Drake, Justin M

Abstract Annual breast cancer screening is a critical piece of women’s health. While mammography remains the gold standard, increased breast density leads to decreased sensitivity, underscoring the need for more sensitive and accessible screening methods. Liquid-based biopsies for early breast cancer detection are emerging but currently remain out of reach for clinical use. Recent data on nucleotide assessment from plasma in breast cancer have been mixed with 87% sensitivity for late-stage disease (stage 3-4) but only 20% sensitivity for early-stage disease (stage 0-2). Proteomics is an exciting area for early cancer screening where improvements in sample preparation and equipment have enabled major advances in early cancer detection. This is particularly true for a deep proteome assay as proteins can be identified which are 8-9 orders of magnitude less abundant than the most common plasma proteins. This study evaluates the presence of breast cancer using label-free shotgun mass spectrometry-based proteomics on less than 1 ml of plasma from 1,259 women classified as either healthy or newly diagnosed treatment naïve breast cancer patients with a focus on early-stage disease. We trained using a cohort of 845 women, comprising of 466 healthy and 379 with breast cancer and validated on 397 women (195 healthy and 202 breast cancer) using a protein-based machine learning classifier to distinguish these groups. All plasma samples were processed in a blinded manner coupled with semi-quantitative, label-free mass spectrometry (MS)-based analysis. The median number of proteins detected per patient across breast cancer and healthy individuals was 7,064 and 7,054, respectively. The validation performance achieved 92.3% specificity for healthy controls and an overall sensitivity of 92.6% with an AUC of 0.975 (95% CI: 0.961-0.987) for breast cancer patients. Sensitivity broken down by clinical stage (0-IV), molecular subtypes (HR+/HER2+, HR-/HER2+, HR+/HER2-, and HR-/HER2-) and pathological subtypes (LCIS, DCIS, ILC, and IDC) were ≥85% and indistinguishable across all stages and subtypes. Gene set enrichment analyses (GSEA) identified pathways including epithelial-to-mesenchymal transition (EMT) and PI3K-AKT signaling as enriched in the breast cancer samples, highlighting that our test can identify cancer-related proteins in early-stage patients. Overall, we have developed a highly sensitive blood-based assay that utilizes deep proteomic profiling to identify distinctive cancer specific signatures in women who are undergoing screening for breast cancer. This work enables us to develop a protein-based classifier from plasma for early detection of breast cancer and enhances screening strategies for women with dense breasts who are at average or high-risk based on family history, specific genetic mutations such as BRCA1/2, race, or other factors. Citation Format: Alec Horrmann, Yash Travadi, Jacob Carey, Kevin Mallery, Ella Boytim, Grant Schaap, Carissa Rungkittikhun, Kaylee Kamalanathan, Nathaniel R. Bristow, Catalina Galeano-Garces, Adam Groth, Alexa R. Hesch, Pooja Advani, Justin Hwang, Badrinath R. Konety, Justin M. Drake. Deep plasma proteomics for early-stage breast cancer detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4073.

Abstract Purpose: Germline alterations in homologous recombination repair (gHRR) genes affect the pathogenesis, treatment options, and survival of patients with cancer. However, distinct gHRR gene alterations may differentially affect treatment response and oncogenic signaling. In this study, we interrogated genomic and transcriptomic data and assessed clinical outcomes of patients with gHRR mutations across four BRCA-associated cancers (breast, ovarian, pancreatic, and prostate cancers) to identify therapeutic vulnerabilities. Experimental Design: We assessed 24,309 patients undergoing matched tumor/normal next-generation DNA and RNA sequencing. Annotated gHRR gene variants [germline BRCA1, germline BRCA2, germline PALB2, germline ATM (gATM), and germline CHEK2] were analyzed. HRs were used to assess survival outcomes comparing germline versus sporadic groups. Somatic alterations and their frequencies were compared across gHRR-altered groups. Differential gene expression and gene set enrichment analysis were used to compare transcriptomic profiles. Results: Somatic TP53 mutations were depleted in gATM carriers (P < 0.05) across all four BRCA-associated cancers by up to 2.5-fold. Tumors with germline BRCA1/2 mutations were associated with improved survival in patients with ovarian cancer and had consistent enrichment of TP53 mutations in all four cancers. gATM mutations displayed elevated p53 transcriptional activity in all four cancers, with significance reached in breast and prostate cancers (P < 0.01). In breast, ovarian, and prostate cancers, gATM tumors demonstrated significantly increased inflammatory pathways (P < 0.001). Finally, using gene dependency data, we found that cell lines that were highly dependent on ATM were co-dependent on canonical p53 function. Conclusions: gATM-associated cancers seem to require intact p53 activity and this synthetic essentiality may be used to guide targeted therapies that perturb canonical TP53 function.

Abstract Purpose: Protein kinases are known to play a prominent role in oncogenic progression across multiple cancer subtypes, yet their role in prostate cancer progression remains underexplored. The purpose of this study was to identify kinases that drive prostate cancer progression. Experimental Design: To discover kinases that drive prostate cancer progression, we investigated the association between gene expression of all known kinases and long-term clinical outcomes in tumor samples from 545 patients with high-risk disease. We evaluated the impact of genetic and pharmacologic inhibition of the most significant kinase associated with metastatic progression in vitro and in vivo. Results: DNA-dependent protein kinase (DNAPK) was identified as the most significant kinase associated with metastatic progression in high-risk prostate cancer. Inhibition of DNAPK suppressed the growth of both AR-dependent and AR-independent prostate cancer cells. Gene set enrichment analysis nominated Wnt as the top pathway associated with DNAPK. We found that DNAPK interacts with the Wnt transcription factor LEF1 and is critical for LEF1-mediated transcription. Conclusions: Our data show that DNAPK drives prostate cancer progression through transcriptional regulation of Wnt signaling and is an attractive therapeutic target in aggressive prostate cancer.

Abstract Emerging evidence demonstrates that the DNA repair kinase DNA-PK exerts divergent roles in transcriptional regulation of unsolved consequence. Here, in vitro and in vivo interrogation demonstrate that DNA-PK functions as a selective modulator of transcriptional networks that induce cell migration, invasion, and metastasis. Accordingly, suppression of DNA-PK inhibits tumor metastases. Clinical assessment revealed that DNA-PK is significantly elevated in advanced disease, and independently predicts for metastases, recurrence, and reduced overall survival. Further investigation demonstrated that DNA-PK in advanced tumors is highly activated, independently of DNA damage indicators. Combined, these findings put forth new paradigms for DNA-PK function, identify DNA-PK as a potent driver of tumor progression and metastases, and nominate DNA-PK as a therapeutic target for advanced malignancies. Citation Format: Jonathan F. Goodwin, Vishal Kothari, Justin M. Drake, Shuang Zhao, Emanuela Dylgjeri, Jeffry L. Dean, Matthew J. Schiewer, Christopher McNair, Michael S. Magee, Robert B. Den, Ziqi Zhu, Nicholas A. Graham, Ajay A. Vashisht, James A. Wohlschlegel, Thomas G. Graeber, R Jeffrey Karnes, Mandeep Takhar, Elai Davicioni, Scott A. Tomlins, Nima Sharifi, Owen N. Witte, Felix Y. Feng, Karen E. Knudsen. DNA-PK-mediated transcriptional regulation drives tumor progression and metastasis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1860. doi:10.1158/1538-7445.AM2015-1860