309 RNA sequencing and in silico analysis identifies an unannotated antisense long non-coding RNA involved in cancer progression

The polysome profiling method was used to separate mRNAs depending on their loading by ribosomes into polysomal and monosomal fractions. Pools separation of such mRNAs and analysis of transcripts (mRNAs) which are associated with each mRNA pool due to RNA sequencing allowed to get an idea of the translational efficiency of individual mRNAs. Moreover, subsequent in silico analysis make possible searching of regulatory contexts in the 5'-UTR of plant A. thaliana, which may be potentially important for efficient translation of mRNA.

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In silico analysis of inner ear development using public whole embryonic body single-cell RNA-sequencing data

Developmental Biology ◽

10.1016/j.ydbio.2020.10.009 ◽

2021 ◽

Vol 469 ◽

pp. 160-171

Author(s):

Ryosuke Yamamoto ◽

Hiroe Ohnishi ◽

Koichi Omori ◽

Norio Yamamoto

Keyword(s):

Single Cell ◽

Inner Ear ◽

Rna Sequencing ◽

In Silico ◽

In Silico Analysis ◽

Sequencing Data ◽

Ear Development ◽

Inner Ear Development ◽

Single Cell Rna Sequencing ◽

Silico Analysis

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SNHG7 has an oncogenic role in colorectal cancer via potential sponging of MIR-485-5P and MIR-193A-5P; in silico approach

Genetika ◽

10.2298/gensr2101065z ◽

2021 ◽

Vol 53 (1) ◽

pp. 65-78

Author(s):

Farinaz Ziaee ◽

Mohammadreza Hajjari ◽

Seyed Kazeminezhad ◽

Mehrdad Behmanesh

Keyword(s):

Colorectal Cancer ◽

Cancer Progression ◽

In Silico ◽

Potential Role ◽

Non Coding Rna ◽

In Silico Study ◽

Competing Endogenous Rnas ◽

Long Non Coding Rna ◽

In Silico Analyses

SNHG7, as a member of the small nucleolar host gene family, is a recently identified long non-coding RNA (lncRNA). Different reports have identified the SNHGs as competing endogenous RNAs (ceRNAs) sponging miRNAs with a role in cancer progression. However, the biological functions of SNHG7 in the colorectal cancer (CRC) remained to be almost unknown. The current in silico study was aimed to find the potential role of SNHG7 in the CRC development. In this study, we showed the up-regulation of SNHG7 as well as its potential correlation with miRNAs, including mir-193a-5p and mir-485-5P. We hypothesized that SNHG7 modulates these miRNAs availability by acting as a molecular sponge. Our findings showed the potential targets of these miRNAs by studying different databases as well as in silico analyses. In summary, we found SNHG7 as a potential ceRNA which may be a promising biomarker for diagnostic and therapeutic target in CRC.

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Co-Regulation of Protein Coding Genes by Transcription Factor and Long Non-Coding RNA in SARS-CoV-2 Infected Cells: An In Silico Analysis

Non-Coding RNA ◽

10.3390/ncrna7040074 ◽

2021 ◽

Vol 7 (4) ◽

pp. 74

Author(s):

Chinmay Saha ◽

Sayantan Laha ◽

Raghunath Chatterjee ◽

Nitai P. Bhattacharyya

Keyword(s):

In Silico Analysis ◽

Expression Data ◽

Signal Transducer ◽

Protein Coding ◽

Altered Expression ◽

Non Coding Rna ◽

Infected Cells ◽

Ifn Treatment ◽

Long Non Coding Rna ◽

Silico Analysis

Altered expression of protein coding gene (PCG) and long non-coding RNA (lncRNA) have been identified in SARS-CoV-2 infected cells and tissues from COVID-19 patients. The functional role and mechanism (s) of transcriptional regulation of deregulated genes in COVID-19 remain largely unknown. In the present communication, reanalyzing publicly available gene expression data, we observed that 66 lncRNA and 5491 PCG were deregulated in more than one experimental condition. Combining our earlier published results and using different publicly available resources, it was observed that 72 deregulated lncRNA interacted with 3228 genes/proteins. Many targets of deregulated lncRNA could also interact with SARS-CoV-2 coded proteins, modulated by IFN treatment and identified in CRISPR screening to modulate SARS-CoV-2 infection. The majority of the deregulated lncRNA and PCG were targets of at least one of the transcription factors (TFs), interferon responsive factors (IRFs), signal transducer, and activator of transcription (STATs), NFκB, MYC, and RELA/p65. Deregulated 1069 PCG was joint targets of lncRNA and TF. These joint targets are significantly enriched with pathways relevant for SARS-CoV-2 infection indicating that joint regulation of PCG could be one of the mechanisms for deregulation. Over all this manuscript showed possible involvement of lncRNA and mechanisms of deregulation of PCG in the pathogenesis of COVID-19.

