Ca2+ regulation of the intracellular Hb distribution.

N-terminal proteoforms may engage in different protein complexes.

Alternative translation initiation and alternative splicing may give rise to N-terminal proteoforms, proteins that differ at their N-terminus compared with their canonical counterparts. Such proteoforms can have altered localizations, stabilities, and functions. Although proteoforms generated from splice variants can be engaged in different protein complexes, it remained to be studied to what extent this applies to N-terminal proteoforms. To address this, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. First, we generated a catalogue of N-terminal proteoforms found in the HEK293T cellular cytosol from which 22 pairs were selected for interactome profiling. In addition, we provide evidence for the expression of several N-terminal proteoforms, identified in our catalogue, across different human tissues, as well as tissue-specific expression, highlighting their biological relevance. Protein-protein interaction profiling revealed that the overlap of the interactomes for both proteoforms is generally high, showing their functional relation. We also showed that N-terminal proteoforms can be engaged in new interactions and/or lose several interactions compared with their canonical counterparts, thus further expanding the functional diversity of proteomes.

Next-generation materials for RNA-lipid nanoparticles: lyophilization and targeted transfection.

RNA, including mRNA, siRNA and miRNA, is part of a new class of patient treatments that prevent and treat several diseases. As an alternative to DNA therapy using plasmid DNA, RNA functions in the cellular cytosol, avoiding the potential risks of insertion into patient genomes. RNA drugs, including mRNA vaccines, need carrier materials for delivery into the patient's body. Several delivery carriers of mRNA, such as cationic polymers, lipoplexes, lipid-polymer nanoparticles and lipid nanoparticles (LNPs), have been investigated. For clinical applications, one of the most commonly selected types of RNA delivery carrier is LNPs, which are typically formed with (a) ionizable lipids, which bind to RNA; (b) cholesterol for stabilization; (c) phospholipids to form the LNPs; and (d) polyethylene glycol-conjugated lipids to prevent aggregation and provide stealth characteristics. Most RNA-LNP research has been devoted to achieving highly efficient RNA expression in vitro and in vivo. It is also necessary to study the extended storage of RNA-LNPs under mild conditions. One of the most efficient methods to store RNA-LNPs for a long time is to prepare freeze-dried (lyophilized) RNA-LNPs. Future research should include investigating LNP materials for the development of freeze-dried RNA-LNPs using optimal lipid components and compositions with optimal cryoprotectants. Furthermore, the development of sophisticated RNA-LNP materials for targeted transfection into specific tissues, organs or cells will be a future direction in the development RNA therapeutics. We will discuss the prospects for the development of next-generation RNA-LNP materials.

Uptake and stability of DNA nanostructures in cells: a cross-sectional overview of the current state of the art.

The physical and chemical properties of synthetic DNA have transformed this prototypical biopolymer into a versatile nanoscale building block material in the form of DNA nanotechnology. DNA nanotechnology is, in turn, providing unprecedented precision bioengineering for numerous biomedical applications at the nanoscale including next generation immune-modulatory materials, vectors for targeted delivery of nucleic acids, drugs, and contrast agents, intelligent sensors for diagnostics, and theranostics, which combines several of these functionalities into a single construct. Assembling a DNA nanostructure to be programmed with a specific number of targeting moieties on its surface to imbue it with concomitant cellular uptake and retention capabilities along with carrying a specific therapeutic dose is now eminently feasible due to the extraordinary self-assembling properties and high formation efficiency of these materials. However, what remains still only partially addressed is how exactly this class of materials is taken up into cells in both the native state and as targeted or chemically facilitated, along with how stable they are inside the cellular cytosol and other cellular organelles. In this minireview, we summarize what is currently reported in the literature about how (i) DNA nanostructures are taken up into cells along with (ii) what is understood about their subsequent stability in the complex multi-organelle environment of the cellular milieu along with biological fluids in general. This allows us to highlight the many challenges that still remain to overcome in understanding DNA nanostructure-cellular interactions in order to fully translate these exciting new materials.

A Novel Piggyback Strategy for mRNA Delivery Exploiting Adenovirus Entry Biology.

Molecular therapies exploiting mRNA vectors embody enormous potential, as evidenced by the utility of this technology for the context of the COVID-19 pandemic. Nonetheless, broad implementation of these promising strategies has been restricted by the limited repertoires of delivery vehicles capable of mRNA transport. On this basis, we explored a strategy based on exploiting the well characterized entry biology of adenovirus. To this end, we studied an adenovirus-polylysine (AdpL) that embodied “piggyback” transport of the mRNA on the capsid exterior of adenovirus. We hypothesized that the efficient steps of Ad binding, receptor-mediated entry, and capsid-mediated endosome escape could provide an effective pathway for transport of mRNA to the cellular cytosol for transgene expression. Our studies confirmed that AdpL could mediate effective gene transfer of mRNA vectors in vitro and in vivo. Facets of this method may offer key utilities to actualize the promise of mRNA-based therapeutics.

