1
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Wang Y, Narasimamurthy R, Qu M, Shi N, Guo H, Xue Y, Barker N. Circadian regulation of cancer stem cells and the tumor microenvironment during metastasis. Nat Cancer 2024:10.1038/s43018-024-00759-4. [PMID: 38654103 DOI: 10.1038/s43018-024-00759-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/07/2024] [Indexed: 04/25/2024]
Abstract
The circadian clock regulates daily rhythms of numerous physiological activities through tightly coordinated modulation of gene expression and biochemical functions. Circadian disruption is associated with enhanced tumor formation and metastasis via dysregulation of key biological processes and modulation of cancer stem cells (CSCs) and their specialized microenvironment. Here, we review how the circadian clock influences CSCs and their local tumor niches in the context of different stages of tumor metastasis. Identifying circadian therapeutic targets could facilitate the development of new treatments that leverage circadian modulation to ablate tumor-resident CSCs, inhibit tumor metastasis and enhance response to current therapies.
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Affiliation(s)
- Yu Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Neurology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rajesh Narasimamurthy
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Meng Qu
- The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Nuolin Shi
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Haidong Guo
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Yuezhen Xue
- Department of Neurology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Nick Barker
- Department of Neurology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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2
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Kagan BJ, Loeffler A, Boyd JL, Savulescu J. Embodied Neural Systems Can Enable Iterative Investigations of Morally Relevant States. J Neurosci 2024; 44:e0431242024. [PMID: 38599798 PMCID: PMC11007307 DOI: 10.1523/jneurosci.0431-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Affiliation(s)
- Brett J Kagan
- Cortical Labs, Melbourne, 3000 Victoria, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, 3010 Victoria, Australia
| | | | - J Lomax Boyd
- Berman Institute of Bioethics, Johns Hopkins University, Baltimore, Maryland 21205
| | - Julian Savulescu
- Murdoch Children's Research Institute, Melbourne, 3052 Victoria, Australia
- Melbourne Law School, University of Melbourne, Melbourne, 3053 Victoria, Australia
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119210, Singapore
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3
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Liang Q, Peng N, Xie Y, Kumar N, Gao W, Miao Y. MolPhase, an advanced prediction algorithm for protein phase separation. EMBO J 2024:10.1038/s44318-024-00090-9. [PMID: 38565952 DOI: 10.1038/s44318-024-00090-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
We introduce MolPhase, an advanced algorithm for predicting protein phase separation (PS) behavior that improves accuracy and reliability by utilizing diverse physicochemical features and extensive experimental datasets. MolPhase applies a user-friendly interface to compare distinct biophysical features side-by-side along protein sequences. By additional comparison with structural predictions, MolPhase enables efficient predictions of new phase-separating proteins and guides hypothesis generation and experimental design. Key contributing factors underlying MolPhase include electrostatic pi-interactions, disorder, and prion-like domains. As an example, MolPhase finds that phytobacterial type III effectors (T3Es) are highly prone to homotypic PS, which was experimentally validated in vitro biochemically and in vivo in plants, mimicking their injection and accumulation in the host during microbial infection. The physicochemical characteristics of T3Es dictate their patterns of association for multivalent interactions, influencing the material properties of phase-separating droplets based on the surrounding microenvironment in vivo or in vitro. Robust integration of MolPhase's effective prediction and experimental validation exhibit the potential to evaluate and explore how biomolecule PS functions in biological systems.
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Affiliation(s)
- Qiyu Liang
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Nana Peng
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Yi Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Nivedita Kumar
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Weibo Gao
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore, Singapore.
