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Takeuchi C, Yamashita S, Liu YY, Takeshima H, Sasaki A, Fukuda M, Hashimoto T, Naka T, Ishizu K, Sekine S, Yoshikawa T, Hamada A, Yamamichi N, Fujishiro M, Ushijima T. Precancerous nature of intestinal metaplasia with increased chance of conversion and accelerated DNA methylation. Gut 2024; 73:255-267. [PMID: 37751933 DOI: 10.1136/gutjnl-2023-329492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
OBJECTIVE The presence of intestinal metaplasia (IM) is a risk factor for gastric cancer. However, it is still controversial whether IM itself is precancerous or paracancerous. Here, we aimed to explore the precancerous nature of IM by analysing epigenetic alterations. DESIGN Genome-wide DNA methylation analysis was conducted by EPIC BeadArray using IM crypts isolated by Alcian blue staining. Chromatin immunoprecipitation sequencing for H3K27ac and single-cell assay for transposase-accessible chromatin by sequencing were conducted using IM mucosa. NOS2 was induced using Tet-on gene expression system in normal cells. RESULTS IM crypts had a methylation profile unique from non-IM crypts, showing extensive DNA hypermethylation in promoter CpG islands, including those of tumour-suppressor genes. Also, the IM-specific methylation profile, namely epigenetic footprint, was present in a fraction of gastric cancers with a higher frequency than expected, and suggested to be associated with good overall survival. IM organoids had remarkably high NOS2 expression, and NOS2 induction in normal cells led to accelerated induction of aberrant DNA methylation, namely epigenetic instability, by increasing DNA methyltransferase activity. IM mucosa showed dynamic enhancer reprogramming, including the regions involved in higher NOS2 expression. NOS2 had open chromatin in IM cells but not in gastric cells, and IM cells had frequent closed chromatin of tumour-suppressor genes, indicating their methylation-silencing. NOS2 expression in IM-derived organoids was upregulated by interleukin-17A, a cytokine secreted by extracellular bacterial infection. CONCLUSIONS IM cells were considered to have a precancerous nature potentially with an increased chance of converting into cancer cells, and an accelerated DNA methylation induction due to abnormal NOS2 expression.
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Affiliation(s)
- Chihiro Takeuchi
- Division of Epigenomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Shinagawa-ku, Tokyo, Japan
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Department of Biotechnology, Maebashi Institute of Technology, Maebashi, Gunma, Japan
| | - Yu-Yu Liu
- Division of Epigenomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Shinagawa-ku, Tokyo, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Shinagawa-ku, Tokyo, Japan
| | - Akiko Sasaki
- Division of Epigenomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kamakura, Kanagawa, Japan
| | - Masahide Fukuda
- Division of Epigenomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Oita, Japan
| | - Taiki Hashimoto
- Department of Diagnostic Pathology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Tomoaki Naka
- Department of Diagnostic Pathology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Kenichi Ishizu
- Department of Gastric Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Shigeki Sekine
- Department of Diagnostic Pathology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Takaki Yoshikawa
- Department of Gastric Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Nobutake Yamamichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Center for Epidemiology and Preventive Medicine, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Shinagawa-ku, Tokyo, Japan
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2
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Huang KK, Ma H, Chong RHH, Uchihara T, Lian BSX, Zhu F, Sheng T, Srivastava S, Tay ST, Sundar R, Tan ALK, Ong X, Lee M, Ho SWT, Lesluyes T, Ashktorab H, Smoot D, Van Loo P, Chua JS, Ramnarayanan K, Lau LHS, Gotoda T, Kim HS, Ang TL, Khor C, Lee JWJ, Tsao SKK, Yang WL, Teh M, Chung H, So JBY, Yeoh KG, Tan P. Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression. Cancer Cell 2023; 41:2019-2037.e8. [PMID: 37890493 PMCID: PMC10729843 DOI: 10.1016/j.ccell.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/08/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]
Abstract
Intestinal metaplasia (IM) is a pre-malignant condition of the gastric mucosa associated with increased gastric cancer (GC) risk. Analyzing 1,256 gastric samples (1,152 IMs) across 692 subjects from a prospective 10-year study, 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. 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.
