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Sho C, Kawano K, Hou DX, Yoshimoto M, Okuno H. Ameliorative effect of the oil components derived from sweet potato shochu on impaired short-term memory in mice after amyloid β 25-35 injection. J Biosci Bioeng 2023; 135:54-62. [PMID: 36336574 DOI: 10.1016/j.jbiosc.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
Abstract
Sweet potato shochu oil is a by-product of shochu production and usually discarded although some physiological functions are considered. In this study, we investigated the effects of shochu oil on short-term memory using a murine model of spontaneous alternating behavior induced by the intracerebroventricular (ICV) administration of amyloid β25-35 (Aβ25-35). Mice were orally administered shochu oil for 15 days. Experiments with a Y-maze model revealed that the Aβ25-35 caused a significant decrease in spontaneous alternation behavior, and supplementation with shochu oil significantly improved this behavior. DNA microarray analysis revealed that the administration of shochu oil downregulated the expression of S100a9 and Ptgs2, which reportedly exacerbate amyloid β deposition in Alzheimer's disease. The administration of shochu oil upregulated the expression of Dnaja1 and PP2A, which is typically downregulated in Alzheimer's disease. These data suggest that shochu oil possible ameliorates on impaired short-term memory in mice after amyloid β25-35 injection, as indicated by its effects on improving spontaneous alternation behavior and modulating the expressions of related genes.
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Affiliation(s)
- Cho Sho
- Kirishima Shuzo Co., Ltd., 4-28-1 Shimokawahigashi, Miyakonojo, Miyazaki 885-8588, Japan.
| | - Kuniaki Kawano
- Kirishima Shuzo Co., Ltd., 4-28-1 Shimokawahigashi, Miyakonojo, Miyazaki 885-8588, Japan
| | - De-Xing Hou
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Makoto Yoshimoto
- MY Food Development Research Institute, 109-3 ichimanjyo, Miyakonojo, Miyazaki 885-0041, Japan
| | - Hironori Okuno
- Kirishima Shuzo Co., Ltd., 4-28-1 Shimokawahigashi, Miyakonojo, Miyazaki 885-8588, Japan
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Matsumoto T, Iizuka T, Nakamura M, Suzuki T, Yamamoto M, Ono M, Kagami K, Kasama H, Wakae K, Muramatsu M, Horike SI, Kyo S, Yamamoto Y, Mizumoto Y, Daikoku T, Fujiwara H. FOXP4 inhibits squamous differentiation of atypical cells in cervical intraepithelial neoplasia via an ELF3-dependent pathway. Cancer Sci 2022; 113:3376-3389. [PMID: 35838233 PMCID: PMC9530870 DOI: 10.1111/cas.15489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/28/2022] [Accepted: 07/03/2022] [Indexed: 11/28/2022] Open
Abstract
Although the human papillomavirus (HPV) vaccine is effective for preventing cervical cancers, this vaccine does not eliminate pre‐existing infections, and alternative strategies have been warranted. Here, we report that FOXP4 is a new target molecule for differentiation therapy of cervical intraepithelial neoplasia (CIN). An immunohistochemical study showed that FOXP4 was expressed in columnar epithelial, reserve, and immature squamous cells, but not in mature squamous cells of the normal uterine cervix. In contrast with normal mature squamous cells, FOXP4 was expressed in atypical squamous cells in CIN and squamous cell carcinoma lesions. The FOXP4‐positive areas significantly increased according to the CIN stages from CIN1 to CIN3. In monolayer cultures, downregulation of FOXP4 attenuated proliferation and induced squamous differentiation in CIN1‐derived HPV 16‐positive W12 cells via an ELF3‐dependent pathway. In organotypic raft cultures, FOXP4‐downregulated W12 cells showed mature squamous phenotypes of CIN lesions. In human keratinocyte‐derived HaCaT cells, FOXP4 downregulation also induced squamous differentiation via an ELF3‐dependent pathway. These findings suggest that downregulation of FOXP4 inhibits cell proliferation and promotes the differentiation of atypical cells in CIN lesions. Based on these results, we propose that FOXP4 is a novel target molecule for nonsurgical CIN treatment that inhibits CIN progression by inducing squamous differentiation.
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Affiliation(s)
- Takeo Matsumoto
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takashi Iizuka
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Mitsuhiro Nakamura
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takuma Suzuki
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Megumi Yamamoto
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masanori Ono
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Obstetrics and Gynecology, Tokyo Medical University, Tokyo, Japan
| | - Kyosuke Kagami
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Haruki Kasama
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kousho Wakae
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shin-Ichi Horike
- Division of Integrated Omics research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine, Izumo, Shimane, Japan
| | - Yasuhiko Yamamoto
- Departments of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Ishikawa, Japan
| | - Yasunari Mizumoto
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takiko Daikoku
- Division of Animal Disease Model, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hiroshi Fujiwara
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
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Ono M, Toyoda N, Kagami K, Hosono T, Matsumoto T, Horike SI, Yamazaki R, Nakamura M, Mizumoto Y, Fujiwara T, Ando H, Fujiwara H, Daikoku T. Uterine Deletion of Bmal1 Impairs Placental Vascularization and Induces Intrauterine Fetal Death in Mice. Int J Mol Sci 2022; 23:ijms23147637. [PMID: 35886985 PMCID: PMC9319876 DOI: 10.3390/ijms23147637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 02/01/2023] Open
Abstract
Recently, it was demonstrated that the expression of BMAL1 was decreased in the endometrium of women suffering from recurrent spontaneous abortion. To investigate the pathological roles of uterine clock genes during pregnancy, we produced conditional deletion of uterine Bmal1 (cKO) mice and found that cKO mice could receive embryo implantation but not sustain pregnancy. Gene ontology analysis of microarray suggested that uterine NK (uNK) cell function was suppressed in cKO mice. Histological examination revealed the poor formation of maternal vascular spaces in the placenta. In contrast to WT mice, uNK cells in the spongiotrophoblast layer, where maternal uNK cells are directly in contact with fetal trophoblast, hardly expressed an immunosuppressive NK marker, CD161, in cKO mice. By progesterone supplementation, pregnancy could be sustained until the end of pregnancy in some cKO mice. Although this treatment did not improve the structural abnormalities of the placenta, it recruited CD161-positive NK cells into the spongiotrophoblast layer in cKO mice. These findings indicate that the uterine clock system may be critical for pregnancy maintenance after embryo implantation.
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Affiliation(s)
- Masanori Ono
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
- Department of Obstetrics and Gynecology, Tokyo Medical University, Shinjuku, Tokyo 160-0023, Japan
| | - Natsumi Toyoda
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
- Division of Animal Disease Model, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan
| | - Kyosuke Kagami
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
| | - Takashi Hosono
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
- Department of Cellular and Molecular Function Analysis, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan;
| | - Takeo Matsumoto
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
| | - Shin-ichi Horike
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa 920-8640, Japan;
| | - Rena Yamazaki
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
| | - Mitsuhiro Nakamura
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
- Department of Obstetrics and Gynecology, Public Central Hospital of Matto Ishikawa, Hakusan 924-8588, Japan
| | - Yasunari Mizumoto
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
| | - Tomoko Fujiwara
- Department of Human Life Environments, Kyoto Notre Dame University, Kyoto 606-0847, Japan;
| | - Hitoshi Ando
- Department of Cellular and Molecular Function Analysis, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan;
| | - Hiroshi Fujiwara
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan; (M.O.); (N.T.); (K.K.); (T.H.); (T.M.); (R.Y.); (M.N.); (Y.M.)
- Correspondence: (H.F.); (T.D.); Tel.: +81-76-265-2425 (H.F.); +81-76-265-2460 (T.D.); Fax: +81-76-234-4266 (H.F.); +81-76-234-4245 (T.D.)
| | - Takiko Daikoku
- Division of Animal Disease Model, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Takaramachi 13-1, Kanazawa 920-8641, Japan
- Correspondence: (H.F.); (T.D.); Tel.: +81-76-265-2425 (H.F.); +81-76-265-2460 (T.D.); Fax: +81-76-234-4266 (H.F.); +81-76-234-4245 (T.D.)
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Chen Y, Chen S, Lei EP. DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma. Bioinformatics 2022; 38:4062-4069. [PMID: 35809062 PMCID: PMC9438959 DOI: 10.1093/bioinformatics/btac498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/20/2022] [Accepted: 07/08/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION ChIP-seq detects protein-DNA interactions within chromatin, such as that of chromatin structural components and transcription machinery. ChIP-seq profiles are often noisy and variable across replicates, posing a challenge to the development of effective algorithms to accurately detect differential peaks. Methods have recently been designed for this purpose but sometimes yield conflicting results that are inconsistent with the underlying biology. Most existing algorithms perform well on limited datasets. To improve differential analysis of ChIP-seq, we present a novel Differential analysis method for ChIP-seq based on Limma (DiffChIPL). RESULTS DiffChIPL is adaptive to asymmetrical or symmetrical data and can accurately report global differences. We used simulated and real datasets for transcription factors (TFs) and histone modification marks to validate and benchmark our algorithm. DiffChIPL shows superior performance in sensitivity and false positive rate in different simulations and control datasets. DiffChIPL also performs well on real ChIP-seq, CUT&RUN, CUT&Tag and ATAC-seq datasets. DiffChIPL is an accurate and robust method, exhibiting better performance in differential analysis for a variety of applications including TF binding, histone modifications and chromatin accessibility. AVAILABILITY AND IMPLEMENTATION https://github.com/yancychy/DiffChIPL. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Chen
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Shue Chen
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
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Rani P, Dutta K, Kumar V. Artificial intelligence techniques for prediction of drug synergy in malignant diseases: Past, present, and future. Comput Biol Med 2022; 144:105334. [DOI: 10.1016/j.compbiomed.2022.105334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/13/2022] [Accepted: 02/13/2022] [Indexed: 12/22/2022]
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Bamba R, Okamura T, Hashimoto Y, Majima S, Senmaru T, Ushigome E, Nakanishi N, Asano M, Yamazaki M, Takakuwa H, Hamaguchi M, Fukui M. Extracellular lipidome change by an SGLT2 inhibitor, luseogliflozin, contributes to prevent skeletal muscle atrophy in db/db mice. J Cachexia Sarcopenia Muscle 2022; 13:574-588. [PMID: 34854254 PMCID: PMC8818690 DOI: 10.1002/jcsm.12814] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 08/18/2021] [Accepted: 09/04/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Diabetes mellitus increases the excretion of urinary glucose from the renal glomeruli due to elevated blood glucose levels. In the renal tubules, SGLT2 is expressed and reabsorbs the excreted urinary glucose. In the pathogenesis of diabetes mellitus, glucose reabsorption by SGLT2 is increased, and SGLT2 inhibitors improve hyperglycaemia by inhibiting this reabsorption. When urinary glucose excretion is enhanced, glucose supply to skeletal muscle may be insufficient and muscle protein catabolism may be accelerated. On the other hand, SGLT2 inhibitors not only ameliorate hyperglycaemia but also improve fatty acid metabolism in muscle, which may prevent muscle atrophy. METHODS Eight-week-old male db/m mice or db/db mice were fed a standard diet with or without the SGLT2i luseogliflozin (0.01% w/w in chow) for 8 weeks. Mice were sacrificed at 16 weeks of age, and skeletal muscle and serum lipidomes, as well as skeletal muscle transcriptome, were analysed. RESULTS Administration of SGLT2i led to not only decreased visceral fat accumulation (P = 0.004) but also increased soleus muscle weight (P = 0.010) and grip strength (P = 0.0001). The levels of saturated fatty acids, especially palmitic acid, decreased in both muscles (P = 0.017) and sera (P = 0.041) upon administration of SGLT2i, while the content of monosaturated fatty acids, especially oleic acid, increased in both muscle (P < 0.0001) and sera (P = 0.009). Finally, the accumulation of transcripts associated with fatty acid metabolism, such as Scd1, Fasn, and Elovl6, and of muscle atrophy-associated transcripts, such as Foxo1, Mstn, Trim63, and Fbxo32, decreased following SGLT2i administration. CONCLUSIONS Intramuscular fatty acid metabolism and gene expression were influenced by the extracellular lipidome, which was modified by SGLT2i. Hence, secondary effects, other than the hypoglycaemic effects of SGLT2i, might lead to the alleviation of sarcopenia.
