Immunogenomics Lab

Selected Publications

S Perotti , E Spierings, P Humburg, M Yabas, H Bergmann, K Horikawa, C Roots, S Lambe, C Young, TD Andrews, M Field, E Enders, JH Reed, CC GoodnowIgD attenuates the IgM-induced anergy response in transitional and mature B cells.  November 2016 Nature Communications.

Reed J, Jackson J, Christ D and Goodnow C. Clonal Redemption of autoantibodies by somatic hypermutation away from self-reactivity during immunization. June 2016 J Exp Med; 213(7)

Goodnow CC & Ohashi PS (2013) Immunological Tolerance. In Fundamental Immunology 7th Edition. Editor Paul WE, Chapter 32, pp 765-794, NLM 101591462.

Wang JQ, Beutler B, Goodnow CC* & Horikawa K*. 2016. Inhibiting TLR9 and other UNC93B1-dependent TLRs paradoxically increases accumulation of MYD88L265P plasmablasts in vivoBlood (in press). *Equal senior and corresponding authors.

Reed JH, Jackson J, Christ D, Goodnow CC. 2016. Clonal redemption of autoantibodies by somatic hypermutation away from self-reactivity during human immunization. J Exp Med. 213:1255-65.

Andrews TD, Jeelall Y, Talaulikar D, Goodnow CC, Field MA. 2016. DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations. PeerJ. 4:e2074.

Hillhouse EE, Liston A, Collin R, Desautels E, Goodnow CC, Lesage S. 2016. TCR transgenic mice reveal the impact of type 1 diabetes loci on early and late disease checkpoints. Immunol Cell Biol. Apr 5. doi: 10.1038/icb.2016.27. 

Dooley J, Tian L, Schonefeldt S, Delghingaro-Augusto V, Garcia-Perez JE, Pasciuto E, Di Marino D, Carr EJ, Oskolkov N, Lyssenko V, Franckaert D, Lagou V, Overbergh L, Vandenbussche J, Allemeersch J, Chabot-Roy G, Dahlstrom JE, Laybutt DR, Petrovsky N, Socha L, Gevaert K, Jetten AM, Lambrechts D, Linterman MA, Goodnow CC, Nolan CJ, Lesage S, Schlenner SM, Liston A. 2016. Genetic predisposition for beta cell fragility underlies type 1 and type 2 diabetes. Nature Genetics 48:519-27.

Field MA, Cho V, Andrews TD, Goodnow CC. 2015. Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies. PLoS One. 10:e0143199.

Field MA, Andrews TD, Cho V, Cook MC, Enders A, Vinuesa C & Goodnow CC. 2015. Reducing the search space for causal genetic variants with VASP: Variant Analysis of Sequenced Pedigrees. Bioinformatics 31(14):2377-9.

Miosge L, Field MA, Sontani Y, Cho E, Johnson S, Palkova A, Balakishnan B, Liang R, Zhang Y, Lyon S, Beutler B, Whittle B, Betram E, Enders A, Goodnow CC* & Andrews TD* 2015. Comparison of predicted and actual consequences of missense mutations. Proc Natl Acad Sci USA 112:E5189-98. *Equal senior and corresponding authors.

Hu DY, Yap JY, Wirasinha RC, Howard DR, Goodnow CC, Daley SR. 2015. A timeline demarcating two waves of clonal deletion and Foxp3 up-regulation during thymocyte development. Immunol Cell Biol. 94(4):357-66.

Ramiscal RR, Parish IA, Lee-Young RS, Babon JJ, Blagih J, Pratama A, Martin J, Hawley N, Cappello JY, Nieto PF, Ellyard J, Kershaw NJ, Sweet RA, Goodnow CC, Jones RG, Febbraio MA, Vinuesa C, Athanasopoulos V. 2015. Attenuation of AMPK signaling by ROQUIN promotes T follicular helper cell formation. Elife. Oct 23;4. pii: e08698.

Wertz IE, Newton K, Kusam S, Seshasayee D, Lam C, Zhang J, Popovych N, Helgason E, Schoeffler A, Jeet S, Ramamoorthi N, Kategaya L, Newman RJ, Horikawa K, Dugger D, Sandoval W, Mukund S, Zindal A, Martin F, Quan C, Tom J, Fairbrother WJ, Townsend M, Warming S, DeVoss J, Dueber E, Caplazi P, Lee WP, Goodnow CC, Balazs M, Yu K, Kolumam G and Dixit VM. 2015. Phosphorylation and linear ubiquitination regulate A20 inhibition of inflammatory signaling. Nature 528:370-375.