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Affiliation(s)
- Kie Kyon Huang
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Haoran Ma
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Roxanne Hui Heng Chong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Tomoyuki Uchihara
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Benedict Shi Xiang Lian
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Taotao Sheng
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Su Ting Tay
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Raghav Sundar
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Haematology-Oncology, National University Health System, Singapore 119074, Singapore
| | - Angie Lay Keng Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Xuewen Ong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Minghui Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Shamaine Wei Ting Ho
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | | | - Duane Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, TN, USA
| | - Peter Van Loo
- The Francis Crick Institute, London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joy Shijia Chua
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kalpana Ramnarayanan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Louis Ho Shing Lau
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Takuji Gotoda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Hyun Soo Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Seoul, Korea
| | - Tiing Leong Ang
- Department of Gastroenterology & Hepatology, Changi General Hospital, Singapore 529889, Singapore
| | - Christopher Khor
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore 169854, Singapore
| | - Jonathan Wei Jie Lee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; iHealthtech, National University of Singapore, Singapore, Singapore; SynCTI, National University of Singapore, Singapore 117599, Singapore; Department of Gastroenterology & Hepatology, National University Hospital, Singapore 119074, Singapore
| | - Stephen Kin Kwok Tsao
- Department of Gastroenterology & Hepatology, Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Wei Lyn Yang
- Department of Gastroenterology & Hepatology, Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Ming Teh
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Hyunsoo Chung
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
| | - Jimmy Bok Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Division of Surgical Oncology, National University Cancer Institute of Singapore (NCIS), Singapore, Singapore.
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Gastroenterology & Hepatology, National University Hospital, Singapore 119074, Singapore.
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore; Singhealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore 168752, Singapore.
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3
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Usui G, Matsusaka K, Huang KK, Zhu F, Shinozaki T, Fukuyo M, Rahmutulla B, Yogi N, Okada T, Minami M, Seki M, Sakai E, Fujibayashi K, Kwok Tsao SK, Khor C, Ang TL, Abe H, Matsubara H, Fukayama M, Gunji T, Matsuhashi N, Morikawa T, Ushiku T, Yeoh KG, Tan P, Kaneda A. Integrated environmental, lifestyle, and epigenetic risk prediction of primary gastric neoplasia using the longitudinally monitored cohorts. EBioMedicine 2023; 98:104844. [PMID: 38251469 PMCID: PMC10755115 DOI: 10.1016/j.ebiom.2023.104844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND DNA methylation accumulates in non-malignant gastric mucosa after exposure to pathogens. To elucidate how environmental, methylation, and lifestyle factors interplay to influence primary gastric neoplasia (GN) risk, we analyzed longitudinally monitored cohorts in Japan and Singapore. METHODS Asymptomatic subjects who underwent a gastric mucosal biopsy on the health check-up were enrolled. We analyzed the association between clinical factors and GN development using Cox hazard models. We further conducted comprehensive methylation analysis on selected tissues, including (i) mucosae from subjects developing GN later, (ii) mucosae from subjects not developing GN later, and (iii) GN tissues and surrounding mucosae. We also use the methylation data of mucosa collected in Singapore. The association between methylation and GN risk, as well as lifestyle and methylation, were analyzed. FINDINGS Among 4234 subjects, GN was developed in 77 subjects. GN incidence was correlated with age, drinking, smoking, and Helicobacter pylori (HP) status. Accumulation of methylation in biopsied gastric mucosae was predictive of higher future GN risk and shorter duration to GN incidence. Whereas methylation levels were associated with HP positivity, lifestyle, and morphological alterations, DNA methylation remained an independent GN risk factor through multivariable analyses. Pro-carcinogenic epigenetic alterations initiated by HP exposure were amplified by unfavorable but modifiable lifestyle choices. Adding DNA methylation to the model with clinical factors improved the predictive ability for the GN risk. INTERPRETATION The integration of environmental, lifestyle, and epigenetic information can provide increased resolution in the stratification of primary GN risk. FUNDING The funds are listed in Acknowledgements section.
