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Shin K, Kim J, Park SJ, Kim H, Lee MA, Kim O, Park J, Kang N, Kim IH. Early Increase in Circulating PD-1 +CD8 + T Cells Predicts Favorable Survival in Patients with Advanced Gastric Cancer Receiving Chemotherapy. Cancers (Basel) 2023; 15:3955. [PMID: 37568771 PMCID: PMC10417033 DOI: 10.3390/cancers15153955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
The clinical significance of PD-1 expression in circulating CD8+ T cells in patients with gastric cancer (GC) receiving chemotherapy remains unelucidated. Therefore, we aimed to examine its prognostic significance in blood samples of 68 patients with advanced GC who received platinum-based chemotherapy. The correlation between peripheral blood mononuclear cells, measured using fluorescence-activated cell sorting, was evaluated. Patients were divided into two groups according to the changes in PD-1+CD8+ T-cell frequencies between day 0 and 7. They were categorized as increased or decreased PD-1+CD8+ T-cell groups. The increased PD-1+CD8+ T-cell group showed longer progression-free survival (PFS) and overall survival (OS) than the decreased PD-1+CD8+ T-cell group (PFS: 8.7 months vs. 6.1 months, p = 0.007; OS: 20.7 months vs. 10.8 months, p = 0.003). The mean duration of response was significantly different between the groups (5.7 months vs. 2.5 months, p = 0.041). Multivariate analysis revealed that an increase in PD-1+CD8+ T-cell frequency was an independent prognostic factor. We concluded that the early increase in PD-1+CD8+ T-cell frequency is a potential predictor of favorable prognoses and durable responses in patients with advanced GC receiving chemotherapy.
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Affiliation(s)
- Kabsoo Shin
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.S.); (J.K.); (S.J.P.); (M.A.L.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (O.K.); (J.P.); (N.K.)
| | - Joori Kim
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.S.); (J.K.); (S.J.P.); (M.A.L.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (O.K.); (J.P.); (N.K.)
| | - Se Jun Park
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.S.); (J.K.); (S.J.P.); (M.A.L.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (O.K.); (J.P.); (N.K.)
| | - Hyunho Kim
- Division of Medical Oncology, Department of Internal Medicine, St. Vincent Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea;
| | - Myung Ah Lee
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.S.); (J.K.); (S.J.P.); (M.A.L.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (O.K.); (J.P.); (N.K.)
| | - Okran Kim
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (O.K.); (J.P.); (N.K.)
| | - Juyeon Park
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (O.K.); (J.P.); (N.K.)
| | - Nahyeon Kang
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (O.K.); (J.P.); (N.K.)
| | - In-Ho Kim
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (K.S.); (J.K.); (S.J.P.); (M.A.L.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (O.K.); (J.P.); (N.K.)
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2
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Liu R, Cao Z, Wu M, Li X, Fan P, Liu Z. Golgi-apparatus genes related signature for predicting the progression-free interval of patients with papillary thyroid carcinoma. BMC Med Genomics 2023; 16:60. [PMID: 36973751 PMCID: PMC10041766 DOI: 10.1186/s12920-023-01485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND We aimed to build a novel model with golgi apparatus related genes (GaGs) signature and relevant clinical parameters for predicting progression-free interval (PFI) after surgery for papillary thyroid carcinoma (PTC). METHODS We performed a bioinformatic analysis of integrated PTC datasets with the GaGs to identify differentially expressed GaGs (DE-GaGs). Then we generated PFI-related DE-GaGs and established a novel GaGs based signature. After that, we validated the signature on multiple external datasets and PTC cell lines. Further, we conducted uni- and multivariate analyses to identify independent prognostic characters. Finally, we established a signature and clinical parameters-based nomogram for predicting the PFI of PTC. RESULTS We identified 260 DE-GaGs related to PFI in PTC. The functional enrichment analysis showed that the DE-MTGs were associated with an essential oncogenic glycoprotein biosynthetic process. Consequently, we established and optimized a novel 11 gene signature that could distinguish patients with poorer prognoses and predicted PFI accurately. The novel signature had a C-index of 0.78, and the relevant nomogram had a C-index of 0.79. Also, it was closely related to the pivotal clinical characters of and anaplastic potential in datasets and PTC cell lines. And the signature was confirmed a significant independent prognostic factor in PTC. Finally, we built a nomogram by including the signature and relevant clinical factors. Validation analysis showed that the nomogram's efficacy was satisfying in predicting PTC's PFI. CONCLUSION The GaGs signature and nomogram were closely associated with PTC prognosis and may help clinicians improve the individualized prediction of PFI, especially for high-risk patients after surgery.
