Pre-analytical variables of circulating cell-free nucleosomes containing 5-methylcytosine DNA or histone modification H3K9Me3

Circulating Histones to Detect and Monitor the Progression of Cancer

Liquid biopsies have emerged as a minimally invasive cancer detection and monitoring method, which could identify cancer-related alterations in nucleosome or histone levels and modifications in blood, saliva, and urine. Histones, the core component of the nucleosome, are essential for chromatin compaction and gene expression modulation. Increasing evidence suggests that circulating histones and histone complexes, originating from cell death or immune cell activation, could act as promising biomarkers for cancer detection and management. In this review, we provide an overview of circulating histones as a powerful liquid biopsy approach and methods for their detection. We highlight current knowledge on circulating histones in hematologic malignancies and solid cancer, with a focus on their role in cancer dissemination, monitoring, and tumorigenesis. Last, we describe recently developed strategies to identify cancer tissue-of-origin in blood plasma based on nucleosome positioning, inferred from nucleosomal DNA fragmentation footprint, which is independent of the genetic landscape.

Sensitivity assessment of workflows detecting rare circulating cell-free DNA targets: A study design proposal

The field of liquid biopsy has seen extensive growth in recent decades, making it one of the most promising areas in molecular diagnostics. Circulating cell-free DNA (ccfDNA) especially is used as an analyte in a growing number of diagnostic assays. These assays require specified preanalytical workflows delivering ccfDNA in qualities and quantities that facilitate correct and reliable results. As each step and component used in the preanalytical process has the potential to influence the assay sensitivity and other performance characteristics, it is key to find an unbiased experimental setup to test these factors in diagnostic or research laboratories. We defined one such setup by using blood from healthy subjects and commercially available products for blood collection, spike-in material, ccfDNA isolation, and qPCR assays. As the primary read-out, we calculated the probit model-based LOD95 (limit of detection of the 95^th percentile) from the qPCR assay results. In a proof of principle study we tested two different but widely used blood ccfDNA profile stabilization technologies in blood collection tubes, the Cell-Free DNA BCT and the PAXgene Blood ccfDNA Tube. We tested assays for three different EGFR gene mutations and one BRAF gene mutation. The study design revealed differences in performance between the two tested technologies for all four mutations. In conclusion, we successfully established a blueprint for a test procedure capable of verifying and validating a liquid biopsy workflow from blood collection to the analytical result.

Pre-analytical issues in liquid biopsy – where do we stand?

It is well documented that in the chain from sample to the result in a clinical laboratory, the pre-analytical phase is the weakest and most vulnerable link. This also holds for the use and analysis of extracellular nucleic acids. In this short review, we will summarize and critically evaluate the most important steps of the pre-analytical phase, i.e. the choice of the best control population for the patients to be analyzed, the actual blood draw, the choice of tubes for blood drawing, the impact of delayed processing of blood samples, the best method for getting rid of cells and debris, the choice of matrix, i.e. plasma vs. serum vs. other body fluids, and the impact of long-term storage of cell-free liquids on the outcome. Even if the analysis of cell-free nucleic acids has already become a routine application in the area of non-invasive prenatal screening (NIPS) and in the care of cancer patients (search for resistance mutations in the EGFR gene), there are still many unresolved issues of the pre-analytical phase which need to be urgently tackled.

Plasma Histone H4 and H4K20 Trimethylation Levels Differ Between Colon Cancer and Precancerous Polyps

BACKGROUND/AIM

No blood-based biomarkers are available to differentiate between colonic tumors and precancerous polyps. Previously we demonstrated levels of trimethylated H4K20 (H4K20me3) to be lower in blood plasma from patients with colon cancer than those from cancer-free individuals. Herein, we added individuals with precancerous polyps for the first time in order to analyze and investigate the usefulness of plasma H4K20me3 and histone H4 to discriminate colon tumors from precancerous polyps.

MATERIALS AND METHODS

The study included a cohort of 185 individuals undergoing colonoscopy. H4K20me3 and histone H4, measured by an enzyme-linked immunosorbent assay-like assay in plasma, were analyzed according to colonoscopy findings.

