Kottyan Lab

Publications

Namjou, B; Lape, M; Malolepsza, E; DeVore, SB; Weirauch, MT; Dikilitas, O; Jarvik, GP; Kiryluk, K; Kullo, IJ; Liu, C; Biagini, JM; Khurana Hershey, GK; Martin, LJ; Kottyan, L. Multiancestral polygenic risk score for pediatric asthma. Journal of Allergy and Clinical Immunology. 2022; 150:1086-1096.

Eapen, AA; Parameswaran, S; Forney, C; Edsall, LE; Miller, D; Donmez, O; Dunn, K; Lu, X; Granitto, M; Rowden, H; Devonshire, AL; Rothenberg, ME; Weirauch, MT; Kottyan, LC. Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis. Editor, Absher DM. PLoS Genetics. 2022; 18:e1009973.

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; de Boer, CG; Harley, JB; Weirauch, MT; Kottyan, LC. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12:1611.

Hong, T; Parameswaran, S; Donmez, OA; Miller, D; Forney, C; Lape, M; Ribeiro, MS J; Liang, J; Edsall, LE; Magnusen, AF; Harley, JB; Zhao, B; Kottyan, LC; Weirauch, MT. Epstein-Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci. Genome research. 2021; 31:2185-2198.

Hass, MR; Brissette, D; Parameswaran, S; Pujato, M; Donmez, O; Kottyan, LC; Weirauch, MT; Kopan, R. Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets. Editor, Greally JM. PLoS Genetics. 2021; 17:e1009574.

Kottyan, LC; Trimarchi, MP; Lu, X; Caldwell, JM; Maddox, A; Parameswaran, S; Lape, M; D'Mello, RJ; Bonfield, M; Ballaban, A; Eapen, AA; Wen, T; Weirauch, MT; Rothenberg, ME. Replication and meta-analyses nominate numerous eosinophilic esophagitis risk genes. Journal of Allergy and Clinical Immunology. 2021; 147:255-266.

Harley, JB; Chen, X; Pujato, M; Miller, D; Maddox, A; Forney, C; Magnusen, AF; Lynch, A; Chetal, K; Yukawa, M; Barski, A; Salomonis, N; Kaufman, KM; Kottyan, LC; Weirauch, MT. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. 2018; 50:699-707.

Zhang, G; Feenstra, B; Bacelis, J; Liu, X; Muglia, LM; Juodakis, J; Miller, DE; Litterman, N; Jiang, P; Russell, L; Smith, GD; Melbye, M; Jacobsson, B; Muglia, LJ. Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. The New England journal of medicine. 2017; 377:1156-1167.

Langefeld, CD; Ainsworth, HC; Graham, DS C; Kelly, JA; Comeau, ME; Marion, MC; Howard, TD; Ramos, PS; Croker, JA; Morris, DL; Wakeland, EK; Graham, RR; Gaffney, PM; Vyse, TJ. Transancestral mapping and genetic load in systemic lupus erythematosus. Nature Communications. 2017; 8:16021.

Kottyan, LC; Davis, BP; Sherrill, JD; Liu, K; Rochman, M; Kaufman, K; Weirauch, MT; Vaughn, S; Lazaro, S; Rupert, AM; Abonia, JP; Martin, LJ; Harley, JB; Rothenberg, ME. Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease. Nature Genetics. 2014; 46:895-900.

Lewis, AC F; Chisholm, RL; Connolly, JJ; Esplin, ED; Glessner, J; Gordon, A; Green, RC; Hakonarson, H; Harr, M; Holm, IA; Sterling, R; Terek, S; Wei, WQ; Fullerton, SM. Managing differential performance of polygenic risk scores across groups: Real-world experience of the eMERGE Network. The American Journal of Human Genetics. 2024; 111:S0002-9297(24)00120-4.

Dourson, AJ; Fadaka, AO; Warshak, AM; Paranjpe, A; Weinhaus, B; Queme, LF; Hofmann, MC; Evans, HM; Donmez, OA; Forney, C; Weirauch, MT; Kottyan, LC; Lucas, D; Deepe, GS; Jankowski, MP. Macrophage memories of early-life injury drive neonatal nociceptive priming. Cell Reports. 2024; 43:114129.

Virolainen, SJ; Satish, L; Biagini, JM; Chaib, H; Chang, WC; Dexheimer, PJ; Dixon, MR; Dunn, K; Fletcher, D; Forney, C; Shook, M; Weirauch, MT; Khurana Hershey, GK; Kottyan, LC. Filaggrin loss-of-function variants are associated with atopic dermatitis phenotypes in a diverse, early-life prospective cohort. JCI insight. 2024; 9:e178258.

