scholarly journals Transcriptomic and proteomic analyses between small yellow follicles and the smallest hierarchical follicles reveal a role of VLDLR in chicken follicle selection

2019 ◽  
Author(s):  
Qiuyue Chen ◽  
Yiya Wang ◽  
Zemin Liu ◽  
Xiaoli Guo ◽  
Yi Sun ◽  
...  

Abstract Background Follicle selection in chicken refers to the process of selecting one from a group of small yellow follicles (SY, 6-8mm in diameter) to enter the 12-15 mm hierarchical follicles (usually F6 follicles), which is a an important process affecting laying performance in the poultry industry. Although transcripromic analysis on chicken ovarian follicles was reported, integrated analysis on chicken follicles around selection by using both transcripromic and proteomic approaches was still lacking. In this study, we compared the proteomes and transcriptomes of SY and F6 follicles of laying hens and found some genes involved in chicken follicle selection.Results Transcriptomic analysis revealed 855 differentially expressed genes (DEGs) between SY follicles and F6 follicles of laying hens, among which 202 were upregulated and 653 were downregulated. Proteomic analysis revealed 259 differentially expressed proteins (DEPs), including 175 upregulated and 84 downregulated proteins. Among the identified DEGs and DEPs, the expression changes of seven genes including VLDLR1,WIF1, NGFR, AMH, BMP15, GDF6 and MMP13 , and nine proteins including VLDLR, VTG1, VTG3, PSCA, APOB, APOV1, F10, ZP2 and ZP3L2 were validated. In addition VLDLR expression was significantly down-regulated in F6 follicles compared with SY follicles, was signifcantly higher in the GCs than in the TCs and was stimulated by FSH in GCs of both hierarchical and prehierarchical follicles.Conclusions By comparing the proteomes and transcriptomes of SY follicles and F6 of laying hens, we identified some differentially expressed proteins/genes that might play certain roles in chicken follicle selection. These data may contribute to identification of the functional genes and proteins involved in chicken follicular development and selection.

2019 ◽  
Author(s):  
Qiuyue Chen ◽  
Yiya Wang ◽  
Zemin Liu ◽  
Xiaoli Guo ◽  
Yi Sun ◽  
...  

Abstract Background Follicle selection in chicken refers to the process of selecting one from a group of small yellow follicles (SY, 6-8mm in diameter) to enter the 12-15 mm hierarchical follicles (usually F6 follicles), which is a an important process affecting laying performance in the poultry industry. Although transcripromic analysis on chicken ovarian follicles was reported, integrated analysis on chicken follicles around selection by using both transcripromic and proteomic approaches was still lacking. In this study, we compared the proteomes and transcriptomes of SY and F6 follicles of laying hens and found some genes involved in chicken follicle selection.Results Transcriptomic analysis revealed 855 differentially expressed genes (DEGs) between SY follicles and F6 follicles of laying hens, among which 202 were upregulated and 653 were downregulated. Proteomic analysis revealed 259 differentially expressed proteins (DEPs), including 175 upregulated and 84 downregulated proteins. Among the identified DEGs and DEPs, the expression changes of seven genes including VLDLR1,WIF1, NGFR, AMH, BMP15, GDF6 and MMP13 , and nine proteins including VLDLR, VTG1, VTG3, PSCA, APOB, APOV1, F10, ZP2 and ZP3L2 were validated. In addition VLDLR expression was significantly down-regulated in F6 follicles compared with SY follicles, was signifcantly higher in the GCs than in the TCs and was stimulated by FSH in GCs of both hierarchical and prehierarchical follicles.Conclusions By comparing the proteomes and transcriptomes of SY follicles and F6 of laying hens, we identified some differentially expressed proteins/genes that might play certain roles in chicken follicle selection. These data may contribute to identification of the functional genes and proteins involved in chicken follicular development and selection.


2020 ◽  
Author(s):  
Qiuyue Chen ◽  
Yiya Wang ◽  
Zemin Liu ◽  
Xiaoli Guo ◽  
Yi Sun ◽  
...  

