1
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Ott S, Xu S, Lee N, Hong I, Anns J, Suresh DD, Zhang Z, Zhang X, Harion R, Ye W, Chandramouli V, Jesuthasan S, Saheki Y, Claridge-Chang A. Kalium channelrhodopsins effectively inhibit neurons. Nat Commun 2024; 15:3480. [PMID: 38658537 DOI: 10.1038/s41467-024-47203-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
The analysis of neural circuits has been revolutionized by optogenetic methods. Light-gated chloride-conducting anion channelrhodopsins (ACRs)-recently emerged as powerful neuron inhibitors. For cells or sub-neuronal compartments with high intracellular chloride concentrations, however, a chloride conductance can have instead an activating effect. The recently discovered light-gated, potassium-conducting, kalium channelrhodopsins (KCRs) might serve as an alternative in these situations, with potentially broad application. As yet, KCRs have not been shown to confer potent inhibitory effects in small genetically tractable animals. Here, we evaluated the utility of KCRs to suppress behavior and inhibit neural activity in Drosophila, Caenorhabditis elegans, and zebrafish. In direct comparisons with ACR1, a KCR1 variant with enhanced plasma-membrane trafficking displayed comparable potency, but with improved properties that include reduced toxicity and superior efficacy in putative high-chloride cells. This comparative analysis of behavioral inhibition between chloride- and potassium-selective silencing tools establishes KCRs as next-generation optogenetic inhibitors for in vivo circuit analysis in behaving animals.
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Affiliation(s)
- Stanislav Ott
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Sangyu Xu
- Institute for Molecular and Cell Biology, A*STAR Agency for Science, Technology and Research, Singapore, Singapore
| | - Nicole Lee
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Ivan Hong
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Jonathan Anns
- Institute for Molecular and Cell Biology, A*STAR Agency for Science, Technology and Research, Singapore, Singapore
- School of Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Danesha Devini Suresh
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Zhiyi Zhang
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Xianyuan Zhang
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Raihanah Harion
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Weiying Ye
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Vaishnavi Chandramouli
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Suresh Jesuthasan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yasunori Saheki
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Adam Claridge-Chang
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore.
- Institute for Molecular and Cell Biology, A*STAR Agency for Science, Technology and Research, Singapore, Singapore.
- Department of Pharmacy, National University of Singapore, Singapore, Singapore.
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2
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Wang F, Zhu S, Chen W, Han J, Duan R, Wang C, Dai M, Sun F, Jin Y, Wang QJ. Multidimensional detection enabled by twisted black arsenic-phosphorus homojunctions. Nat Nanotechnol 2024; 19:455-462. [PMID: 38225358 DOI: 10.1038/s41565-023-01593-y] [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: 05/04/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024]
Abstract
A light field carrying multidimensional optical information, including but not limited to polarization, intensity and wavelength, is essential for numerous applications such as environmental monitoring, thermal imaging, medical diagnosis and free-space communications. Simultaneous acquisition of this multidimensional information could provide comprehensive insights for understanding complex environments but remains a challenge. Here we demonstrate a multidimensional optical information detection device based on zero-bias double twisted black arsenic-phosphorus homojunctions, where the photoresponse is dominated by the photothermoelectric effect. By using a bipolar and phase-offset polarization photoresponse, the device operated in the mid-infrared range can simultaneously detect both the polarization angle and incident intensity information through direct measurement of the photocurrents in the double twisted black arsenic-phosphorus homojunctions. The device's responsivity makes it possible to retrieve wavelength information, typically perceived as difficult to obtain. Moreover, the device exhibits an electrically tunable polarization photoresponse, enabling precise distinction of polarization angles under low-intensity light exposure. These demonstrations offer a promising approach for simultaneous detection of multidimensional optical information, indicating potential for diverse photonic applications.
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Affiliation(s)
- Fakun Wang
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Song Zhu
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Wenduo Chen
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jiayue Han
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ruihuan Duan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Chongwu Wang
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Mingjin Dai
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Fangyuan Sun
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yuhao Jin
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qi Jie Wang
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore.
- Centre for Disruptive Photonic Technologies, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
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3
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Ang DA, Carter JM, Deka K, Tan JHL, Zhou J, Chen Q, Chng WJ, Harmston N, Li Y. Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma. Nat Commun 2024; 15:2513. [PMID: 38514625 PMCID: PMC10957915 DOI: 10.1038/s41467-024-46728-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
In multiple myeloma, abnormal plasma cells establish oncogenic niches within the bone marrow by engaging the NF-κB pathway to nurture their survival while they accumulate pro-proliferative mutations. Under these conditions, many cases eventually develop genetic abnormalities endowing them with constitutive NF-κB activation. Here, we find that sustained NF-κB/p52 levels resulting from such mutations favours the recruitment of enhancers beyond the normal B-cell repertoire. Furthermore, through targeted disruption of p52, we characterise how such enhancers are complicit in the formation of super-enhancers and the establishment of cis-regulatory interactions with myeloma dependencies during constitutive activation of p52. Finally, we functionally validate the pathological impact of these cis-regulatory modules on cell and tumour phenotypes using in vitro and in vivo models, confirming RGS1 as a p52-dependent myeloma driver. We conclude that the divergent epigenomic reprogramming enforced by aberrant non-canonical NF-κB signalling potentiates transcriptional programs beneficial for multiple myeloma progression.
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Affiliation(s)
- Daniel A Ang
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jean-Michel Carter
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Kamalakshi Deka
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Joel H L Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
- NUS Centre for Cancer Research, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
- NUS Centre for Cancer Research, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore
| | - Nathan Harmston
- Division of Science, Yale-NUS College, Singapore, 138527, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
- Molecular Biosciences Division, Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
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4
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Zhou X, Seow WY, Ha N, Cheng TH, Jiang L, Boonruangkan J, Goh JJL, Prabhakar S, Chou N, Chen KH. Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes. Nat Commun 2024; 15:2342. [PMID: 38491027 PMCID: PMC10943009 DOI: 10.1038/s41467-024-46669-y] [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: 08/11/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
High-dimensional, spatially resolved analysis of intact tissue samples promises to transform biomedical research and diagnostics, but existing spatial omics technologies are costly and labor-intensive. We present Fluorescence In Situ Hybridization of Cellular HeterogeneIty and gene expression Programs (FISHnCHIPs) for highly sensitive in situ profiling of cell types and gene expression programs. FISHnCHIPs achieves this by simultaneously imaging ~2-35 co-expressed genes (clustered into modules) that are spatially co-localized in tissues, resulting in similar spatial information as single-gene Fluorescence In Situ Hybridization (FISH), but with ~2-20-fold higher sensitivity. Using FISHnCHIPs, we image up to 53 modules from the mouse kidney and mouse brain, and demonstrate high-speed, large field-of-view profiling of a whole tissue section. FISHnCHIPs also reveals spatially restricted localizations of cancer-associated fibroblasts in a human colorectal cancer biopsy. Overall, FISHnCHIPs enables fast, robust, and scalable cell typing of tissues with normal physiology or undergoing pathogenesis.
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Affiliation(s)
- Xinrui Zhou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Wan Yi Seow
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Norbert Ha
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Teh How Cheng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Lingfan Jiang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jeeranan Boonruangkan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jolene Jie Lin Goh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Nigel Chou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.
| | - Kok Hao Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.
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5
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Preedy MK, White MRH, Tergaonkar V. Cellular heterogeneity in TNF/TNFR1 signalling: live cell imaging of cell fate decisions in single cells. Cell Death Dis 2024; 15:202. [PMID: 38467621 PMCID: PMC10928192 DOI: 10.1038/s41419-024-06559-z] [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: 09/29/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024]
Abstract
Cellular responses to TNF are inherently heterogeneous within an isogenic cell population and across different cell types. TNF promotes cell survival by activating pro-inflammatory NF-κB and MAPK signalling pathways but may also trigger apoptosis and necroptosis. Following TNF stimulation, the fate of individual cells is governed by the balance of pro-survival and pro-apoptotic signalling pathways. To elucidate the molecular mechanisms driving heterogenous responses to TNF, quantifying TNF/TNFR1 signalling at the single-cell level is crucial. Fluorescence live-cell imaging techniques offer real-time, dynamic insights into molecular processes in single cells, allowing for detection of rapid and transient changes, as well as identification of subpopulations, that are likely to be missed with traditional endpoint assays. Whilst fluorescence live-cell imaging has been employed extensively to investigate TNF-induced inflammation and TNF-induced cell death, it has been underutilised in studying the role of TNF/TNFR1 signalling pathway crosstalk in guiding cell-fate decisions in single cells. Here, we outline the various opportunities for pathway crosstalk during TNF/TNFR1 signalling and how these interactions may govern heterogenous responses to TNF. We also advocate for the use of live-cell imaging techniques to elucidate the molecular processes driving cell-to-cell variability in single cells. Understanding and overcoming cellular heterogeneity in response to TNF and modulators of the TNF/TNFR1 signalling pathway could lead to the development of targeted therapies for various diseases associated with aberrant TNF/TNFR1 signalling, such as rheumatoid arthritis, metabolic syndrome, and cancer.
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Affiliation(s)
- Marcus K Preedy
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, D3308, Dover Street, Manchester, M13 9PT, England, UK
| | - Michael R H White
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, D3308, Dover Street, Manchester, M13 9PT, England, UK.
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, MD7, Singapore, 117596, Singapore.
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6
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Liu M, Bertolazzi G, Sridhar S, Lee RX, Jaynes P, Mulder K, Syn N, Hoppe MM, Fan S, Peng Y, Thng J, Chua R, Jayalakshmi, Batumalai Y, De Mel S, Poon L, Chan EHL, Lee J, Hue SSS, Chang ST, Chuang SS, Chandy KG, Ye X, Pan-Hammarström Q, Ginhoux F, Chee YL, Ng SB, Tripodo C, Jeyasekharan AD. Spatially-resolved transcriptomics reveal macrophage heterogeneity and prognostic significance in diffuse large B-cell lymphoma. Nat Commun 2024; 15:2113. [PMID: 38459052 PMCID: PMC10923916 DOI: 10.1038/s41467-024-46220-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
Macrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Macrophage estimation by immunohistochemistry shows varying prognostic significance across studies in DLBCL, and does not provide a comprehensive analysis of macrophage subtypes. Here, using digital spatial profiling with whole transcriptome analysis of CD68+ cells, we characterize macrophages in distinct spatial niches of reactive lymphoid tissues (RLTs) and DLBCL. We reveal transcriptomic differences between macrophages within RLTs (light zone /dark zone, germinal center/ interfollicular), and between disease states (RLTs/ DLBCL), which we then use to generate six spatially-derived macrophage signatures (MacroSigs). We proceed to interrogate these MacroSigs in macrophage and DLBCL single-cell RNA-sequencing datasets, and in gene-expression data from multiple DLBCL cohorts. We show that specific MacroSigs are associated with cell-of-origin subtypes and overall survival in DLBCL. This study provides a spatially-resolved whole-transcriptome atlas of macrophages in reactive and malignant lymphoid tissues, showing biological and clinical significance.
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Affiliation(s)
- Min Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Radiation Oncology, Chongqing University Cancer Hospital, Chongqing, PR China
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Giorgio Bertolazzi
- Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Shruti Sridhar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Rui Xue Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Kevin Mulder
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Nicholas Syn
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michal Marek Hoppe
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jocelyn Thng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Reiya Chua
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Jayalakshmi
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Yogeshini Batumalai
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Sanjay De Mel
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Limei Poon
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Esther Hian Li Chan
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joanne Lee
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Susan Swee-Shan Hue
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sheng-Tsung Chang
- Department of Pathology, Chi-Mei Medical Center, Tainan City, Taiwan, ROC
| | - Shih-Sung Chuang
- Department of Pathology, Chi-Mei Medical Center, Tainan City, Taiwan, ROC
| | - K George Chandy
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Xiaofei Ye
- Kindstar Global Precision Medicine Institute, Wuhan, PR China
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Yen Lin Chee
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
- Histopathology Unit, Institute of Molecular Oncology Foundation (IFOM) ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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7
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Lum FM, Chan YH, Teo TH, Becht E, Amrun SN, Teng KW, Hartimath SV, Yeo NK, Yee WX, Ang N, Torres-Ruesta AM, Fong SW, Goggi JL, Newell EW, Renia L, Carissimo G, Ng LF. Crosstalk between CD64 +MHCII + macrophages and CD4 + T cells drives joint pathology during chikungunya. EMBO Mol Med 2024; 16:641-663. [PMID: 38332201 PMCID: PMC10940729 DOI: 10.1038/s44321-024-00028-y] [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: 07/26/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Communications between immune cells are essential to ensure appropriate coordination of their activities. Here, we observed the infiltration of activated macrophages into the joint-footpads of chikungunya virus (CHIKV)-infected animals. Large numbers of CD64+MHCII+ and CD64+MHCII- macrophages were present in the joint-footpad, preceded by the recruitment of their CD11b+Ly6C+ inflammatory monocyte precursors. Recruitment and differentiation of these myeloid subsets were dependent on CD4+ T cells and GM-CSF. Transcriptomic and gene ontology analyses of CD64+MHCII+ and CD64+MHCII- macrophages revealed 89 differentially expressed genes, including genes involved in T cell proliferation and differentiation pathways. Depletion of phagocytes, including CD64+MHCII+ macrophages, from CHIKV-infected mice reduced disease pathology, demonstrating that these cells play a pro-inflammatory role in CHIKV infection. Together, these results highlight the synergistic dynamics of immune cell crosstalk in driving CHIKV immunopathogenesis. This study provides new insights in the disease mechanism and offers opportunities for development of novel anti-CHIKV therapeutics.
