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Chan JY, Loh JW, Lim JQ, Liany H, Lee ECY, Lee JY, Kannan B, Lim BY, Guo Z, Lim K, Ha JCH, Ng CCY, Ko TK, Huang D, Seow DYB, Cheng CL, Chan SH, Ngeow J, Teh BT, Lim ST, Ong CK. Single-cell landscape of idiopathic multicentric Castleman disease in identical twins. Blood 2024; 143:1837-1844. [PMID: 38170173 DOI: 10.1182/blood.2023021992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
ABSTRACT Idiopathic multicentric Castleman disease (iMCD) is a rare cytokine-driven disorder characterized by systemic inflammation, generalized lymphadenopathy, and organ dysfunction. Here, we present an unusual occurrence of iMCD in identical twins and examined the immune milieu within the affected lymphoid organs and the host circulation using multiomic high-dimensional profiling. Using spatial enhanced resolution omics sequencing (Stereo-seq) transcriptomic profiling, we performed unsupervised spatially constrained clustering to identify different anatomic structures, mapping the follicles and interfollicular regions. After a cell segmentation approach, interleukin 6 (IL-6) pathway genes significantly colocalized with endothelial cells and fibroblastic reticular cells, confirming observations using a single-cell sequencing approach (10× Chromium). Furthermore, single-cell sequencing of peripheral blood mononuclear cells revealed an "inflammatory" peripheral monocytosis enriched for the expression of S100A family genes in both twins. In summary, we provided evidence of the putative cell-of-origin of IL-6 signals in iMCD and described a distinct monocytic host immune response phenotype through a unique identical twin model.
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Affiliation(s)
- Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore
- SingHealth Duke-NUS Blood Cancer Centre, Singapore
- Duke-NUS Medical School, Singapore
| | - Jui Wan Loh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore
| | - Jing Quan Lim
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore
| | - Herty Liany
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore
| | | | - Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore
| | - Bavani Kannan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore
| | - Boon Yee Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore
| | - Zexi Guo
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore
| | - Kerry Lim
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore
| | - Jeslin Chian Hung Ha
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore
| | | | - Tun Kiat Ko
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore
| | - Dachuan Huang
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore
| | | | - Chee Leong Cheng
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, National Cancer Centre Singapore, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, National Cancer Centre Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
| | - Bin Tean Teh
- Duke-NUS Medical School, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore
- Genome Institute of Singapore, Singapore
| | - Soon Thye Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
- SingHealth Duke-NUS Blood Cancer Centre, Singapore
- Duke-NUS Medical School, Singapore
| | - Choon Kiat Ong
- Duke-NUS Medical School, Singapore
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore
- Genome Institute of Singapore, Singapore
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Lee WWL, Lim JQ, Tang TPL, Tan D, Koh SM, Puan KJ, Wang LW, Lim J, Tan KP, Chng WJ, Lim ST, Ong CK, Rotzschke O. Counterproductive effects of anti-CD38 and checkpoint inhibitor for the treatment of NK/T cell lymphoma. Front Immunol 2024; 15:1346178. [PMID: 38680487 PMCID: PMC11045949 DOI: 10.3389/fimmu.2024.1346178] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction Natural killer/T cell lymphoma (NKTL) is an aggressive malignancy associated with poor prognosis. This is largely due to limited treatment options, especially for relapsed patients. Immunotherapies like immune checkpoint inhibitors (ICI) and anti-CD38 therapies have shown promising but variable clinical efficacies. Combining these therapies has been suggested to enhance efficacy. Methods We conducted a case study on a relapsed NKTL patient treated sequentially with anti-CD38 followed by ICI (anti-PD1) using cytometry analyses. Results and Discussion Our analysis showed an expected depletion of peripheral CD38+ B cells following anti-CD38 treatment. Further analysis indicated that circulating anti-CD38 retained their function for up to 13 weeks post-administration. Anti-PD1 treatment triggered re-activation and upregulation of CD38 on the T cells. Consequently, these anti-PD1-activated T cells were depleted by residual circulating anti-CD38, rendering the ICI treatment ineffective. Finally, a meta-analysis confirmed this counterproductive effect, showing a reduced efficacy in patients undergoing combination therapy. In conclusion, our findings demonstrate that sequential anti-CD38 followed by anti-PD1 therapy leads to a counterproductive outcome in NKTL patients. This suggests that the treatment sequence is antithetic and warrants re-evaluation for optimizing cancer immunotherapy strategies.
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Affiliation(s)
- Wendy W. L. Lee
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jing Quan Lim
- Lymphoma Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
- Oncology-Academic Clinical Programme (ONCO-ACP), Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Tiffany P. L. Tang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Daryl Tan
- Clinic for Lymphoma, Myeloma and Blood Disorders, Mount Elizabeth Hospital Novena Specialist Centre, Singapore, Singapore
| | - Ser Mei Koh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Kia Joo Puan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Liang Wei Wang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jackwee Lim
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Kim Peng Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore
| | - Soon Thye Lim
- Director’s Office, National Cancer Centre Singapore, Singapore, Singapore
- Office of Education, Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Choon Kiat Ong
- Lymphoma Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
- Cancer and Stem Cell Biology, Duke-National University of Singapore (NUS) Graduate Medical School, Singapore, Singapore
| | - Olaf Rotzschke
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Liany H, Jayagopal A, Huang D, Lim JQ, Nbh NI, Jeyasekharan A, Ong CK, Rajan V. ASTER: A Method to Predict Clinically Relevant Synthetic Lethal Genetic Interactions. IEEE J Biomed Health Inform 2024; 28:1785-1796. [PMID: 38227408 DOI: 10.1109/jbhi.2024.3354776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
A Synthetic Lethal (SL) interaction is a functional relationship between two genes or functional entities where the loss of either entity is viable but the loss of both is lethal. Such pairs can be used to develop targeted anticancer therapies with fewer side effects and reduced overtreatment. However, finding clinically relevant SL interactions remains challenging. Leveraging unified gene expression data of both disease-free and cancerous samples, we design a new technique based on statistical hypothesis testing, called ASTER, to identify SL pairs. We empirically find that the patterns of mutually exclusivity ASTER finds using genomic and transcriptomic data provides a strong signal of synthetic lethality. For large-scale multiple hypothesis testing, we develop an extension called ASTER++ that can utilize additional input gene features within the hypothesis testing framework. Our computational and functional experiments demonstrate the efficacy of ASTER in identifying SL pairs with potential therapeutic benefits.
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Li Y, Luo C, Jiang J, He S, Liu Y, Yan W, Xia Y, Cui Q, Huang Y, Lim JQ, Huang D, Hussein IN, Gao Y, Lin G, Ling Y, Ma D, Zhang Y, Chan JY, Wei P, Wang X, Cheng CL, Xiong J, Zhao W, Ong CK, Lim ST, Huang H, Peng R, Bei J. Single-Cell Analysis Reveals Malignant Cells Reshape the Cellular Landscape and Foster an Immunosuppressive Microenvironment of Extranodal NK/T-Cell Lymphoma. Adv Sci (Weinh) 2023; 10:e2303913. [PMID: 37949673 PMCID: PMC10754138 DOI: 10.1002/advs.202303913] [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] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/20/2023] [Indexed: 11/12/2023]
Abstract
Extranodal natural killer/T-cell lymphoma (NKTCL) is an aggressive type of lymphoma associated with Epstein-Barr virus (EBV) and characterized by heterogeneous tumor behaviors. To better understand the origins of the heterogeneity, this study utilizes single-cell RNA sequencing (scRNA-seq) analysis to profile the tumor microenvironment (TME) of NKTCL at the single-cell level. Together with in vitro and in vivo models, the study identifies a subset of LMP1+ malignant NK cells contributing to the tumorigenesis and development of heterogeneous malignant cells in NKTCL. Furthermore, malignant NK cells interact with various immunocytes via chemokines and their receptors, secrete substantial DPP4 that impairs the chemotaxis of immunocytes and regulates their infiltration. They also exhibit an immunosuppressive effect on T cells, which is further boosted by LMP1. Moreover, high transcription of EBV-encoded genes and low infiltration of tumor-associated macrophages (TAMs) are favorable prognostic indicators for NKTCL in multiple patient cohorts. This study for the first time deciphers the heterogeneous composition of NKTCL TME at single-cell resolution, highlighting the crucial role of malignant NK cells with EBV-encoded LMP1 in reshaping the cellular landscape and fostering an immunosuppressive microenvironment. These findings provide insights into understanding the pathogenic mechanisms of NKTCL and developing novel therapeutic strategies against NKTCL.
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Affiliation(s)
- Yi‐Qi Li
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Chun‐Ling Luo
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Jia‐Xin Jiang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Shuai He
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Yang Liu
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Wen‐Xin Yan
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Yi Xia
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Qian Cui
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhou510080China
| | - Ying Huang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Jing Quan Lim
- Lymphoma Translational Research LaboratoryCellular and Molecular ResearchNational Cancer Centre Singapore30 Hospital BoulevardSingapore168583Singapore
- ONCO‐ACPDuke‐NUS Medical School8 College RoadSingapore169857Singapore
| | - Dachuan Huang
- Lymphoma Translational Research LaboratoryCellular and Molecular ResearchNational Cancer Centre Singapore30 Hospital BoulevardSingapore168583Singapore
- ONCO‐ACPDuke‐NUS Medical School8 College RoadSingapore169857Singapore
| | - Izzah Nabilah Hussein
- Lymphoma Translational Research LaboratoryCellular and Molecular ResearchNational Cancer Centre Singapore30 Hospital BoulevardSingapore168583Singapore
| | - Yan Gao
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Guo‐Wang Lin
- Microbiome Medicine CenterDivision of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhou510280China
| | - Yi‐Hong Ling
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Dong Ma
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Yue‐Tong Zhang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Jason Yongsheng Chan
- Division of Medical OncologyNational Cancer Centre Singapore30 Hospital BoulevardSingapore168583Singapore
| | - Pan‐Pan Wei
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Xiao‐Xiao Wang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Chee Leong Cheng
- Department of PathologySingapore General Hospital20 College RoadAcademia169856Singapore
| | - Jie Xiong
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyNational Research Center for Translational MedicineShanghai Rui Jin HospitalShanghai Jiao Tong University School of Medicine197 Rui Jin Er RoadShanghai200025China
| | - Wei‐Li Zhao
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyNational Research Center for Translational MedicineShanghai Rui Jin HospitalShanghai Jiao Tong University School of Medicine197 Rui Jin Er RoadShanghai200025China
| | - Choon Kiat Ong
- Lymphoma Translational Research LaboratoryCellular and Molecular ResearchNational Cancer Centre Singapore30 Hospital BoulevardSingapore168583Singapore
- Cancer and Stem Cell BiologyDuke‐NUS Medical School8 College RoadSingapore169857Singapore
| | - Soon Thye Lim
- Director's OfficeNational Cancer Centre Singapore30 Hospital BoulevardSingapore168583Singapore
- Office of EducationDuke‐NUS Medical SchoolSingapore169857Singapore
| | - Hui‐Qiang Huang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Rou‐Jun Peng
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Jin‐Xin Bei
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
- Lymphoma Translational Research LaboratoryCellular and Molecular ResearchNational Cancer Centre Singapore30 Hospital BoulevardSingapore168583Singapore
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Loh JW, Lee JY, Lim AH, Guan P, Lim BY, Kannan B, Lee ECY, Gu NX, Ko TK, Ng CCY, Lim JCT, Yeong J, Lim JQ, Ong CK, Teh BT, Chan JY. Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma. Commun Biol 2023; 6:461. [PMID: 37106027 PMCID: PMC10140281 DOI: 10.1038/s42003-023-04856-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Angiosarcomas are rare malignant tumors of the endothelium, arising commonly from the head and neck region (AS-HN) and recently associated with ultraviolet (UV) exposure and human herpesvirus-7 infection. We examined 81 cases of angiosarcomas, including 47 cases of AS-HN, integrating information from whole genome sequencing, gene expression profiling and spatial transcriptomics (10X Visium). In the AS-HN cohort, we observed recurrent somatic mutations in CSMD3 (18%), LRP1B (18%), MUC16 (18%), POT1 (16%) and TP53 (16%). UV-positive AS-HN harbored significantly higher tumor mutation burden than UV-negative cases (p = 0.0294). NanoString profiling identified three clusters with distinct tumor inflammation signature scores (p < 0.001). Spatial transcriptomics revealed topological profiles of the tumor microenvironment, identifying dominant but tumor-excluded inflammatory signals in immune-hot cases and immune foci even in otherwise immune-cold cases. In conclusion, spatial transcriptomics reveal the tumor immune landscape of angiosarcoma, and in combination with multi-omic information, may improve implementation of treatment strategies.
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Affiliation(s)
- Jui Wan Loh
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Abner Herbert Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Peiyong Guan
- Genome Institute of Singapore, Agency of Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Boon Yee Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Bavani Kannan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Ning Xin Gu
- MGI Tech Singapore PTE LTD, Singapore, Singapore
| | - Tun Kiat Ko
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology, Agency of Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Joe Yeong
- Institute of Molecular and Cell Biology, Agency of Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency of Science, Technology and Research (ASTAR), Singapore, Singapore.
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
| | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore.
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.