Abstract Background: Follicle selection in chickens refers to the process of selecting one follicle from a group of small yellow follicles (SY, 6-8 mm in diameter) for development into 12-15 mm hierarchical follicles (usually F6 follicles), which is an important process affecting laying performance in the poultry industry. Although transcriptomic analysis of chicken ovarian follicles has been reported, integrated analysis of chicken follicles for selection by using both transcriptomic and proteomic approaches is still rarely performed. In this study, we compared the proteomes and transcriptomes of SY and F6 follicles in laying hens and identified several genes involved in chicken follicle selection. Results: Transcriptomic analysis revealed 855 differentially expressed genes (DEGs) between SY follicles and F6 follicles in laying hens, among which 202 were upregulated and 653 were downregulated. Proteomic analysis revealed 259 differentially expressed proteins (DEPs), including 175 upregulated and 84 downregulated proteins. Among the identified DEGs and DEPs, changes in the expression of seven genes, including VLDLR1, WIF1, NGFR, AMH, BMP15, GDF6 and MMP13 , and nine proteins, including VLDLR, VTG1, VTG3, PSCA, APOB, APOV1, F10, ZP2 and ZP3L2, were validated. Further analysis indicated that the mRNA level of chicken VLDLR was higher in F6 follicles than in SY follicles and was also higher in granulosa cells (GCs) than in thecal cells (TCs), and it was stimulated by FSH in GCs of prehierarchical follicles. Conclusions: By comparing the proteomes and transcriptomes of SY and F6 follicles in laying hens, we identified several differentially expressed proteins/genes that might play certain roles in chicken follicle selection. These data may contribute to the identification of functional genes and proteins involved in chicken follicle selection.


2021 ◽  
Author(s):  
Yuzhen Wang ◽  
Bin Yao ◽  
Xianlan Duan ◽  
Jianjun Li ◽  
Wei Song ◽  
...  

Abstract BackgroundEccrine sweat gland (SG) restrictedly exists in mouse foot pads indicating that mouse plantar dermis (PD) contains the SG lineage-restricted niches. However, it is still unclear how niches can affect stem cell fates.MethodsIn this study, we tried to find the key cues by which stem cells sense and interact with the SG lineage-specific niches. Briefly, we used transcriptomics RNA sequencing analysis to screen differentially expressed genes between SG cells and epidermal stem cells (ES), and then we used proteomic analysis to screen differentially expressed proteins between PD and dorsal dermis (DD).ResultsWe found that Notch1 is not only closely related to embryonic SG morphogenesis based on Gene Ontology enrichment analysis but also differentially down-regulated during SG formation in the levels of genes and proteins. Furthermore, immunochemistry and immunofluorescence staining verified that Notch1 was continuously down-regulated along with the process of SG morphogenesis. Especially, Notch1 positive cells almost disappeared neither in the emerging SG buds or in the newly-formed glandular structures.ConclusionHence, we speculated that Notch1 possibly acts as the role of “gatekeeper” during embryonic SG development and is the promising key cue that regulates the interactions between stem cells and the SG lineage-specific niches. Our attempts highlighted the role of Notch1 during embryonic SG organogenesis.Trial registration Not applicable.


2018 ◽  
Vol 50 (5) ◽  
pp. 1638-1658 ◽  
Author(s):  
Hong Li ◽  
Zhenzhen Gu ◽  
Liyu Yang ◽  
Yadong Tian ◽  
Xiangtao Kang ◽  
...  

