Ras Transformation Uncouples the Kinesin-Coordinated Cellular Nutrient Response

Total Page:16

File Type:pdf, Size:1020Kb

Ras Transformation Uncouples the Kinesin-Coordinated Cellular Nutrient Response Ras transformation uncouples the kinesin-coordinated cellular nutrient response Elma Zaganjora,1, Lauren M. Weila, Joshua X. Gonzalesa, John D. Minnaa,b, and Melanie H. Cobba,2 aDepartment of Pharmacology and bHamon Cancer Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041 Contributed by Melanie H. Cobb, June 12, 2014 (sent for review March 13, 2014; reviewed by George S. Bloom and Anning Lin) The kinesin family members (KIFs) KIF2A and KIF2C depolymerize We recently determined that expression of KIF2C and KIF2A microtubules, unlike the majority of other kinesins, which trans- is up-regulated by the Ras-ERK pathway (19). Therefore, we port cargo along microtubules. KIF2A regulates the localization of asked whether ERK1/2 and these kinesins are required to main- lysosomes in the cytoplasm, which assists in activation of the mech- tain lysosomal organization in immortalized human bronchial anistic target of rapamycin complex 1 (mTORC1) on the lysosomal epithelial cells (HBECs) and also whether the elevated expres- surface. We find that the closely related kinesin KIF2C also influen- sion of KIF2C and KIF2A accounts for the nutrient insensitivity ces lysosomal organization in immortalized human bronchial epi- of lysosomal positioning and mTORC1 activity in a mutant thelial cells (HBECs). Expression of KIF2C and, to a lesser extent, K-Ras–dependent cancer and cancer model. KIF2A in untransformed and mutant K-Ras–transformed cells is regulated by ERK1/2. Prolonged inhibition of ERK1/2 activation Results with PD0325901 mimics nutrient deprivation by disrupting lyso- KIF2A and KIF2C Are Required for the Amino Acid-Dependent some organization and decreasing mTORC1 activity in HBEC, sug- Localization of mTORC1 to Lysosomes in Immortalized HBEC. To ex- gesting a long-term mechanism for optimization of mTORC1 plore the relationships among KIF2A and KIF2C expression, activity by ERK1/2. We tested the hypothesis that up-regulation ERK1/2, and lysosomal organization, we used a model system to of KIF2C and KIF2A by ERK1/2 caused aberrant lysosomal position- assess signaling differences between immortalized cells before ing and mTORC1 activity in a mutant K-Ras–dependent cancer and and after transformation under relatively well-defined conditions. cancer model. In Ras-transformed cells, however, mTORC1 activity We examined the characteristics of a nontumor human bronchial and lysosome organization appear independent of ERK1/2 and epithelial cell line (HBEC) that was immortalized by expression these kinesins although ERK1/2 activity and the kinesins are re- of cyclin-dependent kinase 4 (CDK4) and telomerase (hTERT), quired for Ras-dependent proliferation and migration. We conclude yielding HBEC3KT (number distinguishes different cell donors) that mutant K-Ras repurposes these signaling and regulatory pro- as described (20). These cells maintain epithelial morphology and teins to support the transformed phenotype. express E-cadherin but not N-cadherin (19). We compared the behavior of this immortalized untransformed cell line to an iso- omplex signaling pathways are engaged to coordinate cellu- genic non-small cell lung cancer (NSCLC) model that was gen- Clar growth and proliferation as dictated by stimulatory signals, erated by introducing mutant K-Ras and a stable knockdown of such as abundant nutrients and growth factors, or inhibitory sig- p53 to yield HBEC3KTRL53 (21, 22). We also examined the nals, such as limiting nutrients or other cell stresses. Disturbances patient-derived colorectal cancer cell HCT116, which has an in coordination of signaling events are often observed in pathol- oncogenic K-Ras mutation. ogies such as cancer (1). Some cancers use oncogenic mutations of To examine the effects of nutrient restriction, cells were placed ’ the small GTPase K-Ras to promote their survival and pro- in