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Zhou J, Toh SHM, Tan TK, Balan K, Lim JQ, Tan TZ, Xiong S, Jia Y, Ng SB, Peng Y, Jeyasekharan AD, Fan S, Lim ST, Ong CAJ, Ong CK, Sanda T, Chng WJ. Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma. Mol Cancer 2023; 22:69. [PMID: 37032358 PMCID: PMC10084643 DOI: 10.1186/s12943-023-01767-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 03/24/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Extranodal natural killer/T-cell lymphoma (NKTL) is an aggressive type of non-Hodgkin lymphoma with dismal outcome. A better understanding of disease biology and key oncogenic process is necessary for the development of targeted therapy. Super-enhancers (SEs) have been shown to drive pivotal oncogenes in various malignancies. However, the landscape of SEs and SE-associated oncogenes remain elusive in NKTL. METHODS We used Nano-ChIP-seq of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs NKTL primary tumor samples. Integrative analysis of RNA-seq and survival data further pinned down high value, novel SE oncogenes. We utilized shRNA knockdown, CRISPR-dCas9, luciferase reporter assay, ChIP-PCR to investigate the regulation of transcription factor (TF) on SE oncogenes. Multi-color immunofluorescence (mIF) staining was performed on an independent cohort of clinical samples. Various function experiments were performed to evaluate the effects of TOX2 on the malignancy of NKTL in vitro and in vivo. RESULTS SE landscape was substantially different in NKTL samples in comparison with normal tonsils. Several SEs at key transcriptional factor (TF) genes, including TOX2, TBX21(T-bet), EOMES, RUNX2, and ID2, were identified. We confirmed that TOX2 was aberrantly overexpressed in NKTL relative to normal NK cells and high expression of TOX2 was associated with worse survival. Modulation of TOX2 expression by shRNA, CRISPR-dCas9 interference of SE function impacted on cell proliferation, survival and colony formation ability of NKTL cells. Mechanistically, we found that RUNX3 regulates TOX2 transcription by binding to the active elements of its SE. Silencing TOX2 also impaired tumor formation of NKTL cells in vivo. Metastasis-associated phosphatase PRL-3 has been identified and validated as a key downstream effector of TOX2-mediated oncogenesis. CONCLUSIONS Our integrative SE profiling strategy revealed the landscape of SEs, novel targets and insights into molecular pathogenesis of NKTL. The RUNX3-TOX2-SE-TOX2-PRL-3 regulatory pathway may represent a hallmark of NKTL biology. Targeting TOX2 could be a valuable therapeutic intervene for NKTL patients and warrants further study in clinic.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Kalpnaa Balan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Jing Quan Lim
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Tuan Zea Tan
- Genomics and Data Analytics Core (GeDaC), Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Yunlu Jia
- Department of Medical Oncology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Soon Thye Lim
- Director's office, National Cancer Centre, Singapore, 168583, Singapore
- Office of Education, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore, 168583, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, 168583, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673, Singapore
| | - Choon Kiat Ong
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Singapore.
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Yap DRY, Lim JQ, Huang D, Ong CK, Chan JY. Emerging predictive biomarkers for novel therapeutics in peripheral T-cell and natural killer/T-cell lymphoma. Front Immunol 2023; 14:1068662. [PMID: 36776886 PMCID: PMC9909478 DOI: 10.3389/fimmu.2023.1068662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Peripheral T-cell lymphoma (PTCL) and natural killer/T-cell lymphoma (NKTCL) are rare subtypes of non-Hodgkin's lymphoma that are typically associated with poor treatment outcomes. Contemporary first-line treatment strategies generally involve the use of combination chemoimmunotherapy, radiation and/or stem cell transplant. Salvage options incorporate a number of novel agents including epigenetic therapies (e.g. HDAC inhibitors, DNMT inhibitors) as well as immune checkpoint inhibitors. However, validated biomarkers to select patients for individualized precision therapy are presently lacking, resulting in high treatment failure rates, unnecessary exposure to drug toxicities, and missed treatment opportunities. Recent advances in research on the tumor and microenvironmental factors of PTCL and NKTCL, including alterations in specific molecular features and immune signatures, have improved our understanding of these diseases, though several issues continue to impede progress in clinical translation. In this Review, we summarize the progress and development of the current predictive biomarker landscape, highlight potential knowledge gaps, and discuss the implications on novel therapeutics development in PTCL and NKTCL.
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Affiliation(s)
- Daniel Ren Yi Yap
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Dachuan Huang
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
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Lim JQ, Huang D, Chan JY, Laurensia Y, Wong EKY, Cheah DMZ, Chia BKH, Chuang WY, Kuo MC, Su YJ, Cai QQ, Feng Y, Rao H, Feng LN, Wei PP, Chen JR, Han BW, Lin GW, Cai J, Fang Y, Tan J, Hong H, Liu Y, Zhang F, Li W, Poon MLM, Ng SB, Jeyasekharan A, Ha JCH, Khoo LP, Chin ST, Pang WL, Kee R, Cheng CL, Grigoropoulos NF, Tang T, Tao M, Farid M, Puan KJ, Xiong J, Zhao WL, Khor CC, Hwang W, Kim WS, Campo E, Tan P, Teh BT, Chng WJ, Rötzschke O, Tousseyn T, Huang HQ, Rozen S, Lim ST, Shih LY, Bei JX, Ong CK. A genomic-augmented multivariate prognostic model for the survival of Natural-killer/T-cell lymphoma patients from an international cohort. Am J Hematol 2022; 97:1159-1169. [PMID: 35726449 DOI: 10.1002/ajh.26636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/17/2022] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
With lowering costs of sequencing and genetic profiling techniques, genetic drivers can now be detected readily in tumors but current prognostic models for Natural-killer/T cell lymphoma (NKTCL) have yet to fully leverage on them for prognosticating patients. Here, we used next-generation sequencing to sequence 260 NKTCL tumors, and trained a genomic prognostic model (GPM) with the genomic mutations and survival data from this retrospective cohort of patients using LASSO Cox regression. The GPM is defined by the mutational status of 13 prognostic genes and is weakly correlated with the risk-features in International Prognostic Index (IPI), Prognostic Index for Natural-Killer cell lymphoma (PINK) and PINK-Epstein-Barr virus (PINK-E). Cox-proportional hazard multivariate regression also showed that the new GPM is independent and significant for both progression-free survival (PFS, HR: 3.73, 95% CI 2.07-6.73; P<0.001) and overall survival (OS, HR: 5.23, 95% CI 2.57-10.65; P=0.001) with known risk-features of these indices. When we assign an additional risk-score to samples, which are mutant for the GPM, the Harrell's C-indices of GPM-augmented IPI, PINK and PINK-E improved significantly (P<0.001, χ2 test) for both PFS and OS. Thus, we report on how genomic mutational information could steer towards better prognostication of NKTCL patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jing Quan Lim
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore.,ONCO-ACP, Duke-NUS Medical School, 8 College Road, Singapore
| | - Dachuan Huang
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore.,ONCO-ACP, Duke-NUS Medical School, 8 College Road, Singapore
| | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Yurike Laurensia
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Esther Kam Yin Wong
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Daryl Ming Zhe Cheah
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Burton Kuan Hui Chia
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Wen-Yu Chuang
- Department of Anatomic Pathology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.,Chang Gung University, Taoyuan, Taiwan
| | - Ming-Chung Kuo
- Chang Gung University, Taoyuan, Taiwan.,Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yi-Jiun Su
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Qing-Qing Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanfen Feng
- Guangdong Provincial People's Hospital.,Guangdong Academy of Medical Sciences
| | - Huilan Rao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li-Na Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Pan-Pan Wei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jie-Rong Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Bo-Wei Han
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guo-Wang Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu Fang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jing Tan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore.,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Huangming Hong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanhui Liu
- Guangdong Provincial People's Hospital.,Guangdong Academy of Medical Sciences
| | - Fen Zhang
- Guangdong Provincial People's Hospital.,Guangdong Academy of Medical Sciences
| | - Wenyu Li
- Guangdong Provincial People's Hospital.,Guangdong Academy of Medical Sciences
| | - Michelle L M Poon
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore
| | - Siok-Bian Ng
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Anand Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Haematology-Oncology, National University Health System, Singapore
| | - Jeslin Chian Hung Ha
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Lay Poh Khoo
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Suk Teng Chin
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Wan Lu Pang
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Rebecca Kee
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Chee Leong Cheng
- Department of Pathology, Singapore General Hospital, 20 College Road, Academia, Singapore
| | | | - Tiffany Tang
- ONCO-ACP, Duke-NUS Medical School, 8 College Road, Singapore
| | - Miriam Tao
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Mohamad Farid
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore
| | - Kia Joo Puan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, Singapore, Singapore
| | - Jie Xiong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei-Li Zhao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chiea Chuen Khor
- Genome Institute of Singapore, 60 Biopolis Street Genome, Singapore
| | - William Hwang
- Director's office, National Cancer Centre, Singapore
| | - Won Seog Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Elias Campo
- Consorci Institut D'Investigacions Biomediques August Pi I Sunyer, Barcelona, Spain
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Genome Institute of Singapore, 60 Biopolis Street Genome, Singapore.,Division of Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Division of Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore
| | - Wee-Joo Chng
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Olaf Rötzschke
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, Sinagpore, Singapore
| | - Thomas Tousseyn
- KU Leuven, Department of Imaging and Pathology, Translational Cell and Tissue Research Lab, Herestraat 49, Leuven, Belgium.,UZ Leuven, Department of Pathology, Leuven, Belgium
| | - Hui-Qiang Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Steve Rozen
- Division of Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore
| | - Soon Thye Lim
- Director's office, National Cancer Centre, Singapore.,Office of Education, Duke-NUS Medical School, Singapore
| | - Lee-Yung Shih
- Chang Gung University, Taoyuan, Taiwan.,Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore.,Genome Institute of Singapore, 60 Biopolis Street Genome, Singapore.,Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, 8 College Road, Singapore
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9
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Poh J, Ngeow KC, Pek M, Tan KH, Lim JS, Chen H, Ong CK, Lim JQ, Lim ST, Lim CM, Goh BC, Choudhury Y. Analytical and clinical validation of an amplicon-based next generation sequencing assay for ultrasensitive detection of circulating tumor DNA. PLoS One 2022; 17:e0267389. [PMID: 35486650 PMCID: PMC9053827 DOI: 10.1371/journal.pone.0267389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing of circulating tumor DNA presents a promising approach to cancer diagnostics, complementing conventional tissue-based diagnostic testing by enabling minimally invasive serial testing and broad genomic coverage through a simple blood draw to maximize therapeutic benefit to patients. LiquidHALLMARK® is an amplicon-based next-generation sequencing assay developed for the genomic profiling of plasma-derived cell-free DNA (cfDNA). The comprehensive 80-gene panel profiles point mutations, insertions/deletions, copy number alterations, and gene fusions, and further detects oncogenic viruses (Epstein-Barr virus (EBV) and hepatitis B virus (HBV)) and microsatellite instability (MSI). Here, the analytical and clinical validation of the assay is reported. Analytical validation using reference genetic materials demonstrated a sensitivity of 99.38% for point mutations and 95.83% for insertions/deletions at 0.1% variant allele frequency (VAF), and a sensitivity of 91.67% for gene fusions at 0.5% VAF. In non-cancer samples, a high specificity (≥99.9999% per-base) was observed. The limit of detection for copy number alterations, EBV, HBV, and MSI were also empirically determined. Orthogonal comparison of epidermal growth factor receptor (EGFR) variant calls made by LiquidHALLMARK and a reference allele-specific polymerase chain reaction (AS-PCR) method for 355 lung cancer specimens revealed an overall concordance of 93.80%, while external validation with cobas® EGFR Mutation Test v2 for 50 lung cancer specimens demonstrated an overall concordance of 84.00%, with a 100% concordance rate for EGFR variants above 0.4% VAF. Clinical application of LiquidHALLMARK in 1,592 consecutive patients demonstrated a high detection rate (74.8% circulating tumor DNA (ctDNA)-positive in cancer samples) and broad actionability (50.0% of cancer samples harboring alterations with biological evidence for actionability). Among ctDNA-positive lung cancers, 72.5% harbored at least one biomarker with a guideline-approved drug indication. These results establish the high sensitivity, specificity, accuracy, and precision of the LiquidHALLMARK assay and supports its clinical application for blood-based genomic testing.
