Publications


Selected Publications



2022
Cell reports

Cobo I, Cheng A, Murillo-Saich J, Coras R, Torres A, Abe Y, Lana AJ, Schlachetzki J, Liu-Bryan R, Terkeltaub R, Sanchez-Lopez E, Glass CK. Monosodium urate crystals regulate a unique JNK-dependent macrophage metabolic and inflammatory response Cell Reports, 2022. https://doi.org/10.1016/j.celrep.2022.110489

CellMetabolism

Shen Z, Li RZ, Prohaska TA, Hoeksema MA, Spann NJ, Tao J, Fonseca GJ, Le T, Stolze LK, Sakai M, Romanoski CE, Glass CK. Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs. Elife.2022 Jan 20;11:e70878. doi: 10.7554/eLife.70878. Online ahead of print. PMID: 35049498.


2021
Molecular Cell

Troutman TD, Kofman E, Glass CK. Exploiting dynamic enhancer landscapes to decode macrophage and microglia phenotypes in health and disease. Molecular Cell (2021), https://doi.org/10.1016/j.molcel.2021.08.004


Science

Cox N, Crozet L, Holtman IR, Loyher PL, Lazarov T, White JB, Mass E, Stanley ER, Elemento O, Glass CK, Geissmann F. Diet-regulated production of PDGFcc by macrophages controls energy storage. Science. 2021 Jul 2;373(6550):eabe9383. doi: 10.1126/science.abe9383. PMID: 34210853


SciAdv

Hoeksema MA, Shen Z, Holtman IR, Zheng A, Spann NJ, Cobo I, Gymrek M, Glass CK. Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4. Sci Adv. 2021 Jun 16;7(25):eabf9808. doi: 10.1126/sciadv.abf9808. PMID: 34134993.


Science

Reid DA, Reed PJ, Schlachetzki JCM, Nitulescu II, Chou G, Tsui EC, Jones JR, Chandran S, Lu AT, McClain CA, Ooi JH, Wang TW, Lana AJ, Linker SB, Ricciardulli AS, Lau S, Schafer ST, Horvath S, Dixon JR, Hah N, Glass CK, Gage FH. Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons. Science. 2021 Apr 2;372(6537):91-94. doi: 10.1126/science.abb9032. PMID: 33795458


STAR Prot

Troutman TD, Bennett H, Sakai M, Seidman JS, Heinz S, Glass CK. Purification of mouse hepatic non-parenchymal cells or nuclei for use in ChIP-seq and other next-generation sequencing approaches. STAR Protoc. 2021 Mar 10;2(1):100363. doi: 10.1016/j.xpro.2021.100363. eCollection 2021 Mar 19. PMID: 33748781.


NatProt

Nott A, Schlachetzki JCM, Fixsen BR, Glass CK. Nuclei isolation of multiple brain cell types for omics interrogation. Nature Protocols, 2021 Jan 25. https://doi.org/10.1038/s41596-020-00472-3. PMID: 33495627 PMCID: PMC7969463.


2020
Bioinformatics

Shen Z, Hoeksema MA, Ouyang Z, Benner C, Glass CK. MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. Bioinformatics, Volume 36, Issue Supplement_1, July 2020, Pages i84–i92, https://doi.org/10.1093/bioinformatics/btaa476

CellImm

Seidman JS, Troutman TD, Sakai M, Gola A, Spann NJ, Bennett H, Bruni CM, Ouyang Z, Li RZ, Sun X, Vu BT, Pasillas MP, Ego KM, Gosselin D, Link VM, Chong L, Evans RM, Thompson BM, McDonald JG, Hosseini M, Witztum JL, Germain RN, Glass CK. Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis. Immunity. 2020 Apr 28;S1074-7613(20)30159-X. doi: 10.1016/j.immuni.2020.04.001. PMID: 32362324.

NatImm

Sajti E, Link VM, Ouyang Z, Spann NJ, Westin E, Romanoski CE, Fonseca GJ, Prince LS, Glass CK. Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung. Nat Immunol. 2020 Feb;21(2):221-231. doi: 10.1038/s41590-019-0582-z. Epub 2020 Jan 20. PMID: 31959980.


