Introduction: Acridine orange (AO) was first extracted from coal tar in the late nineteenth century and was used as a fluorescent dye. In this paper, we review emergent research about novel applications of AO for fluorescence surgery and cancer therapy.Materials and methods: We performed a systematic search in the MEDLINE, PubMed, Cochrane library, Google Scholar, Embase, Web of Science, and Scopus database using combinations of the term “acridine orange” with the following: “surgical oncology,”...
1h
Emerging evidence suggests that alternative splicing (AS) is modified in cancer and is associated with cancer progression. Systematic analysis of AS signature in glioblastoma (GBM) is lacking and is greatly needed. We profiled genome-wide AS events in 498 GBM patients in TCGA using RNA-seq data, and splicing network and prognostic predictor were built by integrated bioinformatics analysis. Among 45,610 AS events in 10,434 genes, we detected 1,829 AS events in 1,311 genes, and 1,667 AS events in 1,146...
1h
Hodgkin Lymphoma (HL) is a malignancy that frequently affects young adults. Although, there are effective treatments not every patient responds, necessitating the development of novel therapeutic approaches, especially for relapsed and refractory cases. The two TNF receptor family members CD30 and CD137 are expressed on Hodgkin and Reed Sternberg (HRS) cells, the malignant cells in HL. We found that this co-expression is specific for HRS cells. Based on this discovery we developed a bispecific antibody...
1h
Chronic myelogenous leukemia (CML) is a malignancy of the myeloid cell lineage characterized by a recurrent chromosomal abnormality: the Philadelphia chromosome, which results from the reciprocal translocation of the chromosomes 9 and 22. The Philadelphia chromosome contains a fusion gene called BCR-ABL1. The BCR-ABL1 codes for an aberrantly functioning tyrosine kinase that drives the malignant proliferation of the founding clone. The advent of tyrosine kinase inhibitors (TKI) represents a landmark...
13h
Patients' clinical factors and genetics factors such as anaplastic lymphoma kinase (ALK) fusion variants and BIM (Bcl-2-like 11) polymorphism were reported to be associated with clinical outcome in crizotinib-treated advanced non-small cell lung cancer (NSCLC). However, the results were still controversial. We analyzed outcome of 54 patients with known ALK fusion variants who received crizotinib for advanced NSCLC. Thirty of them had successful BIM polymorphism analysis and 6 (20%) had a BIM deletion....
13h
Clinical outcomes for patients with advanced melanoma have improved significantly with the introduction of immune checkpoint inhibitors. These agents have distinct adverse effects with the potential for heightened host immune responses manifesting as an autoimmune reaction in any organ. We report a unique case who developed pembrolizumab induced arthritis, ocular hypotony with vision loss and pulmonary interstitial fibrosis. A 57-year old gentleman with advanced melanoma was treated with pembrolizumab...
13h
Abstract Background Vedolizumab (VDZ) was approved by the Japanese Ministry of Health, Labor and Welfare in 2018 for the treatment of patients with moderate-to-severe active ulcerative colitis (UC). The comparative cost-effectiveness of VDZ compared with other biologics is unknown in Japan. This information could be useful for decision makers at the time of repricing biologics for the treatment of patients with moderate-to-severe UC. ...
1h
Abstract The use of open-source programming languages, such as R, in health decision sciences is growing and has the potential to facilitate model transparency, reproducibility, and shareability. However, realizing this potential can be challenging. Models are complex and primarily built to answer a research question, with model sharing and transparency relegated to being secondary goals. Consequently, code is often neither well documented nor systematically organized in a comprehensible...
2h
Contributors : Ken-Der Wang ; Michael KolomietsSeries Type : Expression profiling by high throughput sequencingOrganism : Zea maysISR is the initiation of a beneficial association by certain fungi in the rhizosphere followed by the establishment of belowground-aboveground signaling communication may result in the induction of heightened host resistance to foliar and stem pathogens, as well as insect pests.
