Transcriptome Dynamics Reveal Stage-Specific and Melatonin-Triggered Gene Expression Patterns During The Cashmere Growth Cycle in Capra Hircus

Abstract Background Cashmere goat is famous for its high-quality fibers. The growth of cashmere in secondary hair follicles exhibits a seasonal pattern arising from circannual changes in the natural photoperiod. Although several studies have compared and analyzed the differences in gene expression between different cashmere growth stages, the selection of samples in these studies relies on research experience or morphological evidence. Distinguishing cashmere growth cycle according to gene expression patterns may help to explore the regulation mechanisms related to cashmere growth and the effect of melatonin from a molecular level more accurately. Results In this study, we applied RNA-sequencing to the hair follicles of three normal and three melatonin-treated Inner Mongolian cashmere goats sampled every month during a whole cashmere growth cycle. A total of 3559 and 988 genes were subjected as seasonal changing genes (SCGs) in the control and treated groups, respectively. The SCGs in the normal group are divided into three clusters, and their specific expression patterns help to group the cashmere growth cycle into anagen, catagen and telogen stages. Some canonical pathways such as Wnt, TGF-beta and Hippo signaling pathways are detected as promoting the cashmere growth, while Cell adhesion molecules (CAMs), Cytokine-cytokine receptor interaction, Jak-STAT, Fc epsilon RI, NOD-like receptor, Rap1, PI3K-Akt, cAMP, NF-kappa B and many immune-related pathways are detected in the catagen and telogen stages. The PI3K-Akt signaling, ECM-receptor interaction and Focal adhesion are found in the transition stage between telogen to anagen, which may serve as candidate biomarkers for telogen-anagen regeneration. Pairwise comparisons between the control and melatonin-treated groups also indicate 941 monthly differentially expressed genes (monthly DEGs). These monthly DEGs are mainly distributed from April and September, which reveal a potential signal pathway map regulating the anagen stage triggered by melatonin. Enrichment analysis shows that Wnt, Hedgehog, ECM, Chemokines and NF-kappa B signaling pathways may be involved in the regulation of non-quiescence and secondary shedding under the influence of melatonin. Conclusions Our study decodes the key regulators of the whole cashmere growth cycle, laying the foundation for the control of cashmere growth and improvement of cashmere yield.

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Transcriptome Dynamics Reveal Stage-specific and Melatonin-triggered Gene Expression Patterns During the Cashmere Growth Cycle in Capra Hircus

10.21203/rs.3.rs-586481/v1 ◽

2021 ◽

Author(s):

Chun Li ◽

Cong Feng ◽

Guangyuan Ma ◽

Shaoyin Fu ◽

Ming Chen ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Expression Patterns ◽

Growth Cycle ◽

Hair Follicles ◽

Receptor Interaction ◽

Morphological Evidence ◽

Gene Expression Patterns ◽

Growth Stages ◽

Nf Kappa B

Abstract Background: Cashmere goat is famous for its high-quality fibers. The growth of cashmere in secondary hair follicles exhibits a seasonal pattern arising from circannual changes in the natural photoperiod. Although several studies have compared and analyzed the differences in gene expression between different cashmere growth stages, the selection of samples in these studies relies on research experience or morphological evidence. Distinguishing cashmere growth cycles according to gene expression patterns may help to explore the regulation mechanisms related to cashmere growth and the effect of melatonin from a molecular level more accurately. Results: In this study, we applied RNA-sequencing to the hair follicles of three normal and three melatonin-treated Inner Mongolian cashmere goats sampled every month during a whole cashmere growth cycle. A total of 3559 and 988 genes were subjected as seasonal changing genes (SCGs) in the control and treated groups, respectively. The SCGs in the normal group are divided into three clusters, and their specific expression patterns help to group the cashmere growth cycle into anagen, catagen and telogen stages. Some canonical pathways such as Wnt, TGF-beta and Hippo signaling pathways are detected as promoting the cashmere growth, while Cell adhesion molecules (CAMs), Cytokine-cytokine receptor interaction, Jak-STAT, Fc epsilon RI, NOD-like receptor, Rap1, PI3K-Akt, cAMP, NF-kappa B and many immune-related pathways are detected in the catagen and telogen stages. The PI3K-Akt signaling, ECM-receptor interaction and Focal adhesion are found in the transition stage between telogen to anagen, which may serve as candidate biomarkers for telogen-anagen regeneration. Pairwise comparisons between the control and melatonin-treated groups also indicate 941 monthly differentially expressed genes (monthly DEGs). These monthly DEGs are mainly distributed from April and September, which reveal a potential signal pathway map regulating the anagen stage triggered by melatonin. Enrichment analysis shows that Wnt, Hedgehog, ECM, Chemokines and NF-kappa B signaling pathways may be involved in the regulation of non-quiescence and secondary shedding under the influence of melatonin. Conclusions: Our study decodes the key regulators of the whole cashmere growth cycle, laying the foundation for the control of cashmere growth and improvement of cashmere yield.