2019
CellMetabolism

Sun X, Seidman JS, Zhao P, Troutman TD, Spann NJ, Que X, Zhou F, Liao Z, Pasillas M, Yang X, Magida JA, Kisseleva T, Brenner DA, Downes M, Evans RM, Saltiel AR, Tsimikas S, Glass CK, Witztum JL. Neutralization of Oxidized Phospholipids Ameliorates Non-alcoholic Steatohepatitis. Cell Metab. 2019 Nov 14. pii: S1550-4131(19)30605-9. doi: 10.1016/j.cmet.2019.10.014. PMID: 31761566.

Science

Nott A*, Holtman IR*, Coufal NG*, Schlachetzki JCM, Yu M, Hu R, Han CZ, Pena M, Xiaoi J, Wu Y, Keulen Z, Pasillas MP, O’Connor C, Nickl CK, Schafer ST, Shen Z, Rissman RA, Brewer JB, Gosselin D, Gonda DD, Levy ML, Rosenfeld MG, McVicker G, Gage FH, Ren B, Glass CK. Brain cell type-specific enhancer-promoter interactome maps and disease risk association. Science. 2019 Nov 14. pii: eaay0793. doi: 10.1126/science.aay0793. PMC7028213.

CellMetabolism

Sakai M, Troutman TD, Seidman JS, Ouyang Z, Spann NJ, Abe Y, Ego KM, Bruni CM, Deng Z, Schlachetzki JCM, Nott A, Bennett H, Chang J, Vu BT, Pasillas MP, Link VM, Texari L, Heinz S, Thompson BM, McDonald JG, Geissmann F, Glass CK. Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity. Immunity. 2019 Oct 3. DOI: https://doi.org/10.1016/j.immuni.2019.09.002.

CellMetabolism

Cohen Katsenelson K, Stender JD, Kawashima AT, Lordén G, Uchiyama S, Nizet V, Glass CK, Newton AC. PHLPP1 counter-regulates STAT1-mediated inflammatory signaling. Elife. 2019 Aug 13;8. pii: e48609. doi: 10.7554/eLife.48609. PMID: 31408005; PMCID: PMC6692130.

CellMetabolism

Fonseca GJ, Tao J, Westin EM, Duttke SH, Spann NJ, Strid T, Shen Z, Stender JD, Sakai M, Link VM, Benner C, Glass CK. Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. Nat Commun. 2019 Jan 24;10(1):414. doi: 10.1038/s41467-018-08236-0. PMID: 30679424 PMCID: PMC6345992.


2018

Carlin AF, Vizcarra EA, Branche E, Viramontes KM, Suarez-Amaran L, Ley K, Heinz S, Benner C, Shresta S, Glass CK. Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages. PNAS USA. 2018 Sep 25;115(39):E9172-E9181. doi: 10.1073/pnas.1807690115. Epub 2018 Sep 11. PMID: 30206152 PMCID: PMC6166801

Link VM, Romanoski CE, Metzler D, Glass CK. MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements. Nucleic Acids Res. 2018 Jun 9. doi: 10.1093/nar/gky491. PMID: 29893919

Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell June 17, 2018. https://doi.org/10.1016/j.cell.2018.04.018

Que X, Hung MY, Yeang C, Gonen A, Prohaska TA, Sun X, Diehl C, Määttä A, Gaddis DE, Bowden K, Pattison J, MacDonald JG, Ylä-Herttuala S, Mellon PL, Hedrick CC, Ley K, Miller YI, Glass CK, Peterson KL, Binder CJ, Tsimikas S,Witztum JL. Oxidized phospholipids are proinflammatory and proatherogenic in hypercholesterolaemic mice. Nature. 2018 Jun;558(7709):301-306. doi: 10.1038/s41586-018-0198-8. Epub 2018 Jun 6.

Muse EM, Yu S, Edillor CR, Tao J, Spann NJ, Troutman TD, Seidman JS, Henke A, Roland JT, Ozeki KA, Thompson BM, McDonald JG, Bahadorani J, Tsimikas S, Grossman TR, Tremblay MS and Glass CK. Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP in macrophages. PNAS April 9, 2018. 201714518; https://doi.org/10.1073/pnas.1714518115.


2017

Pirzgalska RM, Seixas E, Seidman JS, Link VM, Sánchez NM, Mahú I, Mendes R, Gres V, Kubasova N, Morris I, Arús BA, Larabee CM, Vasques M, Tortosa F, Sousa AL, Anandan S, Tranfield E, Hahn MK, Iannacone M, Spann NJ, Glass CK, Domingos AI. Sympathetic neuron-associated macrophages contribute to obesity by importing and metabolizing norepinephrine. Nat Med. 2017 Nov;23(11):1309-1318. doi: 10.1038/nm.4422. Epub 2017 Oct 9. PMID: 29035364.

