Spatiotemporal Genomic Profiling of Intestinal Metaplasia Reveals Clonal Dynamics of Gastric Cancer Progression

Authors
Kie Kyon Huang^1,28, Haoran Ma^1,28, Roxanne Hui Heng Chong^2,28, Tomoyuki Uchihara¹, Benedict Shi Xiang Lian¹, Feng Zhu², Taotao Sheng³, Supriya Srivastava², Su Ting Tay¹, Raghav Sundar^1,2,4, Angie Lay Keng Tan¹, Xuewen Ong¹, Minghui Lee¹, Shamaine Wei Ting Ho³, Tom Lesluyes⁵, Hassan Ashktorab⁶, Duane Smoot⁷, Peter Van Loo^5,8,9, Joy Shijia Chua², Kalpana Ramnarayanan¹, Louis Ho Shing Lau¹⁰, Takuji Gotoda¹¹, Hyun Soo Kim¹², Tiing Leong Ang¹³, Christopher Khor¹⁴, Jonathan Wei Jie Lee^2,15,16,23, Stephen Kin Kwok Tsao¹⁷, Wei Lyn Yang¹⁷, Ming Teh¹⁸, Hyunsoo Chung^19,*, Jimmy Bok Yan So^20,21,22,*, Khay Guan Yeoh^2,23,*, Patrick Tan^{1,3,24,25,26,27,29,*}, Singapore Gastric Cancer Consortium

Affiliations

1. Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
2. Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
3. Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
4. Department of Haematology-Oncology, National University Health System, Singapore 119074, Singapore
5. The Francis Crick Institute, London, UK
6. Department of Medicine, Howard University, Washington, DC, USA
7. Department of Internal Medicine, Meharry Medical College, Nashville, Tennessee, USA
8. Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
9. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
10. Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong
11. Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine
12. Department of Internal Medicine, Yonsei University Wonju College of Medicine
13. Department of Gastroenterology & Hepatology, Changi General Hospital, Singapore 529889, Singapore
14. Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore 169854, Singapore
15. iHealthtech, National University of Singapore, Singapore
16. SynCTI, National University of Singapore, Singapore 117599, Singapore
17. Department of Gastroenterology & Hepatology, Tan Tock Seng Hospital, Singapore 308433, Singapore
18. Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
19. Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
20. Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
21. NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
22. Division of Surgical Oncology, National University Cancer Institute of Singapore (NCIS), Singapore
23. Department of Gastroenterology & Hepatology, National University Hospital, Singapore 119074, Singapore
24. Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
25. Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
26. Cellular and Molecular Research, National Cancer Centre, Singapore
27. Singhealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore 168752, Singapore
28. These authors contributed equally
29. Lead contact

Corresponding Authors
Prof Patrick Tan (gmstanp@duke-nus.edu.sg)
Prof Khay Guan Yeoh (mdcykg@nus.edu.sg)
Prof Jimmy Bok Yan So (jimmyso@nus.edu.sg )
Dr Hyunsoo Chung (h.chung@snu.ac.kr)

Introduction
The Gastric Cancer Epidemiology Program (GCEP) is a prospective multi-center longitudinal cohort study, monitoring 2980 Chinese participants aged ≥50 from 2004 to 2015. At enrolment, GCEP subjects underwent screening gastroscopies with standardised gastric mucosal sampling at multiple stomach regions (antrum, body, cardia), and surveillance endoscopies at years 3 and 5.

Methods
For this study (“TransGCEP1000”), we performed high-depth (>1000x) targeted DNA sequencing of 277 cancer genes on 1217 frozen endoscopic biopsies from 682 unique subjects (1119 samples from 644 subjects with intestinal metaplasia (IM); 98 samples from 38 control subjects without IM) (Figure 1). We also generated bulk RNA-seq transcriptomes of 183 gastric samples from the antrum (24 normal, 31 IM) and body/cardia (22 normal, 106 IM) while additional samples (not from GCEP1000) were profiled using single–cell RNA-seq, and spatial transcriptomics.

Results
We identify 26 IM driver genes in diverse pathways including chromatin regulation (ARID1A) and intestinal homeostasis (SOX9). Single-cell and spatial profiles highlight changes in tissue ecology and IM lineage heterogeneity, including an intestinal stem-cell dominant cellular compartment linked to early malignancy. Expanded transcriptome profiling reveals expression-based molecular subtypes of IM associated with incomplete histology, antral/intestinal cell types, ARID1A mutations, inflammation, and microbial communities normally associated with the healthy oral tract. We demonstrate that combined clinical-genomic models outperform clinical-only models in predicting IMs likely to transform to GC.

Conclusion
By highlighting strategies for accurately identifying IM patients at high GC risk and a role for microbial dysbiosis in IM progression, our results raise opportunities for GC precision prevention and interception (Figure 2).