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Affiliation(s)
- Rui Liu
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, China
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhen Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Mengwei Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaobin Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Peizhi Fan
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, China.
| | - Ziwen Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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3
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Role of IL-6/STAT3 Axis in Resistance to Cisplatin in Gastric Cancers. Biomedicines 2023; 11:biomedicines11030694. [PMID: 36979673 PMCID: PMC10044743 DOI: 10.3390/biomedicines11030694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Gastric cancer, the second most common cause of death worldwide, is characterized by poor prognosis and low responsiveness to chemotherapy. Indeed, multidrug resistance, based mainly on cellular and molecular factors, remains one of the most limiting factors of the current approach to gastric cancer (GC) therapy. We employed a comprehensive gene expression analysis through data mining of publicly available databases to assess the role of the signal transducer and activator of transcription 3 (STAT3) in gastric cancer drug efficiency. It has been proposed that gastric cancer cells are less sensitive to these drugs because they develop resistance to these agents through activating alternative signalling pathways responsible for overcoming pharmacological inhibition. Our study evaluated the hypothesis that activating STAT3 signalling in response to cisplatin reduces the reaction to the drug. Consistent with this hypothesis, inhibition of interleukin 6 (IL-6)/STAT3 in combination therapy with cisplatin prevented both STAT3 activation and more lethality than induction by a single agent. The data suggest that the IL-6/STAT3 axis block associated with cisplatin treatment may represent a strategy to overcome resistance.
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4
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Clinical relevance of PD-1 positive CD8 T-cells in gastric cancer. Gastric Cancer 2023; 26:393-404. [PMID: 36781556 PMCID: PMC10115710 DOI: 10.1007/s10120-023-01364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND We evaluated the relevance of PD-1+CD8+ T-cells in gastric cancer (GC) including prognostic significance, association with chemotherapy and immunotherapy sensitivity and correlations with the tumor microenvironment (TME). METHODS Discovery cohort: GC samples were evaluated for AE1/3, CD8, PD-1, Ki-67 and Granzyme-B expression with fluorescence-based multiplex immunohistochemistry (mIHC). Validation cohorts: we analyzed bulk RNAseq GC datasets from TCGA, the "3G" chemotherapy trial and an immunotherapy phase 2 trial. The cox proportional hazards model was used to identify factors that influenced overall survival (OS). To study the TME, we analyzed single-cell RNAseq performed on GCs. RESULTS In the discovery cohort of 350 GCs, increased PD-1 expression of CD8 T-cells was prognostic for OS (HR 0.822, p = 0.042). PD-1 expression in CD8 T-cells highly correlated with cytolytic [Granzyme-B+] (r = 0.714, p < 0.001) and proliferative [Ki-67+] (r = 0.798, p < 0.001) activity. Analysis of bulk RNAseq datasets showed tumors with high PD-1 and CD8A expression levels had improved OS when treated with immunotherapy (HR 0.117, p = 0.036) and chemotherapy (HR 0.475, p = 0.017). Analysis of an scRNAseq dataset of 152,423 cells from 40 GCs revealed that T-cell and NK-cell proportions were higher (24% vs 18% and 19% vs 15%, p < 0.0001), while macrophage proportions were lower (7% vs 11%, p < 0.0001) in CD8PD-1high compared to CD8PD-1low tumors. CONCLUSION This is one of the largest GC cohorts of mIHC combined with analysis of multiple datasets providing orthogonal validation of the clinical relevance of PD-1+CD8+ T-cells being associated with improved OS. CD8PD-1high tumors have distinct features of an immunologically active, T-cell inflamed TME.
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5
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Ho SWT, Sheng T, Xing M, Ooi WF, Xu C, Sundar R, Huang KK, Li Z, Kumar V, Ramnarayanan K, Zhu F, Srivastava S, Isa ZFBA, Anene-Nzelu CG, Razavi-Mohseni M, Shigaki D, Ma H, Tan ALK, Ong X, Lee MH, Tay ST, Guo YA, Huang W, Li S, Beer MA, Foo RSY, Teh M, Skanderup AJ, Teh BT, Tan P. Regulatory enhancer profiling of mesenchymal-type gastric cancer reveals subtype-specific epigenomic landscapes and targetable vulnerabilities. Gut 2023; 72:226-241. [PMID: 35817555 DOI: 10.1136/gutjnl-2021-326483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/03/2022] [Indexed: 01/28/2023]
Abstract
OBJECTIVE Gastric cancer (GC) comprises multiple molecular subtypes. Recent studies have highlighted mesenchymal-subtype GC (Mes-GC) as a clinically aggressive subtype with few treatment options. Combining multiple studies, we derived and applied a consensus Mes-GC classifier to define the Mes-GC enhancer landscape revealing disease vulnerabilities. DESIGN Transcriptomic profiles of ~1000 primary GCs and cell lines were analysed to derive a consensus Mes-GC classifier. Clinical and genomic associations were performed across >1200 patients with GC. Genome-wide epigenomic profiles (H3K27ac, H3K4me1 and assay for transposase-accessible chromatin with sequencing (ATAC-seq)) of 49 primary GCs and GC cell lines were generated to identify Mes-GC-specific enhancer landscapes. Upstream regulators and downstream targets of Mes-GC enhancers were interrogated using chromatin immunoprecipitation followed by sequencing (ChIP-seq), RNA sequencing, CRISPR/Cas9 editing, functional assays and pharmacological inhibition. RESULTS We identified and validated a 993-gene cancer-cell intrinsic Mes-GC classifier applicable to retrospective cohorts or prospective single samples. Multicohort analysis of Mes-GCs confirmed associations with poor patient survival, therapy resistance and few targetable genomic alterations. Analysis of enhancer profiles revealed a distinctive Mes-GC epigenomic landscape, with TEAD1 as a master regulator of Mes-GC enhancers and Mes-GCs exhibiting preferential sensitivity to TEAD1 pharmacological inhibition. Analysis of Mes-GC super-enhancers also highlighted NUAK1 kinase as a downstream target, with synergistic effects observed between NUAK1 inhibition and cisplatin treatment. CONCLUSION Our results establish a consensus Mes-GC classifier applicable to multiple transcriptomic scenarios. Mes-GCs exhibit a distinct epigenomic landscape, and TEAD1 inhibition and combinatorial NUAK1 inhibition/cisplatin may represent potential targetable options.
