Discovery and Proof-of-Concept Study of Nuclease Activity as a Novel Biomarker for Breast Cancer Tumors

Abstract

Breast cancer is one of the most common pathologies diagnosed in the clinical practice. Despite major advancements in diagnostic approaches, there is no widely accepted biomarker in the clinical practice that can diagnose breast malignancy. Confirmatory diagnosis still relies on the pathological assessment of tissue biopsies by expert pathologists. Thus, there is an unmet need for new types of biomarkers and novel platform technologies that can be easily and robustly integrated into the clinic and that can assist pathologists. Herein, we show that nuclease activity associated to malignant tumors can be used as a novel biomarker in breast cancer, which can be detected via specific degradation of nucleic acid probes. In this study we have identified a set of three chemically modified nucleic acid probes that can diagnose malignancy in biopsy samples with high accuracy (89%), sensitivity (82%) and specificity (94%). This work represents a breakthrough for the potential clinical use of nuclease activity as biomarker, which can be detected via nucleic acids probes, for the clinical diagnosis of malignancy in breast tissue biopsies. This platform technology could be readily implemented into the clinic as adjunct to histopathological diagnostic.

Rational Design and Experimental Analysis of Short-Oligonucleotide Substrate Specificity for Targeting Bacterial Nucleases

“… 1 In particular, the use of nuclease-activatable oligonucleotide probes (NAOPs) as biosensors has proven its potential as a groundbreaking solution in early diagnosis of serious infectious diseases. 2 , 3 The detection of bacterial infection, 4 − 6 malignant cells in biopsies of breast cancer, 7 − 9 or food contamination by pathogenic bacteria 1 has been previously reported to be feasible on the basis of their nuclease activity profile. 10 − 12 A key aspect in the development of any diagnostic tool based on oligonucleotide probes is the necessity of designing probes which are both efficient and specific.…”

“…Nucleic acids have been proven useful recognition molecules for the development of several diagnostic strategies, taking advantage of their flexibility to be adapted to various transduction mechanisms, such as fluorescence, electrochemistry, piezoelectric, and colorimetric mechanisms . In particular, the use of nuclease-activatable oligonucleotide probes (NAOPs) as biosensors has proven its potential as a groundbreaking solution in early diagnosis of serious infectious diseases. , The detection of bacterial infection, − malignant cells in biopsies of breast cancer, − or food contamination by pathogenic bacteria 1 has been previously reported to be feasible on the basis of their nuclease activity profile. − A key aspect in the development of any diagnostic tool based on oligonucleotide probes is the necessity of designing probes which are both efficient and specific . Efficiency is directly related to the extent to which the target nuclease cleavages the synthetic substrate.…”

Nucleases as molecular targets for cancer diagnosis

“…Very promising results were achieved in a study that comprised paired breast samples (cancer and healthy), where a panel of 3 chemically modified nucleic acid probes could successfully differentiate between cancer and healthy samples. Through harnessing cancerassociated nuclease activity towards the probes, discrimination between cancer and healthy was achieved with high accuracy, sensitivity, and specificity [88]. This highlights the great potential of nuclease activity as a functional diagnostic biomarker but also as a complementary diagnostic strategy along with the golden standard of histopathological diagnosis.…”

“…In fact, the reported difference in nuclease profile as protein or mRNA between cancer and normal has led Hernandez et al to anticipate that nuclease activity signature could be recruited as a diagnostic biomarker taking advantage of the dynamic property of these enzymes. Nuclease activity profile has been successfully utilized to differentiate between breast cancer cells and healthy counterparts [84], HNSCC cells from the normal cells (Hernandez Lab, unpublish data), and breast cancer tissue samples from benign samples with high accuracy [88]. This reflects the utility of nuclease activity assaying as a diagnostic approach but also underlines the diversity of nucleases where nucleic acid probes can be tailored to specifically detect each cancer type.…”

Ultra-Sensitive and Specific Detection of S. aureus Bacterial Cultures Using an Oligonucleotide Probe Integrated in a Lateral Flow-Based Device

“…Moreover, nucleic acids have been proven to be useful recognition molecules for the development of several diagnostic strategies, mostly due to their flexibility and adaptability to various transduction mechanisms, such as fluorescence, electrochemical, piezoelectric, and colorimetric [15,16]. In recent years, we have been working on various approaches based on nucleic acid substrates to target specific nucleases that could be used as a blueprint of bacterial infections or specific types of cancer [17][18][19][20]. The Staphylococcus aureus (S. aureus) bacteria, both the methicillin sensitive (MSSA) and methicillin resistant (MRSA) varieties, is the leading cause of nosocomial infections worldwide [21][22][23][24].…”