Identification Of Hypoxia Research Articles

Identification of hypoxia- and immune-related biomarkers in patients with ischemic stroke

BackgroundThe immune microenvironment and hypoxia play crucial roles in the pathophysiology of ischemic stroke (IS). Hence, in this study, we aimed to identify hypoxia- and immune-related biomarkers in IS. MethodsThe IS microarray dataset GSE16561 was examined to determine differentially expressed genes (DEGs) utilizing bioinformatics-based analysis. The intersection of hypoxia-related genes and DEGs was conducted to identify differentially expressed hypoxia-related genes (DEHRGs). Then, using weighted correlation network analysis (WGCNA), all of the genes in GSE16561 dataset were examined to create a co-expression network, and module–clinical trait correlations were examined for the purpose of examining the genes linked to immune cells. The immune-related DEHRGs were submitted to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. A protein–protein interaction (PPI) network was constructed by Cytoscape plugin MCODE, in order to extract hub genes. The miRNet was used to predict hub gene-related transcription factors (TFs) and miRNAs. Finally, a diagnostic model was developed by least absolute shrinkage and selection operator (LASSO) logistic regression. ResultsBetween the control and IS samples, 4171 DEGs were found. Thereafter, the intersection of hypoxia-related genes and DEGs was conducted to obtain 45 DEHRGs. Ten significantly differentially infiltrated immune cells were found—namely, CD56dim natural killer cells, activated CD8 T cells, activated dendritic cells, activated B cells, central memory CD8 T cells, effector memory CD8 T cells, natural killer cells, gamma delta T cells, plasmacytoid dendritic cells, and neutrophils—between IS and control samples. Subsequently, we identified 27 immune-related DEHRGs through the intersection of DEHRGs and genes in important modules of WGCNA. The immune-related DEHRGs were primarily enriched in response to hypoxia, cellular polysaccharide metabolic process, response to decreased oxygen levels, polysaccharide metabolic process, lipid and atherosclerosis, and HIF−1 signaling pathway H. Using MCODE, FOS, DDIT3, DUSP1, and NFIL3 were found to be hub genes. In the validation cohort and training set, the AUC values of the diagnostic model were 0.9188034 and 0.9395085, respectively. ConclusionIn brief, we identified and validated four hub genes—FOS, DDIT3, DUSP1, and NFIL3—which might be involved in the pathological development of IS, potentially providing novel perspectives for the diagnosis and treatment of IS.

Identification of Hypoxia and Mitochondrial-related Gene Signature and Prediction of Prognostic Model in Lung Adenocarcinoma.

Background: The correlation between hypoxia and tumor development is widely acknowledged. Meanwhile, the foremost organelle affected by hypoxia is mitochondria. This study aims to determine whether they possess prognostic characteristics in lung adenocarcinoma (LUAD). For this purpose, a bioinformatics analysis was conducted to assess hypoxia and mitochondrial scores related genes, resulting in the successful establishment of a prognostic model. Methods: Using the single sample Gene Set Enrichment Analysis algorithm, the hypoxia and mitochondrial scores were computed. Differential expression analysis and weighted correlation network analysis were employed to identify genes associated with hypoxia and mitochondrial scores. Prognosis-related genes were obtained through univariate Cox regression, followed by the establishment of a prognostic model using least absolute shrinkage and selection operator Cox regression. Two independent validation datasets were utilized to verify the accuracy of the prognostic model using receiver operating characteristic and calibration curves. Additionally, a nomogram was employed to illustrate the clinical significance of this study. Results: 318 differentially expressed genes associated with hypoxia and mitochondrial scores were identified for the construction of a prognostic model. The prognostic model based on 16 genes, including PKM, S100A16, RRAS, TUBA4A, PKP3, KCTD12, LPGAT1, ITPRID2, MZT2A, LIFR, PTPRM, LATS2, PDIK1L, GORAB, PCDH7, and CPED1, demonstrates good predictive accuracy for LUAD prognosis. Furthermore, tumor microenvironments analysis and drug sensitivity analysis indicate an association between risk scores and certain immune cells, and a higher risk scores suggesting improved chemotherapy efficacy. Conclusion: The research established a prognostic model consisting of 16 genes, and a nomogram was developed to accurately predict the prognosis of LUAD patients. These findings may contribute to guiding clinical decision-making and treatment selection for patients with LUAD, ultimately leading to improved treatment outcomes.

Dissecting a hypoxia-related angiogenic gene signature for predicting prognosis and immune status in hepatocellular carcinoma.

