1
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Narmada BC, Khakpoor A, Shirgaonkar N, Narayanan S, Kim Aw PP, Singh M, Ong KH, Owino CO, Ting Ng JW, Yew HC, Binte Mohamed Nasir NS, Au VB, Sng R, Kaliaperumal N, Toe Wai Khine HH, Casuscelli di Tocco F, Masayuki O, Naikar S, Ng HX, Chia SL, Yi Seah CX, Alnawaz MH, Lee Yoon Wai C, Ling Tay AY, Singh MK, Chew V, Yu W, Connolly JE, Periyasamy G, Plissonnier ML, Levrero M, Lim SG, DasGupta R. Single cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity. J Hepatol 2024:S0168-8278(24)00137-5. [PMID: 38423478 DOI: 10.1016/j.jhep.2024.02.017] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND & AIMS Hepatitis B surface antigen (HBsAg) loss or functional cure (FC), is considered the desirable therapeutic outcome for chronic hepatitis B (CHB) patients. However, the immune-pathological biomarkers and underlying mechanisms remain unclear. In this study we comprehensively interrogate disease-associated cell states (DACS) identified within intra-hepatic tissue and matched PBMCs from either CHB or FC patients, at the resolution of single cells, to provide novel insights into putative mechanisms underlying FC. METHODS We combined single cell transcriptomics (scRNA-seq) with multiparametric flow cytometry-based immune phenotyping, and multiplexed immunofluorescence to elucidate the immunopathological cell states associated with CHB vs FC. RESULTS We find that the intra-hepatic environment of CHB and FC patients displays specific cell identities and molecular signatures that are distinct from those found in matched PBMCs. FC is associated with emergence of an altered adaptive immune response marked by CD4 cytotoxic T lymphocytes (CD4-CTLs), and an activated innate response represented by liver-resident natural killer (LR-NK) cells, specific Kupffer cell (KC) subtypes and marginated neutrophils. Surprisingly, we find that FC patients are also characterized by the presence of MHC class II-expressing hepatocytes and low but persistent levels of cccDNA and pgRNA, which may play an important role in achieving functional cure in HBV patients. CONCLUSIONS Our study provides conceptually novel insights into the immuno-pathological control of HBV cure, and opens exciting new avenues for clinical management, biomarker discovery and therapeutic interventions. We believe that the discoveries from this study, as it relates to the activation of an innate and altered immune response that may facilitate sustained, low-grade inflammation, may have broader implications in the resolution of chronic viral hepatitis.
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Affiliation(s)
- Balakrishnan Chakrapani Narmada
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672; Experimental Drug Development Centre, A*STAR, 10 Biopolis Way, Chromos, Singapore 138670, Singapore
| | - Atefeh Khakpoor
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Niranjan Shirgaonkar
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672
| | - Sriram Narayanan
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Pauline Poh Kim Aw
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672
| | - Malay Singh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671, Singapore
| | - Kok Haur Ong
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671, Singapore
| | - Collins Oduor Owino
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jane Wei Ting Ng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hui Chuing Yew
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Veonice Bijin Au
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Reina Sng
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Nivashini Kaliaperumal
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Htet Htet Toe Wai Khine
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Otsuka Masayuki
- Translational Immunology Institute (TII), SingHealth-DukeNUS Academic Medical Centre, Singapore 169856, Singapore
| | - Shamita Naikar
- Translational Immunology Institute (TII), SingHealth-DukeNUS Academic Medical Centre, Singapore 169856, Singapore
| | - Hui Xin Ng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Su Li Chia
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Myra Hj Alnawaz
- Department of Medicine, National University Hospital, Singapore
| | - Chris Lee Yoon Wai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Amy Yuh Ling Tay
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mangat Kamarjit Singh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Valerie Chew
- Translational Immunology Institute (TII), SingHealth-DukeNUS Academic Medical Centre, Singapore 169856, Singapore
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671, Singapore
| | - John Edward Connolly
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Institute of Biomedical Studies, Baylor University, Waco, TX, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Giridharan Periyasamy
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Way, Chromos, Singapore 138670, Singapore
| | | | - Massimo Levrero
- Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR5286, Lyon, France; Department of Hepatology, Hôpital Croix-Rousse, Hospices Civils de Lyon, Lyon, France; University of Lyon Claude Bernard 1 (UCLB1), Lyon, France; Department of Medicine SCIAC and the Italian Institute of Technology (IIT) Center for Life Nanosciences (CLNS), University of Rome La Sapienza, Rome, Italy
| | - Seng Gee Lim
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore; Department of Medicine, National University Hospital, Singapore; Division of Gastroenterology and Hepatology, National University Hospital, National University Health System, Singapore
| | - Ramanuj DasGupta
- Laboratory of Precision Medicine and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St., #02-01 Genome, Singapore 138672.
