1
|
Geister E, Ard D, Patel H, Findley A, DeSouza G, Martin L, Knox H, Gavara N, Lugea A, Sabbatini ME. The Role of Twist1 in Chronic Pancreatitis-Associated Pancreatic Stellate Cells. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00234-7. [PMID: 39032603 DOI: 10.1016/j.ajpath.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 06/18/2024] [Accepted: 06/28/2024] [Indexed: 07/23/2024]
Abstract
In a healthy pancreas, pancreatic stellate cells (PaSCs) synthesize the basement membrane, which is mainly composed of type IV collagen and laminin. In chronic pancreatitis (CP), PaSCs are responsible for the production of a rigid extracellular matrix (ECM) that is mainly composed of fibronectin and type I/III collagen. Reactive oxygen species evoke the formation of the rigid ECM by PaSCs. One source of reactive oxygen species is NADPH oxidase (Nox) enzymes. Nox1 up-regulates the expression of Twist1 and matrix metalloproteinase-9 (MMP-9) in PaSCs from mice with CP. This study determined the functional relationship between Twist1 and MMP-9, and other PaSC-produced proteins, and the extent to which Twist1 regulates digestion of ECM proteins in CP. Twist1 induced the expression of MMP-9 in mouse PaSCs. The action of Twist1 was not selective to MMP-9 because Twist1 induced the expression of types I and IV collagen, fibronectin, transforming growth factor, and α-smooth muscle actin. Using luciferase assay, Twist1 in human primary PaSCs increased the expression of MMP-9 at the transcriptional level in an NF-κB dependent manner. The digestion of type I/III collagen by MMP-9 secreted by PaSCs from mice with CP depended on Twist1. Thus, Twist1 in PaSCs from mice with CP induces rigid ECM production and MMP-9 transcription in an NF-κB-dependent mechanism that selectively displays proteolytic activity toward type I/III collagen.
Collapse
Affiliation(s)
- Emma Geister
- Department of Biological Sciences, Augusta University, Augusta, Georgia
| | - Dalton Ard
- Department of Biological Sciences, Augusta University, Augusta, Georgia
| | - Heer Patel
- Department of Biological Sciences, Augusta University, Augusta, Georgia
| | - Alyssa Findley
- Department of Biological Sciences, Augusta University, Augusta, Georgia
| | - Godfrey DeSouza
- Department of Biological Sciences, Augusta University, Augusta, Georgia
| | - Lyndsay Martin
- Department of Biological Sciences, Augusta University, Augusta, Georgia
| | - Henry Knox
- Department of Biological Sciences, Augusta University, Augusta, Georgia
| | - Natasha Gavara
- Department of Biological Sciences, Augusta University, Augusta, Georgia
| | - Aurelia Lugea
- Cedars-Sinai Medical Center, Los Angeles, California
| | | |
Collapse
|
2
|
England SJ, Rusnock AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells. Neural Dev 2023; 18:8. [PMID: 38017520 PMCID: PMC10683209 DOI: 10.1186/s13064-023-00176-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/12/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. METHODS To identify candidate members of V0v gene regulatory networks, we FAC-sorted wild-type and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. RESULTS Our data reveal two molecularly distinct subtypes of zebrafish V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuron expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. CONCLUSIONS This study identifies two molecularly distinct subsets of zebrafish V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
Collapse
Affiliation(s)
| | | | - Amra Mujcic
- Biology Department, Syracuse University, Syracuse, NY, USA
| | | | - Sarah de Jager
- Physiology, Development and Neuroscience Department, Cambridge University, Cambridge, UK
| | | | - José L Juárez-Morales
- Biology Department, Syracuse University, Syracuse, NY, USA
- Programa de IxM-CONAHCYT, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), La Paz, Baja California Sur, México
| | | | - Ginny Grieb
- Biology Department, Syracuse University, Syracuse, NY, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, NY, USA
| | | |
Collapse
|
3
|
England SJ, Woodard AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in these Cells. RESEARCH SQUARE 2023:rs.3.rs-3290462. [PMID: 37693471 PMCID: PMC10491344 DOI: 10.21203/rs.3.rs-3290462/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. Results Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions This study identifies two molecularly distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
Collapse
|
4
|
Juárez-Morales JL, Weierud F, England SJ, Demby C, Santos N, Grieb G, Mazan S, Lewis KE. Evolution of lbx spinal cord expression and function. Evol Dev 2021; 23:404-422. [PMID: 34411410 DOI: 10.1111/ede.12387] [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: 01/15/2021] [Revised: 06/04/2021] [Accepted: 06/21/2021] [Indexed: 11/29/2022]
Abstract
Ladybird homeobox (Lbx) transcription factors have crucial functions in muscle and nervous system development in many animals. Amniotes have two Lbx genes, but only Lbx1 is expressed in spinal cord. In contrast, teleosts have three lbx genes and we show here that zebrafish lbx1a, lbx1b, and lbx2 are expressed by distinct spinal cell types, and that lbx1a is expressed in dI4, dI5, and dI6 interneurons, as in amniotes. Our data examining lbx expression in Scyliorhinus canicula and Xenopus tropicalis suggest that the spinal interneuron expression of zebrafish lbx1a is ancestral, whereas lbx1b has acquired a new expression pattern in spinal cord progenitor cells. lbx2 spinal expression was probably acquired in the ray-finned lineage, as this gene is not expressed in the spinal cords of either amniotes or S. canicula. We also show that the spinal function of zebrafish lbx1a is conserved with mouse Lbx1. In zebrafish lbx1a mutants, there is a reduction in the number of inhibitory spinal interneurons and an increase in the number of excitatory spinal interneurons, similar to mouse Lbx1 mutants. Interestingly, the number of inhibitory spinal interneurons is also reduced in lbx1b mutants, although in this case the number of excitatory interneurons is not increased. lbx1a;lbx1b double mutants have a similar spinal interneuron phenotype to lbx1a single mutants. Taken together these data suggest that lbx1b and lbx1a may be required in succession for correct specification of dI4 and dI6 spinal interneurons, although only lbx1a is required for suppression of excitatory fates in these cells.
