Illuminating the role of lncRNAs ROR and MALAT1 in cancer stemness state of anaplastic thyroid cancer: An exploratory study.

Background: Anaplastic thyroid cancer (ATC) is one of the most aggressive malignancies in humans that accounts for a considerable rate of cancer-associated mortality. Since conventional therapies are lacking sufficient efficacy, new treatment approaches are required. This goal could be achieved through a better understanding of the molecular pathogenesis of ATC. Thyroid tumorigenesis is initiated by a subpopulation of cells known as cancer stem cells (CSCs) with specific markers such as CD133 that confers to processes such as self-renewal and metastasis. Besides, some long non-coding RNAs (lncRNAs) promote tumorigenesis by mediating the aforementioned processes. Methods: Here, we designed an exploratory study to investigate the role of lncRNAs ROR and MALAT1 and their related genes in CSC stemness. Using magnetic-activated cell sorting (MACS), the CD133- and CD133+ subpopulations were separated in SW1736 and C643 ATC cell lines. Next, the expression profiles of the CD133 marker, MALAT1, and its associated genes (CCND1, NESTIN, MYBL2, MCL1, IQGAP1), as well as ROR and its related genes (POU5F1, SOX2, NANOG), were explored by qRT-PCR. Results: We found significant up-regulation of ROR, POU5F1, SOX2, NANOG, CD133, MALAT1, IQGAP1, and MCL1 in CD133+ SW1736 cells compared to CD133- cells. As for CD133+ C643 cells, CCND1, IQGAP1, POU5F1, SOX2, NANOG, and NESTIN were significantly up-regulated compared to CD133- cells. Conclusions: This study suggests that these lncRNAs in CD133-positive SW1736 and C643 cells might regulate stemness behaviors in ATC.

CRISPR-Based Fluorescent Reporter (CBFR) Assay for Sensitive, Specific, Inexpensive, and Visual Detection of a Specific EGFR Exon 19 Deletion in NSCLC.

Epidermal growth factor receptor (EGFR) is a transmembrane glycoprotein receptor with intracellular tyrosine kinase activity. Mutations in the EGFR gene, including deletions in exon 19 and the mutation L858R, induce responsiveness of non-small cell lung cancer (NSCLC) to a group of drugs known as tyrosine kinase inhibitors. Here, we report the development of the CRISPR-based fluorescent reporter (CBFR) assay including a two-step strategy combining PCR amplification and Cas12a-driven cleavage to detect the delE746_A750 subtype of EGFR exon 19 deletions. Sensitivity and specificity of the CBFR assay were analyzed with different concentrations of fluorescence reporter and different amounts of PCR product. The results demonstrated that increasing the fluorescent reporter to 4 µM and the PCR product to 5 µl enhanced sensitivity. The CBFR assay could detect EGFR exon 19 deletion even with a frequency of 1% in samples. In clinical NSCLC samples, optimized CBFR assay enabled visual detection of the delE746_A750 subtype in less than 1 h. The CBFR assay provides a sensitive, specific, and simple strategy designed based on a straightforward and inexpensive process. We suggest that the CBFR assay could serve as a diagnostic approach to detect mutations, deletions, and pathogens in underequipped laboratories and promote personalized therapeutic approaches.

Exploring the genetic etiology of drug-resistant epilepsy: incorporation of exome sequencing into practice.

