| 1. |
Ito, Y., Uda, S*., Kokaji, T., Hirayama, A., Soga, T., Suzuki, Y., Kuroda, S., & Kubota, H., Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures, Scientific reports, https://doi.org/10.1038/s41598-023-31547-2, 13, 1, [4758], 2023.03. |
| 2. |
Suguru Fujita, Yasuaki Karasawa, Masashi Fujii, Ken-Ichi Hironaka, Shinsuke Uda, Hiroyuki Kubota, Hiroshi Inoue, Yohei Sumitomo, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda, Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans, NPJ systems biology and applications, https://doi.org/10.1038/s41540-022-00213-0, 8, 1, 6-6, 2022.02. |
| 3. |
Fumiko Matsuzaki, Shinsuke Uda, Yukiyo Yamauchi, Masaki Matsumoto, Tomoyoshi Soga, Kazumitsu Maehara, Yasuyuki Ohkawa, Keiichi I Nakayama, Shinya Kuroda, Hiroyuki Kubota, An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver., Cell reports, 10.1016/j.celrep.2021.109569, 36, 8, 109569-109569, 2021.08. |
| 4. |
Riku Egami, Toshiya Kokaji, Atsushi Hatano, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-ichi Hironaka, Saori Uematsu, Akira Terakawa, Yunfan Bai, Yifei Pan, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Kubota, Yutaka Suzuki, Masaki Matsumoto, Keiichi I. Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda, Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle, iScience, https://doi.org/10.1016/j.isci.2021.102217, 24, 3, 102217-102217, 2021.03. |
| 5. |
Toshiya Kokaji, Atsushi Hatano, Yuki Ito, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-ichi Hironaka, Riku Egami, Akira Terakawa, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Kubota, Yutaka Suzuki, Kazutaka Ikeda, Makoto Arita, Masaki Matsumoto, Keiichi Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda, Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity , SCIENCE SIGNALING, 13, 660, 2020.12. |
| 6. |
Takumi Wada, Ken-ichi Hironaka, Mitsutaka Wataya, Masashi Fujii, Miki Eto, Shinsuke Uda, Daisuke Hoshino, Katsuyuki Kunida, Haruki Inoue, Hiroyuki Kubota, Tsuguto Takizawa, Yasuaki Karasawa, Hirofumi Nakatomi, Nobuhito Saito, Hiroki Hamaguchi, Yasuro Furuichi, Yasuko Manabe, Nobuharu L. Fujii, Shinya Kuroda, Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise , CELL REPORTS, 32, 9, 2020.09. |
| 7. |
Shinsuke Uda, Application of information theory in systems biology, Biophysical Reviews, 10.1007/s12551-020-00665-w, 12, 2, 377-384, 2020.04, Over recent years, new light has been shed on aspects of information processing in cells. The quantification of information, as described by Shannon’s information theory, is a basic and powerful tool that can be applied to various fields, such as communication, statistics, and computer science, as well as to information processing within cells. It has also been used to infer the network structure of molecular species. However, the difficulty of obtaining sufficient sample sizes and the computational burden associated with the high-dimensional data often encountered in biology can result in bottlenecks in the application of information theory to systems biology. This article provides an overview of the application of information theory to systems biology, discussing the associated bottlenecks and reviewing recent work.. |
| 8. |
Shinsuke Uda, Approximate conditional independence test using residuals, 12th International Conference on Agents and Artificial Intelligence, ICAART 2020
ICAART 2020 - Proceedings of the 12th International Conference on Agents and Artificial Intelligence, 297-304, 2020.01, Conditional mutual information is a useful measure for detecting the association between variables that are also affected by other variables. Though permutation tests are used to check whether the conditional mutual information is zero to indicate mutual independence, permutations are difficult to perform because the other variables in a dataset may be associated with the variables in question. This problem is particularly acute when working with datasets of small sample size. This study aims to propose a computational method for approximating conditional mutual information based on the distribution of residuals in regression models. The proposed method can implement the permutation tests for statistical significance by translating the problem of measuring conditional independence into the problem of estimating simple independence. Additionally, a reliability of p-value in permutation test is defined to omit unreliably detected associations. We tested our proposed method's performance in inferring the network structure of an artificial gene network against comparable methods submitted to the Dream4 challenge.. |
| 9. |
Masashi Fujii, Yohei Murakami, Yasuaki Karasawa, Yohei Sumitomo, Suguru Fujita, Masanori Koyama, Shinsuke Uda, Hiroyuki Kubota, Hiroshi Inoue, Katsumi Konishi, Shigeyuki Oba, Shin Ishii, Shinya Kuroda, Logical design of oral glucose ingestion pattern minimizing blood glucose in humans, npj Systems Biology and Applications, 10.1038/s41540-019-0108-1, 5, 1, 2019.12, Excessive increase in blood glucose level after eating increases the risk of macroangiopathy, and a method for not increasing the postprandial blood glucose level is desired. However, a logical design method of the dietary ingestion pattern controlling the postprandial blood glucose level has not yet been established. We constructed a mathematical model of blood glucose control by oral glucose ingestion in three healthy human subjects, and predicted that intermittent ingestion 30 min apart was the optimal glucose ingestion patterns that minimized the peak value of blood glucose level. We confirmed with subjects that this intermittent pattern consistently decreased the peak value of blood glucose level. We also predicted insulin minimization pattern, and found that the intermittent ingestion 30 min apart was optimal, which is similar to that of glucose minimization pattern. Taken together, these results suggest that the glucose minimization is achieved by suppressing the peak value of insulin concentration, rather than by enhancing insulin concentration. This approach could be applied to design optimal dietary ingestion patterns.. |
