Heterogeneity and molecular landscape of melanoma: implications for targeted therapy.

Uveal cancer (UM) offers a complex molecular landscape characterized by substantial heterogeneity, both on the genetic and epigenetic levels. This heterogeneity plays a critical position in shaping the behavior and response to therapy for this uncommon ocular malignancy. Targeted treatments with gene-specific therapeutic molecules may prove useful in overcoming radiation resistance, however, the diverse molecular makeups of UM call for a patient-specific approach in therapy procedures. We need to understand the intricate molecular landscape of UM to develop targeted treatments customized to each patient's specific genetic mutations. One of the promising approaches is using liquid biopsies, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), for detecting and monitoring the disease at the early stages. These non-invasive methods can help us identify the most effective treatment strategies for each patient. Single-cellular is a brand-new analysis platform that gives treasured insights into diagnosis, prognosis, and remedy. The incorporation of this data with known clinical and genomics information will give a better understanding of the complicated molecular mechanisms that UM diseases exploit. In this review, we focused on the heterogeneity and molecular panorama of UM, and to achieve this goal, the authors conducted an exhaustive literature evaluation spanning 1998 to 2023, using keywords like "uveal melanoma, "heterogeneity". "Targeted therapies"," "CTCs," and "single-cellular analysis".

Restoring the epigenetic landscape of lung microbiome: potential therapeutic approach for chronic respiratory diseases.

BACKGROUND: Chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD) and bronchiectasis, present significant threats to global health. Recent studies have revealed the crucial role of the lung microbiome in the development of these diseases. Pathogens have evolved complex strategies to evade the immune response, with the manipulation of host cellular epigenetic mechanisms playing a pivotal role. There is existing evidence regarding the effects of Pseudomonas on epigenetic modifications and their association with pulmonary diseases. Therefore, this study aims to directly assess the connection between Pseudomonas abundance and chronic respiratory diseases. We hope that our findings will shed light on the molecular mechanisms behind lung pathogen infections. METHODS: We analyzed data from 366 participants, including individuals with COPD, acute exacerbations of COPD (AECOPD), bronchiectasis, and healthy individuals. Previous studies have given limited attention to the impact of Pseudomonas on these groups and their comparison with healthy individuals. Two independent datasets from different ethnic backgrounds were used for external validation. Each dataset separately analyzed bacteria at the genus level. RESULTS: The study reveals that Pseudomonas, a bacterium, was consistently found in high concentrations in all chronic lung disease datasets but it was present in very low abundance in the healthy datasets. This suggests that Pseudomonas may influence cellular mechanisms through epigenetics, contributing to the development and progression of chronic respiratory diseases. CONCLUSIONS: This study emphasizes the importance of understanding the relationship between the lung microbiome, epigenetics, and the onset of chronic pulmonary disease. Enhanced recognition of molecular mechanisms and the impact of the microbiome on cellular functions, along with a better understanding of these concepts, can lead to improved diagnosis and treatment.

E74-like Factor 5 Promoter Methylation in Circulating Tumor DNA as a Potential Prognostic Marker in Breast Cancer Patients.

BACKGROUND: Epigenetic alternations, such as DNA methylation, play a crucial role in breast tumor initiation and progression. The identification of noninvasive prognostic biomarkers has great importance in cancer management. Methylated cell-free DNA (cfDNA), circulating in the blood as a convenient tumor-associated DNA marker, can be used as a minimally invasive cancer biomarker. This study aimed to evaluate the promoter methylation status of E74-like factor 5 (ELF5) tumor suppressor gene in both tumors and plasma cell-free DNA of 80 breast cancer patients, compared with normal controls. METHODS: Plasma cfDNA concentrations were measured using quantitative real-time PCR, and methylation pattern in the ELF5 gene promoter region was performed using methylation-specific polymerase chain reaction (MS-PCR) technique. RESULTS: The data revealed a statistically significant increase in cfDNA concentrations in breast cancer patients, particularly in those with higher stages of the disease, triple-negative status, and metastasis (p<0.001). ELF5 promoter region hypermethylation was observed in 70% of breast cancer patients in both plasma cfDNA and tumor tissues. Notably, all patients with lymph node involvement and distant metastatic exhibited promoter hypermethylation in the ELF5 gene. CONCLUSION: Our findings suggest that ELF5 promoter methylation in circulating DNA could serve as a potential non-invasive prognostic molecular marker in breast cancer patients. However, further studies are warranted to evaluate its diagnostic value.

