Tokushima University / Educator and Researcher Directory --- Watanabe, Kengo

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Tokushima University ⟩ Graduate School of Biomedical Sciences ⟩ 医学域 ⟩ Medical Science ⟩ Social Medicine ⟩ Department of Medical AI Data Science ⟩
Tokushima University ⟩ Faculty of Medicine ⟩ School of Medicine ⟩ Course of Social and Environmental Medicine ⟩ Medical AI Data Scienc ⟩

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Research

Personal Web Page

https://researchmap.jp/ken5watanabe (researchmap)

https://orcid.org/0000-0002-0348-1634 (ORCID)

Field of Study

○	Life sciences [Pharmaceuticals - health and biochemistry]
○	Life sciences [Cell biology]
○	Life sciences [Functional biochemistry]
○	Life sciences [Molecular biology]
○	Life sciences [Nutrition and health science]
○	Informatics [Biological, health, and medical informatics]

Subject of Study

Book / Paper

Book:

1.	Kengo Watanabe and Hidenori Ichijo : Osmosensing via liquid-liquid phase separation (BIO Clinica Vol.38 No.4), HOKURYUKAN, Tokyo, Mar. 2023.
2.	Kengo Watanabe : Quantitative evaluation of liquid droplets using image analysis (Jikkenigaku Bessatsu - Phase Separation Analysis Protocol), YODOSHA CO., LTD., Tokyo, Jul. 2022.
3.	Kengo Watanabe, Isao Naguro and Hidenori Ichijo : Cells sense osmotic stress from the inside through liquid-liquid phase separation (Jikkenigaku Vol.39 No.11), YODOSHA CO., LTD., Tokyo, Jun. 2021.
4.	Kengo Watanabe, Isao Naguro and Hidenori Ichijo : A high-content genome-wide siRNA screening for signal transduction research (Jikkenigaku Vol.32 No.9), YODOSHA CO., LTD., Tokyo, May 2014.

Academic Paper (Judged Full Paper):