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Affiliation(s)
- Genki Usui
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Diagnostic Pathology, NTT Medical Center Tokyo, Tokyo, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tomohiro Shinozaki
- Faculty of Engineering, Department of Information and Computer Technology, Tokyo University of Science, Tokyo, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Norikazu Yogi
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoka Okada
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mizuki Minami
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Cancer Genomics Center, Chiba University Hospital, Chiba, Japan
| | - Eiji Sakai
- Department of Gastroenterology, NTT Medical Center Tokyo, Tokyo, Japan; Division of Gastroenterology, Yokohama Sakae Kyosai Hospital, Yokohama, Japan
| | - Kazutoshi Fujibayashi
- Center for Preventive Medicine, NTT Medical Center Tokyo, Tokyo, Japan; Department of General Medicine, Juntendo University Hospital, Tokyo, Japan
| | - Stephen Kin Kwok Tsao
- Department of Gastroenterology and Hepatology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Christopher Khor
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore, Singapore
| | - Tiing Leong Ang
- Department of Gastroenterology and Hepatology, Changi General Hospital, Singapore, Singapore
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiaki Gunji
- Center for Preventive Medicine, NTT Medical Center Tokyo, Tokyo, Japan
| | | | - Teppei Morikawa
- Department of Diagnostic Pathology, NTT Medical Center Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Department of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore.
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore; Genome Institute of Singapore, Singapore, Singapore; Cancer Science Institute of Singapore, Singapore, Singapore.
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Health and Disease Omics Center, Chiba University, Chiba, Japan.
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4
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Gao T, Kastriti ME, Ljungström V, Heinzel A, Tischler AS, Oberbauer R, Loh PR, Adameyko I, Park PJ, Kharchenko PV. A pan-tissue survey of mosaic chromosomal alterations in 948 individuals. Nat Genet 2023; 55:1901-1911. [PMID: 37904053 PMCID: PMC10838621 DOI: 10.1038/s41588-023-01537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/18/2023] [Indexed: 11/01/2023]
Abstract
Genetic mutations accumulate in an organism's body throughout its lifetime. While somatic single-nucleotide variants have been well characterized in the human body, the patterns and consequences of large chromosomal alterations in normal tissues remain largely unknown. Here, we present a pan-tissue survey of mosaic chromosomal alterations (mCAs) in 948 healthy individuals from the Genotype-Tissue Expression project, augmenting RNA-based allelic imbalance estimation with haplotype phasing. We found that approximately a quarter of the individuals carry a clonally-expanded mCA in at least one tissue, with incidence strongly correlated with age. The prevalence and genome-wide patterns of mCAs vary considerably across tissue types, suggesting tissue-specific mutagenic exposure and selection pressures. The mCA landscapes in normal adrenal and pituitary glands resemble those in tumors arising from these tissues, whereas the same is not true for the esophagus and skin. Together, our findings show a widespread age-dependent emergence of mCAs across normal human tissues with intricate connections to tumorigenesis.
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Affiliation(s)
- Teng Gao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Maria Eleni Kastriti
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andreas Heinzel
- Department of Nephrology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Arthur S Tischler
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Rainer Oberbauer
- Department of Nephrology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA.