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Affiliation(s)
- Shamaine Wei Ting Ho
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Taotao Sheng
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Manjie Xing
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Wen Fong Ooi
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, National University Hospital, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore.,Singapore Gastric Cancer Consortium, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Zhimei Li
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Vikrant Kumar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | | | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Montreal Heart Institute, Quebec, Quebec, Canada.,Department of Medicine, University of Montreal, Quebec, Quebec, Canada
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Dustin Shigaki
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Haoran Ma
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ming Hui Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Yu Amanda Guo
- Computational and Systems Biology, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Weitai Huang
- Computational and Systems Biology, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore .,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Singapore Gastric Cancer Consortium, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cellular and Molecular Research, National Cancer Centre, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
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6
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Nargund AM, Xu C, Mandoli A, Okabe A, Chen GB, Huang KK, Sheng T, Yao X, Teo JMN, Sundar R, Kok YJ, See YX, Xing M, Li Z, Yong CH, Anand A, A I ZF, Poon LF, Ng MSW, Koh JYP, Ooi WF, Tay ST, Ong X, Tan ALK, Grabsch HI, Fullwood MJ, Teh TB, Bi X, Kaneda A, Li S, Tan P. Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer. Cancer Res 2022; 82:2538-2551. [PMID: 35583999 DOI: 10.1158/0008-5472.can-21-2072] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 04/04/2022] [Accepted: 05/09/2022] [Indexed: 12/24/2022]
Abstract
Mutations in the DNA mismatch repair gene MSH2 are causative of microsatellite instability (MSI) in multiple cancers. Here, we discovered that besides its well-established role in DNA repair, MSH2 exerts a novel epigenomic function in gastric cancer. Unbiased CRISPR-based mass spectrometry combined with genome-wide CRISPR functional screening revealed that in early-stage gastric cancer MSH2 genomic binding is not randomly distributed but rather is associated specifically with tumor-associated super-enhancers controlling the expression of cell adhesion genes. At these loci, MSH2 genomic binding was required for chromatin rewiring, de novo enhancer-promoter interactions, maintenance of histone acetylation levels, and regulation of cell adhesion pathway expression. The chromatin function of MSH2 was independent of its DNA repair catalytic activity but required MSH6, another DNA repair gene, and recruitment to gene loci by the SWI/SNF chromatin remodeler SMARCA4/BRG1. Loss of MSH2 in advanced gastric cancers was accompanied by deficient cell adhesion pathway expression, epithelial-mesenchymal transition, and enhanced tumorigenesis in vitro and in vivo. However, MSH2-deficient gastric cancers also displayed addiction to BAZ1B, a bromodomain-containing family member, and consequent synthetic lethality to bromodomain and extraterminal motif (BET) inhibition. Our results reveal a role for MSH2 in gastric cancer epigenomic regulation and identify BET inhibition as a potential therapy in MSH2-deficient gastric malignancies. SIGNIFICANCE DNA repair protein MSH2 binds and regulates cell adhesion genes by enabling enhancer-promoter interactions, and loss of MSH2 causes deficient cell adhesion and bromodomain and extraterminal motif inhibitor synthetic lethality in gastric cancer.