Earl s balanced salt solution (EBSS), which contains glucose liferation (2–6). Mutant K-Ras activates central signaling cascades, but lacks serum and amino acids. Because mTORC1 is, at least in among them the phosphatidylinositol 3-kinase (Ras-PI3K) and the extracellular signal-regulated kinase ERK1/2 (Ras-ERK) path- Significance ways, to facilitate continued proliferation under suboptimal con- ditions and bypass inhibitory signals from energy stress pathways. The kinesin family member 2C (KIF2C) that regulates microtu- Mechanistic target of rapamycin (mTOR), a serine/threonine bule depolymerization, is up-regulated in a number of human protein kinase in a PI3K-related family, is a central regulator of cancer cells in a Ras- and ERK1/2-dependent manner. In this events leading to cell growth and proliferation (7–12). It carries out study, we find that KIF2C expression positively regulates sig- this role primarily as part of a complex [mTOR complex 1 naling pathways downstream of Ras, ERK1/2, and mechanistic (mTORC1)], and, in this capacity, it is exquisitely responsive to target of rapamycin complex 1 in nontransformed cells to co- nutrient availability. In certain cancers, positive regulatory signals to ordinate a cellular nutrient response. Transformation by on- mTORC1 can originate from mutant K-Ras, even in nutrient-poor cogenic Ras overrides the need for this level of organization settings (13, 14). Because cancers often use mTORC1 to optimize and repurposes ERK1/2 and KIF2C signaling events. Therefore, cellular functions to promote growth and survival, we have com- this study provides a link for how cytoskeletal transformation pared how the Ras-ERK pathway influences nutrient sensing and may interconnect with cancer metabolism. mTORC1 in untransformed immortalized cells and in cancer cells. Kinesins are motor proteins that transport cargo along micro- Author contributions: E.Z. and M.H.C. designed research; E.Z., L.M.W., and J.X.G. per- formed research; J.D.M. contributed new reagents/analytic tools; E.Z., L.M.W., J.D.M., tubules. Currently, more than 40 kinesins have been found in and M.H.C. analyzed data; and E.Z. and M.H.C. wrote the paper. mammals, most of which have primary functions as cargo carriers. Reviewers: G.S.B., University of Virginia; and A.L., University of Chicago and Shanghai Kinesin family member (KIF) 2A is one of a handful of kinesins Institute of Biochemistry and Cell Biology. that apparently do not transport cargo, but instead depolymerize The authors declare no conflict of interest. microtubules. In HeLa cells, KIF2A was shown to regulate the 1Present address: Department of Cell Biology, Harvard Medical School, Boston, MA 02115. location of lysosomes in the cytoplasm, which is thought to be es- 2To whom correspondence should be addressed. Email: melanie.cobb@utsouthwestern. sential for mTORC1 activation (15–18). We find that KIF2A and edu. the closely related kinesin KIF2C (also known as MCAK) also This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. control lysosomal organization in human bronchial epithelial cells. 1073/pnas.1411016111/-/DCSupplemental. 10568–10573 | PNAS | July 22, 2014 | vol. 111 | no. 29 www.pnas.org/cgi/doi/10.1073/pnas.1411016111 Downloaded by guest on September 27, 2021 part, activated through interaction with Rag small GTPases and and less well-localized with lysosomes (Fig. S1 A, B,andF). Because the Ragulator complex on lysosomes (16), we examined how re- KIF2C has many functions that overlap with KIF2A (19), we tested moval of amino acids and serum affected lysosomes and mTOR its effects as well and found that depletion of KIF2C also prevented localization. After 60–90 min of starvation in EBSS, lysosomes in restoration of lysosomal organization or mTOR activity by amino HBEC3KT lost the typical perinuclear concentrated pattern and acids (Fig. 1 A–C and Fig. S1 D and G), suggesting that more than instead gained a more diffuse and symmetric distribution, similar one kinesin participates in lysosomal positioning. Although KIF2A to what