Case report: Whole exome sequencing of circulating cell-free tumor DNA in a follicular thyroid carcinoma patient with lung and bone metastases

Instrumental variable-based high-dimensional mediation analysis with unmeasured confounders for survival data in the observational epigenetic study

Background: High dimensional mediation analysis is frequently conducted to explore the role of epigenetic modifiers between exposure and health outcome. However, the issue of high dimensional mediation analysis with unmeasured confounders for survival analysis in observational study has not been well solved. Methods: In this study, we proposed an instrumental variable based approach for high dimensional mediation analysis with unmeasured confounders in survival analysis for epigenetic study. We used the Sobel's test, the Joint test, and the Bootstrap method to test the mediation effect. A comprehensive simulation study was conducted to decide the best test strategy. An empirical study based on DNA methylation data of lung cancer patients was conducted to illustrate the performance of the proposed method. Results: Simulation study suggested that the proposed method performed well in the identifying mediating factors. The estimation of the mediation effect by the proposed approach is also reliable with less bias compared with the classical approach. In the empirical study, we identified two DNA methylation signatures including cg21926276 and cg26387355 with a mediation effect of 0.226 (95%CI: 0.108-0.344) and 0.158 (95%CI: 0.065-0.251) between smoking and lung cancer using the proposed approach. Conclusion: The proposed method obtained good performance in simulation and empirical studies, it could be an effective statistical tool for high dimensional mediation analysis.

Liquid biopsy in thyroid cancer: from circulating biomarkers to a new prospective of tumor monitoring and therapy

Recently, liquid biopsy has attracted much interest as a tool for early cancer screening, prognosis, monitoring and response to treatment in many different cancer types. Indeed, liquid biopsies can be repeatedly performed in a noninvasive way, at lower cost and without the risks associated to the classic tissue biopsy. The objective of this monography was to describe the main components studied in liquid biopsy (circulating tumor nucleic acids, circulating tumor cells and extracellular vesicles) and how they have been explored in thyroid cancer, through an in-depth scientific literature review. While circulating tumor cells are the most represented component in the literature of liquid biopsy in thyroid cancer, circulating tumor nucleic acids and extracellular vesicles have also been recently explored. One important challenge in this field of research, especially for differentiated thyroid cancer, has been the low quantity of circulating components with respect to other cancer types, requiring more advanced techniques for both isolation and analysis. Despite these limitations, liquid biopsy showed promise as an additional noninvasive tool for diagnosis, prognosis, to predict outcome and therapeutic response in differentiated, medullary and anaplastic thyroid cancer.

Comprehensive transcriptomic analysis of papillary thyroid cancer: potential biomarkers associated with tumor progression

PURPOSE

Identification of stage-specific prognostic/predictive biomarkers in papillary thyroid carcinoma (PTC) could lead to its more efficient clinical management. The main objective of this study was to characterize the stage-specific deregulation in genes and miRNA expression in PTC to identify potential prognostic biomarkers.

METHODS

495 RNASeq and 499 miRNASeq PTC samples (stage I-IV) as well as, respectively, 56 and 57 normal samples were retrieved from The Cancer Genome Atlas (TCGA). Differential expression analysis was performed using DESeq 2 to identify deregulation of genes and miRNAs between sequential stages. To identify the minority of patients who progress to higher stages, we performed clustering analysis on stage I RNASeq data. An independent PTC RNASeq data set (BioProject accession PRJEB11591) was also used for the validation of the results.

RESULTS

LTF and PLA2R1 were identified as two promising biomarkers down-regulated in a subgroup of stage I (both in TCGA and in the validation data set) and in the majority of stage IV of PTC (in TCGA data set). hsa-miR-205, hsa-miR-509-2, hsa-miR-514-1 and hsa-miR-514-2 were also detected as up-regulated miRNAs in both PTC patients with stage I and stage III. Hierarchical clustering of stage I samples showed substantial heterogeneity in the expression pattern of PTC indicating the necessity of categorizing stage I patients based on the expressional alterations of specific biomarkers.

CONCLUSION

Stage I PTC patients showed large amount of expressional heterogeneity. Therefore, risk stratification based on the expressional alterations of candidate biomarkers could be an important step toward personalized management of these patients.

High-dimensional mediation analysis in survival models

Mediation analysis with high-dimensional DNA methylation markers is important in identifying epigenetic pathways between environmental exposures and health outcomes. There have been some methodology developments of mediation analysis with high-dimensional mediators. However, high-dimensional mediation analysis methods for time-to-event outcome data are still yet to be developed. To address these challenges, we propose a new high-dimensional mediation analysis procedure for survival models by incorporating sure independent screening and minimax concave penalty techniques for variable selection, with the Sobel and the joint method for significance test of indirect effect. The simulation studies show good performance in identifying correct biomarkers, false discovery rate control, and minimum estimation bias of the proposed procedure. We also apply this approach to study the causal pathway from smoking to overall survival among lung cancer patients potentially mediated by 365,307 DNA methylations in the TCGA lung cancer cohort. Mediation analysis using a Cox proportional hazards model estimates that patients who have serious smoking history increase the risk of lung cancer through methylation markers including cg21926276, cg27042065, and cg26387355 with significant hazard ratios of 1.2497(95%CI: 1.1121, 1.4045), 1.0920(95%CI: 1.0170, 1.1726), and 1.1489(95%CI: 1.0518, 1.2550), respectively. The three methylation sites locate in the three genes which have been showed to be associated with lung cancer event or overall survival. However, the three CpG sites (cg21926276, cg27042065 and cg26387355) have not been reported, which are newly identified as the potential novel epigenetic markers linking smoking and survival of lung cancer patients. Collectively, the proposed high-dimensional mediation analysis procedure has good performance in mediator selection and indirect effect estimation.

