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Background: Breast cancer is one of the most prevalent types of cancer in Iranian women and the second cause of death in women worldwide. Gene mutations are the key determinants of the disease; therefore, the genetic study of this disease is of paramount importance. One of the genetic evaluation methods of this disease is microarray technology, which allows the examination of the simultaneous expression of thousands of genes. Clustering is the method for analyzing high-dimension data, which we used in the present research for collecting similar genes in separated clusters. Method: A descriptive and inferential statistical analysis was carried out to evaluate unsupervised learning models of gene expression analysis and five bi-clustering methods (including PLAID (PL), Fabia, Bimax, Cheng & Church (CC), and Xmotif) were compared. For this purpose, we obtained the microarray gene expression data for lapatinib-resistant breast cancer cell lines from previously published research. The enrichment efficacy of the clusters was evaluated with gene ontology, and the results of these five models were compared with the Jaccard index, variance stability, least-square error, and goodness of fit indices. Furthermore, the results of the best model were assessed for building a genes sets network with Bayesian networks. Results: After preprocessing, clustering was performed on the data with the dimension (4710 x 18) of the genes. Four models, except for CC, successfully found bi-clusters in the data set. The data evaluation revealed that the results of the models were almost the same, but the PL model performed better than the others, finding 11 bi-clusters; this model was used to build the network of gene sets. Conclusion: According to the results, the PL method was suitable for clustering the data. Accordingly, it could be recommended for data analysis. In addition, the gene sets network formed on gene expression data was incompetent. [ABSTRACT FROM AUTHOR]

Objective. Sulfur mustard (SM) is a highly reactive alkylating agent which produces ocular, respiratory, and skin damages. Eyes are the most sensitive organ to SM due to high intrinsic metabolic and rapid turnover rate of corneal epithelium and aqueous-mucous interfaces of the cornea and conjunctiva. Here we investigate underlying molecular mechanism of SM exposure delayed effects which is still a controversial issue after about 30 years. Materials and Methods. Following ethical approval, we have analyzed serum proteome of ten severe SM exposed male patients with delayed eye symptoms with two-dimensional electrophoresis followed by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. The western blotting was used to confirm the proteins that have been identified. Results. We have identified thirteen proteins including albumin, haptoglobin, and keratin isoforms as well as immunoglobulin kappa chain which showed upregulation while transferrin and alpha 1 antitrypsin revealed downregulation in these patients in comparison with healthy control group. Conclusions. Our results elevated participation of free iron circulatory imbalance and local matrix-metalloproteinase activity in development of delayed ocular symptoms induced by SM. It demonstrates that SM induced systemic toxicity leads to some serum protein changes that continually and gradually exacerbate the ocular surface injuries. [ABSTRACT FROM AUTHOR]

Patterns obtained in two-dimensional gel electrophoresis (2- DE) in the previously published articles suggest a varying number of proteins. To seek the cause of this variation, we investigated the effect of reduction power on the overall tear proteome maps. To this end, the buffers of two reducing agents, dithiothreitol ( DTT) at nine different concentrations and di-(2-hydroxyethyl) disulfide ( HED), were examined. The assay showed that HED clearly improved 2- DE resolution, increased the number of detectable protein spots, and offered well-resolved chain regions in comparison with those treated with DTT. Furthermore, this study introduced increasing the reduction power as a remedy to increase the reproducibility of two-dimensional human tear proteome maps. In addition, the results of our assessment showed that improved reduction efficiency was accompanied by increased procedure reproducibility from 42% to 89%. [ABSTRACT FROM AUTHOR]

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer (BC) that currently lacks specific therapy options. Thus, chemotherapy continues to be the primary treatment, and developing novel targets is a top clinical focus. The androgen receptor (AR) has emerged as a therapeutic target in a subtype of TNBC, with substantial clinical benefits shown in various clinical studies. Numerous studies have shown that cancer is associated with changes in components of the cell cycle machinery. Although cell cycle cyclin-dependent kinase (CDK) 4/6 inhibitors are successful in the treatment of ER-positive BC, they are not helpful in the treatment of patients with TNBC. We investigated the possibility of combining CDK4/6 inhibitor(ribociclib) with AR inhibitor(enzalutamide) in the AR-positive TNBC cell line. Ribociclib showed an inhibitory effect in TNBC cells. Additionally, we found that enzalutamide reduced cell migration/invasion, clonogenic capacity, cell cycle progression, and cell growth in AR-positive cells. Enzalutamide therapy could increase the cytostatic impact of ribociclib in AR+ TNBC cells. Furthermore, dual inhibition of AR and CDK4/6 demonstrated synergy in an AR+ TNBC model compared to each treatment alone. [ABSTRACT FROM AUTHOR]

Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques. • The application of tags for protein purification will reduce the cost of preparing the chromatographic columns. • A suitable tagging system may provide a sufficient expression yield and high purity of the protein product. • The introduction of the self-cleavable tags and aggregating tags have been influential in the protein purification industry. • The application of the aggregating tags in a column-free manner can facilitate higher protein expression yield. • Emerging technologies, including bioinformatics, SELEX, and nanotechnology, have helped to improve technical limitations. [ABSTRACT FROM AUTHOR]