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Affiliation(s)
- Jonathan Poh
- Lucence Diagnostics Pte Ltd, Singapore, Singapore
| | | | - Michelle Pek
- Lucence Health Inc, Palo Alto, California, United States of America
| | - Kian-Hin Tan
- Lucence Health Inc, Palo Alto, California, United States of America
| | | | - Hao Chen
- Lucence Diagnostics Pte Ltd, Singapore, Singapore
| | | | - Jing Quan Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Soon Thye Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Chwee Ming Lim
- Department of Otolaryngology-Head and Neck Surgery, Singapore General Hospital, Duke-NUS Medical School, Singapore, Singapore
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10
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Kizhakeyil A, Zaini NBM, Poh ZS, Wong BHS, Loh X, Ng AS, Low ZS, Prasannan P, Gong C, Tan MGK, Nagarajan C, Huang D, Lu PW, Lim JQ, Barrans S, Ong CK, Lim ST, Chng WJ, Follows G, Hodson DJ, Du MQ, Goh YT, Tan SH, Grigoropoulos NF, Verma NK. DDX3X loss is an adverse prognostic marker in diffuse large B-cell lymphoma and is associated with chemoresistance in aggressive non-Hodgkin lymphoma subtypes. Mol Cancer 2021; 20:134. [PMID: 34654425 PMCID: PMC8520256 DOI: 10.1186/s12943-021-01437-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/24/2021] [Indexed: 01/03/2023] Open
Affiliation(s)
- Atish Kizhakeyil
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore
| | | | - Zhi Sheng Poh
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Brandon Han Siang Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Xinpeng Loh
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Aik Seng Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Zun Siong Low
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Praseetha Prasannan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Chun Gong
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Michelle Guet Khim Tan
- Clinical Translational Sciences, Singapore General Hospital, The Academia Level 9, 20 College Road, Singapore, 169856, Singapore
| | - Chandramouli Nagarajan
- Department of Haematology, Singapore General Hospital, The Academia, Level 3, 20 College Road, Singapore, 169856, Singapore
| | - Dachuan Huang
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Pang Wan Lu
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service (HMDS), St. James's Institute of Oncology, Leeds, UK
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.,Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Genome Institute of Singapore, 60 Biopolis Street Genome, Singapore, 138672, Singapore
| | - Soon Thye Lim
- Director's office, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.,Office of Education, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Wee Joo Chng
- National University Cancer Institute, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,NUS Center for Cancer Research (N2CR) and Dept of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - George Follows
- Addenbrooke's Hospital NHS Foundation Trust, Cambridge, UK
| | | | - Ming Qing Du
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Yeow Tee Goh
- Department of Haematology, Singapore General Hospital, The Academia, Level 3, 20 College Road, Singapore, 169856, Singapore
| | - Suat Hoon Tan
- National Skin Centre Singapore, 1 Mandalay Road, Singapore, 308205, Singapore
| | - Nicholas Francis Grigoropoulos
- Department of Haematology, Singapore General Hospital, The Academia, Level 3, 20 College Road, Singapore, 169856, Singapore. .,Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Navin Kumar Verma
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore. .,National Skin Centre Singapore, 1 Mandalay Road, Singapore, 308205, Singapore.
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11
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Sun Y, Gao Y, Chen J, Huang L, Deng P, Chen J, Chai KXY, Hong JH, Chan JY, He H, Wang Y, Cheah D, Lim JQ, Chia BKH, Huang D, Liu L, Liu S, Wang X, Teng Y, Pang D, Grigoropoulos NF, Teh BT, Yu Q, Lim ST, Li W, Ong CK, Huang H, Tan J. CREBBP cooperates with the cell cycle machinery to attenuate chidamide sensitivity in relapsed/refractory diffuse large B-cell lymphoma. Cancer Lett 2021; 521:268-280. [PMID: 34481935 DOI: 10.1016/j.canlet.2021.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/25/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL) exhibits frequent inactivating mutations of the histone acetyltransferase CREBBP, highlighting the attractiveness of targeting CREBBP deficiency as a therapeutic strategy. In this study, we demonstrate that chidamide, a novel histone deacetylase (HDAC) inhibitor, is effective in treating a subgroup of relapsed/refractory DLBCL patients, achieving an overall response rate (ORR) of 25.0% and a complete response (CR) rate of 15.0%. However, the clinical response to chidamide remains poor, as most patients exhibit resistance, hampering the clinical utility of the drug. Functional in vitro and in vivo studies have shown that CREBBP loss of function is correlated with chidamide sensitivity, which is associated with modulation of the cell cycle machinery. A combinatorial drug screening of 130 kinase inhibitors targeting cell cycle regulators identified AURKA inhibitors, which inhibit the G2/M transition during the cell cycle, as top candidates that synergistically enhanced the antitumor effects of chidamide in CREBBP-proficient DLBCL cells. Our study demonstrates that CREBBP inactivation can serve as a potential biomarker to predict chidamide sensitivity, while combination of an AURKA inhibitor and chidamide is a novel therapeutic strategy for the treatment of relapsed/refractory DLBCL.
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Affiliation(s)
- Yichen Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jianfeng Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ling Huang
- Lymphoma Division, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology Guangzhou, China
| | - Peng Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jinghong Chen
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Kelila Xin Ye Chai
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Jing Han Hong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jason Yongsheng Chan
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Haixia He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yali Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Daryl Cheah
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Burton Kuan Hui Chia
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Dachuan Huang
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Lizhen Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shini Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoxiao Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Teng
- Lymphoma Division, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology Guangzhou, China
| | - Diwen Pang
- Lymphoma Division, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology Guangzhou, China
| | | | - 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, Singapore; SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore; Genome Institute of Singapore, A*STAR, Singapore
| | - Qiang Yu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore; Genome Institute of Singapore, A*STAR, Singapore
| | - Soon Thye Lim
- Director's Office, National Cancer Centre Singapore, Singapore; Office of Education, Duke-NUS Medical School, Singapore
| | - Wenyu Li
- Lymphoma Division, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology Guangzhou, China
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore; Genome Institute of Singapore, A*STAR, Singapore.
| | - Huiqiang Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jing Tan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.
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12
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Chan JY, Lim JQ, Ong CK. Towards Next Generation Biomarkers in Natural Killer/T-Cell Lymphoma. Life (Basel) 2021; 11:838. [PMID: 34440582 PMCID: PMC8398475 DOI: 10.3390/life11080838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/11/2021] [Accepted: 08/14/2021] [Indexed: 12/22/2022] Open
Abstract
Natural killer/T-cell lymphoma (NKTCL) is an Epstein-Barr virus-associated non-Hodgkin lymphoma linked to an aggressive clinical course and poor prognosis. Despite an improvement in survival outcomes with the incorporation of novel agents including immune checkpoint inhibitors in the treatment of NKTCL, a significant proportion of patients still relapse or remain refractory to treatment. Several clinical prognostic models have been developed for NKTCL patients treated in the modern era, though the optimal approach to risk stratification remains to be determined. Novel molecular biomarkers derived from multi-omic profiling have recently been developed, with the potential to improve diagnosis, prognostication and treatment of this disease. Notably, a number of potential biomarkers have emerged from a better understanding of the tumor immune microenvironment and inflammatory responses. This includes a recently described 3'UTR structural variant in the PD-L1 gene, which confers susceptibility to checkpoint immunotherapy. In this review, we summarize the biomarker landscape of NKTCL and highlight emerging biomarkers with the potential for clinical implementation.
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Affiliation(s)
- Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- SingHealth Duke-NUS Blood Cancer Centre, Singapore 169857, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore;
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore;
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
- Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore
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13
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Ong SY, Lim JQ, Grigoropoulos N, Laurensia Y, Huang D, Chia BKH, Zhe DCM, Saraf SA, Cheng CL, Chuang WY, Kuo MC, Su YJ, Phipps C, Nagarajan C, Lee YS, Lung DTC, Shih LY, Goh YT, Lim ST, Ong CK. No association between <i>ECSIT</i> germline mutations and hemophagocytic lymphohistiocytosis in natural killer/T-cell lymphoma. Haematologica 2021; 106:1737-1739. [PMID: 33054138 PMCID: PMC8168500 DOI: 10.3324/haematol.2020.269209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 12/03/2022] Open
Affiliation(s)
- Shin Yeu Ong
- Department of Haematology, Singapore General Hospital
| | - Jing Quan Lim
- National Cancer Center, Singapore; Duke-NUS Medical School
| | | | | | - Dachuan Huang
- National Cancer Center, Singapore; Duke-NUS Medical School
| | | | | | | | | | - Wen-Yu Chuang
- Department of Pathology, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan
| | - Ming-Chung Kuo
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan
| | - Yi-Jiun Su
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan
| | - Colin Phipps
- Department of Haematology, Singapore General Hospital
| | | | - Yuh Shan Lee
- Department of Haematology, Singapore General Hospital
| | | | - Lee-Yung Shih
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan
| | - Yeow Tee Goh
- Department of Haematology, Singapore General Hospital
| | - Soon Thye Lim
- National Cancer Center, Singapore; Duke-NUS Medical School.
| | - Choon Kiat Ong
- National Cancer Center, Singapore; Duke-NUS Medical School, Singapore; Genome Institute of Singapore, A*STAR.
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14
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Wintachai P, Lim JQ, Techasen A, Lert-itthiporn W, Kongpetch S, Loilome W, Chindaprasirt J, Titapun A, Namwat N, Khuntikeo N, Jusakul A. Diagnostic and Prognostic Value of Circulating Cell-Free DNA for Cholangiocarcinoma. Diagnostics (Basel) 2021; 11:999. [PMID: 34070951 PMCID: PMC8228499 DOI: 10.3390/diagnostics11060999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/21/2022] Open
Abstract
The analysis of cfDNA has been applied as a liquid biopsy in several malignancies. However, its value in the diagnosis and prognosis of cholangiocarcinoma (CCA) have not been well defined. We aimed to investigate the diagnostic and prognostic values of cfDNA level and tumor-specific mutation in circulating DNA (ctDNA) in CCA. The plasma cfDNA levels from 62 CCA patients, 33 benign biliary disease (BBD) patients and 30 normal controls were quantified by fluorescent assay. Targeted probe-based sequencing of 60 genes was applied for mutation profiling in 10 ctDNA samples and their corresponding treatment-naïve tissues. cfDNA levels in CCA were significantly higher than those in BBD and normal controls. We found that cfDNA levels at 0.2175 and 0.3388 ng/µL significantly discriminated CCA from healthy controls and BBD with 88.7 and 82.3% sensitivity and 96.7 and 57.6% specificity, respectively. cfDNA levels showed superior diagnostic efficacy in detecting CCA compared to CEA and CA19-9. ARID1A (30%), PBRM1 (30%), MTOR (30%), and FGFR3 (30%) mutations were the most common. Using nine frequently mutated genes in the ctDNA samples, the diagnostic accuracy of cfDNA sequencing was 90.8%, with 96.7% average sensitivity and 72.4% specificity. This study supports the use of cfDNA as a diagnosis and prognostic biomarker for CCA.
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Affiliation(s)
- Preawwalee Wintachai
- Biomedical Sciences Program, Graduate School, Khon Kaen University, Khon Kaen 40002, Thailand;
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre and Duke-NUS Medical School, Singapore 169857, Singapore;
| | - Anchalee Techasen
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Worachart Lert-itthiporn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Sarinya Kongpetch
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Watcharin Loilome
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Jarin Chindaprasirt
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
- Department of Internal Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Attapol Titapun
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
- Departments of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nisana Namwat
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Narong Khuntikeo
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
- Departments of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Apinya Jusakul
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (A.T.); (S.K.); (W.L.); (J.C.); (A.T.); (N.N.); (N.K.)
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
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15
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Chan JY, Lim JQ, Yeong J, Ravi V, Guan P, Boot A, Tay TKY, Selvarajan S, Md Nasir ND, Loh JH, Ong CK, Huang D, Tan J, Li Z, Ng CCY, Tan TT, Masuzawa M, Sung KWK, Farid M, Quek RHH, Tan NC, Teo MCC, Rozen SG, Tan P, Futreal A, Teh BT, Soo KC. Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma. J Clin Invest 2021; 130:5833-5846. [PMID: 33016928 DOI: 10.1172/jci139080] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [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: 04/13/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022] Open
Abstract
Angiosarcomas are rare, clinically aggressive tumors with limited treatment options and a dismal prognosis. We analyzed angiosarcomas from 68 patients, integrating information from multiomic sequencing, NanoString immuno-oncology profiling, and multiplex immunohistochemistry and immunofluorescence for tumor-infiltrating immune cells. Through whole-genome sequencing (n = 18), 50% of the cutaneous head and neck angiosarcomas exhibited higher tumor mutation burden (TMB) and UV mutational signatures; others were mutationally quiet and non-UV driven. NanoString profiling revealed 3 distinct patient clusters represented by lack (clusters 1 and 2) or enrichment (cluster 3) of immune-related signaling and immune cells. Neutrophils (CD15+), macrophages (CD68+), cytotoxic T cells (CD8+), Tregs (FOXP3+), and PD-L1+ cells were enriched in cluster 3 relative to clusters 2 and 1. Likewise, tumor inflammation signature (TIS) scores were highest in cluster 3 (7.54 vs. 6.71 vs. 5.75, respectively; P < 0.0001). Head and neck angiosarcomas were predominant in clusters 1 and 3, providing the rationale for checkpoint immunotherapy, especially in the latter subgroup with both high TMB and TIS scores. Cluster 2 was enriched for secondary angiosarcomas and exhibited higher expression of DNMT1, BRD3/4, MYC, HRAS, and PDGFRB, in keeping with the upregulation of epigenetic and oncogenic signaling pathways amenable to targeted therapies. Molecular and immunological dissection of angiosarcomas may provide insights into opportunities for precision medicine.