Kayagaki N, Stowe IB, Lee BL, O’Rourke K, Anderson K, Warming S, Cuellar T, Haley B, Roose-Girma M, Phung QT, Liu PS, Lill JR, Li H, Wu J, Kummerfeld S, Zhang J, Lee WP, Snipas SJ, Salvesen GS, Morris LX, Fitzgerald L, Zhang Y, Bertram EM, Goodnow CC & Dixit VM. 2015. Gasdermin-D mediates LPS-induced non-canonical inflammasome signaling downstream of caspase-11. Nature (Article) 526:666-671.

Tangye SG, Brink R, Goodnow CC, Phan TG. 2015. SnapShot: Interactions between B Cells and T Cells. Cell 162:926-926.e1.

Han B, Wu S, Foo C-S, Horton R, Jenne C, Watson S, Whittle B, Goodnow CC & Cyster JG. 2014. Zinc finger protein Zfp335 is required for formation of the naïve T cell compartment. eLIFE Oct 24;3. doi: 10.7554/eLife.03549.

Lee CE, Fulcher DA, Whittle B, Chand R, Fewings N, Field M, Andrews D, Goodnow CC, Cook MC. 2014. Autosomal dominant B cell deficiency with alopecia due to a mutation in NFKB2 that results in non-processible p100. Blood Sep 18. pii: blood-2014-06-578542.

Ellyard JI, Jerjen R, Martin JL, Lee A, Field MA, Jiang SH, Cappello J, Naumann SK, Andrews TD, Scott HS, Casarotto MG, Goodnow CC, Chaitow J, Pascual V, Hertzog P, Alexander SI, Cook MC, Vinuesa CG. 2014. Whole exome sequencing in early-onset cerebral SLE identifies a pathogenic variant in TREX1. Arthritis Rheumatol. Aug 19. doi: 10.1002/art.38824.

Sabouri Z, Schofield P, Horikawa K, Spierings E, Kipling D, Randall KL, Langley D, Roome B, Vazquez-Lombardi R, Rouet R, Hermes JR, Chan TD, Brink R, Dunn-Walters D, Christ D* and Goodnow CC*. 2014. Redemption of autoantibodies on anergic B cells by V-region glycosylation and mutation away from self-reactivity. Proc Natl Acad Sci USA 111:E2567-75. *Equal senior and corresponding authors. Accompanied by expert commentary: Haynes BF, Verkoczy L, Kelsoe G. “Redemption of autoreactive B cells” Proc Natl Acad Sci U S A 111(25):9022-3.

Enders A*, Short A, Miosge LA, Bergmann H, Sontani Y, Bertram EM, Whittle B, Balakishnan B, Yoshida K, Sjollema G, Field MA, Andrews TD, Hagiwara H & Goodnow CC*. 2014. Zinc-finger protein ZFP318 is essential for expression of IgD, the alternatively spliced Igh product made by mature B lymphocytes. Proc Natl Acad Sci USA 111:4513-4518. *Equal senior and corresponding authors.

Cho V, Mei Y, Sanny A, Chan S, Enders A, Bertram EM, Tan A, Goodnow CC* & Andrews TD*. 2014. The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA. Genome Biology 15(1):R26. *Equal senior and corresponding authors. Featured as “Editor’s pick”.

Wang JQ, Jeelall YS, Beutler B, Horikawa K* & Goodnow CC*. 2014. Consequences of the recurrent MYD88L265P somatic mutation for B cell tolerance. J Exp Med 211:413-426. * Equal senior and corresponding authors.

Altin JA, Daley SR, Howitt J, Rickards HJ, Batkin AK, Horikawa K, Prasad SJ, Nelms KA, Kumar S, Wu LC, Tan S-S, Cook MC* & Goodnow CC*. 2014. Ndfip1 mediates peripheral tolerance to self and exogenous antigen by inducing cell cycle exit in responding CD4+ T cells. Proc Natl Acad Sci USA 111:2067-2074. * Equal senior and corresponding authors.

Daley SR, Coakley KM, Hu D, Randall KL, Jenne CN, Limnander A Myers DR, Polakos NK, Enders A, Roots C, Balakishnan B, Miosge LA, Sjollema S, Bertram EM, Field MA, Shao Y, Andrews TD, Whittle B, Barnes SW, Walker JR, Cyster JG, Goodnow CC* & Roose JP*. 2013. Rasgrp1 mutation increases naïve T-cell CD44 expression and drives mTOR-dependent accumulation of Helios+ T cells and autoantibodies.  eLIFE 2:e01020.  * Equal senior and corresponding authors.

