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Contents
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[1]A Frost, VM Unger and P De Camilli: The BAR domain superfamily: membrane-molding macromolecules. Cell 137, 191-196 (2009)
[2]A Shimada, H Niwa, K Tsujita, S Suetsugu, K Nitta, K Hanawa-Suetsugu, R Akasaka, Y Nishino, M Toyama, L Chen, ZJ Liu, BC Wang, M Yamamoto, T Terada, A Miyazawa, A Tanaka, S Sugano, M Shirouzu, K Nagayama, T Takenawa and S Yokoyama: Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis. Cell 129, 761-772 (2007)
[3]S Ahmed, W Bu, RT Lee, S Maurer-Stroh and WI Goh: F-BAR domain proteins: Families and function. Commun Integr Biol 3, 116-121 (2010)
[4]P Aspenstrom: Roles of F-BAR/PCH proteins in the regulation of membrane dynamics and actin reorganization. Int Rev Cell Mol Biol 272, 1-31 (2009)
[5]RJ Heath and RH Insall: F-BAR domains: multifunctional regulators of membrane curvature. J Cell Sci 121, 1951-1954 (2008)
[6]RH Roberts-Galbraith and KL Gould: Setting the F-BAR: functions and regulation of the F-BAR protein family. Cell Cycle 9, 4091-4097 (2010)
[7]T Takenawa and H Miki: WASP and WAVE family proteins: key molecules for rapid rearrangement of cortical actin filaments and cell movement. J Cell Sci 114, 1801-1809 (2001)
[8]S Liu, X Xiong, X Zhao, X Yang and H Wang: F-BAR family proteins, emerging regulators for cell membrane dynamic changes-from structure to human diseases. J Hematol Oncol 8, 47 (2015)
[9]X Li, J Mai, A Virtue, Y Yin, R Gong, X Sha, S Gutchigian, A Frisch, I Hodge, X Jiang, H Wang and XF Yang: IL-35 is a novel responsive anti-inflammatory cytokine--a new system of categorizing anti-inflammatory cytokines. PLoS One 7, e33628 (2012)
[10]J Mai, A Virtue, E Maley, T Tran, Y Yin, S Meng, M Pansuria, X Jiang, H Wang and XF Yang: MicroRNAs and other mechanisms regulate interleukin-17 cytokines and receptors. Front Biosci (Elite Ed) 4, 1478-1495 (2012)
[11]X Huang, R Gong, X Li, A Virtue, F Yang, IH Yang, AH Tran, XF Yang and H Wang: Identification of novel pretranslational regulatory mechanisms for NF-kappaB activation. J Biol Chem 288, 15628-15640 (2013)
[12]S Meng, S Ciment, M Jan, T Tran, H Pham, R Cueto, XF Yang and H Wang: Homocysteine induces inflammatory transcriptional signaling in monocytes. Front Biosci (Landmark Ed) 18, 685-695 (2013)
[13]A Virtue, J Mai, Y Yin, S Meng, T Tran, X Jiang, H Wang and XF Yang: Structural evidence of anti-atherogenic microRNAs. Front Biosci (Landmark Ed) 16, 3133-3145 (2011)
[14]NC Chen, F Yang, LM Capecci, Z Gu, AI Schafer, W Durante, XF Yang and H Wang: Regulation of homocysteine metabolism and methylation in human and mouse tissues. FASEB J 24, 2804-2817 (2010)
[15]J Shen, Y Yin, J Mai, X Xiong, M Pansuria, J Liu, E Maley, NU Saqib, H Wang and XF Yang: Caspase-1 recognizes extended cleavage sites in its natural substrates. Atherosclerosis 210, 422-429 (2010)
[16]Y Yin, Y Yan, X Jiang, J Mai, NC Chen, H Wang and XF Yang: Inflammasomes are differentially expressed in cardiovascular and other tissues. Int J Immunopathol Pharmacol 22, 311-322 (2009)
[17]XF Yang, D Mirkovic, S Zhang, QE Zhang, Y Yan, Z Xiong, F Yang, IH Chen, L Li and H Wang: Processing sites are different in the generation of HLA-A2.1-restricted, T cell reactive tumor antigen epitopes and viral epitopes. Int J Immunopathol Pharmacol 19, 853-870 (2006)
[18]B Ng, F Yang, DP Huston, Y Yan, Y Yang, Z Xiong, LE Peterson, H Wang and XF Yang: Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes. J Allergy Clin Immunol 114, 1463-1470 (2004)
[19]A Osman: Yeast two-hybrid assay for studying protein-protein interactions. Methods Mol Biol 270, 403-422 (2004)