1h
GSE137903 The PedBE clock estimates DNA methylation age in pediatric buccal cells [dataset 3, GECKO]
Contributors : Lisa M McEwen ; Kieran J O’Donnell ; Megan G McGill ; Rachel D Edgar ; Meaghan J Jones ; Julia L MacIsaac ; David T Lin ; Katia Ramadori ; Alexander Morin ; Nicole Gladish ; Elika Garg ; Eva Unternaehrer ; Irina Pokhvisneva ; Neerja Karnani ; Michelle Z Kee ; Torsten Klengel ; Nancy E Adler ; Ronald G Barr ; Nicole Letourneau ; Gerald F Giesbrecht ; James N Reynolds ; Darina Czamara ; Jeffrey M Armstrong ; Marilyn J Essex ; Carolina de Weerth ; Roseriet Beijers ; Marieke...
1h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLong noncoding RNAs regulating diverse cellular processes implicate in many diseases. Here, we report the identification of a novel long intergenic noncoding RNA, Linc-ASEN, expressed in prematurely senescent cells, that associates with UPF1 and represses cellular senescence by reducing p21 production transcriptionally and post-transcriptionally. The Linc-ASEN-UPF1 complex suppressed p21 transcription by recruiting...
1h
Contributors : Jin-Hong Kim ; Sangbin Han ; Sukyeong Kim ; Young-Ran GuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusOsteoarthritis (OA) is a prevalent degenerative disease, which involves progressive and irreversible destruction of cartilage matrix. Despite efforts to reconstruct cartilage matrix in osteoarthritic joints, it has been a difficult task as adult cartilage exhibits marginal repair capacity. Here we report the identification of tankyrase as...
1h
Contributors : Killian Hurley ; Carlos Villacorta-Martin ; Darrell N KottonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensiPSC derived AEC2 cells for independent validation of stable SFTPCtdTomato+ outgrowth by scRNA-seq using iPSCs
1h
Contributors : Lixing Zhan ; Lele Song ; Renxu ChangSeries Type : Non-coding RNA profiling by arrayOrganism : Mus musculusTo identify potential unique miRs that contribute to shaping the intestinal stemness in colitis, we analyzed the miRNome of colonic crypt stem cells from DSS-induced colitis mice.
1h
Contributors : Wei Li ; Chen-Min Sun ; Xu-Dong Yao ; Bo Peng ; Jun-Hua Zheng ; Min LiuSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensWe have employed circRNA microarray expression profiling as a discovery platform to identify the dysregulated circRNAs in RCC.
1h
GSE137890 Effect of miR-494-3p on LPS-treated intestinal epithelial cells isolated from C57BL/6 mice
Contributors : Lixing Zhan ; Lele Song ; Renxu ChangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe microenvironment of injured mucosa has important effects on intestinal stem cell self-renewal and reconstruction of epithelial barrier function in inflammatory bowel disease (IBD). However, the precise status of the interactions between intestinal epithelial cell (IEC) injury, particularly intestinal crypt absence, and microenvironment in IBD is not completely...
1h
Contributors : Killian Hurley ; Carlos Villacorta-Martin ; Darrell N KottonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe perform time-series global transcriptomic profiling of a directed differentiation protocol for generating alveolar epithelial type II cells (AEC2s) from pluripotent stem cells (PSCs). We analyzed 3 different timepoints in the RUES2 differentiation: 1) Day 0 undifferentiated cells, 2) Day 15 lung progenitors highly enriched in NKX2-1+...
1h
Contributors : Lixing Zhan ; Lele Song ; Renxu ChangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe microenvironment of injured mucosa has important effects on intestinal stem cell self-renewal and reconstruction of epithelial barrier function in inflammatory bowel disease (IBD). However, the precise status of the interactions between intestinal epithelial cell (IEC) injury, particularly intestinal crypt absence, and microenvironment in IBD is not completely...
