Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages.

Autor: Sheu KM; Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 611 Charles E. Young Dr S, Los Angeles, CA 90093, USA., Pimplaskar A; Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 611 Charles E. Young Dr S, Los Angeles, CA 90093, USA., Hoffmann A; Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 611 Charles E. Young Dr S, Los Angeles, CA 90093, USA. Electronic address: ahoffmann@ucla.edu.

Publikováno v: Molecular cell [Mol Cell] 2024 Nov 07; Vol. 84 (21), pp. 4095-4110.e6. Date of Electronic Publication: 2024 Oct 15.

Temporal evolution reveals bifurcated lineages in aggressive neuroendocrine small cell prostate cancer trans-differentiation.

Autor: Chen CC; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA., Tran W; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA., Song K; Department of Bioengineering, UCLA, Los Angeles, CA, USA., Sugimoto T; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA., Obusan MB; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA., Wang L; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA., Sheu KM; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA., Cheng D; Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA., Ta L; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA., Varuzhanyan G; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA., Huang A; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA., Xu R; Department of Biological Chemistry, UCLA, Los Angeles, CA, USA., Zeng Y; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA., Borujerdpur A; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA., Bayley NA; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA., Noguchi M; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA., Mao Z; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA., Morrissey C; Department of Urology, University of Washington School of Medicine, Seattle, WA, USA., Corey E; Department of Urology, University of Washington School of Medicine, Seattle, WA, USA., Nelson PS; Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA; Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA., Zhao Y; Department of Pathology, Duke University School of Medicine, Durham, NC, USA; Department of Pathology, College of Basic Medical Sciences and the First Hospital, China Medical University, Shenyang, China., Huang J; Department of Pathology, Duke University School of Medicine, Durham, NC, USA., Park JW; Department of Pathology, Duke University School of Medicine, Durham, NC, USA., Witte ON; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA; Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA; Molecular Biology Institute, UCLA, Los Angeles, CA, USA; Parker Institute for Cancer Immunotherapy, UCLA, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA. Electronic address: owenwitte@mednet.ucla.edu., Graeber TG; Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA, USA; California NanoSystems Institute, UCLA, Los Angeles, CA, USA; Metabolomics Center, UCLA, Los Angeles, CA, USA. Electronic address: tgraeber@mednet.ucla.edu.

Publikováno v: Cancer cell [Cancer Cell] 2023 Dec 11; Vol. 41 (12), pp. 2066-2082.e9. Date of Electronic Publication: 2023 Nov 22.

Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.

Autor: Kim J; Department of Mathematics, Pohang University of Science and Technology, Pohang, South Korea., Sheu KM; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA., Cheng QJ; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California, Los Angeles, Los Angeles, CA, USA., Hoffmann A; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA. Electronic address: ahoffmann@ucla.edu., Enciso G; Department of Mathematics, University of California, Irvine, Irvine, CA, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA. Electronic address: enciso@uci.edu.

Publikováno v: Cell reports [Cell Rep] 2022 Jul 12; Vol. 40 (2), pp. 111076.

Pathogenic TNF-α drives peripheral nerve inflammation in an Aire-deficient model of autoimmunity.

Autor: Wang Y; Department of Neurology, Thomas Jefferson University, Philadelphia, PA 19107., Guo L; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095., Yin X; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095., McCarthy EC; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095., Cheng MI; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095., Hoang AT; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095., Chen HC; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095., Patel AY; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095., Allard Trout D; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132., Xu E; School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599., Yakobian N; St. Louis University School of Medicine, St. Louis, MO 63104., Hugo W; Division of Endocrinology and Diabetes, University of Southern California Keck School of Medicine, Los Angeles, CA 90033., Howard JF Jr; Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599., Sheu KM; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095., Hoffmann A; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095., Lechner MG; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095., Su MA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095; masu@mednet.ucla.edu.; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2022 Jan 25; Vol. 119 (4).

NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages.

Autor: Cheng QJ; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.; Division of Infectious, Diseases Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA., Ohta S; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA., Sheu KM; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA., Spreafico R; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA., Adelaja A; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA., Taylor B; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA., Hoffmann A; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA. ahoffmann@ucla.edu.; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA.

Publikováno v: Science (New York, N.Y.) [Science] 2021 Jun 18; Vol. 372 (6548), pp. 1349-1353.