Advanced strategies for screening and identifying RNA-targeted small molecules: Bridging therapeutic potential and innovation by Zukela Ruzi, Daxiong Han, Kailibinuer Aierken

“…However, their dynamic nature and structural complexity have historically posed challenges in developing small molecules with high affinity and selectivity. In recent years, significant advancements in screening methodologies, such as high-throughput screening (HTS), small molecule microarrays (SMMs), and DNA-encoded libraries (DELs), have facilitated the identification of RNA-binding small molecules with enhanced specificity. …”
Get full text

Genetic Dissection of Learning and Memory in Mice by Yann S. Mineur, Wim E. Crusio, Frans Sluyter

“…Next, we briefly review more recently developed techniques, such as microarrays and RNA interference. In addition, we focus on gene-environment interactions and endophenotypes. …”
Get full text

Genetic heterogeneity in familial forms of genetic generalized epilepsy: from mono- to oligogenism by Maha Dahawi, Jean-Madeleine de Sainte Agathe, Mohamed S. Elmagzoub, Elhami A. Ahmed, Julien Buratti, Thomas Courtin, Eric Noé, Julie Bogoin, Bruno Copin, Fatima A. Elmugadam, Wasma A. Abdelgadir, Ahmed K. M. A. Ahmed, Mohamed A. Daldoum, Rayan Mamoon Ibrahim Altayeb, Mohamed Bashir, Leena Mohamed Khalid, Sahar Gamil, Sara Baldassari, Liena Elsayed, Boris Keren, Gregory Nuel, Ammar E. Ahmed, Eric Leguern

“…Moreover, a polygenic mode of inheritance is suspected in most cases. We performed SNP microarrays and whole exome sequencing in 20 families from Sudan, focusing on those with at least four affected members. …”
Get full text

Comprehensive analysis of microRNA expression profile in malignant glioma tissues by Monika Piwecka, Katarzyna Rolle, Agnieszka Belter, Anna Maria Barciszewska, Marek Żywicki, Marcin Michalak, Stanisław Nowak, Mirosława Z. Naskręt-Barciszewska, Jan Barciszewski

“…We investigated the global miRNA profile of malignant glioma tissues with miRNA microarrays, deep sequencing and meta‐analysis. We selected miRNAs that were most frequently deregulated in glioblastoma tissues, as well as in peritumoral areas, in comparison with normal human brain. …”
Get full text

Revealing new mouse epicardial cell markers through transcriptomics. by Lars Bochmann, Padmini Sarathchandra, Federica Mori, Enrique Lara-Pezzi, Domenico Lazzaro, Nadia Rosenthal

“…<h4>Methodology</h4>Using laser capture microscopy, we isolated the epicardial layer from the adult murine heart before or after cardiac infarction in wildtype mice and mice expressing a transgenic IGF-1 propeptide (mIGF-1) that enhances cardiac repair, and analyzed the transcription profile using DNA microarrays.<h4>Principal findings</h4>Expression of epithelial genes such as basonuclin, dermokine, and glycoprotein M6A are highly enriched in the epicardial layer, which maintains expression of selected embryonic genes involved in epicardial development in mIGF-1 transgenic hearts. …”
Get full text

Multi-Scale Genomic, Transcriptomic and Proteomic Analysis of Colorectal Cancer Cell Lines to Identify Novel Biomarkers. by Romina Briffa, Inhwa Um, Dana Faratian, Ying Zhou, Arran K Turnbull, Simon P Langdon, David J Harrison

“…Selecting colorectal cancer (CRC) patients likely to respond to therapy remains a clinical challenge. …”
Get full text

Nonlinear Quantitative Radiation Sensitivity Prediction Model Based on NCI-60 Cancer Cell Lines by Chunying Zhang, Luc Girard, Amit Das, Sun Chen, Guangqiang Zheng, Kai Song

“…Important radiation therapy (RT) related genes were selected by significance analysis of microarrays (SAM). …”
Get full text

Classification of gliomas based on genome-wide DNA methylation profiles and immunohistochemical analysis: a short study by Olga Taryma-Leśniak, Kamil Buczkowski, Tomasz Klepinowski, Maciej Jankowski, Szymon Retfiński, Bartłomiej Sagan, Leszek Sagan, Ewa Szutowicz, Kacper Winiarski, Marta Masztalewicz, Przemysław Nowacki, Marta Sobalska-Kwapis, Dominik Strapagiel, Wojciech Kloc, Beata Lipska-Ziętkiewicz, Ewa Iżycka-Świeszewska, Tomasz K. Wojdacz

“…The formalin-fixed paraffin-embedded (FFPE) and freshly frozen (FF) samples were analyzed using Infinium Methylation-EPIC microarrays. The diagnosis was changed in two cases, and two other cases were classified as control tissue due to the low content of neoplastic cells in examined frozen samples. …”
Get full text

Biomarker-Based Nomogram to Predict Neoadjuvant Chemotherapy Response in Muscle-Invasive Bladder Cancer by Meritxell Pérez, Juan José Lozano, Mercedes Ingelmo-Torres, Montserrat Domenech, Caterina Fernández Ramón, J. Alfred Witjes, Antoine G. van der Heijden, Maria José Requena, Antonio Coy, Ricard Calderon, Begoña Mellado, Antonio Alcaraz, Antoni Vilaseca, Maria J. Ribal

“…Gene expression patterns were analysed in 34 samples from transurethral resection of the bladder (TURB) using Illumina microarrays. The expression levels of 45 selected differentially expressed genes between responders and non-responders to NAC were validated by quantitative PCR in an independent cohort of 157 patients. …”
Get full text