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2
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Xiang W, Lam YH, Periyasamy G, Chuah C. Application of High Throughput Technologies in the Development of Acute Myeloid Leukemia Therapy: Challenges and Progress. Int J Mol Sci 2022; 23:ijms23052863. [PMID: 35270002 PMCID: PMC8910862 DOI: 10.3390/ijms23052863] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex hematological malignancy characterized by extensive heterogeneity in genetics, response to therapy and long-term outcomes, making it a prototype example of development for personalized medicine. Given the accessibility to hematologic malignancy patient samples and recent advances in high-throughput technologies, large amounts of biological data that are clinically relevant for diagnosis, risk stratification and targeted drug development have been generated. Recent studies highlight the potential of implementing genomic-based and phenotypic-based screens in clinics to improve survival in patients with refractory AML. In this review, we will discuss successful applications as well as challenges of most up-to-date high-throughput technologies, including artificial intelligence (AI) approaches, in the development of personalized medicine for AML, and recent clinical studies for evaluating the utility of integrating genomics-guided and drug sensitivity testing-guided treatment approaches for AML patients.
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Affiliation(s)
- Wei Xiang
- Department of Haematology, Singapore General Hospital, Singapore 169608, Singapore; (W.X.); (Y.H.L.)
| | - Yi Hui Lam
- Department of Haematology, Singapore General Hospital, Singapore 169608, Singapore; (W.X.); (Y.H.L.)
| | - Giridharan Periyasamy
- High Throughput Phenomics Platform, Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore 139632, Singapore;
| | - Charles Chuah
- Department of Haematology, Singapore General Hospital, Singapore 169608, Singapore; (W.X.); (Y.H.L.)
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 169857, Singapore
- Correspondence:
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3
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Wong RLY, Wong MRE, Kuick CH, Saffari SE, Wong MK, Tan SH, Merchant K, Chang KTE, Thangavelu M, Periyasamy G, Chen ZX, Iyer P, Tan EEK, Soh SY, Iyer NG, Fan Q, Loh AHP. Integrated Genomic Profiling and Drug Screening of Patient-Derived Cultures Identifies Individualized Copy Number-Dependent Susceptibilities Involving PI3K Pathway and 17q Genes in Neuroblastoma. Front Oncol 2021; 11:709525. [PMID: 34722256 PMCID: PMC8551924 DOI: 10.3389/fonc.2021.709525] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Neuroblastoma is the commonest extracranial pediatric malignancy. With few recurrent single nucleotide variations (SNVs), mutation-based precision oncology approaches have limited utility, but its frequent and heterogenous copy number variations (CNVs) could represent genomic dependencies that may be exploited for personalized therapy. Patient-derived cell culture (PDC) models can facilitate rapid testing of multiple agents to determine such individualized drug-responses. Thus, to study the relationship between individual genomic aberrations and therapeutic susceptibilities, we integrated comprehensive genomic profiling of neuroblastoma tumors with drug screening of corresponding PDCs against 418 targeted inhibitors. We quantified the strength of association between copy number and cytotoxicity, and validated significantly correlated gene-drug pairs in public data and using machine learning models. Somatic mutations were infrequent (3.1 per case), but copy number losses in 1p (31%) and 11q (38%), and gains in 17q (69%) were prevalent. Critically, in-vitro cytotoxicity significantly correlated only with CNVs, but not SNVs. Among 1278 significantly correlated gene-drug pairs, copy number of GNA13 and DNA damage response genes CBL, DNMT3A, and PPM1D were most significantly correlated with cytotoxicity; the drugs most commonly associated with these genes were PI3K/mTOR inhibitor PIK-75, and CDK inhibitors P276-00, SNS-032, AT7519, flavopiridol and dinaciclib. Predictive Markov random field models constructed from CNVs alone recapitulated the true z-score-weighted associations, with the strongest gene-drug functional interactions in subnetworks involving PI3K and JAK-STAT pathways. Together, our data defined individualized dose-dependent relationships between copy number gains of PI3K and STAT family genes particularly on 17q and susceptibility to PI3K and cell cycle agents in neuroblastoma. Integration of genomic profiling and drug screening of patient-derived models of neuroblastoma can quantitatively define copy number-dependent sensitivities to targeted inhibitors, which can guide personalized therapy for such mutationally quiet cancers.
