Cell free DNA biology and its involvement in breast carcinogenesis

Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

Circulating tumor DNA (ctDNA) methylation, an innovative liquid biopsy biomarker, has emerged as a promising tool in early cancer diagnosis, monitoring, and prognosis prediction. As a noninvasive approach, liquid biopsy overcomes the limitations of traditional tissue biopsy. Among various biomarkers, ctDNA methylation has garnered significant attention due to its high specificity and early detection capability across diverse cancer types. Despite its immense potential, the clinical application of ctDNA methylation faces substantial challenges pertaining to sensitivity, specificity, and standardization. In this review, we begin by introducing the basic biology and common detection techniques of ctDNA methylation. We then explore recent advancements and the challenges faced in the clinical application of ctDNA methylation in liquid biopsies. This includes progress in early screening and diagnosis, identification of clinical molecular subtypes, monitoring of recurrence and minimal residual disease (MRD), prediction of treatment response and prognosis, assessment of tumor burden, and determination of tissue origin. Finally, we discuss the future perspectives and challenges of ctDNA methylation detection in clinical applications. This comprehensive overview underscores the vital role of ctDNA methylation in enhancing cancer diagnostic accuracy, personalizing treatments, and effectively monitoring disease progression, providing valuable insights for future research and clinical practice.

Liquid Biopsy in the Clinical Management of Cancers

Liquid biopsy, a noninvasive diagnosis that examines circulating tumor components in body fluids, is increasingly used in cancer management. An overview of relevant literature emphasizes the current state of liquid biopsy applications in cancer care. Biomarkers in liquid biopsy, particularly circulating tumor DNA (ctDNA), circulating tumor RNAs (ctRNA), circulating tumor cells (CTCs), extracellular vesicles (EVs), and other components, offer promising opportunities for early cancer diagnosis, treatment selection, monitoring, and disease assessment. The implementation of liquid biopsy in precision medicine has shown significant potential in various cancer types, including lung cancer, colorectal cancer, breast cancer, and prostate cancer. Advances in genomic and molecular technologies such as next-generation sequencing (NGS) and digital polymerase chain reaction (dPCR) have expanded the utility of liquid biopsy, enabling the detection of somatic variants and actionable genomic alterations in tumors. Liquid biopsy has also demonstrated utility in predicting treatment responses, monitoring minimal residual disease (MRD), and assessing tumor heterogeneity. Nevertheless, standardizing liquid biopsy techniques, interpreting results, and integrating them into the clinical routine remain as challenges. Despite these challenges, liquid biopsy has significant clinical implications in cancer management, offering a dynamic and noninvasive approach to understanding tumor biology and guiding personalized treatment strategies.

Comprehensive genomic profiling for oncological advancements by precision medicine

Considerable advancements in next generation sequencing (NGS) techniques have sparked the use of comprehensive genomic profiling (CGP) as a guiding tool for precision-centered oncological treatments. The past two decades have seen the completion of the human genome project, and the consequential invention of NGS. High-throughput sequencing technologies support the discovery and commonplace use of individualized cancer treatments, specifically immune-centered checkpoint inhibitor therapies, and oncogene and tumor suppressor gene targeted therapies. Nevertheless, CGP is not commonly used in all clinical settings. This review investigates the clinically relevant applications of CGP. Studies published between the years 2000-2023 have shown substantial evidence of the benefits of integrating CGP into routine care practice, while also making important comparisons to current-standard oncological treatment strategies. Findings of a comprehensive genomic profile includes predictive, prognostic, and diagnostic biomarkers, together with somatic mutation identification which can indicate the efficacy of immunotherapies and molecularly guided therapies. This review highlights the importance of CGP in identifying driver mutations in tumors that subsequently can be effectively targeted with molecular therapeutics and lead to drug discovery, allowing for increased precision in treating tumors selectively based on their specific genetic mutations, thereby improving patient outcomes.

Clinical Efficacy of Pyrotinib Combined with Capecitabine in the Second-Line or Above Treatment for HER-2 Positive Advanced Breast Cancer and Its Association with Cell-Free DNA

Purpose

To evaluate the clinical efficacy of pyrotinib combined with capecitabine in the treatment of HER-2 positive breast cancer in real world and its correlation with cfDNA.

Methods

From September 2020 to June 2021, 181 cases of HER-2 positive advanced breast cancer patients who were treated in Jiangsu Cancer Hospital and Nantong Cancer Hospital were analyzed. Patients were given pyrotinib combined with capecitabine or trastuzumab combined with capecitabine. Eighty-one patients who received pyrotinib+capecitabine second-line or above treatment were included in the pyrotinib group, and 100 patients who received trastuzumab+capecitabine second-line or above treatment were included in the trastuzumab group. The objective response rate (ORR) and clinical benefit rate (CBR) of the two groups were compared. The follow-up results of the patients were analyzed, and the progression-free survival (PFS) and adverse reactions were compared between the two groups. Plasma cfDNA was detected by real-time fluorescence quantitative PCR. The cfDNA levels of patients before and after treatment were compared, and the change of cfDNA levels in patients with different curative effects over time was recorded. The patients were further divided into high cfDNA expression and low cfDNA expression groups, and the PFS of patients with different cfDNA levels was analyzed. COX univariate and multivariate analysis of factors influencing posttreatment survival in patients with HER-2-positive breast cancer were performed.

