Validating amino acid variants in proteogenomics using sequence coverage by multiple reads

Mass spectrometry-based proteome analysis usually implies matching mass spectra of proteolytic peptides to amino acid sequences predicted from nucleic acid sequences. At the same time, due to the stochastic nature of the method when it comes to proteome-wide analysis, in which only a fraction of peptides are selected for sequencing, the completeness of protein sequence identification is undermined. Likewise, the reliability of peptide variant identification in proteogenomic studies is suffering. We propose a way to interpret shotgun proteomics results, specifically in data-dependent acquisition mode, as protein sequence coverage by multiple reads, just as it is done in the field of nucleic acid sequencing for the calling of single nucleotide variants. Multiple reads for each position in a sequence could be provided by overlapping distinct peptides, thus, confirming the presence of certain amino acid residues in the overlapping stretch with much lower false discovery rate than conventional 1%. The source of overlapping distinct peptides are, first, miscleaved tryptic peptides in combination with their properly cleaved counterparts, and, second, peptides generated by several proteases with different specificities after the same specimen is subject to parallel digestion and analyzed separately. We illustrate this approach using publicly available multiprotease proteomic datasets and our own data generated for HEK-293 cell line digests obtained using trypsin, LysC and GluC proteases. From 5000 to 8000 protein groups are identified for each digest corresponding to up to 30% of the whole proteome coverage. Most of this coverage was provided by a single read, while up to 7% of the observed protein sequences were covered two-fold and more. The proteogenomic analysis of HEK-293 cell line revealed 36 peptide variants associated with SNP, seven of which were supported by multiple reads. The efficiency of the multiple reads approach depends strongly on the depth of proteome analysis, the digesting features such as the level of miscleavages, and will increase with the number of different proteases used in parallel proteome digestion.

Optimization and green synthesis of zinc oxide nanoparticle using Garcinia cambogia leaf and evaluation of their antioxidant and anticancer property in kidney cancer (A498) cell lines

Introduction and Aim: In 21stcentury, nanomedicine has turned out to be an emergent modulus operation for the diagnosis and treatment of cancer. The current study includes the optimization and green synthesis of zinc oxide nanoparticles from the leaves of Garcinia cambogia and interpretation of its antioxidant and anticancer activity. Materials and Methods: Synthesized ZnO NPs were investigated by UV–vis, FTIR, XRD, SEM, EDX, HR-TEM, SAED, particle size distribution and DLS analysis. Furthermore, different antioxidant assays were conducted for evaluating the antioxidant activity of (ZnO NPs) and its anticancer activity using (A498) cell lines along with non-cancerous (HEK-293) cell line using MTT assay and XTT assay. Results: The UV–visible spectrum showed an absorption peak at 277 nm that reflects surface plasmon resonance (SPR) ZnONPs. The presence of various functional groups was confirmed by FTIR analysis. XRD patterns indicated that the ZnO NPs had a single-phase nature with the wurtzite structure. SEM, TEM pictures confirmed the size and shape of synthesized Nanoparticles ranges of 11–32 nm and mostly hexagonal forms. The Zeta potential value of 57.9 mV revealed the surface charge of green synthesized ZnONPs. The cytotoxicity of the ZnO NPs with various concentrations (6.25 to 200 µg/mL) was measured in (A498) cell lines along with non-cancerous (HEK-293) cell line. After the exposure, to MTT and XTT assay, cellular morphology studies showed that the cancer cell viability decreased with increasing ZnO NP concentration. Conclusion: The synthesized ZnONPs via a green synthetic route could be developed as anti-cancer agent against cancer cells.