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4
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Chong LM, Wang P, Lee VV, Vijayakumar S, Tan HQ, Wang FQ, Yeoh TDYY, Truong ATL, Tan LWJ, Tan SB, Senthil Kumar K, Hau E, Vellayappan BA, Blasiak A, Ho D. Radiation therapy with phenotypic medicine: towards N-of-1 personalization. Br J Cancer 2024:10.1038/s41416-024-02653-3. [PMID: 38514762 DOI: 10.1038/s41416-024-02653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024] Open
Abstract
In current clinical practice, radiotherapy (RT) is prescribed as a pre-determined total dose divided over daily doses (fractions) given over several weeks. The treatment response is typically assessed months after the end of RT. However, the conventional one-dose-fits-all strategy may not achieve the desired outcome, owing to patient and tumor heterogeneity. Therefore, a treatment strategy that allows for RT dose personalization based on each individual response is preferred. Multiple strategies have been adopted to address this challenge. As an alternative to current known strategies, artificial intelligence (AI)-derived mechanism-independent small data phenotypic medicine (PM) platforms may be utilized for N-of-1 RT personalization. Unlike existing big data approaches, PM does not engage in model refining, training, and validation, and guides treatment by utilizing prospectively collected patient's own small datasets. With PM, clinicians may guide patients' RT dose recommendations using their responses in real-time and potentially avoid over-treatment in good responders and under-treatment in poor responders. In this paper, we discuss the potential of engaging PM to guide clinicians on upfront dose selections and ongoing adaptations during RT, as well as considerations and limitations for implementation. For practicing oncologists, clinical trialists, and researchers, PM can either be implemented as a standalone strategy or in complement with other existing RT personalizations. In addition, PM can either be used for monotherapeutic RT personalization, or in combination with other therapeutics (e.g. chemotherapy, targeted therapy). The potential of N-of-1 RT personalization with drugs will also be presented.
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Affiliation(s)
- Li Ming Chong
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 117583, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Peter Wang
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 117583, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - V Vien Lee
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore
| | - Smrithi Vijayakumar
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore
| | - Hong Qi Tan
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, 168583, Singapore
| | - Fu Qiang Wang
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, 168583, Singapore
| | | | - Anh T L Truong
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 117583, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Lester Wen Jeit Tan
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 117583, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Shi Bei Tan
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 117583, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Kirthika Senthil Kumar
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 117583, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore
| | - Eric Hau
- Department of Radiation Oncology, Westmead Hospital, Sydney, NSW, Australia
- Department of Radiation Oncology, Blacktown Haematology and Cancer Care Centre, Sydney, NSW, Australia
- Westmead Medical School, The University of Sydney, Sydney, NSW, Australia
- Centre for Cancer Research, Westmead Institute of Medical Research, Sydney, NSW, Australia
| | - Balamurugan A Vellayappan
- Department of Radiation Oncology, National University Cancer Institute, Singapore, 119074, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
| | - Agata Blasiak
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 117583, Singapore.
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore.
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.
| | - Dean Ho
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 117583, Singapore.
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore, 117456, Singapore.
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.
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5
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Li X, Ng KK, Wong JJY, Zhou JH, Yow WQ. Brain gray matter morphometry relates to onset age of bilingualism and theory of mind in young and older adults. Sci Rep 2024; 14:3193. [PMID: 38326334 PMCID: PMC10850089 DOI: 10.1038/s41598-023-48710-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/29/2023] [Indexed: 02/09/2024] Open
Abstract
Lifelong bilingualism may result in neural reserve against decline not only in the general cognitive domain, but also in social cognitive functioning. In this study, we show the brain structural correlates that are associated with second language age of acquisition (L2AoA) and theory of mind (the ability to reason about mental states) in normal aging. Participants were bilingual adults (46 young, 50 older) who completed a theory-of-mind task battery, a language background questionnaire, and an anatomical MRI scan to obtain cortical morphometric features (i.e., gray matter volume, thickness, and surface area). Findings indicated a theory-of-mind decline in older adults compared to young adults, controlling for education and general cognition. Importantly, earlier L2AoA and better theory-of-mind performance were associated with larger volume, higher thickness, and larger surface area in the bilateral temporal, medial temporal, superior parietal, and prefrontal brain regions. These regions are likely to be involved in mental representations, language, and cognitive control. The morphometric association with L2AoA in young and older adults were comparable, but its association with theory of mind was stronger in older adults than young adults. The results demonstrate that early bilingual acquisition may provide protective benefits to intact theory-of-mind abilities against normal age-related declines.
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Affiliation(s)
- Xiaoqian Li
- Humanities, Arts and Social Sciences, Singapore University of Technology and Design, Singapore, Singapore
| | - Kwun Kei Ng
- Centre for Sleep and Cognition & Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joey Ju Yu Wong
- Centre for Sleep and Cognition & Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Juan Helen Zhou
- Centre for Sleep and Cognition & Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore.
| | - W Quin Yow
- Humanities, Arts and Social Sciences, Singapore University of Technology and Design, Singapore, Singapore.
