scholarly journals Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes

Biomedicines ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 582
Author(s):  
Yoko Ono ◽  
Hidemasa Bono
Keyword(s):  
Meta Analysis ◽  
Hypoxia Inducible Factor ◽  
Data Driven ◽  
Similarity Coefficients ◽  
Hypoxia Inducible Factor 1 ◽  
Response System ◽  
Inducible Genes ◽  
The Relationship ◽  
G Protein Coupled ◽  
Sufficient Oxygen

Hypoxia is a condition in which cells, tissues, or organisms are deprived of sufficient oxygen supply. Aerobic organisms have a hypoxic response system, represented by hypoxia-inducible factor 1-α (HIF1A), to adapt to this condition. Due to publication bias, there has been little focus on genes other than well-known signature hypoxia-inducible genes. Therefore, in this study, we performed a meta-analysis to identify novel hypoxia-inducible genes. We searched publicly available transcriptome databases to obtain hypoxia-related experimental data, retrieved the metadata, and manually curated it. We selected the genes that are differentially expressed by hypoxic stimulation, and evaluated their relevance in hypoxia by performing enrichment analyses. Next, we performed a bibliometric analysis using gene2pubmed data to examine genes that have not been well studied in relation to hypoxia. Gene2pubmed data provides information about the relationship between genes and publications. We calculated and evaluated the number of reports and similarity coefficients of each gene to HIF1A, which is a representative gene in hypoxia studies. In this data-driven study, we report that several genes that were not known to be associated with hypoxia, including the G protein-coupled receptor 146 gene, are upregulated by hypoxic stimulation.

scholarly journals Multi-omic meta-analysis of transcriptomes and the bibliome uncovers GPR146 as the novel hypoxia-inducible gene

2021 ◽  
Author(s):  
Yoko Ono ◽  
Hidemasa Bono
Keyword(s):  
Meta Analysis ◽  
Hypoxia Inducible Factor ◽  
Enrichment Analysis ◽  
The Novel ◽  
Hypoxia Inducible Factor 1 ◽  
Response System ◽  
The Relationship ◽  
G Protein Coupled ◽  
Inducible Gene ◽  
Sufficient Oxygen

Hypoxia is a condition in which cells, tissues, or organisms are deprived of sufficient oxygen supply. Aerobic organisms have the hypoxic response system, represented by hypoxia-inducible factor 1-α (HIF1A), to avoid this condition. Because of publication bias, the genes other than well-known signature hypoxia-stimulating genes may not be focused. Therefore, in this study, we performed meta-analysis to identify novel hypoxia-responsive genes. We searched publicly available transcriptome databases to obtain hypoxia-related experimental data, retrieved the metadata, and manually curated it. We selected the genes that are differentially expressed by hypoxic stimulation, and evaluated their relevance in hypoxia by performing enrichment analyses. We then calculated the number of reports and similarity coefficient of each gene for HIF1A (surrogate for hypoxia) using gene2pubmed that provides information about the relationship between gene and publication. Enrichment analysis confirmed that the selected genes were related to hypoxic stimulation, as expected. We then performed gene2pubmed analysis to investigate the genes that had not been fully studied under hypoxia. In this data-driven study, we report that the G protein-coupled receptor 146 gene is upregulated by hypoxic stimulation.

scholarly journals Hypoxia-inducible factor–1 and associated upstream and downstream proteins in the pathophysiology and management of glioblastoma

2014 ◽  
Vol 37 (6) ◽  
pp. E8 ◽  
Author(s):  
Matthew Womeldorff ◽  
David Gillespie ◽  
Randy L. Jensen
Keyword(s):  
Cellular Response ◽  
Treatment Options ◽  
Hypoxia Inducible Factor ◽  
Hypoxia Inducible Factor 1 ◽  
Poor Patient ◽  
Growth Development ◽  
The Relationship ◽  
Insight Into ◽  
Upstream Regulators

Glioblastoma multiforme (GBM) is a highly aggressive brain tumor with an exceptionally poor patient outcome despite aggressive therapy including surgery, radiation, and chemotherapy. This aggressive phenotype may be associated with intratumoral hypoxia, which probably plays a key role in GBM tumor growth, development, and angiogenesis. A key regulator of cellular response to hypoxia is the protein hypoxia-inducible factor–1 (HIF-1). An examination of upstream hypoxic and nonhypoxic regulation of HIF-1 as well as a review of the downstream HIF-1–regulated proteins may provide further insight into the role of this transcription factor in GBM pathophysiology. Recent insights into upstream regulators that intimately interact with HIF-1 could provide potential therapeutic targets for treatment of this tumor. The same is potentially true for HIF-1–mediated pathways of glycolysis-, angiogenesis-, and invasion-promoting proteins. Thus, an understanding of the relationship between HIF-1, its upstream protein regulators, and its downstream transcribed genes in GBM pathogenesis could provide future treatment options for the care of patients with these tumors.

scholarly journals Cavefish cope with environmental hypoxia by developing more erythrocytes and overexpression of hypoxia inducible genes

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Corine M van der Weele ◽  
William R Jeffery
Keyword(s):  
Normal Development ◽  
Hypoxia Inducible Factor ◽  
Hypoxia Tolerance ◽  
Astyanax Mexicanus ◽  
Hypoxia Inducible Factor 1 ◽  
Primitive Hematopoiesis ◽  
Cave Environment ◽  
Surface Dwelling ◽  
Inducible Genes ◽  
Lateral Mesoderm

Dark caves lacking primary productivity can expose subterranean animals to hypoxia. We used the surface-dwelling (surface fish) and cave-dwelling (cavefish) morphs of Astyanax mexicanus as a model for understanding the mechanisms of hypoxia tolerance in the cave environment. Primitive hematopoiesis, which is restricted to the posterior lateral mesoderm in other teleosts, also occurs in the anterior lateral mesoderm in Astyanax, potentially pre-adapting surface fish for hypoxic cave colonization. Cavefish have enlarged both hematopoietic domains and develop more erythrocytes than surface fish, which are required for normal development in both morphs. Laboratory induced hypoxia suppresses growth in surface fish but not in cavefish. Both morphs respond to hypoxia by overexpressing hypoxia-inducible factor 1 (hif1) pathway genes, and some hif1 genes are constitutively upregulated in normoxic cavefish to similar levels as in hypoxic surface fish. We conclude that cavefish cope with hypoxia by increasing erythrocyte development and constitutive hif1 gene overexpression.