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Affiliation(s)
| | - Megan R E Wong
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Seyed Ehsan Saffari
- Centre for Quantitative Medicine, Duke NUS Medical School, Singapore, Singapore
| | - Meng Kang Wong
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore
| | - Sheng Hui Tan
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore
| | - Khurshid Merchant
- Duke NUS Medical School, Singapore, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore.,Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Kenneth T E Chang
- Duke NUS Medical School, Singapore, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore.,Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Matan Thangavelu
- Centre for High Throughput Phenomics (CHiP-GIS), Genome Institute of Singapore, Singapore, Singapore
| | - Giridharan Periyasamy
- Centre for High Throughput Phenomics (CHiP-GIS), Genome Institute of Singapore, Singapore, Singapore
| | - Zhi Xiong Chen
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore.,Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Prasad Iyer
- Duke NUS Medical School, Singapore, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore.,Department of Paediatric Subspecialties Haematology Oncology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Enrica E K Tan
- Duke NUS Medical School, Singapore, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore.,Department of Paediatric Subspecialties Haematology Oncology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Shui Yen Soh
- Duke NUS Medical School, Singapore, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore.,Department of Paediatric Subspecialties Haematology Oncology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - N Gopalakrishna Iyer
- Duke NUS Medical School, Singapore, Singapore.,Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Qiao Fan
- Centre for Quantitative Medicine, Duke NUS Medical School, Singapore, Singapore
| | - Amos H P Loh
- Duke NUS Medical School, Singapore, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore.,Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore, Singapore
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4
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Low JL, Lau DP, Zhang X, Kwang XL, Rohatgi N, Chan JV, Chong FT, Wong SQR, Leong HS, Thangavelu MT, Rikka S, Skanderup AMJ, Tan DSW, Periyasamy G, Koh JLY, Iyer NG, DasGupta R. A chemical genetic screen identifies Aurora kinases as a therapeutic target in EGFR T790M negative, gefitinib-resistant head and neck squamous cell carcinoma (HNSCC). EBioMedicine 2021; 64:103220. [PMID: 33529999 PMCID: PMC7851772 DOI: 10.1016/j.ebiom.2021.103220] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 01/03/2021] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Overexpression of epidermal growth factor receptor (EGFR), and downstream pathway activation appears to be a common oncogenic driver in the majority of head and neck squamous cell cancers (HNSCCs); yet targeting EGFR for the treatment of HNSCC has met with limited success. Apart from the anti-EGFR antibody cetuximab, no small molecule EGFR/tyrosine kinase inhibitors (TKIs) have progressed to routine clinical use. The aim of this study was to determine factors contributing to the lack of response to TKIs and identify alternative therapeutic vulnerabilities. METHODS Genomic and transcriptomic sequencing, high-throughput compound screens, overexpression and siRNA knockdown, western blot, in vivo xenograft studies. FINDINGS We derived three pairs of isogenic gefitinib (TKI)-sensitive and resistant patient-derived HNSCC cell lines. Genomic sequencing of gefitinib-resistant cell lines identified a lack of activating and resistance-associated EGFR mutations. Instead, transcriptomic sequencing showed upregulated EMT gene signature in the gefitinib-resistant cells with a corresponding increase in their migratory phenotype. Additionally, the resistant cell displayed reduced growth rate. Surprisingly, while gefitinib-resistant cells were independent of EGFR for survival, they nonetheless displayed activation of downstream ERK and AKT signalling. High-throughput screening (HTS) of druggable, small molecule libraries revealed that the gefitinib-resistant cells were particularly sensitive to inhibitors of genes involved in cell cycle and mitosis, such as Aurora kinase inhibitors (AKIs), cyclin-dependent kinase (CDK) inhibitors, and microtubule inhibitors. Notably our results showed that in the EGFR inhibited state, Aurora kinases are essential for cell survival. INTERPRETATION Our study demonstrates that in the absence of activating EGFR mutations, HNSCCs may gain resistance to gefitinib through decreased cell proliferation, which makes them exceptionally vulnerable to cell-cycle inhibitors. FUNDING Agency for Science, Technology, and Research (A*STAR), National Medical Research Council (NMRC), and the National Institutes of Health (NIH)/National Cancer Institute (NCI).
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Affiliation(s)
- Joo-Leng Low
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - Dawn Pingxi Lau
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Xiaoqian Zhang
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - Xue-Lin Kwang
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Neha Rohatgi
- Laboratory of Computational Cancer Genomics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jane Vin Chan
- Computational Phenomics Platform, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Fui-Teen Chong
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Stephen Qi Rong Wong
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - Hui-Sun Leong
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Matan Thangavelu Thangavelu
- Centre for High Throughput Phenomics (CHiP-GIS), Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Shivaji Rikka
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore; Centre for High Throughput Phenomics (CHiP-GIS), Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Anders Martin Jacobsen Skanderup
- Laboratory of Computational Cancer Genomics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Daniel Shao Weng Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Giridharan Periyasamy
- Centre for High Throughput Phenomics (CHiP-GIS), Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Judice Lie Yong Koh
- Computational Phenomics Platform, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - N Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore.
| | - Ramanuj DasGupta
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore.
