Identification of molecular pathways and candidate genes associated with cocks’ comb size trait by genome-wide transcriptome analysis

Liu, Yifan; Tu, Yan; Zhang, Ming; Ji, Gaige; Wang, Kun; Shan, Yanju; Ju, Xiaojun; Zhang, Di; JingTing, Shu; Zou, Jianmin

doi:10.1038/s41598-018-20373-6

Cited by 9 publications

(8 citation statements)

References 46 publications

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“…More recently, RNA sequencing (RNA-seq) has become a powerful method for precise quantification of not only coding but also non-coding RNAs. With recent improvements of chicken genome information, RNA-seq successfully revealed the intriguing genes affecting egg albumen in layers 9 and comb size of cocks 10 . The latest studies using RNA-seq have also reported differential gene expression profiles in breast muscles of modern and foundation broiler lines 11,12 or those in broiler lines with high- and low-ultimate pH 13 .…”

Section: Introductionmentioning

confidence: 99%

Distinct cell proliferation, myogenic differentiation, and gene expression in skeletal muscle myoblasts of layer and broiler chickens

Nihashi

Umezawa

Shinji

et al. 2019

Sci Rep

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Myoblasts play a central role during skeletal muscle formation and growth. Precise understanding of myoblast properties is thus indispensable for meat production. Herein, we report the cellular characteristics and gene expression profiles of primary-cultured myoblasts of layer and broiler chickens. Broiler myoblasts actively proliferated and promptly differentiated into myotubes compared to layer myoblasts, which corresponds well with the muscle phenotype of broilers. Transcriptomes of layer and broiler myoblasts during differentiation were quantified by RNA sequencing. Ontology analyses of the differentially expressed genes (DEGs) provided a series of extracellular proteins as putative markers for characterization of chicken myogenic cells. Another ontology analyses demonstrated that broiler myogenic cells are rich in cell cycle factors and muscle components. Independent of these semantic studies, principal component analysis (PCA) statistically defined two gene sets: one governing myogenic differentiation and the other segregating layers and broilers. Thirteen candidate genes were identified with a combined study of the DEGs and PCA that potentially contribute to proliferation or differentiation of chicken myoblasts. We experimentally proved that one of the candidates, enkephalin, an opioid peptide, suppresses myoblast growth. Our results present a new perspective that the opioids present in feeds may influence muscle development of domestic animals.

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Section: Introductionmentioning

confidence: 99%

Distinct cell proliferation, myogenic differentiation, and gene expression in skeletal muscle myoblasts of layer and broiler chickens

Nihashi

Umezawa

Shinji

et al. 2019

Sci Rep

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“…Each column represents a sample, and each row represents a gene. The red and blue gradients indicate an increase and a decrease in gene expression abundance, respectively ( Liu et al, 2018 ). (C) Venn diagram analysis showing the number of transcription factors targeting the PD-L1 promoter that can be affected by IFN-γ in HCT116 and HKE-3 cells.…”

Section: Resultsmentioning

confidence: 99%

Regulation of IFN-γ-mediated PD-L1 expression by MYC in colorectal cancer with wild-type KRAS and TP53 and its clinical implications

et al. 2022

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Introduction: In the tumor microenvironment, interferon gamma (IFN-γ) secreted by tumor infiltrating lymphocytes can upregulate programmed cell death 1 ligand 1 (PD-L1) expression in many cancers. The present study evaluated the expression of PD-L1 in selected colorectal cancer cell lines with IFN-γ treatment and explored the correlation between programmed cell death 1 ligand 1 expression and KRAS/TP53 mutation status.Methods: The selected colorectal cancer cell lines had known KRAS mutations or TP53 mutations. TCGA data analysis were used to investigate the correlation between overall survival of patient with anti-PD-1/PD-L1 immunotherapy and KRAS/TP53 mutation status. Besides, the correlation between PD-L1 expression and KRAS/TP53 mutation status were also investigated by using TCGA data analysis. In vitro experiments were used to explore the mechanism underlying KRAS- and TP53-related PD-L1 expression.Results: Firstly, TCGA data analysis for gene expression and overall survival and an in vitro study revealed that the wild-type KRAS/TP53 cell lines exhibited hyperresponsiveness to interferon gamma exposure and correlated with better survival in patients receiving anti-PD-1/PD-L1 treatment. Secondly, experimental data revealed that interferon gamma induced the upregulation of programmed cell death 1 ligand 1 mainly through regulating MYC in wild-type KRAS and TP53 colorectal cancers.Discussion: Our findings revealed that the response to anti-PD-1/PD-L1 cancer immunotherapy frequently happened in wild-type KRAS and TP53 colorectal cancers, which were also found to show higher programmed cell death 1 ligand 1 expression. Our results indicate that the wild-type KRAS/TP53 colorectal cancer cell lines may respond better to interferon gamma treatment, which causes increased programmed cell death 1 ligand 1 expression and may be a mechanism underlying the better responses to anti-PD-1/PD-L1 therapies in wild-type KRAS and wild-type TP53 colorectal cancer. Furthermore, the experimental results suggest that interferon gamma regulated programmed cell death 1 ligand 1 expression through the regulation of MYC, which may further affect the response to PD-1/PD-L1 cancer immunotherapy. These results suggest a novel potential treatment strategy for enhancing the efficacy of PD-1/PD-L1 blockade immunotherapy in most colorectal cancer patients.

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“…This is not the only colour gene with a link with comb size, with the gene PIK3R1 also having prior links to comb size in chickens (Y. Liu et al, 2018).…”

Section: Feral Birds On Kauai and Bermudamentioning

confidence: 99%

Genomics and Transcriptomics of Behaviour and Plumage Colouration

Fogelholm

2020

Linköping Studies in Science and Technology. Dissertations

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The aim throughout this thesis has been to investigate the underlying genetics of behaviours and feather colour and plumage patterns by using chickens as a model organism. Chickens are extremely important as a food source, both in terms of egg, as well as meat production. As such there is a large research interest for them, and they provide an excellent model to study the effects of domestication and evolution, since the ancestor to our domestic breeds the Red Junglefowl can still be found living freely in the wild. This allows us to set up long term crossing experiments where we can harness the power of recombination events and genome wide sequencing to perform genome wide mapping studies. I also want to take the opportunity to integrate the results from all of my work and consider it in perspective of the domestication syndrome. In Paper I we investigated the Social Reinstatement behaviour which combines aspects of sociality and anxiousness. We detected several QTL and some overlap with Open Field behaviour from previous work within the group. By combining genomic and transcriptomic methods three strong candidate genes were found: TTRAP, ACOT9 and PRDX4.

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Identification of molecular pathways and candidate genes associated with cocks’ comb size trait by genome-wide transcriptome analysis

Cited by 9 publications

References 46 publications

Distinct cell proliferation, myogenic differentiation, and gene expression in skeletal muscle myoblasts of layer and broiler chickens

Distinct cell proliferation, myogenic differentiation, and gene expression in skeletal muscle myoblasts of layer and broiler chickens

Regulation of IFN-γ-mediated PD-L1 expression by MYC in colorectal cancer with wild-type KRAS and TP53 and its clinical implications

Genomics and Transcriptomics of Behaviour and Plumage Colouration

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