| 10. |
Izumi Ohigashi, Yu Tanaka, Kenta Kondo, Sayumi Fujimori, Hiroyuki Kondo, Amy C. Palin, Victoria Hoffmann, Mina Kozai, Yosuke Matsushita, Shinsuke Uda, Ryo Motosugi, Jun Hamazaki, Hiroyuki Kubota, Shigeo Murata, Keiji Tanaka, Toyomasa Katagiri, Hidetaka Kosako, Yousuke Takahama, Trans-omics Impact of Thymoproteasome in Cortical Thymic Epithelial Cells, Cell Reports, 10.1016/j.celrep.2019.10.079, 29, 9, 2901-2916.e6, 2019.11, Ohigashi et al. show that the use of cyclin D1-transgenic mice allows quantitative proteomic analysis of cortical and medullary thymic epithelial cells (TECs). Results provide a trans-omics platform for further exploration of TEC biology and reveal the specific impact of the thymoproteasome on proteasome subunit composition in cortical TECs.. |
| 11. |
Kentaro Kawata, Katsuyuki Yugi, Atsushi Hatano, Toshiya Kokaji, Yoko Tomizawa, Masashi Fujii, Shinsuke Uda, Hiroyuki Kubota, Masaki Matsumoto, Keiichi Nakayama, Shinya Kuroda, Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data, Genes to Cells, 10.1111/gtc.12655, 24, 1, 82-93, 2019.01, Cellular signaling regulates various cellular functions via protein phosphorylation. Phosphoproteomic data potentially include information for a global regulatory network from signaling to cellular functions, but a procedure to reconstruct this network using such data has yet to be established. In this paper, we provide a procedure to reconstruct a global regulatory network from signaling to cellular functions from phosphoproteomic data by integrating prior knowledge of cellular functions and inference of the kinase–substrate relationships (KSRs). We used phosphoproteomic data from insulin-stimulated Fao hepatoma cells and identified protein phosphorylation regulated by insulin specifically over-represented in cellular functions in the KEGG database. We inferred kinases for protein phosphorylation by KSRs, and connected the kinases in the insulin signaling layer to the phosphorylated proteins in the cellular functions, revealing that the insulin signal is selectively transmitted via the Pi3k-Akt and Erk signaling pathways to cellular adhesions and RNA maturation, respectively. Thus, we provide a method to reconstruct global regulatory network from signaling to cellular functions based on phosphoproteomic data.. |
| 12. |
Hiroyuki Kubota, Shinsuke Uda, Fumiko Matsuzaki, Yukiyo Yamauchi, Shinya Kuroda, Erratum
In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver (Cell Systems (2018) 7(1) (118–128.e3), (S240547121830231X), (10.1016/j.cels.2018.05.013)), Cell Systems, 10.1016/j.cels.2018.11.002, 7, 5, 562-564, 2018.11, Main Text: (Cell Systems 7, 118–128.e1–e3, July 25, 2018) In the original Figure S1 of this article, the western blotting images included by the authors, labeled “pIR” and “IR” (20 μM), were incorrect. They were duplicated images of pAKT and pGSK3β (20 μM) panels, respectively. However, the correct blots were quantitated and analyzed by the author. This mistake does not affect the other figures in the paper or its conclusions. Figure S1 has been corrected to include the correct images. The authors apologize for any confusion their error may have caused.[Figure presented]. |
| 13. |
Kentaro Kawata, Atsushi Hatano, Katsuyuki Yugi, Hiroyuki Kubota, Takanori Sano, Masashi Fujii, Yoko Tomizawa, Toshiya Kokaji, Kaori Y. Tanaka, Shinsuke Uda, Yutaka Suzuki, Masaki Matsumoto, Keiichi I. Nakayama, Kaori Saitoh, Keiko Kato, Ayano Ueno, Maki Ohishi, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda, Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks, iScience, 10.1016/j.isci.2018.07.022, 7, 212-229, 2018.09, The concentrations of insulin selectively regulate multiple cellular functions. To understand how insulin concentrations are interpreted by cells, we constructed a trans-omic network of insulin action in FAO hepatoma cells using transcriptomic data, western blotting analysis of signaling proteins, and metabolomic data. By integrating sensitivity into the trans-omic network, we identified the selective trans-omic networks stimulated by high and low doses of insulin, denoted as induced and basal insulin signals, respectively. The induced insulin signal was selectively transmitted through the pathway involving Erk to an increase in the expression of immediate-early and upregulated genes, whereas the basal insulin signal was selectively transmitted through a pathway involving Akt and an increase of Foxo phosphorylation and a reduction of downregulated gene expression. We validated the selective trans-omic network in vivo by analysis of the insulin-clamped rat liver. This integrated analysis enabled molecular insight into how liver cells interpret physiological insulin signals to regulate cellular functions.. |
| 14. |