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miR-744/eNOS/NO axis: A novel target to halt triple negative breast cancer progression

Breast Disease ◽

10.3233/bd-200454 ◽

2021 ◽

pp. 1-9

Author(s):

Farah Hady El Kilany ◽

Rana Ahmed Youness ◽

Reem Amr Assal ◽

Mohamed Zakaria Gad

Keyword(s):

Breast Cancer ◽

Cancer Progression ◽

In Silico ◽

In Silico Analysis ◽

No Production ◽

Cellular Viability ◽

Griess Reagent ◽

Normal Tissues ◽

Qrt Pcr ◽

Silico Analysis

BACKGROUND: Nitric oxide (NO) may have a dual role in cancer. At low concentrations, endogenous NO promotes tumor growth and proliferation. However, at very high concentrations, it mediates cancer cell apoptosis and inhibits cancer growth. High levels of NO have been observed in blood of breast cancer (BC) patients, which increases tumor blood flow and promotes angiogenesis. To date, the regulation of NO-synthesizing enzyme, eNOS, by miRNAs has not been adequately investigated in BC. Therefore, the main aim of this study is to unravel the possible regulation of eNOS by miRNAs in BC and to examine their influence on NO production and BC progression. METHODS: Expression profile of eNOS in Egyptian BC patients and MDA-MB-231 cell lines was investigated using qRT-PCR. In-silico analysis was performed to predict a putative upstream regulator of eNOS. miR-744-5p was selected and its expression was quantified in BC tissues using qRT-PCR. MDA-MB-231 cells were cultured and transfected with miR-744-5p using lipofection method. NO levels were determined using Griess Reagent. Cellular viability and colony-forming ability were assessed using MTT and colony-forming assays; respectively. RESULTS: eNOS and miR-744-5p were significantly up-regulated in BC tissues compared to paired normal tissues. In-silico analysis revealed that miR-744-5p putatively binds to eNOS transcript with high binding scores. Transfection of MDA-MB-231 cells with miR-744-5p mimics resulted in a significant up-regulation of eNOS and consequently NO levels. In addition, miR-744-5p transfection led to an increase in cellular viability and colony-forming ability of the MDA-MB-231. CONCLUSION: miR-744-5p acts as an upstream positive regulator of the NO synthesizing enzyme, eNOS which in turn elevates NO levels. Furthermore, miR-744-5p is a novel oncogenic miRNA in BC. Thus, targeting miR-744/eNOS/NO axis may act as a therapeutic tool in TNBC.

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Increased NID1 Expression among Breast Cancer Lung Metastatic Women; A Comparative Analysis between Naive and Treated Cases

Recent Patents on Anti-Cancer Drug Discovery ◽

10.2174/1574892815666200302115438 ◽

2020 ◽

Vol 15 (1) ◽

pp. 59-69

Author(s):

Tabinda Urooj ◽

Bushra Wasim ◽

Shamim Mushtaq ◽

Ghulam Haider ◽

Syed N.N. Shah ◽

...

Keyword(s):

Breast Cancer ◽

Lung Metastasis ◽

Cancer Progression ◽

In Silico ◽

In Silico Analysis ◽

Treated Group ◽

Functional Association ◽

Real Time Quantitative Pcr ◽

Protein Expressions ◽

Silico Analysis

Background: Lungs are the second most common reported site of distant metastasis in Breast cancer after bone. Mostly the studies were conducted in cell lines and animal model. To date, there is no blood biomarker reported that could determine the breast cancer progression in terms of lung metastasis. Objective: The aim of this study is to determine Nidogen-1 (NID1)’s mRNA and protein expressions in non-invasive blood samples of breast cancer, in early (II) and lung metastasis advanced stages (III & IV) of naive and treated groups. To determine the functional association of NID1, we employed an in silico analysis, STRING database version 11. Methods: A total of n = 175 cases of breast cancer were recruited in our study. Real time quantitative PCR and ELISA were performed to analyze the mRNA and protein expressions of NID1 respectively. An in silico method is also used to assess NID1’s interactome. Some significant patents related to this topic were also studied and discussed in this research paper. Results: The results show high levels of NID1’s mRNA in the naive group (Group A) as compared to treated group (Group B). Similar trend of increased NID1’s protein expressions was also observed among naive and treated groups, respectively. Our results also show the significant impact of treatment on NID1’s gene and protein expressions. In silico analysis has revealed the functional association of NID1 with its different interactome protein partners. Conclusions: The increased expression of NID1 in early to advanced naive as compared to the treated groups with lung metastasis makes it a promising marker which has pro-metastatic role in breast cancer.

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