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Zheng S, Chan SW, Liu F, Liu J, Chow PKH, Toh HC, Hong W. Hepatocellular Carcinoma: Current Drug Therapeutic Status, Advances and Challenges. Cancers (Basel) 2024; 16:1582. [PMID: 38672664 PMCID: PMC11048862 DOI: 10.3390/cancers16081582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common form of liver cancer, accounting for ~90% of liver neoplasms. It is the second leading cause of cancer-related deaths and the seventh most common cancer worldwide. Although there have been rapid developments in the treatment of HCC over the past decade, the incidence and mortality rates of HCC remain a challenge. With the widespread use of the hepatitis B vaccine and antiviral therapy, the etiology of HCC is shifting more toward metabolic-associated steatohepatitis (MASH). Early-stage HCC can be treated with potentially curative strategies such as surgical resection, liver transplantation, and radiofrequency ablation, improving long-term survival. However, most HCC patients, when diagnosed, are already in the intermediate or advanced stages. Molecular targeted therapy, followed by immune checkpoint inhibitor immunotherapy, has been a revolution in HCC systemic treatment. Systemic treatment of HCC especially for patients with compromised liver function is still a challenge due to a significant resistance to immune checkpoint blockade, tumor heterogeneity, lack of oncogenic addiction, and lack of effective predictive and therapeutic biomarkers.
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Affiliation(s)
- Shunzhen Zheng
- Key Laboratory of Biopharmaceuticals, Postdoctoral Scientific Research Workstation, Shandong Academy of Pharmaceutical Science, Jinan 250098, China;
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673, Singapore; (S.W.C.); (W.H.)
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China;
| | - Siew Wee Chan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673, Singapore; (S.W.C.); (W.H.)
| | - Fei Liu
- Key Laboratory of Biopharmaceuticals, Postdoctoral Scientific Research Workstation, Shandong Academy of Pharmaceutical Science, Jinan 250098, China;
| | - Jun Liu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China;
| | - Pierce Kah Hoe Chow
- Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore 169610, Singapore;
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583, Singapore;
| | - Wanjin Hong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673, Singapore; (S.W.C.); (W.H.)
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2
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Liu X, Zhang K, Kaya NA, Jia Z, Wu D, Chen T, Liu Z, Zhu S, Hillmer AM, Wuestefeld T, Liu J, Chan YS, Hu Z, Ma L, Jiang L, Zhai W. Tumor phylogeography reveals block-shaped spatial heterogeneity and the mode of evolution in Hepatocellular Carcinoma. Nat Commun 2024; 15:3169. [PMID: 38609353 PMCID: PMC11015015 DOI: 10.1038/s41467-024-47541-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Solid tumors are complex ecosystems with heterogeneous 3D structures, but the spatial intra-tumor heterogeneity (sITH) at the macroscopic (i.e., whole tumor) level is under-explored. Using a phylogeographic approach, we sequence genomes and transcriptomes from 235 spatially informed sectors across 13 hepatocellular carcinomas (HCC), generating one of the largest datasets for studying sITH. We find that tumor heterogeneity in HCC segregates into spatially variegated blocks with large genotypic and phenotypic differences. By dissecting the transcriptomic heterogeneity, we discover that 30% of patients had a "spatially competing distribution" (SCD), where different spatial blocks have distinct transcriptomic subtypes co-existing within a tumor, capturing the critical transition period in disease progression. Interestingly, the tumor regions with more advanced transcriptomic subtypes (e.g., higher cell cycle) often take clonal dominance with a wider geographic range, rejecting neutral evolution for SCD patients. Extending the statistical tests for detecting natural selection to many non-SCD patients reveal varying levels of selective signal across different tumors, implying that many evolutionary forces including natural selection and geographic isolation can influence the overall pattern of sITH. Taken together, tumor phylogeography unravels a dynamic landscape of sITH, pinpointing important evolutionary and clinical consequences of spatial heterogeneity in cancer.
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Affiliation(s)
- Xiaodong Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ke Zhang
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China
| | - Neslihan A Kaya
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Zhe Jia
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China
| | - Dafei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tingting Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zhiyuan Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Sinan Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Axel M Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Torsten Wuestefeld
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jin Liu
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Yun Shen Chan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liang Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Li Jiang
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China.