Hiroyuki Kubota, Shinsuke Uda, Fumiko Matsuzaki, Yukiyo Yamauchi, Shinya Kuroda, In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver, Cell Systems, 10.1016/j.cels.2018.05.013, 7, 1, 118-128.e3, 2018.07, Cells respond to various extracellular stimuli through a limited number of signaling pathways. One strategy to process such stimuli is to code the information into the temporal patterns of molecules. Although we showed that insulin selectively regulated molecules depending on its temporal patterns using Fao cells, the in vivo mechanism remains unknown. Here, we show how the insulin-AKT pathway processes the information encoded into the temporal patterns of blood insulin. We performed hyperinsulinemic-euglycemic clamp experiments and found that, in the liver, all temporal patterns of insulin are encoded into the insulin receptor, and downstream molecules selectively decode them through AKT. S6K selectively decodes the additional secretion information. G6Pase interprets the basal secretion information through FoxO1, while GSK3β decodes all secretion pattern information. Mathematical modeling revealed the mechanism via differences in network structures and from sensitivity and time constants. Given that almost all hormones exhibit distinct temporal patterns, temporal coding may be a general principle of system homeostasis by hormones. Kubota et al. show that the insulin-AKT pathway in the liver processes the information encoded into the temporal patterns of blood insulin and selectively regulates downstream molecules. Given that almost all hormones exhibit distinct temporal patterns, our study demonstrates the possibility of temporal coding as a general principle of systemic homeostasis by hormones.. |
| 15. |
Katsumi Konishi, Masashi Fujii, Katsuyuki Kunida, Shinsuke Uda, Shinya Kuroda, Matrix rank minimization approach to signal recovery and nonlinear function estimation for nonlinear ARX model with input nonlinearity, 2017 11th Asian Control Conference, ASCC 2017
2017 Asian Control Conference, ASCC 2017, 10.1109/ASCC.2017.8287382, 1428-1431, 2018.02, This paper deals with an input/output signal recovery problem for nonlinear multiple-input single-output autoregressive exogenous (ARX) models with input nonlinearity, which are used in data-driven systems biology. A matrix rank minimization approach is applied, and a new signal recovery algorithm for nonlinear ARX models is provided. The proposed algorithm recovers output signals and nonlinear-transformed input signals on a linear subspace using some assumptions about nonlinear functions and does not require the exact knowledge of nonlinear functions. Numerical examples using experimental data of signal transduction of cellular systems show the efficiency of the proposed algorithm.. |
| 16. |
Kaoru Ohashi, Masashi Fujii, Shinsuke Uda, Hiroyuki Kubota, Hisako Komada, Kazuhiko Sakaguchi, Wataru Ogawa, Shinya Kuroda, Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects, npj Systems Biology and Applications, 10.1038/s41540-018-0051-6, 4, 2018, Insulin plays a central role in glucose homeostasis, and impairment of insulin action causes glucose intolerance and leads to type 2 diabetes mellitus (T2DM). A decrease in the transient peak and sustained increase of circulating insulin following an infusion of glucose accompany T2DM pathogenesis. However, the mechanism underlying this abnormal temporal pattern of circulating insulin concentration remains unknown. Here we show that changes in opposite direction of hepatic and peripheral insulin clearance characterize this abnormal temporal pattern of circulating insulin concentration observed in T2DM. We developed a mathematical model using a hyperglycemic and hyperinsulinemic-euglycemic clamp in 111 subjects, including healthy normoglycemic and diabetic subjects. The hepatic and peripheral insulin clearance significantly increase and decrease, respectively, from healthy to borderline type and T2DM. The increased hepatic insulin clearance reduces the amplitude of circulating insulin concentration, whereas the decreased peripheral insulin clearance changes the temporal patterns of circulating insulin concentration from transient to sustained. These results provide further insight into the pathogenesis of T2DM, and thus may contribute to develop better treatment of this condition.. |
| 17. |
Kentaro Kawata, Atsushi Hatano, Katsuyuki Yugi, Takanori Sano, Masashi Fujii, Yoko Tomizawa, Toshiya Kokaji, Kaori Y. Tanaka, Shinsuke Uda, Y. Suzuki, Masaki Matsumoto, Keiichi Nakayama, Kaori Saitoh, Keiko Kato, Ayano Ueno, Maki Ohishi, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda, Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks, iScience, 7, 212-229, 2018, The concentrations of insulin selectively regulate multiple cellular functions. To understand how insulin concentrations are interpreted by cells, we constructed a trans-omic network of insulin action in FAO hepatoma cells using transcriptomic data, western blotting analysis of signaling proteins, and metabolomic data. By integrating sensitivity into the trans-omic network, we identified the selective trans-omic networks stimulated by high and low doses of insulin, denoted as induced and basal insulin signals, respectively. The induced insulin signal was selectively transmitted through the pathway involving Erk to an increase in the expression of immediate-early and upregulated genes, whereas the basal insulin signal was selectively transmitted through a pathway involving Akt and an increase of Foxo phosphorylation and a reduction of downregulated gene expression. We validated the selective trans-omic network in vivo by analysis of the insulin-clamped rat liver. This integrated analysis enabled molecular insight into how liver cells interpret physiological insulin signals to regulate cellular functions.. |