Pratama A, Ramiscal RR, Silva DG, Das SK, Athanasopoulos V, Fitch J, Botelho NK, Chang PP, Hu X, Hogan JJ, Maña P, Bernal D, Korner H, Yu D, Goodnow CC, Cook MC, Vinuesa CG. 2013. Roquin-2 shares functions with its paralog Roquin-1 in the repression of mRNAs controlling T follicular helper cells and systemic inflammation. Immunity 38:669-80.

Teh CE, Horikawa K, Arnold CN, Beutler B, Kucharska EM, Vinuesa CG, Bertram EM, Goodnow CC*, Enders A*. 2013. Heterozygous mis-sense mutations in Prkcb as a critical determinant of anti-polysaccharide antibody formation. Genes Immun. 14:223-33. *Equal senior authors.

Bull KR, Rimmer AJ, Siggs OM, Miosge LA, Roots CM, Enders A, Bertram EM, Crockford TL, Whittle B, Potter PK, Simon MM, Mallon A-M, Brown SDM, Beutler B, Goodnow CC, Lunter G & Cornall RJ. 2012. Unlocking the Bottleneck in Forward Genetics Using Whole Genome Sequencing and Identity by Descent to Isolate Causative Mutations. Plos Genetics 9(1):e1003219.

Daley SR, Hu DY & Goodnow CC. 2013. Helios marks strongly self-reactive CD4+ cells in two major waves of thymic deletion distinguished by induction of PD-1 or NF-κB. J Exp Med 210:269-85.

Bergmann H, Yabas M, Short A, Miosge L,, Barthel N, Teh C, Roots CM, Bull K, Jeelall Y, Horikawa K, Whittle B, Balakishnan B, Sjollema G, Bertram EM, Mackay F, Rimmer A, Cornall R, Field MA, Andrews TD, Goodnow CC* & Enders A*. 2013. B-cell survival, surface BCR and BAFF-R expression, CD74 metabolism and CD8- DCs require the intramembrane endopeptidase SPPL2A. J Exp Med 210:31-40. *Equal senior authors.

Jeelall YS, Wang JQ, Law HD, Domaschenz H, Fung HK, Kallies A, Nutt SL, Goodnow CC*, Horikawa K*. 2012. Human lymphoma mutations reveal CARD11 as the switch between self-antigen-induced B cell death or proliferation and autoantibody production. J Exp Med. 209:1907-17. *Equal senior authors.

Andrews TD, Whittle B, Field MA, Balakishnan B, Zhang Y, Shao Y, Cho V, Kirk M, Singh M, Xia Y, Hager J, Winslade S, Sjollema G, Beutler B, Enders A, Goodnow CC. 2012. Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models. Open Biol. 2012 2:120061.

Randall KL, Chan S, Ma CS, Fung I, Mei Y, Yabas M, Tan A, Arkwright PD, Suwairi WA, Reyes S, Yamazaki-Nakashimada MA, Garcia-Cruz M, Smart JM, Picard C, Okada S, Jouanguy E, Casanova J-L, Lambe T, Cornall RJ, Russell S, Oliaro J*, Tangye S*, Bertram E* & Goodnow CC*. 2011. DOCK8 deficiency impairs CD8 T cell survival and function in humans and mice. Journal of Experimental Medicine 208:2305-2320. *Equal senior authors.

Sontani Y, Chapman G, Papathanasiou P, Dunwoodie S, Goodnow CC*, Hoyne GF*. 2011. Cooperation between somatic Ikaros and Notch1 mutations at the inception of T-ALL. Leuk Res. 35:1512-1519. PMID: 21840596. *Equal senior authors.

Anti-islet autoantibodies trigger autoimmune diabetes in the presence of an increased frequency of islet-reactive CD4 T cells. 2011. Silva DG, Daley SR, Hogan J, Lee SK, Teh CE, Hu DY, Lam KP, Goodnow CC*, Vinuesa CG*. Diabetes. 60:2102-11. *Equal senior authors.

