All Publications

  • Emergent high fatality lung disease in systemic juvenile arthritis. Annals of the rheumatic diseases Saper, V. E., Chen, G. n., Deutsch, G. H., Guillerman, R. P., Birgmeier, J. n., Jagadeesh, K. n., Canna, S. n., Schulert, G. n., Deterding, R. n., Xu, J. n., Leung, A. N., Bouzoubaa, L. n., Abulaban, K. n., Baszis, K. n., Behrens, E. M., Birmingham, J. n., Casey, A. n., Cidon, M. n., Cron, R. Q., De, A. n., De Benedetti, F. n., Ferguson, I. n., Fishman, M. P., Goodman, S. I., Graham, T. B., Grom, A. A., Haines, K. n., Hazen, M. n., Henderson, L. A., Ho, A. n., Ibarra, M. n., Inman, C. J., Jerath, R. n., Khawaja, K. n., Kingsbury, D. J., Klein-Gitelman, M. n., Lai, K. n., Lapidus, S. n., Lin, C. n., Lin, J. n., Liptzin, D. R., Milojevic, D. n., Mombourquette, J. n., Onel, K. n., Ozen, S. n., Perez, M. n., Phillippi, K. n., Prahalad, S. n., Radhakrishna, S. n., Reinhardt, A. n., Riskalla, M. n., Rosenwasser, N. n., Roth, J. n., Schneider, R. n., Schonenberg-Meinema, D. n., Shenoi, S. n., Smith, J. A., Sönmez, H. E., Stoll, M. L., Towe, C. n., Vargas, S. O., Vehe, R. K., Young, L. R., Yang, J. n., Desai, T. n., Balise, R. n., Lu, Y. n., Tian, L. n., Bejerano, G. n., Davis, M. M., Khatri, P. n., Mellins, E. D. 2019


    To investigate the characteristics and risk factors of a novel parenchymal lung disease (LD), increasingly detected in systemic juvenile idiopathic arthritis (sJIA).In a multicentre retrospective study, 61 cases were investigated using physician-reported clinical information and centralised analyses of radiological, pathological and genetic data.LD was associated with distinctive features, including acute erythematous clubbing and a high frequency of anaphylactic reactions to the interleukin (IL)-6 inhibitor, tocilizumab. Serum ferritin elevation and/or significant lymphopaenia preceded LD detection. The most prevalent chest CT pattern was septal thickening, involving the periphery of multiple lobes ± ground-glass opacities. The predominant pathology (23 of 36) was pulmonary alveolar proteinosis and/or endogenous lipoid pneumonia (PAP/ELP), with atypical features including regional involvement and concomitant vascular changes. Apparent severe delayed drug hypersensitivity occurred in some cases. The 5-year survival was 42%. Whole exome sequencing (20 of 61) did not identify a novel monogenic defect or likely causal PAP-related or macrophage activation syndrome (MAS)-related mutations. Trisomy 21 and young sJIA onset increased LD risk. Exposure to IL-1 and IL-6 inhibitors (46 of 61) was associated with multiple LD features. By several indicators, severity of sJIA was comparable in drug-exposed subjects and published sJIA cohorts. MAS at sJIA onset was increased in the drug-exposed, but was not associated with LD features.A rare, life-threatening lung disease in sJIA is defined by a constellation of unusual clinical characteristics. The pathology, a PAP/ELP variant, suggests macrophage dysfunction. Inhibitor exposure may promote LD, independent of sJIA severity, in a small subset of treated patients. Treatment/prevention strategies are needed.

