Interpretable Inflammation Landscape of Circulating Immune cells
Author:
Jiménez-Gracia LauraORCID, Maspero DavideORCID, Aguilar-Fernández SergioORCID, Craighero FrancescoORCID, Ruiz Sara, Marchese DomenicaORCID, Caratù GinevraORCID, Elosua-Bayes Marc, Abdalfatah Mohamed, Sanzo-Machuca Angela, Corraliza Ana M., Massoni-Badosa RamonORCID, Tran Hoang A., Normand Rachelly, Nestor Jacquelyn, Hong Yourae, Kole Tessa, van der Velde Petra, Alleblas Frederique, Pedretti Flaminia, Aterido Adrià, Banchero Martin, Soriano German, Román Eva, van den Berge Maarten, Salas AzucenaORCID, Carrascosa Jose Manuel, Nebro Antonio Fernández, Domènech Eugeni, Cañete Juan, Tornero Jesús, Pérez-Gisbert Javier, Choy Ernest, Girolomoni Giampiero, Siegmund Britta, Julià Antonio, Serra Violeta, Elosua Roberto, Tejpar Sabine, Vidal Silvia, Nawijn Martijn C., Marsal Sara, Vandergheynst Pierre, Villani Alexandra-Chloé, Nieto Juan C.ORCID, Heyn HolgerORCID
Abstract
AbstractInflammation is a biological phenomenon involved in a wide variety of physiological and pathological processes. Although a controlled inflammatory response is beneficial for restoring homeostasis, it can become unfavorable if dysregulated. In recent years, major progress has been made in characterizing acute and chronic inflammation in specific diseases. However, a global, holistic understanding of inflammation is still elusive. This is particularly intriguing, considering the crucial function of inflammation for human health and its potential for modern medicine if fully deciphered. Here, we leverage advances in the field of single-cell genomics to delineate the full spectrum of circulating immune cell activation underlying inflammatory processes during infection, immune-mediated inflammatory diseases and cancer. Our single-cell atlas of >2 million peripheral blood mononuclear cells from 356 patients and 18 diseases allowed us to learn a foundation model of inflammation in circulating immune cells. The atlas expanded our current knowledge of the biology of inflammation of acute (e.g. inflammatory bowel disease, sepsis) and chronic (e.g. cirrhosis, asthma, and chronic obstructive pulmonary disease) disease processes and laid the foundation to develop a precision medicine framework using unsupervised as well as explainable machine learning. Beyond a disease-centered classification, we charted altered activity of inflammatory molecules in peripheral blood cells, depicting functional biomarkers to further understand mechanisms of inflammation. Finally, we have laid the groundwork for developing precision medicine diagnostic tools for patients experiencing severe acute or chronic inflammation by learning a classifier for inflammatory diseases, presenting cells in circulation as a powerful resource for patient stratification.
Publisher
Cold Spring Harbor Laboratory
|
|