Detection of early-stage cancers using circulating orphan non-coding RNAs in blood.

Authors

null

Mehran Karimzadeh

Exai Bio Inc., Palo Alto, CA

Mehran Karimzadeh , Jeffrey Wang , Taylor B. Cavazos , Lee S. Schwartzberg , Michael Multhaup , Jeremy Ku , Xuan Zhao , Jieyang Wang , Kathleen Wang , Rose Hanna , Patrick Arensdorf , Kimberly H Chau , Helen Li , Hani Goodarzi , Lisa Fish , Fereydoun Hormozdiari , Babak Alipanahi

Organizations

Exai Bio Inc., Palo Alto, CA, Renown Health, Reno, NV, University of California, San Francisco, San Francisco, CA

Research Funding

Pharmaceutical/Biotech Company
Exai Bio Inc

Background: Orphan non-coding RNAs (oncRNAs) are a novel category of small RNAs (smRNAs) that are present in tumors and largely absent in healthy tissue. We investigated the utility of oncRNAs extracted from serum for early cancer detection across seven cancer types. Methods: We collected 2,882 serum samples from individuals with known cancers of the bladder (n=152), breast (220), colon and rectum (141), kidney (283), lung (281), pancreas (287), and stomach (280) as well as donors with no history of cancer (1,238). We used 0.5 mL serum aliquots to generate and sequence smRNA libraries at an average depth of 20 million 50-bp single-end reads. Samples were split into age-, sex-, and smoking status-matched training (1,232 cancer; 922 control) and validation (412 cancer; 316 control) cohorts. A large catalog of oncRNAs specific to each cancer was created using tumor and adjacent normal samples from The Cancer Genome Atlas (TCGA) smRNA-seq database. Using TCGA-derived oncRNAs, we trained a machine learning model to predict cancer presence and tissue of origin (TOO) in a 5-fold cross validation setup using our training cohort. For the validation cohort, we averaged the predictions from the five training cohort models. Results: The model ROC-AUC for detecting cancer was 0.95 (95% CI: 0.94–0.95 for training and 0.94–0.97 for validation cohorts). Sensitivities for detecting cancer at 95% specificity were 0.74 (0.70–0.76) for early stage (I/II) and 0.80 (0.76–0.84) for late stage (III/IV) cancers in the training cohort, and 0.77 (0.71–0.81) and 0.81 (0.73–0.87) in the validation cohort. Sensitivities of detection for each cancer type are shown. For samples with cancer and TOO predictions, our top 1 and top 2 TOO accuracy was 0.76 (0.68–0.84) and 0.83 (0.76–0.90) for the validation set. Conclusions: These results demonstrate that oncRNAs detected in serum can be used for accurate, early detection, and localization of multiple cancers.

Training (N: sensitivity at 95% specificity (CI)Validation (N: sensitivity at 95% specificity (CI)
Early stage (I/II)Late stage (III/IV)Early stage (I/II)Late stage (III/IV)
All cancers841: 0.73 (0.7–0.76)391: 0.8 (0.76–0.84)290: 0.77 (0.71–0.81)122: 0.81 (0.73–0.88)
Bladder68: 0.38 (0.27–0.51)45: 0.8 (0.65–0.9)27: 0.37 (0.19–0.58)12: 1.0 (0.74–1)
Breast119: 0.6 (0.5–0.69)46: 0.72 (0.57–0.84)42: 0.57 (0.41–0.72)13: 0.77 (0.46–0.95)
Colorectal51: 0.71 (0.56–0.83)55: 0.78 (0.65–0.88)16: 0.88 (0.62–0.98)19: 0.68 (0.43–0.87)
Gastric128: 0.8 (0.73–0.87)83: 0.88 (0.79–0.94)41: 0.83 (0.68–0.93)28: 0.86 (0.67–0.96)
Kidney154: 0.76 (0.68–0.82)59: 0.73 (0.6–0.84)53: 0.79 (0.66–0.89)17: 0.76 (0.5–0.93)
Lung149: 0.84 (0.77–0.89)61: 0.87 (0.76–0.94)49: 0.94 (0.83–0.99)22: 0.86 (0.65–0.97)
Pancreas172: 0.81 (0.75–0.87)42: 0.79 (0.63–0.9)62: 0.84 (0.72–0.92)11: 0.73 (0.39–0.94)

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Abstract Details

Meeting

2023 ASCO Annual Meeting

Session Type

Poster Session

Session Title

Developmental Therapeutics—Molecularly Targeted Agents and Tumor Biology

Track

Developmental Therapeutics—Molecularly Targeted Agents and Tumor Biology

Sub Track

Circulating Biomarkers

Citation

J Clin Oncol 41, 2023 (suppl 16; abstr 3051)

DOI

10.1200/JCO.2023.41.16_suppl.3051

Abstract #

3051

Poster Bd #

249

Abstract Disclosures

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