has been observed in HEK293 and HeLa cells following siRNA and KIF2C siRNA caused a reduction in mTORC1 activity removal of amino acids (15, 16, 23) (Fig. 1 A and B). mTOR was in amino acid-replete cells, knockdown of either or both had little or no effect on mTORC1 activity in cells in serum-containing also dispersed and less concentrated on lysosomes in HBEC3KT C F G cells, and mTORC1 activity was also reduced (Fig. 1C), as mea- medium (Fig. 1 and Fig. S1 and ). ERK1/2 activation in sured by a decrease in phosphorylation of ribosomal protein S6. HBEC3KT was also reduced following KIF2A or KIF2C siRNA. ERK1/2 were also less active after an hour in EBSS. Readdition of Inhibition of the ERK1/2 Pathway Alters Lysosome Positioning and amino acids or complete medium with amino acids and serum Reduces mTORC1 Activity in Immortalized Cells. mRNAs encoding C reactivated both ERK1/2 and mTORC1 (Fig. 1 ). KIF2C and, to a lesser extent, KIF2A are decreased in both Knockdown studies revealed that the microtubule-depolymerizing HBEC3KT and HBEC3KTRL53 by extended exposure to kinesin KIF2A is required for lysosomal organization and mTORC1 PD0325901, which inhibits the enzymes MEK1 and MEK2 that positioning on lysosomes (15). We recently found that KIF2A activate ERK1/2 (19). These and other studies indicated that and the closely related kinesin KIF2C are both up-regulated in ERK1/2 stimulate KIF2A/C expression. Therefore, we explored many cancers and that their persistent expression is supported by the possibility that ERK1/2 may also influence organelle orga- oncogenic K-Ras and ERK1/2 (19). As previously found in HeLa nization in immortalized cells through their ability to control the and 293 cells, depletion of KIF2A from HBEC3KT prevented expression of proteins that alter microtubule dynamics including typical lysosomal organization, and mTOR also remained diffuse these kinesins. We inhibited ERK1/2 activation by exposure of cells to the MEK inhibitor PD0325901 briefly or for up to 2 d. We showed previously that serum can stimulate ERK1/2 im- mediately after washing out PD0325901 even if cells have been A HBEC3KT B mTOR LAMP2 MERGE treated with the inhibitor for 2 d (19).
Recommended publications
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
    [Show full text]
  • KIF2C (2488C3a): Sc-81305
    SANTA CRUZ BIOTECHNOLOGY, INC. KIF2C (2488C3a): sc-81305 BACKGROUND RECOMMENDED SUPPORT REAGENTS Kinesin family member 2c (KIF2C), alternately known as mitotic centromere- To ensure optimal results, the following support reagents are recommended: associated kinesin (MCAK), is a member of the kinesin-like family of proteins. 1) Western Blotting: use m-IgGk BP-HRP: sc-516102 or m-IgGk BP-HRP (Cruz KIF2C is a cytoplasmic and nuclear protein, present throughout the cell cycle. Marker): sc-516102-CM (dilution range: 1:1000-1:10000), Cruz Marker™ KIF2C associates with the centromere early in prophase, and disassociates Molecular Weight Standards: sc-2035, UltraCruz® Blocking Reagent: after telophase. KIF2C is abundant in thymus and testis, and present at lower sc-516214 and Western Blotting Luminol Reagent: sc-2048. 2) Immunopre- levels in small intestine, the mucosal lining of the colon, and placenta. Human cipitation: use Protein A/G PLUS-Agarose: sc-2003 (0.5 ml agarose/2.0 ml). KIF2C maps to chromosome 1p34.1. 3) Immunofluorescence: use m-IgGk BP-FITC: sc-516140 or m-IgGk BP-PE: sc-516141 (dilution range: 1:50-1:200) with UltraCruz® Mounting Medium: REFERENCES sc-24941 or UltraCruz® Hard-set Mounting Medium: sc-359850. 1. Kim, I.G., et al. 1997. Cloning and expression of human mitotic centromere- associated kinesin gene. Biochim. Biophys. Acta 1359: 181-186. DATA 2. Maney, T., et al. 1998. Mitotic centromere-associated kinesin is important AB CDE F AB for anaphase chromosome segregation. J. Cell Biol. 3: 787-801. 132 K – 3. Hunter, A.W., et al. 2003. The kinesin-related protein MCAK is a micro- 109 K – KIF2C 90 K – tubule depolymerase that forms an ATP-hydrolyzing complex at microtubule 87 K – KIF2C ends.