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5
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Tan JL, Li F, Yeo JZ, Yong KJ, Bassal MA, Ng GH, Lee MY, Leong CY, Tan HK, Wu CS, Liu BH, Chan HM, Tan ZH, Chan YS, Wang S, Lim ZH, Toh TB, Hooi L, Low KN, Ma S, Kong NR, Stein AJ, Wu Y, Thangavelu MT, Suzuki A, Periyasamy G, Asara JM, Dan YY, Bonney GK, Chow EK, Lu GD, Ng HH, Kanagasundaram Y, Ng SB, Tam WL, Chai L, Tenen DG. Abstract 1788: A high-throughput chemical genetic screen reveals SALL4-induced metabolic vulnerabilities in cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1788] [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: 11/16/2022]
Abstract
Abstract
Transcription factors are important drivers of cancer but the development of therapeutics against these factors has had limited success. We developed a stringent high-throughput chemical genetic screening platform to identify compounds that target oncogenic transcription factor SALL4 dependency in liver cancer. The platform comprises SALL4 low- and high-expressing endogenous and engineered isogenic liver cancer cell lines. Unexpectedly, from screening 21,575 natural product extracts, the top hits were four oxidative phosphorylation inhibitors that selectively reduced SALL4-dependent cell viability. The ATP synthase inhibitor oligomycin suppressed SALL4-expressing cancer in lung and liver cancer cell culture models, and in patient-derived xenograft models of liver cancer. Oligomycin also synergized with sorafenib, the standard-of-care targeted therapy in liver cancer, to effectively suppress SALL4-driven tumorigenesis in vivo. When aberrantly expressed in cancer, SALL4 binds ~50% of mitochondrial genes, including many oxidative phosphorylation genes, to predominantly upregulate their expression. SALL4 upregulation also alters the levels of oxidative phosphorylation-related metabolites and functionally increases oxidative phosphorylation activity. Application of our endogenous/isogenic transcription factor-screening platform revealed a therapeutically actionable oxidative phosphorylation vulnerability in SALL4-expressing cancers.
Citation Format: Justin L. Tan, Feng Li, Joanna Z. Yeo, Kol Jia Yong, Mahmoud A. Bassal, Guo Hao Ng, May Yin Lee, Chung Yan Leong, Hong Kee Tan, Chan-Shuo Wu, Bee Hui Liu, Hon Man Chan, Zi Hui Tan, Yun Shen Chan, Siyu Wang, Zhi Han Lim, Tan Boon Toh, Lissa Hooi, Kia Ngee Low, Siming Ma, Nikki R. Kong, Alicia J. Stein, Yue Wu, Matan T. Thangavelu, Atsushi Suzuki, Giridharan Periyasamy, John M. Asara, Yock Young Dan, Glenn K. Bonney, Edward K. Chow, Guo-Dong Lu, Huck Hui Ng, Yoganathan Kanagasundaram, Siew Bee Ng, Wai Leong Tam, Li Chai, Daniel G. Tenen. A high-throughput chemical genetic screen reveals SALL4-induced metabolic vulnerabilities in cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1788.
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Affiliation(s)
- Justin L. Tan
- 1Genome Institute of Singapore, Singapore, Singapore
| | - Feng Li
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Joanna Z. Yeo
- 1Genome Institute of Singapore, Singapore, Singapore
| | - Kol Jia Yong
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | | | - Guo Hao Ng
- 1Genome Institute of Singapore, Singapore, Singapore
| | - May Yin Lee
- 1Genome Institute of Singapore, Singapore, Singapore
| | | | - Hong Kee Tan
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Chan-Shuo Wu
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Bee Hui Liu
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Hon Man Chan
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Zi Hui Tan
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Yun Shen Chan
- 1Genome Institute of Singapore, Singapore, Singapore
| | - Siyu Wang
- 1Genome Institute of Singapore, Singapore, Singapore
| | - Zhi Han Lim
- 1Genome Institute of Singapore, Singapore, Singapore
| | - Tan Boon Toh
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Lissa Hooi
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | | | - Siming Ma
- 1Genome Institute of Singapore, Singapore, Singapore
| | | | | | - Yue Wu
- 4Brigham & Women's Hospital, Boston, MA
| | | | | | | | | | - Yock Young Dan
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | | | - Edward K. Chow
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Guo-Dong Lu
- 2Cancer Science Institute of Singapore, Singapore, Singapore
| | - Huck Hui Ng
- 1Genome Institute of Singapore, Singapore, Singapore
| | | | - Siew Bee Ng
- 3Bioinformatics Institute, Singapore, Singapore
| | - Wai Leong Tam
- 1Genome Institute of Singapore, Singapore, Singapore
| | - Li Chai
- 4Brigham & Women's Hospital, Boston, MA
| | - Daniel G. Tenen
- 2Cancer Science Institute of Singapore, Singapore, Singapore
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6
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Kong LR, Ong RW, Tan TZ, Mohamed Salleh NAB, Thangavelu M, Chan JV, Koh LYJ, Periyasamy G, Lau JA, Le TBU, Wang L, Lee M, Kannan S, Verma CS, Lim CM, Chng WJ, Lane DP, Venkitaraman A, Hung HT, Cheok CF, Goh BC. Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation. Nat Commun 2020; 11:2086. [PMID: 32350249 PMCID: PMC7190866 DOI: 10.1038/s41467-020-15608-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 03/04/2019] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Gain of function (GOF) DNA binding domain (DBD) mutations of TP53 upregulate chromatin regulatory genes that promote genome-wide histone methylation and acetylation. Here, we therapeutically exploit the oncogenic GOF mechanisms of p53 codon 158 (Arg158) mutation, a DBD mutant found to be prevalent in lung carcinomas. Using high throughput compound screening and combination analyses, we uncover that acetylating mutp53R158G could render cancers susceptible to cisplatin-induced DNA stress. Acetylation of mutp53R158G alters DNA binding motifs and upregulates TRAIP, a RING domain-containing E3 ubiquitin ligase which dephosphorylates IĸB and impedes nuclear translocation of RelA (p65), thus repressing oncogenic nuclear factor kappa-B (NF-ĸB) signaling and inducing apoptosis. Given that this mechanism of cytotoxic vulnerability appears inapt in p53 wild-type (WT) or other hotspot GOF mutp53 cells, our work provides a therapeutic opportunity specific to Arg158-mutp53 tumors utilizing a regimen consisting of DNA-damaging agents and mutp53 acetylators, which is currently being pursued clinically. Codon 158 gain-of-function mutant p53 (158-mutp53) promotes tumourigenesis in lung cancer. Here, the authors show that 158-mutp53 render cancers sensitive to cisplatin and p53 acetylation agents through a mechanism where acetylated mutant p53 upregulates TRAIP and inhibits NF-ĸB signaling.
