Joseph David Allen

All Publications

• Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures. Cancer cell Satpathy, S., Clark, N. M., Chen, Y. J., Hosseini, N., Chang, Y. H., Hsiao, Y., Lei, J. T., Petralia, F., Chen, J. S., Geffen, Y., Heiman, D. I., Paul, I., Cho, H., Hollenberg, M., Marino, G. B., Lin, K. T., Mannan, R., White, C. J., Allen, J., Avanessian, S. C., Kane, M. H., Wolfe, A., Kinarivala, M., Liu, W., Anand, S., Lin, M. W., Haines, M., Bergstrom, E. J., Hussey, G., Li, G. X., Mani, D. C., Fang, H., Jaehnig, E. J., Keshishian, H., Miller, B., Su, K. Y., Hsiao, Y. J., Hsu, H. H., Hsieh, M. S., Hsu, K. H., Monovoukas, A., Gohsman, S., Thorup, J. R., Deng, Y., Akiyama, Y., Deng, E., Sheng-Wen Chen, E., Krek, A., Espinoza, R., Ma, W., Charytonowicz, D., Sebra, R., Lin, J. H., Chen, Y. S., Hsu, Y. C., Lin, Z. S., Chen, K. C., Yeh, C. W., Wang, Y. T., Lazar, A. J., Mesri, M., An, E., Zhang, X., Clauser, K. R., Fenyö, D., Chinnaiyan, A. M., Zhang, B., Ding, L., Ruggles, K., Newton, C., Zhang, H., Wang, P., Hostetter, G., Omenn, G. S., Kumar-Sinha, C., Thiagarajan, M., Govindan, R., Paik, P., Parolia, A., Li, Q. K., Ma'ayan, A., Getz, G. A., Dhanasekaran, S. M., Robles, A. I., Chang, G. C., Yang, P. C., Yu, S. L., Chen, H. Y., Nesvizhskii, A. I., Carr, S. A., Mani, D. R., Cieslik, M. P., Chen, Y. J., Gillette, M. A. 2025

  Abstract

  Lung adenocarcinomas (LUAD) are a pressing global health problem with enduring lethality and rapidly shifting epidemiology. Proteogenomic studies integrating proteomics and post-translational modifications with genomics can identify clinical strata and oncogenic mechanisms, but have been underpowered to examine effects of ethnicity, smoking and environmental exposures, or sex on this heterogeneous disease. This comprehensive proteogenomic analysis of LUAD tumors and matched normal adjacent tissues from 406 patients across diverse geographic and demographic backgrounds explores the impact of understudied driver mutations, prognostic role of chromosomal instability, patterns of immune signaling, differential and sex-specific effects of endogenous mutagens and environmental carcinogens, and pathobiology of early-stage tumors with "late-like" characteristics. Candidate protein biomarkers are proposed for unstable tumors with highly fragmented genomes and for carcinogen exposures, and a LUAD subtype-specific atlas of therapeutic vulnerabilities is presented. These observations and the associated data resource advance the objective of precision management strategies for this devastating disease.

  View details for DOI 10.1016/j.ccell.2025.07.011

  View details for PubMedID 40749670

  View details for PubMedCentralID PMC12393171

• Using Circulating Tumor DNA to Monitor Sarcoma Treatment and Recurrence Sun, B. J., Yue, T. M., Hur, D., Allen, J., Delitto, D., Poultsides, G., Lee, B. SPRINGER. 2025: S32-S33

  View details for Web of Science ID 001610671600060

• PSA response and survival based on metastatic site in patients with metastatic castration resistant prostate cancer (mCRPC) treated with lutetium-177-PSMA-vipivotide tetraxetan (Lu177-PVT). Allen, J., Bergstrom, C. P., Song, H., Hoffmann, C., Ruiz, S., Chien, J., Moore, K., Parikh, D., Shah, S., Fan, A. C., Srinivas, S., Iagaru, A., Khaki, A. LIPPINCOTT WILLIAMS & WILKINS. 2025

  View details for DOI 10.1200/JCO.2025.43.5_suppl.107

  View details for Web of Science ID 001454759900041

• Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues. Nature communications Abelin, J. G., Bergstrom, E. J., Rivera, K. D., Taylor, H. B., Klaeger, S., Xu, C., Verzani, E. K., Jackson White, C., Woldemichael, H. B., Virshup, M., Olive, M. E., Maynard, M., Vartany, S. A., Allen, J. D., Phulphagar, K., Harry Kane, M., Rachimi, S., Mani, D. R., Gillette, M. A., Satpathy, S., Clauser, K. R., Udeshi, N. D., Carr, S. A. 2023; 14 (1): 1851

  Abstract

  Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each 'ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.

  View details for DOI 10.1038/s41467-023-37547-0

  View details for PubMedID 37012232

  View details for PubMedCentralID PMC10070353