Epigenetic promoter alterations in GI tumour immune-editing and resistance to immune checkpoint inhibition

Raghav Sundar, Kie Kyon Huang, Vikrant Kumar, Kalpana Ramnarayanan, Deniz Demircioglu, Zhisheng Her, Xuewen Ong, Zul Fazreen Bin Adam Isa, Manjie Xing, Angie Lay Keng Tan, David Wai Meng Tai, Su Pin Choo, Weiwei Zhai, Jia Qi Lim, Meghna Das Thakur, Luciana Molinero, Edward Cha, Marcella Fasso, Monica Niger, Filippo PietrantonioJeeyun Lee, Anand D. Jeyasekharan, Aditi Qamra, Radhika Patnala, Arne Fabritius, Mark De Simone, Joe Yeong, Cedric Chuan Young Ng, Sun Young Rha, Yukiya Narita, Kei Muro, Yu Amanda Guo, Anders Jacobsen Skanderup, Jimmy Bok Yan So, Wei Peng Yong, Qingfeng Chen, Jonathan Göke, Patrick Tan

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)


OBJECTIVES: Epigenomic alterations in cancer interact with the immune microenvironment to dictate tumour evolution and therapeutic response. We aimed to study the regulation of the tumour immune microenvironment through epigenetic alternate promoter use in gastric cancer and to expand our findings to other gastrointestinal tumours. DESIGN: Alternate promoter burden (APB) was quantified using a novel bioinformatic algorithm (proActiv) to infer promoter activity from short-read RNA sequencing and samples categorised into APBhigh, APBint and APBlow. Single-cell RNA sequencing was performed to analyse the intratumour immune microenvironment. A humanised mouse cancer in vivo model was used to explore dynamic temporal interactions between tumour kinetics, alternate promoter usage and the human immune system. Multiple cohorts of gastrointestinal tumours treated with immunotherapy were assessed for correlation between APB and treatment outcomes. RESULTS: APBhigh gastric cancer tumours expressed decreased levels of T-cell cytolytic activity and exhibited signatures of immune depletion. Single-cell RNAsequencing analysis confirmed distinct immunological populations and lower T-cell proportions in APBhigh tumours. Functional in vivo studies using 'humanised mice' harbouring an active human immune system revealed distinct temporal relationships between APB and tumour growth, with APBhigh tumours having almost no human T-cell infiltration. Analysis of immunotherapy-treated patients with GI cancer confirmed resistance of APBhigh tumours to immune checkpoint inhibition. APBhigh gastric cancer exhibited significantly poorer progression-free survival compared with APBlow (median 55 days vs 121 days, HR 0.40, 95% CI 0.18 to 0.93, p=0.032). CONCLUSION: These findings demonstrate an association between alternate promoter use and the tumour microenvironment, leading to immune evasion and immunotherapy resistance.

Original languageEnglish
Pages (from-to)1277-1288
Number of pages12
Issue number7
Publication statusPublished - 2022 Jul 1

Bibliographical note

Publisher Copyright:
© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.

All Science Journal Classification (ASJC) codes

  • Gastroenterology


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