Background/Aims: Accumulating evidences have demonstrated that long noncoding RNAs (lncRNA) play important roles in hepatic lipid metabolism in mammals. However, no systematic screening of the potential lncRNAs in the livers of laying hens has been performed, and few studies have been reported concerning the effects of the lncRNAs on lipid metabolism in the livers of chickens during egg-laying period. The purpose of this study was to compare the difference in lncRNA expression in the livers of pre-laying and peak-laying hens at the age of 20 and 30 weeks old by transcriptome sequencing and to investigate the interaction networks among lncRNAs, mRNAs and miRNAs. Moreover, the regulatory mechanism and biological function of lncLTR, a significantly differentially expressed lncRNA in the liver between pre- and peak-laying hens, was explored in vitro and in vivo. Methods: Bioinformatics analyses were conducted to identify the differentially expressed (DE) lncRNAs between the two groups of hens. The target genes of the DE lncRNA were predicated for further functional enrichment. An integrated analysis was performed among the DE lncRNA datasets, DE mRNAs and DE miRNA datasets obtained from the same samples to predict the interaction relationship. In addition, in vivo and in vitro trials were carried out to determine the expression regulation of lncLTR, and polymorphism association analysis was conducted to detect the biological role of ncLTR. Results: A total of 124 DE lncRNAs with a P-value ≤ 0.05 were identified. Among them, 44 lncRNAs including 30 known and 14 novel lncRNAs were significant differentially expressed (SDE) with FDR ≤ 0.05. Thirty-two lncRNAs were upregulated and 12 were downregulated in peak-laying group compared with pre-laying group. The functional enrichment results revealed that target genes of some lncRNAs are involved in the lipid metabolism process. Integrated analysis suggested that some of the genes involved in lipid metabolism might be regulated by both the lncRNA and the miRNA. In addition, an upregulated lncRNA, designated lncLTR, was demonstrated to be induced by estrogen via ERβ signaling. The c242. G>A SNP in lncLTR was significantly associated with chicken carcass weight, evisceration weight, semi-evisceration weight, head weight, double-wing weight, claw weight traits, and blood biochemical index, especially for the blood triglyceride content. Conclusion: A series of lncRNAs associated with lipid metabolism in the livers of chickens were identified by transcriptome sequencing and functional analysis, providing a valuable data resource for further studies on chicken hepatic metabolism activities. LncLTR was regulated by estrogen via ERβ signaling and associated with chicken carcass trait and blood triglyceride content.


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Hao Bo ◽  
Fang Zhu ◽  
Zhizhong Liu ◽  
Qi Deng ◽  
Guangmin Liu ◽  
...  

AbstractLong noncoding RNAs (lncRNAs) are involved in various physiological and pathological processes. However, the role of lncRNAs in testicular germ cell tumor (TGCT) has been rarely reported. Our purpose is to comprehensively survey the expression and function of lncRNAs in TGCT. In this study, we used RNA sequencing to construct the lncRNA expression profiles of 13 TGCT tissues and 4 paraneoplastic tissues to explore the function of lncRNAs in TGCT. The bioinformatics analysis showed that many lncRNAs are differentially expressed in TGCT. GO and KEGG enrichment analyses revealed that the differentially expressed lncRNAs participated in various biological processes associated with tumorigenesis in cis and trans manners. Further, we found that the expression of LINC00467 was positively correlated with the poor prognosis and pathological grade of TGCT using WGCNA analysis and GEPIA database data mining. In vitro experiments revealed that LNC00467 could promote the migration and invasion of TGCT cells by regulating the expression of AKT3 and influencing total AKT phosphorylation. Further analysis of TCGA data revealed that the expression was negatively correlated with the infiltration of immune cells and the response to PD1 immunotherapy. In summary, this study is the first to construct the expression profile of lncRNAs in TGCT. It is also the first study to identify the metastasis-promoting role of LNC00467, which can be used as a potential predictor of TGCT prognosis and immunotherapeutic response to provide a clinical reference for the treatment and diagnosis of TGCT metastasis.


2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Su Xie ◽  
Mengxun Li ◽  
Yansen Chen ◽  
Yi Liu ◽  
Lipeng Ma ◽  
...  

Abstract Circular RNAs (circRNAs) are a newly discovered class of endogenous non-coding RNAs that play an important role in growth and development by regulating gene expression and participating in a variety of biological processes. However, the role of circRNAs in porcine follicles remains unclear. Therefore, this study examined middle-sized ovarian follicles obtained from Meishan and Duroc sows at day 4 of the follicular phase. High-throughput RNA sequencing (RNA-seq) was utilized to construct circRNAs, and differential expression was identified. The findings were validated using reverse transcription PCR (RT-PCR) and DNA sequencing, GO and KEGG analyses were performed, and potential miRNA targets were identified. The RNA-seq identified a total of 15,866 circRNAs, with 244 differentially expressed in the Meishan relative to the Duroc (111 up-regulated and 133 down-regulated). The RT-PCR finding confirmed the RNA-seq results, and quantitative real-time PCR (qPCR) analysis examining a subset of the circRNAs showed that they are resistant to RNase R digestion. Bioinformatics analysis (GO and KEGG) showed that the host genes associated with the differentially expressed circRNAs are involved in reproduction and follicular development signaling pathways. Furthermore, many of the circRNAs were found to interact with miRNAs that are associated with follicular development. This study presents a new perspective for studying circRNAs and provides a valuable resource for further examination into the potential roles of circRNAs in porcine follicular development.