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Affiliation(s)
- Amrita M Nargund
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Amit Mandoli
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Gao Bin Chen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Taotao Sheng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Xiaosai Yao
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Hematology-Oncology, National University Health System, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Yi Xiang See
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Manjie Xing
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Zhimei Li
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore
| | - Chern Han Yong
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore
| | - Aparna Anand
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Lai Fong Poon
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | | | - Javier Yu Peng Koh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Wen Fong Ooi
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Heike I Grabsch
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.,Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Melissa J Fullwood
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tean Bin Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore, Singapore
| | - Xuezhi Bi
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Bioprocessing Technology Institute, Singapore, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore, Singapore
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7
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Sundar R, Huang KK, Kumar V, Ramnarayanan K, Demircioglu D, Her Z, Ong X, Bin Adam Isa ZF, Xing M, Tan ALK, Tai DWM, Choo SP, Zhai W, Lim JQ, Das Thakur M, Molinero L, Cha E, Fasso M, Niger M, Pietrantonio F, Lee J, Jeyasekharan AD, Qamra A, Patnala R, Fabritius A, De Simone M, Yeong J, Ng CCY, Rha SY, Narita Y, Muro K, Guo YA, Skanderup AJ, So JBY, Yong WP, Chen Q, Göke J, Tan P. Epigenetic promoter alterations in GI tumour immune-editing and resistance to immune checkpoint inhibition. Gut 2022; 71:1277-1288. [PMID: 34433583 PMCID: PMC9185816 DOI: 10.1136/gutjnl-2021-324420] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Raghav Sundar
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Hospital, Singapore .,Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore.,Singapore Gastric Cancer Consortium, Singapore
| | - Kie-Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Vikrant Kumar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | | | - Deniz Demircioglu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Zhisheng Her
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Zul Fazreen Bin Adam Isa
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore,Diagnostic Development Hub (DxD), Agency for Science, Technology and Research, Singapore
| | - Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore,Diagnostic Development Hub (DxD), Agency for Science, Technology and Research, Singapore
| | - Angie Lay-Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | | | - Su Pin Choo
- Division of Medical Oncology, National Cancer Centre, Singapore,Curie Oncology, Singapore
| | - Weiwei Zhai
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jia Qi Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Meghna Das Thakur
- Department of Development Sciences, Genentech, San Francisco, California, USA
| | - Luciana Molinero
- Department of Development Sciences, Genentech, San Francisco, California, USA
| | - Edward Cha
- Department of Development Sciences, Genentech, San Francisco, California, USA
| | - Marcella Fasso
- Department of Development Sciences, Genentech, San Francisco, California, USA
| | - Monica Niger
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Anand D Jeyasekharan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Hospital, Singapore,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Aditi Qamra
- Statistical Programming and Analytics, Roche Canada, Mississauga, Ontario, Canada,University Health Network, Toronto, Ontario, Canada
| | | | | | | | - Joe Yeong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Sun Young Rha
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea,Songdang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Yukiya Narita
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Kei Muro
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yu Amanda Guo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | | | - Jimmy Bok Yan So
- Singapore Gastric Cancer Consortium, Singapore,Department of Surgery, National University Hospital, Singapore,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Wei Peng Yong
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Hospital, Singapore,Singapore Gastric Cancer Consortium, Singapore
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jonathan Göke
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore .,Singapore Gastric Cancer Consortium, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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8
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Sundar R, Barr Kumarakulasinghe N, Huak Chan Y, Yoshida K, Yoshikawa T, Miyagi Y, Rino Y, Masuda M, Guan J, Sakamoto J, Tanaka S, Tan ALK, Hoppe MM, Jeyasekharan AD, Ng CCY, De Simone M, Grabsch HI, Lee J, Oshima T, Tsuburaya A, Tan P. Machine-learning model derived gene signature predictive of paclitaxel survival benefit in gastric cancer: results from the randomised phase III SAMIT trial. Gut 2022; 71:676-685. [PMID: 33980610 PMCID: PMC8921574 DOI: 10.1136/gutjnl-2021-324060] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To date, there are no predictive biomarkers to guide selection of patients with gastric cancer (GC) who benefit from paclitaxel. Stomach cancer Adjuvant Multi-Institutional group Trial (SAMIT) was a 2×2 factorial randomised phase III study in which patients with GC were randomised to Pac-S-1 (paclitaxel +S-1), Pac-UFT (paclitaxel +UFT), S-1 alone or UFT alone after curative surgery. DESIGN The primary objective of this study was to identify a gene signature that predicts survival benefit from paclitaxel chemotherapy in GC patients. SAMIT GC samples were profiled using a customised 476 gene NanoString panel. A random forest machine-learning model was applied on the NanoString profiles to develop a gene signature. An independent cohort of metastatic patients with GC treated with paclitaxel and ramucirumab (Pac-Ram) served as an external validation cohort. RESULTS From the SAMIT trial 499 samples were analysed in this study. From the Pac-S-1 training cohort, the random forest model generated a 19-gene signature assigning patients to two groups: Pac-Sensitive and Pac-Resistant. In the Pac-UFT validation cohort, Pac-Sensitive patients exhibited a significant improvement in disease free survival (DFS): 3-year DFS 66% vs 40% (HR 0.44, p=0.0029). There was no survival difference between Pac-Sensitive and Pac-Resistant in the UFT or S-1 alone arms, test of interaction p<0.001. In the external Pac-Ram validation cohort, the signature predicted benefit for Pac-Sensitive (median PFS 147 days vs 112 days, HR 0.48, p=0.022). CONCLUSION Using machine-learning techniques on one of the largest GC trials (SAMIT), we identify a gene signature representing the first predictive biomarker for paclitaxel benefit. TRIAL REGISTRATION NUMBER UMIN Clinical Trials Registry: C000000082 (SAMIT); ClinicalTrials.gov identifier, 02628951 (South Korean trial).