1.	Adam R. Burns, Jack Wiedrick, Alicia Feryn, Michal Maes, Mukul K. Midha, David H. Baxter, Seamus R. Morrone, Timothy J. Prokop, Charu Kapil, Michael R. Hoopmann, Ulrike Kusebauch, Eric W. Deutsch, Noa Rappaport, Kengo Watanabe, Robert L. Moritz, Richard A. Miller, Jodi A. Lapidus and Eric S. Orwoll : Proteomic changes induced by longevity-promoting interventions in mice., GeroScience, Vol.46, No.2, 1543-1560, 2024. (Summary) Using mouse models and high-throughput proteomics, we conducted an in-depth analysis of the proteome changes induced in response to seven interventions known to increase mouse lifespan. This included two genetic mutations, a growth hormone receptor knockout (GHRKO mice) and a mutation in the Pit-1 locus (Snell dwarf mice), four drug treatments (rapamycin, acarbose, canagliflozin, and 17α-estradiol), and caloric restriction. Each of the interventions studied induced variable changes in the concentrations of proteins across liver, kidney, and gastrocnemius muscle tissue samples, with the strongest responses in the liver and limited concordance in protein responses across tissues. To the extent that these interventions promote longevity through common biological mechanisms, we anticipated that proteins associated with longevity could be identified by characterizing shared responses across all or multiple interventions. Many of the proteome alterations induced by each intervention were distinct, potentially implicating a variety of biological pathways as being related to lifespan extension. While we found no protein that was affected similarly by every intervention, we identified a set of proteins that responded to multiple interventions. These proteins were functionally diverse but tended to be involved in peroxisomal oxidation and metabolism of fatty acids. These results provide candidate proteins and biological mechanisms related to enhancing longevity that can inform research on therapeutic approaches to promote healthy aging. (Keyword) Mice / Animals / Longevity / proteome / proteomics / Transcription Factors / Receptors, Somatotropin (Link to Publication Site) ● Publication site (DOI): 10.1007/s11357-023-00917-z (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 37653270 ● Summary page in Scopus @ Elsevier: 2-s2.0-85169162929 (DOI: 10.1007/s11357-023-00917-z, PubMed: 37653270, Elsevier: Scopus)
2.	Kengo Watanabe, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Gonzalo G. Garcia, Michael R. Hoopmann, Mukul K. Midha, David H. Baxter, Michal Maes, Seamus R. Morrone, Kelly M. Crebs, Charu Kapil, Ulrike Kusebauch, Jack Wiedrick, Jodi Lapidus, Lance Pflieger, Christopher Lausted, Jared C. Roach, Gwênlyn Glusman, Steven R. Cummings, Nicholas J. Schork, Nathan D. Price, Leroy Hood, Richard A. Miller, Robert L. Moritz and Noa Rappaport : Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers, Communications Biology, Vol.6, No.1, 768, 2023. (Summary) Aging manifests as progressive deteriorations in homeostasis, requiring systems-level perspectives to investigate the gradual molecular dysregulation of underlying biological processes. Here, we report systemic changes in the molecular regulation of biological processes under multiple lifespan-extending interventions. Differential Rank Conservation (DIRAC) analyses of mouse liver proteomics and transcriptomics data show that mechanistically distinct lifespan-extending interventions (acarbose, 17α-estradiol, rapamycin, and calorie restriction) generally tighten the regulation of biological modules. These tightening patterns are similar across the interventions, particularly in processes such as fatty acid oxidation, immune response, and stress response. Differences in DIRAC patterns between proteins and transcripts highlight specific modules which may be tightened via augmented cap-independent translation. Moreover, the systemic shifts in fatty acid metabolism are supported through integrated analysis of liver transcriptomics data with a mouse genome-scale metabolic model. Our findings highlight the power of systems-level approaches for identifying and characterizing the biological processes involved in aging and longevity. (Keyword) Animals / Mice / Longevity / Lipid Metabolism / aging / Disease Models, Animal / Liver / Fatty Acids (Link to Publication Site) ● Publication site (DOI): 10.1038/s42003-023-05128-y (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 37481675 ● Summary page in Scopus @ Elsevier: 2-s2.0-85165420884 (DOI: 10.1038/s42003-023-05128-y, PubMed: 37481675, Elsevier: Scopus)
3.	Kazuhiro Morishita, Kengo Watanabe, Isao Naguro and Hidenori Ichijo : Sodium ion influx regulates liquidity of biomolecular condensates in hyperosmotic stress response, Cell Reports, Vol.42, No.4, 112315, 2023. (Summary) Biomolecular condensates are membraneless structures formed through phase separation. Recent studies have demonstrated that the material properties of biomolecular condensates are crucial for their biological functions and pathogenicity. However, the phase maintenance of biomolecular condensates in cells remains elusive. Here, we show that sodium ion (Na+) influx regulates the condensate liquidity under hyperosmotic stress. ASK3 condensates have higher fluidity at the high intracellular Na+ concentration derived from extracellular hyperosmotic solution. Moreover, we identified TRPM4 as a cation channel that allows Na+ influx under hyperosmotic stress. TRPM4 inhibition causes the liquid-to-solid phase transition of ASK3 condensates, leading to impairment of the ASK3 osmoresponse. In addition to ASK3 condensates, intracellular Na+ widely regulates the condensate liquidity and aggregate formation of biomolecules, including DCP1A, TAZ, and polyQ-protein, under hyperosmotic stress. Our findings demonstrate that changes in Na+ contribute to the cellular stress response via liquidity maintenance of biomolecular condensates. (Keyword) Biomolecular Condensates / Ions / Osmoregulation / phase transition (Link to Publication Site) ● Publication site (DOI): 10.1016/j.celrep.2023.112315 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 37019112 ● Search Scopus @ Elsevier (PMID): 37019112 ● Search Scopus @ Elsevier (DOI): 10.1016/j.celrep.2023.112315 (DOI: 10.1016/j.celrep.2023.112315, PubMed: 37019112)
