Center for Autoimmune Genomics and Etiology (CAGE)

Ali, A; Canaday, LM; Feldman, HA; Cevik, H; Moran, MT; Rajaram, S; Lakes, N; Tuazon, JA; Seelamneni, H; Krishnamurthy, D; et al. Natural killer cell immunosuppressive function requires CXCR3-dependent redistribution within lymphoid tissues. Journal of Clinical Investigation. 2021; 131.

Cai, B; Cai, J; Yin, Z; Jiang, X; Yao, C; Ma, J; Xue, Z; Miao, P; Xiao, Q; Cheng, Y; et al. Long non-coding RNA expression profiles in neutrophils revealed potential biomarker for prediction of renal involvement in SLE patients. Rheumatology. 2021; 60:1734-1746.

Caster, DJ; Korte, EA; Merchant, ML; Klein, JB; Barati, MT; Joglekar, A; Wilkey, DW; Coventry, S; Hata, J; Rovin, BH; et al. Patients with Proliferative Lupus Nephritis Have Autoantibodies That React to Moesin and Demonstrate Increased Glomerular Moesin Expression. Journal of Clinical Medicine. 2021; 10.

Chidambaran, V; Zhang, X; Pilipenko, V; Chen, X; Wronowski, B; Geisler, K; Martin, LJ; Barski, A; Weirauch, MT; Ji, H. Methylation quantitative trait locus analysis of chronic postsurgical pain uncovers epigenetic mediators of genetic risk. Epigenomics. 2021; 13:613-630.

Corcoran, D; Maltbie, N; Sudalairaj, S; Baker, FN; Hirschfeld, J; Porollo, A. CoeViz 2: Protein Graphs Derived From Amino Acid Covariance. 2021; 1.

Cox, A; Cevik, H; Feldman, HA; Canaday, LM; Lakes, N; Waggoner, SN. Targeting natural killer cells to enhance vaccine responses. Trends in Pharmacological Sciences. 2021; 42:789-801.

Cushion, MT; Tisdale-Macioce, N; Sayson, SG; Porollo, A. The Persistent Challenge of Pneumocystis Growth Outside the Mammalian Lung: Past and Future Approaches. Frontiers in Microbiology. 2021; 12.

Dey, D; Sciascia, S; Pons-Estel, GJ; Ding, H; Shen, N. Health Disparities in Rheumatic Diseases: Understanding Global Challenges in Africa, Europe, Latin America, and Asia and Proposing Strategies for Improvement. Rheumatic Disease Clinics of North America. 2021; 47:119-132.

Felton, JM; Vallabh, S; Parameswaran, S; Edsall, LE; Ernst, K; Wronowski, B; Malik, A; Kotliar, M; Weirauch, MT; Barski, A; et al. Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. Journal of Immunology. 2021; 207:1044-1054.

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. PLoS Genetics. 2021; 17.

Her, YR; Wang, L; Chepelev, I; Manterola, M; Berkovits, B; Cui, K; Zhao, K; Wolgemuth, DJ. Genome-wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate gene expression during spermatogenesis. Molecular Reproduction and Development. 2021; 88:141-157.

Ho, JS Y; Mok, BW Y; Campisi, L; Jordan, T; Yildiz, S; Parameswaran, S; Wayman, JA; Gaudreault, NN; Meekins, DA; Indran, SV; et al. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell. 2021; 184:2618-2632.e17.

Johansson, E; Martin, LJ; He, H; Chen, X; Weirauch, MT; Kroner, JW; Khurana Hershey, GK; Biagini, JM. Second-hand smoke and NFE2L2 genotype interaction increases paediatric asthma risk and severity. Clinical and Experimental Allergy. 2021; 51:801-810.

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

Korinfskaya, S; Parameswaran, S; Weirauch, MT; Barski, A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development?. Frontiers in Immunology. 2021; 12.

Kottyan, LC; Trimarchi, MP; Lu, X; Caldwell, JM; Maddox, A; Parameswaran, S; Lape, M; D'Mello, RJ; Bonfield, M; Ballaban, A; et al. Replication and meta-analyses nominate numerous eosinophilic esophagitis risk genes. Journal of Allergy and Clinical Immunology. 2021; 147:255-266.

Kuang, Y; Pyo, A; Eafergan, N; Cain, B; Gutzwiller, LM; Axelrod, O; Gagliani, EK; Weirauch, MT; Kopan, R; Kovall, RA; et al. Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor. PLoS Genetics. 2021; 17.

Leader, BA; Koritala, BS C; Moore, CA; Dean, EG; Kottyan, LC; Smith, DF. Epigenetics of obstructive sleep apnea syndrome: a systematic review. Journal of Clinical Sleep Medicine. 2021.

Li, G; Liu, L; Yin, Z; Ye, Z; Shen, N. Glutamine metabolism is essential for the production of IL-17A in γδ T cells and skin inflammation. Tissue and Cell. 2021; 71.