Collapse
Affiliation(s)
| | - Frida Weierud
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | | | - Celia Demby
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Nicole Santos
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Sylvie Mazan
- Biologie Intégrative des Organismes Marins, UMR 7232 CNRS, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | | |
Collapse
|
5
|
Zhang Y, Xin L, Pirrello J, Fang Y, Yang J, Qi J, Montoro P, Tang C. Ethylene response factors regulate expression of HbSUT3, the sucrose influx carrier in laticifers of Hevea brasiliensis. TREE PHYSIOLOGY 2021; 41:1278-1288. [PMID: 33554256 DOI: 10.1093/treephys/tpaa179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
Natural rubber is an important industrial raw material and is commercially produced by rubber trees (Hevea brasiliensis). The sucrose transporter HbSUT3 plays an essential role in rubber production. Its expression in latex (cytoplasm of rubber-producing laticifers) is induced by bark treatment with Ethrel, an ethylene releaser, and the inducing effect correlates well with Ethrel-stimulated rubber yield increase. However, the mechanisms of ethylene induction on HbSUT3 expression are not known. Here, five Ethylene Response Factor (ERF) genes were identified from the cDNA library of Hevea latex by yeast one-hybrid screening with the promoter of HbSUT3 gene as bait. As revealed in a tobacco (Nicotiana tabacum) protoplast transient expression system, these HbERFs were mainly localized in the nucleus and four of them exhibited apparent transactivation activity. Of the five HbERF genes, HbERF-IXc4 was the most frequently screened in yeast one-hybrid, accounting for 65% of the ERF clones obtained. Moreover, among the five HbERFs, HbERF-IXc4 showed the strongest transactivation capacity when expressed in tobacco protoplast, the highest transcript abundance in latex and a close expressional correlation with its target gene, HbSUT3, in response to the Ethrel treatment. Taken together, our results indicate that ERFs, especially HbERF-IXc4, are critically involved in the activation of HbSUT3 expression in latex after Ethrel treatment on Hevea bark, and thus the stimulated latex yield.
Collapse
Affiliation(s)
- Yi Zhang
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, College of Tropical Crops, Hainan University, 58 Renmin Avenue, Haikou 570228, China
| | - Lusheng Xin
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, College of Tropical Crops, Hainan University, 58 Renmin Avenue, Haikou 570228, China
| | - Julien Pirrello
- CIRAD, UMR AGAP, 389 Avenue d'Agropolis - TA A-108/03, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 389 Avenue d'Agropolis - TA A-108/03, F-34398 Montpellier, France
| | - Yongjun Fang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, 4 West Xueyuan Road, Haikou 570100, China; 5Corresponding authors C.Tang ( or ); P. Montoro
| | - Jianghua Yang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, 4 West Xueyuan Road, Haikou 570100, China; 5Corresponding authors C.Tang ( or ); P. Montoro
| | - Jiyan Qi
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, College of Tropical Crops, Hainan University, 58 Renmin Avenue, Haikou 570228, China
| | - Pascal Montoro
- CIRAD, UMR AGAP, 389 Avenue d'Agropolis - TA A-108/03, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 389 Avenue d'Agropolis - TA A-108/03, F-34398 Montpellier, France
| | - Chaorong Tang
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, College of Tropical Crops, Hainan University, 58 Renmin Avenue, Haikou 570228, China
| |
Collapse
|
6
|
Kim YR, Yi M, Cho SA, Kim WY, Min J, Shin JG, Lee SJ. Identification and functional study of genetic polymorphisms in cyclic nucleotide phosphodiesterase 3A (PDE3A). Ann Hum Genet 2020; 85:80-91. [PMID: 33249558 DOI: 10.1111/ahg.12411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022]
Abstract
Phosphodiesterase 3A (PDE3A) is an enzyme that plays an important role in the regulation of cyclic adenosine monophosphate (cAMP)-mediated intracellular signaling in cardiac myocytes and platelets. PDE3A hydrolyzes cAMP, which results in a decrease in intracellular cAMP levels and leads to platelet activation. Whole-exome sequencing of 50 DNA samples from a healthy Korean population revealed a total of 13 single nucleotide polymorphisms including five missense variants, D12N, Y497C, H504Q, C707R, and A980V. Recombinant proteins for the five variants of PDE3A (and wild-type protein) were expressed in a FreeStyle 293 expression system with site-directed mutagenesis. The expression of the recombinant PDE3A proteins was confirmed with Western blotting. Catalytic activity of the PDE3A missense variants and wild-type enzyme was measured with a PDE-based assay. Effects of the missense variants on the inhibition of PDE3A activity by cilostazol were also investigated. All variant proteins showed reduced activity (33-53%; p < .0001) compared to the wild-type protein. In addition, PDE3A activity was inhibited by cilostazol in a dose-dependent manner and was further suppressed in the missense variants. Specifically, the PDE3A Y497C showed significantly reduced activity, consistent with the predictions of in silico analyses. The present study provides evidence that individuals carrying the PDE3A Y497C variant may have lower enzyme activity for cAMP hydrolysis, which could cause interindividual variation in cAMP-mediated physiological functions.
Collapse
Affiliation(s)
- You Ran Kim
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University College of Medicine, Inje University, Busan, South Korea
| | - MyeongJin Yi
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University College of Medicine, Inje University, Busan, South Korea.,Pharmacogenetics Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Sun-Ah Cho
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University College of Medicine, Inje University, Busan, South Korea
| | - Woo-Young Kim
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University College of Medicine, Inje University, Busan, South Korea
| | - JungKi Min
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Jae-Gook Shin
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University College of Medicine, Inje University, Busan, South Korea.,Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Inje University College of Medicine, Inje University, Busan, 47392, South Korea
| | - Su-Jun Lee
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University College of Medicine, Inje University, Busan, South Korea
| |
Collapse
|
7
|
Wu X, Schnitzler GR, Gao GF, Diamond B, Baker AR, Kaplan B, Williamson K, Westlake L, Lorrey S, Lewis TA, Garvie CW, Lange M, Hayat S, Seidel H, Doench J, Cherniack AD, Kopitz C, Meyerson M, Greulich H. Mechanistic insights into cancer cell killing through interaction of phosphodiesterase 3A and schlafen family member 12. J Biol Chem 2020; 295:3431-3446. [PMID: 32005668 DOI: 10.1074/jbc.ra119.011191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/27/2020] [Indexed: 01/08/2023] Open
Abstract
Cytotoxic molecules can kill cancer cells by disrupting critical cellular processes or by inducing novel activities. 6-(4-(Diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one (DNMDP) is a small molecule that kills cancer cells by generation of novel activity. DNMDP induces complex formation between phosphodiesterase 3A (PDE3A) and schlafen family member 12 (SLFN12) and specifically kills cancer cells expressing elevated levels of these two proteins. Here, we examined the characteristics and covariates of the cancer cell response to DNMDP. On average, the sensitivity of human cancer cell lines to DNMDP is correlated with PDE3A expression levels. However, DNMDP could also bind the related protein, PDE3B, and PDE3B supported DNMDP sensitivity in the absence of PDE3A expression. Although inhibition of PDE3A catalytic activity did not account for DNMDP sensitivity, we found that expression of the catalytic domain of PDE3A in cancer cells lacking PDE3A is sufficient to confer sensitivity to DNMDP, and substitutions in the PDE3A active site abolish compound binding. Moreover, a genome-wide CRISPR screen identified the aryl hydrocarbon receptor-interacting protein (AIP), a co-chaperone protein, as required for response to DNMDP. We determined that AIP is also required for PDE3A-SLFN12 complex formation. Our results provide mechanistic insights into how DNMDP induces PDE3A-SLFN12 complex formation, thereby killing cancer cells with high levels of PDE3A and SLFN12 expression.