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Affiliation(s)
- Ryo Bamba
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takuro Okamura
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshitaka Hashimoto
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Saori Majima
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takafumi Senmaru
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Emi Ushigome
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naoko Nakanishi
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mai Asano
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masahiro Yamazaki
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroshi Takakuwa
- Agilent Technologies, Chromatography Mass Spectrometry Sales Department, Life Science and Applied Markets Group, Tokyo, Japan
| | - Masahide Hamaguchi
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Michiaki Fukui
- Department of Endocrinology and Metabolism, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Sato H, Takado Y, Toyoda S, Tsukamoto-Yasui M, Minatohara K, Takuwa H, Urushihata T, Takahashi M, Shimojo M, Ono M, Maeda J, Orihara A, Sahara N, Aoki I, Karakawa S, Isokawa M, Kawasaki N, Kawasaki M, Ueno S, Kanda M, Nishimura M, Suzuki K, Mitsui A, Nagao K, Kitamura A, Higuchi M. Neurodegenerative processes accelerated by protein malnutrition and decelerated by essential amino acids in a tauopathy mouse model. SCIENCE ADVANCES 2021; 7:eabd5046. [PMID: 34678069 PMCID: PMC8535828 DOI: 10.1126/sciadv.abd5046] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Protein malnutrition is epidemiologically suggested as a potential risk factor for senile dementia, although molecular mechanisms linking dietary proteins and amino acids to neurodegeneration remain unknown. Here, we show that a low-protein diet resulted in down-regulated expression of synaptic components and a modest acceleration of brain atrophy in mice modeling neurodegenerative tauopathies. Notably, these abnormal phenotypes were robustly rescued by the administration of seven selected essential amino acids. The up-regulation of inflammation-associated gene expression and progressive brain atrophy in the tauopathy model were profoundly suppressed by treatment with these essential amino acids without modifications of tau depositions. Moreover, the levels of kynurenine, an initiator of a pathway inducing neuroinflammatory gliosis and neurotoxicity in the brain, were lowered by treatment through inhibition of kynurenine uptake in the brain. Our findings highlight the importance of specific amino acids as systemic mediators of brain homeostasis against neurodegenerative processes.
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Affiliation(s)
- Hideaki Sato
- Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Yuhei Takado
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | | | | | - Keiichiro Minatohara
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroyuki Takuwa
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Takuya Urushihata
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Manami Takahashi
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Masafumi Shimojo
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Maiko Ono
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Jun Maeda
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Asumi Orihara
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Naruhiko Sahara
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | - Ichio Aoki
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
| | | | | | | | | | - Satoko Ueno
- Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | | | | | | | | | - Kenji Nagao
- Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Akihiko Kitamura
- Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
- Corresponding author. (M.H.); (A.K.)
| | - Makoto Higuchi
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Sciences and Technology, Chiba 263-8555, Japan
- Corresponding author. (M.H.); (A.K.)
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8
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Osabe T, Shimizu K, Kadota K. Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data. BMC Bioinformatics 2021; 22:511. [PMID: 34670485 PMCID: PMC8527798 DOI: 10.1186/s12859-021-04438-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering is used to classify DEGs with similar expression patterns for the subsequent analyses of data from experiments such as time-courses or multi-group comparisons. However, gene clustering has rarely been used for analyzing simple two-group data or differential expression (DE). In this study, we report that a model-based clustering algorithm implemented in an R package, MBCluster.Seq, can also be used for DE analysis. Results The input data originally used by MBCluster.Seq is DEGs, and the proposed method (called MBCdeg) uses all genes for the analysis. The method uses posterior probabilities of genes assigned to a cluster displaying non-DEG pattern for overall gene ranking. We compared the performance of MBCdeg with conventional R packages such as edgeR, DESeq2, and TCC that are specialized for DE analysis using simulated and real data. Our results showed that MBCdeg outperformed other methods when the proportion of DEG (PDEG) was less than 50%. However, the DEG identification using MBCdeg was less consistent than with conventional methods. We compared the effects of different normalization algorithms using MBCdeg, and performed an analysis using MBCdeg in combination with a robust normalization algorithm (called DEGES) that was not implemented in MBCluster.Seq. The new analysis method showed greater stability than using the original MBCdeg with the default normalization algorithm. Conclusions MBCdeg with DEGES normalization can be used in the identification of DEGs when the PDEG is relatively low. As the method is based on gene clustering, the DE result includes information on which expression pattern the gene belongs to. The new method may be useful for the analysis of time-course and multi-group data, where the classification of expression patterns is often required. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04438-4.
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Affiliation(s)
- Takayuki Osabe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,Interfaculty Initiative in Information Studies, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Interfaculty Initiative in Information Studies, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Park JM, Han YM, Oh JY, Lee DY, Choi SH, Hahm KB. Transcriptome profiling implicated in beneficiary actions of kimchi extracts against Helicobacter pylori infection. J Clin Biochem Nutr 2021; 69:171-187. [PMID: 34616109 PMCID: PMC8482382 DOI: 10.3164/jcbn.20-116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022] Open
Abstract
Dietary intervention to prevent Helicobacter pylori (H. pylori)-gastric cancer might be ideal because of no risk of bacterial resistance, safety, and rejuvenating action of atrophic gastritis. We have published data about the potential of fermented kimchi as nutritional approach for H. pylori. Hence recent advances in RNAseq analysis lead us to investigate the transcriptome analysis to explain these beneficiary actions of kimchi. gastric cells were infected with either H. pylori or H. pylori plus kimchi. 943 genes were identified as significantly increased or decreased genes according to H. pylori infection and 68 genes as significantly changed between H. pylori infection and H. pylori plus kimchi (p<0.05). Gene classification and Medline database showed DLL4, FGF18, PTPRN, SLC7A11, CHAC1, FGF21, ASAN, CTH, and CREBRF were identified as significantly increased after H. pylori, but significantly decreased with kimchi and NEO1, CLDN8, KLRG1, and IGFBP1 were identified as significantly decreased after H. pylori, but increased with kimchi. After KEGG and STRING-GO analysis, oxidative stress, ER stress, cell adhesion, and apoptosis genes were up-regulated with H. pylori infection but down-regulated with kimchi, whereas tissue regeneration, cellular anti-oxidative response, and anti-inflammation genes were reversely regulated with kimchi (p<0.01). Conclusively, transcriptomes of H. pylori plus kimchi showed significant biological actions.
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Affiliation(s)
- Jong Min Park
- Daejeon University School of Oriental Medicine, Daejeon, 34520, Korea
| | - Young Min Han
- Seoul Center, Korea Basic Science Institute, Seoul, 02456, Korea
| | - Ji Young Oh
- CJ Food Research Center, Suwon, 16471, Korea
| | | | | | - Ki Baik Hahm
- CHA Cancer Preventive Research Center, CHA Bio Complex, Pangyo, 13497, Korea
- Medpacto Research Institute, Medpacto, Seoul, 06668, Korea
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10
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Okamura T, Hashimoto Y, Majima S, Senmaru T, Ushigome E, Nakanishi N, Asano M, Yamazaki M, Takakuwa H, Hamaguchi M, Fukui M. Trans Fatty Acid Intake Induces Intestinal Inflammation and Impaired Glucose Tolerance. Front Immunol 2021; 12:669672. [PMID: 33995404 PMCID: PMC8117213 DOI: 10.3389/fimmu.2021.669672] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Aims Many nutritional and epidemiological studies have shown that high consumption of trans fatty acids can cause several adverse effects on human health, including cardiovascular disease, diabetes, and cancer. In the present study, we investigated the effect of trans fatty acids on innate immunity in the gut by observing mice fed with a diet high in trans fatty acids, which have been reported to cause dysbiosis. Methods We used C57BL6/J mice and fed them with normal diet (ND) or high-fat, high-sucrose diet (HFHSD) or high-trans fatty acid, high-sucrose diet (HTHSD) for 12 weeks. 16S rRNA gene sequencing was performed on the mice stool samples, in addition to flow cytometry, real-time PCR, and lipidomics analysis of the mice serum and liver samples. RAW264.7 cells were used for the in vitro studies. Results Mice fed with HTHSD displayed significantly higher blood glucose levels and advanced fatty liver and intestinal inflammation, as compared to mice fed with HFHSD. Furthermore, compared to mice fed with HFHSD, mice fed with HTHSD displayed a significant elevation in the expression of CD36 in the small intestine, along with a reduction in the expression of IL-22. Furthermore, there was a significant increase in the populations of ILC1s and T-bet-positive ILC3s in the lamina propria in mice fed with HTHSD. Finally, the relative abundance of the family Desulfovibrionaceae, which belongs to the phylum Proteobacteria, was significantly higher in mice fed with HFHSD or HTHSD, than in mice fed with ND; between the HFHSD and HTHSD groups, the abundance was slightly higher in the HTHSD group. Conclusions This study revealed that compared to saturated fatty acid intake, trans fatty acid intake significantly exacerbated metabolic diseases such as diabetes and fatty liver.
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Affiliation(s)
- Takuro Okamura
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshitaka Hashimoto
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Saori Majima
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takafumi Senmaru
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Emi Ushigome
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naoko Nakanishi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mai Asano
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masahiro Yamazaki
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroshi Takakuwa
- Chromatography Mass Spectrometry Sales Department, Life Science and Applied Markets Group, Agilent Technologies, Tokyo, Japan
| | - Masahide Hamaguchi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Michiaki Fukui
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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11
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Activation-induced cytidine deaminase is a possible regulator of cross-talk between oocytes and granulosa cells through GDF-9 and SCF feedback system. Sci Rep 2021; 11:3833. [PMID: 33589683 PMCID: PMC7884688 DOI: 10.1038/s41598-021-83529-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/03/2021] [Indexed: 01/08/2023] Open
Abstract
Activation-induced cytidine deaminase (AID, Aicda) is a master gene regulating class switching of immunoglobulin genes. In this study, we investigated the significance of AID expression in the ovary. Immunohistological study and RT-PCR showed that AID was expressed in murine granulosa cells and oocytes. However, using the Aicda-Cre/Rosa-tdRFP reporter mouse, its transcriptional history in oocytes was not detected, suggesting that AID mRNA in oocytes has an exogenous origin. Microarray and qPCR validation revealed that mRNA expressions of growth differentiation factor-9 (GDF-9) in oocytes and stem cell factor (SCF) in granulosa cells were significantly decreased in AID-knockout mice compared with wild-type mice. A 6-h incubation of primary granuloma cells markedly reduced AID expression, whereas it was maintained by recombinant GDF-9. In contrast, SCF expression was induced by more than threefold, whereas GDF-9 completely inhibited its increase. In the presence of GDF-9, knockdown of AID by siRNA further decreased SCF expression. However, in AID-suppressed granulosa cells and ovarian tissues of AID-knockout mice, there were no differences in the methylation of SCF and GDF-9. These findings suggest that AID is a novel candidate that regulates cross-talk between oocytes and granulosa cells through a GDF-9 and SCF feedback system, probably in a methylation-independent manner.
