Publications

Porritt RA, Zemmour D, Abe M, Lee Y, Meena Narayanan M, Teixeira de Carvalho T, Gomez AC, Martinon D, Santiskulvong C, Fishbein MC, Chen S, Crother TR, Shimada K, Arditi M, Noval Rivas M. NLRP3 Inflammasome Mediates Immune-Stromal Interactions in Vasculitis. Circ Res. 2021 Sep 14. doi: 10.1161/CIRCRESAHA.121.319153. Online ahead of print.

Parthiv Haldipur, Silvia Bernardo, Kimberly A. Aldinger, Tarika Sivakumar, Jake Millman, Alexandria H. Sjoboen, Derek Dang,  Danilo Dubocanin, Mei Deng, Andrew E. Timms, Brian D. Davis, Jasmine T. Plummer, Kshitij Mankad, Ozgur Oztekin,  Lucia Manganaro, Fabien Guimiot, Homa Adle‑Biassette, Rosa Russo, Joseph R. Siebert, Debora Kidron, Giulia Petrilli,  Nathalie Roux, Ferechte Razavi, Ian A. Glass, Cira Di Gioia, Evelina Silvestri, Kathleen J. Millen. Evidence of disrupted rhombic lip development in the pathogenesis of Dandy–Walker malformationActa Neuropathologica. 2021 August 4.

Kenneth H. Gouin III, Nathan Ing, Jasmine T. Plummer, Charles J. Rosser, Bassem Ben Cheikh, Catherine Oh, Stephanie S. Chen, Keith Syson Chan, Hideki Furuya , Warren G. Tourtellotte, Simon R. V. Knott, Dan Theodorescu. An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer. Nature Communications. 2021 August.

Xie T, Kulur V, Liu N, Deng N, Wang Y, Rowan SC, Yao C, Huang G, Liu X, Taghavifar F, Liang J, Hogaboam C, Stripp B, Chen P, Jiang D, Noble PW. Mesenchymal growth hormone receptor deficiency leads to failure of alveolar progenitor cell function and severe pulmonary fibrosis. Sci Adv. 2021 Jun 9;7(24):eabg6005. doi: 10.1126/sciadv.abg6005. Print 2021 Jun.

Porritt RA, Paschold L, Rivas MN, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schultheiß C, Santiskulvong C, Van Eyk J, McCormick JK, Fasano A, Bahar I, Binder M, Arditi M. HLA class I-associated expansion of TRBV11-2 T cells in multisystem inflammatory syndrome in children. J Clin Invest. 2021 May 17;131(10):e146614. doi: 10.1172/JCI146614.


Li C, Peng Z, Wang Y, Lam G, Nissen N, Tang J, Yuan X, Lewis M, Greene MI, Pandol SJ, Wang Q. Epithelial cell transforming 2 is regulated by Yes-associated protein 1 and mediates pancreatic cancer progression and metastasis. Am J Physiol Gastrointest Liver Physiol. 2021 Mar 1;320(3):G380-G395. doi: 10.1152/ajpgi.00185.2020. Epub 2021 Jan 27.


Lin YN, Mesquita T, Sanchez L, Chen YH, Liu W, Li C, Rogers R, Wang Y, Li X, Wu D, Zhang R, Ibrahim A, Marbán E, Cingolani E. Extracellular vesicles from immortalized cardiosphere-derived cells attenuate arrhythmogenic cardiomyopathy in desmoglein-2 mutant mice. Eur Heart J. 2021 Sep 14;42(35):3558-3571. doi: 10.1093/eurheartj/ehab419.

Shaharuddin SH, Wang V, Santos RS, Gross A, Wang Y, Jawanda H, Zhang Y, Hasan W, Garcia G Jr, Arumugaswami V, Sareen D. Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells. Front Cell Infect Microbiol. 2021 Jun 23;11:678482. doi: 10.3389/fcimb.2021.678482. eCollection 2021.


Liu X, Rowan SC, Liang J, Yao C, Huang G, Deng N, Xie T, Wu D, Wang Y, Burman A, Parimon T, Borok Z, Chen P, Parks WC, Hogaboam CM, Weigt SS, Belperio J, Stripp BR, Noble PW, Jiang D. Categorization of lung mesenchymal cells in development and fibrosis. iScience. 2021 May 19;24(6):102551. doi: 10.1016/j.isci.2021.102551. eCollection 2021 Jun 25.

