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Hamamoto R, Suvarna K, Yamada M, Kobayashi K, Shinkai N, Miyake M, Takahashi M, Jinnai S, Shimoyama R, Sakai A, Takasawa K, Bolatkan A, Shozu K, Dozen A, Machino H, Takahashi S, Asada K, Komatsu M, Sese J, Kaneko S. Application of Artificial Intelligence Technology in Oncology: Towards the Establishment of Precision Medicine. Cancers (Basel) 2020; 12:E3532. [PMID: 33256107 PMCID: PMC7760590 DOI: 10.3390/cancers12123532] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
In recent years, advances in artificial intelligence (AI) technology have led to the rapid clinical implementation of devices with AI technology in the medical field. More than 60 AI-equipped medical devices have already been approved by the Food and Drug Administration (FDA) in the United States, and the active introduction of AI technology is considered to be an inevitable trend in the future of medicine. In the field of oncology, clinical applications of medical devices using AI technology are already underway, mainly in radiology, and AI technology is expected to be positioned as an important core technology. In particular, "precision medicine," a medical treatment that selects the most appropriate treatment for each patient based on a vast amount of medical data such as genome information, has become a worldwide trend; AI technology is expected to be utilized in the process of extracting truly useful information from a large amount of medical data and applying it to diagnosis and treatment. In this review, we would like to introduce the history of AI technology and the current state of medical AI, especially in the oncology field, as well as discuss the possibilities and challenges of AI technology in the medical field.
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Affiliation(s)
- Ryuji Hamamoto
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kruthi Suvarna
- Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India;
| | - Masayoshi Yamada
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Department of Endoscopy, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku Tokyo 104-0045, Japan
| | - Kazuma Kobayashi
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Norio Shinkai
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Mototaka Miyake
- Department of Diagnostic Radiology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Masamichi Takahashi
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Shunichi Jinnai
- Department of Dermatologic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Ryo Shimoyama
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
| | - Akira Sakai
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Ken Takasawa
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Amina Bolatkan
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Kanto Shozu
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
| | - Ai Dozen
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
| | - Hidenori Machino
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Satoshi Takahashi
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Ken Asada
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Masaaki Komatsu
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Jun Sese
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Humanome Lab, 2-4-10 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.Y.); (K.K.); (N.S.); (M.T.); (R.S.); (A.S.); (K.T.); (A.B.); (K.S.); (A.D.); (H.M.); (S.T.); (K.A.); (M.K.); (J.S.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
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Basu A, Mestres I, Sahu SK, Tiwari N, Khongwir B, Baumgart J, Singh A, Calegari F, Tiwari VK. Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation. Genes Dev 2020; 34:1190-1209. [PMID: 32820037 PMCID: PMC7462064 DOI: 10.1101/gad.333906.119] [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: 10/18/2019] [Accepted: 07/21/2020] [Indexed: 12/24/2022]
Abstract
Cerebral cortical development in mammals involves a highly complex and organized set of events including the transition of neural stem and progenitor cells (NSCs) from proliferative to differentiative divisions to generate neurons. Despite progress, the spatiotemporal regulation of this proliferation-differentiation switch during neurogenesis and the upstream epigenetic triggers remain poorly known. Here we report a cortex-specific PHD finger protein, Phf21b, which is highly expressed in the neurogenic phase of cortical development and gets induced as NSCs begin to differentiate. Depletion of Phf21b in vivo inhibited neuronal differentiation as cortical progenitors lacking Phf21b were retained in the proliferative zones and underwent faster cell cycles. Mechanistically, Phf21b targets the regulatory regions of cell cycle promoting genes by virtue of its high affinity for monomethylated H3K4. Subsequently, Phf21b recruits the lysine-specific demethylase Lsd1 and histone deacetylase Hdac2, resulting in the simultaneous removal of monomethylation from H3K4 and acetylation from H3K27, respectively. Intriguingly, mutations in the Phf21b locus associate with depression and mental retardation in humans. Taken together, these findings establish how a precisely timed spatiotemporal expression of Phf21b creates an epigenetic program that triggers neural stem cell differentiation during cortical development.