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12
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Okamura T, Okada H, Hashimoto Y, Majima S, Senmaru T, Nakanishi N, Asano M, Yamazaki M, Hamaguchi M, Fukui M. Let-7e-5p Regulates IGF2BP2, and Induces Muscle Atrophy. Front Endocrinol (Lausanne) 2021; 12:791363. [PMID: 35002969 PMCID: PMC8741024 DOI: 10.3389/fendo.2021.791363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND AND AIMS To understand the role of microRNAs in muscle atrophy caused by androgen-depletion, we performed microarray analysis of microRNA expression in the skeletal muscles of Sham, orchiectomized (ORX), and androgen-treated ORX mice. METHODS To clarify role and mechanisms of let-7e-5p in the muscle, the effect of let-7e-5p overexpression or knockdown on the expression of myosin heavy chain, glucose uptake, and mitochondrial function was investigated in C2C12 myotube cells. Moreover, we examined serum let-7e-5p levels among male subjects with type 2 diabetes. RESULTS We found that the expression of the miRNA, lethal (let)-7e-5p was significantly lower in ORX mice than that in Sham mice (p = 0.027); however, let-7e-5p expression in androgen-treated ORX mice was higher (p = 0.047). Suppression of let-7e-5p significantly upregulated the expression of myosin heavy chain, glucose uptake, and mitochondrial function. Real-time PCR revealed a possible regulation involving let-7e-5p and Igf2bp2 mRNA and protein in C2C12 cells. The serum let-7e-5p levels were significantly lower, which might be in compensation, in subjects with decreased muscle mass compared to subjects without decreased muscle mass. Let-7e-5p downregulates the expression of Igf2bp2 in myotube cells and inhibits the growth of the myosin heavy chain. CONCLUSIONS Based on our study, serum level of let-7e-5p may be used as a potential diagnostic marker for muscle atrophy.
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Affiliation(s)
- Takuro Okamura
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroshi Okada
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Diabetes and Endocrinology, Matsushita Memorial Hospital, Moriguchi, Japan
| | - Yoshitaka Hashimoto
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Saori Majima
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takafumi Senmaru
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naoko Nakanishi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mai Asano
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masahiro Yamazaki
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masahide Hamaguchi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Michiaki Fukui
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- *Correspondence: Michiaki Fukui,
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Takegami M, Hamaguchi M, Miyoshi T, Munekawa C, Yoshimura T, Nakajima H, Kimura T, Okamura T, Hashimoto Y, Nakanishi N, Kitao Y, Kinoshita K, Fukui M. Effect of matcha consumption on gut microbiota in healthy Japanese individuals: study protocol for a double-blind crossover interventional study. J Clin Biochem Nutr 2021; 70:262-265. [PMID: 35692672 PMCID: PMC9130063 DOI: 10.3164/jcbn.21-110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/13/2021] [Indexed: 11/22/2022] Open
Abstract
This study compares and clarifies the changes in intestinal flora resulting from the continuous consumption of two types of matcha. Healthy adults will consume two types of matcha tea for four weeks, and differences in the intestinal microflora before and after drinking will be compared. Gut microbiota will be identified using next-generation sequencing. Phylogenetic classification of the enterobacteria will be performed based on sequence similarities. The relative proportions of the classified enterobacteria to the total nucleotide sequences will be compared between the samples obtained from the two groups consuming different matcha. The continuous consumption of matcha may improve dysbiosis and prevent atherosclerosis. The effects may vary according to the type of matcha used. Trial registration: The study was registered with university hospital medical information network (UMIN) (UMIN000040303), and all participants gave their written informed consent. Registered 1 November 2020, https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000045982.
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Affiliation(s)
- Maya Takegami
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Masahide Hamaguchi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Tomoki Miyoshi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Chihiro Munekawa
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Takashi Yoshimura
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Hanako Nakajima
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Tomonori Kimura
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Takuro Okamura
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Yoshitaka Hashimoto
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Naoko Nakanishi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Yuki Kitao
- Tea Industry Research Division, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center
| | - Kazutsugu Kinoshita
- Tea Industry Research Division, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center
| | - Michiaki Fukui
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
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14
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Matsunaga M, Kita T, Yamamoto R, Yamamoto N, Okano T, Omori K, Sakamoto S, Nakagawa T. Initiation of Supporting Cell Activation for Hair Cell Regeneration in the Avian Auditory Epithelium: An Explant Culture Model. Front Cell Neurosci 2020; 14:583994. [PMID: 33281558 PMCID: PMC7688741 DOI: 10.3389/fncel.2020.583994] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023] Open
Abstract
Sensorineural hearing loss is a common disability often caused by the loss of sensory hair cells in the cochlea. Hair cell (HCs) regeneration has long been the main target for the development of novel therapeutics for sensorineural hearing loss. In the mammalian cochlea, hair cell regeneration is limited, but the auditory epithelia of non-mammalian organisms retain the capacity for hair cell regeneration. In the avian basilar papilla (BP), supporting cells (SCs), which give rise to regenerated hair cells, are usually quiescent. Hair cell loss induces both direct transdifferentiation and mitotic division of supporting cells. Here, we established an explant culture model for hair cell regeneration in chick basilar papillae and validated it for investigating the initial phase of hair cell regeneration. The histological assessment demonstrated hair cell regeneration via direct transdifferentiation of supporting cells. Labeling with 5-ethynyl-2′-deoxyuridine (EdU) revealed the occurrence of mitotic division in the supporting cells at specific locations in the basilar papillae, while no EdU labeling was observed in newly generated hair cells. RNA sequencing indicated alterations in known signaling pathways associated with hair cell regeneration, consistent with previous findings. Also, unbiased analyses of RNA sequencing data revealed novel genes and signaling pathways that may be related to the induction of supporting cell activation in the chick basilar papillae. These results indicate the advantages of our explant culture model of the chick basilar papillae for exploring the molecular mechanisms of hair cell regeneration.
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Affiliation(s)
- Mami Matsunaga
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoko Kita
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Norio Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Okano
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichi Omori
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Takayuki Nakagawa
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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15
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Kariri YA, Alsaleem M, Joseph C, Alsaeed S, Aljohani A, Shiino S, Mohammed OJ, Toss MS, Green AR, Rakha EA. The prognostic significance of interferon-stimulated gene 15 (ISG15) in invasive breast cancer. Breast Cancer Res Treat 2020; 185:293-305. [PMID: 33073304 PMCID: PMC7867506 DOI: 10.1007/s10549-020-05955-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022]
Abstract
Background Lymphovascular invasion (LVI) is a prognostic factor in early-stage invasive breast cancer (BC). Through bioinformatics, data analyses of multiple BC cohorts revealed the positive association between interferon-stimulated gene 15 (ISG15) LVI status. Thus, we explored the prognostic significance of ISG15 in BC. Methods The prognostic significance of ISG15 mRNA was assessed in METABRIC (n = 1980), TCGA (n = 854) and Kaplan–Meier Plotter (n = 3951). ISG15 protein was evaluated using immunohistochemistry (n = 859) in early-stage invasive BC patients with long-term follow-up. The associations between ISG15 expression and clinicopathological features, expression of immune cell markers and patient outcome data were evaluated. Results High mRNA and protein ISG15 expression were associated with LVI, higher histological grade, larger tumour size, hormonal receptor negativity, HER2 positivity, p53 and Ki67. High ISG15 protein expression was associated with HER2-enriched BC subtypes and immune markers (CD8, FOXP3 and CD68). High ISG15 mRNA and ISG15 expressions were associated with poor patient outcome. Cox proportional multivariate analysis revealed that the elevated ISG15 expression was an independent prognostic factor of shorter BC-specific survival. Conclusion This study provides evidence for the role of ISG15 in LVI development and BC prognosis. Further functional studies in BC are warranted to evaluate the therapeutic potential of ISG15. Electronic supplementary material The online version of this article (10.1007/s10549-020-05955-1) contains supplementary material, which is available to authorised users.
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Affiliation(s)
- Yousif A Kariri
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK.,Department of Laboratory Medical Science, Faculty of Applied Medical Science, Shaqra University, Shaqra, Saudi Arabia
| | - Mansour Alsaleem
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Chitra Joseph
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Sami Alsaeed
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Abrar Aljohani
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Sho Shiino
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Omar J Mohammed
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Michael S Toss
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Andrew R Green
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Emad A Rakha
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK. .,Department of Histopathology, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, NG5 1PB, UK.
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16
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Nakajima H, Takewaki F, Hashimoto Y, Kajiyama S, Majima S, Okada H, Senmaru T, Ushigome E, Nakanishi N, Hamaguchi M, Yamazaki M, Tanaka Y, Oikawa Y, Nakajima S, Ohno H, Fukui M. The Effects of Metformin on the Gut Microbiota of Patients with Type 2 Diabetes: A Two-Center, Quasi-Experimental Study. Life (Basel) 2020; 10:life10090195. [PMID: 32932871 PMCID: PMC7555986 DOI: 10.3390/life10090195] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022] Open
Abstract
Metformin is reported to affect human gut microbiota; however, the nature of this association in Japanese patients with type 2 diabetes mellitus (T2DM) is unknown. We enrolled 31 patients with T2DM who took metformin for the first time in this study. We compared them before and after four weeks of taking metformin. Fecal samples were collected and 16S rDNA sequences were performed to identify the gut microbiota. Blood samples and Gastrointestinal Symptom Rating Scale (GSRS) questionnaire results, denoting gastro-intestinal symptoms, were also collected. In the whole-group analysis, no significant differences were found at the phylum level. In a subgroup of 21 patients that excluding those using medications affecting gut microbiota, there was a significant decrease of the phylum Firmicutes (p = 0.042) and of the ratio of the Firmicutes and Bacteroidetes abundances (p = 0.04) after taking metformin. Changes in abdominal pain (r = −0.56, p = 0.008) and regurgitation (r = −0.53, p = 0.01) were associated with Parabacteroides. Despite there being no direct association with abdominal symptoms, our study revealed that the composition of gut microbiota in Japanese individuals with T2DM partially changed after starting metformin.
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Affiliation(s)
- Hanako Nakajima
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
| | - Fumie Takewaki
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
| | - Yoshitaka Hashimoto
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
- Correspondence:
| | - Shizuo Kajiyama
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
- Kajiyama Clinic, Kyoto 600-8898, Japan
| | - Saori Majima
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
| | - Hiroshi Okada
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
- Department of Internal Medicine, Matsushita Memorial Hospital, Moriguchi 570-8540, Japan
| | - Takafumi Senmaru
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
| | - Emi Ushigome
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
| | - Naoko Nakanishi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
| | - Masahide Hamaguchi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
| | - Masahiro Yamazaki
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
| | - Yoshiki Tanaka
- R&D Center, Biofermin Pharmaceutical Co., Ltd., Kobe 650-0021, Japan; (Y.T.); (Y.O.); (S.N.); (H.O.)
| | - Yousuke Oikawa
- R&D Center, Biofermin Pharmaceutical Co., Ltd., Kobe 650-0021, Japan; (Y.T.); (Y.O.); (S.N.); (H.O.)
| | - Shunji Nakajima
- R&D Center, Biofermin Pharmaceutical Co., Ltd., Kobe 650-0021, Japan; (Y.T.); (Y.O.); (S.N.); (H.O.)
| | - Hiroshi Ohno
- R&D Center, Biofermin Pharmaceutical Co., Ltd., Kobe 650-0021, Japan; (Y.T.); (Y.O.); (S.N.); (H.O.)
| | - Michiaki Fukui
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (H.N.); (F.T.); (S.K.); (S.M.); (H.O.); (T.S.); (E.U.); (N.N.); (M.H.); (M.Y.); (M.F.)