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6
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Chen Q, Chia A, Hang SK, Lim A, Koh WK, Peng Y, Gao F, Chen J, Ho Z, Wai LE, Kunasegaran K, Tan AT, Le Bert N, Loh CY, Goh YS, Renia L, Dong T, Vathsala A, Bertoletti A. Engineering immunosuppressive drug-resistant armored (IDRA) SARS-CoV-2 T cells for cell therapy. Cell Mol Immunol 2023; 20:1300-1312. [PMID: 37666955 PMCID: PMC10616128 DOI: 10.1038/s41423-023-01080-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Solid organ transplant (SOT) recipients receive immunosuppressive drugs (ISDs) and are susceptible to developing severe COVID-19. Here, we analyze the Spike-specific T-cell response after 3 doses of mRNA vaccine in a group of SOT patients (n = 136) treated with different ISDs. We demonstrate that a combination of a calcineurin inhibitor (CNI), mycophenolate mofetil (MMF), and prednisone (Pred) treatment regimen strongly suppressed the mRNA vaccine-induced Spike-specific cellular response. Such defects have clinical consequences because the magnitude of vaccine-induced Spike-specific T cells was directly proportional to the ability of SOT patients to rapidly clear SARS-CoV-2 after breakthrough infection. To then compensate for the T-cell defects induced by immunosuppressive treatment and to develop an alternative therapeutic strategy for SOT patients, we describe production of 6 distinct SARS-CoV-2 epitope-specific ISD-resistant T-cell receptor (TCR)-T cells engineered using the mRNA electroporation method with reactivity minimally affected by mutations occurring in Beta, Delta, Gamma, and Omicron variants. This strategy with transient expression characteristics marks an improvement in the immunotherapeutic field and provides an attractive and novel therapeutic possibility for immunosuppressed COVID-19 patients.
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Affiliation(s)
- Qi Chen
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Adeline Chia
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Shou Kit Hang
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Amy Lim
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
| | - Wee Kun Koh
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Fei Gao
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jili Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Zack Ho
- Lion TCR Pte Ltd, Singapore, Singapore
| | - Lu-En Wai
- Lion TCR Pte Ltd, Singapore, Singapore
| | - Kamini Kunasegaran
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Anthony Tanoto Tan
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Nina Le Bert
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Chiew Yee Loh
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yun Shan Goh
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Laurent Renia
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Anantharaman Vathsala
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Antonio Bertoletti
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore.
- Singapore Immunology Network, A*STAR, Singapore, Singapore.
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7
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Koh DHZ, Naito T, Na M, Yeap YJ, Rozario P, Zhong FL, Lim KL, Saheki Y. Visualization of accessible cholesterol using a GRAM domain-based biosensor. Nat Commun 2023; 14:6773. [PMID: 37880244 PMCID: PMC10600248 DOI: 10.1038/s41467-023-42498-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Cholesterol is important for membrane integrity and cell signaling, and dysregulation of the distribution of cellular cholesterol is associated with numerous diseases, including neurodegenerative disorders. While regulated transport of a specific pool of cholesterol, known as "accessible cholesterol", contributes to the maintenance of cellular cholesterol distribution and homeostasis, tools to monitor accessible cholesterol in live cells remain limited. Here, we engineer a highly sensitive accessible cholesterol biosensor by taking advantage of the cholesterol-sensing element (the GRAM domain) of an evolutionarily conserved lipid transfer protein, GRAMD1b. Using this cholesterol biosensor, which we call GRAM-W, we successfully visualize in real time the distribution of accessible cholesterol in many different cell types, including human keratinocytes and iPSC-derived neurons, and show differential dependencies on cholesterol biosynthesis and uptake for maintaining levels of accessible cholesterol. Furthermore, we combine GRAM-W with a dimerization-dependent fluorescent protein (ddFP) and establish a strategy for the ultrasensitive detection of accessible plasma membrane cholesterol. These tools will allow us to obtain important insights into the molecular mechanisms by which the distribution of cellular cholesterol is regulated.
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Affiliation(s)
- Dylan Hong Zheng Koh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Tomoki Naito
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Minyoung Na
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Yee Jie Yeap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Pritisha Rozario
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Franklin L Zhong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- Skin Research Institute of Singapore (SRIS), Singapore, 308232, Singapore
| | - Kah-Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- National Neuroscience Institute, Singapore, 308433, Singapore
| | - Yasunori Saheki
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, 860-0811, Japan.