| 18. |
Takaho Tsuchiya, Masashi Fujii, Naoki Matsuda, Katsuyuki Kunida, Shinsuke Uda, Hiroyuki Kubota, Katsumi Konishi, Shinya Kuroda, System identification of signaling dependent gene expression with different time-scale data, PLoS Computational Biology, 10.1371/journal.pcbi.1005913, 13, 12, 2017.12, Cells decode information of signaling activation at a scale of tens of minutes by downstream gene expression with a scale of hours to days, leading to cell fate decisions such as cell differentiation. However, no system identification method with such different time scales exists. Here we used compressed sensing technology and developed a system identification method using data of different time scales by recovering signals of missing time points. We measured phosphorylation of ERK and CREB, immediate early gene expression products, and mRNAs of decoder genes for neurite elongation in PC12 cell differentiation and performed system identification, revealing the input–output relationships between signaling and gene expression with sensitivity such as graded or switch-like response and with time delay and gain, representing signal transfer efficiency. We predicted and validated the identified system using pharmacological perturbation. Thus, we provide a versatile method for system identification using data with different time scales.. |
| 19. |
Takanori Sano, Kentaro Kawata, Satoshi Ohno, Katsuyuki Yugi, Hiroaki Kakuda, Hiroyuki Kubota, Shinsuke Uda, Masashi Fujii, Katsuyuki Kunida, Daisuke Hoshino, Atsushi Hatano, Yuki Ito, Miharu Sato, Yutaka Suzuki, Shinya Kuroda, Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin, Science Signaling, 10.1126/scisignal.aaf3739, 9, 455, 2016.11, Secretion of insulin transiently increases after eating, resulting in a high circulating concentration. Fasting limits insulin secretion, resulting in a low concentration of insulin in the circulation. We analyzed transcriptional responses to different temporal patterns and doses of insulin in the hepatoma FAO cells and identified 13 up-regulated and 16 down-regulated insulin-responsive genes (IRGs). The up-regulated IRGs responded more rapidly than did the down-regulated IRGs to transient stepwise or pulsatile increases in insulin concentration, whereas the downregulated IRGs were repressed at lower concentrations of insulin than those required to stimulate the up-regulated IRGs. Mathematical modeling of the insulin response as two stages-(i) insulin signaling to transcription and (ii) transcription and mRNA stability-indicated that the first stage was the more rapid stage for the down-regulated IRGs, whereas the second stage of transcription was the more rapid stage for the up-regulated IRGs. A subset of the IRGs that were up-regulated or down-regulated in the FAO cells was similarly regulated in the livers of rats injected with a single dose of insulin. Thus, not only can cells respond to insulin but they can also interpret the intensity and pattern of signal to produce distinct transcriptional responses. These results provide insight that may be useful in treating obesity and type 2 diabetes associated with aberrant insulin production or tissue responsiveness.. |
| 20. |
Takamasa Kudo, Shinsuke Uda, Takaho Tsuchiya, Takumi Wada, Yasuaki Karasawa, Masashi Fujii, Takeshi H. Saito, Shinya Kuroda, Laguerre Filter Analysis with Partial Least Square Regression Reveals a Priming Effect of ERK and CREB on c-FOS Induction, PLoS ONE, 10.1371/journal.pone.0160548, 11, 8, PLoS ONE 11(8): e0160548, 2016.08. |
| 21. |
Takamasa Kudo, Shinsuke Uda, Takaho Tsuchiya, Takumi Wada, Yasuaki Karasawa, Masashi Fujii, Takeshi H. Saito, Shinya Kuroda, Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction, PLoS One, 10.1371/journal.pone.0160548, 11, 8, 2016.08, Signaling networks are made up of limited numbers of molecules and yet can code information that controls different cellular states through temporal patterns and a combination of signaling molecules. In this study, we used a data-driven modeling approach, the Laguerre filter with partial least square regression, to describe how temporal and combinatorial patterns of signaling molecules are decoded by their downstream targets. The Laguerre filter is a time series model used to represent a nonlinear system based on Volterra series expansion. Furthermore, with this approach, each component of the Volterra series expansion is expanded by Laguerre basis functions. We combined two approaches, application of a Laguerre filter and partial least squares (PLS) regression, and applied the combined approach to analysis of a signal transduction network.We applied the Laguerre filter with PLS regression to identify input and output (IO) relationships between MAP kinases and the products of immediate early genes (IEGs).We found that Laguerre filter with PLS regression performs better than Laguerre filter with ordinary regression for the reproduction of a time series of IEGs. Analysis of the nonlinear characteristics extracted using the Laguerre filter revealed a priming effect of ERK and CREB on c-FOS induction. Specifically, we found that the effects of a first pulse of ERK enhance the subsequent effects on c-FOS induction of treatment with a second pulse of ERK, a finding consistent with prior molecular biological knowledge. The variable importance of projections and output loadings in PLS regression predicted the upstream dependency of each IEG. Thus, a Laguerre filter with partial least square regression approach appears to be a powerful method to find the processing mechanism of temporal patterns and combination of signaling molecules by their downstream gene expression.. |