Collapse
Affiliation(s)
- Xiaoyun Wu
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142
| | | | - Galen F Gao
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142
| | - Brett Diamond
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142
| | - Andrew R Baker
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142
| | - Bethany Kaplan
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142
| | | | | | - Selena Lorrey
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142
| | - Timothy A Lewis
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142
| | - Colin W Garvie
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142
| | - Martin Lange
- Research and Development, Pharmaceuticals, Bayer AG, 13342 Berlin, Germany
| | - Sikander Hayat
- Research and Development, Pharmaceuticals, Bayer AG, 13342 Berlin, Germany
| | - Henrik Seidel
- Research and Development, Pharmaceuticals, Bayer AG, 13342 Berlin, Germany
| | - John Doench
- Genetic Perturbation Platform, Broad Institute, Cambridge, Massachusetts 02142
| | - Andrew D Cherniack
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Charlotte Kopitz
- Research and Development, Pharmaceuticals, Bayer AG, 13342 Berlin, Germany
| | - Matthew Meyerson
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Heidi Greulich
- Cancer Program, Broad Institute, Cambridge, Massachusetts 02142; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.
| |
Collapse
|
8
|
Jiang J, Zhao W, Tang Q, Wang B, Li X, Feng Z. Over expression of amphiregulin promoted malignant progression in gastric cancer. Pathol Res Pract 2019; 215:152576. [DOI: 10.1016/j.prp.2019.152576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/17/2019] [Accepted: 07/31/2019] [Indexed: 12/30/2022]
|
9
|
Juárez-Morales JL, Martinez-De Luna RI, Zuber ME, Roberts A, Lewis KE. Zebrafish transgenic constructs label specific neurons in Xenopus laevis spinal cord and identify frog V0v spinal neurons. Dev Neurobiol 2017; 77:1007-1020. [PMID: 28188691 DOI: 10.1002/dneu.22490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022]
Abstract
A correctly functioning spinal cord is crucial for locomotion and communication between body and brain but there are fundamental gaps in our knowledge of how spinal neuronal circuitry is established and functions. To understand the genetic program that regulates specification and functions of this circuitry, we need to connect neuronal molecular phenotypes with physiological analyses. Studies using Xenopus laevis tadpoles have increased our understanding of spinal cord neuronal physiology and function, particularly in locomotor circuitry. However, the X. laevis tetraploid genome and long generation time make it difficult to investigate how neurons are specified. The opacity of X. laevis embryos also makes it hard to connect functional classes of neurons and the genes that they express. We demonstrate here that Tol2 transgenic constructs using zebrafish enhancers that drive expression in specific zebrafish spinal neurons label equivalent neurons in X. laevis and that the incorporation of a Gal4:UAS amplification cassette enables cells to be observed in live X. laevis tadpoles. This technique should enable the molecular phenotypes, morphologies and physiologies of distinct X. laevis spinal neurons to be examined together in vivo. We have used an islet1 enhancer to label Rohon-Beard sensory neurons and evx enhancers to identify V0v neurons, for the first time, in X. laevis spinal cord. Our work demonstrates the homology of spinal cord circuitry in zebrafish and X. laevis, suggesting that future work could combine their relative strengths to elucidate a more complete picture of how vertebrate spinal cord neurons are specified, and function to generate behavior. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 77: 1007-1020, 2017.
Collapse
Affiliation(s)
- José L Juárez-Morales
- Department of Biology, Syracuse University, 107 College Place, Syracuse, New York, 13244.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, United Kingdom
| | - Reyna I Martinez-De Luna
- The Center for Vision Research, Department of Ophthalmology, SUNY Upstate Medical University, Institute for Human Performance, 505 Irving Ave. Syracuse, New York, 13210
| | - Michael E Zuber
- The Center for Vision Research, Department of Ophthalmology, SUNY Upstate Medical University, Institute for Human Performance, 505 Irving Ave. Syracuse, New York, 13210
| | - Alan Roberts
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom
| | - Katharine E Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, New York, 13244
| |
Collapse
|
10
|
Kim E, Ilic N, Shrestha Y, Zou L, Kamburov A, Zhu C, Yang X, Lubonja R, Tran N, Nguyen C, Lawrence MS, Piccioni F, Bagul M, Doench JG, Chouinard CR, Wu X, Hogstrom L, Natoli T, Tamayo P, Horn H, Corsello SM, Lage K, Root DE, Subramanian A, Golub TR, Getz G, Boehm JS, Hahn WC. Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles. Cancer Discov 2016; 6:714-26. [PMID: 27147599 PMCID: PMC4930723 DOI: 10.1158/2159-8290.cd-16-0160] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/26/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic. One rare KRAS allele, D33E, displayed tumorigenicity and constitutive activation of known RAS effector pathways. By comparing gene expression changes induced upon expression of wild-type and mutant alleles, we inferred the activity of specific alleles. Because alleles found to be mutated only once in 5,338 tumors rendered cells tumorigenic, these observations underscore the value of integrating genomic information with functional studies. SIGNIFICANCE Experimentally inferring the functional status of cancer-associated mutations facilitates the interpretation of genomic information in cancer. Pooled in vivo screen and gene expression profiling identified functional variants and demonstrated that expression of rare variants induced tumorigenesis. Variant phenotyping through functional studies will facilitate defining key somatic events in cancer. Cancer Discov; 6(7); 714-26. ©2016 AACR.See related commentary by Cho and Collisson, p. 694This article is highlighted in the In This Issue feature, p. 681.
Collapse
Affiliation(s)
- Eejung Kim
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nina Ilic
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Lihua Zou
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Cong Zhu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Xiaoping Yang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Rakela Lubonja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nancy Tran
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Cindy Nguyen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Mukta Bagul
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Xiaoyun Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Larson Hogstrom
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ted Natoli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medicine, University of California, San Diego, La Jolla, California
| | - Heiko Horn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Steven M Corsello
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kasper Lage
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| |
Collapse
|
11
|
Juárez-Morales JL, Schulte CJ, Pezoa SA, Vallejo GK, Hilinski WC, England SJ, de Jager S, Lewis KE. Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2-independent mechanism. Neural Dev 2016; 11:5. [PMID: 26896392 PMCID: PMC4759709 DOI: 10.1186/s13064-016-0059-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/04/2016] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND For neurons to function correctly in neuronal circuitry they must utilize appropriate neurotransmitters. However, even though neurotransmitter specificity is one of the most important and defining properties of a neuron we still do not fully understand how neurotransmitter fates are specified during development. Most neuronal properties are determined by the transcription factors that neurons express as they start to differentiate. While we know a few transcription factors that specify the neurotransmitter fates of particular neurons, there are still many spinal neurons for which the transcription factors specifying this critical phenotype are unknown. Strikingly, all of the transcription factors that have been identified so far as specifying inhibitory fates in the spinal cord act through Pax2. Even Tlx1 and Tlx3, which specify the excitatory fates of dI3 and dI5 spinal neurons work at least in part by down-regulating Pax2. METHODS In this paper we use single and double mutant zebrafish embryos to identify the spinal cord functions of Evx1 and Evx2. RESULTS We demonstrate that Evx1 and Evx2 are expressed by spinal cord V0v cells and we show that these cells develop into excitatory (glutamatergic) Commissural Ascending (CoSA) interneurons. In the absence of both Evx1 and Evx2, V0v cells still form and develop a CoSA morphology. However, they lose their excitatory fate and instead express markers of a glycinergic fate. Interestingly, they do not express Pax2, suggesting that they are acquiring their inhibitory fate through a novel Pax2-independent mechanism. CONCLUSIONS Evx1 and Evx2 are required, partially redundantly, for spinal cord V0v cells to become excitatory (glutamatergic) interneurons. These results significantly increase our understanding of the mechanisms of neuronal specification and the genetic networks involved in these processes.