4.	Kengo Watanabe, Tomasz Wilmanski, Christian Diener, John C. Earls, Anat Zimmer, Briana Lincoln, Jennifer J. Hadlock, Jennifer C. Lovejoy, Sean M. Gibbons, Andrew T. Magis, Leroy Hood, Nathan D. Price and Noa Rappaport : Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention, Nature Medicine, Vol.29, No.4, 996-1008, 2023. (Summary) Multiomic profiling can reveal population heterogeneity for both health and disease states. Obesity drives a myriad of metabolic perturbations and is a risk factor for multiple chronic diseases. Here we report an atlas of cross-sectional and longitudinal changes in 1,111 blood analytes associated with variation in body mass index (BMI), as well as multiomic associations with host polygenic risk scores and gut microbiome composition, from a cohort of 1,277 individuals enrolled in a wellness program (Arivale). Machine learning model predictions of BMI from blood multiomics captured heterogeneous phenotypic states of host metabolism and gut microbiome composition better than BMI, which was also validated in an external cohort (TwinsUK). Moreover, longitudinal analyses identified variable BMI trajectories for different omics measures in response to a healthy lifestyle intervention; metabolomics-inferred BMI decreased to a greater extent than actual BMI, whereas proteomics-inferred BMI exhibited greater resistance to change. Our analyses further identified blood analyte-analyte associations that were modified by metabolomics-inferred BMI and partially reversed in individuals with metabolic obesity during the intervention. Taken together, our findings provide a blood atlas of the molecular perturbations associated with changes in obesity status, serving as a resource to quantify metabolic health for predictive and preventive medicine. (Keyword) Humans / Body Mass Index / Cross-Sectional Studies / Multiomics / obesity / Phenotype (Link to Publication Site) ● Publication site (DOI): 10.1038/s41591-023-02248-0 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 36941332 ● Summary page in Scopus @ Elsevier: 2-s2.0-85150423431 (DOI: 10.1038/s41591-023-02248-0, PubMed: 36941332, Elsevier: Scopus)
5.	Saki Takayanagi, Kengo Watanabe, Takeshi Maruyama, Motoyuki Ogawa, Kazuhiro Morishita, Mayumi Soga, Tomohisa Hatta, Tohru Natsume, Tomoya Hirano, Hiroyuki Kagechika, Kazuki Hattori, Isao Naguro and Hidenori Ichijo : ASKA technology-based pull-down method reveals a suppressive effect of ASK1 on the inflammatory NOD-RIPK2 pathway in brown adipocytes, Scientific Reports, Vol.11, No.1, 22009, 2021. (Summary) Recent studies have shown that adipose tissue is an immunological organ. While inflammation in energy-storing white adipose tissues has been the focus of intense research, the regulatory mechanisms of inflammation in heat-producing brown adipose tissues remain largely unknown. We previously identified apoptosis signal-regulating kinase 1 (ASK1) as a critical regulator of brown adipocyte maturation; the PKA-ASK1-p38 axis facilitates uncoupling protein 1 (UCP1) induction cell-autonomously. Here, we show that ASK1 suppresses an innate immune pathway and contributes to maintenance of brown adipocytes. We report a novel chemical pull-down method for endogenous kinases using analog sensitive kinase allele (ASKA) technology and identify an ASK1 interactor in brown adipocytes, receptor-interacting serine/threonine-protein kinase 2 (RIPK2). ASK1 disrupts the RIPK2 signaling complex and inhibits the NOD-RIPK2 pathway to downregulate the production of inflammatory cytokines. As a potential biological significance, an in vitro model for intercellular regulation suggests that ASK1 facilitates the expression of UCP1 through the suppression of inflammatory cytokine production. In parallel to our previous report on the PKA-ASK1-p38 axis, our work raises the possibility of an auxiliary role of ASK1 in brown adipocyte maintenance through neutralizing the thermogenesis-suppressive effect of the NOD-RIPK2 pathway. (Keyword) Adipocytes, Brown / Adipocytes, White / Animals / cytokinesis / HEK293 Cells / Humans / inflammation / MAP Kinase Kinase Kinase 5 / Mice / Nod Signaling Adaptor Proteins / Receptor-Interacting Protein Serine-Threonine Kinase 2 / signal transduction / Uncoupling Protein 1 (Link to Publication Site) ● Publication site (DOI): 10.1038/s41598-021-01123-7 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 34759307 ● Summary page in Scopus @ Elsevier: 2-s2.0-85118850723 (DOI: 10.1038/s41598-021-01123-7, PubMed: 34759307, Elsevier: Scopus)
6.	Kengo Watanabe, Kazuhiro Morishita, Xiangyu Zhou, Shigeru Shiizaki, Yasuo Uchiyama, Masato Koike, Isao Naguro and Hidenori Ichijo : Cells recognize osmotic stress through liquid liquid phase separation lubricated with poly(ADP-ribose), Nature Communications, Vol.12, No.1, 1353, 2021. (Summary) Cells are under threat of osmotic perturbation; cell volume maintenance is critical in cerebral edema, inflammation and aging, in which prominent changes in intracellular or extracellular osmolality emerge. After osmotic stress-enforced cell swelling or shrinkage, the cells regulate intracellular osmolality to recover their volume. However, the mechanisms recognizing osmotic stress remain obscured. We previously clarified that apoptosis signal-regulating kinase 3 (ASK3) bidirectionally responds to osmotic stress and regulates cell volume recovery. Here, we show that macromolecular crowding induces liquid-demixing condensates of ASK3 under hyperosmotic stress, which transduce osmosensing signal into ASK3 inactivation. A genome-wide small interfering RNA (siRNA) screen identifies an ASK3 inactivation regulator, nicotinamide phosphoribosyltransferase (NAMPT), related to poly(ADP-ribose) signaling. Furthermore, we clarify that poly(ADP-ribose) keeps ASK3 condensates in the liquid phase and enables ASK3 to become inactivated under hyperosmotic stress. Our findings demonstrate that cells rationally incorporate physicochemical phase separation into their osmosensing systems. (Keyword) Amino Acid Motifs / Amino Acid Sequence / cytokinesis / HEK293 Cells / Humans / Lubrication / MAP Kinase Kinase Kinases / Models, Molecular / Mutation / NAD / Nicotinamide Phosphoribosyltransferase / Osmotic Pressure / Phosphoprotein Phosphatases / Poly Adenosine Diphosphate Ribose / Protein Domains (Link to Publication Site) ● Publication site (DOI): 10.1038/s41467-021-21614-5 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 33649309 ● Summary page in Scopus @ Elsevier: 2-s2.0-85101807116 (DOI: 10.1038/s41467-021-21614-5, PubMed: 33649309, Elsevier: Scopus)