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Affiliation(s)
- Fok-Moon Lum
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore.
| | - Yi-Hao Chan
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Teck-Hui Teo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Etienne Becht
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Siti Naqiah Amrun
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Karen Ww Teng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Siddesh V Hartimath
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Nicholas Kw Yeo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Wearn-Xin Yee
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Nicholas Ang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Anthony M Torres-Ruesta
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Julian L Goggi
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Guillaume Carissimo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Lisa Fp Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZX, UK.
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8
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Luah YH, Wu T, Cheow LF. Identification, sorting and profiling of functional killer cells via the capture of fluorescent target-cell lysate. Nat Biomed Eng 2024; 8:248-262. [PMID: 37652987 DOI: 10.1038/s41551-023-01089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/04/2023] [Indexed: 09/02/2023]
Abstract
Assays for assessing cell-mediated cytotoxicity are largely target-cell-centric and cannot identify and isolate subpopulations of cytotoxic effector cells. Here we describe an assay compatible with flow cytometry for the accurate identification and sorting of functional killer-cell subpopulations in co-cultures. The assay, which we named PAINTKiller (for 'proximity affinity intracellular transfer identification of killer cells'), relies on the detection of an intracellular fluorescent protein 'painted' by a lysed cell on the surface of the lysing cytotoxic cell (specifically, on cell lysis the intracellular fluorescein derivative carboxyfluorescein succinimidyl ester is captured on the surface of the natural killer cell by an antibody for anti-fluorescein isothiocyanate linked to an antibody for the pan-leucocyte surface receptor CD45). The assay can be integrated with single-cell RNA sequencing for the analysis of molecular pathways associated with cell cytotoxicity and may be used to uncover correlates of functional immune responses.
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Affiliation(s)
- Yen Hoon Luah
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Critical Analytics for Manufacturing of Personalized-Medicine Interdisciplinary Research Group, Singapore-MIT Alliance in Research and Technology, Singapore, Singapore
| | - Tongjin Wu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Lih Feng Cheow
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
- Critical Analytics for Manufacturing of Personalized-Medicine Interdisciplinary Research Group, Singapore-MIT Alliance in Research and Technology, Singapore, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
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9
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Cheung CMG. Macular neovascularization and polypoidal choroidal vasculopathy: phenotypic variations, pathogenic mechanisms and implications in management. Eye (Lond) 2024; 38:659-667. [PMID: 37803144 PMCID: PMC10920817 DOI: 10.1038/s41433-023-02764-w] [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: 08/30/2023] [Revised: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023] Open
Abstract
Advances in imaging have led to improved ability to characterize variations in clinical sub-phenotypes of macular neovascularization (MNV) in Age-related macular degeneration (AMD). Polypoidal choroidal vasculopathy (PCV) was initially described based on characteristic features observed in indocyanine green angiography (ICGA) and was thought to be a distinct entity from AMD. However, subsequent careful observations based on confocal scanning laser ophthalmoscopy-based ICGA, optical coherence tomography (OCT) and OCT angiography have led researchers to appreciate similarities between PCV lesion and type 1 MNV in typical neovascular AMD. Concurrently, clinical trials have shown that anti-VEGF monotherapy can achieve favourable visual outcome in the majority of eyes with PCV. These learnings have led to a shift in the way PCV is managed over the past decade. Recent studies have supported the use of non-ICGA based imaging modality to screen for PCV and the adoption of anti-VEGF monotherapy as initial therapy for PCV. A focus of recent research has been in the understanding of the role of choroidal alterations in the pathogenesis of PCV. The concept of pachychoroid in leading to outer retinal ischemia has garnered increasing support. Future research in this area should evaluate the potential of choroidal morphology in guiding personalized therapy in PCV.
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Affiliation(s)
- Chui Ming Gemmy Cheung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.
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10
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Singhal V, Chou N, Lee J, Yue Y, Liu J, Chock WK, Lin L, Chang YC, Teo EML, Aow J, Lee HK, Chen KH, Prabhakar S. BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis. Nat Genet 2024; 56:431-441. [PMID: 38413725 PMCID: PMC10937399 DOI: 10.1038/s41588-024-01664-3] [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: 04/03/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Spatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local neighborhood transcriptome, representing cell state and microenvironment, respectively. BANKSY's spatial feature augmentation strategy improved performance on both tasks when tested on diverse RNA (imaging, sequencing) and protein (imaging) datasets. BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can also be used for quality control of spatial transcriptomics data and for spatially aware batch effect correction. Importantly, it is substantially faster and more scalable than existing methods, enabling the processing of millions of cell datasets. In summary, BANKSY provides an accurate, biologically motivated, scalable and versatile framework for analyzing spatially resolved omics data.
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Affiliation(s)
- Vipul Singhal
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Nigel Chou
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Joseph Lee
- Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Yifei Yue
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Republic of Singapore
| | - Jinyue Liu
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Wan Kee Chock
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Li Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | | | | | - Jonathan Aow
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Hwee Kuan Lee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- School of Computing, National University of Singapore, Singapore, Republic of Singapore
- Singapore Eye Research Institute, Singapore, Republic of Singapore
- International Research Laboratory on Artificial Intelligence, Singapore, Republic of Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Kok Hao Chen
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
| | - Shyam Prabhakar
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Population and Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore.
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11
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Xiao B, Kuruvilla J, Tan EK. Resilience conferred by APOE-R136S: a defense bestowed by nature to combat Alzheimer's disease. Signal Transduct Target Ther 2024; 9:52. [PMID: 38424046 PMCID: PMC10904861 DOI: 10.1038/s41392-024-01775-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Bin Xiao
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore.
- Neuroscience Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.
| | - Joshua Kuruvilla
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore
| | - Eng-King Tan
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore.
- Neuroscience Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.
- Neuroscience and Behavioural Disorders Program, Duke-NUS Medical School, Singapore, Singapore.
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12
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Chang KC, Nagarajan N, Gan YH. Short-chain fatty acids of various lengths differentially inhibit Klebsiella pneumoniae and Enterobacteriaceae species. mSphere 2024; 9:e0078123. [PMID: 38305176 PMCID: PMC10900885 DOI: 10.1128/msphere.00781-23] [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: 12/15/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
The gut microbiota is inextricably linked to human health and disease. It can confer colonization resistance against invading pathogens either through niche occupation and nutrient competition or via its secreted metabolites. Short-chain fatty acids (SCFA) are the primary metabolites in the gut as a result of dietary fiber fermentation by the gut microbiota. In this work, we demonstrate that the interaction of single-species gut commensals on solid media is insufficient for pathogen inhibition, but supernatants from monocultures of these commensal bacteria enriched in acetate confer inhibition against anaerobic growth of the enteric pathogen Klebsiella pneumoniae. The three primary SCFAs (acetate, propionate, and butyrate) strongly inhibit the intestinal commensal Escherichia coli Nissle as well as a panel of enteric pathogens besides K. pneumoniae at physiological pH of the cecum and ascending colon. This inhibition was significantly milder on anaerobic gut commensals Bacteroides thetaiotaomicron and Bifidobacterium adolescentis previously demonstrated to be associated with microbiota recovery after antibiotic-induced dysbiosis. We describe a general suppression of bacterial membrane potential by these SCFAs at physiological cecum and ascending colonic pH. Furthermore, the strength of bacterial inhibition increases with increasing alkyl chain length. Overall, the insights gained in this study shed light on the potential therapeutic use of SCFAs for conferring colonization resistance against invading pathogens in a dysbiotic gut.IMPORTANCERising antimicrobial resistance has made treatment of bacterial infections increasingly difficult. According to the World Health Organization, it has become a burgeoning threat to hospital and public health systems worldwide. This threat is largely attributed to the global rise of carbapenem-resistant Enterobacteriaceae in recent years, with common hospital-acquired pathogens growing increasingly resistant to last-line antibiotics. Antibiotics disrupt the homeostatic balance of the gut microbiota, resulting in the loss of colonization resistance against enteric pathogens. This work describes the ability of short-chain fatty acids (SCFAs) produced by gut microbiota to be effective against a wide panel of enteric pathogens without major impact on common gut commensal species. We also demonstrate a previously undescribed link between alkyl chain length and antibacterial effects of SCFAs. SCFAs, thus, hold promise as an alternative therapeutic option leveraging on the antimicrobial activity of these endogenously produced gut metabolites without disrupting gut microbiota homeostasis.
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Affiliation(s)
- Kai Chirng Chang
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Niranjan Nagarajan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yunn-Hwen Gan
- Department of Biochemistry, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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13
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Chong JSX, Chua KY, Ng KK, Chong SW, Leong RLF, Chee MWL, Koh WP, Zhou JH. Higher handgrip strength is linked to higher salience ventral attention functional network segregation in older adults. Commun Biol 2024; 7:214. [PMID: 38383572 PMCID: PMC10881588 DOI: 10.1038/s42003-024-05862-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Converging evidence suggests that handgrip strength is linked to cognition in older adults, and this may be subserved by shared age-related changes in brain function and structure. However, the interplay among handgrip strength, brain functional connectivity, and cognitive function remains poorly elucidated. Hence, our study sought to examine these relationships in 148 community-dwelling older adults. Specifically, we examined functional segregation, a measure of functional brain organization sensitive to ageing and cognitive decline, and its associations with handgrip strength and cognitive function. We showed that higher handgrip strength was related to better processing speed, attention, and global cognition. Further, higher handgrip strength was associated with higher segregation of the salience/ventral attention network, driven particularly by higher salience/ventral attention intra-network functional connectivity of the right anterior insula to the left posterior insula/frontal operculum and right midcingulate/medial parietal cortex. Importantly, these handgrip strength-related inter-individual differences in salience/ventral attention network functional connectivity were linked to cognitive function, as revealed by functional decoding and brain-cognition association analyses. Our findings thus highlight the importance of the salience/ventral attention network in handgrip strength and cognition, and suggest that inter-individual differences in salience/ventral attention network segregation and intra-network connectivity could underpin the handgrip strength-cognition relationship in older adults.
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Affiliation(s)
- Joanna Su Xian Chong
- Centre for Sleep and Cognition & Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kevin Yiqiang Chua
- Integrative Sciences and Engineering Programme (ISEP), NUS Graduate School, National University of Singapore, 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
| | - Shin Wee Chong
- Centre for Sleep and Cognition & Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ruth L F Leong
- Centre for Sleep and Cognition & Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michael W L Chee
- Centre for Sleep and Cognition & Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Woon Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), 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.
- Integrative Sciences and Engineering Programme (ISEP), NUS Graduate School, National University of Singapore, Singapore, Singapore.
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore.
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14
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Wu Y, Teh YC, Chong SZ. Going Full TeRM: The Seminal Role of Tissue-Resident Macrophages in Organ Remodeling during Pregnancy and Lactation. J Immunol 2024; 212:513-521. [PMID: 38315948 DOI: 10.4049/jimmunol.2300560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/23/2023] [Indexed: 02/07/2024]
Abstract
During pregnancy and lactation, the uterus and mammary glands undergo remarkable structural changes to perform their critical reproductive functions before reverting to their original dormant state upon childbirth and weaning, respectively. Underlying this incredible plasticity are complex remodeling processes that rely on coordinated decisions at both the cellular and tissue-subunit levels. With their exceptional versatility, tissue-resident macrophages play a variety of supporting roles in these organs during each stage of development, ranging from maintaining immune homeostasis to facilitating tissue remodeling, although much remains to be discovered about the identity and regulation of individual macrophage subsets. In this study, we review the increasingly appreciated contributions of these immune cells to the reproductive process and speculate on future lines of inquiry. Deepening our understanding of their interactions with the parenchymal or stromal populations in their respective niches may reveal new strategies to ameliorate complications in pregnancy and breastfeeding, thereby improving maternal health and well-being.
