scholarly journals Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Takahito Ohshiro ◽  
Masamitsu Konno ◽  
Ayumu Asai ◽  
Yuki Komoto ◽  
Akira Yamagata ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Mass Spectrometry ◽  
Cancer Cells ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Simultaneous Detection ◽  
Colorectal Cancer Cells ◽  
Base Modifications ◽  
Cell Propagation ◽  
Methylation Ratio

AbstractEpitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of sequencing methods to map transcriptome-wide RNA base modifications. We have proposed a single-molecule quantum sequencer for mapping RNA base modifications in microRNAs (miRNAs), such as N6-methyladenosine (m6A) or 5-methylcytidine (5mC), which are related to cancer cell propagation and suppression. Here, we investigated 5mC and m6A in hsa-miR-200c-5p extracted from colorectal cancer cells and determined their methylation sites and rates; the data were comparable to those determined by mass spectrometry. Furthermore, we evaluated the methylation ratio of cytidine and adenosine at each site in the sequences and its relationship. These results suggest that the methylation ratio of cytidine and adenosine is facilitated by the presence of vicinal methylation. Our work provides a robust new tool for sequencing various types of RNA base modifications in their RNA context.

scholarly journals TCF7L2 Silencing Reprograms the 4D Nucleome of Colorectal Cancer Cells

2020 ◽  
Author(s):  
Markus A. Brown ◽  
Gabrielle A. Dotson ◽  
Scott Ronquist ◽  
Georg Emons ◽  
Indika Rajapakse ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Time Series ◽  
Stem Cell ◽  
Wnt Signaling ◽  
Cancer Cells ◽  
Rna Sequencing ◽  
Chromatin Structure ◽  
Cell Phenotype ◽  
Colorectal Cancer Cells

AbstractCanonical Wnt signaling is crucial for intestinal homeostasis as the major Wnt signaling effector in the intestines, TCF4, is required for stem cell maintenance. The capability of TCF4 to maintain the stem cell phenotype is contingent upon β-catenin, a potent transcriptional activator which interacts with histone acetyltransferases and chromatin remodeling complexes. In colorectal cancer, mutations result in high levels of nuclear β-catenin causing aberrant cell growth. Here, we used RNAi to explore the influence of TCF4 on chromatin structure (Hi-C) and gene expression (RNA sequencing) across a 72-hour time series in colorectal cancer. We found that TCF4 reduction results in a disproportionate upregulation of gene expression genome-wide, including a powerful induction of SOX2. Hi-C analysis revealed a general increase in chromatin compaction across the entire time series, though this did not influence gene expression. Analysis of local chromosome organization demonstrated a TAD boundary loss which influenced the expression of a cluster of CEACAM genes on chromosome 19. Four-dimensional nucleome (4DN) analysis, which integrates structural (Hi-C) and functional (RNA sequencing) data, identified EMT and E2F as the two most deregulated pathways and LUM, TMPO, and AURKA as highly influential genes in these networks. Results from gene expression, chromatin structure, and centrality analyses were then integrated to generate a list of candidate transcription factors for reprogramming of colorectal cancer cells to a vulnerable state. The top ranked transcription factor in our analysis was c-JUN, an oncoprotein known to interact with TCF4 and β-catenin.

Theragnosis by a miR-141-3p molecular beacon: simultaneous detection and sensitization of 5-fluorouracil resistant colorectal cancer cells through the activation of the TRIM13-associated apoptotic pathway

2019 ◽  
Vol 55 (52) ◽  
pp. 7466-7469 ◽  
Author(s):  
Sung Ung Moon ◽  
Yongkeun Park ◽  
Min Geun Park ◽  
Sung Kyu Song ◽  
Seok Hoo Jeong ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Cells ◽  
Molecular Beacon ◽  
Simultaneous Detection ◽  
Apoptotic Pathway ◽  
Colorectal Cancer Cells ◽  
Therapy And Diagnosis

Schematic of the ‘therapy and diagnosis at once (theragnosis)’ for 5-FU resistant colorectal cancer using the miR-141-3p molecular beacon.

scholarly journals The Genome-Wide Analysis of Carcinoembryonic Antigen Signaling by Colorectal Cancer Cells Using RNA Sequencing

PLoS ONE ◽  
2016 ◽  
Vol 11 (9) ◽  
pp. e0161256 ◽  
Author(s):  
Olga Bajenova ◽  
Anna Gorbunova ◽  
Igor Evsyukov ◽  
Michael Rayko ◽  
Svetlana Gapon ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Carcinoembryonic Antigen ◽  
Cancer Cells ◽  
Rna Sequencing ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Colorectal Cancer Cells

scholarly journals RNA Sequencing Analysis of Molecular Basis of Sodium Butyrate-Induced Growth Inhibition on Colorectal Cancer Cell Lines

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Qianwen Zhou ◽  
Guiqin Li ◽  
Siyu Zuo ◽  
Wenjing Zhu ◽  
Xiaoqin Yuan
Keyword(s):  
Colorectal Cancer ◽  
Cell Death ◽  
Cancer Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Sodium Butyrate ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Inhibition Of Proliferation ◽  
Colorectal Cancer Cells

