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Hu S, Zhang X, Xin H, Guo M, Xiao Y, Chang Z, Luo Q, Li Y, Zhu C. Identification of PI3K-AKT Pathway-Related Genes and Construction of Prognostic Prediction Model for ccRCC. Cancer Rep (Hoboken) 2024; 7:e70010. [PMID: 39233640 PMCID: PMC11375326 DOI: 10.1002/cnr2.70010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 07/23/2024] [Accepted: 08/10/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC), the predominate histological type of renal cell carcinoma (RCC), has been extensively studied, with poor prognosis as the stage increases. Research findings consistently indicated that the PI3K-Akt pathway is commonly dysregulated across various cancer types, including ccRCC. Targeting the PI3K-Akt pathway held promise as a potential therapeutic approach for treating ccRCC. Development and validation of PI3K-Akt pathway-related genes related biomarkers can enhance healthcare management of patients with ccRCC. PURPOSE This study aimed to identify the key genes in the PI3K-Akt pathway associated with the diagnosis and prognosis of CCRCC using data mining from the Cancer Genome Atlas (TCGA) and Gene Expression Synthesis (GEO) datasets. METHODS The purpose of this study is to use bioinformatics methods to screen data sets and clinicopathological characteristics associated with ccRCC patients. The exhibited significantly differential expressed genes (DEGs) associated with the PI3K-Akt pathway were examined by KEGG. In addition, Kaplan-Meier (KM) analysis used to estimate the survival function of the differential genes by using the UALCAN database and graphPad Prism 9.0. And exploring the association between the expression levels of the selected genes and the survival status and time of patients with ccRCC based on SPSS22.0. Finally, a multigene prognostic model was constructed to assess the prognostic risk of ccRCC patients. RESULTS A total of 911 genes with common highly expressed were selected based on the GEO and TCGA databases. According to the KEGG pathway analysis, there were 42 genes enriched in PI3K-Akt signalling pathway. And seven of highly expressed genes were linked to a poor prognosis in ccRCC. And a multigene prognostic model was established based on IL2RG, EFNA3, and MTCP1 synergistic expression might be utilized to predict the survival of ccRCC patients. CONCLUSIONS Three PI3K-Akt pathway-related genes may be helpful to identify the prognosis and molecular characteristics of ccRCC patients and to improve therapeutic regimens, and these risk characteristics might be further applied in the clinic.
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Affiliation(s)
- Shaowen Hu
- Department of Urinary Surgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Xiaoli Zhang
- Department of Urinary Surgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Huiru Xin
- Department of Thoracic and Cardiovascular Surgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Mingjie Guo
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Henan University, Kaifeng, China
| | - Yafei Xiao
- Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Zhongwei Chang
- Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Qingyang Luo
- Department of Urinary Surgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Yang Li
- Department of Urinary Surgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Chaoyang Zhu
- Department of Urinary Surgery, Huaihe Hospital of Henan University, Kaifeng, China
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Liang X, Duan Q, Li B, Wang Y, Bu Y, Zhang Y, Kuang Z, Mao L, An X, Wang H, Yang X, Wan N, Feng Z, Shen W, Miao W, Chen J, Liu S, Storz JF, Liu J, Nevo E, Li K. Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep. Proc Natl Acad Sci U S A 2024; 121:e2322291121. [PMID: 38913905 PMCID: PMC11228492 DOI: 10.1073/pnas.2322291121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/06/2024] [Indexed: 06/26/2024] Open
Abstract
Tibetan sheep were introduced to the Qinghai Tibet plateau roughly 3,000 B.P., making this species a good model for investigating genetic mechanisms of high-altitude adaptation over a relatively short timescale. Here, we characterize genomic structural variants (SVs) that distinguish Tibetan sheep from closely related, low-altitude Hu sheep, and we examine associated changes in tissue-specific gene expression. We document differentiation between the two sheep breeds in frequencies of SVs associated with genes involved in cardiac function and circulation. In Tibetan sheep, we identified high-frequency SVs in a total of 462 genes, including EPAS1, PAPSS2, and PTPRD. Single-cell RNA-Seq data and luciferase reporter assays revealed that the SVs had cis-acting effects on the expression levels of these three genes in specific tissues and cell types. In Tibetan sheep, we identified a high-frequency chromosomal inversion that exhibited modified chromatin architectures relative to the noninverted allele that predominates in Hu sheep. The inversion harbors several genes with altered expression patterns related to heart protection, brown adipocyte proliferation, angiogenesis, and DNA repair. These findings indicate that SVs represent an important source of genetic variation in gene expression and may have contributed to high-altitude adaptation in Tibetan sheep.