• Review of current trends of 2-DE applications in the field of proteomics. • Strengths and shortcomings of 2-DE technique. • Innovative adaptations of 2-DE for alternative applications and future prospects. Two-dimensional gel electrophoresis (2-DE) is a technique that has been widely applied in a variety of proteomics studies. It is capable of resolving complex protein mixtures into individual protein spots based on their isoelectric point and molecular weight, enabling large-scale analysis of protein expression patterns for deciphering their changes in different biological conditions. 2-DE is a powerful tool that empowers researchers to perform differential qualitative and quantitative proteome analysis and is particularly advantageous for characterizing protein isoforms and post-translationally modified proteins. Despite its popularity as the workhorse for proteomics in the past few decades, it has been gradually displaced by the more sophisticated and high-performance mass spectrometry-based methods. However, there are several variations of the 2-DE technique that have emerged as promising approaches that shine new light on specific niches that 2-DE could still contribute. In this review, we first provide an overview of the applications of 2-DE, its merits and pitfalls in the current proteomic research arena, followed by a discussion on several alternative approaches for potential future applications. [ABSTRACT FROM AUTHOR]

Mesenchymal stem cells (MSCs) are earmarked as perfect candidates for cell therapy and tissue engineering due to their capacity to differentiate into different cell types. However, their potential for application in regenerative medicine declines when the levels of the reactive oxygen and nitrogen species (RONS) increase from the physiological levels, a phenomenon which is at least inevitable in ex vivo cultures and air‐exposed damaged tissues. Increased levels of RONS can alter the patterns of osteogenic and adipogenic differentiation and inhibit proliferation, as well. Besides, oxidative stress enhances senescence and cell death, thus lowering the success rates of the MSC engraftment. Hence, in this review, we have selected some representatives of antioxidants and newly emerged nano antioxidants in three main categories, including chemical compounds, biometabolites, and protein precursors/proteins, which are proved to be effective in the treatment of MSCs. We will focus on how antioxidants can be applied to optimize the clinical usage of the MSCs and their associated signaling pathways. We have also reviewed several paralleled properties of some antioxidants and nano antioxidants which can be simultaneously used in real‐time imaging, scaffolding techniques, and other applications in addition to their primary antioxidative function. [ABSTRACT FROM AUTHOR]

Evaluating the effectiveness of drugs on an individual basis before prescribing them has an influential role in choosing a successful treatment plan. The advent of microfluidic devices has provided us with more real platforms capable of mimicking the natural microenvironment (scales, shear stress, diffusion transport, etc.). This research has introduced a truncated microfluidic gradient maker that can create a linear concentration gradient of trastuzumab (showing good correlation (r(9) = 0.9968) with simulation data) with a wide range of flow rates (20–190 µl/min) and investigate its effect on SK-BR-3 spheroid cells. The results of trastuzumab efficacy on 3D spheroid cells in the microchip were compared with the conventional 2D cell cultured by MTT assay at 24 h, 48 h, and 72 h. The results showed that trastuzumab had dose-dependent effects in both 2D and spheroid cell cultures. However, the IC50 values for trastuzumab were significantly higher in 2D cell culture (560 ± 23 µg/mL) compared to 3D spheroid models (407 ± 17 µg/mL). Moreover, compared with conventional drug sensitivity tests, this microchip required fewer samples and reagents and a lower risk of fluctuation and contamination due to automatic medium exchange. [Display omitted] • A novel truncated microfluidic chip which can generate nine different dosages of the drug in a smaller design was constructed. • Effects of the different dosages of trastuzumab on SK-BR-3 spheroids were observed. • The performance of trastuzumab on SK-BR-3 spheroids cultured in chip and 2d conventional model was compared. [ABSTRACT FROM AUTHOR]

• MERS-CoV, SARS-CoV-1/2 as members of β-CoVs family have many similar pathogenicity. • Frequency of emerging β-CoVs infections reported in males are higher than females. • Sex-hormones and X-chromosome related genes may be the cause of these sex differences. • Immune response of women might protect further against MERS, SARS-CoV1/2 infections. • Sex-based immune-responses may provide new insights for upcoming immunotherapies. Emerging beta-coronaviruses (β-CoVs), including Severe Acute Respiratory Syndrome CoV-1 (SARS-CoV-1), Middle East Respiratory Syndrome-CoV (MERS-CoV), and Severe Acute Respiratory Syndrome CoV-2 (SARS-CoV-2, the cause of COVID19) are responsible for acute respiratory illnesses in human. The epidemiological features of the SARS, MERS, and new COVID-19 have revealed sex-dependent variations in the infection, frequency, treatment, and fatality rates of these syndromes. Females are likely less susceptible to viral infections, perhaps due to their steroid hormone levels, the impact of X-linked genes, and the sex-based immune responses. Although mostly inactive, the X chromosome makes the female's immune system more robust. The extra immune-regulatory genes of the X chromosome are associated with lower levels of viral load and decreased infection rate. Moreover, a higher titer of the antibodies and their longer blood circulation half-life are involved in a more durable immune protection in females. The activation rate of the immune cells and the production of TLR7 and IFN are more prominent in females. Although the bi-allelic expression of the immune regulatory genes can sometimes lead to autoimmune reactions, the higher titer of TLR7 in females is further associated with a stronger anti-viral immune response. Considering these sex-related differences and the similarities between the SARS, MERS, and COVID-19, we will discuss them in immune responses against the β-CoVs-associated syndromes. We aim to provide information on sex-based disease susceptibility and response. A better understanding of the evasion strategies of pathogens and the host immune responses can provide worthful insights into immunotherapy, and vaccine development approaches. [ABSTRACT FROM AUTHOR]