Butyrate is a short-chain fatty acid decomposed from dietary fiber and has been shown to have effects on inhibition of proliferation but induction of apoptosis in colorectal cancer cells. However, clinical trials have yielded ambiguous outcomes with regard to its antitumor activities. In this study, we aimed to explore the molecular mechanisms underlying the sensitivity of colorectal cancer cells to sodium butyrate (NaB). RNA sequencing was used to establish the whole-transcriptome profile in NaB-treated versus untreated colorectal cancer cells. Differentially expressed genes were bioinformatically analyzed to predict their possible involvement in NaB-triggered cell death, and the expression of eight dysregulated genes was validated by quantitative real-time PCR. We found that there were a total of 7192 genes (5720 upregulated and 1472 downregulated, fold-change ≥ 2 or ≤ 0.5 for upregulation or downregulation, q-value < 0.05) differentially expressed in NaB-treated cells as compared with the untreated controls. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that the differentially expressed genes were enriched in DNA replication, cell cycle, homologous recombination, pyrimidine metabolism, mismatch repair, and other signaling pathways and may take part in NaB-induced cell death. Among the identified factors, the MCM2-7 complex might be a target of NaB. Our findings provide an important basis for further studies of the complicate network that might regulate sensitivity of colorectal cancer cells to NaB.

scholarly journals A77 FURTHER CARACTERIZATION OF THE 67 KDA LAMININ RECEPTOR (67LR) IN COLORECTAL CANCER CELLS

2020 ◽  
Vol 3 (Supplement_1) ◽  
pp. 91-92
Author(s):  
G Cloutier ◽  
T Khalfaoui ◽  
J Beaulieu
Keyword(s):  
Colorectal Cancer ◽  
Mass Spectrometry ◽  
Cell Surface ◽  
Cancer Cells ◽  
Soluble Fraction ◽  
Laminin Receptor ◽  
Mass Spectrometry Analysis ◽  
Cell Fractionation ◽  
Spectrometry Analysis ◽  
Colorectal Cancer Cells

Abstract Background The 67 kDa laminin receptor (67LR) was the first non-integrin cell surface receptor for laminin isolated on laminin affinity columns from cancer cells in the 1980’s. Initially, 67LR is found as a cytoplasmic precursor of a 37 kDa protein, named 37LR, associated with the small ribosomal subunit. In human cells, 37LR allows the formation of the polyribosome complex and plays a key role in the initiation of translation. The mechanism by which the ribosomal protein becomes the 67LR membrane receptor is still unclear. It is presumed that the process involves post-translational modifications combined with homo or hetero-dimerization with non-associated ribosomal proteins. It has been shown that 37/67LR regulates adhesion and proliferation of normal human intestinal epithelial cells. Interestingly, overexpression of 37/67LR is correlated with aggressiveness and a poor prognosis in a wide variety of cancers. Aims The aim of this study was to confirm the overexpression of 37/67LR at the membrane of colorectal cancer cells and to identify its homo or heterodimerization partners. Methods To detect the expression of 37/67LR in colorectal cancer we performed an indirect immunofluorescence on tissues from normal and diseased colons. To confirm the presence of 67LR at the membrane of Caco-2 cells we used a cellular fractionation extraction protocol combined with ultracentrifugation and detergent treatment to separate ribosome-containing fractions from the membranes and isolate the membrane associated 67LR. Mass spectrometry analysis to study the molecular identity of 67LR was performed on immunoreactive bands corresponding to 37LR and 67LR. Results Immunolocalization of 37/67LR revealed an overexpression in colorectal cancer tissues. Following analysis by western blotting, immunoreactive 67LR protein was found in the soluble fraction after ultracentrifugation at 210,000 x g while 37LR was detected in the insoluble counterpart which was solubilized after treatment with detergent, suggesting that 37LR is associated with the membrane. Mass spectrometry analysis of these fractions indicated that 37LR was not identified in the immunoreactive bands of 67LR in the soluble fraction but identified the 67 kDa elastin binding protein, another 67 kDa cell surface laminin receptor. Conclusions These results indicate that 37LR is overexpressed in colorectal adenocarcinoma cells. Further characterization of the receptor by cell fractionation and mass spectrometry indicated that the 67 kDa immunoreactive form is not related to 37LR. Supported by CIHR. Funding Agencies CIHR

scholarly journals Long noncoding RNA and mRNA profiling in cetuximab‐resistant colorectal cancer cells by RNA sequencing analysis

2019 ◽  
Vol 8 (4) ◽  
pp. 1641-1651 ◽  
Author(s):  
Changwen Jing ◽  
Rong Ma ◽  
Haixia Cao ◽  
Zhuo Wang ◽  
Siwen Liu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Cells ◽  
Rna Sequencing ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Sequencing Analysis ◽  
Mrna Profiling ◽  
Colorectal Cancer Cells
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