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Affiliation(s)
- Yixuan Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Ye Chean Teh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Shu Zhen Chong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
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15
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Suda K, Okabe A, Matsuo J, Chuang LSH, Li Y, Jangphattananont N, Mon NN, Myint KN, Yamamura A, So JBY, Voon DCC, Yang H, Yeoh KG, Kaneda A, Ito Y. Aberrant Upregulation of RUNX3 Activates Developmental Genes to Drive Metastasis in Gastric Cancer. Cancer Res Commun 2024; 4:279-292. [PMID: 38240752 PMCID: PMC10836196 DOI: 10.1158/2767-9764.crc-22-0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/08/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Gastric cancer metastasis is a major cause of mortality worldwide. Inhibition of RUNX3 in gastric cancer cell lines reduced migration, invasion, and anchorage-independent growth in vitro. Following splenic inoculation, CRISPR-mediated RUNX3-knockout HGC-27 cells show suppression of xenograft growth and liver metastasis. We interrogated the potential of RUNX3 as a metastasis driver in gastric cancer by profiling its target genes. Transcriptomic analysis revealed strong involvement of RUNX3 in the regulation of multiple developmental pathways, consistent with the notion that Runt domain transcription factor (RUNX) family genes are master regulators of development. RUNX3 promoted "cell migration" and "extracellular matrix" programs, which are necessary for metastasis. Of note, we found pro-metastatic genes WNT5A, CD44, and VIM among the top differentially expressed genes in RUNX3 knockout versus control cells. Chromatin immunoprecipitation sequencing and HiChIP analyses revealed that RUNX3 bound to the enhancers and promoters of these genes, suggesting that they are under direct transcriptional control by RUNX3. We show that RUNX3 promoted metastasis in part through its upregulation of WNT5A to promote migration, invasion, and anchorage-independent growth in various malignancies. Our study therefore reveals the RUNX3-WNT5A axis as a key targetable mechanism for gastric cancer metastasis. SIGNIFICANCE Subversion of RUNX3 developmental gene targets to metastasis program indicates the oncogenic nature of inappropriate RUNX3 regulation in gastric cancer.
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Affiliation(s)
- Kazuto Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Junichi Matsuo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Naing Naing Mon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Khine Nyein Myint
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Akihiro Yamamura
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jimmy Bok-Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dominic Chih-Cheng Voon
- Innovative Cancer Model Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Japan
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshiaki Ito
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
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16
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Ma W, Ahmad SAI, Hashimoto M, Khalilnezhad A, Kataoka M, Arima Y, Tanaka Y, Yanagi S, Umemoto T, Suda T. MITOL deficiency triggers hematopoietic stem cell apoptosis via ER stress response. EMBO J 2024; 43:339-361. [PMID: 38238476 PMCID: PMC10897143 DOI: 10.1038/s44318-024-00029-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024] Open
Abstract
Hematopoietic stem cell (HSC) divisional fate and function are determined by cellular metabolism, yet the contribution of specific cellular organelles and metabolic pathways to blood maintenance and stress-induced responses in the bone marrow remains poorly understood. The outer mitochondrial membrane-localized E3 ubiquitin ligase MITOL/MARCHF5 (encoded by the Mitol gene) is known to regulate mitochondrial and endoplasmic reticulum (ER) interaction and to promote cell survival. Here, we investigated the functional involvement of MITOL in HSC maintenance by generating MX1-cre inducible Mitol knockout mice. MITOL deletion in the bone marrow resulted in HSC exhaustion and impairment of bone marrow reconstitution capability in vivo. Interestingly, MITOL loss did not induce major mitochondrial dysfunction in hematopoietic stem and progenitor cells. In contrast, MITOL deletion induced prolonged ER stress in HSCs, which triggered cellular apoptosis regulated by IRE1α. In line, dampening of ER stress signaling by IRE1α inihibitor KIRA6 partially rescued apoptosis of long-term-reconstituting HSC. In summary, our observations indicate that MITOL is a principal regulator of hematopoietic homeostasis and protects blood stem cells from cell death through its function in ER stress signaling.
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Affiliation(s)
- Wenjuan Ma
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan
| | - Shah Adil Ishtiyaq Ahmad
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Michihiro Hashimoto
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan
| | - Ahad Khalilnezhad
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan
| | - Miho Kataoka
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan
| | - Yuichiro Arima
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan
| | - Yosuke Tanaka
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan
| | - Shigeru Yanagi
- Laboratory of Molecular Biochemistry, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Terumasa Umemoto
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan.
| | - Toshio Suda
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, 8620811, Japan.
- Cancer Science Institute of Singapore, National University of Singapore; Centre for Translation Medicine, Singapore, 117599, Singapore.
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17
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Tan CAZ, Chong KKL, Yeong DYX, Ng CHM, Ismail MH, Yap ZH, Khetrapal V, Tay VSY, Drautz-Moses DI, Ali Y, Chen SL, Kline KA. Purine and carbohydrate availability drive Enterococcus faecalis fitness during wound and urinary tract infections. mBio 2024; 15:e0238423. [PMID: 38078746 PMCID: PMC10790769 DOI: 10.1128/mbio.02384-23] [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: 09/14/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Although E. faecalis is a common wound pathogen, its pathogenic mechanisms during wound infection are unexplored. Here, combining a mouse wound infection model with in vivo transposon and RNA sequencing approaches, we identified the E. faecalis purine biosynthetic pathway and galactose/mannose MptABCD phosphotransferase system as essential for E. faecalis acute replication and persistence during wound infection, respectively. The essentiality of purine biosynthesis and the MptABCD PTS is driven by the consumption of purine metabolites by E. faecalis during acute replication and changing carbohydrate availability during the course of wound infection. Overall, our findings reveal the importance of the wound microenvironment in E. faecalis wound pathogenesis and how these metabolic pathways can be targeted to better control wound infections.
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Affiliation(s)
- Casandra Ai Zhu Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daryl Yu Xuan Yeong
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Celine Hui Min Ng
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Zhei Hwee Yap
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Varnica Khetrapal
- Infectious Diseases Translational Research Programme, Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vanessa Shi Yun Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, Singapore
| | - Swaine L. Chen
- Infectious Diseases Translational Research Programme, Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore, Singapore
| | - Kimberly A. Kline
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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18
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Huang J, Kee MZL, Law EC, Sum KK, Silveira PP, Godfrey KM, Daniel LM, Tan KH, Chong YS, Chan SY, Eriksson JG, Meaney MJ, Huang JY. Parental and child genetic burden of glycaemic dysregulation and early-life cognitive development: an Asian and European prospective cohort study. Transl Psychiatry 2024; 14:2. [PMID: 38177108 PMCID: PMC10766615 DOI: 10.1038/s41398-023-02694-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024] Open
Abstract
Insulin resistance and glucose metabolism have been associated with neurodevelopmental disorders. However, in the metabolically more susceptible Asian populations, it is not clear whether the genetic burden of glycaemic dysregulation influences early-life neurodevelopment. In a multi-ethnic Asian prospective cohort study in Singapore (Growing Up in Singapore Towards healthy Outcomes (GUSTO)), we constructed child and parental polygenic risk scores (PRS) for glycaemic dysregulation based on the largest genome-wide association studies of type 2 diabetes and fasting glucose among Asians. We found that child PRS for HOMA-IR was associated with a lower perceptual reasoning score at ~7 years (β = -0. 141, p-value = 0.024, 95% CI -0. 264 to -0. 018) and a lower WIAT-III mean score at ~9 years (β = -0.222, p-value = 0.001, 95% CI -0.357 to -0.087). This association were consistent in direction among boys and girls. These inverse associations were not influenced by parental PRS and were likely mediated via insulin resistance rather than mediators such as birth weight and childhood body mass index. Higher paternal PRS for HOMA-IR was suggestively associated with lower child perceptual reasoning at ~7 years (β = -0.172, p-value = 0.002, 95% CI -0.280 to -0.064). Replication analysis in a European cohort, the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort, showed that higher child PRS for fasting glucose was associated with lower verbal IQ score while higher maternal PRS for insulin resistance was associated with lower performance IQ score in their children at ~8.5 years. In summary, our findings suggest that higher child PRS for HOMA-IR was associated with lower cognitive scores in both Asian and European replication cohorts. Differential findings between cohorts may be attributed to genetic and environmental factors. Further investigation of the functions of the genetic structure and ancestry-specific PRS and a more comprehensive investigation of behavioural mediators may help to understand these findings better.
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Affiliation(s)
- Jian Huang
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK.
| | - Michelle Z L Kee
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Evelyn C Law
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Ka Kei Sum
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Patricia Pelufo Silveira
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Psychiatry, Faculty of Medicine and Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, McGill University, Montreal, Quebec, Canada
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Centre and NIHR Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Lourdes Mary Daniel
- Department of Child Development, KK Women's and Children's Hospital, Singapore, Singapore
| | - Kok Hian Tan
- Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Obstetrics & Gynaecology, National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
| | - Shiao-Yng Chan
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Johan G Eriksson
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of general practice and primary health care, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Psychiatry, Faculty of Medicine and Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, McGill University, Montreal, Quebec, Canada
- Brain-Body Initiative, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jonathan Yinhao Huang
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore
- Thompson School of Social Work & Public Health, Office of Public Health Studies, University of Hawai'i at Mānoa, Honolulu, HI, USA
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19
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Affiliation(s)
- Darren Shu Jeng Ting
- Birmingham and Midland Eye Centre, Birmingham, UK
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, UK
| | - Ting Fang Tan
- Artificial Intelligence and Digital Innovation Research Group, Singapore Eye Research Institute, Singapore, Singapore
- Singapore National Eye Centre, Singapore, Singapore
| | - Daniel Shu Wei Ting
- Artificial Intelligence and Digital Innovation Research Group, Singapore Eye Research Institute, Singapore, Singapore.
- Singapore National Eye Centre, Singapore, Singapore.
- Department of Ophthalmology and Visual Sciences, Duke-National University of Singapore Medical School, Singapore, Singapore.
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20
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Feng Z, Zhang X, Zhou J, Li Q, Chu L, Di G, Xu Z, Chen Q, Wang M, Jiang X, Xia H, Chen X. An in vitro-transcribed circular RNA targets the mitochondrial inner membrane cardiolipin to ablate EIF4G2 +/PTBP1 + pan-adenocarcinoma. Nat Cancer 2024; 5:30-46. [PMID: 37845485 DOI: 10.1038/s43018-023-00650-8] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/07/2023] [Indexed: 10/18/2023]
Abstract
In vitro-transcribed (IVT) mRNA has arisen as a rapid method for the production of nucleic acid drugs. Here, we have constructed an oncolytic IVT mRNA that utilizes human rhinovirus type 2 (HRV2) internal ribosomal entry sites (IRESs) to selectively trigger translation in cancer cells with high expression of EIF4G2 and PTBP1. The oncolytic effect was provided by a long hGSDMDc .825 T>A/c.884 A>G-F1LCT mutant mRNA sequence with mitochondrial inner membrane cardiolipin targeting toxicity that triggers mitophagy. Utilizing the permuted intron-exon (PIE) splicing circularization strategy and lipid nanoparticle (LNP) encapsulation reduced immunogenicity of the mRNA and enabled delivery to eukaryotic cells in vivo. Engineered HRV2 IRESs-GSDMDp.D275E/E295G-F1LCT circRNA-LNPs (GSDMDENG circRNA) successfully inhibited EIF4G2+/PTBP1+ pan-adenocarcinoma xenografts growth. Importantly, in a spontaneous tumor model with abnormal EIF4G2 and PTBP1 caused by KRAS G12D mutation, GSDMDENG circRNA significantly prevented the occurrence of pancreatic, lung and colon adenocarcinoma, improved the survival rate and induced persistent KRAS G12D tumor antigen-specific cytotoxic T lymphocyte responses.
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Affiliation(s)
- Zunyong Feng
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore
| | - Xuanbo Zhang
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore
| | - Jing Zhou
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Qiang Li
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Liuxi Chu
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China
| | - Guangfu Di
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Zhengyuan Xu
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Qun Chen
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Ming Wang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaochun Jiang
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China.
| | - Hongping Xia
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China.
- Department of Pathology, Nanjing Drum Tower Hospital Clinical College & Key Laboratory of Antibody Technique of National Health Commission & Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, China.
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore.