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Kurozumi S, Alsaleem M, Monteiro CJ, Bhardwaj K, Joosten SEP, Fujii T, Shirabe K, Green AR, Ellis IO, Rakha EA, Mongan NP, Heery DM, Zwart W, Oesterreich S, Johnston SJ. Targetable ERBB2 mutation status is an independent marker of adverse prognosis in estrogen receptor positive, ERBB2 non-amplified primary lobular breast carcinoma: a retrospective in silico analysis of public datasets. Breast Cancer Res 2020; 22:85. [PMID: 32782013 PMCID: PMC7422515 DOI: 10.1186/s13058-020-01324-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/26/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Invasive lobular carcinoma (ILC) accounts for 10-15% of primary breast cancers and is typically estrogen receptor alpha positive (ER+) and ERBB2 non-amplified. Somatic mutations in ERBB2/3 are emerging as a tractable mechanism underlying enhanced human epidermal growth factor 2 (HER2) activity. We tested the hypothesis that therapeutically targetable ERBB2/3 mutations in primary ILC of the breast associate with poor survival outcome in large public datasets. METHODS We performed in silico comparison of ERBB2 non-amplified cases of ER+ stage I-III primary ILC (N = 279) and invasive ductal carcinoma (IDC, N = 1301) using METABRIC, TCGA, and MSK-IMPACT information. Activating mutations amenable to HER2-directed therapy with neratinib were identified using existing functional data from in vitro cell line and xenograft experiments. Multivariate analysis of 10-year overall survival (OS) with tumor size, grade, and lymph node status was performed using a Cox regression model. Differential gene expression analyses by ERBB2 mutation and amplification status was performed using weighted average differences and an in silico model of response to neratinib derived from breast cancer cell lines. RESULTS ILC tumors comprised 17.7% of all cases in the dataset but accounted for 47.1% of ERBB2-mutated cases. Mutations in ERBB2 were enriched in ILC vs. IDC cases (5.7%, N = 16 vs. 1.4%, N = 18, p < 0.0001) and clustered in the tyrosine kinase domain of HER2. ERBB3 mutations were not enriched in ILC (1.1%, N = 3 vs. 1.8%, N = 23; p = 0.604). Median OS for patients with ERBB2-mutant ILC tumors was 66 months vs. 211 months for ERBB2 wild-type (p = 0.0001), and 159 vs. 166 months (p = 0.733) for IDC tumors. Targetable ERBB2 mutational status was an independent prognostic marker of 10-year OS-but only in ILC (hazard ratio, HR = 3.7, 95% CI 1.2-11.0; p = 0.021). Findings were validated using a novel ERBB2 mutation gene enrichment score (HR for 10-year OS in ILC = 2.3, 95% CI 1.04-5.05; p = 0.040). CONCLUSIONS Targetable ERBB2 mutations are enriched in primary ILC and their detection represents an actionable strategy with the potential to improve patient outcomes. Biomarker-led clinical trials of adjuvant HER-targeted therapy are warranted for patients with ERBB2-mutated primary ILC.
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MESH Headings
- Biomarkers, Tumor/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/metabolism
- Carcinoma, Lobular/pathology
- Computer Simulation
- Databases, Genetic/statistics & numerical data
- Female
- Humans
- Middle Aged
- Mutation
- Prognosis
- Receptor, ErbB-2/genetics
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/metabolism
- Retrospective Studies
- Survival Rate
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Affiliation(s)
- Sasagu Kurozumi
- Nottingham Breast Cancer Research Centre, Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Gunma, Japan
- Department of Breast Surgery, International University of Health and Welfare, Narita, Japan
| | - Mansour Alsaleem
- Nottingham Breast Cancer Research Centre, Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Cíntia J Monteiro
- Nottingham Breast Cancer Research Centre, Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
- Gene Regulation and RNA Biology Laboratory, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Kartikeya Bhardwaj
- Nottingham Breast Cancer Research Centre, Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
- Gene Regulation and RNA Biology Laboratory, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Stacey E P Joosten
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Takaaki Fujii
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Ken Shirabe
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Ian O Ellis
- Nottingham Breast Cancer Research Centre, Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - David M Heery
- Gene Regulation and RNA Biology Laboratory, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Steffi Oesterreich
- Womens Cancer Research Center, UPMC Hillman Cancer Center and Magee-Women Research Institute, Pittsburgh, PA, USA
| | - Simon J Johnston
- Nottingham Breast Cancer Research Centre, Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK.
- Gene Regulation and RNA Biology Laboratory, School of Pharmacy, University of Nottingham, Nottingham, UK.
- Translational Medicine, Oncology Research and Development, AstraZeneca, Darwin Building, Milton, Cambridge, UK.
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18
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Pharmacologically targetable vulnerability in prostate cancer carrying RB1-SUCLA2 deletion. Oncogene 2020; 39:5690-5707. [PMID: 32694611 DOI: 10.1038/s41388-020-1381-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
RB1 gene is often homozygously deleted or mutated in prostate adenocarcinomas following acquirement of castration resistance and/or metastatic ability. We found that SUCLA2 gene is frequently involved in the deletion of the RB1 gene region in advanced prostate cancer. SUCLA2 constitutes the β-subunit of succinate CoA ligase heterodimer that reversibly converts succinyl CoA into succinate. We sought the possibility that deletion of SUCLA2 gives rise to a metabolic vulnerability that could be targeted therapeutically. We found a significant metabolic shift in SUCLA2-deleted prostate cancer cells, including lower mitochondrial respiratory activity. By screening a number of libraries for compounds that induce cell death selectively in SUCLA2-deficient prostate cancer cells, we identified thymoquinone (2-isopropyl-5-methylbenzo-1,4-quinone) and PMA (phorbol-12-myristate-13-acetate) from a natural compound library. These findings indicate that the metabolic vulnerability in SUCLA2-deficient prostate cancer cells is pharmacologically targetable.
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19
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Hashimoto Y, Hamaguchi M, Kaji A, Sakai R, Osaka T, Inoue R, Kashiwagi S, Mizushima K, Uchiyama K, Takagi T, Naito Y, Fukui M. Intake of sucrose affects gut dysbiosis in patients with type 2 diabetes. J Diabetes Investig 2020; 11:1623-1634. [PMID: 32412684 PMCID: PMC7610116 DOI: 10.1111/jdi.13293] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/14/2022] Open
Abstract
Aims/Introduction Gut dysbiosis is generally associated with type 2 diabetes mellitus. However, the effect of habitual dietary intake on gut dysbiosis in Japanese patients with type 2 diabetes mellitus has not yet been explicated. This study investigated whether alteration of the gut microbiota was influenced by dietary intake of sucrose in Japanese patients with type 2 diabetes mellitus. Materials and Methods In this cross‐sectional study, 97 patients with type 2 diabetes mellitus and 97 healthy individuals were matched by age and sex, and then, fecal samples were obtained. Next‐generation sequencing of the 16S ribosomal ribonucleic acid gene was carried out, and functional profiles for the gut microbiota were analyzed. We selected the top 30 gut microbial genera and top 20 functional profiles for the gut microbiota specified by the weighted average difference method. The association between gut microbial genera or functional profiles and habitual dietary intake was investigated by Spearman’s rank correlation coefficient, and then, clustering analysis was carried out to clarify the impact of habitual dietary intake. Results The Actinobacteria phylum was highly abundant in patients with type 2 diabetes mellitus, whereas the Bacteroidetes phylum was less abundant. Diabetic‐type gut microbes, specifically Bacteroides and Bifidobacterium, were altered by sucrose intake at the genus level. Furthermore, sucrose intake was associated with glycolysis/gluconeogenesis in the diabetic‐type functional profiles of the gut microbiota. Conclusions The gut microbiota and functional profiles for the gut microbiota in patients with type 2 diabetes mellitus were significantly different from those in healthy individuals. Furthermore, we showed that sucrose intake was closely associated with these differences.
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Affiliation(s)
- Yoshitaka Hashimoto
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masahide Hamaguchi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ayumi Kaji
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryosuke Sakai
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takafumi Osaka
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Kyoto Prefectural University, Kyoto, Japan.,Laboratory of Animal Science, Setsunan University, Hirakata, Japan
| | - Saori Kashiwagi
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsura Mizushima
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuhiko Uchiyama
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomohisa Takagi
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department for Medical Innovation and Translational Medical Science, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Naito
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Michiaki Fukui
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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20
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Kulathunga N, Kohno S, Linn P, Nishimoto Y, Horike SI, Zaraiskii MI, Kumar S, Muranaka H, Takahashi C. Peripubertal high-fat diet promotes c-Myc stabilization in mammary gland epithelium. Cancer Sci 2020; 111:2336-2348. [PMID: 32437590 PMCID: PMC7385354 DOI: 10.1111/cas.14492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 12/12/2022] Open
Abstract
Dietary fat consumption during accelerated stages of mammary gland development, such as peripubertal maturation or pregnancy, is known to increase the risk for breast cancer. However, the underlying molecular mechanisms are not fully understood. Here we examined the gene expression profile of mouse mammary epithelial cells (MMECs) on exposure to a high-fat diet (HFD) or control diet (CD). Trp53-/- female mice were fed with the experimental diets for 5 weeks during the peripubertal period (3-8 weeks of age). The treatment showed no significant difference in body weight between the HFD-fed mice and CD-fed mice. However, gene set enrichment analysis predicted a significant enrichment of c-Myc target genes in animals fed HFD. Furthermore, we detected enhanced activity and stabilization of c-Myc protein in MMECs exposed to a HFD. This was accompanied by augmented c-Myc phosphorylation at S62 with a concomitant increase in ERK phosphorylation. Moreover, MMECs derived from HFD-fed Trp53-/- mouse showed increased colony- and sphere-forming potential that was dependent on c-Myc. Further, oleic acid, a major fatty acid constituent of the HFD, and TAK-875, an agonist to G protein-coupled receptor 40 (a receptor for oleic acid), enhanced c-Myc stabilization and MMEC proliferation. Overall, our data indicate that HFD influences MMECs by stabilizing an oncoprotein, pointing to a novel mechanism underlying dietary fat-mediated mammary carcinogenesis.
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Affiliation(s)
- Nilakshi Kulathunga
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Susumu Kohno
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Paing Linn
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Yuuki Nishimoto
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Shin-Ichi Horike
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Mikhail I Zaraiskii
- Pavlov First St. Petersburg State Medical University, St. Petersburg, Russia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, Australia
| | - Hayato Muranaka
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.,Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
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21
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Alfarsi LH, El Ansari R, Masisi BK, Parks R, Mohammed OJ, Ellis IO, Rakha EA, Green AR. Integrated Analysis of Key Differentially Expressed Genes Identifies DBN1 as a Predictive Marker of Response to Endocrine Therapy in Luminal Breast Cancer. Cancers (Basel) 2020; 12:cancers12061549. [PMID: 32545448 PMCID: PMC7352383 DOI: 10.3390/cancers12061549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
Endocrine therapy is the mainstay of adjuvant treatment for patients with luminal breast cancer. Despite ongoing advances in endocrine therapy to date, a proportion of patients ultimately develop endocrine resistance, resulting in failure of therapy and poor prognosis. Therefore, as part of the growing concept of personalised medicine, the need for identification of predictive markers of endocrine therapy response at an early stage, is recognised. The METABRIC series was used to identify differentially expressed genes (DEGs) in term of response to adjuvant endocrine therapy. Drebrin 1 (DBN1) was identified as a key DEG associated with response to hormone treatment. Next, large, well-characterised cohorts of primary luminal breast cancer with long-term follow-up were assessed at the mRNA and protein levels for the value of DBN1 as a prognostic marker in luminal breast cancer, as well as its potential for predicting the benefit of endocrine therapy. DBN1 positivity was associated with aggressive clinicopathological variables and poor patient outcomes. Importantly, high DBN1 expression predicted relapse patients who were subject to adjuvant endocrine treatment. Our results further demonstrate that DBN1 is an independent prognostic marker in luminal breast cancer. Its association with the response to endocrine therapy and outcome provides evidence for DBN1 as a potential biomarker in luminal breast cancer, particularly for the benefit of endocrine treatment. Further functional investigations into the mechanisms underlying sensitivity to endocrine therapy is required.
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Affiliation(s)
- Lutfi H. Alfarsi
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (L.H.A.); (R.E.A.); (B.K.M.); (R.P.); (O.J.M.); (I.O.E.); (E.A.R.)
| | - Rokaya El Ansari
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (L.H.A.); (R.E.A.); (B.K.M.); (R.P.); (O.J.M.); (I.O.E.); (E.A.R.)
| | - Brendah K. Masisi
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (L.H.A.); (R.E.A.); (B.K.M.); (R.P.); (O.J.M.); (I.O.E.); (E.A.R.)
| | - Ruth Parks
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (L.H.A.); (R.E.A.); (B.K.M.); (R.P.); (O.J.M.); (I.O.E.); (E.A.R.)
| | - Omar J Mohammed
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (L.H.A.); (R.E.A.); (B.K.M.); (R.P.); (O.J.M.); (I.O.E.); (E.A.R.)
| | - Ian O. Ellis
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (L.H.A.); (R.E.A.); (B.K.M.); (R.P.); (O.J.M.); (I.O.E.); (E.A.R.)