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Affiliation(s)
- Li Ren Kong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Medical Research Council Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK.
| | - Richard Weijie Ong
- Laboratory of Molecular Endocrinology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | | | - Matan Thangavelu
- Genome Institute of Singapore, Agency for Science, Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Jane Vin Chan
- Genome Institute of Singapore, Agency for Science, Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Lie Yong Judice Koh
- Genome Institute of Singapore, Agency for Science, Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Giridharan Periyasamy
- Genome Institute of Singapore, Agency for Science, Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Jieying Amelia Lau
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Thi Bich Uyen Le
- Laboratory of Molecular Endocrinology, National Cancer Centre Singapore, Singapore, Singapore
| | - Lingzhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Miyoung Lee
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Chwee Ming Lim
- Division of Surgical Oncology (Head and Neck Surgery), National University Cancer Institute, Singapore (NCIS), Singapore, 119074, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, 119074, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - David P Lane
- p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore, 138648, Singapore
| | - Ashok Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Huynh The Hung
- Laboratory of Molecular Endocrinology, National Cancer Centre Singapore, Singapore, Singapore
| | - Chit Fang Cheok
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore. .,Department of Haematology-Oncology, National University Cancer Institute, Singapore, 119074, Singapore.
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7
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Tan JL, Li F, Yeo JZ, Yong KJ, Bassal MA, Ng GH, Lee MY, Leong CY, Tan HK, Wu CS, Liu BH, Chan TH, Tan ZH, Chan YS, Wang S, Lim ZH, Toh TB, Hooi L, Low KN, Ma S, Kong NR, Stein AJ, Wu Y, Thangavelu MT, Suzuki A, Periyasamy G, Asara JM, Dan YY, Bonney GK, Chow EK, Lu GD, Ng HH, Kanagasundaram Y, Ng SB, Tam WL, Tenen DG, Chai L. New High-Throughput Screening Identifies Compounds That Reduce Viability Specifically in Liver Cancer Cells That Express High Levels of SALL4 by Inhibiting Oxidative Phosphorylation. Gastroenterology 2019; 157:1615-1629.e17. [PMID: 31446059 PMCID: PMC7309153 DOI: 10.1053/j.gastro.2019.08.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/18/2019] [Accepted: 08/09/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Some oncogenes encode transcription factors, but few drugs have been successfully developed to block their activity specifically in cancer cells. The transcription factor SALL4 is aberrantly expressed in solid tumor and leukemia cells. We developed a screen to identify compounds that reduce the viability of liver cancer cells that express high levels of SALL4, and we investigated their mechanisms. METHODS We developed a stringent high-throughput screening platform comprising unmodified SNU-387 and SNU-398 liver cancer cell lines and SNU-387 cell lines engineered to express low and high levels of SALL4. We screened 1597 pharmacologically active small molecules and 21,575 natural product extracts from plant, bacteria, and fungal sources for those that selectively reduce the viability of cells with high levels of SALL4 (SALL4hi cells). We compared gene expression patterns of SALL4hi cells vs SALL4-knockdown cells using RNA sequencing and real-time polymerase chain reaction analyses. Xenograft tumors were grown in NOD/SCID gamma mice from SALL4hi SNU-398 or HCC26.1 cells or from SALL4lo patient-derived xenograft (PDX) cells; mice were given injections of identified compounds or sorafenib, and the effects on tumor growth were measured. RESULTS Our screening identified 1 small molecule (PI-103) and 4 natural compound analogues (oligomycin, efrapeptin, antimycin, and leucinostatin) that selectively reduced viability of SALL4hi cells. We performed validation studies, and 4 of these compounds were found to inhibit oxidative phosphorylation. The adenosine triphosphate (ATP) synthase inhibitor oligomycin reduced the viability of SALL4hi hepatocellular carcinoma and non-small-cell lung cancer cell lines with minimal effects on SALL4lo cells. Oligomycin also reduced the growth of xenograft tumors grown from SALL4hi SNU-398 or HCC26.1 cells to a greater extent than sorafenib, but oligomycin had little effect on tumors grown from SALL4lo PDX cells. Oligomycin was not toxic to mice. Analyses of chromatin immunoprecipitation sequencing data showed that SALL4 binds approximately 50% of mitochondrial genes, including many oxidative phosphorylation genes, to activate their transcription. In comparing SALL4hi and SALL4-knockdown cells, we found SALL4 to increase oxidative phosphorylation, oxygen consumption rate, mitochondrial membrane potential, and use of oxidative phosphorylation-related metabolites to generate ATP. CONCLUSIONS In a screening for compounds that reduce the viability of cells that express high levels of the transcription factor SALL4, we identified inhibitors of oxidative phosphorylation, which slowed the growth of xenograft tumors from SALL4hi cells in mice. SALL4 activates the transcription of genes that regulate oxidative phosphorylation to increase oxygen consumption, mitochondrial membrane potential, and ATP generation in cancer cells. Inhibitors of oxidative phosphorylation might be used for the treatment of liver tumors with high levels of SALL4.