A new HIF-1 alpha variant induced by zinc ion suppresses HIF-1-mediated hypoxic responses

2001 ◽  
Vol 114 (22) ◽  
pp. 4051-4061
Author(s):  
Yang-Sook Chun ◽  
Eunjoo Choi ◽  
Eun-Jin Yeo ◽  
Jong Ho Lee ◽  
Myung-Suk Kim ◽  
...  
Keyword(s):  
Nuclear Translocation ◽  
Consensus Sequence ◽  
Hypoxia Inducible Factor ◽  
Zinc Ion ◽  
Dominant Negative ◽  
Hypoxia Inducible Factor 1 ◽  
Aryl Hydrocarbon ◽  
Hypoxic Conditions ◽  
Alpha Variant ◽  
Inducible Genes

The expressions of hypoxia-inducible genes are upregulated by hypoxia-inducible factor 1 (HIF-1), which is a heterodimer of HIF-1α and HIF-1β/ARNT (aryl hydrocarbon receptor nuclear transporter). Under hypoxic conditions, HIF-1α becomes stabilized and both HIF-1α and ARNT are translocated into the nucleus and codimerized, binding to the HIF-1 consensus sequence and transactivating hypoxia-inducible genes. Other than hypoxia, cobalt and nickel, which can substitute for iron in the ferroprotein, induce the stabilization of HIF-1α and the activation of HIF-1. We found previously that, although zinc, another example of a metal substitute for iron, stabilized HIF-1α, it suppressed the formation of HIF-1 by blocking the nuclear translocation of ARNT. Here, we identify a new spliced variant of human HIF-1α that is induced by zinc. The isoform lacks the 12th exon, which produced a frame-shift and gave a shorter form of HIF-1α (557 amino acids), designated HIF-1αZ (HIF-1α induced by Zn). This moiety was found to inhibit HIF-1 activity and reduce mRNA expressions of the hypoxia-inducible genes. It blocked the nuclear translocation of ARNT but not that of endogenous HIF-1α, and was associated with ARNT in the cytosol. These results suggest that HIF-1αZ functions as a dominant-negative isoform of HIF-1 by sequestering ARNT in the cytosol. In addition, the generation of HIF-1αZ seems to be responsible for the inhibitory effects of the zinc ion on HIF-1-mediated hypoxic responses, because the expressed HIF-1αZ behaved in the same manner as zinc in terms of inhibited HIF-1 activity and ARNT translocation.

scholarly journals Prognostic role of hypoxia-inducible factor-1 alpha expression in osteosarcoma: a meta-analysis

2016 ◽  
pp. 1477 ◽  
Author(s):  
Hai-Yong Ren ◽  
Heng Yuan Li ◽  
Tao Xie ◽  
Ling Ling Sun ◽  
Ting Zhu ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Hypoxia Inducible Factor ◽  
Prognostic Role ◽  
Hypoxia Inducible Factor 1

scholarly journals Hypoxia-Inducible Factor-1 Expression Predicts Osteosarcoma Patients’ Survival: A Meta-Analysis

2016 ◽  
Vol 31 (3) ◽  
pp. 229-234 ◽  
Author(s):  
Yurong Ouyang ◽  
Hui Li ◽  
Jie Bu ◽  
Xiaoyang Li ◽  
Zhuoyuan Chen ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Hypoxia Inducible Factor ◽  
Disease Free Survival ◽  
Free Survival ◽  
Hypoxia Inducible Factor 1 ◽  
Proliferation And Metastasis ◽  
Primary Bone ◽  
The Stability ◽  
High Level

Osteosarcoma, the most common primary bone malignancy, is characterized by easily relapsing and metastasizing. Hypoxia-inducible factor-1 (HIF-1) plays an essential role in tumorigenesis, affecting tumor metabolism, differentiation, angiogenesis, proliferation and metastasis, and has been found to be associated with survival in patients with osteosarcoma. The possible prognostic value of HIF-1 was investigated in many studies, but the results were inconsistent. We therefore conducted a meta-analysis to elucidate the correlation of HIF-1 expression, analyzed by immunohistochemistry in osteosarcoma tissues, with prognosis. The association degree was assessed by calculation of the hazard ratio (HR) and risk ratio (RR) with corresponding 95% confidence intervals (CIs). Follow-up information was available for 486 patients from 7 studies. The results showed that high HIF-1 expression was associated with a worse prognosis when compared to low or undetectable HIF-1 expression, with an HR of 3.67 (95% CI 2.24-5.99; p<0.001) for overall survival (OS) and an RR of 3.72 (95% CI 2.26-6.13; p<0.001) for OS. The RR of 2.55 for disease-free survival (DFS) did not show any obvious relationship between a high level of HIF-1 and DFS (95% CI 0.95-6.87; p = 0.064). The stability of this result was tested by sensitivity analysis and no significant change was detected. This meta-analysis suggests that HIF-1 is an effective prognostic biomarker to predict OS in patients with osteosarcoma.

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