- Cellular Pathology, Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Hucknall Road, Nottingham NG5 1PB, UK
| | - Emad A. Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (L.H.A.); (R.E.A.); (B.K.M.); (R.P.); (O.J.M.); (I.O.E.); (E.A.R.)
- Cellular Pathology, Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Hucknall Road, Nottingham NG5 1PB, UK
| | - Andrew R. Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, UK; (L.H.A.); (R.E.A.); (B.K.M.); (R.P.); (O.J.M.); (I.O.E.); (E.A.R.)
- Correspondence: ; Tel.: +44-115-8231407
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22
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Wei H. Construction of a hierarchical gene regulatory network centered around a transcription factor. Brief Bioinform 2020; 20:1021-1031. [PMID: 29186304 DOI: 10.1093/bib/bbx152] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/11/2017] [Indexed: 12/24/2022] Open
Abstract
We have modified a multitude of transcription factors (TFs) in numerous plant species and some animal species, and obtained transgenic lines that exhibit phenotypic alterations. Whenever we observe phenotypic changes in a TF's transgenic lines, we are always eager to identify its target genes, collaborative regulators and even upstream high hierarchical regulators. This issue can be addressed by establishing a multilayered hierarchical gene regulatory network (ML-hGRN) centered around a given TF. In this article, a practical approach for constructing an ML-hGRN centered on a TF using a combined approach of top-down and bottom-up network construction methods is described. Strategies for constructing ML-hGRNs are vitally important, as these networks provide key information to advance our understanding of how biological processes are regulated.
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Affiliation(s)
- Hairong Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.,School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
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23
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Aljohani AI, Toss MS, Kurozumi S, Joseph C, Aleskandarany MA, Miligy IM, Ansari RE, Mongan NP, Ellis IO, Green AR, Rakha EA. The prognostic significance of wild-type isocitrate dehydrogenase 2 (IDH2) in breast cancer. Breast Cancer Res Treat 2019; 179:79-90. [PMID: 31599393 PMCID: PMC6985218 DOI: 10.1007/s10549-019-05459-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Lymphovascular invasion (LVI) is a prerequisite step in breast cancer (BC) metastasis. We have previously identified wild-type isocitrate dehydrogenase 2 (IDH2) as a key putative driver of LVI. Thus, we explored the prognostic significance of IDH2 at transcriptome and protein expression levels in pre-invasive and invasive disease. METHODS Utlising tissue microarrays from a large well annotated BC cohort including ductal carcinoma in situ and invasive breast cancer (IBC), IDH2 was assessed at the transcriptomic and proteomic level. The associations between clinicopathological factors including LVI status, prognosis and the expression of IDH2 were evaluated. RESULTS In pure DCIS and IBC, high IDH2 protein expression was associated with features of aggressiveness including high nuclear grade, larger size, comedo necrosis and hormonal receptor negativity and LVI, higher grade, larger tumour size, high NPI, HER2 positivity, and hormonal receptor negativity, respectively. High expression of IDH2 either in mRNA or in protein levels was associated with poor patient's outcome in both DCIS and IBC. Multivariate analysis revealed that IDH2 protein expression was an independent risk factor for shorter BC specific-survival. CONCLUSION Further functional studies to decipher the role of IDH2 and its mechanism of action as a driver of BC progression and LVI are warranted.
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Affiliation(s)
- Abrar I Aljohani
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Michael S Toss
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Sasagu Kurozumi
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Chitra Joseph
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Mohammed A Aleskandarany
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Islam M Miligy
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK.,Histopathology Department, Faculty of Medicine, Menoufia University, Shibin El Kom, Egypt
| | - Rokaya El Ansari
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Nigel P Mongan
- Department of Pharmacology, Weill Cornell Medicine, New York, 10065, USA.,Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Ian O Ellis
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK. .,Histopathology Department, Faculty of Medicine, Menoufia University, Shibin El Kom, Egypt. .,Department of Histopathology, Nottingham University Hospital NHS Trust, City Hospital Campus, Hucknall Road, Nottingham, NG5 1PB, UK.
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24
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Metalloprotease-Dependent Attenuation of BMP Signaling Restricts Cardiac Neural Crest Cell Fate. Cell Rep 2019; 29:603-616.e5. [DOI: 10.1016/j.celrep.2019.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/12/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023] Open
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25
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Katsuda T, Kawamata M, Inoue A, Yamaguchi T, Abe M, Ochiya T. Long‐term maintenance of functional primary human hepatocytes using small molecules. FEBS Lett 2019; 594:114-125. [DOI: 10.1002/1873-3468.13582] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Takeshi Katsuda
- Division of Molecular and Cellular Medicine National Cancer Center Research Institute Tokyo Japan
| | - Masaki Kawamata
- Division of Molecular and Cellular Medicine National Cancer Center Research Institute Tokyo Japan
- Division of Organogenesis and Regeneration Medical Institute of Bioregulation Kyushu University Fukuoka Japan
| | - Ayako Inoue
- Division of Molecular and Cellular Medicine National Cancer Center Research Institute Tokyo Japan
| | - Tomoko Yamaguchi
- Division of Molecular and Cellular Medicine National Cancer Center Research Institute Tokyo Japan
- Department of Molecular and Cellular Medicine, Institute of Medical Science Tokyo Medical University Nishi-Shinjuku, Shinjuku-ku Tokyo Japan
| | - Maki Abe
- Division of Molecular and Cellular Medicine National Cancer Center Research Institute Tokyo Japan
- Department of Molecular and Cellular Medicine, Institute of Medical Science Tokyo Medical University Nishi-Shinjuku, Shinjuku-ku Tokyo Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine National Cancer Center Research Institute Tokyo Japan
- Department of Molecular and Cellular Medicine, Institute of Medical Science Tokyo Medical University Nishi-Shinjuku, Shinjuku-ku Tokyo Japan
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26
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Katsuda T, Matsuzaki J, Yamaguchi T, Yamada Y, Prieto-Vila M, Hosaka K, Takeuchi A, Saito Y, Ochiya T. Generation of human hepatic progenitor cells with regenerative and metabolic capacities from primary hepatocytes. eLife 2019; 8:47313. [PMID: 31393263 PMCID: PMC6731094 DOI: 10.7554/elife.47313] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/08/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatocytes are regarded as the only effective cell source for cell transplantation to treat liver diseases; however, their availability is limited due to a donor shortage. Thus, a novel cell source must be developed. We recently reported that mature rodent hepatocytes can be reprogrammed into progenitor-like cells with a repopulative capacity using small molecule inhibitors. Here, we demonstrate that hepatic progenitor cells can be obtained from human infant hepatocytes using the same strategy. These cells, named human chemically induced liver progenitors (hCLiPs), had a significant repopulative capacity in injured mouse livers following transplantation. hCLiPs redifferentiated into mature hepatocytes in vitro upon treatment with hepatic maturation-inducing factors. These redifferentiated cells exhibited cytochrome P450 (CYP) enzymatic activities in response to CYP-inducing molecules and these activities were comparable with those in primary human hepatocytes. These findings will facilitate liver cell transplantation therapy and drug discovery studies. One of the most successful treatments for liver disease is transplanting a donor liver into a patient. But demands for donor livers far outstrips supply. A promising alternative could be, rather than replacing the whole organ, to transplant patients with individual liver cells called hepatocytes. These cells can then move into the liver, replace damaged cells, and help support the organ. However, hepatocytes are also in short supply, as despite the liver’s amazing regenerative abilities, these cells struggle to divide outside of the body. Improving how these cells multiply, could therefore help more people receive hepatocyte transplants. In 2017, researchers found a way to convert mouse and rat hepatocytes into cells that could divide more rapidly using a cocktail of three small molecules. These 'chemically induced liver progenitors', or CLiPs for short, were able to mature into working hepatocytes and support injured mouse livers. But, discoveries made in rats and mice are not always applicable to humans. Now, Katsuda et al. – including some of the researchers involved in the 2017 work – have set out to investigate whether CLiPs can also be made from human cells, and if so, whether these cells can be used for hepatocyte transplantations. Using a similar cocktail of molecules, Katsuda et al. managed to convert infant human hepatocytes into CLiPs. As with the rodent cells, these human CLiPs were able to turn back into mature, working liver cells. When transplanted into mice with genetic liver diseases, the human CLiPs moved into the liver and became part of the organ. These transplanted cells were able to reconstruct the liver tissue of diseased mice, and in some cases, replaced more than 90% of the liver’s damaged cells. Developing human CLiP technology could provide a new way to support people on the waiting list for liver transplantation. But there are some obstacles still to overcome. At present the technique only works with hepatocytes from infant donors. The next step is to improve the method so that it works with liver cells donated by adults.
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Affiliation(s)
- Takeshi Katsuda
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Juntaro Matsuzaki
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Tomoko Yamaguchi
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan.,Division of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Tokyo, Japan
| | - Yasuhiro Yamada
- Department of Clinical Pharmaceutics, Nihon Pharmaceutical University, Saitama, Japan
| | - Marta Prieto-Vila
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazunori Hosaka
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Atsuko Takeuchi
- Division of Analytical Laboratory, Kobe Pharmaceutical University, Kobe, Japan
| | - Yoshimasa Saito
- Division of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Tokyo, Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan.,Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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A Robust Approach for Identification of Cancer Biomarkers and Candidate Drugs. ACTA ACUST UNITED AC 2019; 55:medicina55060269. [PMID: 31212673 PMCID: PMC6631768 DOI: 10.3390/medicina55060269] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/17/2019] [Accepted: 06/01/2019] [Indexed: 12/31/2022]
Abstract
Background and objectives: Identification of cancer biomarkers that are differentially expressed (DE) between two biological conditions is an important task in many microarray studies. There exist several methods in the literature in this regards and most of these methods designed especially for unpaired samples, those are not suitable for paired samples. Furthermore, the traditional methods use p-values or fold change (FC) values to detect the DE genes. However, sometimes, p-value based results do not comply with FC based results due to the smaller pooled variance of gene expressions, which occurs when variance of each individual condition becomes smaller. There are some methods that combine both p-values and FC values to solve this problem. But, those methods also show weak performance for small sample cases in the presence of outlying expressions. To overcome this problem, in this paper, an attempt is made to propose a hybrid robust SAM-FC approach by combining rank of FC values and rank of p-values computed by SAM statistic using minimum β-divergence method, which is designed for paired samples. Materials and Methods: The proposed method introduces a weight function known as β-weight function. This weight function produces larger weights corresponding to usual and smaller weights for unusual expressions. The β-weight function plays the significant role on the performance of the proposed method. The proposed method uses β-weight function as a measure of outlier detection by setting β = 0.2. We unify both classical and robust estimates using β-weight function, such that maximum likelihood estimators (MLEs) are used in absence of outliers and minimum β-divergence estimators are used in presence of outliers to obtain reasonable p-values and FC values in the proposed method. Results: We examined the performance of proposed method in a comparison of some popular methods (t-test, SAM, LIMMA, Wilcoxon, WAD, RP, and FCROS) using both simulated and real gene expression profiles for both small and large sample cases. From the simulation and a real spike in data analysis results, we observed that the proposed method outperforms other methods for small sample cases in the presence of outliers and it keeps almost equal performance with other robust methods (Wilcoxon, RP, and FCROS) otherwise. From the head and neck cancer (HNC) gene expression dataset, the proposed method identified two additional genes (CYP3A4 and NOVA1) that are significantly enriched in linoleic acid metabolism, drug metabolism, steroid hormone biosynthesis and metabolic pathways. The survival analysis through Kaplan-Meier curve revealed that combined effect of these two genes has prognostic capability and they might be promising biomarker of HNC. Moreover, we retrieved the 12 candidate drugs based on gene interaction from glad4u and drug bank literature based gene associations. Conclusions: Using pathway analysis, disease association study, protein-protein interactions and survival analysis we found that our proposed two additional genes might be involved in the critical pathways of cancer. Furthermore, the identified drugs showed statistical significance which indicates that proteins associated with these genes might be therapeutic target in cancer.
