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Cell free RNA

Xiaolong Wang, Yungang Yan, Chunman Zhang, Wei Wei, Xin Ai, Yongbin Pang, Ying Bian
Prostate cancer-up-regulated long noncoding RNA 1(PlncRNA-1) has been demonstrated to be increased in several cancers, which plays an oncogenic role in the development of cancer. However, the exact functions and molecular mechanism of PlncRNA-1 in the tumorigenesis of glioma has not been studied. In present work, we firstly identified that PlncRNA-1 expression levels were prominently augmented in glioma patient tissues and glioma cell lines compared with adjacent noncancerous tissue and normal cells, respectively...
April 10, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Jin-Shan Wang, Qing-Hong Liu, Xiao-Hua Cheng, Wen-Yuan Zhang, Yong-Chao Jin
The incidence and mortality rate of bladder cancer have dramatically expanded, so it's urgent to discover new biomarker and therapeutic target for bladder cancer. Recently, lncRNA has been identified as oncogene or tumor suppressor to regulate the tumorigenesis. LncRNA ZFAS1 has been confirmed as oncogene in various tumors. However, the expression, function, and underlying mechanism of ZFAS1 in bladder carcinogenesis have yet to be totally clarified. In the current study, our data demonstrated that ZFAS1 expression was significantly upregulated in bladder cancer tissues and cell lines...
April 10, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Youlong Ma, Feiyue Teng, Matthew R Libera
Solid-phase oligonucleotide amplification is of interest because of possible applications to next-generation sequencing, multiplexed microarray-based detection, and cell-free synthetic biology. Its efficiency is, however, less than that of traditional liquid-phase amplification involving unconstrained primers and enzymes, and understanding how to optimize the solid-phase amplification process remains challenging. Here we demonstrate the concept of solid-phase nucleic acid sequence based amplification (SP-NASBA) and use it to study the effect of tethering density on amplification efficiency...
April 13, 2018: Analytical Chemistry
Zhenlu Zhang, Guijuan He, Gil-Soo Han, Jiantao Zhang, Nicholas Catanzaro, Arturo Diaz, Zujian Wu, George M Carman, Lianhui Xie, Xiaofeng Wang
Replication of positive-strand RNA viruses [(+)RNA viruses] takes place in membrane-bound viral replication complexes (VRCs). Formation of VRCs requires virus-mediated manipulation of cellular lipid synthesis. Here, we report significantly enhanced brome mosaic virus (BMV) replication and much improved cell growth in yeast cells lacking PAH1 (pah1Δ), the sole yeast ortholog of human LIPIN genes. PAH1 encodes Pah1p (phosphatidic acid phosphohydrolase), which converts phosphatidate (PA) to diacylglycerol that is subsequently used for the synthesis of the storage lipid triacylglycerol...
April 12, 2018: PLoS Pathogens
Sara Puente-Marin, Iván Nombela, Sergio Ciordia, María Carmen Mena, Verónica Chico, Julio Coll, María Del Mar Ortega-Villaizan
Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of rainbow trout RBCs. For RNA-seq, a de novo assembly was conducted, in order to create a transcriptome database for RBCs. For proteome profiling, we developed a proteomic method that combined: (a) fractionation into cytosolic and membrane fractions, (b) hemoglobin removal of the cytosolic fraction, (c) protein digestion, and (d) a novel step with pH reversed-phase peptide fractionation and final Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC ESI-MS/MS) analysis of each fraction...
April 9, 2018: Genes
Ting-Lin Yen, Chao-Chien Chang, Chi-Li Chung, Wen-Chin Ko, Chih-Hao Yang, Cheng-Ying Hsieh
Traumatic brain injury (TBI) is one of the leading causes of mortality worldwide and leads to persistent cognitive, sensory, motor dysfunction, and emotional disorders. TBI-caused primary injury results in structural damage to brain tissues. Following the primary injury, secondary injuries which are accompanied by neuroinflammation, microglial activation, and additional cell death subsequently occur. Platonin, a cyanine photosensitizing dye, has been used to treat trauma, ulcers, and some types of acute inflammation...
April 6, 2018: International Journal of Molecular Sciences
Yan Zhu, Peizhan Chen, Yisha Gao, Na Ta, Yunshuo Zhang, Jialin Cai, Yong Zhao, Shupeng Liu, Jianming Zheng
The long non-coding RNA maternally expressed gene 3 (MEG3) is frequently dysregulated in human cancers; however, its roles in colorectal cancer (CRC) development are largely unknown. Here, we reported that MEG3 was down-regulated in CRC tissues and CRC patients with lower MEG3 showed poorer overall survival and disease-free survival than those with higher MEG3 level. MEG3 over-expression represses CRC cells proliferation and migration in vivo and in vitro, while MEG3 knockdown leads to the enhanced proliferation and metastasis of CRC cells...
