All Publications

  • Medial HOXA genes demarcate haematopoietic stem cell fate during human development NATURE CELL BIOLOGY Dou, D. R., Calvanese, V., Sierra, M. I., Nguyen, A. T., Minasian, A., Saarikoski, P., Sasidharan, R., Ramirez, C. M., Zack, J. A., Crooks, G. M., Galic, Z., Mikkola, H. K. 2016; 18 (6): 595-?


    Pluripotent stem cells (PSCs) may provide a potential source of haematopoietic stem/progenitor cells (HSPCs) for transplantation; however, unknown molecular barriers prevent the self-renewal of PSC-HSPCs. Using two-step differentiation, human embryonic stem cells (hESCs) differentiated in vitro into multipotent haematopoietic cells that had the CD34(+)CD38(-/lo)CD90(+)CD45(+)GPI-80(+) fetal liver (FL) HSPC immunophenotype, but exhibited poor expansion potential and engraftment ability. Transcriptome analysis of immunophenotypic hESC-HSPCs revealed that, despite their molecular resemblance to FL-HSPCs, medial HOXA genes remained suppressed. Knockdown of HOXA7 disrupted FL-HSPC function and caused transcriptome dysregulation that resembled hESC-derived progenitors. Overexpression of medial HOXA genes prolonged FL-HSPC maintenance but was insufficient to confer self-renewal to hESC-HSPCs. Stimulation of retinoic acid signalling during endothelial-to-haematopoietic transition induced the HOXA cluster and other HSC/definitive haemogenic endothelium genes, and prolonged HSPC maintenance in culture. Thus, medial HOXA gene expression induced by retinoic acid signalling marks the establishment of the definitive HSPC fate and controls HSPC identity and function.

    View details for DOI 10.1038/ncb3354

    View details for Web of Science ID 000376750100006

    View details for PubMedID 27183470

    View details for PubMedCentralID PMC4981340

  • Xist ribonucleoproteins promote female sex-biased autoimmunity. Cell Dou, D. R., Zhao, Y., Belk, J. A., Zhao, Y., Casey, K. M., Chen, D. C., Li, R., Yu, B., Srinivasan, S., Abe, B. T., Kraft, K., Hellström, C., Sjöberg, R., Chang, S., Feng, A., Goldman, D. W., Shah, A. A., Petri, M., Chung, L. S., Fiorentino, D. F., Lundberg, E. K., Wutz, A., Utz, P. J., Chang, H. Y. 2024; 187 (3): 733-749.e16


    Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.

    View details for DOI 10.1016/j.cell.2023.12.037

    View details for PubMedID 38306984

  • Xist Ribonucleoproteins Promote Female Sex-biased Autoimmunity Dou, D., Zhao, Y., Belk, J., Zhao, Y., Casey, K., Chen, D., Li, R., Yu, B., Srinivasan, S., Abe, B., Kraft, K., Hellstroem, C., Sjoeberg, R., Chang, S., Feng, A., Goldman, D., Shah, A., Petri, M., Chung, L., Fiorentino, D., Lundberg, E., Wutz, A., Utz, P., Chang, H. WILEY. 2023: 25-26
  • Structural modularity of the XIST ribonucleoprotein complex. Nature communications Lu, Z., Guo, J. K., Wei, Y., Dou, D. R., Zarnegar, B., Ma, Q., Li, R., Zhao, Y., Liu, F., Choudhry, H., Khavari, P. A., Chang, H. Y. 2020; 11 (1): 6163


    Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m6A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.

    View details for DOI 10.1038/s41467-020-20040-3

    View details for PubMedID 33268787

  • Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. eLife Carter, A. C., Xu, J., Nakamoto, M. Y., Wei, Y., Zarnegar, B. J., Shi, Q., Broughton, J. P., Ransom, R. C., Salhotra, A., Nagaraja, S. D., Li, R., Dou, D. R., Yost, K. E., Cho, S., Mistry, A., Longaker, M. T., Khavari, P. A., Batey, R. T., Wuttke, D. S., Chang, H. Y. 2020; 9


    The Xist lncRNA mediates X chromosome inactivation (XCI)1,2. Here we show that Spen, an Xist-binding repressor protein essential for XCI3-9, binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation activates a subset of endogenous retroviral (ERV) elements in mouse embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing10-11. ERV RNA and Xist A-repeat bind the RRM domains of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in strictly local gene silencing in cis. These results suggest that Xist may coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.