    [Show full text]
  • Supplementary Table S1. Correlation Between the Mutant P53-Interacting Partners and PTTG3P, PTTG1 and PTTG2, Based on Data from Starbase V3.0 Database
    Supplementary Table S1. Correlation between the mutant p53-interacting partners and PTTG3P, PTTG1 and PTTG2, based on data from StarBase v3.0 database. PTTG3P PTTG1 PTTG2 Gene ID Coefficient-R p-value Coefficient-R p-value Coefficient-R p-value NF-YA ENSG00000001167 −0.077 8.59e-2 −0.210 2.09e-6 −0.122 6.23e-3 NF-YB ENSG00000120837 0.176 7.12e-5 0.227 2.82e-7 0.094 3.59e-2 NF-YC ENSG00000066136 0.124 5.45e-3 0.124 5.40e-3 0.051 2.51e-1 Sp1 ENSG00000185591 −0.014 7.50e-1 −0.201 5.82e-6 −0.072 1.07e-1 Ets-1 ENSG00000134954 −0.096 3.14e-2 −0.257 4.83e-9 0.034 4.46e-1 VDR ENSG00000111424 −0.091 4.10e-2 −0.216 1.03e-6 0.014 7.48e-1 SREBP-2 ENSG00000198911 −0.064 1.53e-1 −0.147 9.27e-4 −0.073 1.01e-1 TopBP1 ENSG00000163781 0.067 1.36e-1 0.051 2.57e-1 −0.020 6.57e-1 Pin1 ENSG00000127445 0.250 1.40e-8 0.571 9.56e-45 0.187 2.52e-5 MRE11 ENSG00000020922 0.063 1.56e-1 −0.007 8.81e-1 −0.024 5.93e-1 PML ENSG00000140464 0.072 1.05e-1 0.217 9.36e-7 0.166 1.85e-4 p63 ENSG00000073282 −0.120 7.04e-3 −0.283 1.08e-10 −0.198 7.71e-6 p73 ENSG00000078900 0.104 2.03e-2 0.258 4.67e-9 0.097 3.02e-2 Supplementary Table S2.
    [Show full text]
  • Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes
    Tohoku J. Exp. Med., 2011,Differential 223, 161-176 Gene Expression in OPCs, Oligodendrocytes and Type II Astrocytes 161 Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes Jian-Guo Hu,1,2,* Yan-Xia Wang,3,* Jian-Sheng Zhou,2 Chang-Jie Chen,4 Feng-Chao Wang,1 Xing-Wu Li1 and He-Zuo Lü1,2 1Department of Clinical Laboratory Science, The First Affiliated Hospital of Bengbu Medical College, Bengbu, P.R. China 2Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, P.R. China 3Department of Neurobiology, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China 4Department of Laboratory Medicine, Bengbu Medical College, Bengbu, P.R. China Oligodendrocyte precursor cells (OPCs) are bipotential progenitor cells that can differentiate into myelin-forming oligodendrocytes or functionally undetermined type II astrocytes. Transplantation of OPCs is an attractive therapy for demyelinating diseases. However, due to their bipotential differentiation potential, the majority of OPCs differentiate into astrocytes at transplanted sites. It is therefore important to understand the molecular mechanisms that regulate the transition from OPCs to oligodendrocytes or astrocytes. In this study, we isolated OPCs from the spinal cords of rat embryos (16 days old) and induced them to differentiate into oligodendrocytes or type II astrocytes in the absence or presence of 10% fetal bovine serum, respectively. RNAs were extracted from each cell population and hybridized to GeneChip with 28,700 rat genes. Using the criterion of fold change > 4 in the expression level, we identified 83 genes that were up-regulated and 89 genes that were down-regulated in oligodendrocytes, and 92 genes that were up-regulated and 86 that were down-regulated in type II astrocytes compared with OPCs.
    [Show full text]
  • Supplementary Data
    Supplementary Appendix Table of contents: Genes selected for real-time quantitative reverse transcriptase PCR………2 Table 1s: Microarrays results for genes selected for RQ-PCR…………….……...5 Table 2s: Gene list of TaqMan expression assays ……………………………...…6 Figure 1s: An example for a RQ-PCR matrix plate……………………………...….7 Figure 2s: Distribution of quantitative real time RT-PCR values before and after normalization for the various gene…………………………………………………….8 Table 3s: Distribution of means of quantitative real time RT-PCR values for the various genes………………………………………………………….………………….9 Table 4s: Summary of the ranks in Multivariate Cox Regression analysis of quantitative real time RT-PCR results (1- low, 2- medium, 3- high).....……………...………..………………………………………………………….9 Figure 3s: Microarrays results verification. Immunostaning with anti-CDH2.….10 Reference......……………...………..…………………………………...……………11 Genes selected for real-time quantitative reverse transcriptase PCR (RQ- PCR) We hypothesized that increased expression of certain genes in primary NSCLC could identify patients at high risk for the development of brain metastasis. The selection of genes for the RQ-PCR studies was based on results from our exploratory microarray gene expression profiling (GEP) studies (table 1s) [1, 2] and published data linking the expression of these genes either to metastasis (there was no published data on brain metastasis) or to survival in lung cancers or other non- hematological cancers. We focused on genes whose expression was higher either in primary NSCLC with brain metastasis and/or in brain metastasis compared with primary NSCLC. Our microarray study included 26 primary NSCLC (6 metastasized to the brain), 8 normal lungs, 7 brain metastases (not from the same primary NSCLC included in the arrays), and one pooled RNA from normal brain.
