1
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Zeng G, Xu X, Kok YJ, Deng FS, Ling Chow EW, Gao J, Bi X, Wang Y. Cytochrome c regulates hyphal morphogenesis by interfering with cAMP-PKA signaling in Candida albicans. Cell Rep 2023; 42:113473. [PMID: 37980562 DOI: 10.1016/j.celrep.2023.113473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
In the human fungal pathogen Candida albicans, invasive hyphal growth is a well-recognized virulence trait. We employed transposon-mediated genome-wide mutagenesis, revealing that inactivating CTM1 blocks hyphal growth. CTM1 encodes a lysine (K) methyltransferase, which trimethylates cytochrome c (Cyc1) at K79. Mutants lacking CTM1 or expressing cyc1K79A grow as yeast under hyphae-inducing conditions, indicating that unmethylated Cyc1 suppresses hyphal growth. Transcriptomic analyses detected increased levels of the hyphal repressor NRG1 and decreased levels of hyphae-specific genes in ctm1Δ/Δ and cyc1K79A mutants, suggesting cyclic AMP (cAMP)-protein kinase A (PKA) signaling suppression. Co-immunoprecipitation and in vitro kinase assays demonstrated that unmethylated Cyc1 inhibits PKA kinase activity. Surprisingly, hyphae-defective ctm1Δ/Δ and cyc1K79A mutants remain virulent in mice due to accelerated proliferation. Our results unveil a critical role for cytochrome c in maintaining the virulence of C. albicans by orchestrating proliferation, growth mode, and metabolism. Importantly, this study identifies a biological function for lysine methylation on cytochrome c.
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Affiliation(s)
- Guisheng Zeng
- A(∗)STAR Infectious Diseases Labs (A(∗)STAR ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore.
| | - Xiaoli Xu
- A(∗)STAR Infectious Diseases Labs (A(∗)STAR ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Fu-Sheng Deng
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Eve Wai Ling Chow
- A(∗)STAR Infectious Diseases Labs (A(∗)STAR ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore
| | - Jiaxin Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuezhi Bi
- Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yue Wang
- A(∗)STAR Infectious Diseases Labs (A(∗)STAR ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
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2
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Ingavat N, Wang X, Liew JM, Mahfut FB, But KP, Kok YJ, Bi X, Yang Y, Shintaro K, Tsoumpra M, Zhang W. Harnessing ceramic hydroxyapatite as an effective polishing strategy to remove product- and process-related impurities in bispecific antibody purification. BIORESOUR BIOPROCESS 2023; 10:93. [PMID: 38647984 PMCID: PMC10992335 DOI: 10.1186/s40643-023-00713-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/06/2023] [Indexed: 04/25/2024] Open
Abstract
Bispecific antibody (bsAb), a novel therapeutic modality, provides excellent treatment efficacy, yet poses numerous challenges to downstream process development, which are mainly due to the intricate diversity of bsAb structures and impurity profiles. Ceramic hydroxyapatite (CHT), a mixed-mode medium, allows proteins to interact with its calcium sites (C-sites) through metal affinity and/or its phosphate sites (P-sites) through cation exchange interactions. This dual-binding capability potentially offers unique bind and elute behaviours for different proteins of interest, resulting in optimal product purity when suitable elution conditions are employed. In this study, the effectiveness of CHT as a polishing step for bsAb purification was investigated across three model molecules and benchmarked against the traditional cation exchange chromatography (CEX). For both asymmetric and symmetric IgG-like bsAb post Protein A eluates, at least 97% product purity was achieved after CHT polishing. CHT delivered a superior aggregate clearance to CEX, resulting in low high molecular weight (HMW) impurities (0.5%) and low process-related impurities in the product pools. Moreover, CHT significantly mitigated "chromatography-induced aggregation" whereas eightfold more HMW was generated by CEX. This study illustrated the developability of CHT in effectively eliminating low molecular weight (LMW) impurities through post-load-wash (PLW) optimization, resulting in an additional reduction of up to 48% in LMW impurities. A mechanistic explanation regarding the performance of impurity removal and mitigation of the chromatography-induced aggregation by CHT was proposed, illustrating unique CHT capability is potentially driven by C-site cooperation, of which effectiveness could depend on the bsAb composition and size.