BACKGROUND: By affecting about 50 million people worldwide, epilepsy is considered a global concern in neurology. Intolerable enough, up to » of all patients do not respond to antiepileptic drugs and have recurring seizures. Therefore, revealing the underlying etiology is quite demanding in a clinical context to improve diagnosis and disease management. METHODS: Initially, 85 patients suspected of epilepsy underwent thorough clinical and paraclinical evaluation and 24 individuals with drug-resistant epilepsy entered the study. Using whole-exome sequencing, the genetic etiology of drug-resistant epilepsy was investigated and discerned whether this method could facilitate the management of drug-resistant epilepsy through personalized medicine. Eventually, functional annotation was performed and drug-gene interaction networks were constructed to find potential therapeutic targets. RESULTS: We found eleven novel variants in various genes including IRF2BPL, ST3GAL3, and GPAA1, for which a few epilepsy-related variants are available in public databases. The overall diagnostic yield for likely pathogenic and pathogenic variants and the detection rate of novel variants were 25% and 84.6%, respectively. Based on the results, two patients were considered potential candidates for personalized medicine. The highest number of interaction with drugs was demonstrated for SCN1A, SCN2A, and GRIN2A genes. CONCLUSIONS: This study highlighted the importance of consanguineous marriage in drug-resistant epilepsy and suggested the possibility of reduced penetrance and variable expressivity in some of the autosomal dominant cases. We also suggest that whole-exome sequencing could facilitate personalized management of drug-resistant epilepsy. Regarding drug-gene interactions, some genes such as SCN1A and SCN2A might serve as therapeutic targets in drug-resistant epilepsy.

CEP104 gene may involve in the pathogenesis of a new developmental disorder other than joubert syndrome.

BACKGROUND: The CEP104 gene (OMIM: 616,690) encodes the centrosome protein 104 (CEP104) that is involved in cilia function. Pathogenic variants in this gene have been described in four patients diagnosed with Joubert syndrome (JBTS) 25. Here, we challenged the concept that pathogenic variants in CEP104 gene are only involved in the development of JBTS 25. METHODS AND RESULTS: In a clinical setting, whole-exome sequencing (WES) was applied to investigate pathogenic variants in patients with unexplained developmental delay or intellectual disability (DD/ID).WES revealed a novel homozygous nonsense variant (c.643C > T) in CEP104 (NM _014704.3) in a girl with mild intellectual disability, hypotonia, and imbalanced gait. Her brain MRI data did not show molar tooth sign (MTS) or any other brain anomalies. CONCLUSION: Our study introduced a novel variant in the CEP104 gene that results in an ID phenotype other than JBTS25. Comparison of her phenotype with that of eight previously published DD/ID patients harboring pathogenic variants in CEP104 gene revealed that more than half of them did not show JBTS related symptoms. Therefore, we suggest that the CEP104 gene might also be involved in a disorder other than JBTS 25, a point that deserves to be emerged in the OMIM database.

Alginate-based 3D cell culture technique to evaluate the half-maximal inhibitory concentration: an in vitro model of anticancer drug study for anaplastic thyroid carcinoma.

BACKGROUND: Three-dimensional (3D) cell culture methods are identified for simulating the biological microenvironment and demonstrating more similarity to in vivo circumstances. Anaplastic thyroid carcinoma (ATC) is a lethal endocrine malignancy. Despite different treatment approaches, no improvement in the survival rate of the patients has been shown. In this study, we used the 3D in vitro ATC model to investigate the cytotoxic effect of BI-847325 anticancer drug in two-dimensional (2D)- and 3D- cultured cells. METHODS: Human ATC cell lines, C643 and SW1736, were cultured in one percentage (w/v) sodium alginate. Spheroids were incubated in medium for one week. The reproducibility of the fabrication of alginate beads was evaluated. Encapsulation of the cells in alginate was examined by DAPI (4',6-diamidino-2-phenylindole) staining. Survival of alginate-encapsulated cells was evaluated by CFSE (5,6-Carboxyfluorescein N-hydroxysuccinimidyl ester) staining. The population doubling times of C643 and SW1736 cell lines cultured in 2D monolayer as well as in 3D system were calculated. The cytotoxic effect of BI-847325 on 2D- and 3D- cultured cell lines was assessed for 24-72 h by MTT [3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide] assay. Finally, the 3D culture results were compared with the 2D culture method. RESULTS: The half-maximal inhibitory concentration (IC50) values of BI-847325 were higher in 3D culture compared to 2D culture. The cytotoxicity data indicated that 3D in vitro models were more resistant to chemotherapy agents. CONCLUSIONS: The findings of this study are beneficial for developing in vitro ATC 3D models to analyze the efficacy of different chemotherapy drugs and formulations.

Circular RNA-associated ceRNA network involved in HIF-1 signalling in triple-negative breast cancer: circ_0047303 as a potential key regulator.

