Murine breast cancers disorganize the liver transcriptome in a zonated manner

[1]  S. Kawaoka,et al.  Remote solid cancers rewire hepatic nitrogen metabolism via host nicotinamide-N-methyltransferase , 2022, Nature Communications.

[2]  N. Henderson,et al.  Liver zonation, revisited , 2022, Hepatology.

[3]  Yushui Ma,et al.  Bile acid metabolism dysregulation associates with cancer cachexia: roles of liver and gut microbiome , 2021, Journal of cachexia, sarcopenia and muscle.

[4]  Natalie Porat-Shliom,et al.  Liver Zonation – Revisiting Old Questions With New Technologies , 2021, Frontiers in Physiology.

[5]  R. Skoda,et al.  Remodeling of metabolism and inflammation by exercise ameliorates tumor-associated anemia , 2021, Science advances.

[6]  Cholsoon Jang,et al.  Glucagon regulates the stability of REV-ERBα to modulate hepatic glucose production in a model of lung cancer–associated cachexia , 2021, Science Advances.

[7]  Shubhada R. Kulkarni,et al.  A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie–Wnt signaling axis in the liver , 2021, Developmental cell.

[8]  Patrice D Cani,et al.  Multi‐compartment metabolomics and metagenomics reveal major hepatic and intestinal disturbances in cancer cachectic mice , 2021, Journal of cachexia, sarcopenia and muscle.

[9]  D. Gabrilovich,et al.  Myeloid-derived suppressor cells in the era of increasing myeloid cell diversity , 2021, Nature Reviews Immunology.

[10]  J. Lundeberg,et al.  Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver , 2020, Nature Communications.

[11]  David Haussler,et al.  The UCSC Genome Browser database: 2021 update , 2020, Nucleic Acids Res..

[12]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[13]  P. Coupland,et al.  Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy , 2020, Nature Communications.

[14]  S. Itzkovitz,et al.  Liver zonation. , 2020, Journal of hepatology.

[15]  Andrea J. Radtke,et al.  Commensal-driven immune zonation of the liver promotes host defence , 2020, Nature.

[16]  J. Yamate,et al.  Dietary Iron Overload Differentially Modulates Chemically-Induced Liver Injury in Rats , 2020, Nutrients.

[17]  T. Baumert,et al.  Single-cell genomics and spatial transcriptomics: Discovery of novel cell states and cellular interactions in liver physiology and disease biology , 2020, Journal of hepatology.

[18]  Kamir J. Hiam,et al.  Systemic dysfunction and plasticity of the immune macroenvironment in cancer models , 2020, Nature Medicine.

[19]  Swarnali Acharyya,et al.  Understanding cachexia in the context of metastatic progression , 2020, Nature Reviews Cancer.

[20]  A. Vandenbon,et al.  A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data , 2019, Nature Communications.

[21]  C. Ponting,et al.  Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis , 2019, Cell reports.

[22]  M. Ronis,et al.  Improved method for isolating high-quality RNA from mouse bone with RNAlater at room temperature , 2019, Bone reports.

[23]  J. Klausner,et al.  CD11b+Ly6G+ myeloid‐derived suppressor cells promote liver regeneration in a murine model of major hepatectomy , 2019, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[24]  S. Itzkovitz,et al.  Spatial sorting enables comprehensive characterization of liver zonation , 2019, Nature Metabolism.

[25]  T. M. O’Connell,et al.  Cachexia induced by cancer and chemotherapy yield distinct perturbations to energy metabolism , 2019, Journal of cachexia, sarcopenia and muscle.

[26]  Gary D Bader,et al.  Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations , 2018, Nature Communications.

[27]  J. Hampe,et al.  Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control , 2018, Nature Communications.

[28]  David M. Wilson,et al.  Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures , 2018, Cell.

[29]  Erik Sundström,et al.  RNA velocity of single cells , 2018, Nature.

[30]  K. Kawakami,et al.  A novel zebrafish intestinal tumor model reveals a role for cyp7a1-dependent tumor–liver crosstalk in causing adverse effects on the host , 2018, Disease Models & Mechanisms.

[31]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[32]  Yong-long Han,et al.  Serum and urine metabolomics study reveals a distinct diagnostic model for cancer cachexia , 2017, Journal of cachexia, sarcopenia and muscle.

[33]  Yutaka Suzuki,et al.  Remote reprogramming of hepatic circadian transcriptome by breast cancer , 2017, Oncotarget.

[34]  T. Kietzmann.  Metabolic zonation of the liver: The oxygen gradient revisited , 2017, Redox biology.

[35]  I. Amit,et al.  Single-cell spatial reconstruction reveals global division of labor in the mammalian liver , 2016, Nature.

[36]  D. Fearon,et al.  Tumor-Induced IL-6 Reprograms Host Metabolism to Suppress Anti-tumor Immunity , 2016, Cell metabolism.

[37]  Pierre Baldi,et al.  Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis , 2016, Cell.

[38]  K. Pienta,et al.  Murine Hind Limb Long Bone Dissection and Bone Marrow Isolation , 2016, Journal of visualized experiments : JoVE.

[39]  E. Wagner,et al.  Mechanisms of metabolic dysfunction in cancer-associated cachexia , 2016, Genes & development.

[40]  J. Vierling,et al.  Autoimmune hepatitis , 2015, Frontiers of Medicine.

[41]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[42]  M. Yeh,et al.  Pathological features of fatty liver disease. , 2014, Gastroenterology.

[43]  R. Roeder,et al.  Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia , 2013, Proceedings of the National Academy of Sciences.

[44]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[45]  M. Kaplan,et al.  Primary biliary cirrhosis , 1998, Hepatology.

[46]  O. Cummings,et al.  Relationship of steatosis grade and zonal location to histological features of steatohepatitis in adult patients with non-alcoholic fatty liver disease. , 2008, Journal of hepatology.

[47]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  S. Ostrand-Rosenberg,et al.  Mouse 4T1 Breast Tumor Model , 2000, Current protocols in immunology.