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5
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Huang RJ, Wichmann IA, Su A, Sathe A, Shum MV, Grimes SM, Meka R, Almeda A, Bai X, Shen J, Nguyen Q, Amieva MR, Hwang JH, Ji HP. A spatially mapped gene expression signature for intestinal stem-like cells identifies high-risk precursors of gastric cancer. bioRxiv 2023:2023.09.20.558462. [PMID: 37786704 PMCID: PMC10541579 DOI: 10.1101/2023.09.20.558462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Objective Gastric intestinal metaplasia (GIM) is a precancerous lesion that increases gastric cancer (GC) risk. The Operative Link on GIM (OLGIM) is a combined clinical-histopathologic system to risk-stratify patients with GIM. The identification of molecular biomarkers that are indicators for advanced OLGIM lesions may improve cancer prevention efforts. Methods This study was based on clinical and genomic data from four cohorts: 1) GAPS, a GIM cohort with detailed OLGIM severity scoring (N=303 samples); 2) the Cancer Genome Atlas (N=198); 3) a collation of in-house and publicly available scRNA-seq data (N=40), and 4) a spatial validation cohort (N=5) consisting of annotated histology slides of patients with either GC or advanced GIM. We used a multi-omics pipeline to identify, validate and sequentially parse a highly-refined signature of 26 genes which characterize high-risk GIM. Results Using standard RNA-seq, we analyzed two separate, non-overlapping discovery (N=88) and validation (N=215) sets of GIM. In the discovery phase, we identified 105 upregulated genes specific for high-risk GIM (defined as OLGIM III-IV), of which 100 genes were independently confirmed in the validation set. Spatial transcriptomic profiling revealed 36 of these 100 genes to be expressed in metaplastic foci in GIM. Comparison with bulk GC sequencing data revealed 26 of these genes to be expressed in intestinal-type GC. Single-cell profiling resolved the 26-gene signature to both mature intestinal lineages (goblet cells, enterocytes) and immature intestinal lineages (stem-like cells). A subset of these genes was further validated using single-molecule multiplex fluorescence in situ hybridization. We found certain genes (TFF3 and ANPEP) to mark differentiated intestinal lineages, whereas others (OLFM4 and CPS1) localized to immature cells in the isthmic/crypt region of metaplastic glands, consistent with the findings from scRNAseq analysis. Conclusions using an integrated multi-omics approach, we identified a novel 26-gene expression signature for high-OLGIM precursors at increased risk for GC. We found this signature localizes to aberrant intestinal stem-like cells within the metaplastic microenvironment. These findings hold important translational significance for future prevention and early detection efforts.
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Affiliation(s)
- Robert J. Huang
- Division of Gastroenterology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ignacio A. Wichmann
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
- Division of Obstetrics and Gynecology, Department of Obstetrics, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Andrew Su
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anuja Sathe
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Miranda V. Shum
- Division of Gastroenterology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Susan M. Grimes
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Rithika Meka
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Alison Almeda
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Xiangqi Bai
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Jeanne Shen
- Department of Pathology, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Manuel R. Amieva
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Joo Ha Hwang
- Division of Gastroenterology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
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6
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Kumagai K, Shimizu T, Nikaido M, Hirano T, Kakiuchi N, Takeuchi Y, Minamiguchi S, Sakurai T, Teramura M, Utsumi T, Hiramatsu Y, Nakanishi Y, Takai A, Miyamoto S, Ogawa S, Seno H. On the origin of gastric tumours: analysis of a case with intramucosal gastric carcinoma and oxyntic gland adenoma. J Pathol 2023; 259:362-368. [PMID: 36625379 DOI: 10.1002/path.6050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/01/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Most gastric cancers develop in inflamed gastric mucosa due to Helicobacter pylori infection, typically with metaplastic changes. However, the origins of gastric cancer remain unknown. Here, we present a case of intramucosal gastric carcinoma (IGC) and oxyntic gland adenoma (OGA) derived from spasmolytic polypeptide-expressing metaplasia (SPEM). Early gastric cancer adjacent to a polyp was found in the upper corpus of a 71-year-old woman without H. pylori infection and was endoscopically resected. Histological examination showed IGC and OGA, both of which had predominant MUC6 expression. Interestingly, gastric glands with enriched MUC6-positive mucous cells, referred to as SPEM, expanded between them. Whole-exome sequencing analysis revealed a truncating KRAS(G12D) mutation in IGC, OGA, and SPEM. In addition, TP53 and CDKN2A mutations and a loss of chromosome 17p were found in the IGC, whereas a GNAS mutation was observed in the OGA. These results indicated that IGC and OGA originated from the KRAS-mutated SPEM. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ken Kumagai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Shimizu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mitsuhiro Nikaido
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomonori Hirano
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhide Takeuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan.,Clinical Bio Resource Center, Kyoto University Hospital, Kyoto, Japan
| | | | - Takaki Sakurai
- Department of Diagnostic Pathology, Kansai Electric Power Hospital, Osaka, Japan
| | - Mari Teramura
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Utsumi
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukiko Hiramatsu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shin'ichi Miyamoto
- Department of Gastroenterology and Hepatology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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