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Affiliation(s)
- Nattha Ingavat
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xinhui Wang
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jia Min Liew
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Farouq Bin Mahfut
- Cell Line Development Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ka Pui But
- Protein Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yee Jiun Kok
- Protein Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xuezhi Bi
- Protein Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yuansheng Yang
- Cell Line Development Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kobayashi Shintaro
- Chromatography Media Business Division, HOYA Technosurgical Corporation, Singapore Branch, Singapore
| | - Maria Tsoumpra
- Chromatography Media Business Division, HOYA Technosurgical Corporation, Singapore Branch, Singapore
| | - Wei Zhang
- Downstream Processing Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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3
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Nargund AM, Xu C, Mandoli A, Okabe A, Chen GB, Huang KK, Sheng T, Yao X, Teo JMN, Sundar R, Kok YJ, See YX, Xing M, Li Z, Yong CH, Anand A, Bin Adam Isa ZF, Poon LF, Ng MSW, Koh JYP, Ooi WF, Tay ST, Ong X, Tan ALK, Smoot DT, Ashktorab H, Grabsch HI, Fullwood MJ, Teh BT, Bi X, Kaneda A, Li S, Tan P. Correction: Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer. Cancer Res 2023; 83:804. [PMID: 36861360 DOI: 10.1158/0008-5472.can-22-4060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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4
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Nargund AM, Xu C, Mandoli A, Okabe A, Chen GB, Huang KK, Sheng T, Yao X, Teo JMN, Sundar R, Kok YJ, See YX, Xing M, Li Z, Yong CH, Anand A, A I ZF, Poon LF, Ng MSW, Koh JYP, Ooi WF, Tay ST, Ong X, Tan ALK, Grabsch HI, Fullwood MJ, Teh TB, Bi X, Kaneda A, Li S, Tan P. Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer. Cancer Res 2022; 82:2538-2551. [PMID: 35583999 DOI: 10.1158/0008-5472.can-21-2072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 04/04/2022] [Accepted: 05/09/2022] [Indexed: 12/24/2022]
Abstract
Mutations in the DNA mismatch repair gene MSH2 are causative of microsatellite instability (MSI) in multiple cancers. Here, we discovered that besides its well-established role in DNA repair, MSH2 exerts a novel epigenomic function in gastric cancer. Unbiased CRISPR-based mass spectrometry combined with genome-wide CRISPR functional screening revealed that in early-stage gastric cancer MSH2 genomic binding is not randomly distributed but rather is associated specifically with tumor-associated super-enhancers controlling the expression of cell adhesion genes. At these loci, MSH2 genomic binding was required for chromatin rewiring, de novo enhancer-promoter interactions, maintenance of histone acetylation levels, and regulation of cell adhesion pathway expression. The chromatin function of MSH2 was independent of its DNA repair catalytic activity but required MSH6, another DNA repair gene, and recruitment to gene loci by the SWI/SNF chromatin remodeler SMARCA4/BRG1. Loss of MSH2 in advanced gastric cancers was accompanied by deficient cell adhesion pathway expression, epithelial-mesenchymal transition, and enhanced tumorigenesis in vitro and in vivo. However, MSH2-deficient gastric cancers also displayed addiction to BAZ1B, a bromodomain-containing family member, and consequent synthetic lethality to bromodomain and extraterminal motif (BET) inhibition. Our results reveal a role for MSH2 in gastric cancer epigenomic regulation and identify BET inhibition as a potential therapy in MSH2-deficient gastric malignancies. SIGNIFICANCE DNA repair protein MSH2 binds and regulates cell adhesion genes by enabling enhancer-promoter interactions, and loss of MSH2 causes deficient cell adhesion and bromodomain and extraterminal motif inhibitor synthetic lethality in gastric cancer.