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Affiliation(s)
- Justin L Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Feng Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Joanna Z Yeo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kol Jia Yong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Mahmoud A Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Guo Hao Ng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - May Yin Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chung Yan Leong
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Hong Kee Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Chan-Shuo Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Bee Hui Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tim H Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Zi Hui Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yun Shen Chan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Siyu Wang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Zhi Han Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Tan Boon Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lissa Hooi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Kia Ngee Low
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Siming Ma
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Nikki R Kong
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Alicia J Stein
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yue Wu
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Clinical Laboratory, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Matan T Thangavelu
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Atsushi Suzuki
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Giridharan Periyasamy
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - John M Asara
- Department of Medicine, Division of Signal Transduction, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Yock Young Dan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Health System, Singapore
| | - Glenn K Bonney
- Department of Hepatobiliary, Pancreatic Surgery and Liver Transplantation, Department of Surgery, University Surgical Cluster, National University Health System, Singapore; National University Centre for Organ Transplantation, National University Hospital, Singapore
| | - Edward K Chow
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Guo-Dong Lu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China; Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education of China, Nanning, China
| | - Huck Hui Ng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Siew Bee Ng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wai Leong Tam
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts.
| | - Li Chai
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
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8
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Bharath M, Arun T, Kumar P, Netto A, Chickabasaviah Y, Periyasamy G, Sekar D. Familial amyloid polyneuropathy with transthyretin P.V173 mutation: A report of the FIRST case from India. J Neurol Sci 2019. [DOI: 10.1016/j.jns.2019.10.959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Loo SY, Toh L, Pathak E, Tan W, Ma S, Yuan J, Periyasamy G, Torta F, Chan J, Tan T, Sim YR, Tan V, Tan B, Madhukumar P, Yong WS, Ong KW, Wong CY, Wenk MR, Foo R, Yap YS, Lim E, Tam WL. Abstract B22: Inducing cell state transitions in triple-negative breast cancer (TNBC). Mol Cancer Res 2018. [DOI: 10.1158/1557-3125.advbc17-b22] [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: 11/16/2022]
Abstract
Abstract
Triple-negative breast cancer (TNBC), as immunohistochemically defined by its estrogen receptor (ER)-negative, progesterone receptor (PR)-negative and human epidermal growth factor receptor-2 (HER2)-negative status, is an important subtype due to its biologically aggressive behavior and limited treatment options available. TNBC is associated with an overall poorer prognosis, with higher risk of disease recurrence/progression and shorter duration of treatment response, i.e., treatment resistance. Treatment resistance may be largely attributed to cancer stem cells (CSCs), which are intrinsically treatment resistant and continually self-renew, proliferate, and differentiate into different phenotypes. Activation of the cell biologic program, epithelial-mesenchymal transition (EMT), has been demonstrated to promote the dedifferentiation of heterogeneous subpopulations of cancer cells towards CSC phenotypes. We hypothesized that induction of the mesenchymal-epithelial transition (MET) program might disrupt CSC function, drive differentiation, and render greater susceptibility to conventional chemotherapy. In this study, we utilized high-throughput chemical-genetic screens to uncover a potent class of MET mediators. With the use of in vitro and in vivo models of TNBC, we showed that changing the malignant cell state to a differentiated phenotype by inducing MET reduced mammosphere formation, increased chemosensitivity, and decreased the tumor burden in NSG mice. Delving into the mechanisms of tumor differentiation via ChIP-seq, RNA-seq, and Gene Ontology analysis revealed differences in metabolic status between cell states, which might be exploited in the treatment of TNBC. We also assessed combinations of MET mediators, in order to increase the potency and durability of differentiation. Hence, this study assessed the role of differentiation in the treatment of TNBC and the efficacy of various MET mediators, singly and in combination, in inducing differentiation.
