Xuanying Li

All Publications

• Reduced chromatin accessibility to CD4 T cell super-enhancers encompassing susceptibility loci of rheumatoid arthritis. EBioMedicine Jadhav, R. R., Hu, B., Ye, Z., Sheth, K., Li, X., Greenleaf, W. J., Weyand, C. M., Goronzy, J. J. 1800; 76: 103825

  Abstract

  BACKGROUND: Rheumatoid arthritis (RA) is an inflammatory disease that manifests as a preclinical stage of systemic autoimmunity followed by chronic progressive synovitis. Disease-associated genetic SNP variants predominantly map to non-coding, regulatory regions of functional importance in CD4 T cells, implicating these cells as key regulators. A better understanding of the epigenome of CD4 T cells holds the promise of providing information on the interaction between genetic susceptibility and exogenous factors.METHODS: We mapped regions of chromatin accessibility using ATAC-seq in peripheral CD4 T cell subsets of patients with RA (n=18) and compared them to T cells from patients with psoriatic arthritis (n=11) and age-matched healthy controls (n=10). Transcripts of selected genes were quantified using qPCR.FINDINGS: RA-associated epigenetic signatures were identified that in part overlapped between central and effector memory CD4 T cells and that were to a lesser extent already present in naive cells. Sites more accessible in RA were highly enriched for the motif of the transcription factor (TF) CTCF suggesting differences in the three-dimensional chromatin structure. Unexpectedly, sites with reduced chromatin accessibility were enriched for motifs of TFs pertinent for T cell function. Most strikingly, super-enhancers encompassing RA-associated SNPs were less accessible. Analysis of selected transcripts and published DNA methylation patterns were consistent with this finding. The preferential loss in accessibility at these super-enhancers was seen in patients with high and low disease activity and on a variety of immunosuppressive treatment modalities.INTERPRETATION: Disease-associated genes are epigenetically less poised to respond in CD4 T cells from patients with established RA.FUNDING: This work was supported by I01 BX001669 from the Veterans Administration.

  View details for DOI 10.1016/j.ebiom.2022.103825

  View details for PubMedID 35085847

• The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters PLOS GENETICS Soffers, J. M., Alcantara, S., Li, X., Shao, W., Seidel, C. W., Li, H., Zeitlinger, J., Abmayr, S. M., Workman, J. L. 2021; 17 (11): e1009668

  Abstract

  The Spt/Ada-Gcn5 Acetyltransferase (SAGA) coactivator complex has multiple modules with different enzymatic and non-enzymatic functions. How each module contributes to gene expression is not well understood. During Drosophila oogenesis, the enzymatic functions are not equally required, which may indicate that different genes require different enzymatic functions. An analogy for this phenomenon is the handyman principle: while a handyman has many tools, which tool he uses depends on what requires maintenance. Here we analyzed the role of the non-enzymatic core module during Drosophila oogenesis, which interacts with TBP. We show that depletion of SAGA-specific core subunits blocked egg chamber development at earlier stages than depletion of enzymatic subunits. These results, as well as additional genetic analyses, point to an interaction with TBP and suggest a differential role of SAGA modules at different promoter types. However, SAGA subunits co-occupied all promoter types of active genes in ChIP-seq and ChIP-nexus experiments, and the complex was not specifically associated with distinct promoter types in the ovary. The high-resolution genomic binding profiles were congruent with SAGA recruitment by activators upstream of the start site, and retention on chromatin by interactions with modified histones downstream of the start site. Our data illustrate that a distinct genetic requirement for specific components may conceal the fact that the entire complex is physically present and suggests that the biological context defines which module functions are critical.

  View details for DOI 10.1371/journal.pgen.1009668

  View details for Web of Science ID 000745154000002

  View details for PubMedID 34807910

  View details for PubMedCentralID PMC8648115

• Activation of mTORC1 at late endosomes misdirects T cell fate decision in older individuals. Science immunology Jin, J., Kim, C., Xia, Q., Gould, T. M., Cao, W., Zhang, H., Li, X., Weiskopf, D., Grifoni, A., Sette, A., Weyand, C. M., Goronzy, J. J. 2021; 6 (60)