Subcellular localization and compartment-specific toxicokinetics of cadmium, arsenic, and zinc in brandling worm Eisenia fetida

Awareness of toxicokinetics at the subcellular level is crucial to deciphering the underlying intoxication processes of metal(loid)s, although this information is often lacking. Here, the toxicokinetics of two non-essential metal(loid)s (Cd and As) and one essential metal (Zn) in both the whole body and subcellular fractions of earthworm (Eisenia fetida) were assessed. Earthworms were exposed to natural soils originating from a gradient of metal(loid) pollution for 14 days followed by a 14-day elimination phase in clean soil. Clearly distinct toxicokinetic patterns were found in the earthworms according to the metal(loid) considered. An obvious concentration-dependent increase was observed in earthworms or subcellular compartments where no equilibrium was reached (with slow or no elimination) for Cd and As throughout the experiment. As for Zn, the earthworms were able to retain a steady-state concentration of Zn in its body or each fraction without a clear intake behavior via the dynamic trade-off between uptake and elimination at different pollution levels. These differences in toxicokinetics at the subcellular level supported the observed differences in bioaccumulation patterns and were indicative of the strategy by which non-essential and essential elements are handled by earthworms. Notably, the concentration of Cd and As in subcellular compartments showed the same pattern as for Zn in the order of cellular cytosol > cellular debris > metal-rich granules, which might be associated with the binding of non-essential/essential elements with metallothionein enriched in the cytosol. Our findings enhance the understanding of the underlying mechanisms for metal(loid) accumulation kinetics in earthworms from the perspective of subcellular partitioning, and will be beneficial for accurate risk assessment of Cd, As, and Zn.

Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol.

Ribosome profiling has revealed translation outside canonical coding sequences, including translation of short upstream ORFs, long noncoding RNAs, overlapping ORFs, ORFs in UTRs, or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling, and CRISPR-based screens showed that hundreds of ORFs derived from noncoding transcripts produce (micro)proteins, whereas other studies failed to find evidence for such types of noncanonical translation products. Here, we attempted to discover translation products from noncoding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from noncoding regions but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap-based interactome analysis of two N-terminal proteoforms originating from noncoding regions showed the functional potential of these novel proteins.

B-adrenergic/cAMP signaling in doxorubicin-induced cardiotoxicity

Doxorubicin (Dox) is one of the most commonly used chemotherapy but also one of the most cardiotoxic. As of today, only the iron chelator Dexrazoxane has been FDA and EMA approved as a cardioprotective agent for Dox but its usage is still controversial. Thus, there is an urgent need to identify new targets to develop an effective protection against Dox-induced cardiotoxicity (DIC) without compromising its anti-tumor action. Well-characterized DIC mechanisms include topoisomerase II inhibition, DNA damages, induction of ROS and bioenergetic distress that lead to cardiomyocyte death. Alternative mechanisms are emerging such as an alteration of the β-adrenergic system. Our objective here was to study DIC mechanisms with a specific focus on how Dox treatment affects the β-adrenergic/cAMP signaling cascade. We used FRET-based sensors for cAMP targeted to two different cellular compartments, cytosol and nucleus, and measured the cAMP response to the β-adrenergic agonist isoprenaline (Iso, 10 nM) in adult rat ventricular myocytes after 24 h treatment with 1 or 10 μM Dox. Basal cAMP concentration was measured by Elisa. Adenylyl cyclase (AC5 and AC6 isoforms) mRNA was measured by RT-qPCR and phosphodiesterase (PDE) isoform expression and activity by western blot and radioenzymatic assay, respectively. cAMP response to Iso was decreased by 25% at 1 μM and > 50% at 10 μM Dox in both cytosol and nucleus. The maximal response to 20 μM L858051 (a forskolin analog) + 200 μM IBMX (a PDE inhibitor) on top of Iso was also decreased by Dox. Dox treatment did not change basal cAMP level nor PDE activity, but decreased AC5 and AC6 mRNA and PDE4 protein expression. Doxorubicin treatment downregulates the β-adrenergic/cAMP cascade in ventricular myocytes by decreasing adenylyl cyclase expression and maximal activity. This may contribute to the Dox-induced cardiotoxicity mechanisms.

Effects of Functional Phenolics Dietary Supplementation on Athletes' Performance and Recovery: A Review.

In recent years, many efforts have been made to identify micronutrients or nutritional strategies capable of preventing, or at least, attenuating, exercise-induced muscle damage and oxidative stress, and improving athlete performance. The reason is that most exercises induce various changes in mitochondria and cellular cytosol that lead to the generation of reactive species and free radicals whose accumulation can be harmful to human health. Among them, supplementation with phenolic compounds seems to be a promising approach since their chemical structure, composed of catechol, pyrogallol, and methoxy groups, gives them remarkable health-promoting properties, such as the ability to suppress inflammatory processes, counteract oxidative damage, boost the immune system, and thus, reduce muscle soreness and accelerate recovery. Phenolic compounds have also already been shown to be effective in improving temporal performance and reducing psychological stress and fatigue. Therefore, the aim of this review is to summarize and discuss the current knowledge on the effects of dietary phenolics on physical performance and recovery in athletes and sports practitioners. Overall, the reports show that phenolics exert important benefits on exercise-induced muscle damage as well as play a biological/physiological role in improving physical performance.

