Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in hepatocellular carcinoma: the PLANET study
Weiwei Zhai, Hannah Lai, Neslihan Arife Kaya, Jianbin Chen, Hechuan Yang, Bingxin Lu, Jia Qi Lim, Siming Ma, Sin Chi Chew, Khi Pin Chua, Jacob J.S. Alvarez, Pauline Jieqi Chen, Mei Mei Chang, Lingyan Wu, Brian K. P. Goh, Alexander Chung, Chung Yip Chan, Peng Chung Cheow, Ser Yee Lee, Juinn Huar Kam, Alfred Wei Chieh Kow, Shridhar Ganpathi Iyer, Rawisak Chanwat, Jidapa Thammasiri, Boon Koon Yoong, Diana Bee‐Lan Ong, Vanessa H. de Villa, Rouchelle D.dela Cruz, Tracy Jiezhen Loh, Wei Wan, Zeng Zeng, Anders J. Skanderup, Yin Huei Pang, Krishnakumar Madhavan, Tony Kiat Hon Lim, Glenn Kunnath Bonney, Wei Qiang Leow, Valerie Chew, Yock Young Dan, Wai Leong Tam, Han Chong Toh, Roger Foo, Pierce K. H. Chow
Abstract
Intra-tumor heterogeneity (ITH) is a key challenge in cancer treatment, but previous studies have focused mainly on the genomic alterations without exploring phenotypic (transcriptomic and immune) heterogeneity. Using one of the largest prospective surgical cohorts for hepatocellular carcinoma (HCC) with multi-region sampling, we sequenced whole genomes and paired transcriptomes from 67 HCC patients (331 samples). We found that while genomic ITH was rather constant across stages, phenotypic ITH had a very different trajectory and quickly diversified in stage II patients. Most strikingly, 30% of patients were found to contain more than one transcriptomic subtype within a single tumor. Such phenotypic ITH was found to be much more informative in predicting patient survival than genomic ITH and explains the poor efficacy of single-target systemic therapies in HCC. Taken together, we not only revealed an unprecedentedly dynamic landscape of phenotypic heterogeneity in HCC, but also highlighted the importance of studying phenotypic evolution across cancer types.