A deep learning-based framework for predicting survival-associated groups in colon cancer by integrating multi-omics and clinical data.

Precise prognostic classification of patients and identifying survival subgroups and their associated genes can be important clinical references when designing treatment strategies for cancer patients. Multi-omics and data integration techniques are powerful tools to achieve this goal. This study aimed to introduce a machine learning method to integrate three types of biological data, and investigate the performance of two other methods, in identifying the survival dependency of patients. The data included TCGA RNA-seq gene expression, DNA methylation, and clinical data from 368 patients with colon cancer also we use an independent external validation data set, containing 232 samples. Three methods including, hyper-parameter optimized autoencoders (HPOAE), normal autoencoder, and penalized principal component analysis (PPCA) were used for simultaneous data integration and estimation under a COX hazards model. The HPOAE was thought to outperform other methods. The HPOAE had the Log Rank Mantel-Cox value of 14.27 ± 2, and a Breslow-Generalized Wilcoxon value of 13.13 ± 1. Ten miRNA, 11 methylated genes, and 28 mRNA all by (importance of marginal cutoff > 0.95) were identified. The study demonstrated that hsa-miR-485-5p targets both ZMYM1 and tp53, the latter of which has been previously associated with cancer in numerous studies. Furthermore, compared to other methods, the HPOAE exhibited a greater capacity for identifying survival subgroups and the genes associated with them in patients with colon cancer. However, all of the results were obtained by computational methods, and clinical and experimental studies are needed to validate these results.

Study of DACH1 Expression and its Epigenetic Regulators as Possible Breast Cancer-Related Biomarkers.

Background: Breast carcinogenesis involves both genetic and epigenetic changes. DNA methylation, as well as micro-RNA regulations, are the significant epigenetic phenomena dysregulated in breast cancer. Herein, the expression of DACH1 as a tumor suppressor gene and its promoter methylation status was analyzed in breast cancer tumors. Also, the expression of three micro RNAs (miR-217, miR-6807-3p, and miR-552), which had been previously reported to target DACH1, was assessed. Methods: The SYBR green-based Real-Time reverse transcription-PCR was used to determine DACH1 and micro-RNAs (miR-217, miR-6807-3p, and miR-552) expression in 120 ductal breast cancer tumors compared with standard control. Also, the promoter methylation pattern of DACH1 was investigated using the Methylation-specific PCR technique. Results: DACH1 expression was significantly down-regulated in breast tumors (p<0.05). About 33.5% of tumors showed DACH1 promoter hyper-methylation. The studied micro-RNAs, expression was negatively correlated with DACH1 expression. The highest expressions of miRNAs and higher DACH1 promoter methylation were observed in advanced cancer situations. The Kaplan-Meier survival curves indicated that the overall survival was significantly poor in higher miRNAs and lower DACH1 expression in breast cancer patients (p<0.002). Conclusion: DACH1 down-regulation may be associated with a poor breast cancer prognosis. The DACH1 down-regulation may be due to epigenetic regulations such as promoter methylation, especially in triple-negative cases. Other factors, such as micro-RNAs (miR-217, miR-6807-3p, and miR-552), may also have an impact. The elevated expression of miR-217, miR-6807-3p, and miR-552, maybe candidates as possible poor prognostic biomarkers in breast cancer management for further consideration.

Bystander Response Following High-Dose X-irradiation; Time-dependent Nature of GammaH2AX Foci and Cell Death Consequences.