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8
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Khoo BY, Hon PY, Leong J, Sai Rama Sridatta P, Thevasagayam NM, Loy SQD, Chua JJY, Ang BSP, Chow A, Marimuthu K, De PP, Ng OT, Vasoo S. Evaluation of NG-Test CARBA 5 version 2, Cepheid Xpert Carba-R, and carbapenem inactivation methods in comparison to whole-genome sequencing for the identification of carbapenemases in non-fermenting Gram-negative bacilli. J Clin Microbiol 2023; 61:e0031623. [PMID: 37671882 PMCID: PMC10512785 DOI: 10.1128/jcm.00316-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/11/2023] [Indexed: 09/07/2023] Open
Abstract
NG-Test CARBA 5 (NG-Biotech) is a rapid in vitro multiplex immunoassay for the phenotypic detection and differentiation of the "big five" carbapenemase families (KPC, OXA-48-like, VIM, IMP, and NDM). Version 2 of this assay was evaluated alongside the Xpert Carba-R assay (Cepheid, Inc.), the modified carbapenem inactivation method (mCIM), and the CIMTris assay, with a collection of carbapenem-resistant non-fermenting Gram-negative bacilli comprising 138 Pseudomonas aeruginosa and 97 Acinetobacter baumannii isolates. Whole-genome sequencing (WGS) was used as the reference standard. For P. aeruginosa, NG-Test CARBA 5 produced an overall percentage agreement (OPA) with WGS of 97.1%, compared with 92.8% forXpert Carba-R and 90.6% for mCIM. For A. baumannii, as OXA-type carbapenemases (non-OXA-48) are not included, both the NG-Test CARBA 5 and Xpert Carba-R only had an OPA of 6.2%, while the CIMTris performed well with an OPA of 99.0%. The majority of A. baumannii isolates (95.9%) tested falsely positive for IMP on NG-Test CARBA 5; no IMP genes were found on WGS. No clear cause was found for this phenomenon; a cross-reacting protein antigen unique to A. baumannii is a possible culprit. NG-Test CARBA 5 performed well for carbapenemase detection in P. aeruginosa. However, results from A. baumannii isolates should be interpreted with caution.
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Affiliation(s)
- Bo Yan Khoo
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
| | - Pei Yun Hon
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
| | - Janice Leong
- Department of Laboratory Medicine, Tan Tock Seng Hospital, , Singapore
| | | | | | - Song Qi Dennis Loy
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
| | - Jasmine J. Y. Chua
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
| | - Brenda Sze Peng Ang
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, , Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Department of Infection Prevention and Control, Tan Tock Seng Hospital, , Singapore
| | - Angela Chow
- National Centre for Infectious Diseases, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, , Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Department of Preventive and Population Medicine, Office of Clinical Epidemiology, Analytics, and Knowledge (OCEAN), Tan Tock Seng Hospital, , Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, , Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
| | - Partha Pratim De
- Department of Laboratory Medicine, Tan Tock Seng Hospital, , Singapore
| | - Oon Tek Ng
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, , Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, , Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
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9
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Zeller MA, Ma J, Wong FY, Tum S, Hidano A, Holt H, Chhay T, Sorn S, Koeut D, Seng B, Chao S, Ng GGK, Yan Z, Chou M, Rudge JW, Smith GJD, Su YCF. The genomic landscape of swine influenza A viruses in Southeast Asia. Proc Natl Acad Sci U S A 2023; 120:e2301926120. [PMID: 37552753 PMCID: PMC10438389 DOI: 10.1073/pnas.2301926120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/07/2023] [Indexed: 08/10/2023] Open
Abstract
Swine are a primary source for the emergence of pandemic influenza A viruses. The intensification of swine production, along with global trade, has amplified the transmission and zoonotic risk of swine influenza A virus (swIAV). Effective surveillance is essential to uncover emerging virus strains; however gaps remain in our understanding of the swIAV genomic landscape in Southeast Asia. More than 4,000 nasal swabs were collected from pigs in Cambodia, yielding 72 IAV-positive samples by RT-qPCR and 45 genomic sequences. We unmasked the cocirculation of multiple lineages of genetically diverse swIAV of pandemic concern. Genomic analyses revealed a novel European avian-like H1N2 swIAV reassortant variant with North American triple reassortant internal genes, that emerged approximately seven years before its first detection in pigs in 2021. Using phylogeographic reconstruction, we identified south central China as the dominant source of swine viruses disseminated to other regions in China and Southeast Asia. We also identified nine distinct swIAV lineages in Cambodia, which diverged from their closest ancestors between two and 15 B.P., indicating significant undetected diversity in the region, including reverse zoonoses of human H1N1/2009 pandemic and H3N2 viruses. A similar period of cryptic circulation of swIAVs occurred in the decades before the H1N1/2009 pandemic. The hidden diversity of swIAV observed here further emphasizes the complex underlying evolutionary processes present in this region, reinforcing the importance of genomic surveillance at the human-swine interface for early warning of disease emergence to avoid future pandemics.