Epithelial cell transforming 2 is regulated by Yes-associated protein 1 and mediates pancreatic cancer progression and metastasis.
Li C, Peng Z, Wang Y, Lam G, Nissen N, Tang J, Yuan X, Lewis M, Greene MI, Pandol SJ, Wang Q. Commensal bacteria and fungi differentially regulate tumor responses to radiation therapy. Am J Physiol Gastrointest Liver Physiol. 2021 Mar 1;320(3):G380-G395. doi: 10.1152/ajpgi.00185.2020. Epub 2021 Jan 27.


Shiao SL, Kershaw KM, Limon JJ, You S, Yoon J, Ko EY, Guarnerio J, Potdar AA, McGovern DPB, Bose S, Dar TB, Noe P, Lee J, Kubota Y, Maymi VI, Davis MJ, Henson RM, Choi RY, Yang W, Tang J, Gargus M, Prince AD, Zumsteg ZS, Underhill DM. Cancer Cell. 2021 Sep 13;39(9):1202-1213.e6. doi: 10.1016/j.ccell.2021.07.002. Epub 2021 Jul 29.


Gonzalez TL, Eisman LE, Joshi NV, Flowers AE, Wu D, Wang Y, Santiskulvong C, Tang J, Buttle RA, Sauro E, Clark EL, DiPentino R, Jefferies CA, Chan JL, Lin Y, Zhu Y, Afshar Y, Tseng HR, Taylor K, Williams J 3rd, Pisarska MD. High-throughput miRNA sequencing of the human placenta: expression throughout gestation. Epigenomics. 2021 Jul;13(13):995-1012. doi: 10.2217/epi-2021-0055. Epub 2021 May 25.

Wenjuan Zhang, PhD; Brian D. Davis, BSc; Stephanie S. Chen, BSc; Jorge M. Sincuir Martinez, BS; Jasmine T. Plummer, PhD; Eric Vail, MD. Emergence of a Novel SARS-CoV-2 Variant in Southern California. JAMA. January 2021


Sun T, Gonzalez TL, Deng N, DiPentino R, Clark EL, Lee B, Tang J, Wang Y, Stripp BR, Yao C, Tseng HR, Karumanchi SA, Koeppel AF, Turner SD, Farber CR, Rich SS, Wang ET, Williams J, Pisarska MD. Sexually Dimorphic Crosstalk at the Maternal-Fetal Interface. J Clin Endocrinol Metab. 2020 Dec 1;105(12):e4831-47. doi: 10.1210/clinem/dgaa503.


Poe AJ, Kulkarni M, Leszczynska A, Tang J, Shah R, Jami-Alahmadi Y, Wang J, Kramerov AA, Wohlschlegel J, Punj V, Ljubimov AV, Saghizadeh M. Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling. Cells. 2020 Sep 26;9(10):2175. doi: 10.3390/cells9102175.

Wenjuan Zhang, PhD; John Paul Govindavari, DO; Brian D. Davis, BSc; Stephanie S. Chen, BSc; Jong Taek Kim, MD; Jianbo Song, PhD; Jean Lopategui, MD; Jasmine T. Plummer, PhD; Eric Vail, MD. Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic. JAMA Network Open. 2020


Ha CWY, Martin A, Sepich-Poore GD, Shi B, Wang Y, Gouin K, Humphrey G, Sanders K, Ratnayake Y, Chan KSL, Hendrick G, Caldera JR, Arias C, Moskowitz JE, Ho Sui SJ, Yang S, Underhill D, Brady MJ, Knott S, Kaihara K, Steinbaugh MJ, Li H, McGovern DPB, Knight R, Fleshner P, Devkota S. Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans. Cell. 2020 Oct 29;183(3):666-683.e17. doi: 10.1016/j.cell.2020.09.009. Epub 2020 Sep 28.
 

Sharma A, Garcia G Jr, Wang Y, Plummer JT, Morizono K, Arumugaswami V, Svendsen CN. Human iPSC-Derived Cardiomyocytes Are Susceptible to SARS-CoV-2 Infection. Cell Rep Med. 2020 Jul 21; 1(4): 100052.

Rajput PS, Lamb J, Kothari S, Pereira B, Soetkamp D, Wang Y, Tang J, Van Eyk JE, Mullins ES, Lyden PD. Neuron-generated thrombin induces a protective astrocyte response via protease activated receptors. Glia. 2020 Feb;68(2):246-262.