7.	Ryoki Nakamura, Tomohiro Numata, Go Kasuya, Takeshi Yokoyama, Tomohiro Nishizawa, Tsukasa Kusakizako, Takafumi Kato, Tatsuya Hagino, Naoshi Dohmae, Masato Inoue, Kengo Watanabe, Hidenori Ichijo, Masahide Kikkawa, Mikako Shirouzu, Thomas J. Jentsch, Ryuichiro Ishitani, Yasunobu Okada and Osamu Nureki : Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation, Communications Biology, Vol.3, No.1, 240, 2020. (Summary) Members of the leucine-rich repeat-containing 8 (LRRC8) protein family, composed of the five LRRC8A-E isoforms, are pore-forming components of the volume-regulated anion channel (VRAC). LRRC8A and at least one of the other LRRC8 isoforms assemble into heteromers to generate VRAC transport activities. Despite the availability of the LRRC8A structures, the structural basis of how LRRC8 isoforms other than LRRC8A contribute to the functional diversity of VRAC has remained elusive. Here, we present the structure of the human LRRC8D isoform, which enables the permeation of organic substrates through VRAC. The LRRC8D homo-hexamer structure displays a two-fold symmetric arrangement, and together with a structure-based electrophysiological analysis, revealed two key features. The pore constriction on the extracellular side is wider than that in the LRRC8A structures, which may explain the increased permeability of organic substrates. Furthermore, an N-terminal helix protrudes into the pore from the intracellular side and may be critical for gating. (Keyword) Cryoelectron Microscopy / Ion Transport / Protein Domains / Protein Isoforms / signal transduction / Voltage-Dependent Anion Channels (Link to Publication Site) ● Publication site (DOI): 10.1038/s42003-020-0951-z (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 32415200 ● Summary page in Scopus @ Elsevier: 2-s2.0-85084736903 (DOI: 10.1038/s42003-020-0951-z, PubMed: 32415200, Elsevier: Scopus)
8.	Sho Sugawara, Yusuke Kanamaru, Shiori Sekine, Lila Maekawa, Akinori Takahashi, Tadashi Yamamoto, Kengo Watanabe, Takao Fujisawa, Kazuki Hattori and Hidenori Ichijo : The mitochondrial protein PGAM5 suppresses energy consumption in brown adipocytes by repressing expression of uncoupling protein 1, The Journal of Biological Chemistry, Vol.295, No.17, 5588-5601, 2020. (Summary) Accumulating evidence suggests that brown adipose tissue (BAT) is a potential therapeutic target for managing obesity and related diseases. PGAM family member 5, mitochondrial serine/threonine protein phosphatase (PGAM5), is a protein phosphatase that resides in the mitochondria and regulates many biological processes, including cell death, mitophagy, and immune responses. Because BAT is a mitochondria-rich tissue, we have hypothesized that PGAM5 has a physiological function in BAT. We previously reported that PGAM5-knockout (KO) mice are resistant to severe metabolic stress. Importantly, lipid accumulation is suppressed in PGAM5-KO BAT, even under unstressed conditions, raising the possibility that PGAM5 deficiency stimulates lipid consumption. However, the mechanism underlying this observation is undetermined. Here, using an array of biochemical approaches, including quantitative RT-PCR, immunoblotting, and oxygen consumption assays, we show that PGAM5 negatively regulates energy expenditure in brown adipocytes. We found that PGAM5-KO brown adipocytes have an enhanced oxygen consumption rate and increased expression of uncoupling protein 1 (UCP1), a protein that increases energy consumption in the mitochondria. Mechanistically, we found that PGAM5 phosphatase activity and intramembrane cleavage are required for suppression of UCP1 activity. Furthermore, utilizing a genome-wide siRNA screen in HeLa cells to search for regulators of PGAM5 cleavage, we identified a set of candidate genes, including phosphatidylserine decarboxylase (), which catalyzes the formation of phosphatidylethanolamine at the mitochondrial membrane. Taken together, these results indicate that PGAM5 suppresses mitochondrial energy expenditure by down-regulating UCP1 expression in brown adipocytes and that its phosphatase activity and intramembrane cleavage are required for UCP1 suppression. (Keyword) Adipocytes, Brown / Animals / Cells, Cultured / Down-Regulation / energy metabolism / HeLa Cells / Humans / male / Mice, Inbred C57BL / knockout mice / Mitochondrial Proteins / oxygen consumption / Phosphoprotein Phosphatases / Uncoupling Protein 1 (Link to Publication Site) ● Publication site (DOI): 10.1074/jbc.ra119.011508 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 32144202 ● Summary page in Scopus @ Elsevier: 2-s2.0-85083760367 (DOI: 10.1074/jbc.ra119.011508, PubMed: 32144202, Elsevier: Scopus)
9.	Go Kasuya, Takanori Nakane, Takeshi Yokoyama, Yanyan Jia, Masato Inoue, Kengo Watanabe, Ryoki Nakamura, Tomohiro Nishizawa, Tsukasa Kusakizako, Akihisa Tsutsumi, Haruaki Yanagisawa, Naoshi Dohmae, Motoyuki Hattori, Hidenori Ichijo, Zhiqiang Yan, Masahide Kikkawa, Mikako Shirouzu, Ryuichiro Ishitani and Osamu Nureki : Cryo-EM structures of the human volume-regulated anion channel LRRC8, Nature Structural & Molecular Biology, Vol.25, No.9, 797-804, 2018. (Summary) Maintenance of cell volume against osmotic change is crucial for proper cell functions. Leucine-rich repeat-containing 8 proteins are anion-selective channels that extrude anions to decrease the cell volume on cellular swelling. Here, we present the structure of human leucine-rich repeat-containing 8A, determined by single-particle cryo-electron microscopy. The structure shows a hexameric assembly, and the transmembrane region features a topology similar to gap junction channels. The LRR region, with 15 leucine-rich repeats, forms a long, twisted arc. The channel pore is located along the central axis and constricted on the extracellular side, where highly conserved polar and charged residues at the tip of the extracellular helix contribute to permeability to anions and other osmolytes. Two structural populations were identified, corresponding to compact and relaxed conformations. Comparing the two conformations suggests that the LRR region is flexible and mobile, with rigid-body motions, which might be implicated in structural transitions on pore opening. (Keyword) Amino Acid Sequence / Cryoelectron Microscopy / Humans / Ion Channel Gating / Membrane Proteins / Protein Conformation / Sequence Homology, Amino Acid (Link to Publication Site) ● Publication site (DOI): 10.1038/s41594-018-0109-6 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 30127360 ● Summary page in Scopus @ Elsevier: 2-s2.0-85052597609 (DOI: 10.1038/s41594-018-0109-6, PubMed: 30127360, Elsevier: Scopus)
10.	Kengo Watanabe, Tsuyoshi Umeda, Kuniyoshi Niwa, Isao Naguro and Hidenori Ichijo : A PP6-ASK3 Module Coordinates the Bidirectional Cell Volume Regulation under Osmotic Stress, Cell Reports, Vol.22, No.11, 2809-2817, 2018. (Link to Publication Site) ● Publication site (DOI): 10.1016/j.celrep.2018.02.045 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 29539411 ● Summary page in Scopus @ Elsevier: 2-s2.0-85043590434 (DOI: 10.1016/j.celrep.2018.02.045, PubMed: 29539411, Elsevier: Scopus)