BackgroundHypoxia and angiogenesis, as prominent characteristics of malignant tumors, are implicated in the progression of hepatocellular carcinoma (HCC). However, the role of hypoxia in the angiogenesis of liver cancer is unclear. Therefore, we explored the regulatory mechanisms of hypoxia-related angiogenic genes (HRAGs) and the relationship between these genes and the prognosis of HCC.MethodsThe transcriptomic and clinical data of HCC samples were downloaded from public datasets, followed by identification of hypoxia- and angiogenesis-related genes in the database. A gene signature model was constructed based on univariate and multivariate Cox regression analyses, and validated in independent cohorts. Kaplan-Meier survival and time-dependent receiver operating characteristic (ROC) curves were generated to evaluate the model’s predictive capability. Gene set enrichment analysis (GSEA) was performed to explore signaling pathways regulated by the gene signature. Furthermore, the relationships among gene signature, immune status, and response to anti-angiogenesis agents and immune checkpoint blockade (ICB) were analyzed.ResultsThe prognostic model was based on three HRAGs (ANGPT2, SERPINE1 and SPP1). The model accurately predicted that low-risk patients would have longer overall survival than high-risk patients, consistent with findings in other cohorts. GSEA indicated that high-risk group membership was significantly associated with hypoxia, angiogenesis, the epithelial-mesenchymal transition, and activity in immune-related pathways. The high-risk group also had more immunosuppressive cells and higher expression of immune checkpoints such as PD-1 and PD-L1. Conversely, the low-risk group had a better response to anti-angiogenesis and ICB therapy.ConclusionsThe gene signature based on HRAGs was predictive of prognosis and provided an immunological perspective that will facilitate the development of personalized therapies.

Refinement of an Established Procedure and Its Application for Identification of Hypoxia in Prostate Cancer Xenografts

Simple SummaryRegions of low oxygen status (hypoxia) are a characteristic feature of solid tumors. This hypoxia is a major cause of resistance to treatment, especially radiation therapy, and it can increase the likelihood of metastatic spread. Being able to accurately identify tumor hypoxia will allow us to predict a patient’s response to therapy and find alternative approaches to improve outcome. We have refined a dissection method that involves autoradiography and laser-guided microdissection of hypoxic areas in tumors. Using this approach, we were able to test the feasibility of applying a 15-gene signature that was previously developed for head and neck cancer patients to identify hypoxia in pre-clinical models of prostate cancer. Our results demonstrated the potential of this method to identify hypoxia in this tumor type and suggest its applicability for use in patients with prostate cancer.Background: This pre-clinical study was designed to refine a dissection method for validating the use of a 15-gene hypoxia classifier, which was previously established for head and neck squamous cell carcinoma (HNSCC) patients, to identify hypoxia in prostate cancer. Methods: PC3 and DU-145 adenocarcinoma cells, in vitro, were gassed with various oxygen concentrations (0–21%) for 24 h, followed by real-time PCR. Xenografts were established in vivo, and the mice were injected with the hypoxic markers [18F]-FAZA and pimonidazole. Subsequently, tumors were excised, frozen, cryo-sectioned, and analyzed using autoradiography ([18F]-FAZA) and immunohistochemistry (pimonidazole); the autoradiograms used as templates for laser capture microdissection of hypoxic and non-hypoxic areas, which were lysed, and real-time PCR was performed. Results: In vitro, all 15 genes were increasingly up-regulated as oxygen concentrations decreased. With the xenografts, all 15 genes were up-regulated in the hypoxic compared to non-hypoxic areas for both cell lines, although this effect was greater in the DU-145. Conclusions: We have developed a combined autoradiographic/laser-guided microdissection method with broad applicability. Using this approach on fresh frozen tumor material, thereby minimizing the degree of RNA degradation, we showed that the 15-gene hypoxia gene classifier developed in HNSCC may be applicable for adenocarcinomas such as prostate cancer.

Collaborative approach to reducing cardiac arrests in an acute medical unit.

Cardiac arrests are often preceded by a period of physiological deterioration. Preventing potentially avoidable cardiac arrests therefore depends on reliable recognition of, and response to, those deteriorations. Our hospital’s acute medical unit had one of the highest rates of cardiac arrest in our organisation at baseline. The aim was to reduce our unit’s cardiac arrest rate by over 50%. Pareto chart analysis identified unreliable processes in the recognition and response to deteriorating patients. Process mapping exercises were performed, then the model for improvement and rapid cycle tests of change were used to develop standardised processes for clinical observations, recognising deteriorating patients and responding to hypoxia. Multidisciplinary learning from what went well, incorporating resilience engineering principles, helped to identify good practice and then test ways of making good practice happen more reliably. Learning from success also addressed some of the psychological barriers to change by encouraging pride in work and a positive focus within our unit. The cardiac arrest rate reduced from 4.3/1000 (October 2014 to February 2016) to 1.1/1000 (March 2016 to end of 2016), associated with improved reliability of the following process measures: reliability of clinical observations, documentation of target oxygen saturations, identification of hypoxia and completion of structured response to hypoxia. This study is an example of a multidisciplinary team engaging in quality improvement, identifying their own local problems and testing their solutions scientifically. Learning from what went well had a positive impact on the project, and the team plans to spread the successful interventions across the organisation.