Geoffrey de Couto G, Jaghatspanyan E, DeBerge M, Liu W, Luther K, Wang Y, Tang J, Thorp EB, Marbán E. Mechanism of Enhanced MerTK-Dependent Macrophage Efferocytosis by Extracellular Vesicles. Arterioscler Thromb Vasc Biol. 2019 Oct;39(10):2082-2096.

Kim GB, Rincon Fernandez Pacheco D, Saxon D, Yang A, Sabet S, Dutra-Clarke M, Levy R, Watkins A, Park H, Abbasi Akhtar A, Linesch PW, Kobritz N, Chandra SS, Grausam K, Ayala-Sarmiento A, Molina J, Sedivakova K, Hoang K, Tsyporin J, Gareau DS, Filbin MG, Bannykh S, Santiskulvong C, Wang Y, Tang J, Suva ML, Chen B, Danielpour M, Breunig JJ. Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements. Cell. 2019 Sep 19;179(1):251-267.e24.  ​

Hirose S, Wang S, Tormanen K, Wang Y, Tang J, Akbari O, Ghiasi H. Roles of Type 1, 2, and 3 Innate Lymphoid Cells in Herpes Simplex Virus 1 Infection In Vitro and In Vivo.  J Virol. 2019 Jun 14;93(13):e00523-19.  

Tsuda M, Hamade H, Thomas LS, Salumbides BC, Potdar AA, Wong MH, Nunnelee JS, Stamps JT, Neutzsky-Wulff AV, Barrett RJ, Wang Y, Tang J, Funari VA, Targan SR, Michelsen KS. A role for BATF3 in TH9 differentiation and T-cell-driven mucosal pathologies. Mucosal Immunol. 2019 May;12(3):644-655.  

 

Ackerman AL, Anger JT, Khalique MU, Ackerman JE, Tang J, Kim J, Underhill DM, Freeman MR; NIH Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP). Optimization of DNA extraction from human urinary samples for mycobiome community profiling. PLoS One. 2019 Apr 25;14(4):e0210306.  

 

Zhang X, Lei B, Wang Y, Xu S, Liu H. Dual-Sensitive On-Off Switch in Liposome Bilayer for Controllable Drug Release. Langmuir. 2019 Apr 16;35(15):5213-5220. 

Xu J, Reznik E, Lee HJ, Gundem G, Jonsson P, Sarungbam J, Bialik A, Sanchez-Vega F, Creighton CJ, Hoekstra J, Zhang L, Sajjakulnukit P, Kremer D, Tolstyka Z, Casuscelli J, Stirdivant S, Tang J, Schultz N, Jeng P, Dong Y, Su W, Cheng EH, Russo P, Coleman JA, Papaemmanuil E, Chen YB, Reuter VE, Sander C, Kennedy SR, Hsieh JJ, Lyssiotis CA, Tickoo SK, Hakimi AA. Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma. Elife. 2019 Apr 1;8:e38986. 

 

Khan Z, Cao DY, Giani JF, Bernstein EA, Veiras LC, Fuchs S, Wang Y, Peng Z, Kalkum M, Liu GY, Bernstein KE. Overexpression of the C-domain of angiotensin-converting enzyme reduces melanoma growth by stimulating M1 macrophage polarization. J Biol Chem. 2019 Mar 22;294(12):4368-4380.  

Geng Y, Liu X, Liang J, Habiel DM, Kulur V, Coelho AL, Deng N, Xie T, Wang Y, Liu N, Huang G, Kurkciyan A, Liu Z, Tang J, Hogaboam CM, Jiang D, Noble PW. PD-L1 on invasive fibroblasts drives fibrosis in a humanized model of idiopathic pulmonary fibrosis. JCI Insight. 2019 Mar 21;4(6):e125326.

Limon JJ, Tang J, Li D, Wolf AJ, Michelsen KS, Funari V, Gargus M, Nguyen C, Sharma P, Maymi VI, Iliev ID, Skalski JH, Brown J, Landers C, Borneman J, Braun J, Targan SR, McGovern DPB, Underhill DM. Malassezia Is Associated with Crohn's Disease and Exacerbates Colitis in Mouse Models. Cell Host Microbe. 2019 Mar 13;25(3):377-388.e6.