    [Show full text]
  • KIF2C Regulates Synaptic Plasticity and Cognition by Mediating
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.05.455197; this version posted August 5, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 KIF2C regulates synaptic plasticity and cognition by mediating 2 dynamic microtubule invasion of dendritic spines 3 Rui Zheng1,2†, Yong-Lan Du1,2†, Xin-Tai Wang2, Tai-Lin Liao1,2, Zhe Zhang1,2, Na Wang1,2, Xiu- 4 Mao Li3, Ying Shen4, Lei Shi5, Jian-Hong Luo1,2*, Jun Xia6*, Ziyi Wang7*, Junyu Xu1,2* 5 6 1Department of Neurobiology and Department of Rehabilitation of the Children’s 7 Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. 8 2NHC and CAMS Key Laboratory of Medical Neurobiology, Ministry of Education Frontier 9 Science Center for Brain Research and Brain Machine Integration, School of Brain Science and 10 Brain Medicine, Zhejiang University, Hangzhou, 310058, China. 11 3Department of Orthopedic Surgery, the Second Affiliated Hospital, Zhejiang University School 12 of Medicine, Hangzhou, 310058, China. 13 4Department of Physiology and Department of Neurology of First Affiliated Hospital, Zhejiang 14 University School of Medicine, Hangzhou, 310058, China. 15 5JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, 16 Guangzhou, China. 17 6Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong 18 University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. 19 7Innovative Institute of Basic Medical Sciences of Zhejiang University (Yuhang), Hangzhou, 20 310012, China.
    [Show full text]
  • Gene Expression Profiling of MCF10A Breast Epithelial Cells Exposed to IOERT
    ANTICANCER RESEARCH 35: 3223-3234 (2015) Gene Expression Profiling of MCF10A Breast Epithelial Cells Exposed to IOERT LUIGI MINAFRA1*, VALENTINA BRAVATÀ1*, GIORGIO RUSSO1, GIUSI IRMA FORTE1, FRANCESCO PAOLO CAMMARATA1, MARILENA RIPAMONTI1, GIULIANA CANDIANO1, MELCHIORRE CERVELLO2, AGATA GIALLONGO2, GIOVANNI PERCONTI2, CRISTINA MESSA1,4,5 and MARIA CARLA GILARDI1,3,5 1Institute of Bioimaging and Molecular Physiology, National Research Council (IBFM-CNR) -LATO, Cefalù, Italy; 2Institute of Biomedicine and Molecular Immunology “Alberto Monroy”- National Research Council (IBIM-CNR), Palermo, Italy; 3Nuclear Medicine, San Raffaele Scientific Institute, Milan, Italy; 4Nuclear Medicine Center, San Gerardo Hospital, Monza, Italy; 5Department of Health Sciences, Tecnomed Foundation, University of Milano-Bicocca, Milan, Italy Abstract. Background/Aim: Intraoperative electron radiation experiments were carried out to validate candidate IOERT therapy (IOERT) is a therapeutic approach that delivers a biomarkers. Clonogenic tests and morphological evaluations single high dose of ionizing radiation (IR) directly to the to examine cellular effects induced by radiation were also tumor bed during cancer surgery. The main goal of IOERT is conducted. Results: The study revealed a dose-dependent gene- to counteract tumor growth by acting on residual cancer cells expression profile and specific key genes that may be proposed as well as to preserve healthy surrounding tissue from the as novel markers of radiosensitivity. Our results show side-effects of radiation therapy. The radiobiology of the consistent differences in non-tumorigenic cell tolerance and in healthy tissue response to IR is a topic of interest which may the molecular response of MCF10A cells to different IOERTs. contribute to avoiding impairment of normal tissue and organ In particular, after 9 Gy of exposure, the selection of a function and to reducing the risks of secondary cancer.