Background: The paradigm shifts in target theory could be defined as the radiation-triggered bystander response in which the radiation deleterious effects occurred in the adjacent cells. Objective: This study aims to assess bystander response in terms of DNA damage and their possible cell death consequences following high-dose radiotherapy. Temporal characteristics of gH2AX foci as a manifestation of DNA damage were also evaluated. Material and Methods: In this experimental study, bystander response was investigated in human carcinoma cells of HeLa and HN5, neighboring those that received high doses. Medium transfer was performed from 10 Gy-irradiated donors to 1.5 Gy-irradiated recipients. GammaH2AX foci, clonogenic and apoptosis assays were investigated. The gH2AX foci time-point study was implemented 1, 4, and 24 h after the medium exchange. Results: DNA damage was enhanced in HeLa and HN5 bystander cells with the ratio of 1.27 and 1.72, respectively, which terminated in more than two-fold clonogenic survival decrease, along with gradual apoptosis increase. GammH2AX foci temporal characterization revealed maximum foci scoring at the 1 h time-point in HeLa, and also 4 h in HN5, which remained even 24 h after the medium sharing in higher level than the control group. Conclusion: The time-dependent nature of bystander-induced gH2AX foci as a DNA damage surrogate marker was highlighted with the persistent foci at 24 h. considering an outcome of bystander-induced DNA damage, predominant role of clonogenic cell death was also elicited compared to apoptosis. Moreover, the role of high-dose bystander response observed in the current work clarified bystander potential implications in radiotherapy.

Tailored design and preparation of magnetic nanocomposite particles for the isolation of exosomes.

Here, we prepared a magnetic nanocomposite system composed of a cluster of magnetite nanoparticles coated with silica shell (MSNPs) with an average diameter of 140 ± 20 nm and conjugated with CD9 antibody (AntiCD9) using different strategies including adsorption or chemical conjugation of antibody molecules to either aminated MSNPs (AMSNPs) or carboxylated MSNPs (CMSNPs). Then, MSNPs were employed to isolate exosomes from ultracentrifuge-enriched solution, PC3 cell-culture medium, or exosome-spiked simulated plasma samples. Quantitative tests using nanoparticle-tracking analysis confirmed antibody-covalently conjugated MSNPs, i.e. the AntiCD9-AMSNPs and AntiCD9-CMSNPs enabled >90% recovery of exosomes. Additionally, the exosomes isolated with AntiCD9-CMSNPs showed higher recovery efficiency compared to the AntiCD9-AMSNPs. For both nanoadsorbents, lower protein impurities amounts were obtained as compared to that of exosomes isolated by ultracentrifugation and Exocib kit. The mean diameter assessment of the isolated exosomes indicates that particles isolated by using AntiCD9-AMSNPs and AntiCD9-CMSNPs have smaller sizes (136 ± 2.64 nm and 113 ± 11.53 nm, respectively) than those obtained by UC-enriched exosomes (140.9 ± 1.6 nm) and Exocib kit (167 ± 10.53 nm). Such promising results obtained in the isolation of exosomes recommend magnetic nanocomposite as an efficient tool for the simple and fast isolation of exosomes for diagnosis applications.

Association study of Bif-1 gene expression with histopathological characteristics and hormone receptors in breast cancer.

BACKGROUND: Breast cancer is a heterogeneous disease that has various clinical outcomes. Bax-interacting factor-1 (Bif-1) is a member of the endophilin B family that generates the pro-apoptotic BCL2-Associated X (BAX) protein in response to apoptotic signals. Lack of Bif-1 inhibits the intrinsic pathway of apoptosis and enhancements the risk of tumor genesis. The present study aimed to investigate the relationship between hormone receptors (ER, PR, and HER2) status and different levels of Bif-1 gene expression in breast cancer patients. METHODS: Bif-1 gene expression was evaluated in 50 breast cancer tumors and 50 normal breast mammary tissues using the SYBR Green real-time RT-PCR technique. Multivariate and univariate analyses were used to appraise the relationship between the prognostic significance of the Bif-1 gene using SPSS software. In this study, the Bif-1 was selected as a candidate for a molecular biomarker and its expression status in breast cancer patients with hormone receptors (ER, RR, and HER2) compared to patients without these hormone receptors. RESULTS: The study showed that the relative expression of the Bif-1 gene in tissues of patients with hormone receptors in breast cancer compared to those without hormone receptors was not statistically significant. The expression levels of the Bif-1 gene in different groups were evaluated for hormone receptor status. No significant relationship was found between the Bif-1 gene expression and hormone receptors (ER, PR, and HER2) (p > 0.05). CONCLUSION: Bif-1 gene expression may be a useful prognostic marker in breast cancer.

Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers.

BACKGROUND: Aberrant levels of 5-hydroxymethylcytosine (5-hmC) can lead to cancer progression. Identification of 5-hmC-related biological pathways in cancer studies can produce better understanding of gastrointestinal (GI) cancers. We conducted a network-based analysis on 5-hmC levels extracted from circulating free DNAs (cfDNA) in GI cancers including colon, gastric, and pancreatic cancers, and from healthy donors. The co-5-hmC network was reconstructed using the weighted-gene co-expression network method. The cancer-related modules/subnetworks were detected. Preservation of three detected 5-hmC-related modules was assessed in an external dataset. The 5-hmC-related modules were functionally enriched, and biological pathways were identified. The relationship between modules was assessed using the Pearson correlation coefficient (p-value < 0.05). An elastic network classifier was used to assess the potential of the 5-hmC modules in distinguishing cancer patients from healthy individuals. To assess the efficiency of the model, the Area Under the Curve (AUC) was computed using five-fold cross-validation in an external dataset. RESULTS: The main biological pathways were the cell cycle, apoptosis, and extracellular matrix (ECM) organization. Direct association between the cell cycle and apoptosis, inverse association between apoptosis and ECM organization, and inverse association between the cell cycle and ECM organization were detected for the 5-hmC modules in GI cancers. An AUC of 92% (0.73-1.00) was observed for the predictive model including 11 genes. CONCLUSION: The intricate association between biological pathways of identified modules may reveal the hidden significance of 5-hmC in GI cancers. The identified predictive model and new biomarkers may be beneficial in cancer detection and precision medicine using liquid biopsy in the early stages.

miR-888 and E-Cadherin Levels in Ductal Carcinoma Breast Cancer as Possible Cancer-Related Markers.

Background: Cancer occurs due to genetic or epigenetic factors. Breast cancer (BC) is the most common cancer among females and is considered one of the leading causes of cancer death worldwide. Epigenetic biomarkers have proven to be important in cancer management. Methods: E-cadherin gene expression and its associated regulatory microRNA, miR-888, were studied in 60 ductal carcinoma BC patients compared with normal controls using real-time Reverse Transcription Polymerase Chain Reaction. In addition, the association of the gene and microRNA expression with hormone receptors and other clinicopathologic characteristics were assessed. The correlation between plasma and tumor miR-888 expression was studied to evaluate its potential as a marker of noninvasiveness. Results: The results showed a significant increase in expression of miR-888, and a decrease in E-cadherin expression in tumor tissues compared with normal controls. The miR-888 and E-cadherin mRNA levels showed an inverse correlation. The overexpression of miR-888 in both tumor and plasma and downregulation of E-cadherin were particularly prominent when there was nodal involvement and distant metastasis status as we well as being significantly associated with higher disease stages and triple-negative tumor hormone receptor status. The Kaplan-Meier survival curves indicated that overall survival was significantly poor in BC patients with higher miR-888 and lower E-cadherin expression. Conclusions: Our study indicated that elevated eXpression of miR-888 may be a negative prognostic factor in breast cancer.

Pan-cancer analysis of biological events on cell cycle instability in gastrointestinal cancers with integrative scoring method.