RESULTS

Levels of H4K20me3 were lower in patients with colon cancer than in individuals with normal colonoscopy and those with precancerous polyps (p=0.02 and p=0.01, respectively). In contrast, highest quantities of histone H4 were measured in those with colon cancer compared to other groups (all p<0.01).

CONCLUSION

Beside H4K20me3, plasma histone H4 is a useful marker to discriminate colonic tumors from precancerous polyps and other conditions.

Liquid Biopsies to Monitor Solid Organ Transplant Function: A Review of New Biomarkers

Despite modern immunosuppressive therapy, allograft rejection remains a major cause of solid organ transplant dysfunction. For clinical care, organ transplant function is routinely monitored by measuring biomarkers that, depending on the organ transplanted, include serum creatinine, N-terminal pro-hormone of brain natriuretic peptide (NT-proBNP), and aspartate aminotransferase. All can be measured easily in clinical chemistry laboratories. The main problem with these biomarkers is that they have a low sensitivity for the detection of allograft damage and are nonspecific for the detection of allograft rejection. To diagnose rejection, histologic examination of grafted tissue is necessary, which requires an invasive biopsy procedure. There is thus an unmet need in transplantation medicine for biomarkers that are specific for rejection, identify graft injury at an early stage, and may eventually overcome the need for a transplant biopsy. Recently, tremendous progress in the field of biomarkers has been made. In this narrative review, the potential of donor-derived cell-free DNA (ddcfDNA), cell-free nucleosomes, and extracellular vesicles to act as next-generation biomarkers for solid organ transplant is discussed. Based on the fact that cell content is released during rejection, these markers could serve as very specific biomarkers for allograft injury and rejection. These markers have the potential to improve rejection monitoring, evaluate the response to antirejection therapy, and may decrease the need for invasive procedures.

Serological biomarkers in triage of FIT-positive subjects?

FIT-based colorectal cancer screening has been implemented in many countries including Denmark, where 916 colorectal cancer and 4468 high- or medium-risk adenoma patients were identified within April-December 2014, among 16,806 subjects with a positive FIT test. Screening increases the overall requirements for colonoscopy, which may challenge the current capacity. Some countries have increased their initial FIT cut-off level in order to comply with lack of colonoscopy capacity. Many patients with neoplasia will not be detected, however, by using increased FIT cut-off levels. The number of patients with neoplastic lesions missed by increased cut-off levels appears to be much higher than expected. Therefore, tests that identify those patients missed by increased FIT cut-off levels must be developed. Preliminary results of determination of one of several biomarker entities currently under investigation show that nucleosome blood tests may be one option for identifying some of these patients. Implementation of a triage test consisting of FIT, blood-based biomarkers and plus/minus colonoscopy is suggested to identify subjects with FIT levels between the initial and the increased cut-off level that must be offered colonoscopy. In addition, triage may reduce the frequency of unnecessary colonoscopies by 25%.

Circulating Nucleosomes and Nucleosome Modifications as Biomarkers in Cancer

Traditionally the stratification of many cancers involves combining tumour and clinicopathological features (e.g., patient age; tumour size, grade, receptor status and location) to inform treatment options and predict recurrence risk and survival. However, current biomarkers often require invasive excision of the tumour for profiling, do not allow monitoring of the response to treatment and stratify patients into broad heterogeneous groups leading to inconsistent treatment responses. Here we explore and describe the benefits of using circulating biomarkers (nucleosomes and/or modifications to nucleosomes) as a non-invasive method for detecting cancer and monitoring response to treatment. Nucleosomes (DNA wound around eight core histone proteins) are responsible for compacting our genome and their composition and post-translational modifications are responsible for regulating gene expression. Here, we focus on breast and colorectal cancer as examples where utilizing circulating nucleosomes as biomarkers hold real potential as liquid biopsies. Utilizing circulating nucleosomes as biomarkers is an exciting new area of research that promises to allow both the early detection of cancer and monitoring of treatment response. Nucleosome-based biomarkers combine with current biomarkers, increasing both specificity and sensitivity of current tests and have the potential to provide individualised precision-medicine based treatments for patients.