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Affiliation(s)
- Amitava Basu
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Iván Mestres
- Center for Regenerative Therapies Dresden (CRTD), School of Medicine, Technische Universität Dresden, 01307 Dresden, Germany
| | | | - Neha Tiwari
- Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | | | - Jan Baumgart
- Translational Animal Research Center (TARC), University Medical Centre, Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Aditi Singh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, United Kingdom
| | - Federico Calegari
- Center for Regenerative Therapies Dresden (CRTD), School of Medicine, Technische Universität Dresden, 01307 Dresden, Germany
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, United Kingdom
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Silva ILZ, Robert AW, Cabo GC, Spangenberg L, Stimamiglio MA, Dallagiovanna B, Gradia DF, Shigunov P. Effects of PUMILIO1 and PUMILIO2 knockdown on cardiomyogenic differentiation of human embryonic stem cells culture. PLoS One 2020; 15:e0222373. [PMID: 32437472 PMCID: PMC7241771 DOI: 10.1371/journal.pone.0222373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 04/28/2020] [Indexed: 01/31/2023] Open
Abstract
Posttranscriptional regulation plays a fundamental role in the biology of embryonic stem cells (ESCs). Many studies have demonstrated that multiple mRNAs are coregulated by one or more RNA-binding proteins (RBPs) that orchestrate mRNA expression. A family of RBPs, which is known as the Pumilio-FBF (PUF) family, is highly conserved among different species and has been associated with the undifferentiated and differentiated states of different cell lines. In humans, two homologs of the PUF family have been found: Pumilio 1 (PUM1) and Pumilio 2 (PUM2). To understand the role of these proteins in human ESCs (hESCs), we first assessed the influence of the silencing of PUM1 and PUM2 on pluripotency genes and found that the knockdown of Pumilio genes significantly decreased the OCT4 and NANOG mRNA levels and reduced the amount of nuclear OCT4, which suggests that Pumilio proteins play a role in the maintenance of pluripotency in hESCs. Furthermore, we observed that PUM1-and-PUM2-silenced hESCs exhibited improved efficiency of in vitro cardiomyogenic differentiation. Through an in silico analysis, we identified mRNA targets of PUM1 and PUM2 that are expressed at the early stages of cardiomyogenesis, and further investigation will determine whether these target mRNAs are active and involved in the progression of cardiomyogenesis. Our findings contribute to the understanding of the role of Pumilio proteins in hESC maintenance and differentiation.
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Affiliation(s)
| | - Anny Waloski Robert
- Laboratory of Basic Biology of Stem Cells (LABCET), Instituto Carlos Chagas—FIOCRUZ-PR, Curitiba, Paraná, Brazil
| | | | - Lucia Spangenberg
- Bioinformatics Unit, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Marco Augusto Stimamiglio
- Laboratory of Basic Biology of Stem Cells (LABCET), Instituto Carlos Chagas—FIOCRUZ-PR, Curitiba, Paraná, Brazil
| | - Bruno Dallagiovanna
- Laboratory of Basic Biology of Stem Cells (LABCET), Instituto Carlos Chagas—FIOCRUZ-PR, Curitiba, Paraná, Brazil
| | - Daniela Fiori Gradia
- Department of Genetics, Federal University of Parana (UFPR), Curitiba, Paraná, Brazil
| | - Patrícia Shigunov
- Laboratory of Basic Biology of Stem Cells (LABCET), Instituto Carlos Chagas—FIOCRUZ-PR, Curitiba, Paraná, Brazil
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4
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Tietz KT, Gallagher TL, Mannings MC, Morrow ZT, Derr NL, Amacher SL. Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts. Dev Biol 2020; 462:129-140. [PMID: 32246943 DOI: 10.1016/j.ydbio.2020.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.
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Affiliation(s)
- Kiel T Tietz
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Thomas L Gallagher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Monica C Mannings
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary T Morrow
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas L Derr
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharon L Amacher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University, Columbus, OH, 43210, USA.
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5
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Lepesant JMJ, Iampietro C, Galeota E, Augé B, Aguirrenbengoa M, Mercé C, Chaubet C, Rocher V, Haenlin M, Waltzer L, Pelizzola M, Di Stefano L. A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons. Nucleic Acids Res 2020; 48:1206-1224. [PMID: 31799607 PMCID: PMC7026653 DOI: 10.1093/nar/gkz1142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 11/05/2019] [Accepted: 11/23/2019] [Indexed: 11/14/2022] Open
Abstract
The histone demethylase LSD1 is a key chromatin regulator that is often deregulated in cancer. Its ortholog, dLsd1 plays a crucial role in Drosophila oogenesis; however, our knowledge of dLsd1 function is insufficient to explain its role in the ovary. Here, we have performed genome-wide analysis of dLsd1 binding in the ovary, and we document that dLsd1 is preferentially associated to the transcription start site of developmental genes. We uncovered an unanticipated interplay between dLsd1 and the GATA transcription factor Serpent and we report an unexpected role for Serpent in oogenesis. Besides, our transcriptomic data show that reducing dLsd1 levels results in ectopic transposable elements (TE) expression correlated with changes in H3K4me2 and H3K9me2 at TE loci. In addition, our results suggest that dLsd1 is required for Piwi dependent TE silencing. Hence, we propose that dLsd1 plays crucial roles in establishing specific gene expression programs and in repressing transposons during oogenesis.