[20]JH Morris, GM Knudsen, E Verschueren, JR Johnson, P Cimermancic, AL Greninger and AR Pico: Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc 9, 2539-2554 (2014)
[21]J Sambrook and DW Russell: Identification of associated proteins by coimmunoprecipitation. CSH Protoc 2006 (2006)
[22]H Iioka and IG Macara: Detection of RNA-Protein Interactions Using Tethered RNA Affinity Capture. Methods Mol Biol 1316, 67-73 (2015)
[23]R Pires Martins, RE Leach and SA Krawetz: Whole-body gene expression by data mining. Genomics 72, 34-42 (2001)
[24]H Ohno, S Hirabayashi, A Kansaku, I Yao, M Tajima, W Nishimura, H Ohnishi, H Mashima, T Fujita, M Omata and Y Hata: Carom: a novel membrane-associated guanylate kinase-interacting protein with two SH3 domains. Oncogene 22, 8422-8431 (2003)
[25]J Zhu, Y Shang, C Xia, W Wang, W Wen and M Zhang: Guanylate kinase domains of the MAGUK family scaffold proteins as specific phospho-protein-binding modules. EMBO J 30, 4986-4997 (2011)
[26]L Onder, R Danuser, E Scandella, S Firner, Q Chai, T Hehlgans, JV Stein and B Ludewig: Endothelial cell-specific lymphotoxin-beta receptor signaling is critical for lymph node and high endothelial venule formation. J Exp Med 210, 465-473 (2013)
[27]R Zhu, LQ Bi, SL Wu, L Li, H Kong, WP Xie, H Wang and ZL Meng: Iptakalim attenuates hypoxia-induced pulmonary arterial hypertension in rats by endothelial function protection. Mol Med Rep 12, 2945-2952 (2015)
[28]AT Reddy, SP Lakshmi, JM Kleinhenz, RL Sutliff, CM Hart and RC Reddy: Endothelial cell peroxisome proliferator-activated receptor gamma reduces endotoxemic pulmonary inflammation and injury. J Immunol 189, 5411-5420 (2012)
[29]AM Malutan, T Drugan, N Costin, R Ciortea, C Bucuri, MP Rada and D Mihu: Pro-inflammatory cytokines for evaluation of inflammatory status in endometriosis. Cent Eur J Immunol 40, 96-102 (2015)
[30]E Brogi, G Schatteman, T Wu, EA Kim, L Varticovski, B Keyt and JM Isner: Hypoxia-induced paracrine regulation of vascular endothelial growth factor receptor expression. J Clin Invest 97, 469-476 (1996)
[31]AL Rocha, FM Reis and RN Taylor: Angiogenesis and endometriosis. Obstet Gynecol Int 2013, 859619 (2013)
[32]P Anderle, M Duval, S Draghici, A Kuklin, TG Littlejohn, JF Medrano, D Vilanova and MA Roberts: Gene expression databases and data mining. Biotechniques Suppl, 36-44 (2003)
[33]LC Giudice and LC Kao: Endometriosis. Lancet 364, 1789-1799 (2004)
[34]AS Sengar, J Ellegood, AP Yiu, H Wang, W Wang, SC Juneja, JP Lerch, SA Josselyn, RM Henkelman, MW Salter and SE Egan: Vertebrate intersectin1 is repurposed to facilitate cortical midline connectivity and higher order cognition. J Neurosci 33, 4055-4065 (2013)
[35]E Greaves, F Collins, A Esnal-Zufiaurre, S Giakoumelou, AW Horne and PT Saunders: Estrogen receptor (ER) agonists differentially regulate neuroangiogenesis in peritoneal endometriosis via the repellent factor SLIT3. Endocrinology 155, 4015-4026 (2014)
[36]G Chen, X Xu, L Zhang, Y Fu, M Wang, H Gu and X Xie: Blocking autocrine VEGF signaling by sunitinib, an anti-cancer drug, promotes embryonic stem cell self-renewal and somatic cell reprogramming. Cell Res 24, 1121-1136 (2014)
[37]K Takei and V Haucke: Clathrin-mediated endocytosis: membrane factors pull the trigger. Trends Cell Biol 11, 385-391 (2001)
[38]WM Henne, E Boucrot, M Meinecke, E Evergren, Y Vallis, R Mittal and HT McMahon: FCHo proteins are nucleators of clathrin-mediated endocytosis. Science 328, 1281-1284 (2010)
[39]P Samavarchi-Tehrani, A Golipour, L David, HK Sung, TA Beyer, A Datti, K Woltjen, A Nagy and JL Wrana: Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7, 64-77 (2010)
[40]D Subramanyam, S Lamouille, RL Judson, JY Liu, N Bucay, R Derynck and R Blelloch: Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nat Biotechnol 29, 443-448 (2011)