Collapse
Affiliation(s)
- José L Juárez-Morales
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Claus J Schulte
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Sofia A Pezoa
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Grace K Vallejo
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - William C Hilinski
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, 505 Irving Avenue, Syracuse, NY, 13210, USA
| | - Samantha J England
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Sarah de Jager
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Katharine E Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
| |
Collapse
|
12
|
A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. PLoS Genet 2014; 10:e1004819. [PMID: 25502805 PMCID: PMC4263371 DOI: 10.1371/journal.pgen.1004819] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 10/14/2014] [Indexed: 12/13/2022] Open
Abstract
Understanding the functional relevance of DNA variants is essential for all exome and genome sequencing projects. However, current mutagenesis cloning protocols require Sanger sequencing, and thus are prohibitively costly and labor-intensive. We describe a massively-parallel site-directed mutagenesis approach, "Clone-seq", leveraging next-generation sequencing to rapidly and cost-effectively generate a large number of mutant alleles. Using Clone-seq, we further develop a comparative interactome-scanning pipeline integrating high-throughput GFP, yeast two-hybrid (Y2H), and mass spectrometry assays to systematically evaluate the functional impact of mutations on protein stability and interactions. We use this pipeline to show that disease mutations on protein-protein interaction interfaces are significantly more likely than those away from interfaces to disrupt corresponding interactions. We also find that mutation pairs with similar molecular phenotypes in terms of both protein stability and interactions are significantly more likely to cause the same disease than those with different molecular phenotypes, validating the in vivo biological relevance of our high-throughput GFP and Y2H assays, and indicating that both assays can be used to determine candidate disease mutations in the future. The general scheme of our experimental pipeline can be readily expanded to other types of interactome-mapping methods to comprehensively evaluate the functional relevance of all DNA variants, including those in non-coding regions.
Collapse
|
13
|
Van Allen EM, Mouw KW, Kim P, Iyer G, Wagle N, Al-Ahmadie H, Zhu C, Ostrovnaya I, Kryukov GV, O'Connor KW, Sfakianos J, Garcia-Grossman I, Kim J, Guancial EA, Bambury R, Bahl S, Gupta N, Farlow D, Qu A, Signoretti S, Barletta JA, Reuter V, Boehm J, Lawrence M, Getz G, Kantoff P, Bochner BH, Choueiri TK, Bajorin DF, Solit DB, Gabriel S, D'Andrea A, Garraway LA, Rosenberg JE. Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov 2014; 4:1140-53. [PMID: 25096233 DOI: 10.1158/2159-8290.cd-14-0623] [Citation(s) in RCA: 453] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
UNLABELLED Cisplatin-based chemotherapy is the standard of care for patients with muscle-invasive urothelial carcinoma. Pathologic downstaging to pT0/pTis after neoadjuvant cisplatin-based chemotherapy is associated with improved survival, although molecular determinants of cisplatin response are incompletely understood. We performed whole-exome sequencing on pretreatment tumor and germline DNA from 50 patients with muscle-invasive urothelial carcinoma who received neoadjuvant cisplatin-based chemotherapy followed by cystectomy (25 pT0/pTis "responders," 25 pT2+ "nonresponders") to identify somatic mutations that occurred preferentially in responders. ERCC2, a nucleotide excision repair gene, was the only significantly mutated gene enriched in the cisplatin responders compared with nonresponders (q < 0.01). Expression of representative ERCC2 mutants in an ERCC2-deficient cell line failed to rescue cisplatin and UV sensitivity compared with wild-type ERCC2. The lack of normal ERCC2 function may contribute to cisplatin sensitivity in urothelial cancer, and somatic ERCC2 mutation status may inform cisplatin-containing regimen usage in muscle-invasive urothelial carcinoma. SIGNIFICANCE Somatic ERCC2 mutations correlate with complete response to cisplatin-based chemosensitivity in muscle-invasive urothelial carcinoma, and clinically identified mutations lead to cisplatin sensitivity in vitro. Nucleotide excision repair pathway defects may drive exceptional response to conventional chemotherapy.
Collapse
Affiliation(s)
- Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Harvard Radiation Oncology Program, Boston, Massachusetts
| | - Philip Kim
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Weill Cornell Medical College, Cornell University, New York, New York. Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Hikmat Al-Ahmadie
- Weill Cornell Medical College, Cornell University, New York, New York. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cong Zhu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Kevin W O'Connor
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - John Sfakianos
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ilana Garcia-Grossman
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Elizabeth A Guancial
- Division of Hematology/Oncology, Department of Medicine, University of Rochester Medical Center School of Medicine and Dentistry, Rochester, New York
| | - Richard Bambury
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samira Bahl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Deborah Farlow
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Angela Qu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Justine A Barletta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Victor Reuter
- Weill Cornell Medical College, Cornell University, New York, New York. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesse Boehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, Massachusetts
| | - Philip Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York. Weill Cornell Medical College, Cornell University, New York, New York
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Dean F Bajorin
- Weill Cornell Medical College, Cornell University, New York, New York. Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Weill Cornell Medical College, Cornell University, New York, New York. Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stacey Gabriel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Harvard Radiation Oncology Program, Boston, Massachusetts
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
| | - Jonathan E Rosenberg
- Weill Cornell Medical College, Cornell University, New York, New York. Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
14
|
Dittmer TA, Sahni N, Kubben N, Hill DE, Vidal M, Burgess RC, Roukos V, Misteli T. Systematic identification of pathological lamin A interactors. Mol Biol Cell 2014; 25:1493-510. [PMID: 24623722 PMCID: PMC4004598 DOI: 10.1091/mbc.e14-02-0733] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Laminopathies are a collection of phenotypically diverse diseases that include muscular dystrophies, cardiomyopathies, lipodystrophies, and premature aging syndromes. Laminopathies are caused by >300 distinct mutations in the LMNA gene, which encodes the nuclear intermediate filament proteins lamin A and C, two major architectural elements of the mammalian cell nucleus. The genotype-phenotype relationship and the basis for the pronounced tissue specificity of laminopathies are poorly understood. Here we seek to identify on a global scale lamin A-binding partners whose interaction is affected by disease-relevant LMNA mutations. In a screen of a human genome-wide ORFeome library, we identified and validated 337 lamin A-binding proteins. Testing them against 89 known lamin A disease mutations identified 50 disease-associated interactors. Association of progerin, the lamin A isoform responsible for the premature aging disorder Hutchinson-Gilford progeria syndrome, with its partners was largely mediated by farnesylation. Mapping of the interaction sites on lamin A identified the immunoglobulin G (IgG)-like domain as an interaction hotspot and demonstrated that lamin A variants, which destabilize the Ig-like domain, affect protein-protein interactions more globally than mutations of surface residues. Analysis of a set of LMNA mutations in a single residue, which result in three phenotypically distinct diseases, identified disease-specific interactors. The results represent a systematic map of disease-relevant lamin A interactors and suggest loss of tissue-specific lamin A interactions as a mechanism for the tissue-specific appearance of laminopathic phenotypes.