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Affiliation(s)
- Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Joe Yeong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore.,Institute of Molecular and Cell Biology, Singapore
| | - Vinod Ravi
- Department of Sarcoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peiyong Guan
- Integrated Biostatistics and Bioinformatics Programme
| | - Arnoud Boot
- Integrated Biostatistics and Bioinformatics Programme.,Centre for Computational Biology, and
| | | | | | | | - Jie Hua Loh
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Dachuan Huang
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Jing Tan
- Laboratory of Cancer Epigenome, Division of Medical Sciences National Cancer Centre Singapore, Singapore
| | - Zhimei Li
- Laboratory of Cancer Epigenome, Division of Medical Sciences National Cancer Centre Singapore, Singapore
| | - Cedric Chuan-Young Ng
- Laboratory of Cancer Epigenome, Division of Medical Sciences National Cancer Centre Singapore, Singapore
| | - Thuan Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Mikio Masuzawa
- Department of Regulation Biochemistry, School of Allied Health Sciences, Kitasato University, Minato City, Tokyo, Japan
| | - Ken Wing-Kin Sung
- Genome Institute of Singapore, A*STAR, Singapore.,School of Computing, National University of Singapore, Singapore
| | - Mohamad Farid
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore
| | | | - Ngian Chye Tan
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore.,SingHealth Duke-NUS Head and Neck Centre, Singapore
| | | | - Steven George Rozen
- Integrated Biostatistics and Bioinformatics Programme.,Centre for Computational Biology, and.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Genome Institute of Singapore, A*STAR, Singapore
| | - Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bin Tean Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Laboratory of Cancer Epigenome, Division of Medical Sciences National Cancer Centre Singapore, Singapore.,Division of Cellular and Molecular Research, National Cancer Centre Singapore
| | - Khee Chee Soo
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore.,SingHealth Duke-NUS Head and Neck Centre, Singapore
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16
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Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Poon PSY, Lam YN, Lin JS, Tay ST, Lee MH, Tan ALK, Ong X, White K, Rozen SG, Beer M, Foo RSY, Grabsch HI, Skanderup AJ, Li S, Teh BT, Tan P. Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer. J Clin Invest 2021; 130:3005-3020. [PMID: 32364535 DOI: 10.1172/jci126726] [Citation(s) in RCA: 6] [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: 12/10/2018] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Transcriptional reactivation of telomerase catalytic subunit (TERT) is a frequent hallmark of cancer, occurring in 90% of human malignancies. However, specific mechanisms driving TERT reactivation remain obscure for many tumor types and in particular gastric cancer (GC), a leading cause of global cancer mortality. Here, through comprehensive genomic and epigenomic analysis of primary GCs and GC cell lines, we identified the transcription factor early B cell factor 1 (EBF1) as a TERT transcriptional repressor and inactivation of EBF1 function as a major cause of TERT upregulation. Abolishment of EBF1 function occurs through 3 distinct (epi)genomic mechanisms. First, EBF1 is epigenetically silenced via DNA methyltransferase, polycomb-repressive complex 2 (PRC2), and histone deacetylase activity in GCs. Second, recurrent, somatic, and heterozygous EBF1 DNA-binding domain mutations result in the production of dominant-negative EBF1 isoforms. Third, more rarely, genomic deletions and rearrangements proximal to the TERT promoter remobilize or abolish EBF1-binding sites, derepressing TERT and leading to high TERT expression. EBF1 is also functionally required for various malignant phenotypes in vitro and in vivo, highlighting its importance for GC development. These results indicate that multimodal genomic and epigenomic alterations underpin TERT reactivation in GC, converging on transcriptional repressors such as EBF1.
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Affiliation(s)
- Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Jing Tan
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Aditi Qamra
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Po-Hsien Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Zhimei Li
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Nisha Padmanabhan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Yu Amanda Guo
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore
| | - Xiaosai Yao
- Institute of Molecular and Cell Biology, Singapore
| | - Mandoli Amit
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ley Moy Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Taotao Sheng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Jing Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Singapore
| | - Shamaine Wei Ting Ho
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Mohana Ray
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Gregorio Fazzi
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Kevin Junliang Lim
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Giovani Claresta Wijaya
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Shenli Zhang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Tannistha Nandi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Tingdong Yan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Mei Mei Chang
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore
| | - Kakoli Das
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Zul Fazreen Adam Isa
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Jeanie Wu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Polly Suk Yean Poon
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Yue Ning Lam
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Joyce Suling Lin
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Su Ting Tay
- 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
| | - 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
| | - Kevin White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA.,Tempus Labs, Chicago, Illinois, USA
| | - Steven George Rozen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
| | - Michael Beer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Medicine, and.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Singapore
| | - Heike Irmgard Grabsch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands.,Pathology and Data Analyticis, Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds, United Kingdom
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of 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
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, 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
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,Cancer Science Institute of Singapore, National University 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.,Biomedical Research Council, Agency for Science, Technology and Research, Singapore
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17
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Chan JY, Lim JQ, Ong CK. Checkpoint immunotherapy for NK/T cell lymphoma—Time for a showdown? Precision Clinical Medicine 2021; 4:70-72. [PMID: 35693125 PMCID: PMC8982608 DOI: 10.1093/pcmedi/pbab004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 11/13/2022] Open
Abstract
A commentary on “Combination of anti-PD-1 antibody with P-GEMOX as a potentially effective immunochemotherapy for advanced natural killer/T cell lymphoma”.
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Affiliation(s)
- Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, 169610, Singapore
- SingHealth Duke-NUS Blood Cancer Centre, 169610, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, 169610, Singapore
- Duke-NUS Medical School, 169857, Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, 169610, Singapore
- Duke-NUS Medical School, 169857, Singapore
- Genome Institute of Singapore, 138672, Singapore
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18
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Oon ML, Lim JQ, Lee B, Leong SM, Soon GST, Wong ZW, Lim EH, Li Z, Yeoh AEJ, Chen S, Ban KHK, Chung TH, Tan SY, Chuang SS, Kato S, Nakamura S, Takahashi E, Ho YH, Khoury JD, Au-Yeung RKH, Cheng CL, Lim ST, Chng WJ, Tripodo C, Rotzschke O, Ong CK, Ng SB. T-Cell Lymphoma Clonality by Copy Number Variation Analysis of T-Cell Receptor Genes. Cancers (Basel) 2021; 13:cancers13020340. [PMID: 33477749 PMCID: PMC7832336 DOI: 10.3390/cancers13020340] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/11/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary T-cells defend the human body from pathogenic invasion via specific recognition by T-cell receptors (TCRs). The TCR genes undergo recombination (rearrangement) in a myriad of possible ways to generate different TCRs that can recognize a wide diversity of foreign antigens. However, in patients with T-cell lymphoma (TCL), a particular T-cell becomes malignant and proliferates, resulting in a population of genetically identical cells with same TCR rearrangement pattern. To help diagnose patients with TCL, a polymerase chain reaction (PCR)-based assay is currently used to determine if neoplastic cells in patient samples are of T-cell origin and bear identical (monoclonal) TCR rearrangement pattern. Herein, we report the application of a novel segmentation and copy number computation algorithm to accurately identify different TCR rearrangement patterns using data from the whole genome sequencing of patient materials. Our approach may improve the diagnostic accuracy of TCLs and can be similarly applied to the diagnosis of B-cell lymphomas. Abstract T-cell lymphomas arise from a single neoplastic clone and exhibit identical patterns of deletions in T-cell receptor (TCR) genes. Whole genome sequencing (WGS) data represent a treasure trove of information for the development of novel clinical applications. However, the use of WGS to identify clonal T-cell proliferations has not been systematically studied. In this study, based on WGS data, we identified monoclonal rearrangements (MRs) of T-cell receptors (TCR) genes using a novel segmentation algorithm and copy number computation. We evaluated the feasibility of this technique as a marker of T-cell clonality using T-cell lymphomas (TCL, n = 44) and extranodal NK/T-cell lymphomas (ENKTLs, n = 20), and identified 98% of TCLs with one or more TCR gene MRs, against 91% detected using PCR. TCR MRs were absent in all ENKTLs and NK cell lines. Sensitivity-wise, this platform is sufficiently competent, with MRs detected in the majority of samples with tumor content under 25% and it can also distinguish monoallelic from biallelic MRs. Understanding the copy number landscape of TCR using WGS data may engender new diagnostic applications in hematolymphoid pathology, which can be readily adapted to the analysis of B-cell receptor loci for B-cell clonality determination.
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Affiliation(s)
- Ming Liang Oon
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore;
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore; (B.L.); (O.R.)
| | - Sai Mun Leong
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore;
| | - Gwyneth Shook-Ting Soon
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
| | - Zi Wei Wong
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
| | - Evelyn Huizi Lim
- Viva-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; (E.H.L.); (Z.L.); (A.E.J.Y.)
| | - Zhenhua Li
- Viva-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; (E.H.L.); (Z.L.); (A.E.J.Y.)
| | - Allen Eng Juh Yeoh
- Viva-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; (E.H.L.); (Z.L.); (A.E.J.Y.)
- VIVA—University Children’s Cancer Centre, Khoo Teck Puat–National University Children’s Medical Institute, National University Hospital, National University Health System, Singapore 119074, Singapore
| | - Shangying Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; (S.C.); (K.H.K.B.)
| | - Kenneth Hon Kim Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; (S.C.); (K.H.K.B.)
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (T.-H.C.); (W.-J.C.)
| | - Soo-Yong Tan
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore;
| | - Shih-Sung Chuang
- Department of Pathology, Chi-Mei Medical Center, Tainan 71004, Taiwan;
| | - Seiichi Kato
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya 466-8560, Japan; (S.K.); (S.N.)
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya 464-0021, Japan
| | - Shigeo Nakamura
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya 466-8560, Japan; (S.K.); (S.N.)
| | - Emiko Takahashi
- Department of Pathology, Aichi Medical University Hospital, Nagakute 480-1195, Japan;
| | - Yong-Howe Ho
- Department of Pathology, Tan Tock Seng Hospital, Singapore 308433, Singapore;
| | - Joseph D. Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Rex K. H. Au-Yeung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China;
| | - Chee-Leong Cheng
- Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore;
| | - Soon-Thye Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore;
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (T.-H.C.); (W.-J.C.)
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore 119074, Singapore
| | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo School of Medicine, 90134 Palermo, Italy;
| | - Olaf Rotzschke
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore; (B.L.); (O.R.)
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore;
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
- Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore
- Correspondence: (C.K.O.); (S.-B.N.); Tel.: +65-6436-8269 (C.K.O.); +65-6772-4709 (S-B.N.)
| | - Siok-Bian Ng
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore;
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (T.-H.C.); (W.-J.C.)
- Correspondence: (C.K.O.); (S.-B.N.); Tel.: +65-6436-8269 (C.K.O.); +65-6772-4709 (S-B.N.)
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19
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Tan BY, Md Nasir ND, Chang HY, Ng CCY, Guan P, Nagarajan S, Rajasegaran V, Lee JY, Lim JQ, Thike AA, Teh BT, Tan PH. Morphologic and genetic heterogeneity in breast fibroepithelial lesions-a comprehensive mapping study. Mod Pathol 2020; 33:1732-1745. [PMID: 32322022 DOI: 10.1038/s41379-020-0533-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 02/01/2023]
Abstract
Breast fibroepithelial lesions (FELs) encompass the common fibroadenoma (FA) and relatively rare phyllodes tumour (PT); the latter entity is usually classified as benign, borderline or malignant. Intratumoural heterogeneity is frequently present in these tumours, making accurate histologic evaluation challenging. Despite their rarity, PTs are an important clinical problem due to their propensity for recurrence and, in the case of malignant PT, metastasis. Surgical excision is the mainstay of management. Recent work has uncovered myriad genetic alterations in breast FELs. In this study, exome sequencing was performed on seven cases of morphologically heterogeneous breast FELs, including FAs, PTs of all grades, and a case of metaplastic spindle cell carcinoma arising in PT, in order to elucidate their intratumoural genetic repertoire. Gene mutations identified encompassed cell signalling, tumour suppressor, DNA repair and cell cycle regulating pathways. Mutations common to multiple tumour regions generally showed higher variant allele frequency. Frequent mutations included MED12, TP53, RARA and PIK3CA. Histological observations of increased cellular density and pleomorphism correlated with mutational burden. Phylogenetic analyses revealed disparate pathways of possible tumour progression. In summary, histological heterogeneity correlated with genetic changes in breast FELs.
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Affiliation(s)
| | - Nur Diyana Md Nasir
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | | | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Peiyong Guan
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore.,Quantitative Biology and Medicine Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Sanjanaa Nagarajan
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Jing Yi Lee
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Laboratory, National Cancer Centre Singapore, Singapore, Singapore
| | - Aye Aye Thike
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Bin Tean Teh
- Duke-NUS Medical School, Singapore, Singapore. .,Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore.
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore. .,Duke-NUS Medical School, Singapore, Singapore. .,Division of Pathology, Singapore General Hospital, Singapore, Singapore.