Omics data integration plays an essential role in manifesting hidden cancer insights. To detect the main combinatorial/parallel impact of cancer events, integrative approaches in pan-cancer studies must be used. Here, we assessed gastrointestinal (GI) cancers from several perspectives of genomics, transcriptomics, epigenomics, and also combinatorial impacts using a novel integrative approach to score genes. Next, scores were diffused on a signaling network and extracted subnetworks. We also implemented our new scoring method to compare upper-/lower-GI cancers, investigate the regulatory mechanisms of lncRNAs, and detect amplifications/deletions between GI and non-GI cancers. The integrative subnetwork indicated the interplay among essential protein families in the cell cycle. The copy-number-variation-related subnetwork revealed minor cell cycle and immune effects, whereas the methylation-related subnetwork revealed significant immune effects. The top-score lncRNAs indicated a distinct regulatory pattern for lower-/upper-, and accessory-GI categories. In summary, cell cycle dysfunction might be largely the consequence of combinatorial abnormalities.

LRIG1 expression and colorectal cancer prognosis.

BACKGROUND: To make the right treatment decisions about colorectal cancer (CRC) patients reliable predictive and prognostic data are needed. However, in many cases this data is not enough. Some studies suggest that LRIG1 gene (leucine-rich repeats and immunoglobulin-like domains1) has prognostic implications in different kinds of cancers. METHODS: One hundred and two patients with colorectal cancer were retrospectively analyzed for LRIG1 expression at both mRNA and protein levels. SYBR Green Real-Time RT-PCR technique was used for mRNA expression analyses and Glyceraldehyde-3-Phosphate Dehydrogenase gene (GAPDH) was considered as a reference gene for data normalization. LRIG1 protein expression was analyzed using Immunohistochemistry. Additionally, appropriate statistic analyses were used to assess the expression of LRIG1 in test and control groups. The prognostic significance of LRIG1 expression was analyzed using the univariate and multivariate analyses. RESULTS: The data revealed that the expression of LRIG1 in both mRNA and protein levels was down regulated in colorectal tumor tissues (P < 0.01) but is not clinically relevant prognostic indicator in CRC. CONCLUSIONS: Therefore, it is suggested that LRIG1 expression analyses may not be considered as an important issue when making informed and individualized clinical decisions regarding the management of colorectal cancer patients.

Association study of miR-22 and miR-335 expression levels and G2 assay related inherent radiosensitivity in peripheral blood of ductal carcinoma breast cancer patients.

Identifying patient's cellular radiosensitivity before radiotherapy (RT) in breast cancer (BC) patients allows proper alternations in routinely used treatment programs and reduces the adverse side effects in exposed patients. This study was conducted on blood samples taken from 60 women diagnosed with Invasive Ductal Carcinoma (IDC) BC (mean age: 47±9.93) and 30 healthy women (mean age: 44.43±6.7). The standard G2 assay was performed to predict cellular radiosensitivity. To investigate miR-22 and miR-335 expression levels in peripheral blood mononuclear cells (PBMCs), qPCR was performed. The sensitivity and specificity of the mentioned miRNAs were assessed by plotting the Receiver Operating Characteristic (ROC) curve. Binary logistic regression was performed to identify the miRNA involvement in BC and cellular radiosensitivity (CR) of BC patients. The frequency of spontaneous and radiation-induced chromatid breaks (CBs) was significantly different between control and patient groups (p<0.05). A cut-off value was determined to differentiate the patients with and without cellular radiosensitivity. miR-22 and miR-335 were significantly downregulated in BC patients. miRNAs expression levels were directly associated with CR. ROC curve assessment identified that both miRNAs had acceptable specificity and sensitivity in the prediction of BC and CR of BC patients. Binary logistic regression showed that both miRNAs could also predict BC successfully. Although only miR-22 was shown potent to predict CR of BC patients, both miR-22 and miR-335 might act as tumor suppressor miRNAs in BC. miR-22 and miR-335 may be promising potential biomarkers in BC prediction along with other important biomarkers. Moreover, mirR-22 might be a potential biomarker for the prediction of CR in BC patients.

Plasma GBP2 promoter methylation is associated with advanced stages in breast cancer.