1996 ◽  
Vol 5 (3) ◽  
pp. 151-168 ◽  
Author(s):  
Ghanim Almahbobi ◽  
Alan O Trounson

The present review demonstrates that the availability of bioactive FSH and LH in PCOS is normal and that granulosa cells of PCO are not apoptotic and instead hyperexpress functional FSH receptors and may possess intact aromatase activity. Consequently, these cells respond excessively to exogenous FSH stimulation and produce high amounts of oestradiol both in vivo and in vitro. The altered developmental capacity of follicles from PCO in vivo is most likely due to the abnormal follicular milieu of PCO and the culminating effects of intrafollicular inhibitors and stimulators. The failure of ovarian oestradiol production and follicular maturation to dominance in vivo may be due to a mechanism that interferes with the function of FSH, such as intraovarian steroids and growth factors. It has previously been shown that EGF and TGFα have inhibitory actions on follicular development, aromatization and LH receptor formation. In contrast, EGF enhances early follicular recruitment and growth. Therefore, it is hypothesized that EGF/TGFα may have a causal relationship in the mechanisms of anovulatory infertility in women with PCOS. Thus, an aberration in the regulation of follicular fluid EGF and/or TGFα may result in reduced numbers of granulosa cells, cessation of follicle selection and ultimately in the creation and maintenance of PCOS. The exact mechanism by which the hyperfunction of EGF/TGFα occurs and the trigger for this hyperactivity in the ovary remain to be determined. An experimental animal model may be required to assist such investigations in the future.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chang Zhao ◽  
Shi Shu ◽  
Yunlong Bai ◽  
Dong Wang ◽  
Cheng Xia ◽  
...  

Abstract To screen differentially expressed proteins in the blood dairy cows with inactive ovaries caused by a negative energy balance and to determine the roles of the identified proteins in the development of inactive ovaries.Holstein cows at 14 to 21 days postpartum in an intensive dairy farm were examined for their energy balance (EB) status by blood β-hydroxybutyrate (BHBA) and assigned to the inactive ovary (IO) group (n = 50) and the normal oestrus control (CON) group (n = 50) at 60 to 90 days postpartum by means of the oestrus manifestation, rectal examination and B-ultrasound examination. Fourteen differentially expressed proteins from 61 proteins in the plasma of dairy cows with IOs were identified by iTRAQ/LC-MS/MS and GO, KEGG, and PATHWAY analysis. Eleven expressed proteins were upregulated, and 3 expressed proteins were downregulated. Among the 10 differentially expressed proteins verified by Western blot or ELISA, the relative expression levels of ALDOB, IGFBP2, ITIH3 and LDHB in mixed samples and single samples were consistent with the proteomic protein results. PKM2, GPX3, ALDOB, RBP4 and AHSG were significantly different between the two groups (P < 0.05); APOA4 and SPAM1 were not significantly different (P > 0.05) but were still downregulated in the ovarian resting group. This study confirmed that 14 plasma differential proteins in the inactive ovaries of postpartum dairy cows were associated with follicular development, and these findings provide a foundation for further research on the mechanism and prevention of inactive ovaries in dairy cows.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2407-2407
Author(s):  
Rodney R. Miles ◽  
Zhaosheng Lin ◽  
Megan S. Lim ◽  
Kojo S.J. Elenitoba-Johnson