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Affiliation(s)
- Xiaolong Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Qijiao Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yinjia Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yueting Bu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yonglu Zhang
- Fengjia Town Health Center, Rushan City, Weihai City264200, China
| | - Zhuoran Kuang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Leyan Mao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Xuan An
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Xiaojie Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Na Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Zhilong Feng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Wei Shen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Weilan Miao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jiaqi Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Sanyuan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE68588
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa3498838, Israel
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
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Zhu L, Jiao H, Gao W, Gong P, Shi C, Zhang F, Zhao J, Lu X, Liu B, Luo J. MiR-103-5p deficiency suppresses lipid accumulation via upregulating PLSCR4 and its host gene PANK3 in goat mammary epithelial cells. Int J Biol Macromol 2024; 267:131240. [PMID: 38583827 DOI: 10.1016/j.ijbiomac.2024.131240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/09/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Lipids are intimately related to the unique flavor and nutritional values of goat milk. MicroRNAs (miRNA) participate in the regulation of various biological functions, including the synthesis and degradation of lipids. Several studies have shown that miR-103 is involved in the regulation of lipid metabolism, however, the molecular mechanism by which miR-103 regulates lipid metabolism in goat mammary gland is poorly understood. In this study, miR-103 was knocked out in goat mammary epithelial cells (GMECs) by CRISPR/Cas9, and the accumulation of lipid droplets, triglycerides, and cholesterol in the cells was suppressed subsequently. Overexpression or knockdown of miR-103-5p and miR-103-3p in GMECs revealed that it was miR-103-5p that promoted lipid accumulation but not miR-103-3p. In addition, Pantothenate Kinase 3 (PANK3), the host gene of miR-103, and Phospholipid Scramblase 4 (PLSCR4) were identified as the target genes of miR-103-5p by dual fluorescein and miRNA pulldown. Furthermore, we identified that cellular lipid levels were negatively regulated by PANK3 and PLSCR4. Lastly, in miR-103 knockout GMECs, the knockdown of PANK and PLSCR4 rescued the lipid accumulation. These findings suggest that miR-103-5p promotes lipid accumulation by targeting PLSCR4 and the host gene PANK3 in GMECs, providing new insights for the regulation of goat milk lipids via miRNAs.
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Affiliation(s)
- Lu Zhu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hongyun Jiao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenchang Gao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, China
| | - Chenbo Shi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fuhong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianqing Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xuefeng Lu
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, China
| | - Baolong Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Geng P, Zhao J, Li Q, Wang X, Qin W, Wang T, Shi X, Liu X, Chen J, Qiu H, Xu G. Z-Ligustilide Combined with Cisplatin Reduces PLPP1-Mediated Phospholipid Synthesis to Impair Cisplatin Resistance in Lung Cancer. Int J Mol Sci 2023; 24:17046. [PMID: 38069368 PMCID: PMC10706864 DOI: 10.3390/ijms242317046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Lung cancer is a malignant tumor with one of the highest morbidity and mortality rates in the world. Approximately 80-85% of lung cancer is diagnosed as non-small lung cancer (NSCLC), and its 5-year survival rate is only 21%. Cisplatin is a commonly used chemotherapy drug for the treatment of NSCLC. Its efficacy is often limited by the development of drug resistance after long-term treatment. Therefore, determining how to overcome cisplatin resistance, enhancing the sensitivity of cancer cells to cisplatin, and developing new therapeutic strategies are urgent clinical problems. Z-ligustilide is the main active ingredient of the Chinese medicine Angelica sinensis, and has anti-tumor activity. In the present study, we investigated the effect of the combination of Z-ligustilide and cisplatin (Z-ligustilide+cisplatin) on the resistance of cisplatin-resistant lung cancer cells and its mechanism of action. We found that Z-ligustilide+cisplatin decreased the cell viability, induced cell cycle arrest, and promoted the cell apoptosis of cisplatin-resistant lung cancer cells. Metabolomics combined with transcriptomics revealed that Z-ligustilide+cisplatin inhibited phospholipid synthesis by upregulating the expression of phospholipid phosphatase 1 (PLPP1). A further study showed that PLPP1 expression was positively correlated with good prognosis, whereas the knockdown of PLPP1 abolished the effects of Z-ligustilide+cisplatin on cell cycle and apoptosis. Specifically, Z-ligustilide+cisplatin inhibited the activation of protein kinase B (AKT) by reducing the levels of phosphatidylinositol 3,4,5-trisphosphate (PIP3). Z-ligustilide+cisplatin induced cell cycle arrest and promoted the cell apoptosis of cisplatin-resistant lung cancer cells by inhibiting PLPP1-mediated phospholipid synthesis. Our findings demonstrate that the combination of Z-Ligustilide and cisplatin is a promising approach to the chemotherapy of malignant tumors that are resistant to cisplatin.
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Affiliation(s)
- Pengyu Geng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Jinhui Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Qi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Xiaolin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Wangshu Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Ting Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Jia Chen
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China; (J.C.); (H.Q.)
| | - Hongdeng Qiu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China; (J.C.); (H.Q.)
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (P.G.); (J.Z.); (Q.L.); (X.W.); (W.Q.); (T.W.); (X.S.); (X.L.)
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
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