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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3
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Chew V, Chuang CH, Hsu C. Translational research on drug development and biomarker discovery for hepatocellular carcinoma. J Biomed Sci 2024; 31:22. [PMID: 38368324 PMCID: PMC10874078 DOI: 10.1186/s12929-024-01011-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 02/10/2024] [Indexed: 02/19/2024] Open
Abstract
Translational research plays a key role in drug development and biomarker discovery for hepatocellular carcinoma (HCC). However, unique challenges exist in this field because of the limited availability of human tumor samples from surgery, the lack of homogenous oncogenic driver mutations, and the paucity of adequate experimental models. In this review, we provide insights into these challenges and review recent advancements, with a particular focus on the two main agents currently used as mainstream therapies for HCC: anti-angiogenic agents and immunotherapy. First, we examine the pre-clinical and clinical studies to highlight the challenges of determining the optimal therapeutic combinations with biologically effective dosage for HCC. Second, we discuss biomarker studies focusing on anti-PD1/anti-PD-L1-based combination therapy. Finally, we discuss the progress made in our collective understanding of tumor immunology and in multi-omics analysis technology, which enhance our understanding of the mechanisms underlying immunotherapy, characterize different patient subgroups, and facilitate the development of novel combination approaches to improve treatment efficacy. In summary, this review provides a comprehensive overview of efforts in translational research aiming at advancing our understanding of and improving the treatment of HCC.
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Affiliation(s)
- Valerie Chew
- Translational Immunology Institute, SingHealth-DukeNUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Chien-Huai Chuang
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Chiun Hsu
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan.
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan.
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan.
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4
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Chung F, Zavadil J. New risk factors and molecular landscapes of hepatic angiosarcoma in the Taiwanese population †. J Pathol 2024; 262:1-3. [PMID: 37929656 DOI: 10.1002/path.6224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Hepatic angiosarcoma is a rare, highly aggressive malignancy of the liver. The tumorigenesis of hepatic angiosarcoma has been relatively understudied in terms of aetiology and molecular properties. A recent study published in The Journal of Pathology revealed a strong association between hepatic angiosarcoma incidence and chronic kidney disease, particularly in end-stage renal disease using population-based data from the National Health Insurance Research Database in Taiwan and an institutional cohort. The study also revealed enrichment in the mutational signature of aristolochic acid exposure and is the first reported observation of this mutational signature in human sarcomas. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Felicia Chung
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia
| | - Jiri Zavadil
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, Rhône-Alpes, France
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Kwok DW, Stevers NO, Nejo T, Chen LH, Etxeberria I, Jung J, Okada K, Cove MC, Lakshmanachetty S, Gallus M, Barpanda A, Hong C, Chan GKL, Wu SH, Ramos E, Yamamichi A, Liu J, Watchmaker P, Ogino H, Saijo A, Du A, Grishanina N, Woo J, Diaz A, Chang SM, Phillips JJ, Wiita AP, Klebanoff CA, Costello JF, Okada H. Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563178. [PMID: 37904942 PMCID: PMC10614978 DOI: 10.1101/2023.10.19.563178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22 , respectively. TCR-engineered CD8 + T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.
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6
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Jeon AJ, Anene-Nzelu CG, Teo YY, Chong SL, Sekar K, Wu L, Chew SC, Chen J, Kendarsari RI, Lai H, Ling WH, Kaya NA, Lim JQ, Chung AYF, Cheow PC, Kam JH, Madhavan K, Kow A, Ganpathi IS, Lim TKH, Leow WQ, Loong S, Loh TJ, Wan WK, Soon GST, Pang YH, Yoong BK, Bee-Lan Ong D, Lim J, de Villa VH, dela Cruz RD, Chanwat R, Thammasiri J, Bonney GK, Goh BK, Foo RSY, Chow PKH. A genomic enhancer signature associates with hepatocellular carcinoma prognosis. JHEP Rep 2023; 5:100715. [PMID: 37168287 PMCID: PMC10165154 DOI: 10.1016/j.jhepr.2023.100715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 05/13/2023] Open
Abstract
Background & Aims Lifestyle and environmental-related exposures are important risk factors for hepatocellular carcinoma (HCC), suggesting that epigenetic dysregulation significantly underpins HCC. We profiled 30 surgically resected tumours and the matched adjacent normal tissues to understand the aberrant epigenetic events associated with HCC. Methods We identified tumour differential enhancers and the associated genes by analysing H3K27 acetylation (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) and Hi-C/HiChIP data from the resected tumour samples of 30 patients with early-stage HCC. This epigenome dataset was analysed with previously reported genome and transcriptome data of the overlapping group of patients from the same cohort. We performed patient-specific differential expression testing using multiregion sequencing data to identify genes that undergo both enhancer and gene expression changes. Based on the genes selected, we identified two patient groups and performed a recurrence-free survival analysis. Results We observed large-scale changes in the enhancer distribution between HCC tumours and the adjacent normal samples. Many of the gain-in-tumour enhancers showed corresponding upregulation of the associated genes and vice versa, but much of the enhancer and gene expression changes were patient-specific. A subset of the upregulated genes was activated in a subgroup of patients' tumours. Recurrence-free survival analysis revealed that the patients with a more robust upregulation of those genes showed a worse prognosis. Conclusions We report the genomic enhancer signature associated with differential prognosis in HCC. Findings that cohere with oncofoetal reprogramming in HCC were underpinned by genome-wide enhancer rewiring. Our results present the epigenetic changes in HCC that offer the rational selection of epigenetic-driven gene targets for therapeutic intervention or disease prognostication in HCC. Impact and Implications Lifestyle and environmental-related exposures are the important risk factors of hepatocellular carcinoma (HCC), suggesting that tumour-associated epigenetic dysregulations may significantly underpin HCC. We profiled tumour tissues and their matched normal from 30 patients with early-stage HCC to study the dysregulated epigenetic changes associated with HCC. By also analysing the patients' RNA-seq and clinical data, we found the signature genes - with epigenetic and transcriptomic dysregulation - associated with worse prognosis. Our findings suggest that systemic approaches are needed to consider the surrounding cellular environmental and epigenetic changes in HCC tumours.