Shook, MS; Lu, X; Chen, X; Parameswaran, S; Edsall, L; Trimarchi, MP; Ernst, K; Granitto, M; Forney, C; Donmez, OA; Diouf, AA; VonHandorf, A; Rothenberg, ME; Weirauch, MT; Kottyan, LC. Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis. The American Journal of Human Genetics. 2024; 111:280-294.

Dai, D; Gu, S; Han, X; Ding, H; Jiang, Y; Zhang, X; Yao, C; Hong, S; Zhang, J; Shen, Y; Kottyan, LC; Weirauch, MT; Vinuesa, CG; Shen, N. The transcription factor ZEB2 drives the formation of age-associated B cells. Science. 2024; 383:413-421.

Dourson, AJ; Fadaka, AO; Warshak, AM; Paranjpe, A; Weinhaus, B; Queme, LF; Hofmann, MC; Evans, HM; Donmez, OA; Forney, C; Weirauch, MT; Kottyan, LT; Lucas, D; Deepe, GS; Jankowski, MP. Macrophage epigenetic memories of early life injury drive neonatal nociceptive priming. 2023; 4:2023.02.13.528015.

Wang, C; Liu, X; Liang, J; Narita, Y; Ding, W; Li, D; Zhang, L; Wang, H; Leong, MM L; Hou, I; Zeng, MS; Jiang, S; Teng, M; Zhao, B. A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth. Nature Communications. 2023; 14:1598.

Wang, L; Rossi, RM; Chen, X; Chen, J; Runyon, J; Chawla, M; Miller, D; Forney, C; Lynch, A; Zhang, X; Kottyan, LC; Weirauch, MT; Zhang, G; Muglia, LJ. A functional mechanism for a non-coding variant near AGTR2 associated with risk for preterm birth. BMC Medicine. 2023; 21:258.

Chehade, M; Wright, BL; Atkins, D; Aceves, SS; Ackerman, SJ; Assa'ad, AH; Bauer, M; Collins, MH; Commins, SP; Davis, CM; Wechsler, J; Zimmermann, N; Furuta, GT; Rothenberg, ME. Breakthroughs in understanding and treating eosinophilic gastrointestinal diseases presented at the CEGIR/TIGERs Symposium at the 2022 American Academy of Allergy, Asthma & Immunology Meeting. Journal of Allergy and Clinical Immunology. 2023; 152:1382-1393.

Haas, KM; McGregor, MJ; Bouhaddou, M; Polacco, BJ; Kim, EY; Nguyen, TT; Newton, BW; Urbanowski, M; Kim, H; Williams, MA P; Hultquist, JF; Kaake, RM; García-Sastre, A; Krogan, NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nature Communications. 2023; 14:6030.

Meibers, HE; Warrick, KA; VonHandorf, A; Vallez, CN; Kawarizadeh, K; Saha, I; Donmez, O; Jain, VG; Kottyan, LC; Weirauch, MT; Pasare, C. Effector memory T cells induce innate inflammation by triggering DNA damage and a non-canonical STING pathway in dendritic cells. Cell Reports. 2023; 42:113180.

Kiryluk, K; Sanchez-Rodriguez, E; Zhou, XJ; Zanoni, F; Liu, L; Mladkova, N; Khan, A; Marasa, M; Zhang, JY; Balderes, O; Savoldi, S; Spotti, D; Zamboli, P; Izzi, C. Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy. Nature Genetics. 2023; 55:1091-1105.

Song, J; Forrest, N; Gordon, A; Kottyan, L; Mittendorf, KF; Wei, WQ; Ramsey-Goldman, R; Walunas, T; Kho, A. Utilization of electronic health record data to evaluate the association of urban environment with systemic lupus erythematosus symptoms. Rheumatology. 2023; 62:e180-e181.

Gautam, Y; Caldwell, J; Kottyan, L; Chehade, M; Dellon, ES; Rothenberg, ME; Mersha, TB; Wechsler, J; Davis, C; Furuta, G; Falk, G; Hirano, I; Gonsalves, NP; Peterson, K. Genome-wide admixture and association analysis identifies African ancestry-specific risk loci of eosinophilic esophagitis in African Americans. Journal of Allergy and Clinical Immunology. 2023; 151:1337-1350.

Wayman, JA; Thomas, A; Bejjani, A; Katko, A; Almanan, M; Godarova, A; Korinfskaya, S; Cazares, TA; Yukawa, M; Kottyan, LC; Barski, A; Chougnet, CA; Hildeman, DA; Miraldi, ER. An atlas of gene regulatory networks for memory CD4 + T cells in youth and old age. 2023; 4:2023.03.07.531590.