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Affiliation(s)
- Amrita M Nargund
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Amit Mandoli
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Gao Bin Chen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Taotao Sheng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Xiaosai Yao
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Hematology-Oncology, National University Health System, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Yi Xiang See
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Manjie Xing
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Zhimei Li
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore
| | - Chern Han Yong
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore
| | - Aparna Anand
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Lai Fong Poon
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | | | - Javier Yu Peng Koh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Wen Fong Ooi
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Heike I Grabsch
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.,Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Melissa J Fullwood
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tean Bin Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore, Singapore
| | - Xuezhi Bi
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Bioprocessing Technology Institute, Singapore, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore, Singapore
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5
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Lee AP, Kok YJ, Lakshmanan M, Leong D, Zheng L, Lim HL, Chen S, Mak SY, Ang KS, Templeton N, Salim T, Wei X, Gifford E, Tan AHM, Bi X, Ng SK, Lee DY, Ling WLW, Ho YS. Multi-omics profiling of a CHO cell culture system unravels the effect of culture pH on cell growth, antibody titer, and product quality. Biotechnol Bioeng 2021; 118:4305-4316. [PMID: 34289087 DOI: 10.1002/bit.27899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/23/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022]
Abstract
A robust monoclonal antibody (mAb) bioprocess requires physiological parameters such as temperature, pH, or dissolved oxygen to be well-controlled as even small variations in them could potentially impact the final product quality. For instance, pH substantially affects N-glycosylation, protein aggregation, and charge variant profiles, as well as mAb productivity. However, relatively less is known about how pH jointly influences product quality and titer. In this study, we investigated the effect of pH on culture performance, product titer, and quality profiles by applying longitudinal multi-omics profiling, including transcriptomics, proteomics, metabolomics, and glycomics, at three different culture pH set points. The subsequent systematic analysis of multi-omics data showed that pH set points differentially regulated various intracellular pathways including intracellular vesicular trafficking, cell cycle, and apoptosis, thereby resulting in differences in specific productivity, product titer, and quality profiles. In addition, a time-dependent variation in mAb N-glycosylation profiles, independent of pH, was identified to be mainly due to the accumulation of mAb proteins in the endoplasmic reticulum disrupting cellular homeostasis over culture time. Overall, this multi-omics-based study provides an in-depth understanding of the intracellular processes in mAb-producing CHO cell line under varied pH conditions, and could serve as a baseline for enabling the quality optimization and control of mAb production.
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Affiliation(s)
- Alison P Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dawn Leong
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lu Zheng
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hsueh Lee Lim
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shi Ya Mak
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kok Siong Ang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Neil Templeton
- Process Research and Development, Merck & Co. Inc., West Point, Pennsylvania, USA
| | - Taha Salim
- Process Research and Development, Merck & Co. Inc., Kenilworth, New Jersey, USA
| | - Xiaona Wei
- Scientific Informatics, MSD International GmbH (Singapore Branch), Singapore, Singapore
| | - Eric Gifford
- Scientific Informatics, MSD International GmbH (Singapore Branch), Singapore, Singapore
| | - Andy Hee-Meng Tan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Say Kong Ng
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,School of Chemical Engineering, Sungkyunkwan University, Seoul, Gyeonggi-do, Republic of Korea
| | - Wai Lam W Ling
- Process Research and Development, Merck & Co. Inc., Kenilworth, New Jersey, USA
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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6
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Lay C, Chu CW, Purbojati RW, Acerbi E, Drautz-Moses DI, de Sessions PF, Jie S, Ho E, Kok YJ, Bi X, Chen S, Mak SY, Chua MC, Goh AEN, Chiang WC, Rao R, Chaithongwongwatthana S, Khemapech N, Chongsrisawat V, Martin R, Roeselers G, Ho YS, Hibberd ML, Schuster SC, Knol J. A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants. BMC Microbiol 2021; 21:191. [PMID: 34172012 PMCID: PMC8229302 DOI: 10.1186/s12866-021-02230-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD. RESULTS As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome. CONCLUSIONS This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development. TRIAL REGISTRATION The study was registered in the Dutch Trial Register (Number: 2838 ) on 4th April 2011.
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Affiliation(s)
| | | | - Rikky Wenang Purbojati
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Enzo Acerbi
- Danone Nutricia Research, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | | | - Song Jie
- Genome Institute of Singapore, Singapore, Singapore
| | - Eliza Ho
- Genome Institute of Singapore, Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Shi Ya Mak
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Mei Chien Chua
- KK Women's and Children's Hospital, Singapore, Singapore
| | - Anne E N Goh
- KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Rajeshwar Rao
- KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Nipon Khemapech
- King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voranush Chongsrisawat
- King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rocio Martin
- Danone Nutricia Research, Utrecht, The Netherlands
| | | | - Ying Swan Ho
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Martin L Hibberd
- Genome Institute of Singapore, Singapore, Singapore
- London School of Hygiene and Tropical Medicine, London, UK
| | - Stephan C Schuster
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands.
- Wageningen University, Wageningen, The Netherlands.