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Affiliation(s)
- Ah-Jung Jeon
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Quebec, Canada
| | - Yue-Yang Teo
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Shay Lee Chong
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Karthik Sekar
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Lingyan Wu
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Sin-Chi Chew
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Raden Indah Kendarsari
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Hannah Lai
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Wen Huan Ling
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Neslihan Arife Kaya
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Jia Qi Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Alexander Yaw Fui Chung
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Peng-Chung Cheow
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Juinn Huar Kam
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Krishnakumar Madhavan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Alfred Kow
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Iyer Shridhar Ganpathi
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Wei-Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Shihleone Loong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Tracy Jiezhen Loh
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Wei Keat Wan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | | | - Yin Huei Pang
- Department of Pathology, National University Hospital, Singapore
| | - Boon Koon Yoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Diana Bee-Lan Ong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanessa H. de Villa
- Department of Surgery and Center for Liver Health and Transplantation, The Medical City, Pasig City, Philippines
| | - Rouchelle D. dela Cruz
- Department of Laboratory Medicine and Pathology, The Medical City, Pasig City, Philippines
| | - Rawisak Chanwat
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | | | - Glenn K. Bonney
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Brian K.P. Goh
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Roger Sik Yin Foo
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pierce Kah-Hoe Chow
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
- Corresponding author. Address: National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore 168583, Singapore. Tel.: +65-63065424.
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Jeon AJ, Teo YY, Sekar K, Chong SL, Wu L, Chew SC, Chen J, Kendarsari RI, Lai H, Ling WH, Kaya NA, Lim JQ, Ramasamy A, Oguz G, Chung AYF, Chan CY, Cheow PC, Kam JH, Madhavan K, Kow A, Ganpathi IS, Lim TKH, Leow WQ, Loong S, Loh TJ, Wan WK, Soon GST, Pang YH, Yoong BK, Ong DBL, Lim J, de Villa VH, Cruz RD, Chanwat R, Thammasiri J, Bonney GK, Goh BKP, Tucker-Kellogg G, Foo RSY, Chow PKH. Multi-region sampling with paired sample sequencing analyses reveals sub-groups of patients with novel patient-specific dysregulation in Hepatocellular Carcinoma. BMC Cancer 2023; 23:118. [PMID: 36737737 PMCID: PMC9896715 DOI: 10.1186/s12885-022-10444-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/13/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Conventional differential expression (DE) testing compares the grouped mean value of tumour samples to the grouped mean value of the normal samples, and may miss out dysregulated genes in small subgroup of patients. This is especially so for highly heterogeneous cancer like Hepatocellular Carcinoma (HCC). METHODS Using multi-region sampled RNA-seq data of 90 patients, we performed patient-specific differential expression testing, together with the patients' matched adjacent normal samples. RESULTS Comparing the results from conventional DE analysis and patient-specific DE analyses, we show that the conventional DE analysis omits some genes due to high inter-individual variability present in both tumour and normal tissues. Dysregulated genes shared in small subgroup of patients were useful in stratifying patients, and presented differential prognosis. We also showed that the target genes of some of the current targeted agents used in HCC exhibited highly individualistic dysregulation pattern, which may explain the poor response rate. DISCUSSION/CONCLUSION Our results highlight the importance of identifying patient-specific DE genes, with its potential to provide clinically valuable insights into patient subgroups for applications in precision medicine.