Using CRISPR/Cas9 System to Knock out Exon 48 in DMD Gene

Background: Out of frame mutations in DMD gene cause Duchenne Muscular Dystrophy (DMD) which is a neuromuscular progressive genetic disorder. In DMD patients, lack of dystrophin causes progressive muscle degeneration, which results in heart and respiratory failure leading to premature death. At present, there is no certain treatment for DMD. DMD gene is the largest gene in human genome by 2.2 mega base pairs and contains 79 exons. In the past few years, gene therapy has been considered a promising DMD treatment, and among various gene-editing technologies, CRISPR/Cas9 system is shown to be more precise and reliable. The aim of this study was to assess the possibility of knocking out exon 48 by using a pair of sgRNAs. Methods: A pair of guide RNAs (gRNAs) was designed to cleave DMD gene and induce deletion of exon 48. gRNAs were transfected to the HEK-293 cell line and then the deletion in genomic DNA was analyzed by PCR and subsequent Sanger sequencing. Results: Exon 48 was successfully deleted and therefore exon 47 was joined to exon 49. Conclusion: This result indicated that CRISPR/Cas9 system could be used to edit DMD gene precisely.

Phytol-Loaded Solid Lipid Nanoparticles as a Novel Anticandidal Nanobiotechnological Approach

Phytol is a diterpene alcohol and can be found as a product of the metabolism of chlorophyll in plants. This compound has been explored as a potential antimicrobial agent, but it is insoluble in water. In this study, we describe a novel approach for an interesting anticandidal drug delivery system containing phytol. Different formulations of phytol-loaded solid lipid nanoparticles (SLN) were designed and tested using a natural lipid, 1,3-distearyl-2-oleyl-glycerol (TG1). Different compositions were considered to obtain three formulations with 1:10, 1:5, and 1:3 w/w phytol/TG1 ratios. All the formulations were prepared by emulsification solvent evaporation method and had their physicochemical properties assessed. The biocompatibility assay was performed in the HEK-293 cell line and the antifungal efficacy was demonstrated in different strains of Candida ssp., including different clinical isolates. Spherical and uniform SLN (<300 nm, PdI < 0.2) with phytol-loading efficiency >65% were achieved. Phytol-loaded SLN showed a dose-dependent cytotoxic effect in the HEK-293 cell line. The three tested formulations of phytol-loaded SLN considerably enhanced the minimal inhibitory concentration of phytol against 15 strains of Candida spp. Considering the clinical isolates, the formulations containing the highest phytol/TG1 ratios showed MICs at 100%. Thus, the feasibility and potential of phytol-loaded SLN was demonstrated in vitro, being a promising nanocarrier for phytol delivery from an anticandidal approach.

S-Palmitoylation of the sodium channel Nav1.6 regulates its activity and neuronal excitability

S-Palmitoylation is a reversible post-translational lipid modification that dynamically regulates protein functions. Voltage-gated sodium channels are subjected to S-palmitoylation and exhibit altered functions in different S-palmitoylation states. Our aim was to investigate whether and how S-palmitoylation regulates Nav1.6 channel function and to identify S-palmitoylation sites that can potentially be pharmacologically targeted. Acyl-biotin exchange assay showed that Nav1.6 is modified by S-palmitoylation in the mouse brain and in a Nav1.6 stable HEK 293 cell line. Using whole-cell voltage clamp, we discovered that enhancing S-palmitoylation with palmitic acid increases Nav1.6 current, whereas blocking S-palmitoylation with 2-bromopalmitate reduces Nav1.6 current and shifts the steady-state inactivation in the hyperpolarizing direction. Three S-palmitoylation sites (Cys1169, Cys1170, and Cys1978) were identified. These sites differentially modulate distinct Nav1.6 properties. Interestingly, Cys1978 is exclusive to Nav1.6 among all Nav isoforms and is evolutionally conserved in Nav1.6 among most species. Cys1978S-palmitoylation regulates current amplitude uniquely in Nav1.6. Furthermore, we showed that eliminating S-palmitoylation at specific sites alters Nav1.6-mediated excitability in dorsal root ganglion neurons. Therefore, our study reveals S-palmitoylation as a potential isoform-specific mechanism to modulate Nav activity and neuronal excitability in physiological and diseased conditions.