Proteogenomic characterization of the molecular determinants of prostate cancer radioresistance

Roni Haas ^1,2,3,4 Shahbaz Khan ⁵ Gavin Frame ⁶ Wenyan Zhao ^1,2,3,4 Benjamin Carlin ^1,2,3,4 Takafumi N. Yamaguchi ^1,2,3,4 Yuan Zhe Bugh ^1,2,3,4 Julie Livingstone ^1,2,3,4 Chenghao Zhu ^1,2,3,4 Rupert Hugh-White ^1,2,3,4 Shu Tao ^1,2,3,4 Andrew Macklin ⁵ Vladimir Ignatchenko ⁵ Natalie Kurganovs ⁵ Geoff S. Higgins ⁷ Michelle R. Downes ^8,9 Danny Vesprini ¹⁰ Andrew Loblaw ¹⁰ Thomas Kislinger ^5,6 Paul C. Boutros ^1,2,3,4,6 Stanley K. Liu ^6,10,11

¹Department of Human Genetics, University of California, Los Angeles, USA
²Department of Urology, University of California, Los Angeles, USA
³Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA
⁴Institute for Precision Health, University of California, Los Angeles, USA
⁵Princess Margaret Cancer Centre, University Health Network, Canada
⁶Department of Medical Biophysics, University of Toronto, Canada
⁷MRC Oxford Institute for Radiation Oncology, University of Oxford, UK
⁸Division of Anatomic Pathology, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Canada
⁹Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
¹⁰Department of Radiation Oncology, University of Toronto, Canada
¹¹Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Canada

Prostate Cancer (PC), the second most common cause of cancer death in men, is frequently treated using radiotherapy with curative intent. Despite its effectiveness, radiotherapy often results in aggressive PC relapse characterized by radioresistance. The diversity in therapeutic response to radiotherapy, and the molecular processes underlining radioresistance are not fully understood. Here we integrated genomic, transcriptomic, and proteomic investigations to comprehensively characterize the molecular determinants of PC radioresistance. To model radioresistance, we have created Conventional-Fractionation (CF) and Hypo-Fractionated (HF) isogenic radioresistant cells that represent different therapeutic regimens: the traditional CF radiotherapy with daily small radiation doses over weeks, and the relatively new HF radiotherapy with high radiation doses across several single treatments. We discovered that CF radioresistant cells gained twice the number of somatic single-nucleotide variants than HF. Nevertheless, the gained mutations, irrespective of the treatment schedule, converged on mutational signatures associated with mismatch DNA repair. CF radioresistant cells demonstrated strong and exclusive dysregulation of driver and hallmark-cancer genes in RNA abundance profiles. The differences in protein abundance display cell-fraction-dependent clusters, foremost of which are elevated levels of DNA repair proteins in CF radioresistant cell nuclei. Collectively, we observed a far more aggressive phenotype in CF radioresistant cells compared to HF. The clinical relevance of our top potential therapeutic targets was assessed using a cohort of 380 PC patients. Our study provides a platform for the development of therapies for radio-recurrent PC. Ongoing proteogenomic integration will help understand the relationships amongst radioresistance-associated changes at the DNA, RNA, and protein levels.