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Affiliation(s)
- Ah-Jung Jeon
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Yue-Yang Teo
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Karthik Sekar
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Shay Lee Chong
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Lingyan Wu
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Sin-Chi Chew
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Jianbin Chen
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Raden Indah Kendarsari
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hannah Lai
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wen Huan Ling
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Neslihan Arife Kaya
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jia Qi Lim
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Adaikalavan Ramasamy
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Gokce Oguz
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alexander Yaw-Fui Chung
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Chung Yip Chan
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Peng-Chung Cheow
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Juinn Huar Kam
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Krishnakumar Madhavan
- grid.410759.e0000 0004 0451 6143Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Alfred Kow
- grid.410759.e0000 0004 0451 6143Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Iyer Shridhar Ganpathi
- grid.410759.e0000 0004 0451 6143Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Tony Kiat Hon Lim
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Wei-Qiang Leow
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Shihleone Loong
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Tracy Jiezhen Loh
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Wei Keat Wan
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Gwyneth Shook Ting Soon
- grid.412106.00000 0004 0621 9599Department of Pathology, National University Hospital, Singapore, 119074 Singapore
| | - Yin Huei Pang
- grid.412106.00000 0004 0621 9599Department of Pathology, National University Hospital, Singapore, 119074 Singapore
| | - Boon Koon Yoong
- grid.10347.310000 0001 2308 5949Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Diana Bee-Lan Ong
- grid.10347.310000 0001 2308 5949Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- grid.10347.310000 0001 2308 5949Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanessa H. de Villa
- Department of Surgery and Center for Liver Health and Transplantation, The Medical City, Pasig City, Metro Manila Philippines
| | - Rouchelle D.dela Cruz
- Department of Laboratory Medicine and Pathology, The Medical City, Pasig City, Metro Manila Philippines
| | - Rawisak Chanwat
- grid.419173.90000 0000 9607 5779Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | - Jidapa Thammasiri
- grid.419173.90000 0000 9607 5779Division of Pathology, National Cancer Institute, Bangkok, Thailand
| | - Glenn K. Bonney
- grid.410759.e0000 0004 0451 6143Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Brian K. P. Goh
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Greg Tucker-Kellogg
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Roger Sik Yin Foo
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pierce K. H. Chow
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
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8
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Toh MR, Wong EYT, Wong SH, Ng AWT, Loo LH, Chow PKH, Ngeow JYY. Global Epidemiology and Genetics of Hepatocellular Carcinoma. Gastroenterology 2023; 164:766-782. [PMID: 36738977 DOI: 10.1053/j.gastro.2023.01.033] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading cancers worldwide. Classically, HCC develops in genetically susceptible individuals who are exposed to risk factors, especially in the presence of liver cirrhosis. Significant temporal and geographic variations exist for HCC and its etiologies. Over time, the burden of HCC has shifted from the low-moderate to the high sociodemographic index regions, reflecting the transition from viral to nonviral causes. Geographically, the hepatitis viruses predominate as the causes of HCC in Asia and Africa. Although there are genetic conditions that confer increased risk for HCC, these diagnoses are rarely recognized outside North America and Europe. In this review, we will evaluate the epidemiologic trends and risk factors of HCC, and discuss the genetics of HCC, including monogenic diseases, single-nucleotide polymorphisms, gut microbiome, and somatic mutations.
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Affiliation(s)
- Ming Ren Toh
- Cancer Genetics Service, National Cancer Centre Singapore, Singapore
| | | | - Sunny Hei Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Alvin Wei Tian Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute, Agency for Science, Technology, and Research (A∗STAR), Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pierce Kah-Hoe Chow
- Department of Hepato-Pancreato-Biliary and Transplant Surgery, National Cancer Center Singapore and Singapore General Hospital, Singapore; Duke-NUS Medical School Singapore, Singapore
| | - Joanne Yuen Yie Ngeow
- Cancer Genetics Service, National Cancer Centre Singapore, Singapore; Division of Medical Oncology, National Cancer Centre Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Duke-NUS Medical School Singapore, Singapore.
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9
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Tian Y, Xiao H, Yang Y, Zhang P, Yuan J, Zhang W, Chen L, Fan Y, Zhang J, Cheng H, Deng T, Yang L, Wang W, Chen G, Wang P, Gong P, Niu X, Zhang X. Crosstalk between 5-methylcytosine and N 6-methyladenosine machinery defines disease progression, therapeutic response and pharmacogenomic landscape in hepatocellular carcinoma. Mol Cancer 2023; 22:5. [PMID: 36627693 PMCID: PMC9830866 DOI: 10.1186/s12943-022-01706-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Accumulated evidence highlights the significance of the crosstalk between epigenetic and epitranscriptomic mechanisms, notably 5-methylcytosine (5mC) and N6-methyladenosine (m6A). Herein, we conducted a widespread analysis regarding the crosstalk between 5mC and m6A regulators in hepatocellular carcinoma (HCC). METHODS Pan-cancer genomic analysis of the crosstalk between 5mC and m6A regulators was presented at transcriptomic, genomic, epigenetic, and other multi-omics levels. Hub 5mC and m6A regulators were summarized to define an epigenetic and epitranscriptomic module eigengene (EME), which reflected both the pre- and post-transcriptional modifications. RESULTS 5mC and m6A regulators interacted with one another at the multi-omic levels across pan-cancer, including HCC. The EME scoring system enabled to greatly optimize risk stratification and accurately predict HCC patients' clinical outcomes and progression. Additionally, the EME accurately predicted the responses to mainstream therapies (TACE and sorafenib) and immunotherapy as well as hyper-progression. In vitro, 5mC and m6A regulators cooperatively weakened apoptosis and facilitated proliferation, DNA damage repair, G2/M arrest, migration, invasion and epithelial-to-mesenchymal transition (EMT) in HCC cells. The EME scoring system was remarkably linked to potential extrinsic and intrinsic immune escape mechanisms, and the high EME might contribute to a reduced copy number gain/loss frequency. Finally, we determined potential therapeutic compounds and druggable targets (TUBB1 and P2RY4) for HCC patients with high EME. CONCLUSIONS Our findings suggest that HCC may result from a unique synergistic combination of 5mC-epigenetic mechanism mixed with m6A-epitranscriptomic mechanism, and their crosstalk defines therapeutic response and pharmacogenomic landscape.