March 31, 2018: EBioMedicine
Zhihua Gong, Junying Chen, Jia-Nan Cheng, Chengdu Sun, Qingzhu Jia, Xinwei Diao, Bo Zhu
BACKGROUND: The benefits of immune checkpoint inhibitors for first-line treatment in patients with lung adenocarcinoma harboring EGFR mutations are unclear. The effects of ICIs depend on the tumor microenvironment (TME). Differences in TME properties between mutant and wild-type EGFR have not been fully characterized. PATIENTS AND METHODS: We collected 105 surgically resected (50 EGFR mutated and 55 EGFR wild-type), treatment-naïve lung adenocarcinoma tissues with clinical data to investigate the landscape and compartmentalization of tumor-infiltrating immune cells with respect to EGFR status by immunohistochemistry...
March 17, 2018: Clinical Lung Cancer
Megan E Capozzi, Meredith J Giblin, John S Penn
Chronic hyperglycemia is thought to be the major stimulator of retinal dysfunction in diabetic retinopathy (DR). Thus, many diabetes-related systemic factors have been overlooked as inducers of DR pathology. Cell culture models of retinal cell types are frequently used to mechanistically study DR, but appropriate stimulators of DR-like factors are difficult to identify. Furthermore, elevated glucose, a gold standard for cell culture treatments, yields little to no response from many primary human retinal cells...
April 3, 2018: Scientific Reports
Hosna Jabbari, Ian Wark, Carlo Montemagno
MOTIVATION: RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades...
2018: PloS One
Xiaowei Fu, Yaqiong Zhu, Bingbing Zheng, Yeqing Zou, Chao Wang, Peng Wu, Jun Wang, Haimin Chen, Pengcheng Du, Bo Liang, Lu Fang
Kinesin family member C1 (KIFC1, also known as HSET) is a minus end-directed motor protein, which is critical in centrosome clustering. The present study investigated the expression of KIFC1 in paired hepatocellular carcinoma (HCC) tissues and adjacent non-cancerous tissues from 91 patients by immunohistochemical analysis; clinical data were concomitantly collected. KIFC1 was expressed at high levels in HCC tissues, compared with that in peritumoral tissues (54.9 vs. 14.3%; P<0.01), and its expression correlated with tumor emboli, metastasis, recurrence and time of recurrence...
March 29, 2018: International Journal of Oncology
Huan-Huan Wang, Zhi-Qiang Wu, Dong Qian, Nicholas G Zaorsky, Ming-Han Qiu, Jing-Jing Cheng, Chao Jiang, Juan Wang, Xian-Liang Zeng, Chun-Lei Liu, Li-Jun Tian, Guo-Guang Ying, Mao-Bin Meng, Xi-Shan Hao, Zhi-Yong Yuan
PURPOSE: To investigate how necroptosis (ie, programmed necrosis) is involved in killing of non-small cell lung cancer (NSCLC) after ablative hypofractionated radiation therapy (HFRT). METHODS AND MATERIALS: Deoxyribonucleic acid damage, DNA repair, and the death form of NSCLC cells were assessed after radiation therapy. The overexpression and silencing of receptor-interacting protein kinases 3 (RIP3, a key protein involved activation of necroptosis)-stable NSCLC cell lines were successfully constructed...
May 1, 2018: International Journal of Radiation Oncology, Biology, Physics
Lucy Golden-Mason, Rachel H McMahan, Michael S Kriss, Alexandra L Kilgore, Linling Cheng, Rachael J Dran, Amanda Wieland, Hugo R Rosen
Chronic hepatitis C virus (HCV) infection is characterized by dysregulated natural killer (NK) cell responses. NKs play a critical role in achieving sustained responses to interferon (IFN)-α-based therapy. Rapid sustained HCV-RNA clearance is now achieved with direct-acting antivirals (DAAs). Studies of patients receiving first-wave DAAs suggest NK functional restoration. Here, we investigate the effect of mainstream DAA treatment on NKs. We collected a prospective cohort of male HCV genotype 1-infected patients treated with ledipasvir/sofosbuvir (n = 22)...