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21
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Kim JJ, Vitale D, Otani DV, Lian MM, Heilbron K, Iwaki H, Lake J, Solsberg CW, Leonard H, Makarious MB, Tan EK, Singleton AB, Bandres-Ciga S, Noyce AJ, Blauwendraat C, Nalls MA, Foo JN, Mata I. Multi-ancestry genome-wide association meta-analysis of Parkinson's disease. Nat Genet 2024; 56:27-36. [PMID: 38155330 PMCID: PMC10786718 DOI: 10.1038/s41588-023-01584-8] [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: 08/26/2022] [Accepted: 10/20/2023] [Indexed: 12/30/2023]
Abstract
Although over 90 independent risk variants have been identified for Parkinson's disease using genome-wide association studies, most studies have been performed in just one population at a time. Here we performed a large-scale multi-ancestry meta-analysis of Parkinson's disease with 49,049 cases, 18,785 proxy cases and 2,458,063 controls including individuals of European, East Asian, Latin American and African ancestry. In a meta-analysis, we identified 78 independent genome-wide significant loci, including 12 potentially novel loci (MTF2, PIK3CA, ADD1, SYBU, IRS2, USP8, PIGL, FASN, MYLK2, USP25, EP300 and PPP6R2) and fine-mapped 6 putative causal variants at 6 known PD loci. By combining our results with publicly available eQTL data, we identified 25 putative risk genes in these novel loci whose expression is associated with PD risk. This work lays the groundwork for future efforts aimed at identifying PD loci in non-European populations.
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Affiliation(s)
- Jonggeol Jeffrey Kim
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Preventive Neurology Unit, Centre for Prevention Diagnosis and Detection, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.
| | - Dan Vitale
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Diego Véliz Otani
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - Michelle Mulan Lian
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, A*STAR, Singapore, Singapore
| | | | - Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Warly Solsberg
- Pharmaceutical Sciences and Pharmacogenomics, UCSF, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, UCSF, San Francisco, CA, USA
| | - Hampton Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - Eng-King Tan
- Department of Neurology, National Neuroscience Institute, Duke NUS Medical School, Singapore, Singapore
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Alastair J Noyce
- Preventive Neurology Unit, Centre for Prevention Diagnosis and Detection, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Data Tecnica International, Washington, DC, USA.
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore.
- Genome Institute of Singapore, Agency for Science, Technology and Research, A*STAR, Singapore, Singapore.
| | - Ignacio Mata
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
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22
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Walden SL, Nguyen PHD, Li HK, Liu X, Le MTN, Xian Jun L, Barner-Kowollik C, Truong VX. Visible light-induced switching of soft matter materials properties based on thioindigo photoswitches. Nat Commun 2023; 14:8298. [PMID: 38097621 PMCID: PMC10721821 DOI: 10.1038/s41467-023-44128-8] [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: 07/31/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Thioindigos are visible light responsive photoswitches with excellent spatial control over the conformational change between their trans- and cis- isomers. However, they possess limited solubility in all conventional organic solvents and polymers, hindering their application in soft matter materials. Herein, we introduce a strategy for the covalent insertion of thioindigo units into polymer main chains, enabling thioindigos to function within crosslinked polymeric hydrogels. We overcome their solubility issue by developing a thioindigo bismethacrylate linker able to undergo radical initiated thiol-ene reaction for step-growth polymerization, generating indigo-containing polymers. The optimal wavelength for the reversible trans-/cis- isomerisation of thioindigo was elucidated by constructing a detailed photochemical action plot of their switching efficiencies at a wide range of monochromatic wavelengths. Critically, indigo-containing polymers display significant photoswitching of the materials' optical and physical properties in organic solvents and water. Furthermore, the photoswitching of thioindigo within crosslinked structures enables visible light induced modulation of the hydrogel stiffness. Both the thioindigo-containing hydrogels and photoswitching processes are non-toxic to cells, thus offering opportunities for advanced applications in soft matter materials and biology-related research.
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Affiliation(s)
- Sarah L Walden
- Centre for Materials Science, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- School of Chemistry and Physics, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
| | - Phuong H D Nguyen
- Department of Pharmacology and Institute for Digital Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Republic of Singapore
| | - Hao-Kai Li
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore, Republic of Singapore
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore, Republic of Singapore
| | - Minh T N Le
- Department of Pharmacology and Institute for Digital Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Republic of Singapore
| | - Loh Xian Jun
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore, 138634, Republic of Singapore.
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore, 627833, Republic of Singapore.
| | - Christopher Barner-Kowollik
- Centre for Materials Science, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia.
- School of Chemistry and Physics, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
| | - Vinh X Truong
- School of Chemistry and Physics, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia.
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore, 138634, Republic of Singapore.
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23
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Yeow J, Luo M, Chng SS. Molecular mechanism of phospholipid transport at the bacterial outer membrane interface. Nat Commun 2023; 14:8285. [PMID: 38092770 PMCID: PMC10719372 DOI: 10.1038/s41467-023-44144-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry.
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Affiliation(s)
- Jiang Yeow
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117558, Singapore
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, 117456, Singapore.
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24
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Gautam N, Wojciech L, Yap J, Chua YL, Ding EM, Sim DC, Tan AS, Ahl PJ, Prasad M, Tung DW, Connolly JE, Adriani G, Brzostek J, Gascoigne NR. Themis controls T cell activation, effector functions, and metabolism of peripheral CD8 + T cells. Life Sci Alliance 2023; 6:e202302156. [PMID: 37739454 PMCID: PMC10517225 DOI: 10.26508/lsa.202302156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023] Open
Abstract
Themis is important in regulating positive selection of thymocytes during T cell development, but its role in peripheral T cells is less understood. Here, we investigated T cell activation and its sequelae using a tamoxifen-mediated, acute Themis deletion mouse model. We find that proliferation, effector functions including anti-tumor killing, and up-regulation of energy metabolism are severely compromised. This study reveals the phenomenon of peripheral adaptation to loss of Themis, by demonstrating direct TCR-induced defects after acute deletion of Themis that were not evident in peripheral T cells chronically deprived of Themis in dLck-Cre deletion model. Peripheral adaptation to long-term loss was compared using chronic versus acute tamoxifen-mediated deletion and with the (chronic) dLck-Cre deletion model. We found that upon chronic tamoxifen-mediated Themis deletion, there was modulation in the gene expression profile for both TCR and cytokine signaling pathways. This profile overlapped with (chronic) dLck-Cre deletion model. Hence, we found that peripheral adaptation induced changes to both TCR and cytokine signaling modules. Our data highlight the importance of Themis in the activation of CD8+ T cells.
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Affiliation(s)
- Namrata Gautam
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lukasz Wojciech
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jiawei Yap
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yen Leong Chua
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Eyan Mw Ding
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Don Cn Sim
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Alrina Sm Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Patricia J Ahl
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mukul Prasad
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Desmond Wh Tung
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - John E Connolly
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Giulia Adriani
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore
| | - Joanna Brzostek
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nicholas Rj Gascoigne
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Translational Cancer Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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25
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Chow EWL, Song Y, Chen J, Xu X, Wang J, Chen K, Gao J, Wang Y. The transcription factor Rpn4 activates its own transcription and induces efflux pump expression to confer fluconazole resistance in Candida auris. mBio 2023; 14:e0268823. [PMID: 38014938 PMCID: PMC10746192 DOI: 10.1128/mbio.02688-23] [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: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Candida auris is a recently emerged pathogenic fungus of grave concern globally due to its resistance to conventional antifungals. This study takes a whole-genome approach to explore how C. auris overcomes growth inhibition imposed by the common antifungal drug fluconazole. We focused on gene disruptions caused by a "jumping genetic element" called transposon, leading to fluconazole resistance. We identified mutations in two genes, each encoding a component of the Ubr2/Mub1 ubiquitin-ligase complex, which marks the transcription regulator Rpn4 for degradation. When either protein is absent, stable Rpn4 accumulates in the cell. We found that Rpn4 activates the expression of itself as well as the main drug efflux pump gene CDR1 by binding to a PACE element in the promoter. Furthermore, we identified an amino acid change in Ubr2 in many resistant clinical isolates, contributing to Rpn4 stabilization and increased fluconazole resistance.
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Affiliation(s)
- Eve W. L. Chow
- Infectious Diseases Labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yabing Song
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinxin Chen
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Xu
- Infectious Diseases Labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Kun Chen
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiaxin Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yue Wang
- Infectious Diseases Labs, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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26
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Choo Z, Koh X, Wong MRE, Ashokan RM, Ali Ahamed NSB, Kang C, Kuick CH, Chang KTE, Larisch S, Loh AHP, Chen ZX. Targeted Degradation of XIAP is Sufficient and Specific to Induce Apoptosis in MYCN-overexpressing High-risk Neuroblastoma. Cancer Res Commun 2023; 3:2386-2399. [PMID: 37874199 PMCID: PMC10681007 DOI: 10.1158/2767-9764.crc-23-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/22/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
XIAP, the most potent mammalian inhibitor of apoptosis protein (IAP), critically restricts developmental culling of sympathetic neuronal progenitors, and is correspondingly overexpressed in most MYCN-amplified neuroblastoma tumors. Because apoptosis-related protein in the TGFβ signaling pathway (ARTS) is the only XIAP antagonist that directly binds and degrades XIAP, we evaluated the preclinical effectiveness and tolerability of XIAP antagonism as a novel targeting strategy for neuroblastoma. We found that antagonism of XIAP, but not other IAPs, triggered apoptotic death in neuroblastoma cells. XIAP silencing induced apoptosis while overexpression conferred protection from drug-induced apoptosis. From a screen of IAP inhibitors, first-in-class ARTS mimetic A4 was most effective against high-risk and high XIAP-expressing neuroblastoma cells, and least toxic toward normal liver- and bone marrow-derived cells, compared with pan-IAP antagonists. On target engagement assays and nuclear magnetic resonance spectroscopy, A4 was observed to degrade rather than inhibit XIAP, catalyzing rapid degradation of XIAP through the ubiquitin-proteasome pathway. In MYCN-amplified neuroblastoma patient-derived xenografts, A4 significantly prolonged survival as a single agent, and demonstrated synergism with standard-of-care agents to reduce their effective required doses 3- to 6-fold. Engagement and degradation of XIAP by ARTS mimetics is a novel targeting strategy for neuroblastoma that may be especially effective against MYCN-amplified disease with intrinsically high XIAP expression. First-in-class ARTS mimetic A4 demonstrates preclinical efficacy and warrants further development and study. SIGNIFICANCE XIAP degradation is sufficient to kill MYCN-amplified neuroblastoma which overexpresses and relies on XIAP as a brake against cell death, without affecting normal cells.
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Affiliation(s)
- Zhang'E Choo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xiaoying Koh
- Experimental Drug Development Centre, A*STAR, Singapore
| | - Megan Rui En Wong
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore
| | - Ruth Minothini Ashokan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Nurul Suhana Binte Ali Ahamed
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - CongBao Kang
- Experimental Drug Development Centre, A*STAR, Singapore
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
| | - Kenneth Tou En Chang
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
- Duke NUS Medical School, Singapore
| | - Sarit Larisch
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, Israel
| | - Amos Hong Pheng Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore
- Duke NUS Medical School, Singapore
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, Israel
- Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore
| | - Zhi Xiong Chen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore
- National University Cancer Institute, Singapore, National University Health System, Singapore
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27
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Iakovleva V, Wuestefeld A, Ong ABL, Gao R, Kaya NA, Lee MY, Zhai W, Tam WL, Dan YY, Wuestefeld T. Mfap4: a promising target for enhanced liver regeneration and chronic liver disease treatment. NPJ Regen Med 2023; 8:63. [PMID: 37935709 PMCID: PMC10630300 DOI: 10.1038/s41536-023-00337-9] [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: 03/27/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023] Open
Abstract
The liver has a remarkable regenerative capacity. Nevertheless, under chronic liver-damaging conditions, this capacity becomes exhausted, allowing the accumulation of fibrotic tissue and leading to end-stage liver disease. Enhancing the endogenous regenerative capacity by targeting regeneration breaks is an innovative therapeutic approach. We set up an in vivo functional genetic screen to identify such regeneration breaks. As the top hit, we identified Microfibril associated protein 4 (Mfap4). Knockdown of Mfap4 in hepatocytes enhances cell proliferation, accelerates liver regeneration, and attenuates chronic liver disease by reducing liver fibrosis. Targeting Mfap4 modulates several liver regeneration-related pathways including mTOR. Our research opens the way to siRNA-based therapeutics to enhance hepatocyte-based liver regeneration.
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Affiliation(s)
- Viktoriia Iakovleva
- Laboratory of In Vivo Genetics and Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Republic of Singapore
| | - Anna Wuestefeld
- Laboratory of In Vivo Genetics and Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
| | - Agnes Bee Leng Ong
- Laboratory of In Vivo Genetics and Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
| | - Rong Gao
- Laboratory of In Vivo Genetics and Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
| | - Neslihan Arife Kaya
- Laboratory of Translational Cancer Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
| | - May Yin Lee
- Laboratory of Translational Cancer Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wai Leong Tam
- Laboratory of Translational Cancer Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Republic of Singapore
| | - Yock Young Dan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Republic of Singapore
- Division of Gastroenterology and Hepatology, National University Health System, Singapore, 119074, Republic of Singapore
| | - Torsten Wuestefeld
- Laboratory of In Vivo Genetics and Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- School of Biological Science, Nanyang University of Singapore, Singapore, 637551, Republic of Singapore.
