Genome-wide identification and characterization of long non-coding RNAs in MDCK cell lines with high and low tumorigenicities

Qiao, Zhihua; Yang, Di; Liu, Lixia; Liu, Zhenbin; Wang, Jiamin; He, Dan; Wu, Huihao; Wang, Jiao; Ma, Zhiyong

doi:10.1016/j.ygeno.2019.08.002

Cited by 9 publications

(8 citation statements)

References 28 publications

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“…In addition, while MM is a rare cancer in humans, the high frequency of MM in particular breeds enabled the identification of ~ 10 breed-specific lncRNAs, which were shown to be specifically differentially expressed in one breed versus the others (Hitte et al 2019 ). Beside melanomas, a number of studies have established lncRNA atlases in canine cancers, such as B-cell lymphoma (DLBCL) (Cascione et al 2019 ; Verma et al 2015 ) or canine kidney cancer (MDCK) (Qiao et al 2020 ) (Table 2 A) and also linked GWAS hits to overlapping lncRNAs such as in hematopoietic cancers (Hédan et al 2021 ).…”

Section: De Novo Transcriptome Reconstruction Of New Long Non-coding ...mentioning

confidence: 99%

LncRNAs in domesticated animals: from dog to livestock species

et al. 2021

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Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

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Section: De Novo Transcriptome Reconstruction Of New Long Non-coding ...mentioning

confidence: 99%

LncRNAs in domesticated animals: from dog to livestock species

et al. 2021

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“…The lncRNA and mRNA were submitted to Novogene (Beijing Novogene Technology Co. LTD.) for the transcriptome analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/) and Gene Ontology (GO, http://www.geneontology.org) were conducted (Qiao et al, 2019). KOBAS (2.0) was used to analyze for KEGG (Mao et al, 2005).…”

Section: Methodsmentioning

confidence: 99%

“…Differential expression of lncRNA and mRNA have been focused on following infectious salmon anemia virus and hepatitis B virus infections, respectively (Boltana et al, 2016; Sato et al, 2020). Moreover, the characterization of lncRNA expression is analyzed in Madin–Darby canine kidney cell line (MDCK) cells with human adenovirus and neoplasia (Qiao et al, 2019; Zhao et al, 2016). But, lncRNA and mRNA expression has not been explored in MDCK cells infected with CAdV‐1.…”

Section: Introductionmentioning

confidence: 99%

The biological characteristics of the canine adenovirus type 1 from fox and the transcriptome analysis of the infected MDCK cell

Zhu

Sun²,

Yan

et al. 2021

Cell Biology International

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Canine adenovirus type 1 (CAdV‐1) is the etiologic agent of fox encephalitis, and a virus strain from fox encephalitis is isolated and related research are conducted. In this experiment, the results showed that the F1301 strain was confirmed to be the CAdV‐1. The whole genome of the CAdV‐1 F1301 strain isolated from fox was 30,535 bp and had higher homology to the other reported CAdV‐1 strains. After 0, 12, and 36 h of CAdV‐1 infection, the difference gene of the 592 long noncoding RNA and 11,215 microRNA were involved in cell responses to CAdV‐1 infection through the PI3K‐AKT, Wnt, Herpes simplex, hepatitis C, and Epstein–Barr virus infection pathway in Madin–Darby canine kidney cell line (MDCK). The results indicate that the biological characterization of the CAdV‐1 and the MDCK cell‐CAdV‐1 interaction are clarified.

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“…Of relevance, 417 differentially expressed lncRNAs were identified in canine oral melanomas in comparison with control samples, including the well-studied lncRNA ZEB2-AS, a lncRNA involved in the regulation of the transcription factor Zinc Finger E-Box Binding Homeobox 2 ( Zeb2 ) during EMT in human colon, pancreatic, and breast cancer cell lines, as well as SOX21 Antisense Divergent Transcript 1( Sox21-as1 ) and Cancer Susceptibility 15( Casc15) ( 211 , 221 , 222 ). Finally, long non-coding transcripts from telomeres, called telomeric repeat-containing RNA (TERRA), were identified as blocking telomerase activity in canine tumor cell lines originated from soft tissue sarcomas ( 223 ). MDCK cells were also tested for the presence of tumorigenic lncRNAs, with the aim of preparing a safer and more reliable non-neoplastic MDCK cell line for vaccine production, founding several tumor-associated lncRNAs ( 224 ).…”

Section: Lncrnasmentioning

confidence: 99%

An Update on Molecular Pathways Regulating Vasculogenic Mimicry in Human Osteosarcoma and Their Role in Canine Oncology

et al. 2021

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Canine tumors are valuable comparative models for human counterparts, especially to explore novel biomarkers and to understand pathways and processes involved in metastasis. Vasculogenic mimicry (VM) is a unique property of malignant cancer cells which promote metastasis. Thus, it represents an opportunity to investigate both the molecular mechanisms and the therapeutic targets of a crucial phenotypic malignant switch. Although this biological process has been largely investigated in different human cancer types, including osteosarcoma, it is still largely unknown in veterinary pathology, where it has been mainly explored in canine mammary tumors. The presence of VM in human osteosarcoma is associated with poor clinical outcome, reduced patient survival, and increased risk of metastasis and it shares the main pathways involved in other type of human tumors. This review illustrates the main findings concerning the VM process in human osteosarcoma, search for the related current knowledge in canine pathology and oncology, and potential involvement of multiple pathways in VM formation, in order to provide a basis for future investigations on VM in canine tumors.

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Genome-wide identification and characterization of long non-coding RNAs in MDCK cell lines with high and low tumorigenicities

Cited by 9 publications

References 28 publications

LncRNAs in domesticated animals: from dog to livestock species

LncRNAs in domesticated animals: from dog to livestock species

The biological characteristics of the canine adenovirus type 1 from fox and the transcriptome analysis of the infected MDCK cell

An Update on Molecular Pathways Regulating Vasculogenic Mimicry in Human Osteosarcoma and Their Role in Canine Oncology

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