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Transcriptomic analysis to affirm the regulatory role of long non-coding RNA in horn cancer of Indian zebu cattle breed Kankrej (Bos indicus)

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Abstract

Long non-coding RNA (lncRNA) was previously considered as a non-functional transcript, which now established as part of regulatory elements of biological events such as chromosome structure, remodeling, and regulation of gene expression. The study presented here showed the role of lncRNA through differential expression analysis on cancer-related coding genes in horn squamous cell carcinoma of Indian zebu cattle. A total of 10,360 candidate lncRNAs were identified and further analyzed for its coding potential ability using three tools (CPC, CPAT, and PLEK) that provide 8862 common lncRNAs. Pfam analysis of these common lncRNAs gave 8612 potential candidates for lncRNA differential expression analysis. Differential expression analysis showed a total of 59 significantly differentially expressed genes and 19 lncRNAs. Pearson’s correlation analysis was used to identify co-expressed mRNA-lncRNAs to established relation of the regulatory role of lncRNAs in horn cancer. We established a positive relation of seven upregulated (XLOC_000016, XLOC_002198, XLOC_002851, XLOC_ 007383, XLOC_010701, XLOC_010272, and XLOC_011517) and one downregulated (XLOC_011302) lncRNAs with eleven genes that are related to keratin family protein, keratin-associated protein family, cornifelin, corneodesmosin, serpin family protein, and metallothionein that have well-established role in squamous cell carcinoma through cellular communication, cell growth, cell invasion, and cell migration. These biological events were found to be related to the MAPK pathway of cell cycle regulation indicating the role of lncRNAs in manipulating cell cycle regulation during horn squamous cell carcinomas that will be useful in identifying molecular portraits related to the development of horn cancer.

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Data availability

All data generated or analyzed during this study are included in this published article as supplementary information files. In addition, the datasets generated and analyzed during the current study are available in the NCBI-SRA with bioproject number PRJNA497667 and biosample numbers as given in supplementary data. The following link can be used by the reviewer to access data as a part of data share at NCBI-SRA that are publically available. https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA497667

Abbreviations

HN:

horn normal

HC:

horn cancer

CPC:

Coding Potential Calculator

CPAT:

Coding-Potential Assessment Tools

PLEK:

predictor of long non-coding RNAs and messenger RNAs based on an improved K-mer scheme

lncRNA:

long non-coding RNA

FPKM:

fragments per kilobase of transcripts per millions mapped reads

KEGG:

Kyoto Encyclopedia of Genes and Genomes

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Funding

We thank the Department of Biotechnology (DBT), Government of India, New Delhi, India, for providing financial support (Grant Letter No. BT/PR13649/AAQ/1/627/2015) for this project.

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Authors and Affiliations

  1. Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India

    Pritesh H. Sabara, Subhash J. Jakhesara, Ketankumar J. Panchal, Chaitanya G. Joshi & Prakash G. Koringa

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  1. Pritesh H. Sabara
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  2. Subhash J. Jakhesara
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  3. Ketankumar J. Panchal
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  4. Chaitanya G. Joshi
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Contributions

PHS and KJP participated in sample collection, library preparation, and sequencing; PHS analyzed data and drafted manuscript; PGK conceptualized actual research project, participated in sample collection, and improved manuscript; SJJ helped in data analysis and improved manuscript; CGJ provided all facilities to carryout research. All authors read and approved the final manuscript.

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Correspondence to Prakash G. Koringa.

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All animal ethics guidelines were followed and complied as per permission from Ethical Committee norms and letter No. IAEC 525-2015.

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Figure S1

Heatmap showing expression level based upon FPKM value for A) Genes and B) LncRNAs. (PNG 348 kb)

High resolution image (TIF 8077 kb)

Figure S2

Protein-protein interaction analysis of significant differentially expressed genes. (PNG 105 kb)

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Figure S3

Gene ontology analysis based upon significant differentially expressed genes. (PNG 220 kb)

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Figure S4

Interaction between different gene ontology terms identified based upon significant differentially expressed genes. (PNG 303 kb)

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Figure S5

Interaction between different gene ontology terms identified based upon target genes of lncRNAs. (PNG 249 kb)

High resolution image (TIF 7373 kb)

Figure S6

Comparison of RT-qPCR and transcriptome analysis results of selected genes and lncRNAs based upon their log2 fold change value. (PNG 86 kb)

High resolution image (TIF 5257 kb)

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Sabara, P.H., Jakhesara, S.J., Panchal, K.J. et al. Transcriptomic analysis to affirm the regulatory role of long non-coding RNA in horn cancer of Indian zebu cattle breed Kankrej (Bos indicus). Funct Integr Genomics 20, 75–87 (2020). https://doi.org/10.1007/s10142-019-00700-4

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