Academic Paper (Unrefereed Paper):

1.	Dylan S Ellis, Kengo Watanabe, Tomasz Wilmanski, Michael S Lustgarten, Andres Ardisson V Korat, Gwênlyn Glusman, Jennifer J Hadlock, Oliver Fiehn, Paola Sebastiani, Nathan D Price, Leroy Hood, Andrew T Magis, Simon J Evans, Lance Pflieger, Jennifer C Lovejoy, Sean M Gibbons, Cory C Funk, Priyanka Baloni and Noa Rappaport : APOE Genotype and Biological Age Impact Inter-Omic Associations Related to Bioenergetics, bioRxiv, 2024. (Summary) Apolipoprotein E (APOE) modifies human aging; specifically, the epsilon2 and epsilon4 alleles are among the strongest genetic predictors of longevity and Alzheimer's disease (AD) risk, respectively. However, detailed mechanisms for their influence on aging remain unclear. Herein, we analyzed inter-omic, context-dependent association patterns across APOE genotypes, sex, and health axes in 2,229 community-dwelling individuals to test APOE genotypes for variation in metabolites and metabolite-associations tied to a previously-validated metric of biological aging (BA) based on blood biomarkers. Our analysis, supported by validation in an independent cohort, identified top APOE-associated plasma metabolites as diacylglycerols, which were increased in epsilon2-carriers and trended higher in epsilon4-carriers compared to epsilon3-homozygotes, despite the known opposing aging effects of the allele variants. 'Omics association patterns of epsilon2-carriers and increased biological age were also counter-intuitively similar, displaying increased associations between insulin resistance markers and energy-generating pathway metabolites. These results provide an atlas of APOE-related 'omic associations and support the involvement of bioenergetic pathways in mediating the impact of APOE on aging. (Link to Publication Site) ● Publication site (DOI): 10.1101/2024.10.17.618322 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 39605362 ● Search Scopus @ Elsevier (PMID): 39605362 ● Search Scopus @ Elsevier (DOI): 10.1101/2024.10.17.618322 (DOI: 10.1101/2024.10.17.618322, PubMed: 39605362)
2.	Kengo Watanabe, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Oliver Fiehn, Robert Moritz, Richard Miller and Noa Rappaport : MULTIOMIC SYSTEMS ANALYSIS OF LIFESPAN-EXTENDING INTERVENTIONS IN MOUSE TISSUES, Innovation in Aging, Vol.7, No.Supplement_1, 934, 2023. (Summary) Aging is associated with dysregulation of molecular, cellular, and physiological processes. Nutritional and pharmacological interventions with different postulated modes of action have been shown to extend lifespan and delay aging-related diseases in model organisms, suggesting the existence of core cellular processes that mediate the effect on lifespan and healthspan. However, these underlying molecular processes remain largely uncharacterized. In this study, we analyzed multiomic tissue-derived data of lifespan-extending interventions in mice including metabolomics and proteomics from the NIA Longevity Consortium and previously reported transcriptomics. We applied three systems techniques, differential rank conservation (DIRAC) analysis, weighted gene co-expression network analysis (WGCNA), and mouse genome-scale metabolic model (GEM) reconstruction, to the mouse liver proteomic and transcriptomic datasets of lifespan-extending interventions (e.g., acarbose, 17α-estradiol, and rapamycin). We found that these interventions generally strengthen the rank conservation of biological processes and shift metabolic fluxes, with fatty acid metabolism emerging as a common process affected by multiple interventions. We then applied these approaches to an expanded experimental data with additional interventions (e.g., canagliflozin) and tissues (e.g., kidney, muscle, and plasma), confirming our results and further observing varied inter-omic and inter-tissue patterns exerted by lifespan-extending interventions. Our findings highlight the potential of integrative systems analysis to elucidate common and unique cellular and physiological changes relating to aging and lifespan-extending interventions, which have translational potential as preventive and prognostic measures to improve human health. (Link to Publication Site) ● Publication site (DOI): 10.1093/geroni/igad104.3000 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1093/geroni/igad104.3000 (DOI: 10.1093/geroni/igad104.3000)
3.	Lance Pflieger, Kengo Watanabe, Max Robinson, Gustavo Glusman, Jodi Lapidus, Oliver Fiehn, Robert Moritz and Noa Rappaport : PROSPECTIVE MULTI-OMIC ANALYSIS OF HUMAN LONGEVITY COHORTS IDENTIFIES ANALYTE NETWORKS ASSOCIATED WITH LONGEVITY, Innovation in Aging, Vol.7, No.Supplement_1, 691-692, 2023. (Summary) Serum based biomarkers of longevity have long been sought to explain the mechanisms of healthy aging and longevity. Using a 1:3 case cohort design, the Longevity Consortium has produced untargeted mass spectrometry based proteomic and metabolomic datasets from serum of four cohorts with longevity status, defined as those that reached the age corresponding to the 98th percentile of survival using sex specific and birth cohort specific survival percentiles. The cohorts are the Osteoporotic Fractures in Men study, the Study of Osteoporotic Fractures, the Health, Aging, and Body Composition Study, and the Cardiovascular Health Study. In this study, we integrate metabolomics and proteomics using machine learning and system biology approaches to construct multi-omic signatures predictive of longevity and healthy aging. We identify networks enriched for biomarkers previously shown to be associated with longevity such as apolipoproteins, along with novel associations, and we further compare with our findings in a mouse omics LC dataset of molecular changes induced by life-extending interventions. We show substantial differences between male and female longevity networks. The study highlights the effectiveness of using integrative systems biology methods to capture the heterogeneity of underlying molecular aging phenotypes, in order to generate a robust signature of longevity. The identified biomarker signatures may have significant implications for the development of personalized interventions aimed at promoting healthy aging and preventing age-related diseases. (Link to Publication Site) ● Publication site (DOI): 10.1093/geroni/igad104.2245 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1093/geroni/igad104.2245 (DOI: 10.1093/geroni/igad104.2245)
4.	Noa Rappaport, Dylan Ellis, Kengo Watanabe, Tomasz Wilmanski, Leroy Hood, Nathan Price, Cory Funk and Priyanka Baloni : BIOLOGICAL AGING AND APOE STATUS REWIRE INTER-OMIC ASSOCIATIONS RELATED TO BIOENERGETICS IN HUMANS, Innovation in Aging, Vol.7, No.Supplement_1, 631-632, 2023. (Summary) Apolipoprotein E (APOE) modifies human aging, with the ϵ2 and ϵ4 alleles being among the strongest genetic predictors of longevity and Alzheimer's disease, respectively. However, the mechanisms of APOE's impact on aging and cognition remain largely uncharacterized. In this study, we analyzed inter-omic context-dependent association patterns across APOE genotype, sex, and health in an undiagnosed cohort of 1950 individuals. We hypothesized that APOE genotypes would show variation in energy metabolites tied to previously-validated metrics of 'biological aging', a modifiable health metric based on blood biomarkers. Our analysis identified top APOE-associated metabolites as diacylglycerols, including oleoyl- and linoleoyl-arachidonoyl-glycerols, similarly increased in APOE ϵ2- and ϵ4- carriers compared to ϵ3-homozygotes. Male ϵ2-carriers and biologically-older males displayed a similar increase in associations between insulin resistance and bioenergetic metabolites including pyruvate, glucose, gluconate, and lactate, a trend which was validated in an independent cohort of TwinsUK females. These results provide an atlas of APOE allele-rewired associations and support the involvement of bioenergetic pathways in mediating APOE impact on longevity and AD risk, suggesting targets for enhancing healthspan via lifestyle-modifications or drug-repurposing. (Link to Publication Site) ● Publication site (DOI): 10.1093/geroni/igad104.2058 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1093/geroni/igad104.2058 (DOI: 10.1093/geroni/igad104.2058)
5.	Kengo Watanabe, Tomasz Wilmanski, Lance Pflieger, Christian Diener, John Earls, Jennifer Hadlock, Jennifer Lovejoy, Sean Gibbons, Andrew Magis, Leroy Hood, Nathan Price and Noa Rappapor : Characterization of Blood Multiomics-Based Metabolic Health Measure, Obesity, Vol.31, No.S2, 259, 2023. (Link to Publication Site) ● Publication site (DOI): 10.1002/oby.23939 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1002/oby.23939 (DOI: 10.1002/oby.23939)
6.	Xiangyu Zhou, Kengo Watanabe, Kazuhiro Morishita, Jun Hamazaki, Shigeo Murata, Isao Naguro and Hidenori Ichijo : Proteasomal regulation of ASK family kinases dictates cell fate under hyperosmotic stress, bioRxiv, 2023. (Summary) Summary The proteasome has an essential role in proteostasis maintenance and is critical for cell survival under proteotoxic conditions including hyperosmotic stress. However, it is unknown how proteasome activity is linked to cell survival/death under hyperosmotic stress. We have previously reported that apoptosis signal-regulating kinase 3 (ASK3) contributes to cell survival through its inactivation under hyperosmotic stress. 19S regulatory particle subunits of the proteasome were enriched in the ASK3 inactivator candidates identified through our genome-wide small interfering RNA (siRNA) screen. In this study, we demonstrate that the proteasome regulates ASK3 inactivation through its proteolytic activity. Intriguingly, the proteasome inactivates ASK3 via degradation of not ASK3 per se but another ASK family member ASK1 which activates ASK3 in a kinase activity-dependent manner. Furthermore, the elevated ASK1 level under proteasome inhibition sensitizes cells to hyperosmotic stress. These findings suggest that ASK family maintenance links proteasome capacity to cell fate bifurcation under hyperosmotic stress. (Link to Publication Site) ● Publication site (DOI): 10.1101/2023.05.23.541899 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1101/2023.05.23.541899 (DOI: 10.1101/2023.05.23.541899)