Citation Format: Ser Yue Loo, Liping Toh, Elina Pathak, Wilson Tan, Siming Ma, Ju Yuan, Giridharan Periyasamy, Federico Torta, Jack Chan, Tira Tan, Yi Rong Sim, Veronique Tan, Benita Tan, Preetha Madhukumar, Wei Sean Yong, Kong Wee Ong, Chow Yin Wong, Markus R. Wenk, Roger Foo, Yoon-Sim Yap, Elaine Lim, Wai Leong Tam. Inducing cell state transitions in triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr B22.
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Affiliation(s)
- Ser Yue Loo
- 1Genome Institute of Singapore, Singapore, Singapore,
| | - Liping Toh
- 1Genome Institute of Singapore, Singapore, Singapore,
| | - Elina Pathak
- 1Genome Institute of Singapore, Singapore, Singapore,
| | - Wilson Tan
- 1Genome Institute of Singapore, Singapore, Singapore,
| | - Siming Ma
- 1Genome Institute of Singapore, Singapore, Singapore,
| | - Ju Yuan
- 1Genome Institute of Singapore, Singapore, Singapore,
| | | | - Federico Torta
- 2National University of Singapore, Singapore, Singapore,
| | - Jack Chan
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Tira Tan
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Yi Rong Sim
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Veronique Tan
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Benita Tan
- 3National Cancer Centre Singapore, Singapore, Singapore
| | | | - Wei Sean Yong
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Kong Wee Ong
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Chow Yin Wong
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Markus R. Wenk
- 2National University of Singapore, Singapore, Singapore,
| | - Roger Foo
- 1Genome Institute of Singapore, Singapore, Singapore,
| | - Yoon-Sim Yap
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Elaine Lim
- 3National Cancer Centre Singapore, Singapore, Singapore
| | - Wai Leong Tam
- 1Genome Institute of Singapore, Singapore, Singapore,
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10
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Low J, Koh J, Leong H, Lau D, Zhang X, Kwang X, Chan J, Rikka S, Tan DSW, Periyasamy G, Iyer N, Dasgupta R. A chemical genetics approach to identify therapeutic vulnerabilities in Gefitinib resistant, EGFR T790M. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx511.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Chia S, Low JL, Zhang X, Kwang XL, Chong FT, Sharma A, Bertrand D, Toh SY, Leong HS, Thangavelu MT, Hwang JSG, Lim KH, Skanthakumar T, Tan HK, Su Y, Hui Choo S, Hentze H, Tan IBH, Lezhava A, Tan P, Tan DSW, Periyasamy G, Koh JLY, Gopalakrishna Iyer N, DasGupta R. Phenotype-driven precision oncology as a guide for clinical decisions one patient at a time. Nat Commun 2017; 8:435. [PMID: 28874669 PMCID: PMC5585361 DOI: 10.1038/s41467-017-00451-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [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] [Received: 02/20/2017] [Accepted: 06/30/2017] [Indexed: 12/22/2022] Open
Abstract
Genomics-driven cancer therapeutics has gained prominence in personalized cancer treatment. However, its utility in indications lacking biomarker-driven treatment strategies remains limited. Here we present a "phenotype-driven precision-oncology" approach, based on the notion that biological response to perturbations, chemical or genetic, in ex vivo patient-individualized models can serve as predictive biomarkers for therapeutic response in the clinic. We generated a library of "screenable" patient-derived primary cultures (PDCs) for head and neck squamous cell carcinomas that reproducibly predicted treatment response in matched patient-derived-xenograft models. Importantly, PDCs could guide clinical practice and predict tumour progression in two n = 1 co-clinical trials. Comprehensive "-omics" interrogation of PDCs derived from one of these models revealed YAP1 as a putative biomarker for treatment response and survival in ~24% of oral squamous cell carcinoma. We envision that scaling of the proposed PDC approach could uncover biomarkers for therapeutic stratification and guide real-time therapeutic decisions in the future.Treatment response in patient-derived models may serve as a biomarker for response in the clinic. Here, the authors use paired patient-derived mouse xenografts and patient-derived primary culture models from head and neck squamous cell carcinomas, including metastasis, as models for high-throughput screening of anti-cancer drugs.
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Affiliation(s)
- Shumei Chia
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Joo-Leng Low
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Xiaoqian Zhang
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Xue-Lin Kwang
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Fui-Teen Chong
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Ankur Sharma
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Denis Bertrand
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Shen Yon Toh
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Hui-Sun Leong
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Matan T Thangavelu
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Jacqueline S G Hwang
- Department of Anatomical Pathology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Kok-Hing Lim
- Department of Anatomical Pathology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Thakshayeni Skanthakumar
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Hiang-Khoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Yan Su
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Siang Hui Choo
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Hannes Hentze
- Biological Resource Centre (BRC), A*STAR, 20 Biopolis Way, #07-01 Centros, Singapore, 138668, Singapore
| | - Iain B H Tan
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Alexander Lezhava
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Daniel S W Tan
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Giridharan Periyasamy
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Judice L Y Koh
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - N Gopalakrishna Iyer
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore.
| | - Ramanuj DasGupta
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore.
