Fonseca Lab - Publications

2022
	Helminth-induced reprogramming of the stem cell compartment inhibits type 2 immunity Karo-Atar, Danielle; Ouladan, Shaida; Javkar, Tanvi; Joumier, Loick; Matheson, Macy K.; Merritt, Sydney; Westfall, Susan; Rochette, Annie; Gentile, Maria E.; Fontes, Ghislaine; Fonseca, Gregory J.; Parisien, Marc; Diatchenko, Luda; von Moltke, Jakob; Malleshaiah, Mohan; Gregorieff, Alex; King, Irah L. Journal of Experimental Medicine doi:10.1084/jem.20212311 TLR4 is a regulator of trained immunity in a murine model of Duchenne muscular dystrophy Bhattarai, Salyan; Li, Qian; Ding, Jun; Liang, Feng; Gusev, Ekaterina; Lapohos, Orsolya; Fonseca, Gregory J.; Kaufmann, Eva; Divangahi, Maziar; Petrof, Basil J. Nature Communications doi:10.1038/s41467-022-28531-1 Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs Shen, Zeyang; Li, Rick Z.; Prohaska, Thomas A.; Hoeksema, Marten A.; Spann, Nathan J.; Tao, Jenhan; Fonseca, Gregory J.; Le, Thomas; Stolze, Lindsey K.; Sakai, Mashito; Romanoski, Casey E.; Glass, Christopher K. Elife doi:10.7554/eLife.70878
2021
	A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19 Ding, Jun; Hostallero, David E.; El Khili, Mohamed R.; Fonseca, Gregory J.; Milette, Simon; Noorah, Nuzha; Guay-Belzile, Myriam; Spicer, Jonathan; Daneshtalab, Noriko; Sirois, Martin; Tremblay, Karine; Emad, Amin; Rousseau, Simon PLoS Computational Biology doi:10.1371/journal.pcbi.1008810. Angiotensin-converting enzyme 2 expression in COPD and IPF fibroblasts: the forgotten cell in COVID-19 Aloufi, Noof; Traboulsi, Hussein; Ding, Jun; Fonseca, Gregory J.; Nair, Parameswaran; Huang, Steven K.; Hussain, Sabah N. A.; Eidelman, David H.; Baglole, Carolyn J. American Journal of Physiology-Lung Cellular and Molecular Physiology doi:10.1152/ajplung.00455.2020
2020
	Infiltrating Hematogenous Macrophages Aggregate Around β-Amyloid Plaques in an Age- and Sex-Dependent Manner in a Mouse Model of Alzheimer Disease Kozyrev, Natalie; Albers, Shawn; Yang, Jennifer; Prado, Vania F.; Prado, Marco A.M.; Fonseca, Gregory J.; Rylett, R. Jane; Dekaban, Gregory A. Journal of neuropathology and experimental neurology doi:10.1093/jnen/nlaa093 Differential effects of human adenovirus E1A protein isoforms on aerobic glycolysis in A549 human lung epithelial cells Prusinkiewicz, Martin A.; Tu, Jessie; Dodge, MacKenzie J.; MacNeil, Katelyn M.; Radko-Juettner, Sandi; Fonseca, Gregory J.; Pelka, Peter; Mymryk, Joe S. Viruses doi:10.3390/v12060610 Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung Sajti, Eniko; Link, Verena M.; Ouyang, Zhengyu; Spann, Nathanael J.; Westin, Emma; Romanoski, Casey E.; Fonseca, Gregory J.; Prince, Lawrence S.; Glass, Christopher K. Nature Immunology doi:10.1038/s41590-019-0582-z
2019
	Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages Fonseca, Gregory J.; Tao, Jenhan; Westin, Emma M.; Duttke, Sascha H.; Spann, Nathanael J.; Strid, Tobias; Shen, Zeyang; Stender, Joshua D.; Sakai, Mashito; Link, Verena M.; Benner, Christopher; Glass, Christopher K. Nature Communications doi:10.1038/s41467-018-08236-0
2018
	Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function Link, Verena M.; Duttke, Sascha H.; Chun, Hyun B.; Holtman, Inge R.; Westin, Emma; Hoeksema, Marten A.; Abe, Yohei; Skola, Dylan; Romanoski, Casey E.; Tao, Jenhan; Fonseca, Gregory J.; Troutman, Ty D.; Spann, Nathanael J.; Strid, Tobias; Sakai, Mashito; Yu, Miao; Hu, Rong; Fang, Rongxin; Metzler, Dirk; Ren, Bing; Glass, Christopher K. Cell doi:10.1016/j.cell.2018.04.018
2016