Imaging of brain oxygenation with magnetic resonance imaging: A validation with positron emission tomography in the healthy and tumoural brain

The partial pressure in oxygen remains challenging to map in the brain. Two main strategies exist to obtain surrogate measures of tissue oxygenation: the tissue saturation studied by magnetic resonance imaging (StO2-MRI) and the identification of hypoxia by a positron emission tomography (PET) biomarker with 3-[18F]fluoro-1-(2-nitro-1-imidazolyl)-2-propanol ([18F]-FMISO) as the leading radiopharmaceutical. Nonetheless, a formal validation of StO2-MRI against FMISO-PET has not been performed. The objective of our studies was to compare the two approaches in (a) the normal rat brain when the rats were submitted to hypoxemia; (b) animals implanted with four tumour types differentiated by their oxygenation. Rats were submitted to normoxic and hypoxemic conditions. For the brain tumour experiments, U87-MG, U251-MG, 9L and C6 glioma cells were orthotopically inoculated in rats. For both experiments, StO2-MRI and [18F]-FMISO PET were performed sequentially. Under hypoxemia conditions, StO2-MRI revealed a decrease in oxygen saturation in the brain. Nonetheless, [18F]-FMISO PET, pimonidazole immunohistochemistry and molecular biology were insensitive to hypoxia. Within the context of tumours, StO2-MRI was able to detect hypoxia in the hypoxic models, mimicking [18F]-FMISO PET with high sensitivity/specificity. Altogether, our data clearly support that, in brain pathologies, StO2-MRI could be a robust and specific imaging biomarker to assess hypoxia.

Hyperpolarized magnetic resonance spectroscopy for assessing tumor hypoxia

ABSTRACTIntroduction. Hypoxic tumor cells are radioresistant, therefore, identification of hypoxia is crucial. Hyperpolarized magnetic resonance spectroscopy (HPMRS) allows real time measurements of the conversion of pyruvate to lactate, the final step of anaerobic energy production, and may thus allow non-invasive identification of hypoxia or treatment-induced changes in oxygenation. The aim of the study was to investigate the usefulness of HPMRS as a means to assess tumor hypoxia and its dynamics during intervention.Material and methods. C3H mammary carcinomas grown in CDF1 mice were used. To manipulate with tumor oxygenation, non-anaesthetized mice were gassed with air, 10% or 100% oxygen prior to administration of hyperpolarized [1-¹³C]pyruvate and HPMRS analysis. A direct assessment of tumor oxygen partial pressure (pO2) distributions were made using the Eppendorf oxygen electrode in a separate, but similarly treated, group of mice.Results. Even though breathing 100% oxygen improved tumor oxygenation as evidenced by pO2 measurements, the mean (with 1 S.E.) [1-¹³C]lactate/[1-¹³C]pyruvate ratio was unaffected by this intervention, being 34 (30–37) in mice breathing air and 37 (33–42) in mice breathing 100% oxygen. In contrast, and in accordance with pO2 measurements, a significant increase in the [1-¹³C]lactate/[1-¹³C]pyruvate ratio was seen in 10% oxygen-breathing mice with a ratio of 46 (42–50).Conclusions. Although, no metabolic change was observed during 100% O2 breathing using HPMRS, the significant increase in the [1-¹³C]lactate/[1-¹³C]pyruvate ratio during 10% oxygen breathing suggests, that HPMRS can detect hypoxia-driven changes in the metabolic fate of pyruvate. To what extent and for what purposes HPMRS may best supplement or complement established techniques like hypoxia PET needs to be unraveled in future research.

Early identification of acute hypoxia based on brain NADH fluorescence and cerebral blood flow

Hypoxia is closely related to many diseases and often leads to death. Early detection and identification of the hypoxia causes may help to promptly determine the right rescue plan and reduce the mortality. We proposed a new multiparametric monitoring method employing mitochondrial reduced nicotinamide adenine dinucleotide (NADH) fluorescence, regional reflectance, regional cerebral blood flow (CBF), electrocardiography (ECG), and respiration under six kinds of acute hypoxia in four categories to investigate a correlation between the parameter variances and the hypoxia causes. The variation patterns of the parameters were discussed, and the combination of NADH and CBF may contribute to the identification of the causes of hypoxia.

