The molecular mechanisms and gene expression profiling for shikonin-induced apoptotic and necroptotic cell death in U937 cells

Mammalian ooplasm supports the preimplantation development and reprograms the introduced nucleus transferred from a somatic cell to confer pluripotency in a cloning experiment. However, the underlying molecular mechanisms of oocyte competence remain unknown. Recent advances in microarray technologies have allowed gene expression profiling of such tiny specimens as oocytes and preimplantation embryos, generating a flood of information about gene expressions. So, what can we learn from it? Here, we review the initiative global gene expression studies of mouse and/or human oocytes, focusing on the lists of maternal transcripts and their expression patterns during oogenesis and preimplantation development. Especially, the genes expressed exclusively in oocytes should contribute to the uniqueness of oocyte competence, driving mammalian development systems of oocytes and preimplantation embryos. Furthermore, we discuss future directions for oocyte gene expression profiling, including discovering biomarkers of oocyte quality and exploiting the microarray data for ‘making oocytes’.

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Gene expression profiling reveals underlying molecular mechanisms of the early stages of tamoxifen-induced rat hepatocarcinogenesis☆

Toxicology and Applied Pharmacology ◽

10.1016/j.taap.2007.07.001 ◽

2007 ◽

Vol 225 (1) ◽

pp. 61-69 ◽

Cited By ~ 22

Author(s):

Igor P. Pogribny ◽

Tetyana V. Bagnyukova ◽

Volodymyr P. Tryndyak ◽

Levan Muskhelishvili ◽

Rocio Rodriguez-Juarez ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Molecular Mechanisms ◽

Early Stages

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Investigation of the molecular mechanisms underlying postoperative recurrence in prostate cancer by gene expression profiling

Experimental and Therapeutic Medicine ◽

10.3892/etm.2017.5510 ◽

2017 ◽

Author(s):

Cheng Yajun ◽

Tang Yuan ◽

Wang Zhong ◽

Xu Bin

Keyword(s):

Gene Expression ◽

Prostate Cancer ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Molecular Mechanisms ◽

Postoperative Recurrence

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Comprehensive analyses reveal three-gene signatures in ovarian cancer

10.21203/rs.3.rs-28741/v1 ◽

2020 ◽

Author(s):

Chuang Li ◽

Yuan Lyu ◽

Caixia Liu

Keyword(s):

Gene Expression ◽

Ovarian Cancer ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Molecular Mechanisms ◽

Hub Genes ◽

Clinical Prognosis ◽

Gene Signatures ◽

Cancer Tissues ◽

Differently Expressed Genes

Abstract Background: Ovarian cancer is a common cancer that affects the quality of women’s life. With the limitation of the early diagnosis of the disease, ovarian cancer has a high mortality rate worldwide. However, the molecular mechanisms underlying tumor invasion, proliferation, and metastasis in ovarian cancer remain unclear. We aimed to identify, using bioinformatics, important genes and pathways that may serve crucial roles in the prevention, diagnosis, and treatment of ovarian cancer. Methods: Three microarray datasets (GSE14407, GSE36668, and GSE26712) were selected for whole-genome gene expression profiling , and differentially expressed genes were identified between normal and ovarian cancer tissues. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using DAVID. Additionally, a protein-protein interaction network was constructed to reveal possible interactions among the differently expressed genes. The prognostic values of the hub genes were investigated using Gene Expression Profiling Interactive Analysis (GEPIA) and the KM plotter database. Meanwhile, the mRNA expression analysis of the hub genes was performed using the GEPIA database. Results: We obtained 247 upregulated and 530 downregulated differently expressed genes, and 52 hub genes in the significant gene modules. Enrichment analysis revealed that the hub genes were significantly ( P < 0.05) associated with proliferation. Additionally, BIRC5, CXCL13, and PBK were revealed to be significantly associated with the clinical prognosis of patients with ovarian cancer. Immunohistochemical staining results obtained from the Human Protein Atlas revealed that BIRC5, PBK, and CXCL13 were highly expressed in ovaria cancer tissues. Conclusion Three-gene signatures ( BIRC5, CXCL13 , and PBK ) are associated with the occurrence, development, and prognosis of OC, and may therefore serve as biological markers of the disease.

