SNiPER: a novel hypermethylation biomarker panel for liquid biopsy based early breast cancer detection

Abstract

IntroductionMammography is the gold standard for early breast cancer detection, but shows important limitations. Blood-based approaches on basis of cell-free DNA (cfDNA) provide minimally invasive screening tools to characterize epigenetic alterations of tumor suppressor genes and could serve as a liquid biopsy, complementing mammography.MethodsPotential biomarkers were identified from The Cancer Genome Atlas (TCGA), using HumanMethylation450-BeadChip data. Promoter methylation status was evaluated quantitatively by pyrosequencing in a serum test cohort (n = 103), a serum validation cohort (n = 368) and a plasma cohort (n = 125).Results SPAG6, NKX2-6 and PER1 were identified as novel biomarker candidates. ITIH5 was included on basis of our previous work. In the serum test cohort, a panel of SPAG6 and ITIH5 showed 63% sensitivity for DCIS and 51% sensitivity for early invasive tumor (pT1, pN0) detection at 80% specificity. The serum validation cohort revealed 50% sensitivity for DCIS detection on basis of NKX2-6 and ITIH5. Furthermore, an inverse correlation between methylation frequency and cfDNA concentration was uncovered. Therefore, markers were tested in a plasma cohort, achieving a 64% sensitivity for breast cancer detection using SPAG6, PER1 and ITIH5. ConclusionsAlthough liquid biopsy remains challenging, a combination of SPAG6, NKX2-6, ITIH5 and PER1 (SNiPER) provides a promising tool for blood-based breast cancer detection.

Aberrant expression of SPAG6 may affect the disease phenotype and serve as a tumor biomarker in BCR/ABL1‑negative myeloproliferative neoplasms

“…In mammals, SPAG6 is predominately expressed in the sperm, lungs, nervous system and inner ear, and is considered to be mainly involved in sperm maturation and nervous system development under normal physiological conditions (11,12). Accumulating evidence has demonstrated that aberrant SPAG6 expression in hematological malignancies, and ovarian, bladder, breast and lung cancer, may affect the occurrence and development of human cancer types by regulating the proliferation, apoptosis, invasion and metastasis of tumor cells (13)(14)(15)(16)(17)(18)(19)(20). In addition, SPAG6 has been reported to enhance the effect of apoptosis-inducing drugs and induce cell cycle arrest (21).…”

Detection and relevance of epigenetic markers on ctDNA: recent advances and future outlook

“…According to a recent review based on 14 studies, cfDNA methylation analysis is highly promising for both early detection and disease relapse [29]. Methylation of SPAG6, NKX2-6, ITIH5, and PER1 genes was detected early in serum of breast cancer patients [30].…”

Liquid Biopsy is Instrumental for 3PM Dimensional Solutions in Cancer Management

“…Cancer-associated changes in DNA methylation can be identified in blood, stool, urine or other biofluids [ 110 , 111 ]. As was demonstrated by an example of breast cancer, blood-based approaches associated with cell-free DNA are minimally invasive screening tools used to define epigenetic alterations of genes serving as liquid biopsy, complementing conventional detection tools such as mammography [ 112 ]. Moreover, the detection of DNA methylation in plasma or serum samples may help to understand tumor heterogeneity better than tissue biopsy [ 89 ].…”

“…Moreover, the detection of DNA methylation in plasma or serum samples may help to understand tumor heterogeneity better than tissue biopsy [ 89 ]. An evaluation of promoter methylation in a serum test, serum validation, and a plasma cohort revealed that the promising potential for early breast cancer detection could be attributed to the novel hypermethylation biomarker panel including SPAG6 , NKX2-6 , ITIH5, and PER1 [ 112 ]. Additionally, the assessment of the methylation level of selected genes in circulating cell-free DNA in plasma samples may be considered an effective procedure for the subtyping of lung cancer in addition to standard diagnostic procedures [ 89 ].…”

“…Therefore, the clinical utilization of non-invasive methods such as liquid biopsy represent a promising approach for early cancer detection and improvements of survival rates of patients with various cancer types [ 197 ]. As discussed above, an evaluation of biomarkers from various types of liquid biopsy is associated with high applicability in the framework of early detection of various cancer types, such as lung [ 86 , 118 , 177 ], breast [ 112 , 151 ], bladder [ 120 ], gastric [ 95 ], cervical [ 98 ], endometrial [ 192 ], or ovarian cancer [ 35 , 121 ] ( Figure 3 ). The application of liquid biopsy in cancer screening and early diagnosis represent the most promising aspects of its clinical utilization [ 46 ].…”