1h
Series Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensLong noncoding RNAs regulating diverse cellular processes implicate in many diseases. Here, we report the identification of a novel long intergenic noncoding RNA, Linc-ASEN, expressed in prematurely senescent cells, that associates with UPF1 and represses cellular senescence by reducing p21 production transcriptionally and post-transcriptionally. The Linc-ASEN-UPF1 complex suppressed p21 transcription...
1h
GSE137883 Ultra-deep sequencing reveals pre-mRNA splicing as a sequence driven high-fidelity process
Contributors : Derrick J Reynolds ; Klemens J HertelSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAlternative splicing diversifies mRNA transcripts in human cells. While the spliceosome pairs exons with a high degree of accuracy, the rates of rare aberrant and non-canonical pre-mRNA splicing have not been evaluated at the nucleotide level to determine the quantity and identity of these events across splice junctions. Using ultra-deep sequencing the frequency...
1h
Contributors : Lisa M McEwen ; Kieran J O’Donnell ; Megan G McGill ; Rachel D Edgar ; Meaghan J Jones ; Julia L MacIsaac ; David T Lin ; Katia Ramadori ; Alexander Morin ; Nicole Gladish ; Elika Garg ; Eva Unternaehrer ; Irina Pokhvisneva ; Neerja Karnani ; Michelle Z Kee ; Torsten Klengel ; Nancy E Adler ; Ronald G Barr ; Nicole Letourneau ; Gerald F Giesbrecht ; James N Reynolds ; Darina Czamara ; Jeffrey M Armstrong ; Marilyn J Essex ; Carolina de Weerth ; Roseriet Beijers ; Marieke...
1h
Series Type : Expression profiling by high throughput sequencingOrganism : Petromyzon marinusThis SuperSeries is composed of the SubSeries listed below.
1h
Contributors : Anna Zinovyeva ; Li Li ; Isana Veksler-LublinskySeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Caenorhabditis elegansmicroRNAs (miRNAs) are potent regulators of gene expression that function in diverse developmental and physiological processes. Argonaute proteins loaded with miRNAs form the miRNA Induced Silencing Complexes (miRISCs) that repress gene expression at the post-transcriptional level. miRISCs target genes through partial sequence complementarity...
1h
Contributor : Diego RobledoSeries Type : Expression profiling by high throughput sequencingOrganism : Petromyzon marinusWe have previously shown that GABA ainhibits caspase activation and promote axon regeneration in descending neurons of the sea lamprey brainstem after a complete spinal cord injury. Here, we repeated this treatment and performed Illumina RNA sequencing studies in the brainstems of control and GABA treated animals.
1h
Contributors : Sara McArdle ; Konrad Buscher ; Yanal Ghosheh ; Akula Bala Pramod ; Jacqueline Miller ; Holger Winkels ; Dennis Wolf ; Klaus LeySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMacrophage heterogeneity within atherosclerotic plaques was explored with intravital imaging, flow cytometry, and RNA sequencing. 4 populations of cells were found with varying expression profiles and functions relevant to atherosclerosis and inflammation.
1h
Contributor : Diego RobledoSeries Type : Expression profiling by high throughput sequencingOrganism : Petromyzon marinusWe have previously shown that baclofen treatments inhibit caspase activation and promote axon regeneration in descending neurons of the sea lamprey brainstem after a complete spinal cord injury. Here, we repeated this treatment and performed Illumina RNA sequencing studies in the brainstems of control and baclofen treated animals.
1h
Contributors : Killian Hurley ; Carlos Villacorta-Martin ; Darrell N KottonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLineage tracing of individual cells during directed differentiation human iPSC into alveolospheres was performed using a lentiviral barcode labeling system (Weinreb et al., 2019).
1h
Contributors : Hoi-Hung Cheung ; Wai-Yee ChanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWS iPSC (iWS780) is a WRN-null iPSC line derived from AG00780 fibroblast. This iPSC line showed normal 46,XY karyotype. iWS780 was gene-edited by CRIPSR/Cas9 to correct the WRN point mutation. Two clones (C21 & C24) were characterized and showed expression of wild-type WRN protein after gene editing. The iPSC lines (isogenic) were subsequently differentiated into...