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The Fibrosis-Targeted Collagen/Integrins Gene Profile Predicts Risk of Metastasis in Pulmonary Neuroendocrine Neoplasms

Frontiers in Oncology ◽

10.3389/fonc.2021.706141 ◽

2021 ◽

Vol 11 ◽

Author(s):

Tabatha Gutierrez Prieto ◽

Juliana Machado-Rugolo ◽

Camila Machado Baldavira ◽

Ana Paula Pereira Velosa ◽

Walcy Rosolia Teodoro ◽

...

Keyword(s):

Gene Expression ◽

Lymph Node ◽

Gene Expression Profiling ◽

Distant Metastasis ◽

Expression Profiling ◽

Molecular Mechanisms ◽

Metastatic Potential ◽

Neuroendocrine Neoplasms ◽

Stage Design ◽

Integrin Gene

Recently, collagen/integrin genes have shown promise as predictors of metastasis mainly in non-small cell lung cancer and breast cancer. However, it is unknown if these gene expression profiling differ in metastatic potential of pulmonary neuroendocrine neoplasms (PNENs). In this study, we sought to identify differentially expressed collagen/integrin genes in PNENs in order to understand the molecular mechanisms underlying the development of stroma-associated fibrosis for invasion and metastasis. We compared collagen/integrin gene expression profiling between PNE tumors (PNETs) and PNE carcinomas (PNECs) using a two-stage design. First, we used PCR Array System for 84 ECM-related genes, and among them, we found COL1A2, COL3A1, COL5A2, ITGA5, ITGAV, and ITGB1 functionally involved in the formation of the stroma-associated fibrosis among PNENs histological subtypes. Second, we examined the clinical association between the six collagen/integrin genes in tumor tissues from 24 patients with surgically excised PNENs. However, the pathological exam of their resected tissues demonstrated that 10 developed lymph node metastasis and 7 distant metastasis. We demonstrated and validated up regulation of the six fibrogenic genes in PNECs and down regulation in PNETs that were significantly associated with metastasis-free and overall survival (P<0.05). Our study implicates up regulation of fibrogenic genes as a critical molecular event leading to lymph node and distant metastasis in PNENs.

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Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2020125118 ◽

2021 ◽

Vol 118 (18) ◽

pp. e2020125118

Author(s):

Yoshiaki Kita ◽

Hirozumi Nishibe ◽

Yan Wang ◽

Tsutomu Hashikawa ◽

Satomi S. Kikuchi ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Large Scale ◽

Molecular Mechanisms ◽

Neural Circuit ◽

Expression Patterns ◽

Three Dimensional ◽

Control Of Gene Expression ◽

Cellular Resolution

Precise spatiotemporal control of gene expression in the developing brain is critical for neural circuit formation, and comprehensive expression mapping in the developing primate brain is crucial to understand brain function in health and disease. Here, we developed an unbiased, automated, large-scale, cellular-resolution in situ hybridization (ISH)–based gene expression profiling system (GePS) and companion analysis to reveal gene expression patterns in the neonatal New World marmoset cortex, thalamus, and striatum that are distinct from those in mice. Gene-ontology analysis of marmoset-specific genes revealed associations with catalytic activity in the visual cortex and neuropsychiatric disorders in the thalamus. Cortically expressed genes with clear area boundaries were used in a three-dimensional cortical surface mapping algorithm to delineate higher-order cortical areas not evident in two-dimensional ISH data. GePS provides a powerful platform to elucidate the molecular mechanisms underlying primate neurobiology and developmental psychiatric and neurological disorders.

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