| 22. |
Shinsuke Uda, Shinya Kuroda, Analysis of cellular signal transduction from an information theoretic approach, Seminars in Cell & Developmental Biology, 51, 24-31, 2016.03. |
| 23. |
Shinsuke Uda, Shinya Kuroda, Analysis of cellular signal transduction from an information theoretic approach, Seminars in Cell and Developmental Biology, 10.1016/j.semcdb.2015.12.011, 51, 24-31, 2016.03, Signal transduction processes the information of various cellular functions, including cell proliferation, differentiation, and death. The information for controlling cell fate is transmitted by concentrations of cellular signaling molecules. However, how much information is transmitted in signaling pathways has thus far not been investigated. Shannon's information theory paves the way to quantitatively analyze information transmission in signaling pathways. The theory has recently been applied to signal transduction, and mutual information of signal transduction has been determined to be a measure of information transmission. We review this work and provide an overview of how signal transduction transmits informational input and exerts biological output.. |
| 24. |
Kaoru Ohashi, Hisako Komada, Shinsuke Uda, Kubota Hiroyuki, Toshinao Iwaki, Hiroki Fukuzawa, Yasunori Komori, Masashi Fujii, Yu Toyoshima, Kazuhiko Sakaguchi, Wataru Ogawa, Shinya Kuroda, Glucose Homeostatic Law: Insulin Clearance Predicts the Progression of Glucose Intolerance in Humans, PLoS ONE, doi:10.1371/journal.pone.0143880, 10, 12, 2015.12. |
| 25. |
Kaoru Ohashi, Hisako Komada, Shinsuke Uda, Hiroyuki Kubota, Toshinao Iwaki, Hiroki Fukuzawa, Yasunori Komori, Masashi Fujii, Yu Toyoshima, Kazuhiko Sakaguchi, Wataru Ogawa, Shinya Kuroda, Glucose homeostatic law
Insulin clearance predicts the progression of glucose intolerance in humans, PLoS One, 10.1371/journal.pone.0143880, 10, 12, 2015.12, Homeostatic control of blood glucose is regulated by a complex feedback loop between glucose and insulin, of which failure leads to diabetes mellitus. However, physiological and pathological nature of the feedback loop is not fully understood. We made a mathematical model of the feedback loop between glucose and insulin using time course of blood glucose and insulin during consecutive hyperglycemic and hyperinsulinemic-euglycemic clamps in 113 subjects with variety of glucose tolerance including normal glucose tolerance (NGT), impaired glucose tolerance (IGT) and type 2 diabetes mellitus (T2DM). We analyzed the correlation of the parameters in the model with the progression of glucose intolerance and the conserved relationship between parameters. The model parameters of insulin sensitivity and insulin secretion significantly declined from NGT to IGT, and from IGT to T2DM, respectively, consistent with previous clinical observations. Importantly, insulin clearance, an insulin degradation rate, significantly declined from NGT, IGT to T2DM along the progression of glucose intolerance in the mathematical model. Insulin clearance was positively correlated with a product of insulin sensitivity and secretion assessed by the clamp analysis or determined with the mathematical model. Insulin clearance was correlated negatively with postprandial glucose at 2h after oral glucose tolerance test. We also inferred a square-law between the rate constant of insulin clearance and a product of rate constants of insulin sensitivity and secretion in the model, which is also conserved among NGT, IGT and T2DM subjects. Insulin clearance shows a conserved relationship with the capacity of glucose disposal among the NGT, IGT and T2DM subjects. The decrease of insulin clearance predicts the progression of glucose intolerance.. |
| 26. |
Yugi, K., Kubota Hiroyuki, Toyoshima, Y., Noguchi, R., Kawata, K., Komori, Y., Shinsuke Uda, Kunida, K., Tomizawa, Y., Funato, Y., Miki, H., Masaki Matsumoto, Keiichi Nakayama, Kashikura, K., Endo, K., Ikeda, K., Soga, T., Kuroda, S., Reconstruction of insulin signal flow from phosphoproteome and metabolome data, Cell Reports, 2014.08. |
| 27. |
Katsuyuki Yugi, Hiroyuki Kubota, Yu Toyoshima, Rei Noguchi, Kentaro Kawata, Yasunori Komori, Shinsuke Uda, Katsuyuki Kunida, Yoko Tomizawa, Yosuke Funato, Hiroaki Miki, Masaki Matsumoto, Keiichi Nakayama, Kasumi Kashikura, Keiko Endo, Kazutaka Ikeda, Tomoyoshi Soga, Shinya Kuroda, Reconstruction of insulin signal flow from phosphoproteome and metabolome data, Cell Reports, 10.1016/j.celrep.2014.07.021, 8, 4, 1171-1183, 2014.08, Cellular homeostasis is regulated by signals through multiple molecular networks that include protein phosphorylation and metabolites. However, where and when the signal flows through a network and regulates homeostasis has not been explored. We have developed a reconstruction method for the signal flow based on time-course phosphoproteome and metabolome data, using multiple databases, and have applied it to acute action of insulin, an important hormone for metabolic homeostasis. An insulin signal flows through a network, through signaling pathways that involve 13 protein kinases, 26 phosphorylated metabolic enzymes, and 35 allosteric effectors, resulting in quantitative changes in 44 metabolites. Analysis of the network reveals that insulin induces phosphorylation and activation of liver-type phosphofructokinase 1, thereby controlling a key reaction in glycolysis. We thus provide a versatile method of reconstruction of signal flow through the network using phosphoproteome and metabolome data.. |