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28
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Kurozumi S, Joseph C, Sonbul S, Alsaeed S, Kariri Y, Aljohani A, Raafat S, Alsaleem M, Ogden A, Johnston SJ, Aleskandarany MA, Fujii T, Shirabe K, Caldas C, Ashankyty I, Dalton L, Ellis IO, Desmedt C, Green AR, Mongan NP, Rakha EA. A key genomic subtype associated with lymphovascular invasion in invasive breast cancer. Br J Cancer 2019; 120:1129-1136. [PMID: 31114020 PMCID: PMC6738092 DOI: 10.1038/s41416-019-0486-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Lymphovascular invasion (LVI) is associated with the development of metastasis in invasive breast cancer (BC). However, the complex molecular mechanisms of LVI, which overlap with other oncogenic pathways, remain unclear. This study, using available large transcriptomic datasets, aims to identify genes associated with LVI in early-stage BC patients. METHODS Gene expression data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort (n = 1565) was used as a discovery dataset, and The Cancer Genome Atlas (TCGA; n = 854) cohort was used as a validation dataset. Key genes were identified on the basis of differential mRNA expression with respect to LVI status as characterised by histological review. The relationships among LVI-associated genomic subtype, clinicopathological features and patient outcomes were explored. RESULTS A 99-gene set was identified that demonstrated significantly different expression between LVI-positive and LVI-negative cases. Clustering analysis with this gene set further divided cases into two molecular subtypes (subtypes 1 and 2), which were significantly associated with pathology-determined LVI status in both cohorts. The 10-year overall survival of subtype 2 was significantly worse than that of subtype 1. CONCLUSION This study demonstrates that LVI in BC is associated with a specific transcriptomic profile with potential prognostic value.
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Affiliation(s)
- Sasagu Kurozumi
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Chitra Joseph
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Sultan Sonbul
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Sami Alsaeed
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Yousif Kariri
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Abrar Aljohani
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Sara Raafat
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Mansour Alsaleem
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Angela Ogden
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Simon J Johnston
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Mohammed A Aleskandarany
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
- Faculty of Medicine, Menoufyia University, Shebin al Kawm, Egypt
| | - Takaaki Fujii
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Ken Shirabe
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ibraheem Ashankyty
- Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Leslie Dalton
- Department of Histopathology, St. David's South Austin Medical Center, Austin, TX, USA
| | - Ian O Ellis
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Nigel P Mongan
- Biology and Translational Research, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK.
- Faculty of Medicine, Menoufyia University, Shebin al Kawm, Egypt.
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29
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Kubota A, Suto A, Suzuki K, Kobayashi Y, Nakajima H. Matrix metalloproteinase-12 produced by Ly6C low macrophages prolongs the survival after myocardial infarction by preventing neutrophil influx. J Mol Cell Cardiol 2019; 131:41-52. [PMID: 31009606 DOI: 10.1016/j.yjmcc.2019.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/01/2019] [Accepted: 04/09/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Various immune cells are involved in different phases of cardiac repair after myocardial infarction (MI). Especially, Ly6Clow M2-like macrophages (Ly6Clo macrophages) are vital for cardiac repair after MI. However, the molecular mechanisms how Ly6Clo macrophages promote wound healing after MI are still largely unknown. METHODS AND RESULTS Transcriptome analysis of Ly6Clo macrophages and Ly6Chigh M1-like macrophages (Ly6Chi macrophages) harvested from the infarcted heart revealed that Ly6Clo macrophages highly expressed matrix metalloproteinase (MMP)-12 mRNA compared to Ly6Chi macrophages. MMP-12 expression was enhanced in the infarcted heart and preferentially observed in Ly6Clo macrophages. Importantly, the survival rate and cardiac function after MI were significantly impaired in MMP-12-deficient (mmp12-/-) mice compared with those in wild-type mice. In addition, the extent of myocardial fibrosis and the number of myofibroblasts in the infarct area were decreased in mmp12-/- mice. MMP-9 expression and neutrophils, which are the major cellular source of MMP-9, in the infarcted heart were increased in mmp12-/- mice. Moreover, mRNA expression of neutrophil-attracting chemokines including CXCL1, CXCL2, and CXCL5 was significantly higher in mmp12-/- mice. Consistently, treatment with anti-CXCR2 antibody significantly decreased neutrophil numbers and MMP-9 expression in the infarcted heart in mmp12-/- mice. Finally, the administration of recombinant MMP-12 into the infarcted heart decreased neutrophil numbers in the infarcted heart and promoted wound healing in both wild-type mice and mmp12-/- mice. CONCLUSION MMP-12 produced by Ly6Clo macrophages improves the survival after MI possibly through the promotion of wound healing by reducing neutrophil infiltration.
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Affiliation(s)
- Akihiko Kubota
- Department of Cardiovascular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akira Suto
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan; Institute for Global Prominent Research, Chiba University, Chiba, Japan.
| | - Kotaro Suzuki
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshio Kobayashi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.
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30
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Segawa S, Kondo Y, Nakai Y, Iizuka A, Kaneko S, Yokosawa M, Furuyama K, Tsuboi H, Goto D, Matsumoto I, Sumida T. Placenta Specific 8 Suppresses IL-18 Production through Regulation of Autophagy and Is Associated with Adult Still Disease. THE JOURNAL OF IMMUNOLOGY 2018; 201:3534-3545. [PMID: 30404814 DOI: 10.4049/jimmunol.1800667] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/03/2018] [Indexed: 11/19/2022]
Abstract
Adult Still disease (ASD) is a systemic disorder of unknown etiology characterized by high spiking fever, rash, and arthritis. The purpose of this study was to identify genes specifically associated with the active phase of the disease. In this study, we have reported that placenta specific 8 (PLAC8) was a newly specific gene involved in ASD. DNA microarray and validation analysis using human monocytes revealed that the expression of PLAC8 was significantly higher in active-ASD patients than in inactive-ASD patients and healthy controls. In ASD, PLAC8 expression level correlated with serum levels of CRP, ferritin, IL-1β, and IL-18. Stimulation of monocytes with LPS results in PLAC8 upregulation. LPS or nigericin stimulation of PLAC8-overexpressing human monocytic cell line (THP-1), but not mock THP-1 cells, was associated with a significant decrease in IL-1β and IL-18 production. PLAC8 overexpression in THP-1 cells was associated with enhanced autophagy and suppression of IL-1β and IL-18 production. Therefore, we found that PLAC8 was upregulated in activated monocytes, as was IL-1β and IL-18. The upregulated PLAC8 acts on the synthesis of inactive precursors of IL-1β and IL-18 and seemed to suppress the production of IL-1β and IL-18 by negative feedback through enhanced autophagy, resulting in the suppression of ASD. The results highlight the role of PLAC8 in the pathogenesis of ASD and suggest its potential suitability as an activity marker and therapeutic target in ASD.
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Affiliation(s)
- Seiji Segawa
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Yuya Kondo
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Yuji Nakai
- Institute for Food Sciences, Hirosaki University, Hirosaki 038-0012, Japan
| | - Akira Iizuka
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Shunta Kaneko
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Masahiro Yokosawa
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Kotona Furuyama
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Hiroto Tsuboi
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Daisuke Goto
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Isao Matsumoto
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
| | - Takayuki Sumida
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; and
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31
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Chen G, Tsoi A, Xu H, Zheng WJ. Predict effective drug combination by deep belief network and ontology fingerprints. J Biomed Inform 2018; 85:149-154. [DOI: 10.1016/j.jbi.2018.07.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 11/17/2022]
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32
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Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A. Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. Mol Omics 2018; 14:218-236. [PMID: 29917034 PMCID: PMC6080592 DOI: 10.1039/c8mo00042e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022]
Abstract
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in order to study systems-level responses to compound treatments. In recent years there has been a rapid increase in publicly available toxicological and 'omics' data, particularly gene expression data, and a corresponding development of methods for its analysis. In this review, we summarize recent progress relating to the analysis of RNA-Seq and microarray data, review relevant databases, and highlight recent applications of toxicogenomics data for understanding and predicting compound toxicity. These include the analysis of differentially expressed genes and their enrichment, signature matching, methods based on interaction networks, and the analysis of co-expression networks. In the future, these state-of-the-art methods will likely be combined with new technologies, such as whole human body models, to produce a comprehensive systems-level understanding of toxicity that reduces the necessity of in vivo toxicity assessment in animal models.
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Affiliation(s)
- Benjamin Alexander-Dann
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Lavinia Lorena Pruteanu
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
- Babeş-Bolyai University
, Institute for Doctoral Studies
,
1 Kogălniceanu Street
, Cluj-Napoca 400084
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
| | - Erin Oerton
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Nitin Sharma
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Ioana Berindan-Neagoe
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, Research Center for Functional Genomics
, Biomedicine and Translational Medicine
,
23 Marinescu Street
, Cluj-Napoca 400337
, Romania
- The Oncology Institute “Prof. Dr Ion Chiricuţă”
, Department of Functional Genomics and Experimental Pathology
,
34-36 Republicii Street
, Cluj-Napoca 400015
, Romania
| | - Dezső Módos
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Andreas Bender
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
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33
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Shimoyama Y, Tamai K, Shibuya R, Nakamura M, Mochizuki M, Yamaguchi K, Kakuta Y, Kinouchi Y, Sato I, Kudo A, Shimosegawa T, Satoh K. Periostin attenuates tumor growth by inducing apoptosis in colitis-related colorectal cancer. Oncotarget 2018; 9:20008-20017. [PMID: 29731999 PMCID: PMC5929442 DOI: 10.18632/oncotarget.25026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/17/2018] [Indexed: 11/29/2022] Open
Abstract
Inflammatory bowel diseases, which are multifactorial autoimmune colitis diseases, are occurring with increasing prevalence. One of the most serious complications of these diseases is colorectal cancer. Here we investigated the role of periostin (Postn), a matricellular protein that interacts with various integrin molecules on the cell surface, in colitis-induced colorectal cancer. Immunohistochemistry of mouse and human colorectal cancer samples revealed that Postn was expressed in the stroma and was upregulated in close proximity to the cancer cells. The colonic tumorigenesis in an inflammation-related colon carcinogenesis mouse model was increased in Postn knock-out (Postn−/−) mice compared to Postn+/+ mice. Although no difference was found in the degree of colitis between Postn+/+ and Postn−/− mice, Postn inhibited tumor growth and induced the apoptosis of mouse rectal cancer cells in vitro. Furthermore, fewer apoptotic colorectal cancer cells were observed in Postn−/− than in Postn+/+ mice. These data suggested that Postn has an anti-tumor effect on colitis-induced colorectal cancer.
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Affiliation(s)
- Yusuke Shimoyama
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan.,Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Keiichi Tamai
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Rie Shibuya
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Mao Nakamura
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Mai Mochizuki
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Kazunori Yamaguchi
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Yoichi Kakuta
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Kinouchi
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuro Sato
- Department of Pathology, Miyagi Cancer Center, Natori, Japan
| | - Akira Kudo
- Department of Biological Information, Tokyo Institute of Technology, Yokohama, Japan
| | - Tooru Shimosegawa
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kennichi Satoh
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
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Abstract
High-throughput biological technologies are routinely used to generate gene expression profiling or cytogenetics data. To achieve high performance, methods available in the literature become more specialized and often require high computational resources. Here, we propose a new versatile method based on the data-ordering rank values. We use linear algebra, the Perron-Frobenius theorem and also extend a method presented earlier for searching differentially expressed genes for the detection of recurrent copy number aberration. A result derived from the proposed method is a one-sample Student's t-test based on rank values. The proposed method is to our knowledge the only that applies to gene expression profiling and to cytogenetics data sets. This new method is fast, deterministic, and requires a low computational load. Probabilities are associated with genes to allow a statistically significant subset selection in the data set. Stability scores are also introduced as quality parameters. The performance and comparative analyses were carried out using real data sets. The proposed method can be accessed through an R package available from the CRAN (Comprehensive R Archive Network) website: https://cran.r-project.org/web/packages/fcros .