Mehta SR, Tom CM, Wang Y, Bresee C, Rushton D, Mathkar PP, Tang J, Mattis VB. Human Huntington’s Disease iPSC-derived cortical neurons display altered transcriptomics, morphology, and maturation. Cell Reports. 2018 Oct 23;25(4):1081-1096. 

 

Skalski JH, Limon-Tello JJ, Sharma P, Gargus MD, Ngyuen C, Tang J, Coelho AL, Hogaboam CM, Crother TR, Underhill DM. (2018). Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice. PLOS Pathogens. 2018 Sept 2014(9):e1007260

 

Rajamani U, Gross AR, Hjelm BE, Sequeira A, Vawter MP, Tang J, Gangalapudi V, Wang Y, Andres AM, Gottlieb RA, Sareen D. Super-Obese Patient-Derived iPSC Hypothalamic Neurons Exhibit Obesogenic Signatures and Hormone Responses. Cell Stem Cell. 2018 May 3;22(5):698-712.e9. 

Ljubimova JY, Braubach O, Patil R, Chiechi A, Tang J, Galstyan A, Shatalova ES, Kleinman MT, Black KL, Holler E. Coarse particulate matter (PM2.5-10) in Los Angeles Basin air induces expression of inflammation and cancer biomarkers in rat brains. Sci Rep. 2018 Apr 9;8(1):5708. 

Xie T, Wang Y, Deng N, Huang G, Taghavifar F, Geng Y, Liu N, Kulur V, Yao C, Chen P, Liu Z, Stripp B, Tang J, Liang J, Noble PW, Jiang D. Single-Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis. Cell Rep. 2018 Mar 27;22(13):3625-3640. 

Seehus CR, Kadavallore A, Torre B, Yeckes AR, Wang Y, Tang J, Kaye J. Alternative activation generates IL-10 producing type 2 innate lymphoid cells. Nat Commun. 2017 Dec 1;8(1):1900. 

Bankoti R, Ogawa C, Nguyen T, Emadi L, Couse M, Salehi S, Fan X, Dhall D, Wang Y, Brown J, Funari V, Tang J, Martins GA. Differential regulation of Effector and Regulatory T cell function by Blimp1. Sci Rep. 2017 Sep 21;7(1):12078.

Kulkarni M, Leszczynska A, Wei G, Winkler MA, Tang J, Funari VA, Deng N, Liu Z, Punj V, Deng SX, Ljubimov AV, Saghizadeh M. Genome-wide analysis suggests a differential microRNA signature associated with normal and diabetic human corneal limbus. Sci Rep. 2017 Jun 14;7(1):3448.

Xu Y, Mizuno T, Sridharan A, Du Y, Guo M, Tang J, Wikenheiser-Brokamp KA, Perl AK, Funari VA, Gokey JJ, Stripp BR and Whitsett JA. Single Cell RNA-Sequencing Identifies Diverse Roles of Epithelial Cells in Idiopathic Pulmonary Fibrosis. JCI Insight. 2016 1(20):e90558. 

McConnell AM, Yao C, Yeckes AR, Wang Y, Selvaggio AS, Tang J, Kirsch DG, Stripp BR. p53 Regulates Progenitor Cell Quiescence and Differentiation in the Airway. Cell Rep. 2016 Nov 22;17(9):2173-2182. 

Lee B, Kroener LL, Xu N, Wang ET, Banks A, Williams J 3rd, Goodarzi MO, Chen YI, Tang J, Wang Y, Gangalapudi V, Pisarska MD. Function and Hormonal Regulation of GATA3 in Human First Trimester Placentation. Biol Reprod. 2016 Nov;95(5):113. 

Wheeler ML, Limon JJ, Bar AS, Leal CA, Gargus M, Tang J, Brown J, Funari VA, Wang HL, Crother TR, Arditi M, Underhill DM, Iliev ID. Immunological Consequences of Intestinal Fungal Dysbiosis. Cell Host Microbe. 2016 Jun 8;19(6):865-73.

Demehri FR, Frykman PK, Cheng Z, Ruan C, Wester T, Nordenskjöld A, Kawaguchi A, Hui TT, Granström AL, Funari V, Teitelbaum DH; HAEC Collaborative Research Group (HCRG). Altered fecal short chain fatty acid composition in children with a history of Hirschsprung-associated enterocolitis. J Pediatr Surg. 2016 Jan;51(1):81-6. 