Gap Junction-Mediated Delivery of Polymeric Macromolecules.

Cellular delivery of therapeutic macromolecules such as proteins, peptides, and nucleic acids remains limited due to inefficient transport across the cellular plasma membrane. Gap junction channels, composed of connexin proteins, provide a mechanism for direct transfer of small molecules across membranes, and recent evidence suggests that the transfer of larger, polymer-like molecules such as microRNAs may be possible. Here, we report direct evidence of gap junction-mediated transfer of polymeric macromolecules. Specifically, we examined the transport of dextran chains with molecular weights ranging from 10 to 70 kDa. We found that dextran chains of up to 40 kDa can diffuse through at least five cell layers in a gap junction-dependent manner within a 30 min time frame. Further, we evaluated the ability of connectosomes, cell-derived vesicles containing functional connexin proteins, to be loaded with dextran chains. By opening connexon hemichannel pores within the membranes of connectosomes, we found that 10 kDa dextran was loaded into more than 90% of vesicles, with reduced levels of loading for dextran chains of larger molecular weight. Upon delivering 10 kDa dextran-loaded connectosomes to cells, we further found that connectosomes transferred these membrane-impermeable molecules to the cellular cytosol with dramatically improved efficiency in comparison to the delivery of free, unencapsulated dextran. Collectively, these results reveal that polymeric macromolecules can be delivered to cells via gap junctions, suggesting that the gap junction route may be useful for the delivery of polymeric therapeutic molecules, such as nucleic acids and peptides.

MOF effectively deliver CRISPR and enhance gene-editing efficiency via MOF’s hydrolytic activity of phosphate ester bonds

Activity enhancement of gene-editing toolsets is critical not only to reverse the intractable endogenous mutagenesis, but also to develop new therapeutic modalities for clinical translation. However, the gene editing efficiency was often not fully satisfactory due to the deficient catalytic activity of CRISPR protein. Herein, we report a cocatalysis approach to improve gene editing efficiency using Zr6(μ3-O)4(μ3-OH)4-cluster-containing metal–organic framework (MOF), which can efficiently package Cpf1-encoding plasmids and deliver them into cellular cytosols. Importantly, Zr6(μ3-O)4(μ3-OH)4 cluster (building block of nanoPCN-8908) can pre-activate and hydrolyze the phosphate ester bonds (a type of key chemical bonds in between genomic DNAs needed to be cleaved before gene editing), assisting expressed Cpf1 to edit genomic loci. The editing efficiency of VEGFA and DNMT1 (two genes crucial to oncogenesis) by plasmid@nanoPCN-8908 is 5-fold and 7-fold, respectively, higher than did another MOF (ZIF-8) often used as the CRISPR vehicle. This MOF-based cocatalysis approach shows huge potential to promote the development of CRISPR gene editing technologies.

Specific changes of zinc and metallothioneins during the in vitro maturation and ageing of a retinal pigment epithelium cellular model

AbstractPurposeDuring ageing, the retinal pigment epithelium (RPE) undergoes several morphological and physiological alterations such as loss of melanin, formation of extracellular deposits and metal dyshomeostasis. We examined the age‐related changes in the transcriptome and metallome (metal content in cellular cytosol, membrane and culture media) of the ageing RPE to give an insight into the origin of risk factors linked with neurodegenerative eye diseases like AMD.MethodsWe established a primary human RPE cells culture model to study the maturation (10, 21 and 59 days in culture) and ageing (91 and 133 days in culture) of cells in vitro. We analyzed the transcriptome by RNA sequencing (RNAseq) and determined the metallome by inductively coupled plasma mass spectrometry (ICP‐MS). Localization of specific proteins was carried out by immunocytochemistry.ResultsRPE differentiation markers increased significantly from 10 to 59 days in culture, followed by a decrease from 91 days onwards, as determined by RNAseq and immunocytochemistry assays. After 59 days in culture, there was an alteration in the expression of genes associated with essential biological processes, some of them being phosphorylation, oxidation‐reduction and ion transport. Metal content (i.e., Na, P, Mg, Ca, Cu and Zn) in the cellular cytosol and membranes showed mixed tendencies with time. Interestingly, cytosolic zinc levels decreased from 10 to 59 days (maturing RPE) but increased at 91 and 133 days (ageing RPE). This biphasic change was mirrored by the gene expression changes of specific isoforms of the zinc‐binding metallothioneins including MT1G and MT2A.ConclusionsGene expression and metal content showed time‐dependent changes in the in vitro RPE cell culture model. We observed a specific association between zinc levels and metallothionein expressions during maturation and ageing that, if confirmed by further evidences, may shed light for the metal dyshomeostasis observed during AMD.

Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach

Key messagePSV infection changed the abundance of host plant’s transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and cytosol, affecting photosynthesis, translation, transcription, and splicing.Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)–Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The ‘omic’ results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)–seq data were obtained to provide new insights into PSV-P–satRNA–plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.