Linder, JE; Allworth, A; Bland, HT; Caraballo, PJ; Chisholm, RL; Clayton, EW; Crosslin, DR; Dikilitas, O; DiVietro, A; Esplin, ED; Thayer, J; Tiwari, HK; Trinidad, SB; Walunas, T. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genetics in Medicine. 2023; 25:100006.

Xiao, B; Edwards, DR V; Lucas, A; Drivas, T; Gray, K; Keating, B; Weng, C; Jarvik, GP; Hakonarson, H; Kottyan, L; Luo, Y; Kim, D; Ritchie, M; Verma, SS. Inference of Causal Relationships Between Genetic Risk Factors for Cardiometabolic Phenotypes and Female-Specific Health Conditions. Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease. 2023; 12:e026561.

Gill, K; Moore, C; Nwogu, O; Kroner, JW; Chang, W; Stevens, ML; Kyzy, AB; Biagini, JM; Devonshire, AL; Kottyan, L; Martin, LJ; Andorf, S; Hershey, GK K; Roskin, KM. B cell repertoire in children with skin barrier dysfunction supports altered IgE maturation associated with allergic food sensitization. 2023; 4:2023.02.01.526538.

Virolainen, SJ; VonHandorf, A; Viel, KC M F; Weirauch, MT; Kottyan, LC. Gene-environment interactions and their impact on human health. Genes and Immunity. 2023; 24:1-11.

Cazares, TA; Rizvi, FW; Iyer, B; Chen, X; Kotliar, M; Bejjani, AT; Wayman, JA; Donmez, O; Wronowski, B; Parameswaran, S; Kottyan, LC; Barski, A; Weirauch, MT; Surya Prasath, VB; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. Editor, Przytycka TM. PLoS Computational Biology. 2023; 19:e1010863.

Hui, D; Xiao, B; Dikilitas, O; Freimuth, RR; Irvin, MR; Jarvik, GP; Kottyan, L; Kullo, I; Limdi, NA; Liu, C; Wei, WQ; Verma, S; Kim, D; Ritchie, MD. Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2023; 28:437-448.

Levin, MG; Tsao, NL; Singhal, P; Liu, C; Vy, HM T; Paranjpe, I; Backman, JD; Bellomo, TR; Bone, WP; Biddinger, KJ; Joseph, J; Sun, YV; Voight, BF; Damrauer, SM. Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure. Nature Communications. 2022; 13:6914.

Zhou, T; Zhu, X; Ye, Z; Wang, YF; Yao, C; Xu, N; Zhou, M; Ma, J; Qin, Y; Shen, Y; Kottyan, LC; Weirauch, MT; Hou, G; Shen, N. Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery. Nature Communications. 2022; 13:1855.

Liu, L; Khan, A; Sanchez-Rodriguez, E; Zanoni, F; Li, Y; Steers, N; Balderes, O; Zhang, J; Krithivasan, P; LeDesma, RA; Ionita-Laza, I; Novak, J; Gharavi, AG; Kiryluk, K. Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits. Nature Communications. 2022; 13:6859.

Ge, T; Irvin, MR; Patki, A; Srinivasasainagendra, V; Lin, YF; Tiwari, HK; Armstrong, ND; Benoit, B; Chen, CY; Choi, KW; Lebo, MS; Meigs, JB; Limdi, NA; Karlson, EW. Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations. Genome Medicine: medicine in the post-genomic era. 2022; 14:70.

Namjou, B; Lape, M; Malolepsza, E; DeVore, SB; Weirauch, MT; Dikilitas, O; Jarvik, GP; Kiryluk, K; Kullo, IJ; Liu, C; Biagini, JM; Khurana Hershey, GK; Martin, LJ; Kottyan, L. Multiancestral polygenic risk score for pediatric asthma. Journal of Allergy and Clinical Immunology. 2022; 150:1086-1096.

Sawyer, RP; Stone, HK; Salim, H; Lu, X; Weirauch, MT; Kottyan, L. Frontotemporal degeneration genetic risk loci and transcription regulation as a possible mechanistic link to disease risk. Medicine; analytical reviews of general medicine, neurology, psychiatry, dermatology, and pediatries. 2022; 101:e31078.

Eapen, AA; Parameswaran, S; Forney, C; Edsall, LE; Miller, D; Donmez, O; Dunn, K; Lu, X; Granitto, M; Rowden, H; Devonshire, AL; Rothenberg, ME; Weirauch, MT; Kottyan, LC. Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis. Editor, Absher DM. PLoS Genetics. 2022; 18:e1009973.