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Affiliation(s)
- Doulaye Dembélé
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 1258, Université de Strasbourg, Illkirch-Graffenstaden, France
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35
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Zhao S, Sun J, Shimizu K, Kadota K. Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results. Biol Proced Online 2018; 20:5. [PMID: 29507534 PMCID: PMC5831220 DOI: 10.1186/s12575-018-0067-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/12/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hierarchical Sample clustering (HSC) is widely performed to examine associations within expression data obtained from microarrays and RNA sequencing (RNA-seq). Researchers have investigated the HSC results with several possible criteria for grouping (e.g., sex, age, and disease types). However, the evaluation of arbitrary defined groups still counts in subjective visual inspection. RESULTS To objectively evaluate the degree of separation between groups of interest in the HSC dendrogram, we propose to use Silhouette scores. Silhouettes was originally developed as a graphical aid for the validation of data clusters. It provides a measure of how well a sample is classified when it was assigned to a cluster by according to both the tightness of the clusters and the separation between them. It ranges from 1.0 to - 1.0, and a larger value for the average silhouette (AS) over all samples to be analyzed indicates a higher degree of cluster separation. The basic idea to use an AS is to replace the term cluster by group when calculating the scores. We investigated the validity of this score using simulated and real data designed for differential expression (DE) analysis. We found that larger (or smaller) AS values agreed well with both higher (or lower) degrees of separation between different groups and higher percentages of differentially expressed genes (PDEG). We also found that the AS values were generally independent on the number of replicates (Nrep). Although the PDEG values depended on Nrep, we confirmed that both AS and PDEG values were close to zero when samples in the data showed an intermingled nature between the groups in the HSC dendrogram. CONCLUSION Silhouettes is useful for exploring data with predefined group labels. It would help provide both an objective evaluation of HSC dendrograms and insights into the DE results with regard to the compared groups.
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Affiliation(s)
- Shitao Zhao
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Jianqiang Sun
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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36
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Kontou PI, Pavlopoulou A, Bagos PG. Methods of Analysis and Meta-Analysis for Identifying Differentially Expressed Genes. Methods Mol Biol 2018; 1793:183-210. [PMID: 29876898 DOI: 10.1007/978-1-4939-7868-7_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microarray approaches are widely used high-throughput techniques to assess simultaneously the expression of thousands of genes under certain conditions and study the effects of certain treatments, diseases, and developmental stages. The traditional way to perform such experiments is to design oligonucleotide hybridization probes that correspond to specific genes and then measure the expression of the genes in order to determine which of them are up- or down-regulated compared to a condition that is used as a control. Hitherto, individual experiments cannot capture the bigger picture of how a biological system works and, therefore, data integration from multiple experimental studies and external data repositories is necessary to understand the function of genes and their expression patterns under certain conditions. Therefore, the development of methods for handling, integrating, comparing, interpreting and visualizing microarray data is necessary. The selection of an appropriate method for analysing microarray datasets is not an easy task. In this chapter, we provide an overview of the various methods developed for microarray data analysis, as well as suggestions for choosing the appropriate method for microarray meta-analysis.
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Affiliation(s)
- Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Athanasia Pavlopoulou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece.,International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eylul University, Izmir, 35340, Turkey
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece.
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37
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Fujisaka Y, Iwata T, Tamai K, Nakamura M, Mochizuki M, Shibuya R, Yamaguchi K, Shimosegawa T, Satoh K. Long non-coding RNA HOTAIR up-regulates chemokine (C-C motif) ligand 2 and promotes proliferation of macrophages and myeloid-derived suppressor cells in hepatocellular carcinoma cell lines. Oncol Lett 2017; 15:509-514. [PMID: 29387231 DOI: 10.3892/ol.2017.7322] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/19/2017] [Indexed: 12/27/2022] Open
Abstract
Accumulating evidence demonstrated that Hox antisense intergenic RNA (HOTAIR) serves essential roles in the development and metastasis of several types of cancer. In hepatocellular carcinoma (HCC), high expression of HOTAIR is associated with poor prognosis, and HOTAIR regulates cell migration and proliferation. However, the downstream molecular targets of HOTAIR depend on the cancer cell types, and little is known about the precise molecular mechanisms of HOTAIR involved in cancer development. The present study investigated the role of HOTAIR in HCC cell lines. Notably, the overexpression of HOTAIR in HCC cell lines did not affect cell migration and proliferation capability. In the microarray analysis, C-C motif chemokine ligand (CCL)2 was identified to be differentially expressed in HOTAIR-overexpressing cells, and it was confirmed that HOTAIR promotes the secretion of CCL2. Furthermore, it was revealed that the proportion of macrophages and myeloid-derived suppressor cells (MDSCs) were increased when peripheral blood mononuclear cells were co-cultured with HOTAIR-overexpressing cells. Collectively, these data suggest that HOTAIR regulates CCL2 expression, which may be involved in the recruitment of macrophages and MDSCs to the tumor microenvironment.
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Affiliation(s)
- Yasuyuki Fujisaka
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Miyagi 981-1293, Japan.,Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Tomoaki Iwata
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Miyagi 981-1293, Japan.,Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Keiichi Tamai
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Miyagi 981-1293, Japan
| | - Mao Nakamura
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Miyagi 981-1293, Japan
| | - Mai Mochizuki
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Miyagi 981-1293, Japan
| | - Rie Shibuya
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Miyagi 981-1293, Japan
| | - Kazunori Yamaguchi
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Miyagi 981-1293, Japan
| | - Tooru Shimosegawa
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Kennichi Satoh
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Miyagi 981-1293, Japan
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38
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Ito T, Hirose K, Saku A, Kono K, Takatori H, Tamachi T, Goto Y, Renauld JC, Kiyono H, Nakajima H. IL-22 induces Reg3γ and inhibits allergic inflammation in house dust mite-induced asthma models. J Exp Med 2017; 214:3037-3050. [PMID: 28811323 PMCID: PMC5626396 DOI: 10.1084/jem.20162108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 05/29/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022] Open
Abstract
Previous studies have shown that IL-22, one of the Th17 cell-related cytokines, plays multiple roles in regulating allergic airway inflammation caused by antigen-specific Th2 cells; however, the underlying mechanism remains unclear. Here, we show that allergic airway inflammation and Th2 and Th17 cytokine production upon intratracheal administration of house dust mite (HDM) extract, a representative allergen, were exacerbated in IL-22-deficient mice. We also found that IL-22 induces Reg3γ production from lung epithelial cells through STAT3 activation and that neutralization of Reg3γ significantly exacerbates HDM-induced eosinophilic airway inflammation and Th2 cytokine induction. Moreover, exostatin-like 3 (EXTL3), a functional Reg3γ binding protein, is expressed in lung epithelial cells, and intratracheal administration of recombinant Reg3γ suppresses HDM-induced thymic stromal lymphopoietin and IL-33 expression and accumulation of type 2 innate lymphoid cells in the lung. Collectively, these results suggest that IL-22 induces Reg3γ production from lung epithelial cells and inhibits the development of HDM-induced allergic airway inflammation, possibly by inhibiting cytokine production from lung epithelial cells.
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Affiliation(s)
- Takashi Ito
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Koichi Hirose
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Aiko Saku
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kenta Kono
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Takatori
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomohiro Tamachi
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshiyuki Goto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Jean-Christophe Renauld
- Ludwig Institute for Cancer Research, Brussels Branch, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Hiroshi Kiyono
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Kawasawa YI, Mohammad S, Son AI, Morizono H, Basha A, Salzberg AC, Torii M, Hashimoto-Torii K. WITHDRAWN:Genome-wide profiling of differentially spliced mRNAs in human fetal cortical tissue exposed to alcohol. Alcohol 2017. [DOI: 10.1016/j.alcohol.2017.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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40
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DNA hypermethyation and silencing of PITX1 correlated with advanced stage and poor postoperative prognosis of esophageal squamous cell carcinoma. Oncotarget 2017; 8:84434-84448. [PMID: 29137437 PMCID: PMC5663609 DOI: 10.18632/oncotarget.21375] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/03/2017] [Indexed: 11/25/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is associated with the accumulation of genetic and epigenetic changes in the background mucosa. Dysregulated DNA methylation is known to lead to the inactivation of tumor suppressor genes and the activation of oncogenes. To identify the genes whose expression is perturbed by abnormal DNA methylation in ESCC, integrative transcriptomics by serial analysis of gene expression (SAGE) and methylome sequencing by methyl-DNA immunoprecipitation (MeDIP) analysis were performed. We found 159 genes with significantly decreased expression in ESCC compared to that in noncancerous esophageal mucosa. MeDIP-seq analysis identified hypermethylation in the promoter region of 56 of these genes. Using surgically resected tissues of 40 cases, we confirmed that the paired-like homeodomain 1 (PITX1) gene was hypermethylated in ESCC compared to that in normal tissues (P < 0.0001) by pyrosequencing. PITX1 overexpression in ESCC cell lines inhibited cell growth and colony formation, whereas PITX1 knockdown accelerated cell growth. A PITX1-transfected ESCC cell line, KYSE30, formed smaller tumors in nude mice than in mock-transfected cells. Hypermethylation of PITX1 was associated with tumor depth (P = 0.0011) and advanced tumor stage (P = 0.0052) and predicted poor survival in ESCC (hazard ratio, 0.1538; 95% confidence interval, 0.03159–0.7488; P = 0.0169). In this study, we found a novel tumor suppressor gene of ESCC, PITX1, which is silenced by DNA hypermethylation. Downregulation of PITX1 contributes to the growth and progression of ESCC. Hypermethylation of the PITX1 in ESCC correlated with tumor progression and advanced stage cancer, and may predict a poor prognosis.
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41
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Sato N, Sudo K, Mori M, Imai C, Muramatsu M, Sugimoto M. Early gestational maternal low-protein diet diminishes hepatic response to fasting in young adult male mice. Sci Rep 2017; 7:9812. [PMID: 28852200 PMCID: PMC5575317 DOI: 10.1038/s41598-017-10380-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/08/2017] [Indexed: 12/25/2022] Open
Abstract
Maternal low-protein (MLP) diet can lead to hepatic steatosis, which only develops with ageing. It is still unclear whether the young offspring show any signs of past exposure to prenatal adverse conditions. We hypothesized that early nutritional insult would first affect the dynamic responsiveness to nutritional challenges rather than the static state. We analyzed the transcriptome and metabolome profiles of the hepatic response to fasting/refeeding in young male mice offspring to identify changes induced by early gestational MLP diet. Restricted MLP exposure strictly to early gestation was achieved by the embryo transfer method. As a result, the fasting-induced upregulation of genes related to long-chain fatty acid metabolism and of stress response genes related to protein folding were significantly diminished in MLP pups. Lipid profiling after fasting showed that the hepatic signature of triacylglycerols was shifted to longer acyl-chains and higher saturation by the MLP diet. Bioinformatic analyses suggested that these phenomenological changes may be partially linked to the peroxisome proliferator activated receptor α (PPARα) pathway. Taken together, early gestational MLP diet affected the hepatic dynamic response to nutritional stress in seemingly healthy young offspring, accompanied with partial deterioration of PPARα action.