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Affiliation(s)
- Yu Tian
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
| | - Haijuan Xiao
- grid.508012.eDepartment of Oncology, Shaanxi Province, Affiliated Hospital of the Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi 712046 China
| | - Yanhui Yang
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China ,grid.453074.10000 0000 9797 0900Department of Trauma Surgery, The First Affiliated Hospital and College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003 Henan China
| | - Pingping Zhang
- grid.411525.60000 0004 0369 1599Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433 China
| | - Jiahui Yuan
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
| | - Wei Zhang
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
| | - Lijie Chen
- grid.412449.e0000 0000 9678 1884China Medical University, Shenyang, 110122 Liaoning China
| | - Yibao Fan
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
| | - Jinze Zhang
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
| | - Huan Cheng
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
| | - Tingwei Deng
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
| | - Lin Yang
- grid.440299.2Department of Hepatobiliary Surgery, Shaanxi Province, Xianyang Central Hospital, Xianyang, 712099 Shaanxi China
| | - Weiwei Wang
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China ,grid.414011.10000 0004 1808 090XHepatobiliary Surgery, People’s Hospital of Zhengzhou University and Henan Provincial People’s Hospital, Zhengzhou, 450001 Henan China
| | - Guoyong Chen
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China ,grid.414011.10000 0004 1808 090XHepatobiliary Surgery, People’s Hospital of Zhengzhou University and Henan Provincial People’s Hospital, Zhengzhou, 450001 Henan China
| | - Peiqin Wang
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, 200003 China
| | - Peng Gong
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
| | - Xing Niu
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China ,grid.412449.e0000 0000 9678 1884China Medical University, Shenyang, 110122 Liaoning China
| | - Xianbin Zhang
- grid.263488.30000 0001 0472 9649Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055 China
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10
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Xiang Y, Xiang P, Zhang L, Li Y, Zhang J. A narrative review for platelets and their RNAs in cancers: New concepts and clinical perspectives. Medicine (Baltimore) 2022; 101:e32539. [PMID: 36596034 PMCID: PMC9803462 DOI: 10.1097/md.0000000000032539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recent years have witnessed a growing body of evidence suggesting that platelets are involved in several stages of the metastatic process via direct or indirect interactions with cancer cells, contributing to the progression of neoplastic malignancies. Cancer cells can dynamically exchange components with platelets in and out of blood vessels, and directly phagocytose platelets to hijack their proteome, transcriptome, and secretome, or be remotely regulated by metabolites or microparticles released by platelets, resulting in phenotypic, genetic, and functional modifications. Moreover, platelet interactions with stromal and immune cells in the tumor microenvironment lead to alterations in their components, including the ribonucleic acid (RNA) profile, and complicate the impact of platelets on cancers. A deeper understanding of the roles of platelets and their RNAs in cancer will contribute to the development of anticancer strategies and the optimization of clinical management. Encouragingly, advances in high-throughput sequencing, bioinformatics data analysis, and machine learning have allowed scientists to explore the potential of platelet RNAs for cancer diagnosis, prognosis, and guiding treatment. However, the clinical application of this technique remains controversial and requires larger, multicenter studies with standardized protocols. Here, we integrate the latest evidence to provide a broader insight into the role of platelets in cancer progression and management, and propose standardized recommendations for the clinical utility of platelet RNAs to facilitate translation and benefit patients.