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Affiliation(s)
- Raghav Sundar
- Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Hospital, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore,The N.1 Institute for Health, National University of Singapore, Singapore
| | | | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University Singapore, Singapore
| | - Kazuhiro Yoshida
- Department of Surgical Oncology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takaki Yoshikawa
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yohei Miyagi
- Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Yasushi Rino
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Munetaka Masuda
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Jia Guan
- Department of Clinical Biostatistics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Shiro Tanaka
- Department of Clinical Biostatistics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Angie Lay-Keng Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Michal Marek Hoppe
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Anand D. Jeyasekharan
- Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Hospital, Singapore,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre Singapore, Singapore
| | | | - Heike I. Grabsch
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands,Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jeeyun Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Gangnam-gu, Republic of Korea
| | - Takashi Oshima
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | | | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore .,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Genome Institute of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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9
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Choi YY, Jang E, Kim H, Kim KM, Noh SH, Sohn TS, Huh YM, An JY, Cheong JH. Single patient classifier as a prognostic biomarker in pT1N1 gastric cancer: Results from two large Korean cohorts. Chin J Cancer Res 2021; 33:583-591. [PMID: 34815632 PMCID: PMC8580794 DOI: 10.21147/j.issn.1000-9604.2021.05.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/17/2021] [Indexed: 12/23/2022] Open
Abstract
Objective Benefits of adjuvant treatment in pT1N1 gastric cancer (GC) remain controversial. Additionally, an effective biomarker for early GC is the need of the hour. The prognostic and predictive roles of single patient classifier (SPC) were validated in stage II/III GC. In this study, we aimed to elucidate the role of SPC as a biomarker for pT1N1 GC. Methods The present retrospective biomarker study (NCT03485105) enrolled patients treated for pT1N1 GC between 1996 and 2012 from two large hospitals (the Y cohort and S cohort). For SPC, mRNA expression of four classifier genes (GZMB, WARS, SFRP4 and CDX1) were evaluated by real-time reverse transcription-polymerase chain reaction assay. The SPC was revised targeting pT1 stages and the prognosis was stratified as high- and low-risk group by the expression of SFRP4, a representative epithelial-mesenchymal transition marker.
Results SPC was evaluated in 875 patients (n=391 and 484 in the Y and S cohorts, respectively). Among 864 patients whose SPC result was available, 41 (4.7%) patients experience GC recurrence. According to revised SPC, 254 (29.4%) patients were classified as high risk [123 (31.5%) and 131 (27.1%) in the Y and S cohorts, respectively]. The high risk was related to frequent recurrence in both Y and S cohort (log-rank P=0.023, P<0.001, respectively), while there was no difference byGZMB and WARS expression. Multivariable analyses of the overall-cohort confirmed the high risk of revised SPC as a significant prognostic factor [hazard ratio (HR): 4.402 (2.293−8.449), P<0.001] of GC. A significant difference was not detected by SPC in the prognosis of patients in the presence and absence of adjuvant treatment (log-rank P=0.670).
Conclusions The present study revealed the revised SPC as a prognostic biomarker of pT1N1 GC and suggested the use of the revised SPC for early-stage GC as like stage II/III.
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Affiliation(s)
- Yoon Young Choi
- Department of Surgery, CHA Ilsan Medical Center, CHA University School of Medicine, Goyang-si 1205, Korea.,Department of Surgery, Yonsei University Health System, Seoul 03722, Korea
| | - Eunji Jang
- Department of Radiology, Yonsei University Health System, Seoul 03722, Korea
| | - Hyunki Kim
- Department of Pathology, Yonsei University Health System, Seoul 03722, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Sung Hoon Noh
- Department of Surgery, Yonsei University Health System, Seoul 03722, Korea
| | - Tae Sung Sohn
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Yong-Min Huh
- Department of Radiology, Yonsei University Health System, Seoul 03722, Korea
| | - Ji Yeong An
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jae-Ho Cheong
- Department of Surgery, Yonsei University Health System, Seoul 03722, Korea.,YUHS-KRIBB Medical Convergence Research Institute, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
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10
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Kunisaki C, Sato S, Tsuchiya N, Kubo H, Watanabe J, Sato T, Takeda K, Tamura Y, Kasahara K, Kosaka T, Akiyama H, Endo I. Real-World Therapeutic Outcomes of S-1 Adjuvant Chemotherapy for pStage II/III Gastric Cancer in the Elderly. Eur Surg Res 2021; 62:40-52. [PMID: 33794520 DOI: 10.1159/000515175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 02/08/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND The predictive factors for discontinuation of S-1 administration and prognostic factors in elderly patients with pStage II/III gastric cancer receiving S-1 adjuvant chemotherapy remain unclear. METHODS Between January 2004 and December 2016, 80 elderly gastric cancer patients (≥70 years) undergoing curative D2 gastrectomy were enrolled in this study. Predictive factors for completion of S-1 administration over 1 year, adverse events due to S-1 administration, and prognostic factors for overall survival (OS) and relapse-free survival (RFS) were evaluated. RESULTS Twenty-eight patients (35%) completed 8 courses of S-1. The median relative dose intensity was 82.1% (IQR 31.1-100%). The incidence rates of hematological and nonhematological adverse events were acceptable. Distal gastrectomy was an independent predictive factor for completion of S-1 administration (odds ratio [OR] 0.364; 95% confidence interval [CI] 0.141-0.939; p = 0.037). Higher postoperative neutrophil count/lymphocyte count (N/L) ratio and more advanced stage adversely influenced OS. Multivariate analysis revealed that a higher postoperative N/L ratio and more advanced stage adversely affected RFS. CONCLUSION To complete adjuvant S-1 administration to elderly patients with pStage II/III gastric cancer, total gastrectomy should be avoided if possible. A new regimen for elderly gastric cancer patients with higher postoperative N/L ratios and more advanced stage should be established.