- National Cancer Centre, Singapore, 169610, Republic of Singapore.
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28
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Lau MS, Hu Z, Zhao X, Tan YS, Liu J, Huang H, Yeo CJ, Leong HF, Grinchuk OV, Chan JK, Yan J, Tee WW. Transcriptional repression by a secondary DNA binding surface of DNA topoisomerase I safeguards against hypertranscription. Nat Commun 2023; 14:6464. [PMID: 37833256 PMCID: PMC10576097 DOI: 10.1038/s41467-023-42078-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Regulation of global transcription output is important for normal development and disease, but little is known about the mechanisms involved. DNA topoisomerase I (TOP1) is an enzyme well-known for its role in relieving DNA supercoils for enabling transcription. Here, we report a non-enzymatic function of TOP1 that downregulates RNA synthesis. This function is dependent on specific DNA-interacting residues located on a conserved protein surface. A loss-of-function knock-in mutation on this surface, R548Q, is sufficient to cause hypertranscription and alter differentiation outcomes in mouse embryonic stem cells (mESCs). Hypertranscription in mESCs is accompanied by reduced TOP1 chromatin binding and change in genomic supercoiling. Notably, the mutation does not impact TOP1 enzymatic activity; rather, it diminishes TOP1-DNA binding and formation of compact protein-DNA structures. Thus, TOP1 exhibits opposing influences on transcription through distinct activities which are likely to be coordinated. This highlights TOP1 as a safeguard of appropriate total transcription levels in cells.
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Affiliation(s)
- Mei Sheng Lau
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Zhenhua Hu
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaodan Zhao
- Department of Physics, National University of Singapore, Singapore, 117551, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
| | - Jinyue Liu
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Hua Huang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Electrophysiology Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Clarisse Jingyi Yeo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwei Fen Leong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Oleg V Grinchuk
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Justin Kaixuan Chan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, 117551, Singapore.
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117557, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
| | - Wee-Wei Tee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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29
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Ng SMS, Low R, Pak C, Lai S, Lee B, McCluskey P, Symes R, Invernizzi A, Tsui E, Sitaula RK, Kharel M, Khatri A, Utami AN, La Distia Nora R, Putera I, Sen A, Agarwal M, Mahendradas P, Biswas J, Pavesio C, Cimino L, Sobrin L, Kempen JH, Gupta V, Agrawal R. The role of a multicentre data repository in ocular inflammation: The Ocular Autoimmune Systemic Inflammatory Infectious Study (OASIS). Eye (Lond) 2023; 37:3084-3096. [PMID: 36918629 PMCID: PMC10564879 DOI: 10.1038/s41433-023-02472-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/04/2022] [Revised: 01/19/2023] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
In the current literature, clinical registry cohorts related to ocular inflammation are few and far between, and there are none involving multi-continental international data. Many existing registries comprise administrative databases, data related to specific uveitic diseases, or are designed to address a particular clinical problem. The existing data, although useful and serving their intended purposes, are segmented and may not be sufficiently robust to design prognostication tools or draw epidemiological conclusions in the field of uveitis and ocular inflammation. To solve this, we have developed the Ocular Autoimmune Systemic Inflammatory Infectious Study (OASIS) Clinical Registry. OASIS collects prospective and retrospective data on patients with all types of ocular inflammatory conditions from centers all around the world. It is a primarily web-based platform with alternative offline modes of access. A comprehensive set of clinical data ranging from demographics, past medical history, clinical presentation, working diagnosis to visual outcomes are collected over a range of time points. Additionally, clinical images such as optical coherence tomography, fundus fluorescein angiography and indocyanine green angiography studies may be uploaded. Through the capturing of diverse, well-structured, and clinically meaningful data in a simplified and consistent fashion, OASIS will deliver a comprehensive and well organized data set ripe for data analysis. The applications of the registry are numerous, and include performing epidemiological analysis, monitoring drug side effects, and studying treatment safety efficacy. Furthermore, the data compiled in OASIS will be used to develop new classification and diagnostic systems, as well as treatment and prognostication guidelines for uveitis.
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Affiliation(s)
- Sean Ming Sheng Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Rebecca Low
- Department of Ophthalmology, National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Clara Pak
- University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
| | - SerSei Lai
- Department of Ophthalmology, National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Bernett Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Peter McCluskey
- Save Sight Institute, The University of Sydney, Sydney, NSW, Australia
| | - Richard Symes
- Save Sight Institute, The University of Sydney, Sydney, NSW, Australia
| | - Alessandro Invernizzi
- Save Sight Institute, The University of Sydney, Sydney, NSW, Australia
- Eye Clinic, Department of Biomedical and Clinical Science "Luigi Sacco," Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Edmund Tsui
- Stein Eye Institute, David Geffen of Medicine at UCLA, Los Angeles, CA, USA
| | - Ranju Kharel Sitaula
- Department of Ophthalmology, B. P. Koirala Lions Centre for Ophthalmic Studies, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Muna Kharel
- Nepal Army Institute of Health Sciences, Kathmandu, Nepal
| | | | | | | | | | - Alok Sen
- Sadguru Netra Chikitsalaya, Chitrakoot, Madhya Pradesh, India
| | - Manisha Agarwal
- Department of Ophthalmology, Dr Shroff's Charity Eye Hospital Daryaganj, New Delhi, India
| | | | | | - Carlos Pavesio
- Moorfields Eye Hospital, NHS Foundation Trust, London, UK
| | - Luca Cimino
- Department of Surgery, Medicine Dentistry and Morphological Sciences with Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
- Ocular Immunology Unit, Azienda USL-IRCCS di Reggio Emilia, 42121, Reggio Emilia, Italy
| | - Lucia Sobrin
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Schepens Eye Research Institute, Boston, MA, USA
| | - John H Kempen
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Schepens Eye Research Institute, Boston, MA, USA
- MyungSung Christian Medical Center (MCM) Eye Unit, MCM General Hospital and MyungSung Medical School, Addis Ababa, Ethiopia
- Department of Ophthalmology, Addis Ababa University Faculty of Medicine, Addis Ababa, Ethiopia
- Sight for Souls, Fort Myers, FL, USA
| | - Vishali Gupta
- Advanced Eye Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rupesh Agrawal
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- Department of Ophthalmology, National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore.
- Moorfields Eye Hospital, NHS Foundation Trust, London, UK.
- Singapore Eye Research Institute, The Academia, Singapore, Singapore.
- Department of Ophthalmology and Visual Sciences, Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.
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30
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Tan SH, Tan TK, Yokomori R, Liao M, Huang XZ, Yeoh AEJ, Sanda T. TAL1 hijacks MYCN enhancer that induces MYCN expression and dependence on mevalonate pathway in T-cell acute lymphoblastic leukemia. Leukemia 2023; 37:1969-1981. [PMID: 37591943 DOI: 10.1038/s41375-023-01993-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/18/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023]
Abstract
A hallmark of T-cell acute lymphoblastic leukemia (T-ALL) is the dysregulated expression of oncogenic transcription factors (TFs), including TAL1, NOTCH1 and MYC. Rewiring of the transcriptional program disrupts the tightly controlled spatiotemporal expression of downstream target genes, thereby contributing to leukemogenesis. In this study, we first identify an evolutionarily conserved enhancer element controlling the MYCN oncogene (named enhMYCN) that is aberrantly activated by the TAL1 complex in T-ALL cells. TAL1-positive T-ALL cells are highly dependent on MYCN expression for their maintenance in vitro and in xenograft models. Interestingly, MYCN drives the expression of multiple genes involved in the mevalonate pathway, and T-ALL cells are sensitive to inhibition of HMG-CoA reductase (HMGCR), a rate-limiting enzyme of this pathway. Importantly, MYC and MYCN regulate the same targets and compensate for each other. Thus, MYCN-positive T-ALL cells display a dual dependence on the TAL1-MYCN and NOTCH1-MYC pathways. Together, our results demonstrate that enhMYCN-mediated MYCN expression is required for human T-ALL cells and implicate the TAL1-MYCN-HMGCR axis as a potential therapeutic target in T-ALL.
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Affiliation(s)
- Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Rui Yokomori
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Minghui Liao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Xiao Zi Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Allen Eng Juh Yeoh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Paediatrics, National University of Singapore, Singapore, 119228, Singapore.
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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31
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Tapia Del Fierro A, den Hamer B, Benetti N, Jansz N, Chen K, Beck T, Vanyai H, Gurzau AD, Daxinger L, Xue S, Ly TTN, Wanigasuriya I, Iminitoff M, Breslin K, Oey H, Krom YD, van der Hoorn D, Bouwman LF, Johanson TM, Ritchie ME, Gouil QA, Reversade B, Prin F, Mohun T, van der Maarel SM, McGlinn E, Murphy JM, Keniry A, de Greef JC, Blewitt ME. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nat Commun 2023; 14:5466. [PMID: 37749075 PMCID: PMC10519958 DOI: 10.1038/s41467-023-40992-6] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets. Moreover, it also results in enhanced silencing at the facioscapulohumeral muscular dystrophy associated macrosatellite-array, D4Z4, resulting in enhanced repression of DUX4 encoded by this repeat. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against other epigenetic regulators, including PRC2 and CTCF, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1's role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.
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Affiliation(s)
- Andres Tapia Del Fierro
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Natalia Benetti
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Hannah Vanyai
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lucia Daxinger
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Iromi Wanigasuriya
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Harald Oey
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dinja van der Hoorn
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Linde F Bouwman
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Quentin A Gouil
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Timothy Mohun
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | | | - Edwina McGlinn
- EMBL Australia, Monash University, Clayton, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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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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Martinez N, Smulan LJ, Jameson ML, Smith CM, Cavallo K, Bellerose M, Williams J, West K, Sassetti CM, Singhal A, Kornfeld H. Glycerol contributes to tuberculosis susceptibility in male mice with type 2 diabetes. Nat Commun 2023; 14:5840. [PMID: 37730757 PMCID: PMC10511404 DOI: 10.1038/s41467-023-41519-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/01/2023] [Indexed: 09/22/2023] Open
Abstract
Diabetes mellitus increases risk for tuberculosis disease and adverse outcomes. Most people with both conditions have type 2 diabetes, but it is unknown if type 1 and type 2 diabetes have identical effects on tuberculosis susceptibility. Here we show that male mice receiving a high-fat diet and streptozotocin to model type 2 diabetes, have higher mortality, more lung pathology, and higher bacterial burden following Mycobacterium tuberculosis infection compared to mice treated with streptozotocin or high-fat diet alone. Type 2 diabetes model mice have elevated plasma glycerol, which is a preferred carbon source for M. tuberculosis. Infection studies with glycerol kinase mutant M. tuberculosis reveal that glycerol utilization contributes to the susceptibility of the type 2 diabetes mice. Hyperglycemia impairs protective immunity against M. tuberculosis in both forms of diabetes, but our data show that elevated glycerol contributes to an additional adverse effect uniquely relevant to type 2 diabetes.
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Affiliation(s)
- Nuria Martinez
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lorissa J Smulan
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael L Jameson
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Clare M Smith
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kelly Cavallo
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michelle Bellerose
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - John Williams
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kim West
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amit Singhal
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- A*STAR Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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34
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Fan Q, Li H, Wang X, Tham YC, Teo KYC, Yasuda M, Lim WK, Kwan YP, Teo JX, Chen CJ, Chen LJ, Ahn J, Davila S, Miyake M, Tan P, Park KH, Pang CP, Khor CC, Wong TY, Yanagi Y, Cheung CMG, Cheng CY. Contribution of common and rare variants to Asian neovascular age-related macular degeneration subtypes. Nat Commun 2023; 14:5574. [PMID: 37696869 PMCID: PMC10495468 DOI: 10.1038/s41467-023-41256-z] [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: 05/29/2022] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Neovascular age-related macular degeneration (nAMD), along with its clinical subtype known as polypoidal choroidal vasculopathy (PCV), are among the leading causes of vision loss in elderly Asians. In a genome-wide association study (GWAS) comprising 3,128 nAMD (1,555 PCV and 1,573 typical nAMD), and 5,493 controls of East Asian ancestry, we identify twelve loci, of which four are novel ([Formula: see text]). Substantial genetic sharing between PCV and typical nAMD is noted (rg = 0.666), whereas collagen extracellular matrix and fibrosis-related pathways are more pronounced for PCV. Whole-exome sequencing in 259 PCV patients revealed functional rare variants burden in collagen type I alpha 1 chain gene (COL1A1; [Formula: see text]) and potential enrichment of functional rare mutations at AMD-associated loci. At the GATA binding protein 5 (GATA5) locus, the most significant GWAS novel loci, the expressions of genes including laminin subunit alpha 5 (Lama5), mitochondrial ribosome associated GTPase 2 (Mtg2), and collagen type IX alpha 3 chain (Col9A3), are significantly induced during retinal angiogenesis and subretinal fibrosis in murine models. Furthermore, retinoic acid increased the expression of LAMA5 and MTG2 in vitro. Taken together, our data provide insights into the genetic basis of AMD pathogenesis in the Asian population.