[41]G Scita and PP Di Fiore: The endocytic matrix. Nature 463, 464-473 (2010)
[42]H Qin, A Diaz, L Blouin, RJ Lebbink, W Patena, P Tanbun, EM LeProust, MT McManus, JS Song and M Ramalho-Santos: Systematic identification of barriers to human iPSC generation. Cell 158, 449-461 (2014)
[43]TC He, AB Sparks, C Rago, H Hermeking, L Zawel, LT da Costa, PJ Morin, B Vogelstein and KW Kinzler: Identification of c-MYC as a target of the APC pathway. Science 281, 1509-1512 (1998)
[44]A Marson, R Foreman, B Chevalier, S Bilodeau, M Kahn, RA Young and R Jaenisch: Wnt signaling promotes reprogramming of somatic cells to pluripotency. Cell Stem Cell 3, 132-135 (2008)
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Frontiers in Bioscience-Landmark (FBL) is published by IMR Press from Volume 26 Issue 5 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on imrpress.com as a courtesy and upon agreement with Frontiers in Bioscience.
Analysis for Carom complex, signaling and function by database mining
1 Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
2 Center for Metabolic Disease Research,Temple University School of Medicine, Philadelphia, PA, 19140, USA
3 Cardiovascular Research, Temple University School of Medicine, Philadelphia, PA, 19140, USA
4 Thrombosis Research, Temple University School of Medicine, Philadelphia, PA, 19140, USA
5 Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
6 Department of Cardiology, Second Hospital of Nanchang University, Institute of Cardiovascular Disease in Nanchang University, Nan Chang, Jiang Xi, 330006, China
Abstract
Carom is a novel protein that regulates membrane curvature and transmits pathophysiological signaling. The tissue expression of Carom is unclear and its functional role and signaling are unknown. We employed a group of combined database mining strategies and established a working model of Carom signaling. We identified 26 Carom partners and established their expression profiles in human and mouse tissues. We classified three tiers of tissues for Carom/partner expression and found lymph node was the tier 1 tissue expressing Carom and most of its partners. Using GEO database, we discovered that four conditions (hypoxia, endometriosis, PPARγ deletion and iPSC reprogramming) altered Carom/partner expression in endothelial cells. We identified 26 Carom partner signalings by Ingenuity pathway analysis. Ten of the 26 pathways and three genes (ITSN1, UBC and HSPA5) were reported to be regulated in the above four conditions. Paired induction of Carom/ITSN1 elevation was associated with pathological angiogenesis. Whereas, paired reduction of Carom/HSPA5 or UBC was associated with iPSC generation. These results provide an insight on identifying Carom complex model and predicting its functional implications.
Keywords
- F-BAR proteins
- Membrane dynamics
- Cellular functions
- Inflammation
- Angiogenesis
References
- [1] A Frost, VM Unger and P De Camilli: The BAR domain superfamily: membrane-molding macromolecules. Cell 137, 191-196 (2009)
- [2] A Shimada, H Niwa, K Tsujita, S Suetsugu, K Nitta, K Hanawa-Suetsugu, R Akasaka, Y Nishino, M Toyama, L Chen, ZJ Liu, BC Wang, M Yamamoto, T Terada, A Miyazawa, A Tanaka, S Sugano, M Shirouzu, K Nagayama, T Takenawa and S Yokoyama: Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis. Cell 129, 761-772 (2007)
- [3] S Ahmed, W Bu, RT Lee, S Maurer-Stroh and WI Goh: F-BAR domain proteins: Families and function. Commun Integr Biol 3, 116-121 (2010)
- [4] P Aspenstrom: Roles of F-BAR/PCH proteins in the regulation of membrane dynamics and actin reorganization. Int Rev Cell Mol Biol 272, 1-31 (2009)