    [Show full text]
  • Gene- and Tissue-Level Interactions in Normal Gastrointestinal Development and Hirschsprung Disease
    Gene- and tissue-level interactions in normal gastrointestinal development and Hirschsprung disease Sumantra Chatterjeea,b,1, Priyanka Nandakumara,1, Dallas R. Auera,b, Stacey B. Gabrielc, and Aravinda Chakravartia,b,2 aCenter for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205; bCenter for Human Genetics and Genomics, New York University School of Medicine, New York, NY 10016; and cGenomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142 Contributed by Aravinda Chakravarti, November 1, 2019 (sent for review May 21, 2019; reviewed by William J. Pavan and Tatjana Sauka-Spengler) The development of the gut from endodermal tissue to an organ between the longitudinal and circular muscles, and the sub- with multiple distinct structures and functions occurs over a mucosal (Meissner’s) plexus, between the circular muscle and prolonged time during embryonic days E10.5–E14.5 in the mouse. the submucosal layer. The myenteric and submucoal plexuses During this process, one major event is innervation of the gut by provide motor innervation to both muscular layers of the gut, enteric neural crest cells (ENCCs) to establish the enteric nervous and secretomotor innervation of the mucosa nearest the lumen system (ENS). To understand the molecular processes underpinning of the gut, respectively (6). gut and ENS development, we generated RNA-sequencing profiles The many stages of gut development require numerous initiat- from wild-type mouse guts at E10.5, E12.5, and E14.5 from both ing signaling events activating transcription factors (TFs) targeting sexes. We also generated these profiles from homozygous Ret null diverse genes and pathways varying across development (7, 8).
    [Show full text]
  • A Microrna Program Controls the Transition of Cardiomyocyte Hyperplasia to Hypertrophy and Stimulates Mammalian Cardiac Regeneration
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.25.432908; this version posted February 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A microRNA program controls the transition of cardiomyocyte hyperplasia to hypertrophy and stimulates mammalian cardiac regeneration 1 Andrea Raso; 1 Ellen Dirkx; 1 Vasco Sampaio-Pinto; 1,2 Hamid el Azzouzi; 3,4 Ryan J. Cubero; 5 Daniel W. Sorensen; 1 Lara Ottaviani; 1 Servé Olieslagers; 6 Manon M. Huibers; 6 Roel de Weger; 7 Sailay Siddiqi; 8 Silvia Moimas; 8 Consuelo Torrini; 8 Lorena Zentillin; 8 Luca Braga; 1,9 Paula A. da Costa Martins; 5 Jop H. van Berlo; 8 Serena Zacchigna; 8,10 Mauro Giacca and 1 Leon J. De Windt* 1Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; 2Department of Molecular Genetics, Erasmus University MC, 3015 GD Rotterdam, The Netherlands; 3The Abdus Salam International Centre for Theoretical Physics, 34151 Trieste, Italy; 4Centre for Neural Computation, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, 7030 Trondheim, Norway 5Stem Cell Institute and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, U.S.A. 6Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; 7Department of Cardiothoracic Surgery, Radboud University Medical Center, Nijmegen, the Netherlands; 8International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy; 9Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
    [Show full text]
  • Comparative Proteomic Analysis of Buffalo Oocytes Matured in Vitro
    www.nature.com/scientificreports OPEN Comparative Proteomic Analysis of Buffalo Oocytes Maturedin vitro Using iTRAQ Technique Received: 29 April 2016 Lingsheng Chen1,2, Linhui Zhai2,3, Chunfeng Qu1,4, Chengpu Zhang2, Sheng Li1, Feilin Wu2, Accepted: 26 July 2016 Yingzi Qi2, Fenghua Lu1, Ping Xu2,5, Xiangping Li1 & Deshun Shi1 Published: 26 August 2016 To investigate the protein profiling of buffalo oocytes at the germinal vesicle (GV) stage and metaphase II (MII) stage, an iTRAQ-based strategy was applied. A total of 3,763 proteins were identified, which representing the largest buffalo oocytes proteome dataset to date. Among these proteins identified, 173 proteins were differentially expressed in GV oocytes and competent MII oocytes, and 146 proteins were differentially abundant in competent and incompetent matured oocytes. Functional and KEGG pathway analysis revealed that the up-regulated proteins in competent MII oocytes were related to chromosome segregation, microtubule-based process, protein transport, oxidation reduction, ribosome, and oxidative phosphorylation, etc., in comparison with GV and incompetent MII oocytes. This is the first proteomic report on buffalo oocytes from different maturation stages and developmental competent status. These data will provide valuable information for understanding the molecular mechanism underlying buffalo oocyte maturation, and these proteins may potentially act as markers to predict developmental competence of buffalo oocyte duringin vitro maturation. In vitro maturation (IVM) of mammalian oocytes is an important technique for animal embryo technology, which directly affects the efficiencies of in vitro fertilization (IVF), nuclear transfer and transgenic etc. The devel- opmental competence of oocytes matured in vitro is generally lower than those matured in vivo1,2, which are caused by the desynchronization of nuclear and cytoplasmic maturation3, and insufficient cytoplasmic mat- uration4.