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7
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Ong ST, Ng AS, Ng XR, Zhuang Z, Wong BHS, Prasannan P, Kok YJ, Bi X, Shim H, Wulff H, Chandy KG, Verma NK. Extracellular K + Dampens T Cell Functions: Implications for Immune Suppression in the Tumor Microenvironment. Bioelectricity 2019; 1:169-179. [PMID: 34471819 DOI: 10.1089/bioe.2019.0016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background: Dying tumor cells release intracellular potassium (K+), raising extracellular K+ ([K+]e) in the tumor microenvironment (TME) to 40-50 mM (high-[K+]e). Here, we investigated the effect of high-[K+]e on T cell functions. Materials and Methods: Functional impacts of high-[K+]e on human T cells were determined by cellular, molecular, and imaging assays. Results: Exposure to high-[K+]e suppressed the proliferation of central memory and effector memory T cells, while T memory stem cells were unaffected. High-[K+]e inhibited T cell cytokine production and dampened antitumor cytotoxicity, by modulating the Akt signaling pathway. High-[K+]e caused significant upregulation of the immune checkpoint protein PD-1 in activated T cells. Although the number of KCa3.1 calcium-activated potassium channels expressed in T cells remained unaffected under high-[K+]e, a novel KCa3.1 activator, SKA-346, rescued T cells from high-[K+]e-mediated suppression. Conclusion: High-[K+]e represents a so far overlooked secondary checkpoint in cancer. KCa3.1 activators could overcome such "ionic-checkpoint"-mediated immunosuppression in the TME, and be administered together with known PD-1 inhibitors and other cancer therapeutics to improve outcomes.
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Affiliation(s)
- Seow Theng Ong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Aik Seng Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Xuan Rui Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Zhong Zhuang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Brandon Han Siang Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Praseetha Prasannan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Duke-NUS Medical School, National University of Singapore, Singapore
| | - Heesung Shim
- Department of Pharmacology, School of Medicine, University of California, Davis, Davis, California.,Department of Chemistry, University of California, Davis, Davis, California
| | - Heike Wulff
- Department of Pharmacology, School of Medicine, University of California, Davis, Davis, California
| | | | - Navin Kumar Verma
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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8
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Lakshmanan M, Kok YJ, Lee AP, Kyriakopoulos S, Lim HL, Teo G, Poh SL, Tang WQ, Hong J, Tan AH, Bi X, Ho YS, Zhang P, Ng SK, Lee D. Multi‐omics profiling of CHO parental hosts reveals cell line‐specific variations in bioprocessing traits. Biotechnol Bioeng 2019; 116:2117-2129. [DOI: 10.1002/bit.27014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/03/2019] [Accepted: 05/02/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Meiyappan Lakshmanan
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Alison P. Lee
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Sarantos Kyriakopoulos
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Hsueh Lee Lim
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Gavin Teo
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Swan Li Poh
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Wen Qin Tang
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Jongkwang Hong
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Andy Hee‐Meng Tan
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Xuezhi Bi
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Ying Swan Ho
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Peiqing Zhang
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Say Kong Ng
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
| | - Dong‐Yup Lee
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR) Singapore
- School of Chemical EngineeringSungkyunkwan UniversitySuwon Republic of Korea
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Kok YJ, Ye L, Muller J, Ow DSW, Bi X. Brewing with malted barley or raw barley: what makes the difference in the processes? Appl Microbiol Biotechnol 2018; 103:1059-1067. [PMID: 30515549 DOI: 10.1007/s00253-018-9537-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 12/30/2022]
Abstract
Malted barley is the main source for fermentable sugars used by yeasts in the traditional brewing of beers but its use has been increasingly substituted by unmalted barley and other raw grain adjuncts in recent years. The incorporation of raw grains is mainly economically driven, with the added advantage of improved sustainability, by reducing reliance on the malting process and its associated cost. The use of raw grains however, especially in high proportion, requires modifications to the brewing process to accommodate the lack of malt enzymes and the differences in structural and chemical composition between malted and raw grains. This review describes the traditional malting and brewing processes for the production of full malt beer, compares the modifications to these processes, namely milling and mashing, when raw barley or other grains are used in the production of wort-a solution of fermentable extracts metabolized by yeast and converted into beer, and discusses the activity of endogenous malt enzymes and the use of commercial brewing enzyme cocktails which enable high adjunct brewing.