| 28. |
Yuki Akimoto, Katsuyuki Yugi, Shinsuke Uda, Takamasa Kudo, Yasunori Komori, Hiroyuki Kubota, Shinya Kuroda, The Extraction of Simple Relationships in Growth Factor-Specific Multiple-Input and Multiple-Output Systems in Cell-Fate Decisions by Backward Elimination PLS Regression, PLoS One, 10.1371/journal.pone.0072780, 8, 9, 2013.09, Cells use common signaling molecules for the selective control of downstream gene expression and cell-fate decisions. The relationship between signaling molecules and downstream gene expression and cellular phenotypes is a multiple-input and multiple-output (MIMO) system and is difficult to understand due to its complexity. For example, it has been reported that, in PC12 cells, different types of growth factors activate MAP kinases (MAPKs) including ERK, JNK, and p38, and CREB, for selective protein expression of immediate early genes (IEGs) such as c-FOS, c-JUN, EGR1, JUNB, and FOSB, leading to cell differentiation, proliferation and cell death; however, how multiple-inputs such as MAPKs and CREB regulate multiple-outputs such as expression of the IEGs and cellular phenotypes remains unclear. To address this issue, we employed a statistical method called partial least squares (PLS) regression, which involves a reduction of the dimensionality of the inputs and outputs into latent variables and a linear regression between these latent variables. We measured 1,200 data points for MAPKs and CREB as the inputs and 1,900 data points for IEGs and cellular phenotypes as the outputs, and we constructed the PLS model from these data. The PLS model highlighted the complexity of the MIMO system and growth factor-specific input-output relationships of cell-fate decisions in PC12 cells. Furthermore, to reduce the complexity, we applied a backward elimination method to the PLS regression, in which 60 input variables were reduced to 5 variables, including the phosphorylation of ERK at 10 min, CREB at 5 min and 60 min, AKT at 5 min and JNK at 30 min. The simple PLS model with only 5 input variables demonstrated a predictive ability comparable to that of the full PLS model. The 5 input variables effectively extracted the growth factor-specific simple relationships within the MIMO system in cell-fate decisions in PC12 cells.. |
| 29. |
Takeshi H. Saito, Shinsuke Uda, Takaho Tsuchiya, Yu ichi Ozaki, Shinya Kuroda, Temporal Decoding of MAP Kinase and CREB Phosphorylation by Selective Immediate Early Gene Expression, PLoS One, 10.1371/journal.pone.0057037, 8, 3, 2013.03, A wide range of growth factors encode information into specific temporal patterns of MAP kinase (MAPK) and CREB phosphorylation, which are further decoded by expression of immediate early gene products (IEGs) to exert biological functions. However, the IEG decoding system remain unknown. We built a data-driven based on time courses of MAPK and CREB phosphorylation and IEG expression in response to various growth factors to identify how signal is processed. We found that IEG expression uses common decoding systems regardless of growth factors and expression of each IEG differs in upstream dependency, switch-like response, and linear temporal filters. Pulsatile ERK phosphorylation was selectively decoded by expression of EGR1 rather than c-FOS. Conjunctive NGF and PACAP stimulation was selectively decoded by synergistic JUNB expression through switch-like response to c-FOS. Thus, specific temporal patterns and combinations of MAPKs and CREB phosphorylation can be decoded by selective IEG expression via distinct temporal filters and switch-like responses. The data-driven modeling is versatile for analysis of signal processing and does not require detailed prior knowledge of pathways.. |
| 30. |
Shinsuke Uda, Takeshi H. Saito, Takamasa Kudo, Toshiya Kokaji, Takaho Tsuchiya, Hiroyuki Kubota, Yasunori Komori, Yu Ichi Ozaki, Shinya Kuroda, Robustness and compensation of information transmission of signaling pathways, Science, 10.1126/science.1234511, 341, 6145, 558-561, 2013.01, Robust transmission of information despite the presence of variation is a fundamental problem in cellular functions. However, the capability and characteristics of information transmission in signaling pathways remain poorly understood. We describe robustness and compensation of information transmission of signaling pathways at the cell population level. We calculated the mutual information transmitted through signaling pathways for the growth factor-mediated gene expression. Growth factors appeared to carry only information sufficient for a binary decision. Information transmission was generally more robust than average signal intensity despite pharmacological perturbations, and compensation of information transmission occurred. Information transmission to the biological output of neurite extension appeared robust. Cells may use information entropy as information so that messages can be robustly transmitted despite variation in molecular activities among individual cells.. |