Li, J; Wang, R; Bao, CD; Shen, N; Fu, Q. Application of adjusted global antiphospholipid syndrome score to risk assessment of new thromboembolic events in patients with systemic lupus erythematosus. Journal of Shanghai Jiaotong University (Medical Science). 2021; 41:1046-1050.

Liang, K; He, J; Wei, Y; Zeng, Q; Gong, D; Qin, J; Ding, H; Chen, Z; Zhou, P; Niu, P; et al. Sustained low-dose interleukin-2 therapy alleviates pathogenic humoral immunity via elevating the Tfr/Tfh ratio in lupus. Clinical and Translational Immunology. 2021; 10.

Liu, G; Shi, M; Mosley, JD; Weng, C; Zhang, Y; Lee, MT M; Jarvik, GP; Hakonarson, H; Namjou-Khales, B; Sleiman, P; et al. A Mendelian Randomization Approach Using 3-HMG-Coenzyme-A Reductase Gene Variation to Evaluate the Association of Statin-Induced Low-Density Lipoprotein Cholesterol Lowering With Noncardiovascular Disease Phenotypes. JAMA Network Open. 2021; 4.

López-Isac, E; Smith, SL; Marion, MC; Wood, A; Sudman, M; Yarwood, A; Shi, C; Gaddi, VP; Martin, P; Prahalad, S; et al. Combined genetic analysis of juvenile idiopathic arthritis clinical subtypes identifies novel risk loci, target genes and key regulatory mechanisms. Annals of the Rheumatic Diseases. 2021.

Luo, S; Clarke, SL N; Ramanan, AV; Thompson, SD; Langefeld, CD; Marion, MC; Grom, AA; Schooling, CM; Gaunt, TR; Yeung, SL A; et al. Platelet Glycoprotein Ib α-Chain as a Putative Therapeutic Target for Juvenile Idiopathic Arthritis: A Mendelian Randomization Study. Arthritis and Rheumatology. 2021; 73:693-701.

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.

Miraldi, ER; Chen, X; Weirauch, MT. Deciphering cis-regulatory grammar with deep learning. Nature Genetics. 2021; 53:266-268.

Moreno-Fernandez, ME; Giles, DA; Oates, JR; Chan, CC; Damen, MS M A; Doll, JR; Stankiewicz, TE; Chen, X; Chetal, K; Karns, R; et al. PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease. Cell Metabolism. 2021; 33:1187-1204.e9.

Murrison, LB; Ren, X; Preusse, K; He, H; Kroner, J; Chen, X; Jenkins, S; Johansson, E; Biagini, JM; Weirauch, MT; et al. TSLP disease-associated genetic variants combined with airway TSLP expression influence asthma risk. Journal of Allergy and Clinical Immunology. 2021.

Namjou, B; Stanaway, IB; Lingren, T; Mentch, FD; Benoit, B; Dikilitas, O; Niu, X; Shang, N; Shoemaker, AH; Carey, DJ; et al. Evaluation of the MC4R gene across eMERGE network identifies many unreported obesity-associated variants. International Journal of Obesity. 2021; 45:155-169.

Nigrovic, PA; Colbert, RA; Holers, VM; Ozen, S; Ruperto, N; Thompson, SD; Wedderburn, LR; Yeung, RS M; Martini, A. Biological classification of childhood arthritis: roadmap to a molecular nomenclature. Nature reviews. Rheumatology. 2021; 17:257-269.

Oatman, N; Dasgupta, N; Arora, P; Choi, K; Gawali, MV; Gupta, N; Parameswaran, S; Salomone, J; Reisz, JA; Lawler, S; et al. Mechanisms of stearoyl CoA desaturase inhibitor sensitivity and acquired resistance in cancer. Science advances. 2021; 7.

Ochayon, DE; Waggoner, SN. The Effect of Unconventional Cytokine Combinations on NK-Cell Responses to Viral Infection. Frontiers in Immunology. 2021; 12.

Porollo, A; Cushion, MT. Advances in Genomics Research of Pneumocystis Species. Encyclopedia of Mycology. 2021.

Qin, J; Huang, X; Wang, N; Zhou, P; Zhang, H; Chen, Z; Liang, K; Gong, D; Zeng, Q; Niu, P; et al. Supranutritional selenium suppresses ROS-induced generation of RANKL-expressing osteoclastogenic CD4+ T cells and ameliorates rheumatoid arthritis. Clinical and Translational Immunology. 2021; 10.

Qu, B; Jiang, X; Shen, N. Chapter 30 MicroRNA in systemic lupus erythematosus. Systemic Lupus Erythematosus. 2021.

Rao, R; Han, R; Ogurek, S; Xue, C; Wu, LM; Zhang, L; Zhang, L; Hu, J; Phoenix, TN; Waggoner, SN; et al. Glioblastoma Genetic Drivers Dictate the Function of Tumor-Associated Macrophages/Microglia and Responses to CSF1R Inhibition. Neuro-Oncology. 2021.