	Functional and Structural Mimicry of Cellular Protein Kinase A Anchoring Proteins by a Viral Oncoprotein King, Cason R.; Cohen, Michael J.; Fonseca, Gregory J.; Dirk, Brennan S.; Dikeakos, Jimmy D.; Mymryk, Joe S. PLoS Pathogens doi:10.1371/journal.ppat.1005621
2014
	Environment drives selection and function of enhancers controlling tissue-specific macrophage identities Gosselin, David; Link, Verena M.; Romanoski, Casey E.; Fonseca, Gregory J.; Eichenfield, Dawn Z.; Spann, Nathanael J.; Stender, Joshua D.; Chun, Hyun B.; Garner, Hannah; Geissmann, Frederic; Glass, Christopher K. Cell doi:10.1016/j.cell.2014.11.023 The adenovirus 55 residue E1A protein is a transcriptional activator and binds the unliganded thyroid hormone receptor. Arulsundaram, Vishnuka D; Webb, Paul; Yousef, Ahmed F; Pelka, Peter; Fonseca, Greg J; Baxter, John D; Walfish, Paul G; Mymryk, Joe S The Journal of general virology doi:10.1099/vir.0.056838-0 Adenovirus E1A Recruits the Human Paf1 Complex To Enhance Transcriptional Elongation Fonseca, G. J.; Cohen, M. J.; Mymryk, J. S. Journal of Virology doi:10.1128/jvi.03518-13 Identification and characterization of multiple conserved nuclear localization signals within adenovirus E1A Marshall, Kris S.; Cohen, Michael J.; Fonseca, Greg J.; Todorovic, Biljana; King, Cason R.; Yousef, Ahmed F.; Zhang, Zhiying; Mymryk, Joe S. Virology doi:10.1016/j.virol.2014.02.020
2013
	Dissection of the C-Terminal Region of E1A Redefines the Roles of CtBP and Other Cellular Targets in Oncogenic Transformation Cohen, M. J.; Yousef, A. F.; Massimi, P.; Fonseca, G. J.; Todorovic, B.; Pelka, P.; Turnell, A. S.; Banks, L.; Mymryk, J. S. Journal of Virology doi:10.1128/jvi.00786-13 Viral Retasking of hBre1/RNF20 to Recruit hPaf1 for Transcriptional Activation Fonseca, Gregory J.; Cohen, Michael J.; Nichols, Anthony C.; Barrett, John W.; Mymryk, Joe S. PLoS Pathogens doi:10.1371/journal.ppat.1003411
2012
	Adenovirus evasion of interferon-mediated innate immunity by direct antagonism of a cellular histone posttranslational modification Fonseca, G. J.; Thillainadesan, G.; Yousef, A. F.; Ablack, J. N.; Mossman, K. L.; Torchia, J.; Mymryk, J. S. Cell Host and Microbe doi:10.1016/j.chom.2012.05.005 Characterization of the 55-Residue Protein Encoded by the 9S E1A mRNA of Species C Adenovirus Miller, Matthew S.; Pelka, Peter; Fonseca, Gregory J.; Cohen, Michael J.; Kelly, Jenna N.; Barr, Stephen D.; Grand, Roger J. A.; Turnell, Andrew S.; Whyte, Peter; Mymryk, Joe S. Journal of Virology doi:10.1128/jvi.06399-11 Cellular GCN5 Is a Novel Regulator of Human Adenovirus E1A-Conserved Region 3 Transactivation Ablack, J. N. G.; Cohen, M.; Thillainadesan, G.; Fonseca, G. J.; Pelka, P.; Torchia, J.; Mymryk, J. S. Journal of Virology doi:10.1128/jvi.00289-12
2010
	Identification of a molecular recognition feature in the E1A oncoprotein that binds the SUMO conjugase UBC9 and likely interferes with polySUMOylation Yousef, A. F.; Fonseca, G. J.; Pelka, P.; Ablack, J. N.G.; Walsh, C.; Dick, F. A.; Bazett-Jones, D. P.; Shaw, G. S.; Mymryk, J. S. Oncogene doi:10.1038/onc.2010.226
2008
	Identification of a Second CtBP Binding Site in Adenovirus Type 5 E1A Conserved Region 3 Bruton, Rachel K.; Pelka, Peter; Mapp, Katie L.; Fonseca, Gregory J.; Torchia, Joseph; Turnell, Andrew S.; Mymryk, Joe S.; Grand, Roger J. A. Journal of Virology doi:10.1128/jvi.00248-08 Intrinsic Structural Disorder in Adenovirus E1A: a Viral Molecular Hub Linking Multiple Diverse Processes Pelka, Peter; Ablack, Jailal N. G.; Fonseca, Gregory J.; Yousef, Ahmed F.; Mymryk, Joe S. Journal of Virology doi:10.1128/jvi.00104-08