Kim, E; Forney, C; Viel, K; O'Brien, M; Nelson, C; Gecaine, P; Zabeti, A; Weirauch, M; Kottyan, L. Enrichment of Epstein Barr Virus in patients with Multiple Sclerosis. Journal of immunology (Baltimore, Md. : 1950). 2022; 208:104.09.

Bray, D; Hook, H; Zhao, R; Keenan, JL; Penvose, A; Osayame, Y; Mohaghegh, N; Chen, X; Parameswaran, S; Kottyan, LC; Weirauch, MT; Siggers, T. CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants. Cell Genomics. 2022; 2:100098.

Hou, G; Harley, IT W; Lu, X; Zhou, T; Xu, N; Yao, C; Qin, Y; Ouyang, Y; Ma, J; Zhu, X; Weirauch, MT; Kottyan, LC; Harley, JB; Shen, N. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. Nature Communications. 2021; 12:135.

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; de Boer, CG; Harley, JB; Weirauch, MT; Kottyan, LC. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12:1611.

Leader, BA; Koritala, BS C; Moore, CA; Grigg Dean, EH; Kottyan, LC; Smith, DF. Epigenetics of obstructive sleep apnea syndrome: a systematic review. The Journal of Clinical Sleep Medicine. 2021; 17:2533-2541.

Shoda, T; Kaufman, KM; Wen, T; Caldwell, JM; Osswald, GA; Purnima, P; Zimmermann, N; Collins, MH; Rehn, K; Foote, H; Mukkada, VA; Putnam, PE; Martin, LJ; Rothenberg, ME. Desmoplakin and periplakin genetically and functionally contribute to eosinophilic esophagitis. Nature Communications. 2021; 12:6795.

Hong, T; Parameswaran, S; Donmez, OA; Miller, D; Forney, C; Lape, M; Ribeiro, MS J; Liang, J; Edsall, LE; Magnusen, AF; Harley, JB; Zhao, B; Kottyan, LC; Weirauch, MT. Epstein-Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci. Genome research. 2021; 31:2185-2198.

Kiryluk, K; Sanchez-Rodriguez, E; Zhou, X; Zanoni, F; Liu, L; Mladkova, N; Khan, A; Marasa, M; Zhang, J; Balderes, O; Novak, J; Scolari, F; Zhang, H; Gharavi, A. GWAS defines pathogenic signaling pathways and prioritizes drug targets for IgA nephropathy. 2021; 2021.11.19.21265383.

Devonshire, AL; Fan, H; Pujato, M; Paranjpe, A; Gursel, D; Schipma, M; Dunn, JM; Andorf, S; Pongracic, JA; Kottyan, LC; Kumar, R. Whole blood transcriptomics identifies gene expression associated with peanut allergy in infants at high risk. Clinical and Experimental Allergy. 2021; 51:1396-1400.

Khan, A; Shang, N; Petukhova, L; Zhang, J; Shen, Y; Hebbring, SJ; Moncrieffe, H; Kottyan, LC; Namjou-Khales, B; Knevel, R; Gharavi, AG; Hripcsak, G; Weng, C; Kiryluk, K. Medical Records-Based Genetic Studies of the Complement System. Journal of the American Society of Nephrology : JASN. 2021; 32:2031-2047.

Zhou, T; Zhu, X; Ye, Z; Wang, Y; Yao, C; Xu, N; Zhou, M; Ma, J; Qin, Y; Shen, Y; Kottyan, L; Weirauch, M; Hou, G; Shen, N. CRISPRa screen on a genetic risk locus shared by multiple autoimmune diseases identifies a dysfunctional enhancer that affects IRF8 expression through cooperative lncRNA and DNA methylation machinery. 2021; 2021.06.11.448156.

Hass, MR; Brissette, D; Parameswaran, S; Pujato, M; Donmez, O; Kottyan, LC; Weirauch, MT; Kopan, R. Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets. Editor, Greally JM. PLoS Genetics. 2021; 17:e1009574.

Yin, X; Kim, K; Suetsugu, H; Bang, SY; Wen, L; Koido, M; Ha, E; Liu, L; Sakamoto, Y; Jo, S; Zhang, X; Terao, C; Cui, Y; Bae, SC. Meta-analysis of 208370 East Asians identifies 113 susceptibility loci for systemic lupus erythematosus. Annals of the Rheumatic Diseases. 2021; 80:632-640.