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20
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Ooi WF, Nargund AM, Lim KJ, Zhang S, Xing M, Mandoli A, Lim JQ, Ho SWT, Guo Y, Yao X, Lin SJ, Nandi T, Xu C, Ong X, Lee M, Tan ALK, Lam YN, Teo JX, Kaneda A, White KP, Lim WK, Rozen SG, Teh BT, Li S, Skanderup AJ, Tan P. Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma. Gut 2020; 69:1039-1052. [PMID: 31542774 DOI: 10.1136/gutjnl-2018-317612] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 08/22/2019] [Accepted: 09/01/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Genomic structural variations (SVs) causing rewiring of cis-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (enhancer-based SVs), we integrated epigenomic enhancer profiles revealed by paired-end H3K27ac ChIP-sequencing from primary GCs with tumour whole-genome sequencing (WGS) data (PeNChIP-seq/WGS). DESIGN We applied PeNChIP-seq to 11 primary GCs and matched normal tissues combined with WGS profiles of >200 GCs. Epigenome profiles were analysed alongside matched RNA-seq data to identify tumour-associated enhancer-based SVs with altered cancer transcription. Functional validation of candidate enhancer-based SVs was performed using CRISPR/Cas9 genome editing, chromosome conformation capture assays (4C-seq, Capture-C) and Hi-C analysis of primary GCs. RESULTS PeNChIP-seq/WGS revealed ~150 enhancer-based SVs in GC. The majority (63%) of SVs linked to target gene deregulation were associated with increased tumour expression. Enhancer-based SVs targeting CCNE1, a key driver of therapy resistance, occurred in 8% of patients frequently juxtaposing diverse distal enhancers to CCNE1 proximal regions. CCNE1-rearranged GCs were associated with high CCNE1 expression, disrupted CCNE1 topologically associating domain (TAD) boundaries, and novel TAD interactions in CCNE1-rearranged primary tumours. We also observed IGF2 enhancer-based SVs, previously noted in colorectal cancer, highlighting a common non-coding genetic driver alteration in gastric and colorectal malignancies. CONCLUSION Integrated paired-end NanoChIP-seq and WGS of gastric tumours reveals tumour-associated regulatory SV in regions associated with both simple and complex genomic rearrangements. Genomic rearrangements may thus exploit enhancer-hijacking as a common mechanism to drive oncogene expression in GC.
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Affiliation(s)
- Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Amrita M Nargund
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kevin Junliang Lim
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Shenli Zhang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Manjie Xing
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Amit Mandoli
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Laboratory, National Cancer Centre Singapore, Singapore
| | - Shamaine Wei Ting Ho
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yu Guo
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Xiaosai Yao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Suling Joyce Lin
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Tannistha Nandi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Minghui Lee
- 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
| | - Yue Ning Lam
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Jing Xian Teo
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Chiba University, Chiba, Japan
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, Illinois, USA.,Tempus Labs, Chicago, Illinois, USA
| | - Weng Khong Lim
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
| | - Steven G Rozen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore.,Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Anders J Skanderup
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore .,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
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21
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Ngeow KC, Choudhury Y, Tan KH, Pek M, Ng KT, Lim ST, Lim JQ, Huang D, Ong CK, Tan MH. Ultrasensitive multiplex detection of structural rearrangements in ALK, RET, ROS1 and PD-L1 using a comprehensive next-generation sequencing assay. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3572 Background: Oncogenic structural rearrangements (SR) in ALK, RET and ROS1 are well-described in lung cancer, and confer sensitivity to targeted therapy. SR disrupting the 3’UTR of PD-L1 gene have been reported in multiple cancer types and can potentially predict response to checkpoint immunotherapy. An amplicon-based next-generation sequencing (NGS) platform technology (AmpliMARK), previously optimized for detection of single nucleotide variations (SNVs), microsatellite instability and viral DNA, was extended to the multiplex detection of SR in ALK, RET, ROS1 and PD-L1 in cell-free DNA (cfDNA) and tumor tissue DNA. Methods: A hybrid primer-extension and adapter-ligation based method allowing detection of SR in a fusion-partner agnostic manner was utilized for multiplex target capture of genomic regions of ALK, RET, ROS1 and PD-L1 SR. Analytical validation was performed using admixtures of fragmented genomic DNA from an ALK SR-positive cell line, commercial standards containing RET and ROS1 SR, and synthetic PD-L1 SR gene constructs. Clinical performance was assessed in cfDNA samples from lung cancer patients and tumor tissue DNA samples from natural killer(NK)/T-cell lymphoma patients. Results: Detection of SR could be achieved to an allele frequency detection limit of 0.5% with sensitivity of 89.5% and specificity of 100% in admixture samples mimicking cfDNA. In an unselected series of 374 lung cancer cases, actionable SR for ALK, RET and ROS1 were detected in cfDNA of 9 samples, for an overall detection rate of 2.4%, and 1.8% (3 out of 168) when restricted to treatment-naive lung cancer cases only. In 29 NK/T-cell lymphoma tumor tissue samples, 9 samples were positive for PD-L1 SR, which were orthogonally confirmed by whole-genome sequencing, targeted sequencing or Sanger sequencing for a concordance rate of 100% across all samples. For 1 NK/T-cell lymphoma tumor tissue sample where matched plasma was available, the same PD-L1 SR was also detected in cfDNA. Conclusions: We have demonstrated and validated a comprehensive amplicon-based NGS assay for ultrasensitive multiplex detection of structural rearrangements in ALK, RET, ROS1 and PD-L1 across both cfDNA and tumor tissue DNA in analytical and clinical contexts. Ongoing studies will further evaluate the performance and utility of this assay across a larger number of clinical samples for the detection of these SR as well as additional cancer-associated SR involving NTRK1/2/3, FGFR2/3 and TMPRSS2.
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Affiliation(s)
| | | | | | | | | | - Soon Thye Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Quan Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Dachuan Huang
- National Cancer Centre Singapore, Singapore, Singapore
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22
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Yang VS, Lim JQ, Tay TKY, Selvarajan S, Ng CCY, Farid M, Teh BT, Chan JY. Clinicopathologic Features and Whole Genome Sequencing of a Primary Osteosarcoma of the Uterus. J Immunother Precis Oncol 2020; 3:90-95. [PMID: 36751521 PMCID: PMC9179399 DOI: 10.36401/jipo-19-34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/06/2020] [Indexed: 12/18/2022]
Abstract
Primary osteosarcoma (OS) of the uterus is a distinctly rare and aggressive disease with fewer than 20 cases reported worldwide. We describe a case of primary uterine OS with rapid development of pulmonary and brain metastasis in a 50-year-old woman. Histopathologic examination of the uterine tumor showed atypical spindle cells producing an osteoid matrix with calcification in keeping with OS. Despite initial response to doxorubicin and ifosfamide, the patient succumbed to brain metastases just 8 months from diagnosis. Whole genome sequencing was performed on tumor and blood samples to analyze genetic alterations in this highly aggressive tumor. A pathogenic somatic missense mutation resulting in substitution of glutamate for lysine at position 653 within the protein kinase domain of the platelet-derived growth factor receptor beta (PDGFRB) was found. The PDGF pathway is involved in cell proliferation and angiogenesis, and it has been implicated in malignancy. Crucially, this pathogenic mutation may be amenable to PDGFR tyrosine kinase inhibition, representing a possible treatment approach in this rare sarcoma.
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Affiliation(s)
- Valerie Shiwen Yang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
,Institute of Molecular and Cell Biology, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | | | | | | | - Mohamad Farid
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Bin Tean Teh
- Institute of Molecular and Cell Biology, Singapore
,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
,Cancer Science Institute of Singapore, National University of Singapore, Singapore
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23
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Kongpetch S, Jusakul A, Lim JQ, Ng CCY, Chan JY, Rajasegaran V, Lim TH, Lim KH, Choo SP, Dima S, Popescu I, Duda DG, Kukongviriyapan V, Khuntikeo N, Pairojkul C, Rozen SG, Tan P, Teh BT. Lack of Targetable FGFR2 Fusions in Endemic Fluke-Associated Cholangiocarcinoma. JCO Glob Oncol 2020; 6:628-638. [PMID: 32315234 PMCID: PMC7193781 DOI: 10.1200/go.20.00030] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2020] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Cholangiocarcinoma (CCA) remains a disease with poor prognosis and limited therapeutic options. Identification of driver genetic alterations may lead to the discovery of more effective targeted therapies. CCAs harboring FGFR2 fusions have recently demonstrated promising responses to FGFR inhibitors, highlighting their potential relevance as predictive biomarkers. CCA incidence is high in the northeast of Thailand and its neighboring countries because of chronic infection with the liver fluke Opisthorchis viverrini (Ov). However, there are currently no available data on the prevalence of FGFR alterations in fluke-associated CCA in endemic countries. MATERIALS AND METHODS In this study, we performed anchored multiplex polymerase chain reaction target enrichment RNA sequencing of FGFR1-3, validated by fluorescence in situ hybridization and Sanger sequencing, in 121 Ov-associated and 95 non-Ov-associated CCA tumors. RESULTS Compared with non-fluke-associated CCA (11/95; 11.6%), FGFR2 fusions were significantly less common in fluke-associated CCA (1/121; 0.8%; P = .0006). All FGFR fusions were detected exclusively in intrahepatic CCAs and were mutually exclusive with KRAS/ERBB2/BRAF/FGFR mutations, pointing to their potential roles as oncogenic drivers. CONCLUSION FGFR2 fusions are rare in fluke-associated CCA, underscoring how distinct etiologies may affect molecular landscapes in tumors and highlighting the need to discover other actionable genomic alterations in endemic fluke-associated CCA.
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Affiliation(s)
- Sarinya Kongpetch
- Cholangiocarcinoma Screening and Care Program and Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
- Department of Pharmacology, Khon Kaen University, Khon Kaen, Thailand
| | - Apinya Jusakul
- Cholangiocarcinoma Screening and Care Program and Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
- The Centre for Research and Development of Medical Diagnostic Laboratories and Department of Clinical Immunology and Transfusion Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Jing Quan Lim
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | | | - Vikneswari Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | - Tse Hui Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Su Pin Choo
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Simona Dima
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Irinel Popescu
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Dan G. Duda
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Veerapol Kukongviriyapan
- Cholangiocarcinoma Screening and Care Program and Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
- Department of Pharmacology, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Cholangiocarcinoma Screening and Care Program and Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
- Department of Surgery, Khon Kaen University, Khon Kaen, Thailand
| | | | - Steven G. Rozen
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Genome Institute of Singapore, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Genome Institute of Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore
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24
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Tan KM, Chia B, Lim JQ, Khoo LP, Cheng CL, Tan L, Poon E, Somasundaram N, Farid M, Tang TPL, Tao M, Cheah DMZ, Laurensia Y, Pang JWL, Song T, Tan J, Huang D, Kim SJ, Kim WS, Ong CK, Lim ST, Chan JY. A clinicohaematological prognostic model for nasal-type natural killer/T-cell lymphoma: A multicenter study. Sci Rep 2019; 9:14961. [PMID: 31628410 PMCID: PMC6802199 DOI: 10.1038/s41598-019-51522-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/01/2019] [Indexed: 02/06/2023] Open
Abstract
Extranodal NK/T-cell lymphoma, nasal type (NKTL) is an aggressive type of non-Hodgkin lymphoma closely associated with Epstein-Barr virus and characterized by varying degrees of systemic inflammation. We aim to examine the prognostic significance of peripheral blood neutrophil-lymphocyte ratio (NLR) in patients with NKTL. Therefore, we conducted a retrospective review of 178 patients with biopsy-proven NKTL from the National Cancer Centre Singapore and Samsung Medical Center, South Korea. Using receiver operating curve analysis, an optimal cut-off for high NLR (>3.5) in predicting overall survival (OS) was derived. Survival analysis was performed using the Kaplan-Meier method and multivariable Cox proportional regression. In patients with high NLR, estimated 5-year OS was 25% compared to 53% in those with low NLR. In multivariable analysis, high NLR, in addition to age ≥60 years, presence of B-symptoms and stage III/IV at diagnosis, was independently correlated with worse OS (HR 2.08; 95% CI 1.36 to 3.18; p = 0.0008) and progression-free survival (HR 1.66; 95% CI 1.11 to 2.46; p = 0.0128). A new prognostic index (NABS score) derived from these factors stratified patients into low (0), low-intermediate (1), high-intermediate (2) and high (3-4) risk subgroups, which were associated with 5-year OS of 76.5%, 55.7%, 29.2% and 0% respectively. In conclusion, high NLR is an independent prognostic marker and the NABS model can be used to risk-stratify NKTL patients.