  Abstract

  The nutrient-sensing mammalian target of rapamycin (mTOR) is integral to cell fate decisions after T cell activation. Sustained mTORC1 activity favors the generation of terminally differentiated effector T cells instead of follicular helper and memory T cells. This is particularly pertinent for T cell responses of older adults who have sustained mTORC1 activation despite dysfunctional lysosomes. Here, we show that lysosome-deficient T cells rely on late endosomes rather than lysosomes as an mTORC1 activation platform, where mTORC1 is activated by sensing cytosolic amino acids. T cells from older adults have an increased expression of the plasma membrane leucine transporter SLC7A5 to provide a cytosolic amino acid source. Hence, SLC7A5 and VPS39 deficiency (a member of the HOPS complex promoting early to late endosome conversion) substantially reduced mTORC1 activities in T cells from older but not young individuals. Late endosomal mTORC1 is independent of the negative-feedback loop involving mTORC1-induced inactivation of the transcription factor TFEB that controls expression of lysosomal genes. The resulting sustained mTORC1 activation impaired lysosome function and prevented lysosomal degradation of PD-1 in CD4+ T cells from older adults, thereby inhibiting their proliferative responses. VPS39 silencing of human T cells improved their expansion to pertussis and to SARS-CoV-2 peptides in vitro. Furthermore, adoptive transfer of CD4+ Vps39-deficient LCMV-specific SMARTA cells improved germinal center responses, CD8+ memory T cell generation, and recall responses to infection. Thus, curtailing late endosomal mTORC1 activity is a promising strategy to enhance T cell immunity.

  View details for DOI 10.1126/sciimmunol.abg0791

  View details for PubMedID 34145066

• FOXO1 deficiency impairs proteostasis in aged T cells SCIENCE ADVANCES Jin, J., Li, X., Hu, B., Kim, C., Cao, W., Zhang, H., Weyand, C. M., Goronzy, J. J. 2020; 6 (17)

  View details for DOI 10.1126/sciadv.aba1808

  View details for Web of Science ID 000530628100043

• Distinct Age-Related Epigenetic Signatures in CD4 and CD8 T Cells. Frontiers in immunology Hu, B., Jadhav, R. R., Gustafson, C. E., Le Saux, S., Ye, Z., Li, X., Tian, L., Weyand, C. M., Goronzy, J. J. 2020; 11: 585168

  Abstract

  Healthy immune aging is in part determined by how well the sizes of naive T cell compartments are being maintained with advancing age. Throughout adult life, replenishment largely derives from homeostatic proliferation of existing naive and memory T cell populations. However, while the subpopulation composition of CD4 T cells is relatively stable, the CD8 T cell compartment undergoes more drastic changes with loss of naive CD8 T cells and accumulation of effector T cells, suggesting that CD4 T cells are more resilient to resist age-associated changes. To determine the epigenetic basis for these differences in behaviors, we compared chromatin accessibility maps of CD4 and CD8 T cell subsets from young and old individuals and related the results to the expressed transcriptome. The dominant age-associated signatures resembled hallmarks of differentiation, which were more pronounced for CD8 naive and memory than the corresponding CD4 T cell subsets, indicating that CD8 T cells are less able to keep cellular quiescence upon homeostatic proliferation. In parallel, CD8 T cells from old adults, irrespective of their differentiation state, displayed greater reduced accessibility to genes of basic cell biological function, including genes encoding ribosomal proteins. One possible mechanism is the reduced expression of the transcription factors YY1 and NRF1. Our data suggest that chromatin accessibility signatures can be identified that distinguish CD4 and CD8 T cells from old adults and that may confer the higher resilience of CD4 T cells to aging.

  View details for DOI 10.3389/fimmu.2020.585168

  View details for PubMedID 33262764

• Ecto-NTPDase CD39 is a negative checkpoint that inhibits follicular helper cell generation. The Journal of clinical investigation Cao, W. n., Fang, F. n., Gould, T. n., Li, X. n., Kim, C. n., Gustafson, C. n., Lambert, S. n., Weyand, C. M., Goronzy, J. J. 2020

  Abstract

  Vaccination is a mainstay in preventive medicine, reducing morbidity and mortality from infection, largely by generating pathogen-specific neutralizing antibodies. However, standard immunization strategies are insufficient with increasing age due to immunological impediments, including defects in T follicular helper (Tfh) cells. Here, we found that Tfh generation is inversely linked to the expression of the ecto-NTPDase CD39 that modifies purinergic signaling. The lineage-determining transcription factor BCL6 inhibited CD39 expression, while increased Tfh frequencies were found in individuals with a germline polymorphism preventing transcription of ENTPD1, encoding CD39. In in vitro human and in vivo mouse studies, Tfh generation and germinal center responses were enhanced by reducing CD39 expression through the inhibition of the cAMP/PKA/p-CREB pathway, or by blocking adenosine signaling downstream of CD39 using the selective adenosine A2a receptor antagonist istradefylline. Thus, purinergic signaling in differentiating T cells can be targeted to improve vaccine responses, in particular in older individuals who have increased CD39 expression.