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Affiliation(s)
- Yunhui Xiang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Pinpin Xiang
- Department of Laboratory Medicine, Xiping Community Health Service Center of Longquanyi District Chengdu City, Chengdu, China
| | - Liuyun Zhang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanying Li
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Juan Zhang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- * Correspondence: Juan Zhang, Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, 32# West Second Section, First Ring Road, Qingyang District, Chengdu City, Sichuan Province 610072, China (e-mail: )
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11
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Yang C, Zhang S, Cheng Z, Liu Z, Zhang L, Jiang K, Geng H, Qian R, Wang J, Huang X, Chen M, Li Z, Qin W, Xia Q, Kang X, Wang C, Hang H. Multi-region sequencing with spatial information enables accurate heterogeneity estimation and risk stratification in liver cancer. Genome Med 2022; 14:142. [PMID: 36527145 PMCID: PMC9758830 DOI: 10.1186/s13073-022-01143-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Numerous studies have used multi-region sampling approaches to characterize intra-tumor heterogeneity (ITH) in hepatocellular carcinoma (HCC). However, conventional multi-region sampling strategies do not preserve the spatial details of samples, and thus, the potential influences of spatial distribution on patient-wise ITH (represents the overall heterogeneity level of the tumor in a given patient) have long been overlooked. Furthermore, gene-wise transcriptional ITH (represents the expression pattern of genes across different intra-tumor regions) in HCC is also under-explored, highlighting the need for a comprehensive investigation. METHODS To address the problem of spatial information loss, we propose a simple and easy-to-implement strategy called spatial localization sampling (SLS). We performed multi-region sampling and sequencing on 14 patients with HCC, collecting a total of 75 tumor samples with spatial information and molecular data. Normalized diversity score and integrated heterogeneity score (IHS) were then developed to measure patient-wise and gene-wise ITH, respectively. RESULTS A significant correlation between spatial and molecular heterogeneity was uncovered, implying that spatial distribution of sampling sites did influence ITH estimation in HCC. We demonstrated that the normalized diversity score had the ability to overcome sampling location bias and provide a more accurate estimation of patient-wise ITH. According to this metric, HCC tumors could be divided into two classes (low-ITH and high-ITH tumors) with significant differences in multiple biological properties. Through IHS analysis, we revealed a highly heterogenous immune microenvironment in HCC and identified some low-ITH checkpoint genes with immunotherapeutic potential. We also constructed a low-heterogeneity risk stratification (LHRS) signature based on the IHS results which could accurately predict the survival outcome of patients with HCC on a single tumor biopsy sample. CONCLUSIONS This study provides new insights into the complex phenotypes of HCC and may serve as a guide for future studies in this field.
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Affiliation(s)
- Chen Yang
- grid.16821.3c0000 0004 0368 8293Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Senquan Zhang
- grid.16821.3c0000 0004 0368 8293Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhuoan Cheng
- grid.16821.3c0000 0004 0368 8293Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhicheng Liu
- grid.412793.a0000 0004 1799 5032Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linmeng Zhang
- grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Jiang
- grid.16821.3c0000 0004 0368 8293Renji Biobank, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haigang Geng
- grid.16821.3c0000 0004 0368 8293Department of Gastrointestinal Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ruolan Qian
- grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Wang
- grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaowen Huang
- grid.16821.3c0000 0004 0368 8293Key Laboratory of Gastroenterology and Hepatology, Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mo Chen
- grid.16821.3c0000 0004 0368 8293Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhe Li
- grid.16821.3c0000 0004 0368 8293Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenxin Qin
- grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiang Xia
- grid.16821.3c0000 0004 0368 8293Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaonan Kang
- grid.16821.3c0000 0004 0368 8293Renji Biobank, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cun Wang
- grid.16821.3c0000 0004 0368 8293Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hualian Hang
- grid.16821.3c0000 0004 0368 8293Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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12
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Das S, Thakur S, Korenjak M, Sidorenko VS, Chung FFL, Zavadil J. Aristolochic acid-associated cancers: a public health risk in need of global action. Nat Rev Cancer 2022; 22:576-591. [PMID: 35854147 DOI: 10.1038/s41568-022-00494-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 11/09/2022]
Abstract
Aristolochic acids (AAs) are a group of naturally occurring compounds present in many plant species of the Aristolochiaceae family. Exposure to AA is a significant risk factor for severe nephropathy, and urological and hepatobiliary cancers (among others) that are often recurrent and characterized by the prominent mutational fingerprint of AA. However, herbal medicinal products that contain AA continue to be manufactured and marketed worldwide with inadequate regulation, and possible environmental exposure routes receive little attention. As the trade of food and dietary supplements becomes increasingly globalized, we propose that further inaction on curtailing AA exposure will have far-reaching negative effects on the disease trends of AA-associated cancers. Our Review aims to systematically present the historical and current evidence for the mutagenicity and carcinogenicity of AA, and the effect of removing sources of AA exposure on cancer incidence trends. We discuss the persisting challenges of assessing the scale of AA-related carcinogenicity, and the obstacles that must be overcome in curbing AA exposure and preventing associated cancers. Overall, this Review aims to strengthen the case for the implementation of prevention measures against AA's multifaceted, detrimental and potentially fully preventable effects on human cancer development.
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Affiliation(s)
- Samrat Das
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France
| | - Shefali Thakur
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael Korenjak
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France
| | - Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Felicia Fei-Lei Chung
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France.
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Malaysia.
| | - Jiri Zavadil
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France.
