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Wu Y, Pegoraro AF, Weitz DA, Janmey P, Sun SX. The correlation between cell and nucleus size is explained by an eukaryotic cell growth model. PLoS Comput Biol 2022; 18:e1009400. [PMID: 35180215 PMCID: PMC8893647 DOI: 10.1371/journal.pcbi.1009400] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 03/03/2022] [Accepted: 01/12/2022] [Indexed: 12/19/2022] Open
Abstract
In eukaryotes, the cell volume is observed to be strongly correlated with the nuclear volume. The slope of this correlation depends on the cell type, growth condition, and the physical environment of the cell. We develop a computational model of cell growth and proteome increase, incorporating the kinetics of amino acid import, protein/ribosome synthesis and degradation, and active transport of proteins between the cytoplasm and the nucleoplasm. We also include a simple model of ribosome biogenesis and assembly. Results show that the cell volume is tightly correlated with the nuclear volume, and the cytoplasm-nucleoplasm transport rates strongly influence the cell growth rate as well as the cell/nucleus volume ratio (C/N ratio). Ribosome assembly and the ratio of ribosomal proteins to mature ribosomes also influence the cell volume and the cell growth rate. We find that in order to regulate the cell growth rate and the cell/nucleus volume ratio, the cell must optimally control groups of kinetic and transport parameters together, which could explain the quantitative roles of canonical growth pathways. Finally, although not explicitly demonstrated in this work, we point out that it is possible to construct a detailed proteome distribution using our model and RNAseq data, provided that a quantitative cell division mechanism is known.
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Affiliation(s)
- Yufei Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - David A. Weitz
- Department of Physics, Harvard University, Boston, Massachusetts, United States of America
| | - Paul Janmey
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sean X. Sun
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Zhao J, Xu W, Zhang Y, Lv X, Chen Y, Ju G, Yang F, Lin L, Rao X, Guo Z, Xing T, Li L, Liang J. Decreased expression of ARID1A invasively downregulates the expression of ribosomal proteins in hepatocellular carcinoma. Biomark Med 2021; 15:497-508. [PMID: 33769075 DOI: 10.2217/bmm-2020-0464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: There was increasing evidence showing that ARID1A alterations correlated with higher tumor mutational burden, but there were limited studies focusing on the adaptive mechanisms for tumor cells to survive under excessive genomic alterations. Materials & methods: To further explore the adaptive mechanisms under ARID1A alterations, we performed RNA sequencing in ARID1A knockdown hepatocellular carcinoma cell lines, and demonstrated that decreased expression of ARID1A controlled global ribosomal proteins synthesis. The results were further confirmed by quantitative reverse transcription-PCR and bioinformatic analysis in The Cancer Genome Atlas Liver Hepatocellular Carcinoma database. Conclusion: The present study was the first to demonstrate that ARID1A might be involved in the translation pathway and served as an adaptive mechanism for tumor cells to survive under stress.
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Affiliation(s)
- Jing Zhao
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, China
| | - Weiran Xu
- Department of Oncology, Peking University International Hospital, Peking University, Beijing, 102206, China
| | - Yu Zhang
- Department of Medical Oncology & Radiation Sickness, Peking University Third Hospital, Peking University, Beijing, 100191, China
| | - Xiaomin Lv
- Department of Neurology, The First Hospital of Jilin University, Jilin University, Changchun, 130021, China
| | - Yiran Chen
- Department of Medical Oncology, Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Beijing, 102206, China
| | - Gaoda Ju
- Department of Medical Oncology, Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Beijing, 102206, China
| | - Fang Yang
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, 215000, China
| | - Li Lin
- Department of Oncology, Peking University International Hospital, Peking University, Beijing, 102206, China
| | - Xiaosong Rao
- Department of Pathology, Peking University International Hospital, Peking University, Beijing, 102206, China
| | - Ziwei Guo
- Department of Oncology, Peking University International Hospital, Peking University, Beijing, 102206, China
| | - Tao Xing
- Department of Medical Oncology, Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Beijing, 102206, China
| | - Li Li
- Department of Oncology, Peking University International Hospital, Peking University, Beijing, 102206, China
| | - Jun Liang
- Department of Oncology, Peking University International Hospital, Peking University, Beijing, 102206, China
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3
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Smekalova EM, Gerashchenko MV, O'Connor PBF, Whittaker CA, Kauffman KJ, Fefilova AS, Zatsepin TS, Bogorad RL, Baranov PV, Langer R, Gladyshev VN, Anderson DG, Koteliansky V. In Vivo RNAi-Mediated eIF3m Knockdown Affects Ribosome Biogenesis and Transcription but Has Limited Impact on mRNA-Specific Translation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:252-266. [PMID: 31855834 PMCID: PMC6926209 DOI: 10.1016/j.omtn.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/20/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
Abstract
Translation is an essential biological process, and dysregulation is associated with a range of diseases including ribosomopathies, diabetes, and cancer. Here, we examine translation dysregulation in vivo using RNAi to knock down the m-subunit of the translation initiation factor eIF3 in the mouse liver. Transcriptome sequencing, ribosome profiling, whole proteome, and phosphoproteome analyses show that eIF3m deficiency leads to the transcriptional response and changes in cellular translation that yield few detectable differences in the translation of particular mRNAs. The transcriptional response fell into two main categories: ribosome biogenesis (increased transcription of ribosomal proteins) and cell metabolism (alterations in lipid, amino acid, nucleic acid, and drug metabolism). Analysis of ribosome biogenesis reveals inhibition of rRNA processing, highlighting decoupling of rRNA synthesis and ribosomal protein gene transcription in response to eIF3m knockdown. Interestingly, a similar reduction in eIF3m protein levels is associated with induction of the mTOR pathway in vitro but not in vivo. Overall, this work highlights the utility of a RNAi-based in vivo approach for studying the regulation of mammalian translation in vivo.
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Affiliation(s)
- Elena M Smekalova
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Patrick B F O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Charles A Whittaker
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kevin J Kauffman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Anna S Fefilova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia; Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia.
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Wang H, Ling MH, Chua TK, Poh CL. Two cellular resource‐based models linking growth and parts characteristics aids the study and optimisation of synthetic gene circuits. ENGINEERING BIOLOGY 2017. [DOI: 10.1049/enb.2017.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Huijuan Wang
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Maurice H.T. Ling
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Tze Kwang Chua
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering National University of Singapore Singapore 117583 Singapore
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