Cancer Detection and Classification by CpG Island Hypermethylation Signatures in Plasma Cell-Free DNA.

Cell-free DNA (cfDNA) methylation has emerged as a promising biomarker for early cancer detection, tumor type classification, and treatment response monitoring. Enrichment-based cfDNA methylation profiling methods such as cfMeDIP-seq have shown high accuracy in the classification of multiple cancer types. We have previously optimized another enrichment-based approach for ultra-low input cfDNA methylome profiling, termed cfMBD-seq. We reported that cfMBD-seq outperforms cfMeDIP-seq in the enrichment of high-CpG-density regions, such as CpG islands. However, the clinical feasibility of cfMBD-seq is unknown. In this study, we applied cfMBD-seq to profiling the cfDNA methylome using plasma samples from cancer patients and non-cancer controls. We identified 1759, 1783, and 1548 differentially hypermethylated CpG islands (DMCGIs) in lung, colorectal, and pancreatic cancer patients, respectively. Interestingly, the vast majority of DMCGIs were overlapped with aberrant methylation changes in corresponding tumor tissues, indicating that DMCGIs detected by cfMBD-seq were mainly driven by tumor-specific DNA methylation patterns. From the overlapping DMCGIs, we carried out machine learning analyses and identified a set of discriminating methylation signatures that had robust performance in cancer detection and classification. Overall, our study demonstrates that cfMBD-seq is a powerful tool for sensitive detection of tumor-derived epigenomic signals in cfDNA.

Anti-PD-1-Induced Pneumonitis Is Associated with Persistent Imaging Abnormalities in Melanoma Patients.

Pneumonitis may complicate anti-programmed death-1 (PD-1) therapy, although symptoms usually resolve with steroids. The long-term effects on respiratory function, however, are not well defined. We screened melanoma patients treated with anti-PD-1, with and without ipilimumab (anti-CTLA-4), and identified 31 patients with pneumonitis. Median time to radiographic findings was 4.8 months. Twenty-three patients (74%) presented with respiratory symptoms, whereas 8 (26%) were asymptomatic, and 11 (35%) were hospitalized. With 22.1 months median follow-up, 27 patients (87%) had resolution of symptoms, whereas 4 had persistent cough, dyspnea, and/or wheezing. By contrast, the rate of radiographic resolution was lower: Only 11 (35%) had complete radiographic resolution, whereas 14 (45%) had improvement of pneumonitis with persistent scarring or opacities, and 6 (19%) had persistent or worsened ground-glass opacities and/or nodular densities. Persistence (vs. resolution) of radiographic findings was associated with older age and initial need for steroids but not with need for hospitalization, timing of onset, or treatment regimen (combination vs. monotherapy). Among patients with serial pulmonary function tests, lung function improved with time. Although symptoms of anti-PD-1-induced pneumonitis resolved quickly, scarring or inflammation frequently persisted on computerized tomography. Therefore, further study of subclinical pulmonary effects of anti-PD-1 is needed.