Abstract Follicular lymphoma (FL) is the most common form of low-grade non-Hodgkin lymphoma in the western hemisphere. The vast majority of cases are incurable and transformation to diffuse large B-cell lymphoma (DLBCL) is an important cause of death. The molecular and biologic mechanisms underlying FL transformation are largely uncharacterized. In this study, we utilized a global quantitative proteomics approach for the identification of differentially expressed proteins associated with follicular lymphoma transformation. Five matched pairs of clonally identical cases of follicular lymphoma and their transformed counterparts (DLBCL) arising in the same individual were utilized. Quantitative analysis of differentially expressed proteins was performed by isotope-coded affinity tagging (ICAT™) followed by liquid chromatography (LC) and tandem mass spectrometry (MS/MS). Equivalent quantities of total cell lysates obtained from the FLs and the DLBCLs were ICAT™ labeled, and subjected to avidin affinity chromatography. Offline fractions were collected, digested with trypsin, and analyzed by automated reverse phase nanospray LC-MS/MS. Our proteomic studies revealed upregulation of the IGF-1R (3–5 fold) in the transformed lymphomas. Western blot analysis using an antibody to the a-subunit of IGF-1R revealed overexpression in the transformed lymphoma samples as compared to their preceding FL counterparts (discovery set). Similarly, IGF-1R upregulation was demonstrated in an additional independent set of 6/7 DLBCL samples as compared to their preceding FL counterparts. Immunohistochemical studies were performed on formalin-fixed paraffin-embedded tissue sections of 15 matched pairs of FL and their transformed DLBCL counterparts. The neoplastic cells of FL demonstrated negligible levels of IGF-1R whereas in 5/15 cases, the neoplastic cells of DLBCL demonstrated strong cytoplasmic and membranous expression of IGF-1R. We carried out studies to determine the functional role of IGF-1R in the survival of lymphoma cells in vitro. Blocking antibodies to IGF-1R caused a significant reduction of cell viability in all three transformed FL cell lines (SUDHL-4, OCI-LY1, Karpas 4224) as determined by MTT assays. In contrast, antibodies against EGFR, EphA and Frizzled 8 protein did not affect the cell viability of any of the transformed FL cell lines, indicating specificity. Furthermore, knockdown of IGF-1R expression in SUDHL-4 cells by RNA interference resulted in significant reduction in cell viability whereas the control “scramble” siRNA or EGFR siRNA did not have an effect. Cell cycle analysis of the IGF-1R siRNA transfected cells indicated an increase in cells undergoing apoptosis relative to control cells. We utilized a synthetic tyrphostin compound (AG1024) which selectively inhibits the IGF-1R tyrosine kinase activity to determine the effects of pharmacologic inhibition of IGF-1R on the viability of transformed FL cells. Inhibition of IGF-1R resulted in inhibition of cell viability with IC50 of 22mM. This study, for the first time, reveals the role of deregulated expression of IGF-1R in transformed FL and provides a rational basis for the use of IGF-1R blocking agents in the therapy of these neoplasms.


2022 ◽  
Vol 12 ◽  
Author(s):  
Ying Huang ◽  
Wei Luo ◽  
Xuliang Luo ◽  
Xiaohui Wu ◽  
Jinqiu Li ◽  
...  

The differences in reproductive processes at the molecular level between viviparous and oviparous animals are evident, and the site in the ovary that synthesizes sex hormones (androgens and oestrogens) and the trends for enriching sex hormones during follicle development in chickens are different from those in mammals, suggesting that the effect of sex hormones on follicle development in chickens is probably different from that in viviparous animals. To explore the specific role of androgen receptors (ARs) on chicken follicular development, we matched the correspondence of follicular development stages among chickens, humans, cows and identified chicken-specific genes related to follicle development (GAL-SPGs) by comparing follicle development-related genes and their biological functions among species (chickens, humans, and cows). A comparison of the core transcription factor regulatory network of granulosa cells (or ovaries) based on super-enhancers among species (chicken, human, and mouse) revealed that AR is a core transcriptional regulator specific to chickens. In vivo experiments showed that inhibition of AR significantly reduced the number of syf (selected stage follicles) in chickens and decreased the expression of GAL-SPGs in F5 follicles, while in vitro experiments showed that inhibition of AR expression in chicken granulosa cells (GCs) significantly down-regulated the expression levels of GAL-SPGs, indicating that AR could regulate follicle selection through chicken-specific genes related to follicle development. A comparison among species (77 vertebrates) of the conserved genomic regions, where chicken super-enhancers are located, revealed that the chicken AR super-enhancer region is conserved in birds, suggesting that the role of AR in follicle selection maybe widespread in birds. In summary, we found that AR can regulate follicle selection through chicken-specific genes related to follicle development, which also emphasizes the important role of AR in follicle selection in chickens and provides a new perspective for understanding the unique process of follicle development in chickens. Our study will contribute to the application of androgens to the control of egg production in chickens and suggests that researchers can delve into the mechanisms of follicle development in birds based on androgen/androgen receptors.


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