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Affiliation(s)
- Chikara Kunisaki
- Department of Surgery, Gastroenterological Center, Yokohama City University, Yokohama, Japan
| | - Sho Sato
- Department of Surgery, Gastroenterological Center, Yokohama City University, Yokohama, Japan
| | - Nobuhiro Tsuchiya
- Department of Surgery, Gastroenterological Center, Yokohama City University, Yokohama, Japan
| | - Hirokazu Kubo
- Department of Surgery, Gastroenterological Center, Yokohama City University, Yokohama, Japan
| | - Jun Watanabe
- Department of Surgery, Gastroenterological Center, Yokohama City University, Yokohama, Japan
| | - Tsutomu Sato
- Department of Surgery, Gastroenterological Center, Yokohama City University, Yokohama, Japan
| | - Kazuhisa Takeda
- Department of Surgery, Gastroenterological Center, Yokohama City University, Yokohama, Japan
| | - Yuko Tamura
- Department of Gastroenterological Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Kohei Kasahara
- Department of Gastroenterological Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Takashi Kosaka
- Department of Gastroenterological Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Hirotoshi Akiyama
- Department of Gastroenterological Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
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11
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An O, Song Y, Ke X, So JBY, Sundar R, Yang H, Rha SY, Lee MH, Tay ST, Ong X, Tan ALK, Ng MCH, Tantoso E, Chen L, Tan P, Yong WP. "3G" Trial: An RNA Editing Signature to Guide Gastric Cancer Chemotherapy. Cancer Res 2021; 81:2788-2798. [PMID: 33558338 DOI: 10.1158/0008-5472.can-20-2872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/29/2020] [Accepted: 02/03/2021] [Indexed: 12/24/2022]
Abstract
Gastric cancer cases are often diagnosed at an advanced stage with poor prognosis. Platinum-based chemotherapy has been internationally accepted as first-line therapy for inoperable or metastatic gastric cancer. To achieve greater benefits, selection of patients eligible for this treatment is critical. Although gene expression profiling has been widely used as a genomic classifier to identify molecular subtypes of gastric cancer and to stratify patients for different chemotherapy regimens, its prediction accuracy can be improved. Adenosine-to-inosine (A-to-I) RNA editing has emerged as a new player contributing to gastric cancer development and progression, offering potential clinical utility for diagnosis and treatment. Using a systematic computational approach followed by both in vitro validations and in silico validations in The Cancer Genome Atlas (TCGA), we conducted a transcriptome-wide RNA editing analysis of a cohort of 104 patients with advanced gastric cancer and identified an RNA editing (GCRE) signature to guide gastric cancer chemotherapy. RNA editing events stood as a prognostic and predictive biomarker in advanced gastric cancer. A GCRE score based on the GCRE signature consisted of 50 editing sites associated with 29 genes, predicting response to chemotherapy with a high accuracy (84%). Of note, patients demonstrating higher editing levels of this panel of sites presented a better overall response. Consistently, gastric cancer cell lines with higher editing levels showed higher chemosensitivity. Applying the GCRE score on TCGA dataset confirmed that responders had significantly higher levels of editing in advanced gastric cancer. Overall, this newly defined GCRE signature reliably stratifies patients with advanced gastric cancer and predicts response from chemotherapy. SIGNIFICANCE: This study describes a novel A-to-I RNA editing signature as a prognostic and predictive biomarker in advanced gastric cancer, providing a new tool to improve patient stratification and response to therapy.