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Affiliation(s)
- Qiao Fan
- Center for Quantitative Medicine, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore.
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.
| | - Hengtong Li
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiaomeng Wang
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Center for Vision Research, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Yih-Chung Tham
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kelvin Yi Chong Teo
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Masayuki Yasuda
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Laboratory of Genome Variation Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yuet Ping Kwan
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Ching-Jou Chen
- Center for Vision Research, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jeeyun Ahn
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sonia Davila
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Patrick Tan
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chiea Chuan Khor
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Tien Yin Wong
- Tsinghua Medicine, Tsinghua University, Beijing, China
| | - Yasuo Yanagi
- Department of Ophthalmology and Microtechnology, Yokohama City University, Yokohama, Japan
| | - Chui Ming Gemmy Cheung
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Ching-Yu Cheng
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Ma J, Chan JJ, Toh CH, Yap YS. Emerging systemic therapy options beyond CDK4/6 inhibitors for hormone receptor-positive HER2-negative advanced breast cancer. NPJ Breast Cancer 2023; 9:74. [PMID: 37684290 PMCID: PMC10491615 DOI: 10.1038/s41523-023-00578-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 04/06/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Endocrine therapy (ET) with cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) is currently the standard first-line treatment for most patients with hormone receptor (HR) positive, human epidermal growth factor receptor (HER2) negative advanced breast cancer. However, resistance to ET and CDK4/6i inevitably ensues. The optimal post-progression treatment regimens and their sequencing continue to evolve in the rapidly changing treatment landscape. In this review, we summarize the mechanisms of resistance to ET and CDK4/6i, which can be broadly classified as alterations affecting cell cycle mediators and activation of alternative signaling pathways. Recent clinical trials have been directed at the targets and pathways implicated, including estrogen and androgen receptors, PI3K/AKT/mTOR and MAPK pathways, tyrosine kinase receptors such as FGFR and HER2, homologous recombination repair pathway, other components of the cell cycle and cell death. We describe the findings from these clinical trials using small molecule inhibitors, antibody-drug conjugates and immunotherapy, providing insights into how these novel strategies may circumvent treatment resistance, and discuss how some have not translated into clinical benefit. The challenges posed by tumor heterogeneity, adaptive rewiring of signaling pathways and dose-limiting toxicities underscore the need to elucidate the latest tumor biology in each patient, and develop treatments with improved therapeutic index in the era of precision medicine.
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Affiliation(s)
- Jun Ma
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Jack Junjie Chan
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
- Oncology Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ching Han Toh
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore.
- Oncology Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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36
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Ng AS, Chan DKH. Commonalities and differences in the mutational signature and somatic driver mutation landscape across solid and hollow viscus organs. Oncogene 2023; 42:2713-2724. [PMID: 37573406 PMCID: PMC10491491 DOI: 10.1038/s41388-023-02802-7] [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: 06/08/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Advances in sequencing have revealed a highly variegated landscape of mutational signatures and somatic driver mutations in a range of normal tissues. Normal tissues accumulate mutations at varying rates ranging from 11 per cell per year in the liver, to 1879 per cell per year in the bladder. In addition, some normal tissues are also comprised of a large proportion of cells which possess driver mutations while appearing phenotypically normal, as in the oesophagus where a majority of cells harbour driver mutations. Individual tissue proliferation and mutation rate, unique mutagenic stimuli, and local tissue architecture contribute to this highly variegated landscape which confounds the functional characterization of driver mutations found in normal tissue. In particular, our understanding of the relationship between normal tissue somatic mutations and tumour initiation or future cancer risk remains poor. Here, we describe the mutational signatures and somatic driver mutations in solid and hollow viscus organs, highlighting unique characteristics in a tissue-specific manner, while simultaneously seeking to describe commonalities which can bring forward a basic unified theory on the role of these driver mutations in tumour initiation. We discuss novel findings which can be used to inform future research in this field.
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Affiliation(s)
- Aik Seng Ng
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Dedrick Kok Hong Chan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Division of Colorectal Surgery, University Surgical Cluster, National University Hospital, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
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37
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Chu WHW, Tan YH, Tan SY, Chen Y, Yong M, Lye DC, Kalimuddin S, Archuleta S, Gan YH. Acquisition of regulator on virulence plasmid of hypervirulent Klebsiella allows bacterial lifestyle switch in response to iron. mBio 2023; 14:e0129723. [PMID: 37530523 PMCID: PMC10470599 DOI: 10.1128/mbio.01297-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 08/03/2023] Open
Abstract
Hypervirulent Klebsiella pneumoniae causes liver abscess and potentially devastating metastatic complications. The majority of Klebsiella-induced liver abscess are caused by the CG23-I sublineage of hypervirulent Klebsiella pneumoniae. This and some other lineages possess a >200-kb virulence plasmid. We discovered a novel protein IroP nestled in the virulence plasmid-encoded salmochelin operon that cross-regulates and suppresses the promoter activity of chromosomal type 3 fimbriae (T3F) gene transcription. IroP is itself repressed by iron through the ferric uptake regulator. Iron-rich conditions increase T3F and suppress capsule mucoviscosity, leading to biofilm formation and cell adhesion. Conversely, iron-poor conditions cause a transcriptional switch to hypermucoid capsule production and T3F repression. The likely acquisition of iroP on mobile genetic elements and successful adaptive integration into the genetic circuitry of a major lineage of hypervirulent K. pneumoniae reveal a powerful example of plasmid chromosomal cross talk that confers an evolutionary advantage. Our discovery also addresses the conundrum of how the hypermucoid capsule that impedes adhesion could be regulated to facilitate biofilm formation and colonization. The acquired ability of the bacteria to alternate between a state favoring dissemination and one that favors colonization in response to iron availability through transcriptional regulation offers novel insights into the evolutionary success of this pathogen. IMPORTANCE Hypervirulent Klebsiella pneumoniae contributes to the majority of monomicrobial-induced liver abscess infections that can lead to several other metastatic complications. The large virulence plasmid is highly stable in major lineages, suggesting that it provides survival benefits. We discovered a protein IroP encoded on the virulence plasmid that suppresses expression of the type 3 fimbriae. IroP itself is regulated by iron, and we showed that iron regulates hypermucoid capsule production while inversely regulating type 3 fimbriae expression through IroP. The acquisition and integration of this inverse transcriptional switch between fimbriae and capsule mucoviscosity shows an evolved sophisticated plasmid-chromosomal cross talk that changes the behavior of hypervirulent K. pneumoniae in response to a key nutrient that could contribute to the evolutionary success of this pathogen.
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Affiliation(s)
- Wilson H. W. Chu
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yi Han Tan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Si Yin Tan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yahua Chen
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Melvin Yong
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David C. Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
- Program in Emerging Infectious Disease, Duke-NUS Medical School, Singapore, Singapore
| | - Sophia Archuleta
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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38
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Wang Z, Kennedy BK, Wong LW, Sajikumar S. Aging inverts the effects of p75 NTR -modulated mTOR manipulation on hippocampal neuron synaptic plasticity in male mice. FASEB J 2023; 37:e23067. [PMID: 37401900 DOI: 10.1096/fj.202201640rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/05/2023]
Abstract
Age-induced impairments in learning and memory are in part caused by changes to hippocampal synaptic plasticity during aging. The p75 neurotrophin receptor (p75NTR ) and mechanistic target of rapamycin (mTOR) are implicated in synaptic plasticity processes. mTOR is also well known for its involvement in aging. Recently, p75NTR and mTOR were shown to be mechanistically linked, and that p75NTR mediates age-induced impairment of hippocampal synaptic plasticity. Yet the consequences of p75NTR -mTOR interaction on hippocampal synaptic plasticity, and the role of mTOR in age-induced cognitive decline, are unclear. In this study, we utilize field electrophysiology to study the effects of mTOR inhibition and activation on long-term potentiation (LTP) in male young and aged wild-type (WT) mice. We then repeated the experiments on p75NTR knockout mice. The results demonstrate that mTOR inhibition blocks late-LTP in young WT mice but rescues age-related late-LTP impairment in aged WT mice. mTOR activation suppresses late-LTP in aged WT mice while lacking observable effects on young WT mice. These effects were not observed in p75NTR knockout mice. These results demonstrate that the role of mTOR in hippocampal synaptic plasticity is distinct between young and aged mice. Such effects could be explained by differing sensitivity of young and aged hippocampal neurons to changes in protein synthesis or autophagic activity levels. Additionally, elevated mTOR in the aged hippocampus could cause excessive mTOR signaling, which is worsened by activation and alleviated by inhibition. Further research on mTOR and p75NTR may prove useful for advancing understanding and, ultimately, mitigation of age-induced cognitive decline.
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Affiliation(s)
- Zijun Wang
- Department of Physiology, National University of Singapore, Singapore, Singapore
- Life Sciences Institute Neurobiology Programme, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Brian K Kennedy
- Department of Physiology, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
- Centre for Healthy Longevity, National University Health System, Singapore, Singapore
| | - Lik-Wei Wong
- Department of Physiology, National University of Singapore, Singapore, Singapore
- Life Sciences Institute Neurobiology Programme, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sreedharan Sajikumar
- Department of Physiology, National University of Singapore, Singapore, Singapore
- Life Sciences Institute Neurobiology Programme, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Liu X, Jiang L, Ke M, Sigal IA, Chua J, Hoang QV, Chia AW, Najjar RP, Tan B, Cheong J, Bellemo V, Chong RS, Girard MJA, Ang M, Liu M, Garhöfer G, Barathi VA, Saw SM, Villiger M, Schmetterer L. Posterior scleral birefringence measured by triple-input polarization-sensitive imaging as a biomarker of myopia progression. Nat Biomed Eng 2023; 7:986-1000. [PMID: 37365268 PMCID: PMC10427432 DOI: 10.1038/s41551-023-01062-w] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
In myopic eyes, pathological remodelling of collagen in the posterior sclera has mostly been observed ex vivo. Here we report the development of triple-input polarization-sensitive optical coherence tomography (OCT) for measuring posterior scleral birefringence. In guinea pigs and humans, the technique offers superior imaging sensitivities and accuracies than dual-input polarization-sensitive OCT. In 8-week-long studies with young guinea pigs, scleral birefringence was positively correlated with spherical equivalent refractive errors and predicted the onset of myopia. In a cross-sectional study involving adult individuals, scleral birefringence was associated with myopia status and negatively correlated with refractive errors. Triple-input polarization-sensitive OCT may help establish posterior scleral birefringence as a non-invasive biomarker for assessing the progression of myopia.
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Affiliation(s)
- Xinyu Liu
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- SERI-NTU Advanced Ocular Engineering (STANCE) programme, Singapore, Singapore
| | - Liqin Jiang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Mengyuan Ke
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Ian A Sigal
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jacqueline Chua
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- SERI-NTU Advanced Ocular Engineering (STANCE) programme, Singapore, Singapore
| | - Quan V Hoang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine National University of Singapore, Singapore, Singapore
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Audrey Wi Chia
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Raymond P Najjar
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine National University of Singapore, Singapore, Singapore
| | - Bingyao Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- SERI-NTU Advanced Ocular Engineering (STANCE) programme, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Jocelyn Cheong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Valentina Bellemo
- SERI-NTU Advanced Ocular Engineering (STANCE) programme, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Rachel S Chong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Michaël J A Girard
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Marcus Ang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Mengyang Liu
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Gerhard Garhöfer
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Veluchamy A Barathi
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine National University of Singapore, Singapore, Singapore
- Translational Pre-Clinical Model Platform, Singapore Eye Research Institute, Singapore, Singapore
| | - Seang-Mei Saw
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- Saw Swee Hock School of Public Health, ,National University of Singapore, National University Health System, Singapore, Singapore
| | - Martin Villiger
- Wellman Center for Photomedicine, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Leopold Schmetterer
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.
- Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.
- SERI-NTU Advanced Ocular Engineering (STANCE) programme, Singapore, Singapore.
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria.
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland.
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria.
