Exosome-based microRNA Biomarkers for Non-invasive and Early Detection of Pancreatic Cancer in PLCO Biospecimens
Limitations of current PDAC biomarkers and the promise of miRNAs as PDAC biomarkers - Previous attempts to develop PDAC early detection tests have suffered from flaws in their study design, including 1) failure to enroll early-stage PDAC cases, 2) the assumption that a biomarker developed in metastatic settings would also detect early-stage PDAC, or 3) the idea that a tissue-derived biomarker would also function in the blood. MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes implicated in every human cancer, including PDAC, and may thus be ideal biomarkers. Indeed, circulating cell-free miRNAs (cf-miRNAs) have been shown to have diagnostic potential. Furthermore, the recent discovery that cancer cells actively excrete miRNAs in small extracellular vesicles called exosomes (exo miRNAs) has revolutionized the field, as tumor-derived exosomal cargo enables the identification of cancer-specific molecular markers.
Importance of exosome-based miRNAs for early detection of PDAC - To address the limitations of cf-miRNA biomarkers and to interrogate the potential clinical significance of exo-mRNAs, during the previous cycle of funding (U01-CA214254), we completed a systematic and comprehensive biomarker discovery and validation effort in patients with PDAC and non-disease control participants. Utilizing the power of unbiased and genome-wide sequencing-based miRNA profiling approaches, together with rigorous bioinformatics and machine-learning algorithms, we: 1) identified panels of 5 cf-miRNAs and 8 exo-miRNAs that could robustly identify patients with early-stage PDAC (area under the curve [AUC] for cf-miRNAs = 0.90; AUC for exo-miRNAs = 0.96); 2) combined the cf- and exo-miRNAs into a “transcriptomic signature” that was superior to individual biomarker panels in identifying patients with all stages of PDAC (AUC = 0.98), including patients with early-stage (stage I/II) disease (AUC = 0.93; sensitivity = 80%; specificity = 91%); 3) showed that combining our transcriptomic signature with established serological tumor marker CA19-9 further improved diagnostic performance (AUC = 0.99); and 4) most importantly, showed that our transcriptomic signature accurately identified patients with PDAC who were CA19-9-negative (<37 U/ml; AUC = 0.96; sensitivity = 91%; specificity = 90%). Of note, we hold patent-pending intellectual property for our transcriptomic signature with the USPTO. These successes collectively demonstrate our ability to establish a transcriptomic signature for the early detection of PDAC.
In this renewed cycle of this funding (5 U01 CA214254-07), we are building upon our previous success, and our large-scale validation demonstrates the clinical significance of our transcriptomic signature in real-life clinical settings. We have evaluated its performance as a non-invasive assay in large, racially/ethnically diverse, prospective cohorts of PDAC patients with various risk profiles; we are currently deciphering its diagnostic potential for detecting PCNs with high-grade dysplasia (HGD) or invasive disease and, important to this proposal, we intend to use it to determine lead-time for disease development in pre-diagnosis specimens from individuals who later developed PDAC.
The current four milestone-based specific aims of this proposal were:
Aim #1: Expand our biorepository via continued prospective enrollment of patients with PDAC and PNs, including those with PCNs and familial risk, with an additional focus on enrollment of and specimen collection from patients of racial/ethnic minority populations, to support our project and NCI’s PCDC biobanking efforts.
Aim #2: Further validate the transcriptomic signature and establish its performance in prospective cohorts of patients with early-stage PDAC for its clinical translation.
Aim #3: Determine the clinical significance of our transcriptomic signature to detect the presence of HGD and invasive cancer in pre-operative serum collected from patients clinically diagnosed as PCNs with high-risk stigmata.
Aim #4: Evaluate the ability of our transcriptomic signature to detect PDAC at its earliest stages in pre-diagnosis serum specimens and to determine lead time before disease presentation. This specific aim pertains to the use of PLCO samples; we plan to evaluate the performance of our signature alone or in combination with other markers (e.g., CA19-9) in longitudinally collected samples from patients with PDAC that include pre-, at-, and post-diagnosis timepoints and use it to determine the lead time before disease presentation.
Ajay Goel (City of Hope)
Alessandro Mannucci (City of Hope)
Han Haiyong (Translational Genomics Research Institute)
Daniel D. Von Hoff (Translational Genomics Research Institute)
Robert Rick Selby (St Jude Medical center, Fullerton, CA)
John S Bolton (Ochsner Clinic Foundation, New Orleans, LA)
Erkut Hasan Borazanci (Honor Health Research Institute, Scottsdale, AZ)
Vincent Chung (City of Hope)
Michael J Demeure (Hoag family center institute, Newport beach, CA)
Wayne Alix Ian Frederick (Howard University)
Stanley Hamilton (City of Hope)
Masamichi Hayashi (Nagoya University Graduate School of Medicine, Nagoya, Japan)
Yasuhiro Kodera (Nagoya University Graduate School of Medicine, Nagoya, Japan)
Eyal Meiri (Piedmont Oncology, Atlanta, GA)
Joon Oh Park (Samsung Research Institute for Future Medicine, Seoul, Korea)
Gagandeep Singh (City of Hope)
Sierra Min Talley (City of Hope)
Susan Tsai (Medical college of wisconsin, Milwaukee, WI)