Song, R; Gao, Y; Dozmorov, I; Malladi, V; Saha, I; McDaniel, MM; Parameswaran, S; Liang, C; Arana, C; Zhang, B; Weirauch, MT; Kottyan, LC; Wakeland, EK; Pasare, C. IRF1 governs the differential interferon-stimulated gene responses in human monocytes and macrophages by regulating chromatin accessibility. Cell Reports. 2021; 34:108891.

Lyles, JL; Martin, LJ; Shoda, T; Collins, MH; Trimarchi, MP; He, H; Kottyan, LC; Mukkada, VA; Rothenberg, ME. Very early onset eosinophilic esophagitis is common, responds to standard therapy, and demonstrates enrichment for CAPN14 genetic variants. Journal of Allergy and Clinical Immunology. 2021; 147:244-254.e6.

Stone, HK; Parameswaran, S; Eapen, AA; Chen, X; Harley, JB; Devarajan, P; Weirauch, MT; Kottyan, L. Comprehensive Review of Steroid-Sensitive Nephrotic Syndrome Genetic Risk Loci and Transcriptional Regulation as a Possible Mechanistic Link to Disease Risk. Kidney International Reports. 2021; 6:187-195.

Kottyan, LC; Trimarchi, MP; Lu, X; Caldwell, JM; Maddox, A; Parameswaran, S; Lape, M; D'Mello, RJ; Bonfield, M; Ballaban, A; Eapen, AA; Wen, T; Weirauch, MT; Rothenberg, ME. Replication and meta-analyses nominate numerous eosinophilic esophagitis risk genes. Journal of Allergy and Clinical Immunology. 2021; 147:255-266.

Rajaram, S; Canaday, LM; Ochayon, DE; Rangel, KM; Ali, A; Gyurova, IE; Krishnamurthy, D; Fletcher, JS; Reighard, SD; Cox, A; Deshmukh, H; Zacharias, WJ; Borchers, MT; Waggoner, SN. The Promise and Peril of Natural Killer Cell Therapies in Pulmonary Infection. Immunity. 2020; 52:887-889.

Moncrieffe, H; Dunn, K; Huang, Y; Chen, X; Langefeld, CD; Weirauch, MT; Harley, JB; Kottyan, LC; Thompson, SD. 4277 Functional consequences of the juvenile idiopathic arthritis risk variant at 1q24.3. Journal of Clinical and Translational Science. 2020; 4:95-96.

McDaniel, MM; Kottyan, LC; Singh, H; Pasare, C. Suppression of Inflammasome Activation by IRF8 and IRF4 in cDCs Is Critical for T Cell Priming. Cell Reports. 2020; 31:107604.

Laurynenka, V; Ho, D; Huang, Y; Parameswaran, S; Kottyan, LC; Weirauch, MT; Perentesis, J; Kaufman, KM; Mizukawa, B; Harley, JB. The Ikaros1, IKZF1 , risk locus for Acute Lymphoblastic Leukemia (ALL) at chromosome 7p12.2 regulates the expression of the FIGNL1 gene. Journal of immunology (Baltimore, Md. : 1950). 2020; 204:163.15.

Laurynenka, V; Chen, X; Carter, M; Parameswaran, S; Eswar, S; Kaufman, KM; Namjou, B; Weirauch, MT; Kottyan, LC; Harley, JB. Latency III gene products of Epstein-Barr Virus (EBV) are associated with Systemic Lupus Erythematosus (SLE) genetic risk loci. Journal of immunology (Baltimore, Md. : 1950). 2020; 204:141.2.

Reighard, SD; Cranert, SA; Rangel, KM; Ali, A; Gyurova, IE; de la Cruz-Lynch, AT; Tuazon, JA; Khodoun, MV; Kottyan, LC; Smith, DF; Brunner, HI; Waggoner, SN. Therapeutic Targeting of Follicular T Cells with Chimeric Antigen Receptor-Expressing Natural Killer Cells. Cell Reports Medicine. 2020; 1:100003.

Ochayon, DE; Ali, A; Alarcon, PC; Krishnamurthy, D; Kottyan, LC; Borchers, MT; Waggoner, SN. IL-33 promotes type 1 cytokine expression via p38 MAPK in human NK cells. Journal of Leukocyte Biology. 2020; 107:663-671.

Javier, E; Lu, X; Kottyan, LC. Noncoding Variants as Genetic Contributors to Autoimmune Disease Pathogenesis. Journal of Investigative Dermatology. 2020; 140:277-278.

Kottyan, LC; Parameswaran, S; Weirauch, MT; Rothenberg, ME; Martin, LJ. The genetic etiology of eosinophilic esophagitis. Journal of Allergy and Clinical Immunology. 2020; 145:9-15.