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Affiliation(s)
- Michael A. Zeller
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Jordan Ma
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Sothyra Tum
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Arata Hidano
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Hannah Holt
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Ty Chhay
- Livestock Development for Community Livelihood, Phnom Penh120108, Cambodia
| | - San Sorn
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Dina Koeut
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Bunnary Seng
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Sovanncheypo Chao
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Giselle G. K. Ng
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Zhuang Yan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Monidarin Chou
- University of Health Sciences, Phnom Penh120210, Cambodia
| | - James W. Rudge
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore169857, Singapore
- SingHealth Duke-NUS Global Health Institute,SingHealth Duke-NUS Academic Medical Centre, Singapore169857, Singapore
- Duke Global Health Institute, Duke University, Durham, NC27708
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
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10
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Zhu Y, Mei Y, Baby N, Teo HY, Binte Hanafi Z, Mohd Salleh SN, Sajikumar S, Liu H. Tumor-mediated microbiota alteration impairs synaptic tagging/capture in the hippocampal CA1 area via IL-1β production. Commun Biol 2023; 6:685. [PMID: 37400621 DOI: 10.1038/s42003-023-05036-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 06/12/2023] [Indexed: 07/05/2023] Open
Abstract
Cancer patients often experience impairments in cognitive function. However, the evidence for tumor-mediated neurological impairment and detailed mechanisms are still lacking. Gut microbiota has been demonstrated to be involved in the immune system homeostasis and brain functions. Here we find that hepatocellular carcinoma (HCC) growth alters the gut microbiota and impedes the cognitive functions. The synaptic tagging and capture (STC), an associative cellular mechanism for the formation of associative memory, is impaired in the tumor-bearing mice. STC expression is rescued after microbiota sterilization. Transplantation of microbiota from HCC tumor-bearing mice induces similar STC impairment in wide type mice. Mechanistic study reveals that HCC growth significantly elevates the serum and hippocampus IL-1β levels. IL-1β depletion in the HCC tumor-bearing mice restores the STC. Taken together, these results demonstrate that gut microbiota plays a crucial role in mediating the tumor-induced impairment of the cognitive function via upregulating IL-1β production.
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Affiliation(s)
- Ying Zhu
- Immunology Translational Research Programme, Department of Microbiology of Immunology, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Yu Mei
- Immunology Translational Research Programme, Department of Microbiology of Immunology, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Nimmi Baby
- Department of Physiology, National University of Singapore, Singapore, 117597, Singapore
| | - Huey Yee Teo
- Immunology Translational Research Programme, Department of Microbiology of Immunology, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Zuhairah Binte Hanafi
- Immunology Translational Research Programme, Department of Microbiology of Immunology, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Siti Nazihah Mohd Salleh
- Human Monoclonal Antibody Platform, Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Sreedharan Sajikumar
- Department of Physiology, National University of Singapore, Singapore, 117597, Singapore.
- Life Sciences Institute Neurobiology Programme, National University of Singapore, Singapore, 117456, Singapore.
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore.
| | - Haiyan Liu
- Immunology Translational Research Programme, Department of Microbiology of Immunology, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.
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11
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Oei V, Chuang LSH, Matsuo J, Srivastava S, Teh M, Ito Y. RUNX3 inactivates oncogenic MYC through disruption of MYC/MAX complex and subsequent recruitment of GSK3β-FBXW7 cascade. Commun Biol 2023; 6:689. [PMID: 37400551 DOI: 10.1038/s42003-023-05037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/12/2023] [Indexed: 07/05/2023] Open
Abstract
MYC is one of the most commonly dysregulated proto-oncogenes in cancer. MYC promotes cancer initiation and maintenance by regulating multiple biological processes, such as proliferation and stem cell function. Here, we show that developmental regulator RUNX3 targets MYC protein for rapid degradation through the glycogen synthase kinase-3 beta-F-box/WD repeat-containing protein 7 (GSK3β-FBXW7) proteolytic pathway. The evolutionarily conserved Runt domain of RUNX3 interacts directly with the basic helix-loop-helix leucine zipper of MYC, resulting in the disruption of MYC/MAX and MYC/MIZ-1 interactions, enhanced GSK3β-mediated phosphorylation of MYC protein at threonine-58 and its subsequent degradation via the ubiquitin-proteasomal pathway. We therefore uncover a previously unknown mode of MYC destabilization by RUNX3 and provide an explanation as to why RUNX3 inhibits early-stage cancer development in gastrointestinal and lung mouse cancer models.