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Affiliation(s)
- Noriko Sato
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Katsuko Sudo
- Animal Research Center, Tokyo Medical University, 6-1-1, Shinjyuku, Shinjyuku-ku, Tokyo, 160-0022, Japan
| | - Masayo Mori
- Institute for Advanced Biosciences, Keio University, Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Chihiro Imai
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Masaaki Muramatsu
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
- AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda-Ku, Tokyo, 100-0004, Japan
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42
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Abstract
Excessive alcohol consumption results in significant changes in gene expression and isoforms due to altered mRNA splicing. As such, an intriguing possibility is that disturbances in alternative splicing are involved in key pathological pathways triggered by alcohol exposure. However, no resources have been available to systematically analyze this possibility at a genome-wide scale. Here, we performed RNA sequencing of human fetal cortical slices that were obtained at the late first trimester and exposed to ethanol or control medium. We report 382 events that were identified as changes affecting the ratio of splicing isoforms in the ethanol-exposed fetal human cortex. Additionally, previously unreported novel isoforms of several genes were also identified. These results provide a broad perspective on the post-transcriptional regulatory network underlying ethanol-induced pathogenesis in the developing human cortex.
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43
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Yoshihara M, Sasamoto Y, Hayashi R, Ishikawa Y, Tsujikawa M, Hayashizaki Y, Itoh M, Kawaji H, Nishida K. High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor. Sci Rep 2017; 7:2845. [PMID: 28588247 PMCID: PMC5460231 DOI: 10.1038/s41598-017-02824-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/19/2017] [Indexed: 12/27/2022] Open
Abstract
An in vitro model of corneal epithelial cells (CECs) has been developed to study and treat corneal disorders. Nevertheless, conventional CEC culture supplemented with epidermal growth factor (EGF) results in a loss of CEC characteristics. It has recently been reported that limbal epithelial cells (LECs) cultured with keratinocyte growth factor (KGF) and the rho kinase inhibitor Y-27632 could maintain the expression of several CEC-specific markers. However, the molecular mechanism underlying the effect of culture media on LECs remains to be elucidated. To elucidate this mechanism, we performed comprehensive gene expression analysis of human LECs cultured with EGF or KGF/Y-27632, by cap analysis of gene expression (CAGE). Here, we found that LECs cultured with KGF and Y-27632 presented a gene expression profile highly similar to that of CECs in vivo. In contrast, LECs cultured with EGF lost the characteristic CEC gene expression profile. We further discovered that CEC-specific PAX6 promoters are highly activated in LECs cultured with KGF and Y-27632. Our results provide strong evidence that LECs cultured with KGF and Y-27632 would be an improved in vitro model in the context of gene expression. These findings will accelerate basic studies of CECs and clinical applications in regenerative medicine.
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Affiliation(s)
- Masahito Yoshihara
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.,Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yuzuru Sasamoto
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Ryuhei Hayashi
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.,Department of Stem Cells and Applied Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuki Ishikawa
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Motokazu Tsujikawa
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | | | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan. .,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan. .,Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Kanagawa, Japan.
| | - Kohji Nishida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
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Overexpression of KCNJ2 in induced pluripotent stem cell-derived cardiomyocytes for the assessment of QT-prolonging drugs. J Pharmacol Sci 2017; 134:75-85. [DOI: 10.1016/j.jphs.2017.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 05/14/2017] [Accepted: 05/17/2017] [Indexed: 02/05/2023] Open
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45
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Zyla J, Marczyk M, Weiner J, Polanska J. Ranking metrics in gene set enrichment analysis: do they matter? BMC Bioinformatics 2017; 18:256. [PMID: 28499413 PMCID: PMC5427619 DOI: 10.1186/s12859-017-1674-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/03/2017] [Indexed: 11/29/2022] Open
Abstract
Background There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment Analysis seems to be one of the most commonly used (over 10,000 citations). An important parameter, which could affect the final result, is the choice of a metric for the ranking of genes. Applying a default ranking metric may lead to poor results. Methods and results In this work 28 benchmark data sets were used to evaluate the sensitivity and false positive rate of gene set analysis for 16 different ranking metrics including new proposals. Furthermore, the robustness of the chosen methods to sample size was tested. Using k-means clustering algorithm a group of four metrics with the highest performance in terms of overall sensitivity, overall false positive rate and computational load was established i.e. absolute value of Moderated Welch Test statistic, Minimum Significant Difference, absolute value of Signal-To-Noise ratio and Baumgartner-Weiss-Schindler test statistic. In case of false positive rate estimation, all selected ranking metrics were robust with respect to sample size. In case of sensitivity, the absolute value of Moderated Welch Test statistic and absolute value of Signal-To-Noise ratio gave stable results, while Baumgartner-Weiss-Schindler and Minimum Significant Difference showed better results for larger sample size. Finally, the Gene Set Enrichment Analysis method with all tested ranking metrics was parallelised and implemented in MATLAB, and is available at https://github.com/ZAEDPolSl/MrGSEA. Conclusions Choosing a ranking metric in Gene Set Enrichment Analysis has critical impact on results of pathway enrichment analysis. The absolute value of Moderated Welch Test has the best overall sensitivity and Minimum Significant Difference has the best overall specificity of gene set analysis. When the number of non-normally distributed genes is high, using Baumgartner-Weiss-Schindler test statistic gives better outcomes. Also, it finds more enriched pathways than other tested metrics, which may induce new biological discoveries. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1674-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joanna Zyla
- Data Mining Group, Institute of Automatic Control, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, Gliwice, 44-100, Poland
| | - Michal Marczyk
- Data Mining Group, Institute of Automatic Control, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, Gliwice, 44-100, Poland.
| | - January Weiner
- Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin, 10117, Germany
| | - Joanna Polanska
- Data Mining Group, Institute of Automatic Control, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, Gliwice, 44-100, Poland
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46
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The RB–IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity. Oncogene 2017; 36:5145-5157. [DOI: 10.1038/onc.2017.124] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 12/12/2022]
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47
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Identification of Novel and Noninvasive Biomarkers of Acute Cellular Rejection After Liver Transplantation by Protein Microarray. Transplant Direct 2016; 2:e118. [PMID: 27990483 PMCID: PMC5142373 DOI: 10.1097/txd.0000000000000630] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/13/2016] [Indexed: 12/20/2022] Open
Abstract
Background Acute cellular rejection (ACR) is one of the main factors in transplanted organ failure in liver transplantation. A precise marker for diagnosing or predicting rejection is not currently available; therefore, invasive liver biopsy is standard procedure. To develop a noninvasive method for precise diagnosis of ACR, we evaluated autoantibodies from patient sera as potential biomarkers using protein microarrays (seromics). Methods Sera from hepatitis C virus–positive ACR patients were compared to three hepatitis C virus cirrhosis control groups and healthy volunteers. The control groups consisted of 2 no-ACR groups obtained on postoperative day 28 and 1 year after transplantation and a preoperative group obtained 1 day before transplantation. For validation, we evaluated whether the candidate antibodies can distinguish ACR from other types of liver dysfunction after liver transplantation using enzyme-linked immunosorbent assay. Results Seromic analysis by weighted average difference (WAD) ranking and Mann-Whitney U test revealed a significant increase of 57 autoantibodies in the sera of ACR patients with liver dysfunction. Among the 57 candidates, autoantibodies to charged multivesicular body protein 2B, potassium channel tetramerization domain containing 14, voltage gated subfamily A regulatory beta subunit 3, and triosephosphate isomerase 1 were regarded as potential biomarkers of ACR after liver transplantation. Using 20 ACR patients with variable backgrounds for validation, the autoantibodies to charged multivesicular body protein 2B and triosephosphate isomerase 1 were significantly increased in ACR patients compared to other control groups. Conclusions A panel of autoantibodies identified by seromics as potential noninvasive biomarkers was clinically useful for diagnosing ACR after liver transplantation.
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48
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Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues. Oncotarget 2016; 6:41216-27. [PMID: 26515599 PMCID: PMC4747401 DOI: 10.18632/oncotarget.5649] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/12/2015] [Indexed: 12/13/2022] Open
Abstract
Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.
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49
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Mochizuki M, Tamai K, Imai T, Sugawara S, Ogama N, Nakamura M, Matsuura K, Yamaguchi K, Satoh K, Sato I, Motohashi H, Sugamura K, Tanaka N. CD271 regulates the proliferation and motility of hypopharyngeal cancer cells. Sci Rep 2016; 6:30707. [PMID: 27469492 PMCID: PMC4965829 DOI: 10.1038/srep30707] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/07/2016] [Indexed: 11/25/2022] Open
Abstract
CD271 (p75 neurotrophin receptor) plays both positive and negative roles in cancer development, depending on the cell type. We previously reported that CD271 is a marker for tumor initiation and is correlated with a poor prognosis in human hypopharyngeal cancer (HPC). To clarify the role of CD271 in HPC, we established HPC cell lines and knocked down the CD271 expression using siRNA. We found that CD271-knockdown completely suppressed the cells’ tumor-forming capability both in vivo and in vitro. CD271-knockdown also induced cell-cycle arrest in G0 and suppressed ERK phosphorylation. While treatment with an ERK inhibitor only partially inhibited cell growth, CDKN1C, which is required for maintenance of quiescence, was strongly upregulated in CD271-depleted HPC cells, and the double knockdown of CD271 and CDKN1C partially rescued the cells from G0 arrest. In addition, either CD271 depletion or the inhibition of CD271-RhoA signaling by TAT-Pep5 diminished the in vitro migration capability of the HPC cells. Collectively, CD271 initiates tumor formation by increasing the cell proliferation capacity through CDKN1C suppression and ERK-signaling activation, and by accelerating the migration signaling pathway in HPC.
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Affiliation(s)
- Mai Mochizuki
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan.,Department of Oncovirology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Keiichi Tamai
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan.,Department of Cancer Stem Cell Research, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takayuki Imai
- Department of Head and Neck Surgery, Miyagi Cancer Center, Natori, Japan
| | - Sayuri Sugawara
- Division of Cancer Biology and Therapeutics, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Naoko Ogama
- Division of Cancer Biology and Therapeutics, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Mao Nakamura
- Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Kazuto Matsuura
- Department of Head and Neck Surgery, Miyagi Cancer Center, Natori, Japan.,Department of Head and Neck Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazunori Yamaguchi
- Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan.,Department of Oncovirology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kennichi Satoh
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan.,Department of Cancer Stem Cell Research, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuro Sato
- Department of Pathology, Miyagi Cancer Center, Natori, Japan.,Department of Cancer Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kazuo Sugamura
- Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Nobuyuki Tanaka
- Division of Cancer Biology and Therapeutics, Miyagi Cancer Center Research Institute, Natori, Japan.,Department of Cancer Biology and Therapeutics, Tohoku University Graduate School of Medicine, Sendai, Japan
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Maruyama R, Shimizu M, Ishijima T, Nakai Y, Inoue J, Sato R. Searching for novel ATF4 target genes in human hepatoma cells by microarray analysis. Biosci Biotechnol Biochem 2016; 80:1149-54. [PMID: 26967115 DOI: 10.1080/09168451.2016.1146072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Activating transcription factor 4 (ATF4) is a transcription factor with an important biological activity. ATF4 is induced by various stresses, such as endoplasmic reticulum stress, through the phosphorylation of eukaryotic translation initiation factor 2α. ATF4 is also involved in lipid metabolism. In the present study, we performed a microarray experiment to identify new ATF4 target genes, particularly those involved in lipid metabolism, and identified C12orf39, CSTA, and CALCB as novel ATF4 target genes. An amino acid response element (AARE) as an ATF4-binding site is present in the promoter regions of these genes. In a detailed analysis using luciferase assay, we showed that ATF4 activated C12orf39 promoter activity and that this activation was diminished by deletion or mutation of the AARE sequence in the promoter region. Our results suggest that C12orf39, CSTA, and CALCB are novel ATF4 target genes and that C12orf39 promoter activity is activated by ATF4 through AARE.
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Affiliation(s)
- Ryuto Maruyama
- a Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences , The University of Tokyo , Tokyo , Japan
| | - Makoto Shimizu
- a Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences , The University of Tokyo , Tokyo , Japan
| | - Tomoko Ishijima
- a Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences , The University of Tokyo , Tokyo , Japan
| | - Yuji Nakai
- b Institute for Food Sciences , Hirosaki University , Aomori , Japan
| | - Jun Inoue
- a Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences , The University of Tokyo , Tokyo , Japan
| | - Ryuichiro Sato
- a Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences , The University of Tokyo , Tokyo , Japan
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