7.	Kengo Watanabe, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Gonzalo G. Garcia, Michael R. Hoopmann, Mukul K. Midha, David H. Baxter, Michal Maes, Seamus R. Morrone, Kelly M. Crebs, Charu Kapil, Ulrike Kusebauch, Jack Wiedrick, Jodi Lapidus, Jennifer C. Lovejoy, Andrew T. Magis, Christopher Lausted, Jared C. Roach, Gustavo Glusman, Steven R. Cummings, Nicholas J. Schork, Nathan D. Price, Leroy Hood, Richard A. Miller, Robert L. Moritz and Noa Rappaport : Systems-level patterns in biological processes are changed under prolongevity interventions and across biological age, medRxiv, 2022. (Summary) Aging manifests as progressive deterioration in cellular and systemic homeostasis, requiring systems-level perspectives to understand the gradual molecular dysregulation of underlying biological processes. Here, we report systems-level changes in the molecular regulation of biological processes under multiple lifespan-extending interventions in mice and across age in humans. In mouse cohorts, Differential Rank Conservation (DIRAC) analyses of liver proteomics and transcriptomics show that mechanistically distinct prolongevity interventions tighten the regulation of aging-related biological modules, including fatty acid metabolism and inflammation processes. An integrated analysis of liver transcriptomics with mouse genome-scale metabolic model supports the shifts in fatty acid metabolism. Additionally, the difference in DIRAC patterns between proteins and transcripts suggests biological modules which may be tightly regulated via cap-independent translation. In a human cohort spanning the majority of the adult lifespan, DIRAC analyses of blood proteomics and metabolomics demonstrate that regulation of biological modules does not monotonically loosen with age; instead, the regulatory patterns shift according to both chronological and biological ages. Our findings highlight the power of systems-level approaches to identifying and characterizing the biological processes involved in aging and longevity. (Link to Publication Site) ● Publication site (DOI): 10.1101/2022.07.11.22277435 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1101/2022.07.11.22277435 (DOI: 10.1101/2022.07.11.22277435)
8.	Kazuhiro Morishita, Kengo Watanabe, Isao Naguro and Hidenori Ichijo : Sodium ion regulates liquidity of biomolecular condensates in hyperosmotic stress response, bioRxiv, 2022. (Summary) Summary Biomolecular condensates are membraneless structures formed through phase separation. Recent studies have demonstrated that the material properties of biomolecular condensates are crucial for their biological functions and pathogenicity. However, the phase maintenance of biomolecular condensates in cells remains elusive. Here, we show that sodium ion (Na<sup>+</sup>) influx regulates the condensate liquidity under hyperosmotic stress. The fluidity of ASK3 condensates increases at the high intracellular Na<sup>+</sup> concentration derived from extracellular hyperosmotic solution. Moreover, we identified TRPM4 as a cation channel that allows Na<sup>+</sup> influx under hyperosmotic stress. TRPM4 inhibition causes the liquid-to-solid phase transition of ASK3 condensates, leading to impairment of the ASK3 osmoresponse. In addition to ASK3 condensates, intracellular Na<sup>+</sup> widely regulates the condensate liquidity and aggregate formation of biomolecules, including DCP1A, TAZ and polyQ-protein, under hyperosmotic stress. Our findings demonstrate that changes in Na<sup>+</sup> contribute to the cellular stress response via liquidity maintenance of biomolecular condensates. (Link to Publication Site) ● Publication site (DOI): 10.1101/2022.06.10.495571 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1101/2022.06.10.495571 (DOI: 10.1101/2022.06.10.495571)
9.	Kengo Watanabe, Tomasz Wilmanski, Christian Diener, John C. Earls, Anat Zimmer, Briana Lincoln, Jennifer J. Hadlock, Jennifer C. Lovejoy, Sean M. Gibbons, Andrew T. Magis, Leroy Hood, Nathan D. Price and Noa Rappaport : Multiomic Body Mass Index signatures in blood reveal clinically relevant population heterogeneity and variable responses to a healthy lifestyle intervention, medRxiv, 2022. (Summary) Multiomic profiling can reveal population heterogeneity for both health and disease states. Obesity drives a myriad of metabolic perturbations in individuals and is a risk factor for multiple chronic diseases. Here, we report a global atlas of cross-sectional and longitudinal changes in 1,111 blood analytes associated with variation in Body Mass Index (BMI), as well as the multiomic associations with host polygenic risk scores and gut microbiome composition, from a cohort of 1,277 individuals enrolled in a wellness program. Machine learning model predictions of BMI from blood multiomics captured heterogeneous phenotypic states of host metabolism and gut microbiome composition, better than classically-measured BMI. Moreover, longitudinal analyses identified variable BMI trajectories for different omics measures in response to a healthy lifestyle intervention; metabolomics-inferred BMI decreased to a greater extent than actual BMI, while proteomics-inferred BMI exhibited greater resistance to change. Our analyses further revealed blood analyte–analyte associations that were significantly modified by metabolomics-inferred BMI and partially reversed in the metabolically obese population during the intervention. Taken together, our findings provide a blood atlas of the molecular perturbations associated with changes in obesity status, serving as a valuable resource to robustly quantify metabolic health for predictive and preventive medicine. (Link to Publication Site) ● Publication site (DOI): 10.1101/2022.01.20.22269601 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1101/2022.01.20.22269601 (DOI: 10.1101/2022.01.20.22269601)
10.	Kengo Watanabe, Kazuhiro Morishita, Xiangyu Zhou, Shigeru Shiizaki, Yasuo Uchiyama, Masato Koike, Isao Naguro and Hidenori Ichijo : Cells recognize osmotic stress through liquid-liquid phase separation lubricated with poly(ADP-ribose), bioRxiv, 2020. (Summary) Cells are under threat of osmotic perturbation; and cell volume maintenance is critical in cerebral edema, inflammation and aging, in which prominent changes in intracellular or extracellular osmolality emerge. After osmotic stress-enforced cell swelling or shrinkage, the cells regulate intracellular osmolality to recover their volume. However, the mechanisms recognizing osmotic stress remain obscured. We previously clarified that apoptosis signal-regulating kinase 3 (ASK3) bidirectionally responds to osmotic stress and regulates cell volume recovery. Here, we report that macromolecular crowding induces liquid-demixing condensates of ASK3 under hyperosmotic stress, which transduce osmosensing signal into ASK3 inactivation. A genome-wide small interfering RNA (siRNA) screen identified an ASK3 inactivation regulator, nicotinamide phosphoribosyltransferase (NAMPT), related to poly(ADP-ribose) signaling. Furthermore, we clarify that poly(ADP-ribose) keeps ASK3 condensates in the liquid phase and enables ASK3 to become inactivated under hyperosmotic stress. Our findings demonstrate that cells rationally incorporate physicochemical phase separation into their osmosensing systems. (Link to Publication Site) ● Publication site (DOI): 10.1101/2020.04.20.049759 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1101/2020.04.20.049759 (DOI: 10.1101/2020.04.20.049759)
11.	Go Kasuya, Takanori Nakane, Takeshi Yokoyama, Yanyan Jia, Masato Inoue, Kengo Watanabe, Ryoki Nakamura, Tomohiro Nishizawa, Kusakizako Tsukasa, Tsutsumi Akihisa, Haruaki Yanagisawa, Naoshi Dohmae, Motoyuki Hattori, Hidenori Ichijo, Zhiqiang Yan, Masahide Kikkawa, Mikako Shirouzu, Ryuichiro Ishitani and Osamu Nureki : Cryo-EM structure of the volume-regulated anion channel LRRC8, bioRxiv, 2018. (Summary) Maintenance of cell volume against osmotic change is crucial for proper cell functions, such as cell proliferation and migration. The leucine-rich repeat-containing 8 (LRRC8) proteins are anion selective channels, and were recently identified as pore components of the volume-regulated anion channels (VRACs), which extrude anions to decrease the cell volume upon cell-swelling. Here, we present the human LRRC8A structure, determined by a single-particle cryo-electron microscopy analysis. The sea anemone-like structure represents a trimer of dimers assembly, rather than a symmetrical hexameric assembly. The four-spanning transmembrane region has a gap junction channel-like membrane topology, while the LRR region containing 15 leucine-rich repeats forms a long twisted arc. The channel pore is along the central axis and constricted on the extracellular side, where the highly conserved polar and charged residues at the tip of the extracellular helix contribute to the anion and other osmolyte permeability. Comparing the two structural populations facilitated the identification of both compact and relaxed conformations, suggesting that the LRR region is flexible and mobile with rigid-body motions, which might be implicated in structural transitions upon pore opening. Overall, our structure provides a framework for understanding the molecular mechanisms of this unique class of ion channels. (Link to Publication Site) ● Publication site (DOI): 10.1101/331207 (Link to Search Site for Scientific Articles) ● Search Scopus @ Elsevier (DOI): 10.1101/331207 (DOI: 10.1101/331207)