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Lyons-Reid J, Ward LC, Derraik JGB, Thway-Tint M, Monnard CR, Ramos Nieves JM, Albert BB, Kenealy T, Godfrey KM, Chan SY, Cutfield WS. Prediction of fat-free mass in young children using bioelectrical impedance spectroscopy. Eur J Clin Nutr 2023:10.1038/s41430-023-01317-4. [PMID: 37524804 DOI: 10.1038/s41430-023-01317-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Bioimpedance devices are practical for measuring body composition in preschool children, but their application is limited by the lack of validated equations. OBJECTIVES To develop and validate fat-free mass (FFM) bioimpedance prediction equations among New Zealand 3.5-year olds, with dual-energy X-ray absorptiometry (DXA) as the reference method. METHODS Bioelectrical impedance spectroscopy (SFB7, ImpediMed) and DXA (iDXA, GE Lunar) measurements were conducted on 65 children. An equation incorporating weight, sex, ethnicity, and impedance was developed and validated. Performance was compared with published equations and mixture theory prediction. RESULTS The equation developed in ~70% (n = 45) of the population (FFM [kg] = 1.39 + 0.30 weight [kg] + 0.39 length2/resistance at 50 kHz [cm2/Ω] + 0.30 sex [M = 1/F = 0] + 0.28 ethnicity [1 = Asian/0 = non-Asian]) explained 88% of the variance in FFM and predicted FFM with a root mean squared error of 0.39 kg (3.4% of mean FFM). When internally validated (n = 20), bias was small (40 g, 0.3% of mean FFM), with limits of agreement (LOA) ±7.6% of mean FFM (95% LOA: -0.82, 0.90 kg). Published equations evaluated had similar LOA, but with marked bias (>12.5% of mean FFM) when validated in our cohort, likely due to DXA differences. Of mixture theory methods assessed, the SFB7 inbuilt equation with personalized body geometry values performed best. However, bias and LOA were larger than with the empirical equations (-0.43 kg [95% LOA: -1.65, 0.79], p < 0.001). CONCLUSIONS We developed and validated a bioimpedance equation that can accurately predict FFM. Further external validation of the equation is required.
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Affiliation(s)
- Jaz Lyons-Reid
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Leigh C Ward
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - José G B Derraik
- Liggins Institute, University of Auckland, Auckland, New Zealand
- Department of Paediatrics: Child and Youth Health, University of Auckland, Auckland, New Zealand
- Environmental-Occupational Health Sciences and Non-communicable Diseases Research Group, Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Mya Thway-Tint
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Human Potential Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Cathriona R Monnard
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - J Manuel Ramos Nieves
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Timothy Kenealy
- Liggins Institute, University of Auckland, Auckland, New Zealand
- Department of Medicine and Department of General Practice and Primary Health Care, University of Auckland, Auckland, New Zealand
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Shiao-Yng Chan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Obstetrics & Gynaecology, National University of Singapore, Singapore, Singapore
| | - Wayne S Cutfield
- Liggins Institute, University of Auckland, Auckland, New Zealand.
- A Better Start - National Science Challenge, University of Auckland, Auckland, New Zealand.
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41
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Zhang Y, Wong CY, Lim CZJ, Chen Q, Yu Z, Natalia A, Wang Z, Pang QY, Lim SW, Loh TP, Ang BT, Tang C, Shao H. Multiplexed RNA profiling by regenerative catalysis enables blood-based subtyping of brain tumors. Nat Commun 2023; 14:4278. [PMID: 37460561 DOI: 10.1038/s41467-023-39844-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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] [Received: 01/11/2023] [Accepted: 06/29/2023] [Indexed: 07/20/2023] Open
Abstract
Current technologies to subtype glioblastoma (GBM), the most lethal brain tumor, require highly invasive brain biopsies. Here, we develop a dedicated analytical platform to achieve direct and multiplexed profiling of circulating RNAs in extracellular vesicles for blood-based GBM characterization. The technology, termed 'enzyme ZIF-8 complexes for regenerative and catalytic digital detection of RNA' (EZ-READ), leverages an RNA-responsive transducer to regeneratively convert and catalytically enhance signals from rare RNA targets. Each transducer comprises hybrid complexes - protein enzymes encapsulated within metal organic frameworks - to configure strong catalytic activity and robust protection. Upon target RNA hybridization, the transducer activates directly to liberate catalytic complexes, in a target-recyclable manner; when partitioned within a microfluidic device, these complexes can individually catalyze strong chemifluorescence reactions for digital RNA quantification. The EZ-READ platform thus enables programmable and reliable RNA detection, across different-sized RNA subtypes (miRNA and mRNA), directly in sample lysates. When clinically evaluated, the EZ-READ platform established composite signatures for accurate blood-based GBM diagnosis and subtyping.
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Affiliation(s)
- Yan Zhang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Chi Yan Wong
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Carine Z J Lim
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Qingchang Chen
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Zhonglang Yu
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Auginia Natalia
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Zhigang Wang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
| | - Qing You Pang
- Neuro-Oncology Research Laboratory, Department of Research, National Neuroscience Institute, Singapore, Singapore
| | - See Wee Lim
- Neuro-Oncology Research Laboratory, Department of Research, National Neuroscience Institute, Singapore, Singapore
| | - Tze Ping Loh
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Beng Ti Ang
- Department of Neurosurgery, National Neuroscience Institute, Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Carol Tang
- Neuro-Oncology Research Laboratory, Department of Research, National Neuroscience Institute, Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- National Neuroscience Institute, Singapore, Singapore.
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.
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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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43
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Chan DKH, Mandal A, Hester S, Yu Z, Higgins GS, Kessler BM, Fischer R, Buczacki SJA. Biallelic FBXW7 knockout induces AKAP8-mediated DNA damage in neighbouring wildtype cells. Cell Death Discov 2023; 9:200. [PMID: 37386001 DOI: 10.1038/s41420-023-01494-y] [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: 02/22/2023] [Revised: 05/24/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Colorectal cancer possesses marked intratumoral heterogeneity. While subclonal interactions between Vogelstein driver mutations have been extensively studied, less is known about competitive or cooperative effects between subclonal populations with other cancer driver mutations. FBXW7 is a cancer driver mutation which is present in close to 17% of colorectal cancer cells. In this study, we generated isogenic FBXW7 mutant cells using CRISPR-Cas9. We identified an upregulation of oxidative phosphorylation and DNA damage in FBXW7 mutant cells, which surprisingly proliferated at a decreased rate compared to wildtype cells. To determine subclonal interactions, wildtype and mutant FBXW7 cells were cocultured using a Transwell system. Wildtype cells cocultured with FBXW7 mutant cells similarly developed DNA damage which was not observed when wildtype cells were co-cultured with other wildtype cells, suggesting that FBXW7 mutant cells were inducing DNA damage in neighbouring wildtype cells. Using mass spectrometry, we identified AKAP8 as being secreted by FBXW7 mutant cells into the coculture media. Furthermore, overexpression of AKAP8 in wildtype cells recapitulated the DNA damage phenotype observed during coculture, while co-culture of wildtype cells with double mutant FBXW7-/-/AKAP8-/- cells abrogated the DNA damage phenotype. Here, we describe a hitherto unknown phenomenon of AKAP8-mediated DNA damage from FBXW7 mutant to neighbouring wildtype cells. Our findings demonstrate the importance of elucidating the local effect of cancer driver mutations between subclonal populations.
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Affiliation(s)
- Dedrick Kok Hong Chan
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Amit Mandal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Svenja Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Zhanru Yu
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | | | - Benedikt Mathias Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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Parikh BH, Blakeley P, Regha K, Liu Z, Yang B, Bhargava M, Wong DSL, Tan QSW, Wong CSW, Wang HF, Al-Mubaarak A, Chou C, Cheung CMG, Lim KL, Barathi VA, Hunziker W, Lingam G, Hu TX, Su X. Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state. Proc Natl Acad Sci U S A 2023; 120:e2214842120. [PMID: 37339216 DOI: 10.1073/pnas.2214842120] [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: 09/02/2022] [Accepted: 05/11/2023] [Indexed: 06/22/2023] Open
Abstract
Transplantation of stem cell-derived retinal pigment epithelial (RPE) cells is considered a viable therapeutic option for age-related macular degeneration (AMD). Several landmark Phase I/II clinical trials have demonstrated safety and tolerability of RPE transplants in AMD patients, albeit with limited efficacy. Currently, there is limited understanding of how the recipient retina regulates the survival, maturation, and fate specification of transplanted RPE cells. To address this, we transplanted stem cell-derived RPE into the subretinal space of immunocompetent rabbits for 1 mo and conducted single-cell RNA sequencing analyses on the explanted RPE monolayers, compared to their age-matched in vitro counterparts. We observed an unequivocal retention of RPE identity, and a trajectory-inferred survival of all in vitro RPE populations after transplantation. Furthermore, there was a unidirectional maturation toward the native adult human RPE state in all transplanted RPE, regardless of stem cell resource. Gene regulatory network analysis suggests that tripartite transcription factors (FOS, JUND, and MAFF) may be specifically activated in posttransplanted RPE cells, to regulate canonical RPE signature gene expression crucial for supporting host photoreceptor function, and to regulate prosurvival genes required for transplanted RPE's adaptation to the host subretinal microenvironment. These findings shed insights into the transcriptional landscape of RPE cells after subretinal transplantation, with important implications for cell-based therapy for AMD.
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Affiliation(s)
- Bhav Harshad Parikh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Paul Blakeley
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kakkad Regha
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Zengping Liu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
| | - Binxia Yang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Mayuri Bhargava
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Department of Ophthalmology, National University Hospital, Singapore 119074, Singapore
| | - Daniel Soo Lin Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Queenie Shu Woon Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Claudine See Wei Wong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Hao Fei Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Abdurrahmaan Al-Mubaarak
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Chai Chou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | | | - Kah Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Veluchamy Amutha Barathi
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Academic Clinical Program in Ophthalmology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Walter Hunziker
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Gopal Lingam
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Department of Ophthalmology, National University Hospital, Singapore 119074, Singapore
| | - Tim Xiaoming Hu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Xinyi Su
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Department of Ophthalmology, National University Hospital, Singapore 119074, Singapore
- Institute of Health Innovation and Technology, National University of Singapore, Singapore 119276, Singapore
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Teo JQM, Chang HY, Tan SH, Tang CY, Ong RTH, Ko KKK, Chung SJ, Tan TT, Kwa ALH. Comparative Activities of Novel Therapeutic Agents against Molecularly Characterized Clinical Carbapenem-Resistant Enterobacterales Isolates. Microbiol Spectr 2023; 11:e0100223. [PMID: 37184408 PMCID: PMC10269625 DOI: 10.1128/spectrum.01002-23] [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: 03/12/2023] [Accepted: 05/01/2023] [Indexed: 05/16/2023] Open
Abstract
Limited treatment options exist for the treatment of carbapenem-resistant Enterobacterales (CRE) bacteria. Fortunately, there are several recently approved antibiotics indicated for CRE infections. Here, we examine the in vitro activity of various novel agents (eravacycline, plazomicin, ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam) and comparators (tigecycline, amikacin, levofloxacin, fosfomycin, polymyxin B) against 365 well-characterized CRE clinical isolates with various genotypes. Nonduplicate isolates collected from the largest public health hospital in Singapore between 2007 and 2020 were subjected to antimicrobial susceptibility testing (broth microdilution or antibiotic gradient test strips). Susceptibilities were defined using Clinical and Laboratory Standards Institute (CLSI) or Food and Drug Administration (FDA) interpretative criteria. Sequence types and resistance mechanisms were characterized using short-read whole-genome sequencing. Overall, tigecycline and plazomicin exhibited the highest susceptibility rates (89.6% and 80.8%, respectively). However, the tigecycline susceptibility breakpoint utilized here may be outdated in view of prevailing pharmacokinetic-pharmacodynamic (PK/PD) data. Susceptibility varied by carbapenemase genotype; the β-lactam/β-lactamase inhibitor combinations were equally active (92.3 to 99.2% susceptible) against KPC producers, but only ceftazidime-avibactam retained high susceptibility (98.7%) against OXA-48-like producers. Against metallo-β-lactamase producers, only plazomicin exhibited moderate activity (77.0% susceptible). Aminoglycoside activity was also influenced by carbapenemase genotypes. This work provides an insight into the comparative activity and presumptive utility of novel agents in this geographic region. IMPORTANCE This study determined the susceptibilities of carbapenem-resistant Enterobacterales isolates to various novel antimicrobial agents (ceftazidime-avibactam, imipenem-relebactam, meropenem-vaborbactam, eravacycline, and plazomicin). Whole-genome sequencing was performed for all strains. Our study findings provide insights into the comparative activities of novel agents in this geographic region. Plazomicin and ceftazidime-avibactam exhibited the lowest nonsusceptibility rates and may be considered promising agents in the management of carbapenem-resistant Enterobacterales infections. We note also that antibiotic activity is influenced by genotypes and that understanding the geographic region's molecular epidemiology could aid in the definition of the presumptive utility of novel agents and contribute to antibiotic decision-making.