1h
Series Type : Other ; Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
1h
Contributors : Yaou Zhang ; Ziqiang WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo understand the global effects of B2M knock-down on host gene expression, the RNA-seq study was carried out using HSV-1 infected HeLa cells transfected with B2M siRNAs (siB2M) or negative control siRNAs (siCTRL)
1h
Series Type : OtherOrganism : Homo sapiensLong noncoding RNAs regulating diverse cellular processes implicate in many diseases. Here, we report the identification of a novel long intergenic noncoding RNA, Linc-ASEN, expressed in prematurely senescent cells, that associates with UPF1 and represses cellular senescence by reducing p21 production transcriptionally and post-transcriptionally. The Linc-ASEN-UPF1 complex suppressed p21 transcription by recruiting Polycomb Repressive Complex 1 (PRC1) and...
1h
Contributor : Penelope OttewellSeries Type : Expression profiling by arrayOrganism : Homo sapiensMDA-MB-231 human breast cancer cells were injected orthotopiclly into mammary glands 4 of female NOD SCID mice 4-weeks after sub-cutaneous implantation of human femoral bone chips. Primary tumour, bone chips containing metastatic deposits and naive bone chips were isolated and mRNA analysed for gene expression to determine genetic signitures associated with breast cancer bone metastasis.
1h
Contributors : Yaqing Zhang ; Marina Pasca di Magliano ; Richard McEachinSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRegulatory T cells (Treg) are common in the tumor microenvironment in both human pancreatic cancer and in genetically engineered mouse models of the disease. Previous studies in orthotopic syngeneic models of pancreatic cancer -recapitulated in our own data- indicated that Treg depletion results CD8+ T cell-mediated tumor regression. In...
1h
Contributors : Divyesh Patel ; Manthan Patel ; Umashankar SinghSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo study the role of CGGBP1 in regulation of CTCF occupancy, we performed CTCF ChIP-seq in HEK293T cells with three different levels of CGGBP1: (i) endogenous levels of CGGBP1 (ii) CGGBP1 knockdown, and (iii) CGGBP1 overexpression. Here, we show that CTCF binds to repeats as well as canonical CTCF-motifs and CGGBP1 determines the CTCF...
2h
Contributors : Akihito Harada ; Sumiaki Fukuda ; Yasuyuki Ohkawa ; So-ichiro FukadaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSkeletal muscle possesses the ability to adapt its size in response to milieus, which is called plasticity. Overload like resistance training induces the increment of muscle mass called muscle hypertrophy. Muscle stem cells (also known as muscle stem cells) function to supply new nuclei for myofiber during the overload in muscle....
4h
Contributors : X Wang ; D Z RudnerSeries Type : Other ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Bacillus subtilis PY79To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with...
4h
Contributors : Donghoon Lee ; Timothy E HolySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe report an approach called photoactivated intersectional physiology sequencing (PIPseq), a technique for tagging cells based on their functional properties and then harvesting them for RNA sequencing. We demonstrate that PIPseq is capable of selecting physiologically rare (
8h
Contributors : Di Wang ; Weiwei YuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Mouse BMDM is the universal cell type of studying innate immunity.This study was to analyze LPS induced innate immune respone and the relationship between serine synthesis pathway and LPS induced innate immune responeMethods: BMDM cells were treated with or without LPS for 6 hours in the pressence of phgdh inhibitor or not. Then mRNA profiles of these samles were generated...
9h
Contributors : Xiang Lu ; Yapeng SuSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensA mechanistic relationship between tumor epigenetic plasticity and nongenetic adaptive resistance to therapy is described, with MAPK inhibition of BRAF-mutant melanoma cells providing the model system. Upon inhibition, these largely melanocytic cells undergo reversible cell-state changes, ultimately yielding...