Review, Commentary:

1.	Noa Rappapor and Kengo Watanabe : Biological BMI uncovers hidden health risks and is more responsive to lifestyle shifts, Nature Medicine, Vol.29, No.4, 801-802, Apr. 2023. (Keyword) Humans / Body Mass Index / Life Style / Obesity (Link to Publication Site) ● Publication site (DOI): 10.1038/s41591-023-02283-x (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 37041385 ● Summary page in Scopus @ Elsevier: 2-s2.0-85153122084 (DOI: 10.1038/s41591-023-02283-x, PubMed: 37041385, Elsevier: Scopus)
2.	Shunya Ishihara, Hidenori Ichijo and Kengo Watanabe : A Novel Lens for Cell Volume Regulation: Liquid Liquid Phase Separation, Cellular Physiology and Biochemistry, Vol.55, No.S1, 135-160, Apr. 2021. (Summary) Cells are constantly exposed to the risk of volume perturbation under physiological conditions. The increase or decrease in cell volume accompanies intracellular changes in cell membrane tension, ionic strength/concentration and macromolecular crowding. To avoid deleterious consequences caused by cell volume perturbation, cells have volume recovery systems that regulate osmotic water flow by transporting ions and organic osmolytes across the cell membrane. Thus far, a number of biomolecules have been reported to regulate cell volume. However, the question of how cells sense volume change and modulate volume regulatory systems is not fully understood. Recently, the existence and significance of phaseseparated biomolecular condensates have been revealed in numerous physiological events, including cell volume perturbation. In this review, we summarize the current understanding of cell volume-sensing mechanisms, introduce recent studies on biomolecular condensates induced by cell volume change and discuss how biomolecular condensates contribute to cell volume sensing and cell volume maintenance. In addition to previous studies of biochemistry, molecular biology and cell biology, a phase separation perspective will allow us to understand the complicated volume regulatory systems of cells. (Link to Publication Site) ● Publication site (DOI): 10.33594/000000357 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 33877747 ● Summary page in Scopus @ Elsevier: 2-s2.0-85105692822 (DOI: 10.33594/000000357, PubMed: 33877747, Elsevier: Scopus)
3.	Kazuhiro Morishita, Kengo Watanabe and Hidenori Ichijo : Cell volume regulation in cancer cell migration driven by osmotic water flow, Cancer Science, Vol.110, No.8, 2337-2347, May 2019. (Link to Publication Site) ● Publication site (DOI): 10.1111/cas.14079 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 31120184 ● Summary page in Scopus @ Elsevier: 2-s2.0-85068384441 (DOI: 10.1111/cas.14079, PubMed: 31120184, Elsevier: Scopus)
4.	Takuto Nishida, Kazuki Hattori and Kengo Watanabe : The regulatory and signaling mechanisms of the ASK family, Advances in Biological Regulation, Vol.66, 2-22, Dec. 2017. (Link to Publication Site) ● Publication site (DOI): 10.1016/j.jbior.2017.05.004 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 28669716 ● Summary page in Scopus @ Elsevier: 2-s2.0-85021371885 (DOI: 10.1016/j.jbior.2017.05.004, PubMed: 28669716, Elsevier: Scopus)
5.	Xiangyu Zhou, Isao Naguro, Hidenori Ichijo and Kengo Watanabe : Mitogen-activated protein kinases as key players in osmotic stress signaling, Biochimica et Biophysica Acta (BBA) - General Subjects, Vol.1860, No.9, 2037-2052, Sep. 2016. (Link to Publication Site) ● Publication site (DOI): 10.1016/j.bbagen.2016.05.032 (Link to Search Site for Scientific Articles) ● PubMed @ National Institutes of Health, US National Library of Medicine (PMID): 27261090 ● Summary page in Scopus @ Elsevier: 2-s2.0-84976525679 (DOI: 10.1016/j.bbagen.2016.05.032, PubMed: 27261090, Elsevier: Scopus)