Blood methylated cell-free DNA (cfDNA) as a minimally invasive cancer biomarker has great importance in cancer management. Guanylate binding protein 2 (GBP2) has been considered as a possible controlling factor in tumor development. GBP2 gene expression and its promoter methylation status in both plasma cfDNA and tumor tissues of ductal carcinoma breast cancer patients were analyzed using SYBR green comparative Real-Time RT-PCR and, Methyl-specific PCR techniques, respectively in order to find a possible cancer-related marker. The results revealed that GBP2 gene expression and promoter methylation were inversely associated. GBP2 was down-regulated in tumors with emphasis on triple negative status, nodal involvement and higher cancer stages (p<0.0001). GBP2 promoter methylation on both cfDNA and tumor tissues were positively correlated and was detected in about 88% of breast cancer patients mostly in (Lymph node positive) LN+ and higher stages. Data provided shreds of evidence that GBP2 promoter methylation in circulating DNA may be considered as a possible effective non-invasive molecular marker in poor prognostic breast cancer patients with the evidence of its relation to disease stage and lymph node metastasis. However further studies need to evaluate the involvement of GBP2 promoter methylation in progression-free survival or overall survival of the patients.

Enhanced response of radioresistant carcinoma cell line to heterogeneous dose distribution of grid; the role of high-dose bystander effect.

PURPOSE: The classical dogma that restricted the radiation effect to the directly irradiated cells has been challenged by the bystander effect. This off-target phenomenon which was manifested in adjacent cells via signaling of fully exposed cells might be involved in high-dose Grid therapy as well. Here, an in-vitro study was performed to examine the possible extent of carcinoma cells response to the inhomogeneous dose distribution of Grid irradiation in the context of the bystander effect. MATERIALS AND METHODS: Bystander effect was investigated in human carcinoma cell lines of HeLa and HN5 adjacent to those received high-dose Grid irradiation using 'medium transfer' and 'cell-to-cell contact' strategies. Based on the Grid peak-to-valley dose profile, medium transfer was exerted from 10 Gy uniformly exposed donors to 1.5 Gy uniformly irradiated recipients. Cell-contact bystander was evaluated after nonuniform dose distribution of 10 Gy Grid irradiation using cloning cylinders. GammaH2AX foci, micronucleus and clonogenic assays besides gene expression analysis were performed. RESULTS: Various parameters (ɑ/ß, D37, D50) extracted from survival curve which fitted to the Linear Quadratic model, verified more radioresistance of HN5. Survival fraction at 2 Gy (SF2) indicated as 0.42 ± 0.06 in HeLa and 0.5 ± 0.03 in HN5. The level of survival decrease, DNA damages and micronucleus of cells located in the Grid shielded areas (1.5 Gy cell-to-cell contact bystander cells) were significantly more than the values obtained from cells which were irradiated by merely uniform dose of 1.5 Gy. The gH2AX foci and micronuclei frequencies were enhanced in cell-contact bystander approximately more than 1.8 times. Relative expression of DNA damage repair pathway genes (Xrcc6 and H2afx) in bystander cells increased significantly. The most cell survival reduction (11.6 times) was revealed in the Grid bystander cells of radioresistant cell line (HN5). No statistically significant difference between 10 Gy uniform beam and Grid non-uniform beam was observed. CONCLUSIONS: Various endpoints confirmed an augmented response of cells in the valley dose region of the Grid block significantly (compared with the cells irradiated by identical dose of uniform beam), suggesting the role of high-dose bystander effect which was more pronounced in resistant carcinoma cell lines. These findings could provide a partial explanation for the Grid beneficial response seen in a number of pre-clinical and clinical studies.

Enhanced cytotoxic and genotoxic effects of gadolinium-doped ZnO nanoparticles on irradiated lung cancer cells at megavoltage radiation energies.