9h
Contributors : Aaron D Viny ; Ross L Levine ; Richard P KocheSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTranscriptional regulators, including the cohesin complex member STAG2, are recurrently mutated in cancer. The role of STAG2 in gene regulation, hematopoiesis, and tumor suppression remains unresolved. We show Stag2 deletion in hematopoietic stem/progenitor cells (HSPC) results in altered hematopoietic function, increased self-renewal, and...
10h
Contributors : Freddy Gonzalez Badillo ; Flavia Zisi Tegou ; Anthony J Griswold ; Alice TomeiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTumors induce tolerance towards their antigens by producing the chemokine CCL21, leading to the formation of tertiary lymphoid organs (TLOs). Ins2-CCL21 transgenic, non-obese diabetic (NOD) mice express CCL21 in pancreatic β-cells and do not develop autoimmune diabetes. We investigated by which mechanisms CCL21 expression...
10h
Contributors : Constantina Christodoulou ; Joel A Spencer ; Raphael Turcotte ; Konstantinos D Kokkaliaris ; Riccardo Panero ; Azucena Ramos ; Tatiana V Esipova ; Sergei A Vinogradov ; Sarah Rudzinskas ; Yi Zhang ; Archibald S Perkins ; Raffaele A Calogero ; Timm Schroeder ; Charles P Lin ; Fernando D CamargoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAs the biology of hematopoietic stem cells (HSCs) has been predominantly studied under transplantation...
10h
Contributors : Parmanand Malvi ; Narendra WajapeyeeSeries Type : Expression profiling by arrayOrganism : Homo sapiensMetabolic alterations that are critical for cancer cell growth and metastasis are one of the key hallmarks of cancer. Here, we show that thymidine kinase 1 (TK1) is significantly overexpressed in tumor samples from lung adenocarcinoma (LUAD) patients relative to normal controls, and this TK1 overexpression is associated with significantly reduced overall survival and cancer recurrence....
11h
Contributors : David A Tuveson ; Lindsey A BakerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis study aimed to determine what genes are differentially expressed following 2 hours' treatment with napabucasin (BBI-608) alone or in combination with NQO1 depletion.
12h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
15h
Contributors : Mafalda Santiago ; Claudia Antunes ; Marta Guedes ; Michelina Iacovino ; Michael Kyba ; Wolf Reik ; Nuno Sousa ; Luisa Pinto ; Miguel R Branco ; C J MarquesSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusTET enzymes oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), a process thought to be intermediary in an active DNA demethylation mechanism. Notably, 5hmC is highly abundant in the brain and in neuronal cells. Here we...
15h
Contributors : Ting Lu ; Hui ChengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe used RNA-seq to evaluate the global programme of gene expression after Dox inducible Yamanaka factors ectopic expression during this biological process.
15h
Contributors : Liang Cheng ; Haiyun Gan ; Xu Hua ; Tamas Ordog ; Zhiguo ZhangSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusEstablishment and subsequent maintenance of distinct chromatin domains during embryonic stem cell (ESC) differentiation are crucial for lineage specification and cell fate determination. Here we show that the histone chaperone Chromatin Assembly Factor 1 (CAF-1), which...
15h
Contributors : M Menon ; S Mohammadi ; J Davila-Velderrain ; B A Goods ; T D Cadwell ; Y Xing ; Rachamimov A Stemmer ; A K Shalek ; J C Love ; K Kellis ; B P HaflerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHere we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we...
15h
Contributors : Ting Lu ; Hui ChengSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusWe used ATAC-seq to evaluate the global programme of chromtain accessibility after Dox inducible Yamanaka factors ectopic expression during this biological process.
15h
Contributors : Farah Chali ; Serge Marty ; Giampaolo Milior ; Mélanie Morin-Brureau ; Caroline Le Duigou ; Corinne Blugeon ; Laurent Jourdren ; Etienne Savary ; Richard MilesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusLipid homeostasis is dysregulated in several forms of neurodegeneration. Here we examined changes in sterols, neutral lipids and transcripts that control their homeostasis during the neuronal death induced in the CA1 region of mouse...
15h
Future Oncology, Ahead of Print.
1h
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