    [Show full text]
  • Decreased DNA Methylation at Promoters and Gene-Specific Neuronal
    medRxiv preprint doi: https://doi.org/10.1101/2020.12.10.20246405; this version posted December 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Decreased DNA methylation at promoters and gene-specific neuronal hypermethylation in the prefrontal cortex of patients with bipolar disorder Miki Bundo1†, Junko Ueda1,2†, Yutaka Nakachi1, Kiyoto Kasai3,4, Tadafumi Kato2,5#, Kazuya Iwamoto1# 1Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Japan 2Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Japan 3Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Japan 4The International Research Center for Neurointelligence (WPI-IRCN) at The University of Tokyo Institutes for Advanced Study (UTIAS), 5Department of Psychiatry and Behavioral Science, Graduate School of Medicine, Juntendo University †contributed equally to this work #corresponding authors: Kazuya Iwamoto Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University. 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan [email protected] Tadadumi Kato Department of Psychiatry and Behavioral Science, Graduate School of Medicine, Juntendo University. 2-1-1 Hongo, Bunkyo, Tokyo 113-8421, Japan [email protected]. Running title: DNA methylation analysis in bipolar disorder 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.10.20246405; this version posted December 11, 2020.
    [Show full text]
  • Supplementary Materials: Molecular Signature of Subtypes of Non- Small Cell Lung Cancer by Large-Scale Transcriptional Profiling
    Cancers 2020 S1 of S18 Supplementary Materials: Molecular Signature of Subtypes of Non- Small Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co- Expression Network Analysis (WGCNA) Magdalena Niemira, Francois Collin, Anna Szalkowska, Agnieszka Bielska, Karolina Chwialkowska, Joanna Reszec, Jacek Niklinski, Miroslaw Kwasniewski and Adam Kretowski Cancers 2020 S2 of S18 A B Figure S1. The top-ranked enriched canonical pathway identified in (A) SCC and (B) ADC using IPA: Eicosanoid signalling pathway. Cancers 2020 S3 of S18 A Cancers 2020 S4 of S18 Figure S2. The second-ranked enriched canonical pathway identified in (A) SCC and (B) ADC using IPA: Agranulocyte adhesion and diapedesis. Cancers 2020 S5 of S18 Figure S3. The top-ranked enriched canonical pathway identified only in lung ADC: MIF regulation of innate immunity. A B Figure S4. Cluster dendograms of the gene clusters of (A) LUAD and (B) LUSC subset from TCGA database. Cancers 2020 S6 of S18 A B C D Figure S5. Protein-protein interaction (PPI) network of genes in the red (A), lightcyan (B), darkorange (C), yellow (D) modules in ADC. The networks were constructed using Cytoscape v. 3.7.2. software. Cancers 2020 S7 of S18 A B Figure S6. Protein-protein interaction (PPI) network of genes in the blue (A) and (B) modules in SCC. The networks were constructed using Cytoscape v. 3.7.2. software. Cancers 2020 S8 of S18 Table S1. Upstream regulator analysis of DEGs in lung SCC predicted by IPA. Upstream Prediction Target
    [Show full text]