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Affiliation(s)
- Khee Ming Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Burton Chia
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Lay Poh Khoo
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Chee Leong Cheng
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Leonard Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Eileen Poon
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore, Singapore
| | - Nagavalli Somasundaram
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore, Singapore
| | - Mohamad Farid
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore, Singapore
| | - Tiffany Pooi Ling Tang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore, Singapore
| | - Miriam Tao
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore, Singapore
| | - Daryl Ming Zhe Cheah
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Yurike Laurensia
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Jane Wan Lu Pang
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Tammy Song
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Tan
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Dachuan Huang
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | | | | | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore. .,Genome Institute of Singapore, A*STAR, Singapore, Singapore. .,Duke-NUS Medical School, Singapore, Singapore.
| | - Soon Thye Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore. .,SingHealth Duke-NUS Blood Cancer Centre, Singapore, Singapore. .,Duke-NUS Medical School, Singapore, Singapore.
| | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore. .,SingHealth Duke-NUS Blood Cancer Centre, Singapore, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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25
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Md Nasir ND, Ng CCY, Rajasegaran V, Wong SF, Liu W, Ng GXP, Lee JY, Guan P, Lim JQ, Thike AA, Koh VCY, Loke BN, Chang KTE, Gudi MA, Lian DWQ, Madhukumar P, Tan BKT, Tan VKM, Wong CY, Yong WS, Ho GH, Ong KW, Tan P, Teh BT, Tan PH, Rahman NA, Nahar Begum SMK, Cheah PL, Chen CJ, Dela Fuente E, Han A, Harada O, Kanomata N, Lee CS, Han Lee JY, Kamal M, Nishimura R, Ohi Y, Sawyer EJ, Teoh KH, Tsang AKH, Tsang JY, Tse GMK, Yamaguchi R. Genomic characterisation of breast fibroepithelial lesions in an international cohort. J Pathol 2019; 249:447-460. [DOI: 10.1002/path.5333] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/11/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
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26
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Toh MR, Chong ST, Chan SH, Low CE, Ishak NDB, Lim JQ, Courtney E, Ngeow J. Functional analysis of clinical BARD1 germline variants. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004093. [PMID: 31371347 PMCID: PMC6672023 DOI: 10.1101/mcs.a004093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 12/31/2022] Open
Abstract
Germline pathogenic variants in BRCA1/2 account for one-third of familial breast cancers. The majority of BRCA1 function requires heterodimerization with BARD1. In contrast to BRCA1, BARD1 is a low-penetrance gene with an unclear clinical relevance, partly because of limited functional evidence. Using patient-derived lymphoblastoid cells, we functionally characterized two pathogenic variants (c.1833dupT, c.2099delG) and three variants of uncertain significance (VUSs) (c.73G>C, c.1217G>A, c.1918C>A). Three of these patients had breast cancers, whereas the remaining had colorectal cancers (n = 3). Both patients with pathogenic variants (c.1833dupT, c.2099delG) developed breast cancers with aggressive disease phenotypes such as triple-negative breast cancer and high cancer grades. As BARD1 encompasses multiple functional domains, including those of apoptosis and homologous recombination repair, we hypothesized that the function being impaired would correspond with the domain where the variant was located. Variants c.1918C>A, c.1833dupT, c.1217G>A, and c.2099delG, located within and proximal to apoptotic domains of ankyrin and BRCT, were associated with impaired apoptosis. Conversely, apoptosis function was preserved in c.73G>C, which was distant from the ankyrin domain. All variants displayed normal BRCA1 heterodimerization and RAD51 colocalization, consistent with their location being distal to BRCA1—and RAD51-binding domains. In view of deficient apoptosis, VUSs (c.1217G>A and c.1918C>A) may be pathogenic or likely pathogenic variants. In summary, functional analysis of BARD1 VUSs requires a combination of assays and, more importantly, the use of appropriate functional assays with consideration to the variant's location.
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Affiliation(s)
- Ming Ren Toh
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Siao Ting Chong
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Sock Hoai Chan
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Chen Ee Low
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | | | - Jing Quan Lim
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Eliza Courtney
- Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore
| | - Joanne Ngeow
- Duke-NUS Medical School, Singapore, 169857, Singapore.,Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 639798, Singapore.,Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138673, Singapore
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27
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Chan JY, Lim JQ, Ravi V, Guan P, Tay TKY, Selvarajan S, Ong CK, Huang D, Jing T, Ng CCY, Sung KWK, Harunal Rashid MFR, Quek RHH, Tan NC, Teo MCC, Rozen S, Tan P, Futreal A, Teh BT, Soo KC. Metagenomic discovery of a distinct inflammatory subtype of human angiosarcoma associated with human herpesvirus 7. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.11047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11047 Background: Angiosarcomas are rare, clinically-aggressive endothelial tumors with remarkable heterogeneity in terms of anatomical and etiological origins, amongst which UV-radiation and oncogenic viruses have been implicated. Methods: The genomic and transcriptomic landscapes of human angiosarcomas were examined using whole genome sequencing (n = 18) and RNAseq (n = 14). Results were validated in an extended cohort of FFPE tissue (n = 57) on various platforms. Results: We observed recurrent mutations in known angiosarcoma-associated genes including TP53, KDR, POT1 and PTPRB. The median tumor mutation burden (TMB) was 1.95 mutations per megabase and was highest in a subset of head and neck angiosarcomas (HN-AS, n = 6) harboring UV signatures. The remaining cases, including seven HN-AS, contained a significantly lower TMB (5.04 vs 0.91, p= 0.0007). In corroboration, UV exposures were validated by cyclobutane pyrimidine dimer immunohistochemistry in 15 of 35 (42.9%) HN-AS and cutaneous angiosarcomas, but not in visceral or breast angiosarcomas. Gene set enrichment analysis (GSEA) revealed upregulation of “cell cycle” and “inflammation” pathways in angiosarcomas. Notably, drug inhibition of overexpressed kinases including aurora kinase, polo-like kinase and checkpoint kinase-1 potently reduced viability in two angiosarcoma cell lines, achieving IC50s of < 1µM. Metagenomic analysis detected viral reads mapping to the human herpesvirus-7 (HHV-7) genome, which were verified by PCR and immunohistochemistry. Genomic integration of HHV-7 was demonstrated at its flanking DRR telomeric repeat sequence adjoining the subtelomeric region of chromosome 17p. Overall, HHV-7 was detected in 38 of 57 (66.7%) angiosarcomas and inversely correlated with UV exposure ( p= 0.01). GSEA and Nanostring IO360 profiling showed that “inflammation” pathways were enriched in viral-positive angiosarcomas, while “cell cycle” pathways were enriched in viral-negative cases. Compared with HHV-7 negative cases, HHV-7 positive angiosarcomas were associated with high tumor inflammation scores (TIS ≥ median 6.74) (73.3% vs 25.0%, p = 0.02). Conclusions: We identified distinct subtypes of angiosarcoma characterized by HHV7-positive “inflammation” and UV-associated “cell cycle” phenotypes.
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Affiliation(s)
| | - Jing Quan Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Vinod Ravi
- The University of Texas MD Anderson Cancer Center, Department of Sarcoma Medical Oncology, Houston, TX
| | | | | | | | | | | | - Tan Jing
- National Cancer Centre Singapore, Singapore, Singapore
| | - Cedric Chuan Young Ng
- Biomedical Research Council, Agency for Science, Technology and Research Singapore, Singapore, Singapore
| | | | | | | | | | | | | | - Patrick Tan
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Department of Genomic Medicine, Houston, TX
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Khee Chee Soo
- National Cancer Centre Singapore, Singapore, Singapore
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28
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Guan P, Wong SF, Lim JQ, Ng CCY, Soong PL, Sim CQX, Ong CK, Rajasegaran V, Myint SS, Lee JY, Tan HK, Iyer NG, Soo KC, Teh BT, Tay ABG. Mutational Signatures in Mandibular Ameloblastoma Correlate with Smoking. J Dent Res 2019; 98:652-658. [PMID: 30917298 DOI: 10.1177/0022034519837248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Ameloblastoma is a rare tumor of odontogenic epithelium, the low incidence rate of which precludes statistical determination of its molecular characterizations. Despite recent genomic and transcriptomic profiling, the etiology of ameloblastomas remains poorly understood. Risk factors of ameloblastoma development are also largely unknown. Whole exome sequencing was performed on 11 mandibular ameloblastoma samples. We identified 2 convergent mutational signatures in ameloblastoma: 1) a signature found in multiple types of lung cancers with probable etiology of tobacco carcinogens (COSMIC signature 4) and 2) a signature present in gingivobuccal oral squamous cell carcinoma and correlated with tobacco-chewing habits (COSMIC signature 29). These mutational signatures highlight tobacco usage or related mutagens as one possible risk factor of ameloblastoma, since the association of BRAF mutations and smoking was demonstrated in multiple studies. In addition to BRAF hotspot mutations (V600E), we observed clear inter- and intratumor heterogeneities. Interestingly, prior to BRAF mutation, important genes regulating odontogenesis mutated (e.g., corepressor BCOR), possibly playing important roles in tumorigenesis. Furthermore, recurrent mutations in the CDC73 gene, the germline mutations of which predispose patients to the development of jaw tumors, were found in 2 patients, which may lead to recurrence if not targeted by therapeutic drugs. Our unbiased profiling of coding regions of ameloblastoma genomes provides insights to the possible etiology of mandibular ameloblastoma and highlights potential disease risk factors for screening and prevention, especially for Asian patients. Because of the limited sample size and incomplete habitual, dietary, and occupational data, a causal link between tobacco usage and ameloblastoma still requires further investigations.
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Affiliation(s)
- P Guan
- 1 Integrated Biostatistics and Bioinformatics Programme, Duke-NUS Medical School, Singapore.,2 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore.,3 Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - S F Wong
- 2 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - J Q Lim
- 2 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore.,4 Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore
| | - C C Y Ng
- 2 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - P L Soong
- 5 Department of Oral and Maxillofacial Surgery, National Dental Centre Singapore, Singapore
| | - C Q X Sim
- 5 Department of Oral and Maxillofacial Surgery, National Dental Centre Singapore, Singapore
| | - C K Ong
- 4 Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore
| | - V Rajasegaran
- 2 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - S S Myint
- 2 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - J Y Lee
- 2 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - H K Tan
- 6 Division of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - N G Iyer
- 6 Division of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - K C Soo
- 6 Division of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - B T Teh
- 2 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore.,7 Cancer Science Institute of Singapore, National University of Singapore, Singapore.,8 Institute of Molecular and Cell Biology, Singapore.,9 Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore.,10 SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
| | - A B G Tay
- 5 Department of Oral and Maxillofacial Surgery, National Dental Centre Singapore, Singapore
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29
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Abstract
Natural killer T cell lymphoma (NKTL) is an aggressive disease with very poor treatment outcomes in the advanced stages. With chemotherapy, initial response rates to treatment are high but responses are short lived. A better understanding of the complex molecular pathogenesis of this disease is essential in order to design and develop better therapeutics with improved efficacy. This review aims to summarise the key pathogenic mechanisms in NKTL which may have significant prognostic and therapeutic implications.
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Affiliation(s)
- Nagavalli Somasundaram
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Choon Kiat Ong
- Duke-NUS Medical School, Singapore, Singapore
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
- Genome Institute of Singapore A*STAR, Singapore, Singapore
| | - Soon Thye Lim
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
- Singhealth Duke- NUS Blood Cancer Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
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30
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Ng AWT, Poon SL, Huang MN, Lim JQ, Boot A, Yu W, Suzuki Y, Thangaraju S, Ng CCY, Tan P, Pang ST, Huang HY, Yu MC, Lee PH, Hsieh SY, Chang AY, Teh BT, Rozen SG. Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia. Sci Transl Med 2018; 9:9/412/eaan6446. [PMID: 29046434 DOI: 10.1126/scitranslmed.aan6446] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/31/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022]
Abstract
Many traditional pharmacopeias include Aristolochia and related plants, which contain nephrotoxins and mutagens in the form of aristolochic acids and similar compounds (collectively, AA). AA is implicated in multiple cancer types, sometimes with very high mutational burdens, especially in upper tract urothelial cancers (UTUCs). AA-associated kidney failure and UTUCs are prevalent in Taiwan, but AA's role in hepatocellular carcinomas (HCCs) there remains unexplored. Therefore, we sequenced the whole exomes of 98 HCCs from two hospitals in Taiwan and found that 78% showed the distinctive mutational signature of AA exposure, accounting for most of the nonsilent mutations in known cancer driver genes. We then searched for the AA signature in 1400 HCCs from diverse geographic regions. Consistent with exposure through known herbal medicines, 47% of Chinese HCCs showed the signature, albeit with lower mutation loads than in Taiwan. In addition, 29% of HCCs from Southeast Asia showed the signature. The AA signature was also detected in 13 and 2.7% of HCCs from Korea and Japan as well as in 4.8 and 1.7% of HCCs from North America and Europe, respectively, excluding one U.S. hospital where 22% of 87 "Asian" HCCs had the signature. Thus, AA exposure is geographically widespread. Asia, especially Taiwan, appears to be much more extensively affected, which is consistent with other evidence of patterns of AA exposure. We propose that additional measures aimed at primary prevention through avoidance of AA exposure and investigation of possible approaches to secondary prevention are warranted.
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Affiliation(s)
- Alvin W T Ng
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Song Ling Poon
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Mi Ni Huang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jing Quan Lim
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore.,Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Arnoud Boot
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Willie Yu
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yuka Suzuki
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Saranya Thangaraju
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Cedric C Y Ng
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,SingHealth/Duke-NUS Precision Medicine Institute, Singapore 169609, Singapore.,Genome Institute of Singapore, Singapore 138672, Singapore
| | - See-Tong Pang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital, Linkou, Taoyuan 33305, Taiwan
| | - Hao-Yi Huang
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan
| | - Ming-Chin Yu
- Department of General Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan
| | - Po-Huang Lee
- Department of Surgery, National Taiwan University, Taipei 10051, Taiwan
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan.
| | - Alex Y Chang
- Johns Hopkins Singapore, Singapore 308433, Singapore.
| | - Bin T Teh
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore. .,Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore.,SingHealth/Duke-NUS Precision Medicine Institute, Singapore 169609, Singapore.,Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore. .,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore.,SingHealth/Duke-NUS Precision Medicine Institute, Singapore 169609, Singapore
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31
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Nairismägi ML, Gerritsen ME, Li ZM, Wijaya GC, Chia BKH, Laurensia Y, Lim JQ, Yeoh KW, Yao XS, Pang WL, Bisconte A, Hill RJ, Bradshaw JM, Huang D, Song TLL, Ng CCY, Rajasegaran V, Tang T, Tang QQ, Xia XJ, Kang TB, Teh BT, Lim ST, Ong CK, Tan J. Oncogenic activation of JAK3-STAT signaling confers clinical sensitivity to PRN371, a novel selective and potent JAK3 inhibitor, in natural killer/T-cell lymphoma. Leukemia 2018; 32:1147-1156. [PMID: 29434279 PMCID: PMC5940653 DOI: 10.1038/s41375-017-0004-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/17/2017] [Accepted: 12/04/2017] [Indexed: 02/06/2023]
Abstract
Aberrant activation of the JAK3-STAT signaling pathway is a characteristic feature of many hematological malignancies. In particular, hyperactivity of this cascade has been observed in natural killer/T-cell lymphoma (NKTL) cases. Although the first-in-class JAK3 inhibitor tofacitinib blocks JAK3 activity in NKTL both in vitro and in vivo, its clinical utilization in cancer therapy has been limited by the pan-JAK inhibition activity. To improve the therapeutic efficacy of JAK3 inhibition in NKTL, we have developed a highly selective and durable JAK3 inhibitor PRN371 that potently inhibits JAK3 activity over the other JAK family members JAK1, JAK2, and TYK2. PRN371 effectively suppresses NKTL cell proliferation and induces apoptosis through abrogation of the JAK3-STAT signaling. Moreover, the activity of PRN371 has a more durable inhibition on JAK3 compared to tofacitinib in vitro, leading to significant tumor growth inhibition in a NKTL xenograft model harboring JAK3 activating mutation. These findings provide a novel therapeutic approach for the treatment of NKTL.