Reighard, SD; Krishnamurthy, D; Cevik, H; Ochayon, DE; Ali, A; Seelamneni, H; Brunner, HI; Waggoner, SN. Immunomodulatory effects of cytokine-induced expansion of cytotoxic lymphocytes in a mouse model of lupus-like disease. Cytotherapy. 2021; 23:37-45.

Santiago, IJ; Zhang, D; Saras, A; Pontillo, N; Xu, C; Chen, X; Weirauch, MT; Mistry, M; Ginty, DD; Pecot, MY; et al. Drosophila Fezf functions as a transcriptional repressor to direct layer-specific synaptic connectivity in the fly visual system. Proceedings of the National Academy of Sciences of the United States of America. 2021; 118.

Satterfield, BA; Dikilitas, O; Safarova, MS; Clarke, SL; Tcheandjieu, C; Zhu, X; Bastarache, L; Larson, EB; Justice, AE; Shang, N; et al. Associations of Genetically Predicted Lp(a) (Lipoprotein [a]) Levels With Cardiovascular Traits in Individuals of European and African Ancestry. Circulation: Genomic and Precision Medicine. 2021; 14.

Schott, G; Munoz, GG; Trevino, N; Chen, X; Weirauch, MT; Gregory, SG; Bradrick, SS; Blanco, MA G. U2AF2 binds IL7R exon 6 ectopically and represses its inclusion. RNA. 2021.

Shen, N; Lipsky, PE. In memoriam: Shunle Chen, MD, 1932-2021. Lupus. 2021; 30:861-862.

Song, R; Gao, Y; Dozmorov, I; Malladi, V; Saha, I; McDaniel, MM; Parameswaran, S; Liang, C; Arana, C; Zhang, B; et al. IRF1 governs the differential interferon-stimulated gene responses in human monocytes and macrophages by regulating chromatin accessibility. Cell Reports. 2021; 34.

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.

Suri, P; Stanaway, IB; Zhang, Y; Freidin, MB; Tsepilov, YA; Carrell, DS; Williams, FM K; Aulchenko, YS; Hakonarson, H; Namjou, B; et al. Genome-wide association studies of low back pain and lumbar spinal disorders using electronic health record data identify a locus associated with lumbar spinal stenosis. Pain. 2021; 162:2263-2272.

Tang, Y; Xu, Q; Hu, L; Yan, X; Feng, X; Yokota, A; Wang, W; Zhan, D; Krishnamurthy, D; Ochayon, DE; et al. Tumor Microenvironment-Derived R-spondins Enhance Anti-Tumor Immunity to Suppress Tumor Growth and Sensitize for Immune Checkpoint Blockade Therapy. Cancer Discovery. 2021.

Thomas, M; Sakoda, LC; Hoffmeister, M; Rosenthal, EA; Lee, JK; van Duijnhoven, FJ B; Platz, EA; Wu, AH; Dampier, CH; de la Chapelle, A; et al. Response to Li and Hopper. American Journal of Human Genetics. 2021; 108:527-529.

Wu, L; Jiang, X; Qi, C; Zhang, C; Qu, B; Shen, N. EZH2 Inhibition Interferes With the Activation of Type I Interferon Signaling Pathway and Ameliorates Lupus Nephritis in NZB/NZW F1 Mice. Frontiers in Immunology. 2021; 12.

Xu, N; Zhou, T; Hou, GJ; Shen, N; Tang, YJ. Application of CRISPR/Cas9-mediated homologous recombination to the functional study of disease-associated genetic variants located in non-coding region. Journal of Shanghai Jiaotong University (Medical Science). 2021; 41:8-15.

Yang, Z; Slone, J; Wang, X; Zhan, J; Huang, Y; Namjou, B; Kaufman, KM; Pauciulo, M; Harley, JB; Muglia, LJ; et al. Validation of low-coverage whole-genome sequencing for mitochondrial DNA variants suggests mitochondrial DNA as a genetic cause of preterm birth. Human Mutation. 2021.

Yao, Y; Chen, Z; Zhang, H; Chen, C; Zeng, M; Yunis, J; Wei, Y; Wan, Y; Zhou, M; Qiu, C; et al. Selenium-GPX4 axis protects follicular helper T cells from ferroptosis. Nature Immunology. 2021; 22:1127-1139.

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

Zhang, H; Dai, D; Hu, Q; Yang, F; Xue, Y; Li, F; Shen, N; Zhang, M; Huang, C. Bach2 attenuates IL-2R signaling to control Treg homeostasis and Tfr development. Cell Reports. 2021; 35.

Zhao, YN; Qiu, R; Shen, N; Tang, YJ. Construction of inducible CRISPR/Cas9 system for studying gene function in mouse. Journal of Shanghai Jiaotong University (Medical Science). 2021; 41:297-301.

Zhu, T; Zhang, X; Chen, X; Brown, AP; Weirauch, MT; Guilbert, TW; Khurana Hershey, GK; Biagini, JM; Ji, H. Nasal DNA methylation differentiates severe from non-severe asthma in African-American children. Allergy: European Journal of Allergy and Clinical Immunology. 2021; 76:1836-1845.