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Affiliation(s)
- Yee Jiun Kok
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Lijuan Ye
- Nestlé R&D Center (Pte) Ltd, 29 Quality Road, Singapore, 618802, Singapore
| | - Jeroen Muller
- Nestlé Research Center, Lausanne 26, CH-1000, Lausanne, Switzerland
| | - Dave Siak-Wei Ow
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.
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Haryadi R, Ho S, Kok YJ, Pu HX, Zheng L, Pereira NA, Li B, Bi X, Goh LT, Yang Y, Song Z. Optimization of heavy chain and light chain signal peptides for high level expression of therapeutic antibodies in CHO cells. PLoS One 2015; 10:e0116878. [PMID: 25706993 PMCID: PMC4338144 DOI: 10.1371/journal.pone.0116878] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 12/16/2014] [Indexed: 11/18/2022] Open
Abstract
Translocation of a nascent protein from the cytosol into the ER mediated by its signal peptide is a critical step in protein secretion. The aim of this work was to develop a platform technology to optimize the signal peptides for high level production of therapeutic antibodies in CHO cells. A database of signal peptides from a large number of human immunoglobulin (Ig) heavy chain (HC) and kappa light chain (LC) was generated. Most of the HC signal peptides contain 19 amino acids which can be divided into three domains and the LC signal peptides contain 22 amino acids. The signal peptides were then clustered according to sequence similarity. Based on the clustering, 8 HC and 2 LC signal peptides were analyzed for their impacts on the production of 5-top selling antibody therapeutics, namely, Herceptin, Avastin, Remicade, Rituxan, and Humira. The best HC and LC signal peptides for producing these 5 antibodies were identified. The optimized signal peptides for Rituxan is 2-fold better compared to its native signal peptides which are available in the public database. Substitution of a single amino acid in the optimized HC signal peptide for Avastin reduced its production significantly. Mass spectrometry analyses revealed that all optimized signal peptides are accurately removed in the mature antibodies. The results presented in this report are particularly important for the production of these 5 antibodies as biosimilar drugs. They also have the potential to be the best signal peptides for the production of new antibodies in CHO cells.
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Affiliation(s)
- Ryan Haryadi
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Steven Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Helen X. Pu
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lu Zheng
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Natasha A. Pereira
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Bin Li
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lin-Tang Goh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yuansheng Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhiwei Song
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- * E-mail:
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Nissom PM, Sanny A, Kok YJ, Hiang YT, Chuah SH, Shing TK, Lee YY, Wong KTK, Hu WS, Sim MYG, Philp R. Transcriptome and proteome profiling to understanding the biology of high productivity CHO cells. Mol Biotechnol 2007; 34:125-40. [PMID: 17172658 DOI: 10.1385/mb:34:2:125] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 12/23/2022]
Abstract
A combined transcriptome and proteome analysis was carried out to identify key genes and proteins differentially expressed in Chinese hamster ovary (CHO) cells producing high and low levels of dhfr-GFP fusion protein. Comparison of transcript levels was performed using a proprietary 15K CHO cDNA microarray chip, whereas proteomic analysis was performed using iTRAQ quantitative protein profiling technique. Microarray analysis revealed 77 differentially expressed genes, with 53 genes upregulated and 24 genes downregulated. Proteomic analysis gave 75 and 80 proteins for the midexponential and stationary phase, respectively. Although there was a general lack of correlation between mRNA levels and quantitated protein abundance, results from both datasets concurred on groups of proteins/genes based on functional categorization. A number of genes (20%) and proteins (45 and 23%) were involved in processes related to protein biosynthesis. We also identified three genes/proteins involved in chromatin modification. Enzymes responsible for opening up chromatin, Hmgn3 and Hmgb1, were upregulated whereas enzymes that condense chromatin, histone H1.2, were downregulated. Genes and proteins that promote cell growth (Igfbp4, Ptma, S100a6, and Lgals3) were downregulated, whereas those that deter cell growth (Ccng2, Gsg2, and S100a11) were upregulated. Other main groups of genes and proteins include carbohydrate metabolism, signal transduction, and transport. Our findings show that an integrated genomic and proteomics approach can be effectively utilized to monitor transcriptional and posttranscriptional events of mammalian cells in culture.
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Affiliation(s)
- Peter Morin Nissom
- Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore, 138668.
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