The purpose of this study was to investigate the radiation dose enhancement effects of gadolinium-doped zinc oxide nanoparticles (Gd-doped ZnO NPs) under the megavoltage (MV) X-ray irradiation. ZnO NPs have preferred photocatalytic properties under UV light for cancer killing. UV light has limited applications in cancer treatment and it is necessary to use X-ray photons with MV energies. In order to increase the absorption of radiation and also to enhance the imaging visualization capabilities of ZnO NPs, gadolinium (Gd) as a high atomic number element was selected for doping into the structure of ZnO NPs. Gd-doped ZnO NPs were synthesized by a chemical precipitation method and characterized by transmission electron microscopy, powder X-ray diffraction, ultraviolet-visible spectroscopy, and energy-dispersive X-ray techniques. Cellular uptake was assessed by TEM and inductively coupled plasma mass spectrometry. NPs cytotoxicity was analyzed by MTT assay and radiation dose enhancement was measured by clonogenic survival assay. Apoptosis induction, cell cycle progression, micronucleus formation and expression of DNA double-strand break repair genes of XRCC2 and XRCC4 were determined by flow cytometry, micronucleus assay, and quantitative real-time polymerase chain reaction. CT and MR imaging were used to analyze the image visualization capabilities of NPs. NPs characterization showed that highly pure crystalline Gd-doped ZnO NPs with a narrow size distribution and grain size of 9 nm were synthesized. Gd-doped ZnO NPs were distributed in the cells and showed dose-dependent toxicity. Combination of Gd-doped ZnO NPs with 6 MV X-rays induced dose-dependent radiosensitivity with sensitizer enhancement ratios (SER) of 1.47 and 1.61 for 10 and 20 µg/mL NPs concentrations. Cancer cells blocked in G1, apoptosis rates, and micronuclei formation was enhanced and inversely, the DNA repair efficiency was impaired by down regulation of the mRNA levels of XRCC2 and XRCC4 genes. Gd-doped ZnO NPs enhanced the contrasts of CT and MR images of cancer cells. Overall, the results of this study provide detailed biological insights on the dose enhancement of Gd-doped ZnO NPs at MV radiations, which would contribute to the further development of this potent theranostic platform for clinical applications.

Unearthing Regulatory Axes of Breast Cancer circRNAs Networks to Find Novel Targets and Fathom Pivotal Mechanisms.

Circular RNAs (circRNAs) possess valuable characteristics for both diagnosis and treatment of several human cancers including breast cancer (BC). In this study, we combined several systems, biology tools and approaches to identify influential BC circRNAs, miRNAs, and related mRNAs as the members of competing endogenous RNAs (ceRNAs) networks and related RNA binding proteins (RBPs) to study and decipher the BC-triggering biological processes and pathways. Rooting from the identified total of 25 co-differentially expressed circRNAs (DECs) between triple negative (TN) and luminal A subtypes of BC from microarray analysis, five hub DECs (hsa_circ_0003227, hsa_circ_0001955, hsa_circ_0020080, hsa_circ_0001666, and hsa_circ_0065173) and top eleven RBPs (AGO1, AGO2, EIF4A3, FMRP, HuR (ELAVL1), IGF2BP1, IGF2BP2, IGF2BP3, EWSR1, FUS, and PTB) were explored to form the upper stream regulatory elements. All the hub circRNAs were regarded as a super sponge having multiple miRNA response elements (MREs). Then, three BC leading miRNAs (hsa-miR-149, hsa-miR-182, and hsa-miR-383) were also introduced from merging several established ceRNAs networks. The predicted 7- and 8-mer MREs matches between hub circRNAs and leading miRNAs ensured their enduring regulatory capability. The mined downstream mRNAs of the circRNAs-miRNAs network then were presented to STRING database to form the PPI network and to decipher the issue from another point of view. The BC interconnected enriched pathways and processes guarantee the merits of the ceRNAs network's members as targetable therapeutic elements. This study suggested extensive panels of novel therapeutic targets that are in charge of BC progression, hence their impressive role cannot be excluded and needs deeper empirical laboratory designs.

Integrity and Quantity Evaluation of Plasma Cell-Free DNA in Triple Negative Breast Cancer.