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Affiliation(s)
- Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xinyu Ke
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jimmy Bok-Yan So
- Department of Surgery, National University Hospital, Singapore. .,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Raghav Sundar
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sun Young Rha
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Ming Hui Lee
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore
| | | | - Erwin Tantoso
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore. .,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore
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12
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An JY, Choi YY, Lee J, Hyung WJ, Kim KM, Noh SH, Choi MG, Cheong JH. A Multi-cohort Study of the Prognostic Significance of Microsatellite Instability or Mismatch Repair Status after Recurrence of Resectable Gastric Cancer. Cancer Res Treat 2020; 52:1153-1161. [PMID: 32599987 PMCID: PMC7577808 DOI: 10.4143/crt.2020.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/01/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE High microsatellite instability (MSI) is related to good prognosis in gastric cancer. We aimed to identify the prognostic factors of patients with recurrent gastric cancer and investigate the role of MSI as a prognostic and predictive biomarker of survival after tumor recurrence. Materials and Methods This retrospective cohort study enrolled patients treated for stage II/III gastric cancer who developed tumor recurrence and in whom the MSI status or mismatch repair (MMR) status of the tumor was known. MSI status and the expression of MMR proteins were evaluated using polymerase chain reaction and immunohistochemical analysis, respectively. RESULTS Of the 790 patients included, 64 (8.1%) had high MSI status or MMR deficiency. The tumor-node-metastasis stage, type of recurrence, Lauren classification, chemotherapy after recurrence, and interval to recurrence were independently associated with survival after tumor recurrence. The MSI/MMR status and receiving adjuvant chemotherapy were not associated with survival after recurrence. In a subgroup analysis of patients with high MSI or MMR-deficient gastric cancer, those who did not receive adjuvant chemotherapy had better treatment response to chemotherapy after recurrence than those who received adjuvant chemotherapy. CONCLUSION Patients with high MSI/MMR-deficient gastric cancer should be spared from adjuvant chemotherapy after surgery, but aggressive chemotherapy after recurrence should be considered. Higher tumor-node-metastasis stage, Lauren classification, interval to recurrence, and type of recurrence are associated with survival after tumor recurrence and should thus be considered when establishing a treatment plan and designing clinical trials targeting recurrent gastric cancer.
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Affiliation(s)
- Ji Yeong An
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon Young Choi
- Department of Surgery, Yonsei University Health System, Seoul, Korea.,Yonsei Biomedical Research Institute, Yonsei University Health System, Seoul, Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Woo Jin Hyung
- Department of Surgery, Yonsei University Health System, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Hoon Noh
- Department of Surgery, Yonsei University Health System, Seoul, Korea
| | - Min-Gew Choi
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae-Ho Cheong
- Department of Surgery, Yonsei University Health System, Seoul, Korea.,Yonsei Biomedical Research Institute, Yonsei University Health System, Seoul, Korea.,YUHS-KRIBB Medical Convergence Research Institute, Seoul, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
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13
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Ho D, Quake SR, McCabe ERB, Chng WJ, Chow EK, Ding X, Gelb BD, Ginsburg GS, Hassenstab J, Ho CM, Mobley WC, Nolan GP, Rosen ST, Tan P, Yen Y, Zarrinpar A. Enabling Technologies for Personalized and Precision Medicine. Trends Biotechnol 2020; 38:497-518. [PMID: 31980301 PMCID: PMC7924935 DOI: 10.1016/j.tibtech.2019.12.021] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023]
Abstract
Individualizing patient treatment is a core objective of the medical field. Reaching this objective has been elusive owing to the complex set of factors contributing to both disease and health; many factors, from genes to proteins, remain unknown in their role in human physiology. Accurately diagnosing, monitoring, and treating disorders requires advances in biomarker discovery, the subsequent development of accurate signatures that correspond with dynamic disease states, as well as therapeutic interventions that can be continuously optimized and modulated for dose and drug selection. This work highlights key breakthroughs in the development of enabling technologies that further the goal of personalized and precision medicine, and remaining challenges that, when addressed, may forge unprecedented capabilities in realizing truly individualized patient care.
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Affiliation(s)
- Dean Ho
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore; The Institute for Digital Medicine (WisDM), National University of Singapore, Singapore; Department of Biomedical Engineering, NUS Engineering, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, CA, USA; Department of Applied Physics, Stanford University, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Wee Joo Chng
- Department of Haematology and Oncology, National University Cancer Institute, National University Health System, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Edward K Chow
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xianting Ding
- Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, NC, USA
| | - Jason Hassenstab
- Department of Neurology, Washington University in St. Louis, MO, USA; Psychological & Brain Sciences, Washington University in St. Louis, MO, USA
| | - Chih-Ming Ho
- Department of Mechanical Engineering, University of California, Los Angeles, CA, USA
| | - William C Mobley
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University, CA, USA
| | - Steven T Rosen
- Comprehensive Cancer Center and Beckman Research Institute, City of Hope, CA, USA
| | - Patrick Tan
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yun Yen
- College of Medical Technology, Center of Cancer Translational Research, Taipei Cancer Center of Taipei Medical University, Taipei, Taiwan
| | - Ali Zarrinpar
- Department of Surgery, Division of Transplantation & Hepatobiliary Surgery, University of Florida, FL, USA
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14
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Roy AC, Shapiro J, Burge M, Karapetis CS, Pavlakis N, Segelov E, Chau I, Lordick F, Chen LT, Barbour A, Tebbutt N, Price T. Management of early-stage gastro-esophageal cancers: expert perspectives from the Australasian Gastrointestinal Trials Group (AGITG) with invited international faculty. Expert Rev Anticancer Ther 2020; 20:305-324. [PMID: 32202178 DOI: 10.1080/14737140.2020.1746185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Introduction: A multimodal approach in operable early-stage oesophago-gastric (OG) cancer has evolved in the last decade, leading to improvement in overall outcomes.Areas covered: A review of the published literature and conference abstracts was undertaken on the topic of optimal adjunctive chemotherapy or chemoradiotherapy in early-stage OG cancers. This review article focuses on the current evidence pertaining to neoadjuvant and perioperative strategies in curable OG cancers including the evolving landscape of immunotherapy and targeted drugs in this setting.Expert commentary: Adjunctive therapies in the form of preoperative chemo-radiotherapy (CRT) or chemotherapy and perioperative chemotherapy over surgery alone improve outcomes in patients with operable OG cancer. Although there are variations in practice around the world, a multi-disciplinary approach to patient care is of paramount importance. Immunotherapy and on treatment functional imaging are two examples of emerging strategies to improve the outcome for early-stage patients. A better understanding of the molecular biology of this disease may help overcome the problem of tumor heterogeneity and enable more rationally designed and targeted therapeutic interventions in the future.