The aggressive and highly metastatic nature of triple-negative breast cancer (TNBC) causes patients to suffer from the poor outcome. HIF-1 signalling pathway is a prominent pathway that contributes to angiogenesis and metastasis progression in tumours. On the contrary, the undeniable importance of circular RNAs (circRNAs) as multifunctional non-coding RNAs (ncRNAs) has been identified in breast cancer. These ncRNAs owing to their high stability and specificity have been becoming a hotspot in cancer researches. circRNAs act as competing endogenous RNAs (ceRNAs) and compete with mRNAs for shared miRNAs, thus modulate gene expression. Since the most dysregulated biological functions in TNBC are associated with cellular invasion, understanding the molecular pathogenesis of these processes is a crucial step towards the development of new treatment approaches. The purpose of this study is to undermine the circRNA-associated ceRNA network involved in HIF-1 signalling in TNBC using an integrative bioinformatics approach. In the next step, the novel circ_0047303-mediated ceRNA regulatory axes have been extracted and validated across TNBC samples. We show that circ_0047303 has the highest degree in the circRNA-associated ceRNA network and shows a significant up-expression in TNBC. Moreover, our results suggest that circ_0047303 could mediate the upregulation of key angiogenesis-related genes, including HIF-1, EIF4E2 and VEGFA in TNBC through sponging the tumour-suppressive miRNAs. The circ_0047303 could be a promising molecular biomarker and/or therapeutic target for TNBC.

Interindividual immunogenic variants: Susceptibility to coronavirus, respiratory syncytial virus and influenza virus.

The coronavirus disease (Covid-19) pandemic is the most serious event of the year 2020, causing considerable global morbidity and mortality. The goal of this review is to provide a comprehensive summary of reported associations between inter-individual immunogenic variants and disease susceptibility or symptoms caused by the coronavirus strains severe acute respiratory syndrome-associated coronavirus, severe acute respiratory syndrome-associated coronavirus-2, and two of the main respiratory viruses, respiratory syncytial virus and influenza virus. The results suggest that the genetic background of the host could affect the levels of proinflammatory and anti-inflammatory cytokines and might modulate the progression of Covid-19 in affected patients. Notably, genetic variations in innate immune components such as toll-like receptors and mannose-binding lectin 2 play critical roles in the ability of the immune system to recognize coronavirus and initiate an early immune response to clear the virus and prevent the development of severe symptoms. This review provides promising clues related to the potential benefits of using immunotherapy and immune modulation for respiratory infectious disease treatment in a personalized manner.

Association of OLR1 gene polymorphisms with the risk of coronary artery disease: A systematic review and meta-analysis.

BACKGROUND: Oxidized LDL receptor 1 (OLR1) encodes LOX-1, LOXIN, and OLR1D4 transcript variants. Up-regulation of LOX-1 and down-regulation of LOXIN have an essential role in causing coronary artery disease (CAD). Discovery of risk single nucleotide polymorphisms (SNPs) in OLR1 gene is clinically important as these polymorphisms could be candidate biomarkers of CAD. OBJECTIVES: The purpose of this study is quantitative evidence synthesis on how OLR1 polymorphisms in the haplotype block impact the risk of CAD. METHODS: First, a systematic keyword-based search in PubMed, Web of Science, and Scopus was conducted. After data extraction, pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for OLR1 polymorphisms and CAD. Twelve case-control studies, including 6,238 cases and 15,773 controls, were concluded in the meta-analysis. RESULTS: Our findings demonstrate significant association of OLR1 polymorphisms in the haplotype block with CAD risk in all genetic models (allelic model: OR = 1.19, 95%CI = 1.06-1.34; additive model: OR = 1.54, 95%CI = 1.16-2.05; recessive model: OR = 1.26, 95%CI = 1.04-1.53; dominant model: OR = 1.28, 95%CI = 1.09-1.51). Subgroup analysis based on the type of polymorphism revealed that rs1050283 (3'UTR*188 C > T) and rs3736235 (IVS4-14 A > G) are more significantly associated with the risk of CAD compared to other polymorphisms in the haplotype block. CONCLUSIONS: We found a significant association between OLR1 polymorphisms in the haplotype block, especially rs1050283 and rs3736235, with CAD. We also suggest that precise determination of disease association with polymorphisms in a haplotype requires investigation of all SNPs rather than a single SNP in that specific haplotype.