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Affiliation(s)
- Julie M J Lepesant
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France
| | - Carole Iampietro
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France
| | - Eugenia Galeota
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan 20139, Italy
| | - Benoit Augé
- CBD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France
| | - Marion Aguirrenbengoa
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France
| | - Clemèntine Mercé
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France.,School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Camille Chaubet
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France
| | - Vincent Rocher
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France
| | - Marc Haenlin
- CBD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France
| | - Lucas Waltzer
- CBD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France.,Université Clermont Auvergne, CNRS, INSERM, GReD, Clermont-Ferrand F-63000, France
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan 20139, Italy
| | - Luisa Di Stefano
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31062, France
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6
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Kolawole OA, Banjo S. In Vitro Biological Estimation of 1,2,3-Triazolo[4,5-d]pyrimidine Derivatives as Anti-breast Cancer Agent: DFT, QSAR and Docking Studies. Curr Pharm Biotechnol 2020; 21:70-78. [DOI: 10.2174/1389201020666190904163003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/03/2019] [Accepted: 08/18/2019] [Indexed: 11/22/2022]
Abstract
Background & Objective:
Series of synthesized molecular compounds were considered as
anti-breast cancer. The molecular descriptors which describe the microbial activities of the studied
compounds were calculated using theoretical approach.
Methods:
The calculated parameters obtained EHOMO (eV), ELUMO (eV), dipole moment (Debye), log P,
molecular weight (amu), HBA, HBD, Vol and Ovality were screened. The obtained calculated descriptors
were used to develop QSAR model for prediction of experimental inhibition concentration
(IC50) using SPSS and Gretl software packages for multiple linear regression (MLR) and MATLAB for
the artificial neural network (ANN).
Results:
From this statistical analysis, MLR and ANN were observed to be predictive, however, ANNQSAR
model predicted more efficiently than MLR.
Conclusion:
Furthermore, molecular docking study was executed with breast cancer cell line
(PDB ID: 1hi7); it was observed that BS20 with binding energy of -7.0 kcal/mol bounded more efficiently
than other compounds also, it inhibited more than the standard used (5-FU).
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Affiliation(s)
- Oyebamiji A. Kolawole
- Computational Chemistry Laboratory, Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Oyo State, Nigeria
| | - Semire Banjo
- Computational Chemistry Laboratory, Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Oyo State, Nigeria
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7
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Zhang L, Chen Y, Li C, Liu J, Ren H, Li L, Zheng X, Wang H, Han Z. RNA binding protein PUM2 promotes the stemness of breast cancer cells via competitively binding to neuropilin-1 (NRP-1) mRNA with miR-376a. Biomed Pharmacother 2019; 114:108772. [PMID: 30909144 DOI: 10.1016/j.biopha.2019.108772] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 12/20/2022] Open
Abstract
Others and ours studies have established the promoting roles of NRP-1 (neuropilin-1) in breast cancer, however, the underlying mechanisms by which NRP-1 is regulated are still confused. Here, bioinformatics analysis indicated that RNA binding protein PUM2 could bind to NRP-1 mRNA. Clinical samples showed that PUM2 expression was significantly increased in breast cancer tissues, negatively correlated with the overall survival and relapse-free survival of breast cancer patients, and positively correlated with NRP-1 expression. Meanwhile, PUM2 expression was remarkably increased in non-adherent spheroids. in vitro experiments demonstrated that PUM2 knockdown attenuated the stemness of breast cancer cells, evident by the decrease of spheroid formation capacity, ALDH1 activity and stemness marker expression. Mechanistically, RNA immunoprecipitation (RIP) and luciferase reporter analysis indicated that PUM2 competitively bound to NRP 3'UTR with miR-376a, which had been previously confirmed by us to suppress the stemness of breast cancer cells, and increased NRP-1 mRNA stability and expression. Furthermore, ectopic expression of NRP-1 or miR-376a knockdown rescued the inhibitory effects of NRP-1 knockdown on the stemness of breast cancer cells. Thus, our results suggest that PUM2 could facilitate the stemness of breast cancer cells by competitively binding to NRP-1 3'UTR with miR-376a.
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Affiliation(s)
- Lansheng Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, China
| | - Yanwei Chen
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Caihong Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, China
| | - Jinyang Liu
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Huiwen Ren
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Lishan Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, China
| | - Xia Zheng
- Department of Radiation Oncology, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, China
| | - Hui Wang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Zhengxiang Han
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China.
