Center for Autoimmune Genomics and Etiology (CAGE)

Publications

Alex Feldman, H; Cevik, H; Waggoner, SN. Negativity begets longevity in T cells. The Journal of Clinical Investigation. 2023; 133:e171027.

Bedard, MC; Chihanga, T; Carlile, A; Jackson, R; Brusadelli, MG; Lee, D; VonHandorf, A; Rochman, M; Dexheimer, PJ; Chalmers, J; Lambert, PF; Adam, M; Steven Potter, S; Wells, SI. Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer. Nature Communications. 2023; 14:1975.

Brusilovsky, M; Rochman, M; Shoda, T; Kotliar, M; Caldwell, JM; Mack, LE; Besse, JA; Chen, X; Weirauch, MT; Barski, A; Rothenberg, ME. Vitamin D receptor and STAT6 interactome governs oesophageal epithelial barrier responses to IL-13 signalling. Gut. 2023; 72:834-845.

Burkes, RM; Bailey, E; Hwalek, T; Osterburg, A; Lach, L; Panos, R; Waggoner, SN; Borchers, MT. Associations of Smoking, Cytomegalovirus Serostatus, and Natural Killer Cell Phenotypes in Smokers With and At Risk for COPD. Chronic obstructive pulmonary diseases (Miami, Fla.). 2023; 10:286-296.

Cain, B; Webb, J; Yuan, Z; Cheung, D; Lim, HW; Kovall, RA; Weirauch, MT; Gebelein, B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Research. 2023; 51:6055-6072.

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.

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.

Cheng, Z; Hou, G; Shen, N. Evolving understandings for the roles of non-coding RNAs in autoimmunity and autoimmune disease. Journal of Autoimmunity. 2023; 137:102948.

Daamen, AR; Wang, H; Bachali, P; Shen, N; Kingsmore, KM; Robl, RD; Grammer, AC; Fu, SM; Lipsky, PE. Molecular mechanisms governing the progression of nephritis in lupus prone mice and human lupus patients. Frontiers in Immunology. 2023; 14:1147526.

Dexheimer, PJ; Pujato, M; Roskin, KM; Weirauch, MT. VExD: a curated resource for human gene expression alterations following viral infection. Editor, McIntyre L. G3-Genes Genomes Genetics. 2023; 13:jkad176.

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.

Elliott, KH; Balchand, SK; Paese, CL B; Chang, CF; Yang, Y; Brown, KM; Rasicci, DT; He, H; Thorner, K; Chaturvedi, P; Murray, SA; Chen, J; Porollo, A; Peterson, KA; Brugmann, SA. Identification of a heterogeneous and dynamic ciliome during embryonic development and cell differentiation. Development (Cambridge). 2023; 150:dev201237.

Fu, H; Zheng, H; Chen, X; Weirauch, MT; Muglia, LJ; Wang, L; Liu, Y. NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome Biology: biology for the post-genomic era. 2023; 24:50.

Gao, X; Luo, K; Wang, D; Wei, Y; Yao, Y; Deng, J; Yang, Y; Zeng, Q; Dong, X; Xiong, L; Liu, Z; Cockburn, IA; Luo, W; Yu, D. T follicular helper 17 (Tfh17) cells are superior for immunological memory maintenance. eLife. 2023; 12:e82217.

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.

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.

Gu, S; Zhang, J; Han, X; Ding, H; Yao, C; Ye, Z; Yin, Z; Hou, G; Jiang, Y; Qian, J; Zhou, H; Guo, Q; Chen, S; Dai, D; Shen, N. Involvement of Transcriptional Factor Pbx1 in Peripheral B Cell Homeostasis to Constrain Lupus Autoimmunity. Arthritis and Rheumatology. 2023; 75:1381-1394.

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.

Han, X; Gu, S; Hong, SM; Jiang, Y; Zhang, J; Yao, C; Yin, Z; Ye, Z; Ding, H; Chen, S; Dai, D; Shen, N. Amelioration of Autoimmunity in a Lupus Mouse Model by Modulation of T-Bet-Promoted Energy Metabolism in Pathogenic Age/Autoimmune-Associated B Cells. Arthritis and Rheumatology. 2023; 75:1203-1215.

Hou, G; Zhou, T; Xu, N; Yin, Z; Zhu, X; Zhang, Y; Cui, Y; Ma, J; Tang, Y; Cheng, Z; Guo, Y; Ding, H; Ye, Z; Shen, N. Integrative Functional Genomics Identifies Systemic Lupus Erythematosus Causal Genetic Variant in the IRF5 Risk Locus. Arthritis and Rheumatology. 2023; 75:574-585.

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.

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.

Lakes, N; Canaday, LM; Waggoner, SN. Can't drop the MIC(A/B): Preventing stress-ligand shedding to enhance pan-cancer targeting. 2023; 4:398-400.

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.

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.

Owen, KA; Bell, KA; Price, A; Bachali, P; Ainsworth, H; Marion, MC; Howard, TD; Langefeld, CD; Shen, N; Yazdany, J; Dall’era, M; Grammer, AC; Lipsky, PE. Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry. Scientific Reports. 2023; 13:5339.