Collapse
Affiliation(s)
- Travis A Dittmer
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 Department of Genetics, Harvard Medical School, Boston, MA 02215
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Sahni N, Yi S, Zhong Q, Jailkhani N, Charloteaux B, Cusick ME, Vidal M. Edgotype: a fundamental link between genotype and phenotype. Curr Opin Genet Dev 2013; 23:649-57. [PMID: 24287335 DOI: 10.1016/j.gde.2013.11.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/06/2013] [Accepted: 11/01/2013] [Indexed: 11/17/2022]
Abstract
Classical 'one-gene/one-disease' models cannot fully reconcile with the increasingly appreciated prevalence of complicated genotype-to-phenotype associations in human disease. Genes and gene products function not in isolation but as components of intricate networks of macromolecules (DNA, RNA, or proteins) and metabolites linked through biochemical or physical interactions, represented in 'interactome' network models as 'nodes' and 'edges', respectively. Accordingly, mechanistic understanding of human disease will require understanding of how disease-causing mutations affect systems or interactome properties. The study of 'edgetics' uncovers specific loss or gain of interactions (edges) to interpret genotype-to-phenotype relationships. We review how distinct genetic variants, the genotype, lead to distinct phenotypic outcomes, the phenotype, through edgetic perturbations in interactome networks altogether representing the 'edgotype'.
Collapse
Affiliation(s)
- Nidhi Sahni
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | |
Collapse
|
16
|
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 2013; 342:1235587. [PMID: 24092746 PMCID: PMC3947637 DOI: 10.1126/science.1235587] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating the latter. We found regions particularly sensitive to mutations ("ultrasensitive") and variants that are disruptive because of mechanistic effects on transcription-factor binding (that is, "motif-breakers"). We also found variants in regions with higher network centrality tend to be deleterious. Insertions and deletions followed a similar pattern to single-nucleotide variants, with some notable exceptions (e.g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers.
Collapse
Affiliation(s)
- Ekta Khurana
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Yao Fu
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
| | - Vincenza Colonna
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, CB10 1SA, UK
- Institute of Genetics and Biophysics, National Research Council
(CNR), 80131 Naples, Italy
| | - Xinmeng Jasmine Mu
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
| | - Hyun Min Kang
- Center for Statistical Genetics, Biostatistics, University of
Michigan, Ann Arbor, MI 48109, USA
| | - Tuuli Lappalainen
- Department of Genetic Medicine and Development, University of Geneva
Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of
Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Andrea Sboner
- Institute for Precision Medicine and the Department of Pathology and
Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian
Hospital, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute
for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021,
USA
| | - Lucas Lochovsky
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
| | - Jieming Chen
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology,
Yale University, New Haven, CT 06520, USA
| | - Arif Harmanci
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Jishnu Das
- Department of Biological Statistics and Computational Biology,
Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University,
Ithaca, NY 14853, USA
| | - Alexej Abyzov
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Suganthi Balasubramanian
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dimple Chakravarty
- Institute for Precision Medicine and the Department of Pathology and
Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian
Hospital, New York, NY 10065, USA
| | - Daniel Challis
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, CB10 1SA, UK
| | - Declan Clarke
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Uday S. Evani
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert Fragoza
- Weill Institute for Cell and Molecular Biology, Cornell University,
Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University,
Ithaca, NY 14853, USA
| | - Erik Garrison
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Richard Gibbs
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | - Zeynep H. Gümüş
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute
for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021,
USA
- Department of Physiology and Biophysics, Weill Cornell Medical
College, New York, NY, 10065, USA
| | - Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Naoki Kitabayashi
- Institute for Precision Medicine and the Department of Pathology and
Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian
Hospital, New York, NY 10065, USA
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
- Keck Biotechnology Resource Laboratory, Yale University, New Haven,
CT 06511, USA
| | - Kasper Lage
- Pediatric Surgical Research Laboratories, MassGeneral Hospital for
Children, Massachusetts General Hospital, Boston, MA 02114, USA
- Analytical and Translational Genetics Unit, Massachusetts General
Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
- Center for Biological Sequence Analysis, Department of Systems
Biology, Technical University of Denmark, Lyngby, Denmark
- Center for Protein Research, University of Copenhagen, Copenhagen,
Denmark
| | - Vaja Liluashvili
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute
for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021,
USA
- Department of Physiology and Biophysics, Weill Cornell Medical
College, New York, NY, 10065, USA
| | - Steven M. Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, NY
10065, USA
| | - Daniel G. MacArthur
- Analytical and Translational Genetics Unit, Massachusetts General
Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of
Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142,
USA
| | - Gabor Marth
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Donna Muzny
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | - Tune H. Pers
- Center for Biological Sequence Analysis, Department of Systems
Biology, Technical University of Denmark, Lyngby, Denmark
- Division of Endocrinology and Center for Basic and Translational
Obesity Research, Children’s Hospital, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Graham R. S. Ritchie
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeffrey A. Rosenfeld
- Department of Medicine, Rutgers New Jersey Medical School, Newark,
NJ 07101, USA
- IST/High Performance and Research Computing, Rutgers University
Newark, NJ 07101, USA
- Sackler Institute for Comparative Genomics, American Museum of
Natural History, New York, NY 10024, USA
| | - Cristina Sisu
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Xiaomu Wei
- Weill Institute for Cell and Molecular Biology, Cornell University,
Ithaca, NY 14853, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY
10065, USA
| | - Michael Wilson
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, CB10 1SA, UK
| | - Fuli Yu
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | | | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva
Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of
Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology,
Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University,
Ithaca, NY 14853, USA
| | - Mark A. Rubin
- Institute for Precision Medicine and the Department of Pathology and
Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian
Hospital, New York, NY 10065, USA
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, CB10 1SA, UK
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT
06520, USA
| |
Collapse
|
17
|
Guo Y, Wei X, Das J, Grimson A, Lipkin S, Clark A, Yu H. Dissecting disease inheritance modes in a three-dimensional protein network challenges the "guilt-by-association" principle. Am J Hum Genet 2013; 93:78-89. [PMID: 23791107 DOI: 10.1016/j.ajhg.2013.05.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 05/02/2013] [Accepted: 05/23/2013] [Indexed: 10/26/2022] Open
Abstract
To better understand different molecular mechanisms by which mutations lead to various human diseases, we classified 82,833 disease-associated mutations according to their inheritance modes (recessive versus dominant) and molecular types (in-frame [missense point mutations and in-frame indels] versus truncating [nonsense mutations and frameshift indels]) and systematically examined the effects of different classes of disease mutations in a three-dimensional protein interactome network with the atomic-resolution interface resolved for each interaction. We found that although recessive mutations affecting the interaction interface of two interacting proteins tend to cause the same disease, this widely accepted "guilt-by-association" principle does not apply to dominant mutations. Furthermore, recessive truncating mutations in regions encoding the same interface are much more likely to cause the same disease, even for interfaces close to the N terminus of the protein. Conversely, dominant truncating mutations tend to be enriched in regions encoding areas between interfaces. These results suggest that a significant fraction of truncating mutations can generate functional protein products. For example, TRIM27, a known cancer-associated protein, interacts with three proteins (MID2, TRIM42, and SIRPA) through two different interfaces. A dominant truncating mutation (c.1024delT [p.Tyr342Thrfs*30]) associated with ovarian carcinoma is located between the regions encoding the two interfaces; the altered protein retains its interaction with MID2 and TRIM42 through the first interface but loses its interaction with SIRPA through the second interface. Our findings will help clarify the molecular mechanisms of thousands of disease-associated genes and their tens of thousands of mutations, especially for those carrying truncating mutations, often erroneously considered "knockout" alleles.