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Affiliation(s)
- Amitesh C Roy
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, Australia
| | | | - Matt Burge
- Department of Cancer Care Services, Royal Brisbane Hospital, University Of Queensland, Herston, Australia
| | - Christos S Karapetis
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, Australia
| | - Nick Pavlakis
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, Australia
| | - Eva Segelov
- Department of Medical Oncology, Monash University and Monash Health, Melbourne, Australia
| | - Ian Chau
- Department of Medical Oncology, Royal Marsden Hospital, Institute of Cancer Research, Surrey, London, UK
| | - Florian Lordick
- Leipzig University Medical Centre, University Cancer Centre Leipzig, Leipzig, Germany
| | - Li-Tong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Andrew Barbour
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Australia
| | - Niall Tebbutt
- Department of Medical Oncology, Austin Health, Heidelberg, Australia
| | - Tim Price
- Queen Elizabeth Hospital, University of Adelaide, Adelaide, Australia
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15
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Ho SWT, Tan P. Dissection of gastric cancer heterogeneity for precision oncology. Cancer Sci 2019; 110:3405-3414. [PMID: 31495054 PMCID: PMC6825006 DOI: 10.1111/cas.14191] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer (GC) remains the fifth most prevalent cancer worldwide and the third leading cause of global cancer mortality. Comprehensive ‐omic studies have unveiled a heterogeneous GC landscape, with considerable molecular diversity both between and within tumors. Given the complex nature of GC, a long‐sought goal includes effective identification of distinct patient subsets with prognostic and/or predictive outcomes to enable tailoring of specific treatments (“precision oncology”). In this review, we highlight various approaches to molecular classification in GC, covering recent genomic, transcriptomic, proteomic and epigenomic features. We pay special attention to the translational significance of classifier systems and examine potential confounding factors which deserve further investigation. In particular, we discuss recent advancements in our knowledge of intra‐subtype, intra‐patient and intra‐tumor heterogeneity, and the pivotal role of the tumor stromal microenvironment.
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Affiliation(s)
- Shamaine Wei Ting Ho
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore.,Cellular and Molecular Research, National Cancer Centre, Singapore.,Singapore Gastric Cancer Consortium, Singapore
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Tirino G, Pompella L, Petrillo A, Laterza MM, Pappalardo A, Caterino M, Orditura M, Ciardiello F, Galizia G, De Vita F. What's New in Gastric Cancer: The Therapeutic Implications of Molecular Classifications and Future Perspectives. Int J Mol Sci 2018; 19:E2659. [PMID: 30205505 PMCID: PMC6165492 DOI: 10.3390/ijms19092659] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 02/05/2023] Open
Abstract
Despite some remarkable innovations and the advent of novel molecular classifications the prognosis of patients with advanced gastric cancer (GC) remains overall poor and current clinical application of new advances is disappointing. During the last years only Trastuzumab and Ramucirumab have been approved and currently used as standard of care targeted therapies, but the systemic management of advanced disease did not radically change in contrast with the high number of molecular drivers identified. The Cancer Genome Atlas (TCGA) and Asian Cancer Research Group (ACRG) classifications paved the way, also for GC, to that more contemporary therapeutic approach called "precision medicine" even if tumor heterogeneity and a complex genetic landscape still represent a strong barrier. The identification of specific cancer subgroups is also making possible a better selection of patients that are most likely to respond to immunotherapy. This review aims to critically overview the available molecular classifications summarizing the main druggable molecular drivers and their possible therapeutic implications also taking advantage of new technologies and acquisitions.
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Affiliation(s)
- Giuseppe Tirino
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Luca Pompella
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Angelica Petrillo
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Maria Maddalena Laterza
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Annalisa Pappalardo
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Marianna Caterino
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Michele Orditura
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Fortunato Ciardiello
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Gennaro Galizia
- Division of GI Tract Surgical Oncology, Department of Cardio-Thoracic and Respiratory Sciences, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
| | - Ferdinando De Vita
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via Pansini n.5, 80131 Naples, Italy.
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