Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR

Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L^-1] and hypoxia (DO = 4‒5 mg L^-1) in 10 and 18° temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; P < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.

The Potential Role of Radiomics and Radiogenomics in Patient Stratification by Tumor Hypoxia Status

BACKGROUND

Despite the clinical knowledge accumulated over a century about tumor hypoxia, this biologic parameter remains a major challenge in cancer treatment. Patients presenting with hypoxic tumors are more resistant to radiotherapy and often poor responders to chemotherapy. Treatment failure because of hypoxia is, therefore, very common. Several methods have been trialed to measure and quantify tumor hypoxia, with varied success. Over the last couple of decades, hypoxia-specific functional imaging has started to play an important role in personalized treatment planning and delivery. Yet, there are no gold standards in place, owing to inter- and intrapatient phenotypic variations that further complicate the overall picture. The aim of the current article is to analyze, through the review of the literature, the potential role of radiomics and radiogenomics in patient stratification by tumor hypoxia status.

METHODS

Search of literature published in English since 2000 was conducted using Medline. Additional articles were retrieved via pearling of identified literature. Publications were reviewed and summarized in text and in a tabulated format.

RESULTS

Although still an immature area of science, radiomics has shown its potential in the quantification of hypoxia within the heterogeneous tumor, quantification of changes regarding the degree of hypoxia after radiotherapy and drug delivery, monitoring tumor response to anti-angiogenic therapy, and assisting with patient stratification and outcome prediction based on the hypoxic status.

CONCLUSIONS

The lack of technique standardization to measure and quantify tumor hypoxia presents an opportunity for data mining and machine learning in radiogenomics.