Collapse
|
18
|
Fukunaga T, Cha-aim K, Hirakawa Y, Sakai R, Kitagawa T, Nakamura M, Nonklang S, Hoshida H, Akada R. Designed construction of recombinant DNA at theura3Δ0locus in the yeastSaccharomyces cerevisiae. Yeast 2013; 30:243-53. [DOI: 10.1002/yea.2957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/08/2013] [Accepted: 04/15/2013] [Indexed: 11/08/2022] Open
Affiliation(s)
- Tomoaki Fukunaga
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Kamonchai Cha-aim
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Yuki Hirakawa
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Ryota Sakai
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Takao Kitagawa
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Mikiko Nakamura
- Innovation Centre; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Sanom Nonklang
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Hisashi Hoshida
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Rinji Akada
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| |
Collapse
|
19
|
Gateway vectors for efficient artificial gene assembly in vitro and expression in yeast Saccharomyces cerevisiae. PLoS One 2013; 8:e64419. [PMID: 23675537 PMCID: PMC3651225 DOI: 10.1371/journal.pone.0064419] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 04/15/2013] [Indexed: 11/19/2022] Open
Abstract
Construction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created a series of Gateway shuttle vectors and an integration vector, which facilitate the assembly of artificial genes and their expression in the budding yeast Saccharomyces cerevisiae. Our method enables the rapid construction of an artificial gene from a promoter and an open reading frame (ORF) cassette by one-step recombination reaction in vitro. Furthermore, the plasmid thus created can readily be introduced into yeast cells to test the assembled gene's functionality. As flexible regulatory components of a synthetic genetic network, we also created new versions of the tetracycline-regulated transactivators tTA and rtTA by fusing them to the auxin-inducible degron (AID). Using our gene assembly approach, we made yeast expression vectors of these engineered transactivators, AIDtTA and AIDrtTA and then tested their functions in yeast. We showed that these factors can be regulated by doxycycline and degraded rapidly after addition of auxin to the medium. Taken together, the method for combinatorial gene assembly described here is versatile and would be a valuable tool for yeast synthetic biology.
Collapse
|
20
|
Jakobi AJ, Huizinga EG. A rapid cloning method employing orthogonal end protection. PLoS One 2012; 7:e37617. [PMID: 22685543 PMCID: PMC3369885 DOI: 10.1371/journal.pone.0037617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 04/27/2012] [Indexed: 11/30/2022] Open
Abstract
We describe a novel in vitro cloning strategy that combines standard tools in molecular biology with a basic protecting group concept to create a versatile framework for the rapid and seamless assembly of modular DNA building blocks into functional open reading frames. Analogous to chemical synthesis strategies, our assembly design yields idempotent composite synthons amenable to iterative and recursive split-and-pool reaction cycles. As an example, we illustrate the simplicity, versatility and efficiency of the approach by constructing an open reading frame composed of tandem arrays of a human fibronectin type III (FNIII) domain and the von Willebrand Factor A2 domain (VWFA2), as well as chimeric (FNIII)n-VWFA2-(FNIII)n constructs. Although we primarily designed this strategy to accelerate assembly of repetitive constructs for single-molecule force spectroscopy, we anticipate that this approach is equally applicable to the reconstitution and modification of complex modular sequences including structural and functional analysis of multi-domain proteins, synthetic biology or the modular construction of episomal vectors.
Collapse
Affiliation(s)
- Arjen J. Jakobi
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Eric G. Huizinga
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- * E-mail:
| |
Collapse
|
21
|
Richie CT, Bembenek JN, Chestnut B, Furuta T, Schumacher JM, Wallenfang M, Golden A. Protein phosphatase 5 is a negative regulator of separase function during cortical granule exocytosis in C. elegans. J Cell Sci 2012; 124:2903-13. [PMID: 21878498 DOI: 10.1242/jcs.073379] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in the Caenorhabditis elegans separase gene, sep-1, are embryonic lethal. Newly fertilized mutant embryos have defects in polar body extrusion, fail to undergo cortical granule exocytosis, and subsequently fail to complete cytokinesis. Chromosome nondisjunction during the meiotic divisions is readily apparent after depletion of sep-1 by RNAi treatment, but much less so in hypomorphic mutant embryos. To identify factors that influence the activity of separase in cortical granule exocytosis and cytokinesis, we carried out a genetic suppressor screen. A mutation in the protein phosphatase 5 (pph-5) gene was identified as an extragenic suppressor of sep-1. This mutation suppressed the phenotypes of hypomorphic separase mutants but not RNAi depleted animals. Depletion of pph-5 caused no phenotypes on its own, but was effective in restoring localization of mutant separase to vesicles and suppressing cortical granule exocytosis and cytokinesis phenotypes. The identification of PPH-5 as a suppressor of separase suggests that a new phospho-regulatory pathway plays an important role in regulating anaphase functions of separase.
Collapse
|
22
|
Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol 2012; 30:159-64. [PMID: 22252508 DOI: 10.1038/nbt.2106] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 12/19/2011] [Indexed: 01/13/2023]
Abstract
To better understand the molecular mechanisms and genetic basis of human disease, we systematically examine relationships between 3,949 genes, 62,663 mutations and 3,453 associated disorders by generating a three-dimensional, structurally resolved human interactome. This network consists of 4,222 high-quality binary protein-protein interactions with their atomic-resolution interfaces. We find that in-frame mutations (missense point mutations and in-frame insertions and deletions) are enriched on the interaction interfaces of proteins associated with the corresponding disorders, and that the disease specificity for different mutations of the same gene can be explained by their location within an interface. We also predict 292 candidate genes for 694 unknown disease-to-gene associations with proposed molecular mechanism hypotheses. This work indicates that knowledge of how in-frame disease mutations alter specific interactions is critical to understanding pathogenesis. Structurally resolved interaction networks should be valuable tools for interpreting the wealth of data being generated by large-scale structural genomics and disease association studies.