Ignatius Irudayam J, Contreras D, Spurka L, Subramanian A, Allen J, Ren S, Kanagavel V, Nguyen Q, Ramaiah A, Ramamoorthy K, French SW, Klein AS, Funari V, Arumugaswami V. Characterization of type I interferon pathway during hepatic differentiation of human pluripotent stem cells and hepatitis C virus infection. Stem Cell Res. 2015 Sep;15(2):354-64. 

Xu N, Geller DH, Jones MR, Funari VA, Azziz R, Goodarzi MO. Comprehensive assessment of expression of insulin signaling pathway components in subcutaneous adipose tissue of women with and without polycystic ovary syndrome. J Clin Transl Endocrinol. 2015 Sep;2(3):99-104. 

Hatada S, Subramanian A, Mandefro B, Ren S, Kim HW, Tang J, Funari V, Baloh RH, Sareen D, Arumugaswami V, Svendsen CN. Low-Dose Irradiation Enhances Gene Targeting in Human Pluripotent Stem Cells. Stem Cells Transl Med. 2015 Sep;4(9):998-1010. 

Seehus CR, Aliahmad P, de la Torre B, Iliev ID, Spurka L, Funari VA, Kaye J. The development of innate lymphoid cells requires TOX-dependent generation of a common innate lymphoid cell progenitor. Nat Immunol. 2015 Jun;16(6):599-608.

Giamarellos-Bourboulis E, Tang J, Pyleris E, Pistiki A, Barbatzas C, Brown J, Lee CC, Harkins TT, Kim G, Weitsman S, Barlow GM, Funari VA, Pimentel M. Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome. Scand J Gastroenterol. 2015;50(9):1076-87. 

Frykman PK, Nordenskjöld A, Kawaguchi A, Hui TT, Granström AL, Cheng Z, Tang J, Underhill DM, Iliev I, Funari VA, Wester T; HAEC Collaborative Research Group (HCRG). Characterization of Bacterial and Fungal Microbiome in Children with Hirschsprung Disease with and without a History of Enterocolitis: A Multicenter Study. PLoS One. 2015 Apr 24;10(4):e0124172. 

Tang J, Iliev ID, Brown J, Underhill DM, Funari VA. Mycobiome: Approaches to analysis of intestinal fungi. J Immunol Methods. 2015 Jun;421:112-21. 

Seksenyan A, Kadavallore A, Walts AE, de la Torre B, Berel D, Strom SP, Aliahmad P, Funari VA, Kaye J. TOX3 is expressed in mammary ER(+) epithelial cells and regulates ER target genes in luminal breast cancer. BMC Cancer. 2015 Jan 30;15:22.

Taylor-Harding B, Aspuria PJ, Agadjanian H, Cheon DJ, Mizuno T, Greenberg D, Allen JR, Spurka L, Funari V, Spiteri E, Wang Q, Orsulic S, Walsh C, Karlan BY, Wiedemeyer WR. Cyclin E1 and RTK/RAS signaling drive CDK inhibitor resistance via activation of E2F and ETS. Oncotarget. 2015 Jan 20;6(2):696-714. 

Sareen D, Saghizadeh M, Ornelas L, Winkler MA, Narwani K, Sahabian A, Funari VA, Tang J, Spurka L, Punj V, Maguen E, Rabinowitz YS, Svendsen CN, Ljubimov AV. Differentiation of human limbal-derived induced pluripotent stem cells into limbal-like epithelium. Stem Cells Transl Med. 2014 Sep;3(9):1002-12. 

Funari VA, Winkler M, Brown J, Dimitrijevich SD, Ljubimov AV, Saghizadeh M. Differentially expressed wound healing-related microRNAs in the human diabetic cornea. PLoS One. 2013 Dec 20;8(12):e84425. 

Li P, Grigorenko E, Funari V, Enright E, Zhang H, Kim HL. Evaluation of a high-throughput, microfluidics platform for performing TaqMan™ qPCR using formalin-fixed paraffin-embedded tumors. Bioanalysis. 2013 Jul;5(13):1623-33.

Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, Brown J, Becker CA, Fleshner PR, Dubinsky M, Rotter JI, Wang HL, McGovern DP, Brown GD, Underhill DM. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science. 2012 Jun 8;336(6086):1314-7.