The Epigenetic Biomarker γH2AX: From Bench to Clinical Trials

Cystic fibrosis (CF) is a chronic genetic disease that mainly affects the respiratory and gastrointestinal systems. No curative treatments are available, but the follow-up in specialized centers has greatly improved the patient life expectancy. Robust biomarkers are required to monitor the disease, guide treatments, stratify patients, and provide outcome measures in clinical trials. In the present study, we outline a strategy to select putative DNA methylation biomarkers of lung disease severity in cystic fibrosis patients. In the discovery step, we selected seven potential biomarkers using a genome-wide DNA methylation dataset that we generated in nasal epithelial samples from the MethylCF cohort. In the replication step, we assessed the same biomarkers using sputum cell samples from the MethylBiomark cohort. Of interest, DNA methylation at the cg11702988 site (ATP11A gene) positively correlated with lung function and BMI, and negatively correlated with lung disease severity, P. aeruginosa chronic infection, and the number of exacerbations. These results were replicated in prospective sputum samples collected at four time points within an 18-month period and longitudinally. To conclude, (i) we identified a DNA methylation biomarker that correlates with CF severity, (ii) we provided a method to easily assess this biomarker, and (iii) we carried out the first longitudinal analysis of DNA methylation in CF patients. This new epigenetic biomarker could be used to stratify CF patients in clinical trials.

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A Computational Solution to Bolster Epigenetic Clock Reliability for Clinical Trials and Longitudinal Tracking

Innovation in Aging ◽

10.1093/geroni/igab046.015 ◽

2021 ◽

Vol 5 (Supplement_1) ◽

pp. 5-5

Author(s):

Albert Higgins-Chen ◽

Kyra Thrush ◽

Tina Hu-Seliger ◽

Yunzhang Wang ◽

Sara Hagg ◽

...

Keyword(s):

Clinical Trials ◽

High Reliability ◽

Principal Component ◽

Epigenetic Clock ◽

Age Related ◽

Longitudinal Tracking ◽

Short And Long Term ◽

Epigenetic Biomarker ◽

Computational Solution

Abstract Epigenetic clocks are widely used aging biomarkers, but they are calculated from methylation data for individual CpGs that can be surprisingly unreliable. We report that technical noise causes six major epigenetic clocks to deviate by 3 to 9 years between replicates. We present a novel computational solution: we perform principal component analysis followed by biological age prediction using principal components, extracting shared age-related changes across CpGs while ignoring noise from individual CpGs. Our novel principal-component versions of six clocks show agreement between most technical replicates within 1 year, and increased stability in short- and long-term longitudinal studies. This requires only one additional step compared to traditional clocks, does not require prior knowledge of CpG reliabilities, and can improve the reliability of any existing or future epigenetic biomarker. The extremely high reliability of principal component epigenetic clocks makes them particularly useful for personalized medicine and clinical trials evaluating novel aging interventions.

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A computational solution for bolstering reliability of epigenetic clocks: Implications for clinical trials and longitudinal tracking

10.1101/2021.04.16.440205 ◽

2021 ◽

Author(s):

Albert T. Higgins-Chen ◽

Kyra L. Thrush ◽

Yunzhang Wang ◽

Pei-Lun Kuo ◽

Meng Wang ◽

...

Keyword(s):

Clinical Trials ◽

High Reliability ◽

Random Noise ◽

Principal Component ◽

Methylation Data ◽

Technical Noise ◽

Longitudinal Tracking ◽

Level Data ◽

Epigenetic Biomarker ◽

Age Prediction

Epigenetic clocks are widely used aging biomarkers calculated from DNA methylation data. Unfortunately, measurements for individual CpGs can be surprisingly unreliable due to technical noise, and this may limit the utility of epigenetic clocks. We report that noise produces deviations up to 3 to 9 years between technical replicates for six major epigenetic clocks. The elimination of low-reliability CpGs does not ameliorate this issue. Here, we present a novel computational multi-step solution to address this noise, involving performing principal component analysis on the CpG-level data followed by biological age prediction using principal components as input. This method extracts shared systematic variation in DNAm while minimizing random noise from individual CpGs. Our novel principal-component versions of six clocks show agreement between most technical replicates within 0 to 1.5 years, equivalent or improved prediction of outcomes, and more stable trajectories in longitudinal studies and cell culture. This method entails only one additional step compared to traditional clocks, does not require prior knowledge of CpG reliabilities, and can improve the reliability of any existing or future epigenetic biomarker. The high reliability of principal component-based epigenetic clocks will make them particularly useful for applications in personalized medicine and clinical trials evaluating novel aging interventions.

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Localization of Gallium-67 in Peritoneal Cells by Electron Microscopic Autoradiography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100072460 ◽

1973 ◽

Vol 31 ◽

pp. 404-405

Author(s):

D. C. Swartzendruber ◽

Norma L. Idoyaga-Vargas

Keyword(s):

Clinical Trials ◽

Soft Tissue ◽

Tumor Tissue ◽

Soft Tissue Tumors ◽

Clinical Usefulness ◽

Electron Microscopic ◽

Normal Cells ◽

Electron Microscopic Autoradiography ◽

Peritoneal Cells ◽

Gallium 67

The radionuclide gallium-67 (67Ga) localizes preferentially but not specifically in many human and experimental soft-tissue tumors. Because of this localization, 67Ga is used in clinical trials to detect humar. cancers by external scintiscanning methods. However, the fact that 67Ga does not localize specifically in tumors requires for its eventual clinical usefulness a fuller understanding of the mechanisms that control its deposition in both malignant and normal cells. We have previously reported that 67Ga localizes in lysosomal-like bodies, notably, although not exclusively, in macrophages of the spocytaneous AKR thymoma. Further studies on the uptake of 67Ga by macrophages are needed to determine whether there are factors related to malignancy that might alter the localization of 67Ga in these cells and thus provide clues to discovering the mechanism of 67Ga localization in tumor tissue.

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