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Affiliation(s)
- M -L Nairismägi
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Z M Li
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - G C Wijaya
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - B K H Chia
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Y Laurensia
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - J Q Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - K W Yeoh
- Department of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - X S Yao
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - W L Pang
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - A Bisconte
- Principia Biopharma, South San Francisco, CA, USA
| | - R J Hill
- Principia Biopharma, South San Francisco, CA, USA
| | - J M Bradshaw
- Principia Biopharma, South San Francisco, CA, USA
| | - D Huang
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - T L L Song
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - C C Y Ng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - V Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - T Tang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Q Q Tang
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - X J Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - T B Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - B T Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - S T Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Office of Education, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - C K Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore. .,Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - J Tan
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
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32
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Lim WK, Davila S, Teo JX, Yang C, Pua CJ, Blöcker C, Lim JQ, Ching J, Yap JJL, Tan SY, Sahlén A, Chin CWL, Teh BT, Rozen SG, Cook SA, Yeo KK, Tan P. Beyond fitness tracking: The use of consumer-grade wearable data from normal volunteers in cardiovascular and lipidomics research. PLoS Biol 2018; 16:e2004285. [PMID: 29485983 PMCID: PMC5828350 DOI: 10.1371/journal.pbio.2004285] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/23/2018] [Indexed: 12/14/2022] Open
Abstract
The use of consumer-grade wearables for purposes beyond fitness tracking has not been comprehensively explored. We generated and analyzed multidimensional data from 233 normal volunteers, integrating wearable data, lifestyle questionnaires, cardiac imaging, sphingolipid profiling, and multiple clinical-grade cardiovascular and metabolic disease markers. We show that subjects can be stratified into distinct clusters based on daily activity patterns and that these clusters are marked by distinct demographic and behavioral patterns. While resting heart rates (RHRs) performed better than step counts in being associated with cardiovascular and metabolic disease markers, step counts identified relationships between physical activity and cardiac remodeling, suggesting that wearable data may play a role in reducing overdiagnosis of cardiac hypertrophy or dilatation in active individuals. Wearable-derived activity levels can be used to identify known and novel activity-modulated sphingolipids that are in turn associated with insulin sensitivity. Our findings demonstrate the potential for wearables in biomedical research and personalized health.
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Affiliation(s)
- Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
- Cancer and Stem Biology Program, Duke-NUS Medical School, Singapore
| | - Sonia Davila
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Chengxi Yang
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
| | - Chee Jian Pua
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
| | | | - Jing Quan Lim
- Lymphoma Genomic Translational Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jianhong Ching
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | | | - Swee Yaw Tan
- Department of Cardiology, National Heart Centre Singapore, Singapore
| | - Anders Sahlén
- Department of Cardiology, National Heart Centre Singapore, Singapore
| | | | - Bin Tean Teh
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
- Cancer and Stem 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
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Steven G. Rozen
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
- Cancer and Stem Biology Program, Duke-NUS Medical School, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Stuart Alexander Cook
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
- National Heart and Lung Institute, Imperial College London, United Kingdom
- MRC Clinical Sciences Centre, Imperial College London, United Kingdom
| | - Khung Keong Yeo
- Department of Cardiology, National Heart Centre Singapore, Singapore
| | - Patrick Tan
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
- Cancer and Stem Biology Program, Duke-NUS Medical School, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Biomedical Research Council, Agency for Science, Technology and Research, Singapore
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33
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Ler LD, Ghosh S, Chai X, Thike AA, Heng HL, Siew EY, Dey S, Koh LK, Lim JQ, Lim WK, Myint SS, Loh JL, Ong P, Sam XX, Huang D, Lim T, Tan PH, Nagarajan S, Cheng CWS, Ho H, Ng LG, Yuen J, Lin PH, Chuang CK, Chang YH, Weng WH, Rozen SG, Tan P, Creasy CL, Pang ST, McCabe MT, Poon SL, Teh BT. Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2. Sci Transl Med 2017; 9:9/378/eaai8312. [PMID: 28228601 DOI: 10.1126/scitranslmed.aai8312] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/02/2017] [Indexed: 12/12/2022]
Abstract
Trithorax-like group complex containing KDM6A acts antagonistically to Polycomb-repressive complex 2 (PRC2) containing EZH2 in maintaining the dynamics of the repression and activation of gene expression through H3K27 methylation. In urothelial bladder carcinoma, KDM6A (a H3K27 demethylase) is frequently mutated, but its functional consequences and therapeutic targetability remain unknown. About 70% of KDM6A mutations resulted in a total loss of expression and a consequent loss of demethylase function in this cancer type. Further transcriptome analysis found multiple deregulated pathways, especially PRC2/EZH2, in KDM6A-mutated urothelial bladder carcinoma. Chromatin immunoprecipitation sequencing analysis revealed enrichment of H3K27me3 at specific loci in KDM6A-null cells, including PRC2/EZH2 and their downstream targets. Consequently, we targeted EZH2 (an H3K27 methylase) and demonstrated that KDM6A-null urothelial bladder carcinoma cell lines were sensitive to EZH2 inhibition. Loss- and gain-of-function assays confirmed that cells with loss of KDM6A are vulnerable to EZH2. IGFBP3, a direct KDM6A/EZH2/H3K27me3 target, was up-regulated by EZH2 inhibition and contributed to the observed EZH2-dependent growth suppression in KDM6A-null cell lines. EZH2 inhibition delayed tumor onset in KDM6A-null cells and caused regression of KDM6A-null bladder tumors in both patient-derived and cell line xenograft models. In summary, our study demonstrates that inactivating mutations of KDM6A, which are common in urothelial bladder carcinoma, are potentially targetable by inhibiting EZH2.
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Affiliation(s)
- Lian Dee Ler
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, 28 Medical Drive, Singapore 117456, Singapore
| | - Sujoy Ghosh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Xiaoran Chai
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Aye Aye Thike
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Hong Lee Heng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Ee Yan Siew
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sucharita Dey
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore
| | - Liang Kai Koh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jing Quan Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Weng Khong Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jia Liang Loh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Pauline Ong
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Xin Xiu Sam
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Dachuan Huang
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Tony Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Puay Hoon Tan
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Sanjanaa Nagarajan
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | | | - Henry Ho
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Lay Guat Ng
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - John Yuen
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Po-Hung Lin
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Cheng-Keng Chuang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Ying-Hsu Chang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Wen-Hui Weng
- Department of Chemical Engineering and Biotechnology and Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Steven G Rozen
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.,Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore.,Genome Institute of Singapore, 60 Biopolis Street Genome, Singapore 138672, Singapore
| | - Caretha L Creasy
- Cancer Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - See-Tong Pang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan.
| | - Michael T McCabe
- Cancer Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.
| | - Song Ling Poon
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore. .,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore. .,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, #07-18, Singapore 138673, Singapore
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34
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Jusakul A, Cutcutache I, Yong CH, Lim JQ, Huang MN, Padmanabhan N, Nellore V, Kongpetch S, Ng AWT, Ng LM, Choo SP, Myint SS, Thanan R, Nagarajan S, Lim WK, Ng CCY, Boot A, Liu M, Ong CK, Rajasegaran V, Lie S, Lim AST, Lim TH, Tan J, Loh JL, McPherson JR, Khuntikeo N, Bhudhisawasdi V, Yongvanit P, Wongkham S, Totoki Y, Nakamura H, Arai Y, Yamasaki S, Chow PKH, Chung AYF, Ooi LLPJ, Lim KH, Dima S, Duda DG, Popescu I, Broet P, Hsieh SY, Yu MC, Scarpa A, Lai J, Luo DX, Carvalho AL, Vettore AL, Rhee H, Park YN, Alexandrov LB, Gordân R, Rozen SG, Shibata T, Pairojkul C, Teh BT, Tan P. Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma. Cancer Discov 2017; 7:1116-1135. [PMID: 28667006 DOI: 10.1158/2159-8290.cd-17-0368] [Citation(s) in RCA: 556] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/07/2017] [Accepted: 06/28/2017] [Indexed: 02/07/2023]
Abstract
Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined 4 CCA clusters-fluke-positive CCAs (clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations; conversely, fluke-negative CCAs (clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3' untranslated region deletion as a mechanism of FGFR2 upregulation. Integration of noncoding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation of H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores-mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Our results exemplify how genetics, epigenetics, and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer.Significance: Integrated whole-genome and epigenomic analysis of CCA on an international scale identifies new CCA driver genes, noncoding promoter mutations, and structural variants. CCA molecular landscapes differ radically by etiology, underscoring how distinct cancer subtypes in the same organ may arise through different extrinsic and intrinsic carcinogenic processes. Cancer Discov; 7(10); 1116-35. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 1047.
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Affiliation(s)
- Apinya Jusakul
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore.,The Centre for Research and Development of Medical Diagnostic Laboratories and Department of Clinical Immunology and Transfusion Sciences, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Ioana Cutcutache
- Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Chern Han Yong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Jing Quan Lim
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore.,Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Division of Medical Oncology, Singapore
| | - Mi Ni Huang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Nisha Padmanabhan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Vishwa Nellore
- Department of Biostatistics and Bioinformatics, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Sarinya Kongpetch
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore.,Cholangiocarcinoma Screening and Care Program and Liver Fluke and Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Alvin Wei Tian Ng
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Ley Moy Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Su Pin Choo
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sanjanaa Nagarajan
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | - Weng Khong Lim
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | - Arnoud Boot
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Mo Liu
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Division of Medical Oncology, Singapore
| | - Vikneswari Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | - Stefanus Lie
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore.,Division of Radiation Oncology, National Cancer Centre Singapore, Singapore
| | - Alvin Soon Tiong Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Tse Hui Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Jing Tan
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | - Jia Liang Loh
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore
| | - John R McPherson
- Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Narong Khuntikeo
- Cholangiocarcinoma Screening and Care Program and Liver Fluke and Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | - Puangrat Yongvanit
- Cholangiocarcinoma Screening and Care Program and Liver Fluke and Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamasaki
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Japan
| | - Pierce Kah-Hoe Chow
- Division of Surgical Oncology, National Cancer Center Singapore and Office of Clinical Sciences, Duke-NUS Medical School, Singapore
| | - Alexander Yaw Fui Chung
- Department of Hepatopancreatobiliary/Transplant Surgery, Singapore General Hospital, Singapore
| | | | - Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Simona Dima
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Dan G Duda
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Irinel Popescu
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Philippe Broet
- DHU Hepatinov, Hôpital Paul Brousse, AP-HP, Villejuif, France
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Ming-Chin Yu
- Department of General Surgery, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Aldo Scarpa
- Applied Research on Cancer Centre (ARC-Net), University and Hospital Trust of Verona, Verona, Italy
| | - Jiaming Lai
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. China
| | - Di-Xian Luo
- National and Local Joint Engineering Laboratory of High-through Molecular Diagnostic Technology, the First People's Hospital of Chenzhou, Southern Medical University, Chenzhou, P. R. China
| | | | - André Luiz Vettore
- Laboratory of Cancer Molecular Biology, Department of Biological Sciences, Federal University of São Paulo, Rua Pedro de Toledo, São Paulo, Brazil
| | - Hyungjin Rhee
- Department of Pathology, Brain Korea 21 PLUS Project for Medical Science, Integrated Genomic Research Center for Metabolic Regulation, Yonsei University College of Medicine, Seoul, Korea
| | - Young Nyun Park
- Department of Pathology, Brain Korea 21 PLUS Project for Medical Science, Integrated Genomic Research Center for Metabolic Regulation, Yonsei University College of Medicine, Seoul, Korea
| | - Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Raluca Gordân
- Department of Biostatistics and Bioinformatics, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina. .,Department of Computer Science, Duke University, Durham, North Carolina
| | - Steven G Rozen
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore. .,Centre for Computational Biology, Duke-NUS Medical School, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan. .,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Japan
| | - Chawalit Pairojkul
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
| | - Bin Tean Teh
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore. .,Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore.,Institute of Molecular and Cell Biology, Singapore
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore.,Genome Institute of Singapore, Singapore
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35
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Lim ST, Song T, Lim JQ, Laurensia Y, Pang JWL, Nagarajan S, Claresta G, Jing T, Tang TPL, Nairismagi ML, Ong CK. Oncogenic activation of STAT3 pathway drives PD-L1 expression in natural killer/T cell lymphoma. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.7549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
7549 Background: Natural killer/T-cell lymphoma (NKTL) is a rare type of non-Hodgkin lymphoma that occurs more frequently in East Asia and Latin America and is associated with Epstein–Barr virus infection. Recent whole-exome sequencing studies in NKTL have reported recurrent somatic mutations in genes associated with JAK-STAT pathway, however the role of aberrant JAK-STAT signaling in tumor immune escape through PD-L1 regulation is unclear. Methods: To determine the prevalence of JAK-STAT pathway alteration in NKTL, we performed targeted sequencing of 188 genes associated with JAK-STAT pathway in 109 NKTL (22 Singapore cases, 79 China cases and 8 cell lines). Single nucleotide variants and micro-indels were called using Freebayes and candidate variants annotated using ANNOVAR. Ba/F3 model system was used to test the transformation capacity of identified variants. Cell lines were evaluated for PD-L1 expression by immunoblotting and flow cytometry. Tissue microarrays were examined for p-STAT3 and PD-L1 expression by immunohistochemistry. Results: We identified a total of 284 non-synonymous somatic mutations candidates in 114 genes, including 243 missense, 10 nonsense, 4 splice-site and 27 indel mutations. Recurrent mutations were most frequently located in STAT3 (25/109 cases, 23%) followed by TP53 (16/109 cases, 16%) and JAK3 (8/109 cases, 7%). A total of 18 STAT3 variants were identified including known hotspot mutations and novel mutations in the SH2, coiled coil and DNA-binding domains. Characterization of novel E616K mutant residing in the SH2 domain showed that E616K conferred IL3 independent growth to Ba/F3 cells, increased STAT3 phosphorylation and PD-L1 expression. Consistent with these findings, PD-L1 was over expressed in cell lines harboring STAT3 mutations. A positive correlation between PD-L1 and p-STAT3 expression was also observed in tumor tissue (R = 0.51, P = 0.02). Conclusions: We characterized a novel activating STAT3 mutant and demonstrated its ability to drive PD-L1 expression, which may promote tumor evasion from the antitumor immune response. The combination of PD-1/PD-L1 antibodies and STAT3 inhibitors might be a promising and novel therapeutic approach for NKTL in the future.