    View details for DOI 10.7554/eLife.54508

    View details for PubMedID 32379046

  • Interferon Stimulated Gene Expression in HIV/HCV Coinfected Patients Treated with Nitazoxanide/Peginterferon-Alfa-2a and Ribavirin AIDS RESEARCH AND HUMAN RETROVIRUSES Petersen, T., Lee, Y., Osinusi, A., Amorosa, V. K., Wang, C., Kang, M., Matining, R., Zhang, X., Dou, D., Umbleja, T., Kottilil, S., Peters, M. G. 2016; 32 (7): 660-667


    A combination of nitazoxanide (NTZ), peginterferon (PegIFN), and ribavirin (RBV) may result in higher sustained virologic response (SVR) rates in hepatitis C virus (HCV) monoinfected patients. This study evaluated the effect of NTZ on interferon-stimulated gene (ISG) expression in vitro and in vivo among HIV/HCV genotype-1 (GT-1) treatment-naive patients. The ability of NTZ to enhance host response to interferon (IFN) signaling using the HCV cell culture system was initially evaluated. Second, ISG expression in 53 patients with treatment outcomes [21 SVR and 32 nonresponders (NR)] in the ACTG A5269 trial, a phase-II study (4-week lead in of NTZ 500 mg daily followed by 48 weeks of NTZ, PegIFN, and weight-based RBV), was assessed. The relative expression of 48 ISGs in peripheral blood mononuclear cells (PBMCs) was measured at baseline, week 4, and week 8 of treatment in a blinded manner. In vitro NTZ produced a direct and additive antiviral effect with IFN-alfa, with pretreatment of NTZ resulting in maximal HCV suppression. NTZ augmented IFN-mediated ISG induction in PBMCs from relapsers and SVRs (p < 0.05), but not NR. In ACTG A5269, baseline expression of most ISGs was similar between NR and SVR. NTZ minimally induced 17 genes in NR and 13 genes in SVR after 4 weeks of therapy. However, after initiation of PegIFN and RBV, ISG induction was predominantly observed in the SVR group and not NR group. NTZ treatment facilitates IFN-induced suppression of HCV replication. Inability to achieve SVR with IFN-based therapy in this clinical trial is associated with diminished ISG response to therapy that is refractory to NTZ.

    View details for DOI 10.1089/aid.2015.0236

    View details for Web of Science ID 000379609100007

    View details for PubMedID 26974581

    View details for PubMedCentralID PMC4931749

  • High interferon-stimulated gene ISG-15 expression affects HCV treatment outcome in patients co-infected with HIV and HCV JOURNAL OF MEDICAL VIROLOGY Katsounas, A., Hubbard, J. J., Wang, C. H., Zhang, X., Dou, D., Shivakumar, B., Winter, S., Schlaak, J. F., Lempicki, R. A., Masur, H., Polis, M., Kottilil, S., Osinusi, A. 2013; 85 (6): 959-963


    Increased baseline expression and lack of induction of interferon-stimulated genes (ISG) are strong negative predictors of therapeutic response to PegIFN/RBV in patients co-infected with HIV and hepatitis C virus (HCV). This study specifically addressed whether ISG-15 expression influences therapeutic responses in 20 HIV/HCV genotype-1 subjects undergoing HCV treatment. Non-responders had significantly higher baseline expression and selective induction of ISG-15 after IFN-α treatment relative to participants with sustained virological response. High baseline levels of ISG-15 were also associated with less induction of ISG with treatment. These results support a role for ISG-15 as a prognostic indicator and resistance factor to IFN-α.

    View details for DOI 10.1002/jmv.23576

    View details for Web of Science ID 000317906300004

    View details for PubMedID 23588721