- [5] RJ Heath and RH Insall: F-BAR domains: multifunctional regulators of membrane curvature. J Cell Sci 121, 1951-1954 (2008)
- [6] RH Roberts-Galbraith and KL Gould: Setting the F-BAR: functions and regulation of the F-BAR protein family. Cell Cycle 9, 4091-4097 (2010)
- [7] T Takenawa and H Miki: WASP and WAVE family proteins: key molecules for rapid rearrangement of cortical actin filaments and cell movement. J Cell Sci 114, 1801-1809 (2001)
- [8] S Liu, X Xiong, X Zhao, X Yang and H Wang: F-BAR family proteins, emerging regulators for cell membrane dynamic changes-from structure to human diseases. J Hematol Oncol 8, 47 (2015)
- [9] X Li, J Mai, A Virtue, Y Yin, R Gong, X Sha, S Gutchigian, A Frisch, I Hodge, X Jiang, H Wang and XF Yang: IL-35 is a novel responsive anti-inflammatory cytokine--a new system of categorizing anti-inflammatory cytokines. PLoS One 7, e33628 (2012)
- [10] J Mai, A Virtue, E Maley, T Tran, Y Yin, S Meng, M Pansuria, X Jiang, H Wang and XF Yang: MicroRNAs and other mechanisms regulate interleukin-17 cytokines and receptors. Front Biosci (Elite Ed) 4, 1478-1495 (2012)
- [11] X Huang, R Gong, X Li, A Virtue, F Yang, IH Yang, AH Tran, XF Yang and H Wang: Identification of novel pretranslational regulatory mechanisms for NF-kappaB activation. J Biol Chem 288, 15628-15640 (2013)
- [12] S Meng, S Ciment, M Jan, T Tran, H Pham, R Cueto, XF Yang and H Wang: Homocysteine induces inflammatory transcriptional signaling in monocytes. Front Biosci (Landmark Ed) 18, 685-695 (2013)
- [13] A Virtue, J Mai, Y Yin, S Meng, T Tran, X Jiang, H Wang and XF Yang: Structural evidence of anti-atherogenic microRNAs. Front Biosci (Landmark Ed) 16, 3133-3145 (2011)
- [14] NC Chen, F Yang, LM Capecci, Z Gu, AI Schafer, W Durante, XF Yang and H Wang: Regulation of homocysteine metabolism and methylation in human and mouse tissues. FASEB J 24, 2804-2817 (2010)
- [15] J Shen, Y Yin, J Mai, X Xiong, M Pansuria, J Liu, E Maley, NU Saqib, H Wang and XF Yang: Caspase-1 recognizes extended cleavage sites in its natural substrates. Atherosclerosis 210, 422-429 (2010)
- [16] Y Yin, Y Yan, X Jiang, J Mai, NC Chen, H Wang and XF Yang: Inflammasomes are differentially expressed in cardiovascular and other tissues. Int J Immunopathol Pharmacol 22, 311-322 (2009)
- [17] XF Yang, D Mirkovic, S Zhang, QE Zhang, Y Yan, Z Xiong, F Yang, IH Chen, L Li and H Wang: Processing sites are different in the generation of HLA-A2.1-restricted, T cell reactive tumor antigen epitopes and viral epitopes. Int J Immunopathol Pharmacol 19, 853-870 (2006)
- [18] B Ng, F Yang, DP Huston, Y Yan, Y Yang, Z Xiong, LE Peterson, H Wang and XF Yang: Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes. J Allergy Clin Immunol 114, 1463-1470 (2004)
- [19] A Osman: Yeast two-hybrid assay for studying protein-protein interactions. Methods Mol Biol 270, 403-422 (2004)
- [20] JH Morris, GM Knudsen, E Verschueren, JR Johnson, P Cimermancic, AL Greninger and AR Pico: Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc 9, 2539-2554 (2014)
- [21] J Sambrook and DW Russell: Identification of associated proteins by coimmunoprecipitation. CSH Protoc 2006 (2006)
- [22] H Iioka and IG Macara: Detection of RNA-Protein Interactions Using Tethered RNA Affinity Capture. Methods Mol Biol 1316, 67-73 (2015)
- [23] R Pires Martins, RE Leach and SA Krawetz: Whole-body gene expression by data mining. Genomics 72, 34-42 (2001)
- [24] H Ohno, S Hirabayashi, A Kansaku, I Yao, M Tajima, W Nishimura, H Ohnishi, H Mashima, T Fujita, M Omata and Y Hata: Carom: a novel membrane-associated guanylate kinase-interacting protein with two SH3 domains. Oncogene 22, 8422-8431 (2003)