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Sex-specific variation in signaling pathways and gene expression patterns in human leukocytes in response to endotoxin and exercise

Journal of Neuroinflammation ◽

10.1186/s12974-016-0758-5 ◽

2016 ◽

Vol 13 (1) ◽

Cited By ~ 10

Author(s):

Asghar Abbasi ◽

Rodolfo de Paula Vieira ◽

Felix Bischof ◽

Michael Walter ◽

Masoud Movassaghi ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Human Leukocytes ◽

Specific Variation

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Gene expression patterns of oncogenic signaling pathways provide a novel approach to targeted therapeutics in advanced non-small cell lung cancer (NSCLC)

Journal of Clinical Oncology ◽

10.1200/jco.2007.25.18_suppl.7503 ◽

2007 ◽

Vol 25 (18_suppl) ◽

pp. 7503-7503

Author(s):

A. Potti ◽

A. Bild ◽

H. Dressman ◽

M. Kelley ◽

D. Harpole ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Metastatic Disease ◽

Cancer Biology ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Targeted Therapeutics ◽

Oncogenic Signaling ◽

Novel Approach ◽

Oncogenic Signaling Pathways

7503 Gene expression profiles reflect unique aspects of individual tumors and may characterize tumor heterogeneity in NSCLC. We used gene expression signatures that reflect the deregulation of major oncogenic signaling pathways (Ras, PI3 kinase, Akt, Src, β-catenin, E2F, and Myc) to identify patterns of pathway activation in 118 samples from patients with recurrent (n = 69) and metastatic (n = 49) NSCLC. These individuals, in particular, the patients with metastatic disease are likely to be resistant to standard chemotherapy pointing to the need for alternative therapeutic options. As one approach to this challenge, we used Affymetrix expression data to identify patterns of pathway deregulation in patients with advanced (recurrent/metastatic) disease and compared them to our previously described data on early stage NSCLC (n = 91). Unique to the recurrent and metastatic disease cohorts, a majority of the tumors (greater than 80%) had deregulation of multiple signaling pathways. In particluar, NSCLC tumors with deregulated Src and Myc pathways had a much worse prognosis than those with deregulated Ras and Akt pathways [median survival: 15.5 months vs. 55.3 months, hazard ratio: 2.6, p < 0.01]. Further, using cell proliferation assays, we have shown that the predicted deregulation of Ras, Src and PI3K pathways was directly proportional (p < 0.01, log rank test) to the sensitivity of NSCLC cell lines (n = 17) to agents that specifically target these pathways, suggesting that an ability to profile the status of oncogenic pathways in a tumor sample provides an opportunity to better characterize the oncogenic process in patients with recurrent and advanced NSCLC. More importantly, such a strategy provides a novel approach to targeted therapeutics in NSCLC by guiding the appropriate use of pathway specific inhibitors. Finally, data on gene expression patterns involving other signatures representing unique cancer biology relevant to NSCLC (e.g. hypoxia, chromosomal instability, and angiogenesis) will be also be presented. No significant financial relationships to disclose.

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RNA-Seq-Based Gene Expression Pattern and Morphological Alterations in Chick Thymus during Postnatal Development

International Journal of Genomics ◽

10.1155/2019/6905194 ◽

2019 ◽

Vol 2019 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Zhouyiyuan Xue ◽

Abdur Rahman Ansari ◽

Xing Zhao ◽

Kun Zang ◽

Yu Liang ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Postnatal Development ◽

Expression Pattern ◽

Expression Patterns ◽

Critical Role ◽

Gene Expression Pattern ◽

Receptor Interaction ◽

Rna Seq ◽

Morphological Alterations

The thymus is a lobulated unique lymphoid immune organ that plays a critical role in the selection, development, proliferation, and differentiation of T cells. The thymus of developing chickens undergoes continued morphological alterations; however, the biomolecular and transcriptional dynamics of the postnatal thymus in avian species is not clear yet. Therefore, the thymuses from chickens at different stages of development (at weeks 0, 1, 5, 9, 18, and 27) were used in the present study. The RNA-seq method was used to study the gene expression patterns. On average, 24120819 clean reads were mapped, differentially expressed genes (DEGs) were identified on the basis of log values (fold change), including 744 upregulated and 425 downregulated genes. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are PCNA, CCNA2, CCNB2, and CDK1. Thus, the current study revealed that during postnatal development, the thymus undergoes severe atrophy. Thymus structure was damaged and gene expression changed dramatically, especially at the 27th week of age. Moreover, we found significant changes of several signaling pathways such as the cytokine-cytokine receptor interaction and cell cycle signaling pathways. Hence, it may be inferred that those signaling pathways might be closely related to the postnatal chicken thymus development.

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