Whole exome sequencing of cell-free DNA - A systematic review and Bayesian individual patient data meta-analysis

Molecular profiling of tumor derived cell free DNA (cfDNA) is gaining ground as a prognostic and predictive biomarker. However to what extent cfDNA reflects the full metastatic landscape as currently determined by tumor tissue analysis remains controversial. Though technically challenging, whole exome sequencing (WES) of cfDNA enables thorough evaluation of somatic alterations. Here, we review the feasibility of WES of cfDNA and determine the sensitivity of WES-detected single nucleotide variants (SNVs) in cfDNA on individual patient data level using paired tumor tissue as reference (sharedSNVsAlltissueSNVs×100%). The pooled sensitivity was 50% (95% credible interval (CI): 29-72%). The tissue mutant allele frequency (MAF) of variants exclusively identified in tissue was significantly lower (12.5%, range: 0.5-18%) than the tissue MAF of variants identified in both tissue and cfDNA (23.9%, range: 17-38%), p = 0.004. The overall agreement (sharedSNVsAllSNVs×100%)between SNVs in cfDNA and tumor tissue was 31% (95% CI: 15-49%). The number of detected SNVs was positively correlated with circulating tumor DNA (ctDNA) fraction (p = 0.016). A sub analysis of samples with ctDNA fractions ≥ 25% improved the sensitivity to 69% (95% CI: 46-89%) and agreement to 46% (95% CI: 36-59%), suggesting that WES is mainly feasible for patients with high ctDNA fractions. Pre- and post-analytical procedures were highly variable between studies rendering comparisons problematic. In conclusion, various aspects of WES of cfDNA are largely in its investigative phase, standardization of methodologies is highly needed to bring this promising technique to its clinical potential.

Extracellular Vesicles from Thyroid Carcinoma: The New Frontier of Liquid Biopsy

The diagnostic approach to thyroid cancer is one of the most challenging issues in oncology of the endocrine system because of its high incidence (3.8% of all new cancer cases in the US) and the difficulty to distinguish benign from malignant non-functional thyroid nodules and establish the cervical lymph node involvement during staging. Routine diagnosis of thyroid nodules usually relies on a fine-needle aspirate biopsy, which is invasive and often inaccurate. Therefore, there is an urgent need to identify novel, accurate, and non-invasive diagnostic procedures. Liquid biopsy, as a non-invasive approach for the detection of diagnostic biomarkers for early tumor diagnosis, prognosis, and disease monitoring, may be of particular benefit in this context. Extracellular vesicles (EVs) are a consistent source of tumor-derived RNA due to their prevalence in circulating bodily fluids, the well-established isolation protocols, and the fact that RNA in phospholipid bilayer-enclosed vesicles is protected from blood-borne RNases. Recent results in other types of cancer, including our recent study on plasma EVs from glioblastoma patients suggest that information derived from analysis of EVs from peripheral blood plasma can be integrated in the routine diagnostic tumor approach. In this review, we will examine the diagnostic and prognostic potential of liquid biopsy to detect tumor-derived nucleic acids in circulating EVs from patients with thyroid carcinoma.

Evaluation of the Possibility to Detect Circulating Tumor DNA From Pituitary Adenoma

Objective: Circulating free DNA (cfDNA) in general and circulating tumor DNA (ctDNA) in particular is becoming an increasingly used form of liquid biopsy biomarkers. In this study, we are investigating the ability to detect ctDNA from the plasma of pituitary adenoma (PA) patients. Design: Tumor tissue samples were obtained from planed PA resections, before which blood plasma samples were taken. Somatic variants found in PA tissue samples were evaluated in related cfDNA, isolated from plasma samples. Methods: Sanger sequencing, as well as previously obtained whole-exome sequencing data, were used to evaluate somatic variants composition in tumor tissue samples. cfDNA was isolated from the same PA patients and competitive allele-specific TaqMan PCR and amplicon-based next-generation sequencing (NGS) approach were used for targeted detection of variants found in corresponding tumor tissue samples. Results: Using NGS-based analysis, we detected five out of 17 somatic variants in 40 to 60% of total reads, three variants in 0.50-5.00% of total read count, including GNAS c.601C>T, which was detected using ultra-deep NGS (1.78 million X) in 0.77% of amplicons reads. Nine variants were not detected. We also detected We were not able to detect variant found in PA tissue in cfDNA using cast-PCR, indicating that the portion of variant-containing ctDNA in total isolated cfDNA is too small to be detected with this method. Conclusions: For the first time, we demonstrate the possibility to detect somatic variants of PA in cfDNA isolated from patients' blood plasma. Whether the source of variant detected in cfDNA is PA should be further tested.