| 31. |
Hiroyuki Kubota, Rei Noguchi, Yu Toyoshima, Yu ichi Ozaki, Shinsuke Uda, Kanako Watanabe, Wataru Ogawa, Shinya Kuroda, Temporal Coding of Insulin Action through Multiplexing of the AKT Pathway, Molecular Cell, 10.1016/j.molcel.2012.04.018, 46, 6, 820-832, 2012.06, One of the unique characteristics of cellular signaling pathways is that a common signaling pathway can selectively regulate multiple cellular functions of a hormone; however, this selective downstream control through a common signaling pathway is poorly understood. Here we show that the insulin-dependent AKT pathway uses temporal patterns multiplexing for selective regulation of downstream molecules. Pulse and sustained insulin stimulations were simultaneously encoded into transient and sustained AKT phosphorylation, respectively. The downstream molecules, including ribosomal protein S6 kinase (S6K), glucose-6-phosphatase (G6Pase), and glycogen synthase kinase-3β (GSK3β) selectively decoded transient, sustained, and both transient and sustained AKT phosphorylation, respectively. Selective downstream decoding is mediated by the molecules' network structures and kinetics. Our results demonstrate that the AKT pathway can multiplex distinct patterns of blood insulin, such as pulse-like additional and sustained-like basal secretions, and the downstream molecules selectively decode secretion patterns of insulin.. |
| 32. |
Kanako Watanabe, Yuki Akimoto, Katsuyuki Yugi, Shinsuke Uda, Jaehoon Chung, Shinichi Nakamuta, Kozo Kaibuchi, Shinya Kuroda, Latent process genes for cell differentiation are common decoders of neurite extension length, Journal of Cell Science, 10.1242/jcs.097709, 125, 9, 2198-2211, 2012.05, A latent process involving signal transduction and gene expression is needed as a preparation step for cellular function. We previously found that nerve growth factor (NGF)-induced cell differentiation has a latent process, which is dependent on ERK activity and gene expression and required for subsequent neurite extension. A latent process can be considered as a preparation step that decodes extracellular stimulus information into cellular functions; however, molecular mechanisms of this process remain unknown. We identified Metrnl, Dclk1 and Serpinb1a as genes that are induced during the latent process (LP) with distinct temporal expression profiles and are required for subsequent neurite extension in PC12 cells. The LP genes showed distinct dependency on the duration of ERK activity, and they were also induced during the latent process of PACAP- and forskolin-induced cell differentiation. Regardless of neurotrophic factors, expression levels of the LP genes during the latent process (0-12 hours), but not phosphorylation levels of ERK, always correlated with subsequent neurite extension length (12-24 hours). Overexpression of all LP genes together, but not of each gene separately, enhanced NGF-induced neurite extension. The LP gene products showed distinct spatial localization. Thus, the LP genes appear to be the common decoders for neurite extension length regardless of neurotrophic factors, and they might function in distinct temporal and spatial manners during the latent process. Our findings provide molecular insight into the physiological meaning of the latent process as the preparation step for decoding information for future phenotypic change.. |
| 33. |
Yu Toyoshima, Hiroaki Kakuda, Kazuhiro A. Fujita, Shinsuke Uda, Shinya Kuroda, Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling, Nature Communications, 10.1038/ncomms1745, 3, 2012.04, Sensitivity is one of the hallmarks of biological and pharmacological responses. However, the principle of controlling sensitivity remains unclear. Here we theoretically analyse a simple biochemical reaction and find that the signal transfer efficiency of the transient peak amplitude attenuates depending on the strength of negative regulation. We experimentally find that many signalling pathways in various cell lines, including the Akt and ERK pathways, can be approximated by simple biochemical reactions and that the same property of the attenuation of signal transfer efficiency was observed for such pathways. Because of this property, a downstream molecule should show higher sensitivity to an activator and lower sensitivity to an inhibitor than an upstream molecule. Indeed, we experimentally verify that S6, which lies downstream of Akt, shows lower sensitivity to an epidermal growth factor receptor inhibitor than Akt. Thus, cells can control downstream sensitivity through the attenuation of signal transfer efficiency by changing the expression level of negative regulators.. |
| 34. |