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Affiliation(s)
- Vincent Oei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Graduate School, Integrative Sciences and Engineering Programme, Singapore, Singapore
| | - Linda Shyue Huey Chuang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Junichi Matsuo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, Singapore
| | - Yoshiaki Ito
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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12
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Li Z, Milionis A, Zheng Y, Yee M, Codispoti L, Tan F, Poulikakos D, Yap CH. Superhydrophobic hemostatic nanofiber composites for fast clotting and minimal adhesion. Nat Commun 2019; 10:5562. [PMID: 31804481 PMCID: PMC6895059 DOI: 10.1038/s41467-019-13512-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [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: 10/26/2018] [Accepted: 11/11/2019] [Indexed: 11/17/2022] Open
Abstract
Hemostatic materials are of great importance in medicine. However, their successful implementation is still challenging as it depends on two, often counteracting, attributes; achieving blood coagulation rapidly, before significant blood loss, and enabling subsequent facile wound-dressing removal, without clot tears and secondary bleeding. Here we illustrate an approach for achieving hemostasis, rationally targeting both attributes, via a superhydrophobic surface with immobilized carbon nanofibers (CNFs). We find that CNFs promote quick fibrin growth and cause rapid clotting, and due to their superhydrophobic nature they severely limit blood wetting to prevent blood loss and drastically reduce bacteria attachment. Furthermore, minimal contact between the clot and the superhydrophobic CNF surface yields an unforced clot detachment after clot shrinkage. All these important attributes are verified in vitro and in vivo with rat experiments. Our work thereby demonstrates that this strategy for designing hemostatic patch materials has great potential.
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Affiliation(s)
- Zhe Li
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Athanasios Milionis
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Yu Zheng
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Marcus Yee
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Lukas Codispoti
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Freddie Tan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Dimos Poulikakos
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
| | - Choon Hwai Yap
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore.
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13
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Leidy-Davis T, Cheng K, Goodwin LO, Morgan JL, Juan WC, Roca X, Ong ST, Bergstrom DE. Viable Mice with Extensive Gene Humanization (25-kbp) Created Using Embryonic Stem Cell/Blastocyst and CRISPR/Zygote Injection Approaches. Sci Rep 2018; 8:15028. [PMID: 30301924 PMCID: PMC6177426 DOI: 10.1038/s41598-018-33408-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
Here, we describe an expansion of the typical DNA size limitations associated with CRISPR knock-in technology, more specifically, the physical extent to which mouse genomic DNA can be replaced with donor (in this case, human) DNA at an orthologous locus by zygotic injection. Driving our efforts was the desire to create a whole animal model that would replace 17 kilobase pairs (kbp) of the mouse Bcl2l11 gene with the corresponding 25-kbp segment of human BCL2L11, including a conditionally removable segment (2.9-kbp) of intron 2, a cryptic human exon immediately 3' of this, and a native human exon some 20 kbp downstream. Using two methods, we first carried out the replacement by employing a combination of bacterial artificial chromosome recombineering, classic embryonic stem cell (ESC) targeting, dual selection, and recombinase-driven cassette removal (ESC/Blastocyst Approach). Using a unique second method, we employed the same vector (devoid of its selectable marker cassettes), microinjecting it along with redundant single guide RNAs (sgRNAs) and Cas9 mRNA into mouse zygotes (CRISPR/Zygote Approach). In both instances, we were able to achieve humanization of Bcl2l11 to the extent designed, remove all selection cassettes, and demonstrate the functionality of the conditionally removable, loxP-flanked, 2.9-kbp intronic segment.
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Affiliation(s)
| | - Kai Cheng
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
- Genetically Engineered Models and Services, Charles River Laboratories, Wilmington, USA
| | - Leslie O Goodwin
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
| | - Judith L Morgan
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
- Center for Biometric Analysis, The Jackson Laboratory, Bar Harbor, USA
| | - Wen Chun Juan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- MSD Pharma (Singapore) Private Limited, Singapore, Republic of Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - S Tiong Ong
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
- Department of Haematology, Singapore General Hospital, Singapore, Republic of Singapore
- Department of Medical Oncology, National Cancer Centre, Singapore, Republic of Singapore
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - David E Bergstrom
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA.
- Cancer Center, The Jackson Laboratory, Bar Harbor, ME, USA.
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