April 2018: Hepatology Communications
Sören Müller, Sameer Agnihotri, Karsen E Shoger, Max I Myers, Nicholas Smith, Srilakshmi Chaparala, Clarence R Villanueva, Ansuman Chattopadhyay, Adrian V Lee, Lisa H Butterfield, Aaron Diaz, Hideho Okada, Ian F Pollack, Gary Kohanbash
Low-grade gliomas (LGGs) are the most common brain tumor affecting children. We recently reported an early phase clinical trial of a peptide-based vaccine, which elicited consistent antigen-specific T cell responses in pediatric LGG patients. Additionally, we observed radiologic responses of stable disease (SD), partial response (PR), and near-complete/complete response (CR) following therapy. To identify biomarkers of clinical response in peripheral blood, we performed RNA sequencing on PBMC samples collected at multiple time points...
April 5, 2018: JCI Insight
Satoshi Watanabe, Takayuki Sakurai, Shingo Nakamura, Kazuchika Miyoshi, Masahiro Sato
Recent advances in genome editing systems such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease (CRISPR/Cas9) have facilitated genomic modification in mammalian cells. However, most systems employ transient treatment with selective drugs such as puromycin to obtain the desired genome-edited cells, which often allows some untransfected cells to survive and decreases the efficiency of generating genome-edited cells. Here, we developed a novel targeted toxin-based drug-free selection system for the enrichment of genome-edited cells...
April 4, 2018: International Journal of Molecular Sciences
Anis Senoussi, Jonathan Lee Tin Wah, Yoshihiro Shimizu, Jérôme Robert, Alfonso Jaramillo, Sven Findeiss, Ilka M Axmann, André Estevez-Torres
Riboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo. However, riboregulators are generally designed in silico and tested in vivo, which provides little quantitative information about their performances, thus hindering the improvement of design algorithms...
April 4, 2018: ACS Synthetic Biology
Gloria Lozano, Rosario Francisco-Velilla, Encarnacion Martinez-Salas
Internal ribosome entry site (IRES) elements are RNA regions that recruit the translation machinery internally. Here we investigated the conformational changes and RNA dynamics of a picornavirus IRES upon incubation with distinct ribosomal fractions. Differential SHAPE analysis of the free RNA showed that nucleotides reaching the final conformation on long timescales were placed at domains 4 and 5, while candidates for long-range interactions were located in domain 3. Salt-washed ribosomes induced a fast RNA local flexibility modification of domains 2 and 3, while ribosome-associated factors changed domains 4 and 5...
April 3, 2018: Scientific Reports
Camille A Bayas, Jiarui Wang, Marissa K Lee, Jared M Schrader, Lucy Shapiro, W E Moerner
We report the dynamic spatial organization of Caulobacter crescentus RNase E (RNA degradosome) and ribosomal protein L1 (ribosome) using 3D single-particle tracking and superresolution microscopy. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. These results contrast with RNase E and ribosome distribution in Escherichia coli , where RNase E colocalizes with the cytoplasmic membrane and ribosomes accumulate in polar nucleoid-free zones...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
Jie-Feng Geng, Xing Liu, Hai-Biao Zhao, Wen-Fei Fan, Jun-Jie Geng, Xian-Zhi Liu
BACKGROUND: Both LncRNA UCA1 and miR-495 are crucial gene regulators in various disorders. This study aims to investigate their role in epilepsy and seizure-induced brain injury. METHODS: In this research, rat model of epilepsy was established by pilocarpine induction. The RNA and protein expression in hippocampal tissues and neurons were determined by qRT-PCR and western blot, respectively. The hippocampal neurons were isolated from hippocampal tissues, and treated with magnesium-free (MGF) physiological solution for epileptiform activity induction...
March 30, 2018: International Journal of Biochemistry & Cell Biology
Philipp Rosendahl, Katarzyna Plak, Angela Jacobi, Martin Kraeter, Nicole Toepfner, Oliver Otto, Christoph Herold, Maria Winzi, Maik Herbig, Yan Ge, Salvatore Girardo, Katrin Wagner, Buzz Baum, Jochen Guck
The throughput of cell mechanical characterization has recently approached that of conventional flow cytometers. However, this very sensitive, label-free approach still lacks the specificity of molecular markers. Here we developed an approach that combines real-time 1D-imaging fluorescence and deformability cytometry in one instrument (RT-FDC), thus opening many new research avenues. We demonstrated its utility by using subcellular fluorescence localization to identify mitotic cells and test for mechanical changes in those cells in an RNA interference screen...
April 2, 2018: Nature Methods
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