Collapse
Affiliation(s)
- Xiujuan Wang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | | | | | | | | | | |
Collapse
|
23
|
Yuan Z, Qiao C, Hu P, Li J, Xiao X. A versatile adeno-associated virus vector producer cell line method for scalable vector production of different serotypes. Hum Gene Ther 2011; 22:613-24. [PMID: 21186998 PMCID: PMC3081441 DOI: 10.1089/hum.2010.241] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Accepted: 12/25/2010] [Indexed: 02/04/2023] Open
Abstract
Application of adeno-associated virus (AAV) vector in large animal studies and clinical trials often requires high-titer and high-potency vectors. A number of currently used vector production methods, based on either transient transfection or helper virus infection of cell lines, have their advantages and limitations. We previously developed a 293-cell-based producer cell line method for high-titer and high-potency AAV2 vectors. Similar to several other methods, however, it requires multiple cloning steps for the vector and packaging plasmids and a two-step transfection and selection for stable cell lines. Here we report a simplified method with several key improvements and advantages: (1) a one-step cloning of AAV vector cassette into the serotype-specific packaging plasmid; (2) a single plasmid transfection and selection for stable AAV vector producer cell lines; (3) high vector yields of different serotypes, e.g., AAV2, 8, and 9, upon infection with an E1A/E1B-deleted helper adenovirus; (4) efficient packaging of both single-stranded and double-stranded (self-complementary) AAV vectors; and (5) efficient packaging of large AAV cassettes such as a mini-dystrophin vector (5.0 kb). All cell lines were stable with growth rates identical to the parental 293 cells. The vector yields were consistent among serotypes, with 5 × 10(13) to 8 × 10(13) vector genome particles per Nunc cell factory (equivalent to 40 15-cm plates). The vectors showed high potency for in vitro and in vivo transduction. In conclusion, the simple and versatile AAV producer cell line method can be useful for large scale AAV vector production in preclinical and clinical studies.
Collapse
Affiliation(s)
- Zhenhua Yuan
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | | |
Collapse
|
24
|
Charloteaux B, Zhong Q, Dreze M, Cusick ME, Hill DE, Vidal M. Protein-protein interactions and networks: forward and reverse edgetics. Methods Mol Biol 2011; 759:197-213. [PMID: 21863489 DOI: 10.1007/978-1-61779-173-4_12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Phenotypic variations of an organism may arise from alterations of cellular networks, ranging from the complete loss of a gene product to the specific perturbation of a single molecular interaction. In interactome networks that are modeled as nodes (macromolecules) connected by edges (interactions), these alterations can be thought of as node removal and edge-specific or "edgetic" perturbations, respectively. Here we present two complementary strategies, forward and reverse edgetics, to investigate the phenotypic outcomes of edgetic perturbations of binary protein-protein interaction networks. Both approaches are based on the yeast two-hybrid system (Y2H). The first allows the determination of the interaction profile of proteins encoded by alleles with known phenotypes to identify edgetic alleles. The second is used to directly isolate edgetic alleles for subsequent in vivo characterization.
Collapse
Affiliation(s)
- Benoit Charloteaux
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | | | | |
Collapse
|
25
|
Abstract
Gene deletion is one of the most powerful tools to study gene function. In the genomics era there is great demand for fast, simple high-throughput methods for gene deletion to study the roles of the large numbers of genes that are being identified. Here we present an approach that speeds up the process of generation of deletion mutants by greatly simplifying the production of gene deletion constructs. With this purpose we have developed a method, which we named DelsGate (Deletion via Gateway), that combines PCR and Gateway cloning technology together with the use of the I-SceI homing endonuclease to generate precise deletion constructs in a very simple, universal and robust manner in just 2 days. DelsGate consists of standard PCR of only the 5' and 3' 1 kb gene flanks directly followed by in vitro Gateway cloning and final generation of the circular deletion construct by in vivo recombination in Escherichia coli. For use in DelsGate we have modified a Gateway cloning vector to include selectable markers for the transformation of Ascomycetes and the Basidiomycete fungus Ustilago maydis. The PCR and transformation steps of DelsGate should be well suited for high-throughput approaches to gene deletion construction in fungal species. We describe here the entire process, from the generation of the deletion construct with DelsGate to the analysis of the fungal transformants to test for gene replacement, with the Basidiomycete fungus Ustilago maydis. Application of DelsGate to other fungal species is also underway. Additionally, we describe how this basic approach can be adapted to other genetic manipulations with minor changes. We specifically describe its application to create unmarked deletions in Ralstonia solanacearum, a Gram-negative phytopathogenic bacterium.
Collapse
|
26
|
Marotta F, Koike K, Lorenzetti A, Jain S, Signorelli P, Metugriachuk Y, Mantello P, Locorotondo N. Regulating redox balance gene expression in healthy individuals by nutraceuticals: a pilot study. Rejuvenation Res 2010; 13:175-8. [PMID: 20370494 DOI: 10.1089/rej.2009.0950] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We tested the effect of a fermented papaya preparation (FPP; ORI, Gifu, Japan) on redox balance gene expression in 11 healthy nonsmoker, teetotaller individuals subjected to a detailed dietary and lifestyle questionnaire who refrained from any multivitamin supplement or fortified food. Redox status was assessed by erythrocyte and plasma parameters together with related leukocyte mRNA (glutathione peroxidase [GPx], superoxide dismutase [SOD], catalase, 8-oxoguanine glycosylase [hOGG1]) before/after 6 grams of FPP supplementation. At 2 and 4 weeks after FPP administration, plasma parameters remained unchanged, whereas FPP significantly upregulated all tested gene expression (p < 0.05). Although posttranscriptional/translation protein modifications do occur and larger and longer studies are awaited, these preliminary data suggest that a transcriptomic modification of key redox and DNA repair genes may offer further insights when attempting to interrelate "nutragenomics" to clinical phenomena.
Collapse
|
27
|
Young J, Ménétrey J, Goud B. RAB6C is a retrogene that encodes a centrosomal protein involved in cell cycle progression. J Mol Biol 2010; 397:69-88. [PMID: 20064528 DOI: 10.1016/j.jmb.2010.01.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 12/08/2009] [Accepted: 01/05/2010] [Indexed: 10/20/2022]
Abstract
Rab-GTPases are key regulators of membrane transport, and growing evidence indicates that their expression levels are altered in certain human malignancies, including cancer. Rab6C, a newly identified Rab6 subfamily member, has attracted recent attention because its reduced expression might confer a selective advantage to drug-resistant breast cancer cells. Here, we report that RAB6C is a primate-specific retrogene derived from a RAB6A' transcript. RAB6C is transcribed in a limited number of human tissues including brain, testis, prostate, and breast. Endogenous Rab6C is considerably less abundant and has a much shorter half-life than Rab6A'. Comparison of the GTP-binding motifs of Rab6C and Rab6A', homology modeling, and GTP-blot overlay assays indicate that amino acid changes in Rab6C have greatly reduced its GTP-binding affinity. Instead, the noncanonical GTP-binding domain of Rab6C mediates localization of the protein to the centrosome. Overexpression of Rab6C results in G1 arrest, and its specific depletion generates tetraploid cells with supernumerary centrosomes, revealing a role of Rab6C in events related to the centrosome and cell cycle progression. Thus, RAB6C is a rare example of a recently emerged retrogene that has acquired the status of a new gene, encoding a functional protein with altered characteristics compared to Rab6A'.