Understanding the role of integrins in breast cancer invasion, metastasis, angiogenesis, and drug resistance.

Integrins are cell adhesion receptors, which are typically transmembrane glycoproteins that connect to the extracellular matrix (ECM). The function of integrins regulated by biochemical events within the cells. Understanding the mechanisms of cell growth by integrins is important in elucidating their effects on tumor progression. One of the major events in integrin signaling is integrin binding to extracellular ligands. Another event is distant signaling that gathers chemical signals from outside of the cell and transmit the signals upon cell adhesion to the inside of the cell. In normal breast tissue, integrins function as checkpoints to monitor effects on cell proliferation, while in cancer tissue these functions altered. The combination of tumor microenvironment and its associated components determines the cell fate. Hypoxia can increase the expression of several integrins. The exosomal integrins promote the growth of metastatic cells. Expression of certain integrins is associated with increased metastasis and decreased prognosis in cancers. In addition, integrin-binding proteins promote invasion and metastasis in breast cancer. Targeting specific integrins and integrin-binding proteins may provide new therapeutic approaches for breast cancer therapies. This review will examine the current knowledge of integrins' role in breast cancer.

Investigation of promoter methylation of FSCN1 gene and FSCN1 protein expression in differentiated thyroid carcinomas.

FSCN1 gene encodes an actin-bundling protein, FSCN1, which is involved in formation of actin-based structures that contribute to cell migration. High levels of FSCN1 expression is observed in cells with extended membranes and protrusions. Moreover, up-regulation of FSCN1 has been reported in several epithelial carcinomas. Therefore, FSCN1 is thought to play a role in cell movement and invasion. However, the mechanism behind FSCN1 up-regulation is not known. We investigated the expression of FSCN1 using immunohistochemistry. Methylation-specific PCR was adopted to analyze the methylation status of FSCN1 promoter as a potential regulatory mechanism in FSCN1 expression. The samples included papillary thyroid carcinoma, follicular thyroid carcinoma and goiter samples (controls). Methylation of FSCN1 promoter was observed in 50% of follicular, 48.6% of papillary and 60% of controls. The promoter was unmethylated in 16.7% of follicular samples, 5.7% of papillary samples and 26.7% of controls. In the remaining 33.3% of follicular and 45.7% of papillary samples as well as 13.3% of controls, both methylated and unmethylated alleles were amplified, a condition referred to as semi-methylation. The results showed that FSCN1 promoter was significantly hypomethylated in papillary cases while the methylation status was not significantly altered in follicular cases. On the other hand, FSCN1 was expressed in only nine papillary samples. Regarding protein expression and methylation status, we suggest that hypomethylation of FSCN1 promoter in papillary thyroid carcinoma does not lead to overexpression of FSCN1 and that there might be other regulatory mechanisms involved in FSCN1 up-regulation.

An innovative paradigm of methods in microRNAs detection: highlighting DNAzymes, the illuminators.

miRNAs are short regulatory sequences that monitor gene expression at post-transcriptional level. miRNAs play outstanding roles in cellular processes and their altered expression or aberrant function has been reported in diseases such as cancer. Furthermore, some of them serve as biomarkers for prognosis, diagnosis, and prediction of drug effectiveness as well as probable utility in the field of personalized medicine. As a result, proper and sensitive detection of miRNAs is a crucial matter. Traditional approaches including Northern blotting, Microarray, and Quantitative reverse transcription polymerase chain reaction have been extensively employed by means of miRNA detection for decades. However, these methods lack sufficient sensitivity, specificity and are labor intensive. In the recent years, DNAzyme-based assays have become strikingly attractive. The principal element in these techniques is a G-rich sequence, called the G-quadruplex, which turns into a DNAzyme with catalytic activity by addition of hemin, and subsequently allows simple and rapid detection of the target. In this review, different methods of miRNA detection, along with related advantages and disadvantages are discussed, with a special focus on DNAzymes and DNAzyme-derived methods.