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13
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Ng CCY, Lim S, Lim AH, Md Nasir ND, Zhang J, Rajasegaran V, Lee JY, Kok JST, Thike AA, Lim JX, Weng R, Yee S, Choudhury Y, Chan JY, Tan PH, Tan MH, Teh BT. A comprehensive next generation sequencing tissue assay for Asian-prevalent cancers—Analytical validation and performance evaluation with clinical samples. Front Mol Biosci 2022; 9:963243. [PMID: 36213130 PMCID: PMC9532579 DOI: 10.3389/fmolb.2022.963243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: A well-validated diagnostic assay with curated biomarkers complements clinicopathological factors to facilitate early diagnosis and ensure timely treatment delivery. This study focuses on an Asian-centric cancer diagnostic assay designed and thoroughly validated against commercially available standard references and a cohort of over 200 clinical specimens spanning 12 diverse Asian-centric cancer types. Methods: The assay uses hybrid-capture probes capable of profiling DNA aberrations from 572 cancer-related genes and 91 RNA fusion partners. The panel can detect clinically-tractable biomarkers such as microsatellite instability (MSI) and tumor mutation burden (TMB). Results: Analytical evaluation demonstrated 100% specificity and 99.9% sensitivity within a ≥5% VAF limit of detection (LoD) for SNV/Indels. RNA-based fusion features an LoD of ≥5 copies per nanogram input when evaluated against commercial references. Excellent linearity and concordance were observed when benchmarking against orthogonal methods in identifying MSI status, TMB scores and RNA fusions. Actionable genetic alterations were identified in 65% of the clinical samples. Conclusion: These results demonstrate a molecular diagnostic assay that accurately detects genomic alterations and complex biomarkers. The data also supports an excellent performance of this assay for making critical diagnoses and well-informed therapeutic decisions in Asian prevalent cancers.
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Affiliation(s)
- Cedric Chuan-Young Ng
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Sandy Lim
- Diagnostics Development Hub (DxD Hub), A National Platform Hosted by A*STAR, Singapore, Singapore
| | - Abner Herbert Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Nur Diyana Md Nasir
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Jingxian Zhang
- Diagnostics Development Hub (DxD Hub), A National Platform Hosted by A*STAR, Singapore, Singapore
| | - Vikneswari Rajasegaran
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Jessica Sook Ting Kok
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Aye Aye Thike
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | | | - Ruifen Weng
- Diagnostics Development Hub (DxD Hub), A National Platform Hosted by A*STAR, Singapore, Singapore
| | - Sidney Yee
- Diagnostics Development Hub (DxD Hub), A National Platform Hosted by A*STAR, Singapore, Singapore
| | | | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Min-Han Tan
- Lucence Diagnostics Pte Ltd, Singapore, Singapore
- *Correspondence: Bin Tean Teh, ; Min-Han Tan,
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
- *Correspondence: Bin Tean Teh, ; Min-Han Tan,
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14
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Ozeki Y, Kanogawa N, Ogasawara S, Ogawa K, Ishino T, Nakagawa M, Fujiwara K, Unozawa H, Iwanaga T, Sakuma T, Fujita N, Kojima R, Kanzaki H, Koroki K, Kobayashi K, Nakamura M, Kiyono S, Kondo T, Saito T, Nakagawa R, Suzuki E, Ooka Y, Nakamoto S, Muroyama R, Tawada A, Chiba T, Arai M, Kato J, Ikeda JI, Takiguchi Y, Kato N. Liver biopsy technique in the era of genomic cancer therapies: a single-center retrospective analysis. Int J Clin Oncol 2022; 27:1459-1466. [PMID: 35704154 DOI: 10.1007/s10147-022-02195-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/22/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND With the evolution of personalized medicine in the field of oncology, which includes optimal treatment selection using next-generation sequencing-based companion diagnostic systems and tumor-agnostic treatments according to common biomarkers, a liver tumor biopsy technique that can obtain a sufficient specimen volume must be established. The current study aimed to evaluate the safety and availability of a liver tumor biopsy technique with multiple puncture sites made using a coaxial introducer needle and embolization with gelatin sponge particles. METHODS Patients with primary or metastatic liver cancer who underwent liver tumor biopsies with puncture tract embolization using gelatin sponge (Spongel®) from October 2019 to September 2020 were included in the study. The complication and diagnostic rates were evaluated, and whether the specimen volume was sufficient for Foundation® CDx was investigated. RESULTS In total, 96 patients were enrolled in this analysis. The median total number of puncture times per patient was 3 (range 1-8). The pathological diagnostic rate was 79.2%. Using the FoundationOne® CDx, specimens with a sufficient volume required for genomic medicine were collected in 84.9% of patients. The incidence rate of bleeding was 4.2% (n = 4), and only one patient presented with major bleeding requiring transfusion. CONCLUSIONS Liver biopsy with puncture tract embolization using a gelatin sponge may be safe and effective for collecting specimens with a volume sufficient for modern cancer treatments.