Collapse
Affiliation(s)
- Joanne Young
- Molecular Mechanisms of Intracellular Transport, CNRS, UMR144, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | | | | |
Collapse
|
28
|
Edgetic perturbation models of human inherited disorders. Mol Syst Biol 2009; 5:321. [PMID: 19888216 PMCID: PMC2795474 DOI: 10.1038/msb.2009.80] [Citation(s) in RCA: 278] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/02/2009] [Indexed: 01/20/2023] Open
Abstract
Cellular functions are mediated through complex systems of macromolecules and metabolites linked through biochemical and physical interactions, represented in interactome models as ‘nodes' and ‘edges', respectively. Better understanding of genotype-to-phenotype relationships in human disease will require modeling of how disease-causing mutations affect systems or interactome properties. Here we investigate how perturbations of interactome networks may differ between complete loss of gene products (‘node removal') and interaction-specific or edge-specific (‘edgetic') alterations. Global computational analyses of ∼50 000 known causative mutations in human Mendelian disorders revealed clear separations of mutations probably corresponding to those of node removal versus edgetic perturbations. Experimental characterization of mutant alleles in various disorders identified diverse edgetic interaction profiles of mutant proteins, which correlated with distinct structural properties of disease proteins and disease mechanisms. Edgetic perturbations seem to confer distinct functional consequences from node removal because a large fraction of cases in which a single gene is linked to multiple disorders can be modeled by distinguishing edgetic network perturbations. Edgetic network perturbation models might improve both the understanding of dissemination of disease alleles in human populations and the development of molecular therapeutic strategies.
Collapse
|
29
|
Manini P, De Palma G, Andreoli R, Marczynski B, Hanova M, Mozzoni P, Naccarati A, Vodickova L, Hlavac P, Mutti A, Vodicka P. Biomarkers of nucleic acid oxidation, polymorphism in, and expression of, hOGG1 gene in styrene-exposed workers. Toxicol Lett 2009; 190:41-7. [DOI: 10.1016/j.toxlet.2009.06.862] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/18/2009] [Accepted: 06/22/2009] [Indexed: 11/25/2022]
|
30
|
Toivanen PI, Nieminen T, Viitanen L, Alitalo A, Roschier M, Jauhiainen S, Markkanen JE, Laitinen OH, Airenne TT, Salminen TA, Johnson MS, Airenne KJ, Ylä-Herttuala S. Novel vascular endothelial growth factor D variants with increased biological activity. J Biol Chem 2009; 284:16037-48. [PMID: 19366703 DOI: 10.1074/jbc.m109.001123] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Members of the vascular endothelial growth factor (VEGF) family play a pivotal role in angiogenesis and lymphangiogenesis. They are potential therapeutics to induce blood vessel formation in myocardium and skeletal muscle, when normal blood flow is compromised. Most members of the VEGF/platelet derived growth factor protein superfamily exist as covalently bound antiparallel dimers. However, the mature form of VEGF-D (VEGF-D(DeltaNDeltaC)) is predominantly a non-covalent dimer even though the cysteine residues (Cys-44 and Cys-53) forming the intersubunit disulfide bridges in the other members of the VEGF family are also conserved in VEGF-D. Moreover, VEGF-D bears an additional cysteine residue (Cys-25) at the subunit interface. Guided by our model of VEGF-D(DeltaNDeltaC), the cysteines at the subunit interface were mutated to study the effect of these residues on the structural and functional properties of VEGF-D(DeltaNDeltaC). The conserved cysteines Cys-44 and Cys-53 were found to be essential for the function of VEGF-D(DeltaNDeltaC). More importantly, the substitution of the Cys-25 at the dimer interface by various amino acids improved the activity of the recombinant VEGF-D(DeltaNDeltaC) and increased the dimer to monomer ratio. Specifically, substitutions to hydrophobic amino acids Ile, Leu, and Val, equivalent to those found in other VEGFs, most favorably affected the activity of the recombinant VEGF-D(DeltaNDeltaC). The increased activity of these mutants was mainly due to stabilization of the protein. This study enables us to better understand the structural determinants controlling the biological activity of VEGF-D. The novel variants of VEGF-D(DeltaNDeltaC) described here are potential agents for therapeutic applications, where induction of vascular formation is required.
Collapse
Affiliation(s)
- Pyry I Toivanen
- Department of Biotechnology and Molecular Medicine, A. I. Virtanen Institute for Molecular Sciences, FI-70211 Kuopio, Finland
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Han YW, Aleyas AG, George JA, Kim SJ, Kim HK, Yoon HA, Yoo DJ, Kang SH, Kim K, Eo SK. Polarization of protective immunity induced by replication-incompetent adenovirus expressing glycoproteins of pseudorabies virus. Exp Mol Med 2008; 40:583-95. [PMID: 19116444 PMCID: PMC2679340 DOI: 10.3858/emm.2008.40.6.583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2008] [Indexed: 11/04/2022] Open
Abstract
Replication-incompetent adenoviruses expressing three major glycoproteins (gB, gC, and gD) of pseudorabies virus (PrV) were constructed and used to examine the ability of these glycoproteins to induce protective immunity against a lethal challenge. Among three constructs, recombinant adenovirus expressing gB (rAd-gB) was found to induce the most potent immunity biased to Th1-type, as determined by the IgG isotype ratio and the profile of the Th1/Th2 cytokine production. Conversely, the gC-expressing adenovirus (rAd-gC) revealed Th2-type immunity and the gD-expressing adenovirus (rAd-gD) induced lower levels of IFN-? and IL-4 production than other constructs, except IL-2 production. Mucosal delivery of rAd-gB induced mucosal IgA and serum IgG responses and biased toward Th2-type immune responses. However, these effects were not observed in response to systemic delivery of rAd-gB. In addition, rAd-gB appeared to induce effective protective immunity against a virulent viral infection, regardless of whether it was administered via the muscular or systemic route. These results suggest that administration of replication-incompetent adenoviruses can induce different types of immunity depending on the expressed antigen and that recombinant adenoviruses expressing gB induced the most potent Th1-biased humoral and cellular immunity and provided effective protection against PrV infection.
Collapse
Affiliation(s)
- Young Woo Han
- Laboratory of Microbiology, College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Jeonju 561-756, Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
DelsGate, a robust and rapid gene deletion construction method. Fungal Genet Biol 2008; 45:379-88. [DOI: 10.1016/j.fgb.2007.11.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Revised: 10/10/2007] [Accepted: 11/08/2007] [Indexed: 11/24/2022]
|