Browsing by Author "Xi, Yuanxin"

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    Contextual cues from cancer cells govern cancer-associated fibroblast heterogeneity
    (Cell Press, 2021) Bota-Rabassedas, Neus; Banerjee, Priyam; Niu, Yichi; Cao, Wenjian; Luo, Jiayi; Xi, Yuanxin; Tan, Xiaochao; Sheng, Kuanwei; Ahn, Young-Ho; Lee, Sieun; Parra, Edwin Roger; Rodriguez-Canales, Jaime; Albritton, Jacob; Weiger, Michael; Liu, Xin; Guo, Hou-Fu; Yu, Jiang; Rodriguez, B. Leticia; Firestone, Joshua J.A.; Mino, Barbara; Creighton, Chad J.; Solis, Luisa M.; Villalobos, Pamela; Raso, Maria Gabriela; Sazer, Daniel W.; Gibbons, Don L.; Russell, William K.; Longmore, Gregory D.; Wistuba, Ignacio I.; Wang, Jing; Chapman, Harold A.; Miller, Jordan S.; Zong, Chenghang; Kurie, Jonathan M.
    Cancer cells function as primary architects of the tumor microenvironment. However, the molecular features of cancer cells that govern stromal cell phenotypes remain unclear. Here, we show that cancer-associated fibroblast (CAF) heterogeneity is driven by lung adenocarcinoma (LUAD) cells at either end of the epithelial-to-mesenchymal transition (EMT) spectrum. LUAD cells that have high expression of the EMT-activating transcription factor ZEB1 reprogram CAFs through a ZEB1-dependent secretory program and direct CAFs to the tips of invasive projections through a ZEB1-driven CAF repulsion process. The EMT, in turn, sensitizes LUAD cells to pro-metastatic signals from CAFs. Thus, CAFs respond to contextual cues from LUAD cells to promote metastasis.
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    Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes
    (EMBO, 2015) Li, Xu; Wang, Wenqi; Wang, Jiadong; Malovannaya, Anna; Xi, Yuanxin; Li, Wei; Guerra, Rudy; Hawke, David H.; Qin, Jun; Chen, Junjie
    The current knowledge on how transcription factors (TFs), the ultimate targets and executors of cellular signalling pathways, are regulated by protein–protein interactions remains limited. Here, we performed proteomics analyses of soluble and chromatin‐associated complexes of 56 TFs, including the targets of many signalling pathways involved in development and cancer, and 37 members of the Forkhead box (FOX) TF family. Using tandem affinity purification followed by mass spectrometry (TAP/MS), we performed 214 purifications and identified 2,156 high‐confident protein–protein interactions. We found that most TFs form very distinct protein complexes on and off chromatin. Using this data set, we categorized the transcription‐related or unrelated regulators for general or specific TFs. Our study offers a valuable resource of protein–protein interaction networks for a large number of TFs and underscores the general principle that TFs form distinct location‐specific protein complexes that are associated with the different regulation and diverse functions of these Tfs.