- [25] J Zhu, Y Shang, C Xia, W Wang, W Wen and M Zhang: Guanylate kinase domains of the MAGUK family scaffold proteins as specific phospho-protein-binding modules. EMBO J 30, 4986-4997 (2011)
- [26] L Onder, R Danuser, E Scandella, S Firner, Q Chai, T Hehlgans, JV Stein and B Ludewig: Endothelial cell-specific lymphotoxin-beta receptor signaling is critical for lymph node and high endothelial venule formation. J Exp Med 210, 465-473 (2013)
- [27] R Zhu, LQ Bi, SL Wu, L Li, H Kong, WP Xie, H Wang and ZL Meng: Iptakalim attenuates hypoxia-induced pulmonary arterial hypertension in rats by endothelial function protection. Mol Med Rep 12, 2945-2952 (2015)
- [28] AT Reddy, SP Lakshmi, JM Kleinhenz, RL Sutliff, CM Hart and RC Reddy: Endothelial cell peroxisome proliferator-activated receptor gamma reduces endotoxemic pulmonary inflammation and injury. J Immunol 189, 5411-5420 (2012)
- [29] AM Malutan, T Drugan, N Costin, R Ciortea, C Bucuri, MP Rada and D Mihu: Pro-inflammatory cytokines for evaluation of inflammatory status in endometriosis. Cent Eur J Immunol 40, 96-102 (2015)
- [30] E Brogi, G Schatteman, T Wu, EA Kim, L Varticovski, B Keyt and JM Isner: Hypoxia-induced paracrine regulation of vascular endothelial growth factor receptor expression. J Clin Invest 97, 469-476 (1996)
- [31] AL Rocha, FM Reis and RN Taylor: Angiogenesis and endometriosis. Obstet Gynecol Int 2013, 859619 (2013)
- [32] P Anderle, M Duval, S Draghici, A Kuklin, TG Littlejohn, JF Medrano, D Vilanova and MA Roberts: Gene expression databases and data mining. Biotechniques Suppl, 36-44 (2003)
- [33] LC Giudice and LC Kao: Endometriosis. Lancet 364, 1789-1799 (2004)
- [34] AS Sengar, J Ellegood, AP Yiu, H Wang, W Wang, SC Juneja, JP Lerch, SA Josselyn, RM Henkelman, MW Salter and SE Egan: Vertebrate intersectin1 is repurposed to facilitate cortical midline connectivity and higher order cognition. J Neurosci 33, 4055-4065 (2013)
- [35] E Greaves, F Collins, A Esnal-Zufiaurre, S Giakoumelou, AW Horne and PT Saunders: Estrogen receptor (ER) agonists differentially regulate neuroangiogenesis in peritoneal endometriosis via the repellent factor SLIT3. Endocrinology 155, 4015-4026 (2014)
- [36] G Chen, X Xu, L Zhang, Y Fu, M Wang, H Gu and X Xie: Blocking autocrine VEGF signaling by sunitinib, an anti-cancer drug, promotes embryonic stem cell self-renewal and somatic cell reprogramming. Cell Res 24, 1121-1136 (2014)
- [37] K Takei and V Haucke: Clathrin-mediated endocytosis: membrane factors pull the trigger. Trends Cell Biol 11, 385-391 (2001)
- [38] WM Henne, E Boucrot, M Meinecke, E Evergren, Y Vallis, R Mittal and HT McMahon: FCHo proteins are nucleators of clathrin-mediated endocytosis. Science 328, 1281-1284 (2010)
- [39] P Samavarchi-Tehrani, A Golipour, L David, HK Sung, TA Beyer, A Datti, K Woltjen, A Nagy and JL Wrana: Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7, 64-77 (2010)
- [40] D Subramanyam, S Lamouille, RL Judson, JY Liu, N Bucay, R Derynck and R Blelloch: Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nat Biotechnol 29, 443-448 (2011)
- [41] G Scita and PP Di Fiore: The endocytic matrix. Nature 463, 464-473 (2010)
- [42] H Qin, A Diaz, L Blouin, RJ Lebbink, W Patena, P Tanbun, EM LeProust, MT McManus, JS Song and M Ramalho-Santos: Systematic identification of barriers to human iPSC generation. Cell 158, 449-461 (2014)
- [43] TC He, AB Sparks, C Rago, H Hermeking, L Zawel, LT da Costa, PJ Morin, B Vogelstein and KW Kinzler: Identification of c-MYC as a target of the APC pathway. Science 281, 1509-1512 (1998)
- [44] A Marson, R Foreman, B Chevalier, S Bilodeau, M Kahn, RA Young and R Jaenisch: Wnt signaling promotes reprogramming of somatic cells to pluripotency. Cell Stem Cell 3, 132-135 (2008)