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Affiliation(s)
- Jocelyn Qi-Min Teo
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Hong Yi Chang
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Si Hui Tan
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Cheng Yee Tang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Karrie Kwan Ki Ko
- Department of Microbiology, Singapore General Hospital, Singapore, Singapore
| | - Shimin Jasmine Chung
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Thuan Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore
- Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
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Mah MG, Linster M, Low DHW, Zhuang Y, Jayakumar J, Samsudin F, Wong FY, Bond PJ, Mendenhall IH, Su YCF, Smith GJD. Spike-Independent Infection of Human Coronavirus 229E in Bat Cells. Microbiol Spectr 2023; 11:e0348322. [PMID: 37199653 PMCID: PMC10269751 DOI: 10.1128/spectrum.03483-22] [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: 09/06/2022] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
Bats are the reservoir for numerous human pathogens, including coronaviruses. Despite many coronaviruses having descended from bat ancestors, little is known about virus-host interactions and broader evolutionary history involving bats. Studies have largely focused on the zoonotic potential of coronaviruses with few infection experiments conducted in bat cells. To determine genetic changes derived from replication in bat cells and possibly identify potential novel evolutionary pathways for zoonotic virus emergence, we serially passaged six human 229E isolates in a newly established Rhinolophus lepidus (horseshoe bat) kidney cell line. Here, we observed extensive deletions within the spike and open reading frame 4 (ORF4) genes of five 229E viruses after passaging in bat cells. As a result, spike protein expression and infectivity of human cells was lost in 5 of 6 viruses, but the capability to infect bat cells was maintained. Only viruses that expressed the spike protein could be neutralized by 229E spike-specific antibodies in human cells, whereas there was no neutralizing effect on viruses that did not express the spike protein inoculated on bat cells. However, one isolate acquired an early stop codon, abrogating spike expression but maintaining infection in bat cells. After passaging this isolate in human cells, spike expression was restored due to acquisition of nucleotide insertions among virus subpopulations. Spike-independent infection of human coronavirus 229E may provide an alternative mechanism for viral maintenance in bats that does not rely on the compatibility of viral surface proteins and known cellular entry receptors. IMPORTANCE Many viruses, including coronaviruses, originated from bats. Yet, we know little about how these viruses switch between hosts and enter human populations. Coronaviruses have succeeded in establishing in humans at least five times, including endemic coronaviruses and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In an approach to identify requirements for host switches, we established a bat cell line and adapted human coronavirus 229E viruses by serial passage. The resulting viruses lost their spike protein but maintained the ability to infect bat cells, but not human cells. Maintenance of 229E viruses in bat cells appears to be independent of a canonical spike receptor match, which in turn might facilitate cross-species transmission in bats.
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Affiliation(s)
- Marcus G. Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dolyce H. W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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Zhou Q, Jiang Y, Cai C, Li W, Leow MKS, Yang Y, Liu J, Xu D, Sun L. Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs. Life Sci Alliance 2023; 6:e202302002. [PMID: 37024123 PMCID: PMC10078953 DOI: 10.26508/lsa.202302002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
Although long noncoding RNAs (lncRNAs) experience weaker evolutionary constraints and exhibit lower sequence conservation than coding genes, they can still conserve their features in various aspects. Here, we used multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1,731 conserved lncRNAs with 427 high-confidence ones meeting multiple criteria. Conserved lncRNAs, compared with non-conserved ones, generally have longer gene bodies, more exons and transcripts, stronger connections with human diseases, and are more abundant and widespread across different tissues. Transcription factor (TF) profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger regulation on conserved than non-conserved lncRNAs. Our study has reconciled some discrepant interpretations of lncRNA conservation and revealed a new set of transcriptional factors ruling the expression of conserved lncRNAs.
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Affiliation(s)
- Qiuzhong Zhou
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
| | - Yuxi Jiang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chaoqun Cai
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wen Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Melvin Khee-Shing Leow
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yi Yang
- Program in Health Services & Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Jin Liu
- Program in Health Services & Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Dan Xu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Sun
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore, Singapore
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48
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Lim DWT, Kao HF, Suteja L, Li CH, Quah HS, Tan DSW, Tan SH, Tan EH, Tan WL, Lee JN, Wee FYT, Jain A, Goh BC, Chua MLK, Liao BC, Ng QS, Hong RL, Ang MK, Yeong JPS, Iyer NG. Clinical efficacy and biomarker analysis of dual PD-1/CTLA-4 blockade in recurrent/metastatic EBV-associated nasopharyngeal carcinoma. Nat Commun 2023; 14:2781. [PMID: 37188668 PMCID: PMC10184620 DOI: 10.1038/s41467-023-38407-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 05/02/2023] [Indexed: 05/17/2023] Open
Abstract
Single-agent checkpoint inhibitor (CPI) activity in Epstein-Barr Virus (EBV) related nasopharyngeal carcinoma (NPC) is limited. Dual CPI shows increased activity in solid cancers. In this single-arm phase II trial (NCT03097939), 40 patients with recurrent/metastatic EBV-positive NPC who failed prior chemotherapy receive nivolumab 3 mg/kg every 2 weeks and ipilimumab 1 mg/kg every 6 weeks. Primary outcome of best overall response rate (BOR) and secondary outcomes (progression-free survival [PFS], clinical benefit rate, adverse events, duration of response, time to progression, overall survival [OS]) are reported. The BOR is 38% with median PFS and OS of 5.3 and 19.5 months, respectively. This regimen is well-tolerated and treatment-related adverse events requiring discontinuation are low. Biomarker analysis shows no correlation of outcomes to PD-L1 expression or tumor mutation burden. While the BOR does not meet pre-planned estimates, patients with low plasma EBV-DNA titre (<7800 IU/ml) trend to better response and PFS. Deep immunophenotyping of pre- and on-treatment tumor biopsies demonstrate early activation of the adaptive immune response, with T-cell cytotoxicity seen in responders prior to any clinically evident response. Immune-subpopulation profiling also identifies specific PD-1 and CTLA-4 expressing CD8 subpopulations that predict for response to combined immune checkpoint blockade in NPC.
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Affiliation(s)
- Darren Wan-Teck Lim
- National Cancer Centre Singapore, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
| | - Hsiang-Fong Kao
- National Taiwan University Hospital, Taipei, Taiwan
- National Taiwan University Cancer Center, Taipei, Taiwan
| | - Lisda Suteja
- National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Constance H Li
- National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Hong Sheng Quah
- National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Daniel Shao-Weng Tan
- National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Sze-Huey Tan
- National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Eng-Huat Tan
- National Cancer Centre Singapore, Singapore, Singapore
| | - Wan-Ling Tan
- National Cancer Centre Singapore, Singapore, Singapore
| | - Justina Nadia Lee
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | | | - Amit Jain
- National Cancer Centre Singapore, Singapore, Singapore
| | - Boon-Cher Goh
- National University Health System, Singapore, Singapore
| | - Melvin L K Chua
- National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Bin-Chi Liao
- National Taiwan University Hospital, Taipei, Taiwan
- National Taiwan University Cancer Center, Taipei, Taiwan
| | - Quan Sing Ng
- National Cancer Centre Singapore, Singapore, Singapore
| | - Ruey-Long Hong
- National Taiwan University Hospital, Taipei, Taiwan
- National Taiwan University Cancer Center, Taipei, Taiwan
| | - Mei-Kim Ang
- National Cancer Centre Singapore, Singapore, Singapore
| | - Joe Poh-Sheng Yeong
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Singapore General Hospital, Singapore, Singapore
| | - N Gopalakrishna Iyer
- National Cancer Centre Singapore, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
- Singapore General Hospital, Singapore, Singapore.
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49
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Teo A, Chan LLY, Cheung C, Chia PY, Ong SWX, Fong SW, Ng LFP, Renia L, Lye DC, Young BE, Yeo TW. Myeloperoxidase inhibition may protect against endothelial glycocalyx shedding induced by COVID-19 plasma. Commun Med (Lond) 2023; 3:62. [PMID: 37147421 PMCID: PMC10160718 DOI: 10.1038/s43856-023-00293-x] [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: 08/19/2022] [Accepted: 04/27/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2, the causative agent of COVID-19, is a threat to public health. Evidence suggests increased neutrophil activation and endothelial glycocalyx (EG) damage are independently associated with severe COVID-19. Here, we hypothesised that an increased level of blood neutrophil myeloperoxidase (MPO) is associated with soluble EG breakdown, and inhibiting MPO activity may reduce EG damage. METHODS Analysing a subset of acute and convalescent COVID-19 plasma, 10 from severe and 15 from non-severe COVID-19 cases, and 9 from pre-COVID-19 controls, we determined MPO levels, MPO activity and soluble EG proteins (syndecan-1 and glypican-1) levels by enzyme-linked immunosorbent assay. In vitro primary human aortic endothelial cells were cultured with plasma untreated or treated with specific MPO inhibitors (MPO-IN-28, AZD5904) to determine EG shedding. We then investigated whether inhibiting MPO activity decreased EG degradation. RESULTS In COVID-19 plasma, MPO levels, MPO activity and levels of soluble EG proteins are significantly raised compared to controls, and concentrations increase in proportion to disease severity. Despite clinical recovery, protein concentrations remain significantly elevated. Interestingly, there is a trend of increasing MPO activity in convalescent plasma in both severe and non-severe groups. MPO levels and MPO activity correlate significantly with soluble EG levels and inhibiting MPO activity leads to reduced syndecan-1 shedding, in vitro. CONCLUSIONS Neutrophil MPO may increase EG shedding in COVID-19, and inhibiting MPO activity may protect against EG degradation. Further research is needed to evaluate the utility of MPO inhibitors as potential therapeutics against severe COVID-19.
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Affiliation(s)
- Andrew Teo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- Department of Medicine, The Doherty Institute, University of Melbourne, Melbourne, VIC, Australia.
- National Centre for Infectious Diseases, Singapore, Singapore.
| | - Louisa L Y Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science and Technology and Research (A*STAR), Singapore, Singapore
| | - Po Ying Chia
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Siew Wai Fong
- A*STAR Infectious Diseases Lab (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Lab (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Laurent Renia
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- A*STAR Infectious Diseases Lab (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - David Chien Lye
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Ling School of Medicine, National University of Singapore, Singapore, Singapore
| | - Barnaby Edward Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tsin Wen Yeo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
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50
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Zhang J, Hu Z, Chung HH, Tian Y, Lau KW, Ser Z, Lim YT, Sobota RM, Leong HF, Chen BJ, Yeo CJ, Tan SYX, Kang J, Tan DEK, Sou IF, McClurg UL, Lakshmanan M, Vaiyapuri TS, Raju A, Wong ESM, Tergaonkar V, Rajarethinam R, Pathak E, Tam WL, Tan EY, Tee WW. Dependency of NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis. Nat Commun 2023; 14:2439. [PMID: 37117180 PMCID: PMC10147683 DOI: 10.1038/s41467-023-38132-1] [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: 03/04/2022] [Accepted: 04/17/2023] [Indexed: 04/30/2023] Open
Abstract
Cancer cells undergo transcriptional reprogramming to drive tumor progression and metastasis. Using cancer cell lines and patient-derived tumor organoids, we demonstrate that loss of the negative elongation factor (NELF) complex inhibits breast cancer development through downregulating epithelial-mesenchymal transition (EMT) and stemness-associated genes. Quantitative multiplexed Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins (qPLEX-RIME) further reveals a significant rewiring of NELF-E-associated chromatin partners as a function of EMT and a co-option of NELF-E with the key EMT transcription factor SLUG. Accordingly, loss of NELF-E leads to impaired SLUG binding on chromatin. Through integrative transcriptomic and genomic analyses, we identify the histone acetyltransferase, KAT2B, as a key functional target of NELF-E-SLUG. Genetic and pharmacological inactivation of KAT2B ameliorate the expression of EMT markers, phenocopying NELF ablation. Elevated expression of NELF-E and KAT2B is associated with poorer prognosis in breast cancer patients, highlighting the clinical relevance of our findings. Taken together, we uncover a crucial role of the NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis.
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Affiliation(s)
- Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Republic of Singapore
| | - Zhenhua Hu
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwa Hwa Chung
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Yun Tian
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, 210004, Nanjing, People's Republic of China
| | - Kah Weng Lau
- Department of Pathology, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Republic of Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwei Fen Leong
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Benjamin Jieming Chen
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Clarisse Jingyi Yeo
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Jian Kang
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Dennis Eng Kiat Tan
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Ieng Fong Sou
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Urszula Lucja McClurg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Manikandan Lakshmanan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Thamil Selvan Vaiyapuri
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Anandhkumar Raju
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Esther Sook Miin Wong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Vinay Tergaonkar
- Department of Pathology, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Republic of Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore
| | - Ravisankar Rajarethinam
- Advanced Molecular Pathology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Elina Pathak
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Drive, Genome, Singapore, 138672, Republic of Singapore
| | - Wai Leong Tam
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Drive, Genome, Singapore, 138672, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
| | - Ern Yu Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, 308433, Republic of Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Republic of Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Republic of Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore.
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