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12
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Sharma A, Kumar V, Cao EY, Leong HS, Hakimullah M, Ramakrishnan N, Zhang X, Chong FT, Chia S, Thangavelu MT, Wong AML, Kwang XL, Tan DSW, Periyasamy G, Gopalakrishna Iyer N, DasGupta R. Single-cell RNA-seq unveils divergent modes of chemoresistance in squamous cell carcinoma. Mech Dev 2017. [DOI: 10.1016/j.mod.2017.04.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Linding R, Kubicek S, Periyasamy G. New technologies for translational research: Applying high-content screening in cancer research and personalized medicine. Science 2015. [DOI: 10.1126/science.348.6231.246-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
New techniques and technologies are constantly being introduced that deepen our understanding of disease and therapeutic pathways. Biochemical screening methods have long been used in drug discovery labs, and more recently also in academic settings. Recent advances in both imaging technology and high throughput automation have led to the development of high-content screening (HCS) and integrated liquid handling systems that have broad application in academia and industry. These advances in image acquisition and automation have transformed numerous fields and have yielded increased data capture and throughput. This webinar will discuss how integrated HCS imaging systems that have been coupled with novel computer modeling are being applied to systems biology, translational cancer research, and personalized medicine.
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14
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Subramaniam D, Periyasamy G, Ponnurangam S, Chakrabarti D, Sugumar A, Padigaru M, Weir SJ, Balakrishnan A, Sharma S, Anant S. CDK-4 inhibitor P276 sensitizes pancreatic cancer cells to gemcitabine-induced apoptosis. Mol Cancer Ther 2012; 11:1598-608. [PMID: 22532602 DOI: 10.1158/1535-7163.mct-12-0102] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Despite advances in molecular pathogenesis, pancreatic cancer remains a major unsolved health problem. It is a rapidly invasive, metastatic tumor that is resistant to standard therapies. The phosphatidylinositol-3-kinase/Akt and mTOR signaling pathways are frequently dysregulated in pancreatic cancer. Gemcitabine is the mainstay treatment for metastatic pancreatic cancer. P276 is a novel CDK inhibitor that induces G(2)/M arrest and inhibits tumor growth in vivo models. Here, we determined that P276 sensitizes pancreatic cancer cells to gemcitabine-induced apoptosis, a mechanism-mediated through inhibition of Akt-mTOR signaling. In vitro, the combination of P276 and gemcitabine resulted in a dose- and time-dependent inhibition of proliferation and colony formation of pancreatic cancer cells but not with normal pancreatic ductal cells. This combination also induced apoptosis, as seen by activated caspase-3 and increased Bax/Bcl2 ratio. Gene profiling studies showed that this combination downregulated Akt-mTOR signaling pathway, which was confirmed by Western blot analyses. There was also a downregulation of VEGF and interleukin-8 expression suggesting effects on angiogenesis pathway. In vivo, intraperitoneal administration of the P276-Gem combination significantly suppressed the growth of pancreatic cancer tumor xenografts. There was a reduction in CD31-positive blood vessels and reduced VEGF expression, again suggesting an effect on angiogenesis. Taken together, these data suggest that P276-Gem combination is a novel potent therapeutic agent that can target the Akt-mTOR signaling pathway to inhibit both tumor growth and angiogenesis.
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Affiliation(s)
- Dharmalingam Subramaniam
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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15
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Chauthe SK, Bharate SB, Periyasamy G, Khanna A, Bhutani KK, Mishra PD, Singh IP. One pot synthesis and anticancer activity of dimeric phloroglucinols. Bioorg Med Chem Lett 2012; 22:2251-6. [DOI: 10.1016/j.bmcl.2012.01.089] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 01/05/2012] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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16
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Deshmukh SK, Mishra PD, Kulkarni-Almeida A, Verekar S, Sahoo MR, Periyasamy G, Goswami H, Khanna A, Balakrishnan A, Vishwakarma R. Anti-inflammatory and anticancer activity of ergoflavin isolated from an endophytic fungus. Chem Biodivers 2009; 6:784-9. [PMID: 19479845 DOI: 10.1002/cbdv.200800103] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Biodiversity is a major resource for identification of new molecules with specific therapeutic activities. To identify such an active resource, high throughput screening (HTS) of the extracts prepared from such diversity are examined on specific functional assays. Based on such HTS studies and bioactivity-based fractionation, we have isolated ergoflavin, a pigment from an endophytic fungus, growing on the leaves of an Indian medicinal plant Mimosops elengi (bakul). We report here the isolation, structure elucidation, and biological properties of this compound, which showed good anti-inflammatory and anticancer activities.
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Affiliation(s)
- Sunil Kumar Deshmukh
- Piramal Life Sciences Limited, 1 Nirlon Complex, Off Western Express Highway, Near NSE Complex, Goregaon (East), Mumbai, India.
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