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Affiliation(s)
- Yusuke Ozeki
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Naoya Kanogawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Sadahisa Ogasawara
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan. .,Translational Research and Development Center, Chiba University Hospital, Chiba, Japan.
| | - Keita Ogawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Takamasa Ishino
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Miyuki Nakagawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Kisako Fujiwara
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Hidemi Unozawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Terunao Iwanaga
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Takafumi Sakuma
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Naoto Fujita
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Ryuta Kojima
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Hiroaki Kanzaki
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Keisuke Koroki
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Kazufumi Kobayashi
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan.,Translational Research and Development Center, Chiba University Hospital, Chiba, Japan
| | - Masato Nakamura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Soichiro Kiyono
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Takayuki Kondo
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Tomoko Saito
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Ryo Nakagawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Eiichiro Suzuki
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Yoshihiko Ooka
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Shingo Nakamoto
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Ryosuke Muroyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Akinobu Tawada
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan.,Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Makoto Arai
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan.,Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Jun Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
| | - Jun-Ichiro Ikeda
- Department of Diagnostic Pathology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuichi Takiguchi
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
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15
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Chan JJ, Zhang B, Chew XH, Salhi A, Kwok ZH, Lim CY, Desi N, Subramaniam N, Siemens A, Kinanti T, Ong S, Sanchez-Mejias A, Ly PT, An O, Sundar R, Fan X, Wang S, Siew BE, Lee KC, Chong CS, Lieske B, Cheong WK, Goh Y, Fam WN, Ooi MG, Koh BTH, Iyer SG, Ling WH, Chen J, Yoong BK, Chanwat R, Bonney GK, Goh BKP, Zhai W, Fullwood MJ, Wang W, Tan KK, Chng WJ, Dan YY, Pitt JJ, Roca X, Guccione E, Vardy LA, Chen L, Gao X, Chow PKH, Yang H, Tay Y. Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis. Nat Cell Biol 2022; 24:928-939. [PMID: 35618746 PMCID: PMC9203280 DOI: 10.1038/s41556-022-00913-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/07/2022] [Indexed: 11/15/2022]
Abstract
Most mammalian genes generate messenger RNAs with variable untranslated regions (UTRs) that are important post-transcriptional regulators. In cancer, shortening at 3′ UTR ends via alternative polyadenylation can activate oncogenes. However, internal 3′ UTR splicing remains poorly understood as splicing studies have traditionally focused on protein-coding alterations. Here we systematically map the pan-cancer landscape of 3′ UTR splicing and present this in SpUR (http://www.cbrc.kaust.edu.sa/spur/home/). 3′ UTR splicing is widespread, upregulated in cancers, correlated with poor prognosis and more prevalent in oncogenes. We show that antisense oligonucleotide-mediated inhibition of 3′ UTR splicing efficiently reduces oncogene expression and impedes tumour progression. Notably, CTNNB1 3′ UTR splicing is the most consistently dysregulated event across cancers. We validate its upregulation in hepatocellular carcinoma and colon adenocarcinoma, and show that the spliced 3′ UTR variant is the predominant contributor to its oncogenic functions. Overall, our study highlights the importance of 3′ UTR splicing in cancer and may launch new avenues for RNA-based anti-cancer therapeutics. Chan et al. report that 3′ UTR splicing is widespread and enhanced across different cancer types and is associated with more advanced tumour progression.
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Affiliation(s)
- Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xiao Hong Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Adil Salhi
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA, USA
| | - Chun You Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ng Desi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Nagavidya Subramaniam
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore, Singapore
| | - Angela Siemens
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,The University of British Columbia, Vancouver, British Columbia, Canada
| | - Tyas Kinanti
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shane Ong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Avencia Sanchez-Mejias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Integra Therapeutics S.L., Barcelona, Spain
| | - Phuong Thao Ly
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Raghav Sundar
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
| | - Xiaonan Fan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shi Wang
- Department of Pathology, National University Health System, Singapore, Singapore
| | - Bei En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kuok Chung Lee
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Choon Seng Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Bettina Lieske
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Yufen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee Nih Fam
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Melissa G Ooi
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan T H Koh
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shridhar Ganpathi Iyer
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Hepatobiliary & Pancreatic Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wen Huan Ling
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Boon-Koon Yoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rawisak Chanwat
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | - Glenn Kunnath Bonney
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Hepatobiliary & Pancreatic Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Brian K P Goh
- Department of Hepatopancreatobiliary and Transplantation Surgery, Singapore General Hospital and National Cancer Center Singapore, Singapore, Singapore
| | - Weiwei Zhai
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wilson Wang
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yock Young Dan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ernesto Guccione
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Leah A Vardy
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,BioMap, Beijing, China
| | - Pierce K H Chow
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore.,Department of Hepatopancreatobiliary and Transplantation Surgery, Singapore General Hospital and National Cancer Center Singapore, Singapore, Singapore.,Academic Clinical Programme for Surgery, SingHealth Duke-NUS Academic Medical Centre (AMC), Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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