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Affiliation(s)
- Soon Thye Lim
- National Cancer Centre Singapore, Sinagpore, Singapore
| | - Tammy Song
- National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Quan Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | | | | | | | | | - Tan Jing
- National Cancer Centre Singapore, Singapore, Singapore
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36
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Nastase A, Teo JY, Heng HL, Ng CCY, Myint SS, Rajasegaran V, Loh JL, Lee SY, Ooi LL, Chung AYF, Chow PKH, Cheow PC, Wan WK, Azhar R, Khoo A, Xiu SX, Alkaff SMF, Cutcutache I, Lim JQ, Ong CK, Herlea V, Dima S, Duda DG, Teh BT, Popescu I, Lim TKH. Genomic and proteomic characterization of ARID1A chromatin remodeller in ampullary tumors. Am J Cancer Res 2017; 7:484-502. [PMID: 28401006 PMCID: PMC5385638] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 01/02/2017] [Indexed: 06/07/2023] Open
Abstract
AT rich interactive domain 1A (ARID1A) is one of the most commonly mutated genes in a broad variety of tumors. The mechanisms that involve ARID1A in ampullary cancer progression remains elusive. Here, we evaluated the frequency of ARID1A and KRAS mutations in ampullary adenomas and adenocarcinomas and in duodenal adenocarcinomas from two cohorts of patients from Singapore and Romania, correlated with clinical and pathological tumor features, and assessed the functional role of ARID1A. In the ampullary adenocarcinomas, the frequency of KRAS and ARID1A mutations was 34.7% and 8.2% respectively, with a loss or reduction of ARID1A protein in 17.2% of the cases. ARID1A mutational status was significantly correlated with ARID1A protein expression level (P=0.023). There was a significant difference in frequency of ARID1A mutation between Romania and Singapore (2.7% versus 25%, P=0.04), suggestive of different etiologies. One somatic mutation was detected in the ampullary adenoma group. In vitro studies indicated the tumor suppressive role of ARID1A. Our results warrant further investigation of this chromatin remodeller as a potential early biomarker of the disease, as well as identification of therapeutic targets in ARID1A mutated ampullary cancers.
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Affiliation(s)
- Anca Nastase
- Laboratory of Cancer Epigenome, National Cancer Centre SingaporeSingapore
- Centre of Digestive Diseases and Liver Transplantation, Fundeni Clinical InstituteBucharest, Romania
| | - Jin Yao Teo
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General HospitalSingapore
| | - Hong Lee Heng
- Laboratory of Cancer Epigenome, National Cancer Centre SingaporeSingapore
| | | | - Swe Swe Myint
- Laboratory of Cancer Epigenome, National Cancer Centre SingaporeSingapore
| | | | - Jia Liang Loh
- Laboratory of Cancer Epigenome, National Cancer Centre SingaporeSingapore
| | - Ser Yee Lee
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General HospitalSingapore
| | - London Lucien Ooi
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General HospitalSingapore
| | - Alexander Yaw Fui Chung
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General HospitalSingapore
| | | | - Peng Chung Cheow
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General HospitalSingapore
| | - Wei Keat Wan
- Department of Pathology, Singapore General HospitalSingapore, Singapore
| | - Rafy Azhar
- Department of Pathology, Singapore General HospitalSingapore, Singapore
| | - Avery Khoo
- Department of Pathology, Singapore General HospitalSingapore, Singapore
| | - Sam Xin Xiu
- Department of Pathology, Singapore General HospitalSingapore, Singapore
| | | | - Ioana Cutcutache
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical SchoolSingapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical SchoolSingapore, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, National Cancer Centre SingaporeSingapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, National Cancer Centre SingaporeSingapore
| | - Vlad Herlea
- Department of Pathology, Fundeni Clinical InstituteBucharest, Romania
- Faculty of Medicine, Titu Maiorescu UniversityBucharest, Romania
| | - Simona Dima
- Centre of Digestive Diseases and Liver Transplantation, Fundeni Clinical InstituteBucharest, Romania
| | - Dan G Duda
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical SchoolBoston, Massachusetts, USA
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, National Cancer Centre SingaporeSingapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical SchoolSingapore, Singapore
- Cancer Science Institute of Singapore, National University of SingaporeSingapore, Singapore
- Institute of Molecular and Cell Biology, A*STARSingapore, Singapore
| | - Irinel Popescu
- Centre of Digestive Diseases and Liver Transplantation, Fundeni Clinical InstituteBucharest, Romania
| | - Tony Kiat Hon Lim
- Department of Pathology, Singapore General HospitalSingapore, Singapore
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37
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Chan SH, Lim WK, Michalski ST, Lim JQ, Ishak NDB, Met-Domestici M, Young CNC, Vikstrom K, Esplin ED, Fulbright J, Ang MK, Wee J, Sittampalam K, Farid M, Lincoln SE, Itahana K, Abdullah S, Teh BT, Ngeow J. Germline hemizygous deletion of CDKN2A-CDKN2B locus in a patient presenting with Li-Fraumeni syndrome. NPJ Genom Med 2016; 1:16015. [PMID: 29263814 PMCID: PMC5685299 DOI: 10.1038/npjgenmed.2016.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 04/27/2016] [Indexed: 11/09/2022] Open
Abstract
Li–Fraumeni syndrome (LFS) is a rare cancer predisposition syndrome usually associated with TP53 germline alterations. Its genetic basis in TP53 wild-type pedigrees is less understood. Using whole-genome sequencing, we identified a germline hemizygous deletion ablating CDKN2A–CDKN2B in a TP53 wild-type patient presenting with high-grade sarcoma, laryngeal squamous cell carcinoma and a family history suggestive of LFS. Patient-derived cells demonstrated reduced basal gene and protein expression of the CDKN2A-encoded tumour suppressors p14ARF and p16INK4A with concomitant decrease in p21 and faster cell proliferation, implying potential deregulation of p53-mediated cell cycle control. Review of 13 additional patients with pathogenic CDKN2A variants suggested associations of germline CDKN2A mutations with an expanded spectrum of non-melanoma familial cancers. To our knowledge, this is the first report of a germline gross deletion of the CDKN2A–CDKN2B locus in an LFS family. These findings highlight the potential contribution of germline CDKN2A deletions to cancer predisposition and the importance of interrogating the full extent of CDKN2A locus in clinical testing gene panels.
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Affiliation(s)
- Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Weng Khong Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore, Singapore
| | | | - Jing Quan Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Nur Diana Binte Ishak
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Marie Met-Domestici
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Cedric Ng Chuan Young
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | | | | | | | - Mei Kim Ang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Joseph Wee
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Mohamad Farid
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Koji Itahana
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore, Singapore
| | | | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University Singapore, Singapore, Singapore.,Institute of Molecular and Cellular Biology, ASTAR, Singapore, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Oncology Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, Singapore
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38
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Nairismägi ML, Tan J, Lim JQ, Nagarajan S, Ng CCY, Rajasegaran V, Huang D, Lim WK, Laurensia Y, Wijaya GC, Li ZM, Cutcutache I, Pang WL, Thangaraju S, Ha J, Khoo LP, Chin ST, Dey S, Poore G, Tan LHC, Koh HKM, Sabai K, Rao HL, Chuah KL, Ho YH, Ng SB, Chuang SS, Zhang F, Liu YH, Pongpruttipan T, Ko YH, Cheah PL, Karim N, Chng WJ, Tang T, Tao M, Tay K, Farid M, Quek R, Rozen SG, Tan P, Teh BT, Lim ST, Tan SY, Ong CK. JAK-STAT and G-protein-coupled receptor signaling pathways are frequently altered in epitheliotropic intestinal T-cell lymphoma. Leukemia 2016; 30:1311-9. [PMID: 26854024 PMCID: PMC4895162 DOI: 10.1038/leu.2016.13] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 12/11/2022]
Abstract
Epitheliotropic intestinal T-cell lymphoma (EITL, also known as type II enteropathy-associated T-cell lymphoma) is an aggressive intestinal disease with poor prognosis and its molecular alterations have not been comprehensively characterized. We aimed to identify actionable easy-to-screen alterations that would allow better diagnostics and/or treatment of this deadly disease. By performing whole-exome sequencing of four EITL tumor-normal pairs, followed by amplicon deep sequencing of 42 tumor samples, frequent alterations of the JAK-STAT and G-protein-coupled receptor (GPCR) signaling pathways were discovered in a large portion of samples. Specifically, STAT5B was mutated in a remarkable 63% of cases, JAK3 in 35% and GNAI2 in 24%, with the majority occurring at known activating hotspots in key functional domains. Moreover, STAT5B locus carried copy-neutral loss of heterozygosity resulting in the duplication of the mutant copy, suggesting the importance of mutant STAT5B dosage for the development of EITL. Dysregulation of the JAK-STAT and GPCR pathways was also supported by gene expression profiling and further verified in patient tumor samples. In vitro overexpression of GNAI2 mutants led to the upregulation of pERK1/2, a member of MEK-ERK pathway. Notably, inhibitors of both JAK-STAT and MEK-ERK pathways effectively reduced viability of patient-derived primary EITL cells, indicating potential therapeutic strategies for this neoplasm with no effective treatment currently available.
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Affiliation(s)
- M-L Nairismägi
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - J Tan
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - J Q Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - S Nagarajan
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - C C Y Ng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - V Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - D Huang
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - W K Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Y Laurensia
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - G C Wijaya
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Z M Li
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - I Cutcutache
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - W L Pang
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - S Thangaraju
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - J Ha
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - L P Khoo
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - S T Chin
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - S Dey
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - G Poore
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - L H C Tan
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - H K M Koh
- Advanced Molecular Pathology Laboratory, Singapore Health Services, Singapore, Singapore
| | - K Sabai
- Advanced Molecular Pathology Laboratory, Singapore Health Services, Singapore, Singapore
| | - H-L Rao
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - K L Chuah
- Department of Pathology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Y-H Ho
- Department of Pathology, Tan Tock Seng Hospital, Singapore, Singapore
| | - S-B Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - S-S Chuang
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan.,Department of Pathology, Taipei Medical University and National Taiwan University, Taipei, Taiwan
| | - F Zhang
- Department of Pathology, Guangdong General Hospital, Guangzhou, China
| | - Y-H Liu
- Department of Pathology, Guangdong General Hospital, Guangzhou, China
| | - T Pongpruttipan
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Y H Ko
- Department of Pathology, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - P-L Cheah
- Department of Pathology, University of Malaya, Kuala Lumpur, Malaysia
| | - N Karim
- Department of Pathology, Hospital Raja Permaisuri Bainun, Ipoh, Malaysia
| | - W-J Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Hospital, National University Health System, Singapore, Singapore
| | - T Tang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - M Tao
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - K Tay
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - M Farid
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - R Quek
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - S G Rozen
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - P Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - B T Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - S T Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Office of Education, Duke-NUS Medical School, Singapore, Singapore
| | - S-Y Tan
- Department of Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore.,Department of Pathology, Guangdong General Hospital, Guangzhou, China.,Department of Pathology, University of Malaya, Kuala Lumpur, Malaysia.,Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - C K Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
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