Identification of components associated with thermal acclimation of photosystem II in Synechocystis sp. PCC6803. by John G Rowland, Xin Pang, Iwane Suzuki, Norio Murata, William J Simon, Antoni R Slabas

“…<h4>Methodology/findings</h4>We have analysed gene expression using whole-genome microarrays and monitored alterations in physiology during acclimation of PSII to elevated growth temperature in Synechocystis sp. …”
Get full text

Dual-targeting and steric hindrance resolution in HER2 IHC: a novel approach to improve diagnostic sensitivity by Li Luo, Xi Zhang, Linqiong Chen, Zhuohan Chen, Yuchen Wang, Kaihao Huang, Xiaoyun Lin, Hongxiang Zhu, Wangqi Du

“…Additionally, significantly higher HER2 scores were observed in most BC tissues on tissue microarrays (TMAs) compared to those diagnosed using the traditional method. …”
Get full text

p53 activation by knockdown technologies. by Mara E Robu, Jon D Larson, Aidas Nasevicius, Soraya Beiraghi, Charles Brenner, Steven A Farber, Stephen C Ekker

“…Interestingly, quantitative reverse-transcriptase PCR, microarrays and whole-mount in situ hybridization assays show that MO off-targeting effects are accompanied by diagnostic transcription of an N-terminal truncated p53 isoform that uses a recently recognized internal p53 promoter. …”
Get full text

Electrochemical Strategies for MicroRNA Quantification Leveraging Amplification and Nanomaterials: A Review by Alexander Hunt, Gymama Slaughter

“…However, conventional detection methods, such as Northern blotting, RT-PCR, and microarrays, are limited by low sensitivity, lengthy protocols, and limited specificity. …”
Get full text

Serum LncRNAs Profiles Serve as Novel Potential Biomarkers for the Diagnosis of HBV-Positive Hepatocellular Carcinoma. by Kang Wang, Wei Xing Guo, Nan Li, Chun Fang Gao, Jie Shi, Yu Fu Tang, Feng Shen, Meng Chao Wu, Shan Rong Liu, Shu Qun Cheng

“…<h4>Methods</h4>lncRNA microarrays were utilized to measure the differential expression of lncRNAs between tumor tissues and corresponding non-tumor tissues in HBV-positive hapatocellular carcinoma. uc001ncr and AX800134 were selected as candidate lncRNAs and detected in three independent cohorts containing a total of 684 participants (healthy individuals and chronic HBV patients and HBV-positive HCC patients) who were recruited between March 2011 and December 2012. …”
Get full text

Distinct roles of non-canonical poly(A) polymerases in RNA metabolism. by Salvatore San Paolo, Stepanka Vanacova, Luca Schenk, Tanja Scherrer, Diana Blank, Walter Keller, André P Gerber

“…In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA-related processes. …”
Get full text

Interleukin-13 receptor alpha 2 expression in tumor cells is associated with reduced disease-free survival in patients with luminal subtype invasive breast cancer by Hee Jung Kwon, Jung Eun Choi, Young Kyung Bae

“…Interleukin-13 receptor alpha 2 expressions were assessed by immunohistochemistry in tissue microarrays of 1283 invasive breast cancer samples, and associations between these expressions and clinicopathological variables and clinical outcomes were investigated. …”
Get full text

Inhibition of PDK modulates radiotherapy resistance in gastric cancer by Qi Zhang, Wanjia Qiao, Xiaoyu Liu, Jun Lu, Farooq Benish, Shuping Li, Xiaojun Liu

“…Abstract To explore the effect of sodium dichloroacetate (DCA), a pyruvate dehydrogenase kinase (PDK) inhibitor, on the progression of gastric cancer and resistance to radiotherapy, we analyzed histopathological microarrays from 60 gastric cancer and paracancerous tissues to determine PDK expression and its prognostic significance. 5-Ethynyl-2′-deoxyuridine (EdU) incorporation assay and Transwell migration assay were used to investigate the effects of PDK inhibition on gastric cancer cell proliferation and migration. …”
Get full text

The Response of Enterococcus faecalis V583 to Chloramphenicol Treatment by Ågot Aakra, Heidi Vebø, Ulf Indahl, Lars Snipen, Øystein Gjerstad, Merete Lunde, Ingolf F. Nes

“…Efflux of drug out of the cells may be one mechanism used by V583 to overcome the effect of chloramphenicol.…”
Get full text

Elucidation of Dysregulated Pathways Associated With Hypoxia in Oestrogen Receptor‐Negative Breast Cancer by Suad A. K. Shamis, Jean Quinn, Sara Al‐Badran, Molly McKenzie, Phimmada Hatthakarnkul, Gerard Lynch, Guang‐Yu Lian, Warapan Numprasit, Laszlo Romics Jr., Ditte Andersen, Elizabeth Mallon, Donald C. McMillan, Joanne Edwards

“…Methods Immunohistochemistry was performed to identify the prognostic role of CAIX protein expression in ER− tissue microarrays (TMAs) (n = 191). CAIX‐positive samples (n = 37) were transcriptionally profiled by TempO‐Seq and analysed by STRING. …”
Get full text

Comprehensive analysis of single-cell and bulk RNA sequencing data unveils antigen-presenting and processing fibroblasts and establishes a predictive model in gastric cancer by Chenggang Zhang, Fangqi Chen, Jie Li, Yixuan He, Juan Sun, Zicheng Zheng, Guanmo Liu, Yihua Wang, Weiming Kang, Xin Ye

“…The predictive model based on APPFRGs effectively predicts the prognosis and tumor immune status of GC.…”
Get full text