Yu Ichi Ozaki, Shinsuke Uda, Takeshi H. Saito, Jaehoon Chung, Hiroyuki Kubota, Shinya Kuroda, A quantitative image cytometry technique for time series or population analyses of signaling networks, PLoS One, 10.1371/journal.pone.0009955, 5, 4, 2010.09, Background: Modeling of cellular functions on the basis of experimental observation is increasingly common in the field of cellular signaling. However, such modeling requires a large amount of quantitative data of signaling events with high spatio-temporal resolution. A novel technique which allows us to obtain such data is needed for systems biology of cellular signaling. Methodology/Principal Findings: We developed a fully automatable assay technique, termed quantitative image cytometry (QIC), which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification. With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. The signaling activities quantified by the assay system showed good correlation with, as well as comparable reproducibility to, western blot analysis. Taking advantage of the high spatio-temporal resolution, we investigated the signaling dynamics of the ERK pathway in PC12 cells. Conclusions/Significance: The QIC technique appears as a highly quantitative and versatile technique, which can be a convenient replacement for the most conventional techniques including western blot, flow cytometry and live cell imaging. Thus, the QIC technique can be a powerful tool for investigating the systems biology of cellular signaling.. |
| 35. |
Kazuhiro A. Fujita, Yu Toyoshima, Shinsuke Uda, Yu Ichi Ozaki, Hiroyuki Kubota, Shinya Kuroda, Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics, Science Signaling, 10.1126/scisignal.2000810, 3, 132, 2010.07, In cellular signal transduction, the information in an external stimulus is encoded in temporal patterns in the activities of signaling molecules; for example, pulses of a stimulus may produce an increasing response or may produce pulsatile responses in the signaling molecules. Here, we show how the Akt pathway, which is involved in cell growth, specifically transmits temporal information contained in upstream signals to downstream effectors. We modeled the epidermal growth factor (EGF)-dependent Akt pathway in PC12 cells on the basis of experimental results. We obtained counterintuitive results indicating that the sizes of the peak amplitudes of receptor and downstream effector phosphorylation were decoupled; weak, sustained EGF receptor (EGFR) phosphorylation, rather than strong, transient phosphorylation, strongly induced phosphorylation of the ribosomal protein S6, a molecule downstream of Akt. Using frequency response analysis, we found that a three-component Akt pathway exhibited the property of a low-pass filter and that this property could explain decoupling of the peak amplitudes of receptor phosphorylation and that of downstream effectors. Furthermore, we found that lapatinib, an EGFR inhibitor used as an anticancer drug, converted strong, transient Akt phosphorylation into weak, sustained Akt phosphorylation, and, because of the low-pass filter characteristics of the Akt pathway, this led to stronger S6 phosphorylation than occurred in the absence of the inhibitor. Thus, an EGFR inhibitor can potentially act as a downstream activator of some effectors.. |
| 36. |
Jaehoon Chung, Hiroyuki Kubota, Yu Ichi Ozaki, Shinsuke Uda, Shinya Kuroda, Timing-dependent actions of NGF required for cell differentiation, PLoS One, 10.1371/journal.pone.0009011, 5, 2, 2010.02, Background: Continuous NGF stimulation induces PC12 cell differentiation. However, why continuous NGF stimulation is required for differentiation is unclear. In this study, we investigated the underlying mechanisms of the timing-dependent requirement of NGF action for cell differentiation. Methodology/Principal Findings: To address the timing-dependency of the NGF action, we performed a discontinuous stimulation assay consisting of a first transient stimulation followed by an interval and then a second sustained stimulation and quantified the neurite extension level. Consequently, we observed a timing-dependent action of NGF on cell differentiation, and discontinuous NGF stimulation similarly induced differentiation. The first stimulation did not induce neurite extension, whereas the second stimulation induced fast neurite extension; therefore, the first stimulation is likely required as a prerequisite condition. These observations indicate that the action of NGF can be divided into two processes: an initial stimulation-driven latent process and a second stimulation-driven extension process. The latent process appears to require the activities of ERK and transcription, but not PI3K, whereas the extension-process requires the activities of ERK and PI3K, but not transcription. We also found that during the first stimulation, the activity of NGF can be replaced by PACAP, but not by insulin, EGF, bFGF or forskolin; during the second stimulation, however, the activity of NGF cannot be replaced by any of these stimulants. These findings allowed us to identify potential genes specifically involved in the latent process, rather than in other processes, using a microarray. Conclusions/Significance: These results demonstrate that NGF induces the differentiation of PC12 cells via mechanically distinct processes: an ERK-driven and transcription-dependent latent process, and an ERK- and PI3K-driven and transcription-independent extension process.. |
| 37. |
Koujin Takeda, Shinsuke Uda, Yoshiyuki Kabashima, Analysis of CDMA systems that are characterized by eigenvalue spectrum, Europhysics Letters, 76, 1193-1199, 2006. |
| 38. |
Shinsuke Uda, Yoshiyuki Kabashima, Statistical mechanical development of a sparse Bayesian classifier, Journal of the Physical Society of Japan, 74, 2233-2242, 2005. |
| 39. |
Koji Tsuda, Shinsuke Uda, Taishin Kin, Kiyoshi Asai, Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data, Neural Processing Letters, 19, 63-72, 2004. |