Proceeding of Domestic Conference:

1.	Kengo Watanabe : Osmotic stress-sensing mechanism via liquid-liquid phase separation, The 97th Annual Meeting of the Japanese Biochemical Society (2024 Young Investigator Award Lecture SK1-05), Nov. 2024.
2.	Kengo Watanabe, Isao Naguro and Hidenori Ichijo : Phase separation governs PP6-mediated ASK3 inactivation under hyperosmotic stress, The 92nd Annual Meeting of the Japanese Biochemical Society (Symposium 2S09m), Sep. 2019.
3.	Kengo Watanabe : ASK3 and cell volume regulation: common mechanism in cellular osmotic stress response and cell death induction, IMSUT Young Scientists Symposium, Jan. 2019.
4.	Kengo Watanabe, Isao Naguro and Hidenori Ichijo : PP6-ASK3 module is a key converter under bidirectional osmotic stress, Consortium of Biological Sciences 2017 (ConBio2017, Workshop 2PW15), Dec. 2017.

Et cetera, Workshop:

1.	Kengo Watanabe : Rise of the age of discovery in life science researches, Divisional seminar (Division of Biological Science, Nara Institute of Science and Technology), Aug. 2024.
2.	Kengo Watanabe : Rise of the age of discovery in health science researches, The 32nd Young Talent Development Seminar (COI-NEXT integrated health industry city site that will be a world model for self-sustained growth of human resources and technology), Apr. 2024.
3.	Kengo Watanabe : Beyond the Scale with Biological BMI: Integrated Multiomic Measures of Metabolic Health, Oike Lab seminar (Kumamoto University), Dec. 2023.
4.	Kengo Watanabe : Rise of the age of discovery in stress response researches, Nex-Gen Symposium on Cell Signaling, Aug. 2023.
5.	Kengo Watanabe : Beyond the Scale with Biological BMI: Integrated Multiomic Measures of Metabolic Health, RIKEN BDR seminar, Aug. 2023.
6.	Kengo Watanabe : Beyond the Scale with Biological BMI: Integrated Multiomic Measures of Metabolic Health, Long Lab seminar (Vanderbilt University Medical Center), Jul. 2023.
7.	Kengo Watanabe : Poly(ADP-ribose) regulates osmoresponsive kinase ASK3 via liquid-liquid phase separation, Atomi & Shimizu Lab seminar (Tokyo University of Agriculture and Technology), Nov. 2019.

Patent:

1.	Noa Rappapor, Kengo Watanabe, Tomasz Wilmanski and Nathan Price : OMICS-INFERRED BODY INDEX METHOD AND SYSTEM, 63/480,814 (Jan. 2023), US-20240249847-A1 (Jul. 2024), .

Grants-in-Aid for Scientific Research (KAKEN Grants Database @ NII.ac.jp)

An exploration of the common principles in the cellular osmotic stress response and cell death induction (Project/Area Number: 19K16067 )
Genome-wide screen-based identification of non-selective hypertonicity-induced cation channel (Project/Area Number: 17K15086 )
Search by Researcher Number (20781727)