THE FONSECA LAB

Helminth-induced reprogramming of the stem cell compartment inhibits type 2 immunity

Journal of Experimental Medicine

doi:10.1084/jem.20212311

TLR4 is a regulator of trained immunity in a murine model of Duchenne muscular dystrophy

Nature Communications

doi:10.1038/s41467-022-28531-1

Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs

Elife

doi:10.7554/eLife.70878

A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19

PLoS Computational Biology

doi:10.1371/journal.pcbi.1008810.

Angiotensin-converting enzyme 2 expression in COPD and IPF fibroblasts: the forgotten cell in COVID-19

American Journal of Physiology-Lung Cellular and Molecular Physiology

doi:10.1152/ajplung.00455.2020

Infiltrating Hematogenous Macrophages Aggregate Around β-Amyloid Plaques in an Age- and Sex-Dependent Manner in a Mouse Model of Alzheimer Disease

Journal of neuropathology and experimental neurology

doi:10.1093/jnen/nlaa093

Differential effects of human adenovirus E1A protein isoforms on aerobic glycolysis in A549 human lung epithelial cells

Viruses

doi:10.3390/v12060610

Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung

Nature Immunology

doi:10.1038/s41590-019-0582-z

Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages

Nature Communications

doi:10.1038/s41467-018-08236-0

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

Cell

doi:10.1016/j.cell.2018.04.018

Functional and Structural Mimicry of Cellular Protein Kinase A Anchoring Proteins by a Viral Oncoprotein

PLoS Pathogens

doi:10.1371/journal.ppat.1005621

Environment drives selection and function of enhancers controlling tissue-specific macrophage identities

Cell

doi:10.1016/j.cell.2014.11.023

The adenovirus 55 residue E1A protein is a transcriptional activator and binds the unliganded thyroid hormone receptor.

The Journal of general virology

doi:10.1099/vir.0.056838-0

Adenovirus E1A Recruits the Human Paf1 Complex To Enhance Transcriptional Elongation

Journal of Virology

doi:10.1128/jvi.03518-13

Identification and characterization of multiple conserved nuclear localization signals within adenovirus E1A

Virology

doi:10.1016/j.virol.2014.02.020

Dissection of the C-Terminal Region of E1A Redefines the Roles of CtBP and Other Cellular Targets in Oncogenic Transformation

Journal of Virology

doi:10.1128/jvi.00786-13

Viral Retasking of hBre1/RNF20 to Recruit hPaf1 for Transcriptional Activation

PLoS Pathogens

doi:10.1371/journal.ppat.1003411

Adenovirus evasion of interferon-mediated innate immunity by direct antagonism of a cellular histone posttranslational modification

Cell Host and Microbe

doi:10.1016/j.chom.2012.05.005

Characterization of the 55-Residue Protein Encoded by the 9S E1A mRNA of Species C Adenovirus

Journal of Virology

doi:10.1128/jvi.06399-11

Cellular GCN5 Is a Novel Regulator of Human Adenovirus E1A-Conserved Region 3 Transactivation

Journal of Virology

doi:10.1128/jvi.00289-12

Identification of a molecular recognition feature in the E1A oncoprotein that binds the SUMO conjugase UBC9 and likely interferes with polySUMOylation

Oncogene

doi:10.1038/onc.2010.226

Identification of a Second CtBP Binding Site in Adenovirus Type 5 E1A Conserved Region 3

Journal of Virology

doi:10.1128/jvi.00248-08

Intrinsic Structural Disorder in Adenovirus E1A: a Viral Molecular Hub Linking Multiple Diverse Processes

Journal of Virology

doi:10.1128/jvi.00104-08