Results

The ORR of the pyrotinib group (58.02%) was significantly higher than that of the trastuzumab group (42.00%, P = 0.0369). Similarly, the CBR of the pyrotinib group (65.43%) was significantly higher than that of the trastuzumab group (49.00%, P = 0.0347). The incidence of adverse reactions between the two groups was not statistically significant (P > 0.05). The results of survival analysis showed that the PFS of the pyrotinib group was 8.02 ± 3.05 months, the PFS of the trastuzumab group was 7.11 ± 3.06 months, and the PFS of the pyrotinib group was significantly longer than that of the trastuzumab group (P = 0.035). The comparison of cfDNA levels between the two groups showed that on the 28th and 56th day of treatment, the cfDNA levels in the pyrotinib group were significantly lower than those in the trastuzumab group (P < 0.05). Long-term follow-up results showed that compared with patients with high cfDNA expression, the PFS of patients with low cfDNA expression was significantly prolonged (P < 0.05). The level of cfDNA is an independent risk factor affecting the prognosis of patients with HER-2-positive breast cancer.

Conclusion

The combined use of pyrotinib and capecitabine has good clinical efficacy and high safety in patients with HER-2 positive breast cancer. The combined use of pyrotinib and capecitabine prolongs the PFS of patients and reduces the level of plasma cfDNA. Changes in cfDNA levels can reflect the therapeutic efficacy of patients with HER-2-positive breast cancer to a certain extent and can be used as a potential indicator for evaluating the prognosis of patients with HER-2-positive breast cancer.

Size and Methylation Index of Cell-Free and Cell-Surface-Bound DNA in Blood of Breast Cancer Patients in the Contest of Liquid Biopsy

Aberrantly methylated circulating DNA (cirDNA) has proven to be a good cancer marker, but its detection is limited by low concentrations, fragmentation, and insufficiency. Since the methylated cirDNA was shown to be more stable in circulation than the unmethylated one and was shown to bind with the blood cell surface, we studied the concentration, representation, and fragmentation of tumor-derived methylated DNA in cell-free and cell-surface-associated DNA. We found that long DNA fragments (more than 10 kb) are mainly associated with the surface of blood cells. However, in plasma short DNA fragments (100–1000 bp) were also found along with long DNA fragments. Isolation of short fragments after separation of cirDNA in 6% PAGE followed by quantitative PCR (L1 element) has shown that short DNA fragments in healthy females represent 22% versus 0.5–4.4% in breast cancer patients. The methylated form of the RARβ2 gene was detected only in long DNA fragments by Real-time TaqMan PCR of bisulfite-converted DNA. The methylation index of cirDNA from healthy women was estimated at 0%, 9%, and 7% in plasma, PBS-EDTA, and trypsin eluates from the surface of blood cells, respectively. The methylation index of breast cancer patients’ DNA was found to be 33%, 15%, and 61% in the same fractions confirming the overrepresentation of methylated DNA in csbDNA.

Cohesin RAD21 Gene Promoter Methylation Correlated with Better Prognosis in Breast Cancer Patients

RAD21 plays multiple roles in numerous cancers. In breast cancer (BC), a high level of RAD21 correlates with poor disease outcomes and resistance to chemotherapy. However, data regarding RAD21 promoter methylation in BC tissue and its correlation with clinical outcomes in patients with BC remain limited. Here, we investigated the clinicopathological features associated with the methylation status of RAD21 in BC to figure out its possible role in pathogenesis and the formation of breast carcinogenesis. The methylation status of the RAD21 gene was significantly associated with better clinical outcomes in patients with BC.

Cell-free DNA comparative analysis of the genomic landscape of first-line hormone receptor-positive metastatic breast cancer from the US and China

PURPOSE

Meaningful comparison of mutational landscapes across ethnic groups requires the use of standardized platform technology. We have used a harmonized NGS-based liquid biopsy assay to explore the differential genomic landscape of patients with initially hormone receptor-positive (HR+), HER2-negative MBC of first line metastasis or primary Stage IV at diagnosis from the United States (US) and China (CN).

METHODS

Plasma circulating tumor DNA (ctDNA) from 27 US patients and 65 CN patients was sequenced using the harmonized CLIA-certified, 152-gene PredicineCare™ liquid biopsy assay. Kaplan-Meier survival analysis was performed to analyze the correlation between genomic alterations and progression-free survival (PFS), and p-values were calculated using the log-rank test.

RESULTS

All patients in the CN cohort received chemotherapy and/or hormonal therapy, while 85.2% (23/27) patients in the US cohort received hormonal therapy plus CDK4/6 inhibitors. Mutations were detected in 23 of 27 (85%) US patients and 54 of 65 (83%) CN patients. The prevalence of AKT1 (P = 0.008) and CDH1 (P = 0.021) alterations were both higher in the US vs. CN cohort. In addition, FGFR1 amplification were more frequent in the CN vs. US cohort (P = 0.048). PTEN deletions (P = 0.03) and ESR1 alterations (P = 0.02) were associated with shorter PFS in the CN cohort, neither of these associations were observed in the US cohort. Interestingly, a reduced association between PTEN deletion and PFS was observed in patients receiving CDK4/6 inhibitor treatment.

CONCLUSION

The differential prevalence of ctDNA-based alterations such as FGFR1, AKT1, and CDH1 was observed in initially HR+/HER2- MBC patients in the US vs. CN. In addition, the association of PTEN deletions with shorter PFS was found in the CN but not the US cohort. The differential genomic landscapes across the two ethnic groups may reflect biologic differences and clinical implications.