Pividori, M; Lu, S; Li, B; Su, C; Johnson, ME; Wei, WQ; Feng, Q; Namjou, B; Kiryluk, K; Kullo, IJ; Skarke, C; Ritchie, MD; Grant, SF A; Greene, CS. Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. Nature Communications. 2023; 14:5562.

Shen, N; Zhao, Y; Duan, LH; Song, LJ; Zeng, XF; Liu, Y; Zhao, Y. [Recommendations for diagnosis and treatment of systemic lupus erythematosus]. Zhonghua nei ke za zhi [Chinese journal of internal medicine]. 2023; 62:775-784.

Shen, Y; Vanarsa, K; Yin, Z; Zhang, T; Castillo, J; Dai, M; Zou, L; Qin, L; Wang, J; Guo, Q; Shen, N; Ye, Z; Mohan, C; Ding, H. Urine L-selectin reflects clinical and histological renal disease activity and treatment response in lupus nephritis across multi-ethnicity. Frontiers in Immunology. 2023; 14:1200167.

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.

Spotnitz, M; Acharya, N; Cimino, JJ; Murphy, S; Namjou, B; Crimmins, N; Walunas, T; Liu, C; Crosslin, D; Benoit, B; Chung, W; Wei, WQ; Natarajan, K; Weng, C. A metadata framework for computational phenotypes. JAMIA Open. 2023; 6:ooad032.

Sun, F; Wu, H; Wang, Z; Wu, T; Wu, X; Chen, J; Zhang, D; Bao, C; Shen, N; Wu, L; Zhu, J; Ye, S. Effectiveness and Safety of Belimumab in Chinese Lupus Patients: A Multicenter, Real-World Observational Study. Biomedicines. 2023; 11:962.

Torre, D; Fstkchyan, YS; Ho, JS Y; Cheon, Y; Patel, RS; Degrace, EJ; Mzoughi, S; Schwarz, M; Mohammed, K; Seo, JS; Rosenberg, BR; Benner, C; Guccione, E; Marazzi, I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Molecular Cell. 2023; 83:4255-4271.e9.

Tran, C; Khadkikar, S; Porollo, A. Survey of Protein Sequence Embedding Models. International Journal of Molecular Sciences. 2023; 24:3775.

Van Camp, PJ; Prasath, VB S; Haslam, DB; Porollo, A. MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile. Microbiome. 2023; 11:223.

Vinuesa, CG; Shen, N; Ware, T. Genetics of SLE: mechanistic insights from monogenic disease and disease-associated variants. Nature Reviews Nephrology. 2023; 19:558-572.

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.

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.

Wang, Q; Martínez-Bonet, M; Kim, T; Sparks, JA; Ishigaki, K; Chen, X; Sudman, M; Aguiar, V; Sim, S; Hernandez, MC; Weirauch, MT; Langefeld, CD; Thompson, SD; Nigrovic, PA. Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant. Cell Genomics. 2023; 3:100420.

Wang, R; Hao, M; Kou, X; Sui, B; Sanmillan, ML; Zhang, X; Liu, D; Tian, J; Yu, W; Chen, C; Giraudo, C; Rao, DA; Shen, N; Shi, S. Apoptotic vesicles ameliorate lupus and arthritis via phosphatidylserine-mediated modulation of T cell receptor signaling. Bioactive Materials. 2023; 25:472-484.

Wang, Y; Lin, S; Wu, J; Jiang, M; Lin, J; Zhang, Y; Ding, H; Zhou, H; Shen, N; Di, W. Control of lupus activity during pregnancy via the engagement of IgG sialylation: novel crosstalk between IgG sialylation and pDC functions. Frontiers of Medicine. 2023; 17:549-561.

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.

Williams, AT; Shrine, N; Naghra-van Gijzel, H; Betts, JC; Chen, J; Hessel, EM; John, C; Packer, R; Reeve, NF; Yeo, AJ; Hall, IP; Wain, LV; Michalovich, D; Tobin, MD. Genome-wide association study of susceptibility to hospitalised respiratory infections. Wellcome Open Research. 2023; 6:290.

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.

Xie, C; Zhou, H; Athanasopoulos, V; Shen, Q; Zhang, Y; Meng, X; Burgio, G; Arsov, T; Lungu, AC; Zhang, P; Meng, Y; Shen, N; He, Y; Vinuesa, CG. De Novo PACSIN1 Gene Variant Found in Childhood Lupus and a Role for PACSIN1/TRAF4 Complex in Toll-like Receptor 7 Activation. Arthritis and Rheumatology. 2023; 75:1058-1071.

Zhang, D; Sun, F; Chen, J; Ding, H; Wang, X; Shen, N; Li, T; Ye, S. Four trajectories of 24-hour urine protein levels in real-world lupus nephritis cohorts. RMD Open. 2023; 9:e002930.

Zhang, F; Zhang, B; Ding, H; Li, X; Wang, X; Zhang, X; Liu, Q; Feng, Q; Han, M; Chen, L; Tang, H; Shen, N; Wang, H; Wei, B. The Oxysterol Receptor EBI2 Links Innate and Adaptive Immunity to Limit IFN Response and Systemic Lupus Erythematosus. Advanced Science. 2023; 10:e2207108.