Yabas M, Teh CE, Frankenreiter S, Lal D, Roots CM, Whittle B, Andrews DT, Zhang Y, Teoh NC, Sprent J, Tze LE, Kucharska EM, Kofler J, Farell GC, Bröer S, Goodnow CC* & Enders A*. 2011. ATP11C is critical for the internalization of phosphatidylserine and differentiation of B lymphocytes. Nature Immunol. 12:441-449. *equal senior authors. commentaries published: “Flippin’ lipids” Nat Immunol. 2011 May; 12(5):373-5; and “B cells need their flip-flops” Immunol Cell Biol. 2011 Oct; 89(7):751-2.

Altin JA, Tian L, Liston A, Bertram EM, Goodnow CC* & Cook MC*. 2011. Decreased T-cell receptor signaling through CARD11 differentially compromises forkhead box protein 3-positive regulatory versus T(H)2 effector cells to cause allergy. J Allergy Clin Immunol. 127:1277-1285 *equal senior authors.

Tze LE, Horikawa K, Domaschenz H, Howard DR, Roots C, RigbyRJ, Way DA, Ohmura-Hoshino M, Ishido S, Andoniou CE, Degli-Esposti MA & Goodnow CC. 2011. CD83 opposes IL-10-driven MARCH1-mediated ubiquitination and degradation of MHC class II on dendritic cells. J Exp Med 208:149-65.

Teh CE, Daley SR, Enders A, Goodnow CC. 2010. T-cell regulation by casitas B-lineage lymphoma (Cblb) is a critical failsafe against autoimmune disease due to autoimmune regulator (Aire) deficiency. Proc Natl Acad Sci USA 107:14709-14.

Randall KL, Lambe T, Johnson A, Treanor B, Kucharska E, Domaschenz H, Whittle B, Tze LE, Enders A, Crockford TL, Bouriez-Jones T, Alston D, Cyster JG, Lenardo MJ, Mackay F, Deenick EK, Tangye SG, Chan TD, Camidge T, Brink R, Vinuesa CG, Batista FD, Cornall RJ, Goodnow CC. 2009. Dock8 mutations cripple B cell immunological synapses, germinal centers and long-lived antibody production. Nature Immunol. 10:1283-91. Accompanied by expert commentary: “B cell memory: how to start and when to end” N Pelletier1 & MG McHeyzer-Williams, Nature Immunology 10, 1233 – 1235.

Johnson AL, Aravind L, Shulzhenko N, Morgun A, Choi S-Y, Crockford TL, Lambe T, Domaschenz H, Kucharska E, Zheng L, Vinuesa CG, Lenardo MJ, Goodnow CC, Cornall RJ and Schwartz RH. 2009. Themis is a member of a new metazoan gene family required for completion of thymocyte positive selection. Nature Immunology  10:831-839.

Wu Z, Jia X, de la Cruz L, Su X, Marzolf B, Troisch P, Zak D, Hamilton A, Whittle B, Yu D, Sheahan D, Bertram E, Aderem A, Otting G, Goodnow CC* & Hoyne GF. 2008. Memory T cell RNA rearrangement programmed by heterogeneous nuclear ribonucleoprotein hnRNPLL.  Immunity 29:863-875. *corresponding author and equal senior author. (Cover article)

Shiow LR, Roadcap DW, Paris K, Watson SR, Grigorova IL, Lebet T, An J, Xu Y, Jenne CN, Föger N, Sorensen RU, Goodnow CC, Bear JE, Puck JM, Cyster JG. 2008. The actin regulator coronin 1A is mutant in a thymic egress-deficient mouse strain and in a patient with severe combined immunodeficiency. Nature Immunol. 9:1307-15. Accompanied by expert commentary: “Immunodeficiency: when T cells are stuck at home.” Hogquist KA Nature Immunol. 2008 9:1207-8

Liu M, Duke JL, Richter DJ, Vinuesa CG, Goodnow CC, Kleinstein SH, Schatz DG.  2007. Two levels of protection for the B cell genome during somatic hypermutation. Nature 451:841-845

Siggs OM, Miosge LA, Yates AL, Kucharska EM, Sheahan D, Brdicka T, Weiss A, Liston A, Goodnow CC. 2007. Opposing functions of the T cell receptor kinase ZAP-70 in immunity and tolerance differentially titrate in response to nucleotide substitutions. Immunity 27:912-26.

Yu D , Tan A, Hu X, Athanasopoulos V, Hutloff A, Lam KP, Simpson N, Giles KM, Leedman PJ, Goodnow CC* & Vinuesa CG*. 2007 Roquin represses autoimmunity by limiting T cell Inducible CoStimulator mRNA.  Nature 450:299-305. *Equal senior authors.


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