BACKGROUND: Triple-Negative Breast Cancer (TNBC) is a subtype of breast cancer that lacks expression of the estrogen and progesterone receptor and does not overex-press human epidermal growth factor 2 receptor protein. TNBC is associated with special characteristics, including aggressiveness, poor prognosis, and treatment response. Non-invasive blood-based molecular markers such as cell-free DNA (cfDNA) variables have been shown to be putative markers in breast cancer prognosis. METHODS: The cfDNA quantity and integrity were assessed in a case-control study of 96 breast cancer patients including 46 triple negative and 50 non-triple negative compared with 50 unaffected controls. A quantitative real-time PCR approach based on the quantification of two amplicons of the ß-actin gene with different lengths (99 and 394 bp) was used to evaluate the integrity index 394/99. RESULTS: Both cfDNA integrity index and quality were significantly elevated in breast cancer patients but integrity index can be considered as the more reliable diagnostic marker. The statistically significant increase of cfDNA quantity and integrity was observed in TNBC patients, somehow associated with nodal metastasis (p<0.001). CONCLUSION: Elevated cfDNA concentration and integrity index in breast cancer patients compared with normal control and significant difference observed between TNBC and non-TNBC may be considered as a possible effective non-invasive diagnostic and prognostic molecular marker in breast cancer.

Association of Elevated Peripheral Blood Micronucleus Frequency and Bmi-1 mRNA Expression with Metastasis in Iranian Breast Cancer Patients

Background: In order to find cytogenetic and molecular metastasis biomarkers detectable in peripheral blood the spontaneous genomic instability expressed as micronuclei and Bmi-1 expression in peripheral blood of breast cancer (BC) patients were studied in different stages of the disease compared with unaffected first-degree relatives (FDRs) and normal control. Methods: The Cytokinesis Block Micronuclei Cytome (CBMN cyt) and nested real-time Reverse Transcription-Polymerase Chain Reaction (RT-PCR) assays, were respectively used to measure genomic instability and Bmi-1 gene expression in 160 Iranian individuals comprised of BC patients in different stages of the disease, unaffected FDRs and normal control groups. Result: The frequency of micronuclei and Bmi-1 expression were dramatically higher in distant metastasis compared with non-metastatic BC. In spite of micronucleus frequency with no association with lymph node (LN) involvement and hormone receptor status, the Bmi-1 expression level was higher in LN positive and triple negative patients. Conclusion: Our results indicate that increased genomic instability expressed as micronuclei and higher Bmi-1 expression in peripheral blood are associated with metastasis in breast cancer. Therefore implementation of micronucleus assay and Bmi-1 expression analysis in blood as possible cytogenetic and molecular biomarkers in clinical level may potentially enhance the quality of management of patients with breast cancer.

Insulin Receptor Substrate 2 mRNA Expression in Urinary Sediment Cells as a Diagnostic Marker of Nephropathy in Diabetic Patients.

INTRODUCTION: The initiation and progression of diabetic nephropathy (DN) is complex. Quantification of mRNA expression in urinary sediment cells (USCs) has emerged as a novel strategy for studying kidney diseases. Insulin requires a family of insulin receptor substrate (IRS) proteins for its physiological effects, and many reports have highlighted the role of insulin and IRS proteins in kidney physiology and disease. This study aimed to assess IRS2 expression in USCs of patients with diabetes mellitus, DN, and nondiabetic chronic kidney disease. MATERIALS AND METHODS: To quantify IRS2 expression, RNA was extracted from USCs of 223 individuals comprised of diabetes mellitus, DN, and nondiabetic chronic kidney disease as well as a healthy control group. The cDNA was synthesized and comparative TaqMan real-time reverse transcript polymerase chain reaction was used in the presence of beta actin gene as a reference gene for normalization, relative to the control. RESULTS: Our data showed that the USCs expression of IRS2 gene was significantly increased in the DN patients compared with other groups (P < .001). The IRS2 expression was not significantly different between microalbuminuria and macroalbuminuria conditions or different stages of DN, except for the end-stage renal disease where the expression was lower. CONCLUSIONS: In patients with DN, urinary mRNA expression of the IRS2 gene is associated with kidney function. Our result suggests that serial measurement of urinary expression of this gene may have a value for early detection of kidney injury in diabetic patients.