  View details for DOI 10.1172/JCI132417

  View details for PubMedID 32452837

• Characterization of a metazoan ADA acetyltransferase complex NUCLEIC ACIDS RESEARCH Soffers, J. M., Li, X., Saraf, A., Seidel, C. W., Florens, L., Washburn, M. P., Abmayr, S. M., Workman, J. L. 2019; 47 (7): 3383–94

  Abstract

  The Gcn5 acetyltransferase functions in multiple acetyltransferase complexes in yeast and metazoans. Yeast Gcn5 is part of the large SAGA (Spt-Ada-Gcn5 acetyltransferase) complex and a smaller ADA acetyltransferase complex. In flies and mammals, Gcn5 (and its homolog pCAF) is part of various versions of the SAGA complex and another large acetyltransferase complex, ATAC (Ada2A containing acetyltransferase complex). However, a complex analogous to the small ADA complex in yeast has never been described in metazoans. Previous studies in Drosophila hinted at the existence of a small complex which contains Ada2b, a partner of Gcn5 in the SAGA complex. Here we have purified and characterized the composition of this complex and show that it is composed of Gcn5, Ada2b, Ada3 and Sgf29. Hence, we have named it the metazoan 'ADA complex'. We demonstrate that the fly ADA complex has histone acetylation activity on histones and nucleosome substrates. Moreover, ChIP-Sequencing experiments identified Ada2b peaks that overlap with another SAGA subunit, Spt3, as well as Ada2b peaks that do not overlap with Spt3 suggesting that the ADA complex binds chromosomal sites independent of the larger SAGA complex.

  View details for DOI 10.1093/nar/gkz042

  View details for Web of Science ID 000467965900017

  View details for PubMedID 30715476

  View details for PubMedCentralID PMC6468242

• Enzymatic modules of the SAGA chromatin-modifying complex play distinct roles in Drosophila gene expression and development GENES & DEVELOPMENT Li, X., Seidel, C. W., Szerszen, L. T., Lange, J. J., Workman, J. L., Abmayr, S. M. 2017; 31 (15): 1588–1600

  Abstract

  The Spt-Ada-Gcn5-acetyltransferase (SAGA) chromatin-modifying complex is a transcriptional coactivator that contains four different modules of subunits. The intact SAGA complex has been well characterized for its function in transcription regulation and development. However, little is known about the roles of individual modules within SAGA and whether they have any SAGA-independent functions. Here we demonstrate that the two enzymatic modules of Drosophila SAGA are differently required in oogenesis. Loss of the histone acetyltransferase (HAT) activity blocks oogenesis, while loss of the H2B deubiquitinase (DUB) activity does not. However, the DUB module regulates a subset of genes in early embryogenesis, and loss of the DUB subunits causes defects in embryogenesis. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) analysis revealed that both the DUB and HAT modules bind most SAGA target genes even though many of these targets do not require the DUB module for expression. Furthermore, we found that the DUB module can bind to chromatin and regulate transcription independently of the HAT module. Our results suggest that the DUB module has functions within SAGA and independent functions.

  View details for DOI 10.1101/gad.300988.117

  View details for Web of Science ID 000410655400007

  View details for PubMedID 28887412

  View details for PubMedCentralID PMC5630023

• Reading and Interpreting the Histone Acylation Code GENOMICS PROTEOMICS & BIOINFORMATICS Soffers, J. M., Li, X., Abmayr, S. M., Workman, J. L. 2016; 14 (6): 329–32

  View details for DOI 10.1016/j.gpb.2016.12.001

  View details for Web of Science ID 000391081100001

  View details for PubMedID 28007607

  View details for PubMedCentralID PMC5200937

• Follicular T-helper cell recruitment governed by bystander B cells and ICOS-driven motility NATURE Xu, H., Li, X., Liu, D., Li, J., Zhang, X., Chen, X., Hou, S., Peng, L., Xu, C., Liu, W., Zhang, L., Qi, H. 2013; 496 (7446): 523-+

  Abstract

  Germinal centres support antibody affinity maturation and memory formation. Follicular T-helper cells promote proliferation and differentiation of antigen-specific B cells inside the follicle. A genetic deficiency in the inducible co-stimulator (ICOS), a classic CD28 family co-stimulatory molecule highly expressed by follicular T-helper cells, causes profound germinal centre defects, leading to the view that ICOS specifically co-stimulates the follicular T-helper cell differentiation program. Here we show that ICOS directly controls follicular recruitment of activated T-helper cells in mice. This effect is independent from ICOS ligand (ICOSL)-mediated co-stimulation provided by antigen-presenting dendritic cells or cognate B cells, and does not rely on Bcl6-mediated programming as an intermediate step. Instead, it requires ICOSL expression by follicular bystander B cells, which do not present cognate antigen to T-helper cells but collectively form an ICOS-engaging field. Dynamic imaging reveals ICOS engagement drives coordinated pseudopod formation and promotes persistent T-cell migration at the border between the T-cell zone and the B-cell follicle in vivo. When follicular bystander B cells cannot express ICOSL, otherwise competent T-helper cells fail to develop into follicular T-helper cells normally, and fail to promote optimal germinal centre responses. These results demonstrate a co-stimulation-independent function of ICOS, uncover a key role for bystander B cells in promoting the development of follicular T-helper cells, and reveal unsuspected sophistication in dynamic T-cell positioning in vivo.

  View details for DOI 10.1038/nature12058

  View details for Web of Science ID 000317984400045

  View details for PubMedID 23619696