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia.

BackgroundIn mammalians, HIF is a master regulator of hypoxia gene expression through direct binding to DNA, while its role in microRNA expression regulation, critical in the hypoxia response, is not elucidated genome wide. Our aim is to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression.MethodsMCF-7 cells were incubated at 1% Oxygen for 16, 32 and 48 h. SiRNA against HIF-1α and HIF-2α were performed as previously published. MicroRNA and mRNA expression were assessed using microRNA microarrays, small RNA sequencing, gene expression microarrays and Real time PCR. The Kraken pipeline was applied for microRNA-seq analysis along with Bioconductor packages. Microarray data was analysed using Limma (Bioconductor), ChIP-seq data were analysed using Gene Set Enrichment Analysis and multiple testing correction applied in all analyses.ResultsHypoxia time course microRNA sequencing data analysis identified 41 microRNAs significantly up- and 28 down-regulated, including hsa-miR-4521, hsa-miR-145-3p and hsa-miR-222-5p reported in conjunction with hypoxia for the first time. Integration of HIF-1α and HIF-2α ChIP-seq data with expression data showed overall association between binding sites and microRNA up-regulation, with hsa-miR-210-3p and microRNAs of miR-27a/23a/24-2 and miR-30b/30d clusters as predominant examples. Moreover the expression of hsa-miR-27a-3p and hsa-miR-24-3p was found positively associated to a hypoxia gene signature in breast cancer. Gene expression analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts involved in microRNA processing were found regulated by hypoxia, of which DICER (down-regulated) and AGO4 (up-regulated) were HIF dependent. DICER expression was found inversely correlated to hypoxia in breast cancer.ConclusionsIntegrated analysis of microRNA, mRNA and ChIP-seq data in a model cell line supports the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level, with the presence of HIF binding sites at microRNA genomic loci associated with up-regulation. The identification of hypoxia and HIF regulated microRNAs relevant for breast cancer is important for our understanding of disease development and design of therapeutic interventions.

20 Identification of hypoxia regulated genes unaffected by pH

20 Identification of hypoxia regulated genes unaffected by pH

Identification of hypoxia in cells and tissues of epigastric 9L rat glioma using EF5 [2-(2-nitro-1H-imidazol-1-yl)-N-(2,2,3,3,3-pentafluoropropyl) acetamide

One of the most sensitive hypoxia detection methods is based on the observation that binding of nitroimidazoles to cellular macromolecules occurs as a result of hypoxia-dependent bioreduction by cellular nitroreductases. Nitroimidazole-binding techniques provide measurements of hypoxia to virtually any degree of spatial resolution and with a multiplicity of techniques. This paper demonstrates hypoxia imaging using in vivo EF5 binding with detection by a fluorochrome-conjugated monoclonal antibody. We investigated these techniques in the 9L glioma tumour, in part because the exact nature of the hypoxia in this tumour system is controversial. Our results demonstrate that following intravenous injection of EF5, binding and detection using a monoclonal antibody in 9L gliomas is specific and oxygen dependent. Detection of binding using fluorescence microscopy can be performed on frozen tissues; tissue sections can be counterstained with haematoxylin and eosin for light microscopic analysis. Alternatively, the distribution of hypoxia in a tumour can be inferred by examining individual tumour cells using flow cytometric techniques. Based upon the results presented herein, the radiation-resistant phenotype of 9L epigastric tumours grown in our laboratories can be associated with the presence of hypoxic cells.

The influence of upper respiratory tract surgery on respiratory function evaluated by oxygen saturation.

To evaluate the influence of upper respiratory tract surgery on respiratory function, we used a pulse oximeter to measure the arterial oxygen saturation in 40 patients (ASA 1 or 2) during surgery under local anesthesia. The patients were divided into four groups: a control group of 10 patients who underwent surgery not involving the upper respiratory tract, and three upper respiratory tract surgery groups of 10 patients each underwent surgery on the nasal cavity alone (group 1), on the oral cavity alone (group 2), and on both the oral and nasal cavities (group 3). Groups 1 and 2 showed little desaturation compared to their baseline levels and the control group, while group 3 showed a mild desaturation even at the beginning of surgery and this gradually turned to a moderate or severe desaturation. This was due to both the extension of the surgical zone to the nasal and oral cavities and to ventilatory distress produced by massive bleeding and aspiration of secretions. Thus, the pulse oximeter is a useful monitor for upper respiratory tract surgery involving both general and local anesthesia. It allows the identification of hypoxia so that remedial therapy can be instituted.