Rahnamoun H, Lu H, Duttke SH, Benner C, Glass CK, Lauberth SM. Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling. Nat Commun. 2017 Sep 29;8(1):754. doi: 10.1038/s41467-017-01117-y. PMID: 28963538; PMCID: PMC5622043.

Holtman IR, Skola D, Glass CK. Transcriptional control of microglia phenotypes in health and disease. J Clin Invest. 2017 Jul 31. pii: 90604. doi: 10.1172/JCI90604. Epub 2017 Jul 31. PMID: 28758903.

Hogan NT, Whalen MB, Stolze LK, Hadeli NK, Lam MT, Springstead JR, Glass CK, Romanoski CE. Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells. Elife. 2017 Jun 6;6. pii: e22536. doi: 10.7554/eLife.22536. PMID: 28585919.

Gosselin D, Skola D, Coufal NG, Holtman IR, Schlachetzki JCM, Sajti E, Jaeger BN, O'Connor C, Fitzpatrick C, Pasillas MP, Pena M, Adair A, Gonda DG, Levy ML, Ransohoff RM, Gage FH, Glass CK. An environment-dependent transcriptional network specifies human microglia identity. Science. 2017 May 25. pii: eaal3222. doi: 10.1126/science.aal3222. Epub 2017 May 25. PMID: 28546318.

Phan AT, Goldrath AW, Glass CK. Metabolic and Epigenetic Coordination of TCell and Macrophage Immunity. Immunity. 2017 May 16;46(5):714-729. doi:10.1016/j.immuni.2017.04.016. Review. PMID: 28514673.

Stender JD, Nwachukwu JC, Kastrati I, Kim Y, Strid T, Yakir M, Srinivasan S, Nowak J, Izard T, Rangarajan ES, Carlson KE, Katzenellenbogen JA, Yao X, Grant BJ, Leong HS, Lin C, Frasor J, Nettles KW, Glass CK. Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells. Mol Cell. 2017 Mar 16;65(6):1122-1135.e5. doi: 10.1016/j.molcel.2017.02.008. PMID: 27814941.


2016

Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, Lam MT, Manabe I, Shimano H, Saghatelian A, Glass CK. SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism. Cell Metab. 2016 Dec 21. pii: S1550-4131(16)30588-5. doi: 10.1016/j.cmet.2016.11.009. PMID: 27814941.

Thomas GD, Hanna RN, Vasudevan NT, Hamers AA, Romanoski CE, McArdle S, Ross KD, Blatchley A, Yoakum D, Hamilton BA, Mikulski Z, Jain MK, Glass CK, Hedrick CC. Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6Clow Monocytes while Preserving Macrophage Gene Function.Immunity. 2016 Nov 15;45(5):975-987. doi: 10.1016/j.immuni.2016.10.011. PMID: 27814941

Eichenfield DZ, Troutman TD, Link VM, Lam MT, Cho H, Gosselin D, Spann NJ, Lesch HP, Tao J, Muto J, Gallo RL, Evans RM, Glass CK. Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. Elife. 2016 Jul 27;5. pii: e13024. doi: 10.7554/eLife.13024. PMID: 27462873.

Allison KA, Sajti E, Collier JG, Gosselin D, Troutman TD, Stone EL, Hedrick SM, Glass CK. Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells. Elife. 2016 Jul 4;5. pii: e10134. doi: 10.7554/eLife.10134. PMID: 27376549.


2015

Romanoski CE, Link VM, Heinz S, Glass CK. Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends Immunol. 2015 Sep;36(9):507-18. doi: 10.1016/j.it.2015.07.006. Epub 2015 Aug 19. Review. PMID: 26298065. PMC4548828.

Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol. 2015 Mar;16(3):144-54. doi:10.1038/nrm3949. Epub 2015 Feb 4. Review. PMID: 25650801. PMC4517609.


2014

Gosselin D, Link VM, Romanoski CE, Fonseca GJ, Eichenfield DZ, Spann NJ, Stender JD, Chun HB, Garner H, Geissmann F, Glass CK. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell. 2014 Dec 4;159(6):1327-40. PMID:25480297.

Allison KA, Kaikkonen MU, Gaasterland T, Glass CK. Vespucci: a system for building annotated databases of nascent transcripts. Nucleic Acids Res. Feb 2014; 42(4): 2433–2447. PMC3936758.