    View details for DOI 10.1136/annrheumdis-2019-216040

    View details for PubMedID 31562126

  • Targeting the adaptability of heterogeneous aneuploids. Cell Chen, G., Mulla, W. A., Kucharavy, A., Tsai, H. J., Rubinstein, B., Conkright, J., McCroskey, S., Bradford, W. D., Weems, L., Haug, J. S., Seidel, C. W., Berman, J., Li, R. 2015; 160 (4): 771-784


    Aneuploid genomes, characterized by unbalanced chromosome stoichiometry (karyotype), are associated with cancer malignancy and drug resistance of pathogenic fungi. The phenotypic diversity resulting from karyotypic diversity endows the cell population with superior adaptability. We show here, using a combination of experimental data and a general stochastic model, that the degree of phenotypic variation, thus evolvability, escalates with the degree of overall growth suppression. Such scaling likely explains the challenge of treating aneuploidy diseases with a single stress-inducing agent. Instead, we propose the design of an "evolutionary trap" (ET) targeting both karyotypic diversity and fitness. This strategy entails a selective condition "channeling" a karyotypically divergent population into one with a predominant and predictably drugable karyotypic feature. We provide a proof-of-principle case in budding yeast and demonstrate the potential efficacy of this strategy toward aneuploidy-based azole resistance in Candida albicans. By analyzing existing pharmacogenomics data, we propose the potential design of an ET against glioblastoma.

    View details for DOI 10.1016/j.cell.2015.01.026

    View details for PubMedID 25679766

    View details for PubMedCentralID PMC4328141

  • Whole chromosome aneuploidy: big mutations drive adaptation by phenotypic leap. BioEssays : news and reviews in molecular, cellular and developmental biology Chen, G., Rubinstein, B., Li, R. 2012; 34 (10): 893-900


    Despite its widespread existence, the adaptive role of aneuploidy (the abnormal state of having an unequal number of different chromosomes) has been a subject of debate. Cellular aneuploidy has been associated with enhanced resistance to stress, whereas on the organismal level it is detrimental to multicellular species. Certain aneuploid karyotypes are deleterious for specific environments, but karyotype diversity in a population potentiates adaptive evolution. To reconcile these paradoxical observations, this review distinguishes the role of aneuploidy in cellular versus organismal evolution. Further, it proposes a population genetics perspective to examine the behavior of aneuploidy on a populational versus individual level. By altering the copy number of a significant portion of the genome, aneuploidy introduces large phenotypic leaps that enable small cell populations to explore a wide phenotypic landscape, from which adaptive traits can be selected. The production of chromosome number variation can be further increased by stress- or mutation-induced chromosomal instability, fueling rapid cellular adaptation.

    View details for DOI 10.1002/bies.201200069

    View details for PubMedID 22926916

    View details for PubMedCentralID PMC3526072

  • Hsp90 stress potentiates rapid cellular adaptation through induction of aneuploidy. Nature Chen, G., Bradford, W. D., Seidel, C. W., Li, R. 2012; 482 (7384): 246-50


    Aneuploidy--the state of having uneven numbers of chromosomes--is a hallmark of cancer and a feature identified in yeast from diverse habitats. Recent studies have shown that aneuploidy is a form of large-effect mutation that is able to confer adaptive phenotypes under diverse stress conditions. Here we investigate whether pleiotropic stress could induce aneuploidy in budding yeast (Saccharomyces cerevisae). We show that whereas diverse stress conditions can induce an increase in chromosome instability, proteotoxic stress, caused by transient Hsp90 (also known as Hsp82 or Hsc82) inhibition or heat shock, markedly increased chromosome instability to produce a cell population with high karyotype diversity. The induced chromosome instability is linked to an evolutionarily conserved role for the Hsp90 chaperone complex in kinetochore assembly. Continued growth in the presence of an Hsp90 inhibitor resulted in the emergence of drug-resistant colonies with chromosome XV gain. This drug-resistance phenotype is a quantitative trait involving copy number increases of at least two genes located on chromosome XV. Short-term exposure to Hsp90 stress potentiated fast adaptation to unrelated cytotoxic compounds by means of different aneuploid chromosome stoichiometries. These findings demonstrate that aneuploidy is a form of stress-inducible mutation in eukaryotes, capable of fuelling rapid phenotypic evolution and drug resistance, and reveal a new role for Hsp90 in regulating the emergence of adaptive traits under stress.

    View details for DOI 10.1038/nature10795

    View details for PubMedID 22286062

    View details for PubMedCentralID PMC3276732