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Abstract
The most common type of head and neck cancer, head and neck squamous cell carcinoma (HNSCC), can develop therapeutic resistance that complicates its treatment. The 5-y survival rate for HNSCC remains at ~50%, and improving these outcomes requires a better understanding of the pathogenesis of HNSCC. Studies of HNSCC using in vitro, ex vivo, and in vivo approaches provide a novel conceptual framework based on epigenetic mechanisms for developing future clinical applications. Normal oral tissues are influenced by environmental factors that induce pathological changes affecting the network of epigenetic enzymes and signaling pathways to induce HNSCC growth and metastasis. Although various epigenetic regulator families, such as DNA methyltransferases, ten-eleven translocation proteins, histone acetyltransferases, histone deacetylases, BET bromodomain proteins, protein arginine methyltransferases, histone lysine methyltransferases, and histone lysine demethylases, have a role in diverse cancers, specific members have a function in HNSCC. Recently, lysine-specific demethylases have been identified as a potential, attractive, and novel target of HNSCC. Lysine-specific demethylase 1 (LSD1) expression is inappropriately upregulated in HNSCC and an orthotopic HNSCC mouse model. LSD1 can demethylate lysine at specific histone positions to repress gene expression or stimulate transcription, indicating a dual and context-dependent role in transcriptional regulation. Our study showed that LSD1 promotes HNSCC growth and metastasis. Pharmacological attenuation of LSD1 inhibits orthotopic and patient-derived HNSCC xenograft growth-specific target genes and signaling pathways. This review provides recent evidence demonstrating the function of epigenetic regulator enzymes in HNSCC progression, including potential therapeutic applications for such enzymes in combination and immunotherapy.
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Affiliation(s)
- M.V. Bais
- Department of Molecular and Cell Biology, Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, USA
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Lee CYS, Lu T, Seydoux G. Nanos promotes epigenetic reprograming of the germline by down-regulation of the THAP transcription factor LIN-15B. eLife 2017; 6:30201. [PMID: 29111977 PMCID: PMC5734877 DOI: 10.7554/elife.30201] [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: 07/06/2017] [Accepted: 11/06/2017] [Indexed: 12/15/2022] Open
Abstract
Nanos RNA-binding proteins are required for germline development in metazoans, but the underlying mechanisms remain poorly understood. We have profiled the transcriptome of primordial germ cells (PGCs) lacking the nanos homologs nos-1 and nos-2 in C. elegans. nos-1nos-2 PGCs fail to silence hundreds of transcripts normally expressed in oocytes. We find that this misregulation is due to both delayed turnover of maternal transcripts and inappropriate transcriptional activation. The latter appears to be an indirect consequence of delayed turnover of the maternally-inherited transcription factor LIN-15B, a synMuvB class transcription factor known to antagonize PRC2 activity. PRC2 is required for chromatin reprogramming in the germline, and the transcriptome of PGCs lacking PRC2 resembles that of nos-1nos-2 PGCs. Loss of maternal LIN-15B restores fertility to nos-1nos-2 mutants. These findings suggest that Nanos promotes germ cell fate by downregulating maternal RNAs and proteins that would otherwise interfere with PRC2-dependent reprogramming of PGC chromatin.
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Affiliation(s)
- Chih-Yung Sean Lee
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Tu Lu
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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10
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Li ZH, Liu XQ, Zhao TQ, Geng PF, Guo WG, Yu B, Liu HM. Design, synthesis and preliminary biological evaluation of new [1,2,3]triazolo[4,5-d]pyrimidine/thiourea hybrids as antiproliferative agents. Eur J Med Chem 2017; 139:741-749. [PMID: 28863355 DOI: 10.1016/j.ejmech.2017.08.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/18/2017] [Accepted: 08/19/2017] [Indexed: 01/06/2023]
Abstract
A series of new [1,2,3]triazolo[4,5-d]pyrimidine/thiourea hybrids were designed and synthesized through the scaffold replacement/ring cleavage strategy. SARs studies revealed that the N-heteroarene moiety attached to the thiourea is preferred over the phenyl ring for the R2 substituents, while the hydrophobic aromatic group is beneficial for improving the activity. Among these compounds, compound 5r significantly inhibited cell growth of lung cancer cell lines H1650 and A549 (IC50 = 1.91, 3.28 μM, respectively), but was less toxic against the normal cell line GES-1 (IC50 = 27.43 μM). Mechanistic studies showed that compound 5r could remarkably inhibit the colony formation of H1650 cells, induced apoptosis possibly through the intrinsic apoptotic pathways, and arrested the cell cycle at G2/M phase. Our studies suggest that the [1,2,3]triazolo[4,5-d]pyrimidine/thiourea hybrids are a new class of chemotypes possessing interesting antiproliferative activity against lung cancer cells and could be potentially utilized for designing new antitumor agents.
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Affiliation(s)
- Zhong-Hua Li
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China
| | - Xue-Qi Liu
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China
| | - Tao-Qian Zhao
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China
| | - Peng-Fei Geng
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China
| | - Wen-Ge Guo
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China
| | - Bin Yu
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China.
| | - Hong-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China.
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