Crotti A, Benner C, Kerman BE, Gosselin D, Lagier-Tourenne C, Zuccato C, Cattaneo E, Gage FH, Cleveland DW, Glass CK. Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors. Nat Neurosci. 2014 Apr;17(4):513-21. PMID:24584051.


2013

Shibata N, Carlin AF, Spann NJ, Saijo K, Morello CS, McDonald JG, Romanoski CE, Maurya MR, Kaikkonen MU, Lam MT, Crotti A, Reichart D, Fox JN, Quehenberger O, Raetz CR, Sullards MC, Murphy RC, Merrill AH Jr, Brown HA, Dennis EA, Fahy E, Subramaniam S, Cavener DR, Spector DH, Russell DW, Glass CK. 25-Hydroxycholesterol activates the integrated stress response to reprogram transcription and translation in macrophages. J Biol Chem. 2013 Dec 13;288(50):35812-23. PMID: 24189069. PMC3861632.

Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK. Effect of natural genetic variation on enhancer selection and function. Nature. 2013 Nov 28;503(7477):487-92. PMID: 24121437. PMC3994126.

Li P, Spann NJ, Kaikkonen MU, Lu M, Oh da Y, Fox JN, Bandyopadhyay G, Talukdar S, Xu J, Lagakos WS, Patsouris D, Armando A, Quehenberger O, Dennis EA, Watkins SM, Auwerx J, Glass CK, Olefsky JM. NCoR repression of LXRs restricts macrophage biosynthesis of insulin-sensitizing omega 3 fatty acids. Cell. 2013 Sep 26;155(1):200-14. PMID: 24074869.

Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell. 2013 Aug 8;51(3):310-25. PMID:23932714. PMCID: PMC3779836.

Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, Lee CY, Watt A, Grossman TR, Rosenfeld MG, Evans RM, Glass CK. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature. 2013 Jun 2. PMID: 2372830.

Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim HS, Glass CK, Rosenfeld MG. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature. 2013 Jun 2. PMID: 23728302.


2012

Lin YC, Benner C, Mansson R, Heinz S, Miyazaki K, Miyazaki M, Chandra V, Bossen C, Glass CK, Murre C. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol. 2012 Dec;13(12):1196-204. PMID:2306443.

Spann NJ, Garmire LX, McDonald JG, Myers DS, Milne SB, Shibata N, Reichart D, Fox JN, Shaked I, Heudobler D, Raetz CRH, Wang EW, Kelly SL, Sullards MC, Murphy RC, Merrill AH, Brown HA, Dennis EA, Li AC, Ley K, Tsimikas S, Fahy E, Subramaniam S, Quehenberger O, Russell DW, Glass CK. Regulated accumulation of desmosterol integrates macrophage lipid metabolism and inflammatory responses. Cell. 2012 Sep 28;151(1):138-52. PMID: 23021221. PMC3464912.

Stender JD, Pascual G, Liu W, Kaikkonen MU, Do K, Spann NJ, Boutros M, Perrimon N, Rosenfeld MG, Glass CK. Control of Proinflammatory Gene Programs by Regulated Trimethylation and Demethylation of Histone H4K20. Mol Cell. 2012 Aug 21. PMID: 22921934.


2011

Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet. 2011 Dec;7(12):e1002401. Epub 2011 Dec 8. PMID: 22174696.

Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature. 2011 May 15;474(7351):390-4. doi: 10.1038/nature10006. PMID: 21572438.

Saijo K, Collier JG, Li AC, Katzenellenbogen JA, Glass CK. An ADIOL-ERβ-CtBP transrepression pathway negatively regulates microglia-mediated inflammation. Cell. 2011 May 13;145(4):584-95. PMID: 21565615.

Huang W, Ghisletti S, Saijo K, Gandhi M, Aouadi M, Tesz GJ, Zhang DX, Yao J, Czech MP, Goode BL, Rosenfeld MG, Glass CK. Coronin 2A mediates actin-dependent de-repression of inflammatory response genes. Nature. 2011 Feb 17;470(7334):414-8. PMID: 21331046.


2010

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010 May 28;38(4):576-89. PMID: 20513432. PMC2898526.

© 2021 Christopher Glass Laboratory
Issues with this site?  Contact Leslie Van Ael

University of California, San Diego School of Medicine
University of California, San Diego