Transcriptome-based screening of intracellular pathways and angiogenesis related genes at different stages of thiram induced tibial lesions in broiler chickens

Jahejo, Ali Raza; Zhang, Ding; Niu, Sheng; Mangi, Raza Ali; Khan, Afrasyab; Qadir, Muhammad Farhan; Khan, Abad; Chen, Huanchun; Tian, Wen‐xia

doi:10.1186/s12864-020-6456-9

Cited by 23 publications

(9 citation statements)

References 62 publications

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“…The expression of RPL17 is significantly increased in organs with increased protein synthesis, such as ovaries, bone marrow, and lymph nodes ( Wang et al, 2015 ; Huang et al, 2016 ). Some studies have pointed out that under the pathological condition, the protein synthesis and metabolism of some organs will be enhanced, which is consistent with our research results ( Yuan et al, 2018 ; Jahejo et al, 2020 ). However, a study has suggested that RPL17 may act outside the ribosome.…”

Section: Discussionsupporting

confidence: 93%

Identification of Hub Genes Associated With Tuberculous Pleurisy by Integrated Bioinformatics Analysis

Shi

Zhu

et al. 2021

Front. Genet.

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Improving the understanding of the molecular mechanism of tuberculous pleurisy is required to develop diagnosis and new therapy strategies of targeted genes. The purpose of this study is to identify important genes related to tuberculous pleurisy. In this study, the expression profile obtained by sequencing the surgically resected pleural tissue was used to explore the differentially co-expressed genes between tuberculous pleurisy tissue and normal tissue. 29 differentially co-expressed genes were screened by weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis methods. According to the functional annotation analysis of R clusterProfiler software package, these genes are mainly enriched in nucleotide−sugar biosynthetic process (biological process), ficolin−1−rich granule lumen (cell component), and electron transfer activity (molecular function). In addition, in the protein-protein interaction (PPI) network, 20 hub genes of DEGs and WCGNA genes were identified using the CytoHubba plug-in of Cytoscape. In the end, RPL17 was identified as a gene that can be the biomarker of tuberculous pleurisy. At the same time, there are seven genes that may have relationship with the disease (UBA7, NDUFB8, UQCRFS1, JUNB, PSMC4, PHPT1, and MAPK11).

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Section: Discussionsupporting

confidence: 93%

Identification of Hub Genes Associated With Tuberculous Pleurisy by Integrated Bioinformatics Analysis

Shi

Zhu

et al. 2021

Front. Genet.

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“…GREM1 and FMN1 play an important role in mouse and chick limb development [ 100 ], with the former being located within a chicken QTL related to limb development [ 41 ]. MEIS2 is related to angiogenesis at tibial lesions in broiler chickens [ 101 ] and overlapped with a QTL for body weight [ 41 ] ( Table S7 ).…”

Section: Discussionmentioning

confidence: 99%

“…ELL is also a positional candidate gene for egg number in broiler breeders [ 107 ] and a candidate gene associated with egg quality (yolk weight) [ 108 ]. The KLF2 gene is related to angiogenesis at tibial lesions in broiler chickens [ 101 ]. Our findings extend knowledge about genes under selection within this region on GGA28 in meat-type chickens.…”

Section: Discussionmentioning

confidence: 99%

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Abdelmanova

Dotsev

Romanov

et al. 2021

Biology

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Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

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“…The fluorescence intensity of FA as a function of time was evaluated from the time‐lapse series, by quantifying the intensity of pixels with the Image J software. As previously described, [ 46 ] FA lifetime analysis was defined as the time during which the fluorescence intensity remained above the half‐maximum and was calculated from the assembly and disassembly curve done using the Solver function in Excel (Microsoft). The spatiotemporal correlation of focal adhesion with GFP‐TAPP1‐PHx3 or PI3KC2 α ‐GFP as a function of time was quantified based on the focal adhesion drawn regions and the intensity of GFP‐TAPP1‐PHx3 or PI3KC2 α ‐GFP was measured with the ImageJ software.…”

Section: Methodsmentioning

confidence: 99%

Phosphoinositide Conversion Inactivates R‐RAS and Drives Metastases in Breast Cancer

Prever

Hsu

et al. 2022

Advanced Science

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Breast cancer is the most prevalent cancer and a major cause of death in women worldwide. Although early diagnosis and therapeutic intervention significantly improve patient survival rate, metastasis still accounts for most deaths. Here it is reported that, in a cohort of more than 2000 patients with breast cancer, overexpression of PI3KC2α occurs in 52% of cases and correlates with high tumor grade as well as increased probability of distant metastatic events, irrespective of the subtype. Mechanistically, it is demonstrated that PI3KC2α synthetizes a pool of PI(3,4)P2 at focal adhesions that lowers their stability and directs breast cancer cell migration, invasion, and metastasis. PI(3,4)P2 locally produced by PI3KC2α at focal adhesions recruits the Ras GTPase activating protein 3 (RASA3), which inactivates R‐RAS, leading to increased focal adhesion turnover, migration, and invasion both in vitro and in vivo. Proof‐of‐concept is eventually provided that inhibiting PI3KC2α or lowering RASA3 activity at focal adhesions significantly reduces the metastatic burden in PI3KC2α‐overexpressing breast cancer, thereby suggesting a novel strategy for anti‐breast cancer therapy.

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Transcriptome-based screening of intracellular pathways and angiogenesis related genes at different stages of thiram induced tibial lesions in broiler chickens

Cited by 23 publications

References 62 publications

Identification of Hub Genes Associated With Tuberculous Pleurisy by Integrated Bioinformatics Analysis

Identification of Hub Genes Associated With Tuberculous Pleurisy by Integrated Bioinformatics Analysis

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Phosphoinositide Conversion Inactivates R‐RAS and Drives Metastases in Breast Cancer

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